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Diff for /imach/src/imach.c between versions 1.222 and 1.225

version 1.222, 2016/02/17 08:14:50	version 1.225, 2016/07/12 08:40:03
Line 1	Line 1
/* $Id$	/* $Id$
$State$	$State$
$Log$	$Log$
	Revision 1.225 2016/07/12 08:40:03 brouard
	Summary: saving but not running

	Revision 1.224 2016/07/01 13:16:01 brouard
	Summary: Fixes

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

Revision 1.222 2016/02/17 08:14:50 brouard	Revision 1.222 2016/02/17 08:14:50 brouard
Summary: Probably last 0.98 stable version 0.98r6	Summary: Probably last 0.98 stable version 0.98r6

Line 742 Back prevalence and projections:	Line 751 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 838 typedef struct {	Line 847 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 847 int nagesqr=0, nforce=0; /* nagesqr=1 if	Line 856 int nagesqr=0, nforce=0; /* nagesqr=1 if
/* Number of covariates model=V2+V1+ V3age+V2V4 */	/* Number of covariates model=V2+V1+ V3age+V2V4 */
int cptcovn=0; /*< cptcovn number of covariates added in the model (excepting constant and age and ageproduct) */	int cptcovn=0; /*< cptcovn number of covariates added in the model (excepting constant and age and ageproduct) */
int cptcovt=0; /*< cptcovt number of covariates added in the model (excepting constant and age) /	int cptcovt=0; /*< cptcovt number of covariates added in the model (excepting constant and age) /
int cptcovs=0; /*< cptcovs number of simple covariates V2+V1 =2 /	int cptcovs=0; /*< cptcovs number of simple covariates in the model V2+V1 =2 /
	int cptcovsnq=0; /*< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 /
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 nqfveff=0; /*< nqfveff Number of Quantitative Fixed Variables Effective /
	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;
int nlstate=2; /* Number of live states */	int nlstate=2; /* Number of live states */
int ndeath=1; /* Number of dead states */	int ndeath=1; /* Number of dead states */
int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a121 +b12x ncovmodel=2 */	int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a121 +b12x ncovmodel=2 */
	int nqv=0, ntv=0, nqtv=0; /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */
int popbased=0;	int popbased=0;

int wav; / Number of waves for this individuual 0 is possible */	int wav; / Number of waves for this individuual 0 is possible */
Line 995 double *agedc;	Line 1010 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 iqv */
	double **cotvar; / Time varying covariate itv */
	double **cotqvar; / Time varying quantitative covariate itqv */
double idx;	double idx;
int *nbcode, Tvar; /*< model=V2 => Tvar[1]= 2 /	int *nbcode, Tvar; /*< model=V2 => Tvar[1]= 2 /
	int Typevar; /< 1 for qualitative fixed, 2 for quantitative fixed, 3 for qualitive varying, 4 for quanti varying/
int *Tage;	int *Tage;
int Ndum; /* Freq of modality (tricode */	int Ndum; /* Freq of modality (tricode */
/* int *codtab;/ /*< codtab=imatrix(1,100,1,10); /	/* int *codtab;/ /*< codtab=imatrix(1,100,1,10); /
Line 1542 double brent(double ax, double bx, doubl	Line 1561 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 1561 double brent(double ax, double bx, doubl	Line 1580 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 1608 values at the three points, fa, fb , and	Line 1627 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 1624 values at the three points, fa, fb , and	Line 1643 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 1658 values at the three points, fa, fb , and	Line 1677 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 1671 values at the three points, fa, fb , and	Line 1693 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 1717 int ncom;	Line 1746 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 1761 void linmin(double p[], double xi[], int	Line 1794 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 1832 such that failure to decrease by more th	Line 1878 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, flatd=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 1876 void powell(double p[], double **xi, int	Line 1938 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 1899 void powell(double p[], double **xi, int	Line 1961 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)=%.12e",j,p[j]);
fprintf(ficlog," p(%d)=%.12e",j,p[j]);	fprintf(ficlog," p(%d)=%.12e",j,p[j]);
}	}
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
Line 1928 void powell(double p[], double **xi, int	Line 1995 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++) {
	if(flatdir[j] >0){
	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 1936 void powell(double p[], double **xi, int	Line 2011 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 1964 void powell(double p[], double **xi, int	Line 2039 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 1978 void powell(double p[], double **xi, int	Line 2056 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
	#endif
	#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 1987 void powell(double p[], double **xi, int	Line 2069 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 2010 void powell(double p[], double **xi, int	Line 2100 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
	for (j=1, flatd=0;j<=n;j++) {
	if(flatdir[j]>0)
	flatd++;
	}
	if(flatd >0){
	printf("%d flat directions\n",flatd);
	fprintf(ficlog,"%d flat directions\n",flatd);
	for (j=1;j<=n;j++) {
	if(flatdir[j]>0){
	printf("%d ",j);
	fprintf(ficlog,"%d ",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
	#ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
	} /NODIRECTIONCHANGEDUNTILNITER No change in drections until some iterations are done /
	#else
	#endif
} /* loop iteration */	} /* loop iteration */
}	}

Line 2334 double pmij(double ps, double *cov,	Line 2453 double pmij(double ps, double *cov,
/double t34;/	/double t34;/
int i,j, nc, ii, jj;	int i,j, nc, ii, jj;

for(i=1; i<= nlstate; i++){	for(i=1; i<= nlstate; i++){
for(j=1; j<i;j++){	for(j=1; j<i;j++){
for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){	for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
/lnpijopii += param[i][j][nc]cov[nc];*/	/lnpijopii += param[i][j][nc]cov[nc];*/
lnpijopii += x[nc+((i-1)(nlstate+ndeath-1)+j-1)ncovmodel]*cov[nc];	lnpijopii += x[nc+((i-1)(nlstate+ndeath-1)+j-1)ncovmodel]*cov[nc];
/* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */	/* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
}	}
ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */	ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
/* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */	/* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
}	}
for(j=i+1; j<=nlstate+ndeath;j++){	for(j=i+1; j<=nlstate+ndeath;j++){
for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){	for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
/lnpijopii += x[(i-1)nlstatencovmodel+(j-2)ncovmodel+nc+(i-1)(ndeath-1)ncovmodel]cov[nc];/	/lnpijopii += x[(i-1)nlstatencovmodel+(j-2)ncovmodel+nc+(i-1)(ndeath-1)ncovmodel]cov[nc];/
lnpijopii += x[nc + ((i-1)(nlstate+ndeath-1)+(j-2))ncovmodel]*cov[nc];	lnpijopii += x[nc + ((i-1)(nlstate+ndeath-1)+(j-2))ncovmodel]*cov[nc];
/* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */	/* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
}	}
ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */	ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
}	}
}	}

for(i=1; i<= nlstate; i++){	for(i=1; i<= nlstate; i++){
s1=0;	s1=0;
for(j=1; j<i; j++){	for(j=1; j<i; j++){
s1+=exp(ps[i][j]); /* In fact sums pij/pii */	s1+=exp(ps[i][j]); /* In fact sums pij/pii */
/printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); /	/printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); /
}	}
for(j=i+1; j<=nlstate+ndeath; j++){	for(j=i+1; j<=nlstate+ndeath; j++){
s1+=exp(ps[i][j]); /* In fact sums pij/pii */	s1+=exp(ps[i][j]); /* In fact sums pij/pii */
/printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); /	/printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); /
}	}
/* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */	/* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
ps[i][i]=1./(s1+1.);	ps[i][i]=1./(s1+1.);
/* Computing other pijs */	/* Computing other pijs */
for(j=1; j<i; j++)	for(j=1; j<i; j++)
ps[i][j]= exp(ps[i][j])*ps[i][i];	ps[i][j]= exp(ps[i][j])*ps[i][i];
for(j=i+1; j<=nlstate+ndeath; j++)	for(j=i+1; j<=nlstate+ndeath; j++)
ps[i][j]= exp(ps[i][j])*ps[i][i];	ps[i][j]= exp(ps[i][j])*ps[i][i];
/* ps[i][nlstate+1]=1.-s1- ps[i][i];/ / Sum should be 1 */	/* ps[i][nlstate+1]=1.-s1- ps[i][i];/ / Sum should be 1 */
} /* end i */	} /* end i */

for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){	for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
for(jj=1; jj<= nlstate+ndeath; jj++){	for(jj=1; jj<= nlstate+ndeath; jj++){
ps[ii][jj]=0;	ps[ii][jj]=0;
ps[ii][ii]=1;	ps[ii][ii]=1;
}	}
}	}


/* for(ii=1; ii<= nlstate+ndeath; ii++){ */	/* for(ii=1; ii<= nlstate+ndeath; ii++){ */
/* for(jj=1; jj<= nlstate+ndeath; jj++){ */	/* for(jj=1; jj<= nlstate+ndeath; jj++){ */
/* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */	/* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
/* } */	/* } */
/* printf("\n "); */	/* printf("\n "); */
/* } */	/* } */
/* printf("\n ");printf("%lf ",cov[2]);*/	/* printf("\n ");printf("%lf ",cov[2]);*/
/*	/*
for(i=1; i<= npar; i++) printf("%f ",x[i]);	for(i=1; i<= npar; i++) printf("%f ",x[i]);
goto end;*/	goto end;*/
return ps;	return ps;
}	}

