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Diff for /imach/src/imach.c between versions 1.115 and 1.130

version 1.115, 2006/02/27 12:17:45	version 1.130, 2009/05/26 06:44:34
Line 1	Line 1
/* $Id$	/* $Id$
$State$	$State$
$Log$	$Log$
	Revision 1.130 2009/05/26 06:44:34 brouard
	(Module): Max Covariate is now set to 20 instead of 8. A
	lot of cleaning with variables initialized to 0. Trying to make
	V2+V3age+V1+V4 strb=V3age+V1+V4 working better.

	Revision 1.129 2007/08/31 13:49:27 lievre
	Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting

	Revision 1.128 2006/06/30 13:02:05 brouard
	(Module): Clarifications on computing e.j

	Revision 1.127 2006/04/28 18:11:50 brouard
	(Module): Yes the sum of survivors was wrong since
	imach-114 because nhstepm was no more computed in the age
	loop. Now we define nhstepma in the age loop.
	(Module): In order to speed up (in case of numerous covariates) we
	compute health expectancies (without variances) in a first step
	and then all the health expectancies with variances or standard
	deviation (needs data from the Hessian matrices) which slows the
	computation.
	In the future we should be able to stop the program is only health
	expectancies and graph are needed without standard deviations.

	Revision 1.126 2006/04/28 17:23:28 brouard
	(Module): Yes the sum of survivors was wrong since
	imach-114 because nhstepm was no more computed in the age
	loop. Now we define nhstepma in the age loop.
	Version 0.98h

	Revision 1.125 2006/04/04 15:20:31 lievre
	Errors in calculation of health expectancies. Age was not initialized.
	Forecasting file added.

	Revision 1.124 2006/03/22 17:13:53 lievre
	Parameters are printed with %lf instead of %f (more numbers after the comma).
	The log-likelihood is printed in the log file

	Revision 1.123 2006/03/20 10:52:43 brouard
	* imach.c (Module): <title> changed, corresponds to .htm file
	name. <head> headers where missing.

	* imach.c (Module): Weights can have a decimal point as for
	English (a comma might work with a correct LC_NUMERIC environment,
	otherwise the weight is truncated).
	Modification of warning when the covariates values are not 0 or
	1.
	Version 0.98g

	Revision 1.122 2006/03/20 09:45:41 brouard
	(Module): Weights can have a decimal point as for
	English (a comma might work with a correct LC_NUMERIC environment,
	otherwise the weight is truncated).
	Modification of warning when the covariates values are not 0 or
	1.
	Version 0.98g

	Revision 1.121 2006/03/16 17:45:01 lievre
	* imach.c (Module): Comments concerning covariates added

	* imach.c (Module): refinements in the computation of lli if
	status=-2 in order to have more reliable computation if stepm is
	not 1 month. Version 0.98f

	Revision 1.120 2006/03/16 15:10:38 lievre
	(Module): refinements in the computation of lli if
	status=-2 in order to have more reliable computation if stepm is
	not 1 month. Version 0.98f

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

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

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

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

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

Line 206	Line 296
hPijx.	hPijx.

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

Authors: Nicolas Brouard (brouard@ined.fr) and Agn�s Li�vre (lievre@ined.fr).	Authors: Nicolas Brouard (brouard@ined.fr) and Agn�s Li�vre (lievre@ined.fr).
Institut national d'�tudes d�mographiques, Paris.	Institut national d'�tudes d�mographiques, Paris.
Line 235	Line 325
begin-prev-date,...	begin-prev-date,...
open gnuplot file	open gnuplot file
open html file	open html file
stable prevalence	period (stable) prevalence
for age prevalim()	for age prevalim()
h Pij x	h Pij x
variance of p varprob	variance of p varprob
Line 247	Line 337
varevsij()	varevsij()
if popbased==1 varevsij(,popbased)	if popbased==1 varevsij(,popbased)
total life expectancies	total life expectancies
Variance of stable prevalence	Variance of period (stable) prevalence
end	end
*/	*/

Line 288 extern int errno;	Line 378 extern int errno;
#define NINTERVMAX 8	#define NINTERVMAX 8
#define NLSTATEMAX 8 /* Maximum number of live states (for func) */	#define NLSTATEMAX 8 /* Maximum number of live states (for func) */
#define NDEATHMAX 8 /* Maximum number of dead states (for func) */	#define NDEATHMAX 8 /* Maximum number of dead states (for func) */
#define NCOVMAX 8 /* Maximum number of covariates */	#define NCOVMAX 20 /* Maximum number of covariates */
#define MAXN 20000	#define MAXN 20000
#define YEARM 12. /* Number of months per year */	#define YEARM 12. /* Number of months per year */
#define AGESUP 130	#define AGESUP 130
Line 307 extern int errno;	Line 397 extern int errno;
/* $Id$ */	/* $Id$ */
/* $State$ */	/* $State$ */

