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Diff for /imach/src/imach.c between versions 1.186 and 1.197

version 1.186, 2015/04/23 12:01:52	version 1.197, 2015/09/01 18:24:39
Line 1	Line 1
/* $Id$	/* $Id$
$State$	$State$
$Log$	$Log$
	Revision 1.197 2015/09/01 18:24:39 brouard
	* empty log message *

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

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

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

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

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

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

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

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

	Fix 1+age+.

	Revision 1.189 2015/04/30 14:45:16 brouard
	Summary: 0.98q2

	Revision 1.188 2015/04/30 08:27:53 brouard
	* empty log message *

	Revision 1.187 2015/04/29 09:11:15 brouard
	* empty log message *

Revision 1.186 2015/04/23 12:01:52 brouard	Revision 1.186 2015/04/23 12:01:52 brouard
Summary: V1*age is working now, version 0.98q1	Summary: V1*age is working now, version 0.98q1

Line 585	Line 625
end	end
*/	*/

	/* #define DEBUG */
	/* #define DEBUGBRENT */
#define POWELL /* Instead of NLOPT */	#define POWELL /* Instead of NLOPT */
	#define POWELLF1F3 /* Skip test */
/* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test \/ /	/* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test \/ /
/* #define MNBRAKORIGINAL /\* Don't use mnbrak fix \/ /	/* #define MNBRAKORIGINAL /\* Don't use mnbrak fix \/ /

Line 654 typedef struct {	Line 697 typedef struct {
#define NLSTATEMAX 8 /*< Maximum number of live states (for func) /	#define NLSTATEMAX 8 /*< Maximum number of live states (for func) /
#define NDEATHMAX 8 /*< Maximum number of dead states (for func) /	#define NDEATHMAX 8 /*< Maximum number of dead states (for func) /
#define NCOVMAX 20 /*< Maximum number of covariates, including generated covariates V1V2 */	#define NCOVMAX 20 /*< Maximum number of covariates, including generated covariates V1V2 */
#define codtabm(h,k) 1 & (h-1) >> (k-1) ;	#define codtabm(h,k) (1 & (h-1) >> (k-1))+1
#define MAXN 20000	#define MAXN 20000
#define YEARM 12. /*< Number of months per year /	#define YEARM 12. /*< Number of months per year /
#define AGESUP 130	#define AGESUP 130
#define AGEBASE 40	#define AGEBASE 40
	#define AGEOVERFLOW 1.e20
#define AGEGOMP 10 /*< Minimal age for Gompertz adjustment /	#define AGEGOMP 10 /*< Minimal age for Gompertz adjustment /
#ifdef _WIN32	#ifdef _WIN32
#define DIRSEPARATOR '\\'	#define DIRSEPARATOR '\\'
Line 672 typedef struct {	Line 716 typedef struct {

/* $Id$ */	/* $Id$ */
/* $State$ */	/* $State$ */
	#include "version.h"
char version[]="Imach version 0.98q1, April 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";	char version[]=__IMACH_VERSION__;
	char copyright[]="September 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
char fullversion[]="$Revision$ $Date$";	char fullversion[]="$Revision$ $Date$";
char strstart[80];	char strstart[80];
char optionfilext[10], optionfilefiname[FILENAMELENGTH];	char optionfilext[10], optionfilefiname[FILENAMELENGTH];
int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */	int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
int nvar=0, nforce=0; /* Number of variables, number of forces */	int nagesqr=0, nforce=0; /* nagesqr=1 if model is including ageage, number of forces /
/* Number of covariates model=V2+V1+ V3age+V2V4 */	/* Number of covariates model=V2+V1+ V3age+V2V4 */
int cptcovn=0; /*< cptcovn number of covariates added in the model (excepting constant and age and ageproduct) */	int cptcovn=0; /*< cptcovn number of covariates added in the model (excepting constant and age and ageproduct) */
int cptcovt=0; /*< cptcovt number of covariates added in the model (excepting constant and age) /	int cptcovt=0; /*< cptcovt number of covariates added in the model (excepting constant and age) /
Line 808 int estepm;	Line 853 int estepm;

int m,nb;	int m,nb;
long *num;	long *num;
int firstpass=0, lastpass=4,cod, ncodemax, Tage,cens;	int firstpass=0, lastpass=4,cod, cens;
	int ncodemax; / ncodemax[j]= Number of modalities of the j th
	covariate for which somebody answered excluding
	undefined. Usually 2: 0 and 1. */
	int ncodemaxwundef; / ncodemax[j]= Number of modalities of the j th
	covariate for which somebody answered including
	undefined. Usually 3: -1, 0 and 1. */
double *agev,moisnais, annais, moisdc, andc,mint, *anint;	double *agev,moisnais, annais, moisdc, andc,mint, *anint;
double pmmij, *probs;	double pmmij, *probs;
double ageexmed,agecens;	double ageexmed,agecens;
Line 819 int *s; / Status */	Line 870 int *s; / Status */
double *agedc;	double *agedc;
double covar; /< covar[j,i], value of jth covariate for individual i,	double covar; /< covar[j,i], value of jth covariate for individual i,
* covar=matrix(0,NCOVMAX,1,n);	* covar=matrix(0,NCOVMAX,1,n);
* cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]cov[2]; /	* cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]age; /
double idx;	double idx;
int *nbcode, Tvar; /*< model=V2 => Tvar[1]= 2 /	int *nbcode, Tvar; /*< model=V2 => Tvar[1]= 2 /
	int *Tage;
int Ndum; /* Freq of modality (tricode */	int Ndum; /* Freq of modality (tricode */
int codtab; /< codtab=imatrix(1,100,1,10); */	int codtab; /< codtab=imatrix(1,100,1,10); */
int *Tvard, Tprod, cptcovprod, *Tvaraff;	int *Tvard, Tprod, cptcovprod, *Tvaraff;
Line 915 char trimbb(char out, char *in)	Line 967 char trimbb(char out, char *in)
return s;	return s;
}	}

	/* char substrchaine(char out, char in, char chain) */
	/* { */
	/* /\* Substract chain 'chain' from 'in', return and output 'out' \/ /
	/* char s, t; */
	/* t=in;s=out; */
	/* while ((in != chain) && (in != '\0')){ /
	/* out++ = in++; */
	/* } */

	/* /\* in matches chain \/ /
	/* while ((in++ == chain++) && (in != '\0')){ /
	/* printf("in = %c, out= %c chain= %c \n", in, out, chain); */
	/* } */
	/* in--; chain--; */
	/* while ( (in != '\0')){ /
	/* printf("Bef in = %c, out= %c chain= %c \n", in, out, chain); */
	/* out++ = in++; */
	/* printf("Aft in = %c, out= %c chain= %c \n", in, out, chain); */
	/* } */
	/* out='\0'; /
	/* out=s; */
	/* return out; */
	/* } */
	char substrchaine(char out, char in, char chain)
	{
	/* Substract chain 'chain' from 'in', return and output 'out' */
	/* in="V1+V1age+ageage+V2", chain="ageage" /

	char *strloc;

	strcpy (out, in);
	strloc = strstr(out, chain); /* strloc points to out at ageage+V2 /
	printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
	if(strloc != NULL){
	/* will affect out / / strloc+strlenc(chain)=+V2 / / Will also work in Unicode */
	memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
	/* strcpy (strloc, strloc +strlen(chain));*/
	}
	printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
	return out;
	}


char cutl(char blocc, char alocc, char in, char occ)	char cutl(char blocc, char alocc, char in, char occ)
{	{
/* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'	/* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')	and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
gives blocc="abcdef2ghi" and alocc="j".	gives blocc="abcdef" and alocc="ghi2j".
If occ is not found blocc is null and alocc is equal to in. Returns blocc	If occ is not found blocc is null and alocc is equal to in. Returns blocc
*/	*/
char s, t;	char s, t;
Line 945 char cutl(char blocc, char *alocc, cha	Line 1040 char cutl(char blocc, char *alocc, cha
}	}
char cutv(char blocc, char alocc, char in, char occ)	char cutv(char blocc, char alocc, char in, char occ)
{	{
/* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'	/* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')	and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
gives blocc="abcdef2ghi" and alocc="j".	gives blocc="abcdef2ghi" and alocc="j".
If occ is not found blocc is null and alocc is equal to in. Returns alocc	If occ is not found blocc is null and alocc is equal to in. Returns alocc
Line 1256 double f1dim(double x)	Line 1351 double f1dim(double x)

/***************brent ***********************/	/***************brent ***********************/
double brent(double ax, double bx, double cx, double (f)(double), double tol, double xmin)	double brent(double ax, double bx, double cx, double (f)(double), double tol, double xmin)
{	{
	/* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
	* between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
	* the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
	* the minimum is returned as xmin, and the minimum function value is returned as brent , the
	* returned function value.
	*/
int iter;	int iter;
double a,b,d,etemp;	double a,b,d,etemp;
double fu=0,fv,fw,fx;	double fu=0,fv,fw,fx;
Line 1339 values at the three points, fa, fb , and	Line 1440 values at the three points, fa, fb , and
*/	*/
double ulim,u,r,q, dum;	double ulim,u,r,q, dum;
double fu;	double fu;

fa=(func)(*ax);	double scale=10.;
fb=(func)(*bx);	int iterscale=0;

	fa=(func)(ax); / xta[j]=pcom[j]+(ax)xicom[j]; fa=f(xta[j])*/
	fb=(func)(bx); / xtb[j]=pcom[j]+(bx)xicom[j]; fb=f(xtb[j]) */


