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Diff for /imach/src/imach.c between versions 1.246 and 1.314

version 1.246, 2016/09/02 08:49:22	version 1.314, 2022/04/13 17:43:09
Line 1	Line 1
/* $Id$	/* $Id$
$State$	$State$
$Log$	$Log$
	Revision 1.314 2022/04/13 17:43:09 brouard
	* imach.c (Module): Adding link to text data files

	Revision 1.313 2022/04/11 15:57:42 brouard
	* imach.c (Module): Error in rewriting the 'r' file with yearsfproj or yearsbproj fixed

	Revision 1.312 2022/04/05 21:24:39 brouard
	* empty log message *

	Revision 1.311 2022/04/05 21:03:51 brouard
	Summary: Fixed quantitative covariates

	Fixed covariates (dummy or quantitative)
	with missing values have never been allowed but are ERRORS and
	program quits. Standard deviations of fixed covariates were
	wrongly computed. Mean and standard deviations of time varying
	covariates are still not computed.

	Revision 1.310 2022/03/17 08:45:53 brouard
	Summary: 99r25

	Improving detection of errors: result lines should be compatible with
	the model.

	Revision 1.309 2021/05/20 12:39:14 brouard
	Summary: Version 0.99r24

	Revision 1.308 2021/03/31 13:11:57 brouard
	Summary: Version 0.99r23


	* imach.c (Module): Still bugs in the result loop. Thank to Holly Benett

	Revision 1.307 2021/03/08 18:11:32 brouard
	Summary: 0.99r22 fixed bug on result:

	Revision 1.306 2021/02/20 15:44:02 brouard
	Summary: Version 0.99r21

	* imach.c (Module): Fix bug on quitting after result lines!
	(Module): Version 0.99r21

	Revision 1.305 2021/02/20 15:28:30 brouard
	* imach.c (Module): Fix bug on quitting after result lines!

	Revision 1.304 2021/02/12 11:34:20 brouard
	* imach.c (Module): The use of a Windows BOM (huge) file is now an error

	Revision 1.303 2021/02/11 19:50:15 brouard
	* (Module): imach.c Someone entered 'results:' instead of 'result:'. Now it is an error which is printed.

	Revision 1.302 2020/02/22 21:00:05 brouard
	* (Module): imach.c Update mle=-3 (for computing Life expectancy
	and life table from the data without any state)

	Revision 1.301 2019/06/04 13:51:20 brouard
	Summary: Error in 'r'parameter file backcast yearsbproj instead of yearsfproj

	Revision 1.300 2019/05/22 19:09:45 brouard
	Summary: version 0.99r19 of May 2019

	Revision 1.299 2019/05/22 18:37:08 brouard
	Summary: Cleaned 0.99r19

	Revision 1.298 2019/05/22 18:19:56 brouard
	* empty log message *

	Revision 1.297 2019/05/22 17:56:10 brouard
	Summary: Fix bug by moving date2dmy and nhstepm which gaefin=-1

	Revision 1.296 2019/05/20 13:03:18 brouard
	Summary: Projection syntax simplified


	We can now start projections, forward or backward, from the mean date
	of inteviews up to or down to a number of years of projection:
	prevforecast=1 yearsfproj=15.3 mobil_average=0
	or
	prevforecast=1 starting-proj-date=1/1/2007 final-proj-date=12/31/2017 mobil_average=0
	or
	prevbackcast=1 yearsbproj=12.3 mobil_average=1
	or
	prevbackcast=1 starting-back-date=1/10/1999 final-back-date=1/1/1985 mobil_average=1

	Revision 1.295 2019/05/18 09:52:50 brouard
	Summary: doxygen tex bug

	Revision 1.294 2019/05/16 14:54:33 brouard
	Summary: There was some wrong lines added

	Revision 1.293 2019/05/09 15:17:34 brouard
	* empty log message *

	Revision 1.292 2019/05/09 14:17:20 brouard
	Summary: Some updates

	Revision 1.291 2019/05/09 13:44:18 brouard
	Summary: Before ncovmax

	Revision 1.290 2019/05/09 13:39:37 brouard
	Summary: 0.99r18 unlimited number of individuals

	The number n which was limited to 20,000 cases is now unlimited, from firstobs to lastobs. If the number is too for the virtual memory, probably an error will occur.

	Revision 1.289 2018/12/13 09:16:26 brouard
	Summary: Bug for young ages (<-30) will be in r17

	Revision 1.288 2018/05/02 20:58:27 brouard
	Summary: Some bugs fixed

	Revision 1.287 2018/05/01 17:57:25 brouard
	Summary: Bug fixed by providing frequencies only for non missing covariates

	Revision 1.286 2018/04/27 14:27:04 brouard
	Summary: some minor bugs

	Revision 1.285 2018/04/21 21:02:16 brouard
	Summary: Some bugs fixed, valgrind tested

	Revision 1.284 2018/04/20 05:22:13 brouard
	Summary: Computing mean and stdeviation of fixed quantitative variables

	Revision 1.283 2018/04/19 14:49:16 brouard
	Summary: Some minor bugs fixed

	Revision 1.282 2018/02/27 22:50:02 brouard
	* empty log message *

	Revision 1.281 2018/02/27 19:25:23 brouard
	Summary: Adding second argument for quitting

	Revision 1.280 2018/02/21 07:58:13 brouard
	Summary: 0.99r15

	New Makefile with recent VirtualBox 5.26. Bug in sqrt negatve in imach.c

	Revision 1.279 2017/07/20 13:35:01 brouard
	Summary: temporary working

	Revision 1.278 2017/07/19 14:09:02 brouard
	Summary: Bug for mobil_average=0 and prevforecast fixed(?)

	Revision 1.277 2017/07/17 08:53:49 brouard
	Summary: BOM files can be read now

	Revision 1.276 2017/06/30 15:48:31 brouard
	Summary: Graphs improvements

	Revision 1.275 2017/06/30 13:39:33 brouard
	Summary: Saito's color

	Revision 1.274 2017/06/29 09:47:08 brouard
	Summary: Version 0.99r14

	Revision 1.273 2017/06/27 11:06:02 brouard
	Summary: More documentation on projections

	Revision 1.272 2017/06/27 10:22:40 brouard
	Summary: Color of backprojection changed from 6 to 5(yellow)

	Revision 1.271 2017/06/27 10:17:50 brouard
	Summary: Some bug with rint

	Revision 1.270 2017/05/24 05:45:29 brouard
	* empty log message *

	Revision 1.269 2017/05/23 08:39:25 brouard
	Summary: Code into subroutine, cleanings

	Revision 1.268 2017/05/18 20:09:32 brouard
	Summary: backprojection and confidence intervals of backprevalence

	Revision 1.267 2017/05/13 10:25:05 brouard
	Summary: temporary save for backprojection

	Revision 1.266 2017/05/13 07:26:12 brouard
	Summary: Version 0.99r13 (improvements and bugs fixed)

	Revision 1.265 2017/04/26 16:22:11 brouard
	Summary: imach 0.99r13 Some bugs fixed

	Revision 1.264 2017/04/26 06:01:29 brouard
	Summary: Labels in graphs

	Revision 1.263 2017/04/24 15:23:15 brouard
	Summary: to save

	Revision 1.262 2017/04/18 16:48:12 brouard
	* empty log message *

	Revision 1.261 2017/04/05 10:14:09 brouard
	Summary: Bug in E_ as well as in T_ fixed nres-1 vs k1-1

	Revision 1.260 2017/04/04 17:46:59 brouard
	Summary: Gnuplot indexations fixed (humm)

	Revision 1.259 2017/04/04 13:01:16 brouard
	Summary: Some errors to warnings only if date of death is unknown but status is death we could set to pi3

	Revision 1.258 2017/04/03 10:17:47 brouard
	Summary: Version 0.99r12

	Some cleanings, conformed with updated documentation.

	Revision 1.257 2017/03/29 16:53:30 brouard
	Summary: Temp

	Revision 1.256 2017/03/27 05:50:23 brouard
	Summary: Temporary

	Revision 1.255 2017/03/08 16:02:28 brouard
	Summary: IMaCh version 0.99r10 bugs in gnuplot fixed

	Revision 1.254 2017/03/08 07:13:00 brouard
	Summary: Fixing data parameter line

	Revision 1.253 2016/12/15 11:59:41 brouard
	Summary: 0.99 in progress

	Revision 1.252 2016/09/15 21:15:37 brouard
	* empty log message *

	Revision 1.251 2016/09/15 15:01:13 brouard
	Summary: not working

	Revision 1.250 2016/09/08 16:07:27 brouard
	Summary: continue

	Revision 1.249 2016/09/07 17:14:18 brouard
	Summary: Starting values from frequencies

	Revision 1.248 2016/09/07 14:10:18 brouard
	* empty log message *

	Revision 1.247 2016/09/02 11:11:21 brouard
	* empty log message *

Revision 1.246 2016/09/02 08:49:22 brouard	Revision 1.246 2016/09/02 08:49:22 brouard
* empty log message *	* empty log message *

Line 113	Line 350
Author: Nicolas Brouard	Author: Nicolas Brouard

Revision 1.210 2015/11/18 17:41:20 brouard	Revision 1.210 2015/11/18 17:41:20 brouard
Summary: Start working on projected prevalences	Summary: Start working on projected prevalences Revision 1.209 2015/11/17 22:12:03 brouard

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

Line 758 Back prevalence and projections:	Line 993 Back prevalence and projections:
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
oldm=oldms;savm=savms;	oldm=oldms;savm=savms;

- hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);	- hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
Computes the transition matrix starting at age 'age' over	Computes the transition matrix starting at age 'age' over
'nhstepmhstepmstepm' months (i.e. until	'nhstepmhstepmstepm' months (i.e. until
age (in years) age+nhstepmhstepmstepm/12) by multiplying	age (in years) age+nhstepmhstepmstepm/12) by multiplying
Line 903 typedef struct {	Line 1138 typedef struct {
/* #include <libintl.h> */	/* #include <libintl.h> */
/* #define _(String) gettext (String) */	/* #define _(String) gettext (String) */

#define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */	#define MAXLINE 2048 /* Was 256 and 1024. Overflow with 312 with 2 states and 4 covariates. Should be ok */

#define GNUPLOTPROGRAM "gnuplot"	#define GNUPLOTPROGRAM "gnuplot"
/#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"/	/#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"/
Line 918 typedef struct {	Line 1153 typedef struct {
#define NINTERVMAX 8	#define NINTERVMAX 8
#define NLSTATEMAX 8 /*< Maximum number of live states (for func) /	#define NLSTATEMAX 8 /*< Maximum number of live states (for func) /
#define NDEATHMAX 8 /*< Maximum number of dead states (for func) /	#define NDEATHMAX 8 /*< Maximum number of dead states (for func) /
#define NCOVMAX 20 /*< Maximum number of covariates, including generated covariates V1V2 */	#define NCOVMAX 20 /*< Maximum number of covariates, including generated covariates V1V2 */
#define codtabm(h,k) (1 & (h-1) >> (k-1))+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<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)/
#define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1	#define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
#define MAXN 20000	/#define MAXN 20000 / /* Should by replaced by nobs, real number of observations and unlimited */
#define YEARM 12. /*< Number of months per year /	#define YEARM 12. /*< Number of months per year /
/* #define AGESUP 130 */	/* #define AGESUP 130 */
#define AGESUP 150	/* #define AGESUP 150 */
	#define AGESUP 200
	#define AGEINF 0
#define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */	#define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
#define AGEBASE 40	#define AGEBASE 40
#define AGEOVERFLOW 1.e20	#define AGEOVERFLOW 1.e20
Line 944 typedef struct {	Line 1181 typedef struct {
/* $State$ */	/* $State$ */
#include "version.h"	#include "version.h"
char version[]=__IMACH_VERSION__;	char version[]=__IMACH_VERSION__;
char copyright[]="February 2016,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018";	char copyright[]="March 2021,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2020, Nihon University 2021, INED 2000-2021";
char fullversion[]="$Revision$ $Date$";	char fullversion[]="$Revision$ $Date$";
char strstart[80];	char strstart[80];
char optionfilext[10], optionfilefiname[FILENAMELENGTH];	char optionfilext[10], optionfilefiname[FILENAMELENGTH];
Line 968 int nqfveff=0; /**< nqfveff Number of Qu	Line 1205 int nqfveff=0; /**< nqfveff Number of Qu
int ntveff=0; /*< ntveff number of effective time varying variables /	int ntveff=0; /*< ntveff number of effective time varying variables /
int nqtveff=0; /*< ntqveff number of effective time varying quantitative variables /	int nqtveff=0; /*< ntqveff number of effective time varying quantitative variables /
int cptcov=0; /* Working variable */	int cptcov=0; /* Working variable */
	int nobs=10; /* Number of observations in the data lastobs-firstobs */
int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */	int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
int npar=NPARMAX;	int npar=NPARMAX; /* Number of parameters (nlstate+ndeath-1)nlstatencovmodel; */
int nlstate=2; /* Number of live states */	int nlstate=2; /* Number of live states */
int ndeath=1; /* Number of dead states */	int ndeath=1; /* Number of dead states */
int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a121 +b12x ncovmodel=2 */	int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a121 +b12x ncovmodel=2 */
Line 1017 FILE *ficrescveij;	Line 1255 FILE *ficrescveij;
char filerescve[FILENAMELENGTH];	char filerescve[FILENAMELENGTH];
FILE *ficresvij;	FILE *ficresvij;
char fileresv[FILENAMELENGTH];	char fileresv[FILENAMELENGTH];
FILE *ficresvpl;
char fileresvpl[FILENAMELENGTH];
char title[MAXLINE];	char title[MAXLINE];
char model[MAXLINE]; /*< The model line /	char model[MAXLINE]; /*< The model line /
char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], fileresplb[FILENAMELENGTH];	char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], fileresplb[FILENAMELENGTH];
Line 1109 double pmmij, probs; / Global poin	Line 1346 double pmmij, probs; / Global poin
double *mobaverage, mobaverages; / New global variable */	double *mobaverage, mobaverages; / New global variable */
double ageexmed,agecens;	double ageexmed,agecens;
double dateintmean=0;	double dateintmean=0;
	double anprojd, mprojd, jprojd; /* For eventual projections */
	double anprojf, mprojf, jprojf;

