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Diff for /imach/src/imach.c between versions 1.195 and 1.215

version 1.195, 2015/08/18 16:28:39	version 1.215, 2015/12/16 08:52:24
Line 1	Line 1
/* $Id$	/* $Id$
$State$	$State$
$Log$	$Log$
	Revision 1.215 2015/12/16 08:52:24 brouard
	Summary: 0.98r4 working

	Revision 1.214 2015/12/16 06:57:54 brouard
	Summary: temporary not working

	Revision 1.213 2015/12/11 18:22:17 brouard
	Summary: 0.98r4

	Revision 1.212 2015/11/21 12:47:24 brouard
	Summary: minor typo

	Revision 1.211 2015/11/21 12:41:11 brouard
	Summary: 0.98r3 with some graph of projected cross-sectional

	Author: Nicolas Brouard

	Revision 1.210 2015/11/18 17:41:20 brouard
	Summary: Start working on projected prevalences

	Revision 1.209 2015/11/17 22:12:03 brouard
	Summary: Adding ftolpl parameter
	Author: N Brouard

	We had difficulties to get smoothed confidence intervals. It was due
	to the period prevalence which wasn't computed accurately. The inner
	parameter ftolpl is now an outer parameter of the .imach parameter
	file after estepm. If ftolpl is small 1.e-4 and estepm too,
	computation are long.

	Revision 1.208 2015/11/17 14:31:57 brouard
	Summary: temporary

	Revision 1.207 2015/10/27 17:36:57 brouard
	* empty log message *

	Revision 1.206 2015/10/24 07:14:11 brouard
	* empty log message *

	Revision 1.205 2015/10/23 15:50:53 brouard
	Summary: 0.98r3 some clarification for graphs on likelihood contributions

	Revision 1.204 2015/10/01 16:20:26 brouard
	Summary: Some new graphs of contribution to likelihood

	Revision 1.203 2015/09/30 17:45:14 brouard
	Summary: looking at better estimation of the hessian

	Also a better criteria for convergence to the period prevalence And
	therefore adding the number of years needed to converge. (The
	prevalence in any alive state shold sum to one

	Revision 1.202 2015/09/22 19:45:16 brouard
	Summary: Adding some overall graph on contribution to likelihood. Might change

	Revision 1.201 2015/09/15 17:34:58 brouard
	Summary: 0.98r0

	- Some new graphs like suvival functions
	- Some bugs fixed like model=1+age+V2.

	Revision 1.200 2015/09/09 16:53:55 brouard
	Summary: Big bug thanks to Flavia

	Even model=1+age+V2. did not work anymore

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

Line 621	Line 699

/* #define DEBUG */	/* #define DEBUG */
/* #define DEBUGBRENT */	/* #define DEBUGBRENT */
	/* #define DEBUGLINMIN */
	/* #define DEBUGHESS */
	#define DEBUGHESSIJ
	/* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan)\/ /
#define POWELL /* Instead of NLOPT */	#define POWELL /* Instead of NLOPT */
#define POWELLF1F3 /* Skip test */	#define 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 \/ /
Line 691 typedef struct {	Line 773 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 decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)/
	#define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 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
Line 710 typedef struct {	Line 794 typedef struct {

/* $Id$ */	/* $Id$ */
/* $State$ */	/* $State$ */
	#include "version.h"
char version[]="Imach version 0.98q5, August 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[]="October 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
char fullversion[]="$Revision$ $Date$";	char fullversion[]="$Revision$ $Date$";
char strstart[80];	char strstart[80];
char optionfilext[10], optionfilefiname[FILENAMELENGTH];	char optionfilext[10], optionfilefiname[FILENAMELENGTH];
Line 748 double *matprod2(); / test */	Line 833 double *matprod2(); / test */
double oldm, newm, *savm; / Working pointers to matrices */	double oldm, newm, *savm; / Working pointers to matrices */
double oldms, newms, *savms; / Fixed working pointers to matrices */	double oldms, newms, *savms; / Fixed working pointers to matrices */
/FILE fic ; / / Used in readdata only */	/FILE fic ; / / Used in readdata only */
FILE ficpar, ficparo,ficres, ficresp, ficrespl, ficrespij, ficrest,ficresf,*ficrespop;	FILE ficpar, ficparo,ficres, ficresp, ficresphtm, ficresphtmfr, ficrespl, ficrespij, ficrest,ficresf,*ficrespop;
FILE ficlog, ficrespow;	FILE ficlog, ficrespow;
int globpr=0; /* Global variable for printing or not */	int globpr=0; /* Global variable for printing or not */
double fretone; /* Only one call to likelihood */	double fretone; /* Only one call to likelihood */
Line 778 char command[FILENAMELENGTH];	Line 863 char command[FILENAMELENGTH];
int outcmd=0;	int outcmd=0;

char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];	char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
	char fileresu[FILENAMELENGTH]; /* fileres without r in front */
char filelog[FILENAMELENGTH]; /* Log file */	char filelog[FILENAMELENGTH]; /* Log file */
char filerest[FILENAMELENGTH];	char filerest[FILENAMELENGTH];
char fileregp[FILENAMELENGTH];	char fileregp[FILENAMELENGTH];
Line 846 int estepm;	Line 931 int estepm;

int m,nb;	int m,nb;
long *num;	long *num;
int firstpass=0, lastpass=4,cod, Tage,*cens;	int firstpass=0, lastpass=4,cod, cens;
int ncodemax; / ncodemax[j]= Number of modalities of the j th	int ncodemax; / ncodemax[j]= Number of modalities of the j th
covariate for which somebody answered excluding	covariate for which somebody answered excluding
undefined. Usually 2: 0 and 1. */	undefined. Usually 2: 0 and 1. */
Line 866 double covar; /< covar[j,i], value	Line 951 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;
double lsurv, lpop, *tpop;	double lsurv, lpop, *tpop;

Line 901 static int split( char path, char dirc	Line 987 static int split( char path, char dirc
}	}
/* got dirc from getcwd*/	/* got dirc from getcwd*/
printf(" DIRC = %s \n",dirc);	printf(" DIRC = %s \n",dirc);
} else { /* strip direcotry from path */	} else { /* strip directory from path */
ss++; /* after this, the filename */	ss++; /* after this, the filename */
l2 = strlen( ss ); /* length of filename */	l2 = strlen( ss ); /* length of filename */
if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );	if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
Line 1309 char subdirf3(char fileres[], char pre	Line 1395 char subdirf3(char fileres[], char pre
strcat(tmpout,fileres);	strcat(tmpout,fileres);
return tmpout;	return tmpout;
}	}

	/************* function subdirfext *********/
	char subdirfext(char fileres[], char preop, char *postop)
	{

	strcpy(tmpout,preop);
	strcat(tmpout,fileres);
	strcat(tmpout,postop);
	return tmpout;
	}

	/************* function subdirfext3 *********/
	char subdirfext3(char fileres[], char preop, char *postop)
	{

	/* Caution optionfilefiname is hidden */
	strcpy(tmpout,optionfilefiname);
	strcat(tmpout,"/");
	strcat(tmpout,preop);
	strcat(tmpout,fileres);
	strcat(tmpout,postop);
	return tmpout;
	}

char *asc_diff_time(long time_sec, char ascdiff[])	char *asc_diff_time(long time_sec, char ascdiff[])
{	{
long sec_left, days, hours, minutes;	long sec_left, days, hours, minutes;
Line 1573 void linmin(double p[], double xi[], int	Line 1682 void linmin(double p[], double xi[], int
double xx,xmin,bx,ax;	double xx,xmin,bx,ax;
double fx,fb,fa;	double fx,fb,fa;

double scale=10., axs, xxs, xxss; /* Scale added for infinity */	#ifdef LINMINORIGINAL
	#else
	double scale=10., axs, xxs; /* Scale added for infinity */
	#endif

ncom=n;	ncom=n;
pcom=vector(1,n);	pcom=vector(1,n);
xicom=vector(1,n);	xicom=vector(1,n);
nrfunc=func;	nrfunc=func;
for (j=1;j<=n;j++) {	for (j=1;j<=n;j++) {
pcom[j]=p[j];	pcom[j]=p[j];
xicom[j]=xi[j];	xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
}	}

/* axs=0.0; */	#ifdef LINMINORIGINAL
/* xxss=1; /\* 1 and using scale \/ /	xx=1.;
xxs=1;	#else
/* do{ */	axs=0.0;
ax=0.;	xxs=1.;
	do{
xx= xxs;	xx= xxs;
	#endif
	ax=0.;
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]) */
/* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */	/* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
/* xt[x,j]=pcom[j]+xxicom[j] f(ax) = f(xt(a,j=1,n)) = f(p(j) + 0 xi(j)) and f(xx) = f(xt(x, j=1,n)) = f(p(j) + 1 * xi(j)) */	/* xt[x,j]=pcom[j]+xxicom[j] f(ax) = f(xt(a,j=1,n)) = f(p(j) + 0 xi(j)) and f(xx) = f(xt(x, j=1,n)) = f(p(j) + 1 * xi(j)) */
Line 1597 void linmin(double p[], double xi[], int	Line 1712 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){ */	#ifdef LINMINORIGINAL
/* xxs=xxs/scale; /\* Trying a smaller xx, closer to initial ax=0 \/ /	#else
/* 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); */	if (fx != fx){
/* } */	xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
/* }while(fx != fx); */	printf("\|");
	fprintf(ficlog,"\|");
	#ifdef DEBUGLINMIN
	printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n", axs, xxs, fx,fb, fa, xx, ax, bx);
	#endif
	}
	}while(fx != fx);
	#endif

#ifdef DEBUGLINMIN	#ifdef DEBUGLINMIN
printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n", ax,xx,bx,fa,fx,fb);	printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n", ax,xx,bx,fa,fx,fb);
	fprintf(ficlog,"\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n", ax,xx,bx,fa,fx,fb);
#endif	#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]) */
Line 1617 void linmin(double p[], double xi[], int	Line 1740 void linmin(double p[], double xi[], int
#endif	#endif
#ifdef DEBUGLINMIN	#ifdef DEBUGLINMIN
printf("linmin end ");	printf("linmin end ");
	fprintf(ficlog,"linmin end ");
#endif	#endif
for (j=1;j<=n;j++) {	for (j=1;j<=n;j++) {
/* printf(" before xi[%d]=%12.8f", j,xi[j]); */	#ifdef LINMINORIGINAL
xi[j] = xmin; / xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */	xi[j] *= xmin;
/* if(xxs <1.0) */	#else
/* printf(" after xi[%d]=%12.8f, xmin=%12.8f, ax=%12.8f, xx=%12.8f, bx=%12.8f, xxs=%12.8f", j,xi[j], xmin, ax, xx, bx,xxs ); */	#ifdef DEBUGLINMIN
	if(xxs <1.0)
	printf(" before xi[%d]=%12.8f", j,xi[j]);
	#endif
	xi[j] = xminxxs; /* xi rescaled by xmin and number of loops: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
	#ifdef DEBUGLINMIN
	if(xxs <1.0)
	printf(" after xi[%d]=%12.8f, xmin=%12.8f, ax=%12.8f, xx=%12.8f, bx=%12.8f, xxs=%12.8f", j,xi[j], xmin, ax, xx, bx,xxs );
	#endif
	#endif
p[j] += xi[j]; /* Parameters values are updated accordingly */	p[j] += xi[j]; /* Parameters values are updated accordingly */
}	}
/* printf("\n"); */
#ifdef DEBUGLINMIN	#ifdef DEBUGLINMIN
	printf("\n");
printf("Comparing last frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, fret, (*func)(p));	printf("Comparing last frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, fret, (*func)(p));
	fprintf(ficlog,"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++) {	for (j=1;j<=n;j++) {
printf(" xi[%d]= %12.7f p[%d]= %12.7f",j,xi[j],j,p[j]);	printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
if(j % ncovmodel == 0)	fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
	if(j % ncovmodel == 0){
printf("\n");	printf("\n");
	fprintf(ficlog,"\n");
	}
}	}
	#else
#endif	#endif
free_vector(xicom,1,n);	free_vector(xicom,1,n);
free_vector(pcom,1,n);	free_vector(pcom,1,n);
Line 1666 void powell(double p[], double **xi, int	Line 1804 void powell(double p[], double **xi, int
xits=vector(1,n);	xits=vector(1,n);
fret=(func)(p);	fret=(func)(p);
for (j=1;j<=n;j++) pt[j]=p[j];	for (j=1;j<=n;j++) pt[j]=p[j];
rcurr_time = time(NULL);	rcurr_time = time(NULL);
for (iter=1;;++(iter)) {	for (iter=1;;++(iter)) {
fp=(fret); / From former iteration or initial value */	fp=(fret); / From former iteration or initial value */
ibig=0;	ibig=0;
Line 1710 void powell(double p[], double **xi, int	Line 1848 void powell(double p[], double **xi, int
for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */	for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
fptt=(*fret);	fptt=(*fret);
#ifdef DEBUG	#ifdef DEBUG
printf("fret=%lf, %lf, %lf \n", fret, fret, *fret);	printf("fret=%lf, %lf, %lf \n", fret, fret, *fret);
fprintf(ficlog, "fret=%lf, %lf, %lf \n", fret, fret, *fret);	fprintf(ficlog, "fret=%lf, %lf, %lf \n", fret, fret, *fret);
#endif	#endif
printf("%d",i);fflush(stdout); /* print direction (parameter) i */	printf("%d",i);fflush(stdout); /* print direction (parameter) i */
fprintf(ficlog,"%d",i);fflush(ficlog);	fprintf(ficlog,"%d",i);fflush(ficlog);
linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/	linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
/* Outputs are fret(new point p) p is updated and xit rescaled */	/* Outputs are fret(new point p) p is updated and xit rescaled */
Line 1811 void powell(double p[], double **xi, int	Line 1949 void powell(double p[], double **xi, int
t=2.0(fp-2.0(fret)+fptt)SQR(fp-(fret)-del); / Intel compiler doesn't work on one line; bug reported */	t=2.0(fp-2.0(fret)+fptt)SQR(fp-(fret)-del); / Intel compiler doesn't work on one line; bug reported */
t= t- del*SQR(fp-fptt);	t= t- del*SQR(fp-fptt);
#endif	#endif
directest = fp-2.0(fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */	directest = fp-2.0(fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
#ifdef DEBUG	#ifdef DEBUG
printf("t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0(fp-2.0(fret)+fptt)SQR(fp-(fret)-del),delSQR(fp-fptt),t,directest);	printf("t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0(fp-2.0(fret)+fptt)SQR(fp-(fret)-del),delSQR(fp-fptt),t,directest);
fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0(fp-2.0(fret)+fptt)SQR(fp-(fret)-del),delSQR(fp-fptt),t,directest);	fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0(fp-2.0(fret)+fptt)SQR(fp-(fret)-del),delSQR(fp-fptt),t,directest);
Line 1826 void powell(double p[], double **xi, int	Line 1964 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 (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0(fret)+fptt, fp -(*fret) -del, fp-fptt);	printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0(fret)+fptt, fp -(*fret) -del, fp-fptt);
fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);	fprintf(ficlog,"directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
fprintf(ficlog,"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 */
Line 1836 void powell(double p[], double **xi, int	Line 1974 void powell(double p[], double **xi, int
#ifdef DEBUGLINMIN	#ifdef DEBUGLINMIN
printf("Before linmin in direction P%d-P0\n",n);	printf("Before linmin in direction P%d-P0\n",n);
for (j=1;j<=n;j++) {	for (j=1;j<=n;j++) {
printf("Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);	printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
if(j % ncovmodel == 0)	fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
	if(j % ncovmodel == 0){
printf("\n");	printf("\n");
	fprintf(ficlog,"\n");
	}
}	}
#endif	#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	#ifdef DEBUGLINMIN
for (j=1;j<=n;j++) {	for (j=1;j<=n;j++) {
printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);	printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
if(j % ncovmodel == 0)	fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
	if(j % ncovmodel == 0){
printf("\n");	printf("\n");
	fprintf(ficlog,"\n");
	}
}	}
#endif	#endif
for (j=1;j<=n;j++) {	for (j=1;j<=n;j++) {
Line 1876 void powell(double p[], double **xi, int	Line 2020 void powell(double p[], double **xi, int