	/* while(fb != fb){ /\* ax should be ok, reducing distance to ax \/ /
	/* printf("Warning mnbrak fb = %lf, bx=%lf ax=%lf fa==%lf iter=%d\n",fb, bx, ax, fa, iterscale++); */
	/* bx = ax - (ax - bx)/scale; */
	/* fb=(func)(bx); /\ xtb[j]=pcom[j]+(bx)xicom[j]; fb=f(xtb[j]) \/ /
	/* } */

if (fb > fa) {	if (fb > fa) {
SHFT(dum,ax,bx,dum)	SHFT(dum,ax,bx,dum)
SHFT(dum,fb,fa,dum)	SHFT(dum,fb,fa,dum)
Line 1374 values at the three points, fa, fb , and	Line 1486 values at the three points, fa, fb , and
#endif	#endif
#ifdef MNBRAKORIGINAL	#ifdef MNBRAKORIGINAL
#else	#else
if (fu > *fc) {	/* if (fu > fc) { /
#ifdef DEBUG	/* #ifdef DEBUG */
printf("mnbrak4 fu > fc \n");	/* printf("mnbrak4 fu > fc \n"); */
fprintf(ficlog, "mnbrak4 fu > fc\n");	/* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
#endif	/* #endif */
/* SHFT(u,cx,cx,u) /\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and \/ /	/* /\* SHFT(u,cx,cx,u) /\\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and \\/ \/ */
/* SHFT(fa,fc,fu,fc) /\ (b, u, c) is a bracket while test fb > fc will be fu > fc will exit \/ /	/* /\* SHFT(fa,fc,fu,fc) /\\ (b, u, c) is a bracket while test fb > fc will be fu > fc will exit \\/ \/ */
dum=u; /* Shifting c and u */	/* dum=u; /\* Shifting c and u \/ /
u = *cx;	/* u = cx; /
*cx = dum;	/* cx = dum; /
dum = fu;	/* dum = fu; */
fu = *fc;	/* fu = fc; /
*fc =dum;	/* fc =dum; /
} else { /* end */	/* } else { /\* end \/ /
	/* #ifdef DEBUG */
	/* printf("mnbrak3 fu < fc \n"); */
	/* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
	/* #endif */
	/* dum=u; /\* Shifting c and u \/ /
	/* u = cx; /
	/* cx = dum; /
	/* dum = fu; */
	/* fu = fc; /
	/* fc =dum; /
	/* } */
#ifdef DEBUG	#ifdef DEBUG
printf("mnbrak3 fu < fc \n");	printf("mnbrak34 fu < or >= fc \n");
fprintf(ficlog, "mnbrak3 fu < fc\n");	fprintf(ficlog, "mnbrak34 fu < fc\n");
#endif	#endif
dum=u; /* Shifting c and u */	dum=u; /* Shifting c and u */
u = *cx;	u = *cx;
*cx = dum;	*cx = dum;
dum = fu;	dum = fu;
fu = *fc;	fu = *fc;
*fc =dum;	*fc =dum;
}
#endif	#endif
} else if ((cx-u)(u-ulim) > 0.0) { /* u is after c but before ulim */	} else if ((cx-u)(u-ulim) > 0.0) { /* u is after c but before ulim */
#ifdef DEBUG	#ifdef DEBUG
Line 1458 void linmin(double p[], double xi[], int	Line 1580 void linmin(double p[], double xi[], int
int j;	int j;
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 */

ncom=n;	ncom=n;
pcom=vector(1,n);	pcom=vector(1,n);
Line 1467 void linmin(double p[], double xi[], int	Line 1591 void linmin(double p[], double xi[], int
pcom[j]=p[j];	pcom[j]=p[j];
xicom[j]=xi[j];	xicom[j]=xi[j];
}	}
ax=0.0;
xx=1.0;	/* axs=0.0; */
mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */	/* xxss=1; /\* 1 and using scale \/ /
fret=brent(ax,xx,bx,f1dim,TOL,&xmin); / Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */	xxs=1;
	/* do{ */
	ax=0.;
	xx= xxs;
	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) */
	/* 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)) */
	/* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
	/* 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) */
	/* 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){ */
	/* xxs=xxs/scale; /\* Trying a smaller xx, closer to initial ax=0 \/ /
	/* printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n", axs, xxs, fx,fb, fa, xx, ax, bx); */
	/* } */
	/* }while(fx != fx); */

	#ifdef DEBUGLINMIN
	printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n", ax,xx,bx,fa,fx,fb);
	#endif
	fret=brent(ax,xx,bx,f1dim,TOL,&xmin); / Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, fret(xmin),/
	/* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
	/* fmin = f(p[j] + xmin * xi[j]) */
	/* P+lambda n in that direction (lambdamin), with TOL between abscisses */
	/* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xminxicom[j]; /
#ifdef DEBUG	#ifdef DEBUG
printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);	printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);	fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
#endif	#endif
	#ifdef DEBUGLINMIN
	printf("linmin end ");
	#endif
for (j=1;j<=n;j++) {	for (j=1;j<=n;j++) {
xi[j] *= xmin;	/* printf(" before xi[%d]=%12.8f", j,xi[j]); */
p[j] += xi[j];	xi[j] = xmin; / xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
	/* 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 ); */
	p[j] += xi[j]; /* Parameters values are updated accordingly */
}	}
	/* printf("\n"); */
	#ifdef DEBUGLINMIN
	printf("Comparing last frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, fret, (*func)(p));
	for (j=1;j<=n;j++) {
	printf(" xi[%d]= %12.7f p[%d]= %12.7f",j,xi[j],j,p[j]);
	if(j % ncovmodel == 0)
	printf("\n");
	}
	#endif
free_vector(xicom,1,n);	free_vector(xicom,1,n);
free_vector(pcom,1,n);	free_vector(pcom,1,n);
}	}
Line 1513 void powell(double p[], double **xi, int	Line 1676 void powell(double p[], double **xi, int
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);	fp=(fret); / From former iteration or initial value */
ibig=0;	ibig=0;
del=0.0;	del=0.0;
rlast_time=rcurr_time;	rlast_time=rcurr_time;
Line 1523 void powell(double p[], double **xi, int	Line 1686 void powell(double p[], double **xi, int
printf("\nPowell iter=%d -2LL=%.12f %ld sec. %ld sec.",iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);	printf("\nPowell iter=%d -2LL=%.12f %ld sec. %ld sec.",iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
fprintf(ficlog,"\nPowell iter=%d -2LL=%.12f %ld sec. %ld sec.",iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);	fprintf(ficlog,"\nPowell iter=%d -2LL=%.12f %ld sec. %ld sec.",iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
/* fprintf(ficrespow,"%d %.12f %ld",iter,fret,curr_time.tm_sec-start_time.tm_sec); */	/* fprintf(ficrespow,"%d %.12f %ld",iter,fret,curr_time.tm_sec-start_time.tm_sec); */
for (i=1;i<=n;i++) {	for (i=1;i<=n;i++) {
printf(" %d %.12f",i, p[i]);	printf(" %d %.12f",i, p[i]);
fprintf(ficlog," %d %.12lf",i, p[i]);	fprintf(ficlog," %d %.12lf",i, p[i]);
fprintf(ficrespow," %.12lf", p[i]);	fprintf(ficrespow," %.12lf", p[i]);
Line 1551 void powell(double p[], double **xi, int	Line 1714 void powell(double p[], double **xi, int
fprintf(ficlog," - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);	fprintf(ficlog," - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
}	}
}	}
for (i=1;i<=n;i++) {	for (i=1;i<=n;i++) { /* For each direction i */
for (j=1;j<=n;j++) xit[j]=xi[j][i];	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);	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); /* xit[n] has been loaded for direction i */	linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
if (fabs(fptt-(fret)) > del) { / We are keeping the max gain on each of the n directions	/* Outputs are fret(new point p) p is updated and xit rescaled */
because that direction will be replaced unless the gain del is small	if (fabs(fptt-(fret)) > del) { / We are keeping the max gain on each of the n directions */
in comparison with the 'probable' gain, mu^2, with the last average direction.	/* because that direction will be replaced unless the gain del is small */
Unless the n directions are conjugate some gain in the determinant may be obtained	/* in comparison with the 'probable' gain, mu^2, with the last average direction. */
with the new direction.	/* Unless the n directions are conjugate some gain in the determinant may be obtained */
*/	/* with the new direction. */
del=fabs(fptt-(*fret));	del=fabs(fptt-(*fret));
ibig=i;	ibig=i;
}	}
Line 1585 void powell(double p[], double **xi, int	Line 1748 void powell(double p[], double **xi, int
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
#endif	#endif
} /* end i */	} /* end loop on each direction i */
	/* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
	/* But p and xit have been updated at the end of linmin, fret corresponds to new p, xit /
	/* New value of last point Pn is not computed, P(n-1) */
if (2.0fabs(fp-(fret)) <= ftol(fabs(fp)+fabs(fret))) { /* Did we reach enough precision? */	if (2.0fabs(fp-(fret)) <= ftol(fabs(fp)+fabs(fret))) { /* Did we reach enough precision? */
	/* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
	/* By adding ageage in a model, the new -2LL should be lower and the difference follows a /
	/* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
	/* decreased of more than 3.84 */
	/* By adding ageage and V1age the gain (-2LL) should be more than 5.99 (ddl=2) */
	/* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
	/* By adding 10 parameters more the gain should be 18.31 */

