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Diff for /imach/src/imach.c between versions 1.185 and 1.191

version 1.185, 2015/03/11 13:26:42	version 1.191, 2015/07/14 10:00:33
Line 1	Line 1
/* $Id$	/* $Id$
$State$	$State$
$Log$	$Log$
	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
	Summary: V1*age is working now, version 0.98q1

	Some codes had been disabled in order to simplify and Vn*age was
	working in the optimization phase, ie, giving correct MLE parameters,
	but, as usual, outputs were not correct and program core dumped.

Revision 1.185 2015/03/11 13:26:42 brouard	Revision 1.185 2015/03/11 13:26:42 brouard
Summary: Inclusion of compile and links command line for Intel Compiler	Summary: Inclusion of compile and links command line for Intel Compiler

Line 578	Line 602
end	end
*/	*/

	/* #define DEBUG */
	/* #define DEBUGBRENT */
#define POWELL /* Instead of NLOPT */	#define POWELL /* Instead of NLOPT */
/* #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 \/ /

#include <math.h>	#include <math.h>
#include <stdio.h>	#include <stdio.h>
Line 666 typedef struct {	Line 692 typedef struct {
/* $Id$ */	/* $Id$ */
/* $State$ */	/* $State$ */

char version[]="Imach version 0.98q0, March 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 0.98q2, April 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
char 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 812 int *s; / Status */	Line 838 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 Ndum; /* Freq of modality (tricode */	int Ndum; /* Freq of modality (tricode */
Line 830 static int split( char path, char dirc	Line 856 static int split( char path, char dirc
the name of the file (name), its extension only (ext) and its first part of the name (finame)	the name of the file (name), its extension only (ext) and its first part of the name (finame)
*/	*/
char ss; / pointer */	char ss; / pointer */
int l1, l2; /* length counters */	int l1=0, l2=0; /* length counters */

l1 = strlen(path ); /* length of path */	l1 = strlen(path ); /* length of path */
if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );	if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
Line 856 static int split( char path, char dirc	Line 882 static int split( char path, char dirc
if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );	if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
strcpy( name, ss ); /* save file name */	strcpy( name, ss ); /* save file name */
strncpy( dirc, path, l1 - l2 ); /* now the directory */	strncpy( dirc, path, l1 - l2 ); /* now the directory */
dirc[l1-l2] = 0; /* add zero */	dirc[l1-l2] = '\0'; /* add zero */
printf(" DIRC2 = %s \n",dirc);	printf(" DIRC2 = %s \n",dirc);
}	}
/* We add a separator at the end of dirc if not exists */	/* We add a separator at the end of dirc if not exists */
Line 908 char trimbb(char out, char *in)	Line 934 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 938 char cutl(char blocc, char *alocc, cha	Line 1007 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 1249 double f1dim(double x)	Line 1318 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 1332 values at the three points, fa, fb , and	Line 1407 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 1367 values at the three points, fa, fb , and	Line 1453 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 1451 void linmin(double p[], double xi[], int	Line 1547 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 1460 void linmin(double p[], double xi[], int	Line 1558 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 1506 void powell(double p[], double **xi, int	Line 1643 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 1544 void powell(double p[], double **xi, int	Line 1681 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 1578 void powell(double p[], double **xi, int	Line 1715 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 1653 void powell(double p[], double **xi, int	Line 1805 void powell(double p[], double **xi, int
}	}
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 1702 double prevalim(double prlim, int nl	Line 1869 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]]);/
}	}
/* 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<=cptcovprod;k++) /\* Useless \/ /	for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2];
/* cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */	for (k=1; k<=cptcovprod;k++) /* Useless */
	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];