char version[]="Imach version 0.98c, February 2006, INED-EUROREVES ";	char version[]="Imach version 0.98i, June 2006, INED-EUROREVES-Institut de longevite ";
char fullversion[]="$Revision$ $Date$";	char fullversion[]="$Revision$ $Date$";
int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */	char strstart[80];
int nvar;	char optionfilext[10], optionfilefiname[FILENAMELENGTH];
int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;	int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
	int nvar=0;
	int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with 'age' /
int npar=NPARMAX;	int npar=NPARMAX;
int nlstate=2; /* Number of live states */	int nlstate=2; /* Number of live states */
int ndeath=1; /* Number of dead states */	int ndeath=1; /* Number of dead states */
int ncovmodel, ncovcol; /* Total number of covariables including constant a121 +b12x ncovmodel=2 */	int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a121 +b12x ncovmodel=2 */
int popbased=0;	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=0; /* Maxim number of waves */
int jmin, jmax; /* min, max spacing between 2 waves */	int jmin=0, jmax=0; /* min, max spacing between 2 waves */
int ijmin, ijmax; /* Individuals having jmin and jmax */	int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
int gipmx, gsw; /* Global variables on the number of contributions	int gipmx=0, gsw=0; /* Global variables on the number of contributions
to the likelihood and the sum of weights (done by funcone)*/	to the likelihood and the sum of weights (done by funcone)*/
int mle, weightopt;	int mle=1, weightopt=0;
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 */
int *bh; / bh[mi][i] is the bias (+ or -) for this individual if the delay between	int *bh; / bh[mi][i] is the bias (+ or -) for this individual if the delay between
* wave mi and wave mi+1 is not an exact multiple of stepm. */	* wave mi and wave mi+1 is not an exact multiple of stepm. */
double jmean; /* Mean space between 2 waves */	double jmean=1; /* Mean space between 2 waves */
double oldm, newm, *savm; / Working pointers to matrices */	double oldm, newm, *savm; / Working pointers to matrices */
double oldms, newms, *savms; / Fixed working pointers to matrices */	double oldms, newms, *savms; / Fixed working pointers to matrices */
FILE fic,ficpar, ficparo,ficres, ficrespl, ficrespij, ficrest,ficresf,*ficrespop;	FILE fic,ficpar, ficparo,ficres, ficresp, ficrespl, ficrespij, ficrest,ficresf,ficrespop;
FILE ficlog, ficrespow;	FILE ficlog, ficrespow;
int globpr; /* Global variable for printing or not */	int globpr=0; /* Global variable for printing or not */
double fretone; /* Only one call to likelihood */	double fretone; /* Only one call to likelihood */
long ipmx; /* Number of contributions */	long ipmx=0; /* Number of contributions */
double sw; /* Sum of weights */	double sw; /* Sum of weights */
char filerespow[FILENAMELENGTH];	char filerespow[FILENAMELENGTH];
char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */	char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
Line 346 FILE *ficresprobmorprev;	Line 438 FILE *ficresprobmorprev;
FILE fichtm, fichtmcov; /* Html File */	FILE fichtm, fichtmcov; /* Html File */
FILE *ficreseij;	FILE *ficreseij;
char filerese[FILENAMELENGTH];	char filerese[FILENAMELENGTH];
	FILE *ficresstdeij;
	char fileresstde[FILENAMELENGTH];
	FILE *ficrescveij;
	char filerescve[FILENAMELENGTH];
FILE *ficresvij;	FILE *ficresvij;
char fileresv[FILENAMELENGTH];	char fileresv[FILENAMELENGTH];
FILE *ficresvpl;	FILE *ficresvpl;
char fileresvpl[FILENAMELENGTH];	char fileresvpl[FILENAMELENGTH];
char title[MAXLINE];	char title[MAXLINE];
char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];	char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];	char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];	char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
char command[FILENAMELENGTH];	char command[FILENAMELENGTH];
int outcmd=0;	int outcmd=0;
Line 376 char strcurr[80], strfor[80];	Line 472 char strcurr[80], strfor[80];

char *endptr;	char *endptr;
long lval;	long lval;
	double dval;

#define NR_END 1	#define NR_END 1
#define FREE_ARG char*	#define FREE_ARG char*
Line 941 void powell(double p[], double **xi, int	Line 1038 void powell(double p[], double **xi, int
last_time=curr_time;	last_time=curr_time;
(void) gettimeofday(&curr_time,&tzp);	(void) gettimeofday(&curr_time,&tzp);
printf("\nPowell iter=%d -2LL=%.12f %ld sec. %ld sec.",iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);	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(ficlog,"\nPowell iter=%d -2LL=%.12f %ld sec. %ld sec.",iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
fprintf(ficrespow,"%d %.12f %ld",iter,fret,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 1065 void powell(double p[], double **xi, int	Line 1161 void powell(double p[], double **xi, int
}	}
}	}

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

double prevalim(double prlim, int nlstate, double x[], double age, double oldm, double savm, double ftolpl, int ij)	double prevalim(double prlim, int nlstate, double x[], double age, double oldm, double savm, double ftolpl, int ij)
{	{
Line 1259 double *hpxij(double *po, int nhstep	Line 1355 double *hpxij(double *po, int nhstep
for(i=1; i<=nlstate+ndeath; i++)	for(i=1; i<=nlstate+ndeath; i++)
for(j=1;j<=nlstate+ndeath;j++) {	for(j=1;j<=nlstate+ndeath;j++) {
po[i][j][h]=newm[i][j];	po[i][j][h]=newm[i][j];
/*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);	/if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);/
*/
}	}
	/printf("h=%d ",h);/
} /* end h */	} /* end h */
	/* printf("\n H=%d \n",h); */
return po;	return po;
}	}

Line 1358 double func( double *x)	Line 1455 double func( double *x)

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

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

else if (s2==-5) {	else if (s2==-4) {
for (j=1,survp=0. ; j<=2; j++)	for (j=3,survp=0. ; j<=nlstate; j++)
survp += out[s1][j];	survp += (1.+bbh)out[s1][j]- bbhsavm[s1][j];
lli= survp;	lli= log(survp);
}	}


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

else{	else{
lli= log((1.+bbh)out[s1][s2]- bbhsavm[s1][s2]); /* linear interpolation */	lli= log((1.+bbh)out[s1][s2]- bbhsavm[s1][s2]); /* linear interpolation */
/* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)out[s1][s2]- bbh(savm[s1][s2])):log((1.+bbh)out[s1][s2]));/ /* linear interpolation */	/* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)out[s1][s2]- bbh(savm[s1][s2])):log((1.+bbh)out[s1][s2]));/ /* linear interpolation */
Line 1569 double funcone( double *x)	Line 1666 double funcone( double *x)
*/	*/
if( s2 > nlstate && (mle <5) ){ /* Jackson */	if( s2 > nlstate && (mle <5) ){ /* Jackson */
lli=log(out[s1][s2] - savm[s1][s2]);	lli=log(out[s1][s2] - savm[s1][s2]);
} else if (mle==1){	} else if (s2==-2) {
	for (j=1,survp=0. ; j<=nlstate; j++)
	survp += (1.+bbh)out[s1][j]- bbhsavm[s1][j];
	lli= log(survp);
	}else if (mle==1){
lli= log((1.+bbh)out[s1][s2]- bbhsavm[s1][s2]); /* linear interpolation */	lli= log((1.+bbh)out[s1][s2]- bbhsavm[s1][s2]); /* linear interpolation */
} else if(mle==2){	} else if(mle==2){
lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)out[s1][s2]- bbhsavm[s1][s2]):log((1.+bbh)out[s1][s2])); / linear interpolation */	lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)out[s1][s2]- bbhsavm[s1][s2]):log((1.+bbh)out[s1][s2])); / linear interpolation */
Line 1585 double funcone( double *x)	Line 1686 double funcone( double *x)
ll[s[mw[mi][i]][i]] += 2weight[i]lli;	ll[s[mw[mi][i]][i]] += 2weight[i]lli;
/* printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */	/* printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
if(globpr){	if(globpr){
fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\	fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
%10.6f %10.6f %10.6f ", \	%11.6f %11.6f %11.6f ", \
num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],	num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2weight[i]lli,out[s1][s2],savm[s1][s2]);	2weight[i]lli,out[s1][s2],savm[s1][s2]);
for(k=1,llt=0.,l=0.; k<=nlstate; k++){	for(k=1,llt=0.,l=0.; k<=nlstate; k++){
Line 1939 void lubksb(double *a, int n, int indx	Line 2040 void lubksb(double *a, int n, int indx
}	}
}	}

