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Diff for /imach/src/imach.c between versions 1.208 and 1.215

version 1.208, 2015/11/17 14:31:57	version 1.215, 2015/12/16 08:52:24
Line 1	Line 1
/* $Id$	/* $Id$
$State$	$State$
$Log$	$Log$
	Revision 1.215 2015/12/16 08:52:24 brouard
	Summary: 0.98r4 working

	Revision 1.214 2015/12/16 06:57:54 brouard
	Summary: temporary not working

	Revision 1.213 2015/12/11 18:22:17 brouard
	Summary: 0.98r4

	Revision 1.212 2015/11/21 12:47:24 brouard
	Summary: minor typo

	Revision 1.211 2015/11/21 12:41:11 brouard
	Summary: 0.98r3 with some graph of projected cross-sectional

	Author: Nicolas Brouard

	Revision 1.210 2015/11/18 17:41:20 brouard
	Summary: Start working on projected prevalences

	Revision 1.209 2015/11/17 22:12:03 brouard
	Summary: Adding ftolpl parameter
	Author: N Brouard

	We had difficulties to get smoothed confidence intervals. It was due
	to the period prevalence which wasn't computed accurately. The inner
	parameter ftolpl is now an outer parameter of the .imach parameter
	file after estepm. If ftolpl is small 1.e-4 and estepm too,
	computation are long.

Revision 1.208 2015/11/17 14:31:57 brouard	Revision 1.208 2015/11/17 14:31:57 brouard
Summary: temporary	Summary: temporary

Line 744 typedef struct {	Line 774 typedef struct {
#define NDEATHMAX 8 /*< Maximum number of dead states (for func) /	#define NDEATHMAX 8 /*< Maximum number of dead states (for func) /
#define NCOVMAX 20 /*< Maximum number of covariates, including generated covariates V1V2 */	#define NCOVMAX 20 /*< Maximum number of covariates, including generated covariates V1V2 */
#define codtabm(h,k) (1 & (h-1) >> (k-1))+1	#define codtabm(h,k) (1 & (h-1) >> (k-1))+1
	/#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)/
	#define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
#define MAXN 20000	#define MAXN 20000
#define YEARM 12. /*< Number of months per year /	#define YEARM 12. /*< Number of months per year /
#define AGESUP 130	#define AGESUP 130
Line 801 double *matprod2(); / test */	Line 833 double *matprod2(); / test */
double oldm, newm, *savm; / Working pointers to matrices */	double oldm, newm, *savm; / Working pointers to matrices */
double oldms, newms, *savms; / Fixed working pointers to matrices */	double oldms, newms, *savms; / Fixed working pointers to matrices */
/FILE fic ; / / Used in readdata only */	/FILE fic ; / / Used in readdata only */
FILE ficpar, ficparo,ficres, ficresp, ficrespl, ficrespij, ficrest,ficresf,*ficrespop;	FILE ficpar, ficparo,ficres, ficresp, ficresphtm, ficresphtmfr, ficrespl, ficrespij, ficrest,ficresf,*ficrespop;
FILE ficlog, ficrespow;	FILE ficlog, ficrespow;
int globpr=0; /* Global variable for printing or not */	int globpr=0; /* Global variable for printing or not */
double fretone; /* Only one call to likelihood */	double fretone; /* Only one call to likelihood */
Line 1363 char subdirf3(char fileres[], char pre	Line 1395 char subdirf3(char fileres[], char pre
strcat(tmpout,fileres);	strcat(tmpout,fileres);
return tmpout;	return tmpout;
}	}

	/************* function subdirfext *********/
	char subdirfext(char fileres[], char preop, char *postop)
	{

	strcpy(tmpout,preop);
	strcat(tmpout,fileres);
	strcat(tmpout,postop);
	return tmpout;
	}

	/************* function subdirfext3 *********/
	char subdirfext3(char fileres[], char preop, char *postop)
	{

	/* Caution optionfilefiname is hidden */
	strcpy(tmpout,optionfilefiname);
	strcat(tmpout,"/");
	strcat(tmpout,preop);
	strcat(tmpout,fileres);
	strcat(tmpout,postop);
	return tmpout;
	}

char *asc_diff_time(long time_sec, char ascdiff[])	char *asc_diff_time(long time_sec, char ascdiff[])
{	{
long sec_left, days, hours, minutes;	long sec_left, days, hours, minutes;
Line 1988 double prevalim(double prlim, int nl	Line 2043 double prevalim(double prlim, int nl
/* If we start from prlim again, prlim tends to a constant matrix */	/* If we start from prlim again, prlim tends to a constant matrix */

int i, ii,j,k;	int i, ii,j,k;
double min, max, maxmin, maxmax,sumnew=0.;	double min, max, *meandiff, maxmax,sumnew=0.;
/* double *matprod2(); / /* test */	/* double *matprod2(); / /* test */
double out, cov[NCOVMAX+1], pmij();	double out, cov[NCOVMAX+1], pmij();
double **newm;	double **newm;
double agefin, delaymax=100. ; /* 100 Max number of years to converge */	double agefin, delaymax=200. ; /* 100 Max number of years to converge */
int ncvloop=0;	int ncvloop=0;

	min=vector(1,nlstate);
	max=vector(1,nlstate);
	meandiff=vector(1,nlstate);

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);
Line 2032 double prevalim(double prlim, int nl	Line 2091 double prevalim(double prlim, int nl

savm=oldm;	savm=oldm;
oldm=newm;	oldm=newm;
maxmax=0.;
for(j=1;j<=nlstate;j++){	for(j=1; j<=nlstate; j++){
min=1.;	max[j]=0.;
max=0.;	min[j]=1.;
for(i=1; i<=nlstate; i++) {	}
sumnew=0;	for(i=1;i<=nlstate;i++){
for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];	sumnew=0;
	for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
	for(j=1; j<=nlstate; j++){
prlim[i][j]= newm[i][j]/(1-sumnew);	prlim[i][j]= newm[i][j]/(1-sumnew);
max=FMAX(max,prlim[i][j]);	max[j]=FMAX(max[j],prlim[i][j]);
min=FMIN(min,prlim[i][j]);	min[j]=FMIN(min[j],prlim[i][j]);
/* printf(" age= %d prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d max=%f min=%f\n", (int)age, i, j, i, j, prlim[i][j],(int)agefin, max, min); */	}
}	}
maxmin=(max-min)/(max+min)*2;
maxmax=FMAX(maxmax,maxmin);	maxmax=0.;
/* for(i=1; i<=nlstate; i++) { */	for(j=1; j<=nlstate; j++){
/* sumnew=0.; */	meandiff[j]=(max[j]-min[j])/(max[j]+min[j])2.; / mean difference for each column */
/* sumnew+=prlim[i][j]; */	maxmax=FMAX(maxmax,meandiff[j]);
/* } */	/* printf(" age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, j, meandiff[j],(int)agefin, j, max[j], j, min[j],maxmax); */
/* prmimj = sumnew/(float)nlstate; /\* Means of various prevalence limits. */
} /* j loop */	} /* j loop */
*ncvyear= (int)age- (int)agefin;	*ncvyear= (int)age- (int)agefin;
/* printf("maxmax=%lf maxmin=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, ncvyear); /	/* printf("maxmax=%lf maxmin=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, ncvyear); /
if(maxmax < ftolpl){	if(maxmax < ftolpl){
/* printf("maxmax=%lf maxmin=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, ncvyear); /	/* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, ncvyear); /
	free_vector(min,1,nlstate);
	free_vector(max,1,nlstate);
	free_vector(meandiff,1,nlstate);
return prlim;	return prlim;
}	}
} /* age loop */	} /* age loop */
/* After some age loop it doesn't converge */	/* After some age loop it doesn't converge */
printf("Warning: the stable prevalence at age %d did not converge with the required precision %g > ftolpl=%g within %.0f years. \n\	printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);	Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
/* printf(" age= %d newm\n",(int)age); */
/* for(i=1; i<=nlstate+ndeath; i++) { */
/* for(j=1;j<=nlstate+ndeath;j++){ */
/* printf(" %lf", newm[i][j]); */
/* } */
/* printf("\n"); */
/* } */
/* printf("\n"); */
/* printf("prlim\n"); */
/* for(i=1; i<=nlstate; i++) { */
/* sumnew=0; */
/* for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k]; */
/* for(j=1;j<=nlstate;j++){ */
/* prlim[i][j]= newm[i][j]/(1-sumnew); */
/* printf(" %lf", prlim[i][j]); */
/* } */
/* printf("\n"); */
/* } */
/* printf("\n"); */

/* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */	/* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
	free_vector(min,1,nlstate);
	free_vector(max,1,nlstate);
	free_vector(meandiff,1,nlstate);

return prlim; /* should not reach here */	return prlim; /* should not reach here */
}	}

