imach/src/imach.c - diff

Return to imach.c CVS log

Up to [Local Repository] / imach / src

Diff for /imach/src/imach.c between versions 1.68 and 1.78

version 1.68, 2003/02/04 12:40:59	version 1.78, 2003/05/27 17:26:53
Line 48	Line 48
It is copyrighted identically to a GNU software product, ie programme and	It is copyrighted identically to a GNU software product, ie programme and
software can be distributed freely for non commercial use. Latest version	software can be distributed freely for non commercial use. Latest version
can be accessed at http://euroreves.ined.fr/imach .	can be accessed at http://euroreves.ined.fr/imach .

	Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
	or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so

**********************************************************************/	**********************************************************************/
	/*
	main
	read parameterfile
	read datafile
	concatwav
	if (mle >= 1)
	mlikeli
	print results files
	if mle==1
	computes hessian
	read end of parameter file: agemin, agemax, bage, fage, estepm
	begin-prev-date,...
	open gnuplot file
	open html file
	stable prevalence
	for age prevalim()
	h Pij x
	variance of p varprob
	forecasting if prevfcast==1 prevforecast call prevalence()
	health expectancies
	Variance-covariance of DFLE
	prevalence()
	movingaverage()
	varevsij()
	if popbased==1 varevsij(,popbased)
	total life expectancies
	Variance of stable prevalence
	end
	*/




#include <math.h>	#include <math.h>
#include <stdio.h>	#include <stdio.h>
Line 83	Line 119
#define ODIRSEPARATOR '\\'	#define ODIRSEPARATOR '\\'
#endif	#endif

char version[80]="Imach version 0.91, November 2002, INED-EUROREVES ";	char version[80]="Imach version 0.95a, May 2003, INED-EUROREVES ";
int erreur; /* Error number */	int erreur; /* Error number */
int nvar;	int nvar;
int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;	int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
Line 105 double jmean; /* Mean space between 2 wa	Line 141 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 *ficlog;	FILE ficlog, ficrespow;
FILE ficgp,ficresprob,ficpop, ficresprobcov, *ficresprobcor;	FILE ficgp,ficresprob,ficpop, ficresprobcov, *ficresprobcor;
FILE *ficresprobmorprev;	FILE *ficresprobmorprev;
FILE fichtm; / Html File */	FILE fichtm; / Html File */
Line 188 static int split( char path, char dirc	Line 224 static int split( char path, char dirc
if ( ss == NULL ) { /* no directory, so use current */	if ( ss == NULL ) { /* no directory, so use current */
/*if(strrchr(path, ODIRSEPARATOR )==NULL)	/*if(strrchr(path, ODIRSEPARATOR )==NULL)
printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/	printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
#if defined(__bsd__) /* get current working directory */	/* get current working directory */
extern char *getwd( );	/* extern char* getcwd ( char buf , int len);/

if ( getwd( dirc ) == NULL ) {
#else
extern char *getcwd( );

if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {	if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
#endif
return( GLOCK_ERROR_GETCWD );	return( GLOCK_ERROR_GETCWD );
}	}
strcpy( name, path ); /* we've got it */	strcpy( name, path ); /* we've got it */
Line 297 void free_vector(double*v, int nl, int n	Line 327 void free_vector(double*v, int nl, int n
}	}

/**********************ivector *****************************/	/**********************ivector *****************************/
	char *cvector(long nl,long nh)
	{
	char *v;
	v=(char ) malloc((size_t)((nh-nl+1+NR_END)sizeof(char)));
	if (!v) nrerror("allocation failure in cvector");
	return v-nl+NR_END;
	}

	/****************free ivector ************************/
	void free_cvector(char *v, long nl, long nh)
	{
	free((FREE_ARG)(v+nl-NR_END));
	}

	/**********************ivector *****************************/
int *ivector(long nl,long nh)	int *ivector(long nl,long nh)
{	{
int *v;	int *v;
Line 365 double **matrix(long nrl, long nrh, long	Line 410 double **matrix(long nrl, long nrh, long

for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;	for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
return m;	return m;
	/* print ((m+1)+70) ou print m[1][70]; print m+1 or print &(m[1])
	*/
}	}

/***********************free matrix **********************/	/***********************free matrix **********************/
Line 404 double ***ma3x(long nrl, long nrh, long	Line 451 double ***ma3x(long nrl, long nrh, long
for (j=ncl+1; j<=nch; j++)	for (j=ncl+1; j<=nch; j++)
m[i][j]=m[i][j-1]+nlay;	m[i][j]=m[i][j-1]+nlay;
}	}
return m;	return m;
	/* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
	&(m[i][j][k]) <=> (((m+i) + j)+k)
	*/
}	}

/***********************free ma3x **********************/	/***********************free ma3x **********************/
Line 612 void powell(double p[], double **xi, int	Line 662 void powell(double p[], double **xi, int
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);	fprintf(ficlog,"\nPowell iter=%d -2LL=%.12f",iter,*fret);
for (i=1;i<=n;i++)	fprintf(ficrespow,"%d %.12f",iter,fret);
	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]);	fprintf(ficlog," %d %.12lf",i, p[i]);
	fprintf(ficrespow," %.12lf", p[i]);
	}
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
	fprintf(ficrespow,"\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);
Line 972 double func( double *x)	Line 1026 double func( double *x)
* is higher than the multiple of stepm and negative otherwise.	* is higher than the multiple of stepm and negative otherwise.
*/	*/
/* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]):log((1.+bbh)out[s1][s2]));/	/* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]):log((1.+bbh)out[s1][s2]));/
/* if s2=-2 lli=out[1][1]+out[1][2];*/	if( s2 > nlstate){
if (s2==-2) {	/* i.e. if s2 is a death state and if the date of death is known then the contribution
for (j=1,survp=0. ; j<=nlstate; j++)	to the likelihood is the probability to die between last step unit time and current
survp += out[s1][j];	step unit time, which is also the differences between probability to die before dh
lli= survp;	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
else	health state: the date of the interview describes the actual state
lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)out[s1][s2]- bbh(savm[s1][s2])):log((1.+bbh)out[s1][s2])); / linear interpolation */	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((1.+bbh)out[s1][s2]- bbhsavm[s1][s2]); /* linear interpolation */
	/* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)out[s1][s2]- bbh(savm[s1][s2])):log((1.+bbh)out[s1][s2]));/ /* linear interpolation */
	}
/lli=(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]);/	/lli=(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]);/
/if(lli ==000.0)/	/if(lli ==000.0)/
/printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); /	/printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][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;
} /* end of wave */	} /* end of wave */
Line 1131 double func( double *x)	Line 1204 double func( double *x)
void mlikeli(FILE ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (func)(double []))	void mlikeli(FILE ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (func)(double []))
{	{
int i,j, iter;	int i,j, iter;
double *xi,delti;	double **xi;
double fret;	double fret;
	char filerespow[FILENAMELENGTH];
xi=matrix(1,npar,1,npar);	xi=matrix(1,npar,1,npar);
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"); fprintf(ficlog,"Powell\n");	printf("Powell\n"); fprintf(ficlog,"Powell\n");
	strcpy(filerespow,"pow");
	strcat(filerespow,fileres);
	if((ficrespow=fopen(filerespow,"w"))==NULL) {
	printf("Problem with resultfile: %s\n", filerespow);
	fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
	}
	fprintf(ficrespow,"# Powell\n# iter -2*LL");
	for (i=1;i<=nlstate;i++)
	for(j=1;j<=nlstate+ndeath;j++)
	if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
	fprintf(ficrespow,"\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));	fclose(ficrespow);
	printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));	fprintf(ficlog,"\n#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 1404 void lubksb(double *a, int n, int indx	Line 1490 void lubksb(double *a, int n, int indx
}	}

