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Diff for /imach/src/imach.c between versions 1.190 and 1.199

version 1.190, 2015/05/05 08:51:13	version 1.199, 2015/09/07 14:09:23
Line 1	Line 1
/* $Id$	/* $Id$
$State$	$State$
$Log$	$Log$
	Revision 1.199 2015/09/07 14:09:23 brouard
	Summary: 0.98q6 changing default small png format for graph to vectorized svg.

	Revision 1.198 2015/09/03 07:14:39 brouard
	Summary: 0.98q5 Flavia

	Revision 1.197 2015/09/01 18:24:39 brouard
	* empty log message *

	Revision 1.196 2015/08/18 23:17:52 brouard
	Summary: 0.98q5

	Revision 1.195 2015/08/18 16:28:39 brouard
	Summary: Adding a hack for testing purpose

	After reading the title, ftol and model lines, if the comment line has
	a q, starting with #q, the answer at the end of the run is quit. It
	permits to run test files in batch with ctest. The former workaround was
	$ echo q \| imach foo.imach

	Revision 1.194 2015/08/18 13:32:00 brouard
	Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.

	Revision 1.193 2015/08/04 07:17:42 brouard
	Summary: 0.98q4

	Revision 1.192 2015/07/16 16:49:02 brouard
	Summary: Fixing some outputs

	Revision 1.191 2015/07/14 10:00:33 brouard
	Summary: Some fixes

Revision 1.190 2015/05/05 08:51:13 brouard	Revision 1.190 2015/05/05 08:51:13 brouard
Summary: Adding digits in output parameters (7 digits instead of 6)	Summary: Adding digits in output parameters (7 digits instead of 6)

Line 602	Line 634
/* #define DEBUG */	/* #define DEBUG */
/* #define DEBUGBRENT */	/* #define DEBUGBRENT */
#define POWELL /* Instead of NLOPT */	#define POWELL /* Instead of NLOPT */
	#define POWELLF1F3 /* 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 670 typedef struct {	Line 703 typedef struct {
#define NLSTATEMAX 8 /*< Maximum number of live states (for func) /	#define NLSTATEMAX 8 /*< Maximum number of live states (for func) /
#define NDEATHMAX 8 /*< Maximum number of dead states (for func) /	#define NDEATHMAX 8 /*< Maximum number of dead states (for func) /
#define NCOVMAX 20 /*< Maximum number of covariates, including generated covariates V1V2 */	#define NCOVMAX 20 /*< Maximum number of covariates, including generated covariates V1V2 */
#define codtabm(h,k) 1 & (h-1) >> (k-1) ;	#define codtabm(h,k) (1 & (h-1) >> (k-1))+1
#define MAXN 20000	#define MAXN 20000
#define YEARM 12. /*< Number of months per year /	#define YEARM 12. /*< Number of months per year /
#define AGESUP 130	#define AGESUP 130
#define AGEBASE 40	#define AGEBASE 40
	#define AGEOVERFLOW 1.e20
#define AGEGOMP 10 /*< Minimal age for Gompertz adjustment /	#define AGEGOMP 10 /*< Minimal age for Gompertz adjustment /
#ifdef _WIN32	#ifdef _WIN32
#define DIRSEPARATOR '\\'	#define DIRSEPARATOR '\\'
Line 688 typedef struct {	Line 722 typedef struct {

/* $Id$ */	/* $Id$ */
/* $State$ */	/* $State$ */
	#include "version.h"
char version[]="Imach version 0.98q2, April 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";	char version[]=__IMACH_VERSION__;
	char copyright[]="September 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
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 824 int estepm;	Line 859 int estepm;

int m,nb;	int m,nb;
long *num;	long *num;
int firstpass=0, lastpass=4,cod, ncodemax, Tage,cens;	int firstpass=0, lastpass=4,cod, cens;
	int ncodemax; / ncodemax[j]= Number of modalities of the j th
	covariate for which somebody answered excluding
	undefined. Usually 2: 0 and 1. */
	int ncodemaxwundef; / ncodemax[j]= Number of modalities of the j th
	covariate for which somebody answered including
	undefined. Usually 3: -1, 0 and 1. */
double *agev,moisnais, annais, moisdc, andc,mint, *anint;	double *agev,moisnais, annais, moisdc, andc,mint, *anint;
double pmmij, *probs;	double pmmij, *probs;
double ageexmed,agecens;	double ageexmed,agecens;
Line 838 double covar; /< covar[j,i], value	Line 879 double covar; /< covar[j,i], value
* cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]age; /	* cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]age; /
double idx;	double idx;
int *nbcode, Tvar; /*< model=V2 => Tvar[1]= 2 /	int *nbcode, Tvar; /*< model=V2 => Tvar[1]= 2 /
	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); */
int *Tvard, Tprod, cptcovprod, *Tvaraff;	int *Tvard, Tprod, cptcovprod, *Tvaraff;
Line 1450 values at the three points, fa, fb , and	Line 1492 values at the three points, fa, fb , and
#endif	#endif
#ifdef MNBRAKORIGINAL	#ifdef MNBRAKORIGINAL
#else	#else
if (fu > *fc) {	/* if (fu > fc) { /
#ifdef DEBUG	/* #ifdef DEBUG */
printf("mnbrak4 fu > fc \n");	/* printf("mnbrak4 fu > fc \n"); */
fprintf(ficlog, "mnbrak4 fu > fc\n");	/* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
#endif	/* #endif */
/* SHFT(u,cx,cx,u) /\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and \/ /	/* /\* SHFT(u,cx,cx,u) /\\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and \\/ \/ */
/* SHFT(fa,fc,fu,fc) /\ (b, u, c) is a bracket while test fb > fc will be fu > fc will exit \/ /	/* /\* SHFT(fa,fc,fu,fc) /\\ (b, u, c) is a bracket while test fb > fc will be fu > fc will exit \\/ \/ */
dum=u; /* Shifting c and u */	/* dum=u; /\* Shifting c and u \/ /
u = *cx;	/* u = cx; /
*cx = dum;	/* cx = dum; /
dum = fu;	/* dum = fu; */
fu = *fc;	/* fu = fc; /
*fc =dum;	/* fc =dum; /
} else { /* end */	/* } else { /\* end \/ /
	/* #ifdef DEBUG */
	/* printf("mnbrak3 fu < fc \n"); */
	/* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
	/* #endif */
	/* dum=u; /\* Shifting c and u \/ /
	/* u = cx; /
	/* cx = dum; /
	/* dum = fu; */
	/* fu = fc; /
	/* fc =dum; /
	/* } */
#ifdef DEBUG	#ifdef DEBUG
printf("mnbrak3 fu < fc \n");	printf("mnbrak34 fu < or >= fc \n");
fprintf(ficlog, "mnbrak3 fu < fc\n");	fprintf(ficlog, "mnbrak34 fu < fc\n");
#endif	#endif
dum=u; /* Shifting c and u */	dum=u; /* Shifting c and u */
u = *cx;	u = *cx;
*cx = dum;	*cx = dum;
dum = fu;	dum = fu;
fu = *fc;	fu = *fc;
*fc =dum;	*fc =dum;
}
#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
Line 1546 void linmin(double p[], double xi[], int	Line 1598 void linmin(double p[], double xi[], int
xicom[j]=xi[j];	xicom[j]=xi[j];
}	}

axs=0.0;	/* axs=0.0; */
xxss=1; /* 1 and using scale */	/* xxss=1; /\* 1 and using scale \/ /
xxs=1;	xxs=1;
do{	/* do{ */
ax=0.;	ax=0.;
xx= xxs;	xx= xxs;
mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(xx)xicom[j]; fx=f(xtx[j]) */	mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(xx)xicom[j]; fx=f(xtx[j]) */
Line 1559 void linmin(double p[], double xi[], int	Line 1611 void linmin(double p[], double xi[], int
/* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */	/* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
/* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */	/* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
/* Find a bracket a,x,b in direction n=xi ie xicom, order may change. Scale is [0:xxsxi[j]] et non plus [0:xi[j]]/	/* Find a bracket a,x,b in direction n=xi ie xicom, order may change. Scale is [0:xxsxi[j]] et non plus [0:xi[j]]/
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("\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); */
}	/* } */
}while(fx != fx);	/* }while(fx != fx); */