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

double prevalim(double prlim, int nlstate, double x[], double age, double oldm, double savm, double ftolpl, int ij)	double prevalim(double prlim, int nlstate, double x[], double age, double oldm, double savm, double ftolpl, int *ncvyear, int ij)
{	{
/* Computes the prevalence limit in each live state at age x by left multiplying the unit	/* Computes the prevalence limit in each live state at age x by left multiplying the unit
matrix by transitions matrix until convergence is reached */	matrix by transitions matrix until convergence is reached with precision ftolpl */
	/* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
	/* Wx is row vector: population in state 1, population in state 2, population dead */
	/* or prevalence in state 1, prevalence in state 2, 0 */
	/* newm is the matrix after multiplications, its rows are identical at a factor */
	/* Initial matrix pimij */
	/* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
	/* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
	/* 0, 0 , 1} */
	/*
	* and after some iteration: */
	/* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
	/* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
	/* 0, 0 , 1} */
	/* And prevalence by suppressing the deaths are close to identical rows in prlim: */
	/* {0.51571254859325999, 0.4842874514067399, */
	/* 0.51326036147820708, 0.48673963852179264} */
	/* If we start from prlim again, prlim tends to a constant matrix */

int i, ii,j,k;	int i, ii,j,k;
double min, max, maxmin, maxmax,sumnew=0.;	double min, max, *meandiff, maxmax,sumnew=0.;
/* double *matprod2(); / /* test */	/* double *matprod2(); / /* test */
double out, cov[NCOVMAX+1], pmij();	double out, cov[NCOVMAX+1], pmij();
double **newm;	double **newm;
double agefin, delaymax=50 ; /* Max number of years to converge */	double agefin, delaymax=200. ; /* 100 Max number of years to converge */
	int ncvloop=0;

	min=vector(1,nlstate);
	max=vector(1,nlstate);
	meandiff=vector(1,nlstate);

for (ii=1;ii<=nlstate+ndeath;ii++)	for (ii=1;ii<=nlstate+ndeath;ii++)
for (j=1;j<=nlstate+ndeath;j++){	for (j=1;j<=nlstate+ndeath;j++){
oldm[ii][j]=(ii==j ? 1.0 : 0.0);	oldm[ii][j]=(ii==j ? 1.0 : 0.0);
Line 1896 double prevalim(double prlim, int nl	Line 2062 double prevalim(double prlim, int nl
cov[1]=1.;	cov[1]=1.;

/* Even if hstepm = 1, at least one multiplication by the unit matrix */	/* Even if hstepm = 1, at least one multiplication by the unit matrix */
	/* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){	for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
	ncvloop++;
newm=savm;	newm=savm;
/* Covariates have to be included here again */	/* Covariates have to be included here again */
cov[2]=agefin;	cov[2]=agefin;
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]]);/	cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,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<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,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])]; */
	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];

/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 1920 double prevalim(double prlim, int nl	Line 2091 double prevalim(double prlim, int nl

savm=oldm;	savm=oldm;
oldm=newm;	oldm=newm;
maxmax=0.;
for(j=1;j<=nlstate;j++){	for(j=1; j<=nlstate; j++){
min=1.;	max[j]=0.;
max=0.;	min[j]=1.;
for(i=1; i<=nlstate; i++) {	}
sumnew=0;	for(i=1;i<=nlstate;i++){
for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];	sumnew=0;
	for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
	for(j=1; j<=nlstate; j++){
prlim[i][j]= newm[i][j]/(1-sumnew);	prlim[i][j]= newm[i][j]/(1-sumnew);
/printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);/	max[j]=FMAX(max[j],prlim[i][j]);
max=FMAX(max,prlim[i][j]);	min[j]=FMIN(min[j],prlim[i][j]);
min=FMIN(min,prlim[i][j]);
}	}
maxmin=max-min;	}
maxmax=FMAX(maxmax,maxmin);
	maxmax=0.;
	for(j=1; j<=nlstate; j++){
	meandiff[j]=(max[j]-min[j])/(max[j]+min[j])2.; / mean difference for each column */
	maxmax=FMAX(maxmax,meandiff[j]);
	/* printf(" age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, j, meandiff[j],(int)agefin, j, max[j], j, min[j],maxmax); */
} /* j loop */	} /* j loop */
	*ncvyear= (int)age- (int)agefin;
	/* printf("maxmax=%lf maxmin=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, ncvyear); /
if(maxmax < ftolpl){	if(maxmax < ftolpl){
	/* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, ncvyear); /
	free_vector(min,1,nlstate);
	free_vector(max,1,nlstate);
	free_vector(meandiff,1,nlstate);
return prlim;	return prlim;
}	}
} /* age loop */	} /* age loop */
	/* After some age loop it doesn't converge */
	printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
	Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
	/* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
	free_vector(min,1,nlstate);
	free_vector(max,1,nlstate);
	free_vector(meandiff,1,nlstate);

return prlim; /* should not reach here */	return prlim; /* should not reach here */
}	}

Line 2064 double *hpxij(double *po, int nhstep	Line 2255 double *hpxij(double *po, int nhstep
double **out, cov[NCOVMAX+1];	double **out, cov[NCOVMAX+1];
double **newm;	double **newm;
double agexact;	double agexact;
	double agebegin, ageend;

/* Hstepm could be zero and should return the unit matrix */	/* Hstepm could be zero and should return the unit matrix */
for (i=1;i<=nlstate+ndeath;i++)	for (i=1;i<=nlstate+ndeath;i++)
Line 2077 double *hpxij(double *po, int nhstep	Line 2269 double *hpxij(double *po, int nhstep
newm=savm;	newm=savm;
/* Covariates have to be included here again */	/* Covariates have to be included here again */
cov[1]=1.;	cov[1]=1.;
agexact=age+((h-1)hstepm + (d-1))stepm/YEARM;	agexact=age+((h-1)hstepm + (d-1))stepm/YEARM; /* age just before transition */
cov[2]=agexact;	cov[2]=agexact;
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,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,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,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
	/* 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 2445 double funcone( double *x)	Line 2640 double funcone( double *x)
int s1, s2;	int s1, s2;
double bbh, survp;	double bbh, survp;
double agexact;	double agexact;
	double agebegin, ageend;
/extern weight /	/extern weight /
/* We are differentiating ll according to initial status */	/* We are differentiating ll according to initial status */
/* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/	/* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
Line 2463 double funcone( double *x)	Line 2659 double funcone( double *x)
oldm[ii][j]=(ii==j ? 1.0 : 0.0);	oldm[ii][j]=(ii==j ? 1.0 : 0.0);
savm[ii][j]=(ii==j ? 1.0 : 0.0);	savm[ii][j]=(ii==j ? 1.0 : 0.0);
}	}
for(d=0; d<dh[mi][i]; d++){
	agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
	ageend=agev[mw[mi][i]][i] + (dh[mi][i])stepm/YEARM; / Age at end of effective wave and at the end of transition */
	for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */
	/*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
	and mw[mi+1][i]. dh depends on stepm.*/
newm=savm;	newm=savm;
agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;	agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
cov[2]=agexact;	cov[2]=agexact;
Line 2511 double funcone( double *x)	Line 2712 double funcone( double *x)
ll[s[mw[mi][i]][i]] += 2weight[i]lli;	ll[s[mw[mi][i]][i]] += 2weight[i]lli;
/printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); /	/printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); /
if(globpr){	if(globpr){
fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\	fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f %8.3f\
%11.6f %11.6f %11.6f ", \	%11.6f %11.6f %11.6f ", \
num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],	num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
2weight[i]lli,out[s1][s2],savm[s1][s2]);	2weight[i]lli,out[s1][s2],savm[s1][s2]);
for(k=1,llt=0.,l=0.; k<=nlstate; k++){	for(k=1,llt=0.,l=0.; k<=nlstate; k++){
llt +=ll[k]*gipmx/gsw;	llt +=ll[k]*gipmx/gsw;
Line 2545 void likelione(FILE *ficres,double p[],	Line 2746 void likelione(FILE *ficres,double p[],
int k;	int k;

if(globpri !=0){ / Just counts and sums, no printings */	if(globpri !=0){ / Just counts and sums, no printings */
strcpy(fileresilk,"ilk");	strcpy(fileresilk,"ILK_");
strcat(fileresilk,fileres);	strcat(fileresilk,fileresu);
if((ficresilk=fopen(fileresilk,"w"))==NULL) {	if((ficresilk=fopen(fileresilk,"w"))==NULL) {
printf("Problem with resultfile: %s\n", fileresilk);	printf("Problem with resultfile: %s\n", fileresilk);
fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);	fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
}	}
fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2llweightXnumber_of_contribs/sum_of_weights) and_total\n");	fprintf(ficresilk, "#individual(line's_record) count ageb ageend s1 s2 wave# effective_wave# number_of_matrices_product pij weight weight/gpw -2ln(pij)weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2llweightXnumber_of_contribs/sum_of_weights) and_total\n");
fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");	fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
/* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2weight[i]lli,out[s1][s2],savm[s1][s2]); */	/* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2weight[i]lli,out[s1][s2],savm[s1][s2]); */
for(k=1; k<=nlstate; k++)	for(k=1; k<=nlstate; k++)
fprintf(ficresilk," -2gipw/gswweight*ll[%d]++",k);	fprintf(ficresilk," -2gipw/gswweight*ll[%d]++",k);
Line 2562 void likelione(FILE *ficres,double p[],	Line 2763 void likelione(FILE *ficres,double p[],
fretone=(funcone)(p);	fretone=(funcone)(p);
if(*globpri !=0){	if(*globpri !=0){
fclose(ficresilk);	fclose(ficresilk);
fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));	if (mle ==0)
fflush(fichtm);	fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
}	else if(mle >=1)
	fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
	fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));


	for (k=1; k<= nlstate ; k++) {
	fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Dot's sizes are related to corresponding weight: <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
	<img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
	}
	fprintf(fichtm,"<br>- The function drawn is -2Log(L) in Log scale: by state of origin <a href=\"%s-ori.png\">%s-ori.png</a><br> \
	<img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
	fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
	<img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
	fflush(fichtm);
	}
return;	return;
}	}

Line 2595 void mlikeli(FILE *ficres,double p[], in	Line 2810 void mlikeli(FILE *ficres,double p[], in
for (j=1;j<=npar;j++)	for (j=1;j<=npar;j++)
xi[i][j]=(i==j ? 1.0 : 0.0);	xi[i][j]=(i==j ? 1.0 : 0.0);
printf("Powell\n"); fprintf(ficlog,"Powell\n");	printf("Powell\n"); fprintf(ficlog,"Powell\n");
strcpy(filerespow,"pow");	strcpy(filerespow,"POW_");
strcat(filerespow,fileres);	strcat(filerespow,fileres);
if((ficrespow=fopen(filerespow,"w"))==NULL) {	if((ficrespow=fopen(filerespow,"w"))==NULL) {
printf("Problem with resultfile: %s\n", filerespow);	printf("Problem with resultfile: %s\n", filerespow);
Line 2638 void mlikeli(FILE *ficres,double p[], in	Line 2853 void mlikeli(FILE *ficres,double p[], in
#endif	#endif
free_matrix(xi,1,npar,1,npar);	free_matrix(xi,1,npar,1,npar);
fclose(ficrespow);	fclose(ficrespow);
printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));	printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));	fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));	fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));

}	}

/** Computes Hessian and covariance matrix */	/** Computes Hessian and covariance matrix */
void hesscov(double *matcov, double p[], int npar, double delti[], double ftolhess, double (func)(double []))	void hesscov(double matcov, double hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
{	{
double a,y,*x,pd;	double a,y,*x,pd;
double **hess;	/* double *hess; /
int i, j;	int i, j;
int *indx;	int *indx;

double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);	double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);	double hessij(double p[], double *hess, double delti[], int i, int j,double (func)(double []),int npar);
void lubksb(double *a, int npar, int indx, double b[]) ;	void lubksb(double *a, int npar, int indx, double b[]) ;
void ludcmp(double *a, int npar, int indx, double *d) ;	void ludcmp(double *a, int npar, int indx, double *d) ;
double gompertz(double p[]);	double gompertz(double p[]);
hess=matrix(1,npar,1,npar);	/* hess=matrix(1,npar,1,npar); */

printf("\nCalculation of the hessian matrix. Wait...\n");	printf("\nCalculation of the hessian matrix. Wait...\n");
fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");	fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
for (i=1;i<=npar;i++){	for (i=1;i<=npar;i++){
printf("%d",i);fflush(stdout);	printf("%d-",i);fflush(stdout);
fprintf(ficlog,"%d",i);fflush(ficlog);	fprintf(ficlog,"%d-",i);fflush(ficlog);

hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);	hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);

Line 2674 void hesscov(double **matcov, double p[]	Line 2889 void hesscov(double **matcov, double p[]
for (i=1;i<=npar;i++) {	for (i=1;i<=npar;i++) {
for (j=1;j<=npar;j++) {	for (j=1;j<=npar;j++) {
if (j>i) {	if (j>i) {
printf(".%d%d",i,j);fflush(stdout);	printf(".%d-%d",i,j);fflush(stdout);
fprintf(ficlog,".%d%d",i,j);fflush(ficlog);	fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
hess[i][j]=hessij(p,delti,i,j,func,npar);	hess[i][j]=hessij(p,hess, delti,i,j,func,npar);

hess[j][i]=hess[i][j];	hess[j][i]=hess[i][j];
/printf(" %lf ",hess[i][j]);/	/printf(" %lf ",hess[i][j]);/
Line 2710 void hesscov(double **matcov, double p[]	Line 2925 void hesscov(double **matcov, double p[]
fprintf(ficlog,"\n#Hessian matrix#\n");	fprintf(ficlog,"\n#Hessian matrix#\n");
for (i=1;i<=npar;i++) {	for (i=1;i<=npar;i++) {
for (j=1;j<=npar;j++) {	for (j=1;j<=npar;j++) {
printf("%.3e ",hess[i][j]);	printf("%.6e ",hess[i][j]);
fprintf(ficlog,"%.3e ",hess[i][j]);	fprintf(ficlog,"%.6e ",hess[i][j]);
}	}
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
}	}

	/* printf("\n#Covariance matrix#\n"); */
	/* fprintf(ficlog,"\n#Covariance matrix#\n"); */
	/* for (i=1;i<=npar;i++) { */
	/* for (j=1;j<=npar;j++) { */
	/* printf("%.6e ",matcov[i][j]); */
	/* fprintf(ficlog,"%.6e ",matcov[i][j]); */
	/* } */
	/* printf("\n"); */
	/* fprintf(ficlog,"\n"); */
	/* } */

/* Recompute Inverse */	/* Recompute Inverse */
for (i=1;i<=npar;i++)	/* for (i=1;i<=npar;i++) */
for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];	/* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
ludcmp(a,npar,indx,&pd);	/* ludcmp(a,npar,indx,&pd); */

	/* printf("\n#Hessian matrix recomputed#\n"); */

	/* for (j=1;j<=npar;j++) { */
	/* for (i=1;i<=npar;i++) x[i]=0; */
	/* x[j]=1; */
	/* lubksb(a,npar,indx,x); */
	/* for (i=1;i<=npar;i++){ */
	/* y[i][j]=x[i]; */
	/* printf("%.3e ",y[i][j]); */
	/* fprintf(ficlog,"%.3e ",y[i][j]); */
	/* } */
	/* printf("\n"); */
	/* fprintf(ficlog,"\n"); */
	/* } */

/* printf("\n#Hessian matrix recomputed#\n");	/* Verifying the inverse matrix */
	#ifdef DEBUGHESS
	y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);

	printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
	fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");

for (j=1;j<=npar;j++) {	for (j=1;j<=npar;j++) {
for (i=1;i<=npar;i++) x[i]=0;
x[j]=1;
lubksb(a,npar,indx,x);
for (i=1;i<=npar;i++){	for (i=1;i<=npar;i++){
y[i][j]=x[i];	printf("%.2f ",y[i][j]);
printf("%.3e ",y[i][j]);	fprintf(ficlog,"%.2f ",y[i][j]);
fprintf(ficlog,"%.3e ",y[i][j]);
}	}
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
}	}
*/	#endif

free_matrix(a,1,npar,1,npar);	free_matrix(a,1,npar,1,npar);
free_matrix(y,1,npar,1,npar);	free_matrix(y,1,npar,1,npar);
free_vector(x,1,npar);	free_vector(x,1,npar);
free_ivector(indx,1,npar);	free_ivector(indx,1,npar);
free_matrix(hess,1,npar,1,npar);	/* free_matrix(hess,1,npar,1,npar); */


}	}

/************* hessian matrix **************/	/************* hessian matrix **************/
double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)	double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
{	{ /* Around values of x, computes the function func and returns the scales delti and hessian */
int i;	int i;
int l=1, lmax=20;	int l=1, lmax=20;
double k1,k2;	double k1,k2, res, fx;
double p2[MAXPARM+1]; /* identical to x */	double p2[MAXPARM+1]; /* identical to x */
double res;
double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;	double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
double fx;
int k=0,kmax=10;	int k=0,kmax=10;
double l1;	double l1;

Line 2772 double hessii(double x[], double delta,	Line 3012 double hessii(double x[], double delta,
p2[theta]=x[theta]-delt;	p2[theta]=x[theta]-delt;
k2=func(p2)-fx;	k2=func(p2)-fx;
/res= (k1-2.0fx+k2)/delt/delt; */	/res= (k1-2.0fx+k2)/delt/delt; */
res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2L /	res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2L /

#ifdef DEBUGHESS	#ifdef DEBUGHESSII
printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);	printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);	fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
#endif	#endif
Line 2788 double hessii(double x[], double delta,	Line 3028 double hessii(double x[], double delta,
else if((k1 >khi/nkhi) \|\| (k2 >khi/nkhi)){	else if((k1 >khi/nkhi) \|\| (k2 >khi/nkhi)){
delts=delt;	delts=delt;
}	}
}	} /* End loop k */
}	}
delti[theta]=delts;	delti[theta]=delts;
return res;	return res;