	/* Starting the program with initial values given by a former maximization will simply change */
	/* the scales of the directions and the directions, because the are reset to canonical directions */
	/* Thus the first calls to linmin will give new points and better maximizations until fp-(fret) is /
	/* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
#ifdef DEBUG	#ifdef DEBUG
int k[2],l;	int k[2],l;
k[0]=1;	k[0]=1;
Line 1616 void powell(double p[], double **xi, int	Line 1794 void powell(double p[], double **xi, int
free_vector(ptt,1,n);	free_vector(ptt,1,n);
free_vector(pt,1,n);	free_vector(pt,1,n);
return;	return;
}	} /* enough precision */
if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");	if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */	for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
ptt[j]=2.0*p[j]-pt[j];	ptt[j]=2.0*p[j]-pt[j];
Line 1624 void powell(double p[], double **xi, int	Line 1802 void powell(double p[], double **xi, int
pt[j]=p[j];	pt[j]=p[j];
}	}
fptt=(func)(ptt); / f_3 */	fptt=(func)(ptt); / f_3 */
	#ifdef POWELLF1F3
	#else
if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */	if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
	#endif
/* (x1 f1=fp), (x2 f2=fret), (x3 f3=fptt), (xm fm) /	/* (x1 f1=fp), (x2 f2=fret), (x3 f3=fptt), (xm fm) /
/* From x1 (P0) distance of x2 is at h and x3 is 2h */	/* From x1 (P0) distance of x2 is at h and x3 is 2h */
/* Let f"(x2) be the 2nd derivative equal everywhere. */	/* Let f"(x2) be the 2nd derivative equal everywhere. */
Line 1653 void powell(double p[], double **xi, int	Line 1834 void powell(double p[], double **xi, int
if (t < 0.0) { /* Then we use it for new direction */	if (t < 0.0) { /* Then we use it for new direction */
#else	#else
if (directestt < 0.0) { / Contradiction between both tests */	if (directestt < 0.0) { / Contradiction between both tests */
printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);	printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0(fret)+fptt, fp -(*fret) -del, fp-fptt);	printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0(fret)+fptt, fp -(*fret) -del, fp-fptt);
fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);	fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0(fret)+fptt, fp -(*fret) -del, fp-fptt);	fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0(fret)+fptt, fp -(*fret) -del, fp-fptt);
}	}
if (directest < 0.0) { /* Then we use it for new direction */	if (directest < 0.0) { /* Then we use it for new direction */
#endif	#endif
linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction.*/	#ifdef DEBUGLINMIN
	printf("Before linmin in direction P%d-P0\n",n);
	for (j=1;j<=n;j++) {
	printf("Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
	if(j % ncovmodel == 0)
	printf("\n");
	}
	#endif
	linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
	#ifdef DEBUGLINMIN
	for (j=1;j<=n;j++) {
	printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
	if(j % ncovmodel == 0)
	printf("\n");
	}
	#endif
for (j=1;j<=n;j++) {	for (j=1;j<=n;j++) {
xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */	xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */	xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
Line 1678 void powell(double p[], double **xi, int	Line 1874 void powell(double p[], double **xi, int
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
#endif	#endif
} /* end of t negative */	} /* end of t or directest negative */
	#ifdef POWELLF1F3
	#else
} /* end if (fptt < fp) */	} /* end if (fptt < fp) */
}	#endif
	} /* loop iteration */
}	}

/** Prevalence limit (stable or period prevalence) **************/	/** Prevalence limit (stable or period prevalence) **************/
Line 1709 double prevalim(double prlim, int nl	Line 1908 double prevalim(double prlim, int nl
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)
	cov[3]= agefin*agefin;;
for (k=1; k<=cptcovn;k++) {	for (k=1; k<=cptcovn;k++) {
cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];	cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
/printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);/	/* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf 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]]);*/
}	}
/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+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]][codtab[ij][Tvar[k]]]*cov[2];
for (k=1; k<=cptcovprod;k++) /* Useless */	for (k=1; k<=cptcovprod;k++) /* Useless */
cov[2+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]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];

/printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);/	/printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);/
/printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);/	/printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);/
Line 1871 double *hpxij(double *po, int nhstep	Line 2071 double *hpxij(double *po, int nhstep
int i, j, d, h, k;	int i, j, d, h, k;
double **out, cov[NCOVMAX+1];	double **out, cov[NCOVMAX+1];
double **newm;	double **newm;
	double agexact;

/* 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 1884 double *hpxij(double *po, int nhstep	Line 2085 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.;
cov[2]=age+((h-1)hstepm + (d-1))stepm/YEARM;	agexact=age+((h-1)hstepm + (d-1))stepm/YEARM;
	cov[2]=agexact;
	if(nagesqr==1)
	cov[3]= agexact*agexact;
for (k=1; k<=cptcovn;k++)	for (k=1; k<=cptcovn;k++)
cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];	cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[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+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];	cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[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+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]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];


/printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);/	/printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);/
Line 1943 double func( double *x)	Line 2147 double func( double *x)
int s1, s2;	int s1, s2;
double bbh, survp;	double bbh, survp;
long ipmx;	long ipmx;
	double agexact;
/extern weight /	/extern weight /
/* We are differentiating ll according to initial status */	/* We are differentiating ll according to initial status */
/* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/	/* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
Line 1964 double func( double *x)	Line 2169 double func( double *x)
to be observed in j being in i according to the model.	to be observed in j being in i according to the model.
*/	*/
for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */	for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
cov[2+k]=covar[Tvar[k]][i];	cov[2+nagesqr+k]=covar[Tvar[k]][i];
}	}
/* In model V2+V1V4+ageV3+V3V2 Tvar[1] is V2, Tvar[2=V1V4]	/* In model V2+V1V4+ageV3+V3V2 Tvar[1] is V2, Tvar[2=V1V4]
is 6, Tvar[3=ageV3] should not be computed because of age Tvar[4=V3V2]	is 6, Tvar[3=ageV3] should not be computed because of age Tvar[4=V3V2]
Line 1977 double func( double *x)	Line 2182 double func( double *x)
}	}
for(d=0; d<dh[mi][i]; d++){	for(d=0; d<dh[mi][i]; d++){
newm=savm;	newm=savm;
cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;	agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
	cov[2]=agexact;
	if(nagesqr==1)
	cov[3]= agexact*agexact;
for (kk=1; kk<=cptcovage;kk++) {	for (kk=1; kk<=cptcovage;kk++) {
cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]cov[2]; / Tage[kk] gives the data-covariate associated with age */	cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]agexact; / Tage[kk] gives the data-covariate associated with age */
}	}
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));	1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
Line 2090 double func( double *x)	Line 2298 double func( double *x)
} /* end of individual */	} /* end of individual */
} else if(mle==2){	} else if(mle==2){
for (i=1,ipmx=0, sw=0.; i<=imx; i++){	for (i=1,ipmx=0, sw=0.; i<=imx; i++){
for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];	for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
for(mi=1; mi<= wav[i]-1; mi++){	for(mi=1; mi<= wav[i]-1; mi++){
for (ii=1;ii<=nlstate+ndeath;ii++)	for (ii=1;ii<=nlstate+ndeath;ii++)
for (j=1;j<=nlstate+ndeath;j++){	for (j=1;j<=nlstate+ndeath;j++){
Line 2099 double func( double *x)	Line 2307 double func( double *x)
}	}
for(d=0; d<=dh[mi][i]; d++){	for(d=0; d<=dh[mi][i]; d++){
newm=savm;	newm=savm;
cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;	agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
	cov[2]=agexact;
	if(nagesqr==1)
	cov[3]= agexact*agexact;
for (kk=1; kk<=cptcovage;kk++) {	for (kk=1; kk<=cptcovage;kk++) {
cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];	cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
}	}
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));	1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
Line 2120 double func( double *x)	Line 2331 double func( double *x)
} /* end of individual */	} /* end of individual */
} else if(mle==3){ /* exponential inter-extrapolation */	} else if(mle==3){ /* exponential inter-extrapolation */
for (i=1,ipmx=0, sw=0.; i<=imx; i++){	for (i=1,ipmx=0, sw=0.; i<=imx; i++){
for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];	for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
for(mi=1; mi<= wav[i]-1; mi++){	for(mi=1; mi<= wav[i]-1; mi++){
for (ii=1;ii<=nlstate+ndeath;ii++)	for (ii=1;ii<=nlstate+ndeath;ii++)
for (j=1;j<=nlstate+ndeath;j++){	for (j=1;j<=nlstate+ndeath;j++){
Line 2129 double func( double *x)	Line 2340 double func( double *x)
}	}
for(d=0; d<dh[mi][i]; d++){	for(d=0; d<dh[mi][i]; d++){
newm=savm;	newm=savm;
cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;	agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
	cov[2]=agexact;
	if(nagesqr==1)
	cov[3]= agexact*agexact;
for (kk=1; kk<=cptcovage;kk++) {	for (kk=1; kk<=cptcovage;kk++) {
cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];	cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
}	}
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));	1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
Line 2150 double func( double *x)	Line 2364 double func( double *x)
} /* end of individual */	} /* end of individual */
}else if (mle==4){ /* ml=4 no inter-extrapolation */	}else if (mle==4){ /* ml=4 no inter-extrapolation */
for (i=1,ipmx=0, sw=0.; i<=imx; i++){	for (i=1,ipmx=0, sw=0.; i<=imx; i++){
for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];	for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
for(mi=1; mi<= wav[i]-1; mi++){	for(mi=1; mi<= wav[i]-1; mi++){
for (ii=1;ii<=nlstate+ndeath;ii++)	for (ii=1;ii<=nlstate+ndeath;ii++)
for (j=1;j<=nlstate+ndeath;j++){	for (j=1;j<=nlstate+ndeath;j++){
Line 2159 double func( double *x)	Line 2373 double func( double *x)
}	}
for(d=0; d<dh[mi][i]; d++){	for(d=0; d<dh[mi][i]; d++){
newm=savm;	newm=savm;
cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;	agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
	cov[2]=agexact;
	if(nagesqr==1)
	cov[3]= agexact*agexact;
for (kk=1; kk<=cptcovage;kk++) {	for (kk=1; kk<=cptcovage;kk++) {
cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];	cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
}	}

