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Diff for /imach/src/imach.c between versions 1.144 and 1.148

version 1.144, 2014/02/10 22:17:31	version 1.148, 2014/06/17 17:38:48
Line 1	Line 1
/* $Id$	/* $Id$
$State$	$State$
$Log$	$Log$
Revision 1.144 2014/02/10 22:17:31 brouard	Revision 1.148 2014/06/17 17:38:48 brouard
	Summary: Nothing new
	Author: Brouard

	Just a new packaging for OS/X version 0.98nS

	Revision 1.147 2014/06/16 10:33:11 brouard
* empty log message *	* empty log message *

	Revision 1.146 2014/06/16 10:20:28 brouard
	Summary: Merge
	Author: Brouard

	Merge, before building revised version.

	Revision 1.145 2014/06/10 21:23:15 brouard
	Summary: Debugging with valgrind
	Author: Nicolas Brouard

	Lot of changes in order to output the results with some covariates
	After the Edimburgh REVES conference 2014, it seems mandatory to
	improve the code.
	No more memory valgrind error but a lot has to be done in order to
	continue the work of splitting the code into subroutines.
	Also, decodemodel has been improved. Tricode is still not
	optimal. nbcode should be improved. Documentation has been added in
	the source code.

Revision 1.143 2014/01/26 09:45:38 brouard	Revision 1.143 2014/01/26 09:45:38 brouard
Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising	Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising

Line 377	Line 402
begin-prev-date,...	begin-prev-date,...
open gnuplot file	open gnuplot file
open html file	open html file
period (stable) prevalence	period (stable) prevalence \| pl_nom 1-1 2-2 etc by covariate
for age prevalim()	for age prevalim() \| #**** V1=0 V2=1 V3=1 V4=0 ****
h Pij x	\| 65 1 0 2 1 3 1 4 0 0.96326 0.03674
variance of p varprob	freexexit2 possible for memory heap.

	h Pij x \| pij_nom ficrestpij
	# Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
	1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
	1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907

	1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
	1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
	variance of p one-step probabilities varprob \| prob_nom ficresprob #One-step probabilities and stand. devi in ()
	Standard deviation of one-step probabilities \| probcor_nom ficresprobcor #One-step probabilities and correlation matrix
	Matrix of variance covariance of one-step probabilities \| probcov_nom ficresprobcov #One-step probabilities and covariance matrix

forecasting if prevfcast==1 prevforecast call prevalence()	forecasting if prevfcast==1 prevforecast call prevalence()
health expectancies	health expectancies
Variance-covariance of DFLE	Variance-covariance of DFLE
Line 439 extern int errno;	Line 476 extern int errno;
#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 MAXN 20000	#define MAXN 20000
#define YEARM 12. /*< Number of months per year /	#define YEARM 12. /*< Number of months per year /
#define AGESUP 130	#define AGESUP 130
Line 457 extern int errno;	Line 495 extern int errno;
/* $Id$ */	/* $Id$ */
/* $State$ */	/* $State$ */

char version[]="Imach version 0.98nR2, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";	char version[]="Imach version 0.98nS, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
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 nvar=0, nforce=0; /* Number of variables, number of forces */
int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with 'age' /	/* 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 cptcovt=0; /*< cptcovt number of covariates added in the model (excepting constant and age) /
	int cptcovs=0; /*< cptcovs number of simple covariates V2+V1 =2 /
	int cptcovage=0; /*< Number of covariates with age: V3age only =1 */
	int cptcovprodnoage=0; /*< Number of covariate products without age /
	int cptcoveff=0; /* Total number of covariates to vary for printing results */
	int cptcov=0; /* Working variable */
int npar=NPARMAX;	int npar=NPARMAX;
int nlstate=2; /* Number of live states */	int nlstate=2; /* Number of live states */
int ndeath=1; /* Number of dead states */	int ndeath=1; /* Number of dead states */
Line 482 int *dh; / dh[mi][i] is number of step	Line 527 int *dh; / dh[mi][i] is number of step
int *bh; / bh[mi][i] is the bias (+ or -) for this individual if the delay between	int *bh; / bh[mi][i] is the bias (+ or -) for this individual if the delay between
* wave mi and wave mi+1 is not an exact multiple of stepm. */	* wave mi and wave mi+1 is not an exact multiple of stepm. */
double jmean=1; /* Mean space between 2 waves */	double jmean=1; /* Mean space between 2 waves */
	double *matprod2(); / test */
double oldm, newm, *savm; / Working pointers to matrices */	double oldm, newm, *savm; / Working pointers to matrices */
double oldms, newms, *savms; / Fixed working pointers to matrices */	double oldms, newms, *savms; / Fixed working pointers to matrices */
/FILE fic ; / / Used in readdata only */	/FILE fic ; / / Used in readdata only */
Line 582 double dateintmean=0;	Line 628 double dateintmean=0;
double *weight;	double *weight;
int *s; / Status */	int *s; / Status */
double *agedc;	double *agedc;
double covar; /< covar[i,j], 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]cov[2]; /
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 codtab; /< codtab=imatrix(1,100,1,10); */	int codtab; /< codtab=imatrix(1,100,1,10); */
int *Tvard, Tprod, cptcovprod, *Tvaraff;	int *Tvard, Tprod, cptcovprod, *Tvaraff;
double lsurv, lpop, *tpop;	double lsurv, lpop, *tpop;
Line 675 char trimbb(char out, char *in)	Line 722 char trimbb(char out, char *in)
return s;	return s;
}	}

	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'
	and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
	gives blocc="abcdef2ghi" and alocc="j".
	If occ is not found blocc is null and alocc is equal to in. Returns blocc
	*/
	char s, t, *bl;
	t=in;s=in;
	while ((in != occ) && (in != '\0')){
	alocc++ = in++;
	}
	if( *in == occ){
	*(alocc)='\0';
	s=++in;
	}

	if (s == t) {/* occ not found */
	*(alocc-(in-s))='\0';
	in=s;
	}
	while ( *in != '\0'){
	blocc++ = in++;
	}

	*blocc='\0';
	return t;
	}
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'
Line 845 double **matrix(long nrl, long nrh, long	Line 920 double **matrix(long nrl, long nrh, long

for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;	for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
return m;	return m;
/* print ((m+1)+70) or print m[1][70]; print m+1 or print &(m[1])	/* print ((m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
	m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
	that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
*/	*/
}	}

Line 1280 double prevalim(double prlim, int nl	Line 1357 double prevalim(double prlim, int nl

int i, ii,j,k;	int i, ii,j,k;
double min, max, maxmin, maxmax,sumnew=0.;	double min, max, maxmin, maxmax,sumnew=0.;
double **matprod2();	/* double *matprod2(); / /* test */
double out, cov[NCOVMAX+1], pmij();	double out, cov[NCOVMAX+1], pmij();
double **newm;	double **newm;
double agefin, delaymax=50 ; /* Max number of years to converge */	double agefin, delaymax=50 ; /* Max number of years to converge */
Line 1300 double prevalim(double prlim, int nl	Line 1377 double prevalim(double prlim, int nl

for (k=1; k<=cptcovn;k++) {	for (k=1; k<=cptcovn;k++) {
cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];	cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
/* printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+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];	/* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]cov[2]; /
for (k=1; k<=cptcovprod;k++)	/* 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+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]);/
/printf("ij=%d cov[3]=%lf \n",ij, cov[3]);/	/printf("ij=%d cov[3]=%lf \n",ij, cov[3]);/
	/* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
	/* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind \/ /
out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */	out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */

savm=oldm;	savm=oldm;
Line 1321 double prevalim(double prlim, int nl	Line 1400 double prevalim(double prlim, int nl
sumnew=0;	sumnew=0;
for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];	for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
prlim[i][j]= newm[i][j]/(1-sumnew);	prlim[i][j]= newm[i][j]/(1-sumnew);
	/printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);/
max=FMAX(max,prlim[i][j]);	max=FMAX(max,prlim[i][j]);
min=FMIN(min,prlim[i][j]);	min=FMIN(min,prlim[i][j]);
}	}
Line 1401 double pmij(double ps, double *cov,	Line 1481 double pmij(double ps, double *cov,
}	}
}	}


