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Diff for /imach/src/imach.c between versions 1.41.2.2 and 1.50

version 1.41.2.2, 2003/06/13 07:45:28	version 1.50, 2002/06/26 23:25:02
Line 56	Line 56
#include <unistd.h>	#include <unistd.h>

#define MAXLINE 256	#define MAXLINE 256
#define GNUPLOTPROGRAM "wgnuplot"	#define GNUPLOTPROGRAM "gnuplot"
/#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"/	/#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"/
#define FILENAMELENGTH 80	#define FILENAMELENGTH 80
/#define DEBUG/	/#define DEBUG/
	#define windows
/#define windows/
#define GLOCK_ERROR_NOPATH -1 /* empty path */	#define GLOCK_ERROR_NOPATH -1 /* empty path */
#define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */	#define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */

Line 76	Line 75
#define YEARM 12. /* Number of months per year */	#define YEARM 12. /* Number of months per year */
#define AGESUP 130	#define AGESUP 130
#define AGEBASE 40	#define AGEBASE 40
	#ifdef windows
	#define DIRSEPARATOR '\\'
	#define ODIRSEPARATOR '/'
	#else
	#define DIRSEPARATOR '/'
	#define ODIRSEPARATOR '\\'
	#endif

	char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";
int erreur; /* Error number */	int erreur; /* Error number */
int nvar;	int nvar;
int cptcovn, cptcovage=0, cptcoveff=0,cptcov;	int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
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 97 double jmean; /* Mean space between 2 wa	Line 103 double jmean; /* Mean space between 2 wa
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,ficpar, ficparo,ficres, ficrespl, ficrespij, ficrest,ficresf,*ficrespop;	FILE fic,ficpar, ficparo,ficres, ficrespl, ficrespij, ficrest,ficresf,*ficrespop;
FILE ficgp,ficresprob,*ficpop;	FILE *ficlog;
	FILE ficgp,ficresprob,ficpop, ficresprobcov, *ficresprobcor;
	FILE *ficresprobmorprev;
	FILE fichtm; / Html File */
FILE *ficreseij;	FILE *ficreseij;
char filerese[FILENAMELENGTH];	char filerese[FILENAMELENGTH];
FILE *ficresvij;	FILE *ficresvij;
char fileresv[FILENAMELENGTH];	char fileresv[FILENAMELENGTH];
FILE *ficresvpl;	FILE *ficresvpl;
char fileresvpl[FILENAMELENGTH];	char fileresvpl[FILENAMELENGTH];
	char title[MAXLINE];
	char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
	char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];

	char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
	char filelog[FILENAMELENGTH]; /* Log file */
	char filerest[FILENAMELENGTH];
	char fileregp[FILENAMELENGTH];
	char popfile[FILENAMELENGTH];

	char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];

#define NR_END 1	#define NR_END 1
#define FREE_ARG char*	#define FREE_ARG char*
Line 162 static int split( char path, char dirc	Line 182 static int split( char path, char dirc

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 );
#ifdef windows	s= strrchr( path, DIRSEPARATOR ); /* find last / */
s = strrchr( path, '\\' ); /* find last / */
#else
s = strrchr( path, '/' ); /* find last / */
#endif
if ( s == NULL ) { /* no directory, so use current */	if ( s == NULL ) { /* no directory, so use current */
	/*if(strrchr(path, ODIRSEPARATOR )==NULL)
	printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
#if defined(__bsd__) /* get current working directory */	#if defined(__bsd__) /* get current working directory */
extern char *getwd( );	extern char *getwd( );

Line 233 int nbocc(char *s, char occ)	Line 251 int nbocc(char *s, char occ)

void cutv(char u,char v, char*t, char occ)	void cutv(char u,char v, char*t, char occ)
{	{
	/* cuts string t into u and v where u is ended by char occ excluding it
	and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
	gives u="abcedf" and v="ghi2j" */
int i,lg,j,p=0;	int i,lg,j,p=0;
i=0;	i=0;
for(j=0; j<=strlen(t)-1; j++) {	for(j=0; j<=strlen(t)-1; j++) {
Line 429 double brent(double ax, double bx, doubl	Line 450 double brent(double ax, double bx, doubl
tol2=2.0(tol1=tolfabs(x)+ZEPS);	tol2=2.0(tol1=tolfabs(x)+ZEPS);
/* if (2.0fabs(fp-(fret)) <= ftol(fabs(fp)+fabs(fret)))*/	/* if (2.0fabs(fp-(fret)) <= ftol(fabs(fp)+fabs(fret)))*/
printf(".");fflush(stdout);	printf(".");fflush(stdout);
	fprintf(ficlog,".");fflush(ficlog);
#ifdef DEBUG	#ifdef DEBUG
printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);	printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
	fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
/* if ((fabs(x-xm) <= (tol2-0.5(b-a)))\|\|(2.0fabs(fu-ftemp) <= ftol1.e-2(fabs(fu)+fabs(ftemp)))) { */	/* if ((fabs(x-xm) <= (tol2-0.5(b-a)))\|\|(2.0fabs(fu-ftemp) <= ftol1.e-2(fabs(fu)+fabs(ftemp)))) { */
#endif	#endif
if (fabs(x-xm) <= (tol2-0.5*(b-a))){	if (fabs(x-xm) <= (tol2-0.5*(b-a))){
Line 555 void linmin(double p[], double xi[], int	Line 578 void linmin(double p[], double xi[], int
*fret=brent(ax,xx,bx,f1dim,TOL,&xmin);	*fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
#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);
#endif	#endif
for (j=1;j<=n;j++) {	for (j=1;j<=n;j++) {
xi[j] *= xmin;	xi[j] *= xmin;
Line 585 void powell(double p[], double **xi, int	Line 609 void powell(double p[], double **xi, int
ibig=0;	ibig=0;
del=0.0;	del=0.0;
printf("\nPowell iter=%d -2LL=%.12f",iter,*fret);	printf("\nPowell iter=%d -2LL=%.12f",iter,*fret);
	fprintf(ficlog,"\nPowell iter=%d -2LL=%.12f",iter,*fret);
for (i=1;i<=n;i++)	for (i=1;i<=n;i++)
printf(" %d %.12f",i, p[i]);	printf(" %d %.12f",i, p[i]);
	fprintf(ficlog," %d %.12f",i, p[i]);
printf("\n");	printf("\n");
	fprintf(ficlog,"\n");
for (i=1;i<=n;i++) {	for (i=1;i<=n;i++) {
for (j=1;j<=n;j++) xit[j]=xi[j][i];	for (j=1;j<=n;j++) xit[j]=xi[j][i];
fptt=(*fret);	fptt=(*fret);
#ifdef DEBUG	#ifdef DEBUG
printf("fret=%lf \n",*fret);	printf("fret=%lf \n",*fret);
	fprintf(ficlog,"fret=%lf \n",*fret);
#endif	#endif
printf("%d",i);fflush(stdout);	printf("%d",i);fflush(stdout);
	fprintf(ficlog,"%d",i);fflush(ficlog);
linmin(p,xit,n,fret,func);	linmin(p,xit,n,fret,func);
if (fabs(fptt-(*fret)) > del) {	if (fabs(fptt-(*fret)) > del) {
del=fabs(fptt-(*fret));	del=fabs(fptt-(*fret));
Line 602 void powell(double p[], double **xi, int	Line 631 void powell(double p[], double **xi, int
}	}
#ifdef DEBUG	#ifdef DEBUG
printf("%d %.12e",i,(*fret));	printf("%d %.12e",i,(*fret));
	fprintf(ficlog,"%d %.12e",i,(*fret));
for (j=1;j<=n;j++) {	for (j=1;j<=n;j++) {
xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);	xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
printf(" x(%d)=%.12e",j,xit[j]);	printf(" x(%d)=%.12e",j,xit[j]);
	fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
}	}
for(j=1;j<=n;j++)	for(j=1;j<=n;j++) {
printf(" p=%.12e",p[j]);	printf(" p=%.12e",p[j]);
	fprintf(ficlog," p=%.12e",p[j]);
	}
printf("\n");	printf("\n");
	fprintf(ficlog,"\n");
#endif	#endif
}	}
if (2.0fabs(fp-(fret)) <= ftol(fabs(fp)+fabs(fret))) {	if (2.0fabs(fp-(fret)) <= ftol(fabs(fp)+fabs(fret))) {
Line 617 void powell(double p[], double **xi, int	Line 651 void powell(double p[], double **xi, int
k[0]=1;	k[0]=1;
k[1]=-1;	k[1]=-1;
printf("Max: %.12e",(*func)(p));	printf("Max: %.12e",(*func)(p));
for (j=1;j<=n;j++)	fprintf(ficlog,"Max: %.12e",(*func)(p));
	for (j=1;j<=n;j++) {
printf(" %.12e",p[j]);	printf(" %.12e",p[j]);
	fprintf(ficlog," %.12e",p[j]);
	}
printf("\n");	printf("\n");
	fprintf(ficlog,"\n");
for(l=0;l<=1;l++) {	for(l=0;l<=1;l++) {
for (j=1;j<=n;j++) {	for (j=1;j<=n;j++) {
ptt[j]=p[j]+(p[j]-pt[j])*k[l];	ptt[j]=p[j]+(p[j]-pt[j])*k[l];
printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);	printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
	fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
}	}
printf("func(ptt)=%.12e, deriv=%.12e\n",(func)(ptt),(ptt[j]-p[j])/((func)(ptt)-(*func)(p)));	printf("func(ptt)=%.12e, deriv=%.12e\n",(func)(ptt),(ptt[j]-p[j])/((func)(ptt)-(*func)(p)));
	fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(func)(ptt),(ptt[j]-p[j])/((func)(ptt)-(*func)(p)));
}	}
#endif	#endif

Line 653 void powell(double p[], double **xi, int	Line 693 void powell(double p[], double **xi, int
}	}
#ifdef DEBUG	#ifdef DEBUG
printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);	printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
for(j=1;j<=n;j++)	fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
	for(j=1;j<=n;j++){
printf(" %.12e",xit[j]);	printf(" %.12e",xit[j]);
	fprintf(ficlog," %.12e",xit[j]);
	}
printf("\n");	printf("\n");
	fprintf(ficlog,"\n");
#endif	#endif
}	}
}	}
Line 870 double func( double *x)	Line 914 double func( double *x)
double **out;	double **out;
double sw; /* Sum of weights */	double sw; /* Sum of weights */
double lli; /* Individual log likelihood */	double lli; /* Individual log likelihood */
int s1, s2;
long ipmx;	long ipmx;
/extern weight /	/extern weight /
/* We are differentiating ll according to initial status */	/* We are differentiating ll according to initial status */
Line 885 double func( double *x)	Line 928 double func( double *x)
for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];	for (k=1; k<=cptcovn;k++) cov[2+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++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
oldm[ii][j]=(ii==j ? 1.0 : 0.0);
savm[ii][j]=(ii==j ? 1.0 : 0.0);
}
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;	cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
Line 904 double func( double *x)	Line 944 double func( double *x)