	#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);
	#endif
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]) */
Line 1574 void linmin(double p[], double xi[], int	Line 1629 void linmin(double p[], double xi[], int
printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);	printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);	fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
#endif	#endif
/* printf("linmin end "); */	#ifdef DEBUGLINMIN
	printf("linmin end ");
	#endif
for (j=1;j<=n;j++) {	for (j=1;j<=n;j++) {
/* printf(" before xi[%d]=%12.8f", j,xi[j]); */	/* printf(" before xi[%d]=%12.8f", j,xi[j]); */
xi[j] = xmin; / xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */	xi[j] = xmin; / xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
Line 1583 void linmin(double p[], double xi[], int	Line 1640 void linmin(double p[], double xi[], int
p[j] += xi[j]; /* Parameters values are updated accordingly */	p[j] += xi[j]; /* Parameters values are updated accordingly */
}	}
/* printf("\n"); */	/* printf("\n"); */
/* printf("Comparing last frec(xmin)=%12.8f from Brent and frec(0.)=%12.8f \n", fret, (func)(p)); /	#ifdef DEBUGLINMIN
	printf("Comparing last frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, fret, (*func)(p));
	for (j=1;j<=n;j++) {
	printf(" xi[%d]= %12.7f p[%d]= %12.7f",j,xi[j],j,p[j]);
	if(j % ncovmodel == 0)
	printf("\n");
	}
	#endif
free_vector(xicom,1,n);	free_vector(xicom,1,n);
free_vector(pcom,1,n);	free_vector(pcom,1,n);
}	}
Line 1628 void powell(double p[], double **xi, int	Line 1692 void powell(double p[], double **xi, int
printf("\nPowell iter=%d -2LL=%.12f %ld sec. %ld sec.",iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);	printf("\nPowell iter=%d -2LL=%.12f %ld sec. %ld sec.",iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
fprintf(ficlog,"\nPowell iter=%d -2LL=%.12f %ld sec. %ld sec.",iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);	fprintf(ficlog,"\nPowell iter=%d -2LL=%.12f %ld sec. %ld sec.",iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
/* fprintf(ficrespow,"%d %.12f %ld",iter,fret,curr_time.tm_sec-start_time.tm_sec); */	/* fprintf(ficrespow,"%d %.12f %ld",iter,fret,curr_time.tm_sec-start_time.tm_sec); */
for (i=1;i<=n;i++) {	for (i=1;i<=n;i++) {
printf(" %d %.12f",i, p[i]);	printf(" %d %.12f",i, p[i]);
fprintf(ficlog," %d %.12lf",i, p[i]);	fprintf(ficlog," %d %.12lf",i, p[i]);
fprintf(ficrespow," %.12lf", p[i]);	fprintf(ficrespow," %.12lf", p[i]);
Line 1736 void powell(double p[], double **xi, int	Line 1800 void powell(double p[], double **xi, int
free_vector(ptt,1,n);	free_vector(ptt,1,n);
free_vector(pt,1,n);	free_vector(pt,1,n);
return;	return;
}	} /* enough precision */
if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");	if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */	for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
ptt[j]=2.0*p[j]-pt[j];	ptt[j]=2.0*p[j]-pt[j];
Line 1744 void powell(double p[], double **xi, int	Line 1808 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
	#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
/* (x1 f1=fp), (x2 f2=fret), (x3 f3=fptt), (xm fm) /	/* (x1 f1=fp), (x2 f2=fret), (x3 f3=fptt), (xm fm) /
/* From x1 (P0) distance of x2 is at h and x3 is 2h */	/* From x1 (P0) distance of x2 is at h and x3 is 2h */
/* Let f"(x2) be the 2nd derivative equal everywhere. */	/* Let f"(x2) be the 2nd derivative equal everywhere. */
Line 1773 void powell(double p[], double **xi, int	Line 1840 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, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);	printf("directest= %.12lf, 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, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);	fprintf(ficlog,"directest= %.12lf, 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
	printf("Before linmin in direction P%d-P0\n",n);
	for (j=1;j<=n;j++) {
	printf("Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
	if(j % ncovmodel == 0)
	printf("\n");
	}
	#endif
linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/	linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
	#ifdef DEBUGLINMIN
	for (j=1;j<=n;j++) {
	printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
	if(j % ncovmodel == 0)
	printf("\n");
	}
	#endif
for (j=1;j<=n;j++) {	for (j=1;j<=n;j++) {
xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */	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 */	xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
Line 1798 void powell(double p[], double **xi, int	Line 1880 void powell(double p[], double **xi, int
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
#endif	#endif
} /* end of t negative */	} /* end of t or directest negative */
	#ifdef POWELLF1F3
	#else
} /* end if (fptt < fp) */	} /* end if (fptt < fp) */
}	#endif
	} /* loop iteration */
}	}

/** Prevalence limit (stable or period prevalence) **************/	/** Prevalence limit (stable or period prevalence) **************/
Line 1832 double prevalim(double prlim, int nl	Line 1917 double prevalim(double prlim, int nl
if(nagesqr==1)	if(nagesqr==1)
cov[3]= agefin*agefin;;	cov[3]= agefin*agefin;;
for (k=1; k<=cptcovn;k++) {	for (k=1; k<=cptcovn;k++) {
cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];	cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])];
/printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);/	/* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); */
}	}
/wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]cov[2]; */	/wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]cov[2]; */
for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2];	for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2];
for (k=1; k<=cptcovprod;k++) /* Useless */	for (k=1; k<=cptcovprod;k++) /* Useless */
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])];

/printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);/	/printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);/
/printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);/	/printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);/
Line 2011 double *hpxij(double *po, int nhstep	Line 2096 double *hpxij(double *po, int nhstep
if(nagesqr==1)	if(nagesqr==1)
cov[3]= agexact*agexact;	cov[3]= agexact*agexact;
for (k=1; k<=cptcovn;k++)	for (k=1; k<=cptcovn;k++)
cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];	cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])];
for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */	for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
/* cov[2+Tage[k]]=cov[2+Tage[k]]cov[2]; /	/* cov[2+Tage[k]]=cov[2+Tage[k]]cov[2]; /
cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];	cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2];
for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */	for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])];


/printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);/	/printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);/
Line 2835 void lubksb(double *a, int n, int indx	Line 2920 void lubksb(double *a, int n, int indx

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

/********** Frequencies ******************/	/********** Frequencies ******************/
Line 2887 void freqsummary(char fileres[], int ia	Line 2972 void freqsummary(char fileres[], int ia
bool=1;	bool=1;
if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */	if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
for (z1=1; z1<=cptcoveff; z1++)	for (z1=1; z1<=cptcoveff; z1++)
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){	if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
/* Tests if the value of each of the covariates of i is equal to filter j1 */	/* Tests if the value of each of the covariates of i is equal to filter j1 */
bool=0;	bool=0;
/* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%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,codtab[j1][z1],	bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/	j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
/* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/	/* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
}	}
}	}