/* for(ii=1; ii<= nlstate+ndeath; ii++){ */	/* for(ii=1; ii<= nlstate+ndeath; ii++){ */
/* for(jj=1; jj<= nlstate+ndeath; jj++){ */	/* for(jj=1; jj<= nlstate+ndeath; jj++){ */
/* printf("ddd %lf ",ps[ii][jj]); */	/* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
/* } */	/* } */
/* printf("\n "); */	/* printf("\n "); */
/* } */	/* } */
/* printf("\n ");printf("%lf ",cov[2]); */	/* printf("\n ");printf("%lf ",cov[2]);*/
/*	/*
for(i=1; i<= npar; i++) printf("%f ",x[i]);	for(i=1; i<= npar; i++) printf("%f ",x[i]);
goto end;*/	goto end;*/
return ps;	return ps;
Line 1417 double pmij(double ps, double *cov,	Line 1497 double pmij(double ps, double *cov,

/************** Product of 2 matrices ****************/	/************** Product of 2 matrices ****************/

double matprod2(double out, double in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double b)	double matprod2(double out, double in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double b)
{	{
/* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times	/* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */	b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
/* in, b, out are matrice of pointers which should have been initialized	/* in, b, out are matrice of pointers which should have been initialized
before: only the contents of out is modified. The function returns	before: only the contents of out is modified. The function returns
a pointer to pointers identical to out */	a pointer to pointers identical to out */
long i, j, k;	int i, j, k;
for(i=nrl; i<= nrh; i++)	for(i=nrl; i<= nrh; i++)
for(k=ncolol; k<=ncoloh; k++)	for(k=ncolol; k<=ncoloh; k++){
for(j=ncl,out[i][k]=0.; j<=nch; j++)	out[i][k]=0.;
out[i][k] +=in[i][j]*b[j][k];	for(j=ncl; j<=nch; j++)
	out[i][k] +=in[i][j]*b[j][k];
	}
return out;	return out;
}	}

Line 1471 double *hpxij(double *po, int nhstep	Line 1552 double *hpxij(double *po, int nhstep
cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];	cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
for (k=1; k<=cptcovage;k++)	for (k=1; k<=cptcovage;k++)
cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];	cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
for (k=1; k<=cptcovprod;k++)	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+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];


Line 1522 double func( double *x)	Line 1603 double func( double *x)
Then computes with function pmij which return a matrix p[i][j] giving the elementary probability	Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
to be observed in j being in i according to the model.	to be observed in j being in i according to the model.
*/	*/
for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];	for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
	cov[2+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]
has been calculated etc */	has been calculated etc */
Line 1790 double funcone( double *x)	Line 1873 double funcone( double *x)
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]=covar[Tvar[Tage[kk]]][i]*cov[2];
}	}
	/* 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));
	/* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
	/* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
savm=oldm;	savm=oldm;
oldm=newm;	oldm=newm;
} /* end mult */	} /* end mult */
Line 2037 double hessii(double x[], double delta,	Line 2123 double hessii(double x[], double delta,

fx=func(x);	fx=func(x);
for (i=1;i<=npar;i++) p2[i]=x[i];	for (i=1;i<=npar;i++) p2[i]=x[i];
for(l=0 ; l <=lmax; l++){	for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
l1=pow(10,l);	l1=pow(10,l);
delts=delt;	delts=delt;
for(k=1 ; k <kmax; k=k+1){	for(k=1 ; k <kmax; k=k+1){
delt = delta(l1k);	delt = delta(l1k);
p2[theta]=x[theta] +delt;	p2[theta]=x[theta] +delt;
k1=func(p2)-fx;	k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
p2[theta]=x[theta]-delt;	p2[theta]=x[theta]-delt;
k2=func(p2)-fx;	k2=func(p2)-fx;
/res= (k1-2.0fx+k2)/delt/delt; */	/res= (k1-2.0fx+k2)/delt/delt; */
Line 2212 void freqsummary(char fileres[], int ia	Line 2298 void freqsummary(char fileres[], int ia

first=1;	first=1;

for(k1=1; k1<=j ; k1++){ /* Loop on covariates */	/* for(k1=1; k1<=j ; k1++){ /* Loop on covariates */
for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */	/* for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
j1++;	/* j1++;
	*/
	for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
/*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);	/*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
scanf("%d", i);*/	scanf("%d", i);*/
for (i=-5; i<=nlstate+ndeath; i++)	for (i=-5; i<=nlstate+ndeath; i++)
Line 2233 void freqsummary(char fileres[], int ia	Line 2321 void freqsummary(char fileres[], int ia
if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */	if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
for (z1=1; z1<=cptcoveff; z1++)	for (z1=1; z1<=cptcoveff; z1++)
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){	if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
	/* Tests if the value of each of the covariates of i is equal to filter j1 */
bool=0;	bool=0;
printf("bool=%d i=%d, z1=%d, i1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n",	/* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n",
bool,i,z1, i1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],	bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);	j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
/* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/	/* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
}	}
}	}
Line 2260 void freqsummary(char fileres[], int ia	Line 2349 void freqsummary(char fileres[], int ia
/}/	/}/
}	}
}	}
}	} /* end i */

/* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/	/* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
pstamp(ficresp);	pstamp(ficresp);
Line 2347 void freqsummary(char fileres[], int ia	Line 2436 void freqsummary(char fileres[], int ia
printf("Others in log...\n");	printf("Others in log...\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
}	}
}	/}/
}	}
dateintmean=dateintsum/k2cpt;	dateintmean=dateintsum/k2cpt;