/********** Frequencies ******************/	/********** Frequencies ******************/
void freqsummary(char fileres[], int agemin, int agemax, int s, double agev, int nlstate, int imx, int Tvaraff, int nbcode, int ncodemax,double mint,double anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)	void freqsummary(char fileres[], int iagemin, int iagemax, int s, double agev, int nlstate, int imx, int Tvaraff, int nbcode, int ncodemax,double mint,double anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
{ /* 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;	int first;
double **freq; / Frequencies */	double **freq; / Frequencies */
double *pp;	double pp, *prop;
double pos, k2, dateintsum=0,k2cpt=0;	double pos,posprop, k2, dateintsum=0,k2cpt=0;
FILE *ficresp;	FILE *ficresp;
char fileresp[FILENAMELENGTH];	char fileresp[FILENAMELENGTH];

pp=vector(1,nlstate);	pp=vector(1,nlstate);
probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);	prop=matrix(1,nlstate,iagemin,iagemax+3);
strcpy(fileresp,"p");	strcpy(fileresp,"p");
strcat(fileresp,fileres);	strcat(fileresp,fileres);
if((ficresp=fopen(fileresp,"w"))==NULL) {	if((ficresp=fopen(fileresp,"w"))==NULL) {
Line 1424 void freqsummary(char fileres[], int ag	Line 1510 void freqsummary(char fileres[], int ag
fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);	fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
exit(0);	exit(0);
}	}
freq= ma3x(-2,nlstate+ndeath,-2,nlstate+ndeath,agemin,agemax+3);	freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
j1=0;	j1=0;

j=cptcoveff;	j=cptcoveff;
Line 1439 void freqsummary(char fileres[], int ag	Line 1525 void freqsummary(char fileres[], int ag
scanf("%d", i);*/	scanf("%d", i);*/
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=iagemin; m <= iagemax+3; m++)
freq[i][jk][m]=0;	freq[i][jk][m]=0;

	for (i=1; i<=nlstate; i++)
	for(m=iagemin; m <= iagemax+3; m++)
	prop[i][m]=0;

dateintsum=0;	dateintsum=0;
k2cpt=0;	k2cpt=0;
Line 1455 void freqsummary(char fileres[], int ag	Line 1545 void freqsummary(char fileres[], int ag
for(m=firstpass; m<=lastpass; m++){	for(m=firstpass; m<=lastpass; m++){
k2=anint[m][i]+(mint[m][i]/12.);	k2=anint[m][i]+(mint[m][i]/12.);
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]=iagemax+1;
if(agev[m][i]==1) agev[m][i]=agemax+2;	if(agev[m][i]==1) agev[m][i]=iagemax+2;
	if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
if (m<lastpass) {	if (m<lastpass) {
freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += 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];	freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
}	}

if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {	if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
dateintsum=dateintsum+k2;	dateintsum=dateintsum+k2;
k2cpt++;	k2cpt++;
}	}
Line 1482 void freqsummary(char fileres[], int ag	Line 1573 void freqsummary(char fileres[], int ag
fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);	fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
fprintf(ficresp, "\n");	fprintf(ficresp, "\n");

for(i=(int)agemin; i <= (int)agemax+3; i++){	for(i=iagemin; i <= iagemax+3; i++){
if(i==(int)agemax+3){	if(i==iagemax+3){
fprintf(ficlog,"Total");	fprintf(ficlog,"Total");
}else{	}else{
if(first==1){	if(first==1){
Line 1514 void freqsummary(char fileres[], int ag	Line 1605 void freqsummary(char fileres[], int ag
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,posprop=0; jk <=nlstate ; jk++){
for(jk=1,pos=0; jk <=nlstate ; jk++)
pos += pp[jk];	pos += pp[jk];
	posprop += prop[jk][i];
	}
for(jk=1; jk <=nlstate ; jk++){	for(jk=1; jk <=nlstate ; jk++){
if(pos>=1.e-5){	if(pos>=1.e-5){
if(first==1)	if(first==1)
Line 1528 void freqsummary(char fileres[], int ag	Line 1620 void freqsummary(char fileres[], int ag
printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);	printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
fprintf(ficlog," %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 <= iagemax){
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,prop[jk][i]/posprop, prop[jk][i],posprop);
probs[i][jk][j1]= pp[jk]/pos;	probs[i][jk][j1]= pp[jk]/pos;
/printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);/	/printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);/
}	}
else	else
fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);	fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
}	}
}	}

for(jk=-2; jk <=nlstate+ndeath; jk++)	for(jk=-1; jk <=nlstate+ndeath; jk++)
for(m=-2; m <=nlstate+ndeath; m++)	for(m=-1; m <=nlstate+ndeath; m++)
if(freq[jk][m][i] !=0 ) {	if(freq[jk][m][i] !=0 ) {
if(first==1)	if(first==1)
printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);	printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);	fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
}	}
if(i <= (int) agemax)	if(i <= iagemax)
fprintf(ficresp,"\n");	fprintf(ficresp,"\n");
if(first==1)	if(first==1)
printf("Others in log...\n");	printf("Others in log...\n");
Line 1557 void freqsummary(char fileres[], int ag	Line 1649 void freqsummary(char fileres[], int ag
dateintmean=dateintsum/k2cpt;	dateintmean=dateintsum/k2cpt;

fclose(ficresp);	fclose(ficresp);
free_ma3x(freq,-2,nlstate+ndeath,-2,nlstate+ndeath,(int) agemin,(int) agemax+3);	free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
free_vector(pp,1,nlstate);	free_vector(pp,1,nlstate);
	free_matrix(prop,1,nlstate,iagemin, iagemax+3);
/* End of Freq */	/* End of Freq */
}	}