} /* end mult */	} /* end mult */

s1=s[mw[mi][i]][i];	lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);
s2=s[mw[mi+1][i]][i];	/* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
if( s2 > nlstate){
/* i.e. if s2 is a death state and if the date of death is known then the contribution
to the likelihood is the probability to die between last step unit time and current
step unit time, which is also the differences between probability to die before dh
and probability to die before dh-stepm .
In version up to 0.92 likelihood was computed
as if date of death was unknown. Death was treated as any other
health state: the date of the interview describes the actual state
and not the date of a change in health state. The former idea was
to consider that at each interview the state was recorded
(healthy, disable or death) and IMaCh was corrected; but when we
introduced the exact date of death then we should have modified
the contribution of an exact death to the likelihood. This new
contribution is smaller and very dependent of the step unit
stepm. It is no more the probability to die between last interview
and month of death but the probability to survive from last
interview up to one month before death multiplied by the
probability to die within a month. Thanks to Chris
Jackson for correcting this bug. Former versions increased
mortality artificially. The bad side is that we add another loop
which slows down the processing. The difference can be up to 10%
lower mortality.
*/
lli=log(out[s1][s2] - savm[s1][s2]);
}else{
lli=log(out[s1][s2]); /* or lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); */
/* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
}
ipmx +=1;	ipmx +=1;
sw += weight[i];	sw += weight[i];
ll[s[mw[mi][i]][i]] += 2weight[i]lli;	ll[s[mw[mi][i]][i]] += 2weight[i]lli;
/printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d lli=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],lli,weight[i],out[s1][s2],savm[s1][s2]);/
} /* end of wave */	} /* end of wave */
} /* end of individual */	} /* end of individual */

for(k=1,l=0.; k<=nlstate; k++) l += ll[k];	for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
/* printf("l1=%f l2=%f ",ll[1],ll[2]); */	/* printf("l1=%f l2=%f ",ll[1],ll[2]); */
l= lipmx/sw; / To get the same order of magnitude as if weight=1 for every body */	l= lipmx/sw; / To get the same order of magnitude as if weight=1 for every body */
/exit(0);/
return -l;	return -l;
}	}

Line 960 void mlikeli(FILE *ficres,double p[], in	Line 970 void mlikeli(FILE *ficres,double p[], in
for (i=1;i<=npar;i++)	for (i=1;i<=npar;i++)
for (j=1;j<=npar;j++)	for (j=1;j<=npar;j++)
xi[i][j]=(i==j ? 1.0 : 0.0);	xi[i][j]=(i==j ? 1.0 : 0.0);
printf("Powell\n");	printf("Powell\n"); fprintf(ficlog,"Powell\n");
powell(p,xi,npar,ftol,&iter,&fret,func);	powell(p,xi,npar,ftol,&iter,&fret,func);

printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));	printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
	fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));	fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));

}	}
Line 984 void hesscov(double **matcov, double p[]	Line 995 void hesscov(double **matcov, double p[]
hess=matrix(1,npar,1,npar);	hess=matrix(1,npar,1,npar);

printf("\nCalculation of the hessian matrix. Wait...\n");	printf("\nCalculation of the hessian matrix. Wait...\n");
	fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
for (i=1;i<=npar;i++){	for (i=1;i<=npar;i++){
printf("%d",i);fflush(stdout);	printf("%d",i);fflush(stdout);
	fprintf(ficlog,"%d",i);fflush(ficlog);
hess[i][i]=hessii(p,ftolhess,i,delti);	hess[i][i]=hessii(p,ftolhess,i,delti);
/printf(" %f ",p[i]);/	/printf(" %f ",p[i]);/
/printf(" %lf ",hess[i][i]);/	/printf(" %lf ",hess[i][i]);/
Line 995 void hesscov(double **matcov, double p[]	Line 1008 void hesscov(double **matcov, double p[]
for (j=1;j<=npar;j++) {	for (j=1;j<=npar;j++) {
if (j>i) {	if (j>i) {
printf(".%d%d",i,j);fflush(stdout);	printf(".%d%d",i,j);fflush(stdout);
	fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
hess[i][j]=hessij(p,delti,i,j);	hess[i][j]=hessij(p,delti,i,j);
hess[j][i]=hess[i][j];	hess[j][i]=hess[i][j];
/printf(" %lf ",hess[i][j]);/	/printf(" %lf ",hess[i][j]);/
Line 1002 void hesscov(double **matcov, double p[]	Line 1016 void hesscov(double **matcov, double p[]
}	}
}	}
printf("\n");	printf("\n");
	fprintf(ficlog,"\n");

printf("\nInverting the hessian to get the covariance matrix. Wait...\n");	printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
	fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");

a=matrix(1,npar,1,npar);	a=matrix(1,npar,1,npar);
y=matrix(1,npar,1,npar);	y=matrix(1,npar,1,npar);
Line 1023 void hesscov(double **matcov, double p[]	Line 1039 void hesscov(double **matcov, double p[]
}	}

printf("\n#Hessian matrix#\n");	printf("\n#Hessian matrix#\n");
	fprintf(ficlog,"\n#Hessian matrix#\n");
for (i=1;i<=npar;i++) {	for (i=1;i<=npar;i++) {
for (j=1;j<=npar;j++) {	for (j=1;j<=npar;j++) {
printf("%.3e ",hess[i][j]);	printf("%.3e ",hess[i][j]);
	fprintf(ficlog,"%.3e ",hess[i][j]);
}	}
printf("\n");	printf("\n");
	fprintf(ficlog,"\n");
}	}

/* Recompute Inverse */	/* Recompute Inverse */
Line 1044 void hesscov(double **matcov, double p[]	Line 1063 void hesscov(double **matcov, double p[]
for (i=1;i<=npar;i++){	for (i=1;i<=npar;i++){
y[i][j]=x[i];	y[i][j]=x[i];
printf("%.3e ",y[i][j]);	printf("%.3e ",y[i][j]);
	fprintf(ficlog,"%.3e ",y[i][j]);
}	}
printf("\n");	printf("\n");
	fprintf(ficlog,"\n");
}	}
*/	*/

Line 1087 double hessii( double x[], double delta,	Line 1108 double hessii( double x[], double delta,

#ifdef DEBUG	#ifdef DEBUG
printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);	printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
	fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
#endif	#endif
/if(fabs(k1-2.0fx+k2) <1.e-13){ */	/if(fabs(k1-2.0fx+k2) <1.e-13){ */
if((k1 <khi/nkhi/2.) \|\| (k2 <khi/nkhi/2.)){	if((k1 <khi/nkhi/2.) \|\| (k2 <khi/nkhi/2.)){
Line 1134 double hessij( double x[], double delti[	Line 1156 double hessij( double x[], double delti[
res=(k1-k2-k3+k4)/4.0/delti[thetai]k/delti[thetaj]k/2.; /* Because of L not 2L /	res=(k1-k2-k3+k4)/4.0/delti[thetai]k/delti[thetaj]k/2.; /* Because of L not 2L /
#ifdef DEBUG	#ifdef DEBUG
printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);	printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
	fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
#endif	#endif
}	}
return res;	return res;
Line 1218 void freqsummary(char fileres[], int ag	Line 1241 void freqsummary(char fileres[], int ag
{ /* Some frequencies */	{ /* Some frequencies */

int i, m, jk, k1,i1, j1, bool, z1,z2,j;	int i, m, jk, k1,i1, j1, bool, z1,z2,j;
	int first;
double **freq; / Frequencies */	double **freq; / Frequencies */
double *pp;	double *pp;
double pos, k2, dateintsum=0,k2cpt=0;	double pos, k2, dateintsum=0,k2cpt=0;
Line 1230 void freqsummary(char fileres[], int ag	Line 1254 void freqsummary(char fileres[], int ag
strcat(fileresp,fileres);	strcat(fileresp,fileres);
if((ficresp=fopen(fileresp,"w"))==NULL) {	if((ficresp=fopen(fileresp,"w"))==NULL) {
printf("Problem with prevalence resultfile: %s\n", fileresp);	printf("Problem with prevalence resultfile: %s\n", fileresp);
	fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
exit(0);	exit(0);
}	}
freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);	freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
Line 1237 void freqsummary(char fileres[], int ag	Line 1262 void freqsummary(char fileres[], int ag

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

	first=1;

for(k1=1; k1<=j;k1++){	for(k1=1; k1<=j;k1++){
for(i1=1; i1<=ncodemax[k1];i1++){	for(i1=1; i1<=ncodemax[k1];i1++){
j1++;	j1++;
Line 1289 void freqsummary(char fileres[], int ag	Line 1316 void freqsummary(char fileres[], int ag
fprintf(ficresp, "\n");	fprintf(ficresp, "\n");

for(i=(int)agemin; i <= (int)agemax+3; i++){	for(i=(int)agemin; i <= (int)agemax+3; i++){
if(i==(int)agemax+3)	if(i==(int)agemax+3){
printf("Total");	fprintf(ficlog,"Total");
else	}else{
printf("Age %d", i);	if(first==1){
	first=0;
	printf("See log file for details...\n");
	}
	fprintf(ficlog,"Age %d", i);
	}
for(jk=1; jk <=nlstate ; jk++){	for(jk=1; jk <=nlstate ; jk++){
for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)	for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
pp[jk] += freq[jk][m][i];	pp[jk] += freq[jk][m][i];
Line 1300 void freqsummary(char fileres[], int ag	Line 1332 void freqsummary(char fileres[], int ag
for(jk=1; jk <=nlstate ; jk++){	for(jk=1; jk <=nlstate ; jk++){
for(m=-1, pos=0; m <=0 ; m++)	for(m=-1, pos=0; m <=0 ; m++)
pos += freq[jk][m][i];	pos += freq[jk][m][i];
if(pp[jk]>=1.e-10)	if(pp[jk]>=1.e-10){
	if(first==1){
printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);	printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
else	}
printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);	fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
	}else{
	if(first==1)
	printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
	fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
	}
}	}

for(jk=1; jk <=nlstate ; jk++){	for(jk=1; jk <=nlstate ; jk++){
Line 1314 void freqsummary(char fileres[], int ag	Line 1352 void freqsummary(char fileres[], int ag
for(jk=1,pos=0; jk <=nlstate ; jk++)	for(jk=1,pos=0; jk <=nlstate ; jk++)
pos += pp[jk];	pos += pp[jk];
for(jk=1; jk <=nlstate ; jk++){	for(jk=1; jk <=nlstate ; jk++){
if(pos>=1.e-5)	if(pos>=1.e-5){
printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);	if(first==1)
else	printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);	fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
	}else{
	if(first==1)
	printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
	fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
	}
if( i <= (int) agemax){	if( i <= (int) agemax){
if(pos>=1.e-5){	if(pos>=1.e-5){
fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);	fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
Line 1331 void freqsummary(char fileres[], int ag	Line 1374 void freqsummary(char fileres[], int ag

for(jk=-1; jk <=nlstate+ndeath; jk++)	for(jk=-1; jk <=nlstate+ndeath; jk++)
for(m=-1; m <=nlstate+ndeath; m++)	for(m=-1; m <=nlstate+ndeath; m++)
if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);	if(freq[jk][m][i] !=0 ) {
	if(first==1)
	printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
	fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
	}
if(i <= (int) agemax)	if(i <= (int) agemax)
fprintf(ficresp,"\n");	fprintf(ficresp,"\n");
printf("\n");	if(first==1)
	printf("Others in log...\n");
	fprintf(ficlog,"\n");
}	}
}	}
}	}
Line 1365 void prevalence(int agemin, float agemax	Line 1414 void prevalence(int agemin, float agemax
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++){	for(k1=1; k1<=j;k1++){
for(i1=1; i1<=ncodemax[k1];i1++){	for(i1=1; i1<=ncodemax[k1];i1++){
j1++;	j1++;