/************* backward transition probabilities *************/	/************* backward transition probabilities *************/
Line 2771 double *hbxij(double *po, int nhstep	Line 2890 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;
double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];	int ioffset=0;
double **out;	double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
double sw; /* Sum of weights */	double **out;
double lli; /* Individual log likelihood */	double sw; /* Sum of weights */
int s1, s2;	double lli; /* Individual log likelihood */
double bbh, survp;	int s1, s2;
long ipmx;	int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quatitative time varying covariate */
double agexact;	double bbh, survp;
/extern weight /	long ipmx;
/* We are differentiating ll according to initial status */	double agexact;
/* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/	/extern weight /
/*for(i=1;i<imx;i++)	/* We are differentiating ll according to initial status */
printf(" %d\n",s[4][i]);	/* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
*/	/*for(i=1;i<imx;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 <= nqfveff; iqv++){ /* Quantitatives and Fixed 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 variying (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];
for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */	s2=s[mw[mi+1][i]][i];
cov[2+nagesqr+k]=covar[Tvar[k]][i];	And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
}	But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
/* In model V2+V1V4+ageV3+V3V2 Tvar[1] is V2, Tvar[2=V1V4]	meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
is 6, Tvar[3=ageV3] should not be computed because of age Tvar[4=V3V2]	*/
has been calculated etc */	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 */
for (ii=1;ii<=nlstate+ndeath;ii++)	cov[ioffset+itv]=cotvar[mw[mi][i]][itv][i];
for (j=1;j<=nlstate+ndeath;j++){	}
oldm[ii][j]=(ii==j ? 1.0 : 0.0);	for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */
savm[ii][j]=(ii==j ? 1.0 : 0.0);	if(cotqvar[mw[mi][i]][iqtv][i] == -1){
}	printf("i=%d, mi=%d, iqtv=%d, cotqvar[mw[mi][i]][iqtv][i]=%f",i,mi,iqtv,cotqvar[mw[mi][i]][iqtv][i]);
for(d=0; d<dh[mi][i]; d++){	}
newm=savm;	cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][iqtv][i];
agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;	}
cov[2]=agexact;	/* ioffset=2+nagesqr+cptcovn+nqv+ntv+nqtv; */
if(nagesqr==1)	for (ii=1;ii<=nlstate+ndeath;ii++)
cov[3]= agexact*agexact;	for (j=1;j<=nlstate+ndeath;j++){
for (kk=1; kk<=cptcovage;kk++) {	oldm[ii][j]=(ii==j ? 1.0 : 0.0);
cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]agexact; / Tage[kk] gives the data-covariate associated with age */	savm[ii][j]=(ii==j ? 1.0 : 0.0);
}	}
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,	for(d=0; d<dh[mi][i]; d++){
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));	newm=savm;
savm=oldm;	agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
oldm=newm;	cov[2]=agexact;
} /* end mult */	if(nagesqr==1)
	cov[3]= agexactagexact; / Should be changed here */
/lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);/ /* Original formula */	for (kk=1; kk<=cptcovage;kk++) {
/* But now since version 0.9 we anticipate for bias at large stepm.	cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]agexact; / Tage[kk] gives the data-covariate associated with age */
* If stepm is larger than one month (smallest stepm) and if the exact delay	}
* (in months) between two waves is not a multiple of stepm, we rounded to	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
* the nearest (and in case of equal distance, to the lowest) interval but now	1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
* we keep into memory the bias bh[mi][i] and also the previous matrix product	savm=oldm;
* (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the	oldm=newm;
* probability in order to take into account the bias as a fraction of the way	} /* end mult */
* from savm to out if bh is negative or even beyond if bh is positive. bh varies
* -stepm/2 to stepm/2 .	/lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);/ /* Original formula */
* For stepm=1 the results are the same as for previous versions of Imach.	/* But now since version 0.9 we anticipate for bias at large stepm.
* For stepm > 1 the results are less biased than in previous versions.	* If stepm is larger than one month (smallest stepm) and if the exact delay
*/	* (in months) between two waves is not a multiple of stepm, we rounded to
s1=s[mw[mi][i]][i];	* the nearest (and in case of equal distance, to the lowest) interval but now
s2=s[mw[mi+1][i]][i];	* we keep into memory the bias bh[mi][i] and also the previous matrix product
bbh=(double)bh[mi][i]/(double)stepm;	* (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
/* bias bh is positive if real duration	* probability in order to take into account the bias as a fraction of the way
* is higher than the multiple of stepm and negative otherwise.	* from savm to out if bh is negative or even beyond if bh is positive. bh varies
*/	* -stepm/2 to stepm/2 .
/* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]):log((1.+bbh)out[s1][s2]));/	* For stepm=1 the results are the same as for previous versions of Imach.
if( s2 > nlstate){	* For stepm > 1 the results are less biased than in previous versions.
/* i.e. if s2 is a death state and if the date of death is known	*/
then the contribution to the likelihood is the probability to	s1=s[mw[mi][i]][i];
die between last step unit time and current step unit time,	s2=s[mw[mi+1][i]][i];
which is also equal to probability to die before dh	bbh=(double)bh[mi][i]/(double)stepm;
minus probability to die before dh-stepm .	/* bias bh is positive if real duration
In version up to 0.92 likelihood was computed	* is higher than the multiple of stepm and negative otherwise.
as if date of death was unknown. Death was treated as any other	*/
health state: the date of the interview describes the actual state	/* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]):log((1.+bbh)out[s1][s2]));/
and not the date of a change in health state. The former idea was	if( s2 > nlstate){
to consider that at each interview the state was recorded	/* i.e. if s2 is a death state and if the date of death is known
(healthy, disable or death) and IMaCh was corrected; but when we	then the contribution to the likelihood is the probability to
introduced the exact date of death then we should have modified	die between last step unit time and current step unit time,
the contribution of an exact death to the likelihood. This new	which is also equal to probability to die before dh
contribution is smaller and very dependent of the step unit	minus probability to die before dh-stepm .
stepm. It is no more the probability to die between last interview	In version up to 0.92 likelihood was computed
and month of death but the probability to survive from last	as if date of death was unknown. Death was treated as any other
interview up to one month before death multiplied by the	health state: the date of the interview describes the actual state
probability to die within a month. Thanks to Chris	and not the date of a change in health state. The former idea was
Jackson for correcting this bug. Former versions increased	to consider that at each interview the state was recorded
mortality artificially. The bad side is that we add another loop	(healthy, disable or death) and IMaCh was corrected; but when we
which slows down the processing. The difference can be up to 10%	introduced the exact date of death then we should have modified
lower mortality.	the contribution of an exact death to the likelihood. This new
*/	contribution is smaller and very dependent of the step unit
/* If, at the beginning of the maximization mostly, the	stepm. It is no more the probability to die between last interview
cumulative probability or probability to be dead is	and month of death but the probability to survive from last
constant (ie = 1) over time d, the difference is equal to	interview up to one month before death multiplied by the
0. out[s1][3] = savm[s1][3]: probability, being at state	probability to die within a month. Thanks to Chris
s1 at precedent wave, to be dead a month before current	Jackson for correcting this bug. Former versions increased
wave is equal to probability, being at state s1 at	mortality artificially. The bad side is that we add another loop
precedent wave, to be dead at mont of the current	which slows down the processing. The difference can be up to 10%
wave. Then the observed probability (that this person died)	lower mortality.
is null according to current estimated parameter. In fact,	*/
it should be very low but not zero otherwise the log go to	/* If, at the beginning of the maximization mostly, the
infinity.	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 2891 double func( double *x)	Line 3037 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 3079 double funcone( double *x)	Line 3225 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 3096 double funcone( double *x)	Line 3244 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 <= nqfveff; iqv++){ /* Quantitatives Fixed 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);
Line 3119 double funcone( double *x)	Line 3281 double funcone( double *x)
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;
}	}
	/* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
/* 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));
Line 3162 double funcone( double *x)	Line 3324 double funcone( double *x)
ll[s[mw[mi][i]][i]] += 2weight[i]lli;	ll[s[mw[mi][i]][i]] += 2weight[i]lli;
/printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); /	/printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); /
if(globpr){	if(globpr){
fprintf(ficresilk,"%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]);
Line 3687 void pstamp(FILE *fichier)	Line 3849 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 3697 void pstamp(FILE *fichier)	Line 3861 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,nqfveff); /* Number of Quantitative Fixed Variables Effective */
	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 3739 Title=%s <br>Datafile=%s Firstpass=%d La	Line 3905 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 3751 Title=%s <br>Datafile=%s Firstpass=%d La	Line 3917 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 3766 Title=%s <br>Datafile=%s Firstpass=%d La	Line 3932 Title=%s <br>Datafile=%s Firstpass=%d La
posprop[i]=0;	posprop[i]=0;
pospropt[i]=0;	pospropt[i]=0;
}	}
	for (z1=1; z1<= nqfveff; 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 (nqfveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
for (z1=1; z1<=cptcoveff; z1++) {	for (z1=1; z1<= nqfveff; 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 3785 Title=%s <br>Datafile=%s Firstpass=%d La	Line 3965 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 3825 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4005 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 3838 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4018 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 3989 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4169 Title=%s <br>Datafile=%s Firstpass=%d La
fclose(ficresp);	fclose(ficresp);
fclose(ficresphtm);	fclose(ficresphtm);
fclose(ficresphtmfr);	fclose(ficresphtmfr);
	free_vector(meanq,1,nqfveff);
	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 4101 void concatwav(int wav[], int **dh, int	Line 4283 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 4114 void concatwav(int wav[], int **dh, int	Line 4296 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 */
mw[++mi][i]=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 */
if(m >=lastpass){	mw[++mi][i]=m;
if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){	mli=m;
if(firsthree == 0){	} /* else might be a useless wave -1 and mi is not incremented and mw[mi] not updated */
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);	if(m < lastpass){ /* m < lastpass, standard case */
firsthree=1;	m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing 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.\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;
}
if(s[m][i]==-2){ /* Vital status is really unknown */
nbwarn++;
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);
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);
}
break;
}
break;
}	}
else	else{ /* m >= lastpass, eventual special issue with warning */
m++;	#ifdef UNKNOWNSTATUSNOTCONTRIBUTING
	break;
	#else
	if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
	if(firsthree == 0){
	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;
	}
	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;
	mli=m;
	}
	if(s[m][i]==-2){ /* Vital status is really unknown */
	nbwarn++;
	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);
	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;
	#endif
	}/* End m >= lastpass */
}/* 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 );
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 );	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 );
	}
}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){
printf("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.\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 );	printf("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.\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 );
firstfour=1;	firstfour=1;
}	}
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){
printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);	printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
first=1;	first=1;
}	}
if(first==1){	if(first==1){
fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);	fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
}	}
} /* end mi==0 */	} /* end mi==0 */
} /* End individuals */	} /* End individuals */
/* wav and mw are no more changed */	/* wav and mw are no more changed */


for(i=1; i<=imx; i++){	for(i=1; i<=imx; i++){
for(mi=1; mi<wav[i];mi++){	for(mi=1; mi<wav[i];mi++){
if (stepm <=0)	if (stepm <=0)
dh[mi][i]=1;	dh[mi][i]=1;
else{	else{
if (s[mw[mi+1][i]][i] > nlstate) { /* A death */	if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
if (agedc[i] < 2*AGESUP) {	if (agedc[i] < 2*AGESUP) {
j= rint(agedc[i]12-agev[mw[mi][i]][i]12);	j= rint(agedc[i]12-agev[mw[mi][i]][i]12);
if(j==0) j=1; /* Survives at least one month after exam */	if(j==0) j=1; /* Survives at least one month after exam */
else if(j<0){	else if(j<0){
nberr++;	nberr++;
printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);	printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
j=1; /* Temporary Dangerous patch */	j=1; /* Temporary Dangerous patch */
printf(" We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);	printf(" We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);	fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
fprintf(ficlog," We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);	fprintf(ficlog," We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
}	}
k=k+1;	k=k+1;
if (j >= jmax){	if (j >= jmax){
jmax=j;	jmax=j;
ijmax=i;	ijmax=i;
}	}
if (j <= jmin){	if (j <= jmin){
jmin=j;	jmin=j;
ijmin=i;	ijmin=i;
}	}
sum=sum+j;	sum=sum+j;
/if (j<0) printf("j=%d num=%d \n",j,i);/	/if (j<0) printf("j=%d num=%d \n",j,i);/
/* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/	/* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
}	}
}	}
else{	else{
j= rint( (agev[mw[mi+1][i]][i]12 - agev[mw[mi][i]][i]12));	j= rint( (agev[mw[mi+1][i]][i]12 - agev[mw[mi][i]][i]12));
/* if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */	/* if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */

k=k+1;	k=k+1;
if (j >= jmax) {	if (j >= jmax) {
jmax=j;	jmax=j;
ijmax=i;	ijmax=i;
}	}
else if (j <= jmin){	else if (j <= jmin){
jmin=j;	jmin=j;
ijmin=i;	ijmin=i;
}	}
/* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */	/* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
/printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);/	/printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);/
if(j<0){	if(j<0){
nberr++;	nberr++;
printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);	printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);	fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
}	}
sum=sum+j;	sum=sum+j;
}	}
jk= j/stepm;	jk= j/stepm;
jl= j -jk*stepm;	jl= j -jk*stepm;
ju= j -(jk+1)*stepm;	ju= j -(jk+1)*stepm;
if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */	if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
if(jl==0){	if(jl==0){
dh[mi][i]=jk;	dh[mi][i]=jk;
bh[mi][i]=0;	bh[mi][i]=0;
}else{ /* We want a negative bias in order to only have interpolation ie	}else{ /* We want a negative bias in order to only have interpolation ie
* to avoid the price of an extra matrix product in likelihood */	* to avoid the price of an extra matrix product in likelihood */
dh[mi][i]=jk+1;	dh[mi][i]=jk+1;
bh[mi][i]=ju;	bh[mi][i]=ju;
}	}
}else{	}else{
if(jl <= -ju){	if(jl <= -ju){
dh[mi][i]=jk;	dh[mi][i]=jk;
bh[mi][i]=jl; /* bias is positive if real duration	bh[mi][i]=jl; /* bias is positive if real duration
* is higher than the multiple of stepm and negative otherwise.	* is higher than the multiple of stepm and negative otherwise.
*/	*/
}	}
else{	else{
dh[mi][i]=jk+1;	dh[mi][i]=jk+1;
bh[mi][i]=ju;	bh[mi][i]=ju;
}	}
if(dh[mi][i]==0){	if(dh[mi][i]==0){
dh[mi][i]=1; /* At least one step */	dh[mi][i]=1; /* At least one step */
bh[mi][i]=ju; /* At least one step */	bh[mi][i]=ju; /* At least one step */
/* printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/	/* printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
}	}
} /* end if mle */	} /* end if mle */
}	}
} /* end wave */	} /* end wave */
}	}
Line 4282 void concatwav(int wav[], int **dh, int	Line 4494 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 4293 void concatwav(int wav[], int **dh, int	Line 4505 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<=cptcovsnq; 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	switch(Typevar[j]) {
* If product of VnVm, still boolean :	case 1: /* A real fixed dummy covariate */
* If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables	ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
* 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */	* If product of VnVm, still boolean :
/* Finds for covariate j, n=Tvar[j] of Vn . ij is the	* If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
modality of the nth covariate of individual i. */	* 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
if (ij > modmaxcovj)	/* Finds for covariate j, n=Tvar[j] of Vn . ij is the
modmaxcovj=ij;	modality of the nth covariate of individual i. */
else if (ij < modmincovj)	if (ij > modmaxcovj)
modmincovj=ij;	modmaxcovj=ij;
if ((ij < -1) && (ij > NCOVMAX)){	else if (ij < modmincovj)
printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );	modmincovj=ij;
exit(1);	if ((ij < -1) && (ij > NCOVMAX)){
}else	printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
Ndum[ij]++; /counts and stores the occurence of this modality 0, 1, -1/	exit(1);
/* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */	}else
/printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);/	Ndum[ij]++; /counts and stores the occurence of this modality 0, 1, -1/
/* getting the maximum value of the modality of the covariate	/* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
(should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and	/printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);/
female is 1, then modmaxcovj=1.*/	/* 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
	female ies 1, then modmaxcovj=1.*/
	break;
	case 2:
	break;

	}
} /* 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]);
if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */	if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
if( k != -1){	if( k != -1){
ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th	ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th
covariate for which somebody answered excluding	covariate for which somebody answered excluding
undefined. Usually 2: 0 and 1. */	undefined. Usually 2: 0 and 1. */
}	}
ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th	ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
covariate for which somebody answered including	covariate for which somebody answered including
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 */
/* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.	/* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;	If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
Line 4360 void concatwav(int wav[], int **dh, int	Line 4580 void concatwav(int wav[], int **dh, int
*/	*/
ij=0; /* ij is similar to i but can jump over null modalities */	ij=0; /* ij is similar to i but can jump over null modalities */
for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/	for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
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 4383 void concatwav(int wav[], int **dh, int	Line 4603 void concatwav(int wav[], int **dh, int
/* } /\* end of loop on modality k \/ /	/* } /\* end of loop on modality k \/ /
} /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/	} /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/

for (k=-1; k< maxncov; k++) Ndum[k]=0;	for (k=-1; k< maxncov; k++) Ndum[k]=0;

for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually ageage /	for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually ageage /
/* 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 if((Ndum[i]!=0) && (i<=ncovcol+nqv)){
}else{	Tvaraff[++ij]=-10; /* Dont'n know how to treat quantitative variables yet */
/* Tvaraff[ij]=0; */	}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)){
/* ij--; */	Tvaraff[++ij]=-20; /* Dont'n know how to treat quantitative variables yet */
/* cptcoveff=ij; /\Number of total covariates\/ */	}
cptcov=ij; /Number of total covariates*/	} /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
	/* ij--; */
	/* cptcoveff=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 5256 To be simple, these graphs help to under	Line 5480 To be simple, these graphs help to under
tj = (int) pow(2,cptcoveff);	tj = (int) pow(2,cptcoveff);
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<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
Line 5670 See page 'Matrix of variance-covariance	Line 5894 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<=cptcoveff;cpt++) /*< cptcoveff number of variables /
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 5697 true period expectancies (those weighted	Line 5921 true period expectancies (those weighted
}	}

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

char dirfileres[132],optfileres[132];	char dirfileres[132],optfileres[132];
char gplotcondition[132];	char gplotcondition[132];
int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;	int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
int lv=0, vlv=0, kl=0;	int lv=0, vlv=0, kl=0;
int ng=0;	int ng=0;
int vpopbased;	int vpopbased;
int ioffset; /* variable offset for columns */	int ioffset; /* variable offset for columns */

/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */	/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
/* printf("Problem with file %s",optionfilegnuplot); */	/* printf("Problem with file %s",optionfilegnuplot); */
Line 5714 true period expectancies (those weighted	Line 5938 true period expectancies (those weighted

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

/* Contribution to likelihood */	/* Contribution to likelihood */
/* Plot the probability implied in the likelihood */	/* Plot the probability implied in the likelihood */
fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");	fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");	fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
/* fprintf(ficgp,"\nset ter svg size 640, 480"); / / Too big for svg */	/* fprintf(ficgp,"\nset ter svg size 640, 480"); / / Too big for svg */
fprintf(ficgp,"\nset ter pngcairo size 640, 480");	fprintf(ficgp,"\nset ter pngcairo size 640, 480");
/* nice for mle=4 plot by number of matrix products.	/* nice for mle=4 plot by number of matrix products.
replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */	replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
/* replot exp(p1+p2x)/(1+exp(p1+p2x)+exp(p3+p4x)+exp(p5+p6x)) t "p12(x)" */	/* replot exp(p1+p2x)/(1+exp(p1+p2x)+exp(p3+p4x)+exp(p5+p6x)) t "p12(x)" */
/* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */	/* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));	fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$13):6 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));	fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$13):6 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));
fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));	fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$13):5 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));	fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$13):5 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));
for (i=1; i<= nlstate ; i ++) {	for (i=1; i<= nlstate ; i ++) {
fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);	fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));	fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
fprintf(ficgp," u 2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);	fprintf(ficgp," u 2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);
for (j=2; j<= nlstate+ndeath ; j ++) {	for (j=2; j<= nlstate+ndeath ; j ++) {
fprintf(ficgp,",\\\n \"\" u 2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j);	fprintf(ficgp,",\\\n \"\" u 2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j);
}	}
fprintf(ficgp,";\nset out; unset ylabel;\n");	fprintf(ficgp,";\nset out; unset ylabel;\n");
}	}
/* unset log; plot "rrtest1_sorted_4/ILK_rrtest1_sorted_4.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with points lc variable */	/* unset log; plot "rrtest1_sorted_4/ILK_rrtest1_sorted_4.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with points lc variable */
/* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */	/* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
/* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */	/* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
fprintf(ficgp,"\nset out;unset log\n");	fprintf(ficgp,"\nset out;unset log\n");
/* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */	/* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */

strcpy(dirfileres,optionfilefiname);	strcpy(dirfileres,optionfilefiname);
strcpy(optfileres,"vpl");	strcpy(optfileres,"vpl");
/* 1eme*/	/* 1eme*/
for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */	for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
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<=cptcoveff; 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,cptcoveff); /* 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 */
vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */	vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
/* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */	/* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
}	}
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
continue;	continue;
}	}

fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);	fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);	fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
fprintf(ficgp,"set xlabel \"Age\" \n\	fprintf(ficgp,"set xlabel \"Age\" \n\
set ylabel \"Probability\" \n \	set ylabel \"Probability\" \n \
set ter svg size 640, 480\n \	set ter svg size 640, 480\n \
plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);	plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);

for (i=1; i<= nlstate ; i ++) {	for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," %%lf (%%lf)");	if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%lf (%%lf)");	else fprintf(ficgp," %%lf (%%lf)");
}	}
fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);	fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
for (i=1; i<= nlstate ; i ++) {	for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," %%lf (%%lf)");	if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%lf (%%lf)");	else fprintf(ficgp," %%lf (%%lf)");
}	}
fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);	fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
for (i=1; i<= nlstate ; i ++) {	for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," %%lf (%%lf)");	if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%lf (%%lf)");	else fprintf(ficgp," %%lf (%%lf)");
}	}
fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));	fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */	if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
/* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%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:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */	fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */
kl=0;	if(cptcoveff ==0){
for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */	fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line ", 2+(cpt-1), cpt );
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */	}else{
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	kl=0;
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
vlv= nbcode[Tvaraff[k]][lv];	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
kl++;	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* kl=6+(cpt-1)(nlstate+1)+1+(i-1); /\ 6+(1-1)(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 \/ */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
/6+(cpt-1)(nlstate+1)+1+(i-1)+(nlstate+1)nlstate; 6+(1-1)(2+1)+1+(1-1) +(2+1)2=13 /	vlv= nbcode[Tvaraff[k]][lv];
/6+1+(i-1)+(nlstate+1)nlstate; 6+1+(1-1) +(2+1)2=13 /	kl++;
/* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/	/* kl=6+(cpt-1)(nlstate+1)+1+(i-1); /\ 6+(1-1)(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 \/ */
if(k==cptcoveff){	/6+(cpt-1)(nlstate+1)+1+(i-1)+(nlstate+1)nlstate; 6+(1-1)(2+1)+1+(1-1) +(2+1)2=13 /
fprintf(ficgp,"$%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+1+(i-1)+(nlstate+1)nlstate; 6+1+(1-1) +(2+1)2=13 /
6+(cpt-1), cpt );	/* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
}else{	if(k==cptcoveff){
fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);	fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' with line ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
kl++;	6+(cpt-1), cpt );
}	}else{
} /* end covariate */	fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
}	kl++;
fprintf(ficgp,"\nset out \n");	}
	} /* end covariate */
	} /* end if no covariate */
	} /* end if backcast */
	fprintf(ficgp,"\nset out \n");
} /* k1 */	} /* k1 */
} /* cpt */	} /* cpt */
/2 eme/	/2 eme/
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<=cptcoveff; 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,cptcoveff); /* 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 */
vlv= nbcode[Tvaraff[k]][lv];	vlv= nbcode[Tvaraff[k]][lv];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
}	}
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
continue;	continue;
}	}

fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);	fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/	for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
if(vpopbased==0)	if(vpopbased==0)
fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);	fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
else	else
fprintf(ficgp,"\nreplot ");	fprintf(ficgp,"\nreplot ");
for (i=1; i<= nlstate+1 ; i ++) {	for (i=1; i<= nlstate+1 ; i ++) {
k=2*i;	k=2*i;
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);	fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);
for (j=1; j<= nlstate+1 ; j ++) {	for (j=1; j<= nlstate+1 ; j ++) {
if (j==i) fprintf(ficgp," %%lf (%%lf)");	if (j==i) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%lf (%%lf)");	else fprintf(ficgp," %%lf (%%lf)");
}	}
if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);	if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);	else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);	fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
for (j=1; j<= nlstate+1 ; j ++) {	for (j=1; j<= nlstate+1 ; j ++) {
if (j==i) fprintf(ficgp," %%lf (%%lf)");	if (j==i) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%lf (%%lf)");	else fprintf(ficgp," %%lf (%%lf)");
}	}
fprintf(ficgp,"\" t\"\" w l lt 0,");	fprintf(ficgp,"\" t\"\" w l lt 0,");
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);	fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
for (j=1; j<= nlstate+1 ; j ++) {	for (j=1; j<= nlstate+1 ; j ++) {
if (j==i) fprintf(ficgp," %%lf (%%lf)");	if (j==i) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%lf (%%lf)");	else fprintf(ficgp," %%lf (%%lf)");
}	}
if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");	if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");	else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
} /* state */	} /* state */
} /* vpopbased */	} /* vpopbased */
fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */	fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
} /* k1 */	} /* k1 */


Line 5875 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 6103 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<=cptcoveff; 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,cptcoveff); /* 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 */
vlv= nbcode[Tvaraff[k]][lv];	vlv= nbcode[Tvaraff[k]][lv];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
}	}
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
continue;	continue;
}	}

/* k=2+nlstate(2cpt-2); */	/* k=2+nlstate(2cpt-2); */
k=2+(nlstate+1)*(cpt-1);	k=2+(nlstate+1)*(cpt-1);
Line 5894 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 6122 plot [%.f:%.f] \"%s\" every :::%d::%d u
fprintf(ficgp,"set ter svg size 640, 480\n\	fprintf(ficgp,"set ter svg size 640, 480\n\
plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);	plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
/fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);	/fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");	for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
fprintf(ficgp,"\" t \"e%d1\" w l",cpt);	fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);	fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");	for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
fprintf(ficgp,"\" t \"e%d1\" w l",cpt);	fprintf(ficgp,"\" t \"e%d1\" w l",cpt);

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

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

/* 4eme */	/* 4eme */
/* Survival functions (period) from state i in state j by initial state i */	/* Survival functions (period) from state i in state j by initial state i */
for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */	for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */

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<=cptcoveff; 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,cptcoveff); /* 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 */
vlv= nbcode[Tvaraff[k]][lv];	vlv= nbcode[Tvaraff[k]][lv];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
}	}
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
continue;	continue;
}	}

fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);	fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
Line 5937 unset log y\n	Line 6165 unset log y\n
plot [%.f:%.f] ", ageminpar, agemaxpar);	plot [%.f:%.f] ", ageminpar, agemaxpar);
k=3;	k=3;
for (i=1; i<= nlstate ; i ++){	for (i=1; i<= nlstate ; i ++){
if(i==1){	if(i==1){
fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));	fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
}else{	}else{
fprintf(ficgp,", '' ");	fprintf(ficgp,", '' ");
}	}
l=(nlstate+ndeath)*(i-1)+1;	l=(nlstate+ndeath)*(i-1)+1;
fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);	fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
for (j=2; j<= nlstate+ndeath ; j ++)	for (j=2; j<= nlstate+ndeath ; j ++)
fprintf(ficgp,"+$%d",k+l+j-1);	fprintf(ficgp,"+$%d",k+l+j-1);
fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);	fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
} /* nlstate */	} /* nlstate */
fprintf(ficgp,"\nset out\n");	fprintf(ficgp,"\nset out\n");
} /* end cpt state*/	} /* end cpt state*/
Line 5956 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6184 plot [%.f:%.f] ", ageminpar, agemaxpar)
/* Survival functions (period) from state i in state j by final state j */	/* Survival functions (period) from state i in state j by final state j */
for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */	for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
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<=cptcoveff; 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,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
Line 5967 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6195 plot [%.f:%.f] ", ageminpar, agemaxpar)
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
}	}
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
continue;	continue;
}	}

fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);	fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
Line 6006 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6234 plot [%.f:%.f] ", ageminpar, agemaxpar)
/* CV preval stable (period) for each covariate */	/* CV preval stable (period) for each covariate */
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 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<=cptcoveff; 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,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
Line 6017 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6245 plot [%.f:%.f] ", ageminpar, agemaxpar)
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
}	}
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
continue;	continue;
}	}

fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);	fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
set ter svg size 640, 480\n\	set ter svg size 640, 480\n \
unset log y\n\	unset log y\n \
plot [%.f:%.f] ", ageminpar, agemaxpar);	plot [%.f:%.f] ", ageminpar, agemaxpar);
k=3; /* Offset */	k=3; /* Offset */
for (i=1; i<= nlstate ; i ++){	for (i=1; i<= nlstate ; i ++){
Line 6042 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6270 plot [%.f:%.f] ", ageminpar, agemaxpar)
fprintf(ficgp,"\nset out\n");	fprintf(ficgp,"\nset out\n");
} /* end cpt state*/	} /* end cpt state*/
} /* end covariate */	} /* end covariate */


/* 7eme */	/* 7eme */
if(backcast == 1){	if(backcast == 1){
/* CV back preval stable (period) for each covariate */	/* CV back preval stable (period) for each covariate */
Line 6054 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6282 plot [%.f:%.f] ", ageminpar, agemaxpar)
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	lv= decodtabm(k1,k,cptcoveff); /* 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 */
vlv= nbcode[Tvaraff[k]][lv];	vlv= nbcode[Tvaraff[k]][lv];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
}	}
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
continue;	continue;
}	}

fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);	fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);
Line 6090 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6318 plot [%.f:%.f] ", ageminpar, agemaxpar)
} /* end covariate */	} /* end covariate */
} /* End if backcast */	} /* End if backcast */

/* 8eme */	/* 8eme */
if(prevfcast==1){	if(prevfcast==1){
/* Projection from cross-sectional to stable (period) for each covariate */	/* Projection from cross-sectional to stable (period) for each covariate */

Line 6107 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6335 plot [%.f:%.f] ", ageminpar, agemaxpar)
}	}
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
continue;	continue;
}	}

fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");	fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);	fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
set ter svg size 640, 480\n \	set ter svg size 640, 480\n \
unset log y\n \	unset log y\n \
plot [%.f:%.f] ", ageminpar, agemaxpar);	plot [%.f:%.f] ", ageminpar, agemaxpar);
for (i=1; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */	for (i=1; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
/# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3/	/# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3/
Line 6145 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6373 plot [%.f:%.f] ", ageminpar, agemaxpar)
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 */
/# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3/	/# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3/
/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 /	/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 /
}	}
fprintf(ficgp," u %d:(",ioffset);	fprintf(ficgp," u %d:(",ioffset);
kl=0;	kl=0;
Line 6172 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6400 plot [%.f:%.f] ", ageminpar, agemaxpar)
fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \	fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \
ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)nlstate,cpt );	ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)nlstate,cpt );
}else{	}else{
fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \	fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
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 );
}	}
} /* end if covariate */	} /* end if covariate */
} /* nlstate */	} /* nlstate */
fprintf(ficgp,"\nset out\n");	fprintf(ficgp,"\nset out\n");
} /* end cpt state*/	} /* end cpt state*/
} /* end covariate */	} /* end covariate */
} /* End if prevfcast */	} /* End if prevfcast */


/* proba elementaires */	/* proba elementaires */
fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");	fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
for(i=1,jk=1; i <=nlstate; i++){	for(i=1,jk=1; i <=nlstate; i++){
fprintf(ficgp,"# initial state %d\n",i);	fprintf(ficgp,"# initial state %d\n",i);
for(k=1; k <=(nlstate+ndeath); k++){	for(k=1; k <=(nlstate+ndeath); k++){
if (k != i) {	if (k != i) {
fprintf(ficgp,"# current state %d\n",k);	fprintf(ficgp,"# current state %d\n",k);
for(j=1; j <=ncovmodel; j++){	for(j=1; j <=ncovmodel; j++){
fprintf(ficgp,"p%d=%f; ",jk,p[jk]);	fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
jk++;	jk++;
}	}
fprintf(ficgp,"\n");	fprintf(ficgp,"\n");
}	}
}	}
}	}
fprintf(ficgp,"##############\n#\n");	fprintf(ficgp,"##############\n#\n");