/********** Prevalence ******************/	/********** Prevalence ******************/
void prevalence(int agemin, float agemax, int s, double agev, int nlstate, int imx, int Tvar, int nbcode, int ncodemax,double mint,double anint, double dateprev1,double dateprev2, double calagedate)	void prevalence(double agemin, double agemax, int s, double agev, int nlstate, int imx, int Tvar, int nbcode, int ncodemax,double mint,double anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
{ /* Some frequencies */	{
	/* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
	in each health status at the date of interview (if between dateprev1 and dateprev2).
	We still use firstpass and lastpass as another selection.
	*/

int i, m, jk, k1, i1, j1, bool, z1,z2,j;	int i, m, jk, k1, i1, j1, bool, z1,z2,j;
double **freq; / Frequencies */	double **freq; / Frequencies */
double *pp;	double pp, *prop;
double pos, k2;	double pos,posprop;
	double y2; /* in fractional years */
pp=vector(1,nlstate);	int iagemin, iagemax;

freq=ma3x(-2,nlstate+ndeath,-2,nlstate+ndeath,agemin,agemax+3);	iagemin= (int) agemin;
	iagemax= (int) agemax;
	/pp=vector(1,nlstate);/
	prop=matrix(1,nlstate,iagemin,iagemax+3);
	/* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
j1=0;	j1=0;

j=cptcoveff;	j=cptcoveff;
Line 1584 void prevalence(int agemin, float agemax	Line 1684 void prevalence(int agemin, float agemax
for(i1=1; i1<=ncodemax[k1];i1++){	for(i1=1; i1<=ncodemax[k1];i1++){
j1++;	j1++;

for (i=-2; i<=nlstate+ndeath; i++)	for (i=1; i<=nlstate; i++)
for (jk=-2; jk<=nlstate+ndeath; jk++)	for(m=iagemin; m <= iagemax+3; m++)
for(m=agemin; m <= agemax+3; m++)	prop[i][m]=0.0;
freq[i][jk][m]=0;

for (i=1; i<=imx; i++) {	for (i=1; i<=imx; i++) { /* Each individual */
bool=1;	bool=1;
if (cptcovn>0) {	if (cptcovn>0) {
for (z1=1; z1<=cptcoveff; z1++)	for (z1=1; z1<=cptcoveff; z1++)
Line 1597 void prevalence(int agemin, float agemax	Line 1696 void prevalence(int agemin, float agemax
bool=0;	bool=0;
}	}
if (bool==1) {	if (bool==1) {
for(m=firstpass; m<=lastpass; m++){	for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
k2=anint[m][i]+(mint[m][i]/12.);	y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
if ((k2>=dateprev1) && (k2<=dateprev2)) {	if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
if(agev[m][i]==0) agev[m][i]=agemax+1;	if(agev[m][i]==0) agev[m][i]=iagemax+1;
if(agev[m][i]==1) agev[m][i]=agemax+2;	if(agev[m][i]==1) agev[m][i]=iagemax+2;
if (m<lastpass) {	if((int)agev[m][i] <iagemin \|\| (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m);
if (calagedate>0)	if (s[m][i]>0 && s[m][i]<=nlstate) {
freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];	/if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);/
else	prop[s[m][i]][(int)agev[m][i]] += weight[i];
freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];	prop[s[m][i]][iagemax+3] += weight[i];
freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];	}
}
}	}
}	} /* end selection of waves */
}	}
}	}
for(i=(int)agemin; i <= (int)agemax+3; i++){	for(i=iagemin; i <= iagemax+3; i++){
for(jk=1; jk <=nlstate ; jk++){
for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
pp[jk] += freq[jk][m][i];
}
for(jk=1; jk <=nlstate ; jk++){
for(m=-1, pos=0; m <=0 ; m++)
pos += freq[jk][m][i];
}

for(jk=1; jk <=nlstate ; jk++){	for(jk=1,posprop=0; jk <=nlstate ; jk++) {
for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)	posprop += prop[jk][i];
pp[jk] += freq[jk][m][i];	}
}
	for(jk=1; jk <=nlstate ; jk++){
for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];	if( i <= iagemax){
	if(posprop>=1.e-5){
for(jk=1; jk <=nlstate ; jk++){	probs[i][jk][j1]= prop[jk][i]/posprop;
if( i <= (int) agemax){	}
if(pos>=1.e-5){	}
probs[i][jk][j1]= pp[jk]/pos;	}/* end jk */
}	}/* end i */
}
}/* end jk */
}/* end i */
} /* end i1 */	} /* end i1 */
} /* end k1 */	} /* end k1 */


free_ma3x(freq,-2,nlstate+ndeath,-2,nlstate+ndeath,(int) agemin,(int) agemax+3);
free_vector(pp,1,nlstate);

} /* End of Freq */	/* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
	/free_vector(pp,1,nlstate);/
	free_matrix(prop,1,nlstate, iagemin,iagemax+3);
	} /* End of prevalence */

/*********** Waves Concatenation *************/	/*********** Waves Concatenation *************/

Line 1672 void concatwav(int wav[], int **dh, int	Line 1758 void concatwav(int wav[], int **dh, int
mi=0;	mi=0;
m=firstpass;	m=firstpass;
while(s[m][i] <= nlstate){	while(s[m][i] <= nlstate){
if(s[m][i]>=1 \|\| s[m][i]==-2)	if(s[m][i]>=1)
mw[++mi][i]=m;	mw[++mi][i]=m;
if(m >=lastpass)	if(m >=lastpass)
break;	break;
Line 1689 void concatwav(int wav[], int **dh, int	Line 1775 void concatwav(int wav[], int **dh, int
wav[i]=mi;	wav[i]=mi;
if(mi==0){	if(mi==0){
if(first==0){	if(first==0){
printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);	printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);
first=1;	first=1;
}	}
if(first==1){	if(first==1){
fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);	fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i);
}	}
} /* end mi==0 */	} /* end mi==0 */
}	} /* End individuals */

for(i=1; i<=imx; i++){	for(i=1; i<=imx; i++){
for(mi=1; mi<wav[i];mi++){	for(mi=1; mi<wav[i];mi++){
if (stepm <=0)	if (stepm <=0)
dh[mi][i]=1;	dh[mi][i]=1;
else{	else{
if (s[mw[mi+1][i]][i] > nlstate) {	if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
if (agedc[i] < 2*AGESUP) {	if (agedc[i] < 2*AGESUP) {
j= rint(agedc[i]12-agev[mw[mi][i]][i]12);	j= rint(agedc[i]12-agev[mw[mi][i]][i]12);
if(j==0) j=1; /* Survives at least one month after exam */	if(j==0) j=1; /* Survives at least one month after exam */
Line 1711 void concatwav(int wav[], int **dh, int	Line 1797 void concatwav(int wav[], int **dh, int
if (j >= jmax) jmax=j;	if (j >= jmax) jmax=j;
if (j <= jmin) jmin=j;	if (j <= jmin) jmin=j;
sum=sum+j;	sum=sum+j;
/if (j<0) printf("j=%d num=%d \n",j,i); /	/if (j<0) printf("j=%d num=%d \n",j,i);/
/* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/	/* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
	if(j<0)printf("Error! Negative delay (%d to death) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
}	}
}	}
else{	else{
Line 1722 void concatwav(int wav[], int **dh, int	Line 1809 void concatwav(int wav[], int **dh, int
if (j >= jmax) jmax=j;	if (j >= jmax) jmax=j;
else if (j <= jmin)jmin=j;	else if (j <= jmin)jmin=j;
/* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */	/* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
	/printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);/
	if(j<0)printf("Error! Negative delay (%d) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
sum=sum+j;	sum=sum+j;
}	}
jk= j/stepm;	jk= j/stepm;
Line 1750 void concatwav(int wav[], int **dh, int	Line 1839 void concatwav(int wav[], int **dh, int
if(dh[mi][i]==0){	if(dh[mi][i]==0){
dh[mi][i]=1; /* At least one step */	dh[mi][i]=1; /* At least one step */
bh[mi][i]=ju; /* At least one step */	bh[mi][i]=ju; /* At least one step */
printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);	/* printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
}	}
}	}
} /* end if mle */	} /* end if mle */
Line 1835 void evsij(char fileres[], double ***eij	Line 1924 void evsij(char fileres[], double ***eij
double *gradg, *trgradg;	double *gradg, *trgradg;
int theta;	int theta;