Line 2922 void freqsummary(char fileres[], int ia	Line 3007 void freqsummary(char fileres[], int ia
pstamp(ficresp);	pstamp(ficresp);
if (cptcovn>0) {	if (cptcovn>0) {
fprintf(ficresp, "\n#********** Variable ");	fprintf(ficresp, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficresp, "**********\n#");	fprintf(ficresp, "**********\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]][codtab[j1][z1]]);	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficlog, "**********\n#");	fprintf(ficlog, "**********\n#");
}	}
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
Line 3053 void prevalence(double ***probs, double	Line 3138 void prevalence(double ***probs, double
bool=1;	bool=1;
if (cptcovn>0) {	if (cptcovn>0) {
for (z1=1; z1<=cptcoveff; z1++)	for (z1=1; z1<=cptcoveff; z1++)
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])	if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
bool=0;	bool=0;
}	}
if (bool==1) {	if (bool==1) {
Line 3258 void tricode(int Tvar, int *nbcode, in	Line 3343 void tricode(int Tvar, int *nbcode, in

cptcoveff=0;	cptcoveff=0;

for (k=-1; k < maxncov; k++) Ndum[k]=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 */
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 (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	ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
Line 3285 void tricode(int Tvar, int *nbcode, in	Line 3370 void tricode(int Tvar, int *nbcode, in
/* getting the maximum value of the modality of the covariate	/* getting the maximum value of the modality of the covariate
(should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and	(should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
female is 1, then modmaxcovj=1.*/	female is 1, then modmaxcovj=1.*/
} /* end for loop on individuals */	} /* 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);
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 (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1// For each value 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], i, Ndum[i]);	printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */	fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */	if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
	if( k != -1){
	ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th
	covariate for which somebody answered excluding
	undefined. Usually 2: 0 and 1. */
	}
	ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
	covariate for which somebody answered including
	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 */
Line 3310 void tricode(int Tvar, int *nbcode, in	Line 3404 void tricode(int Tvar, int *nbcode, in
nbcode[Tvar[j]][1]=0;	nbcode[Tvar[j]][1]=0;
nbcode[Tvar[j]][2]=1;	nbcode[Tvar[j]][2]=1;
nbcode[Tvar[j]][3]=2;	nbcode[Tvar[j]][3]=2;
	To be continued (not working yet).
*/	*/
ij=1; /* ij is similar to i but can jumps 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 */	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 (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 // Could be 1 to 4 */	if (Ndum[i] == 0) { /* If nobody responded to this modality k */
/recode from 0 /	break;
if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */	}
nbcode[Tvar[j]][ij]=k; /* stores the modality k in an array nbcode.	ij++;
k is a modality. If we have model=V1+V1*sex	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.*/
then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */	cptcode = ij; /* New max modality for covar j */
ij++;	} /* end of loop on modality i=-1 to 1 or more */
}
if (ij > ncodemax[j]) break;	/* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 \//\ Could be 1 to 4 \//\ cptcode=modmaxcovj \/ /
} /* end of loop on */	/* /\recode from 0 \/ */
} /* end of loop on modality */	/* k is a modality. If we have model=V1+V1sex /
	/* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
	/* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode \/ /
	/* } */
	/* /\* cptcode = ij; \/ /\ New max modality for covar j \/ /
	/* if (ij > ncodemax[j]) { */
	/* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
	/* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
	/* break; */
	/* } */
	/* } /\* 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;
Line 3334 void tricode(int Tvar, int *nbcode, in	Line 3439 void tricode(int Tvar, int *nbcode, in
Ndum[ij]++; /* Might be supersed V1 + V1age /	Ndum[ij]++; /* Might be supersed V1 + V1age /
}	}

ij=1;	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) /
ij++;	}else{
}else	/* Tvaraff[ij]=0; */
Tvaraff[ij]=0;	}
}	}
ij--;	/* ij--; */
cptcoveff=ij; /Number of total covariates/	cptcoveff=ij; /Number of total covariates/

}	}
Line 3948 void varevsij(char optionfilefiname[], d	Line 4054 void varevsij(char optionfilefiname[], d
free_vector(gmp,nlstate+1,nlstate+ndeath);	free_vector(gmp,nlstate+1,nlstate+ndeath);
free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);	free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/	free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");	/* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
	fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
/* for(j=nlstate+1; j<= nlstate+ndeath; j++){ // Only the first actually */	/* for(j=nlstate+1; j<= nlstate+ndeath; j++){ // Only the first actually */
fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");	fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
/* fprintf(ficgp,"\n plot \"%s\" u 1:($3%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); /	/* fprintf(ficgp,"\n plot \"%s\" u 1:($3%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); /
Line 3958 void varevsij(char optionfilefiname[], d	Line 4065 void varevsij(char optionfilefiname[], d
fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));	fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));	fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));	fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);	fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.svg\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
/* fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);	/* fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.svg\"> <br>\n", stepm,YEARM,digitp,digit);
*/	*/
/* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */	/* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);	fprintf(ficgp,"\nset out \"%s%s.svg\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);

free_vector(xp,1,npar);	free_vector(xp,1,npar);
free_matrix(doldm,1,nlstate,1,nlstate);	free_matrix(doldm,1,nlstate,1,nlstate);
Line 4135 void varprob(char optionfilefiname[], do	Line 4242 void varprob(char optionfilefiname[], do
fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");	fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
fprintf(fichtm,"\n");	fprintf(fichtm,"\n");

fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);	fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4></br>this page is important in order to visualize confidence intervals and especially correlation between disability and recovery</li>\n",optionfilehtmcov);
fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\	fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);
file %s<br>\n",optionfilehtmcov);	fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
and drawn. It helps understanding how is the covariance between two incidences.\	and drawn. It helps understanding how is the covariance between two incidences.\
They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");	They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \	fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
Line 4159 To be simple, these graphs help to under	Line 4265 To be simple, these graphs help to under
/j1++;/	/j1++;/
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]][codtab[j1][z1]]);	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficresprob, "**********\n#\n");	fprintf(ficresprob, "**********\n#\n");
fprintf(ficresprobcov, "\n#********** Variable ");	fprintf(ficresprobcov, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficresprobcov, "**********\n#\n");	fprintf(ficresprobcov, "**********\n#\n");

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


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

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

Line 4188 To be simple, these graphs help to under	Line 4294 To be simple, these graphs help to under
if(nagesqr==1)	if(nagesqr==1)
cov[3]= age*age;	cov[3]= age*age;
for (k=1; k<=cptcovn;k++) {	for (k=1; k<=cptcovn;k++) {
cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4	cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];/* j1 1 2 3 4
* 1 1 1 1 1	* 1 1 1 1 1
* 2 2 1 1 1	* 2 2 1 1 1
* 3 1 2 1 1	* 3 1 2 1 1
Line 4196 To be simple, these graphs help to under	Line 4302 To be simple, these graphs help to under
/* nbcode[1][1]=0 nbcode[1][2]=1;*/	/* nbcode[1][1]=0 nbcode[1][2]=1;*/
}	}
/* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]cov[2]; /	/* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]cov[2]; /
for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[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];
for (k=1; k<=cptcovprod;k++)	for (k=1; k<=cptcovprod;k++)
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])];


for(theta=1; theta <=npar; theta++){	for(theta=1; theta <=npar; theta++){
Line 4348 To be simple, these graphs help to under	Line 4454 To be simple, these graphs help to under
first=0;	first=0;
fprintf(ficgp,"\nset parametric;unset label");	fprintf(ficgp,"\nset parametric;unset label");
fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);	fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
fprintf(ficgp,"\nset ter png small size 320, 240");	fprintf(ficgp,"\nset ter svg size 640, 480");
fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\	fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
:<a href=\"%s%d%1d%1d-%1d%1d.png\">\	:<a href=\"%s%d%1d%1d-%1d%1d.svg\">\
%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\	%s%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\	subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);	subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);	fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);	fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);	fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);	fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);	fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)), %11.3e +%.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)) not",\	fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)), %11.3e +%.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)) not",\
Line 4373 To be simple, these graphs help to under	Line 4479 To be simple, these graphs help to under
}/* if first */	}/* if first */
} /* age mod 5 */	} /* age mod 5 */
} /* end loop age */	} /* end loop age */
fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);	fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.svg\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
first=1;	first=1;
} /l12 /	} /l12 /
} /* k12 */	} /* k12 */
Line 4430 fprintf(fichtm," \n<ul><li><b>Graphs</b>	Line 4536 fprintf(fichtm," \n<ul><li><b>Graphs</b>