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

/********** Frequencies ******************/	/********** Frequencies ******************/
void freqsummary(char fileres[], int iagemin, int iagemax, int s, double agev, int nlstate, int imx, int Tvaraff, int nbcode, int ncodemax,double mint,double anint, char strstart[])	void freqsummary(char fileres[], int iagemin, int iagemax, int s, double agev, int nlstate, int imx, int Tvaraff, int nbcode, int ncodemax,double mint,double anint, char strstart[])
{ /* Some frequencies */	{ /* Some frequencies */

int i, m, jk, k1,i1, j1, bool, z1,z2,j;	int i, m, jk, k1,i1, j1, bool, z1,j;
int first;	int first;
double **freq; / Frequencies */	double **freq; / Frequencies */
double pp, *prop;	double pp, *prop;
double pos,posprop, k2, dateintsum=0,k2cpt=0;	double pos,posprop, k2, dateintsum=0,k2cpt=0;
FILE *ficresp;
char fileresp[FILENAMELENGTH];	char fileresp[FILENAMELENGTH];

pp=vector(1,nlstate);	pp=vector(1,nlstate);
Line 2013 void freqsummary(char fileres[], int ia	Line 2118 void freqsummary(char fileres[], int ia
}	}

/* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/	/* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
fprintf(ficresp, "#Local time at start: %s", strstart);	pstamp(ficresp);
if (cptcovn>0) {	if (cptcovn>0) {
fprintf(ficresp, "\n#********** Variable ");	fprintf(ficresp, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
Line 2113 void prevalence(double ***probs, double	Line 2218 void prevalence(double ***probs, double
We still use firstpass and lastpass as another selection.	We still use firstpass and lastpass as another selection.
*/	*/

int i, m, jk, k1, i1, j1, bool, z1,z2,j;	int i, m, jk, k1, i1, j1, bool, z1,j;
double **freq; / Frequencies */	double **freq; / Frequencies */
double pp, *prop;	double pp, *prop;
double pos,posprop;	double pos,posprop;
Line 2171 void prevalence(double ***probs, double	Line 2276 void prevalence(double ***probs, double
if( i <= iagemax){	if( i <= iagemax){
if(posprop>=1.e-5){	if(posprop>=1.e-5){
probs[i][jk][j1]= prop[jk][i]/posprop;	probs[i][jk][j1]= prop[jk][i]/posprop;
}	} else
	printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
}	}
}/* end jk */	}/* end jk */
}/* end i */	}/* end i */
Line 2329 void concatwav(int wav[], int **dh, int	Line 2435 void concatwav(int wav[], int **dh, int
void tricode(int Tvar, int *nbcode, int imx)	void tricode(int Tvar, int *nbcode, int imx)
{	{

int Ndum[20],ij=1, k, j, i, maxncov=19;	/* Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */

	int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=19;
int cptcode=0;	int cptcode=0;
cptcoveff=0;	cptcoveff=0;

Line 2386 void tricode(int Tvar, int *nbcode, in	Line 2494 void tricode(int Tvar, int *nbcode, in

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

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

{	{
/* Health expectancies */	/* Health expectancies, no variances */
int i, j, nhstepm, hstepm, h, nstepm, k, cptj;	int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
	int nhstepma, nstepma; /* Decreasing with age */
double age, agelim, hf;	double age, agelim, hf;
double *p3mat,*varhe;	double ***p3mat;
	double eip;

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


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

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

	agelim=AGESUP;
	/* If stepm=6 months */
	/* Computed by stepm unit matrices, product of hstepm matrices, stored
	in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */

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

	for (age=bage; age<=fage; age ++){
	nstepma=(int) rint((agelim-bage)YEARM/stepm); / Biggest nstepm */
	/* Typically if 20 years nstepm = 2012/6=40 stepm /
	/* if (stepm >= YEARM) hstepm=1;*/
	nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */

	/* If stepm=6 months */
	/* Computed by stepm unit matrices, product of hstepma matrices, stored
	in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */

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

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

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

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

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

	}

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

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

	}

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

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

	double eip, vip;

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

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

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

if(estepm < stepm){	if(estepm < stepm){
printf ("Problem %d lower than %d\n",estepm, stepm);	printf ("Problem %d lower than %d\n",estepm, stepm);
}	}
Line 2441 void evsij(char fileres[], double ***eij	Line 2680 void evsij(char fileres[], double ***eij
*/	*/
hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */	hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */

	/* If stepm=6 months */
	/* nhstepm age range expressed in number of stepm */
agelim=AGESUP;	agelim=AGESUP;
for (age=bage; age<=fage; age ++){ /* If stepm=6 months */	nstepm=(int) rint((agelim-bage)*YEARM/stepm);
/* nhstepm age range expressed in number of stepm */	/* Typically if 20 years nstepm = 2012/6=40 stepm /
nstepm=(int) rint((agelim-age)*YEARM/stepm);	/* if (stepm >= YEARM) hstepm=1;*/
	nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */

	p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
	p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
	gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
	trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
	gp=matrix(0,nhstepm,1,nlstate*nlstate);
	gm=matrix(0,nhstepm,1,nlstate*nlstate);

	for (age=bage; age<=fage; age ++){
	nstepma=(int) rint((agelim-bage)YEARM/stepm); / Biggest nstepm */
/* Typically if 20 years nstepm = 2012/6=40 stepm /	/* Typically if 20 years nstepm = 2012/6=40 stepm /
/* if (stepm >= YEARM) hstepm=1;*/	/* if (stepm >= YEARM) hstepm=1;*/
nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */	nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
gp=matrix(0,nhstepm,1,nlstate*nlstate);
gm=matrix(0,nhstepm,1,nlstate*nlstate);