varhe=ma3x(1,nlstate2,1,nlstate2,(int) bage, (int) fage);	varhe=ma3x(1,nlstatenlstate,1,nlstatenlstate,(int) bage, (int) fage);
xp=vector(1,npar);	xp=vector(1,npar);
dnewm=matrix(1,nlstate*2,1,npar);	dnewm=matrix(1,nlstate*nlstate,1,npar);
doldm=matrix(1,nlstate2,1,nlstate2);	doldm=matrix(1,nlstatenlstate,1,nlstatenlstate);

fprintf(ficreseij,"# Health expectancies\n");	fprintf(ficreseij,"# Health expectancies\n");
fprintf(ficreseij,"# Age");	fprintf(ficreseij,"# Age");
Line 1884 void evsij(char fileres[], double ***eij	Line 1973 void evsij(char fileres[], double ***eij
/* if (stepm >= YEARM) hstepm=1;*/	/* if (stepm >= YEARM) hstepm=1;*/
nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */	nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);	gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
gp=matrix(0,nhstepm,1,nlstate*2);	gp=matrix(0,nhstepm,1,nlstate*nlstate);
gm=matrix(0,nhstepm,1,nlstate*2);	gm=matrix(0,nhstepm,1,nlstate*nlstate);

/* Computed by stepm unit matrices, product of hstepm matrices, stored	/* Computed by stepm unit matrices, product of hstepm matrices, stored
in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */	in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
Line 1923 void evsij(char fileres[], double ***eij	Line 2012 void evsij(char fileres[], double ***eij
for(i=1;i<=nlstate;i++){	for(i=1;i<=nlstate;i++){
cptj=cptj+1;	cptj=cptj+1;
for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){	for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){

gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;	gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
}	}
}	}
}	}
for(j=1; j<= nlstate*2; j++)	for(j=1; j<= nlstate*nlstate; 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];
}	}
Line 1935 void evsij(char fileres[], double ***eij	Line 2025 void evsij(char fileres[], double ***eij

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

trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);	trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);

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

printf("%d\|",(int)age);fflush(stdout);	printf("%d\|",(int)age);fflush(stdout);
fprintf(ficlog,"%d\|",(int)age);fflush(ficlog);	fprintf(ficlog,"%d\|",(int)age);fflush(ficlog);
for(h=0;h<=nhstepm-1;h++){	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*nlstate,1,npar,1,npar,matcov);
matprod2(doldm,dnewm,1,nlstate2,1,npar,1,nlstate2,gradg[k]);	matprod2(doldm,dnewm,1,nlstatenlstate,1,npar,1,nlstatenlstate,gradg[k]);
for(i=1;i<=nlstate*2;i++)	for(i=1;i<=nlstate*nlstate;i++)
for(j=1;j<=nlstate*2;j++)	for(j=1;j<=nlstate*nlstate;j++)
varhe[i][j][(int)age] += doldm[i][j]hfhf;	varhe[i][j][(int)age] += doldm[i][j]hfhf;
}	}
}	}
Line 1977 void evsij(char fileres[], double ***eij	Line 2067 void evsij(char fileres[], double ***eij
}	}
fprintf(ficreseij,"\n");	fprintf(ficreseij,"\n");

free_matrix(gm,0,nhstepm,1,nlstate*2);	free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
free_matrix(gp,0,nhstepm,1,nlstate*2);	free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);	free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);	free_ma3x(trgradg,0,nhstepm,1,nlstate*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);
}	}
printf("\n");	printf("\n");
fprintf(ficlog,"\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*nlstate,1,npar);
free_matrix(doldm,1,nlstate2,1,nlstate2);	free_matrix(doldm,1,nlstatenlstate,1,nlstatenlstate);
free_ma3x(varhe,1,nlstate2,1,nlstate2,(int) bage, (int)fage);	free_ma3x(varhe,1,nlstatenlstate,1,nlstatenlstate,(int) bage, (int)fage);
}	}

/********** Variance ****************/	/********** Variance ****************/
Line 2144 void varevsij(char optionfilefiname[], d	Line 2234 void varevsij(char optionfilefiname[], d
computed over hstepm matrices product = hstepm*stepm months)	computed over hstepm matrices product = hstepm*stepm months)
as a weighted average of prlim.	as a weighted average of prlim.
*/	*/
for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){	for(j=nlstate+1;j<=nlstate+ndeath;j++){
for(i=1,gpp[j]=0.; i<= nlstate; i++)	for(i=1,gpp[j]=0.; i<= nlstate; i++)
gpp[j] += prlim[i][i]*p3mat[i][j][1];	gpp[j] += prlim[i][i]*p3mat[i][j][1];
}	}
Line 2175 void varevsij(char optionfilefiname[], d	Line 2265 void varevsij(char optionfilefiname[], d
computed over hstepm matrices product = hstepm*stepm months)	computed over hstepm matrices product = hstepm*stepm months)
as a weighted average of prlim.	as a weighted average of prlim.
*/	*/
for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){	for(j=nlstate+1;j<=nlstate+ndeath;j++){
for(i=1,gmp[j]=0.; i<= nlstate; i++)	for(i=1,gmp[j]=0.; i<= nlstate; i++)
gmp[j] += prlim[i][i]*p3mat[i][j][1];	gmp[j] += prlim[i][i]*p3mat[i][j][1];
}	}
Line 2200 void varevsij(char optionfilefiname[], d	Line 2290 void varevsij(char optionfilefiname[], d
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(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
for(theta=1; theta <=npar; theta++) {	for(theta=1; theta <=npar; theta++)
trgradgp[j][theta]=gradgp[theta][j];	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++)
Line 2218 void varevsij(char optionfilefiname[], d	Line 2308 void varevsij(char optionfilefiname[], d
vareij[i][j][(int)age] += doldm[i][j]hfhf;	vareij[i][j][(int)age] += doldm[i][j]hfhf;
}	}
}	}

/* pptj */	/* pptj */
matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);	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);	matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
	for(j=nlstate+1;j<=nlstate+ndeath;j++)
for(j=nlstate+1;j<=nlstate+ndeath;j++)	for(i=nlstate+1;i<=nlstate+ndeath;i++)
for(i=nlstate+1;i<=nlstate+ndeath;i++){
varppt[j][i]=doldmp[j][i];	varppt[j][i]=doldmp[j][i];
}

/* end ppptj */	/* end ppptj */
/* x centered again */	/* x centered again */
hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);	hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
Line 2242 void varevsij(char optionfilefiname[], d	Line 2329 void varevsij(char optionfilefiname[], d
prlim[i][i]=mobaverage[(int)age][i][ij];	prlim[i][i]=mobaverage[(int)age][i][ij];
}	}
}	}