out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
Line 2185 double func( double *x)	Line 2402 double func( double *x)
} /* end of individual */	} /* end of individual */
}else{ /* ml=5 no inter-extrapolation no jackson =0.8a */	}else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
for (i=1,ipmx=0, sw=0.; i<=imx; i++){	for (i=1,ipmx=0, sw=0.; i<=imx; i++){
for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];	for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
for(mi=1; mi<= wav[i]-1; mi++){	for(mi=1; mi<= wav[i]-1; mi++){
for (ii=1;ii<=nlstate+ndeath;ii++)	for (ii=1;ii<=nlstate+ndeath;ii++)
for (j=1;j<=nlstate+ndeath;j++){	for (j=1;j<=nlstate+ndeath;j++){
Line 2194 double func( double *x)	Line 2411 double func( double *x)
}	}
for(d=0; d<dh[mi][i]; d++){	for(d=0; d<dh[mi][i]; d++){
newm=savm;	newm=savm;
cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;	agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
	cov[2]=agexact;
	if(nagesqr==1)
	cov[3]= agexact*agexact;
for (kk=1; kk<=cptcovage;kk++) {	for (kk=1; kk<=cptcovage;kk++) {
cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];	cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
}	}

out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
Line 2232 double funcone( double *x)	Line 2452 double funcone( double *x)
double llt;	double llt;
int s1, s2;	int s1, s2;
double bbh, survp;	double bbh, survp;
	double agexact;
/extern weight /	/extern weight /
/* We are differentiating ll according to initial status */	/* We are differentiating ll according to initial status */
/* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/	/* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
Line 2243 double funcone( double *x)	Line 2464 double funcone( double *x)
for(k=1; k<=nlstate; k++) ll[k]=0.;	for(k=1; k<=nlstate; k++) ll[k]=0.;

for (i=1,ipmx=0, sw=0.; i<=imx; i++){	for (i=1,ipmx=0, sw=0.; i<=imx; i++){
for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];	for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
for(mi=1; mi<= wav[i]-1; mi++){	for(mi=1; mi<= wav[i]-1; mi++){
for (ii=1;ii<=nlstate+ndeath;ii++)	for (ii=1;ii<=nlstate+ndeath;ii++)
for (j=1;j<=nlstate+ndeath;j++){	for (j=1;j<=nlstate+ndeath;j++){
Line 2252 double funcone( double *x)	Line 2473 double funcone( double *x)
}	}
for(d=0; d<dh[mi][i]; d++){	for(d=0; d<dh[mi][i]; d++){
newm=savm;	newm=savm;
cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;	agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
	cov[2]=agexact;
	if(nagesqr==1)
	cov[3]= agexact*agexact;
for (kk=1; kk<=cptcovage;kk++) {	for (kk=1; kk<=cptcovage;kk++) {
cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];	cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
}	}

/* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */	/* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));	1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
Line 2689 void lubksb(double *a, int n, int indx	Line 2914 void lubksb(double *a, int n, int indx

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

/********** Frequencies ******************/	/********** Frequencies ******************/
Line 3112 void tricode(int Tvar, int *nbcode, in	Line 3337 void tricode(int Tvar, int *nbcode, in

cptcoveff=0;	cptcoveff=0;

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

/* Loop on covariates without age and products */	/* Loop on covariates without age and products */
for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2age+ V3 + V3V4 keeps V1 + V3 = 2 only */	for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2age+ V3 + V3V4 keeps V1 + V3 = 2 only */
	for (k=-1; k < maxncov; k++) Ndum[k]=0;
for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the	for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
modality of this covariate Vj*/	modality of this covariate Vj*/
ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i	ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
Line 3139 void tricode(int Tvar, int *nbcode, in	Line 3364 void tricode(int Tvar, int *nbcode, in
/* getting the maximum value of the modality of the covariate	/* getting the maximum value of the modality of the covariate
(should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and	(should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
female is 1, then modmaxcovj=1.*/	female is 1, then modmaxcovj=1.*/
}	} /* end for loop on individuals i */
printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);	printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
	fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
cptcode=modmaxcovj;	cptcode=modmaxcovj;
/* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */	/* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
/for (i=0; i<=cptcode; i++) {/	/for (i=0; i<=cptcode; i++) {/
for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1// For each value of the modality of model-cov j */	for (k=modmincovj; k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1// For each value k of the modality of model-cov j */
printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);	printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */	fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */	if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
	if( k != -1){
	ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th
	covariate for which somebody answered excluding
	undefined. Usually 2: 0 and 1. */
	}
	ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
	covariate for which somebody answered including
	undefined. Usually 3: -1, 0 and 1. */
}	}
/* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for	/* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */	historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
Line 3164 void tricode(int Tvar, int *nbcode, in	Line 3398 void tricode(int Tvar, int *nbcode, in
nbcode[Tvar[j]][1]=0;	nbcode[Tvar[j]][1]=0;
nbcode[Tvar[j]][2]=1;	nbcode[Tvar[j]][2]=1;
nbcode[Tvar[j]][3]=2;	nbcode[Tvar[j]][3]=2;
	To be continued (not working yet).
*/	*/
ij=1; /* ij is similar to i but can jumps over null modalities */	ij=0; /* ij is similar to i but can jump over null modalities */
for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */	for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 // Could be 1 to 4 */	if (Ndum[i] == 0) { /* If nobody responded to this modality k */
/recode from 0 /	break;
if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */	}
nbcode[Tvar[j]][ij]=k; /* stores the modality k in an array nbcode.	ij++;
k is a modality. If we have model=V1+V1*sex	nbcode[Tvar[j]][ij]=i; /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/
then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */	cptcode = ij; /* New max modality for covar j */
ij++;	} /* end of loop on modality i=-1 to 1 or more */
}
if (ij > ncodemax[j]) break;	/* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 \//\ Could be 1 to 4 \//\ cptcode=modmaxcovj \/ /
} /* end of loop on */	/* /\recode from 0 \/ */
} /* end of loop on modality */	/* k is a modality. If we have model=V1+V1sex /
	/* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
	/* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode \/ /
	/* } */
	/* /\* cptcode = ij; \/ /\ New max modality for covar j \/ /
	/* if (ij > ncodemax[j]) { */
	/* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
	/* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
	/* break; */
	/* } */
	/* } /\* end of loop on modality k \/ /
} /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/	} /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/

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

for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */	for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually ageage /
/* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1V2./	/* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1V2./
ij=Tvar[i]; /* Tvar might be -1 if status was unknown */	ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
Ndum[ij]++;	Ndum[ij]++; /* Might be supersed V1 + V1age /
}	}

ij=1;	ij=0;
for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(ageV3), 5(V3V2) 6(V1V4) /	for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(ageV3), 5(V3V2) 6(V1V4) /
/printf("Ndum[%d]=%d\n",i, Ndum[i]);/	/printf("Ndum[%d]=%d\n",i, Ndum[i]);/
if((Ndum[i]!=0) && (i<=ncovcol)){	if((Ndum[i]!=0) && (i<=ncovcol)){
	ij++;
/printf("diff Ndum[%d]=%d\n",i, Ndum[i]);/	/printf("diff Ndum[%d]=%d\n",i, Ndum[i]);/
Tvaraff[ij]=i; /For printing (unclear) /	Tvaraff[ij]=i; /For printing (unclear) /
ij++;	}else{
}else	/* Tvaraff[ij]=0; */
Tvaraff[ij]=0;	}
}	}
ij--;	/* ij--; */
cptcoveff=ij; /Number of total covariates/	cptcoveff=ij; /Number of total covariates/

}	}
Line 3989 void varprob(char optionfilefiname[], do	Line 4235 void varprob(char optionfilefiname[], do
fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");	fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
fprintf(fichtm,"\n");	fprintf(fichtm,"\n");

fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);	fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4></br>this page is important in order to visualize confidence intervals and especially correlation between disability and recovery</li>\n",optionfilehtmcov);
fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\	fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);
file %s<br>\n",optionfilehtmcov);	fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
and drawn. It helps understanding how is the covariance between two incidences.\	and drawn. It helps understanding how is the covariance between two incidences.\
They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");	They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \	fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
Line 4039 To be simple, these graphs help to under	Line 4284 To be simple, these graphs help to under
gm=vector(1,(nlstate)*(nlstate+ndeath));	gm=vector(1,(nlstate)*(nlstate+ndeath));
for (age=bage; age<=fage; age ++){	for (age=bage; age<=fage; age ++){
cov[2]=age;	cov[2]=age;
	if(nagesqr==1)
	cov[3]= age*age;
for (k=1; k<=cptcovn;k++) {	for (k=1; k<=cptcovn;k++) {
cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4	cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[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 4050 To be simple, these graphs help to under	Line 4297 To be simple, these graphs help to under
/* 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]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
for (k=1; k<=cptcovprod;k++)	for (k=1; k<=cptcovprod;k++)
cov[2+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]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];


for(theta=1; theta <=npar; theta++){	for(theta=1; theta <=npar; theta++){
Line 4282 fprintf(fichtm," \n<ul><li><b>Graphs</b>	Line 4529 fprintf(fichtm," \n<ul><li><b>Graphs</b>

jj1=0;	jj1=0;
for(k1=1; k1<=m;k1++){	for(k1=1; k1<=m;k1++){
for(i1=1; i1<=ncodemax[k1];i1++){	/* for(i1=1; i1<=ncodemax[k1];i1++){ */
jj1++;	jj1++;
if (cptcovn > 0) {	if (cptcovn > 0) {
fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");	fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
for (cpt=1; cpt<=cptcoveff;cpt++)	for (cpt=1; cpt<=cptcoveff;cpt++){
fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);	fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
	printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);fflush(stdout);
	}
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");	fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
}	}
/* Pij */	/* Pij */
Line 4306 fprintf(fichtm," \n<ul><li><b>Graphs</b>	Line 4555 fprintf(fichtm," \n<ul><li><b>Graphs</b>
fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \	fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</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.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
}	}
} /* end i1 */	/* } /\* end i1 \/ /
}/* End k1 */	}/* End k1 */
fprintf(fichtm,"</ul>");	fprintf(fichtm,"</ul>");