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


	/* If stepm=6 months */
	/* Computed by stepm unit matrices, product of hstepma matrices, stored
	in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */

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

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

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

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

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

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

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

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


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

printf("%d\|",(int)age);fflush(stdout);	printf("%d\|",(int)age);fflush(stdout);
fprintf(ficlog,"%d\|",(int)age);fflush(ficlog);	fprintf(ficlog,"%d\|",(int)age);fflush(ficlog);
Line 2519 void evsij(char fileres[], double ***eij	Line 2750 void evsij(char fileres[], double ***eij
for(k=0;k<=nhstepm-1;k++){	for(k=0;k<=nhstepm-1;k++){
matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);	matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
matprod2(doldm,dnewm,1,nlstatenlstate,1,npar,1,nlstatenlstate,gradg[k]);	matprod2(doldm,dnewm,1,nlstatenlstate,1,npar,1,nlstatenlstate,gradg[k]);
for(i=1;i<=nlstate*nlstate;i++)	for(ij=1;ij<=nlstate*nlstate;ij++)
for(j=1;j<=nlstate*nlstate;j++)	for(ji=1;ji<=nlstate*nlstate;ji++)
varhe[i][j][(int)age] += doldm[i][j]hfhf;	varhe[ij][ji][(int)age] += doldm[ij][ji]hfhf;
}	}
}	}

/* Computing expectancies */	/* Computing expectancies */
	hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++)	for(j=1; j<=nlstate;j++)
for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){	for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;	eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;

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

}	}

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

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

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

	free_vector(xm,1,npar);
free_vector(xp,1,npar);	free_vector(xp,1,npar);
free_matrix(dnewm,1,nlstate*nlstate,1,npar);	free_matrix(dnewm,1,nlstate*nlstate,1,npar);
free_matrix(doldm,1,nlstatenlstate,1,nlstatenlstate);	free_matrix(doldm,1,nlstatenlstate,1,nlstatenlstate);
Line 2612 void varevsij(char optionfilefiname[], d	Line 2865 void varevsij(char optionfilefiname[], d
printf("Computing total mortality p.j=w1p1j+w2p2j+..: result on file '%s' \n",fileresprobmorprev);	printf("Computing total mortality p.j=w1p1j+w2p2j+..: result on file '%s' \n",fileresprobmorprev);

fprintf(ficlog,"Computing total mortality p.j=w1p1j+w2p2j+..: result on file '%s' \n",fileresprobmorprev);	fprintf(ficlog,"Computing total mortality p.j=w1p1j+w2p2j+..: result on file '%s' \n",fileresprobmorprev);
fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);	pstamp(ficresprobmorprev);
fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1p1j+w2p2j+... stand dev in()\n",estepm);	fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1p1j+w2p2j+... stand dev in()\n",estepm);
fprintf(ficresprobmorprev,"# Age cov=%-d",ij);	fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
for(j=nlstate+1; j<=(nlstate+ndeath);j++){	for(j=nlstate+1; j<=(nlstate+ndeath);j++){
Line 2627 void varevsij(char optionfilefiname[], d	Line 2880 void varevsij(char optionfilefiname[], d
fprintf(fichtm,"\n<br>%s <br>\n",digitp);	fprintf(fichtm,"\n<br>%s <br>\n",digitp);
/* } */	/* } */
varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);	varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
fprintf(ficresvij, "#Local time at start: %s", strstart);	pstamp(ficresvij);
fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are the stable prevalence in health states i\n");	fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
	if(popbased==1)
	fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
	else
	fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
fprintf(ficresvij,"# Age");	fprintf(ficresvij,"# Age");
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++)	for(j=1; j<=nlstate;j++)
fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);	fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
fprintf(ficresvij,"\n");	fprintf(ficresvij,"\n");

xp=vector(1,npar);	xp=vector(1,npar);
Line 2654 void varevsij(char optionfilefiname[], d	Line 2911 void varevsij(char optionfilefiname[], d
/* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.	/* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
nhstepm is the number of hstepm from age to agelim	nhstepm is the number of hstepm from age to agelim
nstepm is the number of stepm from age to agelin.	nstepm is the number of stepm from age to agelin.
Look at hpijx to understand the reason of that which relies in memory size	Look at function hpijx to understand why (it is linked to memory size questions) */
and note for a fixed period like k years */
/* We decided (b) to get a life expectancy respecting the most precise curvature of the	/* We decided (b) to get a life expectancy respecting the most precise curvature of the
survival function given by stepm (the optimization length). Unfortunately it	survival function given by stepm (the optimization length). Unfortunately it
means that if the survival funtion is printed every two years of age and if	means that if the survival funtion is printed every two years of age and if
Line 2721 void varevsij(char optionfilefiname[], d	Line 2977 void varevsij(char optionfilefiname[], d
}	}
}	}

for(j=1; j<= nlstate; j++){	for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
for(h=0; h<=nhstepm; h++){	for(h=0; h<=nhstepm; h++){
for(i=1, gm[h][j]=0.;i<=nlstate;i++)	for(i=1, gm[h][j]=0.;i<=nlstate;i++)
gm[h][j] += prlim[i][i]*p3mat[i][j][h];	gm[h][j] += prlim[i][i]*p3mat[i][j][h];
Line 2873 void varprevlim(char fileres[], double *	Line 3129 void varprevlim(char fileres[], double *
double gradg, trgradg;	double gradg, trgradg;
double age,agelim;	double age,agelim;
int theta;	int theta;
fprintf(ficresvpl, "#Local time at start: %s", strstart);
fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");	pstamp(ficresvpl);
	fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
fprintf(ficresvpl,"# Age");	fprintf(ficresvpl,"# Age");
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
fprintf(ficresvpl," %1d-%1d",i,i);	fprintf(ficresvpl," %1d-%1d",i,i);
Line 2988 void varprob(char optionfilefiname[], do	Line 3245 void varprob(char optionfilefiname[], do
fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);	fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);	printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);	fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
fprintf(ficresprob, "#Local time at start: %s", strstart);	pstamp(ficresprob);
fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");	fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
fprintf(ficresprob,"# Age");	fprintf(ficresprob,"# Age");
fprintf(ficresprobcov, "#Local time at start: %s", strstart);	pstamp(ficresprobcov);
fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");	fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
fprintf(ficresprobcov,"# Age");	fprintf(ficresprobcov,"# Age");
fprintf(ficresprobcor, "#Local time at start: %s", strstart);	pstamp(ficresprobcor);
fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");	fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
fprintf(ficresprobcov,"# Age");	fprintf(ficresprobcor,"# Age");