/* This for computing probability of death (h=1 means	/* This for computing probability of death (h=1 means
computed over hstepm (estepm) matrices product = hstepm*stepm months)	computed over hstepm (estepm) matrices product = hstepm*stepm months)
as a weighted average of prlim.	as a weighted average of prlim.
Line 2288 void varevsij(char optionfilefiname[], d	Line 2375 void varevsij(char optionfilefiname[], d
fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);	fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);	fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
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> 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. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", estepm,digitp,digit);	fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);
/* fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);	/* fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
*/	*/
fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);	fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);

free_vector(xp,1,npar);	free_vector(xp,1,npar);
free_matrix(doldm,1,nlstate,1,nlstate);	free_matrix(doldm,1,nlstate,1,nlstate);
Line 2303 void varevsij(char optionfilefiname[], d	Line 2390 void varevsij(char optionfilefiname[], d
fclose(ficresprobmorprev);	fclose(ficresprobmorprev);
fclose(ficgp);	fclose(ficgp);
fclose(fichtm);	fclose(fichtm);
}	}

/********** Variance of prevlim ****************/	/********** Variance of prevlim ****************/
void varprevlim(char fileres[], double varpl, double matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double oldm, double savm, double **prlim, double ftolpl, int ij)	void varprevlim(char fileres[], double varpl, double matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double oldm, double savm, double **prlim, double ftolpl, int ij)
Line 2449 void varprob(char optionfilefiname[], do	Line 2536 void varprob(char optionfilefiname[], do
fprintf(ficresprobcov," p%1d-%1d ",i,j);	fprintf(ficresprobcov," p%1d-%1d ",i,j);
fprintf(ficresprobcor," p%1d-%1d ",i,j);	fprintf(ficresprobcor," p%1d-%1d ",i,j);
}	}
fprintf(ficresprob,"\n");	/* fprintf(ficresprob,"\n");
fprintf(ficresprobcov,"\n");	fprintf(ficresprobcov,"\n");
fprintf(ficresprobcor,"\n");	fprintf(ficresprobcor,"\n");
xp=vector(1,npar);	*/
	xp=vector(1,npar);
dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);	dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
doldm=matrix(1,(nlstate)(nlstate+ndeath),1,(nlstate)(nlstate+ndeath));	doldm=matrix(1,(nlstate)(nlstate+ndeath),1,(nlstate)(nlstate+ndeath));
mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);	mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
Line 2491 void varprob(char optionfilefiname[], do	Line 2579 void varprob(char optionfilefiname[], do
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#\n");
fprintf(ficresprobcov, "\n#********** Variable ");	fprintf(ficresprobcov, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
fprintf(ficresprobcov, "**********\n#");	fprintf(ficresprobcov, "**********\n#\n");

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


fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");	fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
Line 2507 void varprob(char optionfilefiname[], do	Line 2595 void varprob(char optionfilefiname[], do

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

for (age=bage; age<=fage; age ++){	for (age=bage; age<=fage; age ++){
Line 2526 void varprob(char optionfilefiname[], do	Line 2614 void varprob(char optionfilefiname[], do

for(theta=1; theta <=npar; theta++){	for(theta=1; theta <=npar; theta++){
for(i=1; i<=npar; i++)	for(i=1; i<=npar; i++)
xp[i] = x[i] + (i==theta ?delti[theta]:0);	xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);

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

Line 2539 void varprob(char optionfilefiname[], do	Line 2627 void varprob(char optionfilefiname[], do
}	}

for(i=1; i<=npar; i++)	for(i=1; i<=npar; i++)
xp[i] = x[i] - (i==theta ?delti[theta]:0);	xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);

pmij(pmmij,cov,ncovmodel,xp,nlstate);	pmij(pmmij,cov,ncovmodel,xp,nlstate);
k=0;	k=0;
Line 2551 void varprob(char optionfilefiname[], do	Line 2639 void varprob(char optionfilefiname[], do
}	}

for(i=1; i<= (nlstate)*(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])/(double)2./delti[theta];
}	}

for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)	for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
Line 2738 fprintf(fichtm," \n<ul><li><b>Graphs</b>	Line 2826 fprintf(fichtm," \n<ul><li><b>Graphs</b>
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");	fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
}	}
/* Pij */	/* Pij */
fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>	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);	<img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
/* Quasi-incidences */	/* Quasi-incidences */
fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>	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>
Line 2769 health expectancies in states (1) and (2	Line 2857 health expectancies in states (1) and (2
- Health expectancies with their variances (no covariance): <a href=\"t%s\">t%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);	- 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 */
- Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n	/* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
<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," <ul><li><b>Graphs</b></li><p>");	fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");

m=cptcoveff;	m=cptcoveff;
Line 2791 fprintf(fichtm," <ul><li><b>Graphs</b></	Line 2879 fprintf(fichtm," <ul><li><b>Graphs</b></
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");	fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
}	}
for(cpt=1; cpt<=nlstate;cpt++) {	for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident	fprintf(fichtm,"<br>- Observed and period prevalence (with confident
interval) in state (%d): v%s%d%d.png <br>	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);	<img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
}	}
Line 2826 m=pow(2,cptcoveff);	Line 2914 m=pow(2,cptcoveff);
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");	if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
else fprintf(ficgp," \%%lf (\%%lf)");	else fprintf(ficgp," \%%lf (\%%lf)");
}	}
fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);	fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
for (i=1; i<= nlstate ; i ++) {	for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");	if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
else fprintf(ficgp," \%%lf (\%%lf)");	else fprintf(ficgp," \%%lf (\%%lf)");
}	}
fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);	fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
for (i=1; i<= nlstate ; i ++) {	for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");	if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
else fprintf(ficgp," \%%lf (\%%lf)");	else fprintf(ficgp," \%%lf (\%%lf)");
Line 2892 m=pow(2,cptcoveff);	Line 2980 m=pow(2,cptcoveff);
}	}
}	}

/* CV preval stat */	/* CV preval stable (period) */
for (k1=1; k1<= m ; k1 ++) {	for (k1=1; k1<= m ; k1 ++) {
for (cpt=1; cpt<nlstate ; cpt ++) {	for (cpt=1; cpt<=nlstate ; cpt ++) {
k=3;	k=3;
fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);	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);	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);
fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);	fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);

Line 3022 int movingaverage(double ***probs, doubl	Line 3110 int movingaverage(double ***probs, doubl