jj1=0;	jj1=0;
for(k1=1; k1<=m;k1++){	for(k1=1; k1<=m;k1++){
for(i1=1; i1<=ncodemax[k1];i1++){	/* for(i1=1; i1<=ncodemax[k1];i1++){ */
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++){
fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);	fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
	printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
	}
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");	fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
}	}
/* Pij */	/* Pij */
fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \	fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.svg\">%s%d_1.svg</a><br> \
<img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);	<img src=\"%s%d_1.svg\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
/* Quasi-incidences */	/* Quasi-incidences */
fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\	fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \	before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.svg\">%s%d_2.svg</a><br> \
<img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);	<img src=\"%s%d_2.svg\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
/* Period (stable) prevalence in each health state */	/* Period (stable) prevalence in each health state */
for(cpt=1; cpt<=nlstate;cpt++){	for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"<br>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \	fprintf(fichtm,"<br>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \
<img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);	<img src=\"%s%d_%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
}	}
for(cpt=1; cpt<=nlstate;cpt++) {	for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \	fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.svg\">%s%d%d.svg</a> <br> \
<img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);	<img src=\"%s%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
}	}
} /* end i1 */	/* } /\* end i1 \/ /
}/* End k1 */	}/* End k1 */
fprintf(fichtm,"</ul>");	fprintf(fichtm,"</ul>");


fprintf(fichtm,"\	fprintf(fichtm,"\
\n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\	\n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
- Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);	- Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
	- 95%% confidence intervals and Wald tests of the estimated parameters are in the log file.<br> \
	But because parameters are usually highly correlated (a higher incidence of disability \
	and a higher incidence of recovery can give very close observed transition) it might \
	be very useful to look not only at linear confidence intervals estimated from the \
	variances but at the covariance matrix. And instead of looking at the estimated coefficients \
	(parameters) of the logistic regression, it might be more meaningful to visualize the \
	covariance matrix of the one-step probabilities. \
	See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);

fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",	fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));	subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",	- Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
Line 4504 fprintf(fichtm," \n<ul><li><b>Graphs</b>	Line 4619 fprintf(fichtm," \n<ul><li><b>Graphs</b>

jj1=0;	jj1=0;
for(k1=1; k1<=m;k1++){	for(k1=1; k1<=m;k1++){
for(i1=1; i1<=ncodemax[k1];i1++){	/* for(i1=1; i1<=ncodemax[k1];i1++){ */
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++)
fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[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\">");
}	}
for(cpt=1; cpt<=nlstate;cpt++) {	for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \	fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\	prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.svg <br>\
<img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);	<img src=\"%s%d_%d.svg\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
}	}
fprintf(fichtm,"\n<br>- Total life expectancy by age and \	fprintf(fichtm,"\n<br>- Total life expectancy by age and \
health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \	health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
true period expectancies (those weighted with period prevalences are also\	true period expectancies (those weighted with period prevalences are also\
drawn in addition to the population based expectancies computed using\	drawn in addition to the population based expectancies computed using\
observed and cahotic prevalences: %s%d.png<br>\	observed and cahotic prevalences: %s%d.svg<br>\
<img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);	<img src=\"%s%d.svg\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
} /* end i1 */	/* } /\* end i1 \/ /
}/* End k1 */	}/* End k1 */
fprintf(fichtm,"</ul>");	fprintf(fichtm,"</ul>");
fflush(fichtm);	fflush(fichtm);
Line 4551 void printinggnuplot(char fileres[], cha	Line 4666 void printinggnuplot(char fileres[], cha
fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");	fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
for (cpt=1; cpt<= nlstate ; cpt ++) {	for (cpt=1; cpt<= nlstate ; cpt ++) {
for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */	for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
fprintf(ficgp,"\nset out \"%s%d_%d.png\" \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.png\" \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 png small size 320, 240\n\	set ter svg size 640, 480\n\
plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);	plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);

for (i=1; i<= nlstate ; i ++) {	for (i=1; i<= nlstate ; i ++) {
Line 4578 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 4693 plot [%.f:%.f] \"%s\" every :::%d::%d u
/2 eme/	/2 eme/
fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");	fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
for (k1=1; k1<= m ; k1 ++) {	for (k1=1; k1<= m ; k1 ++) {
fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);	fprintf(ficgp,"\nset out \"%s%d.svg\" \n",subdirf2(optionfilefiname,"e"),k1);
fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);	fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);

for (i=1; i<= nlstate+1 ; i ++) {	for (i=1; i<= nlstate+1 ; i ++) {
k=2*i;	k=2*i;
Line 4612 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 4727 plot [%.f:%.f] \"%s\" every :::%d::%d u
for (cpt=1; cpt<= nlstate ; cpt ++) {	for (cpt=1; cpt<= nlstate ; cpt ++) {
/* k=2+nlstate(2cpt-2); */	/* k=2+nlstate(2cpt-2); */
k=2+(nlstate+1)*(cpt-1);	k=2+(nlstate+1)*(cpt-1);
fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);	fprintf(ficgp,"\nset out \"%s%d%d.svg\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
fprintf(ficgp,"set ter png small size 320, 240\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(fileres,"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(fileres,"e"),k1-1,k1-1,k,cpt);
/fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);	/fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");	for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
Line 4637 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 4752 plot [%.f:%.f] \"%s\" every :::%d::%d u
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
k=3;	k=3;
fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);	fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
fprintf(ficgp,"\nset out \"%s%d_%d.png\" \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 png small size 320, 240\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 ; i ++){	for (i=1; i<= nlstate ; i ++){
Line 4694 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 4809 plot [%.f:%.f] ", ageminpar, agemaxpar)
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.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);	fprintf(ficgp,"\nset out \"%s%d_%d.svg\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
if (ng==2)	if (ng==2)
fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");	fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
else	else
fprintf(ficgp,"\nset title \"Probability\"\n");	fprintf(ficgp,"\nset title \"Probability\"\n");
fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);	fprintf(ficgp,"\nset ter svg size 640, 480\nset log y\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;
Line 4717 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 4832 plot [%.f:%.f] ", ageminpar, agemaxpar)
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);
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++) {
if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */	/* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);	if(ij <=cptcovage) { /* Bug valgrind */
ij++;	if((j-2)==Tage[ij]) { /* Bug valgrind */
	fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]);
	ij++;
	}
}	}
else	else
fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);	fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
}	}
fprintf(ficgp,")/(1");	fprintf(ficgp,")/(1");

Line 4734 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 4852 plot [%.f:%.f] ", ageminpar, agemaxpar)