Line 2372 void prevalence(double ***probs, double	Line 2461 void prevalence(double ***probs, double
double pos,posprop;	double pos,posprop;
double y2; /* in fractional years */	double y2; /* in fractional years */
int iagemin, iagemax;	int iagemin, iagemax;
	int first; /** to stop verbosity which is redirected to log file */

iagemin= (int) agemin;	iagemin= (int) agemin;
iagemax= (int) agemax;	iagemax= (int) agemax;
Line 2380 void prevalence(double ***probs, double	Line 2470 void prevalence(double ***probs, double
/* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/	/* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
j1=0;	j1=0;

j=cptcoveff;	/j=cptcoveff;/
if (cptcovn<1) {j=1;ncodemax[1]=1;}	if (cptcovn<1) {j=1;ncodemax[1]=1;}

for(k1=1; k1<=j;k1++){	first=1;
for(i1=1; i1<=ncodemax[k1];i1++){	for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
j1++;	/*for(i1=1; i1<=ncodemax[k1];i1++){
	j1++;*/

for (i=1; i<=nlstate; i++)	for (i=1; i<=nlstate; i++)
for(m=iagemin; m <= iagemax+3; m++)	for(m=iagemin; m <= iagemax+3; m++)
Line 2415 void prevalence(double ***probs, double	Line 2506 void prevalence(double ***probs, double
}	}
}	}
for(i=iagemin; i <= iagemax+3; i++){	for(i=iagemin; i <= iagemax+3; i++){

for(jk=1,posprop=0; jk <=nlstate ; jk++) {	for(jk=1,posprop=0; jk <=nlstate ; jk++) {
posprop += prop[jk][i];	posprop += prop[jk][i];
}	}

for(jk=1; jk <=nlstate ; jk++){	for(jk=1; jk <=nlstate ; jk++){
if( i <= iagemax){	if( i <= iagemax){
if(posprop>=1.e-5){	if(posprop>=1.e-5){
probs[i][jk][j1]= prop[jk][i]/posprop;	probs[i][jk][j1]= prop[jk][i]/posprop;
} else	} else{
printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);	if(first==1){
	first=0;
	printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
	}
	}
}	}
}/* end jk */	}/* end jk */
}/* end i */	}/* end i */
} /* end i1 */	/} //* end i1 */
} /* end k1 */	} /* end j1 */

/* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/	/* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
/free_vector(pp,1,nlstate);/	/free_vector(pp,1,nlstate);/
Line 2580 void concatwav(int wav[], int **dh, int	Line 2674 void concatwav(int wav[], int **dh, int
}	}

/********* Tricode **************************/	/********* Tricode **************************/
void tricode(int Tvar, int *nbcode, int imx)	void tricode(int Tvar, int nbcode, int imx, int Ndum)
{	{
/*< Uses cptcovn+2cptcovprod as the number of covariates */	/*< Uses cptcovn+2cptcovprod as the number of covariates */
/* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1	/* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
/* Boring subroutine which should only output nbcode[Tvar[j]][k]	/* Boring subroutine which should only output nbcode[Tvar[j]][k]
/* nbcode[Tvar[j][1]=	* Tvar[5] in V2+V1+V3age+V2V4 is 2 (V2)
	/* nbcode[Tvar[j]][1]=
*/	*/

int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;	int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
int modmaxcovj=0; /* Modality max of covariates j */	int modmaxcovj=0; /* Modality max of covariates j */
	int cptcode=0; /* Modality max of covariates j */
	int modmincovj=0; /* Modality min of covariates j */


cptcoveff=0;	cptcoveff=0;

for (k=0; k < maxncov; k++) Ndum[k]=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 */

for (j=1; j<=(cptcovn+2cptcovprod); j++) { / For each covariate j */	/* Loop on covariates without age and products */
for (i=1; i<=imx; i++) { /*reads the data file to get the maximum value of the	for (j=1; j<=(cptcovs); j++) { /* model V1 + V2age+ V3 + V3V4 : V1 + V3 = 2 only */
	for (i=1; i<=imx; i++) { /* Lopp 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. Finds for covariate j, n=Tvar[j] of Vn . ij is the	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 it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
	* 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
	/* Finds for covariate j, n=Tvar[j] of Vn . ij is the
modality of the nth covariate of individual i. */	modality of the nth covariate of individual i. */
	if (ij > modmaxcovj)
	modmaxcovj=ij;
	else if (ij < modmincovj)
	modmincovj=ij;
	if ((ij < -1) && (ij > NCOVMAX)){
	printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
	exit(1);
	}else
Ndum[ij]++; /counts and stores the occurence of this modality 0, 1, -1/	Ndum[ij]++; /counts and stores the occurence of this modality 0, 1, -1/
	/* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
/printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);/	/printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);/
if (ij > modmaxcovj) modmaxcovj=ij;
/* 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.*/
}	}
	printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, 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<=modmaxcovj; i++) { /* i=-1 ? 0 and 1// For each modality of model-cov j */	/for (i=0; i<=cptcode; i++) {/
if( Ndum[i] != 0 )	for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1// For each value of the modality of model-cov j */
ncodemax[j]++;	printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
/* Number of modalities of the j th covariate. In fact	if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
ncodemax[j]=2 (dichotom. variables only) but it could be more for	ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
historical reasons */	}
	/* 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 */
} /* 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 */
ij=1;	/* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 for dichotomous */	/* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
for (k=0; k<= modmaxcovj; k++) { /* k=-1 ? NCOVMAX// maxncov or modmaxcovj */	modmincovj=3; modmaxcovj = 7;
	There are only 3 modalities non empty (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
	variables V1_1 and V1_2.
	nbcode[Tvar[j]][ij]=k;
	nbcode[Tvar[j]][1]=0;
	nbcode[Tvar[j]][2]=1;
	nbcode[Tvar[j]][3]=2;
	*/
	ij=1; /* ij is similar to i but can jumps over null modalities */
	for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
	for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 // Could be 1 to 4 */
	/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 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
Line 2631 void tricode(int Tvar, int *nbcode, in	Line 2759 void tricode(int Tvar, int *nbcode, in
} /* end of loop on modality */	} /* end of loop on modality */
} /* 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=0; 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; i++) { /* -2, cste and age */
/* 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]++;
}	}

ij=1;	ij=1;
for (i=1; i<= maxncov; 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]);/
if((Ndum[i]!=0) && (i<=ncovcol)){	if((Ndum[i]!=0) && (i<=ncovcol)){
Tvaraff[ij]=i; /For printing /	/printf("diff Ndum[%d]=%d\n",i, Ndum[i]);/
	Tvaraff[ij]=i; /For printing (unclear) /
ij++;	ij++;
}	}else
	Tvaraff[ij]=0;
}	}
ij--;	ij--;
cptcoveff=ij; /Number of total covariates/	cptcoveff=ij; /Number of total covariates/

}	}


/********* Health Expectancies **************/	/********* Health Expectancies **************/

void evsij(double *eij, double x[], int nlstate, int stepm, int bage, int fage, double oldm, double **savm, int cij, int estepm,char strstart[] )	void evsij(double *eij, double x[], int nlstate, int stepm, int bage, int fage, double oldm, double **savm, int cij, int estepm,char strstart[] )
Line 3245 void varevsij(char optionfilefiname[], d	Line 3378 void varevsij(char optionfilefiname[], d
free_vector(gmp,nlstate+1,nlstate+ndeath);	free_vector(gmp,nlstate+1,nlstate+ndeath);
free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);	free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/	free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");	fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
/* for(j=nlstate+1; j<= nlstate+ndeath; j++){ // Only the first actually */	/* for(j=nlstate+1; j<= nlstate+ndeath; j++){ // Only the first actually */
fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");	fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
/* fprintf(ficgp,"\n plot \"%s\" u 1:($3%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); /	/* fprintf(ficgp,"\n plot \"%s\" u 1:($3%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); /
/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96$4)%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */	/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96$4)%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96$4)%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */	/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96$4)%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 2 ",subdirf(fileresprobmorprev));	fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 3 ",subdirf(fileresprobmorprev));	fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 3 ",subdirf(fileresprobmorprev));	fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));	fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);	fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
/* fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);	/* fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
Line 3363 void varprob(char optionfilefiname[], do	Line 3496 void varprob(char optionfilefiname[], do
int i, j=0, i1, k1, l1, t, tj;	int i, j=0, i1, k1, l1, t, tj;
int k2, l2, j1, z1;	int k2, l2, j1, z1;
int k=0,l, cptcode;	int k=0,l, cptcode;
int first=1, first1;	int first=1, first1, first2;
double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;	double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
double dnewm,doldm;	double dnewm,doldm;
double *xp;	double *xp;
double gp, gm;	double gp, gm;
double gradg, trgradg;	double gradg, trgradg;
double **mu;	double **mu;
double age,agelim, cov[NCOVMAX];	double age,agelim, cov[NCOVMAX+1];
double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */	double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
int theta;	int theta;
char fileresprob[FILENAMELENGTH];	char fileresprob[FILENAMELENGTH];
char fileresprobcov[FILENAMELENGTH];	char fileresprobcov[FILENAMELENGTH];
char fileresprobcor[FILENAMELENGTH];	char fileresprobcor[FILENAMELENGTH];