/************ Forecasting ****************/	/************ Forecasting ****************/
prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){	prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
	/* proj1, year, month, day of starting projection
int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;	agemin, agemax range of age
	dateprev1 dateprev2 range of dates during which prevalence is computed
	anproj2 year of en of projection (same day and month as proj1).
	*/
	int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
int *popage;	int *popage;
double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;	double agec; /* generic age */
	double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
double popeffectif,popcount;	double popeffectif,popcount;
double ***p3mat;	double ***p3mat;
double ***mobaverage;	double ***mobaverage;
char fileresf[FILENAMELENGTH];	char fileresf[FILENAMELENGTH];

agelim=AGESUP;	agelim=AGESUP;
calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;	prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);

prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);


strcpy(fileresf,"f");	strcpy(fileresf,"f");
strcat(fileresf,fileres);	strcat(fileresf,fileres);
Line 3059 prevforecast(char fileres[], double anpr	Line 3149 prevforecast(char fileres[], double anpr

stepsize=(int) (stepm+YEARM-1)/YEARM;	stepsize=(int) (stepm+YEARM-1)/YEARM;
if (stepm<=12) stepsize=1;	if (stepm<=12) stepsize=1;
	if(estepm < stepm){
agelim=AGESUP;	printf ("Problem %d lower than %d\n",estepm, stepm);
	}
hstepm=1;	else hstepm=estepm;

hstepm=hstepm/stepm;	hstepm=hstepm/stepm;
yp1=modf(dateintmean,&yp);	yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
	fractional in yp1 */
anprojmean=yp;	anprojmean=yp;
yp2=modf((yp1*12),&yp);	yp2=modf((yp1*12),&yp);
mprojmean=yp;	mprojmean=yp;
Line 3072 prevforecast(char fileres[], double anpr	Line 3164 prevforecast(char fileres[], double anpr
jprojmean=yp;	jprojmean=yp;
if(jprojmean==0) jprojmean=1;	if(jprojmean==0) jprojmean=1;
if(mprojmean==0) jprojmean=1;	if(mprojmean==0) jprojmean=1;

	i1=cptcoveff;
	if (cptcovn < 1){i1=1;}

fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);	fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);

for(cptcov=1;cptcov<=i2;cptcov++){	fprintf(ficresf,"#**** Routine prevforecast \n");

	/* if (h==(int)(YEARMyearp)){ /
	for(cptcov=1, k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){	for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
k=k+1;	k=k+1;
fprintf(ficresf,"\n#******");	fprintf(ficresf,"\n#******");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=cptcoveff;j++) {
fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
}	}
fprintf(ficresf,"******\n");	fprintf(ficresf,"******\n");
fprintf(ficresf,"# StartingAge FinalAge");	fprintf(ficresf,"# Covariate valuofcovar yearproj age");
for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);	for(j=1; j<=nlstate+ndeath;j++){
	for(i=1; i<=nlstate;i++)
	fprintf(ficresf," p%d%d",i,j);
for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {	fprintf(ficresf," p.%d",j);
	}
	for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
fprintf(ficresf,"\n");	fprintf(ficresf,"\n");
fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);	fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);

for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){	for (agec=fage; agec>=(ageminpar-1); agec--){
nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);	nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
nhstepm = nhstepm/hstepm;	nhstepm = nhstepm/hstepm;

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,agec,hstepm,p,nlstate,stepm,oldm,savm, k);

for (h=0; h<=nhstepm; h++){	for (h=0; h<=nhstepm; h++){
if (h==(int) (calagedate+YEARM*cpt)) {	if (hhstepm/YEARMstepm ==yearp) {
fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+hhstepm/YEARMstepm);	fprintf(ficresf,"\n");
	for(j=1;j<=cptcoveff;j++)
	fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
	fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+hhstepm/YEARMstepm);
}	}
for(j=1; j<=nlstate+ndeath;j++) {	for(j=1; j<=nlstate+ndeath;j++) {
kk1=0.;kk2=0;	ppij=0.;
for(i=1; i<=nlstate;i++) {	for(i=1; i<=nlstate;i++) {
if (mobilav==1)	if (mobilav==1)
kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];	ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
else {	else {
kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];	ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
}	}
	if (hhstepm/YEARMstepm== yearp) {
}	fprintf(ficresf," %.3f", p3mat[i][j][h]);
if (h==(int)(calagedate+12*cpt)){	}
fprintf(ficresf," %.3f", kk1);	} /* end i */
	if (hhstepm/YEARMstepm==yearp) {
	fprintf(ficresf," %.3f", ppij);
}	}
}	}/* end j */
}	} /* end h */
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
}	} /* end agec */
}	} /* end yearp */
}	} /* end cptcod */
}	} /* end cptcov */

if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);	if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);

fclose(ficresf);	fclose(ficresf);
}	}
/************ Forecasting ****************/
	/************ Forecasting *not tested NB***********/
populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){	populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){

int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;	int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
int *popage;	int *popage;
double calagedate, agelim, kk1, kk2;	double calagedatem, agelim, kk1, kk2;
double popeffectif,popcount;	double popeffectif,popcount;
double *p3mat,tabpop,**tabpopprev;	double *p3mat,tabpop,**tabpopprev;
double ***mobaverage;	double ***mobaverage;
Line 3143 populforecast(char fileres[], double anp	Line 3247 populforecast(char fileres[], double anp
tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);	tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);	tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
agelim=AGESUP;	agelim=AGESUP;
calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;	calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;

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, firstpass, lastpass);


strcpy(filerespop,"pop");	strcpy(filerespop,"pop");
Line 3191 populforecast(char fileres[], double anp	Line 3295 populforecast(char fileres[], double anp
for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];	for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
}	}

for(cptcov=1;cptcov<=i2;cptcov++){	for(cptcov=1,k=0;cptcov<=i2;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){	for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
k=k+1;	k=k+1;
fprintf(ficrespop,"\n#******");	fprintf(ficrespop,"\n#******");
Line 3206 populforecast(char fileres[], double anp	Line 3310 populforecast(char fileres[], double anp
for (cpt=0; cpt<=0;cpt++) {	for (cpt=0; cpt<=0;cpt++) {
fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);	fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);

for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){	for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);	nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
nhstepm = nhstepm/hstepm;	nhstepm = nhstepm/hstepm;

Line 3215 populforecast(char fileres[], double anp	Line 3319 populforecast(char fileres[], double anp
hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);	hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);

for (h=0; h<=nhstepm; h++){	for (h=0; h<=nhstepm; h++){
if (h==(int) (calagedate+YEARM*cpt)) {	if (h==(int) (calagedatem+YEARM*cpt)) {
fprintf(ficrespop,"\n %3.f ",agedeb+hhstepm/YEARMstepm);	fprintf(ficrespop,"\n %3.f ",agedeb+hhstepm/YEARMstepm);
}	}
for(j=1; j<=nlstate+ndeath;j++) {	for(j=1; j<=nlstate+ndeath;j++) {
Line 3227 populforecast(char fileres[], double anp	Line 3331 populforecast(char fileres[], double anp
kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];	kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
}	}
}	}
if (h==(int)(calagedate+12*cpt)){	if (h==(int)(calagedatem+12*cpt)){
tabpop[(int)(agedeb)][j][cptcod]=kk1;	tabpop[(int)(agedeb)][j][cptcod]=kk1;
/*fprintf(ficrespop," %.3f", kk1);	/*fprintf(ficrespop," %.3f", kk1);
if (popforecast==1) fprintf(ficrespop," [%.f]", kk1popeffectif[(int)agedeb+1]);/	if (popforecast==1) fprintf(ficrespop," [%.f]", kk1popeffectif[(int)agedeb+1]);/
Line 3238 populforecast(char fileres[], double anp	Line 3342 populforecast(char fileres[], double anp
for(j=1; j<=nlstate;j++){	for(j=1; j<=nlstate;j++){
kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];	kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
}	}
tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1popeffectif[(int)(agedeb+(calagedate+12cpt)hstepm/YEARMstepm-1)];	tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1popeffectif[(int)(agedeb+(calagedatem+12cpt)hstepm/YEARMstepm-1)];
}	}

if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)	if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);	fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
}	}
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
Line 3252 populforecast(char fileres[], double anp	Line 3356 populforecast(char fileres[], double anp

for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {	for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);	fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){	for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);	nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
nhstepm = nhstepm/hstepm;	nhstepm = nhstepm/hstepm;