for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
Line 3277 void printinghtml(char fileres[], char t	Line 3534 void printinghtml(char fileres[], char t
- Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",	- Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));	stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",	- Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));	subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Life expectancies by age and initial health status (estepm=%2d months): \	- (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
<a href=\"%s\">%s</a> <br>\n</li>",	<a href=\"%s\">%s</a> <br>\n",
estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));	estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
	fprintf(fichtm,"\
	- Population projections by age and states: \
	<a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));

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

Line 3300 fprintf(fichtm," \n<ul><li><b>Graphs</b>	Line 3560 fprintf(fichtm," \n<ul><li><b>Graphs</b>
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");	fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
}	}
/* Pij */	/* Pij */
fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \	fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
<img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);	<img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
/* Quasi-incidences */	/* Quasi-incidences */
fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\	fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \	before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
<img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);	<img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
/* Stable prevalence in each health state */	/* Period (stable) prevalence in each health state */
for(cpt=1; cpt<nlstate;cpt++){	for(cpt=1; cpt<nlstate;cpt++){
fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \	fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
<img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);	<img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
}	}
for(cpt=1; cpt<=nlstate;cpt++) {	for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \	fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
<img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);	<img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
}	}
} /* end i1 */	} /* end i1 */
}/* End k1 */	}/* End k1 */
Line 3334 fprintf(fichtm," \n<ul><li><b>Graphs</b>	Line 3594 fprintf(fichtm," \n<ul><li><b>Graphs</b>
- Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",	- Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));	subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",	- Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
	<a href=\"%s\">%s</a> <br>\n</li>",
	estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
	fprintf(fichtm,"\
	- (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
	<a href=\"%s\">%s</a> <br>\n</li>",
	estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
	fprintf(fichtm,"\
	- Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));	estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",	- Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
subdirf2(fileres,"t"),subdirf2(fileres,"t"));	estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\	- Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));	subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));

/* if(popforecast==1) fprintf(fichtm,"\n */	/* if(popforecast==1) fprintf(fichtm,"\n */
Line 3371 prevalence (with 95%% confidence interva	Line 3639 prevalence (with 95%% confidence interva
<img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);	<img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
}	}
fprintf(fichtm,"\n<br>- Total life expectancy by age and \	fprintf(fichtm,"\n<br>- Total life expectancy by age and \
health expectancies in states (1) and (2): %s%d.png<br>\	health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
	true period expectancies (those weighted with period prevalences are also\
	drawn in addition to the population based expectancies computed using\
	observed and cahotic prevalences: %s%d.png<br>\
<img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);	<img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
} /* end i1 */	} /* end i1 */
}/* End k1 */	}/* End k1 */
Line 3383 health expectancies in states (1) and (2	Line 3654 health expectancies in states (1) and (2
void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){	void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){

char dirfileres[132],optfileres[132];	char dirfileres[132],optfileres[132];
int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;	int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
int ng;	int ng=0;
/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */	/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
/* printf("Problem with file %s",optionfilegnuplot); */	/* printf("Problem with file %s",optionfilegnuplot); */
/* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */	/* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
Line 3412 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 3683 plot [%.f:%.f] \"%s\" every :::%d::%d u
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");	if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
else fprintf(ficgp," \%%lf (\%%lf)");	else fprintf(ficgp," \%%lf (\%%lf)");
}	}
fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);	fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
for (i=1; i<= nlstate ; i ++) {	for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");	if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
else fprintf(ficgp," \%%lf (\%%lf)");	else fprintf(ficgp," \%%lf (\%%lf)");
Line 3460 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 3731 plot [%.f:%.f] \"%s\" every :::%d::%d u

for (k1=1; k1<= m ; k1 ++) {	for (k1=1; k1<= m ; k1 ++) {
for (cpt=1; cpt<= nlstate ; cpt ++) {	for (cpt=1; cpt<= nlstate ; cpt ++) {
k=2+nlstate(2cpt-2);	/* k=2+nlstate(2cpt-2); */
	k=2+(nlstate+1)*(cpt-1);
fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);	fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
fprintf(ficgp,"set ter png small\n\	fprintf(ficgp,"set ter png small\n\
set size 0.65,0.65\n\	set size 0.65,0.65\n\
Line 3474 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 3746 plot [%.f:%.f] \"%s\" every :::%d::%d u

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

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

Line 4117 void printinggnuplotmort(char fileres[],	Line 4391 void printinggnuplotmort(char fileres[],




/***********************************************/	/***********************************************/
/************** Main Program ***************/	/************** Main Program ***************/
/***********************************************/	/***********************************************/
Line 4130 int main(int argc, char *argv[])	Line 4405 int main(int argc, char *argv[])
int numlinepar=0; /* Current linenumber of parameter file */	int numlinepar=0; /* Current linenumber of parameter file */
int itimes;	int itimes;
int NDIM=2;	int NDIM=2;
	int vpopbased=0;

char ca[32], cb[32], cc[32];	char ca[32], cb[32], cc[32];
char dummy[]=" ";	char dummy[]=" ";
Line 4185 int main(int argc, char *argv[])	Line 4461 int main(int argc, char *argv[])
char z[1]="c", occ;	char z[1]="c", occ;

