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Diff for /imach/src/imach.c between versions 1.223 and 1.224

version 1.223, 2016/02/19 09:23:35	version 1.224, 2016/07/01 13:16:01
Line 1	Line 1
/* $Id$	/* $Id$
$State$	$State$
$Log$	$Log$
	Revision 1.224 2016/07/01 13:16:01 brouard
	Summary: Fixes

Revision 1.223 2016/02/19 09:23:35 brouard	Revision 1.223 2016/02/19 09:23:35 brouard
Summary: temporary	Summary: temporary

Line 745 Back prevalence and projections:	Line 748 Back prevalence and projections:
/* #define DEBUGLINMIN */	/* #define DEBUGLINMIN */
/* #define DEBUGHESS */	/* #define DEBUGHESS */
#define DEBUGHESSIJ	#define DEBUGHESSIJ
/* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan)\/ /	/* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan) \/ /
#define POWELL /* Instead of NLOPT */	#define POWELL /* Instead of NLOPT */
#define POWELLF1F3 /* Skip test */	#define POWELLNOF3INFF1TEST /* Skip test */
/* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test \/ /	/* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test \/ /
/* #define MNBRAKORIGINAL /\* Don't use mnbrak fix \/ /	/* #define MNBRAKORIGINAL /\* Don't use mnbrak fix \/ /

Line 841 typedef struct {	Line 844 typedef struct {
/* $State$ */	/* $State$ */
#include "version.h"	#include "version.h"
char version[]=__IMACH_VERSION__;	char version[]=__IMACH_VERSION__;
char copyright[]="October 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";	char copyright[]="February 2016,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018";
char fullversion[]="$Revision$ $Date$";	char fullversion[]="$Revision$ $Date$";
char strstart[80];	char strstart[80];
char optionfilext[10], optionfilefiname[FILENAMELENGTH];	char optionfilext[10], optionfilefiname[FILENAMELENGTH];
Line 854 int cptcovs=0; /**< cptcovs number of si	Line 857 int cptcovs=0; /**< cptcovs number of si
int cptcovage=0; /*< Number of covariates with age: V3age only =1 */	int cptcovage=0; /*< Number of covariates with age: V3age only =1 */
int cptcovprodnoage=0; /*< Number of covariate products without age /	int cptcovprodnoage=0; /*< Number of covariate products without age /
int cptcoveff=0; /* Total number of covariates to vary for printing results */	int cptcoveff=0; /* Total number of covariates to vary for printing results */
	int ncoveff=0; /* Total number of effective covariates in the model */
	int nqveff=0; /*< nqveff number of effective quantitative variables /
	int ntveff=0; /*< ntveff number of effective time varying variables /
	int nqtveff=0; /*< ntqveff number of effective time varying quantitative variables /
int cptcov=0; /* Working variable */	int cptcov=0; /* Working variable */
int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */	int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
int npar=NPARMAX;	int npar=NPARMAX;
Line 999 double *agedc;	Line 1006 double *agedc;
double covar; /< covar[j,i], value of jth covariate for individual i,	double covar; /< covar[j,i], value of jth covariate for individual i,
* covar=matrix(0,NCOVMAX,1,n);	* covar=matrix(0,NCOVMAX,1,n);
* cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]age; /	* cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]age; /
	double *coqvar; / Fixed quantitative covariate */
double **cotvar; / Time varying covariate */	double **cotvar; / Time varying covariate */
double **cotqvar; / Time varying quantitative covariate */	double **cotqvar; / Time varying quantitative covariate */
double *coqvar; / Fixed quantitative covariate */
double idx;	double idx;
int *nbcode, Tvar; /*< model=V2 => Tvar[1]= 2 /	int *nbcode, Tvar; /*< model=V2 => Tvar[1]= 2 /
int *Tage;	int *Tage;
Line 1549 double brent(double ax, double bx, doubl	Line 1556 double brent(double ax, double bx, doubl
etemp=e;	etemp=e;
e=d;	e=d;
if (fabs(p) >= fabs(0.5qetemp) \|\| p <= q(a-x) \|\| p >= q(b-x))	if (fabs(p) >= fabs(0.5qetemp) \|\| p <= q(a-x) \|\| p >= q(b-x))
d=CGOLD*(e=(x >= xm ? a-x : b-x));	d=CGOLD*(e=(x >= xm ? a-x : b-x));
else {	else {
d=p/q;	d=p/q;
u=x+d;	u=x+d;
if (u-a < tol2 \|\| b-u < tol2)	if (u-a < tol2 \|\| b-u < tol2)
d=SIGN(tol1,xm-x);	d=SIGN(tol1,xm-x);
}	}
} else {	} else {
d=CGOLD*(e=(x >= xm ? a-x : b-x));	d=CGOLD*(e=(x >= xm ? a-x : b-x));
Line 1568 double brent(double ax, double bx, doubl	Line 1575 double brent(double ax, double bx, doubl
} else {	} else {
if (u < x) a=u; else b=u;	if (u < x) a=u; else b=u;
if (fu <= fw \|\| w == x) {	if (fu <= fw \|\| w == x) {
v=w;	v=w;
w=u;	w=u;
fv=fw;	fv=fw;
fw=fu;	fw=fu;
} else if (fu <= fv \|\| v == x \|\| v == w) {	} else if (fu <= fv \|\| v == x \|\| v == w) {
v=u;	v=u;
fv=fu;	fv=fu;
}	}
}	}
}	}
Line 1615 values at the three points, fa, fb , and	Line 1622 values at the three points, fa, fb , and
cx=(bx)+GOLD(bx-*ax);	cx=(bx)+GOLD(bx-*ax);
fc=(func)(*cx);	fc=(func)(*cx);
#ifdef DEBUG	#ifdef DEBUG
printf("mnbrak0 fb=%.12e fc=%.12e\n",fb,fc);	printf("mnbrak0 a=%lf fa=%lf, b=%lf fb=%lf, c=%lf fc=%lf\n",ax,fa,bx,fb,cx, *fc);
fprintf(ficlog,"mnbrak0 fb=%.12e fc=%.12e\n",fb,fc);	fprintf(ficlog,"mnbrak0 a=%lf fa=%lf, b=%lf fb=%lf, c=%lf fc=%lf\n",ax,fa,bx,fb,cx, *fc);
#endif	#endif
while (fb > fc) { /* Declining a,b,c with fa> fb > fc */	while (fb > fc) { /* Declining a,b,c with fa> fb > fc. If fc=inf it exits and if flat fb=fc it exits too.*/
r=(bx-ax)(fb-*fc);	r=(bx-ax)(fb-*fc);
q=(bx-cx)(fb-*fa);	q=(bx-cx)(fb-fa); / What if fa=inf */
u=(bx)-((bx-cx)q-(bx-ax)*r)/	u=(bx)-((bx-cx)q-(bx-ax)*r)/
(2.0SIGN(FMAX(fabs(q-r),TINY),q-r)); / Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */	(2.0SIGN(FMAX(fabs(q-r),TINY),q-r)); / Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
ulim=(bx)+GLIMIT(cx-bx); /* Maximum abscissa where function should be evaluated */	ulim=(bx)+GLIMIT(cx-bx); /* Maximum abscissa where function should be evaluated */
Line 1631 values at the three points, fa, fb , and	Line 1638 values at the three points, fa, fb , and
double A, fparabu;	double A, fparabu;
A= (fb - fa)/(bx-ax)/(bx+ax-2*u);	A= (fb - fa)/(bx-ax)/(bx+ax-2*u);
fparabu= fa - A(ax-u)(*ax-u);	fparabu= fa - A(ax-u)(*ax-u);
printf("mnbrak (ax=%.12f, fa=%.12lf), (bx=%.12f, fb=%.12lf), (cx=%.12f, fc=%.12lf), (u=%.12f, fu=%.12lf, fparabu=%.12f)\n",ax,fa,bx,fb,cx,*fc,u,fu, fparabu);	printf("\nmnbrak (ax=%.12f, fa=%.12lf), (bx=%.12f, fb=%.12lf), (cx=%.12f, fc=%.12lf), (u=%.12f, fu=%.12lf, fparabu=%.12f, q=%lf < %lf=r)\n",ax,fa,bx,fb,cx,*fc,u,fu, fparabu,q,r);
fprintf(ficlog, "mnbrak (ax=%.12f, fa=%.12lf), (bx=%.12f, fb=%.12lf), (cx=%.12f, fc=%.12lf), (u=%.12f, fu=%.12lf, fparabu=%.12f)\n",ax,fa,bx,fb,cx,*fc,u,fu, fparabu);	fprintf(ficlog,"\nmnbrak (ax=%.12f, fa=%.12lf), (bx=%.12f, fb=%.12lf), (cx=%.12f, fc=%.12lf), (u=%.12f, fu=%.12lf, fparabu=%.12f, q=%lf < %lf=r)\n",ax,fa,bx,fb,cx,*fc,u,fu, fparabu,q,r);
/* And thus,it can be that fu > fc even if fparabu < fc */	/* And thus,it can be that fu > fc even if fparabu < fc */
/* mnbrak (ax=7.666299858533, fa=299039.693133272231), (bx=8.595447774979, fb=298976.598289369489),	/* mnbrak (ax=7.666299858533, fa=299039.693133272231), (bx=8.595447774979, fb=298976.598289369489),
(cx=10.098840694817, fc=298946.631474258087), (u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) /	(cx=10.098840694817, fc=298946.631474258087), (u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) /
Line 1665 values at the three points, fa, fb , and	Line 1672 values at the three points, fa, fb , and
/* fu = fc; /	/* fu = fc; /
/* fc =dum; /	/* fc =dum; /
/* } */	/* } */
#ifdef DEBUG	#ifdef DEBUGMNBRAK
printf("mnbrak34 fu < or >= fc \n");	double A, fparabu;
fprintf(ficlog, "mnbrak34 fu < fc\n");	A= (fb - fa)/(bx-ax)/(bx+ax-2*u);
	fparabu= fa - A(ax-u)(*ax-u);
	printf("\nmnbrak35 ax=%lf fa=%lf bx=%lf fb=%lf, u=%lf fp=%lf fu=%lf < or >= fc=%lf cx=%lf, q=%lf < %lf=r \n",ax, fa, bx,fb,u,fparabu,fu,fc,cx,q,r);
	fprintf(ficlog,"\nmnbrak35 ax=%lf fa=%lf bx=%lf fb=%lf, u=%lf fp=%lf fu=%lf < or >= fc=%lf cx=%lf, q=%lf < %lf=r \n",ax, fa, bx,fb,u,fparabu,fu,fc,cx,q,r);
#endif	#endif
dum=u; /* Shifting c and u */	dum=u; /* Shifting c and u */
u = *cx;	u = *cx;
Line 1678 values at the three points, fa, fb , and	Line 1688 values at the three points, fa, fb , and
#endif	#endif
} else if ((cx-u)(u-ulim) > 0.0) { /* u is after c but before ulim */	} else if ((cx-u)(u-ulim) > 0.0) { /* u is after c but before ulim */
#ifdef DEBUG	#ifdef DEBUG
printf("mnbrak2 u after c but before ulim\n");	printf("\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
fprintf(ficlog, "mnbrak2 u after c but before ulim\n");	fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
#endif	#endif
fu=(*func)(u);	fu=(*func)(u);
if (fu < *fc) {	if (fu < *fc) {
#ifdef DEBUG	#ifdef DEBUG
printf("mnbrak2 u after c but before ulim AND fu < fc\n");	printf("\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,cx,ulim,fu, fc);
fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");	fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,cx,ulim,fu, fc);
	#endif
	SHFT(bx,cx,u,cx+GOLD(cx-bx))
	SHFT(fb,fc,fu,(*func)(u))
	#ifdef DEBUG
	printf("\nmnbrak2 shift GOLD c=%lf",cx+GOLD(cx-bx));
#endif	#endif
SHFT(bx,cx,u,cx+GOLD(cx-bx))
SHFT(fb,fc,fu,(*func)(u))
}	}
} else if ((u-ulim)(ulim-cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */	} else if ((u-ulim)(ulim-cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
#ifdef DEBUG	#ifdef DEBUG
printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");	printf("\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");	fprintf(ficlog,"\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
#endif	#endif
u=ulim;	u=ulim;
fu=(*func)(u);	fu=(*func)(u);
} else { /* u could be left to b (if r > q parabola has a maximum) */	} else { /* u could be left to b (if r > q parabola has a maximum) */
#ifdef DEBUG	#ifdef DEBUG
printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");	printf("\nmnbrak2 u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");	fprintf(ficlog,"\nmnbrak2 u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
#endif	#endif
u=(cx)+GOLD(cx-bx);	u=(cx)+GOLD(cx-bx);
fu=(*func)(u);	fu=(*func)(u);
	#ifdef DEBUG
	printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,cx,bx);
	fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,cx,bx);
	#endif
} /* end tests */	} /* end tests */
SHFT(ax,bx,*cx,u)	SHFT(ax,bx,*cx,u)
SHFT(fa,fb,*fc,fu)	SHFT(fa,fb,*fc,fu)
#ifdef DEBUG	#ifdef DEBUG
printf("mnbrak2 (ax=%.12f, fa=%.12lf), (bx=%.12f, fb=%.12lf), (cx=%.12f, fc=%.12lf), (u=%.12f, fu=%.12lf)\n",ax,fa,bx,fb,cx,*fc,u,fu);	printf("\nmnbrak2 shift (ax=%.12f, fa=%.12lf), (bx=%.12f, fb=%.12lf), (cx=%.12f, fc=%.12lf)\n",ax,fa,bx,fb,cx,fc);
fprintf(ficlog, "mnbrak2 (ax=%.12f, fa=%.12lf), (bx=%.12f, fb=%.12lf), (cx=%.12f, fc=%.12lf), (u=%.12f, fu=%.12lf)\n",ax,fa,bx,fb,cx,*fc,u,fu);	fprintf(ficlog, "\nmnbrak2 shift (ax=%.12f, fa=%.12lf), (bx=%.12f, fb=%.12lf), (cx=%.12f, fc=%.12lf)\n",ax,fa,bx,fb,cx,fc);
#endif	#endif
} /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */	} /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
}	}
Line 1724 int ncom;	Line 1741 int ncom;
double pcom,xicom;	double pcom,xicom;
double (*nrfunc)(double []);	double (*nrfunc)(double []);