double ***varpij;	double ***varpij;

strcpy(fileresprob,"prob");	strcpy(fileresprob,"prob");
Line 3449 standard deviations wide on each axis. <	Line 3581 standard deviations wide on each axis. <
To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");	To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");

cov[1]=1;	cov[1]=1;
tj=cptcoveff;	/* tj=cptcoveff; */
	tj = (int) pow(2,cptcoveff);
if (cptcovn<1) {tj=1;ncodemax[1]=1;}	if (cptcovn<1) {tj=1;ncodemax[1]=1;}
j1=0;	j1=0;
for(t=1; t<=tj;t++){	for(j1=1; j1<=tj;j1++){
for(i1=1; i1<=ncodemax[t];i1++){	/for(i1=1; i1<=ncodemax[t];i1++){ /
j1++;	/j1++;/
if (cptcovn>0) {	if (cptcovn>0) {
fprintf(ficresprob, "\n#********** Variable ");	fprintf(ficresprob, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
Line 3477 To be simple, these graphs help to under	Line 3610 To be simple, these graphs help to under
fprintf(ficresprobcor, "**********\n#");	fprintf(ficresprobcor, "**********\n#");
}	}

	gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
	trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
	gp=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;
for (k=1; k<=cptcovn;k++) {	for (k=1; k<=cptcovn;k++) {
cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];	cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
	* 1 1 1 1 1
	* 2 2 1 1 1
	* 3 1 2 1 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<=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+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];

gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
gp=vector(1,(nlstate)*(nlstate+ndeath));
gm=vector(1,(nlstate)*(nlstate+ndeath));

for(theta=1; theta <=npar; theta++){	for(theta=1; theta <=npar; theta++){
for(i=1; i<=npar; i++)	for(i=1; i<=npar; i++)
Line 3527 To be simple, these graphs help to under	Line 3665 To be simple, these graphs help to under

matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);	matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
matprod2(doldm,dnewm,1,(nlstate)(nlstate+ndeath),1,npar,1,(nlstate)(nlstate+ndeath),gradg);	matprod2(doldm,dnewm,1,(nlstate)(nlstate+ndeath),1,npar,1,(nlstate)(nlstate+ndeath),gradg);
free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);

pmij(pmmij,cov,ncovmodel,x,nlstate);	pmij(pmmij,cov,ncovmodel,x,nlstate);

Line 3564 To be simple, these graphs help to under	Line 3698 To be simple, these graphs help to under
i=0;	i=0;
for (k=1; k<=(nlstate);k++){	for (k=1; k<=(nlstate);k++){
for (l=1; l<=(nlstate+ndeath);l++){	for (l=1; l<=(nlstate+ndeath);l++){
i=i++;	i++;
fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);	fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);	fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
for (j=1; j<=i;j++){	for (j=1; j<=i;j++){
	/* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);	fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));	fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
}	}
}	}
}/* end of loop for state */	}/* end of loop for state */
} /* end of loop for age */	} /* end of loop for age */
	free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
	free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
	free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
	free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);

/* Confidence intervalle of pij */	/* Confidence intervalle of pij */
/*	/*
fprintf(ficgp,"\nunset parametric;unset label");	fprintf(ficgp,"\nunset parametric;unset label");
Line 3587 To be simple, these graphs help to under	Line 3726 To be simple, these graphs help to under
*/	*/

/* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/	/* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
first1=1;	first1=1;first2=2;
for (k2=1; k2<=(nlstate);k2++){	for (k2=1; k2<=(nlstate);k2++){
for (l2=1; l2<=(nlstate+ndeath);l2++){	for (l2=1; l2<=(nlstate+ndeath);l2++){
if(l2==k2) continue;	if(l2==k2) continue;
Line 3609 To be simple, these graphs help to under	Line 3748 To be simple, these graphs help to under
lc1=((v1+v2)+sqrt((v1+v2)(v1+v2) - 4(v1v2-cv12cv12)))/2.;	lc1=((v1+v2)+sqrt((v1+v2)(v1+v2) - 4(v1v2-cv12cv12)))/2.;
lc2=((v1+v2)-sqrt((v1+v2)(v1+v2) - 4(v1v2-cv12cv12)))/2.;	lc2=((v1+v2)-sqrt((v1+v2)(v1+v2) - 4(v1v2-cv12cv12)))/2.;
if ((lc2 <0) \|\| (lc1 <0) ){	if ((lc2 <0) \|\| (lc1 <0) ){
printf("Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Continuing by making them positive: WRONG RESULTS.\n", lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);	if(first2==1){
fprintf(ficlog,"Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e\n", lc1, lc2, v1, v2, cv12);fflush(ficlog);	first1=0;
lc1=fabs(lc1);	printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
lc2=fabs(lc2);	}
	fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
	/* lc1=fabs(lc1); / / If we want to have them positive */
	/* lc2=fabs(lc2); */
}	}

/* Eigen vectors */	/* Eigen vectors */
Line 3634 To be simple, these graphs help to under	Line 3776 To be simple, these graphs help to under
first=0;	first=0;
fprintf(ficgp,"\nset parametric;unset label");	fprintf(ficgp,"\nset parametric;unset label");
fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);	fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");	fprintf(ficgp,"\nset ter png small size 320, 240");
fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\	fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
:<a href=\"%s%d%1d%1d-%1d%1d.png\">\	:<a href=\"%s%d%1d%1d-%1d%1d.png\">\
%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\	%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
Line 3665 To be simple, these graphs help to under	Line 3807 To be simple, these graphs help to under
} /* k12 */	} /* k12 */
} /l1 /	} /l1 /
}/* k1 */	}/* k1 */
} /* loop covariates */	/* } /* loop covariates */
}	}
free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);	free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);	free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
Line 3711 void printinghtml(char fileres[], char t	Line 3853 void printinghtml(char fileres[], char t