/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 1863 double *hpxij(double *po, int nhstep	Line 2032 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 1876 double *hpxij(double *po, int nhstep	Line 2046 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++)	for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];	/* cov[2+Tage[k]]=cov[2+Tage[k]]cov[2]; /
	cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
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 1934 double func( double *x)	Line 2108 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 1955 double func( double *x)	Line 2130 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 1968 double func( double *x)	Line 2143 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 2081 double func( double *x)	Line 2259 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 2090 double func( double *x)	Line 2268 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 2111 double func( double *x)	Line 2292 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 2120 double func( double *x)	Line 2301 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 2141 double func( double *x)	Line 2325 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 2150 double func( double *x)	Line 2334 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 2176 double func( double *x)	Line 2363 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 2185 double func( double *x)	Line 2372 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 2223 double funcone( double *x)	Line 2413 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 2234 double funcone( double *x)	Line 2425 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 2243 double funcone( double *x)	Line 2434 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 3107 void tricode(int Tvar, int *nbcode, in	Line 3302 void tricode(int Tvar, int *nbcode, in
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++) { /* model V1 + V2age+ V3 + V3V4 : V1 + V3 = 2 only */	for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2age+ V3 + V3V4 keeps V1 + V3 = 2 only */
for (i=1; i<=imx; i++) { /* Lopp 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
* If product of VnVm, still boolean :	* If product of VnVm, still boolean :
Line 3130 void tricode(int Tvar, int *nbcode, in	Line 3325 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 */
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);
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 (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1// For each value 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], i, Ndum[i]);
if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */	if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */	ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
}	}
Line 3145 void tricode(int Tvar, int *nbcode, in	Line 3340 void tricode(int Tvar, int *nbcode, in
} /* Ndum[-1] number of undefined modalities */	} /* Ndum[-1] number of undefined modalities */

/* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */	/* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
/* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */	/* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
/* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;	If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
modmincovj=3; modmaxcovj = 7;	modmincovj=3; modmaxcovj = 7;
There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;	There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy	which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
variables V1_1 and V1_2.	defining two dummy variables: variables V1_1 and V1_2.
nbcode[Tvar[j]][ij]=k;	nbcode[Tvar[j]][ij]=k;
nbcode[Tvar[j]][1]=0;	nbcode[Tvar[j]][1]=0;
nbcode[Tvar[j]][2]=1;	nbcode[Tvar[j]][2]=1;
Line 3161 void tricode(int Tvar, int *nbcode, in	Line 3356 void tricode(int Tvar, int *nbcode, in
for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 // Could be 1 to 4 */	for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 // Could be 1 to 4 */
/recode from 0 /	/recode from 0 /
if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */	if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.	nbcode[Tvar[j]][ij]=k; /* stores the modality k in an array nbcode.
k is a modality. If we have model=V1+V1*sex	k is a modality. If we have model=V1+V1*sex
then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */	then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
ij++;	ij++;
Line 3173 void tricode(int Tvar, int *nbcode, in	Line 3368 void tricode(int Tvar, int *nbcode, in

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=1;
Line 4030 To be simple, these graphs help to under	Line 4225 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
*/	*/
/* nbcode[1][1]=0 nbcode[1][2]=1;*/	/* nbcode[1][1]=0 nbcode[1][2]=1;*/
}	}
for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];	/* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]cov[2]; /
	for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
for (k=1; k<=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 4500 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 4698 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 4526 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 4746 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 \/ /	if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */
/* /\fprintf(ficgp,"+p%d%dx",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);\/ */	fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
/* ij++; */	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(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
/* fprintf(ficgp,"+p%d%dx",k3+(k1-1)ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); /	fprintf(ficgp,"+p%d%dx",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
/* ij++; */	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 5343 void removespace(char *str) {	Line 5573 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 5360 int decodemodel ( char model[], int last	Line 5591 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 5383 int decodemodel ( char model[], int last	Line 5606 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]]=cov[2+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; /* Tage[1] = 4 */	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 5646 BOOL IsWow64()	Line 5905 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 5654 void syscompilerinfo()	Line 5913 void syscompilerinfo()
/Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D	/Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
"_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D	"_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
"UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo	"UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
/Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"	/Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
/* 64 bits */	*/
	/* 64 bits */
/*	/*
/GS /W3 /Gy	/GS /W3 /Gy
/Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"	/Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
Line 5669 void syscompilerinfo()	Line 5929 void syscompilerinfo()
/Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel	/Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
/Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"	/Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
*/	*/
/* Link is $/ /* /OUT:"visual studio	/* Link is / / /OUT:"visual studio
2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT	2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
/PDB:"visual studio	/PDB:"visual studio
2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE	2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
Line 5694 void syscompilerinfo()	Line 5954 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 5753 void syscompilerinfo()	Line 6013 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 5770 void syscompilerinfo()	Line 6030 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 5789 void syscompilerinfo()	Line 6049 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 5970 int main(int argc, char *argv[])	Line 6230 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=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;