/goto avoid;/	/goto avoid;/
fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");	fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
fprintf(ficgp,"# logi(p12/p11)=a12+b12age+c12ageage+d12V1+e12V1*age\n");	fprintf(ficgp,"# logi(p12/p11)=a12+b12age+c12ageage+d12V1+e12V1*age\n");
Line 6215 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6443 plot [%.f:%.f] ", ageminpar, agemaxpar)
fprintf(ficgp,"# +exp(a13+b13age+c13ageage+d13V1+e13V1*age))\n");	fprintf(ficgp,"# +exp(a13+b13age+c13ageage+d13V1+e13V1*age))\n");
fprintf(ficgp,"# +exp(a14+b14age+c14ageage+d14V1+e14V1*age)+...)\n");	fprintf(ficgp,"# +exp(a14+b14age+c14ageage+d14V1+e14V1*age)+...)\n");
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",cptcoveff,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);
fprintf(ficgp,"\nset ter svg size 640, 480 ");	fprintf(ficgp,"\nset ter svg size 640, 480 ");
if (ng==1){	if (ng==1){
fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12x) could be nice /	fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12x) could be nice /
fprintf(ficgp,"\nunset log y");	fprintf(ficgp,"\nunset log y");
}else if (ng==2){	}else if (ng==2){
fprintf(ficgp,"\nset ylabel \"Probability\"\n");	fprintf(ficgp,"\nset ylabel \"Probability\"\n");
fprintf(ficgp,"\nset log y");	fprintf(ficgp,"\nset log y");
}else if (ng==3){	}else if (ng==3){
fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");	fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
fprintf(ficgp,"\nset log y");	fprintf(ficgp,"\nset log y");
}else	}else
fprintf(ficgp,"\nunset title ");	fprintf(ficgp,"\nunset title ");
fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);	fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
i=1;	i=1;
for(k2=1; k2<=nlstate; k2++) {	for(k2=1; k2<=nlstate; k2++) {
k3=i;	k3=i;
for(k=1; k<=(nlstate+ndeath); k++) {	for(k=1; k<=(nlstate+ndeath); k++) {
if (k != k2){	if (k != k2){
switch( ng) {	switch( ng) {
case 1:	case 1:
if(nagesqr==0)	if(nagesqr==0)
fprintf(ficgp," p%d+p%d*x",i,i+1);	fprintf(ficgp," p%d+p%d*x",i,i+1);
else /* nagesqr =1 */	else /* nagesqr =1 */
fprintf(ficgp," p%d+p%dx+p%dx*x",i,i+1,i+1+nagesqr);	fprintf(ficgp," p%d+p%dx+p%dx*x",i,i+1,i+1+nagesqr);
break;	break;
case 2: /* ng=2 */	case 2: /* ng=2 */
if(nagesqr==0)	if(nagesqr==0)
fprintf(ficgp," exp(p%d+p%d*x",i,i+1);	fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
else /* nagesqr =1 */	else /* nagesqr =1 */
fprintf(ficgp," exp(p%d+p%dx+p%dx*x",i,i+1,i+1+nagesqr);	fprintf(ficgp," exp(p%d+p%dx+p%dx*x",i,i+1,i+1+nagesqr);
break;	break;
case 3:	case 3:
if(nagesqr==0)	if(nagesqr==0)
fprintf(ficgp," %fexp(p%d+p%dx",YEARM/stepm,i,i+1);	fprintf(ficgp," %fexp(p%d+p%dx",YEARM/stepm,i,i+1);
else /* nagesqr =1 */	else /* nagesqr =1 */
fprintf(ficgp," %fexp(p%d+p%dx+p%dxx",YEARM/stepm,i,i+1,i+1+nagesqr);	fprintf(ficgp," %fexp(p%d+p%dx+p%dxx",YEARM/stepm,i,i+1,i+1+nagesqr);
break;	break;
}	}
ij=1;/* To be checked else nbcode[0][0] wrong */	ij=1;/* To be checked else nbcode[0][0] wrong */
for(j=3; j <=ncovmodel-nagesqr; j++) {	for(j=3; j <=ncovmodel-nagesqr; j++) {
/* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */	/* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
if(ij <=cptcovage) { /* Bug valgrind */	if(ij <=cptcovage) { /* Bug valgrind */
if((j-2)==Tage[ij]) { /* Bug valgrind */	if((j-2)==Tage[ij]) { /* Bug valgrind */
fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);	fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
/* fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */	/* fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
ij++;	ij++;
}	}
}	}
else	else
fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);	fprintf(ficgp,"+p%d%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]); / Valgrind bug nbcode */
}	}
}else{	}else{
i=i-ncovmodel;	i=i-ncovmodel;
if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */	if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
fprintf(ficgp," (1.");	fprintf(ficgp," (1.");
}	}

if(ng != 1){	if(ng != 1){
fprintf(ficgp,")/(1");	fprintf(ficgp,")/(1");

for(k1=1; k1 <=nlstate; k1++){	for(k1=1; k1 <=nlstate; k1++){
if(nagesqr==0)	if(nagesqr==0)
fprintf(ficgp,"+exp(p%d+p%dx",k3+(k1-1)ncovmodel,k3+(k1-1)*ncovmodel+1);	fprintf(ficgp,"+exp(p%d+p%dx",k3+(k1-1)ncovmodel,k3+(k1-1)*ncovmodel+1);
else /* nagesqr =1 */	else /* nagesqr =1 */
fprintf(ficgp,"+exp(p%d+p%dx+p%dxx",k3+(k1-1)ncovmodel,k3+(k1-1)ncovmodel+1,k3+(k1-1)ncovmodel+1+nagesqr);	fprintf(ficgp,"+exp(p%d+p%dx+p%dxx",k3+(k1-1)ncovmodel,k3+(k1-1)ncovmodel+1,k3+(k1-1)ncovmodel+1+nagesqr);

ij=1;	ij=1;
for(j=3; j <=ncovmodel-nagesqr; j++){	for(j=3; j <=ncovmodel-nagesqr; j++){
if(ij <=cptcovage) { /* Bug valgrind */	if(ij <=cptcovage) { /* Bug valgrind */
if((j-2)==Tage[ij]) { /* Bug valgrind */	if((j-2)==Tage[ij]) { /* Bug valgrind */
fprintf(ficgp,"+p%d%dx",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);	fprintf(ficgp,"+p%d%dx",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
/* fprintf(ficgp,"+p%d%dx",k3+(k1-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); /	/* fprintf(ficgp,"+p%d%dx",k3+(k1-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); /
ij++;	ij++;
}	}
}	}
else	else
fprintf(ficgp,"+p%d%d",k3+(k1-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);	fprintf(ficgp,"+p%d%d",k3+(k1-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);/* Valgrind bug nbcode */
}	}
fprintf(ficgp,")");	fprintf(ficgp,")");
}	}
fprintf(ficgp,")");	fprintf(ficgp,")");
if(ng ==2)	if(ng ==2)
fprintf(ficgp," t \"p%d%d\" ", k2,k);	fprintf(ficgp," t \"p%d%d\" ", k2,k);
else /* ng= 3 */	else /* ng= 3 */
fprintf(ficgp," t \"i%d%d\" ", k2,k);	fprintf(ficgp," t \"i%d%d\" ", k2,k);
}else{ /* end ng <> 1 */	}else{ /* end ng <> 1 */
if( k !=k2) /* logit p11 is hard to draw */	if( k !=k2) /* logit p11 is hard to draw */
fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);	fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
}	}
if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)	if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
fprintf(ficgp,",");	fprintf(ficgp,",");
if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))	if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
fprintf(ficgp,",");	fprintf(ficgp,",");
i=i+ncovmodel;	i=i+ncovmodel;
} /* end k */	} /* end k */
} /* end k2 */	} /* end k2 */
fprintf(ficgp,"\n set out\n");	fprintf(ficgp,"\n set out\n");
} /* end jk */	} /* end jk */
} /* end ng */	} /* end ng */
/* avoid: */	/* avoid: */
fflush(ficgp);	fflush(ficgp);
} /* end gnuplot */	} /* end gnuplot */


Line 7156 int readdata(char datafile[], int firsto	Line 7384 int readdata(char datafile[], int firsto
/-------- data file ----------/	/-------- data file ----------/
FILE *fic;	FILE *fic;
char dummy[]=" ";	char dummy[]=" ";
int i=0, j=0, n=0;	int i=0, j=0, n=0, iv=0;
	int lstra;
int linei, month, year,iout;	int linei, month, year,iout;
char line[MAXLINE], linetmp[MAXLINE];	char line[MAXLINE], linetmp[MAXLINE];
char stra[MAXLINE], strb[MAXLINE];	char stra[MAXLINE], strb[MAXLINE];
char *stratrunc;	char *stratrunc;
int lstra;


if((fic=fopen(datafile,"r"))==NULL) {	if((fic=fopen(datafile,"r"))==NULL) {
Line 7188 int readdata(char datafile[], int firsto	Line 7417 int readdata(char datafile[], int firsto
}	}
trimbb(linetmp,line); /* Trims multiple blanks in line */	trimbb(linetmp,line); /* Trims multiple blanks in line */
strcpy(line, linetmp);	strcpy(line, linetmp);

	/* Loops on waves */
for (j=maxwav;j>=1;j--){	for (j=maxwav;j>=1;j--){
	for (iv=nqtv;iv>=1;iv--){ /* Loop on time varying quantitative variables */
	cutv(stra, strb, line, ' ');
	if(strb[0]=='.') { /* Missing value */
	lval=-1;
	cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
	if(isalpha(strb[1])) { /* .m or .d Really Missing value */
	printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value. Exiting.\n", strb, linei,i,line,iv, nqtv, j);
	fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value. Exiting.\n", strb, linei,i,line,iv, nqtv, j);fflush(ficlog);
	return 1;
	}
	}else{
	errno=0;
	/* what_kind_of_number(strb); */
	dval=strtod(strb,&endptr);
	/* if( strb[0]=='\0' \|\| (endptr != '\0')){ /
	/* if(strb != endptr && endptr == '\0') /
	/* dval=dlval; */
	/* if (errno == ERANGE && (lval == LONG_MAX \|\| lval == LONG_MIN)) */
	if( strb[0]=='\0' \|\| (*endptr != '\0')){
	printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,iv, nqtv, j,maxwav);
	fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line, iv, nqtv, j,maxwav);fflush(ficlog);
	return 1;
	}
	cotqvar[j][iv][i]=dval;
	}
	strcpy(line,stra);
	}/* end loop ntqv */

	for (iv=ntv;iv>=1;iv--){ /* Loop on time varying dummies */
	cutv(stra, strb, line, ' ');
	if(strb[0]=='.') { /* Missing value */
	lval=-1;
	}else{
	errno=0;
	lval=strtol(strb,&endptr,10);
	/* if (errno == ERANGE && (lval == LONG_MAX \|\| lval == LONG_MIN))*/
	if( strb[0]=='\0' \|\| (*endptr != '\0')){
	printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th dummy covariate out of %d measured at wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,iv, ntv, j,maxwav);
	fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d dummy covariate out of %d measured wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,iv, ntv,j,maxwav);fflush(ficlog);
	return 1;
	}
	}
	if(lval <-1 \|\| lval >1){
	printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
	Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
	for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
	For example, for multinomial values like 1, 2 and 3,\n \
	build V1=0 V2=0 for the reference value (1),\n \
	V1=1 V2=0 for (2) \n \
	and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
	output of IMaCh is often meaningless.\n \
	Exiting.\n",lval,linei, i,line,j);
	fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
	Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
	for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
	For example, for multinomial values like 1, 2 and 3,\n \
	build V1=0 V2=0 for the reference value (1),\n \
	V1=1 V2=0 for (2) \n \
	and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
	output of IMaCh is often meaningless.\n \
	Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
	return 1;
	}
	cotvar[j][iv][i]=(double)(lval);
	strcpy(line,stra);
	}/* end loop ntv */