	double anbackd, mbackd, jbackd; /* For eventual backprojections */
	double anbackf, mbackf, jbackf;
	double jintmean,mintmean,aintmean;
double *weight;	double *weight;
int *s; / Status */	int *s; / Status */
double *agedc;	double *agedc;
double covar; /< covar[j,i], value of jth covariate for individual i,	double covar; /< covar[j,i], value of jth covariate for individual i,
* covar=matrix(0,NCOVMAX,1,n);	* covar=matrix(0,NCOVMAX,1,n);
* cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]age; /	* cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]age; /
double *coqvar; / Fixed quantitative covariate iqv */	double *coqvar; / Fixed quantitative covariate nqv */
double **cotvar; / Time varying covariate itv */	double **cotvar; / Time varying covariate ntv */
double **cotqvar; / Time varying quantitative covariate itqv */	double **cotqvar; / Time varying quantitative covariate itqv */
double idx;	double idx;
int *nbcode, Tvar; /*< model=V2 => Tvar[1]= 2 /	int *nbcode, Tvar; /*< model=V2 => Tvar[1]= 2 /
Line 1146 int *TvarsQind;	Line 1388 int *TvarsQind;

#define MAXRESULTLINES 10	#define MAXRESULTLINES 10
int nresult=0;	int nresult=0;
	int parameterline=0; /* # of the parameter (type) line */
int TKresult[MAXRESULTLINES];	int TKresult[MAXRESULTLINES];
int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */	int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */	int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
Line 1355 char cutl(char blocc, char *alocc, cha	Line 1598 char cutl(char blocc, char *alocc, cha
{	{
/* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'	/* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')	and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
gives blocc="abcdef" and alocc="ghi2j".	gives alocc="abcdef" and blocc="ghi2j".
If occ is not found blocc is null and alocc is equal to in. Returns blocc	If occ is not found blocc is null and alocc is equal to in. Returns blocc
*/	*/
char s, t;	char s, t;
Line 1637 char *subdirf(char fileres[])	Line 1880 char *subdirf(char fileres[])
/************* function subdirf2 *********/	/************* function subdirf2 *********/
char subdirf2(char fileres[], char preop)	char subdirf2(char fileres[], char preop)
{	{
	/* Example subdirf2(optionfilefiname,"FB_") with optionfilefiname="texte", result="texte/FB_texte"
	Errors in subdirf, 2, 3 while printing tmpout is
	rewritten within the same printf. Workaround: many printfs
/* Caution optionfilefiname is hidden */	/* Caution optionfilefiname is hidden */
strcpy(tmpout,optionfilefiname);	strcpy(tmpout,optionfilefiname);
strcat(tmpout,"/");	strcat(tmpout,"/");
Line 2227 void powell(double p[], double **xi, int	Line 2472 void powell(double p[], double **xi, int
/* But p and xit have been updated at the end of linmin, fret corresponds to new p, xit /	/* But p and xit have been updated at the end of linmin, fret corresponds to new p, xit /
/* New value of last point Pn is not computed, P(n-1) */	/* New value of last point Pn is not computed, P(n-1) */
for(j=1;j<=n;j++) {	for(j=1;j<=n;j++) {
if(flatdir[j] >0){	if(flatdir[j] >0){
printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);	printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);	fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
}	}
/* printf("\n"); */	/* printf("\n"); */
/* fprintf(ficlog,"\n"); */	/* fprintf(ficlog,"\n"); */
}	}
/* if (2.0fabs(fp-(fret)) <= ftol(fabs(fp)+fabs(fret))) { /\* Did we reach enough precision? \/ /	/* if (2.0fabs(fp-(fret)) <= ftol(fabs(fp)+fabs(fret))) { /\* Did we reach enough precision? \/ /
if (2.0fabs(fp-(fret)) <= ftol) { /* Did we reach enough precision? */	if (2.0fabs(fp-(fret)) <= ftol) { /* Did we reach enough precision? */
/* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */	/* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
Line 2378 void powell(double p[], double **xi, int	Line 2623 void powell(double p[], double **xi, int
flatd++;	flatd++;
}	}
if(flatd >0){	if(flatd >0){
printf("%d flat directions\n",flatd);	printf("%d flat directions: ",flatd);
fprintf(ficlog,"%d flat directions\n",flatd);	fprintf(ficlog,"%d flat directions :",flatd);
for (j=1;j<=n;j++) {	for (j=1;j<=n;j++) {
if(flatdir[j]>0){	if(flatdir[j]>0){
printf("%d ",j);	printf("%d ",j);
Line 2419 void powell(double p[], double **xi, int	Line 2664 void powell(double p[], double **xi, int

double prevalim(double prlim, int nlstate, double x[], double age, double oldm, double savm, double ftolpl, int *ncvyear, int ij, int nres)	double prevalim(double prlim, int nlstate, double x[], double age, double oldm, double savm, double ftolpl, int *ncvyear, int ij, int nres)
{	{
/* Computes the prevalence limit in each live state at age x and for covariate combination ij	/**< Computes the prevalence limit in each live state at age x and for covariate combination ij
(and selected quantitative values in nres)	* (and selected quantitative values in nres)
by left multiplying the unit	* by left multiplying the unit
matrix by transitions matrix until convergence is reached with precision ftolpl */	* matrix by transitions matrix until convergence is reached with precision ftolpl
/* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */	* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I
/* Wx is row vector: population in state 1, population in state 2, population dead */	* Wx is row vector: population in state 1, population in state 2, population dead
/* or prevalence in state 1, prevalence in state 2, 0 */	* or prevalence in state 1, prevalence in state 2, 0
/* newm is the matrix after multiplications, its rows are identical at a factor */	* newm is the matrix after multiplications, its rows are identical at a factor.
/* Initial matrix pimij */	* Inputs are the parameter, age, a tolerance for the prevalence limit ftolpl.
	* Output is prlim.
	* Initial matrix pimij
	*/
/* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */	/* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
/* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */	/* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
/* 0, 0 , 1} */	/* 0, 0 , 1} */
Line 2448 void powell(double p[], double **xi, int	Line 2696 void powell(double p[], double **xi, int
double **newm;	double **newm;
double agefin, delaymax=200. ; /* 100 Max number of years to converge */	double agefin, delaymax=200. ; /* 100 Max number of years to converge */
int ncvloop=0;	int ncvloop=0;
	int first=0;

min=vector(1,nlstate);	min=vector(1,nlstate);
max=vector(1,nlstate);	max=vector(1,nlstate);
Line 2544 void powell(double p[], double **xi, int	Line 2793 void powell(double p[], double **xi, int
free_vector(meandiff,1,nlstate);	free_vector(meandiff,1,nlstate);
return prlim;	return prlim;
}	}
} /* age loop */	} /* agefin 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. Try to lower 'ftolpl'. \n\	if(!first){
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);	first=1;
	printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d). Others in log file only...\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM), (int)(age-stepm/YEARM), (int)delaymax);
	}
	fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM), (int)(age-stepm/YEARM), (int)delaymax);

/* 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(min,1,nlstate);
free_vector(max,1,nlstate);	free_vector(max,1,nlstate);
Line 2563 Earliest age to start was %d-%d=%d, ncvl	Line 2816 Earliest age to start was %d-%d=%d, ncvl
/* double bprevalim(double bprlim, double *prevacurrent, int nlstate, double x[], double age, double oldm, double savm, double dnewm, double doldm, double dsavm, double ftolpl, int ncvyear, int ij) /	/* double bprevalim(double bprlim, double *prevacurrent, int nlstate, double x[], double age, double oldm, double savm, double dnewm, double doldm, double dsavm, double ftolpl, int ncvyear, int ij) /
double bprevalim(double bprlim, double **prevacurrent, int nlstate, double x[], double age, double ftolpl, int ncvyear, int ij, int nres)	double bprevalim(double bprlim, double **prevacurrent, int nlstate, double x[], double age, double ftolpl, int ncvyear, int ij, int nres)
{	{
/* Computes the prevalence limit in each live state at age x and covariate ij by left multiplying the unit	/* Computes the prevalence limit in each live state at age x and for covariate combination ij (<=2**cptcoveff) by left multiplying the unit
matrix by transitions matrix until convergence is reached with precision ftolpl */	matrix by transitions matrix until convergence is reached with precision ftolpl */
/* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */	/* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
/* Wx is row vector: population in state 1, population in state 2, population dead */	/* Wx is row vector: population in state 1, population in state 2, population dead */
Line 2584 Earliest age to start was %d-%d=%d, ncvl	Line 2837 Earliest age to start was %d-%d=%d, ncvl
/* 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;
	int first=0;
double min, max, *meandiff, maxmax,sumnew=0.;	double min, max, *meandiff, maxmax,sumnew=0.;
/* double *matprod2(); / /* test */	/* double *matprod2(); / /* test */
double out, cov[NCOVMAX+1], bmij();	double out, cov[NCOVMAX+1], bmij();
Line 2598 Earliest age to start was %d-%d=%d, ncvl	Line 2852 Earliest age to start was %d-%d=%d, ncvl
max=vector(1,nlstate);	max=vector(1,nlstate);
meandiff=vector(1,nlstate);	meandiff=vector(1,nlstate);

dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;	dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
oldm=oldms; savm=savms;	oldm=oldms; savm=savms;

/* Starting with matrix unity */	/* Starting with matrix unity */
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 2612 Earliest age to start was %d-%d=%d, ncvl	Line 2866 Earliest age to start was %d-%d=%d, ncvl
/* Even if hstepm = 1, at least one multiplication by the unit matrix */	/* Even if hstepm = 1, at least one multiplication by the unit matrix */
/* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */	/* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
/* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age \/ /	/* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age \/ /
for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */	/* for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /\* A changer en age \/ /
	for(agefin=age; agefin<FMIN(AGESUP,age+delaymax); agefin=agefin+stepm/YEARM){ /* A changer en age */
ncvloop++;	ncvloop++;
newm=savm; /* oldm should be kept from previous iteration or unity at start */	newm=savm; /* oldm should be kept from previous iteration or unity at start */
/* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */	/* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
Line 2623 Earliest age to start was %d-%d=%d, ncvl	Line 2878 Earliest age to start was %d-%d=%d, ncvl
for (k=1; k<=nsd;k++) { /* For single dummy covariates only */	for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
/* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */	/* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];	cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
/* printf("bprevalim Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */	/* printf("bprevalim Dummy agefin=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agefin,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
}	}
/* for (k=1; k<=cptcovn;k++) { */	/* for (k=1; k<=cptcovn;k++) { */
/* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; \/ /	/* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; \/ /
Line 2677 Earliest age to start was %d-%d=%d, ncvl	Line 2932 Earliest age to start was %d-%d=%d, ncvl
/* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, ageminpar, agemaxpar, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind \/ /	/* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, ageminpar, agemaxpar, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind \/ /
/* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind \/ /	/* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind \/ /
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij)); /* Bug Valgrind */	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij)); /* Bug Valgrind */
	/* if((int)age == 86 \|\| (int)age == 87){ */
	/* printf(" Backward prevalim age=%d agefin=%d \n", (int) age, (int) agefin); */
	/* for(i=1; i<=nlstate+ndeath; i++) { */
	/* printf("%d newm= ",i); */
	/* for(j=1;j<=nlstate+ndeath;j++) { */
	/* printf("%f ",newm[i][j]); */
	/* } */
	/* printf("oldm * "); */
	/* for(j=1;j<=nlstate+ndeath;j++) { */
	/* printf("%f ",oldm[i][j]); */
	/* } */
	/* printf(" bmmij "); */
	/* for(j=1;j<=nlstate+ndeath;j++) { */
	/* printf("%f ",pmmij[i][j]); */
	/* } */
	/* printf("\n"); */
	/* } */
	/* } */
savm=oldm;	savm=oldm;
oldm=newm;	oldm=newm;