for (i=-1; i<=nlstate+ndeath; i++)	for (i=-1; i<=nlstate+ndeath; i++)
for (jk=-1; jk<=nlstate+ndeath; jk++)	for (jk=-1; jk<=nlstate+ndeath; jk++)
for(m=agemin; m <= agemax+3; m++)	for(m=agemin; m <= agemax+3; m++)
Line 1387 void prevalence(int agemin, float agemax	Line 1436 void prevalence(int agemin, float agemax
if ((k2>=dateprev1) && (k2<=dateprev2)) {	if ((k2>=dateprev1) && (k2<=dateprev2)) {
if(agev[m][i]==0) agev[m][i]=agemax+1;	if(agev[m][i]==0) agev[m][i]=agemax+1;
if(agev[m][i]==1) agev[m][i]=agemax+2;	if(agev[m][i]==1) agev[m][i]=agemax+2;
if (m<lastpass)	if (m<lastpass) {
if (calagedate>0) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];	if (calagedate>0)
else	freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];	else
freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];	freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
	freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];
	}
}	}
}	}
}	}
}	}
for(i=(int)agemin; i <= (int)agemax+3; i++){	for(i=(int)agemin; i <= (int)agemax+3; i++){
for(jk=1; jk <=nlstate ; jk++){	for(jk=1; jk <=nlstate ; jk++){
for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)	for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
pp[jk] += freq[jk][m][i];	pp[jk] += freq[jk][m][i];
}	}
for(jk=1; jk <=nlstate ; jk++){	for(jk=1; jk <=nlstate ; jk++){
for(m=-1, pos=0; m <=0 ; m++)	for(m=-1, pos=0; m <=0 ; m++)
pos += freq[jk][m][i];	pos += freq[jk][m][i];
}	}

for(jk=1; jk <=nlstate ; jk++){	for(jk=1; jk <=nlstate ; jk++){
for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)	for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
pp[jk] += freq[jk][m][i];	pp[jk] += freq[jk][m][i];
}

for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];

for(jk=1; jk <=nlstate ; jk++){
if( i <= (int) agemax){
if(pos>=1.e-5){
probs[i][jk][j1]= pp[jk]/pos;
}
}
}

}	}
}
}	for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];

	for(jk=1; jk <=nlstate ; jk++){
	if( i <= (int) agemax){
	if(pos>=1.e-5){
	probs[i][jk][j1]= pp[jk]/pos;
	}
	}
	}/* end jk */
	}/* end i */
	} /* end i1 */
	} /* end k1 */


free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);	free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
Line 1445 void concatwav(int wav[], int **dh, int	Line 1495 void concatwav(int wav[], int **dh, int
int i, mi, m;	int i, mi, m;
/* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;	/* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
double sum=0., jmean=0.;*/	double sum=0., jmean=0.;*/
	int first;
int j, k=0,jk, ju, jl;	int j, k=0,jk, ju, jl;
double sum=0.;	double sum=0.;
	first=0;
jmin=1e+5;	jmin=1e+5;
jmax=-1;	jmax=-1;
jmean=0.;	jmean=0.;
Line 1470 void concatwav(int wav[], int **dh, int	Line 1521 void concatwav(int wav[], int **dh, int
}	}

wav[i]=mi;	wav[i]=mi;
if(mi==0)	if(mi==0){
printf("Warning, no any valid information for:%d line=%d\n",num[i],i);	if(first==0){
	printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
	first=1;
	}
	if(first==1){
	fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
	}
	} /* end mi==0 */
}	}

for(i=1; i<=imx; i++){	for(i=1; i<=imx; i++){
Line 1512 void concatwav(int wav[], int **dh, int	Line 1570 void concatwav(int wav[], int **dh, int
}	}
jmean=sum/k;	jmean=sum/k;
printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);	printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
	fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
}	}

/********* Tricode **************************/	/********* Tricode **************************/
void tricode(int Tvar, int *nbcode, int imx)	void tricode(int Tvar, int *nbcode, int imx)
{	{
Line 1552 void tricode(int Tvar, int *nbcode, in	Line 1612 void tricode(int Tvar, int *nbcode, in
for (k=0; k<19; k++) Ndum[k]=0;	for (k=0; k<19; k++) Ndum[k]=0;

for (i=1; i<=ncovmodel-2; i++) {	for (i=1; i<=ncovmodel-2; i++) {
ij=Tvar[i];	ij=Tvar[i];
Ndum[ij]++;	Ndum[ij]++;
}	}

ij=1;	ij=1;
for (i=1; i<=10; i++) {	for (i=1; i<=10; i++) {
Line 1564 void tricode(int Tvar, int *nbcode, in	Line 1624 void tricode(int Tvar, int *nbcode, in
}	}
}	}

cptcoveff=ij-1;	cptcoveff=ij-1;
}	}

/********* Health Expectancies **************/	/********* Health Expectancies **************/
Line 1674 void evsij(char fileres[], double ***eij	Line 1734 void evsij(char fileres[], double ***eij
}	}
}	}
}	}



for(j=1; j<= nlstate*2; j++)	for(j=1; j<= nlstate*2; j++)
for(h=0; h<=nhstepm-1; h++){	for(h=0; h<=nhstepm-1; h++){
gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];	gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
}	}

}	}

/* End theta */	/* End theta */
Line 1691 void evsij(char fileres[], double ***eij	Line 1747 void evsij(char fileres[], double ***eij
for(h=0; h<=nhstepm-1; h++)	for(h=0; h<=nhstepm-1; h++)
for(j=1; j<=nlstate*2;j++)	for(j=1; j<=nlstate*2;j++)
for(theta=1; theta <=npar; theta++)	for(theta=1; theta <=npar; theta++)
trgradg[h][j][theta]=gradg[h][theta][j];	trgradg[h][j][theta]=gradg[h][theta][j];


for(i=1;i<=nlstate*2;i++)	for(i=1;i<=nlstate*2;i++)
for(j=1;j<=nlstate*2;j++)	for(j=1;j<=nlstate*2;j++)
varhe[i][j][(int)age] =0.;	varhe[i][j][(int)age] =0.;

for(h=0;h<=nhstepm-1;h++){	printf("%d\|",(int)age);fflush(stdout);
	fprintf(ficlog,"%d\|",(int)age);fflush(ficlog);
	for(h=0;h<=nhstepm-1;h++){
for(k=0;k<=nhstepm-1;k++){	for(k=0;k<=nhstepm-1;k++){
matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);	matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
matprod2(doldm,dnewm,1,nlstate2,1,npar,1,nlstate2,gradg[k]);	matprod2(doldm,dnewm,1,nlstate2,1,npar,1,nlstate2,gradg[k]);
Line 1707 void evsij(char fileres[], double ***eij	Line 1765 void evsij(char fileres[], double ***eij
varhe[i][j][(int)age] += doldm[i][j]hfhf;	varhe[i][j][(int)age] += doldm[i][j]hfhf;
}	}
}	}


/* Computing expectancies */	/* Computing expectancies */
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++)	for(j=1; j<=nlstate;j++)
Line 1734 void evsij(char fileres[], double ***eij	Line 1790 void evsij(char fileres[], double ***eij
free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);	free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
}	}
	printf("\n");
	fprintf(ficlog,"\n");

free_vector(xp,1,npar);	free_vector(xp,1,npar);
free_matrix(dnewm,1,nlstate*2,1,npar);	free_matrix(dnewm,1,nlstate*2,1,npar);
free_matrix(doldm,1,nlstate2,1,nlstate2);	free_matrix(doldm,1,nlstate2,1,nlstate2);
Line 1741 void evsij(char fileres[], double ***eij	Line 1800 void evsij(char fileres[], double ***eij
}	}

/********** Variance ****************/	/********** Variance ****************/
void varevsij(char fileres[], double *vareij, double matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double oldm, double savm, double **prlim, double ftolpl, int ij, int estepm)	void varevsij(char optionfilefiname[], double *vareij, double matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double oldm, double savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased)
{	{
/* Variance of health expectancies */	/* Variance of health expectancies */
/* double prevalim(double prlim, int nlstate, double xp, double age, double oldm, double * savm,double ftolpl);*/	/* double prevalim(double prlim, int nlstate, double xp, double age, double oldm, double * savm,double ftolpl);*/
double **newm;	/* double *newm;/
double dnewm,doldm;	double dnewm,doldm;
	double dnewmp,doldmp;
int i, j, nhstepm, hstepm, h, nstepm ;	int i, j, nhstepm, hstepm, h, nstepm ;
int k, cptcode;	int k, cptcode;
double *xp;	double *xp;
double gp, gm;	double gp, gm; /* for var eij */
double *gradg, *trgradg;	double *gradg, trgradg; /for var eij */
	double gradgp, trgradgp; /* for var p point j */
	double gpp, gmp; /* for var p point j */
	double *varppt; / for var p point j nlstate to nlstate+ndeath */
double ***p3mat;	double ***p3mat;
double age,agelim, hf;	double age,agelim, hf;
int theta;	int theta;
	char digit[4];
	char digitp[16];

	char fileresprobmorprev[FILENAMELENGTH];

fprintf(ficresvij,"# Covariances of life expectancies\n");	if(popbased==1)
	strcpy(digitp,"-populbased-");
	else
	strcpy(digitp,"-stablbased-");

	strcpy(fileresprobmorprev,"prmorprev");
	sprintf(digit,"%-d",ij);
	/printf("DIGIT=%s, ij=%d ijr=%-d\|\n",digit, ij,ij);/
	strcat(fileresprobmorprev,digit); /* Tvar to be done */
	strcat(fileresprobmorprev,digitp); /* Popbased or not */
	strcat(fileresprobmorprev,fileres);
	if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
	printf("Problem with resultfile: %s\n", fileresprobmorprev);
	fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
	}
	printf("Computing total mortality p.j=w1p1j+w2p2j+..: result on file '%s' \n",fileresprobmorprev);
	fprintf(ficlog,"Computing total mortality p.j=w1p1j+w2p2j+..: result on file '%s' \n",fileresprobmorprev);
	fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1p1j+w2p2j+... stand dev in()\n");
	fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
	for(j=nlstate+1; j<=(nlstate+ndeath);j++){
	fprintf(ficresprobmorprev," p.%-d SE",j);
	for(i=1; i<=nlstate;i++)
	fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
	}
	fprintf(ficresprobmorprev,"\n");
	if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
	printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
	fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
	exit(0);
	}
	else{
	fprintf(ficgp,"\n# Routine varevsij");
	}
	if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
	printf("Problem with html file: %s\n", optionfilehtm);
	fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
	exit(0);
	}
	else{
	fprintf(fichtm,"\n<li><h4> Computing step probabilities of dying and weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
	}
	varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);

	fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are the stable prevalence in health states i\n");
fprintf(ficresvij,"# Age");	fprintf(ficresvij,"# Age");
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++)	for(j=1; j<=nlstate;j++)
Line 1766 void varevsij(char fileres[], double ***	Line 1876 void varevsij(char fileres[], double ***
xp=vector(1,npar);	xp=vector(1,npar);
dnewm=matrix(1,nlstate,1,npar);	dnewm=matrix(1,nlstate,1,npar);
doldm=matrix(1,nlstate,1,nlstate);	doldm=matrix(1,nlstate,1,nlstate);
	dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
	doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);

	gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
	gpp=vector(nlstate+1,nlstate+ndeath);
	gmp=vector(nlstate+1,nlstate+ndeath);
	trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/

if(estepm < stepm){	if(estepm < stepm){
printf ("Problem %d lower than %d\n",estepm, stepm);	printf ("Problem %d lower than %d\n",estepm, stepm);
Line 1793 void varevsij(char fileres[], double ***	Line 1910 void varevsij(char fileres[], double ***
gp=matrix(0,nhstepm,1,nlstate);	gp=matrix(0,nhstepm,1,nlstate);
gm=matrix(0,nhstepm,1,nlstate);	gm=matrix(0,nhstepm,1,nlstate);


for(theta=1; theta <=npar; theta++){	for(theta=1; theta <=npar; theta++){
for(i=1; i<=npar; i++){ /* Computes gradient */	for(i=1; i<=npar; i++){ /* Computes gradient */
xp[i] = x[i] + (i==theta ?delti[theta]:0);	xp[i] = x[i] + (i==theta ?delti[theta]:0);
Line 1811 void varevsij(char fileres[], double ***	Line 1929 void varevsij(char fileres[], double ***
gp[h][j] += prlim[i][i]*p3mat[i][j][h];	gp[h][j] += prlim[i][i]*p3mat[i][j][h];
}	}
}	}
	/* This for computing forces of mortality (h=1)as a weighted average */
	for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
	for(i=1; i<= nlstate; i++)
	gpp[j] += prlim[i][i]*p3mat[i][j][1];
	}
	/* end force of mortality */

for(i=1; i<=npar; i++) /* Computes gradient */	for(i=1; i<=npar; i++) /* Computes gradient */
xp[i] = x[i] - (i==theta ?delti[theta]:0);	xp[i] = x[i] - (i==theta ?delti[theta]:0);
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);	hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
Line 1828 void varevsij(char fileres[], double ***	Line 1952 void varevsij(char fileres[], double ***
gm[h][j] += prlim[i][i]*p3mat[i][j][h];	gm[h][j] += prlim[i][i]*p3mat[i][j][h];
}	}
}	}
	/* This for computing force of mortality (h=1)as a weighted average */
	for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
	for(i=1; i<= nlstate; i++)
	gmp[j] += prlim[i][i]*p3mat[i][j][1];
	}
	/* end force of mortality */

for(j=1; j<= nlstate; j++)	for(j=1; j<= nlstate; j++) /* vareij */
for(h=0; h<=nhstepm; h++){	for(h=0; h<=nhstepm; h++){
gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];	gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
}	}
	for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
	gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
	}

} /* End theta */	} /* End theta */

trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);	trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */

for(h=0; h<=nhstepm; h++)	for(h=0; h<=nhstepm; h++) /* veij */
for(j=1; j<=nlstate;j++)	for(j=1; j<=nlstate;j++)
for(theta=1; theta <=npar; theta++)	for(theta=1; theta <=npar; theta++)
trgradg[h][j][theta]=gradg[h][theta][j];	trgradg[h][j][theta]=gradg[h][theta][j];

	for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
	for(theta=1; theta <=npar; theta++)
	trgradgp[j][theta]=gradgp[theta][j];

hf=hstepmstepm/YEARM; / Duration of hstepm expressed in year unit. */	hf=hstepmstepm/YEARM; / Duration of hstepm expressed in year unit. */
for(i=1;i<=nlstate;i++)	for(i=1;i<=nlstate;i++)
for(j=1;j<=nlstate;j++)	for(j=1;j<=nlstate;j++)
Line 1857 void varevsij(char fileres[], double ***	Line 1995 void varevsij(char fileres[], double ***
}	}
}	}

	/* pptj */
	matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
	matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
	for(j=nlstate+1;j<=nlstate+ndeath;j++)
	for(i=nlstate+1;i<=nlstate+ndeath;i++)
	varppt[j][i]=doldmp[j][i];
	/* end ppptj */
	hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
	prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);

	if (popbased==1) {
	for(i=1; i<=nlstate;i++)
	prlim[i][i]=probs[(int)age][i][ij];
	}

	/* This for computing force of mortality (h=1)as a weighted average */
	for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
	for(i=1; i<= nlstate; i++)
	gmp[j] += prlim[i][i]*p3mat[i][j][1];
	}
	/* end force of mortality */

	fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
	for(j=nlstate+1; j<=(nlstate+ndeath);j++){
	fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
	for(i=1; i<=nlstate;i++){
	fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
	}
	}
	fprintf(ficresprobmorprev,"\n");

fprintf(ficresvij,"%.0f ",age );	fprintf(ficresvij,"%.0f ",age );
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++){	for(j=1; j<=nlstate;j++){
Line 1869 void varevsij(char fileres[], double ***	Line 2038 void varevsij(char fileres[], double ***
free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);	free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
} /* End age */	} /* End age */
	free_vector(gpp,nlstate+1,nlstate+ndeath);
	free_vector(gmp,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*/
	fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
	/* for(j=nlstate+1; j<= nlstate+ndeath; j++){ // Only the first actually */
	fprintf(ficgp,"\n set log y; set nolog 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 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(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
	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(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);

free_vector(xp,1,npar);	free_vector(xp,1,npar);
free_matrix(doldm,1,nlstate,1,npar);	free_matrix(doldm,1,nlstate,1,nlstate);
free_matrix(dnewm,1,nlstate,1,nlstate);	free_matrix(dnewm,1,nlstate,1,npar);
	free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
	free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
	free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
	fclose(ficresprobmorprev);
	fclose(ficgp);
	fclose(fichtm);

}	}

Line 1891 void varprevlim(char fileres[], double *	Line 2079 void varprevlim(char fileres[], double *
double age,agelim;	double age,agelim;
int theta;	int theta;

fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");	fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");
fprintf(ficresvpl,"# Age");	fprintf(ficresvpl,"# Age");
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
fprintf(ficresvpl," %1d-%1d",i,i);	fprintf(ficresvpl," %1d-%1d",i,i);
Line 1960 void varprevlim(char fileres[], double *	Line 2148 void varprevlim(char fileres[], double *
}	}

/********** Variance of one-step probabilities ****************/	/********** Variance of one-step probabilities ****************/
void varprob(char fileres[], double *matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int Tvar, int *nbcode, int ncodemax)	void varprob(char optionfilefiname[], double *matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int Tvar, int *nbcode, int ncodemax)
{	{
int i, j, i1, k1, j1, z1;	int i, j=0, i1, k1, l1, t, tj;
int k=0, cptcode;	int k2, l2, j1, z1;
	int k=0,l, cptcode;
	int first=1, first1;
	double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;
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 age,agelim, cov[NCOVMAX];	double age,agelim, cov[NCOVMAX];
	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 fileresprobcor[FILENAMELENGTH];

	double ***varpij;

strcpy(fileresprob,"prob");	strcpy(fileresprob,"prob");
strcat(fileresprob,fileres);	strcat(fileresprob,fileres);
if((ficresprob=fopen(fileresprob,"w"))==NULL) {	if((ficresprob=fopen(fileresprob,"w"))==NULL) {
printf("Problem with resultfile: %s\n", fileresprob);	printf("Problem with resultfile: %s\n", fileresprob);
	fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
	}
	strcpy(fileresprobcov,"probcov");
	strcat(fileresprobcov,fileres);
	if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
	printf("Problem with resultfile: %s\n", fileresprobcov);
	fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
	}
	strcpy(fileresprobcor,"probcor");
	strcat(fileresprobcor,fileres);
	if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
	printf("Problem with resultfile: %s\n", fileresprobcor);
	fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
}	}
printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);	printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
	fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
	printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
	fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
	printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
	fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);

fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");	fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
fprintf(ficresprob,"# Age");	fprintf(ficresprob,"# Age");
for(i=1; i<=nlstate;i++)	fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
for(j=1; j<=(nlstate+ndeath);j++)	fprintf(ficresprobcov,"# Age");
fprintf(ficresprob," p%1d-%1d (SE)",i,j);	fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
	fprintf(ficresprobcov,"# Age");


	for(i=1; i<=nlstate;i++)
	for(j=1; j<=(nlstate+ndeath);j++){
	fprintf(ficresprob," p%1d-%1d (SE)",i,j);
	fprintf(ficresprobcov," p%1d-%1d ",i,j);
	fprintf(ficresprobcor," p%1d-%1d ",i,j);
	}
fprintf(ficresprob,"\n");	fprintf(ficresprob,"\n");
	fprintf(ficresprobcov,"\n");
	fprintf(ficresprobcor,"\n");
	xp=vector(1,npar);
	dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
	doldm=matrix(1,(nlstate)(nlstate+ndeath),1,(nlstate)(nlstate+ndeath));
	mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
	varpij=ma3x(1,nlstate(nlstate+ndeath),1,nlstate(nlstate+ndeath),(int) bage, (int) fage);
	first=1;
	if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
	printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
	fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
	exit(0);
	}
	else{
	fprintf(ficgp,"\n# Routine varprob");
	}
	if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
	printf("Problem with html file: %s\n", optionfilehtm);
	fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
	exit(0);
	}
	else{
	fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
	fprintf(fichtm,"\n");

	fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
	fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
	fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");

xp=vector(1,npar);	}
dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
doldm=matrix(1,(nlstate+ndeath)(nlstate+ndeath),1,(nlstate+ndeath)(nlstate+ndeath));

cov[1]=1;	cov[1]=1;
j=cptcoveff;	tj=cptcoveff;
if (cptcovn<1) {j=1;ncodemax[1]=1;}	if (cptcovn<1) {tj=1;ncodemax[1]=1;}
j1=0;	j1=0;
for(k1=1; k1<=1;k1++){	for(t=1; t<=tj;t++){
for(i1=1; i1<=ncodemax[k1];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]]);
fprintf(ficresprob, "**********\n#");	fprintf(ficresprob, "**********\n#");
}	fprintf(ficresprobcov, "\n#********** Variable ");
	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
	fprintf(ficresprobcov, "**********\n#");

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


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

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

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]]];

}	}
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,1,9);	gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
trgradg=matrix(1,9,1,npar);	trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));	gp=vector(1,(nlstate)*(nlstate+ndeath));
gm=vector(1,(nlstate+ndeath)*(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 2029 fprintf(ficresprob,"#One-step probabilit	Line 2292 fprintf(ficresprob,"#One-step probabilit
pmij(pmmij,cov,ncovmodel,xp,nlstate);	pmij(pmmij,cov,ncovmodel,xp,nlstate);

k=0;	k=0;
for(i=1; i<= (nlstate+ndeath); i++){	for(i=1; i<= (nlstate); i++){
for(j=1; j<=(nlstate+ndeath);j++){	for(j=1; j<=(nlstate+ndeath);j++){
k=k+1;	k=k+1;
gp[k]=pmmij[i][j];	gp[k]=pmmij[i][j];
Line 2041 fprintf(ficresprob,"#One-step probabilit	Line 2304 fprintf(ficresprob,"#One-step probabilit

pmij(pmmij,cov,ncovmodel,xp,nlstate);	pmij(pmmij,cov,ncovmodel,xp,nlstate);
k=0;	k=0;
for(i=1; i<=(nlstate+ndeath); i++){	for(i=1; i<=(nlstate); i++){
for(j=1; j<=(nlstate+ndeath);j++){	for(j=1; j<=(nlstate+ndeath);j++){
k=k+1;	k=k+1;
gm[k]=pmmij[i][j];	gm[k]=pmmij[i][j];
}	}
}	}

for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)	for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];	gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];
}	}

for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)	for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
for(theta=1; theta <=npar; theta++)	for(theta=1; theta <=npar; theta++)
trgradg[j][theta]=gradg[theta][j];	trgradg[j][theta]=gradg[theta][j];

matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);	matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);	matprod2(doldm,dnewm,1,(nlstate)(nlstate+ndeath),1,npar,1,(nlstate)(nlstate+ndeath),gradg);