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

Line 4236 int main(int argc, char *argv[])	Line 4512 int main(int argc, char *argv[])
while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');	while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
printf("val= \|%s\| pathr=%s\n",val,pathr);	printf("val= \|%s\| pathr=%s\n",val,pathr);
strcpy (pathtot, val);	strcpy (pathtot, val);
if(pathr[0] == '\0') break; /* Un peu sale */	if(pathr[0] == '\0') break; /* Dirty */
}	}
}	}
else{	else{
Line 4255 int main(int argc, char *argv[])	Line 4531 int main(int argc, char *argv[])
/* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */	/* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
split(pathtot,path,optionfile,optionfilext,optionfilefiname);	split(pathtot,path,optionfile,optionfilext,optionfilefiname);
printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);	printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
chdir(path);	chdir(path); /* Can be a relative path */
	if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
	printf("Current directory %s!\n",pathcd);
strcpy(command,"mkdir ");	strcpy(command,"mkdir ");
strcat(command,optionfilefiname);	strcat(command,optionfilefiname);
if((outcmd=system(command)) != 0){	if((outcmd=system(command)) != 0){
Line 4364 int main(int argc, char *argv[])	Line 4642 int main(int argc, char *argv[])
free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);	free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
fclose (ficparo);	fclose (ficparo);
fclose (ficlog);	fclose (ficlog);
	goto end;
exit(0);	exit(0);
}	}
else if(mle==-3) {	else if(mle==-3) {
Line 4394 int main(int argc, char *argv[])	Line 4673 int main(int argc, char *argv[])
j++;	j++;
fscanf(ficpar,"%1d%1d",&i1,&j1);	fscanf(ficpar,"%1d%1d",&i1,&j1);
if ((i1 != i) && (j1 != j)){	if ((i1 != i) && (j1 != j)){
printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);	printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
	It might be a problem of design; if ncovcol and the model are correct\n \
	run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
exit(1);	exit(1);
}	}
fprintf(ficparo,"%1d%1d",i1,j1);	fprintf(ficparo,"%1d%1d",i1,j1);
Line 4521 int main(int argc, char *argv[])	Line 4802 int main(int argc, char *argv[])

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

n= lastobs;	n= lastobs;
Line 4618 int main(int argc, char *argv[])	Line 4899 int main(int argc, char *argv[])

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

for (j=ncovcol;j>=1;j--){	for (j=ncovcol;j>=1;j--){
Line 4635 int main(int argc, char *argv[])	Line 4916 int main(int argc, char *argv[])
exit(1);	exit(1);
}	}
if(lval <-1 \|\| lval >1){	if(lval <-1 \|\| lval >1){
printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a value of the %d covar (meaning 0 for the reference or 1. IMaCh does not build design variables, do it your self). Exiting.\n",lval,linei, i,line,j);	printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
exit(1);	Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
	for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
	For example, for multinomial values like 1, 2 and 3,\n \
	build V1=0 V2=0 for the reference value (1),\n \
	V1=1 V2=0 for (2) \n \
	and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
	output of IMaCh is often meaningless.\n \
	Exiting.\n",lval,linei, i,line,j);
	goto end;
}	}
covar[j][i]=(double)(lval);	covar[j][i]=(double)(lval);
strcpy(line,stra);	strcpy(line,stra);
}	}
lstra=strlen(stra);	lstra=strlen(stra);

if(lstra > 9){ /* More than 2*32 or max of what printf can write with %ld /	if(lstra > 9){ /* More than 2*32 or max of what printf can write with %ld /
stratrunc = &(stra[lstra-9]);	stratrunc = &(stra[lstra-9]);
num[i]=atol(stratrunc);	num[i]=atol(stratrunc);
Line 4684 int main(int argc, char *argv[])	Line 4973 int main(int argc, char *argv[])
j=0, j1=0, k1=1, k2=1;	j=0, j1=0, k1=1, k2=1;
j=nbocc(model,'+'); /* j=Number of '+' */	j=nbocc(model,'+'); /* j=Number of '+' */
j1=nbocc(model,''); / j1=Number of '' /	j1=nbocc(model,''); / j1=Number of '' /
cptcovn=j+1;	cptcovn=j+1; /* Number of covariates V1+V2+V3 =>2+1=3 */
cptcovprod=j1; /Number of products /	cptcovprod=j1; /Number of products V1V2 =1 */

strcpy(modelsav,model);	strcpy(modelsav,model);
if ((strcmp(model,"age")==0) \|\| (strcmp(model,"age*age")==0)){	if ((strcmp(model,"age")==0) \|\| (strcmp(model,"age*age")==0)){
Line 4695 int main(int argc, char *argv[])	Line 4984 int main(int argc, char *argv[])
}	}