for(j=1; j<=nlstate; j++){	for(j=1; j<=nlstate; j++){
max[j]=0.;	max[j]=0.;
min[j]=1.;	min[j]=1.;
Line 2697 Earliest age to start was %d-%d=%d, ncvl	Line 2971 Earliest age to start was %d-%d=%d, ncvl
meandiff[i]=(max[i]-min[i])/(max[i]+min[i])2.; / mean difference for each column */	meandiff[i]=(max[i]-min[i])/(max[i]+min[i])2.; / mean difference for each column */
maxmax=FMAX(maxmax,meandiff[i]);	maxmax=FMAX(maxmax,meandiff[i]);
/* printf("Back age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, i, meandiff[i],(int)agefin, i, max[i], i, min[i],maxmax); */	/* printf("Back age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, i, meandiff[i],(int)agefin, i, max[i], i, min[i],maxmax); */
} /* j loop */	} /* i loop */
*ncvyear= -( (int)age- (int)agefin);	*ncvyear= -( (int)age- (int)agefin);
/* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, ncvyear);/	/* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, ncvyear); /
if(maxmax < ftolpl){	if(maxmax < ftolpl){
/* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, ncvyear); /	/* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, ncvyear); /
free_vector(min,1,nlstate);	free_vector(min,1,nlstate);
Line 2707 Earliest age to start was %d-%d=%d, ncvl	Line 2981 Earliest age to start was %d-%d=%d, ncvl
free_vector(meandiff,1,nlstate);	free_vector(meandiff,1,nlstate);
return bprlim;	return bprlim;
}	}
} /* age loop */	} /* agefin loop */
/* After some age loop it doesn't converge */	/* After some age loop it doesn't converge */
printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\	if(!first){
	first=1;
	printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. Others in log file only...\n\
	Oldest 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);
	}
	fprintf(ficlog,"Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
Oldest 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);	Oldest 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);
/* 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(min,1,nlstate);
Line 2724 Oldest age to start was %d-%d=%d, ncvloo	Line 3003 Oldest age to start was %d-%d=%d, ncvloo
double pmij(double ps, double cov, int ncovmodel, double x, int nlstate )	double pmij(double ps, double cov, int ncovmodel, double x, int nlstate )
{	{
/* According to parameters values stored in x and the covariate's values stored in cov,	/* According to parameters values stored in x and the covariate's values stored in cov,
computes the probability to be observed in state j being in state i by appying the	computes the probability to be observed in state j (after stepm years) being in state i by appying the
model to the ncovmodel covariates (including constant and age).	model to the ncovmodel covariates (including constant and age).
lnpijopii=ln(pij/pii)= aij+bijage+cijv1+dijv2+... = sum_nc=1^ncovmodel xij(nc)cov[nc]	lnpijopii=ln(pij/pii)= aij+bijage+cijv1+dijv2+... = sum_nc=1^ncovmodel xij(nc)cov[nc]
and, according on how parameters are entered, the position of the coefficient xij(nc) of the	and, according on how parameters are entered, the position of the coefficient xij(nc) of the
Line 2733 double pmij(double ps, double *cov,	Line 3012 double pmij(double ps, double *cov,
j>=i nc + ((i-1)(nlstate+ndeath-1)+(j-2))ncovmodel	j>=i nc + ((i-1)(nlstate+ndeath-1)+(j-2))ncovmodel
Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,	Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.	sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
Outputs ps[i][j] the probability to be observed in j being in j according to	Outputs ps[i][j] or probability to be observed in j being in i according to
the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]	the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
	Sum on j ps[i][j] should equal to 1.
*/	*/
double s1, lnpijopii;	double s1, lnpijopii;
/double t34;/	/double t34;/
Line 2786 double pmij(double ps, double *cov,	Line 3066 double pmij(double ps, double *cov,
ps[ii][ii]=1;	ps[ii][ii]=1;
}	}
}	}


/* for(ii=1; ii<= nlstate+ndeath; ii++){ */	/* for(ii=1; ii<= nlstate+ndeath; ii++){ */
/* for(jj=1; jj<= nlstate+ndeath; jj++){ */	/* for(jj=1; jj<= nlstate+ndeath; jj++){ */
/* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */	/* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
Line 2798 double pmij(double ps, double *cov,	Line 3078 double pmij(double ps, double *cov,
/*	/*
for(i=1; i<= npar; i++) printf("%f ",x[i]);	for(i=1; i<= npar; i++) printf("%f ",x[i]);
goto end;*/	goto end;*/
return ps;	return ps; /* Pointer is unchanged since its call */
}	}

/************* backward transition probabilities *************/	/************* backward transition probabilities *************/
Line 2807 double pmij(double ps, double *cov,	Line 3087 double pmij(double ps, double *cov,
/* double bmij(double ps, double cov, int ncovmodel, double x, int nlstate, double *prevacurrent, double dnewm, double doldm, double dsavm, int ij ) /	/* double bmij(double ps, double cov, int ncovmodel, double x, int nlstate, double *prevacurrent, double dnewm, double doldm, double dsavm, int ij ) /
double bmij(double ps, double cov, int ncovmodel, double x, int nlstate, double ***prevacurrent, int ij )	double bmij(double ps, double cov, int ncovmodel, double x, int nlstate, double ***prevacurrent, int ij )
{	{
/* Computes the backward probability at age agefin and covariate ij	/* Computes the backward probability at age agefin, cov[2], and covariate combination 'ij'. In fact cov is already filled and x too.
* and returns in ps as well as bmij.	* Call to pmij(cov and x), call to cross prevalence, sums and inverses, left multiply, and returns in ps as well as bmij.
*/	*/
int i, ii, j,k;	int i, ii, j,k;

double out, pmij();	double out, pmij();
double sumnew=0.;	double sumnew=0.;
double agefin;	double agefin;
	double k3=0.; /* constant of the w_x diagonal matrix (in order for B to sum to 1 even for death state) */
double dnewm, dsavm, **doldm;	double dnewm, dsavm, **doldm;
double **bbmij;	double **bbmij;

Line 2824 double pmij(double ps, double *cov,	Line 3104 double pmij(double ps, double *cov,
dsavm=ddsavms;	dsavm=ddsavms;

agefin=cov[2];	agefin=cov[2];
	/* Bx = Diag(w_x) P_x Diag(Sum_i w^i_x p^ij_x */
/* bmij // age is cov[2], ij is included in cov, but we need for	/* bmij // age is cov[2], ij is included in cov, but we need for
the observed prevalence (with this covariate ij) */	the observed prevalence (with this covariate ij) at beginning of transition */
dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate);	/* dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
/* We do have the matrix Px in savm and we need pij */
	/* P_x */
	pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /This is forward probability from agefin to agefin + stepm /
	/* outputs pmmij which is a stochastic matrix in row */

	/* Diag(w_x) */
	/* Rescaling the cross-sectional prevalence: Problem with prevacurrent which can be zero */
	sumnew=0.;
	/for (ii=1;ii<=nlstate+ndeath;ii++){/
	for (ii=1;ii<=nlstate;ii++){ /* Only on live states */
	/* printf(" agefin=%d, ii=%d, ij=%d, prev=%f\n",(int)agefin,ii, ij, prevacurrent[(int)agefin][ii][ij]); */
	sumnew+=prevacurrent[(int)agefin][ii][ij];
	}
	if(sumnew >0.01){ /* At least some value in the prevalence */
	for (ii=1;ii<=nlstate+ndeath;ii++){
	for (j=1;j<=nlstate+ndeath;j++)
	doldm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij]/sumnew : 0.0);
	}
	}else{
	for (ii=1;ii<=nlstate+ndeath;ii++){
	for (j=1;j<=nlstate+ndeath;j++)
	doldm[ii][j]=(ii==j ? 1./nlstate : 0.0);
	}
	/* if(sumnew <0.9){ */
	/* printf("Problem internal bmij B: sum on i wi <0.9: j=%d, sum_i wi=%lf,agefin=%d\n",j,sumnew, (int)agefin); */
	/* } */
	}
	k3=0.0; /* We put the last diagonal to 0 */
	for (ii=nlstate+1;ii<=nlstate+ndeath;ii++){
	doldm[ii][ii]= k3;
	}
	/* End doldm, At the end doldm is diag[(w_i)] */

	/* Left product of this diag matrix by pmmij=Px (dnewm=dsavmdoldm): diag[(w_i)Px */
	bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* was a Bug Valgrind */

	/* Diag(Sum_i w^i_x p^ij_x, should be the prevalence at age x+stepm */
	/* w1 p11 + w2 p21 only on live states N1./N..N11/N1. + N2./N..N21/N2.=(N11+N21)/N..=N.1/N.. */
for (j=1;j<=nlstate+ndeath;j++){	for (j=1;j<=nlstate+ndeath;j++){
sumnew=0.; /* w1 p11 + w2 p21 only on live states */	sumnew=0.;
for (ii=1;ii<=nlstate;ii++){	for (ii=1;ii<=nlstate;ii++){
sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij];	/* sumnew+=dsavm[ii][j]prevacurrent[(int)agefin][ii][ij]; /
	sumnew+=pmmij[ii][j]doldm[ii][ii]; / Yes prevalence at beginning of transition */
} /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */	} /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
for (ii=1;ii<=nlstate+ndeath;ii++){	for (ii=1;ii<=nlstate+ndeath;ii++){
if(sumnew >= 1.e-10){
/* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */	/* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
/* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */	/* dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
/* }else if(agefin >= agemaxpar+stepm/YEARM){ */	/* }else if(agefin >= agemaxpar+stepm/YEARM){ */
/* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */	/* dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
/* }else */	/* }else */
doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);	dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0);
}else{
;
/* printf("ii=%d, i=%d, doldm=%lf dsavm=%lf, probs=%lf, sumnew=%lf,agefin=%d\n",ii,j,doldm[ii][j],dsavm[ii][j],prevacurrent[(int)agefin][ii][ij],sumnew, (int)agefin); */
}
} /End ii /	} /End ii /
} /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */	} /* End j, At the end dsavm is diag[1/(w_1p1i+w_2 p2i)] for ALL states even if the sum is only for live states */
/* left Product of this diag matrix by dsavm=Px (newm=dsavmdoldm) /
bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */	ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* was a Bug Valgrind */
/* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten\/ /	/* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
/* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] \/ /
/* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] \/ /
/* left Product of this matrix by diag matrix of prevalences (savm) */
for (j=1;j<=nlstate+ndeath;j++){
for (ii=1;ii<=nlstate+ndeath;ii++){
dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);
}
} /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */
ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */
/* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
/* end bmij */	/* end bmij */
return ps;	return ps; /pointer is unchanged /
}	}
/************* transition probabilities *************/	/************* transition probabilities *************/

Line 2930 double bpmij(double ps, double *cov,	Line 3234 double bpmij(double ps, double *cov,
ps[ii][ii]=1;	ps[ii][ii]=1;
}	}
}	}
/* Added for backcast / / Transposed matrix too */	/* Added for prevbcast / / Transposed matrix too */
for(jj=1; jj<= nlstate+ndeath; jj++){	for(jj=1; jj<= nlstate+ndeath; jj++){
s1=0.;	s1=0.;
for(ii=1; ii<= nlstate+ndeath; ii++){	for(ii=1; ii<= nlstate+ndeath; ii++){
Line 3074 double *hpxij(double *po, int nhstep	Line 3378 double *hpxij(double *po, int nhstep
}	}
for(i=1; i<=nlstate+ndeath; i++)	for(i=1; i<=nlstate+ndeath; i++)
for(j=1;j<=nlstate+ndeath;j++) {	for(j=1;j<=nlstate+ndeath;j++) {
po[i][j][h]=newm[i][j];	po[i][j][h]=newm[i][j];
/if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);/	/if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);/
}	}
/printf("h=%d ",h);/	/printf("h=%d ",h);/
} /* end h */	} /* end h */
/* printf("\n H=%d \n",h); */	/* printf("\n H=%d \n",h); */
return po;	return po;
}	}