Line 2208 double *hpxij(double *po, int nhstep	Line 2255 double *hpxij(double *po, int nhstep
double **out, cov[NCOVMAX+1];	double **out, cov[NCOVMAX+1];
double **newm;	double **newm;
double agexact;	double agexact;
	double agebegin, ageend;

/* Hstepm could be zero and should return the unit matrix */	/* Hstepm could be zero and should return the unit matrix */
for (i=1;i<=nlstate+ndeath;i++)	for (i=1;i<=nlstate+ndeath;i++)
Line 2221 double *hpxij(double *po, int nhstep	Line 2269 double *hpxij(double *po, int nhstep
newm=savm;	newm=savm;
/* Covariates have to be included here again */	/* Covariates have to be included here again */
cov[1]=1.;	cov[1]=1.;
agexact=age+((h-1)hstepm + (d-1))stepm/YEARM;	agexact=age+((h-1)hstepm + (d-1))stepm/YEARM; /* age just before transition */
cov[2]=agexact;	cov[2]=agexact;
if(nagesqr==1)	if(nagesqr==1)
cov[3]= agexact*agexact;	cov[3]= agexact*agexact;
Line 2592 double funcone( double *x)	Line 2640 double funcone( double *x)
int s1, s2;	int s1, s2;
double bbh, survp;	double bbh, survp;
double agexact;	double agexact;
	double agebegin, ageend;
/extern weight /	/extern weight /
/* We are differentiating ll according to initial status */	/* We are differentiating ll according to initial status */
/* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/	/* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
Line 2610 double funcone( double *x)	Line 2659 double funcone( double *x)
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);	savm[ii][j]=(ii==j ? 1.0 : 0.0);
}	}
for(d=0; d<dh[mi][i]; d++){
	agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
	ageend=agev[mw[mi][i]][i] + (dh[mi][i])stepm/YEARM; / Age at end of effective wave and at the end of transition */
	for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */
	/*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
	and mw[mi+1][i]. dh depends on stepm.*/
newm=savm;	newm=savm;
agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;	agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
cov[2]=agexact;	cov[2]=agexact;
Line 2658 double funcone( double *x)	Line 2712 double funcone( double *x)
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 dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); /	/printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); /
if(globpr){	if(globpr){
fprintf(ficresilk,"%9ld %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f %8.3f\	fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f %8.3f\
%11.6f %11.6f %11.6f ", \	%11.6f %11.6f %11.6f ", \
num[i], agexact, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,	num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
2weight[i]lli,out[s1][s2],savm[s1][s2]);	2weight[i]lli,out[s1][s2],savm[s1][s2]);
for(k=1,llt=0.,l=0.; k<=nlstate; k++){	for(k=1,llt=0.,l=0.; k<=nlstate; k++){
llt +=ll[k]*gipmx/gsw;	llt +=ll[k]*gipmx/gsw;
Line 2698 void likelione(FILE *ficres,double p[],	Line 2752 void likelione(FILE *ficres,double p[],
printf("Problem with resultfile: %s\n", fileresilk);	printf("Problem with resultfile: %s\n", fileresilk);
fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);	fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
}	}
fprintf(ficresilk, "#individual(line's_record) count age s1 s2 wave# effective_wave# number_of_matrices_product pij weight weight/gpw -2ln(pij)weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2llweightXnumber_of_contribs/sum_of_weights) and_total\n");	fprintf(ficresilk, "#individual(line's_record) count ageb ageend s1 s2 wave# effective_wave# number_of_matrices_product pij weight weight/gpw -2ln(pij)weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2llweightXnumber_of_contribs/sum_of_weights) and_total\n");
fprintf(ficresilk, "#num_i age i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");	fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
/* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2weight[i]lli,out[s1][s2],savm[s1][s2]); */	/* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2weight[i]lli,out[s1][s2],savm[s1][s2]); */
for(k=1; k<=nlstate; k++)	for(k=1; k<=nlstate; k++)
fprintf(ficresilk," -2gipw/gswweight*ll[%d]++",k);	fprintf(ficresilk," -2gipw/gswweight*ll[%d]++",k);
Line 2717 void likelione(FILE *ficres,double p[],	Line 2771 void likelione(FILE *ficres,double p[],


for (k=1; k<= nlstate ; k++) {	for (k=1; k<= nlstate ; k++) {
fprintf(fichtm,"<br>- Probability p%dj by origin %d and destination j <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \	fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Dot's sizes are related to corresponding weight: <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
<img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);	<img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
}	}
fprintf(fichtm,"<br>- The function drawn is -2Log(L) in Log scale: by state of origin <a href=\"%s-ori.png\">%s-ori.png</a><br> \	fprintf(fichtm,"<br>- The function drawn is -2Log(L) in Log scale: by state of origin <a href=\"%s-ori.png\">%s-ori.png</a><br> \
Line 3173 void pstamp(FILE *fichier)	Line 3227 void pstamp(FILE *fichier)
}	}

/********** Frequencies ******************/	/********** Frequencies ******************/
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, char strstart[])	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, char strstart[],\
	int firstpass, int lastpass, int stepm, int weightopt, char model[])
{ /* Some frequencies */	{ /* Some frequencies */

int i, m, jk, j1, bool, z1,j;	int i, m, jk, j1, bool, z1,j;
	int mi; /* Effective wave */
int first;	int first;
double **freq; / Frequencies */	double **freq; / Frequencies */
double pp, *prop;	double pp, *prop;
double pos,posprop, k2, dateintsum=0,k2cpt=0;	double pos,posprop, k2, dateintsum=0,k2cpt=0;
char fileresp[FILENAMELENGTH];	char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
	double agebegin, ageend;

pp=vector(1,nlstate);	pp=vector(1,nlstate);
prop=matrix(1,nlstate,iagemin,iagemax+3);	prop=matrix(1,nlstate,iagemin,iagemax+3);
strcpy(fileresp,"P_");	strcpy(fileresp,"P_");
strcat(fileresp,fileresu);	strcat(fileresp,fileresu);
	/strcat(fileresphtm,fileresu);/
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);	fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
exit(0);	exit(0);
}	}

	strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
	if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
	printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
	fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
	fflush(ficlog);
	exit(70);
	}
	else{
	fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
	<hr size=\"2\" color=\"#EC5E5E\"> \n\
	Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
	fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
	}
	fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition</h4>\n",fileresphtm, fileresphtm);

	strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
	if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
	printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
	fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
	fflush(ficlog);
	exit(70);
	}
	else{
	fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
	<hr size=\"2\" color=\"#EC5E5E\"> \n\
	Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
	fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
	}
	fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions by age at begin of transition </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);

freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);	freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
j1=0;	j1=0;

Line 3200 void freqsummary(char fileres[], int ia	Line 3290 void freqsummary(char fileres[], int ia

first=1;	first=1;

/* for(k1=1; k1<=j ; k1++){ / / Loop on covariates */	for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ /* Loop on covariates combination */
/* for(i1=1; i1<=ncodemax[k1];i1++){ / / Now it is 2 */
/* j1++; */
for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
/*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);	/*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
scanf("%d", i);*/	scanf("%d", i);*/
for (i=-5; i<=nlstate+ndeath; i++)	for (i=-5; i<=nlstate+ndeath; i++)
Line 3217 void freqsummary(char fileres[], int ia	Line 3304 void freqsummary(char fileres[], int ia

dateintsum=0;	dateintsum=0;
k2cpt=0;	k2cpt=0;
for (i=1; i<=imx; i++) {	for (i=1; i<=imx; i++) { /* For each individual i */
bool=1;	bool=1;
if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */	if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
for (z1=1; z1<=cptcoveff; z1++)	for (z1=1; z1<=cptcoveff; z1++)
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){	if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
/* Tests if the value of each of the covariates of i is equal to filter j1 */	/* Tests if the value of each of the covariates of i is equal to filter j1 */
Line 3229 void freqsummary(char fileres[], int ia	Line 3316 void freqsummary(char fileres[], int ia
j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/	j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
/* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/	/* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
}	}
}	} /* cptcovn > 0 */