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

Line 5984 int main(int argc, char *argv[])	Line 6244 int main(int argc, char *argv[])
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;
int jl;	int jl=0;
int i1, j1, jk, stepsize;	int i1, j1, jk, stepsize=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 6056 int main(int argc, char *argv[])	Line 6316 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("\n%s\n%s",version,fullversion);
if(argc <=1){	if(argc <=1){
printf("\nEnter the parameter file name: ");	printf("\nEnter the parameter file name: ");
Line 6113 int main(int argc, char *argv[])	Line 6373 int main(int argc, char *argv[])

/-------- arguments in the command line --------/	/-------- arguments in the command line --------/

/* Log file */	/* Main Log file */
strcat(filelog, optionfilefiname);	strcat(filelog, optionfilefiname);
strcat(filelog,".log"); /* */	strcat(filelog,".log"); /* */
if((ficlog=fopen(filelog,"w"))==NULL) {	if((ficlog=fopen(filelog,"w"))==NULL) {
Line 6129 int main(int argc, char *argv[])	Line 6389 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(0);

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 6142 int main(int argc, char *argv[])	Line 6402 int main(int argc, char *argv[])
strcat(fileres, optionfilefiname);	strcat(fileres, optionfilefiname);
strcat(fileres,".txt"); /* Other files have txt extension */	strcat(fileres,".txt"); /* Other files have txt extension */

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

if((ficpar=fopen(optionfile,"r"))==NULL) {	if((ficpar=fopen(optionfile,"r"))==NULL) {
printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));	printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
Line 6175 int main(int argc, char *argv[])	Line 6435 int main(int argc, char *argv[])
}	}
ungetc(c,ficpar);	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);	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++;
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\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%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 */
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);	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);
Line 6199 int main(int argc, char *argv[])	Line 6471 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 6217 int main(int argc, char *argv[])	Line 6488 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);
goto end;	goto end;
exit(0);	exit(0);
}	}
else if(mle==-3) {	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 choose 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 choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
Line 6385 run imach with mle=-1 to get a correct t	Line 6656 run imach with mle=-1 to get a correct t
fprintf(ficres,"#%s\n",version);	fprintf(ficres,"#%s\n",version);
} /* End of mle != -3 */	} /* End of mle != -3 */

	/* Main data
	*/
n= lastobs;	n= lastobs;
num=lvector(1,n);	num=lvector(1,n);
moisnais=vector(1,n);	moisnais=vector(1,n);
Line 6436 run imach with mle=-1 to get a correct t	Line 6708 run imach with mle=-1 to get a correct t
Tage[1=V3age]= 4; Tage[2=ageV4] = 3	Tage[1=V3age]= 4; Tage[2=ageV4] = 3
*/	*/

	/* Main decodemodel */


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

Line 6479 run imach with mle=-1 to get a correct t	Line 6754 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
	V2+V1age, there are 3 covariates Tvar[2]=1 (V1)./
	/* 1 to ncodemax[j] is the maximum value of this jth covariate */

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


Line 6500 run imach with mle=-1 to get a correct t	Line 6779 run imach with mle=-1 to get a correct t
if (h>m)	if (h>m)
h=1;	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
* h 1 2 3 4	* For k=4 covariates, h goes from 1 to 2**k
	* codtabm(h,k)= 1 & (h-1) >> (k-1) ;
	* h\k 1 2 3 4
*______________________________	*______________________________
* 1 i=1 1 i=1 1 i=1 1 i=1 1	* 1 i=1 1 i=1 1 i=1 1 i=1 1
* 2 2 1 1 1	* 2 2 1 1 1
Line 6520 run imach with mle=-1 to get a correct t	Line 6801 run imach with mle=-1 to get a correct t
* 16 2 2 2 1	* 16 2 2 2 1
*/	*/
codtab[h][k]=j;	codtab[h][k]=j;
	/* codtab[12][3]=1; */
/codtab[h][Tvar[k]]=j;/	/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("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]]);
}	}
Line 6540 run imach with mle=-1 to get a correct t	Line 6822 run imach with mle=-1 to get a correct t



/------------ gnuplot -------------/	/* Initialisation of ----------- gnuplot -------------*/
strcpy(optionfilegnuplot,optionfilefiname);	strcpy(optionfilegnuplot,optionfilefiname);
if(mle==-3)	if(mle==-3)
strcat(optionfilegnuplot,"-mort");	strcat(optionfilegnuplot,"-mort");
Line 6556 run imach with mle=-1 to get a correct t	Line 6838 run imach with mle=-1 to get a correct t
fprintf(ficgp,"set datafile missing 'NaNq'\n");	fprintf(ficgp,"set datafile missing 'NaNq'\n");
}	}
/* fclose(ficgp);*/	/* fclose(ficgp);*/
/--------- index.htm --------/