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

m=cptcoveff;	m=pow(2,cptcoveff);
if (cptcovn < 1) {m=1;ncodemax[1]=1;}	if (cptcovn < 1) {m=1;ncodemax[1]=1;}

jj1=0;	jj1=0;
Line 3725 fprintf(fichtm," \n<ul><li><b>Graphs</b>	Line 3867 fprintf(fichtm," \n<ul><li><b>Graphs</b>
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");	fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
}	}
/* Pij */	/* Pij */
fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \	fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
<img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);	<img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
/* Quasi-incidences */	/* Quasi-incidences */
fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\	fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \	before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
<img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);	<img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
/* Period (stable) prevalence in each health state */	/* Period (stable) prevalence in each health state */
for(cpt=1; cpt<nlstate;cpt++){	for(cpt=1; cpt<nlstate;cpt++){
fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \	fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
<img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);	<img src=\"%s%d_%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
}	}
for(cpt=1; cpt<=nlstate;cpt++) {	for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <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 : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
Line 3785 fprintf(fichtm," \n<ul><li><b>Graphs</b>	Line 3927 fprintf(fichtm," \n<ul><li><b>Graphs</b>
fflush(fichtm);	fflush(fichtm);
fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");	fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");

m=cptcoveff;	m=pow(2,cptcoveff);
if (cptcovn < 1) {m=1;ncodemax[1]=1;}	if (cptcovn < 1) {m=1;ncodemax[1]=1;}

jj1=0;	jj1=0;
Line 3800 fprintf(fichtm," \n<ul><li><b>Graphs</b>	Line 3942 fprintf(fichtm," \n<ul><li><b>Graphs</b>
}	}
for(cpt=1; cpt<=nlstate;cpt++) {	for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \	fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\	prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
<img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);	<img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
}	}
fprintf(fichtm,"\n<br>- Total life expectancy by age and \	fprintf(fichtm,"\n<br>- Total life expectancy by age and \
health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \	health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
Line 3835 void printinggnuplot(char fileres[], cha	Line 3977 void printinggnuplot(char fileres[], cha
strcpy(optfileres,"vpl");	strcpy(optfileres,"vpl");
/* 1eme*/	/* 1eme*/
for (cpt=1; cpt<= nlstate ; cpt ++) {	for (cpt=1; cpt<= nlstate ; cpt ++) {
for (k1=1; k1<= m ; k1 ++) {	for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);	fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);	fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
fprintf(ficgp,"set xlabel \"Age\" \n\	fprintf(ficgp,"set xlabel \"Age\" \n\
set ylabel \"Probability\" \n\	set ylabel \"Probability\" \n\
set ter png small\n\	set ter png small size 320, 240\n\
set size 0.65,0.65\n\
plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);	plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);

for (i=1; i<= nlstate ; i ++) {	for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");	if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
else fprintf(ficgp," \%%lf (\%%lf)");	else fprintf(ficgp," \%%lf (\%%lf)");
}	}
fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 1,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);	fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
for (i=1; i<= nlstate ; i ++) {	for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");	if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
else fprintf(ficgp," \%%lf (\%%lf)");	else fprintf(ficgp," \%%lf (\%%lf)");
}	}
fprintf(ficgp,"\" t\"95\%% CI\" w l lt 2,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);	fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
for (i=1; i<= nlstate ; i ++) {	for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");	if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
else fprintf(ficgp," \%%lf (\%%lf)");	else fprintf(ficgp," \%%lf (\%%lf)");
}	}
fprintf(ficgp,"\" t\"\" w l lt 2,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 3",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));	fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
}	}
}	}
/2 eme/	/2 eme/

for (k1=1; k1<= m ; k1 ++) {	for (k1=1; k1<= m ; k1 ++) {
fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);	fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);	fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);

for (i=1; i<= nlstate+1 ; i ++) {	for (i=1; i<= nlstate+1 ; i ++) {
k=2*i;	k=2*i;
Line 3881 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 4022 plot [%.f:%.f] \"%s\" every :::%d::%d u
if (j==i) fprintf(ficgp," \%%lf (\%%lf)");	if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
else fprintf(ficgp," \%%lf (\%%lf)");	else fprintf(ficgp," \%%lf (\%%lf)");
}	}
fprintf(ficgp,"\" t\"\" w l lt 1,");	fprintf(ficgp,"\" t\"\" w l lt 0,");
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);	fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
for (j=1; j<= nlstate+1 ; j ++) {	for (j=1; j<= nlstate+1 ; j ++) {
if (j==i) fprintf(ficgp," \%%lf (\%%lf)");	if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
else fprintf(ficgp," \%%lf (\%%lf)");	else fprintf(ficgp," \%%lf (\%%lf)");
}	}
if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 1");	if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
else fprintf(ficgp,"\" t\"\" w l lt 1,");	else fprintf(ficgp,"\" t\"\" w l lt 0,");
}	}
}	}

Line 3899 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 4040 plot [%.f:%.f] \"%s\" every :::%d::%d u
/* k=2+nlstate(2cpt-2); */	/* k=2+nlstate(2cpt-2); */
k=2+(nlstate+1)*(cpt-1);	k=2+(nlstate+1)*(cpt-1);
fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);	fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
fprintf(ficgp,"set ter png small\n\	fprintf(ficgp,"set ter png small size 320, 240\n\
set size 0.65,0.65\n\
plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);	plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
/fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);	/fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");	for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
Line 3923 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 4063 plot [%.f:%.f] \"%s\" every :::%d::%d u
for (k1=1; k1<= m ; k1 ++) {	for (k1=1; k1<= m ; k1 ++) {
for (cpt=1; cpt<=nlstate ; cpt ++) {	for (cpt=1; cpt<=nlstate ; cpt ++) {
k=3;	k=3;
fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);	fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
set ter png small\nset size 0.65,0.65\n\	set ter png small size 320, 240\n\
unset log y\n\	unset log y\n\
plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);	plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);

Line 3955 plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1	Line 4095 plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
}	}
}	}
}	}
	/goto avoid;/
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*/
for(jk=1; jk <=m; jk++) {	for(jk=1; jk <=m; 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");
else	else
fprintf(ficgp,"\nset title \"Probability\"\n");	fprintf(ficgp,"\nset title \"Probability\"\n");
fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);	fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
i=1;	i=1;
for(k2=1; k2<=nlstate; k2++) {	for(k2=1; k2<=nlstate; k2++) {
k3=i;	k3=i;
Line 3975 plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1	Line 4115 plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
fprintf(ficgp," exp(p%d+p%d*x",i,i+1);	fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
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; 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-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-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
}	}
fprintf(ficgp,")/(1");	fprintf(ficgp,")/(1");
Line 3988 plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1	Line 4128 plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
fprintf(ficgp,"+exp(p%d+p%dx",k3+(k1-1)ncovmodel,k3+(k1-1)*ncovmodel+1);	fprintf(ficgp,"+exp(p%d+p%dx",k3+(k1-1)ncovmodel,k3+(k1-1)*ncovmodel+1);
ij=1;	ij=1;
for(j=3; j <=ncovmodel; j++){	for(j=3; j <=ncovmodel; 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,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,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
}	}
fprintf(ficgp,")");	fprintf(ficgp,")");
Line 4005 plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1	Line 4145 plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
} /* end k2 */	} /* end k2 */
} /* end jk */	} /* end jk */
} /* end ng */	} /* end ng */
	avoid:
fflush(ficgp);	fflush(ficgp);
} /* end gnuplot */	} /* end gnuplot */

Line 4588 void printinggnuplotmort(char fileres[],	Line 4729 void printinggnuplotmort(char fileres[],
strcpy(optfileres,"vpl");	strcpy(optfileres,"vpl");
fprintf(ficgp,"set out \"graphmort.png\"\n ");	fprintf(ficgp,"set out \"graphmort.png\"\n ");
fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");	fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
fprintf(ficgp, "set ter png small\n set log y\n");	fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
fprintf(ficgp, "set size 0.65,0.65\n");	/* fprintf(ficgp, "set size 0.65,0.65\n"); */
fprintf(ficgp,"plot [%d:100] %lfexp(%lf(x-%d))",agegomp,p[1],p[2],agegomp);	fprintf(ficgp,"plot [%d:100] %lfexp(%lf(x-%d))",agegomp,p[1],p[2],agegomp);