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

fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",	fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));	subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",	- Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
Line 4356 fprintf(fichtm," \n<ul><li><b>Graphs</b>	Line 4612 fprintf(fichtm," \n<ul><li><b>Graphs</b>

jj1=0;	jj1=0;
for(k1=1; k1<=m;k1++){	for(k1=1; k1<=m;k1++){
for(i1=1; i1<=ncodemax[k1];i1++){	/* for(i1=1; i1<=ncodemax[k1];i1++){ */
jj1++;	jj1++;
if (cptcovn > 0) {	if (cptcovn > 0) {
fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");	fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
Line 4375 true period expectancies (those weighted	Line 4631 true period expectancies (those weighted
drawn in addition to the population based expectancies computed using\	drawn in addition to the population based expectancies computed using\
observed and cahotic prevalences: %s%d.png<br>\	observed and cahotic prevalences: %s%d.png<br>\
<img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);	<img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
} /* end i1 */	/* } /\* end i1 \/ /
}/* End k1 */	}/* End k1 */
fprintf(fichtm,"</ul>");	fprintf(fichtm,"</ul>");
fflush(fichtm);	fflush(fichtm);
Line 4510 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 4766 plot [%.f:%.f] ", ageminpar, agemaxpar)
} /* end covariate */	} /* end covariate */

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

/goto avoid;/	/goto avoid;/
	fprintf(ficgp,"\n##############\n#Graphics of of probabilities or incidences\n#############\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(p13/p11)=a13+b13age+c13ageage+d13V1+e13V1*age\n");
	fprintf(ficgp,"# logi(p13/p11)=p6 +p7age +p8ageage+ p9V1+ p10V1age\n");
	fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12age+c12ageage+d12V1+e12V1*age)\n");
	fprintf(ficgp,"# +exp(a13+b13age+c13ageage+d13V1+e13V1*age)+...)\n");
	fprintf(ficgp,"# p11=1/(1+exp(a12+b12age+c12ageage+d12V1+e12V1*age)\n");
	fprintf(ficgp,"# +exp(a13+b13age+c13ageage+d13V1+e13V1*age)+...)\n");
	fprintf(ficgp,"# p12=exp(a12+b12age+c12ageage+d12V1+e12V1*age)/\n");
	fprintf(ficgp,"# (1+exp(a12+b12age+c12ageage+d12V1+e12V1*age)\n");
	fprintf(ficgp,"# +exp(a13+b13age+c13ageage+d13V1+e13V1*age))\n");
	fprintf(ficgp,"# +exp(a14+b14age+c14ageage+d14V1+e14V1*age)+...)\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<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
	fprintf(ficgp,"# ng=%d\n",ng);
	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,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);	fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
if (ng==2)	if (ng==2)
fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");	fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
Line 4536 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 4814 plot [%.f:%.f] ", ageminpar, agemaxpar)
for(k=1; k<=(nlstate+ndeath); k++) {	for(k=1; k<=(nlstate+ndeath); k++) {
if (k != k2){	if (k != k2){
if(ng==2)	if(ng==2)
fprintf(ficgp," %fexp(p%d+p%dx",YEARM/stepm,i,i+1);	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);
else	else
fprintf(ficgp," exp(p%d+p%d*x",i,i+1);	if(nagesqr==0)
	fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
	else /* nagesqr =1 */
	fprintf(ficgp," exp(p%d+p%dx+p%dx*x",i,i+1,i+1+nagesqr);
ij=1;/* To be checked else nbcode[0][0] wrong */	ij=1;/* To be checked else nbcode[0][0] wrong */
for(j=3; j <=ncovmodel; 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-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]][codtab[jk][Tvar[j-2]]]);
	ij++;
	}
}	}
else	else
fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);	fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
}	}
fprintf(ficgp,")/(1");	fprintf(ficgp,")/(1");

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

ij=1;	ij=1;
for(j=3; j <=ncovmodel; 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,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]][codtab[jk][Tvar[j-2]]]);
	ij++;
	}
}	}
else	else
fprintf(ficgp,"+p%d%d",k3+(k1-1)ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);	fprintf(ficgp,"+p%d%d",k3+(k1-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
}	}
fprintf(ficgp,")");	fprintf(ficgp,")");
}	}
Line 5175 int readdata(char datafile[], int firsto	Line 5468 int readdata(char datafile[], int firsto


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

i=1;	i=1;
Line 5353 void removespace(char *str) {	Line 5646 void removespace(char *str) {
}	}

int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:	int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
* Model V1+V2+V3+V8+V7V8+V5V6+V8age+V3age	* Model V1+V2+V3+V8+V7V8+V5V6+V8age+V3age+age*age
* - cptcovt total number of covariates of the model nbocc(+)+1 = 8	* - nagesqr = 1 if age*age in the model, otherwise 0.
* - cptcovn or number of covariates k of the models excluding age*products =6	* - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
	* - cptcovn or number of covariates k of the models excluding ageproducts =6 and ageage
* - cptcovage number of covariates with age*products =2	* - cptcovage number of covariates with age*products =2
* - cptcovs number of simple covariates	* - cptcovs number of simple covariates
* - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10	* - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
Line 5370 int decodemodel ( char model[], int last	Line 5664 int decodemodel ( char model[], int last
int j1, k1, k2;	int j1, k1, k2;
char modelsav[80];	char modelsav[80];
char stra[80], strb[80], strc[80], strd[80],stre[80];	char stra[80], strb[80], strc[80], strd[80],stre[80];
	char *strpt;

/removespace(model);/	/removespace(model);/
if (strlen(model) >1){ /* If there is at least 1 covariate */	if (strlen(model) >1){ /* If there is at least 1 covariate */
j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;	j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
j=nbocc(model,'+'); /*< j=Number of '+' /
j1=nbocc(model,''); /< j1=Number of '' */
cptcovs=j+1-j1; /*< Number of simple covariates V1+V2age+V3 +V3V4=> V1 + V3 =2 /
cptcovt= j+1; /* Number of total covariates in the model V1 + V2age+ V3 + V3V4=> 4*/
/* including age products which are counted in cptcovage.
* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
cptcovprod=j1; /*< Number of products V1V2 +v3age = 2 /
cptcovprodnoage=0; /*< Number of covariate products without age: V3V4 =1 */
strcpy(modelsav,model);
if (strstr(model,"AGE") !=0){	if (strstr(model,"AGE") !=0){
printf("Error. AGE must be in lower case 'age' model=%s ",model);	printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);	fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
return 1;	return 1;
}	}
if (strstr(model,"v") !=0){	if (strstr(model,"v") !=0){
Line 5393 int decodemodel ( char model[], int last	Line 5679 int decodemodel ( char model[], int last
fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);	fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
return 1;	return 1;
}	}
	strcpy(modelsav,model);
/* Design	if ((strpt=strstr(model,"age*age")) !=0){
* V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight	printf(" strpt=%s, model=%s\n",strpt, model);
* < ncovcol=8 >	if(strpt != model){
* Model V2 + V1 + V3age + V3 + V5V6 + V7V8 + V8age + V8	printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
* k= 1 2 3 4 5 6 7 8	'model=1+age+ageage+V1.' or 'model=1+age+ageage+V1+V1*age.', please swap as well as \n \
* cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8	corresponding column of parameters.\n",model);
* covar[k,i], value of kth covariate if not including age for individual i:	fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
* covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)	'model=1+age+ageage+V1.' or 'model=1+age+ageage+V1+V1*age.', please swap as well as \n \
* Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8	corresponding column of parameters.\n",model); fflush(ficlog);
* if multiplied by age: V3age Tvar[3=V3age]=3 (V3) Tvar[7]=8 and	return 1;
* Tage[++cptcovage]=k	}
* if products, new covar are created after ncovcol with k1
* Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
* Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
* Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
* Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
* Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
* V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
* < ncovcol=8 >
* Model V2 + V1 + V3age + V3 + V5V6 + V7V8 + V8age + V8 d1 d1 d2 d2
* k= 1 2 3 4 5 6 7 8 9 10 11 12
* Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
* p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
* p Tprod[1]@2={ 6, 5}
*p Tvard[1][1]@4= {7, 8, 5, 6}
* covar[k][i]= V2 V1 ? V3 V5V6? V7V8? ? V8
* cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
*How to reorganize?
* Model V1 + V2 + V3 + V8 + V5V6 + V7V8 + V3age + V8age
* Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
* {2, 1, 4, 8, 5, 6, 3, 7}
* Struct []
*/