if (bool==1){	if (bool==1){
for(m=firstpass; m<=lastpass; m++){	/* for(m=firstpass; m<=lastpass; m++){ */
k2=anint[m][i]+(mint[m][i]/12.);	for(mi=1; mi<wav[i];mi++){
/if ((k2>=dateprev1) && (k2<=dateprev2)) {/	m=mw[mi][i];
if(agev[m][i]==0) agev[m][i]=iagemax+1;	/* dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective (mi) waves m=mw[mi][i]
if(agev[m][i]==1) agev[m][i]=iagemax+2;	and mw[mi+1][i]. dh depends on stepm. */
if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];	agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
	ageend=agev[m][i]+(dh[m][i])stepm/YEARM; / Age at end of wave and transition */
	if(m >=firstpass && m <=lastpass){
	k2=anint[m][i]+(mint[m][i]/12.);
	/if ((k2>=dateprev1) && (k2<=dateprev2)) {/
	if(agev[m][i]==0) agev[m][i]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
	if(agev[m][i]==1) agev[m][i]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
	if (s[m][i]>0 && s[m][i]<=nlstate) /* If status at wave m is known and a live state */
	prop[s[m][i]][(int)agev[m][i]] += weight[i]; /* At age of beginning of transition, where status is known */
if (m<lastpass) {	if (m<lastpass) {
freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];	/* if(s[m][i]==4 && s[m+1][i]==4) */
freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];	/* printf(" num=%ld m=%d, i=%d s1=%d s2=%d agev at m=%d\n", num[i], m, i,s[m][i],s[m+1][i], (int)agev[m][i]); */
}	if(s[m][i]==-1)
	printf(" num=%ld m=%d, i=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[i], m, i,s[m][i],s[m+1][i], (int)agev[m][i],agebegin, ageend, (int)((agebegin+ageend)/2.));
if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {	freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; /* At age of beginning of transition, where status is known */
dateintsum=dateintsum+k2;	/* freq[s[m][i]][s[m+1][i]][(int)((agebegin+ageend)/2.)] += weight[i]; */
k2cpt++;	freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i]; /* Total is in iagemax+3 // At age of beginning of transition, where status is known */
}	}
/}/	}
}	if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3)) && (anint[m][i]!=9999) && (mint[m][i]!=99)) {
}	dateintsum=dateintsum+k2;
} /* end i */	k2cpt++;
	/* printf("i=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",i, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
	}
	/}/
	} /* end m */
	} /* end bool */
	} /* end i = 1 to imx */

/* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/	/* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
pstamp(ficresp);	pstamp(ficresp);
if (cptcovn>0) {	if (cptcovn>0) {
fprintf(ficresp, "\n#********** Variable ");	fprintf(ficresp, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
fprintf(ficresp, "**********\n#");	fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
	for (z1=1; z1<=cptcoveff; z1++){
	fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
	fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
	fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
	}
	fprintf(ficresp, "**********\n#");
	fprintf(ficresphtm, "**********</h3>\n");
	fprintf(ficresphtmfr, "**********</h3>\n");
fprintf(ficlog, "\n#********** Variable ");	fprintf(ficlog, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficlog, "**********\n#");	fprintf(ficlog, "**********\n");
}	}
for(i=1; i<=nlstate;i++)	fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
	for(i=1; i<=nlstate;i++) {
fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);	fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
	fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
	}
fprintf(ficresp, "\n");	fprintf(ficresp, "\n");
	fprintf(ficresphtm, "\n");

	/* Header of frequency table by age */
	fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
	fprintf(ficresphtmfr,"<th>Age</th> ");
	for(jk=-1; jk <=nlstate+ndeath; jk++){
	for(m=-1; m <=nlstate+ndeath; m++){
	if(jk!=0 && m!=0)
	fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
	}
	}
	fprintf(ficresphtmfr, "\n");

	/* For each age */
for(i=iagemin; i <= iagemax+3; i++){	for(i=iagemin; i <= iagemax+3; i++){
if(i==iagemax+3){	fprintf(ficresphtm,"<tr>");
	if(i==iagemax+1){
	fprintf(ficlog,"1");
	fprintf(ficresphtmfr,"<tr><th>0</th> ");
	}else if(i==iagemax+2){
	fprintf(ficlog,"0");
	fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
	}else if(i==iagemax+3){
fprintf(ficlog,"Total");	fprintf(ficlog,"Total");
	fprintf(ficresphtmfr,"<tr><th>Total</th> ");
}else{	}else{
if(first==1){	if(first==1){
first=0;	first=0;
printf("See log file for details...\n");	printf("See log file for details...\n");
}	}
	fprintf(ficresphtmfr,"<tr><th>%d</th> ",i);
fprintf(ficlog,"Age %d", i);	fprintf(ficlog,"Age %d", i);
}	}
for(jk=1; jk <=nlstate ; jk++){	for(jk=1; jk <=nlstate ; jk++){
Line 3316 void freqsummary(char fileres[], int ia	Line 3450 void freqsummary(char fileres[], int ia
if( i <= iagemax){	if( i <= iagemax){
if(pos>=1.e-5){	if(pos>=1.e-5){
fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);	fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
	fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",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,prop[jk][i],posprop);	fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
	fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",i, prop[jk][i],posprop);
	}
}	}
}	}

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 ) {	if(freq[jk][m][i] !=0 ) { /* minimizing output */
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 <= iagemax)	if(jk!=0 && m!=0)
	fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][i]);
	}
	}
	fprintf(ficresphtmfr,"</tr>\n ");
	if(i <= iagemax){
fprintf(ficresp,"\n");	fprintf(ficresp,"\n");
	fprintf(ficresphtm,"</tr>\n");
	}
if(first==1)	if(first==1)
printf("Others in log...\n");	printf("Others in log...\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
}	} /* end loop i */
	fprintf(ficresphtm,"</table>\n");
	fprintf(ficresphtmfr,"</table>\n");
/}/	/}/
}	} /* end j1 */
dateintmean=dateintsum/k2cpt;	dateintmean=dateintsum/k2cpt;

fclose(ficresp);	fclose(ficresp);
	fclose(ficresphtm);
	fclose(ficresphtmfr);
free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);	free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
free_vector(pp,1,nlstate);	free_vector(pp,1,nlstate);
free_matrix(prop,1,nlstate,iagemin, iagemax+3);	free_matrix(prop,1,nlstate,iagemin, iagemax+3);
Line 3357 void prevalence(double ***probs, double	Line 3506 void prevalence(double ***probs, double
*/	*/

int i, m, jk, j1, bool, z1,j;	int i, m, jk, j1, bool, z1,j;
	int mi; /* Effective wave */
	int iage;
	double agebegin, ageend;

double **prop;	double **prop;
double posprop;	double posprop;
Line 3376 void prevalence(double ***probs, double	Line 3528 void prevalence(double ***probs, double

first=1;	first=1;
for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){	for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
/*for(i1=1; i1<=ncodemax[k1];i1++){	for (i=1; i<=nlstate; i++)
j1++;*/	for(iage=iagemin; iage <= iagemax+3; iage++)
	prop[i][iage]=0.0;
for (i=1; i<=nlstate; i++)
for(m=iagemin; m <= iagemax+3; m++)	for (i=1; i<=imx; i++) { /* Each individual */
prop[i][m]=0.0;	bool=1;
	if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
for (i=1; i<=imx; i++) { /* Each individual */	for (z1=1; z1<=cptcoveff; z1++)
bool=1;	if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
if (cptcovn>0) {	bool=0;
for (z1=1; z1<=cptcoveff; z1++)	}
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])	if (bool==1) {
bool=0;	/* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews\/ /
}	for(mi=1; mi<wav[i];mi++){
if (bool==1) {	m=mw[mi][i];
for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/	agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
	/* ageend=agev[m][i]+(dh[m][i])stepm/YEARM; /\ Age at end of wave and transition \/ /
	if(m >=firstpass && m <=lastpass){
y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */	y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */	if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
if(agev[m][i]==0) agev[m][i]=iagemax+1;	if(agev[m][i]==0) agev[m][i]=iagemax+1;
if(agev[m][i]==1) agev[m][i]=iagemax+2;	if(agev[m][i]==1) agev[m][i]=iagemax+2;
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((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 (s[m][i]>0 && s[m][i]<=nlstate) {	if (s[m][i]>0 && s[m][i]<=nlstate) {
/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]]);/	/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]]);/
prop[s[m][i]][(int)agev[m][i]] += weight[i];	prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
prop[s[m][i]][iagemax+3] += weight[i];	prop[s[m][i]][iagemax+3] += weight[i];
}	} /* end valid statuses */
}	} /* end selection of dates */
} /* end selection of waves */	} /* end selection of waves */
}	} /* end effective waves */
}	} /* end bool */
for(i=iagemin; i <= iagemax+3; i++){	}
for(jk=1,posprop=0; jk <=nlstate ; jk++) {	for(i=iagemin; i <= iagemax+3; i++){
posprop += prop[jk][i];	for(jk=1,posprop=0; jk <=nlstate ; jk++) {
}	posprop += prop[jk][i];
	}
for(jk=1; jk <=nlstate ; jk++){
if( i <= iagemax){	for(jk=1; jk <=nlstate ; jk++){
if(posprop>=1.e-5){	if( i <= iagemax){
probs[i][jk][j1]= prop[jk][i]/posprop;	if(posprop>=1.e-5){
} else{	probs[i][jk][j1]= prop[jk][i]/posprop;
if(first==1){	} else{
first=0;	if(first==1){
printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);	first=0;
}	printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
}	}
}	}
}/* end jk */	}
}/* end i */	}/* end jk */
	}/* end i */
/} //* end i1 */	/} //* end i1 */
} /* end j1 */	} /* end j1 */