	#ifdef LINMINORIGINAL
void linmin(double p[], double xi[], int n, double fret,double (func)(double []))	void linmin(double p[], double xi[], int n, double fret,double (func)(double []))
	#else
	void linmin(double p[], double xi[], int n, double fret,double (func)(double []), int *flat)
	#endif
{	{
double brent(double ax, double bx, double cx,	double brent(double ax, double bx, double cx,
double (f)(double), double tol, double xmin);	double (f)(double), double tol, double xmin);
Line 1768 void linmin(double p[], double xi[], int	Line 1789 void linmin(double p[], double xi[], int
#ifdef LINMINORIGINAL	#ifdef LINMINORIGINAL
#else	#else
if (fx != fx){	if (fx != fx){
xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */	xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
printf("\|");	printf("\|");
fprintf(ficlog,"\|");	fprintf(ficlog,"\|");
#ifdef DEBUGLINMIN	#ifdef DEBUGLINMIN
printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n", axs, xxs, fx,fb, fa, xx, ax, bx);	printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n", axs, xxs, fx,fb, fa, xx, ax, bx);
#endif	#endif
}	}
}while(fx != fx);	}while(fx != fx && xxs > 1.e-5);
#endif	#endif

#ifdef DEBUGLINMIN	#ifdef DEBUGLINMIN
printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n", ax,xx,bx,fa,fx,fb);	printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n", ax,xx,bx,fa,fx,fb);
fprintf(ficlog,"\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n", ax,xx,bx,fa,fx,fb);	fprintf(ficlog,"\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n", ax,xx,bx,fa,fx,fb);
#endif	#endif
	#ifdef LINMINORIGINAL
	#else
	if(fb == fx){ /* Flat function in the direction */
	xmin=xx;
	*flat=1;
	}else{
	*flat=0;
	#endif
	/Flat mnbrak2 shift (ax=0.000000000000, fa=51626.272983130431), (bx=-1.618034000000, fb=51590.149499362531), (cx=-4.236068025156, fc=51590.149499362531) /
fret=brent(ax,xx,bx,f1dim,TOL,&xmin); / Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, fret(xmin),/	fret=brent(ax,xx,bx,f1dim,TOL,&xmin); / Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, fret(xmin),/
/* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */	/* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
/* fmin = f(p[j] + xmin * xi[j]) */	/* fmin = f(p[j] + xmin * xi[j]) */
/* P+lambda n in that direction (lambdamin), with TOL between abscisses */	/* P+lambda n in that direction (lambdamin), with TOL between abscisses */
/* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xminxicom[j]; /	/* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xminxicom[j]; /
#ifdef DEBUG	#ifdef DEBUG
printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);	printf("retour brent from bracket (a=%lf fa=%lf, xx=%lf fx=%lf, b=%lf fb=%lf): fret=%lf xmin=%lf\n",ax,fa,xx,fx,bx,fb,*fret,xmin);
fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);	fprintf(ficlog,"retour brent from bracket (a=%lf fa=%lf, xx=%lf fx=%lf, b=%lf fb=%lf): fret=%lf xmin=%lf\n",ax,fa,xx,fx,bx,fb,*fret,xmin);
	#endif
	#ifdef LINMINORIGINAL
	#else
	}
#endif	#endif
#ifdef DEBUGLINMIN	#ifdef DEBUGLINMIN
printf("linmin end ");	printf("linmin end ");
Line 1839 such that failure to decrease by more th	Line 1873 such that failure to decrease by more th
output, p is set to the best point found, xi is the then-current direction set, fret is the returned	output, p is set to the best point found, xi is the then-current direction set, fret is the returned
function value at p , and iter is the number of iterations taken. The routine linmin is used.	function value at p , and iter is the number of iterations taken. The routine linmin is used.
*/	*/
	#ifdef LINMINORIGINAL
	#else
	int flatdir; / Function is vanishing in that direction */
	int flat=0; /* Function is vanishing in that direction */
	#endif
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 []))
{	{
void linmin(double p[], double xi[], int n, double *fret,	#ifdef LINMINORIGINAL
	void linmin(double p[], double xi[], int n, double *fret,
double (*func)(double []));	double (*func)(double []));
	#else
	void linmin(double p[], double xi[], int n, double *fret,
	double (func)(double []),int flat);
	#endif
int i,ibig,j;	int i,ibig,j;
double del,t,pt,ptt,*xit;	double del,t,pt,ptt,*xit;
double directest;	double directest;
double fp,fptt;	double fp,fptt;
double *xits;	double *xits;
int niterf, itmp;	int niterf, itmp;
	#ifdef LINMINORIGINAL
	#else

	flatdir=ivector(1,n);
	for (j=1;j<=n;j++) flatdir[j]=0;
	#endif

pt=vector(1,n);	pt=vector(1,n);
ptt=vector(1,n);	ptt=vector(1,n);
Line 1883 void powell(double p[], double **xi, int	Line 1933 void powell(double p[], double **xi, int
rforecast_time=rcurr_time;	rforecast_time=rcurr_time;
itmp = strlen(strcurr);	itmp = strlen(strcurr);
if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */	if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
strcurr[itmp-1]='\0';	strcurr[itmp-1]='\0';
printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);	printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);	fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
for(niterf=10;niterf<=30;niterf+=10){	for(niterf=10;niterf<=30;niterf+=10){
rforecast_time=rcurr_time+(niterf-iter)(rcurr_time-rlast_time);	rforecast_time=rcurr_time+(niterf-iter)(rcurr_time-rlast_time);
forecast_time = *localtime(&rforecast_time);	forecast_time = *localtime(&rforecast_time);
strcpy(strfor,asctime(&forecast_time));	strcpy(strfor,asctime(&forecast_time));
itmp = strlen(strfor);	itmp = strlen(strfor);
if(strfor[itmp-1]=='\n')	if(strfor[itmp-1]=='\n')
strfor[itmp-1]='\0';	strfor[itmp-1]='\0';
printf(" - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);	printf(" - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
fprintf(ficlog," - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);	fprintf(ficlog," - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
}	}
}	}
for (i=1;i<=n;i++) { /* For each direction i */	for (i=1;i<=n;i++) { /* For each direction i */
Line 1906 void powell(double p[], double **xi, int	Line 1956 void powell(double p[], double **xi, int
#endif	#endif
printf("%d",i);fflush(stdout); /* print direction (parameter) i */	printf("%d",i);fflush(stdout); /* print direction (parameter) i */
fprintf(ficlog,"%d",i);fflush(ficlog);	fprintf(ficlog,"%d",i);fflush(ficlog);
	#ifdef LINMINORIGINAL
linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/	linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
/* Outputs are fret(new point p) p is updated and xit rescaled */	#else
	linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
	flatdir[i]=flat; /* Function is vanishing in that direction i */
	#endif
	/* Outputs are fret(new point p) p is updated and xit rescaled */
if (fabs(fptt-(fret)) > del) { / We are keeping the max gain on each of the n directions */	if (fabs(fptt-(fret)) > del) { / We are keeping the max gain on each of the n directions */
/* because that direction will be replaced unless the gain del is small */	/* because that direction will be replaced unless the gain del is small */
/* in comparison with the 'probable' gain, mu^2, with the last average direction. */	/* in comparison with the 'probable' gain, mu^2, with the last average direction. */
/* Unless the n directions are conjugate some gain in the determinant may be obtained */	/* Unless the n directions are conjugate some gain in the determinant may be obtained */
/* with the new direction. */	/* with the new direction. */
del=fabs(fptt-(*fret));	del=fabs(fptt-(*fret));
ibig=i;	ibig=i;
}	}
#ifdef DEBUG	#ifdef DEBUG
printf("%d %.12e",i,(*fret));	printf("%d %.12e",i,(*fret));
fprintf(ficlog,"%d %.12e",i,(*fret));	fprintf(ficlog,"%d %.12e",i,(*fret));
for (j=1;j<=n;j++) {	for (j=1;j<=n;j++) {
xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);	xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
printf(" x(%d)=%.12e",j,xit[j]);	printf(" x(%d)=%.12e",j,xit[j]);
fprintf(ficlog," x(%d)=%.12e",j,xit[j]);	fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
}	}
for(j=1;j<=n;j++) {	for(j=1;j<=n;j++) {
printf(" p(%d)=%.12e",j,p[j]);	printf(" p(%d)=%lf ",j,p[j]);
fprintf(ficlog," p(%d)=%.12e",j,p[j]);	fprintf(ficlog," p(%d)=%lf ",j,p[j]);
}	}
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
Line 1935 void powell(double p[], double **xi, int	Line 1990 void powell(double p[], double **xi, int
/* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */	/* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
/* But p and xit have been updated at the end of linmin, fret corresponds to new p, xit /	/* But p and xit have been updated at the end of linmin, fret corresponds to new p, xit /
/* New value of last point Pn is not computed, P(n-1) */	/* New value of last point Pn is not computed, P(n-1) */
	for(j=1;j<=n;j++) {
	printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
	fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
	}
	printf("\n");
	fprintf(ficlog,"\n");

if (2.0fabs(fp-(fret)) <= ftol(fabs(fp)+fabs(fret))) { /* Did we reach enough precision? */	if (2.0fabs(fp-(fret)) <= ftol(fabs(fp)+fabs(fret))) { /* Did we reach enough precision? */
/* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */	/* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
/* By adding ageage in a model, the new -2LL should be lower and the difference follows a /	/* By adding ageage in a model, the new -2LL should be lower and the difference follows a /
Line 1943 void powell(double p[], double **xi, int	Line 2005 void powell(double p[], double **xi, int
/* By adding ageage and V1age the gain (-2LL) should be more than 5.99 (ddl=2) */	/* By adding ageage and V1age the gain (-2LL) should be more than 5.99 (ddl=2) */
/* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */	/* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
/* By adding 10 parameters more the gain should be 18.31 */	/* By adding 10 parameters more the gain should be 18.31 */

/* Starting the program with initial values given by a former maximization will simply change */	/* Starting the program with initial values given by a former maximization will simply change */
/* the scales of the directions and the directions, because the are reset to canonical directions */	/* the scales of the directions and the directions, because the are reset to canonical directions */
/* Thus the first calls to linmin will give new points and better maximizations until fp-(fret) is /	/* Thus the first calls to linmin will give new points and better maximizations until fp-(fret) is /
Line 1971 void powell(double p[], double **xi, int	Line 2033 void powell(double p[], double **xi, int
}	}
#endif	#endif

	#ifdef LINMINORIGINAL
	#else
	free_ivector(flatdir,1,n);
	#endif
free_vector(xit,1,n);	free_vector(xit,1,n);
free_vector(xits,1,n);	free_vector(xits,1,n);
free_vector(ptt,1,n);	free_vector(ptt,1,n);
Line 1985 void powell(double p[], double **xi, int	Line 2050 void powell(double p[], double **xi, int
pt[j]=p[j];	pt[j]=p[j];
}	}
fptt=(func)(ptt); / f_3 */	fptt=(func)(ptt); / f_3 */
#ifdef POWELLF1F3	#ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
	if (*iter <=4) {
	#else
	#ifdef POWELLNOF3INFF1TEST /* skips test F3 <F1 */
#else	#else
if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */	if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
#endif	#endif
Line 1994 void powell(double p[], double **xi, int	Line 2062 void powell(double p[], double **xi, int
/* Let f"(x2) be the 2nd derivative equal everywhere. */	/* Let f"(x2) be the 2nd derivative equal everywhere. */
/* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */	/* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
/* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h*2 /	/* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h*2 /
/* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */	/* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
	/* also lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
	/* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
/* t=2.0(fp-2.0(fret)+fptt)SQR(fp-(fret)-del)-delSQR(fp-fptt); */	/* t=2.0(fp-2.0(fret)+fptt)SQR(fp-(fret)-del)-delSQR(fp-fptt); */
	/* Even if f3 <f1, directest can be negative and t >0 */
	/* mu² and del² are equal when f3=f1 */
	/* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
	/* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
	/* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0 */
	/* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0 */
#ifdef NRCORIGINAL	#ifdef NRCORIGINAL
t=2.0(fp-2.0(fret)+fptt)SQR(fp-(fret)-del)- delSQR(fp-fptt); /* Original Numerical Recipes in C*/	t=2.0(fp-2.0(fret)+fptt)SQR(fp-(fret)-del)- delSQR(fp-fptt); /* Original Numerical Recipes in C*/
#else	#else
Line 2017 void powell(double p[], double **xi, int	Line 2093 void powell(double p[], double **xi, int
if (t < 0.0) { /* Then we use it for new direction */	if (t < 0.0) { /* Then we use it for new direction */
#else	#else
if (directestt < 0.0) { / Contradiction between both tests */	if (directestt < 0.0) { / Contradiction between both tests */
printf("directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);	printf("directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0(fret)+fptt, fp -(*fret) -del, fp-fptt);	printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0(fret)+fptt, fp -(*fret) -del, fp-fptt);
fprintf(ficlog,"directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);	fprintf(ficlog,"directest= %.12lf (if directest<0 or t<0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0(fret)+fptt, fp -(*fret) -del, fp-fptt);	fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0(fret)+fptt, fp -(*fret) -del, fp-fptt);
}	}
if (directest < 0.0) { /* Then we use it for new direction */	if (directest < 0.0) { /* Then we use it for new direction */
#endif	#endif
#ifdef DEBUGLINMIN	#ifdef DEBUGLINMIN
printf("Before linmin in direction P%d-P0\n",n);	printf("Before linmin in direction P%d-P0\n",n);
for (j=1;j<=n;j++) {	for (j=1;j<=n;j++) {
printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);	printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);	fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
if(j % ncovmodel == 0){	if(j % ncovmodel == 0){
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
}	}
}	}
#endif	#endif
linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/	#ifdef LINMINORIGINAL
#ifdef DEBUGLINMIN	linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
for (j=1;j<=n;j++) {	#else
printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);	linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);	flatdir[i]=flat; /* Function is vanishing in that direction i */
if(j % ncovmodel == 0){
printf("\n");
fprintf(ficlog,"\n");
}
}
#endif	#endif
for (j=1;j<=n;j++) {
xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
}
printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);