	/* Statuses at wave */
cutv(stra, strb, line, ' ');	cutv(stra, strb, line, ' ');
if(strb[0]=='.') { /* Missing status */	if(strb[0]=='.') { /* Missing value */
lval=-1;	lval=-1;
}else{	}else{
errno=0;	errno=0;
lval=strtol(strb,&endptr,10);	lval=strtol(strb,&endptr,10);
/* if (errno == ERANGE && (lval == LONG_MAX \|\| lval == LONG_MIN))*/	/* if (errno == ERANGE && (lval == LONG_MAX \|\| lval == LONG_MIN))*/
if( strb[0]=='\0' \|\| (*endptr != '\0')){	if( strb[0]=='\0' \|\| (*endptr != '\0')){
printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);	printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);
fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);	fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
return 1;	return 1;
}	}
}	}

s[j][i]=lval;	s[j][i]=lval;

	/* Date of Interview */
strcpy(line,stra);	strcpy(line,stra);
cutv(stra, strb,line,' ');	cutv(stra, strb,line,' ');
if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){	if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
Line 7221 int readdata(char datafile[], int firsto	Line 7520 int readdata(char datafile[], int firsto
anint[j][i]= (double) year;	anint[j][i]= (double) year;
mint[j][i]= (double)month;	mint[j][i]= (double)month;
strcpy(line,stra);	strcpy(line,stra);
} /* ENd Waves */	} /* End loop on waves */

	/* Date of death */
cutv(stra, strb,line,' ');	cutv(stra, strb,line,' ');
if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){	if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
}	}
Line 7231 int readdata(char datafile[], int firsto	Line 7531 int readdata(char datafile[], int firsto
year=9999;	year=9999;
}else{	}else{
printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);	printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);	fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
return 1;	return 1;
}	}
andc[i]=(double) year;	andc[i]=(double) year;
moisdc[i]=(double) month;	moisdc[i]=(double) month;
strcpy(line,stra);	strcpy(line,stra);

	/* Date of birth */
cutv(stra, strb,line,' ');	cutv(stra, strb,line,' ');
if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){	if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
}	}
Line 7247 int readdata(char datafile[], int firsto	Line 7548 int readdata(char datafile[], int firsto
}else{	}else{
printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);	printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);	fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
return 1;	return 1;
}	}
if (year==9999) {	if (year==9999) {
printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);	printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);
fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);	fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
return 1;	return 1;

}	}
annais[i]=(double)(year);	annais[i]=(double)(year);
moisnais[i]=(double)(month);	moisnais[i]=(double)(month);
strcpy(line,stra);	strcpy(line,stra);

	/* Sample weight */
cutv(stra, strb,line,' ');	cutv(stra, strb,line,' ');
errno=0;	errno=0;
dval=strtod(strb,&endptr);	dval=strtod(strb,&endptr);
Line 7271 int readdata(char datafile[], int firsto	Line 7573 int readdata(char datafile[], int firsto
weight[i]=dval;	weight[i]=dval;
strcpy(line,stra);	strcpy(line,stra);

	for (iv=nqv;iv>=1;iv--){ /* Loop on fixed quantitative variables */
	cutv(stra, strb, line, ' ');
	if(strb[0]=='.') { /* Missing value */
	lval=-1;
	}else{
	errno=0;
	/* what_kind_of_number(strb); */
	dval=strtod(strb,&endptr);
	/* if(strb != endptr && endptr == '\0') /
	/* dval=dlval; */
	/* if (errno == ERANGE && (lval == LONG_MAX \|\| lval == LONG_MIN)) */
	if( strb[0]=='\0' \|\| (*endptr != '\0')){
	printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line, iv, nqv, maxwav);
	fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line, iv, nqv, maxwav);fflush(ficlog);
	return 1;
	}
	coqvar[iv][i]=dval;
	}
	strcpy(line,stra);
	}/* end loop nqv */

	/* Covariate values */
for (j=ncovcol;j>=1;j--){	for (j=ncovcol;j>=1;j--){
cutv(stra, strb,line,' ');	cutv(stra, strb,line,' ');
if(strb[0]=='.') { /* Missing status */	if(strb[0]=='.') { /* Missing covariate value */
lval=-1;	lval=-1;
}else{	}else{
errno=0;	errno=0;
Line 7288 int readdata(char datafile[], int firsto	Line 7612 int readdata(char datafile[], int firsto
printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \	printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \	Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \	for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
For example, for multinomial values like 1, 2 and 3,\n \	For example, for multinomial values like 1, 2 and 3,\n \
build V1=0 V2=0 for the reference value (1),\n \	build V1=0 V2=0 for the reference value (1),\n \
V1=1 V2=0 for (2) \n \	V1=1 V2=0 for (2) \n \
and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \	and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
output of IMaCh is often meaningless.\n \	output of IMaCh is often meaningless.\n \
Exiting.\n",lval,linei, i,line,j);	Exiting.\n",lval,linei, i,line,j);
fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \	fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \	Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \	for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
For example, for multinomial values like 1, 2 and 3,\n \	For example, for multinomial values like 1, 2 and 3,\n \
build V1=0 V2=0 for the reference value (1),\n \	build V1=0 V2=0 for the reference value (1),\n \
V1=1 V2=0 for (2) \n \	V1=1 V2=0 for (2) \n \
and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \	and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
output of IMaCh is often meaningless.\n \	output of IMaCh is often meaningless.\n \
Exiting.\n",lval,linei, i,line,j);fflush(ficlog);	Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
return 1;	return 1;
}	}
Line 7309 int readdata(char datafile[], int firsto	Line 7633 int readdata(char datafile[], int firsto
strcpy(line,stra);	strcpy(line,stra);
}	}
lstra=strlen(stra);	lstra=strlen(stra);

if(lstra > 9){ /* More than 2*32 or max of what printf can write with %ld /	if(lstra > 9){ /* More than 2*32 or max of what printf can write with %ld /
stratrunc = &(stra[lstra-9]);	stratrunc = &(stra[lstra-9]);
num[i]=atol(stratrunc);	num[i]=atol(stratrunc);
Line 7321 int readdata(char datafile[], int firsto	Line 7645 int readdata(char datafile[], int firsto

i=i+1;	i=i+1;
} /* End loop reading data */	} /* End loop reading data */

imax=i-1; / Number of individuals */	imax=i-1; / Number of individuals */
fclose(fic);	fclose(fic);

return (0);	return (0);
/* endread: */	/* endread: */
printf("Exiting readdata: ");	printf("Exiting readdata: ");
fclose(fic);	fclose(fic);
return (1);	return (1);



}	}

void removespace(char *str) {	void removespace(char *str) {
char p1 = str, p2 = str;	char p1 = str, p2 = str;
do	do
Line 7342 void removespace(char *str) {	Line 7664 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 7380 int decodemodel ( char model[], int last	Line 7703 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");
Line 7401 int decodemodel ( char model[], int last	Line 7723 int decodemodel ( char model[], int last
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 */


/* Design	/* Design
* V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight	* V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
* < ncovcol=8 >	* < ncovcol=8 >
Line 7419 int decodemodel ( char model[], int last	Line 7741 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 7445 int decodemodel ( char model[], int last	Line 7767 int decodemodel ( char model[], int last
* {2, 1, 4, 8, 5, 6, 3, 7}	* {2, 1, 4, 8, 5, 6, 3, 7}
* Struct []	* Struct []
*/	*/

/* This loop fills the array Tvar from the string 'model'.*/	/* This loop fills the array Tvar from the string 'model'.*/
/* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */	/* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
/* modelsav=V2+V1+V4+ageV3 strb=ageV3 stra=V2+V1+V4 */	/* modelsav=V2+V1+V4+ageV3 strb=ageV3 stra=V2+V1+V4 */
Line 7460 int decodemodel ( char model[], int last	Line 7782 int decodemodel ( char model[], int last
/* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]cov[2]; /	/* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]cov[2]; /
/*	/*
* Treating invertedly V2+V1+V3age+V2V4 is as if written V2V4 +V3age + V1 + V2 */	* Treating invertedly V2+V1+V3age+V2V4 is as if written V2V4 +V3age + V1 + V2 */
for(k=cptcovt; k>=1;k--) /*< Number of covariates /	for(k=cptcovt; k>=1;k--) /*< Number of covariates not including constant and age, neither ageage*/
Tvar[k]=0;	Tvar[k]=0;
cptcovage=0;	cptcovage=0;
for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */	for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
Line 7476 int decodemodel ( char model[], int last	Line 7798 int decodemodel ( char model[], int last
cptcovprod--;	cptcovprod--;
cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */	cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
Tvar[k]=atoi(stre); /* V2+V1+V4+V3age Tvar[4]=3 ; V1+V2age Tvar[2]=2; V1+V1age Tvar[2]=1 /	Tvar[k]=atoi(stre); /* V2+V1+V4+V3age Tvar[4]=3 ; V1+V2age Tvar[2]=2; V1+V1age Tvar[2]=1 /
	Typevar[k]=1; /* 2 for age product */
cptcovage++; /* Sums the number of covariates which include age as a product */	cptcovage++; /* Sums the number of covariates which include age as a product */
Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1age Tvar[2]=1, Tage[1]=2 /	Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1age Tvar[2]=1, Tage[1]=2 /
/printf("stre=%s ", stre);/	/printf("stre=%s ", stre);/
Line 7483 int decodemodel ( char model[], int last	Line 7806 int decodemodel ( char model[], int last
cptcovprod--;	cptcovprod--;
cutl(stre,strb,strc,'V');	cutl(stre,strb,strc,'V');
Tvar[k]=atoi(stre);	Tvar[k]=atoi(stre);
	Typevar[k]=1; /* 1 for age product */
cptcovage++;	cptcovage++;
Tage[cptcovage]=k;	Tage[cptcovage]=k;
} else { /* Age is not in the model product V2+V1+V1V4+V3age+V3V2 strb=V3V2*/	} else { /* Age is not in the model product V2+V1+V1V4+V3age+V3V2 strb=V3V2*/
Line 7490 int decodemodel ( char model[], int last	Line 7814 int decodemodel ( char model[], int last
cptcovn++;	cptcovn++;
cptcovprodnoage++;k1++;	cptcovprodnoage++;k1++;
cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3V2 stre=3 strc=/	cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3V2 stre=3 strc=/
Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but	Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
because this model-covariate is a construction we invent a new column	because this model-covariate is a construction we invent a new column
ncovcol + k1	which is after existing variables ncovcol+nqv+ntv+nqtv + k1
If already ncovcol=4 and model=V2+V1+V1V4+ageV3+V3*V2	If already ncovcol=4 and model=V2+V1+V1V4+ageV3+V3*V2
Tvar[3=V1V4]=4+1 Tvar[5=V3V2]=4 + 2= 6, etc */	Tvar[3=V1V4]=4+1 Tvar[5=V3V2]=4 + 2= 6, etc */
	Typevar[k]=2; /* 2 for double fixed dummy covariates */
cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */	cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
Tprod[k1]=k; /* Tprod[1]=3(=V1V4) for V2+V1+V1V4+ageV3+V3V2 */	Tprod[k1]=k; /* Tprod[1]=3(=V1V4) for V2+V1+V1V4+ageV3+V3V2 */
Tvard[k1][1] =atoi(strc); /* m 1 for V1*/	Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
Tvard[k1][2] =atoi(stre); /* n 4 for V4*/	Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
k2=k2+2;	k2=k2+2; /* k2 is initialize to -1, We want to store the n and m in VnVm at the end of Tvar /
Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */	/* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) \/ /
Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */	/* Tvar[cptcovt+k2+1]=Tvard[k1][2]; /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) \/ /
	/ncovcol=4 and model=V2+V1+V1V4+ageV3+V3V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */
	/* 1 2 3 4 5 \| Tvar[5+1)=1, Tvar[7]=2 */
for (i=1; i<=lastobs;i++){	for (i=1; i<=lastobs;i++){
/* Computes the new covariate which is a product of	/* Computes the new covariate which is a product of
covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */	covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
Line 7513 int decodemodel ( char model[], int last	Line 7840 int decodemodel ( char model[], int last
/printf("d=%s c=%s b=%s\n", strd,strc,strb);/	/printf("d=%s c=%s b=%s\n", strd,strc,strb);/
/* scanf("%d",i);*/	/* scanf("%d",i);*/
cutl(strd,strc,strb,'V');	cutl(strd,strc,strb,'V');
ks++; /*< Number of simple covariates /	ks++; /*< Number of simple covariates/
cptcovn++;	cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
Tvar[k]=atoi(strd);	Tvar[k]=atoi(strd);
	Typevar[k]=0; /* 0 for simple covariates */
}	}
strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */	strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
/*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);	/*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
scanf("%d",i);*/	scanf("%d",i);*/
} /* end of loop + on total covariates */	} /* end of loop + on total covariates */
} /* end if strlen(modelsave == 0) ageage might exist /	} /* end if strlen(modelsave == 0) ageage might exist /
} /* end if strlen(model == 0) */	} /* end if strlen(model == 0) */