}	}
Line 4656 int readdata(char datafile[], int firsto	Line 4797 int readdata(char datafile[], int firsto
cutv(stra, strb,line,' ');	cutv(stra, strb,line,' ');
if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){	if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
}	}
else if(iout=sscanf(strb,"%s.") != 0){	else if(iout=sscanf(strb,"%s.",dummy) != 0){
month=99;	month=99;
year=9999;	year=9999;
}else{	}else{
Line 4687 int readdata(char datafile[], int firsto	Line 4828 int readdata(char datafile[], int firsto
cutv(stra, strb,line,' ');	cutv(stra, strb,line,' ');
if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){	if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
}	}
else if(iout=sscanf(strb,"%s.") != 0){	else if(iout=sscanf(strb,"%s.", dummy) != 0){
month=99;	month=99;
year=9999;	year=9999;
}else{	}else{
Line 4780 int readdata(char datafile[], int firsto	Line 4921 int readdata(char datafile[], int firsto


}	}
	void removespace(char *str) {
int decodemodel ( char model[], int lastobs)	char p1 = str, p2 = str;
	do
	while (*p2 == ' ')
	p2++;
	while (p1++ = p2++);
	}

	int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
	* Model V1+V2+V3+V8+V7V8+V5V6+V8age+V3age
	* - cptcovt total number of covariates of the model nbocc(+)+1 = 8
	* - cptcovn or number of covariates k of the models excluding age*products =6
	* - cptcovage number of covariates with age*products =2
	* - 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
	* which is a new column after the 9 (ncovcol) variables.
	* - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
	* - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
	* Tprod[1]@2 {5, 6}: position of first product V7V8 is 5, and second V5V6 is 6.
	* - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7V8 and V5V6 .
	*/
{	{
int i, j, k;	int i, j, k, ks;
int i1, j1, k1, k2;	int i1, 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];

	/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=1, k2=1;	j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
j=nbocc(model,'+'); /* j=Number of '+' */	j=nbocc(model,'+'); /*< j=Number of '+' /
j1=nbocc(model,''); / j1=Number of '' /	j1=nbocc(model,''); /< j1=Number of '' */
cptcovn=j+1; /* Number of covariates V1+V2*age+V3 =>(2 plus signs) + 1=3	cptcovs=j+1-j1; /*< Number of simple covariates V1+V2age+V3 +V3V4=> V1 + V3 =2 /
but the covariates which are product must be computed and stored. */	cptcovt= j+1; /* Number of total covariates in the model V1 + V2age+ V3 + V3V4=> 4*/
cptcovprod=j1; /Number of products V1V2 +v3age = 2 /	/* 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);	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=%s ",model);
Line 4808 int decodemodel ( char model[], int last	Line 4971 int decodemodel ( char model[], int last
return 1;	return 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'.*/	/* This loop fills the array Tvar from the string 'model'.*/
/* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */	/* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
/* modelsav=V2+V1+V4+ageV3 strb=ageV3 stra=V2+V1+V4 */	/* modelsav=V2+V1+V4+ageV3 strb=ageV3 stra=V2+V1+V4 */
Line 4820 int decodemodel ( char model[], int last	Line 5017 int decodemodel ( char model[], int last
/* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */	/* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
/* } */	/* } */
/* 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=cptcovn; k>=1;k--){	/*
cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'	* Treating invertedly V2+V1+V3age+V2V4 is as if written V2V4 +V3age + V1 + V2 */
modelsav==V2+V1+V4+V3age strb=V3age stra=V2+V1+V4	for(k=cptcovt; k>=1;k--) /*< Number of covariates /
*/	Tvar[k]=0;
	cptcovage=0;
	for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
	cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
	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 /
cutv(strd,strc,strb,''); / strdstrc VmVn: strb=V3age 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) { /* Vnage /	if (strcmp(strc,"age")==0) { /*< Model includes age: Vnage */
	/* covar is not filled and then is empty */
cptcovprod--;	cptcovprod--;
cutv(strb,stre,strd,'V'); /* stre="V3" */	cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
Tvar[k]=atoi(stre); /* V2+V1+V4+V3age Tvar[4]=2 ; V1+V2age Tvar[2]=2 */	Tvar[k]=atoi(stre); /* V2+V1+V4+V3age Tvar[4]=3 ; V1+V2age Tvar[2]=2 */
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; /* Tage[1] = 4 */
/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--;
cutv(strb,stre,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 */
cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3V2 stre=3 strc=/	cptcovn++;
Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but	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	because this model-covariate is a construction we invent a new column
ncovcol + k1	ncovcol + k1
If already ncovcol=4 and model=V2+V1+V1V4+ageV3+V3*V2	If already ncovcol=4 and model=V2+V1+V1V4+ageV3+V3*V2
Tvar[3=V1V4]=4+1 Tvar[5=V3V2]=4 + 2= 6, etc */	Tvar[3=V1V4]=4+1 Tvar[5=V3V2]=4 + 2= 6, etc */
cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */	cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
Tprod[k1]=k; /* Tprod[1]=3(=V1V4) for V2+V1+V1V4+ageV3+V3V2 */	Tprod[k1]=k; /* Tprod[1]=3(=V1V4) for V2+V1+V1V4+ageV3+V3V2 */
Tvard[k1][1]=atoi(strc); /* m 1 for V1*/	Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
Tvard[k1][2]=atoi(stre); /* n 4 for V4*/	Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
Tvar[cptcovn+k2]=Tvard[k1][1]; /* Tvar[(cptcovn=4+k2=1)=5]= 1 (V1) */	k2=k2+2;
Tvar[cptcovn+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovn=4+(k2=1)+1)=6]= 4 (V4) */	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++){	for (i=1; i<=lastobs;i++){
/* Computes the new covariate which is a product of	/* Computes the new covariate which is a product of
covar[n][i]* covar[m][i] and stores it at ncovol+k1 */	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];	covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
}	}
k1++;
k2=k2+2;
} /* End age is not in the model */	} /* End age is not in the model */
} /* End if model includes a product */	} /* End if model includes a product */
else { /* no more sum */	else { /* no more sum */
/printf("d=%s c=%s b=%s\n", strd,strc,strb);/	/printf("d=%s c=%s b=%s\n", strd,strc,strb);/
/* scanf("%d",i);*/	/* scanf("%d",i);*/
cutv(strd,strc,strb,'V');	cutl(strd,strc,strb,'V');
Tvar[k]=atoi(strc);	ks++; /*< Number of simple covariates /
	cptcovn++;
	Tvar[k]=atoi(strd);
}	}
strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */	strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
/*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);	/*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
Line 5059 int main(int argc, char *argv[])	Line 5264 int main(int argc, char *argv[])
double kk1, kk2;	double kk1, kk2;
double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;	double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
double **ximort;	double **ximort;
char *alph[]={"a","a","b","c","d","e"}, str[4];	char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
int *dcwave;	int *dcwave;

char z[1]="c", occ;	char z[1]="c", occ;
Line 5227 int main(int argc, char *argv[])	Line 5432 int main(int argc, char *argv[])
ungetc(c,ficpar);	ungetc(c,ficpar);