	#ifdef DEBUGLINMIN
	for (j=1;j<=n;j++) {
	printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
	fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
	if(j % ncovmodel == 0){
	printf("\n");
	fprintf(ficlog,"\n");
	}
	}
	#endif
	for (j=1;j<=n;j++) {
	xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
	xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
	}
	#ifdef LINMINORIGINAL
	#else
	printf("Flat directions\n");
	fprintf(ficlog,"Flat directions\n");
	for (j=1;j<=n;j++) {
	printf("flatdir[%d]=%d ",j,flatdir[j]);
	fprintf(ficlog,"flatdir[%d]=%d ",j,flatdir[j]);
	}
	printf("\n");
	fprintf(ficlog,"\n");
	#endif
	printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
	fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);

#ifdef DEBUG	#ifdef DEBUG
printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);	printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);	fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
for(j=1;j<=n;j++){	for(j=1;j<=n;j++){
printf(" %.12e",xit[j]);	printf(" %lf",xit[j]);
fprintf(ficlog," %.12e",xit[j]);	fprintf(ficlog," %lf",xit[j]);
}	}
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
#endif	#endif
} /* end of t or directest negative */	} /* end of t or directest negative */
#ifdef POWELLF1F3	#ifdef POWELLNOF3INFF1TEST
#else	#else
} /* end if (fptt < fp) */	} /* end if (fptt < fp) */
#endif	#endif
	} /NODIRECTIONCHANGEDUNTILNITER No change in drections until some iterations are done /
	#endif
} /* loop iteration */	} /* loop iteration */
}	}

Line 2778 double *hbxij(double *po, int nhstep	Line 2873 double *hbxij(double *po, int nhstep
/************* log-likelihood ***********/	/************* log-likelihood ***********/
double func( double *x)	double func( double *x)
{	{
int i, ii, j, k, mi, d, kk;	int i, ii, j, k, mi, d, kk;
int ioffset;	int ioffset=0;
double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];	double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
double **out;	double **out;
double sw; /* Sum of weights */	double sw; /* Sum of weights */
double lli; /* Individual log likelihood */	double lli; /* Individual log likelihood */
int s1, s2;	int s1, s2;
int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate */	int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate */
double bbh, survp;	double bbh, survp;
long ipmx;	long ipmx;
double agexact;	double agexact;
/extern weight /	/extern weight /
/* We are differentiating ll according to initial status */	/* We are differentiating ll according to initial status */
/* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/	/* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
/*for(i=1;i<imx;i++)	/*for(i=1;i<imx;i++)
printf(" %d\n",s[4][i]);	printf(" %d\n",s[4][i]);
*/	*/

++countcallfunc;	++countcallfunc;

cov[1]=1.;	cov[1]=1.;

for(k=1; k<=nlstate; k++) ll[k]=0.;	for(k=1; k<=nlstate; k++) ll[k]=0.;
	ioffset=0;
	if(mle==1){
	for (i=1,ipmx=0, sw=0.; i<=imx; i++){
	/* Computes the values of the ncovmodel covariates of the model
	depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
	Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
	to be observed in j being in i according to the model.
	*/
	ioffset=2+nagesqr+cptcovage;
	/* for (k=1; k<=cptcovn;k++){ /\* Simple and product covariates without age* products \/ /
	for (k=1; k<=ncoveff;k++){ /* Simple and product covariates without age* products */
	cov[++ioffset]=covar[Tvar[k]][i];
	}
	for(iqv=1; iqv <= nqveff; iqv++){ /* Quantitatives covariates */
	cov[++ioffset]=coqvar[iqv][i];
	}

if(mle==1){	/* In model V2+V1V4+ageV3+V3V2 Tvar[1] is V2, Tvar[2=V1V4]
for (i=1,ipmx=0, sw=0.; i<=imx; i++){	is 6, Tvar[3=ageV3] should not be computed because of age Tvar[4=V3V2]
/* Computes the values of the ncovmodel covariates of the model	has been calculated etc */
depending if the covariates are fixed or varying (age dependent) and stores them in cov[]	/* For an individual i, wav[i] gives the number of effective waves */
Then computes with function pmij which return a matrix p[i][j] giving the elementary probability	/* We compute the contribution to Likelihood of each effective transition
to be observed in j being in i according to the model.	mw[mi][i] is real wave of the mi th effectve wave */
*/	/* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
ioffset=2+nagesqr;	s2=s[mw[mi+1][i]][i];
for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */	And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
cov[++ioffset]=covar[Tvar[k]][i];	But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
}	meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
for(iqv=1; iqv <= nqv; iqv++){ /* Varying quantitatives covariates */	*/
/* cov[2+nagesqr+cptcovn+iqv]=varq[mw[mi+1][i]][iqv][i]; */	for(mi=1; mi<= wav[i]-1; mi++){
}	for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */
	cov[ioffset+itv]=cotvar[mw[mi][i]][itv][i];
/* In model V2+V1V4+ageV3+V3V2 Tvar[1] is V2, Tvar[2=V1V4]	}
is 6, Tvar[3=ageV3] should not be computed because of age Tvar[4=V3V2]	for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */
has been calculated etc */	cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][iqtv][i];
/* For an individual i, wav[i] gives the number of effective waves */	}
/* We compute the contribution to Likelihood of each effective transition	/* ioffset=2+nagesqr+cptcovn+nqv+ntv+nqtv; */
mw[mi][i] is real wave of the mi th effectve wave */	for (ii=1;ii<=nlstate+ndeath;ii++)
/* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];	for (j=1;j<=nlstate+ndeath;j++){
s2=s[mw[mi+1][i]][i];	oldm[ii][j]=(ii==j ? 1.0 : 0.0);
And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]	savm[ii][j]=(ii==j ? 1.0 : 0.0);
But if the variable is not in the model TTvar[iv] is the real variable effective in the model:	}
meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]	for(d=0; d<dh[mi][i]; d++){
*/	newm=savm;
for(mi=1; mi<= wav[i]-1; mi++){	agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
for(itv=1; itv <= ntv; itv++){ /* Varying dummy covariates */	cov[2]=agexact;
cov[++ioffset]=cotvar[mw[mi+1][i]][itv][i];	if(nagesqr==1)
}	cov[3]= agexactagexact; / Should be changed here */
for(iqtv=1; iqtv <= nqtv; iqtv++){ /* Varying quantitatives covariates */	for (kk=1; kk<=cptcovage;kk++) {
/* cov[2+nagesqr+cptcovn+nqv+ntv+iqtv]=varq[mw[mi+1][i]][iqtv][i]; */	cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]agexact; / Tage[kk] gives the data-covariate associated with age */
}	}
ioffset=2+nagesqr+cptcovn+nqv+ntv+nqtv;	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
for (ii=1;ii<=nlstate+ndeath;ii++)	1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
for (j=1;j<=nlstate+ndeath;j++){	savm=oldm;
oldm[ii][j]=(ii==j ? 1.0 : 0.0);	oldm=newm;
savm[ii][j]=(ii==j ? 1.0 : 0.0);	} /* end mult */
}
for(d=0; d<dh[mi][i]; d++){	/lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);/ /* Original formula */
newm=savm;	/* But now since version 0.9 we anticipate for bias at large stepm.
agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;	* If stepm is larger than one month (smallest stepm) and if the exact delay
cov[2]=agexact;	* (in months) between two waves is not a multiple of stepm, we rounded to
if(nagesqr==1)	* the nearest (and in case of equal distance, to the lowest) interval but now
cov[3]= agexactagexact; / Should be changed here */	* we keep into memory the bias bh[mi][i] and also the previous matrix product
for (kk=1; kk<=cptcovage;kk++) {	* (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]agexact; / Tage[kk] gives the data-covariate associated with age */	* probability in order to take into account the bias as a fraction of the way
}	* from savm to out if bh is negative or even beyond if bh is positive. bh varies
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,	* -stepm/2 to stepm/2 .
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));	* For stepm=1 the results are the same as for previous versions of Imach.
savm=oldm;	* For stepm > 1 the results are less biased than in previous versions.
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 */	bbh=(double)bh[mi][i]/(double)stepm;
/* But now since version 0.9 we anticipate for bias at large stepm.	/* bias bh is positive if real duration
* If stepm is larger than one month (smallest stepm) and if the exact delay	* is higher than the multiple of stepm and negative otherwise.
* (in months) between two waves is not a multiple of stepm, we rounded to	*/
* the nearest (and in case of equal distance, to the lowest) interval but now	/* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]):log((1.+bbh)out[s1][s2]));/
* we keep into memory the bias bh[mi][i] and also the previous matrix product	if( s2 > nlstate){
* (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the	/* i.e. if s2 is a death state and if the date of death is known
* probability in order to take into account the bias as a fraction of the way	then the contribution to the likelihood is the probability to
* from savm to out if bh is negative or even beyond if bh is positive. bh varies	die between last step unit time and current step unit time,
* -stepm/2 to stepm/2 .	which is also equal to probability to die before dh
* For stepm=1 the results are the same as for previous versions of Imach.	minus probability to die before dh-stepm .
* For stepm > 1 the results are less biased than in previous versions.	In version up to 0.92 likelihood was computed
*/	as if date of death was unknown. Death was treated as any other
s1=s[mw[mi][i]][i];	health state: the date of the interview describes the actual state
s2=s[mw[mi+1][i]][i];	and not the date of a change in health state. The former idea was
bbh=(double)bh[mi][i]/(double)stepm;	to consider that at each interview the state was recorded
/* bias bh is positive if real duration	(healthy, disable or death) and IMaCh was corrected; but when we
* is higher than the multiple of stepm and negative otherwise.	introduced the exact date of death then we should have modified
*/	the contribution of an exact death to the likelihood. This new
/* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]):log((1.+bbh)out[s1][s2]));/	contribution is smaller and very dependent of the step unit
if( s2 > nlstate){	stepm. It is no more the probability to die between last interview
/* i.e. if s2 is a death state and if the date of death is known	and month of death but the probability to survive from last
then the contribution to the likelihood is the probability to	interview up to one month before death multiplied by the
die between last step unit time and current step unit time,	probability to die within a month. Thanks to Chris
which is also equal to probability to die before dh	Jackson for correcting this bug. Former versions increased
minus probability to die before dh-stepm .	mortality artificially. The bad side is that we add another loop
In version up to 0.92 likelihood was computed	which slows down the processing. The difference can be up to 10%
as if date of death was unknown. Death was treated as any other	lower mortality.
health state: the date of the interview describes the actual state	*/
and not the date of a change in health state. The former idea was	/* If, at the beginning of the maximization mostly, the
to consider that at each interview the state was recorded	cumulative probability or probability to be dead is
(healthy, disable or death) and IMaCh was corrected; but when we	constant (ie = 1) over time d, the difference is equal to
introduced the exact date of death then we should have modified	0. out[s1][3] = savm[s1][3]: probability, being at state
the contribution of an exact death to the likelihood. This new	s1 at precedent wave, to be dead a month before current
contribution is smaller and very dependent of the step unit	wave is equal to probability, being at state s1 at
stepm. It is no more the probability to die between last interview	precedent wave, to be dead at mont of the current
and month of death but the probability to survive from last	wave. Then the observed probability (that this person died)
interview up to one month before death multiplied by the	is null according to current estimated parameter. In fact,
probability to die within a month. Thanks to Chris	it should be very low but not zero otherwise the log go to
Jackson for correcting this bug. Former versions increased	infinity.
mortality artificially. The bad side is that we add another loop	*/
which slows down the processing. The difference can be up to 10%
lower mortality.
*/
/* If, at the beginning of the maximization mostly, the
cumulative probability or probability to be dead is
constant (ie = 1) over time d, the difference is equal to
0. out[s1][3] = savm[s1][3]: probability, being at state
s1 at precedent wave, to be dead a month before current
wave is equal to probability, being at state s1 at
precedent wave, to be dead at mont of the current
wave. Then the observed probability (that this person died)
is null according to current estimated parameter. In fact,
it should be very low but not zero otherwise the log go to
infinity.
*/
/* #ifdef INFINITYORIGINAL */	/* #ifdef INFINITYORIGINAL */
/* lli=log(out[s1][s2] - savm[s1][s2]); */	/* lli=log(out[s1][s2] - savm[s1][s2]); */
/* #else */	/* #else */
Line 2921 double func( double *x)	Line 3017 double func( double *x)
/* else */	/* else */
/* lli=log(out[s1][s2] - savm[s1][s2]); */	/* lli=log(out[s1][s2] - savm[s1][s2]); */
/* #endif */	/* #endif */
lli=log(out[s1][s2] - savm[s1][s2]);	lli=log(out[s1][s2] - savm[s1][s2]);