}	}

double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)	double hessij( double x[], double *hess, double delti[], int thetai,int thetaj,double (func)(double []),int npar)
{	{
int i;	int i;
int l=1, lmax=20;	int l=1, lmax=20;
double k1,k2,k3,k4,res,fx;	double k1,k2,k3,k4,res,fx;
double p2[MAXPARM+1];	double p2[MAXPARM+1];
int k;	int k, kmax=1;
	double v1, v2, cv12, lc1, lc2;

	int firstime=0;

fx=func(x);	fx=func(x);
for (k=1; k<=2; k++) {	for (k=1; k<=kmax; k=k+10) {
for (i=1;i<=npar;i++) p2[i]=x[i];	for (i=1;i<=npar;i++) p2[i]=x[i];
p2[thetai]=x[thetai]+delti[thetai]/k;	p2[thetai]=x[thetai]+delti[thetai]*k;
p2[thetaj]=x[thetaj]+delti[thetaj]/k;	p2[thetaj]=x[thetaj]+delti[thetaj]*k;
k1=func(p2)-fx;	k1=func(p2)-fx;

p2[thetai]=x[thetai]+delti[thetai]/k;	p2[thetai]=x[thetai]+delti[thetai]*k;
p2[thetaj]=x[thetaj]-delti[thetaj]/k;	p2[thetaj]=x[thetaj]-delti[thetaj]*k;
k2=func(p2)-fx;	k2=func(p2)-fx;

p2[thetai]=x[thetai]-delti[thetai]/k;	p2[thetai]=x[thetai]-delti[thetai]*k;
p2[thetaj]=x[thetaj]+delti[thetaj]/k;	p2[thetaj]=x[thetaj]+delti[thetaj]*k;
k3=func(p2)-fx;	k3=func(p2)-fx;

p2[thetai]=x[thetai]-delti[thetai]/k;	p2[thetai]=x[thetai]-delti[thetai]*k;
p2[thetaj]=x[thetaj]-delti[thetaj]/k;	p2[thetaj]=x[thetaj]-delti[thetaj]*k;
k4=func(p2)-fx;	k4=func(p2)-fx;
res=(k1-k2-k3+k4)/4.0/delti[thetai]k/delti[thetaj]k/2.; /* Because of L not 2L /	res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2L /
#ifdef DEBUG	if(k1k2k3*k4 <0.){
printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);	firstime=1;
fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);	kmax=kmax+10;
	}
	if(kmax >=10 \|\| firstime ==1){
	printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
	fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
	printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e deltik=%.12e deltjk=%.12e, xi-dek=%.12e xj-dek=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
	fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e deltik=%.12e deltjk=%.12e, xi-dek=%.12e xj-dek=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
	}
	#ifdef DEBUGHESSIJ
	v1=hess[thetai][thetai];
	v2=hess[thetaj][thetaj];
	cv12=res;
	/* Computing eigen value of Hessian matrix */
	lc1=((v1+v2)+sqrt((v1+v2)(v1+v2) - 4(v1v2-cv12cv12)))/2.;
	lc2=((v1+v2)-sqrt((v1+v2)(v1+v2) - 4(v1v2-cv12cv12)))/2.;
	if ((lc2 <0) \|\| (lc1 <0) ){
	printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
	fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
	printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
	fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
	}
#endif	#endif
}	}
return res;	return res;
}	}

	/* Not done yet: Was supposed to fix if not exactly at the maximum */
	/* double hessij( double x[], double delti[], int thetai,int thetaj,double (func)(double []),int npar) /
	/* { */
	/* int i; */
	/* int l=1, lmax=20; */
	/* double k1,k2,k3,k4,res,fx; */
	/* double p2[MAXPARM+1]; */
	/* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
	/* int k=0,kmax=10; */
	/* double l1; */

	/* fx=func(x); */
	/* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum \/ /
	/* l1=pow(10,l); */
	/* delts=delt; */
	/* for(k=1 ; k <kmax; k=k+1){ */
	/* delt = delti(l1k); */
	/* for (i=1;i<=npar;i++) p2[i]=x[i]; */
	/* p2[thetai]=x[thetai]+delti[thetai]/k; */
	/* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
	/* k1=func(p2)-fx; */

	/* p2[thetai]=x[thetai]+delti[thetai]/k; */
	/* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
	/* k2=func(p2)-fx; */

	/* p2[thetai]=x[thetai]-delti[thetai]/k; */
	/* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
	/* k3=func(p2)-fx; */

	/* p2[thetai]=x[thetai]-delti[thetai]/k; */
	/* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
	/* k4=func(p2)-fx; */
	/* res=(k1-k2-k3+k4)/4.0/delti[thetai]k/delti[thetaj]k/2.; /\* Because of L not 2L \/ */
	/* #ifdef DEBUGHESSIJ */
	/* printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); */
	/* fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); */
	/* #endif */
	/* if((k1 <khi/nkhi/2.) \|\| (k2 <khi/nkhi/2.)\|\| (k4 <khi/nkhi/2.)\|\| (k4 <khi/nkhi/2.)){ */
	/* k=kmax; */
	/* } */
	/* else if((k1 >khi/nkhif) \|\| (k2 >khi/nkhif) \|\| (k4 >khi/nkhif) \|\| (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. \/ /
	/* k=kmax; l=lmax10; /
	/* } */
	/* else if((k1 >khi/nkhi) \|\| (k2 >khi/nkhi)){ */
	/* delts=delt; */
	/* } */
	/* } /\* End loop k \/ /
	/* } */
	/* delti[theta]=delts; */
	/* return res; */
	/* } */


/************ Inverse of matrix ************/	/************ Inverse of matrix ************/
void ludcmp(double *a, int n, int indx, double *d)	void ludcmp(double *a, int n, int indx, double *d)
{	{
Line 2906 void lubksb(double *a, int n, int indx	Line 3223 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 ******************/
void freqsummary(char fileres[], int iagemin, int iagemax, int s, double agev, int nlstate, int imx, int Tvaraff, int nbcode, int ncodemax,double mint,double anint, char strstart[])	void freqsummary(char fileres[], int iagemin, int iagemax, int s, double agev, int nlstate, int imx, \
	int Tvaraff, int nbcode, int ncodemax,double mint,double anint, char strstart[],\
	int firstpass, int lastpass, int stepm, int weightopt, char model[])
{ /* Some frequencies */	{ /* Some frequencies */

int i, m, jk, j1, bool, z1,j;	int i, m, jk, j1, bool, z1,j;
	int mi; /* Effective wave */
int first;	int first;
double **freq; / Frequencies */	double **freq; / Frequencies */
double pp, *prop;	double pp, *prop;
double pos,posprop, k2, dateintsum=0,k2cpt=0;	double pos,posprop, k2, dateintsum=0,k2cpt=0;
char fileresp[FILENAMELENGTH];	char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
	double agebegin, ageend;

pp=vector(1,nlstate);	pp=vector(1,nlstate);
prop=matrix(1,nlstate,iagemin,iagemax+3);	prop=matrix(1,nlstate,iagemin,iagemax+3);
strcpy(fileresp,"p");	strcpy(fileresp,"P_");
strcat(fileresp,fileres);	strcat(fileresp,fileresu);
	/strcat(fileresphtm,fileresu);/
if((ficresp=fopen(fileresp,"w"))==NULL) {	if((ficresp=fopen(fileresp,"w"))==NULL) {
printf("Problem with prevalence resultfile: %s\n", fileresp);	printf("Problem with prevalence resultfile: %s\n", fileresp);
fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);	fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
exit(0);	exit(0);
}	}

	strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
	if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
	printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
	fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
	fflush(ficlog);
	exit(70);
	}
	else{
	fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
	<hr size=\"2\" color=\"#EC5E5E\"> \n\
	Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
	fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
	}
	fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition</h4>\n",fileresphtm, fileresphtm);

	strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
	if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
	printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
	fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
	fflush(ficlog);
	exit(70);
	}
	else{
	fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
	<hr size=\"2\" color=\"#EC5E5E\"> \n\
	Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
	fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
	}
	fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions by age at begin of transition </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);

freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);	freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
j1=0;	j1=0;

Line 2937 void freqsummary(char fileres[], int ia	Line 3290 void freqsummary(char fileres[], int ia

first=1;	first=1;

/* for(k1=1; k1<=j ; k1++){ / / Loop on covariates */	for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ /* Loop on covariates combination */
/* for(i1=1; i1<=ncodemax[k1];i1++){ / / Now it is 2 */
/* j1++; */
for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
/*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);	/*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
scanf("%d", i);*/	scanf("%d", i);*/
for (i=-5; i<=nlstate+ndeath; i++)	for (i=-5; i<=nlstate+ndeath; i++)
Line 2954 void freqsummary(char fileres[], int ia	Line 3304 void freqsummary(char fileres[], int ia

dateintsum=0;	dateintsum=0;
k2cpt=0;	k2cpt=0;
for (i=1; i<=imx; i++) {	for (i=1; i<=imx; i++) { /* For each individual i */
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*/
}	}
}	} /* cptcovn > 0 */

if (bool==1){	if (bool==1){
for(m=firstpass; m<=lastpass; m++){	/* for(m=firstpass; m<=lastpass; m++){ */
k2=anint[m][i]+(mint[m][i]/12.);	for(mi=1; mi<wav[i];mi++){
/if ((k2>=dateprev1) && (k2<=dateprev2)) {/	m=mw[mi][i];
if(agev[m][i]==0) agev[m][i]=iagemax+1;	/* dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective (mi) waves m=mw[mi][i]
if(agev[m][i]==1) agev[m][i]=iagemax+2;	and mw[mi+1][i]. dh depends on stepm. */
if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];	agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
	ageend=agev[m][i]+(dh[m][i])stepm/YEARM; / Age at end of wave and transition */
	if(m >=firstpass && m <=lastpass){
	k2=anint[m][i]+(mint[m][i]/12.);
	/if ((k2>=dateprev1) && (k2<=dateprev2)) {/
	if(agev[m][i]==0) agev[m][i]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
	if(agev[m][i]==1) agev[m][i]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
	if (s[m][i]>0 && s[m][i]<=nlstate) /* If status at wave m is known and a live state */
	prop[s[m][i]][(int)agev[m][i]] += weight[i]; /* At age of beginning of transition, where status is known */
if (m<lastpass) {	if (m<lastpass) {
freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];	/* if(s[m][i]==4 && s[m+1][i]==4) */
freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];	/* printf(" num=%ld m=%d, i=%d s1=%d s2=%d agev at m=%d\n", num[i], m, i,s[m][i],s[m+1][i], (int)agev[m][i]); */
}	if(s[m][i]==-1)
	printf(" num=%ld m=%d, i=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[i], m, i,s[m][i],s[m+1][i], (int)agev[m][i],agebegin, ageend, (int)((agebegin+ageend)/2.));
if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {	freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; /* At age of beginning of transition, where status is known */
dateintsum=dateintsum+k2;	/* freq[s[m][i]][s[m+1][i]][(int)((agebegin+ageend)/2.)] += weight[i]; */
k2cpt++;	freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i]; /* Total is in iagemax+3 // At age of beginning of transition, where status is known */
}	}
/}/	}
}	if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3)) && (anint[m][i]!=9999) && (mint[m][i]!=99)) {
}	dateintsum=dateintsum+k2;
} /* end i */	k2cpt++;
	/* printf("i=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",i, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
	}
	/}/
	} /* end m */
	} /* end bool */
	} /* end i = 1 to imx */

/* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/	/* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
pstamp(ficresp);	pstamp(ficresp);
if (cptcovn>0) {	if (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]]);	fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
fprintf(ficresp, "**********\n#");	fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
	for (z1=1; z1<=cptcoveff; z1++){
	fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
	fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
	fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
	}
	fprintf(ficresp, "**********\n#");
	fprintf(ficresphtm, "**********</h3>\n");
	fprintf(ficresphtmfr, "**********</h3>\n");
fprintf(ficlog, "\n#********** Variable ");	fprintf(ficlog, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][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++)	fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
	for(i=1; i<=nlstate;i++) {
fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);	fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
	fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
	}
fprintf(ficresp, "\n");	fprintf(ficresp, "\n");
	fprintf(ficresphtm, "\n");

	/* Header of frequency table by age */
	fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
	fprintf(ficresphtmfr,"<th>Age</th> ");
	for(jk=-1; jk <=nlstate+ndeath; jk++){
	for(m=-1; m <=nlstate+ndeath; m++){
	if(jk!=0 && m!=0)
	fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
	}
	}
	fprintf(ficresphtmfr, "\n");

	/* For each age */
for(i=iagemin; i <= iagemax+3; i++){	for(i=iagemin; i <= iagemax+3; i++){
if(i==iagemax+3){	fprintf(ficresphtm,"<tr>");
	if(i==iagemax+1){
	fprintf(ficlog,"1");
	fprintf(ficresphtmfr,"<tr><th>0</th> ");
	}else if(i==iagemax+2){
	fprintf(ficlog,"0");
	fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
	}else if(i==iagemax+3){
fprintf(ficlog,"Total");	fprintf(ficlog,"Total");
	fprintf(ficresphtmfr,"<tr><th>Total</th> ");
}else{	}else{
if(first==1){	if(first==1){
first=0;	first=0;
printf("See log file for details...\n");	printf("See log file for details...\n");
}	}
	fprintf(ficresphtmfr,"<tr><th>%d</th> ",i);
fprintf(ficlog,"Age %d", i);	fprintf(ficlog,"Age %d", i);
}	}
for(jk=1; jk <=nlstate ; jk++){	for(jk=1; jk <=nlstate ; jk++){
Line 3053 void freqsummary(char fileres[], int ia	Line 3450 void freqsummary(char fileres[], int ia
if( i <= iagemax){	if( i <= iagemax){
if(pos>=1.e-5){	if(pos>=1.e-5){
fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);	fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
	fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",i,prop[jk][i]/posprop, prop[jk][i],posprop);
/probs[i][jk][j1]= pp[jk]/pos;/	/probs[i][jk][j1]= pp[jk]/pos;/
/printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);/	/printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);/
}	}
else	else{
fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);	fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
	fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",i, prop[jk][i],posprop);
	}
}	}
}	}

for(jk=-1; jk <=nlstate+ndeath; jk++)	for(jk=-1; jk <=nlstate+ndeath; jk++){
for(m=-1; m <=nlstate+ndeath; m++)	for(m=-1; m <=nlstate+ndeath; m++){
if(freq[jk][m][i] !=0 ) {	if(freq[jk][m][i] !=0 ) { /* minimizing output */
if(first==1)	if(first==1){
printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);	printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
	}
fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);	fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
}	}
if(i <= iagemax)	if(jk!=0 && m!=0)
	fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][i]);
	}
	}
	fprintf(ficresphtmfr,"</tr>\n ");
	if(i <= iagemax){
fprintf(ficresp,"\n");	fprintf(ficresp,"\n");
	fprintf(ficresphtm,"</tr>\n");
	}
if(first==1)	if(first==1)
printf("Others in log...\n");	printf("Others in log...\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
}	} /* end loop i */
	fprintf(ficresphtm,"</table>\n");
	fprintf(ficresphtmfr,"</table>\n");
/}/	/}/
}	} /* end j1 */
dateintmean=dateintsum/k2cpt;	dateintmean=dateintsum/k2cpt;

fclose(ficresp);	fclose(ficresp);
	fclose(ficresphtm);
	fclose(ficresphtmfr);
free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);	free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
free_vector(pp,1,nlstate);	free_vector(pp,1,nlstate);
free_matrix(prop,1,nlstate,iagemin, iagemax+3);	free_matrix(prop,1,nlstate,iagemin, iagemax+3);
Line 3094 void prevalence(double ***probs, double	Line 3506 void prevalence(double ***probs, double
*/	*/

int i, m, jk, j1, bool, z1,j;	int i, m, jk, j1, bool, z1,j;
	int mi; /* Effective wave */
	int iage;
	double agebegin, ageend;

double **prop;	double **prop;
double posprop;	double posprop;
Line 3113 void prevalence(double ***probs, double	Line 3528 void prevalence(double ***probs, double

first=1;	first=1;
for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){	for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
/*for(i1=1; i1<=ncodemax[k1];i1++){	for (i=1; i<=nlstate; i++)
j1++;*/	for(iage=iagemin; iage <= iagemax+3; iage++)
	prop[i][iage]=0.0;
for (i=1; i<=nlstate; i++)
for(m=iagemin; m <= iagemax+3; m++)	for (i=1; i<=imx; i++) { /* Each individual */
prop[i][m]=0.0;	bool=1;
	if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
for (i=1; i<=imx; i++) { /* Each individual */	for (z1=1; z1<=cptcoveff; z1++)
bool=1;	if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
if (cptcovn>0) {	bool=0;
for (z1=1; z1<=cptcoveff; z1++)	}
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])	if (bool==1) {
bool=0;	/* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews\/ /
}	for(mi=1; mi<wav[i];mi++){
if (bool==1) {	m=mw[mi][i];
for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/	agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
	/* ageend=agev[m][i]+(dh[m][i])stepm/YEARM; /\ Age at end of wave and transition \/ /
	if(m >=firstpass && m <=lastpass){
y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */	y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */	if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
if(agev[m][i]==0) agev[m][i]=iagemax+1;	if(agev[m][i]==0) agev[m][i]=iagemax+1;
if(agev[m][i]==1) agev[m][i]=iagemax+2;	if(agev[m][i]==1) agev[m][i]=iagemax+2;
if((int)agev[m][i] <iagemin \|\| (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m);	if((int)agev[m][i] <iagemin \|\| (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m);
if (s[m][i]>0 && s[m][i]<=nlstate) {	if (s[m][i]>0 && s[m][i]<=nlstate) {
/if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);/	/if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);/
prop[s[m][i]][(int)agev[m][i]] += weight[i];	prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
prop[s[m][i]][iagemax+3] += weight[i];	prop[s[m][i]][iagemax+3] += weight[i];
}	} /* end valid statuses */
}	} /* end selection of dates */
} /* end selection of waves */	} /* end selection of waves */
}	} /* end effective waves */
}	} /* end bool */
for(i=iagemin; i <= iagemax+3; i++){	}
for(jk=1,posprop=0; jk <=nlstate ; jk++) {	for(i=iagemin; i <= iagemax+3; i++){
posprop += prop[jk][i];	for(jk=1,posprop=0; jk <=nlstate ; jk++) {
}	posprop += prop[jk][i];
	}
for(jk=1; jk <=nlstate ; jk++){
if( i <= iagemax){	for(jk=1; jk <=nlstate ; jk++){
if(posprop>=1.e-5){	if( i <= iagemax){
probs[i][jk][j1]= prop[jk][i]/posprop;	if(posprop>=1.e-5){
} else{	probs[i][jk][j1]= prop[jk][i]/posprop;
if(first==1){	} else{
first=0;	if(first==1){
printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);	first=0;
}	printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
}	}
}	}
}/* end jk */	}
}/* end i */	}/* end jk */
	}/* end i */
/} //* end i1 */	/} //* end i1 */
} /* end j1 */	} /* end j1 */