/* This loop fills the array Tvar from the string 'model'.*/	nagesqr=1;
/* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */	if (strstr(model,"+age*age") !=0)
/* modelsav=V2+V1+V4+ageV3 strb=ageV3 stra=V2+V1+V4 */	substrchaine(modelsav, model, "+age*age");
/* k=4 (ageV3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 /	else if (strstr(model,"age*age+") !=0)
/* k=3 V4 Tvar[k=3]= 4 (from V4) */	substrchaine(modelsav, model, "age*age+");
/* k=2 V1 Tvar[k=2]= 1 (from V1) */	else
/* k=1 Tvar[1]=2 (from V2) */	substrchaine(modelsav, model, "age*age");
/* k=5 Tvar[5] */	}else
/* for (k=1; k<=cptcovn;k++) { */	nagesqr=0;
/* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */	if (strlen(modelsav) >1){
/* } */	j=nbocc(modelsav,'+'); /*< j=Number of '+' /
/* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]cov[2]; /	j1=nbocc(modelsav,''); /< j1=Number of '' */
/*	cptcovs=j+1-j1; /*< Number of simple covariates V1+V1age+V3 +V3V4+ageage=> V1 + V3 =2 */
* Treating invertedly V2+V1+V3age+V2V4 is as if written V2V4 +V3age + V1 + V2 */	cptcovt= j+1; /* Number of total covariates in the model, not including
for(k=cptcovt; k>=1;k--) /*< Number of covariates /	* cst, age and age*age
	* V1+V1age+ V3 + V3V4+ageage=> 4/
	/* including age products which are counted in cptcovage.
	* but the covariates which are products must be treated
	* separately: ncovn=4- 2=2 (V1+V3). */
	cptcovprod=j1; /*< Number of products V1V2 +v3age = 2 /
	cptcovprodnoage=0; /*< Number of covariate products without age: V3V4 =1 */


	/* Design
	* V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
	* < ncovcol=8 >
	* Model V2 + V1 + V3age + V3 + V5V6 + V7V8 + V8age + V8
	* k= 1 2 3 4 5 6 7 8
	* cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
	* covar[k,i], value of kth covariate if not including age for individual i:
	* covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
	* Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
	* if multiplied by age: V3age Tvar[3=V3age]=3 (V3) Tvar[7]=8 and
	* Tage[++cptcovage]=k
	* if products, new covar are created after ncovcol with k1
	* Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
	* Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
	* Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
	* Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
	* Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
	* V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
	* < ncovcol=8 >
	* Model V2 + V1 + V3age + V3 + V5V6 + V7V8 + V8age + V8 d1 d1 d2 d2
	* k= 1 2 3 4 5 6 7 8 9 10 11 12
	* Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
	* p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
	* p Tprod[1]@2={ 6, 5}
	*p Tvard[1][1]@4= {7, 8, 5, 6}
	* covar[k][i]= V2 V1 ? V3 V5V6? V7V8? ? V8
	* cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
	*How to reorganize?
	* Model V1 + V2 + V3 + V8 + V5V6 + V7V8 + V3age + V8age
	* Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
	* {2, 1, 4, 8, 5, 6, 3, 7}
	* Struct []
	*/

	/* This loop fills the array Tvar from the string 'model'.*/
	/* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
	/* modelsav=V2+V1+V4+ageV3 strb=ageV3 stra=V2+V1+V4 */
	/* k=4 (ageV3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 /
	/* k=3 V4 Tvar[k=3]= 4 (from V4) */
	/* k=2 V1 Tvar[k=2]= 1 (from V1) */
	/* k=1 Tvar[1]=2 (from V2) */
	/* k=5 Tvar[5] */
	/* for (k=1; k<=cptcovn;k++) { */
	/* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
	/* } */
	/* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]cov[2]; /
	/*
	* Treating invertedly V2+V1+V3age+V2V4 is as if written V2V4 +V3age + V1 + V2 */
	for(k=cptcovt; k>=1;k--) /*< Number of covariates /
Tvar[k]=0;	Tvar[k]=0;
cptcovage=0;	cptcovage=0;
for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */	for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'	cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
modelsav==V2+V1+V4+V3age strb=V3age stra=V2+V1+V4 */	modelsav==V2+V1+V4+V3age strb=V3age stra=V2+V1+V4 */
if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */	if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
/* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/	/* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
/scanf("%d",i);/	/scanf("%d",i);/
if (strchr(strb,'')) { /< Model includes a product V2+V1+V4+V3age strb=V3age /	if (strchr(strb,'')) { /< Model includes a product V2+V1+V4+V3age strb=V3age /
cutl(strc,strd,strb,''); /< strdstrc VmVn: strb=V3age(input) strc=age strd=V3 ; V3V2 strc=V2, strd=V3 /	cutl(strc,strd,strb,''); /< strdstrc VmVn: strb=V3age(input) strc=age strd=V3 ; V3V2 strc=V2, strd=V3 /
if (strcmp(strc,"age")==0) { /*< Model includes age: Vnage */	if (strcmp(strc,"age")==0) { /*< Model includes age: Vnage */
/* covar is not filled and then is empty */	/* covar is not filled and then is empty */
cptcovprod--;	cptcovprod--;
cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */	cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
Tvar[k]=atoi(stre); /* V2+V1+V4+V3age Tvar[4]=3 ; V1+V2age Tvar[2]=2 */	Tvar[k]=atoi(stre); /* V2+V1+V4+V3age Tvar[4]=3 ; V1+V2age Tvar[2]=2; V1+V1age Tvar[2]=1 /
cptcovage++; /* Sums the number of covariates which include age as a product */	cptcovage++; /* Sums the number of covariates which include age as a product */
Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1age Tvar[2]=1, Tage[1]=2 /	Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1age Tvar[2]=1, Tage[1]=2 /
/printf("stre=%s ", stre);/	/printf("stre=%s ", stre);/
} else if (strcmp(strd,"age")==0) { /* or ageVn /	} else if (strcmp(strd,"age")==0) { /* or ageVn /
cptcovprod--;	cptcovprod--;
cutl(stre,strb,strc,'V');	cutl(stre,strb,strc,'V');
Tvar[k]=atoi(stre);	Tvar[k]=atoi(stre);
cptcovage++;	cptcovage++;
Tage[cptcovage]=k;	Tage[cptcovage]=k;
} else { /* Age is not in the model product V2+V1+V1V4+V3age+V3V2 strb=V3V2*/	} else { /* Age is not in the model product V2+V1+V1V4+V3age+V3V2 strb=V3V2*/
/* loops on k1=1 (V3V2) and k1=2 V4V3 */	/* loops on k1=1 (V3V2) and k1=2 V4V3 */
	cptcovn++;
	cptcovprodnoage++;k1++;
	cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3V2 stre=3 strc=/
	Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
	because this model-covariate is a construction we invent a new column
	ncovcol + k1
	If already ncovcol=4 and model=V2+V1+V1V4+ageV3+V3*V2
	Tvar[3=V1V4]=4+1 Tvar[5=V3V2]=4 + 2= 6, etc */
	cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
	Tprod[k1]=k; /* Tprod[1]=3(=V1V4) for V2+V1+V1V4+ageV3+V3V2 */
	Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
	Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
	k2=k2+2;
	Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
	Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
	for (i=1; i<=lastobs;i++){
	/* Computes the new covariate which is a product of
	covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
	covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
	}
	} /* End age is not in the model */
	} /* End if model includes a product */
	else { /* no more sum */
	/printf("d=%s c=%s b=%s\n", strd,strc,strb);/
	/* scanf("%d",i);*/
	cutl(strd,strc,strb,'V');
	ks++; /*< Number of simple covariates /
cptcovn++;	cptcovn++;
cptcovprodnoage++;k1++;	Tvar[k]=atoi(strd);
cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3V2 stre=3 strc=/	}
Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but	strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
because this model-covariate is a construction we invent a new column	/*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
ncovcol + k1	scanf("%d",i);*/
If already ncovcol=4 and model=V2+V1+V1V4+ageV3+V3*V2	} /* end of loop + on total covariates */
Tvar[3=V1V4]=4+1 Tvar[5=V3V2]=4 + 2= 6, etc */	} /* end if strlen(modelsave == 0) ageage might exist /
cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */	} /* end if strlen(model == 0) */
Tprod[k1]=k; /* Tprod[1]=3(=V1V4) for V2+V1+V1V4+ageV3+V3V2 */
Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
k2=k2+2;
Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
for (i=1; i<=lastobs;i++){
/* Computes the new covariate which is a product of
covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
}
} /* End age is not in the model */
} /* End if model includes a product */
else { /* no more sum */
/printf("d=%s c=%s b=%s\n", strd,strc,strb);/
/* scanf("%d",i);*/
cutl(strd,strc,strb,'V');
ks++; /*< Number of simple covariates /
cptcovn++;
Tvar[k]=atoi(strd);
}
strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
/*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
scanf("%d",i);*/
} /* end of loop + */
} /* end model */

/*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.	/*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
If model=V1+V1age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0/	If model=V1+V1age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0/
Line 5656 BOOL IsWow64()	Line 5978 BOOL IsWow64()
}	}
#endif	#endif

void syscompilerinfo()	void syscompilerinfo(int logged)
{	{
/* #include "syscompilerinfo.h"*/	/* #include "syscompilerinfo.h"*/
/* command line Intel compiler 32bit windows, XP compatible:*/	/* command line Intel compiler 32bit windows, XP compatible:*/
Line 5705 void syscompilerinfo()	Line 6027 void syscompilerinfo()
int cross = CROSS;	int cross = CROSS;
if (cross){	if (cross){
printf("Cross-");	printf("Cross-");
fprintf(ficlog, "Cross-");	if(logged) fprintf(ficlog, "Cross-");
}	}
#endif	#endif

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

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

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

/* __MINGW32__ */	/* __MINGW32__ */
Line 5764 void syscompilerinfo()	Line 6086 void syscompilerinfo()
/* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */	/* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */

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

#if defined(__GNUC__)	#if defined(__GNUC__)
Line 5781 void syscompilerinfo()	Line 6103 void syscompilerinfo()
+ __GNUC_MINOR__ * 100)	+ __GNUC_MINOR__ * 100)
# endif	# endif
printf(" using GNU C version %d.\n", __GNUC_VERSION__);	printf(" using GNU C version %d.\n", __GNUC_VERSION__);
fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);	if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);