	/* Initialisation of --------- index.htm --------*/

strcpy(optionfilehtm,optionfilefiname); /* Main html file */	strcpy(optionfilehtm,optionfilefiname); /* Main html file */
if(mle==-3)	if(mle==-3)
Line 6626 Interval (in months) between two waves:	Line 6910 Interval (in months) between two waves:
p=param[1][1]; /* (((param +1)+1)+0) /	p=param[1][1]; /* (((param +1)+1)+0) /

globpr=0; /* To get the number ipmx of contributions and the sum of weights*/	globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
	/* For mortality only */
if (mle==-3){	if (mle==-3){
ximort=matrix(1,NDIM,1,NDIM);	ximort=matrix(1,NDIM,1,NDIM);
/* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */	/* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
cens=ivector(1,n);	cens=ivector(1,n);
ageexmed=vector(1,n);	ageexmed=vector(1,n);
agecens=vector(1,n);	agecens=vector(1,n);
Line 6719 Interval (in months) between two waves:	Line 7003 Interval (in months) between two waves:

/* Initialize method and iterate */	/* Initialize method and iterate */
/* p[1]=0.0268; p[NDIM]=0.083; */	/* p[1]=0.0268; p[NDIM]=0.083; */
/* gsl_vector_set(x, 0, 0.0268); */	/* gsl_vector_set(x, 0, 0.0268); */
/* gsl_vector_set(x, 1, 0.083); */	/* gsl_vector_set(x, 1, 0.083); */
gsl_vector_set(x, 0, p[1]);	gsl_vector_set(x, 0, p[1]);
gsl_vector_set(x, 1, p[2]);	gsl_vector_set(x, 1, p[2]);

Line 6837 Interval (in months) between two waves:	Line 7121 Interval (in months) between two waves:
free_ivector(dcwave,1,n);	free_ivector(dcwave,1,n);
free_matrix(ximort,1,NDIM,1,NDIM);	free_matrix(ximort,1,NDIM,1,NDIM);
#endif	#endif
} /* Endof if mle==-3 */	} /* Endof if mle==-3 mortality only */
	/* Standard maximisation */
else{ /* For mle >=1 */	else{ /* For mle >=1 */
globpr=0;/* debug */	globpr=0;/* debug */
	/* Computes likelihood for initial parameters */
likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */	likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);	printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
for (k=1; k<=npar;k++)	for (k=1; k<=npar;k++)
printf(" %d %8.5f",k,p[k]);	printf(" %d %8.5f",k,p[k]);
printf("\n");	printf("\n");
globpr=1; /* to print the contributions */	globpr=1; /* again, to print the contributions */
likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */	likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);	printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
for (k=1; k<=npar;k++)	for (k=1; k<=npar;k++)
printf(" %d %8.5f",k,p[k]);	printf(" %d %8.5f",k,p[k]);
printf("\n");	printf("\n");
if(mle>=1){ /* Could be 1 or 2 */	if(mle>=1){ /* Could be 1 or 2, Real Maximisation */
mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);	mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
}	}

/--------- results files --------------/	/--------- results files --------------/
fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%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 6870 Interval (in months) between two waves:	Line 7155 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 7013 Interval (in months) between two waves:	Line 7298 Interval (in months) between two waves:
fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");	fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);	fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);	fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);

	/* Other stuffs, more or less useful */
while((c=getc(ficpar))=='#' && c!= EOF){	while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);	ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);	fgets(line, MAXLINE, ficpar);
Line 7086 Interval (in months) between two waves:	Line 7372 Interval (in months) between two waves:
fclose(ficres);	fclose(ficres);


	/* Other results (useful)*/


/--------------- Prevalence limit (period or stable prevalence) --------------/	/--------------- Prevalence limit (period or stable prevalence) --------------/
/#include "prevlim.h"/ /* Use ficrespl, ficlog */	/#include "prevlim.h"/ /* Use ficrespl, ficlog */
prlim=matrix(1,nlstate,1,nlstate);	prlim=matrix(1,nlstate,1,nlstate);
Line 7125 Interval (in months) between two waves:	Line 7414 Interval (in months) between two waves:
/* fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */	/* fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
/* } */	/* } */
}	}

	/* ------ Other prevalence ratios------------ */

/* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */	/* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */

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

Removed from v.1.185
changed lines
	Added in v.1.191