} else if ( s2==-1 ) { /* alive */	} else if ( s2==-1 ) { /* alive */
for (j=1,survp=0. ; j<=nlstate; j++)	for (j=1,survp=0. ; j<=nlstate; j++)
survp += (1.+bbh)out[s1][j]- bbhsavm[s1][j];	survp += (1.+bbh)out[s1][j]- bbhsavm[s1][j];
/survp += out[s1][j]; /	/survp += out[s1][j]; /
lli= log(survp);	lli= log(survp);
}	}
else if (s2==-4) {	else if (s2==-4) {
for (j=3,survp=0. ; j<=nlstate; j++)	for (j=3,survp=0. ; j<=nlstate; j++)
survp += (1.+bbh)out[s1][j]- bbhsavm[s1][j];	survp += (1.+bbh)out[s1][j]- bbhsavm[s1][j];
lli= log(survp);	lli= log(survp);
}	}
else if (s2==-5) {	else if (s2==-5) {
for (j=1,survp=0. ; j<=2; j++)	for (j=1,survp=0. ; j<=2; j++)
survp += (1.+bbh)out[s1][j]- bbhsavm[s1][j];	survp += (1.+bbh)out[s1][j]- bbhsavm[s1][j];
lli= log(survp);	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 */
}	}
/lli=(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]);/	/lli=(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]);/
/if(lli ==000.0)/	/if(lli ==000.0)/
/printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); /	/printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); /
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;
/* if (lli < log(mytinydouble)){ */	/* if (lli < log(mytinydouble)){ */
/* printf("Close to inf lli = %.10lf < %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */	/* printf("Close to inf lli = %.10lf < %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */
/* fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */	/* fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */
/* } */	/* } */
} /* end of wave */	} /* end of wave */
} /* end of individual */	} /* end of individual */
} else if(mle==2){	} else if(mle==2){
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+nagesqr+k]=covar[Tvar[k]][i];	for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
for(mi=1; mi<= wav[i]-1; mi++){	for(mi=1; mi<= wav[i]-1; mi++){
for (ii=1;ii<=nlstate+ndeath;ii++)	for (ii=1;ii<=nlstate+ndeath;ii++)
for (j=1;j<=nlstate+ndeath;j++){	for (j=1;j<=nlstate+ndeath;j++){
oldm[ii][j]=(ii==j ? 1.0 : 0.0);	oldm[ii][j]=(ii==j ? 1.0 : 0.0);
savm[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++){	for(d=0; d<=dh[mi][i]; d++){
newm=savm;	newm=savm;
agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;	agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
cov[2]=agexact;	cov[2]=agexact;
if(nagesqr==1)	if(nagesqr==1)
cov[3]= agexact*agexact;	cov[3]= agexact*agexact;
for (kk=1; kk<=cptcovage;kk++) {	for (kk=1; kk<=cptcovage;kk++) {
cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;	cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
}	}
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));	1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
savm=oldm;	savm=oldm;
oldm=newm;	oldm=newm;
} /* end mult */	} /* end mult */

s1=s[mw[mi][i]][i];	s1=s[mw[mi][i]][i];
s2=s[mw[mi+1][i]][i];	s2=s[mw[mi+1][i]][i];
bbh=(double)bh[mi][i]/(double)stepm;	bbh=(double)bh[mi][i]/(double)stepm;
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 */
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;
} /* end of wave */	} /* end of wave */
} /* end of individual */	} /* end of individual */
} else if(mle==3){ /* exponential inter-extrapolation */	} else if(mle==3){ /* exponential 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+nagesqr+k]=covar[Tvar[k]][i];	for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
for(mi=1; mi<= wav[i]-1; mi++){	for(mi=1; mi<= wav[i]-1; mi++){
for (ii=1;ii<=nlstate+ndeath;ii++)	for (ii=1;ii<=nlstate+ndeath;ii++)
for (j=1;j<=nlstate+ndeath;j++){	for (j=1;j<=nlstate+ndeath;j++){
oldm[ii][j]=(ii==j ? 1.0 : 0.0);	oldm[ii][j]=(ii==j ? 1.0 : 0.0);
savm[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++){	for(d=0; d<dh[mi][i]; d++){
newm=savm;	newm=savm;
agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;	agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
cov[2]=agexact;	cov[2]=agexact;
if(nagesqr==1)	if(nagesqr==1)
cov[3]= agexact*agexact;	cov[3]= agexact*agexact;
for (kk=1; kk<=cptcovage;kk++) {	for (kk=1; kk<=cptcovage;kk++) {
cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;	cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
}	}
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));	1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
savm=oldm;	savm=oldm;
oldm=newm;	oldm=newm;
} /* end mult */	} /* end mult */

s1=s[mw[mi][i]][i];	s1=s[mw[mi][i]][i];
s2=s[mw[mi+1][i]][i];	s2=s[mw[mi+1][i]][i];
bbh=(double)bh[mi][i]/(double)stepm;	bbh=(double)bh[mi][i]/(double)stepm;
lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]):log((1.+bbh)out[s1][s2])); / exponential inter-extrapolation */	lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]):log((1.+bbh)out[s1][s2])); / exponential inter-extrapolation */
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;
} /* end of wave */	} /* end of wave */
} /* end of individual */	} /* end of individual */
}else if (mle==4){ /* 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+nagesqr+k]=covar[Tvar[k]][i];	for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
for(mi=1; mi<= wav[i]-1; mi++){	for(mi=1; mi<= wav[i]-1; mi++){
for (ii=1;ii<=nlstate+ndeath;ii++)	for (ii=1;ii<=nlstate+ndeath;ii++)
for (j=1;j<=nlstate+ndeath;j++){	for (j=1;j<=nlstate+ndeath;j++){
oldm[ii][j]=(ii==j ? 1.0 : 0.0);	oldm[ii][j]=(ii==j ? 1.0 : 0.0);
savm[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++){	for(d=0; d<dh[mi][i]; d++){
newm=savm;	newm=savm;
agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;	agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
cov[2]=agexact;	cov[2]=agexact;
if(nagesqr==1)	if(nagesqr==1)
cov[3]= agexact*agexact;	cov[3]= agexact*agexact;
for (kk=1; kk<=cptcovage;kk++) {	for (kk=1; kk<=cptcovage;kk++) {
cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;	cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
}	}

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

s1=s[mw[mi][i]][i];	s1=s[mw[mi][i]][i];
s2=s[mw[mi+1][i]][i];	s2=s[mw[mi+1][i]][i];
if( s2 > nlstate){	if( s2 > nlstate){
lli=log(out[s1][s2] - savm[s1][s2]);	lli=log(out[s1][s2] - savm[s1][s2]);
} else if ( s2==-1 ) { /* alive */	} else if ( s2==-1 ) { /* alive */
for (j=1,survp=0. ; j<=nlstate; j++)	for (j=1,survp=0. ; j<=nlstate; j++)
survp += out[s1][j];	survp += out[s1][j];
lli= log(survp);	lli= log(survp);
}else{	}else{
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]); */	/* 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 */
}else{ /* ml=5 no inter-extrapolation no jackson =0.8a */	}else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
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+nagesqr+k]=covar[Tvar[k]][i];	for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
for(mi=1; mi<= wav[i]-1; mi++){	for(mi=1; mi<= wav[i]-1; mi++){
for (ii=1;ii<=nlstate+ndeath;ii++)	for (ii=1;ii<=nlstate+ndeath;ii++)
for (j=1;j<=nlstate+ndeath;j++){	for (j=1;j<=nlstate+ndeath;j++){
oldm[ii][j]=(ii==j ? 1.0 : 0.0);	oldm[ii][j]=(ii==j ? 1.0 : 0.0);
savm[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++){	for(d=0; d<dh[mi][i]; d++){
newm=savm;	newm=savm;
agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;	agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
cov[2]=agexact;	cov[2]=agexact;
if(nagesqr==1)	if(nagesqr==1)
cov[3]= agexact*agexact;	cov[3]= agexact*agexact;
for (kk=1; kk<=cptcovage;kk++) {	for (kk=1; kk<=cptcovage;kk++) {
cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;	cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
}	}

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

s1=s[mw[mi][i]][i];	s1=s[mw[mi][i]][i];
s2=s[mw[mi+1][i]][i];	s2=s[mw[mi+1][i]][i];
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]);/	/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 */
for(k=1,l=0.; k<=nlstate; k++) l += ll[k];	for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
/* printf("l1=%f l2=%f ",ll[1],ll[2]); */	/* 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 */	l= lipmx/sw; / To get the same order of magnitude as if weight=1 for every body */
return -l;	return -l;
}	}

/************* log-likelihood ***********/	/************* log-likelihood ***********/
Line 3109 double funcone( double *x)	Line 3205 double funcone( double *x)
{	{
/* Same as likeli but slower because of a lot of printf and if */	/* Same as likeli but slower because of a lot of printf and if */
int i, ii, j, k, mi, d, kk;	int i, ii, j, k, mi, d, kk;
	int ioffset=0;
double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];	double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
double **out;	double **out;
double lli; /* Individual log likelihood */	double lli; /* Individual log likelihood */
double llt;	double llt;
int s1, s2;	int s1, s2;
	int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate */
double bbh, survp;	double bbh, survp;
double agexact;	double agexact;
double agebegin, ageend;	double agebegin, ageend;
Line 3126 double funcone( double *x)	Line 3224 double funcone( double *x)
cov[1]=1.;	cov[1]=1.;

for(k=1; k<=nlstate; k++) ll[k]=0.;	for(k=1; k<=nlstate; k++) ll[k]=0.;
	ioffset=0;
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+nagesqr+k]=covar[Tvar[k]][i];	ioffset=2+nagesqr+cptcovage;
	/* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
	for (k=1; k<=ncoveff;k++){ /* Simple and product covariates without age* products */
	cov[++ioffset]=covar[Tvar[k]][i];
	}
	for(iqv=1; iqv <= nqveff; iqv++){ /* Quantitatives covariates */
	cov[++ioffset]=coqvar[iqv][i];
	}

for(mi=1; mi<= wav[i]-1; mi++){	for(mi=1; mi<= wav[i]-1; mi++){
	for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */
	cov[ioffset+itv]=cotvar[mw[mi][i]][itv][i];
	}
	for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */
	cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][iqtv][i];
	}
for (ii=1;ii<=nlstate+ndeath;ii++)	for (ii=1;ii<=nlstate+ndeath;ii++)
for (j=1;j<=nlstate+ndeath;j++){	for (j=1;j<=nlstate+ndeath;j++){
oldm[ii][j]=(ii==j ? 1.0 : 0.0);	oldm[ii][j]=(ii==j ? 1.0 : 0.0);
savm[ii][j]=(ii==j ? 1.0 : 0.0);	savm[ii][j]=(ii==j ? 1.0 : 0.0);
}	}

agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */	agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
ageend=agev[mw[mi][i]][i] + (dh[mi][i])stepm/YEARM; / Age at end of effective wave and at the end of transition */	ageend=agev[mw[mi][i]][i] + (dh[mi][i])stepm/YEARM; / Age at end of effective wave and at the end of transition */
for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */	for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */
/*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]	/*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
and mw[mi+1][i]. dh depends on stepm.*/	and mw[mi+1][i]. dh depends on stepm.*/
newm=savm;	newm=savm;
agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;	agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
cov[2]=agexact;	cov[2]=agexact;
if(nagesqr==1)	if(nagesqr==1)
cov[3]= agexact*agexact;	cov[3]= agexact*agexact;
for (kk=1; kk<=cptcovage;kk++) {	for (kk=1; kk<=cptcovage;kk++) {
cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;	cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
}	}