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

k=0;	k=0;
for(i=1; i<=(nlstate+ndeath); i++){	for(i=1; i<=(nlstate); i++){
for(j=1; j<=(nlstate+ndeath);j++){	for(j=1; j<=(nlstate+ndeath);j++){
k=k+1;	k=k+1;
gm[k]=pmmij[i][j];	mu[k][(int) age]=pmmij[i][j];
}	}
}	}
	for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
/*printf("\n%d ",(int)age);	for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){	varpij[i][j][(int)age] = doldm[i][j];

	/*printf("\n%d ",(int)age);
	for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
printf("%e [%e ;%e] ",gm[i],gm[i]-2sqrt(doldm[i][i]),gm[i]+2sqrt(doldm[i][i]));	printf("%e [%e ;%e] ",gm[i],gm[i]-2sqrt(doldm[i][i]),gm[i]+2sqrt(doldm[i][i]));
	fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2sqrt(doldm[i][i]),gm[i]+2sqrt(doldm[i][i]));
}*/	}*/

fprintf(ficresprob,"\n%d ",(int)age);	fprintf(ficresprob,"\n%d ",(int)age);
	fprintf(ficresprobcov,"\n%d ",(int)age);
	fprintf(ficresprobcor,"\n%d ",(int)age);

for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)	for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));	fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
	for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
}	fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
}	fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
	}
	i=0;
	for (k=1; k<=(nlstate);k++){
	for (l=1; l<=(nlstate+ndeath);l++){
	i=i++;
	fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
	fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
	for (j=1; j<=i;j++){
	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]));
	}
	}
	}/* end of loop for state */
	} /* end of loop for age */

	/* Confidence intervalle of pij */
	/*
	fprintf(ficgp,"\nset noparametric;unset label");
	fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
	fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
	fprintf(fichtm,"\n<br>Probability with confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
	fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
	fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
	fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
	*/

	/* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
	first1=1;
	for (k1=1; k1<=(nlstate);k1++){
	for (l1=1; l1<=(nlstate+ndeath);l1++){
	if(l1==k1) continue;
	i=(k1-1)*(nlstate+ndeath)+l1;
	for (k2=1; k2<=(nlstate);k2++){
	for (l2=1; l2<=(nlstate+ndeath);l2++){
	if(l2==k2) continue;
	j=(k2-1)*(nlstate+ndeath)+l2;
	if(j<=i) continue;
	for (age=bage; age<=fage; age ++){
	if ((int)age %5==0){
	v1=varpij[i][i][(int)age]/stepmYEARM/stepmYEARM;
	v2=varpij[j][j][(int)age]/stepmYEARM/stepmYEARM;
	cv12=varpij[i][j][(int)age]/stepmYEARM/stepmYEARM;
	mu1=mu[i][(int) age]/stepm*YEARM ;
	mu2=mu[j][(int) age]/stepm*YEARM;
	/* Computing eigen value of matrix of covariance */
	lc1=(v1+v2)+sqrt((v1+v2)(v1+v2) - 4(v1v2-cv12cv12));
	lc2=(v1+v2)-sqrt((v1+v2)(v1+v2) - 4(v1v2-cv12cv12));
	if(first1==1){
	first1=0;
	printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\nOthers in log...\n",v1,v2,cv12,lc1,lc2);
	}
	fprintf(ficlog,"Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);
	/* Eigen vectors */
	v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
	v21=sqrt(1.-v11*v11);
	v12=-v21;
	v22=v11;
	/printf(fignu/
	/* mu1+ v11lc1cost + v12lc2sin(t) */
	/* mu2+ v21lc1cost + v21lc2sin(t) */
	if(first==1){
	first=0;
	fprintf(ficgp,"\nset parametric;set nolabel");
	fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);
	fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
	fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1);
	fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k2,l2,k1,l1);
	fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k2,l2,k1,l1);
	fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);
	fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);
	/* fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)), %11.3e +%.3f(-%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)) t \"%d\"",\
	mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \
	mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);
	*/
	fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)), %11.3e +%.3f(-%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)) not",\
	mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \
	mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));
	}else{
	first=0;
	fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);
	fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);
	/*
	fprintf(ficgp,"\nreplot %11.3e+ %.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)), %11.3e +%.3f(-%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)) t \"%d\"",\
	mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \
	mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);
	*/
	fprintf(ficgp,"\nreplot %11.3e+ %.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)), %11.3e +%.3f(-%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)) not",\
	mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \
	mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));
	}/* if first */
	} /* age mod 5 */
	} /* end loop age */
	fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k2,l2,k1,l1);
	first=1;
	} /l12 /
	} /* k12 */
	} /l1 /
	}/* k1 */
	} /* loop covariates */
	free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));	free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));	free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
	free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);	free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);	free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
}	}
free_vector(xp,1,npar);	free_vector(xp,1,npar);
fclose(ficresprob);	fclose(ficresprob);
	fclose(ficresprobcov);
	fclose(ficresprobcor);
	fclose(ficgp);
	fclose(fichtm);
}	}


/***************** Printing html file *********/	/***************** Printing html file *********/
void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \	void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
int lastpass, int stepm, int weightopt, char model[],\	int lastpass, int stepm, int weightopt, char model[],\
int imx,int jmin, int jmax, double jmeanint,char optionfile[], \	int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\	int popforecast, int estepm ,\
char version[], int popforecast, int estepm ){	double jprev1, double mprev1,double anprev1, \
	double jprev2, double mprev2,double anprev2){
int jj1, k1, i1, cpt;	int jj1, k1, i1, cpt;
FILE *fichtm;
/char optionfilehtm[FILENAMELENGTH];/	/char optionfilehtm[FILENAMELENGTH];/
	if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
strcpy(optionfilehtm,optionfile);
strcat(optionfilehtm,".htm");
if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
printf("Problem with %s \n",optionfilehtm), exit(0);	printf("Problem with %s \n",optionfilehtm), exit(0);
	fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
}	}

fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n	fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n	- Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
\n	- Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
Total number of observations=%d <br>\n	- Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n	- Life expectancies by age and initial health status (estepm=%2d months):
<hr size=\"2\" color=\"#EC5E5E\">	<a href=\"e%s\">e%s</a> <br>\n</li>", \
<ul><li>Outputs files<br>\n	jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
- Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
- Gnuplot file name: <a href=\"%s\">%s</a><br>\n	fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
- Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n
- Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n	m=cptcoveff;
- Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n	if (cptcovn < 1) {m=1;ncodemax[1]=1;}
- Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
	jj1=0;
fprintf(fichtm,"\n	for(k1=1; k1<=m;k1++){
- Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n	for(i1=1; i1<=ncodemax[k1];i1++){
- Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n	jj1++;
- Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n	if (cptcovn > 0) {
- Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n	fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
- Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);	for (cpt=1; cpt<=cptcoveff;cpt++)
	fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
	fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
	}
	/* Pij */
	fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>
	<img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
	/* Quasi-incidences */
	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: pe%s%d2.png<br>
	<img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
	/* Stable prevalence in each health state */
	for(cpt=1; cpt<nlstate;cpt++){
	fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
	<img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
	}
	for(cpt=1; cpt<=nlstate;cpt++) {
	fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
	<img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
	}
	fprintf(fichtm,"\n<br>- Total life expectancy by age and
	health expectancies in states (1) and (2): e%s%d.png<br>
	<img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
	} /* end i1 */
	}/* End k1 */
	fprintf(fichtm,"</ul>");


	fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
	- Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
	- Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
	- Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
	- Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
	- Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
	- Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
	- Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);

if(popforecast==1) fprintf(fichtm,"\n	if(popforecast==1) fprintf(fichtm,"\n
- Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n	- Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
Line 2134 Interval (in months) between two waves:	Line 2540 Interval (in months) between two waves:
<br>",fileres,fileres,fileres,fileres);	<br>",fileres,fileres,fileres,fileres);
else	else
fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);	fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);
fprintf(fichtm," <li>Graphs</li><p>");	fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");

m=cptcoveff;	m=cptcoveff;
if (cptcovn < 1) {m=1;ncodemax[1]=1;}	if (cptcovn < 1) {m=1;ncodemax[1]=1;}
Line 2142 fprintf(fichtm," <li>Graphs</li><p>");	Line 2548 fprintf(fichtm," <li>Graphs</li><p>");
jj1=0;	jj1=0;
for(k1=1; k1<=m;k1++){	for(k1=1; k1<=m;k1++){
for(i1=1; i1<=ncodemax[k1];i1++){	for(i1=1; i1<=ncodemax[k1];i1++){
jj1++;	jj1++;
if (cptcovn > 0) {	if (cptcovn > 0) {
fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");	fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
for (cpt=1; cpt<=cptcoveff;cpt++)	for (cpt=1; cpt<=cptcoveff;cpt++)
fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);	fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");	fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
}
fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>
<img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
for(cpt=1; cpt<nlstate;cpt++){
fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>
<img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
}
for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
interval) in state (%d): v%s%d%d.gif <br>
<img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
}	}
for(cpt=1; cpt<=nlstate;cpt++) {	for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>	fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
<img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);	interval) in state (%d): v%s%d%d.png <br>
	<img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
}	}
fprintf(fichtm,"\n<br>- Total life expectancy by age and	} /* end i1 */
health expectancies in states (1) and (2): e%s%d.gif<br>	}/* End k1 */
<img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);	fprintf(fichtm,"</ul>");
fprintf(fichtm,"\n</body>");
}
}
fclose(fichtm);	fclose(fichtm);
}	}

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

int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;	int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
	int ng;
strcpy(optionfilegnuplot,optionfilefiname);	if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
strcat(optionfilegnuplot,".gp.txt");
if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
printf("Problem with file %s",optionfilegnuplot);	printf("Problem with file %s",optionfilegnuplot);
	fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
}	}

#ifdef windows	#ifdef windows
Line 2193 m=pow(2,cptcoveff);	Line 2585 m=pow(2,cptcoveff);
for (cpt=1; cpt<= nlstate ; cpt ++) {	for (cpt=1; cpt<= nlstate ; cpt ++) {
for (k1=1; k1<= m ; k1 ++) {	for (k1=1; k1<= m ; k1 ++) {

fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);	#ifdef windows
	fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
	#endif
	#ifdef unix
	fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);
	#endif