/* This loop fills the array Tvar from the string 'model'.*/	/* This loop fills the array Tvar from the string 'model'.*/
	/* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
for(i=(j+1); i>=1;i--){	for(i=(j+1); i>=1;i--){
cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */	cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
	modelsav=V2+V3age+V1+V4 strb=V3age+V1+V4
	stra=V2
	*/
if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */	if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
/* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/	/* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
/scanf("%d",i);/	/scanf("%d",i);/
if (strchr(strb,'')) { / Model includes a product */	if (strchr(strb,'')) { / Model includes a product V1+V3age+V2 strb=V3age*/
cutv(strd,strc,strb,''); / strdstrc VmVn (if not age)/	cutv(strd,strc,strb,''); / strdstrc VmVn: V3age strc=age strd=V3 ; V3V2 strc=V2, strd=V3 */
if (strcmp(strc,"age")==0) { /* Vnage /	if (strcmp(strc,"age")==0) { /* Vnage /
cptcovprod--;	cptcovprod--;
cutv(strb,stre,strd,'V');	cutv(strb,stre,strd,'V');
Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/	Tvar[i]=atoi(stre); /* V1+V3age+V2 Tvar[2]=3 /
cptcovage++;	cptcovage++; /* Sum the number of covariates including ages as a product */
Tage[cptcovage]=i;	Tage[cptcovage]=i; /* Tage[1] =2 */
/printf("stre=%s ", stre);/	/printf("stre=%s ", stre);/
}	}
else if (strcmp(strd,"age")==0) { /* or ageVn /	else if (strcmp(strd,"age")==0) { /* or ageVn /
cptcovprod--;	cptcovprod--;
Line 4718 int main(int argc, char *argv[])	Line 5010 int main(int argc, char *argv[])
cptcovage++;	cptcovage++;
Tage[cptcovage]=i;	Tage[cptcovage]=i;
}	}
else { /* Age is not in the model */	else { /* Age is not in the model V1+V3V2+V2 strb=V3V2*/
cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/	cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3V2 stre=3 strc=/
Tvar[i]=ncovcol+k1;	Tvar[i]=ncovcol+k1; /* find 'n' in Vn and stores in Tvar.
	If already ncovcol=2 and model=V2V1 Tvar[1]=2+1 and Tvar[2]=2+2 etc /
cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */	cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
Tprod[k1]=i;	Tprod[k1]=i; /* Tprod[1] */
Tvard[k1][1]=atoi(strc); /* m*/	Tvard[k1][1]=atoi(strc); /* m*/
Tvard[k1][2]=atoi(stre); /* n */	Tvard[k1][2]=atoi(stre); /* n */
Tvar[cptcovn+k2]=Tvard[k1][1];	Tvar[cptcovn+k2]=Tvard[k1][1];
Line 4739 int main(int argc, char *argv[])	Line 5032 int main(int argc, char *argv[])
cutv(strd,strc,strb,'V');	cutv(strd,strc,strb,'V');
Tvar[i]=atoi(strc);	Tvar[i]=atoi(strc);
}	}
strcpy(modelsav,stra);	strcpy(modelsav,stra); /* modelsav=V2+V3age+V1+V4 strb=V3age+V1+V4 */
/*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);	/*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
scanf("%d",i);*/	scanf("%d",i);*/
} /* end of loop + */	} /* end of loop + */
Line 4885 int main(int argc, char *argv[])	Line 5178 int main(int argc, char *argv[])
for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){	for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
h++;	h++;
if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;	if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
/* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/	printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
}	}
}	}
}	}
Line 4931 int main(int argc, char *argv[])	Line 5224 int main(int argc, char *argv[])
printf("Problem with %s \n",optionfilehtmcov), exit(0);	printf("Problem with %s \n",optionfilehtmcov), exit(0);
}	}
else{	else{
fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \	fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
<hr size=\"2\" color=\"#EC5E5E\"> \n\	<hr size=\"2\" color=\"#EC5E5E\"> \n\
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\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);	optionfilehtmcov,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> \	fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
<hr size=\"2\" color=\"#EC5E5E\"> \n\	<hr size=\"2\" color=\"#EC5E5E\"> \n\
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\	Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
\n\	\n\
<hr size=\"2\" color=\"#EC5E5E\">\	<hr size=\"2\" color=\"#EC5E5E\">\
<ul><li><h4>Parameter files</h4>\n\	<ul><li><h4>Parameter files</h4>\n\
	- Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
- Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\	- Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
- Log file of the run: <a href=\"%s\">%s</a><br>\n\	- Log file of the run: <a href=\"%s\">%s</a><br>\n\
- Gnuplot file name: <a href=\"%s\">%s</a><br>\n\	- Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
- Date and time at start: %s</ul>\n",\	- Date and time at start: %s</ul>\n",\
fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\	optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
	optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
fileres,fileres,\	fileres,fileres,\
filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);	filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
fflush(fichtm);	fflush(fichtm);
Line 5086 Interval (in months) between two waves:	Line 5381 Interval (in months) between two waves:
printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]exp(p[2](k-agegomp)),(p[1]exp(p[2](k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);	printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]exp(p[2](k-agegomp)),(p[1]exp(p[2](k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);


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

printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \	printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
Line 5129 Interval (in months) between two waves:	Line 5424 Interval (in months) between two waves:
fprintf(ficlog,"%d%d ",i,k);	fprintf(ficlog,"%d%d ",i,k);
fprintf(ficres,"%1d%1d ",i,k);	fprintf(ficres,"%1d%1d ",i,k);
for(j=1; j <=ncovmodel; j++){	for(j=1; j <=ncovmodel; j++){
printf("%f ",p[jk]);	printf("%lf ",p[jk]);
fprintf(ficlog,"%f ",p[jk]);	fprintf(ficlog,"%lf ",p[jk]);
fprintf(ficres,"%f ",p[jk]);	fprintf(ficres,"%lf ",p[jk]);
jk++;	jk++;
}	}
printf("\n");	printf("\n");
Line 5323 Interval (in months) between two waves:	Line 5618 Interval (in months) between two waves:
/* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/	/* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
/,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);/	/,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);/

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

printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\	printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
Line 5345 Interval (in months) between two waves:	Line 5640 Interval (in months) between two waves:
fclose(ficres);	fclose(ficres);


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

strcpy(filerespl,"pl");	strcpy(filerespl,"pl");
strcat(filerespl,fileres);	strcat(filerespl,fileres);
if((ficrespl=fopen(filerespl,"w"))==NULL) {	if((ficrespl=fopen(filerespl,"w"))==NULL) {
printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;	printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;	fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
}	}
printf("Computing stable prevalence: result on file '%s' \n", filerespl);	printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);	fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
fprintf(ficrespl, "#Local time at start: %s", strstart);	pstamp(ficrespl);
fprintf(ficrespl,"#Stable prevalence \n");	fprintf(ficrespl,"# Period (stable) prevalence \n");
fprintf(ficrespl,"#Age ");	fprintf(ficrespl,"#Age ");
for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);	for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
fprintf(ficrespl,"\n");	fprintf(ficrespl,"\n");
Line 5416 Interval (in months) between two waves:	Line 5711 Interval (in months) between two waves:
hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */	hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */

/* hstepm=1; aff par mois*/	/* hstepm=1; aff par mois*/
fprintf(ficrespij, "#Local time at start: %s", strstart);	pstamp(ficrespij);
fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");	fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
for(cptcov=1,k=0;cptcov<=i1;cptcov++){	for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){	for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
Line 5478 Interval (in months) between two waves:	Line 5773 Interval (in months) between two waves:
}	}


/---------- Health expectancies and variances ------------/	/* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */

strcpy(filerest,"t");	prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
strcat(filerest,fileres);	/* 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",\
if((ficrest=fopen(filerest,"w"))==NULL) {	ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
printf("Problem with total LE resultfile: %s\n", filerest);goto end;	*/
fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
	if (mobilav!=0) {
	mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
	if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
	fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
	printf(" Error in movingaverage mobilav=%d\n",mobilav);
	}
}	}
printf("Computing Total LEs with variances: file '%s' \n", filerest);
fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);