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

s1=s[mw[mi][i]][i];	s1=s[mw[mi][i]][i];
Line 3170 double funcone( double *x)	Line 3282 double funcone( double *x)
* is higher than the multiple of stepm and negative otherwise.	* is higher than the multiple of stepm and negative otherwise.
*/	*/
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 ( s2==-1 ) { /* alive */	} else if ( s2==-1 ) { /* alive */
for (j=1,survp=0. ; j<=nlstate; j++)	for (j=1,survp=0. ; j<=nlstate; j++)
survp += (1.+bbh)out[s1][j]- bbhsavm[s1][j];	survp += (1.+bbh)out[s1][j]- bbhsavm[s1][j];
lli= log(survp);	lli= log(survp);
}else if (mle==1){	}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 */
} else if(mle==3){ /* exponential inter-extrapolation */	} 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 */	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 */	} else if (mle==4){ /* mle=4 no inter-extrapolation */
lli=log(out[s1][s2]); /* Original formula */	lli=log(out[s1][s2]); /* Original formula */
} else{ /* mle=0 back to 1 */	} else{ /* mle=0 back to 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 */
/lli=log(out[s1][s2]); / /* Original formula */	/lli=log(out[s1][s2]); / /* Original formula */
} /* End of if */	} /* End of if */
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]); /	/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,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f %8.3f\	fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
%11.6f %11.6f %11.6f ", \	%11.6f %11.6f %11.6f ", \
num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,	num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
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++){
llt +=ll[k]*gipmx/gsw;	llt +=ll[k]*gipmx/gsw;
fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);	fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
}	}
fprintf(ficresilk," %10.6f\n", -llt);	fprintf(ficresilk," %10.6f\n", -llt);
}	}
} /* end of wave */	} /* end of wave */
} /* end of individual */	} /* end of individual */
Line 3717 void pstamp(FILE *fichier)	Line 3829 void pstamp(FILE *fichier)
int mi; /* Effective wave */	int mi; /* Effective wave */
int first;	int first;
double **freq; / Frequencies */	double **freq; / Frequencies */
	double *meanq;
	double **meanqt;
double pp, prop, posprop, *pospropt;	double pp, prop, posprop, *pospropt;
double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;	double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];	char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
Line 3727 void pstamp(FILE *fichier)	Line 3841 void pstamp(FILE *fichier)
posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */	posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */	pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
/* prop=matrix(1,nlstate,iagemin,iagemax+3); */	/* prop=matrix(1,nlstate,iagemin,iagemax+3); */
	meanq=vector(1,nqveff);
	meanqt=matrix(1,lastpass,1,nqtveff);
strcpy(fileresp,"P_");	strcpy(fileresp,"P_");
strcat(fileresp,fileresu);	strcat(fileresp,fileresu);
/strcat(fileresphtm,fileresu);/	/strcat(fileresphtm,fileresu);/
Line 3769 Title=%s <br>Datafile=%s Firstpass=%d La	Line 3885 Title=%s <br>Datafile=%s Firstpass=%d La
freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);	freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
j1=0;	j1=0;

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

first=1;	first=1;
Line 3781 Title=%s <br>Datafile=%s Firstpass=%d La	Line 3897 Title=%s <br>Datafile=%s Firstpass=%d La
Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff	Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
*/	*/

for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ /* Loop on covariates combination */	for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on covariates combination excluding varying and quantitatives */
posproptt=0.;	posproptt=0.;
/*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);	/*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
scanf("%d", i);*/	scanf("%d", i);*/
Line 3796 Title=%s <br>Datafile=%s Firstpass=%d La	Line 3912 Title=%s <br>Datafile=%s Firstpass=%d La
posprop[i]=0;	posprop[i]=0;
pospropt[i]=0;	pospropt[i]=0;
}	}
	for (z1=1; z1<= nqveff; z1++) {
	meanq[z1]+=0.;
	for(m=1;m<=lastpass;m++){
	meanqt[m][z1]=0.;
	}
	}

dateintsum=0;	dateintsum=0;
k2cpt=0;	k2cpt=0;
	/* For that comination of covariate j1, we count and print the frequencies */
for (iind=1; iind<=imx; iind++) { /* For each individual iind */	for (iind=1; iind<=imx; iind++) { /* For each individual iind */
bool=1;	bool=1;
if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */	if (nqveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
for (z1=1; z1<=cptcoveff; z1++) {	for (z1=1; z1<= nqveff; z1++) {
	meanq[z1]+=coqvar[Tvar[z1]][iind];
	}
	for (z1=1; z1<=ncoveff; z1++) {
	/* if(Tvaraff[z1] ==-20){ */
	/* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; \/ /
	/* }else if(Tvaraff[z1] ==-10){ */
	/* /\* sumnew+=coqvar[z1][iind]; \/ /
	/* }else */
if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){	if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
/* Tests if the value of each of the covariates of i is equal to filter j1 */	/* Tests if this individual i responded to j1 (V4=1 V3=0) */
bool=0;	bool=0;
/* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n",	/* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n",
bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),	bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
Line 3815 Title=%s <br>Datafile=%s Firstpass=%d La	Line 3945 Title=%s <br>Datafile=%s Firstpass=%d La
} /* end z1 */	} /* end z1 */
} /* cptcovn > 0 */	} /* cptcovn > 0 */

if (bool==1){	if (bool==1){ /* We selected an individual iin satisfying combination j1 */
/* for(m=firstpass; m<=lastpass; m++){ */	/* for(m=firstpass; m<=lastpass; m++){ */
for(mi=1; mi<wav[iind];mi++){	for(mi=1; mi<wav[iind];mi++){
m=mw[mi][iind];	m=mw[mi][iind];
Line 3855 Title=%s <br>Datafile=%s Firstpass=%d La	Line 3985 Title=%s <br>Datafile=%s Firstpass=%d La

/* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/	/* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
pstamp(ficresp);	pstamp(ficresp);
if (cptcovn>0) {	if (ncoveff>0) {
fprintf(ficresp, "\n#********** Variable ");	fprintf(ficresp, "\n#********** Variable ");
fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");	fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");	fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
for (z1=1; z1<=cptcoveff; z1++){	for (z1=1; z1<=ncoveff; z1++){
fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
Line 3868 Title=%s <br>Datafile=%s Firstpass=%d La	Line 3998 Title=%s <br>Datafile=%s Firstpass=%d La
fprintf(ficresphtm, "**********</h3>\n");	fprintf(ficresphtm, "**********</h3>\n");
fprintf(ficresphtmfr, "**********</h3>\n");	fprintf(ficresphtmfr, "**********</h3>\n");
fprintf(ficlog, "\n#********** Variable ");	fprintf(ficlog, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	for (z1=1; z1<=ncoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficlog, "**********\n");	fprintf(ficlog, "**********\n");
}	}
fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");	fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
Line 4019 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4149 Title=%s <br>Datafile=%s Firstpass=%d La
fclose(ficresp);	fclose(ficresp);
fclose(ficresphtm);	fclose(ficresphtm);
fclose(ficresphtmfr);	fclose(ficresphtmfr);
	free_vector(meanq,1,nqveff);
	free_matrix(meanqt,1,lastpass,1,nqtveff);
free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);	free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);
free_vector(pospropt,1,nlstate);	free_vector(pospropt,1,nlstate);
free_vector(posprop,1,nlstate);	free_vector(posprop,1,nlstate);
free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);	free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);
free_vector(pp,1,nlstate);	free_vector(pp,1,nlstate);
/* End of Freq */	/* End of freqsummary */
}	}

/********** Prevalence ******************/	/********** Prevalence ******************/
Line 4057 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4189 Title=%s <br>Datafile=%s Firstpass=%d La
if (cptcovn<1) {j=1;ncodemax[1]=1;}	if (cptcovn<1) {j=1;ncodemax[1]=1;}

first=1;	first=1;
for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */	for(j1=1; j1<= (int) pow(2,nqveff);j1++){ /* For each combination of covariate */
for (i=1; i<=nlstate; i++)	for (i=1; i<=nlstate; i++)
for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)	for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)
prop[i][iage]=0.0;	prop[i][iage]=0.0;
Line 4065 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4197 Title=%s <br>Datafile=%s Firstpass=%d La
for (i=1; i<=imx; i++) { /* Each individual */	for (i=1; i<=imx; i++) { /* Each individual */
bool=1;	bool=1;
if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */	if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
for (z1=1; z1<=cptcoveff; z1++) /* For each covariate, look at the value for individual i and checks if it is equal to the corresponding value of this covariate according to current combination j1*/	for (z1=1; z1<=nqveff; z1++) /* For each covariate, look at the value for individual i and checks if it is equal to the corresponding value of this covariate according to current combination j1*/
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])	if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
bool=0;	bool=0;
}	}
Line 4131 void concatwav(int wav[], int **dh, int	Line 4263 void concatwav(int wav[], int **dh, int
and mw[mi+1][i]. dh depends on stepm.	and mw[mi+1][i]. dh depends on stepm.
*/	*/

int i, mi, m;	int i=0, mi=0, m=0, mli=0;
/* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;	/* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
double sum=0., jmean=0.;*/	double sum=0., jmean=0.;*/
int first, firstwo, firsthree, firstfour;	int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
int j, k=0,jk, ju, jl;	int j, k=0,jk, ju, jl;
double sum=0.;	double sum=0.;
first=0;	first=0;
Line 4144 void concatwav(int wav[], int **dh, int	Line 4276 void concatwav(int wav[], int **dh, int
jmin=100000;	jmin=100000;
jmax=-1;	jmax=-1;
jmean=0.;	jmean=0.;

	/* Treating live states */
for(i=1; i<=imx; i++){ /* For simple cases and if state is death */	for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
mi=0;	mi=0; /* First valid wave */
	mli=0; /* Last valid wave */
m=firstpass;	m=firstpass;
while(s[m][i] <= nlstate){ /* a live state */	while(s[m][i] <= nlstate){ /* a live state */
if(s[m][i]>=1 \|\| s[m][i]==-4 \|\| s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */	if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */
	mli=m-1;/* mw[++mi][i]=m-1; */
	}else if(s[m][i]>=1 \|\| s[m][i]==-4 \|\| s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */
mw[++mi][i]=m;	mw[++mi][i]=m;
	mli=m;
	} /* else might be a useless wave -1 and mi is not incremented and mw[mi] not updated */
	if(m < lastpass){ /* m < lastpass, standard case */
	m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
}	}
if(m >=lastpass){	else{ /* m >= lastpass, eventual special issue with warning */
	#ifdef UNKNOWNSTATUSNOTCONTRIBUTING
	break;
	#else
if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){	if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
if(firsthree == 0){	if(firsthree == 0){
printf("Information! Unknown health status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);	printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
firsthree=1;	firsthree=1;
}	}
fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);	fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
mw[++mi][i]=m;	mw[++mi][i]=m;
	mli=m;
}	}
if(s[m][i]==-2){ /* Vital status is really unknown */	if(s[m][i]==-2){ /* Vital status is really unknown */
nbwarn++;	nbwarn++;
if((int)anint[m][i] == 9999){ /* Has the vital status really been verified? */	if((int)anint[m][i] == 9999){ /* Has the vital status really been verified? */
printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);	printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);	fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
}	}
break;	break;
}	}
break;	break;
}	#endif
else	}/* End m >= lastpass */
m++;
}/* end while */	}/* end while */

	/* mi is the last effective wave, m is lastpass, mw[j][i] gives the # of j-th effective wave for individual i */
/* After last pass */	/* After last pass */
	/* Treating death states */
if (s[m][i] > nlstate){ /* In a death state */	if (s[m][i] > nlstate){ /* In a death state */
	/* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview \/ /
	/* } */
mi++; /* Death is another wave */	mi++; /* Death is another wave */
/* if(mi==0) never been interviewed correctly before death */	/* if(mi==0) never been interviewed correctly before death */
/* Only death is a correct wave */	/* Only death is a correct wave */
mw[mi][i]=m;	mw[mi][i]=m;
}else if ((int) andc[i] != 9999) { /* Status is either death or negative. A death occured after lastpass, we can't take it into account because of potential bias */	}
	#ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
	else if ((int) andc[i] != 9999) { /* Status is negative. A death occured after lastpass, we can't take it into account because of potential bias */
/* m++; */	/* m++; */
/* mi++; */	/* mi++; */
/* s[m][i]=nlstate+1; /\* We are setting the status to the last of non live state \/ /	/* s[m][i]=nlstate+1; /\* We are setting the status to the last of non live state \/ /
/* mw[mi][i]=m; */	/* mw[mi][i]=m; */
nberr++;
if ((int)anint[m][i]!= 9999) { /* date of last interview is known */	if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
if(firstwo==0){	if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */
printf("Error! Death for individual %ld line=%d occurred %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );	nbwarn++;
firstwo=1;	if(firstfiv==0){
	printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
	firstfiv=1;
	}else{
	fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
	}
	}else{ /* Death occured afer last wave potential bias */
	nberr++;
	if(firstwo==0){
	printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
	firstwo=1;
	}
	fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
}	}
fprintf(ficlog,"Error! Death for individual %ld line=%d occurred %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
}else{ /* end date of interview is known */	}else{ /* end date of interview is known */
/* death is known but not confirmed by death status at any wave */	/* death is known but not confirmed by death status at any wave */
if(firstfour==0){	if(firstfour==0){
Line 4200 void concatwav(int wav[], int **dh, int	Line 4360 void concatwav(int wav[], int **dh, int
}	}
fprintf(ficlog,"Error! Death for individual %ld line=%d occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );	fprintf(ficlog,"Error! Death for individual %ld line=%d occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
}	}
}	} /* end if date of death is known */
wav[i]=mi;	#endif
	wav[i]=mi; /* mi should be the last effective wave (or mli) */
	/* wav[i]=mw[mi][i]; */
if(mi==0){	if(mi==0){
nbwarn++;	nbwarn++;
if(first==0){	if(first==0){
Line 4312 void concatwav(int wav[], int **dh, int	Line 4474 void concatwav(int wav[], int **dh, int
/*< Uses cptcovn+2cptcovprod as the number of covariates */	/*< Uses cptcovn+2cptcovprod as the number of covariates */
/* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1	/* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
* Boring subroutine which should only output nbcode[Tvar[j]][k]	* Boring subroutine which should only output nbcode[Tvar[j]][k]
* Tvar[5] in V2+V1+V3age+V2V4 is 2 (V2)	* Tvar[5] in V2+V1+V3age+V2V4 is 4 (V4) even it is a time varying or quantitative variable
* nbcode[Tvar[5]][1]= nbcode[2][1]=0, nbcode[2][2]=1 (usually);	* nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
*/	*/

int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;	int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
Line 4323 void concatwav(int wav[], int **dh, int	Line 4485 void concatwav(int wav[], int **dh, int