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)");
Line 2210 for (i=1; i<= nlstate ; i ++) {	Line 2609 for (i=1; i<= nlstate ; i ++) {
else fprintf(ficgp," \%%lf (\%%lf)");	else fprintf(ficgp," \%%lf (\%%lf)");
}	}
fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));	fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
	#ifdef unix
fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);	fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");
	#endif
}	}
}	}
/2 eme/	/2 eme/

for (k1=1; k1<= m ; k1 ++) {	for (k1=1; k1<= m ; k1 ++) {
fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);	fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
	fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\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 2242 fprintf(ficgp,"\nset out \"v%s%d%d.gif\"	Line 2643 fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");	if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
else fprintf(ficgp,"\" t\"\" w l 0,");	else fprintf(ficgp,"\" t\"\" w l 0,");
}	}
fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);
}	}

/3eme/	/3eme/
Line 2250 fprintf(ficgp,"\nset out \"v%s%d%d.gif\"	Line 2650 fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
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=2+nlstate(2cpt-2);	k=2+nlstate(2cpt-2);
fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);	fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
	fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
/fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);	/fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");	for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
fprintf(ficgp,"\" t \"e%d1\" w l",cpt);	fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
Line 2263 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);	Line 2664 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);	fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);

}	}
fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
}
}	}
	}

/* CV preval stat */	/* CV preval stat */
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,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);	fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);

for (i=1; i< nlstate ; i ++)	for (i=1; i< nlstate ; i ++)
fprintf(ficgp,"+$%d",k+i+1);	fprintf(ficgp,"+$%d",k+i+1);
Line 2284 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);	Line 2685 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
fprintf(ficgp,"+$%d",l+i+1);	fprintf(ficgp,"+$%d",l+i+1);
}	}
fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);	fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
}	}
}	}

Line 2293 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);	Line 2693 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
for(k=1; k <=(nlstate+ndeath); k++){	for(k=1; k <=(nlstate+ndeath); k++){
if (k != i) {	if (k != i) {
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");
}	}
}	}
}	}
}

for(jk=1; jk <=m; jk++) {
fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
i=1;
for(k2=1; k2<=nlstate; k2++) {
k3=i;
for(k=1; k<=(nlstate+ndeath); k++) {
if (k != k2){
fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
ij=1;
for(j=3; j <=ncovmodel; j++) {
if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
fprintf(ficgp,"+p%d%dx",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
ij++;
}
else
fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
}
fprintf(ficgp,")/(1");

for(k1=1; k1 <=nlstate; k1++){
fprintf(ficgp,"+exp(p%d+p%dx",k3+(k1-1)ncovmodel,k3+(k1-1)*ncovmodel+1);
ij=1;
for(j=3; j <=ncovmodel; j++){
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]]]);
ij++;
}
else
fprintf(ficgp,"+p%d%d",k3+(k1-1)ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
}
fprintf(ficgp,")");
}
fprintf(ficgp,") t \"p%d%d\" ", k2,k);
if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
i=i+ncovmodel;
}
}
}	}
fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);
}	for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
	for(jk=1; jk <=m; jk++) {
fclose(ficgp);	fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
	if (ng==2)
	fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
	else
	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);
	i=1;
	for(k2=1; k2<=nlstate; k2++) {
	k3=i;
	for(k=1; k<=(nlstate+ndeath); k++) {
	if (k != k2){
	if(ng==2)
	fprintf(ficgp," %fexp(p%d+p%dx",YEARM/stepm,i,i+1);
	else
	fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
	ij=1;
	for(j=3; j <=ncovmodel; j++) {
	if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
	fprintf(ficgp,"+p%d%dx",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
	ij++;
	}
	else
	fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
	}
	fprintf(ficgp,")/(1");

	for(k1=1; k1 <=nlstate; k1++){
	fprintf(ficgp,"+exp(p%d+p%dx",k3+(k1-1)ncovmodel,k3+(k1-1)*ncovmodel+1);
	ij=1;
	for(j=3; j <=ncovmodel; j++){
	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]]]);
	ij++;
	}
	else
	fprintf(ficgp,"+p%d%d",k3+(k1-1)ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
	}
	fprintf(ficgp,")");
	}
	fprintf(ficgp,") t \"p%d%d\" ", k2,k);
	if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
	i=i+ncovmodel;
	}
	} /* end k */
	} /* end k2 */
	} /* end jk */
	} /* end ng */
	fclose(ficgp);
} /* end gnuplot */	} /* end gnuplot */


Line 2390 calagedate=(anproj1+mproj1/12.+jproj1/36	Line 2797 calagedate=(anproj1+mproj1/12.+jproj1/36
strcat(fileresf,fileres);	strcat(fileresf,fileres);
if((ficresf=fopen(fileresf,"w"))==NULL) {	if((ficresf=fopen(fileresf,"w"))==NULL) {
printf("Problem with forecast resultfile: %s\n", fileresf);	printf("Problem with forecast resultfile: %s\n", fileresf);
	fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
}	}
printf("Computing forecasting: result on file '%s' \n", fileresf);	printf("Computing forecasting: result on file '%s' \n", fileresf);
	fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);

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

Line 2494 populforecast(char fileres[], double anp	Line 2903 populforecast(char fileres[], double anp
strcat(filerespop,fileres);	strcat(filerespop,fileres);
if((ficrespop=fopen(filerespop,"w"))==NULL) {	if((ficrespop=fopen(filerespop,"w"))==NULL) {
printf("Problem with forecast resultfile: %s\n", filerespop);	printf("Problem with forecast resultfile: %s\n", filerespop);
	fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
}	}
printf("Computing forecasting: result on file '%s' \n", filerespop);	printf("Computing forecasting: result on file '%s' \n", filerespop);
	fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);

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

Line 2515 populforecast(char fileres[], double anp	Line 2926 populforecast(char fileres[], double anp
if (popforecast==1) {	if (popforecast==1) {
if((ficpop=fopen(popfile,"r"))==NULL) {	if((ficpop=fopen(popfile,"r"))==NULL) {
printf("Problem with population file : %s\n",popfile);exit(0);	printf("Problem with population file : %s\n",popfile);exit(0);
	fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
}	}
popage=ivector(0,AGESUP);	popage=ivector(0,AGESUP);
popeffectif=vector(0,AGESUP);	popeffectif=vector(0,AGESUP);
Line 2643 int main(int argc, char *argv[])	Line 3055 int main(int argc, char *argv[])
double ***p3mat;	double ***p3mat;
int *indx;	int *indx;
char line[MAXLINE], linepar[MAXLINE];	char line[MAXLINE], linepar[MAXLINE];
char title[MAXLINE];	char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];

char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];

char filerest[FILENAMELENGTH];
char fileregp[FILENAMELENGTH];
char popfile[FILENAMELENGTH];
char path[80],pathc[80],pathcd[80],pathtot[80],model[20];
int firstobs=1, lastobs=10;	int firstobs=1, lastobs=10;
int sdeb, sfin; /* Status at beginning and end */	int sdeb, sfin; /* Status at beginning and end */
int c, h , cpt,l;	int c, h , cpt,l;
Line 2679 int main(int argc, char *argv[])	Line 3082 int main(int argc, char *argv[])
double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;	double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;


char version[80]="Imach version 0.8a1, June 2003, INED-EUROREVES ";
char *alph[]={"a","a","b","c","d","e"}, str[4];	char *alph[]={"a","a","b","c","d","e"}, str[4];


Line 2714 int main(int argc, char *argv[])	Line 3116 int main(int argc, char *argv[])

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

	/* Log file */
	strcat(filelog, optionfilefiname);
	strcat(filelog,".log"); /* */
	if((ficlog=fopen(filelog,"w"))==NULL) {
	printf("Problem with logfile %s\n",filelog);
	goto end;
	}
	fprintf(ficlog,"Log filename:%s\n",filelog);
	fprintf(ficlog,"\n%s",version);
	fprintf(ficlog,"\nEnter the parameter file name: ");
	fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
	fflush(ficlog);

	/* */
strcpy(fileres,"r");	strcpy(fileres,"r");
strcat(fileres, optionfilefiname);	strcat(fileres, optionfilefiname);
strcat(fileres,".txt"); /* Other files have txt extension */	strcat(fileres,".txt"); /* Other files have txt extension */
Line 2722 int main(int argc, char *argv[])	Line 3138 int main(int argc, char *argv[])

if((ficpar=fopen(optionfile,"r"))==NULL) {	if((ficpar=fopen(optionfile,"r"))==NULL) {
printf("Problem with optionfile %s\n",optionfile);	printf("Problem with optionfile %s\n",optionfile);
	fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
goto end;	goto end;
}	}

strcpy(filereso,"o");	strcpy(filereso,"o");
strcat(filereso,fileres);	strcat(filereso,fileres);
if((ficparo=fopen(filereso,"w"))==NULL) {	if((ficparo=fopen(filereso,"w"))==NULL) {
printf("Problem with Output resultfile: %s\n", filereso);goto end;	printf("Problem with Output resultfile: %s\n", filereso);
	fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
	goto end;
}	}

/* Reads comments: lines beginning with '#' */	/* Reads comments: lines beginning with '#' */
Line 2740 int main(int argc, char *argv[])	Line 3159 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\nmodel=%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=%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=%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=%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);	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);
while((c=getc(ficpar))=='#' && c!= EOF){	while((c=getc(ficpar))=='#' && c!= EOF){
Line 2774 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3193 while((c=getc(ficpar))=='#' && c!= EOF){
for(j=1; j <=nlstate+ndeath-1; j++){	for(j=1; j <=nlstate+ndeath-1; j++){
fscanf(ficpar,"%1d%1d",&i1,&j1);	fscanf(ficpar,"%1d%1d",&i1,&j1);
fprintf(ficparo,"%1d%1d",i1,j1);	fprintf(ficparo,"%1d%1d",i1,j1);
printf("%1d%1d",i,j);	if(mle==1)
	printf("%1d%1d",i,j);
	fprintf(ficlog,"%1d%1d",i,j);
for(k=1; k<=ncovmodel;k++){	for(k=1; k<=ncovmodel;k++){
fscanf(ficpar," %lf",&param[i][j][k]);	fscanf(ficpar," %lf",&param[i][j][k]);
printf(" %lf",param[i][j][k]);	if(mle==1){
	printf(" %lf",param[i][j][k]);
	fprintf(ficlog," %lf",param[i][j][k]);
	}
	else
	fprintf(ficlog," %lf",param[i][j][k]);
fprintf(ficparo," %lf",param[i][j][k]);	fprintf(ficparo," %lf",param[i][j][k]);
}	}
fscanf(ficpar,"\n");	fscanf(ficpar,"\n");
printf("\n");	if(mle==1)
	printf("\n");
	fprintf(ficlog,"\n");
fprintf(ficparo,"\n");	fprintf(ficparo,"\n");
}	}