	/---------- Health expectancies, no variances ------------/

strcpy(filerese,"e");	strcpy(filerese,"e");
strcat(filerese,fileres);	strcat(filerese,fileres);
if((ficreseij=fopen(filerese,"w"))==NULL) {	if((ficreseij=fopen(filerese,"w"))==NULL) {
Line 5498 Interval (in months) between two waves:	Line 5799 Interval (in months) between two waves:
}	}
printf("Computing Health Expectancies: result on file '%s' \n", filerese);	printf("Computing Health Expectancies: result on file '%s' \n", filerese);
fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);	fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
	for(cptcov=1,k=0;cptcov<=i1;cptcov++){
	for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
	k=k+1;
	fprintf(ficreseij,"\n#****** ");
	for(j=1;j<=cptcoveff;j++) {
	fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
	}
	fprintf(ficreseij,"******\n");

	eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
	oldm=oldms;savm=savms;
	evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);

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


	/---------- Health expectancies and variances ------------/


	strcpy(filerest,"t");
	strcat(filerest,fileres);
	if((ficrest=fopen(filerest,"w"))==NULL) {
	printf("Problem with total LE resultfile: %s\n", filerest);goto end;
	fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
	}
	printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
	fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);


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

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

strcpy(fileresv,"v");	strcpy(fileresv,"v");
strcat(fileresv,fileres);	strcat(fileresv,fileres);
Line 5508 Interval (in months) between two waves:	Line 5858 Interval (in months) between two waves:
printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);	printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);	fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);

/* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
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",\
ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
*/

if (mobilav!=0) {
mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
printf(" Error in movingaverage mobilav=%d\n",mobilav);
}
}

for(cptcov=1,k=0;cptcov<=i1;cptcov++){	for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){	for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
k=k+1;	k=k+1;
Line 5530 Interval (in months) between two waves:	Line 5866 Interval (in months) between two waves:
fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
fprintf(ficrest,"******\n");	fprintf(ficrest,"******\n");

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

fprintf(ficresvij,"\n#****** ");	fprintf(ficresvij,"\n#****** ");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
Line 5542 Interval (in months) between two waves:	Line 5882 Interval (in months) between two waves:

eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);	eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
oldm=oldms;savm=savms;	oldm=oldms;savm=savms;
evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);	cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);

vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);	vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
oldm=oldms;savm=savms;	pstamp(ficrest);
varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);	for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
if(popbased==1){	oldm=oldms;savm=savms;
varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);	varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are ");
}	if(vpopbased==1)
	fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
fprintf(ficrest, "#Local time at start: %s", strstart);	else
fprintf(ficrest,"#Total LEs with variances: e.. (std) ");	fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);	fprintf(ficrest,"# Age e.. (std) ");
fprintf(ficrest,"\n");	for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
	fprintf(ficrest,"\n");

epj=vector(1,nlstate+1);	epj=vector(1,nlstate+1);
for(age=bage; age <=fage ;age++){	for(age=bage; age <=fage ;age++){
prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);	prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
if (popbased==1) {	if (vpopbased==1) {
if(mobilav ==0){	if(mobilav ==0){
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
prlim[i][i]=probs[(int)age][i][k];	prlim[i][i]=probs[(int)age][i][k];
}else{ /* mobilav */	}else{ /* mobilav */
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
prlim[i][i]=mobaverage[(int)age][i][k];	prlim[i][i]=mobaverage[(int)age][i][k];
	}
}	}
}

fprintf(ficrest," %4.0f",age);	fprintf(ficrest," %4.0f",age);
for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){	for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
for(i=1, epj[j]=0.;i <=nlstate;i++) {	for(i=1, epj[j]=0.;i <=nlstate;i++) {
epj[j] += prlim[i][i]*eij[i][j][(int)age];	epj[j] += prlim[i][i]*eij[i][j][(int)age];
/* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/	/* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
	}
	epj[nlstate+1] +=epj[j];
}	}
epj[nlstate+1] +=epj[j];
}

for(i=1, vepp=0.;i <=nlstate;i++)	for(i=1, vepp=0.;i <=nlstate;i++)
for(j=1;j <=nlstate;j++)	for(j=1;j <=nlstate;j++)
vepp += vareij[i][j][(int)age];	vepp += vareij[i][j][(int)age];
fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));	fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
for(j=1;j <=nlstate;j++){	for(j=1;j <=nlstate;j++){
fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));	fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
	}
	fprintf(ficrest,"\n");
}	}
fprintf(ficrest,"\n");
}	}
free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);	free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);	free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
Line 5599 Interval (in months) between two waves:	Line 5941 Interval (in months) between two waves:
free_matrix(mint,1,maxwav,1,n);	free_matrix(mint,1,maxwav,1,n);
free_ivector(cod,1,n);	free_ivector(cod,1,n);
free_ivector(tab,1,NCOVMAX);	free_ivector(tab,1,NCOVMAX);
fclose(ficreseij);	fclose(ficresstdeij);
	fclose(ficrescveij);
fclose(ficresvij);	fclose(ficresvij);
fclose(ficrest);	fclose(ficrest);
fclose(ficpar);	fclose(ficpar);

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

strcpy(fileresvpl,"vpl");	strcpy(fileresvpl,"vpl");
strcat(fileresvpl,fileres);	strcat(fileresvpl,fileres);
if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {	if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);	printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
exit(0);	exit(0);
}	}
printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);	printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);

for(cptcov=1,k=0;cptcov<=i1;cptcov++){	for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){	for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
Line 5683 Interval (in months) between two waves:	Line 6026 Interval (in months) between two waves:
fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);	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);*/	/* printf("Total time was %d uSec.\n", total_usecs);*/
/* if(fileappend(fichtm,optionfilehtm)){ */	/* if(fileappend(fichtm,optionfilehtm)){ */
fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>",strstart, strtend);	fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
fclose(fichtm);	fclose(fichtm);
	fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
fclose(fichtmcov);	fclose(fichtmcov);
fclose(ficgp);	fclose(ficgp);
fclose(ficlog);	fclose(ficlog);
/------ End -----------/	/------ End -----------/

chdir(path);
	printf("Before Current directory %s!\n",pathcd);
	if(chdir(pathcd) != 0)
	printf("Can't move to directory %s!\n",path);
	if(getcwd(pathcd,MAXLINE) > 0)
	printf("Current directory %s!\n",pathcd);
/strcat(plotcmd,CHARSEPARATOR);/	/strcat(plotcmd,CHARSEPARATOR);/
sprintf(plotcmd,"gnuplot");	sprintf(plotcmd,"gnuplot");
#ifndef UNIX	#ifndef UNIX

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