ij=1;	ij=1;
for(j=3; j <=ncovmodel-nagesqr; j++){	for(j=3; j <=ncovmodel-nagesqr; j++){
if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {	if(ij <=cptcovage) { /* Bug valgrind */
fprintf(ficgp,"+p%d%dx",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);	if((j-2)==Tage[ij]) { /* Bug valgrind */
ij++;	fprintf(ficgp,"+p%d%dx",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]);
	ij++;
	}
}	}
else	else
fprintf(ficgp,"+p%d%d",k3+(k1-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][j-2]]);	fprintf(ficgp,"+p%d%d",k3+(k1-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
}	}
fprintf(ficgp,")");	fprintf(ficgp,")");
}	}
Line 4866 void prevforecast(char fileres[], double	Line 4986 void prevforecast(char fileres[], double
k=k+1;	k=k+1;
fprintf(ficresf,"\n#******");	fprintf(ficresf,"\n#******");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=cptcoveff;j++) {
fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
}	}
fprintf(ficresf,"******\n");	fprintf(ficresf,"******\n");
fprintf(ficresf,"# Covariate valuofcovar yearproj age");	fprintf(ficresf,"# Covariate valuofcovar yearproj age");
Line 4890 void prevforecast(char fileres[], double	Line 5010 void prevforecast(char fileres[], double
if (hhstepm/YEARMstepm ==yearp) {	if (hhstepm/YEARMstepm ==yearp) {
fprintf(ficresf,"\n");	fprintf(ficresf,"\n");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+hhstepm/YEARMstepm);	fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+hhstepm/YEARMstepm);
}	}
for(j=1; j<=nlstate+ndeath;j++) {	for(j=1; j<=nlstate+ndeath;j++) {
Line 4988 void populforecast(char fileres[], doubl	Line 5108 void populforecast(char fileres[], doubl
k=k+1;	k=k+1;
fprintf(ficrespop,"\n#******");	fprintf(ficrespop,"\n#******");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=cptcoveff;j++) {
fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
}	}
fprintf(ficrespop,"******\n");	fprintf(ficrespop,"******\n");
fprintf(ficrespop,"# Age");	fprintf(ficrespop,"# Age");
Line 5303 void printinghtmlmort(char fileres[], ch	Line 5423 void printinghtmlmort(char fileres[], ch
fprintf(fichtm," mu(age) =%lfexp(%lf(age-%d)) per year<br><br>",p[1],p[2],agegomp);	fprintf(fichtm," mu(age) =%lfexp(%lf(age-%d)) per year<br><br>",p[1],p[2],agegomp);
for (i=1;i<=2;i++)	for (i=1;i<=2;i++)
fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2sqrt(matcov[i][i]),p[i]+2sqrt(matcov[i][i]));	fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2sqrt(matcov[i][i]),p[i]+2sqrt(matcov[i][i]));
fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");	fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
fprintf(fichtm,"</ul>");	fprintf(fichtm,"</ul>");

fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");	fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
Line 5332 void printinggnuplotmort(char fileres[],	Line 5452 void printinggnuplotmort(char fileres[],

strcpy(dirfileres,optionfilefiname);	strcpy(dirfileres,optionfilefiname);
strcpy(optfileres,"vpl");	strcpy(optfileres,"vpl");
fprintf(ficgp,"set out \"graphmort.png\"\n ");	fprintf(ficgp,"set out \"graphmort.svg\"\n ");
fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");	fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");	fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
/* fprintf(ficgp, "set size 0.65,0.65\n"); */	/* fprintf(ficgp, "set size 0.65,0.65\n"); */
fprintf(ficgp,"plot [%d:100] %lfexp(%lf(x-%d))",agegomp,p[1],p[2],agegomp);	fprintf(ficgp,"plot [%d:100] %lfexp(%lf(x-%d))",agegomp,p[1],p[2],agegomp);

Line 5355 int readdata(char datafile[], int firsto	Line 5475 int readdata(char datafile[], int firsto


if((fic=fopen(datafile,"r"))==NULL) {	if((fic=fopen(datafile,"r"))==NULL) {
printf("Problem while opening datafile: %s\n", datafile);return 1;	printf("Problem while opening datafile: %s\n", datafile);fflush(stdout);
fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;	fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);fflush(ficlog);return 1;
}	}

i=1;	i=1;
Line 5557 int decodemodel ( char model[], int last	Line 5677 int decodemodel ( char model[], int last
if (strlen(model) >1){ /* If there is at least 1 covariate */	if (strlen(model) >1){ /* If there is at least 1 covariate */
j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;	j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
if (strstr(model,"AGE") !=0){	if (strstr(model,"AGE") !=0){
printf("Error. AGE must be in lower case 'age' model=1+age+%s ",model);	printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s ",model);fflush(ficlog);	fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
return 1;	return 1;
}	}
if (strstr(model,"v") !=0){	if (strstr(model,"v") !=0){
Line 5571 int decodemodel ( char model[], int last	Line 5691 int decodemodel ( char model[], int last
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;
}	}
Line 5645 int decodemodel ( char model[], int last	Line 5765 int decodemodel ( char model[], int last
/* k=1 Tvar[1]=2 (from V2) */	/* k=1 Tvar[1]=2 (from V2) */
/* k=5 Tvar[5] */	/* k=5 Tvar[5] */
/* for (k=1; k<=cptcovn;k++) { */	/* for (k=1; k<=cptcovn;k++) { */
/* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */	/* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
/* } */	/* } */
/* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[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 /
Line 5865 BOOL IsWow64()	Line 5985 BOOL IsWow64()
}	}
#endif	#endif

void syscompilerinfo()	void syscompilerinfo(int logged)
{	{
/* #include "syscompilerinfo.h"*/	/* #include "syscompilerinfo.h"*/
/* command line Intel compiler 32bit windows, XP compatible:*/	/* command line Intel compiler 32bit windows, XP compatible:*/
Line 5914 void syscompilerinfo()	Line 6034 void syscompilerinfo()
int cross = CROSS;	int cross = CROSS;
if (cross){	if (cross){
printf("Cross-");	printf("Cross-");
fprintf(ficlog, "Cross-");	if(logged) fprintf(ficlog, "Cross-");
}	}
#endif	#endif

#include <stdint.h>	#include <stdint.h>

printf("Compiled with:");fprintf(ficlog,"Compiled with:");	printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
#if defined(__clang__)	#if defined(__clang__)
printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */	printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
#endif	#endif
#if defined(__ICC) \|\| defined(__INTEL_COMPILER)	#if defined(__ICC) \|\| defined(__INTEL_COMPILER)
printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */	printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
#endif	#endif
#if defined(__GNUC__) \|\| defined(__GNUG__)	#if defined(__GNUC__) \|\| defined(__GNUG__)
printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */	printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
#endif	#endif
#if defined(__HP_cc) \|\| defined(__HP_aCC)	#if defined(__HP_cc) \|\| defined(__HP_aCC)
printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */	printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
#endif	#endif
#if defined(__IBMC__) \|\| defined(__IBMCPP__)	#if defined(__IBMC__) \|\| defined(__IBMCPP__)
printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */	printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
#endif	#endif
#if defined(_MSC_VER)	#if defined(_MSC_VER)
printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */	printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
#endif	#endif
#if defined(__PGI)	#if defined(__PGI)
printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */	printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
#endif	#endif
#if defined(__SUNPRO_C) \|\| defined(__SUNPRO_CC)	#if defined(__SUNPRO_C) \|\| defined(__SUNPRO_CC)
printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */	printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
#endif	#endif
printf(" for ");fprintf(ficlog," for ");	printf(" for "); if (logged) fprintf(ficlog, " for ");

// http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros	// http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
#ifdef _WIN32 // note the underscore: without it, it's not msdn official!	#ifdef _WIN32 // note the underscore: without it, it's not msdn official!
// Windows (x64 and x86)	// Windows (x64 and x86)
printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) ");	printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
#elif __unix__ // all unices, not all compilers	#elif __unix__ // all unices, not all compilers
// Unix	// Unix
printf("Unix ");fprintf(ficlog,"Unix ");	printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
#elif __linux__	#elif __linux__
// linux	// linux
printf("linux ");fprintf(ficlog,"linux ");	printf("linux ");if(logged) fprintf(ficlog,"linux ");
#elif __APPLE__	#elif __APPLE__
// Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..	// Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
printf("Mac OS ");fprintf(ficlog,"Mac OS ");	printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
#endif	#endif

/* __MINGW32__ */	/* __MINGW32__ */
Line 5973 void syscompilerinfo()	Line 6093 void syscompilerinfo()
/* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */	/* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */

#if UINTPTR_MAX == 0xffffffff	#if UINTPTR_MAX == 0xffffffff
printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */	printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
#elif UINTPTR_MAX == 0xffffffffffffffff	#elif UINTPTR_MAX == 0xffffffffffffffff
printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */	printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
#else	#else
printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */	printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
#endif	#endif