/*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.	/*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
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);*/

	/* Decodemodel knows only the grammar (simple, product, age*) of the model but not what kind
	of variable (dummy vs quantitative, fixed vs time varying) is behind */
	/* ncovcol= 1, nqv=1, ntv=2, nqtv= 1 = 5 possible variables data
	model= V2 + V4 +V3 + V4V3 + V5age + V5 , V1 is not used saving its place
	k = 1 2 3 4 5 6
	Tvar[k]= 2 4 3 1+1+2+1+1=6 5 5
	Typevar[k]=0 0 0 2 1 0
	*/
	/* Dispatching between quantitative and time varying covariates */
	/* Tvar[k] is the value n of Vn with n varying for 1 to nvcol, or p Vp=VnVm for product /
	for(k=1, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */
	if (Tvar[k] <=ncovcol){ /* Simple fixed dummy covariatee */
	ncoveff++;
	}else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){ /* Remind that product VnVm are added in k/
	nqfveff++; /* Only simple fixed quantitative variable */
	}else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){
	ntveff++; /* Only simple time varying dummy variable */
	}else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv && Typevar[k]==0){
	nqtveff++;/* Only simple time varying quantitative variable */
	}else{
	printf("Other types in effective covariates \n");
	}
	}

	printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
	fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
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 7872 int prevalence_limit(double p, double	Line 8225 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 7885 int prevalence_limit(double p, double	Line 8238 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<=nqfveff;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 7901 int prevalence_limit(double p, double	Line 8254 int prevalence_limit(double p, double
}	}

fprintf(ficrespl,"#Age ");	fprintf(ficrespl,"#Age ");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=nqfveff;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 7911 int prevalence_limit(double p, double	Line 8264 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<=nqfveff;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 7959 int back_prevalence_limit(double *p, dou	Line 8312 int back_prevalence_limit(double *p, dou
agelim=agemaxpar;	agelim=agemaxpar;


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

for(k=1; k<=i1;k++){	for(k=1; k<=i1;k++){
Line 7972 int back_prevalence_limit(double *p, dou	Line 8325 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<=nqfveff;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 7988 int back_prevalence_limit(double *p, dou	Line 8341 int back_prevalence_limit(double *p, dou
}	}

fprintf(ficresplb,"#Age ");	fprintf(ficresplb,"#Age ");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=nqfveff;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 8010 int back_prevalence_limit(double *p, dou	Line 8363 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<=nqfveff;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 8058 int hPijx(double *p, int bage, int fage)	Line 8411 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,nqfveff);
/* 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,nqfveff); k++){
fprintf(ficrespij,"\n#****** ");	fprintf(ficrespij,"\n#****** ");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=nqfveff;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 8130 int hPijx(double *p, int bage, int fage)	Line 8483 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,nqfveff);
/* 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,nqfveff); k++){
fprintf(ficrespijb,"\n#****** ");	fprintf(ficrespijb,"\n#****** ");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=nqfveff;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 8457 int main(int argc, char *argv[])	Line 8810 int main(int argc, char *argv[])
}else	}else
break;	break;
}	}
if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \	if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
&ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){	&ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
if (num_filled != 8) {	if (num_filled != 11) {
printf("Not 8 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");	printf("Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
printf("but line=%s\n",line);	printf("but line=%s\n",line);
}	}
printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt);	printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
}	}
/* ftolpl=6ftol1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit \/ /	/* ftolpl=6ftol1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit \/ /
/ftolpl=6.e-4; //* 6.e-3 make convergences in less than 80 loops for the prevalence limit */	/ftolpl=6.e-4; //* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
Line 8501 int main(int argc, char *argv[])	Line 8854 int main(int argc, char *argv[])
/* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */	/* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */
/* numlinepar=numlinepar+3; /\* In general \/ /	/* numlinepar=numlinepar+3; /\* In general \/ /
/* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */	/* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);	fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);
fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);	fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);
fflush(ficlog);	fflush(ficlog);
/* if(model[0]=='#'\|\| model[0]== '\0'){ */	/* if(model[0]=='#'\|\| model[0]== '\0'){ */
if(model[0]=='#'){	if(model[0]=='#'){
Line 8531 int main(int argc, char *argv[])	Line 8884 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); /*< Fixed quantitative covariate /
	cotvar=ma3x(1,maxwav,1,ntv,1,n); /*< Time varying covariate /
	cotqvar=ma3x(1,maxwav,1,nqtv,1,n); /*< Time varying quantitative covariate /
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 8773 Please run with mle=-1 to get a correct	Line 9129 Please run with mle=-1 to get a correct
k=1 Tvar[1]=2 (from V2)	k=1 Tvar[1]=2 (from V2)
*/	*/
Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */	Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
	Typevar=ivector(1,NCOVMAX); /* -1 to 4 */
/* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).	/* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,	For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.	Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
Line 8798 Please run with mle=-1 to get a correct	Line 9155 Please run with mle=-1 to get a correct
/* Main decodemodel */	/* Main decodemodel */


if(decodemodel(model, lastobs) == 1)	if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3 = {4, 3, 5}*/
goto end;	goto end;

if((double)(lastobs-imx)/(double)imx > 1.10){	if((double)(lastobs-imx)/(double)imx > 1.10){
Line 8853 Please run with mle=-1 to get a correct	Line 9210 Please run with mle=-1 to get a correct
nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);	nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
ncodemax[1]=1;	ncodemax[1]=1;
Ndum =ivector(-1,NCOVMAX);	Ndum =ivector(-1,NCOVMAX);
cptcoveff=0;	cptcoveff=0;
if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and ageage /	if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and ageage /
tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /*< Fills nbcode[Tvar[j]][l]; /	tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /*< Fills nbcode[Tvar[j]][l]; /
}	}
Line 9026 Title=%s <br>Datafile=%s Firstpass=%d La	Line 9383 Title=%s <br>Datafile=%s Firstpass=%d La
and for any valid combination of covariates	and for any valid combination of covariates
and prints on file fileres'p'. */	and prints on file fileres'p'. */
freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \	freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
firstpass, lastpass, stepm, weightopt, model);	firstpass, lastpass, stepm, weightopt, model);

fprintf(fichtm,"\n");	fprintf(fichtm,"\n");
fprintf(fichtm,"<br>Total number of observations=%d <br>\n\	fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
Line 9055 Interval (in months) between two waves:	Line 9412 Interval (in months) between two waves:
ageexmed=vector(1,n);	ageexmed=vector(1,n);
agecens=vector(1,n);	agecens=vector(1,n);
dcwave=ivector(1,n);	dcwave=ivector(1,n);

for (i=1; i<=imx; i++){	for (i=1; i<=imx; i++){
dcwave[i]=-1;	dcwave[i]=-1;
for (m=firstpass; m<=lastpass; m++)	for (m=firstpass; m<=lastpass; m++)
Line 9300 Please run with mle=-1 to get a correct	Line 9657 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 9308 Please run with mle=-1 to get a correct	Line 9665 Please run with mle=-1 to get a correct
fprintf(ficlog,"# Parameters nlstatenlstatencov a121 + b12 age + ...\n");	fprintf(ficlog,"# Parameters nlstatenlstatencov a121 + b12 age + ...\n");
for(i=1,jk=1; i <=nlstate; i++){	for(i=1,jk=1; i <=nlstate; i++){
for(k=1; k <=(nlstate+ndeath); k++){	for(k=1; k <=(nlstate+ndeath); k++){
if (k != i) {	if (k != i) {
printf("%d%d ",i,k);	printf("%d%d ",i,k);
fprintf(ficlog,"%d%d ",i,k);	fprintf(ficlog,"%d%d ",i,k);
fprintf(ficres,"%1d%1d ",i,k);	fprintf(ficres,"%1d%1d ",i,k);
for(j=1; j <=ncovmodel; j++){	for(j=1; j <=ncovmodel; j++){
printf("%12.7f ",p[jk]);	printf("%12.7f ",p[jk]);
fprintf(ficlog,"%12.7f ",p[jk]);	fprintf(ficlog,"%12.7f ",p[jk]);
fprintf(ficres,"%12.7f ",p[jk]);	fprintf(ficres,"%12.7f ",p[jk]);
jk++;	jk++;
}	}
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
fprintf(ficres,"\n");	fprintf(ficres,"\n");
}	}
}	}
}	}
if(mle != 0){	if(mle != 0){
Line 9331 Please run with mle=-1 to get a correct	Line 9688 Please run with mle=-1 to get a correct
printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");	printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");	fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
for(i=1,jk=1; i <=nlstate; i++){	for(i=1,jk=1; i <=nlstate; i++){
for(k=1; k <=(nlstate+ndeath); k++){	for(k=1; k <=(nlstate+ndeath); k++){
if (k != i) {	if (k != i) {
printf("%d%d ",i,k);	printf("%d%d ",i,k);
fprintf(ficlog,"%d%d ",i,k);	fprintf(ficlog,"%d%d ",i,k);
for(j=1; j <=ncovmodel; j++){	for(j=1; j <=ncovmodel; j++){
printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96sqrt(matcov[jk][jk]),p[jk]+1.96sqrt(matcov[jk][jk]));	printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96sqrt(matcov[jk][jk]),p[jk]+1.96sqrt(matcov[jk][jk]));
fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96sqrt(matcov[jk][jk]),p[jk]+1.96sqrt(matcov[jk][jk]));	fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96sqrt(matcov[jk][jk]),p[jk]+1.96sqrt(matcov[jk][jk]));
jk++;	jk++;
}	}
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
}	}
}	}
}	}
} /* end of hesscov and Wald tests */	} /* end of hesscov and Wald tests */