/*********** Higher Back Matrix Product *************/	/*********** Higher Back Matrix Product *************/
/* double *hbxij(double po, int nhstepm, double age, int hstepm, double x, double *prevacurrent, int nlstate, int stepm, double oldm, double savm, double dnewm, double doldm, double dsavm, int ij ) */	/* double *hbxij(double po, int nhstepm, double age, int hstepm, double x, double *prevacurrent, int nlstate, int stepm, double oldm, double savm, double dnewm, double doldm, double dsavm, int ij ) */
double *hbxij(double po, int nhstepm, double age, int hstepm, double x, double ***prevacurrent, int nlstate, int stepm, int ij )	double *hbxij(double po, int nhstepm, double age, int hstepm, double x, double ***prevacurrent, int nlstate, int stepm, int ij, int nres )
{	{
/* Computes the transition matrix starting at age 'age' over	/* For a combination of dummy covariate ij, computes the transition matrix starting at age 'age' over
'nhstepmhstepmstepm' months (i.e. until	'nhstepmhstepmstepm' months (i.e. until
age (in years) age+nhstepmhstepmstepm/12) by multiplying	age (in years) age+nhstepmhstepmstepm/12) by multiplying
nhstepm*hstepm matrices.	nhstepm*hstepm matrices.
Line 3095 double *hbxij(double *po, int nhstep	Line 3399 double *hbxij(double *po, int nhstep
(typically every 2 years instead of every month which is too big	(typically every 2 years instead of every month which is too big
for the memory).	for the memory).
Model is determined by parameters x and covariates have to be	Model is determined by parameters x and covariates have to be
included manually here.	included manually here. Then we use a call to bmij(x and cov)
	The addresss of po (p3mat allocated to the dimension of nhstepm) should be stored for output
*/	*/

int i, j, d, h, k;	int i, j, d, h, k;
double **out, cov[NCOVMAX+1];	double out, cov[NCOVMAX+1], bmij();
double **newm;	double newm, *newmm;
double agexact;	double agexact;
double agebegin, ageend;	double agebegin, ageend;
double oldm, savm;	double oldm, savm;

oldm=oldms;savm=savms;	newmm=po; /* To be saved */
	oldm=oldms;savm=savms; /* Global pointers */
/* 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++)
for (j=1;j<=nlstate+ndeath;j++){	for (j=1;j<=nlstate+ndeath;j++){
Line 3119 double *hbxij(double *po, int nhstep	Line 3424 double *hbxij(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; /* age just before transition */	agexact=age-( (h-1)hstepm + (d) )stepm/YEARM; /* age just before transition, d or d-1? */
/* agexact=age+((h-1)hstepm + (d-1))stepm/YEARM; /\* age just before transition \/ /	/* 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;
for (k=1; k<=cptcovn;k++)	for (k=1; k<=cptcovn;k++){
cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];	/* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
/* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */	/* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; \/ /
for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */	cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
/* cov[2+Tage[k]]=cov[2+Tage[k]]cov[2]; /	/* printf("hbxij Dummy agexact=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agexact,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];	}
/* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]cov[2]; /	for (k=1; k<=nsq;k++) { /* For single varying covariates only */
for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */	/* Here comes the value of quantitative after renumbering k with single quantitative covariates */
	cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
	/* printf("hPxij Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
	}
	for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 */
	if(Dummy[Tvar[Tage[k]]]){
	cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
	} else{
	cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
	}
	/* printf("hBxij Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
	}
	for (k=1; k<=cptcovprod;k++){ /* Useless because included in cptcovn */
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; /	}


/printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);/	/printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);/
/printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);/	/printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);/

/* Careful transposed matrix */	/* Careful transposed matrix */
/* age is in cov[2] */	/* age is in cov[2], prevacurrent at beginning of transition. */
/* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */	/* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
/* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */	/* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\	out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
Line 3164 double *hbxij(double *po, int nhstep	Line 3480 double *hbxij(double *po, int nhstep
for(i=1; i<=nlstate+ndeath; i++)	for(i=1; i<=nlstate+ndeath; i++)
for(j=1;j<=nlstate+ndeath;j++) {	for(j=1;j<=nlstate+ndeath;j++) {
po[i][j][h]=newm[i][j];	po[i][j][h]=newm[i][j];
/if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);/	/* if(h==nhstepm) */
	/* printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]); */
}	}
/printf("h=%d ",h);/	/* printf("h=%d %.1f ",h, agexact); */
} /* end h */	} /* end h */
/* printf("\n H=%d \n",h); */	/* printf("\n H=%d nhs=%d \n",h, nhstepm); */
return po;	return po;
}	}

Line 3550 double funcone( double *x)	Line 3867 double funcone( double *x)
/* Fixed */	/* Fixed */
/* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */	/* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
/* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products \/ /	/* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products \/ /
for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */	for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products // Missing values are set to -1 but should be dropped */
cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, only V1 is fixed (k=6)*/	cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, only V1 is fixed (k=6)*/
/* cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i]; */	/* cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i]; */
/* cov[2+6]=covar[Tvar[6]][i]; */	/* cov[2+6]=covar[Tvar[6]][i]; */
Line 3596 double funcone( double *x)	Line 3913 double funcone( double *x)
agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */	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 */	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 */	for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */
	/* for(d=0; d<=0; d++){ /\* Delay between two effective waves Only one matrix to speed up\/ /
/*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][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.*/	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]+dstepm/YEARM; / Here d is needed */
cov[2]=agexact;	cov[2]=agexact;
if(nagesqr==1)	if(nagesqr==1)
cov[3]= agexact*agexact;	cov[3]= agexact*agexact;
Line 3622 double funcone( double *x)	Line 3940 double funcone( double *x)
s1=s[mw[mi][i]][i];	s1=s[mw[mi][i]][i];
s2=s[mw[mi+1][i]][i];	s2=s[mw[mi+1][i]][i];
/* if(s2==-1){ */	/* if(s2==-1){ */
/* printf(" s1=%d, s2=%d i=%d \n", s1, s2, i); */	/* printf(" ERROR s1=%d, s2=%d i=%d \n", s1, s2, i); */
/* /\* exit(1); \/ /	/* /\* exit(1); \/ /
/* } */	/* } */
bbh=(double)bh[mi][i]/(double)stepm;	bbh=(double)bh[mi][i]/(double)stepm;
Line 3655 double funcone( double *x)	Line 3973 double funcone( double *x)
fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\	fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
%11.6f %11.6f %11.6f ", \	%11.6f %11.6f %11.6f ", \
num[i], agebegin, ageend, 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,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: 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;
fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);	fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
Line 3676 return -l;	Line 3994 return -l;


/************* function likelione *********/	/************* function likelione *********/
void likelione(FILE ficres,double p[], int npar, int nlstate, int globpri, long ipmx, double sw, double fretone, double (funcone)(double []))	void likelione(FILE ficres,double p[], int npar, int nlstate, int globpri, long ipmx, double sw, double fretone, double (func)(double []))
{	{
/* This routine should help understanding what is done with	/* This routine should help understanding what is done with
the selection of individuals/waves and	the selection of individuals/waves and
Line 3700 void likelione(FILE *ficres,double p[],	Line 4018 void likelione(FILE *ficres,double p[],
fprintf(ficresilk," -2gipw/gswweight*ll(total)\n");	fprintf(ficresilk," -2gipw/gswweight*ll(total)\n");
}	}

fretone=(funcone)(p);	fretone=(func)(p);
if(*globpri !=0){	if(*globpri !=0){
fclose(ficresilk);	fclose(ficresilk);
if (mle ==0)	if (mle ==0)
Line 3708 void likelione(FILE *ficres,double p[],	Line 4026 void likelione(FILE *ficres,double p[],
else if(mle >=1)	else if(mle >=1)
fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);	fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));	fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
	fprintf(fichtm,"\n<br>Equation of the model: <b>model=1+age+%s</b><br>\n",model);

for (k=1; k<= nlstate ; k++) {	for (k=1; k<= nlstate ; k++) {
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> \	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> \
Line 4100 void ludcmp(double *a, int n, int indx	Line 4418 void ludcmp(double *a, int n, int indx
big=0.0;	big=0.0;
for (j=1;j<=n;j++)	for (j=1;j<=n;j++)
if ((temp=fabs(a[i][j])) > big) big=temp;	if ((temp=fabs(a[i][j])) > big) big=temp;
if (big == 0.0) nrerror("Singular matrix in routine ludcmp");	if (big == 0.0){
	printf(" Singular Hessian matrix at row %d:\n",i);
	for (j=1;j<=n;j++) {
	printf(" a[%d][%d]=%f,",i,j,a[i][j]);
	fprintf(ficlog," a[%d][%d]=%f,",i,j,a[i][j]);
	}
	fflush(ficlog);
	fclose(ficlog);
	nrerror("Singular matrix in routine ludcmp");
	}
vv[i]=1.0/big;	vv[i]=1.0/big;
}	}
for (j=1;j<=n;j++) {	for (j=1;j<=n;j++) {
Line 4166 void pstamp(FILE *fichier)	Line 4493 void pstamp(FILE *fichier)
fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);	fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
}	}

	void date2dmy(double date,double day, double month, double *year){
	double yp=0., yp1=0., yp2=0.;

	yp1=modf(date,&yp);/* extracts integral of date in yp and
	fractional in yp1 */
	*year=yp;
	yp2=modf((yp1*12),&yp);
	*month=yp;
	yp1=modf((yp2*30.5),&yp);
	*day=yp;
	if(day==0) day=1;
	if(month==0) month=1;
	}



/********** Frequencies ******************/	/********** Frequencies ******************/
void freqsummary(char fileres[], int iagemin, int iagemax, int s, double agev, int nlstate, int imx, \	void freqsummary(char fileres[], double p[], double pstart[], int iagemin, int iagemax, int s, double agev, int nlstate, int imx, \
int Tvaraff, int invalidvarcomb, int *nbcode, int ncodemax,double mint,double anint, char strstart[], \	int Tvaraff, int invalidvarcomb, int *nbcode, int ncodemax,double mint,double anint, char strstart[], \
int firstpass, int lastpass, int stepm, int weightopt, char model[])	int firstpass, int lastpass, int stepm, int weightopt, char model[])
{ /* Some frequencies */	{ /* Some frequencies as well as proposing some starting values */

int i, m, jk, j1, bool, z1,j, k, iv;	int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0, s1=1, s2=1;
int iind=0, iage=0;	int iind=0, iage=0;
int mi; /* Effective wave */	int mi; /* Effective wave */
int first;	int first;
double **freq; / Frequencies */	double **freq; / Frequencies */
double *meanq;	double x, y, a=0.,b=0.,r=1., sa=0., sb=0.; /* for regression, y=b+mx and r is the correlation coefficient /
	int no=0, linreg(int ifi, int ila, int no, const double x[], const double y[], double a, double* b, double* r, double* sa, double * sb);
	double meanq, stdq, *idq;
double **meanqt;	double **meanqt;
double pp, prop, posprop, *pospropt;	double pp, prop, posprop, *pospropt;
double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;	double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
Line 4185 void freqsummary(char fileres[], int ia	Line 4530 void freqsummary(char fileres[], int ia
double agebegin, ageend;	double agebegin, ageend;

pp=vector(1,nlstate);	pp=vector(1,nlstate);
prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);	prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */	posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */	pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
/* prop=matrix(1,nlstate,iagemin,iagemax+3); */	/* prop=matrix(1,nlstate,iagemin,iagemax+3); */
meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */	meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
	stdq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
	idq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
meanqt=matrix(1,lastpass,1,nqtveff);	meanqt=matrix(1,lastpass,1,nqtveff);
strcpy(fileresp,"P_");	strcpy(fileresp,"P_");
strcat(fileresp,fileresu);	strcat(fileresp,fileresu);
Line 4229 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4576 Title=%s <br>Datafile=%s Firstpass=%d La
}	}
fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions of the model, by age at begin of transition, and covariate value at the begin of transition (if the covariate is a varying covariate) </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);	fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions of the model, by age at begin of transition, and covariate value at the begin of transition (if the covariate is a varying covariate) </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);

freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);	y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
	x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
	freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
j1=0;	j1=0;

/* j=ncoveff; /\* Only fixed dummy covariates \/ /	/* j=ncoveff; /\* Only fixed dummy covariates \/ /
j=cptcoveff; /* Only dummy covariates of the model */	j=cptcoveff; /* Only dummy covariates of the model */
if (cptcovn<1) {j=1;ncodemax[1]=1;}	if (cptcovn<1) {j=1;ncodemax[1]=1;}

first=1;

/* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:	/* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
reference=low_education V1=0,V2=0	reference=low_education V1=0,V2=0
Line 4244 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4592 Title=%s <br>Datafile=%s Firstpass=%d La
high_educ V1=0 V2=1	high_educ V1=0 V2=1
Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff	Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
*/	*/
	dateintsum=0;
for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on covariates combination in order of model, excluding quantitatives V4=0, V3=0 for example, fixed or varying covariates */	k2cpt=0;
posproptt=0.;
/*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);	if(cptcoveff == 0 )
scanf("%d", i);*/	nl=1; /* Constant and age model only */
for (i=-5; i<=nlstate+ndeath; i++)	else
for (jk=-5; jk<=nlstate+ndeath; jk++)	nl=2;

	/* if a constant only model, one pass to compute frequency tables and to write it on ficresp */
	/* Loop on nj=1 or 2 if dummy covariates j!=0
	* Loop on j1(1 to 2**cptcoveff) covariate combination
	* freq[s1][s2][iage] =0.
	* Loop on iind
	* ++freq[s1][s2][iage] weighted
	* end iind
	* if covariate and j!0
	* headers Variable on one line
	* endif cov j!=0
	* header of frequency table by age
	* Loop on age
	* pp[s1]+=freq[s1][s2][iage] weighted
	* pos+=freq[s1][s2][iage] weighted
	* Loop on s1 initial state
	* fprintf(ficresp
	* end s1
	* end age
	* if j!=0 computes starting values
	* end compute starting values
	* end j1
	* end nl
	*/
	for (nj = 1; nj <= nl; nj++){ /* nj= 1 constant model, nl number of loops. */
	if(nj==1)
	j=0; /* First pass for the constant */
	else{
	j=cptcoveff; /* Other passes for the covariate values */
	}
	first=1;
	for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on all covariates combination of the model, excluding quantitatives, V4=0, V3=0 for example, fixed or varying covariates */
	posproptt=0.;
	/*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
	scanf("%d", i);*/
	for (i=-5; i<=nlstate+ndeath; i++)
	for (s2=-5; s2<=nlstate+ndeath; s2++)
	for(m=iagemin; m <= iagemax+3; m++)
	freq[i][s2][m]=0;

	for (i=1; i<=nlstate; i++) {
for(m=iagemin; m <= iagemax+3; m++)	for(m=iagemin; m <= iagemax+3; m++)
freq[i][jk][m]=0;	prop[i][m]=0;
	posprop[i]=0;
for (i=1; i<=nlstate; i++) {	pospropt[i]=0;
for(m=iagemin; m <= iagemax+3; m++)	}
prop[i][m]=0;	for (z1=1; z1<= nqfveff; z1++) { /* zeroing for each combination j1 as well as for the total */
posprop[i]=0;	idq[z1]=0.;
pospropt[i]=0;	meanq[z1]=0.;
}	stdq[z1]=0.;
/* for (z1=1; z1<= nqfveff; z1++) { */	}
/* meanq[z1]+=0.; */	/* for (z1=1; z1<= nqtveff; z1++) { */
/* for(m=1;m<=lastpass;m++){ */	/* for(m=1;m<=lastpass;m++){ */
/* meanqt[m][z1]=0.; */	/* meanqt[m][z1]=0.; */
/* } */	/* } */
/* } */	/* } */
	/* dateintsum=0; */
dateintsum=0;	/* k2cpt=0; */
k2cpt=0;
/* For that combination of covariate j1, we count and print the frequencies in one pass */	/* For that combination of covariates j1 (V4=1 V3=0 for example), we count and print the frequencies in one pass */
for (iind=1; iind<=imx; iind++) { /* For each individual iind */	for (iind=1; iind<=imx; iind++) { /* For each individual iind */
bool=1;	bool=1;
if(anyvaryingduminmodel==0){ /* If All fixed covariates */	if(j !=0){
if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */	if(anyvaryingduminmodel==0){ /* If All fixed covariates */
/* for (z1=1; z1<= nqfveff; z1++) { */	if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
/* meanq[z1]+=coqvar[Tvar[z1]][iind]; /\* Computes mean of quantitative with selected filter \/ /	for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */
/* } */	/* if(Tvaraff[z1] ==-20){ */
for (z1=1; z1<=cptcoveff; z1++) {	/* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; \/ /
/* if(Tvaraff[z1] ==-20){ */	/* }else if(Tvaraff[z1] ==-10){ */
/* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; \/ /	/* /\* sumnew+=coqvar[z1][iind]; \/ /
/* }else if(Tvaraff[z1] ==-10){ */	/* }else */
/* /\* sumnew+=coqvar[z1][iind]; \/ /	if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */
/* }else */	/* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */
if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){	bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */
/* Tests if this individual iind responded to j1 (V4=1 V3=0) */	/* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n",
bool=0;	bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
/* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n",	j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),	/* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/	} /* Onlyf fixed */
/* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/	} /* end z1 */
} /* Onlyf fixed */	} /* cptcovn > 0 */
} /* end z1 */	} /* end any */
} /* cptcovn > 0 */	}/* end j==0 */
} /* end any */	if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */
if (bool==1){ /* We selected an individual iind satisfying combination j1 or all fixed */	/* for(m=firstpass; m<=lastpass; m++){ */
/* for(m=firstpass; m<=lastpass; m++){ */	for(mi=1; mi<wav[iind];mi++){ /* For each wave */
for(mi=1; mi<wav[iind];mi++){ /* For that wave */	m=mw[mi][iind];
m=mw[mi][iind];	if(j!=0){
if(anyvaryingduminmodel==1){ /* Some are varying covariates */	if(anyvaryingduminmodel==1){ /* Some are varying covariates */
for (z1=1; z1<=cptcoveff; z1++) {	for (z1=1; z1<=cptcoveff; z1++) {
if( Fixed[Tmodelind[z1]]==1){	if( Fixed[Tmodelind[z1]]==1){
iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;	iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */	if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality. If covariate's
bool=0;	value is -1, we don't select. It differs from the
}else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */	constant and age model which counts them. */
if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {	bool=0; /* not selected */
bool=0;	}else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
	if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
	bool=0;
	}
	}
}	}
	}/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop */
	} /* end j==0 */
	/* bool =0 we keep that guy which corresponds to the combination of dummy values */
	if(bool==1){ /Selected /
	/* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
	and mw[mi+1][iind]. dh depends on stepm. */
	agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
	ageend=agev[m][iind]+(dh[m][iind])stepm/YEARM; / Age at end of wave and transition */
	if(m >=firstpass && m <=lastpass){
	k2=anint[m][iind]+(mint[m][iind]/12.);
	/if ((k2>=dateprev1) && (k2<=dateprev2)) {/
	if(agev[m][iind]==0) agev[m][iind]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
	if(agev[m][iind]==1) agev[m][iind]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
	if (s[m][iind]>0 && s[m][iind]<=nlstate) /* If status at wave m is known and a live state */
	prop[s[m][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
	if (m<lastpass) {
	/* if(s[m][iind]==4 && s[m+1][iind]==4) */
	/* printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind]); */
	if(s[m][iind]==-1)
	printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));
	freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
	for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean on known values only */
	if(!isnan(covar[ncovcol+z1][iind])){
	idq[z1]=idq[z1]+weight[iind];
	meanq[z1]+=covar[ncovcol+z1][iind]weight[iind]; / Computes mean of quantitative with selected filter */
	/* stdq[z1]+=covar[ncovcol+z1][iind]covar[ncovcol+z1][iind]weight[iind]weight[iind]; //error/
	stdq[z1]+=covar[ncovcol+z1][iind]covar[ncovcol+z1][iind]weight[iind]; /* weight[iind];/ /* Computes mean of quantitative with selected filter */
	}
	}
	/* if((int)agev[m][iind] == 55) */
	/* printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */
	/* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
	freq[s[m][iind]][s[m+1][iind]][iagemax+3] += weight[iind]; /* Total is in iagemax+3 // At age of beginning of transition, where status is known */
	}
	} /* end if between passes */
	if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99) && (j==0)) {
	dateintsum=dateintsum+k2; /* on all covariates ?*/
	k2cpt++;
	/* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
}	}
}	}else{
}/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop */	bool=1;
/* bool =0 we keep that guy which corresponds to the combination of dummy values */	}/* end bool 2 */
if(bool==1){	} /* end m */
/* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]	/* for (z1=1; z1<= nqfveff; z1++) { /\* Quantitative variables, calculating mean \/ /
and mw[mi+1][iind]. dh depends on stepm. */	/* idq[z1]=idq[z1]+weight[iind]; */
agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/	/* meanq[z1]+=covar[ncovcol+z1][iind]weight[iind]; /\ Computes mean of quantitative with selected filter \/ /
ageend=agev[m][iind]+(dh[m][iind])stepm/YEARM; / Age at end of wave and transition */	/* stdq[z1]+=covar[ncovcol+z1][iind]covar[ncovcol+z1][iind]weight[iind]weight[iind]; /\ weight[iind];\/ /\* Computes mean of quantitative with selected filter \/ /
if(m >=firstpass && m <=lastpass){	/* } */
k2=anint[m][iind]+(mint[m][iind]/12.);	} /* end bool */
/if ((k2>=dateprev1) && (k2<=dateprev2)) {/	} /* end iind = 1 to imx */
if(agev[m][iind]==0) agev[m][iind]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */	/* prop[s][age] is feeded for any initial and valid live state as well as
if(agev[m][iind]==1) agev[m][iind]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */	freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
if (s[m][iind]>0 && s[m][iind]<=nlstate) /* If status at wave m is known and a live state */
prop[s[m][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
if (m<lastpass) {	/* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
/* if(s[m][iind]==4 && s[m+1][iind]==4) */	if(cptcoveff==0 && nj==1) /* no covariate and first pass */
/* printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind]); */	pstamp(ficresp);
if(s[m][iind]==-1)	if (cptcoveff>0 && j!=0){
printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));	pstamp(ficresp);
freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */	printf( "\n#********** Variable ");
/* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */	fprintf(ficresp, "\n#********** Variable ");
freq[s[m][iind]][s[m+1][iind]][iagemax+3] += weight[iind]; /* Total is in iagemax+3 // At age of beginning of transition, where status is known */	fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
}	fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
} /* end if between passes */	fprintf(ficlog, "\n#********** Variable ");
if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {	for (z1=1; z1<=cptcoveff; z1++){
dateintsum=dateintsum+k2;	if(!FixedV[Tvaraff[z1]]){
k2cpt++;	printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
/* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */	fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
}	fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
} /* end bool 2 */	fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
} /* end m */	fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
} /* end bool */	}else{
} /* end iind = 1 to imx */	printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
/* prop[s][age] is feeded for any initial and valid live state as well as	fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */	fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
	fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
	fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
/* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/	}
pstamp(ficresp);	}
if (cptcoveff>0){	printf( "**********\n#");
fprintf(ficresp, "\n#********** Variable ");	fprintf(ficresp, "**********\n#");
fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");	fprintf(ficresphtm, "**********</h3>\n");
fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");	fprintf(ficresphtmfr, "**********</h3>\n");
fprintf(ficlog, "\n#********** Variable ");	fprintf(ficlog, "**********\n");
for (z1=1; z1<=cptcoveff; z1++){	}
if(DummyV[z1]){	/*
fprintf(ficresp, "V%d (fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	Printing means of quantitative variables if any
fprintf(ficresphtm, "V%d (fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	*/
fprintf(ficresphtmfr, "V%d (fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	for (z1=1; z1<= nqfveff; z1++) {
fprintf(ficlog, "V%d (fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	fprintf(ficlog,"Mean of fixed quantitative variable V%d on %.3g (weighted) individuals sum=%f", ncovcol+z1, idq[z1], meanq[z1]);
	fprintf(ficlog,", mean=%.3g\n",meanq[z1]/idq[z1]);
	if(weightopt==1){
	printf(" Weighted mean and standard deviation of");
	fprintf(ficlog," Weighted mean and standard deviation of");
	fprintf(ficresphtmfr," Weighted mean and standard deviation of");
	}
	/* mu = \frac{w x}{\sum w}
	var = \frac{\sum w (x-mu)^2}{\sum w} = \frac{w x^2}{\sum w} - mu^2
	*/
	printf(" fixed quantitative variable V%d on %.3g (weighted) representatives of the population : %8.5g (%8.5g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1]));
	fprintf(ficlog," fixed quantitative variable V%d on %.3g (weighted) representatives of the population : %8.5g (%8.5g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1]));
	fprintf(ficresphtmfr," fixed quantitative variable V%d on %.3g (weighted) representatives of the population : %8.5g (%8.5g)<p>\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1]));
	}
	/* for (z1=1; z1<= nqtveff; z1++) { */
	/* for(m=1;m<=lastpass;m++){ */
	/* fprintf(ficresphtmfr,"V quantitative id %d, pass id=%d, mean=%f<p>\n", z1, m, meanqt[m][z1]); */
	/* } */
	/* } */

	fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
	if((cptcoveff==0 && nj==1)\|\| nj==2 ) /* no covariate and first pass */
	fprintf(ficresp, " Age");
	if(nj==2) for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " V%d=%d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
	for(i=1; i<=nlstate;i++) {
	if((cptcoveff==0 && nj==1)\|\| nj==2 ) fprintf(ficresp," 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);
	}
	if((cptcoveff==0 && nj==1)\|\| nj==2 ) 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(s2=-1; s2 <=nlstate+ndeath; s2++){
	for(m=-1; m <=nlstate+ndeath; m++){
	if(s2!=0 && m!=0)
	fprintf(ficresphtmfr,"<th>%d%d</th> ",s2,m);
	}
	}
	fprintf(ficresphtmfr, "\n");