#if defined(__GNUC__)	#if defined(__GNUC__)
Line 5990 void syscompilerinfo()	Line 6110 void syscompilerinfo()
+ __GNUC_MINOR__ * 100)	+ __GNUC_MINOR__ * 100)
# endif	# endif
printf(" using GNU C version %d.\n", __GNUC_VERSION__);	printf(" using GNU C version %d.\n", __GNUC_VERSION__);
fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);	if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);

if (uname(&sysInfo) != -1) {	if (uname(&sysInfo) != -1) {
printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);	printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);	if(logged) fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
}	}
else	else
perror("uname() error");	perror("uname() error");
//#ifndef __INTEL_COMPILER	//#ifndef __INTEL_COMPILER
#if !defined (__INTEL_COMPILER) && !defined(__APPLE__)	#if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
printf("GNU libc version: %s\n", gnu_get_libc_version());	printf("GNU libc version: %s\n", gnu_get_libc_version());
fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());	if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
#endif	#endif
#endif	#endif

Line 6009 void syscompilerinfo()	Line 6129 void syscompilerinfo()
// {	// {
#if defined(_MSC_VER)	#if defined(_MSC_VER)
if (IsWow64()){	if (IsWow64()){
printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");	printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");	if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
}	}
else{	else{
printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");	printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");	if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
}	}
// printf("\nPress Enter to continue...");	// printf("\nPress Enter to continue...");
// getchar();	// getchar();
Line 6058 int prevalence_limit(double p, double	Line 6178 int prevalence_limit(double p, double
//for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){	//for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
k=k+1;	k=k+1;
/* to clean */	/* to clean */
//printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);	//printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
fprintf(ficrespl,"\n#******");	fprintf(ficrespl,"\n#******");
printf("\n#******");	printf("\n#******");
fprintf(ficlog,"\n#******");	fprintf(ficlog,"\n#******");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=cptcoveff;j++) {
fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
}	}
fprintf(ficrespl,"******\n");	fprintf(ficrespl,"******\n");
printf("******\n");	printf("******\n");
Line 6073 int prevalence_limit(double p, double	Line 6193 int prevalence_limit(double p, double

fprintf(ficrespl,"#Age ");	fprintf(ficrespl,"#Age ");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=cptcoveff;j++) {
fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[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);
fprintf(ficrespl,"\n");	fprintf(ficrespl,"\n");
Line 6083 int prevalence_limit(double p, double	Line 6203 int prevalence_limit(double p, double
prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);	prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
fprintf(ficrespl,"%.0f ",age );	fprintf(ficrespl,"%.0f ",age );
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
fprintf(ficrespl," %.5f", prlim[i][i]);	fprintf(ficrespl," %.5f", prlim[i][i]);
fprintf(ficrespl,"\n");	fprintf(ficrespl,"\n");
Line 6130 int hPijx(double *p, int bage, int fage)	Line 6250 int hPijx(double *p, int bage, int fage)
for (k=1; k <= (int) pow(2,cptcoveff); k++){	for (k=1; k <= (int) pow(2,cptcoveff); k++){
fprintf(ficrespij,"\n#****** ");	fprintf(ficrespij,"\n#****** ");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
fprintf(ficrespij,"******\n");	fprintf(ficrespij,"******\n");

for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */	for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
Line 6182 int main(int argc, char *argv[])	Line 6302 int main(int argc, char *argv[])

int jj, ll, li, lj, lk;	int jj, ll, li, lj, lk;
int numlinepar=0; /* Current linenumber of parameter file */	int numlinepar=0; /* Current linenumber of parameter file */
	int num_filled;
int itimes;	int itimes;
int NDIM=2;	int NDIM=2;
int vpopbased=0;	int vpopbased=0;
Line 6190 int main(int argc, char *argv[])	Line 6311 int main(int argc, char *argv[])
/* FILE fichtm; //* Html File */	/* FILE fichtm; //* Html File */
/* FILE ficgp;/ /Gnuplot File /	/* FILE ficgp;/ /Gnuplot File /
struct stat info;	struct stat info;
double agedeb;	double agedeb=0.;
double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
	double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;

double fret;	double fret;
double dum; /* Dummy variable */	double dum=0.; /* Dummy variable */
double ***p3mat;	double ***p3mat;
double ***mobaverage;	double ***mobaverage;

char line[MAXLINE];	char line[MAXLINE];
char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];	char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];

	char model[MAXLINE], modeltemp[MAXLINE];
char pathr[MAXLINE], pathimach[MAXLINE];	char pathr[MAXLINE], pathimach[MAXLINE];
char tok, val; /* pathtot */	char tok, val; /* pathtot */
int firstobs=1, lastobs=10;	int firstobs=1, lastobs=10;
int c, h , cpt;	int c, h , cpt, c2;
int jl;	int jl=0;
int i1, j1, jk, stepsize;	int i1, j1, jk, stepsize=0;
	int count=0;

int *tab;	int *tab;
int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */	int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
int mobilav=0,popforecast=0;	int mobilav=0,popforecast=0;
int hstepm, nhstepm;	int hstepm=0, nhstepm=0;
int agemortsup;	int agemortsup;
float sumlpop=0.;	float sumlpop=0.;
double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;	double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;	double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;

double bage=0, fage=110, age, agelim, agebase;	double bage=0, fage=110., age, agelim=0., agebase=0.;
double ftolpl=FTOL;	double ftolpl=FTOL;
double **prlim;	double **prlim;
double **param; / Matrix of parameters */	double **param; / Matrix of parameters */
Line 6276 int main(int argc, char *argv[])	Line 6402 int main(int argc, char *argv[])
#else	#else
getcwd(pathcd, size);	getcwd(pathcd, size);
#endif	#endif
	syscompilerinfo(0);
printf("\n%s\n%s",version,fullversion);	printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
if(argc <=1){	if(argc <=1){
printf("\nEnter the parameter file name: ");	printf("\nEnter the parameter file name: ");
fgets(pathr,FILENAMELENGTH,stdin);	fgets(pathr,FILENAMELENGTH,stdin);
Line 6341 int main(int argc, char *argv[])	Line 6467 int main(int argc, char *argv[])
goto end;	goto end;
}	}
fprintf(ficlog,"Log filename:%s\n",filelog);	fprintf(ficlog,"Log filename:%s\n",filelog);
fprintf(ficlog,"\n%s\n%s",version,fullversion);	fprintf(ficlog,"Version %s %s",version,fullversion);
fprintf(ficlog,"\nEnter the parameter file name: \n");	fprintf(ficlog,"\nEnter the parameter file name: \n");
fprintf(ficlog,"pathimach=%s\npathtot=%s\n\	fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
path=%s \n\	path=%s \n\
Line 6349 int main(int argc, char *argv[])	Line 6475 int main(int argc, char *argv[])
optionfilext=%s\n\	optionfilext=%s\n\
optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);	optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);

syscompilerinfo();	syscompilerinfo(1);

printf("Local time (at start):%s",strstart);	printf("Local time (at start):%s",strstart);
fprintf(ficlog,"Local time (at start): %s",strstart);	fprintf(ficlog,"Local time (at start): %s",strstart);
Line 6385 int main(int argc, char *argv[])	Line 6511 int main(int argc, char *argv[])