Line 3183 void concatwav(int wav[], int **dh, int	Line 3601 void concatwav(int wav[], int **dh, int
int i, mi, m;	int i, mi, m;
/* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;	/* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
double sum=0., jmean=0.;*/	double sum=0., jmean=0.;*/
int first;	int first, firstwo;
int j, k=0,jk, ju, jl;	int j, k=0,jk, ju, jl;
double sum=0.;	double sum=0.;
first=0;	first=0;
	firstwo=0;
jmin=100000;	jmin=100000;
jmax=-1;	jmax=-1;
jmean=0.;	jmean=0.;
for(i=1; i<=imx; i++){	for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
mi=0;	mi=0;
m=firstpass;	m=firstpass;
while(s[m][i] <= nlstate){	while(s[m][i] <= nlstate){ /* a live state */
if(s[m][i]>=1 \|\| s[m][i]==-2 \|\| s[m][i]==-4 \|\| s[m][i]==-5)	if(s[m][i]>=1 \|\| s[m][i]==-2 \|\| s[m][i]==-4 \|\| s[m][i]==-5)
mw[++mi][i]=m;	mw[++mi][i]=m;
if(m >=lastpass)	if(m >=lastpass)
Line 3201 void concatwav(int wav[], int **dh, int	Line 3620 void concatwav(int wav[], int **dh, int
else	else
m++;	m++;
}/* end while */	}/* end while */
if (s[m][i] > nlstate){	if (s[m][i] > nlstate){ /* In a death state */
mi++; /* Death is another wave */	mi++; /* Death is another wave */
/* if(mi==0) never been interviewed correctly before death */	/* if(mi==0) never been interviewed correctly before death */
/* Only death is a correct wave */	/* Only death is a correct wave */
mw[mi][i]=m;	mw[mi][i]=m;
	}else if (andc[i] != 9999) { /* A death occured after lastpass */
	m++;
	mi++;
	s[m][i]=nlstate+1; /* We are setting the status to the last of non live state */
	mw[mi][i]=m;
	nbwarn++;
	if(firstwo==0){
	printf("Warning! Death for individual %ld line=%d occurred after last wave %d. Since 0.98r4 we considered a status %d at wave %d\nOthers in log file only\n",num[i],i,lastpass,nlstate+1, m);
	fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred after last wave %d. Since 0.98r4 we considered a status %d at wave %d\n",num[i],i,lastpass,nlstate+1, m);
	firstwo=1;
	}
	if(firstwo==1){
	fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred after last wave %d. Since 0.98r4 we considered a status %d at wave %d\n",num[i],i,lastpass,nlstate+1, m);
	}
}	}

wav[i]=mi;	wav[i]=mi;
if(mi==0){	if(mi==0){
nbwarn++;	nbwarn++;
Line 3220 void concatwav(int wav[], int **dh, int	Line 3652 void concatwav(int wav[], int **dh, int
}	}
} /* end mi==0 */	} /* end mi==0 */
} /* End individuals */	} /* End individuals */
	/* wav and mw are no more changed */


for(i=1; i<=imx; i++){	for(i=1; i<=imx; i++){
for(mi=1; mi<wav[i];mi++){	for(mi=1; mi<wav[i];mi++){
if (stepm <=0)	if (stepm <=0)
Line 3390 void tricode(int Tvar, int *nbcode, in	Line 3824 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=0; /* 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 or from -1 to 1*/	for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
if (Ndum[i] == 0) { /* If at least one individual responded to this modality k */	if (Ndum[i] == 0) { /* If nobody responded to this modality k */
break;	break;
}	}
ij++;	ij++;
nbcode[Tvar[j]][ij]=i; /* stores the original modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/	nbcode[Tvar[j]][ij]=i; /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/
cptcode = ij; /* New max modality for covar j */	cptcode = ij; /* New max modality for covar j */
} /* end of loop on modality i=-1 to 1 or more */	} /* end of loop on modality i=-1 to 1 or more */

Line 3761 void cvevsij(double ***eij, double x[],	Line 4196 void cvevsij(double ***eij, double x[],
}	}

/********** Variance ****************/	/********** Variance ****************/
void varevsij(char optionfilefiname[], double *vareij, double matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double oldm, double savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])	void varevsij(char optionfilefiname[], double *vareij, double matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double oldm, double savm, double *prlim, double ftolpl, int ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
{	{
/* Variance of health expectancies */	/* Variance of health expectancies */
/* double prevalim(double prlim, int nlstate, double xp, double age, double oldm, double * savm,double ftolpl);*/	/* double prevalim(double prlim, int nlstate, double xp, double age, double oldm, double * savm,double ftolpl);*/
Line 3790 void varevsij(char optionfilefiname[], d	Line 4225 void varevsij(char optionfilefiname[], d

if(popbased==1){	if(popbased==1){
if(mobilav!=0)	if(mobilav!=0)
strcpy(digitp,"-populbased-mobilav-");	strcpy(digitp,"-POPULBASED-MOBILAV_");
else strcpy(digitp,"-populbased-nomobil-");	else strcpy(digitp,"-POPULBASED-NOMOBIL_");
}	}
else	else
strcpy(digitp,"-stablbased-");	strcpy(digitp,"-STABLBASED_");

if (mobilav!=0) {	if (mobilav!=0) {
mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);	mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
Line 3804 void varevsij(char optionfilefiname[], d	Line 4239 void varevsij(char optionfilefiname[], d
}	}
}	}

strcpy(fileresprobmorprev,"prmorprev");	strcpy(fileresprobmorprev,"PRMORPREV-");
sprintf(digit,"%-d",ij);	sprintf(digit,"%-d",ij);
/printf("DIGIT=%s, ij=%d ijr=%-d\|\n",digit, ij,ij);/	/printf("DIGIT=%s, ij=%d ijr=%-d\|\n",digit, ij,ij);/
strcat(fileresprobmorprev,digit); /* Tvar to be done */	strcat(fileresprobmorprev,digit); /* Tvar to be done */
strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */	strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
strcat(fileresprobmorprev,fileres);	strcat(fileresprobmorprev,fileresu);
if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {	if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
printf("Problem with resultfile: %s\n", fileresprobmorprev);	printf("Problem with resultfile: %s\n", fileresprobmorprev);
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);	fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
}	}
printf("Computing total mortality p.j=w1p1j+w2p2j+..: result on file '%s' \n",fileresprobmorprev);	printf("Computing total mortality p.j=w1p1j+w2p2j+..: result on file '%s' \n",fileresprobmorprev);

fprintf(ficlog,"Computing total mortality p.j=w1p1j+w2p2j+..: result on file '%s' \n",fileresprobmorprev);	fprintf(ficlog,"Computing total mortality p.j=w1p1j+w2p2j+..: result on file '%s' \n",fileresprobmorprev);
pstamp(ficresprobmorprev);	pstamp(ficresprobmorprev);
fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1p1j+w2p2j+... stand dev in()\n",estepm);	fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1p1j+w2p2j+... stand dev in()\n",estepm);
Line 3826 void varevsij(char optionfilefiname[], d	Line 4260 void varevsij(char optionfilefiname[], d
fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);	fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
}	}
fprintf(ficresprobmorprev,"\n");	fprintf(ficresprobmorprev,"\n");

fprintf(ficgp,"\n# Routine varevsij");	fprintf(ficgp,"\n# Routine varevsij");
/* fprintf(fichtm, "#Local time at start: %s", strstart);*/	fprintf(ficgp,"\nunset title \n");
	/* fprintf(fichtm, "#Local time at start: %s", strstart);*/
fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");	fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
fprintf(fichtm,"\n<br>%s <br>\n",digitp);	fprintf(fichtm,"\n<br>%s <br>\n",digitp);
/* } */	/* } */
Line 3862 void varevsij(char optionfilefiname[], d	Line 4298 void varevsij(char optionfilefiname[], d
/* For example we decided to compute the life expectancy with the smallest unit */	/* For example we decided to compute the life expectancy with the smallest unit */
/* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.	/* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
nhstepm is the number of hstepm from age to agelim	nhstepm is the number of hstepm from age to agelim
nstepm is the number of stepm from age to agelin.	nstepm is the number of stepm from age to agelim.
Look at function hpijx to understand why (it is linked to memory size questions) */	Look at function hpijx to understand why because of memory size limitations,
/* We decided (b) to get a life expectancy respecting the most precise curvature of the	we decided (b) to get a life expectancy respecting the most precise curvature of the
survival function given by stepm (the optimization length). Unfortunately it	survival function given by stepm (the optimization length). Unfortunately it
means that if the survival funtion is printed every two years of age and if	means that if the survival funtion is printed every two years of age and if
you sum them up and add 1 year (area under the trapezoids) you won't get the same	you sum them up and add 1 year (area under the trapezoids) you won't get the same
Line 3885 void varevsij(char optionfilefiname[], d	Line 4321 void varevsij(char optionfilefiname[], d
for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/	for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
xp[i] = x[i] + (i==theta ?delti[theta]:0);	xp[i] = x[i] + (i==theta ?delti[theta]:0);
}	}
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);	prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);

if (popbased==1) {	if (popbased==1) {
if(mobilav ==0){	if(mobilav ==0){
Line 3898 void varevsij(char optionfilefiname[], d	Line 4334 void varevsij(char optionfilefiname[], d
}	}
}	}

	hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); /* Returns p3mat[i][j][h] for h=1 to nhstepm */
for(j=1; j<= nlstate; j++){	for(j=1; j<= nlstate; j++){
for(h=0; h<=nhstepm; h++){	for(h=0; h<=nhstepm; h++){
for(i=1, gp[h][j]=0.;i<=nlstate;i++)	for(i=1, gp[h][j]=0.;i<=nlstate;i++)
gp[h][j] += prlim[i][i]*p3mat[i][j][h];	gp[h][j] += prlim[i][i]*p3mat[i][j][h];
}	}
}	}
/* This for computing probability of death (h=1 means	/* Next for computing probability of death (h=1 means
computed over hstepm matrices product = hstepm*stepm months)	computed over hstepm matrices product = hstepm*stepm months)
as a weighted average of prlim.	as a weighted average of prlim.
*/	*/
Line 3916 void varevsij(char optionfilefiname[], d	Line 4353 void varevsij(char optionfilefiname[], d

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

if (popbased==1) {	if (popbased==1) {
if(mobilav ==0){	if(mobilav ==0){
Line 3929 void varevsij(char optionfilefiname[], d	Line 4366 void varevsij(char optionfilefiname[], d
}	}
}	}

	hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);

for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */	for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
for(h=0; h<=nhstepm; h++){	for(h=0; h<=nhstepm; h++){
for(i=1, gm[h][j]=0.;i<=nlstate;i++)	for(i=1, gm[h][j]=0.;i<=nlstate;i++)
Line 3991 void varevsij(char optionfilefiname[], d	Line 4430 void varevsij(char optionfilefiname[], d
varppt[j][i]=doldmp[j][i];	varppt[j][i]=doldmp[j][i];
/* end ppptj */	/* end ppptj */
/* x centered again */	/* x centered again */
hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);	prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);

if (popbased==1) {	if (popbased==1) {
if(mobilav ==0){	if(mobilav ==0){
Line 4008 void varevsij(char optionfilefiname[], d	Line 4447 void varevsij(char optionfilefiname[], d
computed over hstepm (estepm) matrices product = hstepm*stepm months)	computed over hstepm (estepm) matrices product = hstepm*stepm months)
as a weighted average of prlim.	as a weighted average of prlim.
*/	*/
	hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
for(j=nlstate+1;j<=nlstate+ndeath;j++){	for(j=nlstate+1;j<=nlstate+ndeath;j++){
for(i=1,gmp[j]=0.;i<= nlstate; i++)	for(i=1,gmp[j]=0.;i<= nlstate; i++)
gmp[j] += prlim[i][i]*p3mat[i][j][1];	gmp[j] += prlim[i][i]*p3mat[i][j][1];
Line 4039 void varevsij(char optionfilefiname[], d	Line 4479 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,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
/* fprintf(ficgp,"\n plot \"%s\" u 1:($3%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); /	/* fprintf(ficgp,"\n plot \"%s\" u 1:($3%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); /
/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96$4)%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */	/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96$4)%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96$4)%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */	/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96$4)%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
Line 4049 void varevsij(char optionfilefiname[], d	Line 4491 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;\nset out \"%s%s.svg\";replot;set out;\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 4068 void varevsij(char optionfilefiname[], d	Line 4510 void varevsij(char optionfilefiname[], d
} /* end varevsij */	} /* end varevsij */

/********** Variance of prevlim ****************/	/********** Variance of prevlim ****************/
void varprevlim(char fileres[], double varpl, double matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double oldm, double savm, double **prlim, double ftolpl, int ij, char strstart[])	void varprevlim(char fileres[], double varpl, double matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double oldm, double savm, double *prlim, double ftolpl, int ncvyearp, int ij, char strstart[])
{	{
/* Variance of prevalence limit */	/* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
/* double prevalim(double prlim, int nlstate, double xp, double age, double oldm, double savm,double ftolpl);/	/* double prevalim(double prlim, int nlstate, double xp, double age, double oldm, double savm,double ftolpl);/

double dnewm,doldm;	double dnewm,doldm;
Line 4078 void varprevlim(char fileres[], double *	Line 4520 void varprevlim(char fileres[], double *
double *xp;	double *xp;
double gp, gm;	double gp, gm;
double gradg, trgradg;	double gradg, trgradg;
	double mgm, mgp;
double age,agelim;	double age,agelim;
int theta;	int theta;

Line 4100 void varprevlim(char fileres[], double *	Line 4543 void varprevlim(char fileres[], double *
if (stepm >= YEARM) hstepm=1;	if (stepm >= YEARM) hstepm=1;
nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */	nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
gradg=matrix(1,npar,1,nlstate);	gradg=matrix(1,npar,1,nlstate);
	mgp=matrix(1,npar,1,nlstate);
	mgm=matrix(1,npar,1,nlstate);
gp=vector(1,nlstate);	gp=vector(1,nlstate);
gm=vector(1,nlstate);	gm=vector(1,nlstate);