Line 3446 void concatwav(int wav[], int **dh, int	Line 3601 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 first, firstwo;
int j, k=0,jk, ju, jl;	int j, k=0,jk, ju, jl;
double sum=0.;	double sum=0.;
first=0;	first=0;
	firstwo=0;
jmin=100000;	jmin=100000;
jmax=-1;	jmax=-1;
jmean=0.;	jmean=0.;
for(i=1; i<=imx; i++){	for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
mi=0;	mi=0;
m=firstpass;	m=firstpass;
while(s[m][i] <= nlstate){	while(s[m][i] <= nlstate){ /* a live state */
if(s[m][i]>=1 \|\| s[m][i]==-2 \|\| s[m][i]==-4 \|\| s[m][i]==-5)	if(s[m][i]>=1 \|\| s[m][i]==-2 \|\| s[m][i]==-4 \|\| s[m][i]==-5)
mw[++mi][i]=m;	mw[++mi][i]=m;
if(m >=lastpass)	if(m >=lastpass)
Line 3464 void concatwav(int wav[], int **dh, int	Line 3620 void concatwav(int wav[], int **dh, int
else	else
m++;	m++;
}/* end while */	}/* end while */
if (s[m][i] > nlstate){	if (s[m][i] > nlstate){ /* In a death state */
mi++; /* Death is another wave */	mi++; /* Death is another wave */
/* if(mi==0) never been interviewed correctly before death */	/* if(mi==0) never been interviewed correctly before death */
/* Only death is a correct wave */	/* Only death is a correct wave */
mw[mi][i]=m;	mw[mi][i]=m;
	}else if (andc[i] != 9999) { /* A death occured after lastpass */
	m++;
	mi++;
	s[m][i]=nlstate+1; /* We are setting the status to the last of non live state */
	mw[mi][i]=m;
	nbwarn++;
	if(firstwo==0){
	printf("Warning! Death for individual %ld line=%d occurred after last wave %d. Since 0.98r4 we considered a status %d at wave %d\nOthers in log file only\n",num[i],i,lastpass,nlstate+1, m);
	fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred after last wave %d. Since 0.98r4 we considered a status %d at wave %d\n",num[i],i,lastpass,nlstate+1, m);
	firstwo=1;
	}
	if(firstwo==1){
	fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred after last wave %d. Since 0.98r4 we considered a status %d at wave %d\n",num[i],i,lastpass,nlstate+1, m);
	}
}	}

wav[i]=mi;	wav[i]=mi;
if(mi==0){	if(mi==0){
nbwarn++;	nbwarn++;
Line 3483 void concatwav(int wav[], int **dh, int	Line 3652 void concatwav(int wav[], int **dh, int
}	}
} /* end mi==0 */	} /* end mi==0 */
} /* End individuals */	} /* End individuals */
	/* wav and mw are no more changed */


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)
Line 4025 void cvevsij(double ***eij, double x[],	Line 4196 void cvevsij(double ***eij, double x[],
}	}

/********** Variance ****************/	/********** Variance ****************/
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 ncvyear, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])	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 ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
{	{
/* 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);*/
Line 4128 void cvevsij(double ***eij, double x[],	Line 4299 void cvevsij(double ***eij, double x[],
/* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.	/* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
nhstepm is the number of hstepm from age to agelim	nhstepm is the number of hstepm from age to agelim
nstepm is the number of stepm from age to agelim.	nstepm is the number of stepm from age to agelim.
Look at function hpijx to understand why (it is linked to memory size questions)	Look at function hpijx to understand why because of memory size limitations,
we decided (b) to get a life expectancy respecting the most precise curvature of the	we decided (b) to get a life expectancy respecting the most precise curvature of the
survival function given by stepm (the optimization length). Unfortunately it	survival function given by stepm (the optimization length). Unfortunately it
means that if the survival funtion is printed every two years of age and if	means that if the survival funtion is printed every two years of age and if
Line 4150 void cvevsij(double ***eij, double x[],	Line 4321 void cvevsij(double ***eij, double x[],
for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/	for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
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);
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij);	prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);

if (popbased==1) {	if (popbased==1) {
if(mobilav ==0){	if(mobilav ==0){
Line 4163 void cvevsij(double ***eij, double x[],	Line 4334 void cvevsij(double ***eij, double x[],
}	}
}	}

	hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); /* Returns p3mat[i][j][h] for h=1 to nhstepm */
for(j=1; j<= nlstate; j++){	for(j=1; j<= nlstate; j++){
for(h=0; h<=nhstepm; h++){	for(h=0; h<=nhstepm; h++){
for(i=1, gp[h][j]=0.;i<=nlstate;i++)	for(i=1, gp[h][j]=0.;i<=nlstate;i++)
gp[h][j] += prlim[i][i]*p3mat[i][j][h];	gp[h][j] += prlim[i][i]*p3mat[i][j][h];
}	}
}	}
/* This for computing probability of death (h=1 means	/* Next for computing probability of death (h=1 means
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.
*/	*/
Line 4181 void cvevsij(double ***eij, double x[],	Line 4353 void cvevsij(double ***eij, double x[],

for(i=1; i<=npar; i++) /* Computes gradient x - delta */	for(i=1; i<=npar; i++) /* Computes gradient x - delta */
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);
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear, ij);	prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij);

if (popbased==1) {	if (popbased==1) {
if(mobilav ==0){	if(mobilav ==0){
Line 4194 void cvevsij(double ***eij, double x[],	Line 4366 void cvevsij(double ***eij, double x[],
}	}
}	}

	hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);

for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */	for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
for(h=0; h<=nhstepm; h++){	for(h=0; h<=nhstepm; h++){
for(i=1, gm[h][j]=0.;i<=nlstate;i++)	for(i=1, gm[h][j]=0.;i<=nlstate;i++)
Line 4256 void cvevsij(double ***eij, double x[],	Line 4430 void cvevsij(double ***eij, double x[],
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);
prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyear,ij);	prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);

if (popbased==1) {	if (popbased==1) {
if(mobilav ==0){	if(mobilav ==0){
Line 4273 void cvevsij(double ***eij, double x[],	Line 4447 void cvevsij(double ***eij, double x[],
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.
*/	*/
	hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
for(j=nlstate+1;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 4335 void cvevsij(double ***eij, double x[],	Line 4510 void cvevsij(double ***eij, double x[],
} /* end varevsij */	} /* end varevsij */

/********** 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 ncvyear, int ij, char strstart[])	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 ncvyearp, int ij, char strstart[])
{	{
/* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/	/* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
/* 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);/
Line 4367 void cvevsij(double ***eij, double x[],	Line 4542 void cvevsij(double ***eij, double x[],
nhstepm=(int) rint((agelim-age)YEARM/stepm); / Typically 20 years = 2012/6=40 /	nhstepm=(int) rint((agelim-age)YEARM/stepm); / Typically 20 years = 2012/6=40 /
if (stepm >= YEARM) hstepm=1;	if (stepm >= YEARM) hstepm=1;
nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */	nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
gradg=matrix(1,npar,1,nlstate);	gradg=matrix(1,npar,1,nlstate);
mgp=matrix(1,npar,1,nlstate);	mgp=matrix(1,npar,1,nlstate);
mgm=matrix(1,npar,1,nlstate);	mgm=matrix(1,npar,1,nlstate);
Line 4378 void cvevsij(double ***eij, double x[],	Line 4552 void cvevsij(double ***eij, double x[],
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); /* Missing or not useful because 1 year */	if((int)age==79 \|\|(int)age== 80 \|\|(int)age== 81 )
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij);	prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
	else
	prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
for(i=1;i<=nlstate;i++){	for(i=1;i<=nlstate;i++){
gp[i] = prlim[i][i];	gp[i] = prlim[i][i];
mgp[theta][i] = prlim[i][i];	mgp[theta][i] = prlim[i][i];
}	}
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);
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij);	if((int)age==79 \|\|(int)age== 80 \|\|(int)age== 81 )
	prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
	else
	prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
for(i=1;i<=nlstate;i++){	for(i=1;i<=nlstate;i++){
gm[i] = prlim[i][i];	gm[i] = prlim[i][i];
mgm[theta][i] = prlim[i][i];	mgm[theta][i] = prlim[i][i];
}	}
for(i=1;i<=nlstate;i++)	for(i=1;i<=nlstate;i++)
gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];	gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
	/* gradg[theta][2]= -gradg[theta][1]; / / For testing if nlstate=2 */
} /* End theta */	} /* End theta */