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

Line 5800 void syscompilerinfo()	Line 6122 void syscompilerinfo()
// {	// {
#if defined(_MSC_VER)	#if defined(_MSC_VER)
if (IsWow64()){	if (IsWow64()){
printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");	printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");	if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
}	}
else{	else{
printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");	printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");	if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
}	}
// printf("\nPress Enter to continue...");	// printf("\nPress Enter to continue...");
// getchar();	// getchar();
Line 5973 int main(int argc, char *argv[])	Line 6295 int main(int argc, char *argv[])

int jj, ll, li, lj, lk;	int jj, ll, li, lj, lk;
int numlinepar=0; /* Current linenumber of parameter file */	int numlinepar=0; /* Current linenumber of parameter file */
	int num_filled;
int itimes;	int itimes;
int NDIM=2;	int NDIM=2;
int vpopbased=0;	int vpopbased=0;
Line 5981 int main(int argc, char *argv[])	Line 6304 int main(int argc, char *argv[])
/* FILE fichtm; //* Html File */	/* FILE fichtm; //* Html File */
/* FILE ficgp;/ /Gnuplot File /	/* FILE ficgp;/ /Gnuplot File /
struct stat info;	struct stat info;
double agedeb;	double agedeb=0.;
double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
	double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;

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

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

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

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

double bage=0, fage=110, age, agelim, agebase;	double bage=0, fage=110., age, agelim=0., agebase=0.;
double ftolpl=FTOL;	double ftolpl=FTOL;
double **prlim;	double **prlim;
double **param; / Matrix of parameters */	double **param; / Matrix of parameters */
Line 6067 int main(int argc, char *argv[])	Line 6395 int main(int argc, char *argv[])
#else	#else
getcwd(pathcd, size);	getcwd(pathcd, size);
#endif	#endif
	syscompilerinfo(0);
printf("\n%s\n%s",version,fullversion);	printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
if(argc <=1){	if(argc <=1){
printf("\nEnter the parameter file name: ");	printf("\nEnter the parameter file name: ");
fgets(pathr,FILENAMELENGTH,stdin);	fgets(pathr,FILENAMELENGTH,stdin);
Line 6132 int main(int argc, char *argv[])	Line 6460 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 6140 int main(int argc, char *argv[])	Line 6468 int main(int argc, char *argv[])
optionfilext=%s\n\	optionfilext=%s\n\
optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);	optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);

syscompilerinfo();	syscompilerinfo(1);

printf("Local time (at start):%s",strstart);	printf("Local time (at start):%s",strstart);
fprintf(ficlog,"Local time (at start): %s",strstart);	fprintf(ficlog,"Local time (at start): %s",strstart);
Line 6176 int main(int argc, char *argv[])	Line 6504 int main(int argc, char *argv[])

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

fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
numlinepar++;
/* 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=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n",title, datafile, lastobs, firstpass,lastpass);
/*



*/	/* Third parameter line */
printf("\nftol=%e \n", ftol);	while(fgets(line, MAXLINE, ficpar)) {
printf("stepm=%d \n", stepm);	/* If line starts with a # it is a comment */
printf("ncovcol=%d nlstate=%d \n", ncovcol, nlstate);	if (line[0] == '#') {
printf("ndeath=%d maxwav=%d mle=%d weight=%d\n", ndeath, maxwav, mle, weightopt);	numlinepar++;
printf("model=%s\n",model);	fputs(line,stdout);
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=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);	fputs(line,ficparo);
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=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);	fputs(line,ficlog);
	continue;
	}else
	break;
	}
	if((num_filled=sscanf(line,"model=1+age%[^.\n]\n", model)) !=EOF){
	if (num_filled != 1) {
	printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
	fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
	model[0]='\0';
	goto end;
	}
	else{
	if (model[0]=='+'){
	for(i=1; i<=strlen(model);i++)
	modeltemp[i-1]=model[i];
	}
	strcpy(model,modeltemp);
	}
	printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout);
	}
	/* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */
	/* numlinepar=numlinepar+3; /\* In general \/ /
	/* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
	if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */
	model[strlen(model)-1]='\0';
	fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
	fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
fflush(ficlog);	fflush(ficlog);
	/* if(model[0]=='#'\|\| model[0]== '\0'){ */
	if(model[0]=='#'){
	printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
	'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+ageage+V1+V1age.' or \n \
	'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
	if(mle != -1){
	printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
	exit(1);
	}
	}
while((c=getc(ficpar))=='#' && c!= EOF){	while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);	ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);	fgets(line, MAXLINE, ficpar);
numlinepar++;	numlinepar++;
	if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
	z[0]=line[1];
	}
	/* printf("***line [1] = %c \n",line[1]); /
fputs(line, stdout);	fputs(line, stdout);
//puts(line);	//puts(line);
fputs(line,ficparo);	fputs(line,ficparo);
Line 6221 int main(int argc, char *argv[])	Line 6613 int main(int argc, char *argv[])
v1+v2age+v2v3 makes cptcovn = 3	v1+v2age+v2v3 makes cptcovn = 3
*/	*/
if (strlen(model)>1)	if (strlen(model)>1)
ncovmodel=2+nbocc(model,'+')+1; /Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2v4+v5age makes 5+2=7/	ncovmodel=2+nbocc(model,'+')+1; /Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2v4+v5age makes 5+2=7,ageage makes 3*/
else	else
ncovmodel=2;	ncovmodel=2; /* Constant and age */
nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
nforce= (nlstate+ndeath-1)nlstate; / Number of forces ij from state i to j */	nforce= (nlstate+ndeath-1)nlstate; / Number of forces ij from state i to j */
npar= nforcencovmodel; / Number of parameters like aij*/	npar= nforcencovmodel; / Number of parameters like aij*/
if(npar >MAXPARM \|\| nlstate >NLSTATEMAX \|\| ndeath >NDEATHMAX \|\| ncovmodel>NCOVMAX){	if(npar >MAXPARM \|\| nlstate >NLSTATEMAX \|\| ndeath >NDEATHMAX \|\| ncovmodel>NCOVMAX){
Line 6239 int main(int argc, char *argv[])	Line 6630 int main(int argc, char *argv[])
/delti=vector(1,npar); //* Scale of each paramater (output from hesscov)*/	/delti=vector(1,npar); //* Scale of each paramater (output from hesscov)*/
if(mle==-1){ /* Print a wizard for help writing covariance matrix */	if(mle==-1){ /* Print a wizard for help writing covariance matrix */
prwizard(ncovmodel, nlstate, ndeath, model, ficparo);	prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);	printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);	fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);	free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
fclose (ficparo);	fclose (ficparo);
fclose (ficlog);	fclose (ficlog);
Line 6249 int main(int argc, char *argv[])	Line 6640 int main(int argc, char *argv[])
}	}
else if(mle==-3) { /* Main Wizard */	else if(mle==-3) { /* Main Wizard */
prwizard(ncovmodel, nlstate, ndeath, model, ficparo);	prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);	printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);	fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);	param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
matcov=matrix(1,npar,1,npar);	matcov=matrix(1,npar,1,npar);
}	}
Line 6274 int main(int argc, char *argv[])	Line 6665 int main(int argc, char *argv[])
if(jj==i) continue;	if(jj==i) continue;
j++;	j++;
fscanf(ficpar,"%1d%1d",&i1,&j1);	fscanf(ficpar,"%1d%1d",&i1,&j1);
if ((i1 != i) && (j1 != j)){	if ((i1 != i) \|\| (j1 != jj)){
printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \	printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
It might be a problem of design; if ncovcol and the model are correct\n \	It might be a problem of design; if ncovcol and the model are correct\n \
run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);	run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
Line 6282 run imach with mle=-1 to get a correct t	Line 6673 run imach with mle=-1 to get a correct t
}	}
fprintf(ficparo,"%1d%1d",i1,j1);	fprintf(ficparo,"%1d%1d",i1,j1);
if(mle==1)	if(mle==1)
printf("%1d%1d",i,j);	printf("%1d%1d",i,jj);
fprintf(ficlog,"%1d%1d",i,j);	fprintf(ficlog,"%1d%1d",i,jj);
for(k=1; k<=ncovmodel;k++){	for(k=1; k<=ncovmodel;k++){
fscanf(ficpar," %lf",&param[i][j][k]);	fscanf(ficpar," %lf",&param[i][j][k]);
if(mle==1){	if(mle==1){
Line 6364 run imach with mle=-1 to get a correct t	Line 6755 run imach with mle=-1 to get a correct t
for(i=1; i <=npar; i++)	for(i=1; i <=npar; i++)
for(j=1; j <=npar; j++) matcov[i][j]=0.;	for(j=1; j <=npar; j++) matcov[i][j]=0.;

	/* Scans npar lines */
for(i=1; i <=npar; i++){	for(i=1; i <=npar; i++){
fscanf(ficpar,"%s",str);	count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
	if(count != 3){
	printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
	This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
	Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
	fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
	This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
	Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
	exit(1);
	}else
if(mle==1)	if(mle==1)
printf("%s",str);	printf("%1d%1d%1d",i1,j1,jk);
fprintf(ficlog,"%s",str);	fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
fprintf(ficparo,"%s",str);	fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
for(j=1; j <=i; j++){	for(j=1; j <=i; j++){
fscanf(ficpar," %le",&matcov[i][j]);	fscanf(ficpar," %le",&matcov[i][j]);
if(mle==1){	if(mle==1){
Line 6385 run imach with mle=-1 to get a correct t	Line 6786 run imach with mle=-1 to get a correct t
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
fprintf(ficparo,"\n");	fprintf(ficparo,"\n");
}	}
	/* End of read covariance matrix npar lines */
for(i=1; i <=npar; i++)	for(i=1; i <=npar; i++)
for(j=i+1;j<=npar;j++)	for(j=i+1;j<=npar;j++)
matcov[i][j]=matcov[j][i];	matcov[i][j]=matcov[j][i];
Line 6424 run imach with mle=-1 to get a correct t	Line 6826 run imach with mle=-1 to get a correct t
s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */	s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
tab=ivector(1,NCOVMAX);	tab=ivector(1,NCOVMAX);
ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2*ncov; V1+V2+V3+V4=>16 /	ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2*ncov; V1+V2+V3+V4=>16 /
	ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2*ncov; V1+V2+V3+V4=>16 /