Line 4107 void varprevlim(char fileres[], double *	Line 4552 void varprevlim(char fileres[], double *
for(i=1; i<=npar; i++){ /* Computes gradient */	for(i=1; i<=npar; i++){ /* Computes gradient */
xp[i] = x[i] + (i==theta ?delti[theta]:0);	xp[i] = x[i] + (i==theta ?delti[theta]:0);
}	}
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);	if((int)age==79 \|\|(int)age== 80 \|\|(int)age== 81 )
for(i=1;i<=nlstate;i++)	prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
	else
	prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
	for(i=1;i<=nlstate;i++){
gp[i] = prlim[i][i];	gp[i] = prlim[i][i];
	mgp[theta][i] = prlim[i][i];
	}
for(i=1; i<=npar; i++) /* Computes gradient */	for(i=1; i<=npar; i++) /* Computes gradient */
xp[i] = x[i] - (i==theta ?delti[theta]:0);	xp[i] = x[i] - (i==theta ?delti[theta]:0);
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);	if((int)age==79 \|\|(int)age== 80 \|\|(int)age== 81 )
for(i=1;i<=nlstate;i++)	prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
	else
	prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
	for(i=1;i<=nlstate;i++){
gm[i] = prlim[i][i];	gm[i] = prlim[i][i];
	mgm[theta][i] = prlim[i][i];
	}
for(i=1;i<=nlstate;i++)	for(i=1;i<=nlstate;i++)
gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];	gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
	/* gradg[theta][2]= -gradg[theta][1]; / / For testing if nlstate=2 */
} /* End theta */	} /* End theta */

trgradg =matrix(1,nlstate,1,npar);	trgradg =matrix(1,nlstate,1,npar);
Line 4126 void varprevlim(char fileres[], double *	Line 4580 void varprevlim(char fileres[], double *
for(j=1; j<=nlstate;j++)	for(j=1; j<=nlstate;j++)
for(theta=1; theta <=npar; theta++)	for(theta=1; theta <=npar; theta++)
trgradg[j][theta]=gradg[theta][j];	trgradg[j][theta]=gradg[theta][j];
	/* if((int)age==79 \|\|(int)age== 80 \|\|(int)age== 81 ){ */
	/* printf("\nmgm mgp %d ",(int)age); */
	/* for(j=1; j<=nlstate;j++){ */
	/* printf(" %d ",j); */
	/* for(theta=1; theta <=npar; theta++) */
	/* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
	/* printf("\n "); */
	/* } */
	/* } */
	/* if((int)age==79 \|\|(int)age== 80 \|\|(int)age== 81 ){ */
	/* printf("\n gradg %d ",(int)age); */
	/* for(j=1; j<=nlstate;j++){ */
	/* printf("%d ",j); */
	/* for(theta=1; theta <=npar; theta++) */
	/* printf("%d %lf ",theta,gradg[theta][j]); */
	/* printf("\n "); */
	/* } */
	/* } */

for(i=1;i<=nlstate;i++)	for(i=1;i<=nlstate;i++)
varpl[i][(int)age] =0.;	varpl[i][(int)age] =0.;
	if((int)age==79 \|\|(int)age== 80 \|\|(int)age== 81){
matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);	matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);	matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
	}else{
	matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
	matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
	}
for(i=1;i<=nlstate;i++)	for(i=1;i<=nlstate;i++)
varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */	varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */

Line 4140 void varprevlim(char fileres[], double *	Line 4617 void varprevlim(char fileres[], double *
fprintf(ficresvpl,"\n");	fprintf(ficresvpl,"\n");
free_vector(gp,1,nlstate);	free_vector(gp,1,nlstate);
free_vector(gm,1,nlstate);	free_vector(gm,1,nlstate);
	free_matrix(mgm,1,npar,1,nlstate);
	free_matrix(mgp,1,npar,1,nlstate);
free_matrix(gradg,1,npar,1,nlstate);	free_matrix(gradg,1,npar,1,nlstate);
free_matrix(trgradg,1,nlstate,1,npar);	free_matrix(trgradg,1,nlstate,1,npar);
} /* End age */	} /* End age */
Line 4171 void varprob(char optionfilefiname[], do	Line 4650 void varprob(char optionfilefiname[], do
char fileresprobcor[FILENAMELENGTH];	char fileresprobcor[FILENAMELENGTH];
double ***varpij;	double ***varpij;

strcpy(fileresprob,"prob");	strcpy(fileresprob,"PROB_");
strcat(fileresprob,fileres);	strcat(fileresprob,fileres);
if((ficresprob=fopen(fileresprob,"w"))==NULL) {	if((ficresprob=fopen(fileresprob,"w"))==NULL) {
printf("Problem with resultfile: %s\n", fileresprob);	printf("Problem with resultfile: %s\n", fileresprob);
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);	fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
}	}
strcpy(fileresprobcov,"probcov");	strcpy(fileresprobcov,"PROBCOV_");
strcat(fileresprobcov,fileres);	strcat(fileresprobcov,fileresu);
if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {	if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
printf("Problem with resultfile: %s\n", fileresprobcov);	printf("Problem with resultfile: %s\n", fileresprobcov);
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);	fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
}	}
strcpy(fileresprobcor,"probcor");	strcpy(fileresprobcor,"PROBCOR_");
strcat(fileresprobcor,fileres);	strcat(fileresprobcor,fileresu);
if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {	if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
printf("Problem with resultfile: %s\n", fileresprobcor);	printf("Problem with resultfile: %s\n", fileresprobcor);
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);	fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
Line 4226 void varprob(char optionfilefiname[], do	Line 4705 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> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back.</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 4250 To be simple, these graphs help to under	Line 4728 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 4279 To be simple, these graphs help to under	Line 4757 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,k)];
	/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 4287 To be simple, these graphs help to under	Line 4766 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,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,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];


for(theta=1; theta <=npar; theta++){	for(theta=1; theta <=npar; theta++){
Line 4437 To be simple, these graphs help to under	Line 4916 To be simple, these graphs help to under
/* mu2+ v21lc1cost + v22lc2sin(t) */	/* mu2+ v21lc1cost + v22lc2sin(t) */
if(first==1){	if(first==1){
first=0;	first=0;
	fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
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 4464 To be simple, these graphs help to under	Line 4944 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;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
first=1;	first=1;
} /l12 /	} /l12 /
} /* k12 */	} /* k12 */
Line 4486 To be simple, these graphs help to under	Line 4966 To be simple, these graphs help to under


/***************** Printing html file *********/	/***************** Printing html file *********/
void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \	void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
int lastpass, int stepm, int weightopt, char model[],\	int lastpass, int stepm, int weightopt, char model[],\
int imx,int jmin, int jmax, double jmeanint,char rfileres[],\	int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
int popforecast, int estepm ,\	int popforecast, int prevfcast, int estepm , \
double jprev1, double mprev1,double anprev1, \	double jprev1, double mprev1,double anprev1, double dateprev1, \
double jprev2, double mprev2,double anprev2){	double jprev2, double mprev2,double anprev2, double dateprev2){
int jj1, k1, i1, cpt;	int jj1, k1, i1, cpt;

fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \	fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
<li><a href='#secondorder'>Result files (second order (variance)</a>\n \	<li><a href='#secondorder'>Result files (second order (variance)</a>\n \
</ul>");	</ul>");
fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \	fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
- Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",	fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",
jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));	jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
	fprintf(fichtm,"<li> - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file) ",
	jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
	fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",	- Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));	stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",	- Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));	subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \	- (a) Life expectancies by health status at initial age, e<sub>i.</sub> (b) health expectancies by health status at initial age, e<sub>ij</sub> . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
<a href=\"%s\">%s</a> <br>\n",	<a href=\"%s\">%s</a> <br>\n",
estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));	estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
fprintf(fichtm,"\	if(prevfcast==1){
- Population projections by age and states: \	fprintf(fichtm,"\
<a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));	- Prevalence projections by age and states: \
	<a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
	}

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

Line 4526 fprintf(fichtm," \n<ul><li><b>Graphs</b>	Line 5011 fprintf(fichtm," \n<ul><li><b>Graphs</b>
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]][codtab[jj1][cpt]]);fflush(stdout);	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\">");
}	}
	/* aij, bij */
	fprintf(fichtm,"<br>- Logit model (yours is: 1+age+%s), for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1.svg\">%s_%d-1.svg</a><br> \
	<img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
/* 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>\n- P<sub>ij</sub> or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2.svg\">%s_%d-2.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-2.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>\n- I<sub>ij</sub> 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,\
<img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);	incidence (rates) are the limit when h tends to zero of the ratio of the probability <sub>h</sub>P<sub>ij</sub> \
/* Period (stable) prevalence in each health state */	divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \
for(cpt=1; cpt<=nlstate;cpt++){	<img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
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> \	/* Survival functions (period) in state j */
<img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);	for(cpt=1; cpt<=nlstate;cpt++){
}	fprintf(fichtm,"<br>\n- Survival functions in state %d. Or probability to survive 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.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
	}
	/* State specific survival functions (period) */
	for(cpt=1; cpt<=nlstate;cpt++){
	fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
	Or probability to survive in various states (1 to %d) being in state %d at different ages.\
	<a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> <img src=\"%s_%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1);
	}
	/* Period (stable) prevalence in each health state */
	for(cpt=1; cpt<=nlstate;cpt++){
	fprintf(fichtm,"<br>\n- 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.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
	}
	if(prevfcast==1){
	/* Projection of prevalence up to period (stable) prevalence in each health state */
	for(cpt=1; cpt<=nlstate;cpt++){
	fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f) up 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.svg\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),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) (or area under each survival functions): <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 */
Line 4554 fprintf(fichtm," \n<ul><li><b>Graphs</b>	Line 5063 fprintf(fichtm," \n<ul><li><b>Graphs</b>
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> \	- Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
- 95%% confidence intervals and T statistics are in the log file.<br>\n", rfileres,rfileres);	- 95%% confidence intervals and Wald tests of the estimated parameters are in the log file if optimization has been done (mle != 0).<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," - Standard deviation 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(fileresu,"PROB_"),subdirf2(fileresu,"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",
subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));	subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));

fprintf(fichtm,"\	fprintf(fichtm,"\
- Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",	- Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));	subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \	- Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
<a href=\"%s\">%s</a> <br>\n</li>",	<a href=\"%s\">%s</a> <br>\n</li>",
estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));	estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \	- (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
<a href=\"%s\">%s</a> <br>\n</li>",	<a href=\"%s\">%s</a> <br>\n</li>",
estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));	estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",	- Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));	estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",	- Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));	estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\	- Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));	subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));

/* if(popforecast==1) fprintf(fichtm,"\n */	/* if(popforecast==1) fprintf(fichtm,"\n */
/* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */	/* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
Line 4602 fprintf(fichtm," \n<ul><li><b>Graphs</b>	Line 5118 fprintf(fichtm," \n<ul><li><b>Graphs</b>
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): <a href=\"%s_%d%d.svg\"> %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,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: <a href=\"%s_%d.svg\">%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,subdirf2(optionfilefiname,"E_"),jj1);
/* } /\* end i1 \/ /	/* } /\* end i1 \/ /
}/* End k1 */	}/* End k1 */
fprintf(fichtm,"</ul>");	fprintf(fichtm,"</ul>");
Line 4623 true period expectancies (those weighted	Line 5139 true period expectancies (those weighted
}	}

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

char dirfileres[132],optfileres[132];	char dirfileres[132],optfileres[132];
int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;	int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
	int lv=0, vlv=0, kl=0;
int ng=0;	int ng=0;
	int vpopbased;
/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */	/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
/* printf("Problem with file %s",optionfilegnuplot); */	/* printf("Problem with file %s",optionfilegnuplot); */
/* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */	/* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
Line 4638 void printinggnuplot(char fileres[], cha	Line 5156 void printinggnuplot(char fileres[], cha
/#endif /	/#endif /
m=pow(2,cptcoveff);	m=pow(2,cptcoveff);

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

strcpy(dirfileres,optionfilefiname);	strcpy(dirfileres,optionfilefiname);
strcpy(optfileres,"vpl");	strcpy(optfileres,"vpl");
/* 1eme*/	/* 1eme*/
fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");	for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
for (cpt=1; cpt<= nlstate ; cpt ++) {	for (k1=1; k1<= m ; k1 ++) { /* For each combination of covariate */
for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */	/* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);	fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);	for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
	vlv= nbcode[Tvaraff[lv]][lv];
	fprintf(ficgp," V%d=%d ",k,vlv);
	}
	fprintf(ficgp,"\n#\n");

	fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
	fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
fprintf(ficgp,"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(fileresu,"VPL_"),k1-1,k1-1);

for (i=1; i<= nlstate ; i ++) {	for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," %%lf (%%lf)");	if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%lf (%%lf)");	else fprintf(ficgp," %%lf (%%lf)");
}	}
fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);	fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
for (i=1; i<= nlstate ; i ++) {	for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," %%lf (%%lf)");	if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%lf (%%lf)");	else fprintf(ficgp," %%lf (%%lf)");
}	}
fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);	fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
for (i=1; i<= nlstate ; i ++) {	for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," %%lf (%%lf)");	if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%lf (%%lf)");	else fprintf(ficgp," %%lf (%%lf)");
}	}
fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));	fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
}	fprintf(ficgp,"\nset out \n");
}	} /* k1 */
	} /* cpt */
/2 eme/	/2 eme/
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,"\n# 2nd: Total life expectancy with CI: 't' files ");
fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);	for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
for (i=1; i<= nlstate+1 ; i ++) {	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
k=2*i;	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
for (j=1; j<= nlstate+1 ; j ++) {	vlv= nbcode[Tvaraff[lv]][lv];
if (j==i) fprintf(ficgp," %%lf (%%lf)");	fprintf(ficgp," V%d=%d ",k,vlv);
else fprintf(ficgp," %%lf (%%lf)");	}
}	fprintf(ficgp,"\n#\n");
if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);	fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);	for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
for (j=1; j<= nlstate+1 ; j ++) {	if(vpopbased==0)
if (j==i) fprintf(ficgp," %%lf (%%lf)");	fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
else fprintf(ficgp," %%lf (%%lf)");	else
}	fprintf(ficgp,"\nreplot ");
fprintf(ficgp,"\" t\"\" w l lt 0,");	for (i=1; i<= nlstate+1 ; i ++) {
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);	k=2*i;
for (j=1; j<= nlstate+1 ; j ++) {	fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);
if (j==i) fprintf(ficgp," %%lf (%%lf)");	for (j=1; j<= nlstate+1 ; j ++) {
else fprintf(ficgp," %%lf (%%lf)");	if (j==i) fprintf(ficgp," %%lf (%%lf)");
}	else fprintf(ficgp," %%lf (%%lf)");
if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");	}
else fprintf(ficgp,"\" t\"\" w l lt 0,");	if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
}	else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
}	fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
	for (j=1; j<= nlstate+1 ; j ++) {
	if (j==i) fprintf(ficgp," %%lf (%%lf)");
	else fprintf(ficgp," %%lf (%%lf)");
	}
	fprintf(ficgp,"\" t\"\" w l lt 0,");
	fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
	for (j=1; j<= nlstate+1 ; j ++) {
	if (j==i) fprintf(ficgp," %%lf (%%lf)");
	else fprintf(ficgp," %%lf (%%lf)");
	}
	if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
	else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
	} /* state */
	} /* vpopbased */
	fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
	} /* k1 */


/3eme/	/3eme/

for (k1=1; k1<= m ; k1 ++) {	for (k1=1; k1<= m ; k1 ++) {
for (cpt=1; cpt<= nlstate ; cpt ++) {	for (cpt=1; cpt<= nlstate ; cpt ++) {
	fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: cov=%d state=%d",k1, cpt);
	for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
	vlv= nbcode[Tvaraff[lv]][lv];
	fprintf(ficgp," V%d=%d ",k,vlv);
	}
	fprintf(ficgp,"\n#\n");

/* 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(fileresu,"E_"),k1-1,k1-1,k,cpt);
/fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);	/fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");	for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
fprintf(ficgp,"\" t \"e%d1\" w l",cpt);	fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
Line 4717 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 5302 plot [%.f:%.f] \"%s\" every :::%d::%d u

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

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

/* CV preval stable (period) */	/* Survival functions (period) from state i in state j by initial state i */
for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */	for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
	fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
	for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
	vlv= nbcode[Tvaraff[lv]][lv];
	fprintf(ficgp," V%d=%d ",k,vlv);
	}
	fprintf(ficgp,"\n#\n");

	fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
	set ter svg size 640, 480\n\
	unset log y\n\
	plot [%.f:%.f] ", ageminpar, agemaxpar);
	k=3;
	for (i=1; i<= nlstate ; i ++){
	if(i==1)
	fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
	else
	fprintf(ficgp,", '' ");
	l=(nlstate+ndeath)*(i-1)+1;
	fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
	for (j=2; j<= nlstate+ndeath ; j ++)
	fprintf(ficgp,"+$%d",k+l+j-1);
	fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
	} /* nlstate */
	fprintf(ficgp,"\nset out\n");
	} /* end cpt state*/
	} /* end covariate */

	/* Survival functions (period) from state i in state j by final state j */
	for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
	fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
	for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
	vlv= nbcode[Tvaraff[lv]][lv];
	fprintf(ficgp," V%d=%d ",k,vlv);
	}
	fprintf(ficgp,"\n#\n");

	fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
	set ter svg size 640, 480\n\
	unset log y\n\
	plot [%.f:%.f] ", ageminpar, agemaxpar);
k=3;	k=3;
fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);	for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);	if(j==1)
	fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
	else
	fprintf(ficgp,", '' ");
	l=(nlstate+ndeath)*(cpt-1) +j;
	fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
	/* for (i=2; i<= nlstate+ndeath ; i ++) */
	/* fprintf(ficgp,"+$%d",k+l+i-1); */
	fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
	} /* nlstate */
	fprintf(ficgp,", '' ");
	fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
	for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
	l=(nlstate+ndeath)*(cpt-1) +j;
	if(j < nlstate)
	fprintf(ficgp,"$%d +",k+l);
	else
	fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
	}
	fprintf(ficgp,"\nset out\n");
	} /* end cpt state*/
	} /* end covariate */