trgradg =matrix(1,nlstate,1,npar);	trgradg =matrix(1,nlstate,1,npar);
Line 4400 void cvevsij(double ***eij, double x[],	Line 4580 void cvevsij(double ***eij, double x[],
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[j][theta]=gradg[theta][j];	trgradg[j][theta]=gradg[theta][j];
if((int)age==68 \|\|(int)age== 69 ){	/* if((int)age==79 \|\|(int)age== 80 \|\|(int)age== 81 ){ */
printf("\nmgm mgp %d ",(int)age);	/* printf("\nmgm mgp %d ",(int)age); */
for(j=1; j<=nlstate;j++){	/* for(j=1; j<=nlstate;j++){ */
printf("%d ",j);	/* printf(" %d ",j); */
for(theta=1; theta <=npar; theta++)	/* for(theta=1; theta <=npar; theta++) */
printf("%d %lf %lf",theta,mgm[theta][j],mgp[theta][j]);	/* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
printf("\n ");	/* printf("\n "); */
}	/* } */
}	/* } */
if((int)age==68 \|\|(int)age== 69 ){	/* if((int)age==79 \|\|(int)age== 80 \|\|(int)age== 81 ){ */
printf("\n gradg %d ",(int)age);	/* printf("\n gradg %d ",(int)age); */
for(j=1; j<=nlstate;j++){	/* for(j=1; j<=nlstate;j++){ */
printf("%d ",j);	/* printf("%d ",j); */
for(theta=1; theta <=npar; theta++)	/* for(theta=1; theta <=npar; theta++) */
printf("%d %lf ",theta,gradg[theta][j]);	/* printf("%d %lf ",theta,gradg[theta][j]); */
printf("\n ");	/* printf("\n "); */
}	/* } */
}	/* } */

for(i=1;i<=nlstate;i++)	for(i=1;i<=nlstate;i++)
varpl[i][(int)age] =0.;	varpl[i][(int)age] =0.;
if((int)age==68 \|\|(int)age== 69 ){	if((int)age==79 \|\|(int)age== 80 \|\|(int)age== 81){
matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);	matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);	matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
}else{	}else{
Line 4789 To be simple, these graphs help to under	Line 4969 To be simple, these graphs help to under
void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \	void printinghtml(char fileresu[], 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 rfileres[],\	int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
int popforecast, int estepm ,\	int popforecast, int prevfcast, int estepm , \
double jprev1, double mprev1,double anprev1, \	double jprev1, double mprev1,double anprev1, double dateprev1, \
double jprev2, double mprev2,double anprev2){	double jprev2, double mprev2,double anprev2, double dateprev2){
int jj1, k1, i1, cpt;	int jj1, k1, i1, cpt;

fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \	fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
<li><a href='#secondorder'>Result files (second order (variance)</a>\n \	<li><a href='#secondorder'>Result files (second order (variance)</a>\n \
</ul>");	</ul>");
fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \	fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
- Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",	fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",
jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));	jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
	fprintf(fichtm,"<li> - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file) ",
	jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
	fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",	- Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));	stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
Line 4807 void printinghtml(char fileresu[], char	Line 4990 void printinghtml(char fileresu[], char
- Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",	- Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));	subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \	- (a) Life expectancies by health status at initial age, e<sub>i.</sub> (b) health expectancies by health status at initial age, e<sub>ij</sub> . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
<a href=\"%s\">%s</a> <br>\n",	<a href=\"%s\">%s</a> <br>\n",
estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));	estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
fprintf(fichtm,"\	if(prevfcast==1){
- Population projections by age and states: \	fprintf(fichtm,"\
	- Prevalence projections by age and states: \
<a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));	<a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
	}

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

Line 4832 fprintf(fichtm," \n<ul><li><b>Graphs</b>	Line 5017 fprintf(fichtm," \n<ul><li><b>Graphs</b>
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");	fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
}	}
/* aij, bij */	/* aij, bij */
fprintf(fichtm,"<br>- Logit model, for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1.svg\">%s_%d-1.svg</a><br> \	fprintf(fichtm,"<br>- Logit model (yours is: 1+age+%s), for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1.svg\">%s_%d-1.svg</a><br> \
<img src=\"%s_%d-1.svg\">",subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);	<img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
/* Pij */	/* Pij */
fprintf(fichtm,"<br>\n- Pij or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2.svg\">%s_%d-2.svg</a><br> \	fprintf(fichtm,"<br>\n- P<sub>ij</sub> or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2.svg\">%s_%d-2.svg</a><br> \
<img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);	<img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
/* Quasi-incidences */	/* Quasi-incidences */
fprintf(fichtm,"<br>\n- Iij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\	fprintf(fichtm,"<br>\n- I<sub>ij</sub> 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,\	before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too,\
incidence (rates) are the limit when h tends to zero of the ratio of the probability hPij \	incidence (rates) are the limit when h tends to zero of the ratio of the probability <sub>h</sub>P<sub>ij</sub> \
divided by h: hPij/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \	divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \
<img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);	<img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
/* Survival functions (period) in state j */	/* Survival functions (period) in state j */
for(cpt=1; cpt<=nlstate;cpt++){	for(cpt=1; cpt<=nlstate;cpt++){
Line 4859 divided by h: hPij/h : <a href=\"%s_%d-3	Line 5044 divided by h: hPij/h : <a href=\"%s_%d-3
fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \	fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \
<img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);	<img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
}	}
	if(prevfcast==1){
	/* Projection of prevalence up to period (stable) prevalence in each health state */
	for(cpt=1; cpt<=nlstate;cpt++){
	fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \
	<img src=\"%s_%d-%d.svg\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1);
	}
	}

for(cpt=1; cpt<=nlstate;cpt++) {	for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d%d.svg\">%s_%d%d.svg</a> <br> \	fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d%d.svg\">%s_%d%d.svg</a> <br> \
<img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);	<img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);
Line 4946 true period expectancies (those weighted	Line 5139 true period expectancies (those weighted
}	}

/***************** Gnuplot file ************/	/***************** Gnuplot file ************/
void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){	void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, char pathc[], double p[]){

char dirfileres[132],optfileres[132];	char dirfileres[132],optfileres[132];
int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;	int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
	int lv=0, vlv=0, kl=0;
int ng=0;	int ng=0;
int vpopbased;	int vpopbased;
/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */	/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
Line 4973 void printinggnuplot(char fileresu[], ch	Line 5167 void printinggnuplot(char fileresu[], ch
/* replot exp(p1+p2x)/(1+exp(p1+p2x)+exp(p3+p4x)+exp(p5+p6x)) t "p12(x)" */	/* replot exp(p1+p2x)/(1+exp(p1+p2x)+exp(p3+p4x)+exp(p5+p6x)) t "p12(x)" */
/* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */	/* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));	fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$12):5 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));	fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$13):6 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));
fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));	fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$12):4 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));	fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$13):5 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));
for (i=1; i<= nlstate ; i ++) {	for (i=1; i<= nlstate ; i ++) {
fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);	fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));	fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
fprintf(ficgp," u 2:($4 == %d && $5==%d ? $9 : 1/0):($11/4.):5 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);	fprintf(ficgp," u 2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);
for (j=2; j<= nlstate+ndeath ; j ++) {	for (j=2; j<= nlstate+ndeath ; j ++) {
fprintf(ficgp,",\\\n \"\" u 2:($4 == %d && $5==%d ? $9 : 1/0):($11/4.):5 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j);	fprintf(ficgp,",\\\n \"\" u 2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j);
}	}
fprintf(ficgp,";\nset out; unset ylabel;\n");	fprintf(ficgp,";\nset out; unset ylabel;\n");
}	}
Line 4994 void printinggnuplot(char fileresu[], ch	Line 5188 void printinggnuplot(char fileresu[], ch
strcpy(dirfileres,optionfilefiname);	strcpy(dirfileres,optionfilefiname);
strcpy(optfileres,"vpl");	strcpy(optfileres,"vpl");
/* 1eme*/	/* 1eme*/
fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files\n");	for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
for (cpt=1; cpt<= nlstate ; cpt ++) {	for (k1=1; k1<= m ; k1 ++) { /* For each combination of covariate */
for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */	/* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
	fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
	for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
	vlv= nbcode[Tvaraff[lv]][lv];
	fprintf(ficgp," V%d=%d ",k,vlv);
	}
	fprintf(ficgp,"\n#\n");

fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);	fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);	fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
fprintf(ficgp,"set xlabel \"Age\" \n\	fprintf(ficgp,"set xlabel \"Age\" \n\
Line 5023 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 5228 plot [%.f:%.f] \"%s\" every :::%d::%d u
} /* k1 */	} /* k1 */
} /* cpt */	} /* cpt */
/2 eme/	/2 eme/
fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
for (k1=1; k1<= m ; k1 ++) {	for (k1=1; k1<= m ; k1 ++) {
	fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
	for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
	vlv= nbcode[Tvaraff[lv]][lv];
	fprintf(ficgp," V%d=%d ",k,vlv);
	}
	fprintf(ficgp,"\n#\n");

fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);	fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/	for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
if(vpopbased==0)	if(vpopbased==0)
Line 5057 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 5272 plot [%.f:%.f] \"%s\" every :::%d::%d u
} /* vpopbased */	} /* vpopbased */
fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */	fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
} /* k1 */	} /* k1 */