/* Reads comments: lines beginning with '#' */	/* Reads comments: lines beginning with '#' */
numlinepar=0;	numlinepar=0;
while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);	/* First parameter line */
fgets(line, MAXLINE, ficpar);	while(fgets(line, MAXLINE, ficpar)) {
	/* If line starts with a # it is a comment */
	if (line[0] == '#') {
	numlinepar++;
	fputs(line,stdout);
	fputs(line,ficparo);
	fputs(line,ficlog);
	continue;
	}else
	break;
	}
	if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
	title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
	if (num_filled != 5) {
	printf("Should be 5 parameters\n");
	}
numlinepar++;	numlinepar++;
fputs(line,stdout);	printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
fputs(line,ficparo);	}
fputs(line,ficlog);	/* Second parameter line */
	while(fgets(line, MAXLINE, ficpar)) {
	/* If line starts with a # it is a comment */
	if (line[0] == '#') {
	numlinepar++;
	fputs(line,stdout);
	fputs(line,ficparo);
	fputs(line,ficlog);
	continue;
	}else
	break;
	}
	if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
	&ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
	if (num_filled != 8) {
	printf("Not 8\n");
	}
	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);
}	}
ungetc(c,ficpar);

fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);	/* Third parameter line */
numlinepar++;	while(fgets(line, MAXLINE, ficpar)) {
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);	/* If line starts with a # it is a comment */
	if (line[0] == '#') {
	numlinepar++;
	fputs(line,stdout);
	fputs(line,ficparo);
	fputs(line,ficlog);
	continue;
	}else
	break;
	}
	if((num_filled=sscanf(line,"model=1+age%[^.\n]\n", model)) !=EOF){
	if (num_filled != 1) {
	printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
	fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
	model[0]='\0';
	goto end;
	}
	else{
	if (model[0]=='+'){
	for(i=1; i<=strlen(model);i++)
	modeltemp[i-1]=model[i];
	}
	strcpy(model,modeltemp);
	}
	/* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
	}
	/* 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 \/ /
	/* 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); */
if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */	if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */
model[strlen(model)-1]='\0';	model[strlen(model)-1]='\0';
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 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 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 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);
fflush(ficlog);	fflush(ficlog);
/* if(model[0]=='#'\|\| model[0]== '\0'){ */	/* if(model[0]=='#'\|\| model[0]== '\0'){ */
if(model[0]=='#'){	if(model[0]=='#'){
Line 6417 int main(int argc, char *argv[])	Line 6602 int main(int argc, char *argv[])
ungetc(c,ficpar);	ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);	fgets(line, MAXLINE, ficpar);
numlinepar++;	numlinepar++;
	if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
	z[0]=line[1];
	}
	/* printf("***line [1] = %c \n",line[1]); /
fputs(line, stdout);	fputs(line, stdout);
//puts(line);	//puts(line);
fputs(line,ficparo);	fputs(line,ficparo);
Line 6448 int main(int argc, char *argv[])	Line 6637 int main(int argc, char *argv[])
/delti=vector(1,npar); //* Scale of each paramater (output from hesscov)*/	/delti=vector(1,npar); //* Scale of each paramater (output from hesscov)*/
if(mle==-1){ /* Print a wizard for help writing covariance matrix */	if(mle==-1){ /* Print a wizard for help writing covariance matrix */
prwizard(ncovmodel, nlstate, ndeath, model, ficparo);	prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);	printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);	fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);	free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
fclose (ficparo);	fclose (ficparo);
fclose (ficlog);	fclose (ficlog);
Line 6458 int main(int argc, char *argv[])	Line 6647 int main(int argc, char *argv[])
}	}
else if(mle==-3) { /* Main Wizard */	else if(mle==-3) { /* Main Wizard */
prwizard(ncovmodel, nlstate, ndeath, model, ficparo);	prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);	printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);	fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);	param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
matcov=matrix(1,npar,1,npar);	matcov=matrix(1,npar,1,npar);
}	}
Line 6483 int main(int argc, char *argv[])	Line 6672 int main(int argc, char *argv[])
if(jj==i) continue;	if(jj==i) continue;
j++;	j++;
fscanf(ficpar,"%1d%1d",&i1,&j1);	fscanf(ficpar,"%1d%1d",&i1,&j1);
if ((i1 != i) && (j1 != j)){	if ((i1 != i) \|\| (j1 != jj)){
printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \	printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
It might be a problem of design; if ncovcol and the model are correct\n \	It might be a problem of design; if ncovcol and the model are correct\n \
run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);	run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
Line 6491 run imach with mle=-1 to get a correct t	Line 6680 run imach with mle=-1 to get a correct t
}	}
fprintf(ficparo,"%1d%1d",i1,j1);	fprintf(ficparo,"%1d%1d",i1,j1);
if(mle==1)	if(mle==1)
printf("%1d%1d",i,j);	printf("%1d%1d",i,jj);
fprintf(ficlog,"%1d%1d",i,j);	fprintf(ficlog,"%1d%1d",i,jj);
for(k=1; k<=ncovmodel;k++){	for(k=1; k<=ncovmodel;k++){
fscanf(ficpar," %lf",&param[i][j][k]);	fscanf(ficpar," %lf",&param[i][j][k]);
if(mle==1){	if(mle==1){
Line 6573 run imach with mle=-1 to get a correct t	Line 6762 run imach with mle=-1 to get a correct t
for(i=1; i <=npar; i++)	for(i=1; i <=npar; i++)
for(j=1; j <=npar; j++) matcov[i][j]=0.;	for(j=1; j <=npar; j++) matcov[i][j]=0.;

	/* Scans npar lines */
for(i=1; i <=npar; i++){	for(i=1; i <=npar; i++){
fscanf(ficpar,"%s",str);	count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
	if(count != 3){
	printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
	This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
	Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
	fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
	This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
	Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
	exit(1);
	}else
if(mle==1)	if(mle==1)
printf("%s",str);	printf("%1d%1d%1d",i1,j1,jk);
fprintf(ficlog,"%s",str);	fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
fprintf(ficparo,"%s",str);	fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
for(j=1; j <=i; j++){	for(j=1; j <=i; j++){
fscanf(ficpar," %le",&matcov[i][j]);	fscanf(ficpar," %le",&matcov[i][j]);
if(mle==1){	if(mle==1){
Line 6594 run imach with mle=-1 to get a correct t	Line 6793 run imach with mle=-1 to get a correct t
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
fprintf(ficparo,"\n");	fprintf(ficparo,"\n");
}	}
	/* End of read covariance matrix npar lines */
for(i=1; i <=npar; i++)	for(i=1; i <=npar; i++)
for(j=i+1;j<=npar;j++)	for(j=i+1;j<=npar;j++)
matcov[i][j]=matcov[j][i];	matcov[i][j]=matcov[j][i];
Line 6633 run imach with mle=-1 to get a correct t	Line 6833 run imach with mle=-1 to get a correct t
s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */	s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
tab=ivector(1,NCOVMAX);	tab=ivector(1,NCOVMAX);
ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2*ncov; V1+V2+V3+V4=>16 /	ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2*ncov; V1+V2+V3+V4=>16 /
	ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2*ncov; V1+V2+V3+V4=>16 /

/* Reads data from file datafile */	/* Reads data from file datafile */
if (readdata(datafile, firstobs, lastobs, &imx)==1)	if (readdata(datafile, firstobs, lastobs, &imx)==1)
Line 6721 run imach with mle=-1 to get a correct t	Line 6922 run imach with mle=-1 to get a correct t
/* 1 to ncodemax[j] is the maximum value of this jth covariate */	/* 1 to ncodemax[j] is the maximum value of this jth covariate */

codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2(k-1) )/2(k-1) */	codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2(k-1) )/2(k-1) */
/printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);/	/printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));/
/* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/	/* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
h=0;	h=0;