/* cptcoveff=0; */	/* cptcoveff=0; */
*cptcov=0;	/* cptcov=0; /

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

/* Loop on covariates without age and products */	/* Loop on covariates without age and products and no quantitative variable */
for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2age+ V3 + V3V4 keeps V1 + V3 = 2 only */	/* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2age+ V3 + V3V4 keeps V1 + V3 = 2 only \/ /
	for (j=1; j<=(cptcov); j++) { / From model V1 + V2age + V3 + V3V4 keeps V1 + V3 = 2 only */
for (k=-1; k < maxncov; k++) Ndum[k]=0;	for (k=-1; k < maxncov; k++) Ndum[k]=0;
for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the	for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
modality of this covariate Vj*/	modality of this covariate Vj*/
ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i	if(Tvar[j] >=1 && Tvar[j] <= cptcov){ / A real fixed covariate */
* If product of VnVm, still boolean :	ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
* If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables	* If product of VnVm, still boolean :
* 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */	* If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
/* Finds for covariate j, n=Tvar[j] of Vn . ij is the	* 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
modality of the nth covariate of individual i. */	/* Finds for covariate j, n=Tvar[j] of Vn . ij is the
if (ij > modmaxcovj)	modality of the nth covariate of individual i. */
modmaxcovj=ij;	if (ij > modmaxcovj)
else if (ij < modmincovj)	modmaxcovj=ij;
modmincovj=ij;	else if (ij < modmincovj)
if ((ij < -1) && (ij > NCOVMAX)){	modmincovj=ij;
printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );	if ((ij < -1) && (ij > NCOVMAX)){
exit(1);	printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
}else	exit(1);
Ndum[ij]++; /counts and stores the occurence of this modality 0, 1, -1/	}else
	Ndum[ij]++; /counts and stores the occurence of this modality 0, 1, -1/
/* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */	/* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
/printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);/	/printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);/
/* getting the maximum value of the modality of the covariate	/* getting the maximum value of the modality of the covariate
(should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and	(should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
female is 1, then modmaxcovj=1.*/	female ies 1, then modmaxcovj=1.*/
} /* end for loop on individuals i */	}
	} /* end for loop on individuals i */
printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);	printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);	fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
cptcode=modmaxcovj;	cptcode=modmaxcovj;
/* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */	/* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
/for (i=0; i<=cptcode; i++) {/	/for (i=0; i<=cptcode; i++) {/
for (k=modmincovj; k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1// For each value k of the modality of model-cov j */	for (k=modmincovj; k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1// For each value k of the modality of model-cov j */
printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);	printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);	fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
Line 4372 void concatwav(int wav[], int **dh, int	Line 4537 void concatwav(int wav[], int **dh, int
undefined. Usually 3: -1, 0 and 1. */	undefined. Usually 3: -1, 0 and 1. */
}	}
/* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for	/* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */	* historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
} /* Ndum[-1] number of undefined modalities */	} /* Ndum[-1] number of undefined modalities */

/* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */	/* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
Line 4393 void concatwav(int wav[], int **dh, int	Line 4558 void concatwav(int wav[], int **dh, int
if (Ndum[i] == 0) { /* If nobody responded to this modality k */	if (Ndum[i] == 0) { /* If nobody responded to this modality k */
break;	break;
}	}
ij++;	ij++;
nbcode[Tvar[j]][ij]=i; /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/	nbcode[Tvar[j]][ij]=i; /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/
cptcode = ij; /* New max modality for covar j */	cptcode = ij; /* New max modality for covar j */
} /* end of loop on modality i=-1 to 1 or more */	} /* end of loop on modality i=-1 to 1 or more */

/* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 \//\ Could be 1 to 4 \//\ cptcode=modmaxcovj \/ /	/* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 \//\ Could be 1 to 4 \//\ cptcode=modmaxcovj \/ /
/* /\recode from 0 \/ */	/* /\recode from 0 \/ */
/* k is a modality. If we have model=V1+V1sex /	/* k is a modality. If we have model=V1+V1sex /
Line 4419 void concatwav(int wav[], int **dh, int	Line 4584 void concatwav(int wav[], int **dh, int
/* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1V2./	/* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1V2./
ij=Tvar[i]; /* Tvar might be -1 if status was unknown */	ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
Ndum[ij]++; /* Might be supersed V1 + V1age /	Ndum[ij]++; /* Might be supersed V1 + V1age /
}	} /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */

ij=0;	ij=0;
for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(ageV3), 5(V3V2) 6(V1V4) /	for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(ageV3), 5(V3V2) 6(V1V4) /
/printf("Ndum[%d]=%d\n",i, Ndum[i]);/	/printf("Ndum[%d]=%d\n",i, Ndum[i]);/
if((Ndum[i]!=0) && (i<=ncovcol)){	if((Ndum[i]!=0) && (i<=ncovcol)){
ij++;
/printf("diff Ndum[%d]=%d\n",i, Ndum[i]);/	/printf("diff Ndum[%d]=%d\n",i, Ndum[i]);/
Tvaraff[ij]=i; /For printing (unclear) /	Tvaraff[++ij]=i; /For printing (unclear) /
}else{	}else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){
/* Tvaraff[ij]=0; */	Tvaraff[++ij]=-10; /* Dont'n know how to treat quantitative variables yet */
	}else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){
	Tvaraff[++ij]=i; /For printing (unclear) /
	}else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){
	Tvaraff[++ij]=-20; /* Dont'n know how to treat quantitative variables yet */
}	}
}	} /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
/* ij--; */	/* ij--; */
/* cptcoveff=ij; /\Number of total covariates\/ */	/* cptcoveff=ij; /\Number of total covariates\/ */
cptcov=ij; /Number of total covariates*/	cptcov=ij; /Number of total real effective covariates: effective
	* because they can be excluded from the model and real
	* if in the model but excluded because missing values*/
}	}


Line 5283 To be simple, these graphs help to under	Line 5452 To be simple, these graphs help to under

cov[1]=1;	cov[1]=1;
/* tj=cptcoveff; */	/* tj=cptcoveff; */
tj = (int) pow(2,cptcoveff);	tj = (int) pow(2,nqveff);
if (cptcovn<1) {tj=1;ncodemax[1]=1;}	if (cptcovn<1) {tj=1;ncodemax[1]=1;}
j1=0;	j1=0;
for(j1=1; j1<=tj;j1++){ /* For each valid combination of covariates */	for(j1=1; j1<=tj;j1++){ /* For each valid combination of covariates or only once*/
if (cptcovn>0) {	if (cptcovn>0) {
fprintf(ficresprob, "\n#********** Variable ");	fprintf(ficresprob, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	for (z1=1; z1<=nqveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficresprob, "**********\n#\n");	fprintf(ficresprob, "**********\n#\n");
fprintf(ficresprobcov, "\n#********** Variable ");	fprintf(ficresprobcov, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	for (z1=1; z1<=nqveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficresprobcov, "**********\n#\n");	fprintf(ficresprobcov, "**********\n#\n");

fprintf(ficgp, "\n#********** Variable ");	fprintf(ficgp, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	for (z1=1; z1<=nqveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficgp, "**********\n#\n");	fprintf(ficgp, "**********\n#\n");


fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");	fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	for (z1=1; z1<=nqveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");	fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");

fprintf(ficresprobcor, "\n#********** Variable ");	fprintf(ficresprobcor, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	for (z1=1; z1<=nqveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficresprobcor, "**********\n#");	fprintf(ficresprobcor, "**********\n#");
if(invalidvarcomb[j1]){	if(invalidvarcomb[j1]){
fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);	fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
Line 5571 void printinghtml(char fileresu[], char	Line 5740 void printinghtml(char fileresu[], char

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

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

jj1=0;	jj1=0;
Line 5581 void printinghtml(char fileresu[], char	Line 5750 void printinghtml(char fileresu[], char
jj1++;	jj1++;
if (cptcovn > 0) {	if (cptcovn > 0) {
fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");	fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
for (cpt=1; cpt<=cptcoveff;cpt++){	for (cpt=1; cpt<=nqveff;cpt++){
fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);	fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);	printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
}	}
Line 5691 See page 'Matrix of variance-covariance	Line 5860 See page 'Matrix of variance-covariance
fflush(fichtm);	fflush(fichtm);
fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");	fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");

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

jj1=0;	jj1=0;
Line 5700 See page 'Matrix of variance-covariance	Line 5869 See page 'Matrix of variance-covariance
jj1++;	jj1++;
if (cptcovn > 0) {	if (cptcovn > 0) {
fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");	fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
for (cpt=1; cpt<=cptcoveff;cpt++)	for (cpt=1; cpt<=nqveff;cpt++)
fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);	fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");	fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");

Line 5745 void printinggnuplot(char fileresu[], ch	Line 5914 void printinggnuplot(char fileresu[], ch
/#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,nqveff);

/* Contribution to likelihood */	/* Contribution to likelihood */
/* Plot the probability implied in the likelihood */	/* Plot the probability implied in the likelihood */
Line 5783 void printinggnuplot(char fileresu[], ch	Line 5952 void printinggnuplot(char fileresu[], ch
for (k1=1; k1<= m ; k1 ++) { /* For each valid combination of covariate */	for (k1=1; k1<= m ; k1 ++) { /* For each valid combination of covariate */
/* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */	/* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");	fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */	for (k=1; k<=nqveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */
lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */	lv= decodtabm(k1,k,nqveff); /* Should be the value of the covariate corresponding to k1 combination */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
Line 5823 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 5992 plot [%.f:%.f] \"%s\" every :::%d::%d u
if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */	if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
/* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */	/* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */	fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */
if(cptcoveff ==0){	if(nqveff ==0){
fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line ", 2+(cpt-1), cpt );	fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line ", 2+(cpt-1), cpt );
}else{	}else{
kl=0;	kl=0;
for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */	for (k=1; k<=nqveff; k++){ /* For each combination of covariate */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */	lv= decodtabm(k1,k,nqveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
Line 5838 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 6007 plot [%.f:%.f] \"%s\" every :::%d::%d u
/6+(cpt-1)(nlstate+1)+1+(i-1)+(nlstate+1)nlstate; 6+(1-1)(2+1)+1+(1-1) +(2+1)2=13 /	/6+(cpt-1)(nlstate+1)+1+(i-1)+(nlstate+1)nlstate; 6+(1-1)(2+1)+1+(1-1) +(2+1)2=13 /
/6+1+(i-1)+(nlstate+1)nlstate; 6+1+(1-1) +(2+1)2=13 /	/6+1+(i-1)+(nlstate+1)nlstate; 6+1+(1-1) +(2+1)2=13 /
/* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/	/* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
if(k==cptcoveff){	if(k==nqveff){
fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' with line ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \	fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' with line ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
6+(cpt-1), cpt );	6+(cpt-1), cpt );
}else{	}else{
Line 5855 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 6024 plot [%.f:%.f] \"%s\" every :::%d::%d u
for (k1=1; k1<= m ; k1 ++) {	for (k1=1; k1<= m ; k1 ++) {

fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");	fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */	for (k=1; k<=nqveff; k++){ /* For each covariate and each value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	lv= decodtabm(k1,k,nqveff); /* Should be the covariate number corresponding to k1 combination */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
Line 5908 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 6077 plot [%.f:%.f] \"%s\" every :::%d::%d u

for (cpt=1; cpt<= nlstate ; cpt ++) {	for (cpt=1; cpt<= nlstate ; cpt ++) {
fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: cov=%d state=%d",k1, cpt);	fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: cov=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */	for (k=1; k<=nqveff; k++){ /* For each covariate and each value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	lv= decodtabm(k1,k,nqveff); /* Should be the covariate number corresponding to k1 combination */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
Line 5950 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 6119 plot [%.f:%.f] \"%s\" every :::%d::%d u

for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);	fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */	for (k=1; k<=nqveff; k++){ /* For each covariate and each value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	lv= decodtabm(k1,k,nqveff); /* Should be the covariate number corresponding to k1 combination */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
Line 5992 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6161 plot [%.f:%.f] ", ageminpar, agemaxpar)
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */

fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);	fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */	for (k=1; k<=nqveff; k++){ /* For each covariate and each value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	lv= decodtabm(k1,k,nqveff); /* Should be the covariate number corresponding to k1 combination */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
Line 6042 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6211 plot [%.f:%.f] ", ageminpar, agemaxpar)
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */

fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);	fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */	for (k=1; k<=nqveff; k++){ /* For each covariate and each value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	lv= decodtabm(k1,k,nqveff); /* Should be the covariate number corresponding to k1 combination */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
Line 6084 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6253 plot [%.f:%.f] ", ageminpar, agemaxpar)
for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2*k), if any covariate is present /	for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2*k), if any covariate is present /
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);	fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */	for (k=1; k<=nqveff; k++){ /* For each covariate and each value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	lv= decodtabm(k1,k,nqveff); /* Should be the covariate number corresponding to k1 combination */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
Line 6131 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6300 plot [%.f:%.f] ", ageminpar, agemaxpar)
for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2*k), if any covariate is present /	for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2*k), if any covariate is present /
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);	fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */	for (k=1; k<=nqveff; k++){ /* For each correspondig covariate value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */	lv= decodtabm(k1,k,nqveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
Line 6161 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6330 plot [%.f:%.f] ", ageminpar, agemaxpar)
}else{	}else{
fprintf(ficgp,",\\\n '' ");	fprintf(ficgp,",\\\n '' ");
}	}
if(cptcoveff ==0){ /* No covariate */	if(nqveff ==0){ /* No covariate */
ioffset=2; /* Age is in 2 */	ioffset=2; /* Age is in 2 */
/# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4/	/# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4/
/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 /	/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 /
Line 6175 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6344 plot [%.f:%.f] ", ageminpar, agemaxpar)
fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \	fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)nlstate,i,cpt );	ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)nlstate,i,cpt );
}else{ /* more than 2 covariates */	}else{ /* more than 2 covariates */
if(cptcoveff ==1){	if(nqveff ==1){
ioffset=4; /* Age is in 4 */	ioffset=4; /* Age is in 4 */
}else{	}else{
ioffset=6; /* Age is in 6 */	ioffset=6; /* Age is in 6 */
Line 6185 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6354 plot [%.f:%.f] ", ageminpar, agemaxpar)
fprintf(ficgp," u %d:(",ioffset);	fprintf(ficgp," u %d:(",ioffset);
kl=0;	kl=0;
strcpy(gplotcondition,"(");	strcpy(gplotcondition,"(");
for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */	for (k=1; k<=nqveff; k++){ /* For each covariate writing the chain of conditions */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */	lv= decodtabm(k1,k,nqveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
Line 6194 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6363 plot [%.f:%.f] ", ageminpar, agemaxpar)
kl++;	kl++;
sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);	sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
kl++;	kl++;
if(k <cptcoveff && cptcoveff>1)	if(k <nqveff && nqveff>1)
sprintf(gplotcondition+strlen(gplotcondition)," && ");	sprintf(gplotcondition+strlen(gplotcondition)," && ");
}	}
strcpy(gplotcondition+strlen(gplotcondition),")");	strcpy(gplotcondition+strlen(gplotcondition),")");
Line 6251 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6420 plot [%.f:%.f] ", ageminpar, agemaxpar)
fprintf(ficgp,"#\n");	fprintf(ficgp,"#\n");
for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/	for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
fprintf(ficgp,"# ng=%d\n",ng);	fprintf(ficgp,"# ng=%d\n",ng);
fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);	fprintf(ficgp,"# jk=1 to 2^%d=%d\n",nqveff,m);
for(jk=1; jk <=m; jk++) {	for(jk=1; jk <=m; jk++) {
fprintf(ficgp,"# jk=%d\n",jk);	fprintf(ficgp,"# jk=%d\n",jk);
fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);	fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
Line 6374 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6543 plot [%.f:%.f] ", ageminpar, agemaxpar)
double agemingood, agemaxgood; /* Currently identical for all covariates */	double agemingood, agemaxgood; /* Currently identical for all covariates */


/* modcovmax=2cptcoveff;/\ Max number of modalities. We suppose */	/* modcovmax=2nqveff;/\ Max number of modalities. We suppose */
/* a covariate has 2 modalities, should be equal to ncovcombmax \/ /	/* a covariate has 2 modalities, should be equal to ncovcombmax \/ /

sumnewp = vector(1,ncovcombmax);	sumnewp = vector(1,ncovcombmax);
Line 6515 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6684 plot [%.f:%.f] ", ageminpar, agemaxpar)


/************ Forecasting ****************/	/************ Forecasting ****************/
void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){	void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int nqveff){
/* proj1, year, month, day of starting projection	/* proj1, year, month, day of starting projection
agemin, agemax range of age	agemin, agemax range of age
dateprev1 dateprev2 range of dates during which prevalence is computed	dateprev1 dateprev2 range of dates during which prevalence is computed
Line 6546 void prevforecast(char fileres[], double	Line 6715 void prevforecast(char fileres[], double
printf("Computing forecasting: result on file '%s', please wait... \n", fileresf);	printf("Computing forecasting: result on file '%s', please wait... \n", fileresf);
fprintf(ficlog,"Computing forecasting: result on file '%s', please wait... \n", fileresf);	fprintf(ficlog,"Computing forecasting: result on file '%s', please wait... \n", fileresf);

if (cptcoveff==0) ncodemax[cptcoveff]=1;	if (nqveff==0) ncodemax[nqveff]=1;


stepsize=(int) (stepm+YEARM-1)/YEARM;	stepsize=(int) (stepm+YEARM-1)/YEARM;
Line 6567 void prevforecast(char fileres[], double	Line 6736 void prevforecast(char fileres[], double
if(jprojmean==0) jprojmean=1;	if(jprojmean==0) jprojmean=1;
if(mprojmean==0) jprojmean=1;	if(mprojmean==0) jprojmean=1;

i1=cptcoveff;	i1=nqveff;
if (cptcovn < 1){i1=1;}	if (cptcovn < 1){i1=1;}

fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);	fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
Line 6576 void prevforecast(char fileres[], double	Line 6745 void prevforecast(char fileres[], double

/* if (h==(int)(YEARMyearp)){ /	/* if (h==(int)(YEARMyearp)){ /
for(cptcov=1, k=0;cptcov<=i1;cptcov++){	for(cptcov=1, k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){	for(cptcod=1;cptcod<=ncodemax[nqveff];cptcod++){
k=k+1;	k=k+1;
fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");	fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=nqveff;j++) {
fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
}	}
fprintf(ficresf," yearproj age");	fprintf(ficresf," yearproj age");
Line 6601 void prevforecast(char fileres[], double	Line 6770 void prevforecast(char fileres[], double
for (h=0; h<=nhstepm; h++){	for (h=0; h<=nhstepm; h++){
if (hhstepm/YEARMstepm ==yearp) {	if (hhstepm/YEARMstepm ==yearp) {
fprintf(ficresf,"\n");	fprintf(ficresf,"\n");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=nqveff;j++)
fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+hhstepm/YEARMstepm);	fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+hhstepm/YEARMstepm);
}	}
Line 6635 void prevforecast(char fileres[], double	Line 6804 void prevforecast(char fileres[], double
}	}

/* /\************ Back Forecasting ***************\/ /	/* /\************ Back Forecasting ***************\/ /
/* void prevbackforecast(char fileres[], double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){ */	/* void prevbackforecast(char fileres[], double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int nqveff){ */
/* /\* back1, year, month, day of starting backection */	/* /\* back1, year, month, day of starting backection */
/* agemin, agemax range of age */	/* agemin, agemax range of age */
/* dateprev1 dateprev2 range of dates during which prevalence is computed */	/* dateprev1 dateprev2 range of dates during which prevalence is computed */
Line 6667 void prevforecast(char fileres[], double	Line 6836 void prevforecast(char fileres[], double
/* printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */	/* printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
/* fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */	/* fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */

/* if (cptcoveff==0) ncodemax[cptcoveff]=1; */	/* if (nqveff==0) ncodemax[nqveff]=1; */

/* /\* if (mobilav!=0) { \/ /	/* /\* if (mobilav!=0) { \/ /
/* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); \/ /	/* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); \/ /
Line 6695 void prevforecast(char fileres[], double	Line 6864 void prevforecast(char fileres[], double
/* if(jprojmean==0) jprojmean=1; */	/* if(jprojmean==0) jprojmean=1; */
/* if(mprojmean==0) jprojmean=1; */	/* if(mprojmean==0) jprojmean=1; */

/* i1=cptcoveff; */	/* i1=nqveff; */
/* if (cptcovn < 1){i1=1;} */	/* if (cptcovn < 1){i1=1;} */

/* fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); */	/* fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); */
Line 6704 void prevforecast(char fileres[], double	Line 6873 void prevforecast(char fileres[], double

/* /\* if (h==(int)(YEARMyearp)){ \/ */	/* /\* if (h==(int)(YEARMyearp)){ \/ */
/* for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */	/* for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */
/* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */	/* for(cptcod=1;cptcod<=ncodemax[nqveff];cptcod++){ */
/* k=k+1; */	/* k=k+1; */
/* fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */	/* fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */
/* for(j=1;j<=cptcoveff;j++) { */	/* for(j=1;j<=nqveff;j++) { */
/* fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */	/* fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
/* } */	/* } */
/* fprintf(ficresfb," yearbproj age"); */	/* fprintf(ficresfb," yearbproj age"); */
Line 6729 void prevforecast(char fileres[], double	Line 6898 void prevforecast(char fileres[], double
/* for (h=0; h<=nhstepm; h++){ */	/* for (h=0; h<=nhstepm; h++){ */
/* if (hhstepm/YEARMstepm ==yearp) { */	/* if (hhstepm/YEARMstepm ==yearp) { */
/* fprintf(ficresfb,"\n"); */	/* fprintf(ficresfb,"\n"); */
/* for(j=1;j<=cptcoveff;j++) */	/* for(j=1;j<=nqveff;j++) */
/* fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */	/* fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
/* fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+hhstepm/YEARMstepm); */	/* fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+hhstepm/YEARMstepm); */
/* } */	/* } */
Line 6792 void populforecast(char fileres[], doubl	Line 6961 void populforecast(char fileres[], doubl
printf("Computing forecasting: result on file '%s' \n", filerespop);	printf("Computing forecasting: result on file '%s' \n", filerespop);
fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);	fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);

if (cptcoveff==0) ncodemax[cptcoveff]=1;	if (nqveff==0) ncodemax[nqveff]=1;

/* if (mobilav!=0) { */	/* if (mobilav!=0) { */
/* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */	/* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
Line 6827 void populforecast(char fileres[], doubl	Line 6996 void populforecast(char fileres[], doubl
}	}

for(cptcov=1,k=0;cptcov<=i2;cptcov++){	for(cptcov=1,k=0;cptcov<=i2;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){	for(cptcod=1;cptcod<=ncodemax[nqveff];cptcod++){
k=k+1;	k=k+1;
fprintf(ficrespop,"\n#******");	fprintf(ficrespop,"\n#******");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=nqveff;j++) {
fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
}	}
fprintf(ficrespop,"******\n");	fprintf(ficrespop,"******\n");
Line 7464 void removespace(char *str) {	Line 7633 void removespace(char *str) {
while (p1++ == p2++);	while (p1++ == p2++);
}	}

int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:	int decodemodel ( char model[], int lastobs)
* Model V1+V2+V3+V8+V7V8+V5V6+V8age+V3age+age*age	/**< This routine decode the model and returns:
* - nagesqr = 1 if age*age in the model, otherwise 0.	* Model V1+V2+V3+V8+V7V8+V5V6+V8age+V3age+age*age
* - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age	* - nagesqr = 1 if age*age in the model, otherwise 0.
* - cptcovn or number of covariates k of the models excluding ageproducts =6 and ageage	* - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
* - cptcovage number of covariates with age*products =2	* - cptcovn or number of covariates k of the models excluding ageproducts =6 and ageage
* - cptcovs number of simple covariates	* - cptcovage number of covariates with age*products =2
* - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10	* - cptcovs number of simple covariates
* which is a new column after the 9 (ncovcol) variables.	* - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
* - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual	* which is a new column after the 9 (ncovcol) variables.
* - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage	* - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
* Tprod[1]@2 {5, 6}: position of first product V7V8 is 5, and second V5V6 is 6.	* - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
* - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7V8 and V5V6 .	* Tprod[1]@2 {5, 6}: position of first product V7V8 is 5, and second V5V6 is 6.
*/	* - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7V8 and V5V6 .
	*/
{	{
int i, j, k, ks;	int i, j, k, ks;
int j1, k1, k2;	int j1, k1, k2;
Line 7502 int decodemodel ( char model[], int last	Line 7672 int decodemodel ( char model[], int last
if ((strpt=strstr(model,"age*age")) !=0){	if ((strpt=strstr(model,"age*age")) !=0){
printf(" strpt=%s, model=%s\n",strpt, model);	printf(" strpt=%s, model=%s\n",strpt, model);
if(strpt != model){	if(strpt != model){
printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \	printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
'model=1+age+ageage+V1.' or 'model=1+age+ageage+V1+V1*age.', please swap as well as \n \	'model=1+age+ageage+V1.' or 'model=1+age+ageage+V1+V1*age.', please swap as well as \n \
corresponding column of parameters.\n",model);	corresponding column of parameters.\n",model);
fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \	fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
'model=1+age+ageage+V1.' or 'model=1+age+ageage+V1+V1*age.', please swap as well as \n \	'model=1+age+ageage+V1.' or 'model=1+age+ageage+V1+V1*age.', please swap as well as \n \
corresponding column of parameters.\n",model); fflush(ficlog);	corresponding column of parameters.\n",model); fflush(ficlog);
return 1;	return 1;
}	}

nagesqr=1;	nagesqr=1;
if (strstr(model,"+age*age") !=0)	if (strstr(model,"+age*age") !=0)
substrchaine(modelsav, model, "+age*age");	substrchaine(modelsav, model, "+age*age");
else if (strstr(model,"age*age+") !=0)	else if (strstr(model,"age*age+") !=0)
substrchaine(modelsav, model, "age*age+");	substrchaine(modelsav, model, "age*age+");
else	else
substrchaine(modelsav, model, "age*age");	substrchaine(modelsav, model, "age*age");
}else	}else
nagesqr=0;	nagesqr=0;
if (strlen(modelsav) >1){	if (strlen(modelsav) >1){
j=nbocc(modelsav,'+'); /*< j=Number of '+' /	j=nbocc(modelsav,'+'); /*< j=Number of '+' /
j1=nbocc(modelsav,''); /< j1=Number of '' */	j1=nbocc(modelsav,''); /< j1=Number of '' */
cptcovs=j+1-j1; /*< Number of simple covariates V1+V1age+V3 +V3V4+ageage=> V1 + V3 =2 */	cptcovs=j+1-j1; /*< Number of simple covariates V1+V1age+V3 +V3V4+ageage=> V1 + V3 =5-3=2 */
cptcovt= j+1; /* Number of total covariates in the model, not including	cptcovt= j+1; /* Number of total covariates in the model, not including
* cst, age and age*age	* cst, age and age*age
* V1+V1age+ V3 + V3V4+ageage=> 4/	* V1+V1age+ V3 + V3V4+ageage=> 3+1=4/
/* including age products which are counted in cptcovage.	/* including age products which are counted in cptcovage.
* but the covariates which are products must be treated	* but the covariates which are products must be treated
* separately: ncovn=4- 2=2 (V1+V3). */	* separately: ncovn=4- 2=2 (V1+V3). */
cptcovprod=j1; /*< Number of products V1V2 +v3age = 2 /	cptcovprod=j1; /*< Number of products V1V2 +v3age = 2 /
cptcovprodnoage=0; /*< Number of covariate products without age: V3V4 =1 */	cptcovprodnoage=0; /*< Number of covariate products without age: V3V4 =1 */