/3eme/	/3eme/

for (k1=1; k1<= m ; k1 ++) {	for (k1=1; k1<= m ; k1 ++) {
for (cpt=1; cpt<= nlstate ; cpt ++) {	for (cpt=1; cpt<= nlstate ; cpt ++) {
	fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: cov=%d state=%d",k1, cpt);
	for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
	vlv= nbcode[Tvaraff[lv]][lv];
	fprintf(ficgp," V%d=%d ",k,vlv);
	}
	fprintf(ficgp,"\n#\n");

/* k=2+nlstate(2cpt-2); */	/* k=2+nlstate(2cpt-2); */
k=2+(nlstate+1)*(cpt-1);	k=2+(nlstate+1)*(cpt-1);
fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);	fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
Line 5086 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 5313 plot [%.f:%.f] \"%s\" every :::%d::%d u
/* Survival functions (period) from state i in state j by initial state i */	/* Survival functions (period) from state i in state j by initial state i */
for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */	for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
k=3;	fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'lij' files, cov=%d state=%d",k1, cpt);	for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
	vlv= nbcode[Tvaraff[lv]][lv];
	fprintf(ficgp," V%d=%d ",k,vlv);
	}
	fprintf(ficgp,"\n#\n");

fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);	fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
set ter svg size 640, 480\n\	set ter svg size 640, 480\n\
unset log y\n\	unset log y\n\
plot [%.f:%.f] ", ageminpar, agemaxpar);	plot [%.f:%.f] ", ageminpar, agemaxpar);
	k=3;
for (i=1; i<= nlstate ; i ++){	for (i=1; i<= nlstate ; i ++){
if(i==1)	if(i==1)
fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));	fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
Line 5111 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 5348 plot [%.f:%.f] ", ageminpar, agemaxpar)
/* Survival functions (period) from state i in state j by final state j */	/* Survival functions (period) from state i in state j by final state j */
for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */	for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
k=3;
fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);	fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
	for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
	vlv= nbcode[Tvaraff[lv]][lv];
	fprintf(ficgp," V%d=%d ",k,vlv);
	}
	fprintf(ficgp,"\n#\n");

fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);	fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
set ter svg size 640, 480\n\	set ter svg size 640, 480\n\
unset log y\n\	unset log y\n\
plot [%.f:%.f] ", ageminpar, agemaxpar);	plot [%.f:%.f] ", ageminpar, agemaxpar);
	k=3;
for (j=1; j<= nlstate ; j ++){ /* Lived in state j */	for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
if(j==1)	if(j==1)
fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));	fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
Line 5143 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 5390 plot [%.f:%.f] ", ageminpar, agemaxpar)
} /* end covariate */	} /* end covariate */

/* CV preval stable (period) for each covariate */	/* CV preval stable (period) for each covariate */
for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */	for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2*k), if any covariate is present /
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
k=3;	fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);	for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
	vlv= nbcode[Tvaraff[lv]][lv];
	fprintf(ficgp," V%d=%d ",k,vlv);
	}
	fprintf(ficgp,"\n#\n");

fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);	fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
set ter svg size 640, 480\n\	set ter svg size 640, 480\n\
unset log y\n\	unset log y\n\
plot [%.f:%.f] ", ageminpar, agemaxpar);	plot [%.f:%.f] ", ageminpar, agemaxpar);
	k=3; /* Offset */
for (i=1; i<= nlstate ; i ++){	for (i=1; i<= nlstate ; i ++){
if(i==1)	if(i==1)
fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));	fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
Line 5167 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 5424 plot [%.f:%.f] ", ageminpar, agemaxpar)
} /* end cpt state*/	} /* end cpt state*/
} /* end covariate */	} /* end covariate */

	if(prevfcast==1){
	/* Projection from cross-sectional to stable (period) for each covariate */

	for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2*k), if any covariate is present /
	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
	fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
	for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
	vlv= nbcode[Tvaraff[lv]][lv];
	fprintf(ficgp," V%d=%d ",k,vlv);
	}
	fprintf(ficgp,"\n#\n");

	fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
	fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
	set ter svg size 640, 480\n\
	unset log y\n\
	plot [%.f:%.f] ", ageminpar, agemaxpar);
	for (i=1; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
	/# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3/
	/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 /
	/# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3/
	/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 /
	if(i==1){
	fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
	}else{
	fprintf(ficgp,",\\\n '' ");
	}
	if(cptcoveff ==0){ /* No covariate */
	fprintf(ficgp," u 2:("); /* Age is in 2 */
	/# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4/
	/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 /
	if(i==nlstate+1)
	fprintf(ficgp," $%d/(1.-$%d)) t 'p.%d' with line ", \
	2+(cpt-1)(nlstate+1)+1+(i-1), 2+1+(i-1)+(nlstate+1)nlstate,cpt );
	else
	fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
	2+(cpt-1)(nlstate+1)+1+(i-1), 2+1+(i-1)+(nlstate+1)nlstate,i,cpt );
	}else{
	fprintf(ficgp,"u 6:(("); /* Age is in 6 */
	/# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3/
	/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 /
	kl=0;
	for (k=1; k<=cptcoveff; k++){ /* For each covariate */
	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
	vlv= nbcode[Tvaraff[lv]][lv];
	kl++;
	/* kl=6+(cpt-1)(nlstate+1)+1+(i-1); /\ 6+(1-1)(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 \/ */
	/6+(cpt-1)(nlstate+1)+1+(i-1)+(nlstate+1)nlstate; 6+(1-1)(2+1)+1+(1-1) +(2+1)2=13 /
	/6+1+(i-1)+(nlstate+1)nlstate; 6+1+(1-1) +(2+1)2=13 /
	/* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
	if(k==cptcoveff)
	if(i==nlstate+1)
	fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv], \
	6+(cpt-1)(nlstate+1)+1+(i-1), 6+1+(i-1)+(nlstate+1)nlstate,cpt );
	else
	fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv], \
	6+(cpt-1)(nlstate+1)+1+(i-1), 6+1+(i-1)+(nlstate+1)nlstate,i,cpt );
	else{
	fprintf(ficgp,"$%d==%d && $%d==%d && ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv]);
	kl++;
	}
	} /* end covariate */
	} /* end if covariate */
	} /* nlstate */
	fprintf(ficgp,"\nset out\n");
	} /* end cpt state*/
	} /* end covariate */
	} /* End if prevfcast */


/* proba elementaires */	/* proba elementaires */
fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");	fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
for(i=1,jk=1; i <=nlstate; i++){	for(i=1,jk=1; i <=nlstate; i++){
Line 5358 void prevforecast(char fileres[], double	Line 5693 void prevforecast(char fileres[], double
char fileresf[FILENAMELENGTH];	char fileresf[FILENAMELENGTH];

agelim=AGESUP;	agelim=AGESUP;
	/* 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.
	*/
	/* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
	/* firstpass, lastpass, stepm, weightopt, model); */
prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);	prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);

strcpy(fileresf,"F_");	strcpy(fileresf,"F_");
Line 5366 void prevforecast(char fileres[], double	Line 5707 void prevforecast(char fileres[], double
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);	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', please wait... \n", fileresf);
fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);	fprintf(ficlog,"Computing forecasting: result on file '%s', please wait... \n", fileresf);

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

Line 5408 void prevforecast(char fileres[], double	Line 5749 void prevforecast(char fileres[], double
for(cptcov=1, k=0;cptcov<=i1;cptcov++){	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#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=cptcoveff;j++) {
fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
}	}
fprintf(ficresf,"******\n");	fprintf(ficresf," yearproj age");
fprintf(ficresf,"# Covariate valuofcovar yearproj age");
for(j=1; j<=nlstate+ndeath;j++){	for(j=1; j<=nlstate+ndeath;j++){
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
fprintf(ficresf," p%d%d",i,j);	fprintf(ficresf," p%d%d",i,j);
Line 5463 void prevforecast(char fileres[], double	Line 5803 void prevforecast(char fileres[], double
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);
	printf("End of Computing forecasting \n");
	fprintf(ficlog,"End of Computing forecasting\n");