Line 2829 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3257 while((c=getc(ficpar))=='#' && c!= EOF){
matcov=matrix(1,npar,1,npar);	matcov=matrix(1,npar,1,npar);
for(i=1; i <=npar; i++){	for(i=1; i <=npar; i++){
fscanf(ficpar,"%s",&str);	fscanf(ficpar,"%s",&str);
printf("%s",str);	if(mle==1)
	printf("%s",str);
	fprintf(ficlog,"%s",str);
fprintf(ficparo,"%s",str);	fprintf(ficparo,"%s",str);
for(j=1; j <=i; j++){	for(j=1; j <=i; j++){
fscanf(ficpar," %le",&matcov[i][j]);	fscanf(ficpar," %le",&matcov[i][j]);
printf(" %.5le",matcov[i][j]);	if(mle==1){
	printf(" %.5le",matcov[i][j]);
	fprintf(ficlog," %.5le",matcov[i][j]);
	}
	else
	fprintf(ficlog," %.5le",matcov[i][j]);
fprintf(ficparo," %.5le",matcov[i][j]);	fprintf(ficparo," %.5le",matcov[i][j]);
}	}
fscanf(ficpar,"\n");	fscanf(ficpar,"\n");
printf("\n");	if(mle==1)
	printf("\n");
	fprintf(ficlog,"\n");
fprintf(ficparo,"\n");	fprintf(ficparo,"\n");
}	}
for(i=1; i <=npar; i++)	for(i=1; i <=npar; i++)
for(j=i+1;j<=npar;j++)	for(j=i+1;j<=npar;j++)
matcov[i][j]=matcov[j][i];	matcov[i][j]=matcov[j][i];

printf("\n");	if(mle==1)
	printf("\n");
	fprintf(ficlog,"\n");


/-------- Rewriting paramater file ----------/	/-------- Rewriting paramater file ----------/
Line 2854 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3293 while((c=getc(ficpar))=='#' && c!= EOF){
strcat(rfileres,optionfilext); /* Other files have txt extension */	strcat(rfileres,optionfilext); /* Other files have txt extension */
if((ficres =fopen(rfileres,"w"))==NULL) {	if((ficres =fopen(rfileres,"w"))==NULL) {
printf("Problem writing new parameter file: %s\n", fileres);goto end;	printf("Problem writing new parameter file: %s\n", fileres);goto end;
	fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
}	}
fprintf(ficres,"#%s\n",version);	fprintf(ficres,"#%s\n",version);

/-------- data file ----------/	/-------- data file ----------/
if((fic=fopen(datafile,"r"))==NULL) {	if((fic=fopen(datafile,"r"))==NULL) {
printf("Problem with datafile: %s\n", datafile);goto end;	printf("Problem with datafile: %s\n", datafile);goto end;
	fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
}	}

n= lastobs;	n= lastobs;
Line 2925 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3366 while((c=getc(ficpar))=='#' && c!= EOF){


/* Calculation of the number of parameter from char model*/	/* Calculation of the number of parameter from char model*/
Tvar=ivector(1,15);	Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
Tprod=ivector(1,15);	Tprod=ivector(1,15);
Tvaraff=ivector(1,15);	Tvaraff=ivector(1,15);
Tvard=imatrix(1,15,1,2);	Tvard=imatrix(1,15,1,2);
Line 2941 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3382 while((c=getc(ficpar))=='#' && c!= EOF){
strcpy(modelsav,model);	strcpy(modelsav,model);
if ((strcmp(model,"age")==0) \|\| (strcmp(model,"age*age")==0)){	if ((strcmp(model,"age")==0) \|\| (strcmp(model,"age*age")==0)){
printf("Error. Non available option model=%s ",model);	printf("Error. Non available option model=%s ",model);
	fprintf(ficlog,"Error. Non available option model=%s ",model);
goto end;	goto end;
}	}

for(i=(j+1); i>=1;i--){	for(i=(j+1); i>=1;i--){
cutv(stra,strb,modelsav,'+');	cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);	if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze 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,'*')) {	if (strchr(strb,'')) { / Model includes a product */
cutv(strd,strc,strb,'*');	cutv(strd,strc,strb,''); / strdstrc VmVn (if not age)/
if (strcmp(strc,"age")==0) {	if (strcmp(strc,"age")==0) { /* Vnage /
cptcovprod--;	cptcovprod--;
cutv(strb,stre,strd,'V');	cutv(strb,stre,strd,'V');
Tvar[i]=atoi(stre);	Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
cptcovage++;	cptcovage++;
Tage[cptcovage]=i;	Tage[cptcovage]=i;
/printf("stre=%s ", stre);/	/printf("stre=%s ", stre);/
}	}
else if (strcmp(strd,"age")==0) {	else if (strcmp(strd,"age")==0) { /* or ageVn /
cptcovprod--;	cptcovprod--;
cutv(strb,stre,strc,'V');	cutv(strb,stre,strc,'V');
Tvar[i]=atoi(stre);	Tvar[i]=atoi(stre);
cptcovage++;	cptcovage++;
Tage[cptcovage]=i;	Tage[cptcovage]=i;
}	}
else {	else { /* Age is not in the model */
cutv(strb,stre,strc,'V');	cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
Tvar[i]=ncovcol+k1;	Tvar[i]=ncovcol+k1;
cutv(strb,strc,strd,'V');	cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
Tprod[k1]=i;	Tprod[k1]=i;
Tvard[k1][1]=atoi(strc);	Tvard[k1][1]=atoi(strc); /* m*/
Tvard[k1][2]=atoi(stre);	Tvard[k1][2]=atoi(stre); /* n */
Tvar[cptcovn+k2]=Tvard[k1][1];	Tvar[cptcovn+k2]=Tvard[k1][1];
Tvar[cptcovn+k2+1]=Tvard[k1][2];	Tvar[cptcovn+k2+1]=Tvard[k1][2];
for (k=1; k<=lastobs;k++)	for (k=1; k<=lastobs;k++)
Line 2981 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3423 while((c=getc(ficpar))=='#' && c!= EOF){
k2=k2+2;	k2=k2+2;
}	}
}	}
else {	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');	cutv(strd,strc,strb,'V');
Line 2990 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3432 while((c=getc(ficpar))=='#' && c!= EOF){
strcpy(modelsav,stra);	strcpy(modelsav,stra);
/*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);	/*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
scanf("%d",i);*/	scanf("%d",i);*/
}	} /* end of loop + */
}	} /* end model */

/* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);	/* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
printf("cptcovprod=%d ", cptcovprod);	printf("cptcovprod=%d ", cptcovprod);
	fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
scanf("%d ",i);*/	scanf("%d ",i);*/
fclose(fic);	fclose(fic);

Line 3027 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3470 while((c=getc(ficpar))=='#' && c!= EOF){
else {	else {
if (andc[i]!=9999){	if (andc[i]!=9999){
printf("Warning negative age at death: %d line:%d\n",num[i],i);	printf("Warning negative age at death: %d line:%d\n",num[i],i);
	fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
agev[m][i]=-1;	agev[m][i]=-1;
}	}
}	}
Line 3059 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3503 while((c=getc(ficpar))=='#' && c!= EOF){
for (i=1; i<=imx; i++) {	for (i=1; i<=imx; i++) {
for(m=1; (m<= maxwav); m++){	for(m=1; (m<= maxwav); m++){
if (s[m][i] > (nlstate+ndeath)) {	if (s[m][i] > (nlstate+ndeath)) {
printf("Error: Wrong value in nlstate or ndeath\n");	printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
	fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
goto end;	goto end;
}	}
}	}
}	}

printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);	printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
	fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);

free_vector(severity,1,maxwav);	free_vector(severity,1,maxwav);
free_imatrix(outcome,1,maxwav+1,1,n);	free_imatrix(outcome,1,maxwav+1,1,n);
Line 3141 printf("Total number of individuals= %d,	Line 3587 printf("Total number of individuals= %d,
jk=1;	jk=1;
fprintf(ficres,"# Parameters nlstatenlstatencov a121 + b12 age + ...\n");	fprintf(ficres,"# Parameters nlstatenlstatencov a121 + b12 age + ...\n");
printf("# Parameters nlstatenlstatencov a121 + b12 age + ...\n");	printf("# Parameters nlstatenlstatencov a121 + b12 age + ...\n");
	fprintf(ficlog,"# Parameters nlstatenlstatencov a121 + b12 age + ...\n");
for(i=1,jk=1; i <=nlstate; i++){	for(i=1,jk=1; i <=nlstate; i++){
for(k=1; k <=(nlstate+ndeath); k++){	for(k=1; k <=(nlstate+ndeath); k++){
if (k != i)	if (k != i)
{	{
printf("%d%d ",i,k);	printf("%d%d ",i,k);
	fprintf(ficlog,"%d%d ",i,k);
fprintf(ficres,"%1d%1d ",i,k);	fprintf(ficres,"%1d%1d ",i,k);
for(j=1; j <=ncovmodel; j++){	for(j=1; j <=ncovmodel; j++){
printf("%f ",p[jk]);	printf("%f ",p[jk]);
	fprintf(ficlog,"%f ",p[jk]);
fprintf(ficres,"%f ",p[jk]);	fprintf(ficres,"%f ",p[jk]);
jk++;	jk++;
}	}
printf("\n");	printf("\n");
	fprintf(ficlog,"\n");
fprintf(ficres,"\n");	fprintf(ficres,"\n");
}	}
}	}
}	}
if(mle==1){	if(mle==1){
/* Computing hessian and covariance matrix */	/* Computing hessian and covariance matrix */
ftolhess=ftol; /* Usually correct */	ftolhess=ftol; /* Usually correct */
hesscov(matcov, p, npar, delti, ftolhess, func);	hesscov(matcov, p, npar, delti, ftolhess, func);
}	}
fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");	fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
printf("# Scales (for hessian or gradient estimation)\n");	printf("# Scales (for hessian or gradient estimation)\n");
for(i=1,jk=1; i <=nlstate; i++){	fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
for(j=1; j <=nlstate+ndeath; j++){	for(i=1,jk=1; i <=nlstate; i++){
if (j!=i) {	for(j=1; j <=nlstate+ndeath; j++){
fprintf(ficres,"%1d%1d",i,j);	if (j!=i) {
printf("%1d%1d",i,j);	fprintf(ficres,"%1d%1d",i,j);
for(k=1; k<=ncovmodel;k++){	printf("%1d%1d",i,j);
printf(" %.5e",delti[jk]);	fprintf(ficlog,"%1d%1d",i,j);
fprintf(ficres," %.5e",delti[jk]);	for(k=1; k<=ncovmodel;k++){
jk++;	printf(" %.5e",delti[jk]);
}	fprintf(ficlog," %.5e",delti[jk]);
printf("\n");	fprintf(ficres," %.5e",delti[jk]);
fprintf(ficres,"\n");	jk++;
}	}
}	printf("\n");
	fprintf(ficlog,"\n");
	fprintf(ficres,"\n");
	}
}	}
	}
k=1;
fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");	k=1;
printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");	fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
for(i=1;i<=npar;i++){	if(mle==1)
/* if (k>nlstate) k=1;	printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
i1=(i-1)/(ncovmodel*nlstate)+1;	fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);	for(i=1;i<=npar;i++){
printf("%s%d%d",alph[k],i1,tab[i]);*/	/* if (k>nlstate) k=1;
fprintf(ficres,"%3d",i);	i1=(i-1)/(ncovmodel*nlstate)+1;
printf("%3d",i);	fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
for(j=1; j<=i;j++){	printf("%s%d%d",alph[k],i1,tab[i]);*/
fprintf(ficres," %.5e",matcov[i][j]);	fprintf(ficres,"%3d",i);
printf(" %.5e",matcov[i][j]);	if(mle==1)
}	printf("%3d",i);
fprintf(ficres,"\n");	fprintf(ficlog,"%3d",i);
printf("\n");	for(j=1; j<=i;j++){
k++;	fprintf(ficres," %.5e",matcov[i][j]);
}	if(mle==1)
	printf(" %.5e",matcov[i][j]);
while((c=getc(ficpar))=='#' && c!= EOF){	fprintf(ficlog," %.5e",matcov[i][j]);
ungetc(c,ficpar);	}
fgets(line, MAXLINE, ficpar);	fprintf(ficres,"\n");
puts(line);	if(mle==1)
fputs(line,ficparo);	printf("\n");
}	fprintf(ficlog,"\n");
ungetc(c,ficpar);	k++;
estepm=0;	}
fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
if (estepm==0 \|\| estepm < stepm) estepm=stepm;	while((c=getc(ficpar))=='#' && c!= EOF){
if (fage <= 2) {	ungetc(c,ficpar);
bage = ageminpar;	fgets(line, MAXLINE, ficpar);
fage = agemaxpar;	puts(line);
}	fputs(line,ficparo);
	}
fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");	ungetc(c,ficpar);
fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);	estepm=0;
fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);	fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
	if (estepm==0 \|\| estepm < stepm) estepm=stepm;
while((c=getc(ficpar))=='#' && c!= EOF){	if (fage <= 2) {
ungetc(c,ficpar);	bage = ageminpar;
fgets(line, MAXLINE, ficpar);	fage = agemaxpar;
puts(line);	}
fputs(line,ficparo);
}	fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
ungetc(c,ficpar);	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);