Line 3260 populforecast(char fileres[], double anp	Line 3364 populforecast(char fileres[], double anp
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);
for (h=0; h<=nhstepm; h++){	for (h=0; h<=nhstepm; h++){
if (h==(int) (calagedate+YEARM*cpt)) {	if (h==(int) (calagedatem+YEARM*cpt)) {
fprintf(ficresf,"\n %3.f ",agedeb+hhstepm/YEARMstepm);	fprintf(ficresf,"\n %3.f ",agedeb+hhstepm/YEARMstepm);
}	}
for(j=1; j<=nlstate+ndeath;j++) {	for(j=1; j<=nlstate+ndeath;j++) {
Line 3268 populforecast(char fileres[], double anp	Line 3372 populforecast(char fileres[], double anp
for(i=1; i<=nlstate;i++) {	for(i=1; i<=nlstate;i++) {
kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];	kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
}	}
if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);	if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
}	}
}	}
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
Line 3296 populforecast(char fileres[], double anp	Line 3400 populforecast(char fileres[], double anp
int main(int argc, char *argv[])	int main(int argc, char *argv[])
{	{
int movingaverage(double *probs, double bage,double fage, double *mobaverage, int mobilav);	int movingaverage(double *probs, double bage,double fage, double *mobaverage, int mobilav);
int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;	int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
double agedeb, agefin,hf;	double agedeb, agefin,hf;
double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;	double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;

Line 3315 int main(int argc, char *argv[])	Line 3419 int main(int argc, char *argv[])
int ju,jl, mi;	int ju,jl, mi;
int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;	int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
int jnais,jdc,jint4,jint1,jint2,jint3,*outcome,tab;	int jnais,jdc,jint4,jint1,jint2,jint3,*outcome,tab;
	int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
int mobilav=0,popforecast=0;	int mobilav=0,popforecast=0;
int hstepm, nhstepm;	int hstepm, nhstepm;
double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;	double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
	double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;

double bage, fage, age, agelim, agebase;	double bage, fage, age, agelim, agebase;
double ftolpl=FTOL;	double ftolpl=FTOL;
Line 3332 int main(int argc, char *argv[])	Line 3438 int main(int argc, char *argv[])
double *varpl; / Variances of prevalence limits by age */	double *varpl; / Variances of prevalence limits by age */
double *epj, vepp;	double *epj, vepp;
double kk1, kk2;	double kk1, kk2;
double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;	double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;

char *alph[]={"a","a","b","c","d","e"}, str[4];	char *alph[]={"a","a","b","c","d","e"}, str[4];

Line 3479 int main(int argc, char *argv[])	Line 3585 int main(int argc, char *argv[])
ungetc(c,ficpar);	ungetc(c,ficpar);

delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);	delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */	/* delti=vector(1,npar); // Scale of each paramater (output from hesscov) */
for(i=1; i <=nlstate; i++){	for(i=1; i <=nlstate; i++){
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);
Line 3496 int main(int argc, char *argv[])	Line 3602 int main(int argc, char *argv[])
}	}
}	}
delti=delti3[1][1];	delti=delti3[1][1];


	/* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); / / Hasn't to to freed here otherwise delti is no more allocated */

/* Reads comments: lines beginning with '#' */	/* Reads comments: lines beginning with '#' */
while((c=getc(ficpar))=='#' && c!= EOF){	while((c=getc(ficpar))=='#' && c!= EOF){
Line 3615 int main(int argc, char *argv[])	Line 3724 int main(int argc, char *argv[])
if (s[4][i]==9) s[4][i]=-1;	if (s[4][i]==9) s[4][i]=-1;
printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i]));}*/	printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i]));}*/

	for (i=1; i<=imx; i++)

	/*if ((s[3][i]==3) \|\| (s[4][i]==3)) weight[i]=0.08;
	else weight[i]=1;*/

/* Calculation of the number of parameter from char model*/	/* Calculation of the number of parameter from char model*/
Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */	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);
Line 3707 int main(int argc, char *argv[])	Line 3820 int main(int argc, char *argv[])

for (i=1; i<=imx; i++) {	for (i=1; i<=imx; i++) {
for(m=2; (m<= maxwav); m++) {	for(m=2; (m<= maxwav); m++) {
if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){	if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
anint[m][i]=9999;	anint[m][i]=9999;
s[m][i]=-1;	s[m][i]=-1;
}	}
if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;	if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
	printf("Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
	fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
	s[m][i]=-1;
	}
	if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
	printf("Error! Month of death of individual %d on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
	fprintf(ficlog,"Error! Month of death of individual %d on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
	s[m][i]=-1;
	}
}	}
}	}

for (i=1; i<=imx; i++) {	for (i=1; i<=imx; i++) {
agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);	agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
for(m=1; (m<= maxwav); m++){	for(m=firstpass; (m<= lastpass); m++){
if(s[m][i] >0 \|\| s[m][i]==-2){	if(s[m][i] >0){
if (s[m][i] >= nlstate+1) {	if (s[m][i] >= nlstate+1) {
if(agedc[i]>0)	if(agedc[i]>0)
if(moisdc[i]!=99 && andc[i]!=9999) agev[m][i]=agedc[i];	if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
	agev[m][i]=agedc[i];
/if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;/	/if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;/
else {	else {
if (andc[i]!=9999){	if ((int)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);	fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
agev[m][i]=-1;	agev[m][i]=-1;
}	}
}	}
}	}
else if(s[m][i] !=9){ /* Should no more exist */	else if(s[m][i] !=9){ /* Standard case, age in fractional
	years but with the precision of a
	month */
agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);	agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
if(mint[m][i]==99 \|\| anint[m][i]==9999)	if((int)mint[m][i]==99 \|\| (int)anint[m][i]==9999)
agev[m][i]=1;	agev[m][i]=1;
else if(agev[m][i] <agemin){	else if(agev[m][i] <agemin){
agemin=agev[m][i];	agemin=agev[m][i];
Line 3757 int main(int argc, char *argv[])	Line 3882 int main(int argc, char *argv[])

}	}
for (i=1; i<=imx; i++) {	for (i=1; i<=imx; i++) {
for(m=1; (m<= maxwav); m++){	for(m=firstpass; (m<=lastpass); m++){
if (s[m][i] > (nlstate+ndeath)) {	if (s[m][i] > (nlstate+ndeath)) {
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);	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);	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);
Line 3766 int main(int argc, char *argv[])	Line 3891 int main(int argc, char *argv[])
}	}
}	}

	/*for (i=1; i<=imx; i++){
	for (m=firstpass; (m<lastpass); m++){
	printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
	}