}	}

/************ Forecasting *not tested NB***********/	/************ Forecasting *not tested NB***********/
Line 6302 int calandcheckages(int imx, int maxwav,	Line 6645 int calandcheckages(int imx, int maxwav,
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=firstpass; (m<= lastpass); m++){	for(m=firstpass; (m<= lastpass); m++){
if(s[m][i] >0 \|\| s[m][i]==-2 \|\| s[m][i]==-4 \|\| s[m][i]==-5){	if(s[m][i] >0 \|\| s[m][i]==-1 \|\| s[m][i]==-2 \|\| s[m][i]==-4 \|\| s[m][i]==-5){ /* What if s[m][i]=-1 */
if (s[m][i] >= nlstate+1) {	if (s[m][i] >= nlstate+1) {
if(agedc[i]>0){	if(agedc[i]>0){
if((int)moisdc[i]!=99 && (int)andc[i]!=9999){	if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
agev[m][i]=agedc[i];	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 ((int)andc[i]!=9999){	if ((int)andc[i]!=9999){
nbwarn++;	nbwarn++;
Line 6317 int calandcheckages(int imx, int maxwav,	Line 6660 int calandcheckages(int imx, int maxwav,
}	}
}	}
} /* agedc > 0 */	} /* agedc > 0 */
}	} /* end if */
else if(s[m][i] !=9){ /* Standard case, age in fractional	else if(s[m][i] !=9){ /* Standard case, age in fractional
years but with the precision of a month */	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]);
Line 6333 int calandcheckages(int imx, int maxwav,	Line 6676 int calandcheckages(int imx, int maxwav,
}	}
/agev[m][i]=anint[m][i]-annais[i];/	/agev[m][i]=anint[m][i]-annais[i];/
/* agev[m][i] = age[i]+2m;/	/* agev[m][i] = age[i]+2m;/
}	} /* en if 9*/
else { /* =9 */	else { /* =9 */
	/* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
agev[m][i]=1;	agev[m][i]=1;
s[m][i]=-1;	s[m][i]=-1;
}	}
}	}
else /= 0 Unknown /	else if(s[m][i]==0) /= 0 Unknown /
agev[m][i]=1;	agev[m][i]=1;
}	else{
	printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
	fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
	agev[m][i]=0;
	}
	} /* End for lastpass */
}	}

for (i=1; i<=imx; i++) {	for (i=1; i<=imx; i++) {
for(m=firstpass; (m<=lastpass); m++){	for(m=firstpass; (m<=lastpass); m++){
if (s[m][i] > (nlstate+ndeath)) {	if (s[m][i] > (nlstate+ndeath)) {
Line 6569 void syscompilerinfo(int logged)	Line 6918 void syscompilerinfo(int logged)

}	}

int prevalence_limit(double p, double prlim, double ageminpar, double agemaxpar, double ftolpl, int ncvyear){	int prevalence_limit(double p, double prlim, double ageminpar, double agemaxpar, double ftolpl, int ncvyearp){
/--------------- Prevalence limit (period or stable prevalence) --------------/	/--------------- Prevalence limit (period or stable prevalence) --------------/
int i, j, k, i1 ;	int i, j, k, i1 ;
/* double ftolpl = 1.e-10; */	/* double ftolpl = 1.e-10; */
Line 6625 void syscompilerinfo(int logged)	Line 6974 void syscompilerinfo(int logged)

for (age=agebase; age<=agelim; age++){	for (age=agebase; age<=agelim; age++){
/* for (age=agebase; age<=agebase; age++){ */	/* for (age=agebase; age<=agebase; age++){ */
prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyear, k);	prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
fprintf(ficrespl,"%.0f ",age );	fprintf(ficrespl,"%.0f ",age );
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
Line 6634 void syscompilerinfo(int logged)	Line 6983 void syscompilerinfo(int logged)
tot += prlim[i][i];	tot += prlim[i][i];
fprintf(ficrespl," %.5f", prlim[i][i]);	fprintf(ficrespl," %.5f", prlim[i][i]);
}	}
fprintf(ficrespl," %.3f %d\n", tot, *ncvyear);	fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
} /* Age */	} /* Age */
/* was end of cptcod */	/* was end of cptcod */
} /* cptcov */	} /* cptcov */
Line 6727 int main(int argc, char *argv[])	Line 7076 int main(int argc, char *argv[])
#endif	#endif
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=0,m,size=100, cptcod;	int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
int ncvyearnp=0;	int ncvyear=0; /* Number of years needed for the period prevalence to converge */
int ncvyear=&ncvyearnp; / Number of years needed for the period prevalence to converge */
int jj, ll, li, lj, lk;	int jj, ll, li, lj, lk;
int numlinepar=0; /* Current linenumber of parameter file */	int numlinepar=0; /* Current linenumber of parameter file */
int num_filled;	int num_filled;
Line 6988 int main(int argc, char *argv[])	Line 7336 int main(int argc, char *argv[])
if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \	if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
&ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){	&ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
if (num_filled != 8) {	if (num_filled != 8) {
printf("Not 8\n");	printf("Not 8 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
	printf("but line=%s\n",line);
}	}
printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt);	printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt);
}	}
/* ftolpl=6ftol1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit \/ /	/* ftolpl=6ftol1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit \/ /
ftolpl=6.e-3; /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */	/ftolpl=6.e-4; //* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
/* Third parameter line */	/* Third parameter line */
while(fgets(line, MAXLINE, ficpar)) {	while(fgets(line, MAXLINE, ficpar)) {
/* If line starts with a # it is a comment */	/* If line starts with a # it is a comment */
Line 7342 Please run with mle=-1 to get a correct	Line 7691 Please run with mle=-1 to get a correct
free_vector(annais,1,n);	free_vector(annais,1,n);
/* free_matrix(mint,1,maxwav,1,n);	/* free_matrix(mint,1,maxwav,1,n);
free_matrix(anint,1,maxwav,1,n);*/	free_matrix(anint,1,maxwav,1,n);*/
free_vector(moisdc,1,n);	/* free_vector(moisdc,1,n); */
free_vector(andc,1,n);	/* free_vector(andc,1,n); */
/* */	/* */

wav=ivector(1,imx);	wav=ivector(1,imx);
dh=imatrix(1,lastpass-firstpass+1,1,imx);	/* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
bh=imatrix(1,lastpass-firstpass+1,1,imx);	/* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
mw=imatrix(1,lastpass-firstpass+1,1,imx);	/* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
	dh=imatrix(1,lastpass-firstpass+2,1,imx); /* We are adding a wave if status is unknown at last wave but death occurs after last wave.*/
	bh=imatrix(1,lastpass-firstpass+2,1,imx);
	mw=imatrix(1,lastpass-firstpass+2,1,imx);

/* Concatenates waves */	/* Concatenates waves */
	/* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
	Death is a valid wave (if date is known).
	mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
	dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
	and mw[mi+1][i]. dh depends on stepm.
	*/

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);
/* */	/* */

	free_vector(moisdc,1,n);
	free_vector(andc,1,n);

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

nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);	nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
Line 7362 Please run with mle=-1 to get a correct	Line 7724 Please run with mle=-1 to get a correct
Ndum =ivector(-1,NCOVMAX);	Ndum =ivector(-1,NCOVMAX);
if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and ageage /	if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and ageage /
tricode(Tvar,nbcode,imx, Ndum); /*< Fills nbcode[Tvar[j]][l]; /	tricode(Tvar,nbcode,imx, Ndum); /*< Fills nbcode[Tvar[j]][l]; /
/* Nbcode gives the value of the lth modality of jth covariate, in	/* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
V2+V1age, there are 3 covariates Tvar[2]=1 (V1)./	V2+V1age, there are 3 covariates Tvar[2]=1 (V1)./
/* 1 to ncodemax[j] is the maximum value of this jth covariate */	/* 1 to ncodemax[j] which is the maximum value of this jth covariate */

/* codtab=imatrix(1,100,1,10);/ / codtab[h,k]=( (h-1) - mod(k-1,2(k-1) )/2(k-1) */	/* codtab=imatrix(1,100,1,10);/ / codtab[h,k]=( (h-1) - mod(k-1,2(k-1) )/2(k-1) */
/printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));/	/printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));/
/* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/	/* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
	/* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
	* codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
	* (currently 0 or 1) in the data.
	* In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
	* corresponding modality (h,j).
	*/

h=0;	h=0;


Line 7378 Please run with mle=-1 to get a correct	Line 7747 Please run with mle=-1 to get a correct
m=pow(2,cptcoveff);	m=pow(2,cptcoveff);

/< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2(k-1) )/2**(k-1) + 1	/< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2(k-1) )/2**(k-1) + 1
* For k=4 covariates, h goes from 1 to 2**k	* For k=4 covariates, h goes from 1 to m=2**k
* codtabm(h,k)= 1 & (h-1) >> (k-1) ;	* codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;
	* #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
* h\k 1 2 3 4	* h\k 1 2 3 4
*______________________________	*______________________________
* 1 i=1 1 i=1 1 i=1 1 i=1 1	* 1 i=1 1 i=1 1 i=1 1 i=1 1
Line 7399 Please run with mle=-1 to get a correct	Line 7769 Please run with mle=-1 to get a correct
* 15 i=8 1 2 2 2	* 15 i=8 1 2 2 2
* 16 2 2 2 2	* 16 2 2 2 2
*/	*/
	/* How to do the opposite? From combination h (=1 to 2*k) how to get the value on the covariates? /
	/* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
	* and the value of each covariate?
	* V1=1, V2=1, V3=2, V4=1 ?
	* h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
	* h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
	* In order to get the real value in the data, we use nbcode
	* nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
	* We are keeping this crazy system in order to be able (in the future?)
	* to have more than 2 values (0 or 1) for a covariate.
	* #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
	* h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
	* bbbbbbbb
	* 76543210
	* h-1 00000101 (6-1=5)
	*(h-1)>>(k-1)= 00000001 >> (2-1) = 1 right shift
	* &
	* 1 00000001 (1)
	* 00000001 = 1 & ((h-1) >> (k-1))
	* +1= 00000010 =2
	*
	* h=14, k=3 => h'=h-1=13, k'=k-1=2
	* h' 1101 =2^3+2^2+0x2^1+2^0
	* >>k' 11
	* & 00000001
	* = 00000001
	* +1 = 00000010=2 = codtabm(14,3)
	* Reverse h=6 and m=16?
	* cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
	* for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
	* decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
	* decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
	* V3=decodtabm(14,3,2**4)=2
	* h'=13 1101 =2^3+2^2+0x2^1+2^0
	*(h-1) >> (j-1) 0011 =13 >> 2
	* &1 000000001
	* = 000000001
	* +1= 000000010 =2
	* 2211
	* V1=1+1, V2=0+1, V3=1+1, V4=1+1
	* V3=2
	*/