	/* For each age */
	for(iage=iagemin; iage <= iagemax+3; iage++){
	fprintf(ficresphtm,"<tr>");
	if(iage==iagemax+1){
	fprintf(ficlog,"1");
	fprintf(ficresphtmfr,"<tr><th>0</th> ");
	}else if(iage==iagemax+2){
	fprintf(ficlog,"0");
	fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
	}else if(iage==iagemax+3){
	fprintf(ficlog,"Total");
	fprintf(ficresphtmfr,"<tr><th>Total</th> ");
}else{	}else{
fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
}
}
fprintf(ficresp, "**********\n#");
fprintf(ficresphtm, "**********</h3>\n");
fprintf(ficresphtmfr, "**********</h3>\n");
fprintf(ficlog, "**********\n");
}
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(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
}
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(iage=iagemin; iage <= iagemax+3; iage++){
fprintf(ficresphtm,"<tr>");
if(iage==iagemax+1){
fprintf(ficlog,"1");
fprintf(ficresphtmfr,"<tr><th>0</th> ");
}else if(iage==iagemax+2){
fprintf(ficlog,"0");
fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
}else if(iage==iagemax+3){
fprintf(ficlog,"Total");
fprintf(ficresphtmfr,"<tr><th>Total</th> ");
}else{
if(first==1){
first=0;
printf("See log file for details...\n");
}
fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
fprintf(ficlog,"Age %d", iage);
}
for(jk=1; jk <=nlstate ; jk++){
for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
pp[jk] += freq[jk][m][iage];
}
for(jk=1; jk <=nlstate ; jk++){
for(m=-1, pos=0; m <=0 ; m++)
pos += freq[jk][m][iage];
if(pp[jk]>=1.e-10){
if(first==1){	if(first==1){
printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);	first=0;
	printf("See log file for details...\n");
	}
	fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
	fprintf(ficlog,"Age %d", iage);
	}
	for(s1=1; s1 <=nlstate ; s1++){
	for(m=-1, pp[s1]=0; m <=nlstate+ndeath ; m++)
	pp[s1] += freq[s1][m][iage];
	}
	for(s1=1; s1 <=nlstate ; s1++){
	for(m=-1, pos=0; m <=0 ; m++)
	pos += freq[s1][m][iage];
	if(pp[s1]>=1.e-10){
	if(first==1){
	printf(" %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
	}
	fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
	}else{
	if(first==1)
	printf(" %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
	fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
}	}
fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
}else{
if(first==1)
printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
}	}
}

for(jk=1; jk <=nlstate ; jk++){	for(s1=1; s1 <=nlstate ; s1++){
/* posprop[jk]=0; */	/* posprop[s1]=0; */
for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */	for(m=0, pp[s1]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
pp[jk] += freq[jk][m][iage];	pp[s1] += freq[s1][m][iage];
} /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */	} /* pp[s1] is the total number of transitions starting from state s1 and any ending status until this age */

for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){	for(s1=1,pos=0, pospropta=0.; s1 <=nlstate ; s1++){
pos += pp[jk]; /* pos is the total number of transitions until this age */	pos += pp[s1]; /* pos is the total number of transitions until this age */
posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state	posprop[s1] += prop[s1][iage]; /* prop is the number of transitions from a live state
from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */	from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state	pospropta += prop[s1][iage]; /* prop is the number of transitions from a live state
from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */	from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
}	}
for(jk=1; jk <=nlstate ; jk++){
if(pos>=1.e-5){	/* Writing ficresp */
if(first==1)	if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);	if( iage <= iagemax){
fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);	fprintf(ficresp," %d",iage);
}else{	}
if(first==1)	}else if( nj==2){
printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);	if( iage <= iagemax){
fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);	fprintf(ficresp," %d",iage);
	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
	}
}	}
if( iage <= iagemax){	for(s1=1; s1 <=nlstate ; s1++){
if(pos>=1.e-5){	if(pos>=1.e-5){
fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);	if(first==1)
fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);	printf(" %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
/probs[iage][jk][j1]= pp[jk]/pos;/	fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
/printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);/	}else{
}	if(first==1)
else{	printf(" %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);	fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);	}
	if( iage <= iagemax){
	if(pos>=1.e-5){
	if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
	fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
	}else if( nj==2){
	fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
	}
	fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
	/probs[iage][s1][j1]= pp[s1]/pos;/
	/printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);/
	} else{
	if((cptcoveff==0 && nj==1)\|\| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta);
	fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[s1][iage],pospropta);
	}
}	}
}	pospropt[s1] +=posprop[s1];
pospropt[jk] +=posprop[jk];	} /* end loop s1 */
} /* end loop jk */	/* pospropt=0.; */
/* pospropt=0.; */	for(s1=-1; s1 <=nlstate+ndeath; s1++){
for(jk=-1; jk <=nlstate+ndeath; jk++){	for(m=-1; m <=nlstate+ndeath; m++){
for(m=-1; m <=nlstate+ndeath; m++){	if(freq[s1][m][iage] !=0 ) { /* minimizing output */
if(freq[jk][m][iage] !=0 ) { /* minimizing output */	if(first==1){
if(first==1){	printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]);
printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);	}
	/* printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]); */
	fprintf(ficlog," %d%d=%.0f",s1,m,freq[s1][m][iage]);
}	}
fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);	if(s1!=0 && m!=0)
	fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[s1][m][iage]);
}	}
if(jk!=0 && m!=0)	} /* end loop s1 */
fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);	posproptt=0.;
	for(s1=1; s1 <=nlstate; s1++){
	posproptt += pospropt[s1];
}	}
} /* end loop jk */	fprintf(ficresphtmfr,"</tr>\n ");
posproptt=0.;
for(jk=1; jk <=nlstate; jk++){
posproptt += pospropt[jk];
}
fprintf(ficresphtmfr,"</tr>\n ");
if(iage <= iagemax){
fprintf(ficresp,"\n");
fprintf(ficresphtm,"</tr>\n");	fprintf(ficresphtm,"</tr>\n");
	if((cptcoveff==0 && nj==1)\|\| nj==2 ) {
	if(iage <= iagemax)
	fprintf(ficresp,"\n");
	}
	if(first==1)
	printf("Others in log...\n");
	fprintf(ficlog,"\n");
	} /* end loop age iage */

	fprintf(ficresphtm,"<tr><th>Tot</th>");
	for(s1=1; s1 <=nlstate ; s1++){
	if(posproptt < 1.e-5){
	fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[s1],posproptt);
	}else{
	fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[s1]/posproptt,pospropt[s1],posproptt);
	}
}	}
if(first==1)	fprintf(ficresphtm,"</tr>\n");
printf("Others in log...\n");	fprintf(ficresphtm,"</table>\n");
fprintf(ficlog,"\n");	fprintf(ficresphtmfr,"</table>\n");
} /* end loop age iage */
fprintf(ficresphtm,"<tr><th>Tot</th>");
for(jk=1; jk <=nlstate ; jk++){
if(posproptt < 1.e-5){	if(posproptt < 1.e-5){
fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);	fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
	fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
	fprintf(ficlog,"# This combination (%d) is not valid and no result will be produced\n",j1);
	printf("# This combination (%d) is not valid and no result will be produced\n",j1);
	invalidvarcomb[j1]=1;
}else{	}else{
fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);	fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
	invalidvarcomb[j1]=0;
}	}
}	fprintf(ficresphtmfr,"</table>\n");
fprintf(ficresphtm,"</tr>\n");	fprintf(ficlog,"\n");
fprintf(ficresphtm,"</table>\n");	if(j!=0){
fprintf(ficresphtmfr,"</table>\n");	printf("#Freqsummary: Starting values for combination j1=%d:\n", j1);
if(posproptt < 1.e-5){	for(i=1,s1=1; i <=nlstate; i++){
fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);	for(k=1; k <=(nlstate+ndeath); k++){
fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);	if (k != i) {
fprintf(ficres,"\n This combination (%d) is not valid and no result will be produced\n\n",j1);	for(jj=1; jj <=ncovmodel; jj++){ /* For counting s1 */
invalidvarcomb[j1]=1;	if(jj==1){ /* Constant case (in fact cste + age) */
}else{	if(j1==1){ /* All dummy covariates to zero */
fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);	freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */
invalidvarcomb[j1]=0;	freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */
}	printf("%d%d ",i,k);
fprintf(ficresphtmfr,"</table>\n");	fprintf(ficlog,"%d%d ",i,k);
} /* end selected combination of covariate j1 */	printf("%12.7f ln(%.0f/%.0f)= %f, OR=%f sd=%f \n",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]),freq[i][k][iagemax+3]/freq[i][i][iagemax+3], sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]));
dateintmean=dateintsum/k2cpt;	fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f \n",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
	pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
fclose(ficresp);	}
fclose(ficresphtm);	}else if((j1==1) && (jj==2 \|\| nagesqr==1)){ /* age or ageage parameter without covariate V4age (to be done later) */
	for(iage=iagemin; iage <= iagemax+3; iage++){
	x[iage]= (double)iage;
	y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);
	/* printf("i=%d, k=%d, s1=%d, j1=%d, jj=%d, y[%d]=%f\n",i,k,s1,j1,jj, iage, y[iage]); */
	}
	/* Some are not finite, but linreg will ignore these ages */
	no=0;
	linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+bx with standard errors /
	pstart[s1]=b;
	pstart[s1-1]=a;
	}else if( j1!=1 && (j1==2 \|\| (log(j1-1.)/log(2.)-(int)(log(j1-1.)/log(2.))) <0.010) && ( TvarsDind[(int)(log(j1-1.)/log(2.))+1]+2+nagesqr == jj) && Dummy[jj-2-nagesqr]==0){ /* We want only if the position, jj, in model corresponds to unique covariate equal to 1 in j1 combination */
	printf("j1=%d, jj=%d, (int)(log(j1-1.)/log(2.))+1=%d, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(int)(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]);
	printf("j1=%d, jj=%d, (log(j1-1.)/log(2.))+1=%f, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]);
	pstart[s1]= log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]));
	printf("%d%d ",i,k);
	fprintf(ficlog,"%d%d ",i,k);
	printf("s1=%d,i=%d,k=%d,p[%d]=%12.7f ln((%.0f/%.0f)/(%.0f/%.0f))= %f, OR=%f sd=%f \n",s1,i,k,s1,p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3],freq[i][k][iagemax+4],freq[i][i][iagemax+4], log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4])),(freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]), sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]+1/freq[i][k][iagemax+4]+1/freq[i][i][iagemax+4]));
	}else{ /* Other cases, like quantitative fixed or varying covariates */
	;
	}
	/* printf("%12.7f )", param[i][jj][k]); */
	/* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
	s1++;
	} /* end jj */
	} /* end k!= i */
	} /* end k */
	} /* end i, s1 */
	} /* end j !=0 */
	} /* end selected combination of covariate j1 */
	if(j==0){ /* We can estimate starting values from the occurences in each case */
	printf("#Freqsummary: Starting values for the constants:\n");
	fprintf(ficlog,"\n");
	for(i=1,s1=1; i <=nlstate; i++){
	for(k=1; k <=(nlstate+ndeath); k++){
	if (k != i) {
	printf("%d%d ",i,k);
	fprintf(ficlog,"%d%d ",i,k);
	for(jj=1; jj <=ncovmodel; jj++){
	pstart[s1]=p[s1]; /* Setting pstart to p values by default */
	if(jj==1){ /* Age has to be done */
	pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
	printf("%12.7f ln(%.0f/%.0f)= %12.7f ",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
	fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f ",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
	}
	/* printf("%12.7f )", param[i][jj][k]); */
	/* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
	s1++;
	}
	printf("\n");
	fprintf(ficlog,"\n");
	}
	}
	} /* end of state i */
	printf("#Freqsummary\n");
	fprintf(ficlog,"\n");
	for(s1=-1; s1 <=nlstate+ndeath; s1++){
	for(s2=-1; s2 <=nlstate+ndeath; s2++){
	/* param[i]\|j][k]= freq[s1][s2][iagemax+3] */
	printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
	fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
	/* if(freq[s1][s2][iage] !=0 ) { /\* minimizing output \/ /
	/* printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
	/* fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
	/* } */
	}
	} /* end loop s1 */