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

fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);	fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);
fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);	fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);	fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);

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);
puts(line);	puts(line);
fputs(line,ficparo);	fputs(line,ficparo);
}	}
ungetc(c,ficpar);	ungetc(c,ficpar);


dateprev1=anprev1+mprev1/12.+jprev1/365.;	dateprev1=anprev1+mprev1/12.+jprev1/365.;
Line 3274 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3736 while((c=getc(ficpar))=='#' && c!= EOF){
freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);	freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);

/------------ gnuplot -------------/	/------------ gnuplot -------------/
printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);	strcpy(optionfilegnuplot,optionfilefiname);
	strcat(optionfilegnuplot,".gp");
	if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
	printf("Problem with file %s",optionfilegnuplot);
	}
	fclose(ficgp);
	printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
	/--------- index.htm --------/

	strcpy(optionfilehtm,optionfile);
	strcat(optionfilehtm,".htm");
	if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
	printf("Problem with %s \n",optionfilehtm), exit(0);
	}

	fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
	Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
	\n
	Total number of observations=%d <br>\n
	Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
	<hr size=\"2\" color=\"#EC5E5E\">
	<ul><li><h4>Parameter files</h4>\n
	- Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
	- Log file of the run: <a href=\"%s\">%s</a><br>\n
	- Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
	fclose(fichtm);

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

/------------ free_vector -------------/	/------------ free_vector -------------/
chdir(path);	chdir(path);
Line 3288 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3777 while((c=getc(ficpar))=='#' && c!= EOF){
fclose(ficparo);	fclose(ficparo);
fclose(ficres);	fclose(ficres);

/--------- index.htm --------/

printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);


/--------------- Prevalence limit --------------/	/--------------- Prevalence limit --------------/

strcpy(filerespl,"pl");	strcpy(filerespl,"pl");
strcat(filerespl,fileres);	strcat(filerespl,fileres);
if((ficrespl=fopen(filerespl,"w"))==NULL) {	if((ficrespl=fopen(filerespl,"w"))==NULL) {
printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;	printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;
	fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;
}	}
printf("Computing prevalence limit: result on file '%s' \n", filerespl);	printf("Computing prevalence limit: result on file '%s' \n", filerespl);
	fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);
fprintf(ficrespl,"#Prevalence limit\n");	fprintf(ficrespl,"#Prevalence limit\n");
fprintf(ficrespl,"#Age ");	fprintf(ficrespl,"#Age ");
for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);	for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
Line 3324 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3811 while((c=getc(ficpar))=='#' && c!= EOF){
k=k+1;	k=k+1;
/printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);/	/printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);/
fprintf(ficrespl,"\n#******");	fprintf(ficrespl,"\n#******");
for(j=1;j<=cptcoveff;j++)	printf("\n#******");
	fprintf(ficlog,"\n#******");
	for(j=1;j<=cptcoveff;j++) {
fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][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");	fprintf(ficrespl,"******\n");
	printf("******\n");
	fprintf(ficlog,"******\n");

for (age=agebase; age<=agelim; age++){	for (age=agebase; age<=agelim; age++){
prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);	prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
Line 3344 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3838 while((c=getc(ficpar))=='#' && c!= EOF){
strcpy(filerespij,"pij"); strcat(filerespij,fileres);	strcpy(filerespij,"pij"); strcat(filerespij,fileres);
if((ficrespij=fopen(filerespij,"w"))==NULL) {	if((ficrespij=fopen(filerespij,"w"))==NULL) {
printf("Problem with Pij resultfile: %s\n", filerespij);goto end;	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);	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;	stepsize=(int) (stepm+YEARM-1)/YEARM;
/if (stepm<=24) stepsize=2;/	/if (stepm<=24) stepsize=2;/
Line 3353 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3849 while((c=getc(ficpar))=='#' && c!= EOF){
agelim=AGESUP;	agelim=AGESUP;
hstepm=stepsizeYEARM; / Every year of age */	hstepm=stepsizeYEARM; / Every year of age */
hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */	hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */

	/* hstepm=1; aff par mois*/

k=0;	k=0;
for(cptcov=1;cptcov<=i1;cptcov++){	for(cptcov=1;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){	for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
Line 3366 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3864 while((c=getc(ficpar))=='#' && c!= EOF){
for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */	for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
nhstepm=(int) rint((agelim-agedeb)YEARM/stepm); / Typically 20 years = 2012/6=40 /	nhstepm=(int) rint((agelim-agedeb)YEARM/stepm); / Typically 20 years = 2012/6=40 /
nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */	nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */

	/* nhstepm=nhstepmYEARM; aff par mois/

p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
oldm=oldms;savm=savms;	oldm=oldms;savm=savms;
hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);	hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
Line 3375 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3876 while((c=getc(ficpar))=='#' && c!= EOF){
fprintf(ficrespij," %1d-%1d",i,j);	fprintf(ficrespij," %1d-%1d",i,j);
fprintf(ficrespij,"\n");	fprintf(ficrespij,"\n");
for (h=0; h<=nhstepm; h++){	for (h=0; h<=nhstepm; h++){
fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ hhstepm/YEARMstepm );	fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ hhstepm/YEARMstepm );
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate+ndeath;j++)	for(j=1; j<=nlstate+ndeath;j++)
fprintf(ficrespij," %.5f", p3mat[i][j][h]);	fprintf(ficrespij," %.5f", p3mat[i][j][h]);
Line 3387 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3888 while((c=getc(ficpar))=='#' && c!= EOF){
}	}
}	}

varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);	varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);

fclose(ficrespij);	fclose(ficrespij);

Line 3400 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3901 while((c=getc(ficpar))=='#' && c!= EOF){
else{	else{
erreur=108;	erreur=108;
printf("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);	printf("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);
}	}


Line 3409 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3911 while((c=getc(ficpar))=='#' && c!= EOF){
strcat(filerest,fileres);	strcat(filerest,fileres);
if((ficrest=fopen(filerest,"w"))==NULL) {	if((ficrest=fopen(filerest,"w"))==NULL) {
printf("Problem with total LE resultfile: %s\n", filerest);goto end;	printf("Problem with total LE resultfile: %s\n", filerest);goto end;
	fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
}	}
printf("Computing Total LEs with variances: file '%s' \n", filerest);	printf("Computing Total LEs with variances: file '%s' \n", filerest);
	fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);


strcpy(filerese,"e");	strcpy(filerese,"e");
strcat(filerese,fileres);	strcat(filerese,fileres);
if((ficreseij=fopen(filerese,"w"))==NULL) {	if((ficreseij=fopen(filerese,"w"))==NULL) {
printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);	printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
	fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
}	}
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);

strcpy(fileresv,"v");	strcpy(fileresv,"v");
strcat(fileresv,fileres);	strcat(fileresv,fileres);
if((ficresvij=fopen(fileresv,"w"))==NULL) {	if((ficresvij=fopen(fileresv,"w"))==NULL) {
printf("Problem with variance resultfile: %s\n", fileresv);exit(0);	printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
	fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
}	}
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);
calagedate=-1;	calagedate=-1;
prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);	prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);

k=0;	k=0;
for(cptcov=1;cptcov<=i1;cptcov++){	for(cptcov=1;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){	for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
k=k+1;	k=k+1;
fprintf(ficrest,"\n#****** ");	fprintf(ficrest,"\n#****** ");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
Line 3454 prevalence(ageminpar, agemax, s, agev, n	Line 3962 prevalence(ageminpar, agemax, s, agev, n

vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);	vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
oldm=oldms;savm=savms;	oldm=oldms;savm=savms;
varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);	varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0);
	if(popbased==1){
	varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);
	}


fprintf(ficrest,"#Total LEs with variances: e.. (std) ");	fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
Line 3543 free_matrix(mint,1,maxwav,1,n);	Line 4053 free_matrix(mint,1,maxwav,1,n);
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);

if(erreur >0)	fprintf(fichtm,"\n</body>");
	fclose(fichtm);
	fclose(ficgp);


	if(erreur >0){
printf("End of Imach with error or warning %d\n",erreur);	printf("End of Imach with error or warning %d\n",erreur);
else printf("End of Imach\n");	fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
	}else{
	printf("End of Imach\n");
	fprintf(ficlog,"End of Imach\n");
	}
	printf("See log file on %s\n",filelog);
	fclose(ficlog);
/* gettimeofday(&end_time, (struct timezone)0);/ /* after time */	/* gettimeofday(&end_time, (struct timezone)0);/ /* after time */

/* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/	/* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
Line 3554 free_matrix(mint,1,maxwav,1,n);	Line 4075 free_matrix(mint,1,maxwav,1,n);


end:	end:
	#ifdef windows
/* chdir(pathcd);*/	/* chdir(pathcd);*/
	#endif
/system("wgnuplot graph.plt");/	/system("wgnuplot graph.plt");/
/system("../gp37mgw/wgnuplot graph.plt");/	/system("../gp37mgw/wgnuplot graph.plt");/
/system("cd ../gp37mgw");/	/system("cd ../gp37mgw");/
Line 3564 free_matrix(mint,1,maxwav,1,n);	Line 4087 free_matrix(mint,1,maxwav,1,n);
strcat(plotcmd,optionfilegnuplot);	strcat(plotcmd,optionfilegnuplot);
system(plotcmd);	system(plotcmd);

/#ifdef windows/	#ifdef windows
while (z[0] != 'q') {	while (z[0] != 'q') {
/* chdir(path); */	/* chdir(path); */
printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");	printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
Line 3574 free_matrix(mint,1,maxwav,1,n);	Line 4097 free_matrix(mint,1,maxwav,1,n);
else if (z[0] == 'g') system(plotcmd);	else if (z[0] == 'g') system(plotcmd);
else if (z[0] == 'q') exit(0);	else if (z[0] == 'q') exit(0);
}	}
/#endif /	#endif
}	}

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

Removed from v.1.41.2.2
changed lines
	Added in v.1.50