Line 7541 int decodemodel ( char model[], int last	Line 7711 int decodemodel ( char model[], int last
* k= 1 2 3 4 5 6 7 8	* k= 1 2 3 4 5 6 7 8
* cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8	* cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
* covar[k,i], value of kth covariate if not including age for individual i:	* covar[k,i], value of kth covariate if not including age for individual i:
* covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)	* covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
* Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8	* Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
* if multiplied by age: V3age Tvar[3=V3age]=3 (V3) Tvar[7]=8 and	* if multiplied by age: V3age Tvar[3=V3age]=3 (V3) Tvar[7]=8 and
* Tage[++cptcovage]=k	* Tage[++cptcovage]=k
* if products, new covar are created after ncovcol with k1	* if products, new covar are created after ncovcol with k1
Line 7650 int decodemodel ( char model[], int last	Line 7820 int decodemodel ( char model[], int last
If model=V1+V1age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0/	If model=V1+V1age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0/

/* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);	/* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
printf("cptcovprod=%d ", cptcovprod);	printf("cptcovprod=%d ", cptcovprod);
fprintf(ficlog,"cptcovprod=%d ", cptcovprod);	fprintf(ficlog,"cptcovprod=%d ", cptcovprod);

scanf("%d ",i);*/	scanf("%d ",i);*/
	/* Dispatching in quantitative and time varying covariates */

	for(k=1, ncoveff=0, nqveff=0, ntveff=0, nqtveff=0;k<=cptcovn; k++){ /* or cptocvt */
	if (Tvar[k] <=ncovcol){
	ncoveff++;
	}else if( Tvar[k] <=ncovcol+nqv){
	nqveff++;
	}else if( Tvar[k] <=ncovcol+nqv+ntv){
	ntveff++;
	}else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
	nqtveff++;
	}else
	printf("Error in effective covariates \n");
	}

return (0); /* with covar[new additional covariate if product] and Tage if age */	return (0); /* with covar[new additional covariate if product] and Tage if age */
/endread:/	/endread:/
printf("Exiting decodemodel: ");	printf("Exiting decodemodel: ");
return (1);	return (1);
}	}

int calandcheckages(int imx, int maxwav, double agemin, double agemax, int nberr, int nbwarn )	int calandcheckages(int imx, int maxwav, double agemin, double agemax, int nberr, int nbwarn )
Line 7994 int prevalence_limit(double p, double	Line 8177 int prevalence_limit(double p, double
agebase=ageminpar;	agebase=ageminpar;
agelim=agemaxpar;	agelim=agemaxpar;

i1=pow(2,cptcoveff);	i1=pow(2,ncoveff);
if (cptcovn < 1){i1=1;}	if (cptcovn < 1){i1=1;}

for(k=1; k<=i1;k++){	for(k=1; k<=i1;k++){
Line 8007 int prevalence_limit(double p, double	Line 8190 int prevalence_limit(double p, double
fprintf(ficrespl,"#******");	fprintf(ficrespl,"#******");
printf("#******");	printf("#******");
fprintf(ficlog,"#******");	fprintf(ficlog,"#******");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=nqveff;j++) {
fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
Line 8023 int prevalence_limit(double p, double	Line 8206 int prevalence_limit(double p, double
}	}

fprintf(ficrespl,"#Age ");	fprintf(ficrespl,"#Age ");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=nqveff;j++) {
fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
}	}
for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);	for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
Line 8033 int prevalence_limit(double p, double	Line 8216 int prevalence_limit(double p, double
/* for (age=agebase; age<=agebase; age++){ */	/* for (age=agebase; age<=agebase; age++){ */
prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);	prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
fprintf(ficrespl,"%.0f ",age );	fprintf(ficrespl,"%.0f ",age );
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=nqveff;j++)
fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
tot=0.;	tot=0.;
for(i=1; i<=nlstate;i++){	for(i=1; i<=nlstate;i++){
Line 8081 int back_prevalence_limit(double *p, dou	Line 8264 int back_prevalence_limit(double *p, dou
agelim=agemaxpar;	agelim=agemaxpar;


i1=pow(2,cptcoveff);	i1=pow(2,nqveff);
if (cptcovn < 1){i1=1;}	if (cptcovn < 1){i1=1;}

for(k=1; k<=i1;k++){	for(k=1; k<=i1;k++){
Line 8094 int back_prevalence_limit(double *p, dou	Line 8277 int back_prevalence_limit(double *p, dou
fprintf(ficresplb,"#******");	fprintf(ficresplb,"#******");
printf("#******");	printf("#******");
fprintf(ficlog,"#******");	fprintf(ficlog,"#******");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=nqveff;j++) {
fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
Line 8110 int back_prevalence_limit(double *p, dou	Line 8293 int back_prevalence_limit(double *p, dou
}	}

fprintf(ficresplb,"#Age ");	fprintf(ficresplb,"#Age ");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=nqveff;j++) {
fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
}	}
for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);	for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);
Line 8132 int back_prevalence_limit(double *p, dou	Line 8315 int back_prevalence_limit(double *p, dou
bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k);	bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k);
}	}
fprintf(ficresplb,"%.0f ",age );	fprintf(ficresplb,"%.0f ",age );
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=nqveff;j++)
fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
tot=0.;	tot=0.;
for(i=1; i<=nlstate;i++){	for(i=1; i<=nlstate;i++){
Line 8180 int hPijx(double *p, int bage, int fage)	Line 8363 int hPijx(double *p, int bage, int fage)
/* hstepm=1; aff par mois*/	/* hstepm=1; aff par mois*/
pstamp(ficrespij);	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 ");
i1= pow(2,cptcoveff);	i1= pow(2,nqveff);
/* 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; */
for (k=1; k <= (int) pow(2,cptcoveff); k++){	for (k=1; k <= (int) pow(2,nqveff); k++){
fprintf(ficrespij,"\n#****** ");	fprintf(ficrespij,"\n#****** ");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=nqveff;j++)
fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
fprintf(ficrespij,"******\n");	fprintf(ficrespij,"******\n");

Line 8252 int hPijx(double *p, int bage, int fage)	Line 8435 int hPijx(double *p, int bage, int fage)
/* hstepm=1; aff par mois*/	/* hstepm=1; aff par mois*/
pstamp(ficrespijb);	pstamp(ficrespijb);
fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x ");	fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x ");
i1= pow(2,cptcoveff);	i1= pow(2,nqveff);
/* 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; */
for (k=1; k <= (int) pow(2,cptcoveff); k++){	for (k=1; k <= (int) pow(2,nqveff); k++){
fprintf(ficrespijb,"\n#****** ");	fprintf(ficrespijb,"\n#****** ");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=nqveff;j++)
fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
fprintf(ficrespijb,"******\n");	fprintf(ficrespijb,"******\n");
if(invalidvarcomb[k]){	if(invalidvarcomb[k]){
Line 8655 int main(int argc, char *argv[])	Line 8838 int main(int argc, char *argv[])
covar=matrix(0,NCOVMAX,1,n); /*< used in readdata /	covar=matrix(0,NCOVMAX,1,n); /*< used in readdata /
coqvar=matrix(1,nqv,1,n); /*< used in readdata /	coqvar=matrix(1,nqv,1,n); /*< used in readdata /
cotvar=ma3x(1,maxwav,1,ntv,1,n); /*< used in readdata /	cotvar=ma3x(1,maxwav,1,ntv,1,n); /*< used in readdata /
cotqvar=ma3x(1,maxwav,1,ntqv,1,n); /*< used in readdata /	cotqvar=ma3x(1,maxwav,1,nqtv,1,n); /*< used in readdata /
cptcovn=0; /Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn/	cptcovn=0; /Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn/
/* v1+v2+v3+v2v4+v5age makes cptcovn = 5	/* v1+v2+v3+v2v4+v5age makes cptcovn = 5
v1+v2age+v2v3 makes cptcovn = 3	v1+v2age+v2v3 makes cptcovn = 3
Line 9425 Please run with mle=-1 to get a correct	Line 9608 Please run with mle=-1 to get a correct
printf("\n");	printf("\n");

/--------- results files --------------/	/--------- results files --------------/
fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);	fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, weightopt,model);


fprintf(ficres,"# Parameters nlstatenlstatencov a121 + b12 age + ...\n");	fprintf(ficres,"# Parameters nlstatenlstatencov a121 + b12 age + ...\n");
Line 9772 Please run with mle=-1 to get a correct	Line 9955 Please run with mle=-1 to get a correct
/if((stepm == 1) && (strcmp(model,".")==0)){/	/if((stepm == 1) && (strcmp(model,".")==0)){/
if(prevfcast==1){	if(prevfcast==1){
/* if(stepm ==1){*/	/* if(stepm ==1){*/
prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);	prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, nqveff);
}	}
if(backcast==1){	if(backcast==1){
ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);	ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
Line 9790 Please run with mle=-1 to get a correct	Line 9973 Please run with mle=-1 to get a correct
free_matrix(bprlim,1,nlstate,1,nlstate); /here or after loop ? /	free_matrix(bprlim,1,nlstate,1,nlstate); /here or after loop ? /

/* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,	/* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,
bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */	bage, fage, firstpass, lastpass, anback2, p, nqveff); */
free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);	free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);	free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);	free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
Line 9816 Please run with mle=-1 to get a correct	Line 9999 Please run with mle=-1 to get a correct
printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);	printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);	fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);

for (k=1; k <= (int) pow(2,cptcoveff); k++){	for (k=1; k <= (int) pow(2,nqveff); k++){
fprintf(ficreseij,"\n#****** ");	fprintf(ficreseij,"\n#****** ");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=nqveff;j++) {
fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
}	}
fprintf(ficreseij,"******\n");	fprintf(ficreseij,"******\n");
Line 9876 Please run with mle=-1 to get a correct	Line 10059 Please run with mle=-1 to get a correct
/*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++){*/

for (k=1; k <= (int) pow(2,cptcoveff); k++){	for (k=1; k <= (int) pow(2,nqveff); k++){
fprintf(ficrest,"\n#****** ");	fprintf(ficrest,"\n#****** ");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=nqveff;j++)
fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
fprintf(ficrest,"******\n");	fprintf(ficrest,"******\n");

fprintf(ficresstdeij,"\n#****** ");	fprintf(ficresstdeij,"\n#****** ");
fprintf(ficrescveij,"\n#****** ");	fprintf(ficrescveij,"\n#****** ");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=nqveff;j++) {
fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
}	}
Line 9892 Please run with mle=-1 to get a correct	Line 10075 Please run with mle=-1 to get a correct
fprintf(ficrescveij,"******\n");	fprintf(ficrescveij,"******\n");

fprintf(ficresvij,"\n#****** ");	fprintf(ficresvij,"\n#****** ");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=nqveff;j++)
fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
fprintf(ficresvij,"******\n");	fprintf(ficresvij,"******\n");

Line 10002 Please run with mle=-1 to get a correct	Line 10185 Please run with mle=-1 to get a correct
/*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++){*/

for (k=1; k <= (int) pow(2,cptcoveff); k++){	for (k=1; k <= (int) pow(2,nqveff); k++){
fprintf(ficresvpl,"\n#****** ");	fprintf(ficresvpl,"\n#****** ");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=nqveff;j++)
fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
fprintf(ficresvpl,"******\n");	fprintf(ficresvpl,"******\n");

Line 10030 Please run with mle=-1 to get a correct	Line 10213 Please run with mle=-1 to get a correct
free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);	free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);	free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);	free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
free_ma3x(cotqvar,1,maxwav,1,ntqv,1,n);	free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
free_ma3x(cotvar,1,maxwav,1,ntv,1,n);	free_ma3x(cotvar,1,maxwav,1,ntv,1,n);
free_matrix(coqvar,1,maxwav,1,n);	free_matrix(coqvar,1,maxwav,1,n);
free_matrix(covar,0,NCOVMAX,1,n);	free_matrix(covar,0,NCOVMAX,1,n);

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Removed from v.1.223
changed lines
	Added in v.1.224