/* /\* for(h=1; h <=100 ;h++){ \/ /	/* /\* for(h=1; h <=100 ;h++){ \/ /
/* /\* printf("h=%2d ", h); \/ /	/* /\* printf("h=%2d ", h); \/ /
/* /\* for(k=1; k <=10; k++){ \/ /	/* /\* for(k=1; k <=10; k++){ \/ /
Line 7477 Title=%s <br>Datafile=%s Firstpass=%d La	Line 7890 Title=%s <br>Datafile=%s Firstpass=%d La
optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);	optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
}	}

fprintf(fichtm,"<html><head>\n<head>\n<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n<title>IMaCh %s</title></head>\n <body><font size=\"7\"><a href=http:/euroreves.ined.fr/imach>IMaCh for Interpolated Markov Chain</a> </font><br>\n<font size=\"3\">Sponsored by Copyright (C) 2002-2015 <a href=http://www.ined.fr>INED</a>-EUROREVES-Institut de longévité-Japan Society for the Promotion of Sciences 日本学術振興会 (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - <a href=https://software.intel.com/en-us>Intel Software 2015</a></font><br> \	fprintf(fichtm,"<html><head>\n<head>\n<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n<title>IMaCh %s</title></head>\n <body><font size=\"7\"><a href=http:/euroreves.ined.fr/imach>IMaCh for Interpolated Markov Chain</a> </font><br>\n<font size=\"3\">Sponsored by Copyright (C) 2002-2015 <a href=http://www.ined.fr>INED</a>-EUROREVES-Institut de longévité-2013-2016-Japan Society for the Promotion of Sciences 日本学術振興会 (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - <a href=https://software.intel.com/en-us>Intel Software 2015-2018</a></font><br> \
<hr size=\"2\" color=\"#EC5E5E\"> \n\	<hr size=\"2\" color=\"#EC5E5E\"> \n\
<font size=\"2\">IMaCh-%s <br> %s</font> \	<font size=\"2\">IMaCh-%s <br> %s</font> \
<hr size=\"2\" color=\"#EC5E5E\"> \n\	<hr size=\"2\" color=\"#EC5E5E\"> \n\
Line 7507 Title=%s <br>Datafile=%s Firstpass=%d La	Line 7920 Title=%s <br>Datafile=%s Firstpass=%d La

/* Calculates basic frequencies. Computes observed prevalence at single age	/* Calculates basic frequencies. Computes observed prevalence at single age
and prints on file fileres'p'. */	and prints on file fileres'p'. */
freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);	freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\
	firstpass, lastpass, stepm, weightopt, model);

fprintf(fichtm,"\n");	fprintf(fichtm,"\n");
fprintf(fichtm,"<br>Total number of observations=%d <br>\n\	fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
Line 7929 Please run with mle=-1 to get a correct	Line 8343 Please run with mle=-1 to get a correct

fflush(ficlog);	fflush(ficlog);
fflush(ficres);	fflush(ficres);
	while(fgets(line, MAXLINE, ficpar)) {
while((c=getc(ficpar))=='#' && c!= EOF){	/* If line starts with a # it is a comment */
ungetc(c,ficpar);	if (line[0] == '#') {
fgets(line, MAXLINE, ficpar);	numlinepar++;
fputs(line,stdout);	fputs(line,stdout);
fputs(line,ficparo);	fputs(line,ficparo);
}	fputs(line,ficlog);
ungetc(c,ficpar);	continue;
	}else
	break;
	}

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

estepm=0;	estepm=0;
fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);	if((num_filled=sscanf(line,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm, &ftolpl)) !=EOF){

	if (num_filled != 6) {
	printf("Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n");
	printf("but line=%s\n",line);
	goto end;
	}
	printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
	}
	/* ftolpl=6ftol1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit \/ /
	/ftolpl=6.e-4;/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */

	/* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
if (estepm==0 \|\| estepm < stepm) estepm=stepm;	if (estepm==0 \|\| estepm < stepm) estepm=stepm;
if (fage <= 2) {	if (fage <= 2) {
bage = ageminpar;	bage = ageminpar;
Line 7947 Please run with mle=-1 to get a correct	Line 8384 Please run with mle=-1 to get a correct
}	}

fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");	fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);	fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);	fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);

/* Other stuffs, more or less useful */	/* Other stuffs, more or less useful */
while((c=getc(ficpar))=='#' && c!= EOF){	while((c=getc(ficpar))=='#' && c!= EOF){
Line 8011 Please run with mle=-1 to get a correct	Line 8448 Please run with mle=-1 to get a correct
This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\	This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);	Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
}else	}else
printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);	printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, pathc,p);

printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt,\	printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt,\
model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\	model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,estepm, \
jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);	jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);

/------------ free_vector -------------/	/------------ free_vector -------------/
/* chdir(path); */	/* chdir(path); */

free_ivector(wav,1,imx);	/* free_ivector(wav,1,imx); / / Moved after last prevalence call */
free_imatrix(dh,1,lastpass-firstpass+1,1,imx);	/* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
free_imatrix(bh,1,lastpass-firstpass+1,1,imx);	/* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
free_imatrix(mw,1,lastpass-firstpass+1,1,imx);	/* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */
free_lvector(num,1,n);	free_lvector(num,1,n);
free_vector(agedc,1,n);	free_vector(agedc,1,n);
/free_matrix(covar,0,NCOVMAX,1,n);/	/free_matrix(covar,0,NCOVMAX,1,n);/
Line 8038 Please run with mle=-1 to get a correct	Line 8475 Please run with mle=-1 to get a correct
/--------------- Prevalence limit (period or stable prevalence) --------------/	/--------------- Prevalence limit (period or stable prevalence) --------------/
/#include "prevlim.h"/ /* Use ficrespl, ficlog */	/#include "prevlim.h"/ /* Use ficrespl, ficlog */
prlim=matrix(1,nlstate,1,nlstate);	prlim=matrix(1,nlstate,1,nlstate);
prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, ncvyear);	prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
fclose(ficrespl);	fclose(ficrespl);

#ifdef FREEEXIT2	#ifdef FREEEXIT2
Line 8083 Please run with mle=-1 to get a correct	Line 8520 Please run with mle=-1 to get a correct
/* 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",\	/* 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);	ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
*/	*/
	free_ivector(wav,1,imx);
	free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
	free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
	free_imatrix(mw,1,lastpass-firstpass+2,1,imx);


if (mobilav!=0) {	if (mobilav!=0) {
mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);	mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
Line 8208 Please run with mle=-1 to get a correct	Line 8650 Please run with mle=-1 to get a correct
cptcod= 0; /* To be deleted */	cptcod= 0; /* To be deleted */
printf("varevsij %d \n",vpopbased);	printf("varevsij %d \n",vpopbased);
fprintf(ficlog, "varevsij %d \n",vpopbased);	fprintf(ficlog, "varevsij %d \n",vpopbased);
varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */	varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are ");	fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are ");
if(vpopbased==1)	if(vpopbased==1)
fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);	fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
Line 8222 Please run with mle=-1 to get a correct	Line 8664 Please run with mle=-1 to get a correct
printf("Computing age specific period (stable) prevalences in each health state \n");	printf("Computing age specific period (stable) prevalences in each health state \n");
fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");	fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
for(age=bage; age <=fage ;age++){	for(age=bage; age <=fage ;age++){
prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyear, k); /ZZ Is it the correct prevalim /	prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /ZZ Is it the correct prevalim /
if (vpopbased==1) {	if (vpopbased==1) {
if(mobilav ==0){	if(mobilav ==0){
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
Line 8301 Please run with mle=-1 to get a correct	Line 8743 Please run with mle=-1 to get a correct

varpl=matrix(1,nlstate,(int) bage, (int) fage);	varpl=matrix(1,nlstate,(int) bage, (int) fage);
oldm=oldms;savm=savms;	oldm=oldms;savm=savms;
varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyear, k, strstart);	varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);
free_matrix(varpl,1,nlstate,(int) bage, (int)fage);	free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
/}/	/}/
}	}

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	Added in v.1.215