Line 6731 run imach with mle=-1 to get a correct t	Line 6932 run imach with mle=-1 to get a correct t

m=pow(2,cptcoveff);	m=pow(2,cptcoveff);

for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */
for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2*(3+1-1 or 3+1-3) =1 or 4 /
h++;
if (h>m)
h=1;
/< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2(k-1) )/2**(k-1) + 1	/< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2(k-1) )/2**(k-1) + 1
* For k=4 covariates, h goes from 1 to 2**k	* For k=4 covariates, h goes from 1 to 2**k
* codtabm(h,k)= 1 & (h-1) >> (k-1) ;	* codtabm(h,k)= 1 & (h-1) >> (k-1) ;
Line 6751 run imach with mle=-1 to get a correct t	Line 6945 run imach with mle=-1 to get a correct t
* 6 2 1 2 1	* 6 2 1 2 1
* 7 i=4 1 2 2 1	* 7 i=4 1 2 2 1
* 8 2 2 2 1	* 8 2 2 2 1
* 9 i=5 1 i=3 1 i=2 1 1	* 9 i=5 1 i=3 1 i=2 1 2
* 10 2 1 1 1	* 10 2 1 1 2
* 11 i=6 1 2 1 1	* 11 i=6 1 2 1 2
* 12 2 2 1 1	* 12 2 2 1 2
* 13 i=7 1 i=4 1 2 1	* 13 i=7 1 i=4 1 2 2
* 14 2 1 2 1	* 14 2 1 2 2
* 15 i=8 1 2 2 1	* 15 i=8 1 2 2 2
* 16 2 2 2 1	* 16 2 2 2 2
*/	*/
codtab[h][k]=j;	for(h=1; h <=100 ;h++){
/* codtab[12][3]=1; */	/* printf("h=%2d ", h); */
/codtab[h][Tvar[k]]=j;/	for(k=1; k <=10; k++){
printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);	/* printf("k=%d %d ",k,codtabm(h,k)); */
}	codtab[h][k]=codtabm(h,k);
}	}
}	/* printf("\n"); */
}	}
	/* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate \/ /
	/* for(i=1; i <=pow(2,cptcoveff-k);i++){ /\* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 \/ /
	/* for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2\/ /
	/* for(cpt=1; cpt <=pow(2,k-1); cpt++){ /\* cpt=1 to 8/2*(3+1-1 or 3+1-3) =1 or 4 \/ */
	/* h++; */
	/* if (h>m) */
	/* h=1; */
	/* codtab[h][k]=j; */
	/* /\* codtab[12][3]=1; \/ /
	/* /\codtab[h][Tvar[k]]=j;\/ */
	/* /\* printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]); \/ /
	/* } */
	/* } */
	/* } */
	/* } */
/* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);	/* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
codtab[1][2]=1;codtab[2][2]=2; */	codtab[1][2]=1;codtab[2][2]=2; */
/* for(i=1; i <=m ;i++){	/* for(i=1; i <=m ;i++){ */
for(k=1; k <=cptcovn; k++){	/* for(k=1; k <=cptcovn; k++){ */
printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);	/* printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); */
}	/* } */
printf("\n");	/* printf("\n"); */
}	/* } */
scanf("%d",i);*/	/* scanf("%d",i);*/

free_ivector(Ndum,-1,NCOVMAX);	free_ivector(Ndum,-1,NCOVMAX);

Line 7032 Interval (in months) between two waves:	Line 7241 Interval (in months) between two waves:
}	}

printf("iter=%d MLE=%f Eq=%lfexp(%lf(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);	printf("iter=%d MLE=%f Eq=%lfexp(%lf(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
for (i=1;i<=NDIM;i++)	for (i=1;i<=NDIM;i++) {
printf("%f [%f ; %f]\n",p[i],p[i]-2sqrt(matcov[i][i]),p[i]+2sqrt(matcov[i][i]));	printf("%f [%f ; %f]\n",p[i],p[i]-2sqrt(matcov[i][i]),p[i]+2sqrt(matcov[i][i]));
	fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2sqrt(matcov[i][i]),p[i]+2sqrt(matcov[i][i]));
	}
lsurv=vector(1,AGESUP);	lsurv=vector(1,AGESUP);
lpop=vector(1,AGESUP);	lpop=vector(1,AGESUP);
tpop=vector(1,AGESUP);	tpop=vector(1,AGESUP);
Line 7066 Interval (in months) between two waves:	Line 7276 Interval (in months) between two waves:


replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */	replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);	if(ageminpar == AGEOVERFLOW \|\|agemaxpar == AGEOVERFLOW){
	printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
	This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
	Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
	fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
	This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
	Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
	}else
	printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \	printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
stepm, weightopt,\	stepm, weightopt,\
model,imx,p,matcov,agemortsup);	model,imx,p,matcov,agemortsup);
Line 7102 Interval (in months) between two waves:	Line 7319 Interval (in months) between two waves:
}	}

/--------- 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 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,"# Parameters nlstatenlstatencov a121 + b12 age + ...\n");	fprintf(ficres,"# Parameters nlstatenlstatencov a121 + b12 age + ...\n");
Line 7131 Interval (in months) between two waves:	Line 7348 Interval (in months) between two waves:
ftolhess=ftol; /* Usually correct */	ftolhess=ftol; /* Usually correct */
hesscov(matcov, p, npar, delti, ftolhess, func);	hesscov(matcov, p, npar, delti, ftolhess, func);
}	}
	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");
	for(i=1,jk=1; i <=nlstate; i++){
	for(k=1; k <=(nlstate+ndeath); k++){
	if (k != i) {
	printf("%d%d ",i,k);
	fprintf(ficlog,"%d%d ",i,k);
	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]));
	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++;
	}
	printf("\n");
	fprintf(ficlog,"\n");
	}
	}
	}

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");
Line 7287 Interval (in months) between two waves:	Line 7522 Interval (in months) between two waves:
dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;	dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;

fscanf(ficpar,"pop_based=%d\n",&popbased);	fscanf(ficpar,"pop_based=%d\n",&popbased);
	fprintf(ficlog,"pop_based=%d\n",popbased);
fprintf(ficparo,"pop_based=%d\n",popbased);	fprintf(ficparo,"pop_based=%d\n",popbased);
fprintf(ficres,"pop_based=%d\n",popbased);	fprintf(ficres,"pop_based=%d\n",popbased);

Line 7311 Interval (in months) between two waves:	Line 7547 Interval (in months) between two waves:
/* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */	/* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */

replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */	replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);	if(ageminpar == AGEOVERFLOW \|\|agemaxpar == -AGEOVERFLOW){
	printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
	This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
	Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
	fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
	This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
	Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
	}else
	printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);

printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\	printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\	model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
Line 7498 Interval (in months) between two waves:	Line 7742 Interval (in months) between two waves:


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*/
oldm=oldms;savm=savms; /* Segmentation fault */	oldm=oldms;savm=savms; /* ZZ Segmentation fault */
cptcod= 0; /* To be deleted */	cptcod= 0; /* To be deleted */
varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */	varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are ");	fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are ");
Line 7509 Interval (in months) between two waves:	Line 7753 Interval (in months) between two waves:
fprintf(ficrest,"# Age e.. (std) ");	fprintf(ficrest,"# Age e.. (std) ");
for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);	for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
fprintf(ficrest,"\n");	fprintf(ficrest,"\n");
	/* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
epj=vector(1,nlstate+1);	epj=vector(1,nlstate+1);
for(age=bage; age <=fage ;age++){	for(age=bage; age <=fage ;age++){
prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);	prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); /ZZ Is it the correct prevalim /
if (vpopbased==1) {	if (vpopbased==1) {
if(mobilav ==0){	if(mobilav ==0){
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
Line 7524 Interval (in months) between two waves:	Line 7768 Interval (in months) between two waves:
}	}

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

for(i=1, vepp=0.;i <=nlstate;i++)	for(i=1, vepp=0.;i <=nlstate;i++)
for(j=1;j <=nlstate;j++)	for(j=1;j <=nlstate;j++)
Line 7606 Interval (in months) between two waves:	Line 7853 Interval (in months) between two waves:
free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);	free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);

free_ivector(ncodemax,1,NCOVMAX);	free_ivector(ncodemax,1,NCOVMAX);
	free_ivector(ncodemaxwundef,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);
Line 7713 Interval (in months) between two waves:	Line 7961 Interval (in months) between two waves:
}	}
end:	end:
while (z[0] != 'q') {	while (z[0] != 'q') {
printf("\nType q for exiting: ");	printf("\nType q for exiting: "); fflush(stdout);
scanf("%s",z);	scanf("%s",z);
}	}
}	}

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

Removed from v.1.190
changed lines
	Added in v.1.199