	/* CV preval stable (period) for each covariate */
	for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2*k), if any covariate is present /
	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
	fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
	for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
	vlv= nbcode[Tvaraff[lv]][lv];
	fprintf(ficgp," V%d=%d ",k,vlv);
	}
	fprintf(ficgp,"\n#\n");

	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);
	k=3; /* Offset */
for (i=1; i<= nlstate ; i ++){	for (i=1; i<= nlstate ; i ++){
if(i==1)	if(i==1)
fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));	fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
else	else
fprintf(ficgp,", '' ");	fprintf(ficgp,", '' ");
l=(nlstate+ndeath)*(i-1)+1;	l=(nlstate+ndeath)*(i-1)+1;
fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);	fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
for (j=1; j<= (nlstate-1) ; j ++)	for (j=2; j<= nlstate ; j ++)
fprintf(ficgp,"+$%d",k+l+j);	fprintf(ficgp,"+$%d",k+l+j-1);
fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);	fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
} /* nlstate */	} /* nlstate */
fprintf(ficgp,"\n");	fprintf(ficgp,"\nset out\n");
} /* end cpt state*/	} /* end cpt state*/
} /* end covariate */	} /* end covariate */

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

	for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2*k), if any covariate is present /
	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
	fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
	for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
	vlv= nbcode[Tvaraff[lv]][lv];
	fprintf(ficgp," V%d=%d ",k,vlv);
	}
	fprintf(ficgp,"\n#\n");

	fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
	fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
	set ter svg size 640, 480\n\
	unset log y\n\
	plot [%.f:%.f] ", ageminpar, agemaxpar);
	for (i=1; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
	/# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3/
	/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 /
	/# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3/
	/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 /
	if(i==1){
	fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
	}else{
	fprintf(ficgp,",\\\n '' ");
	}
	if(cptcoveff ==0){ /* No covariate */
	fprintf(ficgp," u 2:("); /* Age is in 2 */
	/# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4/
	/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 /
	if(i==nlstate+1)
	fprintf(ficgp," $%d/(1.-$%d)) t 'p.%d' with line ", \
	2+(cpt-1)(nlstate+1)+1+(i-1), 2+1+(i-1)+(nlstate+1)nlstate,cpt );
	else
	fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
	2+(cpt-1)(nlstate+1)+1+(i-1), 2+1+(i-1)+(nlstate+1)nlstate,i,cpt );
	}else{
	fprintf(ficgp,"u 6:(("); /* Age is in 6 */
	/# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3/
	/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 /
	kl=0;
	for (k=1; k<=cptcoveff; k++){ /* For each covariate */
	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
	vlv= nbcode[Tvaraff[lv]][lv];
	kl++;
	/* kl=6+(cpt-1)(nlstate+1)+1+(i-1); /\ 6+(1-1)(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 \/ */
	/6+(cpt-1)(nlstate+1)+1+(i-1)+(nlstate+1)nlstate; 6+(1-1)(2+1)+1+(1-1) +(2+1)2=13 /
	/6+1+(i-1)+(nlstate+1)nlstate; 6+1+(1-1) +(2+1)2=13 /
	/* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
	if(k==cptcoveff)
	if(i==nlstate+1)
	fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv], \
	6+(cpt-1)(nlstate+1)+1+(i-1), 6+1+(i-1)+(nlstate+1)nlstate,cpt );
	else
	fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv], \
	6+(cpt-1)(nlstate+1)+1+(i-1), 6+1+(i-1)+(nlstate+1)nlstate,i,cpt );
	else{
	fprintf(ficgp,"$%d==%d && $%d==%d && ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv]);
	kl++;
	}
	} /* end covariate */
	} /* end if covariate */
	} /* nlstate */
	fprintf(ficgp,"\nset out\n");
	} /* end cpt state*/
	} /* end covariate */
	} /* End if prevfcast */


/* proba elementaires */	/* proba elementaires */
fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");	fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
for(i=1,jk=1; i <=nlstate; i++){	for(i=1,jk=1; i <=nlstate; i++){
Line 4768 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 5520 plot [%.f:%.f] ", ageminpar, agemaxpar)
fprintf(ficgp,"##############\n#\n");	fprintf(ficgp,"##############\n#\n");

/goto avoid;/	/goto avoid;/
fprintf(ficgp,"\n##############\n#Graphics of of probabilities or incidences\n#############\n");	fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
fprintf(ficgp,"# logi(p12/p11)=a12+b12age+c12ageage+d12V1+e12V1*age\n");	fprintf(ficgp,"# logi(p12/p11)=a12+b12age+c12ageage+d12V1+e12V1*age\n");
fprintf(ficgp,"# logi(p12/p11)=p1 +p2age +p3ageage+ p4V1+ p5V1age\n");	fprintf(ficgp,"# logi(p12/p11)=p1 +p2age +p3ageage+ p4V1+ p5V1age\n");
fprintf(ficgp,"# logi(p13/p11)=a13+b13age+c13ageage+d13V1+e13V1*age\n");	fprintf(ficgp,"# logi(p13/p11)=a13+b13age+c13ageage+d13V1+e13V1*age\n");
Line 4782 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 5534 plot [%.f:%.f] ", ageminpar, agemaxpar)
fprintf(ficgp,"# +exp(a13+b13age+c13ageage+d13V1+e13V1*age))\n");	fprintf(ficgp,"# +exp(a13+b13age+c13ageage+d13V1+e13V1*age))\n");
fprintf(ficgp,"# +exp(a14+b14age+c14ageage+d14V1+e14V1*age)+...)\n");	fprintf(ficgp,"# +exp(a14+b14age+c14ageage+d14V1+e14V1*age)+...)\n");
fprintf(ficgp,"#\n");	fprintf(ficgp,"#\n");
for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/	for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
fprintf(ficgp,"# ng=%d\n",ng);	fprintf(ficgp,"# ng=%d\n",ng);
fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);	fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
for(jk=1; jk <=m; jk++) {	for(jk=1; jk <=m; jk++) {
fprintf(ficgp,"# jk=%d\n",jk);	fprintf(ficgp,"# jk=%d\n",jk);
fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);	fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
if (ng==2)	fprintf(ficgp,"\nset ter svg size 640, 480 ");
	if (ng==1){
	fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12x) could be nice /
	fprintf(ficgp,"\nunset log y");
	}else if (ng==2){
	fprintf(ficgp,"\nset ylabel \"Probability\"\n");
	fprintf(ficgp,"\nset log y");
	}else if (ng==3){
fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");	fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
else	fprintf(ficgp,"\nset log y");
fprintf(ficgp,"\nset title \"Probability\"\n");	}else
fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);	fprintf(ficgp,"\nunset title ");
	fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
i=1;	i=1;
for(k2=1; k2<=nlstate; k2++) {	for(k2=1; k2<=nlstate; k2++) {
k3=i;	k3=i;
for(k=1; k<=(nlstate+ndeath); k++) {	for(k=1; k<=(nlstate+ndeath); k++) {
if (k != k2){	if (k != k2){
if(ng==2)	switch( ng) {
	case 1:
if(nagesqr==0)	if(nagesqr==0)
fprintf(ficgp," %fexp(p%d+p%dx",YEARM/stepm,i,i+1);	fprintf(ficgp," p%d+p%d*x",i,i+1);
else /* nagesqr =1 */	else /* nagesqr =1 */
fprintf(ficgp," %fexp(p%d+p%dx+p%dxx",YEARM/stepm,i,i+1,i+1+nagesqr);	fprintf(ficgp," p%d+p%dx+p%dx*x",i,i+1,i+1+nagesqr);
else	break;
	case 2: /* ng=2 */
if(nagesqr==0)	if(nagesqr==0)
fprintf(ficgp," exp(p%d+p%d*x",i,i+1);	fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
else /* nagesqr =1 */	else /* nagesqr =1 */
fprintf(ficgp," exp(p%d+p%dx+p%dx*x",i,i+1,i+1+nagesqr);	fprintf(ficgp," exp(p%d+p%dx+p%dx*x",i,i+1,i+1+nagesqr);
	break;
	case 3:
	if(nagesqr==0)
	fprintf(ficgp," %fexp(p%d+p%dx",YEARM/stepm,i,i+1);
	else /* nagesqr =1 */
	fprintf(ficgp," %fexp(p%d+p%dx+p%dxx",YEARM/stepm,i,i+1,i+1+nagesqr);
	break;
	}
ij=1;/* To be checked else nbcode[0][0] wrong */	ij=1;/* To be checked else nbcode[0][0] wrong */
for(j=3; j <=ncovmodel-nagesqr; j++) {	for(j=3; j <=ncovmodel-nagesqr; j++) {
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,j-2)]);
	/* 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");	if(ng != 1){
	fprintf(ficgp,")/(1");

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

ij=1;	ij=1;
for(j=3; j <=ncovmodel-nagesqr; j++){	for(j=3; j <=ncovmodel-nagesqr; j++){
if(((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,j-2)]);
	/* fprintf(ficgp,"+p%d%dx",k3+(k1-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); /
	ij++;
	}
	}
	else
	fprintf(ficgp,"+p%d%d",k3+(k1-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
}	}
else	fprintf(ficgp,")");
fprintf(ficgp,"+p%d%d",k3+(k1-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
}	}
fprintf(ficgp,")");	fprintf(ficgp,")");
	if(ng ==2)
	fprintf(ficgp," t \"p%d%d\" ", k2,k);
	else /* ng= 3 */
	fprintf(ficgp," t \"i%d%d\" ", k2,k);
	}else{ /* end ng <> 1 */
	fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
}	}
fprintf(ficgp,") t \"p%d%d\" ", k2,k);
if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");	if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
i=i+ncovmodel;	i=i+ncovmodel;
}	}
} /* end k */	} /* end k */
} /* end k2 */	} /* end k2 */
	fprintf(ficgp,"\n set out\n");
} /* end jk */	} /* end jk */
} /* end ng */	} /* end ng */
/* avoid: */	/* avoid: */
Line 4907 void prevforecast(char fileres[], double	Line 5693 void prevforecast(char fileres[], double
char fileresf[FILENAMELENGTH];	char fileresf[FILENAMELENGTH];

agelim=AGESUP;	agelim=AGESUP;
	/* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
	in each health status at the date of interview (if between dateprev1 and dateprev2).
	We still use firstpass and lastpass as another selection.
	*/
	/* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
	/* firstpass, lastpass, stepm, weightopt, model); */
prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);	prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);

strcpy(fileresf,"f");	strcpy(fileresf,"F_");
strcat(fileresf,fileres);	strcat(fileresf,fileresu);
if((ficresf=fopen(fileresf,"w"))==NULL) {	if((ficresf=fopen(fileresf,"w"))==NULL) {
printf("Problem with forecast resultfile: %s\n", fileresf);	printf("Problem with forecast resultfile: %s\n", fileresf);
fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);	fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
}	}
printf("Computing forecasting: result on file '%s' \n", fileresf);	printf("Computing forecasting: result on file '%s', please wait... \n", fileresf);
fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);	fprintf(ficlog,"Computing forecasting: result on file '%s', please wait... \n", fileresf);

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

Line 4957 void prevforecast(char fileres[], double	Line 5749 void prevforecast(char fileres[], double
for(cptcov=1, k=0;cptcov<=i1;cptcov++){	for(cptcov=1, k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){	for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
k=k+1;	k=k+1;
fprintf(ficresf,"\n#******");	fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=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",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
}	}
fprintf(ficresf,"******\n");	fprintf(ficresf," yearproj age");
fprintf(ficresf,"# Covariate valuofcovar yearproj age");
for(j=1; j<=nlstate+ndeath;j++){	for(j=1; j<=nlstate+ndeath;j++){
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
fprintf(ficresf," p%d%d",i,j);	fprintf(ficresf," p%d%d",i,j);
Line 4983 void prevforecast(char fileres[], double	Line 5774 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 5012 void prevforecast(char fileres[], double	Line 5803 void prevforecast(char fileres[], double
if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);	if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);

fclose(ficresf);	fclose(ficresf);
	printf("End of Computing forecasting \n");
	fprintf(ficlog,"End of Computing forecasting\n");

}	}

/************ Forecasting *not tested NB***********/	/************ Forecasting *not tested NB***********/
Line 5033 void populforecast(char fileres[], doubl	Line 5827 void populforecast(char fileres[], doubl
prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);	prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);


strcpy(filerespop,"pop");	strcpy(filerespop,"POP_");
strcat(filerespop,fileres);	strcat(filerespop,fileresu);
if((ficrespop=fopen(filerespop,"w"))==NULL) {	if((ficrespop=fopen(filerespop,"w"))==NULL) {
printf("Problem with forecast resultfile: %s\n", filerespop);	printf("Problem with forecast resultfile: %s\n", filerespop);
fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);	fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
Line 5081 void populforecast(char fileres[], doubl	Line 5875 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 5387 double gompertz_f(const gsl_vector *v, v	Line 6181 double gompertz_f(const gsl_vector *v, v
#endif	#endif

/***************** Printing html file *********/	/***************** Printing html file *********/
void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \	void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
int lastpass, int stepm, int weightopt, char model[],\	int lastpass, int stepm, int weightopt, char model[],\
int imx, double p[],double **matcov,double agemortsup){	int imx, double p[],double **matcov,double agemortsup){
int i,k;	int i,k;
Line 5396 void printinghtmlmort(char fileres[], ch	Line 6190 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 5411 fprintf(fichtm,"<ul><li><h4>Life table</	Line 6205 fprintf(fichtm,"<ul><li><h4>Life table</
}	}

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

char dirfileres[132],optfileres[132];	char dirfileres[132],optfileres[132];

Line 5425 void printinggnuplotmort(char fileres[],	Line 6219 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 5738 int decodemodel ( char model[], int last	Line 6532 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 5851 int calandcheckages(int imx, int maxwav,	Line 6645 int calandcheckages(int imx, int maxwav,
for (i=1; i<=imx; i++) {	for (i=1; i<=imx; i++) {
agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);	agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
for(m=firstpass; (m<= lastpass); m++){	for(m=firstpass; (m<= lastpass); m++){
if(s[m][i] >0 \|\| s[m][i]==-2 \|\| s[m][i]==-4 \|\| s[m][i]==-5){	if(s[m][i] >0 \|\| s[m][i]==-1 \|\| s[m][i]==-2 \|\| s[m][i]==-4 \|\| s[m][i]==-5){ /* What if s[m][i]=-1 */
if (s[m][i] >= nlstate+1) {	if (s[m][i] >= nlstate+1) {
if(agedc[i]>0){	if(agedc[i]>0){
if((int)moisdc[i]!=99 && (int)andc[i]!=9999){	if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
agev[m][i]=agedc[i];	agev[m][i]=agedc[i];
/if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;/	/if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;/
}else {	}else {
if ((int)andc[i]!=9999){	if ((int)andc[i]!=9999){
nbwarn++;	nbwarn++;
Line 5866 int calandcheckages(int imx, int maxwav,	Line 6660 int calandcheckages(int imx, int maxwav,
}	}
}	}
} /* agedc > 0 */	} /* agedc > 0 */
}	} /* end if */
else if(s[m][i] !=9){ /* Standard case, age in fractional	else if(s[m][i] !=9){ /* Standard case, age in fractional
years but with the precision of a month */	years but with the precision of a month */
agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);	agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
Line 5882 int calandcheckages(int imx, int maxwav,	Line 6676 int calandcheckages(int imx, int maxwav,
}	}
/agev[m][i]=anint[m][i]-annais[i];/	/agev[m][i]=anint[m][i]-annais[i];/
/* agev[m][i] = age[i]+2m;/	/* agev[m][i] = age[i]+2m;/
}	} /* en if 9*/
else { /* =9 */	else { /* =9 */
	/* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
agev[m][i]=1;	agev[m][i]=1;
s[m][i]=-1;	s[m][i]=-1;
}	}
}	}
else /= 0 Unknown /	else if(s[m][i]==0) /= 0 Unknown /
agev[m][i]=1;	agev[m][i]=1;
}	else{
	printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
	fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
	agev[m][i]=0;
	}
	} /* End for lastpass */
}	}

for (i=1; i<=imx; i++) {	for (i=1; i<=imx; i++) {
for(m=firstpass; (m<=lastpass); m++){	for(m=firstpass; (m<=lastpass); m++){
if (s[m][i] > (nlstate+ndeath)) {	if (s[m][i] > (nlstate+ndeath)) {
Line 6118 void syscompilerinfo(int logged)	Line 6918 void syscompilerinfo(int logged)