	}*/

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

Line 3783 int main(int argc, char *argv[])	Line 3915 int main(int argc, char *argv[])
dh=imatrix(1,lastpass-firstpass+1,1,imx);	dh=imatrix(1,lastpass-firstpass+1,1,imx);
bh=imatrix(1,lastpass-firstpass+1,1,imx);	bh=imatrix(1,lastpass-firstpass+1,1,imx);
mw=imatrix(1,lastpass-firstpass+1,1,imx);	mw=imatrix(1,lastpass-firstpass+1,1,imx);


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

Line 3951 int main(int argc, char *argv[])	Line 4082 int main(int argc, char *argv[])
fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);	fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);	fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);	fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
	printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
	fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);

while((c=getc(ficpar))=='#' && c!= EOF){	while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);	ungetc(c,ficpar);
Line 3961 int main(int argc, char *argv[])	Line 4094 int main(int argc, char *argv[])
ungetc(c,ficpar);	ungetc(c,ficpar);


dateprev1=anprev1+mprev1/12.+jprev1/365.;	dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
dateprev2=anprev2+mprev2/12.+jprev2/365.;	dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;

fscanf(ficpar,"pop_based=%d\n",&popbased);	fscanf(ficpar,"pop_based=%d\n",&popbased);
fprintf(ficparo,"pop_based=%d\n",popbased);	fprintf(ficparo,"pop_based=%d\n",popbased);
Line 3976 int main(int argc, char *argv[])	Line 4109 int main(int argc, char *argv[])
}	}
ungetc(c,ficpar);	ungetc(c,ficpar);

fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);	fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);	fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);	printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
	fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
	fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
	/* day and month of proj2 are not used but only year anproj2.*/

while((c=getc(ficpar))=='#' && c!= EOF){	while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);	ungetc(c,ficpar);
Line 3993 int main(int argc, char *argv[])	Line 4128 int main(int argc, char *argv[])
fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);	fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);	fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);

	probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);	freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);

/------------ gnuplot -------------/	/------------ gnuplot -------------/
Line 4021 int main(int argc, char *argv[])	Line 4156 int main(int argc, char *argv[])
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n	Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
\n	\n
Total number of observations=%d <br>\n	Total number of observations=%d <br>\n
	Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n
Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n	Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
<hr size=\"2\" color=\"#EC5E5E\">	<hr size=\"2\" color=\"#EC5E5E\">
<ul><li><h4>Parameter files</h4>\n	<ul><li><h4>Parameter files</h4>\n
- Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\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	- 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);	- Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,agemin,agemax,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
fclose(fichtm);	fclose(fichtm);

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

Line 4087 Interval (in months) between two waves:	Line 4223 Interval (in months) between two waves:

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);
fprintf(ficrespl,"%.0f",age );	fprintf(ficrespl,"%.0f ",age );
	for(j=1;j<=cptcoveff;j++)
	fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
fprintf(ficrespl," %.5f", prlim[i][i]);	fprintf(ficrespl," %.5f", prlim[i][i]);
fprintf(ficrespl,"\n");	fprintf(ficrespl,"\n");
Line 4115 Interval (in months) between two waves:	Line 4253 Interval (in months) between two waves:

/* hstepm=1; aff par mois*/	/* hstepm=1; aff par mois*/

	fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
for(cptcov=1,k=0;cptcov<=i1;cptcov++){	for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){	for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
k=k+1;	k=k+1;
Line 4132 Interval (in months) between two waves:	Line 4271 Interval (in months) between two waves:
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);
fprintf(ficrespij,"# Age");	fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
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," %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 %f %f",k,agedeb, agedeb+ hhstepm/YEARMstepm );	fprintf(ficrespij,"%d %3.f %3.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 4150 Interval (in months) between two waves:	Line 4289 Interval (in months) between two waves:
}	}
}	}

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

fclose(ficrespij);	fclose(ficrespij);


/---------- Forecasting ------------------/	/---------- Forecasting ------------------/
if((stepm == 1) && (strcmp(model,".")==0)){	/if((stepm == 1) && (strcmp(model,".")==0)){/
prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);	if(prevfcast==1){
if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);	/* if(stepm ==1){*/
}	prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
else{	/* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
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);	/* else{ */
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);	/* 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); */
	/* 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); */
	/* } */
	}


/---------- Health expectancies and variances ------------/	/---------- Health expectancies and variances ------------/
Line 4188 Interval (in months) between two waves:	Line 4330 Interval (in months) between two waves:
printf("Computing Health Expectancies: result on file '%s' \n", filerese);	printf("Computing Health Expectancies: result on file '%s' \n", filerese);
fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);	fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);


strcpy(fileresv,"v");	strcpy(fileresv,"v");
strcat(fileresv,fileres);	strcat(fileresv,fileres);
if((ficresvij=fopen(fileresv,"w"))==NULL) {	if((ficresvij=fopen(fileresv,"w"))==NULL) {
Line 4198 Interval (in months) between two waves:	Line 4339 Interval (in months) between two waves:
printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);	printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);	fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);

calagedate=-1;	/* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
	prevalence(agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);	/* printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d, mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
	ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
	*/

if (mobilav!=0) {	if (mobilav!=0) {
mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);	mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
Line 4327 Interval (in months) between two waves:	Line 4470 Interval (in months) between two waves:

free_matrix(covar,0,NCOVMAX,1,n);	free_matrix(covar,0,NCOVMAX,1,n);
free_matrix(matcov,1,npar,1,npar);	free_matrix(matcov,1,npar,1,npar);
free_vector(delti,1,npar);	/free_vector(delti,1,npar);/
	free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
free_matrix(agev,1,maxwav,1,imx);	free_matrix(agev,1,maxwav,1,imx);
free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);	free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);	if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
	free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);

free_ivector(ncodemax,1,8);	free_ivector(ncodemax,1,8);
free_ivector(Tvar,1,15);	free_ivector(Tvar,1,15);
free_ivector(Tprod,1,15);	free_ivector(Tprod,1,15);
Line 4338 Interval (in months) between two waves:	Line 4484 Interval (in months) between two waves:
free_ivector(Tage,1,15);	free_ivector(Tage,1,15);
free_ivector(Tcode,1,100);	free_ivector(Tcode,1,100);

fprintf(fichtm,"\n</body>");	/* fclose(fichtm);*/
fclose(fichtm);	/* fclose(ficgp);/ / ALready done */
fclose(ficgp);


if(erreur >0){	if(erreur >0){
Line 4369 Interval (in months) between two waves:	Line 4514 Interval (in months) between two waves:
strcpy(plotcmd,GNUPLOTPROGRAM);	strcpy(plotcmd,GNUPLOTPROGRAM);
strcat(plotcmd," ");	strcat(plotcmd," ");
strcat(plotcmd,optionfilegnuplot);	strcat(plotcmd,optionfilegnuplot);
printf("Starting: %s\n",plotcmd);fflush(stdout);	printf("Starting graphs with: %s",plotcmd);fflush(stdout);
system(plotcmd);	system(plotcmd);
	printf(" Wait...");

/#ifdef windows/	/#ifdef windows/
while (z[0] != 'q') {	while (z[0] != 'q') {

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

Removed from v.1.68
changed lines
	Added in v.1.78