covar=matrix(0,NCOVMAX,1,n);	covar=matrix(0,NCOVMAX,1,n); /*< used in readdata /
cptcovn=0; /Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn/	cptcovn=0; /Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn/
/* v1+v2+v3+v2v4+v5age makes cptcovn = 5	/* v1+v2+v3+v2v4+v5age makes cptcovn = 5
v1+v2age+v2v3 makes cptcovn = 3	v1+v2age+v2v3 makes cptcovn = 3
*/	*/
if (strlen(model)>1)	if (strlen(model)>1)
cptcovn=nbocc(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/
/* ncovprod */	else
ncovmodel=2+cptcovn; /Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2v4+v5age makes 5+2=7/	ncovmodel=2;
nvar=ncovmodel-1; /* Suppressing age as a basic covariate */	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*/
Line 5267 int main(int argc, char *argv[])	Line 5472 int main(int argc, char *argv[])
matcov=matrix(1,npar,1,npar);	matcov=matrix(1,npar,1,npar);
}	}
else{	else{
/* Read guess parameters */	/* Read guessed parameters */
/* Reads comments: lines beginning with '#' */	/* Reads comments: lines beginning with '#' */
while((c=getc(ficpar))=='#' && c!= EOF){	while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);	ungetc(c,ficpar);
Line 5316 run imach with mle=-1 to get a correct t	Line 5521 run imach with mle=-1 to get a correct t
}	}
fflush(ficlog);	fflush(ficlog);

	/* Reads scales values */
p=param[1][1];	p=param[1][1];

/* Reads comments: lines beginning with '#' */	/* Reads comments: lines beginning with '#' */
Line 5354 run imach with mle=-1 to get a correct t	Line 5560 run imach with mle=-1 to get a correct t
}	}
fflush(ficlog);	fflush(ficlog);

	/* Reads covariance matrix */
delti=delti3[1][1];	delti=delti3[1][1];


Line 5375 run imach with mle=-1 to get a correct t	Line 5582 run imach with mle=-1 to get a correct t
for(j=1; j <=npar; j++) matcov[i][j]=0.;	for(j=1; j <=npar; j++) matcov[i][j]=0.;

for(i=1; i <=npar; i++){	for(i=1; i <=npar; i++){
fscanf(ficpar,"%s",&str);	fscanf(ficpar,"%s",str);
if(mle==1)	if(mle==1)
printf("%s",str);	printf("%s",str);
fprintf(ficlog,"%s",str);	fprintf(ficlog,"%s",str);
Line 5455 run imach with mle=-1 to get a correct t	Line 5662 run imach with mle=-1 to get a correct t
ncovcol + k1	ncovcol + k1
If already ncovcol=4 and model=V2+V1+V1V4+ageV3	If already ncovcol=4 and model=V2+V1+V1V4+ageV3
Tvar[3=V1V4]=4+1 etc /	Tvar[3=V1V4]=4+1 etc /
Tprod=ivector(1,15); /* Gives the position of a product */	Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
/* Tprod[k1=1]=3(=V1V4) for V2+V1+V1V4+age*V3	/* Tprod[k1=1]=3(=V1V4) for V2+V1+V1V4+age*V3
if V2+V1+V1V4+ageV3+V3V2 TProd[k1=2]=5 (V3V2)	if V2+V1+V1V4+ageV3+V3V2 TProd[k1=2]=5 (V3V2)
*/	*/
Tvaraff=ivector(1,15);	Tvaraff=ivector(1,NCOVMAX); /* Unclear */
Tvard=imatrix(1,15,1,2); /* n=Tvard[k1][1] and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm	Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1] and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
* For V3V2 (in V2+V1+V1V4+ageV3+V3V2), V3*V2 position is 2nd.	* For V3V2 (in V2+V1+V1V4+ageV3+V3V2), V3*V2 position is 2nd.
* Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */	* Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
Tage=ivector(1,15); /* Gives the covariate id of covariates associated with age: V2 + V1 + ageV4 + V3age	Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + ageV4 + V3age
4 covariates (3 plus signs)	4 covariates (3 plus signs)
Tage[1=V3age]= 4; Tage[2=ageV4] = 3	Tage[1=V3age]= 4; Tage[2=ageV4] = 3
*/	*/
Line 5495 run imach with mle=-1 to get a correct t	Line 5702 run imach with mle=-1 to get a correct t
free_matrix(anint,1,maxwav,1,n);*/	free_matrix(anint,1,maxwav,1,n);*/
free_vector(moisdc,1,n);	free_vector(moisdc,1,n);
free_vector(andc,1,n);	free_vector(andc,1,n);
	/* */

wav=ivector(1,imx);	wav=ivector(1,imx);
dh=imatrix(1,lastpass-firstpass+1,1,imx);	dh=imatrix(1,lastpass-firstpass+1,1,imx);
bh=imatrix(1,lastpass-firstpass+1,1,imx);	bh=imatrix(1,lastpass-firstpass+1,1,imx);
Line 5504 run imach with mle=-1 to get a correct t	Line 5711 run imach with mle=-1 to get a correct t

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

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

nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);	nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
ncodemax[1]=1;	ncodemax[1]=1;
if (cptcovn > 0) tricode(Tvar,nbcode,imx);	Ndum =ivector(-1,NCOVMAX);
	if (ncovmodel > 2)
codtab=imatrix(1,100,1,10); /< codtab[h,k]=( (h-1) - mod(k-1,2(k-1) )/2**(k-1)	tricode(Tvar,nbcode,imx, Ndum); /*< Fills nbcode[Tvar[j]][l]; /
*/
	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]);/
h=0;	h=0;


	/if (cptcovn > 0) /


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

for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */	for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
Line 5544 run imach with mle=-1 to get a correct t	Line 5759 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[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 5559 run imach with mle=-1 to get a correct t	Line 5774 run imach with mle=-1 to get a correct t
printf("\n");	printf("\n");
}	}
scanf("%d",i);*/	scanf("%d",i);*/

	free_ivector(Ndum,-1,NCOVMAX);



/------------ gnuplot -------------/	/------------ gnuplot -------------/
strcpy(optionfilegnuplot,optionfilefiname);	strcpy(optionfilegnuplot,optionfilefiname);
Line 5682 Interval (in months) between two waves:	Line 5901 Interval (in months) between two waves:
ximort[i][j]=(i == j ? 1.0 : 0.0);	ximort[i][j]=(i == j ? 1.0 : 0.0);
}	}

p[1]=0.0268; p[NDIM]=0.083;	/p[1]=0.0268; p[NDIM]=0.083;/
/printf("%lf %lf", p[1], p[2]);/	/printf("%lf %lf", p[1], p[2]);/


Line 6076 Interval (in months) between two waves:	Line 6295 Interval (in months) between two waves:



/* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/	/* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
/,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);	printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
Line 6102 Interval (in months) between two waves:	Line 6321 Interval (in months) between two waves:


/--------------- Prevalence limit (period or stable prevalence) --------------/	/--------------- Prevalence limit (period or stable prevalence) --------------/
	#include "prevlim.h" /* Use ficrespl, ficlog */
strcpy(filerespl,"pl");
strcat(filerespl,fileres);
if((ficrespl=fopen(filerespl,"w"))==NULL) {
printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
}
printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
pstamp(ficrespl);
fprintf(ficrespl,"# Period (stable) prevalence \n");
fprintf(ficrespl,"#Age ");
for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
fprintf(ficrespl,"\n");

prlim=matrix(1,nlstate,1,nlstate);

agebase=ageminpar;
agelim=agemaxpar;
ftolpl=1.e-10;
i1=pow(2,cptcoveff);
if (cptcovn < 1){i1=1;}

for(cptcov=1,k=0;cptcov<=i1;cptcov++){
//for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
k=k+1;
/* to clean */
//printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
fprintf(ficrespl,"\n#******");
printf("\n#******");
fprintf(ficlog,"\n#******");
for(j=1;j<=cptcoveff;j++) {
fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
}
fprintf(ficrespl,"******\n");
printf("******\n");
fprintf(ficlog,"******\n");

for (age=agebase; age<=agelim; age++){
prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
fprintf(ficrespl,"%.0f ",age );
for(j=1;j<=cptcoveff;j++)
fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
for(i=1; i<=nlstate;i++)
fprintf(ficrespl," %.5f", prlim[i][i]);
fprintf(ficrespl,"\n");
} /* Age */
/* was end of cptcod */
} /* cptcov */
fclose(ficrespl);	fclose(ficrespl);

/------------- h Pij x at various ages ------------/	#ifdef FREEEXIT2
	#include "freeexit2.h"
strcpy(filerespij,"pij"); strcat(filerespij,fileres);	#endif
if((ficrespij=fopen(filerespij,"w"))==NULL) {
printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
}
printf("Computing pij: result on file '%s' \n", filerespij);
fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);

stepsize=(int) (stepm+YEARM-1)/YEARM;
/if (stepm<=24) stepsize=2;/

agelim=AGESUP;
hstepm=stepsizeYEARM; / Every year of age */
hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */

/* hstepm=1; aff par mois*/
pstamp(ficrespij);
fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
k=k+1;
fprintf(ficrespij,"\n#****** ");
for(j=1;j<=cptcoveff;j++)
fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
fprintf(ficrespij,"******\n");

for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
nhstepm=(int) rint((agelim-agedeb)YEARM/stepm); / Typically 20 years = 2012/6=40 /
nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */

/* nhstepm=nhstepmYEARM; aff par mois/

p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	/------------- h Pij x at various ages ------------/
oldm=oldms;savm=savms;	#include "hpijx.h"
hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);	fclose(ficrespij);
fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate+ndeath;j++)
fprintf(ficrespij," %1d-%1d",i,j);
fprintf(ficrespij,"\n");
for (h=0; h<=nhstepm; h++){
fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ hhstepm/YEARMstepm );
for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate+ndeath;j++)
fprintf(ficrespij," %.5f", p3mat[i][j][h]);
fprintf(ficrespij,"\n");
}
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
fprintf(ficrespij,"\n");
}
}
}

	/-------------- Variance of one-step probabilities---/
	k=1;
varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);	varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);

fclose(ficrespij);

probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);	probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
for(i=1;i<=AGESUP;i++)	for(i=1;i<=AGESUP;i++)
Line 6261 Interval (in months) between two waves:	Line 6384 Interval (in months) between two waves:
}	}
printf("Computing Health Expectancies: result on file '%s' \n", filerese);	printf("Computing Health Expectancies: result on file '%s' \n", filerese);
fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);	fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
for(cptcov=1,k=0;cptcov<=i1;cptcov++){	/*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){	for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
k=k+1;
	for (k=1; k <= (int) pow(2,cptcoveff); k++){
fprintf(ficreseij,"\n#****** ");	fprintf(ficreseij,"\n#****** ");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=cptcoveff;j++) {
fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
Line 6275 Interval (in months) between two waves:	Line 6399 Interval (in months) between two waves:
evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);	evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);

free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);	free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
}	/}/
}	}
fclose(ficreseij);	fclose(ficreseij);

Line 6320 Interval (in months) between two waves:	Line 6444 Interval (in months) between two waves:
printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);	printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);	fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);

for(cptcov=1,k=0;cptcov<=i1;cptcov++){	/*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){	for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
k=k+1;
fprintf(ficrest,"\n#****** ");	for (k=1; k <= (int) pow(2,cptcoveff); k++){
	fprintf(ficrest,"\n#****** ");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
fprintf(ficrest,"******\n");	fprintf(ficrest,"******\n");
Line 6345 Interval (in months) between two waves:	Line 6470 Interval (in months) between two waves:
eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);	eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
oldm=oldms;savm=savms;	oldm=oldms;savm=savms;
cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);	cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
	/*
	*/
	/* goto endfree; */

vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);	vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
pstamp(ficrest);	pstamp(ficrest);


for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/	for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
oldm=oldms;savm=savms;	oldm=oldms;savm=savms; /* Segmentation fault */
varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are ");	varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);
	fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are ");
if(vpopbased==1)	if(vpopbased==1)
fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);	fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
else	else
Line 6394 Interval (in months) between two waves:	Line 6525 Interval (in months) between two waves:
free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);	free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);	free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
free_vector(epj,1,nlstate+1);	free_vector(epj,1,nlstate+1);
}	/}/
}	}
free_vector(weight,1,n);	free_vector(weight,1,n);
free_imatrix(Tvard,1,15,1,2);	free_imatrix(Tvard,1,NCOVMAX,1,2);
free_imatrix(s,1,maxwav+1,1,n);	free_imatrix(s,1,maxwav+1,1,n);
free_matrix(anint,1,maxwav,1,n);	free_matrix(anint,1,maxwav,1,n);
free_matrix(mint,1,maxwav,1,n);	free_matrix(mint,1,maxwav,1,n);
Line 6419 Interval (in months) between two waves:	Line 6550 Interval (in months) between two waves:
}	}
printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);	printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);

for(cptcov=1,k=0;cptcov<=i1;cptcov++){	/*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){	for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
k=k+1;
fprintf(ficresvpl,"\n#****** ");	for (k=1; k <= (int) pow(2,cptcoveff); k++){
	fprintf(ficresvpl,"\n#****** ");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
fprintf(ficresvpl,"******\n");	fprintf(ficresvpl,"******\n");
Line 6431 Interval (in months) between two waves:	Line 6563 Interval (in months) between two waves:
oldm=oldms;savm=savms;	oldm=oldms;savm=savms;
varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);	varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
free_matrix(varpl,1,nlstate,(int) bage, (int)fage);	free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
}	/}/
}	}

fclose(ficresvpl);	fclose(ficresvpl);
Line 6453 Interval (in months) between two waves:	Line 6585 Interval (in months) between two waves:
free_matrix(agev,1,maxwav,1,imx);	free_matrix(agev,1,maxwav,1,imx);
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,1,8);	free_ivector(ncodemax,1,NCOVMAX);
free_ivector(Tvar,1,15);	free_ivector(Tvar,1,NCOVMAX);
free_ivector(Tprod,1,15);	free_ivector(Tprod,1,NCOVMAX);
free_ivector(Tvaraff,1,15);	free_ivector(Tvaraff,1,NCOVMAX);
free_ivector(Tage,1,15);	free_ivector(Tage,1,NCOVMAX);

free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);	free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
free_imatrix(codtab,1,100,1,10);	free_imatrix(codtab,1,100,1,10);

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

Removed from v.1.144
changed lines
	Added in v.1.148