}	}

int prevalence_limit(double p, double *prlim, double ageminpar, double agemaxpar){	int prevalence_limit(double p, double prlim, double ageminpar, double agemaxpar, double ftolpl, int ncvyearp){
/--------------- Prevalence limit (period or stable prevalence) --------------/	/--------------- Prevalence limit (period or stable prevalence) --------------/
int i, j, k, i1 ;	int i, j, k, i1 ;
double ftolpl = 1.e-10;	/* double ftolpl = 1.e-10; */
double age, agebase, agelim;	double age, agebase, agelim;
	double tot;

strcpy(filerespl,"pl");	strcpy(filerespl,"PL_");
strcat(filerespl,fileres);	strcat(filerespl,fileresu);
if((ficrespl=fopen(filerespl,"w"))==NULL) {	if((ficrespl=fopen(filerespl,"w"))==NULL) {
printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;	printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;	fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
}	}
printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);	printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);	fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
pstamp(ficrespl);	pstamp(ficrespl);
fprintf(ficrespl,"# Period (stable) prevalence \n");	fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
fprintf(ficrespl,"#Age ");	fprintf(ficrespl,"#Age ");
for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);	for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
fprintf(ficrespl,"\n");	fprintf(ficrespl,"\n");

/* prlim=matrix(1,nlstate,1,nlstate);/ / back in main */	/* prlim=matrix(1,nlstate,1,nlstate);/ / back in main */

Line 6151 int prevalence_limit(double p, double	Line 6952 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,"#******");
printf("\n#******");	printf("#******");
fprintf(ficlog,"\n#******");	fprintf(ficlog,"#******");
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 6166 int prevalence_limit(double p, double	Line 6967 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,"Total Years_to_converge\n");

for (age=agebase; age<=agelim; age++){	for (age=agebase; age<=agelim; age++){
/* for (age=agebase; age<=agebase; age++){ */	/* for (age=agebase; age<=agebase; age++){ */
prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);	prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
fprintf(ficrespl,"%.0f ",age );	fprintf(ficrespl,"%.0f ",age );
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=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++)	tot=0.;
	for(i=1; i<=nlstate;i++){
	tot += prlim[i][i];
fprintf(ficrespl," %.5f", prlim[i][i]);	fprintf(ficrespl," %.5f", prlim[i][i]);
fprintf(ficrespl,"\n");	}
	fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
} /* Age */	} /* Age */
/* was end of cptcod */	/* was end of cptcod */
} /* cptcov */	} /* cptcov */
Line 6198 int hPijx(double *p, int bage, int fage)	Line 7002 int hPijx(double *p, int bage, int fage)
double agedeb;	double agedeb;
double ***p3mat;	double ***p3mat;

strcpy(filerespij,"pij"); strcat(filerespij,fileres);	strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
if((ficrespij=fopen(filerespij,"w"))==NULL) {	if((ficrespij=fopen(filerespij,"w"))==NULL) {
printf("Problem with Pij resultfile: %s\n", filerespij); return 1;	printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;	fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
Line 6223 int hPijx(double *p, int bage, int fage)	Line 7027 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 6272 int main(int argc, char *argv[])	Line 7076 int main(int argc, char *argv[])
#endif	#endif
int movingaverage(double *probs, double bage,double fage, double *mobaverage, int mobilav);	int movingaverage(double *probs, double bage,double fage, double *mobaverage, int mobilav);
int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;	int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
	int ncvyear=0; /* Number of years needed for the period prevalence to converge */
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 6293 int main(int argc, char *argv[])	Line 7098 int main(int argc, char *argv[])
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;
Line 6317 int main(int argc, char *argv[])	Line 7124 int main(int argc, char *argv[])
double **param; / Matrix of parameters */	double **param; / Matrix of parameters */
double *p;	double *p;
double *matcov; / Matrix of covariance */	double *matcov; / Matrix of covariance */
	double *hess; / Hessian matrix */
double **delti3; / Scale */	double **delti3; / Scale */
double delti; / Scale */	double delti; / Scale */
double *eij, *vareij;	double *eij, *vareij;
Line 6373 int main(int argc, char *argv[])	Line 7181 int main(int argc, char *argv[])
getcwd(pathcd, size);	getcwd(pathcd, size);
#endif	#endif
syscompilerinfo(0);	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);	if(!fgets(pathr,FILENAMELENGTH,stdin)){
	printf("ERROR Empty parameter file name\n");
	goto end;
	}
i=strlen(pathr);	i=strlen(pathr);
if(pathr[i-1]=='\n')	if(pathr[i-1]=='\n')
pathr[i-1]='\0';	pathr[i-1]='\0';
i=strlen(pathr);	i=strlen(pathr);
if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */	if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
pathr[i-1]='\0';	pathr[i-1]='\0';
for (tok = pathr; tok != NULL; ){	}
	i=strlen(pathr);
	if( i==0 ){
	printf("ERROR Empty parameter file name\n");
	goto end;
	}
	for (tok = pathr; tok != NULL; ){
printf("Pathr \|%s\|\n",pathr);	printf("Pathr \|%s\|\n",pathr);
while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');	while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
printf("val= \|%s\| pathr=%s\n",val,pathr);	printf("val= \|%s\| pathr=%s\n",val,pathr);
Line 6437 int main(int argc, char *argv[])	Line 7254 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 6445 int main(int argc, char *argv[])	Line 7262 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(0);	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 6456 int main(int argc, char *argv[])	Line 7273 int main(int argc, char *argv[])
/* */	/* */
strcpy(fileres,"r");	strcpy(fileres,"r");
strcat(fileres, optionfilefiname);	strcat(fileres, optionfilefiname);
	strcat(fileresu, optionfilefiname); /* Without r in front */
strcat(fileres,".txt"); /* Other files have txt extension */	strcat(fileres,".txt"); /* Other files have txt extension */
	strcat(fileresu,".txt"); /* Other files have txt extension */

/* Main ---------arguments file --------*/	/* Main ---------arguments file --------*/

Line 6471 int main(int argc, char *argv[])	Line 7290 int main(int argc, char *argv[])


strcpy(filereso,"o");	strcpy(filereso,"o");
strcat(filereso,fileres);	strcat(filereso,fileresu);
if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */	if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
printf("Problem with Output resultfile: %s\n", filereso);	printf("Problem with Output resultfile: %s\n", filereso);
fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);	fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
Line 6481 int main(int argc, char *argv[])	Line 7300 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);
}	}
ungetc(c,ficpar);	/* Second parameter line */
	while(fgets(line, MAXLINE, 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);	/* If line starts with a # it is a comment */
numlinepar=numlinepar+3; /* In general */	if (line[0] == '#') {
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);	numlinepar++;
if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */	fputs(line,stdout);
model[strlen(model)-1]='\0';	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 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
	printf("but line=%s\n",line);
	}
	printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt);
	}
	/* ftolpl=6ftol1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit \/ /
	/ftolpl=6.e-4; //* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
	/* Third 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,"model=1+age%[^.\n]", model)) !=EOF){
	if (num_filled == 0)
	model[0]='\0';
	else 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); */
	printf("model=1+age+%s\n",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); */
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);
Line 6562 int main(int argc, char *argv[])	Line 7443 int main(int argc, char *argv[])
fprintf(ficlog," You chose 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);
	hess=matrix(1,npar,1,npar);
}	}
else{	else{
/* Read guessed parameters */	/* Read guessed parameters */
Line 6670 run imach with mle=-1 to get a correct t	Line 7552 run imach with mle=-1 to get a correct t
ungetc(c,ficpar);	ungetc(c,ficpar);

matcov=matrix(1,npar,1,npar);	matcov=matrix(1,npar,1,npar);
	hess=matrix(1,npar,1,npar);
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.;

Line 6721 Please run with mle=-1 to get a correct	Line 7604 Please run with mle=-1 to get a correct
strcat(rfileres,"."); /* */	strcat(rfileres,"."); /* */
strcat(rfileres,optionfilext); /* Other files have txt extension */	strcat(rfileres,optionfilext); /* Other files have txt extension */
if((ficres =fopen(rfileres,"w"))==NULL) {	if((ficres =fopen(rfileres,"w"))==NULL) {
printf("Problem writing new parameter file: %s\n", fileres);goto end;	printf("Problem writing new parameter file: %s\n", rfileres);goto end;
fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;	fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
}	}
fprintf(ficres,"#%s\n",version);	fprintf(ficres,"#%s\n",version);
} /* End of mle != -3 */	} /* End of mle != -3 */
Line 6808 Please run with mle=-1 to get a correct	Line 7691 Please run with mle=-1 to get a correct
free_vector(annais,1,n);	free_vector(annais,1,n);
/* free_matrix(mint,1,maxwav,1,n);	/* free_matrix(mint,1,maxwav,1,n);
free_matrix(anint,1,maxwav,1,n);*/	free_matrix(anint,1,maxwav,1,n);*/
free_vector(moisdc,1,n);	/* free_vector(moisdc,1,n); */
free_vector(andc,1,n);	/* free_vector(andc,1,n); */
/* */	/* */

wav=ivector(1,imx);	wav=ivector(1,imx);
dh=imatrix(1,lastpass-firstpass+1,1,imx);	/* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
bh=imatrix(1,lastpass-firstpass+1,1,imx);	/* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
mw=imatrix(1,lastpass-firstpass+1,1,imx);	/* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
	dh=imatrix(1,lastpass-firstpass+2,1,imx); /* We are adding a wave if status is unknown at last wave but death occurs after last wave.*/
	bh=imatrix(1,lastpass-firstpass+2,1,imx);
	mw=imatrix(1,lastpass-firstpass+2,1,imx);

/* Concatenates waves */	/* Concatenates waves */
	/* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
	Death is a valid wave (if date is known).
	mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
	dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
	and mw[mi+1][i]. dh depends on stepm.
	*/

concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);	concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
/* */	/* */

	free_vector(moisdc,1,n);
	free_vector(andc,1,n);

/* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */	/* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */

nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);	nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
Line 6828 Please run with mle=-1 to get a correct	Line 7724 Please run with mle=-1 to get a correct
Ndum =ivector(-1,NCOVMAX);	Ndum =ivector(-1,NCOVMAX);
if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and ageage /	if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and ageage /
tricode(Tvar,nbcode,imx, Ndum); /*< Fills nbcode[Tvar[j]][l]; /	tricode(Tvar,nbcode,imx, Ndum); /*< Fills nbcode[Tvar[j]][l]; /
/* Nbcode gives the value of the lth modality of jth covariate, in	/* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
V2+V1age, there are 3 covariates Tvar[2]=1 (V1)./	V2+V1age, there are 3 covariates Tvar[2]=1 (V1)./
/* 1 to ncodemax[j] is the maximum value of this jth covariate */	/* 1 to ncodemax[j] which 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).*/
	/* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
	* codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
	* (currently 0 or 1) in the data.
	* In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
	* corresponding modality (h,j).
	*/

h=0;	h=0;


Line 6843 Please run with mle=-1 to get a correct	Line 7746 Please run with mle=-1 to get a correct

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 m=2**k
* codtabm(h,k)= 1 & (h-1) >> (k-1) ;	* codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;
	* #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
* h\k 1 2 3 4	* h\k 1 2 3 4
*______________________________	*______________________________
* 1 i=1 1 i=1 1 i=1 1 i=1 1	* 1 i=1 1 i=1 1 i=1 1 i=1 1
Line 6863 Please run with mle=-1 to get a correct	Line 7760 Please run with mle=-1 to get a correct
* 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;	/* How to do the opposite? From combination h (=1 to 2*k) how to get the value on the covariates? /
/* codtab[12][3]=1; */	/* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
/codtab[h][Tvar[k]]=j;/	* and the value of each covariate?
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]]);	* V1=1, V2=1, V3=2, V4=1 ?
}	* h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
}	* h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
}	* In order to get the real value in the data, we use nbcode
}	* nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
	* We are keeping this crazy system in order to be able (in the future?)
	* to have more than 2 values (0 or 1) for a covariate.
	* #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
	* h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
	* bbbbbbbb
	* 76543210
	* h-1 00000101 (6-1=5)
	*(h-1)>>(k-1)= 00000001 >> (2-1) = 1 right shift
	* &
	* 1 00000001 (1)
	* 00000001 = 1 & ((h-1) >> (k-1))
	* +1= 00000010 =2
	*
	* h=14, k=3 => h'=h-1=13, k'=k-1=2
	* h' 1101 =2^3+2^2+0x2^1+2^0
	* >>k' 11
	* & 00000001
	* = 00000001
	* +1 = 00000010=2 = codtabm(14,3)
	* Reverse h=6 and m=16?
	* cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
	* for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
	* decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
	* decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
	* V3=decodtabm(14,3,2**4)=2
	* h'=13 1101 =2^3+2^2+0x2^1+2^0
	*(h-1) >> (j-1) 0011 =13 >> 2
	* &1 000000001
	* = 000000001
	* +1= 000000010 =2
	* 2211
	* V1=1+1, V2=0+1, V3=1+1, V4=1+1
	* V3=2
	*/

	/* /\* for(h=1; h <=100 ;h++){ \/ /
	/* /\* printf("h=%2d ", h); \/ /
	/* /\* for(k=1; k <=10; 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 6897 Please run with mle=-1 to get a correct	Line 7852 Please run with mle=-1 to get a correct
/* Initialisation of ----------- gnuplot -------------*/	/* Initialisation of ----------- gnuplot -------------*/
strcpy(optionfilegnuplot,optionfilefiname);	strcpy(optionfilegnuplot,optionfilefiname);
if(mle==-3)	if(mle==-3)
strcat(optionfilegnuplot,"-mort");	strcat(optionfilegnuplot,"-MORT_");
strcat(optionfilegnuplot,".gp");	strcat(optionfilegnuplot,".gp");

if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {	if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
printf("Problem with file %s",optionfilegnuplot);	printf("Problem with file %s",optionfilegnuplot);
}	}
else{	else{
fprintf(ficgp,"\n# %s\n", version);	fprintf(ficgp,"\n# IMaCh-%s\n", version);
fprintf(ficgp,"# %s\n", optionfilegnuplot);	fprintf(ficgp,"# %s\n", optionfilegnuplot);
//fprintf(ficgp,"set missing 'NaNq'\n");	//fprintf(ficgp,"set missing 'NaNq'\n");
fprintf(ficgp,"set datafile missing 'NaNq'\n");	fprintf(ficgp,"set datafile missing 'NaNq'\n");
Line 6916 Please run with mle=-1 to get a correct	Line 7871 Please run with mle=-1 to get a correct

strcpy(optionfilehtm,optionfilefiname); /* Main html file */	strcpy(optionfilehtm,optionfilefiname); /* Main html file */
if(mle==-3)	if(mle==-3)
strcat(optionfilehtm,"-mort");	strcat(optionfilehtm,"-MORT_");
strcat(optionfilehtm,".htm");	strcat(optionfilehtm,".htm");
if((fichtm=fopen(optionfilehtm,"w"))==NULL) {	if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
printf("Problem with %s \n",optionfilehtm);	printf("Problem with %s \n",optionfilehtm);
Line 6931 Please run with mle=-1 to get a correct	Line 7886 Please run with mle=-1 to get a correct
else{	else{
fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \	fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
<hr size=\"2\" color=\"#EC5E5E\"> \n\	<hr size=\"2\" color=\"#EC5E5E\"> \n\
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\	Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);	optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
}	}

fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \	fprintf(fichtm,"<html><head>\n<head>\n<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n<title>IMaCh %s</title></head>\n <body><font size=\"7\"><a href=http:/euroreves.ined.fr/imach>IMaCh for Interpolated Markov Chain</a> </font><br>\n<font size=\"3\">Sponsored by Copyright (C) 2002-2015 <a href=http://www.ined.fr>INED</a>-EUROREVES-Institut de longévité-2013-2016-Japan Society for the Promotion of Sciences 日本学術振興会 (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - <a href=https://software.intel.com/en-us>Intel Software 2015-2018</a></font><br> \
<hr size=\"2\" color=\"#EC5E5E\"> \n\	<hr size=\"2\" color=\"#EC5E5E\"> \n\
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\	<font size=\"2\">IMaCh-%s <br> %s</font> \
	<hr size=\"2\" color=\"#EC5E5E\"> \n\
	Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
\n\	\n\
<hr size=\"2\" color=\"#EC5E5E\">\	<hr size=\"2\" color=\"#EC5E5E\">\
<ul><li><h4>Parameter files</h4>\n\	<ul><li><h4>Parameter files</h4>\n\
Line 6963 Title=%s <br>Datafile=%s Firstpass=%d La	Line 7920 Title=%s <br>Datafile=%s Firstpass=%d La