	printf("\n");
	fprintf(ficlog,"\n");
	} /* end j=0 */
	} /* end j */

	if(mle == -2){ /* We want to use these values as starting values */
	for(i=1, jk=1; i <=nlstate; i++){
	for(j=1; j <=nlstate+ndeath; j++){
	if(j!=i){
	/ca[0]= k+'a'-1;ca[1]='\0';/
	printf("%1d%1d",i,j);
	fprintf(ficparo,"%1d%1d",i,j);
	for(k=1; k<=ncovmodel;k++){
	/* printf(" %lf",param[i][j][k]); */
	/* fprintf(ficparo," %lf",param[i][j][k]); */
	p[jk]=pstart[jk];
	printf(" %f ",pstart[jk]);
	fprintf(ficparo," %f ",pstart[jk]);
	jk++;
	}
	printf("\n");
	fprintf(ficparo,"\n");
	}
	}
	}
	} /* end mle=-2 */
	dateintmean=dateintsum/k2cpt;
	date2dmy(dateintmean,&jintmean,&mintmean,&aintmean);

	fclose(ficresp);
	fclose(ficresphtm);
fclose(ficresphtmfr);	fclose(ficresphtmfr);
	free_vector(idq,1,nqfveff);
free_vector(meanq,1,nqfveff);	free_vector(meanq,1,nqfveff);
	free_vector(stdq,1,nqfveff);
free_matrix(meanqt,1,lastpass,1,nqtveff);	free_matrix(meanqt,1,lastpass,1,nqtveff);
free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);	free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
	free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
	free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
free_vector(pospropt,1,nlstate);	free_vector(pospropt,1,nlstate);
free_vector(posprop,1,nlstate);	free_vector(posprop,1,nlstate);
free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);	free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+4+AGEMARGE);
free_vector(pp,1,nlstate);	free_vector(pp,1,nlstate);
/* End of freqsummary */	/* End of freqsummary */
}	}

	/* Simple linear regression */
	int linreg(int ifi, int ila, int no, const double x[], const double y[], double a, double* b, double* r, double* sa, double * sb) {

	/* y=a+bx regression */
	double sumx = 0.0; /* sum of x */
	double sumx2 = 0.0; /* sum of x*2 /
	double sumxy = 0.0; /* sum of x * y */
	double sumy = 0.0; /* sum of y */
	double sumy2 = 0.0; /* sum of y*2 /
	double sume2 = 0.0; /* sum of square or residuals */
	double yhat;

	double denom=0;
	int i;
	int ne=*no;

	for ( i=ifi, ne=0;i<=ila;i++) {
	if(!isfinite(x[i]) \|\| !isfinite(y[i])){
	/* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
	continue;
	}
	ne=ne+1;
	sumx += x[i];
	sumx2 += x[i]*x[i];
	sumxy += x[i] * y[i];
	sumy += y[i];
	sumy2 += y[i]*y[i];
	denom = (ne * sumx2 - sumx*sumx);
	/* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */
	}

	denom = (ne * sumx2 - sumx*sumx);
	if (denom == 0) {
	// vertical, slope m is infinity
	*b = INFINITY;
	*a = 0;
	if (r) *r = 0;
	return 1;
	}

	b = (ne sumxy - sumx * sumy) / denom;
	a = (sumy sumx2 - sumx * sumxy) / denom;
	if (r!=NULL) {
	r = (sumxy - sumx sumy / ne) / /* compute correlation coeff */
	sqrt((sumx2 - sumxsumx/ne)
	(sumy2 - sumy*sumy/ne));
	}
	*no=ne;
	for ( i=ifi, ne=0;i<=ila;i++) {
	if(!isfinite(x[i]) \|\| !isfinite(y[i])){
	/* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
	continue;
	}
	ne=ne+1;
	yhat = y[i] - a -b* x[i];
	sume2 += yhat * yhat ;

	denom = (ne * sumx2 - sumx*sumx);
	/* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */
	}
	sb = sqrt(sume2/(double)(ne-2)/(sumx2 - sumx sumx /(double)ne));
	sa= sb * sqrt(sumx2/ne);

	return 0;
	}

/********** Prevalence ******************/	/********** Prevalence ******************/
void prevalence(double *probs, double agemin, double agemax, int s, double *agev, int nlstate, int imx, int Tvar, int *nbcode, int ncodemax,double mint,double anint, double dateprev1,double dateprev2, int firstpass, int lastpass)	void prevalence(double *probs, double agemin, double agemax, int s, double *agev, int nlstate, int imx, int Tvar, int *nbcode, int ncodemax,double mint,double anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
{	{
Line 4552 void prevalence(double ***probs, double	Line 5194 void prevalence(double ***probs, double
iagemin= (int) agemin;	iagemin= (int) agemin;
iagemax= (int) agemax;	iagemax= (int) agemax;
/pp=vector(1,nlstate);/	/pp=vector(1,nlstate);/
prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);	prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
/* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/	/* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
j1=0;	j1=0;

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

first=1;	first=0;
for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */	for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
for (i=1; i<=nlstate; i++)	for (i=1; i<=nlstate; i++)
for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)	for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)
prop[i][iage]=0.0;	prop[i][iage]=0.0;
printf("Prevalence combination of varying and fixed dummies %d\n",j1);	printf("Prevalence combination of varying and fixed dummies %d\n",j1);
/* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */	/* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
Line 4593 void prevalence(double ***probs, double	Line 5235 void prevalence(double ***probs, double
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-AGEMARGE \|\| (int)agev[m][i] >iagemax+3+AGEMARGE){	if((int)agev[m][i] <iagemin-AGEMARGE \|\| (int)agev[m][i] >iagemax+4+AGEMARGE){
printf("Error on individual # %d agev[m][i]=%f <%d-%d or > %d+3+%d m=%d; either change agemin or agemax or fix data\n",i, agev[m][i],iagemin,AGEMARGE, iagemax,AGEMARGE,m);	printf("Error on individual # %d agev[m][i]=%f <%d-%d or > %d+3+%d m=%d; either change agemin or agemax or fix data\n",i, agev[m][i],iagemin,AGEMARGE, iagemax,AGEMARGE,m);
exit(1);	exit(1);
}	}
Line 4617 void prevalence(double ***probs, double	Line 5259 void prevalence(double ***probs, double
if(posprop>=1.e-5){	if(posprop>=1.e-5){
probs[i][jk][j1]= prop[jk][i]/posprop;	probs[i][jk][j1]= prop[jk][i]/posprop;
} else{	} else{
if(first==1){	if(!first){
first=0;	first=1;
printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,j1,probs[i][jk][j1]);	printf("Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]);
	}else{
	fprintf(ficlog,"Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases.\n",jk,i,jk, j1,probs[i][jk][j1]);
}	}
}	}
}	}
Line 4630 void prevalence(double ***probs, double	Line 5274 void prevalence(double ***probs, double

/* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/	/* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
/free_vector(pp,1,nlstate);/	/free_vector(pp,1,nlstate);/
free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);	free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+4+AGEMARGE);
} /* End of prevalence */	} /* End of prevalence */

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

void concatwav(int wav[], int dh, int bh, int mw, int s, double agedc, double *agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)	void concatwav(int wav[], int dh, int bh, int mw, int s, double agedc, double *agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)
{	{
/* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.	/* Concatenates waves: wav[i] is the number of effective (useful waves in the sense that a non interview is useless) of individual i.
Death is a valid wave (if date is known).	Death is a valid wave (if date is known).
mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i	mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][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.	and mw[mi+1][i]. dh depends on stepm. s[m][i] exists for any wave from firstpass to lastpass
*/	*/

int i=0, mi=0, m=0, mli=0;	int i=0, mi=0, m=0, mli=0;
Line 4662 void concatwav(int wav[], int **dh, int	Line 5306 void concatwav(int wav[], int **dh, int
for(i=1; i<=imx; i++){ /* For simple cases and if state is death */	for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
mi=0; /* First valid wave */	mi=0; /* First valid wave */
mli=0; /* Last valid wave */	mli=0; /* Last valid wave */
m=firstpass;	m=firstpass; /* Loop on waves */
while(s[m][i] <= nlstate){ /* a live state */	while(s[m][i] <= nlstate){ /* a live state or unknown state */
if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */	if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */
mli=m-1;/* mw[++mi][i]=m-1; */	mli=m-1;/* mw[++mi][i]=m-1; */
}else if(s[m][i]>=1 \|\| s[m][i]==-4 \|\| s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */	}else if(s[m][i]>=1 \|\| s[m][i]==-4 \|\| s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */
mw[++mi][i]=m;	mw[++mi][i]=m; /* Valid wave: incrementing mi and updating mi; mw[mi] is the wave number of mi_th valid transition */
mli=m;	mli=m;
} /* else might be a useless wave -1 and mi is not incremented and mw[mi] not updated */	} /* else might be a useless wave -1 and mi is not incremented and mw[mi] not updated */
if(m < lastpass){ /* m < lastpass, standard case */	if(m < lastpass){ /* m < lastpass, standard case */
m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */	m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
}	}
else{ /* m >= lastpass, eventual special issue with warning */	else{ /* m = lastpass, eventual special issue with warning */
#ifdef UNKNOWNSTATUSNOTCONTRIBUTING	#ifdef UNKNOWNSTATUSNOTCONTRIBUTING
break;	break;
#else	#else
if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){	if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){ /* case -2 (vital status unknown is warned later */
if(firsthree == 0){	if(firsthree == 0){
printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);	printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p_{%d%d} .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath);
firsthree=1;	firsthree=1;
}	}
fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);	fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p_{%d%d} .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath);
mw[++mi][i]=m;	mw[++mi][i]=m; /* Valid transition with unknown status */
mli=m;	mli=m;
}	}
if(s[m][i]==-2){ /* Vital status is really unknown */	if(s[m][i]==-2){ /* Vital status is really unknown */
nbwarn++;	nbwarn++;
if((int)anint[m][i] == 9999){ /* Has the vital status really been verified? */	if((int)anint[m][i] == 9999){ /* Has the vital status really been verified?not a transition */
printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);	printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);	fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
}	}
Line 4709 void concatwav(int wav[], int **dh, int	Line 5353 void concatwav(int wav[], int **dh, int
/* 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 not in a death state */
#ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE	#ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
else if ((int) andc[i] != 9999) { /* Status is negative. A death occured after lastpass, we can't take it into account because of potential bias */	else if ((int) andc[i] != 9999) { /* Date of death is known */
/* m++; */
/* mi++; */
/* s[m][i]=nlstate+1; /\* We are setting the status to the last of non live state \/ /
/* mw[mi][i]=m; */
if ((int)anint[m][i]!= 9999) { /* date of last interview is known */	if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */	if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* month of death occured before last wave month and status should have been death instead of -1 */
nbwarn++;	nbwarn++;
if(firstfiv==0){	if(firstfiv==0){
printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );	printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d, interviewed on %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
firstfiv=1;	firstfiv=1;
}else{	}else{
fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );	fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d, interviewed on %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
}	}
}else{ /* Death occured afer last wave potential bias */	s[m][i]=nlstate+1; /* Fixing the status as death. Be careful if multiple death states */
	}else{ /* Month of Death occured afer last wave month, potential bias */
nberr++;	nberr++;
if(firstwo==0){	if(firstwo==0){
printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );	printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d with status %d. Potential bias if other individuals are still alive on this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictitious wave at the date of last vital status scan, with a dead status. See documentation\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
firstwo=1;	firstwo=1;
}	}
fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );	fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d with status %d. Potential bias if other individuals are still alive on this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictitious wave at the date of last vital status scan, with a dead status. See documentation\n\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
}	}
}else{ /* end date of interview is known */	}else{ /* if date of interview is unknown */
/* death is known but not confirmed by death status at any wave */	/* death is known but not confirmed by death status at any wave */
if(firstfour==0){	if(firstfour==0){
printf("Error! Death for individual %ld line=%d occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );	printf("Error! Death for individual %ld line=%d occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d with status %d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
firstfour=1;	firstfour=1;
}	}
fprintf(ficlog,"Error! Death for individual %ld line=%d occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );	fprintf(ficlog,"Error! Death for individual %ld line=%d occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d with status %d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
}	}
} /* end if date of death is known */	} /* end if date of death is known */
#endif	#endif
wav[i]=mi; /* mi should be the last effective wave (or mli) */	wav[i]=mi; /* mi should be the last effective wave (or mli), */
/* wav[i]=mw[mi][i]; */	/* wav[i]=mw[mi][i]; */
if(mi==0){	if(mi==0){
nbwarn++;	nbwarn++;
if(first==0){	if(first==0){
Line 4764 void concatwav(int wav[], int **dh, int	Line 5405 void concatwav(int wav[], int **dh, int
if (stepm <=0)	if (stepm <=0)
dh[mi][i]=1;	dh[mi][i]=1;
else{	else{
if (s[mw[mi+1][i]][i] > nlstate) { /* A death */	if (s[mw[mi+1][i]][i] > nlstate) { /* A death, but what if date is unknown? */
if (agedc[i] < 2*AGESUP) {	if (agedc[i] < 2*AGESUP) {
j= rint(agedc[i]12-agev[mw[mi][i]][i]12);	j= rint(agedc[i]12-agev[mw[mi][i]][i]12);
if(j==0) j=1; /* Survives at least one month after exam */	if(j==0) j=1; /* Survives at least one month after exam */
Line 4869 void concatwav(int wav[], int **dh, int	Line 5510 void concatwav(int wav[], int **dh, int
/* cptcov=0; /	/* cptcov=0; /

for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */	for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
	for (k=1; k <= maxncov; k++)
	for(j=1; j<=2; j++)
	nbcode[k][j]=0; /* Valgrind */