/* Reads data from file datafile */	/* Reads data from file datafile */
if (readdata(datafile, firstobs, lastobs, &imx)==1)	if (readdata(datafile, firstobs, lastobs, &imx)==1)
Line 6461 run imach with mle=-1 to get a correct t	Line 6864 run imach with mle=-1 to get a correct t

/* Main decodemodel */	/* Main decodemodel */


if(decodemodel(model, lastobs) == 1)	if(decodemodel(model, lastobs) == 1)
goto end;	goto end;

Line 6504 run imach with mle=-1 to get a correct t	Line 6908 run imach with mle=-1 to get a correct t
nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);	nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
ncodemax[1]=1;	ncodemax[1]=1;
Ndum =ivector(-1,NCOVMAX);	Ndum =ivector(-1,NCOVMAX);
if (ncovmodel > 2)	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 of jth covariate, in
V2+V1age, there are 3 covariates Tvar[2]=1 (V1)./	V2+V1age, there are 3 covariates Tvar[2]=1 (V1)./
Line 6521 run imach with mle=-1 to get a correct t	Line 6925 run imach with mle=-1 to get a correct t

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

for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */
for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2*(3+1-1 or 3+1-3) =1 or 4 /
h++;
if (h>m)
h=1;
/< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2(k-1) )/2**(k-1) + 1	/< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2(k-1) )/2**(k-1) + 1
* For k=4 covariates, h goes from 1 to 2**k	* For k=4 covariates, h goes from 1 to 2**k
* codtabm(h,k)= 1 & (h-1) >> (k-1) ;	* codtabm(h,k)= 1 & (h-1) >> (k-1) ;
Line 6541 run imach with mle=-1 to get a correct t	Line 6938 run imach with mle=-1 to get a correct t
* 6 2 1 2 1	* 6 2 1 2 1
* 7 i=4 1 2 2 1	* 7 i=4 1 2 2 1
* 8 2 2 2 1	* 8 2 2 2 1
* 9 i=5 1 i=3 1 i=2 1 1	* 9 i=5 1 i=3 1 i=2 1 2
* 10 2 1 1 1	* 10 2 1 1 2
* 11 i=6 1 2 1 1	* 11 i=6 1 2 1 2
* 12 2 2 1 1	* 12 2 2 1 2
* 13 i=7 1 i=4 1 2 1	* 13 i=7 1 i=4 1 2 2
* 14 2 1 2 1	* 14 2 1 2 2
* 15 i=8 1 2 2 1	* 15 i=8 1 2 2 2
* 16 2 2 2 1	* 16 2 2 2 2
*/	*/
codtab[h][k]=j;	for(h=1; h <=100 ;h++){
/* codtab[12][3]=1; */	/* printf("h=%2d ", h); */
/codtab[h][Tvar[k]]=j;/	for(k=1; k <=10; k++){
printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);	/* printf("k=%d %d ",k,codtabm(h,k)); */
}	codtab[h][k]=codtabm(h,k);
}	}
}	/* printf("\n"); */
}	}
	/* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate \/ /
	/* for(i=1; i <=pow(2,cptcoveff-k);i++){ /\* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 \/ /
	/* for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2\/ /
	/* for(cpt=1; cpt <=pow(2,k-1); cpt++){ /\* cpt=1 to 8/2*(3+1-1 or 3+1-3) =1 or 4 \/ */
	/* h++; */
	/* if (h>m) */
	/* h=1; */
	/* codtab[h][k]=j; */
	/* /\* codtab[12][3]=1; \/ /
	/* /\codtab[h][Tvar[k]]=j;\/ */
	/* /\* printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]); \/ /
	/* } */
	/* } */
	/* } */
	/* } */
/* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);	/* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
codtab[1][2]=1;codtab[2][2]=2; */	codtab[1][2]=1;codtab[2][2]=2; */
/* for(i=1; i <=m ;i++){	/* for(i=1; i <=m ;i++){ */
for(k=1; k <=cptcovn; k++){	/* for(k=1; k <=cptcovn; k++){ */
printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);	/* printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); */
}	/* } */
printf("\n");	/* printf("\n"); */
}	/* } */
scanf("%d",i);*/	/* scanf("%d",i);*/

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

Line 6822 Interval (in months) between two waves:	Line 7234 Interval (in months) between two waves:
}	}

printf("iter=%d MLE=%f Eq=%lfexp(%lf(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);	printf("iter=%d MLE=%f Eq=%lfexp(%lf(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
for (i=1;i<=NDIM;i++)	for (i=1;i<=NDIM;i++) {
printf("%f [%f ; %f]\n",p[i],p[i]-2sqrt(matcov[i][i]),p[i]+2sqrt(matcov[i][i]));	printf("%f [%f ; %f]\n",p[i],p[i]-2sqrt(matcov[i][i]),p[i]+2sqrt(matcov[i][i]));
	fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2sqrt(matcov[i][i]),p[i]+2sqrt(matcov[i][i]));
	}
lsurv=vector(1,AGESUP);	lsurv=vector(1,AGESUP);
lpop=vector(1,AGESUP);	lpop=vector(1,AGESUP);
tpop=vector(1,AGESUP);	tpop=vector(1,AGESUP);
Line 6856 Interval (in months) between two waves:	Line 7269 Interval (in months) between two waves:


replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */	replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);	if(ageminpar == AGEOVERFLOW \|\|agemaxpar == AGEOVERFLOW){
	printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
	This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
	Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
	fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
	This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
	Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
	}else
	printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \	printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
stepm, weightopt,\	stepm, weightopt,\
model,imx,p,matcov,agemortsup);	model,imx,p,matcov,agemortsup);
Line 6892 Interval (in months) between two waves:	Line 7312 Interval (in months) between two waves:
}	}

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


fprintf(ficres,"# Parameters nlstatenlstatencov a121 + b12 age + ...\n");	fprintf(ficres,"# Parameters nlstatenlstatencov a121 + b12 age + ...\n");
Line 6905 Interval (in months) between two waves:	Line 7325 Interval (in months) between two waves:
fprintf(ficlog,"%d%d ",i,k);	fprintf(ficlog,"%d%d ",i,k);
fprintf(ficres,"%1d%1d ",i,k);	fprintf(ficres,"%1d%1d ",i,k);
for(j=1; j <=ncovmodel; j++){	for(j=1; j <=ncovmodel; j++){
printf("%lf ",p[jk]);	printf("%12.7f ",p[jk]);
fprintf(ficlog,"%lf ",p[jk]);	fprintf(ficlog,"%12.7f ",p[jk]);
fprintf(ficres,"%lf ",p[jk]);	fprintf(ficres,"%12.7f ",p[jk]);
jk++;	jk++;
}	}
printf("\n");	printf("\n");
Line 6921 Interval (in months) between two waves:	Line 7341 Interval (in months) between two waves:
ftolhess=ftol; /* Usually correct */	ftolhess=ftol; /* Usually correct */
hesscov(matcov, p, npar, delti, ftolhess, func);	hesscov(matcov, p, npar, delti, ftolhess, func);
}	}
	printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
	fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
	for(i=1,jk=1; i <=nlstate; i++){
	for(k=1; k <=(nlstate+ndeath); k++){
	if (k != i) {
	printf("%d%d ",i,k);
	fprintf(ficlog,"%d%d ",i,k);
	for(j=1; j <=ncovmodel; j++){
	printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96sqrt(matcov[jk][jk]),p[jk]+1.96sqrt(matcov[jk][jk]));
	fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96sqrt(matcov[jk][jk]),p[jk]+1.96sqrt(matcov[jk][jk]));
	jk++;
	}
	printf("\n");
	fprintf(ficlog,"\n");
	}
	}
	}

fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");	fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
printf("# Scales (for hessian or gradient estimation)\n");	printf("# Scales (for hessian or gradient estimation)\n");
fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");	fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
Line 7077 Interval (in months) between two waves:	Line 7515 Interval (in months) between two waves:
dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;	dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;

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

Line 7101 Interval (in months) between two waves:	Line 7540 Interval (in months) between two waves:
/* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */	/* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */

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

printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\	printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\	model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
Line 7396 Interval (in months) between two waves:	Line 7843 Interval (in months) between two waves:
free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);	free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);

free_ivector(ncodemax,1,NCOVMAX);	free_ivector(ncodemax,1,NCOVMAX);
	free_ivector(ncodemaxwundef,1,NCOVMAX);
free_ivector(Tvar,1,NCOVMAX);	free_ivector(Tvar,1,NCOVMAX);
free_ivector(Tprod,1,NCOVMAX);	free_ivector(Tprod,1,NCOVMAX);
free_ivector(Tvaraff,1,NCOVMAX);	free_ivector(Tvaraff,1,NCOVMAX);
Line 7503 Interval (in months) between two waves:	Line 7951 Interval (in months) between two waves:
}	}
end:	end:
while (z[0] != 'q') {	while (z[0] != 'q') {
printf("\nType q for exiting: ");	printf("\nType q for exiting: "); fflush(stdout);
scanf("%s",z);	scanf("%s",z);
}	}
}	}

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

Removed from v.1.186
changed lines
	Added in v.1.197