/* Calculates basic frequencies. Computes observed prevalence at single age	/* Calculates basic frequencies. Computes observed prevalence at single age
and prints on file fileres'p'. */	and prints on file fileres'p'. */
freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);	freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\
	firstpass, lastpass, stepm, weightopt, model);

fprintf(fichtm,"\n");	fprintf(fichtm,"\n");
fprintf(fichtm,"<br>Total number of observations=%d <br>\n\	fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
Line 7032 Interval (in months) between two waves:	Line 7990 Interval (in months) between two waves:
#else	#else
printf("Powell\n"); fprintf(ficlog,"Powell\n");	printf("Powell\n"); fprintf(ficlog,"Powell\n");
#endif	#endif
strcpy(filerespow,"pow-mort");	strcpy(filerespow,"POW-MORT_");
strcat(filerespow,fileres);	strcat(filerespow,fileresu);
if((ficrespow=fopen(filerespow,"w"))==NULL) {	if((ficrespow=fopen(filerespow,"w"))==NULL) {
printf("Problem with resultfile: %s\n", filerespow);	printf("Problem with resultfile: %s\n", filerespow);
fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);	fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
Line 7129 Interval (in months) between two waves:	Line 8087 Interval (in months) between two waves:
#endif	#endif
fclose(ficrespow);	fclose(ficrespow);

hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);	hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);

for(i=1; i <=NDIM; i++)	for(i=1; i <=NDIM; i++)
for(j=i+1;j<=NDIM;j++)	for(j=i+1;j<=NDIM;j++)
matcov[i][j]=matcov[j][i];	matcov[i][j]=matcov[j][i];

printf("\nCovariance matrix\n ");	printf("\nCovariance matrix\n ");
	fprintf(ficlog,"\nCovariance matrix\n ");
for(i=1; i <=NDIM; i++) {	for(i=1; i <=NDIM; i++) {
for(j=1;j<=NDIM;j++){	for(j=1;j<=NDIM;j++){
printf("%f ",matcov[i][j]);	printf("%f ",matcov[i][j]);
	fprintf(ficlog,"%f ",matcov[i][j]);
}	}
printf("\n ");	printf("\n "); fprintf(ficlog,"\n ");
}	}

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);
Line 7187 Please run with mle=-1 to get a correct	Line 8147 Please run with mle=-1 to get a correct
This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\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);	Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
}else	}else
printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);	printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \	printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
stepm, weightopt,\	stepm, weightopt,\
model,imx,p,matcov,agemortsup);	model,imx,p,matcov,agemortsup);

Line 7202 Please run with mle=-1 to get a correct	Line 8162 Please run with mle=-1 to get a correct
free_matrix(ximort,1,NDIM,1,NDIM);	free_matrix(ximort,1,NDIM,1,NDIM);
#endif	#endif
} /* Endof if mle==-3 mortality only */	} /* Endof if mle==-3 mortality only */
/* Standard maximisation */	/* Standard */
else{ /* For mle >=1 */	else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
globpr=0;/* debug */	globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
/* Computes likelihood for initial parameters */	/* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */	likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);	printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
for (k=1; k<=npar;k++)	for (k=1; k<=npar;k++)
printf(" %d %8.5f",k,p[k]);	printf(" %d %8.5f",k,p[k]);
printf("\n");	printf("\n");
globpr=1; /* again, to print the contributions */	if(mle>=1){ /* Could be 1 or 2, Real Maximization */
	/* mlikeli uses func not funcone */
	mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
	}
	if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
	globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
	/* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
	likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
	}
	globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */	likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);	printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
for (k=1; k<=npar;k++)	for (k=1; k<=npar;k++)
printf(" %d %8.5f",k,p[k]);	printf(" %d %8.5f",k,p[k]);
printf("\n");	printf("\n");
if(mle>=1){ /* Could be 1 or 2, Real Maximisation */
mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
}

/--------- 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);
Line 7246 Please run with mle=-1 to get a correct	Line 8212 Please run with mle=-1 to get a correct
}	}
}	}
}	}
if(mle!=0){	if(mle != 0){
/* Computing hessian and covariance matrix */	/* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
ftolhess=ftol; /* Usually correct */	ftolhess=ftol; /* Usually correct */
hesscov(matcov, p, npar, delti, ftolhess, func);	hesscov(matcov, hess, 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");
printf("Parameters and 95%% confidence intervals\n");	fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
fprintf(ficlog, "Parameters, T and confidence intervals\n");	for(i=1,jk=1; i <=nlstate; i++){
for(i=1,jk=1; i <=nlstate; i++){	for(k=1; k <=(nlstate+ndeath); k++){
for(k=1; k <=(nlstate+ndeath); k++){	if (k != i) {
if (k != i) {	printf("%d%d ",i,k);
printf("%d%d ",i,k);	fprintf(ficlog,"%d%d ",i,k);
fprintf(ficlog,"%d%d ",i,k);	for(j=1; j <=ncovmodel; j++){
for(j=1; j <=ncovmodel; j++){	printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96sqrt(matcov[jk][jk]),p[jk]+1.96sqrt(matcov[jk][jk]));
printf("%12.7f T=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-2sqrt(matcov[jk][jk]),p[jk]+2sqrt(matcov[jk][jk]));	fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96sqrt(matcov[jk][jk]),p[jk]+1.96sqrt(matcov[jk][jk]));
fprintf(ficlog,"%12.7f T=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-2sqrt(matcov[jk][jk]),p[jk]+2sqrt(matcov[jk][jk]));	jk++;
jk++;	}
	printf("\n");
	fprintf(ficlog,"\n");
}	}
printf("\n");
fprintf(ficlog,"\n");
}	}
}	}
}	} /* end of hesscov and Wald tests */

	/* */
fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");	fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
printf("# Scales (for hessian or gradient estimation)\n");	printf("# Scales (for hessian or gradient estimation)\n");
fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");	fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
Line 7292 Please run with mle=-1 to get a correct	Line 8259 Please run with mle=-1 to get a correct
}	}

fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");	fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
if(mle>=1)	if(mle >= 1) /* To big for the screen */
printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");	printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");	fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
/* # 121 Var(a12)\n\ */	/* # 121 Var(a12)\n\ */
Line 7355 Please run with mle=-1 to get a correct	Line 8322 Please run with mle=-1 to get a correct
fprintf(ficres," Var(%s%1d%1d)",ca,i,j);	fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
}else{	}else{
if(mle>=1)	if(mle>=1)
printf(" %.5e",matcov[jj][ll]);	printf(" %.7e",matcov[jj][ll]);
fprintf(ficlog," %.5e",matcov[jj][ll]);	fprintf(ficlog," %.7e",matcov[jj][ll]);
fprintf(ficres," %.5e",matcov[jj][ll]);	fprintf(ficres," %.7e",matcov[jj][ll]);
}	}
}	}
}	}
Line 7376 Please run with mle=-1 to get a correct	Line 8343 Please run with mle=-1 to get a correct

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

	/* while((c=getc(ficpar))=='#' && c!= EOF){ */
	/* ungetc(c,ficpar); */
	/* fgets(line, MAXLINE, ficpar); */
	/* fputs(line,stdout); */
	/* fputs(line,ficparo); */
	/* } */
	/* ungetc(c,ficpar); */

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

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

	/* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
if (estepm==0 \|\| estepm < stepm) estepm=stepm;	if (estepm==0 \|\| estepm < stepm) estepm=stepm;
if (fage <= 2) {	if (fage <= 2) {
bage = ageminpar;	bage = ageminpar;
Line 7394 Please run with mle=-1 to get a correct	Line 8384 Please run with mle=-1 to get a correct
}	}

fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");	fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);	fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);	fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);

/* Other stuffs, more or less useful */	/* Other stuffs, more or less useful */
while((c=getc(ficpar))=='#' && c!= EOF){	while((c=getc(ficpar))=='#' && c!= EOF){
Line 7458 Please run with mle=-1 to get a correct	Line 8448 Please run with mle=-1 to get a correct
This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\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);	Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
}else	}else
printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);	printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, pathc,p);

printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\	printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt,\
model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\	model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,estepm, \
jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);	jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);

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

free_ivector(wav,1,imx);	/* free_ivector(wav,1,imx); / / Moved after last prevalence call */
free_imatrix(dh,1,lastpass-firstpass+1,1,imx);	/* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
free_imatrix(bh,1,lastpass-firstpass+1,1,imx);	/* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
free_imatrix(mw,1,lastpass-firstpass+1,1,imx);	/* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */
free_lvector(num,1,n);	free_lvector(num,1,n);
free_vector(agedc,1,n);	free_vector(agedc,1,n);
/free_matrix(covar,0,NCOVMAX,1,n);/	/free_matrix(covar,0,NCOVMAX,1,n);/
Line 7485 Please run with mle=-1 to get a correct	Line 8475 Please run with mle=-1 to get a correct
/--------------- Prevalence limit (period or stable prevalence) --------------/	/--------------- Prevalence limit (period or stable prevalence) --------------/
/#include "prevlim.h"/ /* Use ficrespl, ficlog */	/#include "prevlim.h"/ /* Use ficrespl, ficlog */
prlim=matrix(1,nlstate,1,nlstate);	prlim=matrix(1,nlstate,1,nlstate);
prevalence_limit(p, prlim, ageminpar, agemaxpar);	prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
fclose(ficrespl);	fclose(ficrespl);

#ifdef FREEEXIT2	#ifdef FREEEXIT2
Line 7512 Please run with mle=-1 to get a correct	Line 8502 Please run with mle=-1 to get a correct
/if((stepm == 1) && (strcmp(model,".")==0)){/	/if((stepm == 1) && (strcmp(model,".")==0)){/
if(prevfcast==1){	if(prevfcast==1){
/* if(stepm ==1){*/	/* if(stepm ==1){*/
prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);	prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
/* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/	/* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
/* } */	/* } */
/* else{ */	/* else{ */
Line 7530 Please run with mle=-1 to get a correct	Line 8520 Please run with mle=-1 to get a correct
/* printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d, mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\	/* printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d, mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);	ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
*/	*/
	free_ivector(wav,1,imx);
	free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
	free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
	free_imatrix(mw,1,lastpass-firstpass+2,1,imx);


if (mobilav!=0) {	if (mobilav!=0) {
mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);	mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
Line 7542 Please run with mle=-1 to get a correct	Line 8537 Please run with mle=-1 to get a correct

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

strcpy(filerese,"e");	strcpy(filerese,"E_");
strcat(filerese,fileres);	strcat(filerese,fileresu);
if((ficreseij=fopen(filerese,"w"))==NULL) {	if((ficreseij=fopen(filerese,"w"))==NULL) {
printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);	printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);	fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
}	}
printf("Computing Health Expectancies: result on file '%s' \n", filerese);	printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);	fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
/*for(cptcov=1,k=0;cptcov<=i1;cptcov++){	/*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/	for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/

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

Line 7568 Please run with mle=-1 to get a correct	Line 8563 Please run with mle=-1 to get a correct
/}/	/}/
}	}
fclose(ficreseij);	fclose(ficreseij);
	printf("done evsij\n");fflush(stdout);
	fprintf(ficlog,"done evsij\n");fflush(ficlog);

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


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


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

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

strcpy(fileresv,"v");	strcpy(fileresv,"V_");
strcat(fileresv,fileres);	strcat(fileresv,fileresu);
if((ficresvij=fopen(fileresv,"w"))==NULL) {	if((ficresvij=fopen(fileresv,"w"))==NULL) {
printf("Problem with variance resultfile: %s\n", fileresv);exit(0);	printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);	fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
}	}
printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);	printf(" Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(stdout);
fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);	fprintf(ficlog," Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(ficlog);

/*for(cptcov=1,k=0;cptcov<=i1;cptcov++){	/*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/	for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/

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

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

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

eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);	eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
oldm=oldms;savm=savms;	oldm=oldms;savm=savms;
cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);	printf(" cvevsij %d, ",k);
/*	fprintf(ficlog, " cvevsij %d, ",k);
*/	cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
/* goto endfree; */	printf(" end cvevsij \n ");
	fprintf(ficlog, " end cvevsij \n ");
vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
pstamp(ficrest);	/*
	*/
	/* goto endfree; */
for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
oldm=oldms;savm=savms; /* Segmentation fault */	vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
cptcod= 0; /* To be deleted */	pstamp(ficrest);
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 ");
if(vpopbased==1)	for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);	oldm=oldms;savm=savms; /* ZZ Segmentation fault */
else	cptcod= 0; /* To be deleted */
fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");	printf("varevsij %d \n",vpopbased);
fprintf(ficrest,"# Age e.. (std) ");	fprintf(ficlog, "varevsij %d \n",vpopbased);
for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);	varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
fprintf(ficrest,"\n");	fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are ");
	if(vpopbased==1)
epj=vector(1,nlstate+1);	fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
for(age=bage; age <=fage ;age++){	else
prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);	fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
if (vpopbased==1) {	fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
if(mobilav ==0){	for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
for(i=1; i<=nlstate;i++)	fprintf(ficrest,"\n");
prlim[i][i]=probs[(int)age][i][k];	/* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
}else{ /* mobilav */	epj=vector(1,nlstate+1);
for(i=1; i<=nlstate;i++)	printf("Computing age specific period (stable) prevalences in each health state \n");
prlim[i][i]=mobaverage[(int)age][i][k];	fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
}	for(age=bage; age <=fage ;age++){
}	prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /ZZ Is it the correct prevalim /
	if (vpopbased==1) {
fprintf(ficrest," %4.0f",age);	if(mobilav ==0){
for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){	for(i=1; i<=nlstate;i++)
for(i=1, epj[j]=0.;i <=nlstate;i++) {	prlim[i][i]=probs[(int)age][i][k];
epj[j] += prlim[i][i]*eij[i][j][(int)age];	}else{ /* mobilav */
/* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/	for(i=1; i<=nlstate;i++)
}	prlim[i][i]=mobaverage[(int)age][i][k];
epj[nlstate+1] +=epj[j];
}	}
	}
for(i=1, vepp=0.;i <=nlstate;i++)
for(j=1;j <=nlstate;j++)	fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
vepp += vareij[i][j][(int)age];	/* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); / / to be done */
fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));	/* printf(" age %4.0f ",age); */
for(j=1;j <=nlstate;j++){	for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));	for(i=1, epj[j]=0.;i <=nlstate;i++) {
	epj[j] += 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]); */
}	}
fprintf(ficrest,"\n");	epj[nlstate+1] +=epj[j];
	}
	/* printf(" age %4.0f \n",age); */

	for(i=1, vepp=0.;i <=nlstate;i++)
	for(j=1;j <=nlstate;j++)
	vepp += vareij[i][j][(int)age];
	fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
	for(j=1;j <=nlstate;j++){
	fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
}	}
	fprintf(ficrest,"\n");
}	}
free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);	} /* End vpopbased */
free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);	free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
free_vector(epj,1,nlstate+1);	free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
	free_vector(epj,1,nlstate+1);
	printf("done \n");fflush(stdout);
	fprintf(ficlog,"done\n");fflush(ficlog);

/}/	/}/
}	} /* End k */
free_vector(weight,1,n);	free_vector(weight,1,n);
free_imatrix(Tvard,1,NCOVMAX,1,2);	free_imatrix(Tvard,1,NCOVMAX,1,2);
free_imatrix(s,1,maxwav+1,1,n);	free_imatrix(s,1,maxwav+1,1,n);
Line 7705 Please run with mle=-1 to get a correct	Line 8717 Please run with mle=-1 to get a correct
fclose(ficrescveij);	fclose(ficrescveij);
fclose(ficresvij);	fclose(ficresvij);
fclose(ficrest);	fclose(ficrest);
	printf("done Health expectancies\n");fflush(stdout);
	fprintf(ficlog,"done Health expectancies\n");fflush(ficlog);
fclose(ficpar);	fclose(ficpar);

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

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

/*for(cptcov=1,k=0;cptcov<=i1;cptcov++){	/*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/	for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
Line 7723 Please run with mle=-1 to get a correct	Line 8738 Please run with mle=-1 to get a correct
for (k=1; k <= (int) pow(2,cptcoveff); k++){	for (k=1; k <= (int) pow(2,cptcoveff); k++){
fprintf(ficresvpl,"\n#****** ");	fprintf(ficresvpl,"\n#****** ");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
fprintf(ficresvpl,"******\n");	fprintf(ficresvpl,"******\n");

varpl=matrix(1,nlstate,(int) bage, (int) fage);	varpl=matrix(1,nlstate,(int) bage, (int) fage);
oldm=oldms;savm=savms;	oldm=oldms;savm=savms;
varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);	varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);
free_matrix(varpl,1,nlstate,(int) bage, (int)fage);	free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
/}/	/}/
}	}

fclose(ficresvpl);	fclose(ficresvpl);
	printf("done variance-covariance of period prevalence\n");fflush(stdout);
	fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);

/---------- End : free ----------------/	/---------- End : free ----------------/
if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);	if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
Line 7747 Please run with mle=-1 to get a correct	Line 8764 Please run with mle=-1 to get a correct
free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);	free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
free_matrix(covar,0,NCOVMAX,1,n);	free_matrix(covar,0,NCOVMAX,1,n);
free_matrix(matcov,1,npar,1,npar);	free_matrix(matcov,1,npar,1,npar);
	free_matrix(hess,1,npar,1,npar);
/free_vector(delti,1,npar);/	/free_vector(delti,1,npar);/
free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);	free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
free_matrix(agev,1,maxwav,1,imx);	free_matrix(agev,1,maxwav,1,imx);
Line 7760 Please run with mle=-1 to get a correct	Line 8778 Please run with mle=-1 to get a correct
free_ivector(Tage,1,NCOVMAX);	free_ivector(Tage,1,NCOVMAX);

free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);	free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
free_imatrix(codtab,1,100,1,10);	/* free_imatrix(codtab,1,100,1,10); */
fflush(fichtm);	fflush(fichtm);
fflush(ficgp);	fflush(ficgp);

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

Removed from v.1.195
changed lines
	Added in v.1.215