/* */	/* */
fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");	fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
printf("# Scales (for hessian or gradient estimation)\n");	printf("# Scales (for hessian or gradient estimation)\n");
fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");	fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
for(i=1,jk=1; i <=nlstate; i++){	for(i=1,jk=1; i <=nlstate; i++){
for(j=1; j <=nlstate+ndeath; j++){	for(j=1; j <=nlstate+ndeath; j++){
if (j!=i) {	if (j!=i) {
fprintf(ficres,"%1d%1d",i,j);	fprintf(ficres,"%1d%1d",i,j);
printf("%1d%1d",i,j);	printf("%1d%1d",i,j);
fprintf(ficlog,"%1d%1d",i,j);	fprintf(ficlog,"%1d%1d",i,j);
for(k=1; k<=ncovmodel;k++){	for(k=1; k<=ncovmodel;k++){
printf(" %.5e",delti[jk]);	printf(" %.5e",delti[jk]);
fprintf(ficlog," %.5e",delti[jk]);	fprintf(ficlog," %.5e",delti[jk]);
fprintf(ficres," %.5e",delti[jk]);	fprintf(ficres," %.5e",delti[jk]);
jk++;	jk++;
}	}
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
fprintf(ficres,"\n");	fprintf(ficres,"\n");
}	}
}	}
}	}

Line 9390 Please run with mle=-1 to get a correct	Line 9747 Please run with mle=-1 to get a correct
for(itimes=1;itimes<=2;itimes++){	for(itimes=1;itimes<=2;itimes++){
jj=0;	jj=0;
for(i=1; i <=nlstate; i++){	for(i=1; i <=nlstate; i++){
for(j=1; j <=nlstate+ndeath; j++){	for(j=1; j <=nlstate+ndeath; j++){
if(j==i) continue;	if(j==i) continue;
for(k=1; k<=ncovmodel;k++){	for(k=1; k<=ncovmodel;k++){
jj++;	jj++;
ca[0]= k+'a'-1;ca[1]='\0';	ca[0]= k+'a'-1;ca[1]='\0';
if(itimes==1){	if(itimes==1){
if(mle>=1)	if(mle>=1)
printf("#%1d%1d%d",i,j,k);	printf("#%1d%1d%d",i,j,k);
fprintf(ficlog,"#%1d%1d%d",i,j,k);	fprintf(ficlog,"#%1d%1d%d",i,j,k);
fprintf(ficres,"#%1d%1d%d",i,j,k);	fprintf(ficres,"#%1d%1d%d",i,j,k);
}else{	}else{
if(mle>=1)	if(mle>=1)
printf("%1d%1d%d",i,j,k);	printf("%1d%1d%d",i,j,k);
fprintf(ficlog,"%1d%1d%d",i,j,k);	fprintf(ficlog,"%1d%1d%d",i,j,k);
fprintf(ficres,"%1d%1d%d",i,j,k);	fprintf(ficres,"%1d%1d%d",i,j,k);
}	}
ll=0;	ll=0;
for(li=1;li <=nlstate; li++){	for(li=1;li <=nlstate; li++){
for(lj=1;lj <=nlstate+ndeath; lj++){	for(lj=1;lj <=nlstate+ndeath; lj++){
if(lj==li) continue;	if(lj==li) continue;
for(lk=1;lk<=ncovmodel;lk++){	for(lk=1;lk<=ncovmodel;lk++){
ll++;	ll++;
if(ll<=jj){	if(ll<=jj){
cb[0]= lk +'a'-1;cb[1]='\0';	cb[0]= lk +'a'-1;cb[1]='\0';
if(ll<jj){	if(ll<jj){
if(itimes==1){	if(itimes==1){
if(mle>=1)	if(mle>=1)
printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);	printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);	fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);	fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
}else{	}else{
if(mle>=1)	if(mle>=1)
printf(" %.5e",matcov[jj][ll]);	printf(" %.5e",matcov[jj][ll]);
fprintf(ficlog," %.5e",matcov[jj][ll]);	fprintf(ficlog," %.5e",matcov[jj][ll]);
fprintf(ficres," %.5e",matcov[jj][ll]);	fprintf(ficres," %.5e",matcov[jj][ll]);
}	}
}else{	}else{
if(itimes==1){	if(itimes==1){
if(mle>=1)	if(mle>=1)
printf(" Var(%s%1d%1d)",ca,i,j);	printf(" Var(%s%1d%1d)",ca,i,j);
fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);	fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
fprintf(ficres," Var(%s%1d%1d)",ca,i,j);	fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
}else{	}else{
if(mle>=1)	if(mle>=1)
printf(" %.7e",matcov[jj][ll]);	printf(" %.7e",matcov[jj][ll]);
fprintf(ficlog," %.7e",matcov[jj][ll]);	fprintf(ficlog," %.7e",matcov[jj][ll]);
fprintf(ficres," %.7e",matcov[jj][ll]);	fprintf(ficres," %.7e",matcov[jj][ll]);
}	}
}	}
}	}
} /* end lk */	} /* end lk */
} /* end lj */	} /* end lj */
} /* end li */	} /* end li */
if(mle>=1)	if(mle>=1)
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
fprintf(ficres,"\n");	fprintf(ficres,"\n");
numlinepar++;	numlinepar++;
} /* end k*/	} /* end k*/
} /end j /	} /end j /
} /* end i */	} /* end i */
} /* end itimes */	} /* end itimes */

fflush(ficlog);	fflush(ficlog);
fflush(ficres);	fflush(ficres);
while(fgets(line, MAXLINE, ficpar)) {	while(fgets(line, MAXLINE, ficpar)) {
/* If line starts with a # it is a comment */	/* If line starts with a # it is a comment */
if (line[0] == '#') {	if (line[0] == '#') {
numlinepar++;	numlinepar++;
fputs(line,stdout);	fputs(line,stdout);
fputs(line,ficparo);	fputs(line,ficparo);
fputs(line,ficlog);	fputs(line,ficlog);
continue;	continue;
}else	}else
break;	break;
}	}

/* while((c=getc(ficpar))=='#' && c!= EOF){ */	/* while((c=getc(ficpar))=='#' && c!= EOF){ */
/* ungetc(c,ficpar); */	/* ungetc(c,ficpar); */
/* fgets(line, MAXLINE, ficpar); */	/* fgets(line, MAXLINE, ficpar); */
Line 9477 Please run with mle=-1 to get a correct	Line 9834 Please run with mle=-1 to get a correct

estepm=0;	estepm=0;
if((num_filled=sscanf(line,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm, &ftolpl)) !=EOF){	if((num_filled=sscanf(line,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm, &ftolpl)) !=EOF){

if (num_filled != 6) {	if (num_filled != 6) {
printf("Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line);	printf("Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line);
fprintf(ficlog,"Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line);	fprintf(ficlog,"Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line);
goto end;	goto end;
}	}
printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);	printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
}	}
/* ftolpl=6ftol1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit \/ /	/* ftolpl=6ftol1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit \/ /
/ftolpl=6.e-4;/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */	/ftolpl=6.e-4;/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */

/* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */	/* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
if (estepm==0 \|\| estepm < stepm) estepm=stepm;	if (estepm==0 \|\| estepm < stepm) estepm=stepm;
if (fage <= 2) {	if (fage <= 2) {
Line 9555 Please run with mle=-1 to get a correct	Line 9912 Please run with mle=-1 to get a correct
ungetc(c,ficpar);	ungetc(c,ficpar);

fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);	fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);
fprintf(ficparo,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);	fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
fprintf(ficlog,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);	fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
fprintf(ficres,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);	fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
/* day and month of proj2 are not used but only year anproj2.*/	/* day and month of proj2 are not used but only year anproj2.*/


Line 9576 Please run with mle=-1 to get a correct	Line 9933 Please run with mle=-1 to get a correct
printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p);	printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p);
}	}
printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \	printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \	model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \
jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);	jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);

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

/* free_ivector(wav,1,imx); / / Moved after last prevalence call */	/* free_ivector(wav,1,imx); / / Moved after last prevalence call */
/* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */	/* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
Line 9617 Please run with mle=-1 to get a correct	Line 9974 Please run with mle=-1 to get a correct
probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);	probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
for(i=1;i<=AGESUP;i++)	for(i=1;i<=AGESUP;i++)
for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */	for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
for(k=1;k<=ncovcombmax;k++)	for(k=1;k<=ncovcombmax;k++)
probs[i][j][k]=0.;	probs[i][j][k]=0.;
prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);	prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
if (mobilav!=0 \|\|mobilavproj !=0 ) {	if (mobilav!=0 \|\|mobilavproj !=0 ) {
mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);	mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
Line 9905 Please run with mle=-1 to get a correct	Line 10262 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,nqtv,1,n);
	free_ma3x(cotvar,1,maxwav,1,ntv,1,n);
	free_matrix(coqvar,1,maxwav,1,n);
free_matrix(covar,0,NCOVMAX,1,n);	free_matrix(covar,0,NCOVMAX,1,n);
free_matrix(matcov,1,npar,1,npar);	free_matrix(matcov,1,npar,1,npar);
free_matrix(hess,1,npar,1,npar);	free_matrix(hess,1,npar,1,npar);
Line 9915 Please run with mle=-1 to get a correct	Line 10275 Please run with mle=-1 to get a correct

free_ivector(ncodemax,1,NCOVMAX);	free_ivector(ncodemax,1,NCOVMAX);
free_ivector(ncodemaxwundef,1,NCOVMAX);	free_ivector(ncodemaxwundef,1,NCOVMAX);
	free_ivector(Typevar,-1,NCOVMAX);
free_ivector(Tvar,1,NCOVMAX);	free_ivector(Tvar,1,NCOVMAX);
free_ivector(Tprod,1,NCOVMAX);	free_ivector(Tprod,1,NCOVMAX);
free_ivector(Tvaraff,1,NCOVMAX);	free_ivector(Tvaraff,1,NCOVMAX);

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

Removed from v.1.222
changed lines
	Added in v.1.225