/* Loop on covariates without age and products and no quantitative variable */	/* Loop on covariates without age and products and no quantitative variable */
/* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2age+ V3 + V3V4 keeps V1 + V3 = 2 only \/ /
for (k=1; k<=cptcovt; k++) { /* From model V1 + V2age + V3 + V3V4 keeps V1 + V3 = 2 only */	for (k=1; k<=cptcovt; k++) { /* From model V1 + V2age + V3 + V3V4 keeps V1 + V3 = 2 only */
for (j=-1; (j < maxncov); j++) Ndum[j]=0;	for (j=-1; (j < maxncov); j++) Ndum[j]=0;
if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */	if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
switch(Fixed[k]) {	switch(Fixed[k]) {
case 0: /* Testing on fixed dummy covariate, simple or product of fixed */	case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
	modmaxcovj=0;
	modmincovj=0;
for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the modality of this covariate Vj*/	for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the modality of this covariate Vj*/
ij=(int)(covar[Tvar[k]][i]);	ij=(int)(covar[Tvar[k]][i]);
/* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i	/* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
Line 4889 void concatwav(int wav[], int **dh, int	Line 5534 void concatwav(int wav[], int **dh, int
modmaxcovj=ij;	modmaxcovj=ij;
else if (ij < modmincovj)	else if (ij < modmincovj)
modmincovj=ij;	modmincovj=ij;
if ((ij < -1) && (ij > NCOVMAX)){	if (ij <0 \|\| ij >1 ){
	printf("ERROR, IMaCh doesn't treat covariate with missing values V%d=-1, individual %d will be skipped.\n",Tvar[k],i);
	fprintf(ficlog,"ERROR, currently IMaCh doesn't treat covariate with missing values V%d=-1, individual %d will be skipped.\n",Tvar[k],i);
	fflush(ficlog);
	exit(1);
	}
	if ((ij < -1) \|\| (ij > NCOVMAX)){
printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );	printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
exit(1);	exit(1);
}else	}else
Line 4935 void concatwav(int wav[], int **dh, int	Line 5586 void concatwav(int wav[], int **dh, int
/* nbcode[Tvar[j]][3]=2; */	/* nbcode[Tvar[j]][3]=2; */
/* To be continued (not working yet). */	/* To be continued (not working yet). */
ij=0; /* ij is similar to i but can jump over null modalities */	ij=0; /* ij is similar to i but can jump over null modalities */
for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
	/* for (i=modmincovj; i<=modmaxcovj; i++) { / / i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
	/* Skipping the case of missing values by reducing nbcode to 0 and 1 and not -1, 0, 1 */
	/* model=V1+V2+V3, if V2=-1, 0 or 1, then nbcode[2][1]=0 and nbcode[2][2]=1 instead of
	* nbcode[2][1]=-1, nbcode[2][2]=0 and nbcode[2][3]=1 */
	/, could be restored in the future /
	for (i=0; i<=1; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
if (Ndum[i] == 0) { /* If nobody responded to this modality k */	if (Ndum[i] == 0) { /* If nobody responded to this modality k */
break;	break;
}	}
ij++;	ij++;
nbcode[Tvar[k]][ij]=i; /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1*/	nbcode[Tvar[k]][ij]=i; /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1 . Could be -1*/
cptcode = ij; /* New max modality for covar j */	cptcode = ij; /* New max modality for covar j */
} /* end of loop on modality i=-1 to 1 or more */	} /* end of loop on modality i=-1 to 1 or more */
break;	break;
Line 4956 void concatwav(int wav[], int **dh, int	Line 5613 void concatwav(int wav[], int **dh, int
break;	break;
} /* end switch */	} /* end switch */
} /* end dummy test */	} /* end dummy test */
	if(Dummy[k]==1 && Typevar[k] !=1){ /* Dummy covariate and not age product */
/* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 \//\ Could be 1 to 4 \//\ cptcode=modmaxcovj \/ /	for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the modality of this covariate Vj*/
/* /\recode from 0 \/ */	if(isnan(covar[Tvar[k]][i])){
/* k is a modality. If we have model=V1+V1sex /	printf("ERROR, IMaCh doesn't treat fixed quantitative covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i);
/* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */	fprintf(ficlog,"ERROR, currently IMaCh doesn't treat covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i);
/* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode \/ /	fflush(ficlog);
/* } */	exit(1);
/* /\* cptcode = ij; \/ /\ New max modality for covar j \/ /	}
/* if (ij > ncodemax[j]) { */	}
/* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */	}
/* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */	} /* end of loop on model-covariate k. nbcode[Tvark][1]=-1, nbcode[Tvark][1]=0 and nbcode[Tvark][2]=1 sets the value of covariate k*/
/* break; */
/* } */
/* } /\* end of loop on modality k \/ /
} /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/

for (k=-1; k< maxncov; k++) Ndum[k]=0;	for (k=-1; k< maxncov; k++) Ndum[k]=0;
/* Look at fixed dummy (single or product) covariates to check empty modalities */	/* Look at fixed dummy (single or product) covariates to check empty modalities */
Line 5063 void concatwav(int wav[], int **dh, int	Line 5716 void concatwav(int wav[], int **dh, int
/* 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 agelin.	nstepm is the number of stepm from age to agelin.
Look at hpijx to understand the reason of that which relies in memory size	Look at hpijx to understand the reason which relies in memory size consideration
and note for a fixed period like estepm months */	and note for a fixed period like estepm months */
/* 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
Line 5294 void concatwav(int wav[], int **dh, int	Line 5947 void concatwav(int wav[], int **dh, int
/* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/	/* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/

}	}

	/* Standard deviation of expectancies ij */
fprintf(ficresstdeij,"%3.0f",age );	fprintf(ficresstdeij,"%3.0f",age );
for(i=1; i<=nlstate;i++){	for(i=1; i<=nlstate;i++){
eip=0.;	eip=0.;
Line 5309 void concatwav(int wav[], int **dh, int	Line 5963 void concatwav(int wav[], int **dh, int
}	}
fprintf(ficresstdeij,"\n");	fprintf(ficresstdeij,"\n");

	/* Variance of expectancies ij */
fprintf(ficrescveij,"%3.0f",age );	fprintf(ficrescveij,"%3.0f",age );
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++){	for(j=1; j<=nlstate;j++){
Line 5342 void concatwav(int wav[], int **dh, int	Line 5997 void concatwav(int wav[], int **dh, int
/********** 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 ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[], int nres)	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[], int nres)
{	{
/* Variance of health expectancies */	/** Variance of health expectancies
/* double prevalim(double prlim, int nlstate, double xp, double age, double oldm, double * savm,double ftolpl);*/	* double prevalim(double prlim, int nlstate, double xp, double age, double oldm, double * savm,double ftolpl);
/* double *newm;/	* double **newm;
/* 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 movingaverage(); */	/* int movingaverage(); */
double dnewm,doldm;	double dnewm,doldm;
double dnewmp,doldmp;	double dnewmp,doldmp;
int i, j, nhstepm, hstepm, h, nstepm ;	int i, j, nhstepm, hstepm, h, nstepm ;
	int first=0;
int k;	int k;
double *xp;	double *xp;
double gp, gm; /* for var eij */	double gp, gm; /*< for var eij /
double *gradg, trgradg; /for var eij */	double *gradg, trgradg; /< for var eij /
double gradgp, trgradgp; /* for var p point j */	double gradgp, trgradgp; /*< for var p point j /
double gpp, gmp; /* for var p point j */	double gpp, gmp; /*< for var p point j /
double *varppt; / for var p point j nlstate to nlstate+ndeath */	double varppt; /< for var p point j nlstate to nlstate+ndeath */
double ***p3mat;	double ***p3mat;
double age,agelim, hf;	double age,agelim, hf;
/* double **mobaverage; /	/* double **mobaverage; /
Line 5418 void concatwav(int wav[], int **dh, int	Line 6075 void concatwav(int wav[], int **dh, int
/* fprintf(fichtm, "#Local time at start: %s", strstart);*/	/* fprintf(fichtm, "#Local time at start: %s", strstart);*/
fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");	fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
fprintf(fichtm,"\n<br>%s <br>\n",digitp);	fprintf(fichtm,"\n<br>%s <br>\n",digitp);
/* } */
varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);	varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
pstamp(ficresvij);	pstamp(ficresvij);
fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");	fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
Line 5473 void concatwav(int wav[], int **dh, int	Line 6130 void concatwav(int wav[], int **dh, int
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);
}	}
	/**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and
	* returns into prlim .
	*/
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);	prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);

	/* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */
if (popbased==1) {	if (popbased==1) {
if(mobilav ==0){	if(mobilav ==0){
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
Line 5485 void concatwav(int wav[], int **dh, int	Line 6145 void concatwav(int wav[], int **dh, int
prlim[i][i]=mobaverage[(int)age][i][ij];	prlim[i][i]=mobaverage[(int)age][i][ij];
}	}
}	}
	/**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}x\f$ at horizon h.
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres); /* Returns p3mat[i][j][h] for h=1 to nhstepm */	*/
	hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres); /* Returns p3mat[i][j][h] for h=0 to nhstepm */
	/**< And for each alive state j, sums over i \f$ w^i_x {}{h}_p^{ij}x\f$, which are the probability
	* at horizon h in state j including mortality.
	*/
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];
}	}
}	}
/* Next for computing probability of death (h=1 means	/* Next for computing shifted+ 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(i) * p(i,j) p.3=w1p13 + w2p23 .
*/	*/
for(j=nlstate+1;j<=nlstate+ndeath;j++){	for(j=nlstate+1;j<=nlstate+ndeath;j++){
for(i=1,gpp[j]=0.; i<= nlstate; i++)	for(i=1,gpp[j]=0.; i<= nlstate; i++)
gpp[j] += prlim[i][i]*p3mat[i][j][1];	gpp[j] += prlim[i][i]*p3mat[i][j][1];
}	}
/* end probability of death */
	/* Again with minus shift */

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);

prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);	prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);

if (popbased==1) {	if (popbased==1) {
Line 5534 void concatwav(int wav[], int **dh, int	Line 6199 void concatwav(int wav[], int **dh, int
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];
}	}
/* end probability of death */	/* end shifting computations */

	/**< Computing gradient matrix at horizon h
	*/
for(j=1; j<= nlstate; j++) /* vareij */	for(j=1; j<= nlstate; j++) /* vareij */
for(h=0; h<=nhstepm; h++){	for(h=0; h<=nhstepm; h++){
gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];	gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
}	}
	/**< Gradient of overall mortality p.3 (or p.j)
for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */	*/
	for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu mortality from j */
gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];	gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
}	}

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

	/* We got the gradient matrix for each theta and state j */
trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */	trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */

for(h=0; h<=nhstepm; h++) /* veij */	for(h=0; h<=nhstepm; h++) /* veij */
Line 5557 void concatwav(int wav[], int **dh, int	Line 6226 void concatwav(int wav[], int **dh, int
for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */	for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
for(theta=1; theta <=npar; theta++)	for(theta=1; theta <=npar; theta++)
trgradgp[j][theta]=gradgp[theta][j];	trgradgp[j][theta]=gradgp[theta][j];
	/**< as well as its transposed matrix
	*/

hf=hstepmstepm/YEARM; / Duration of hstepm expressed in year unit. */	hf=hstepmstepm/YEARM; / Duration of hstepm expressed in year unit. */
for(i=1;i<=nlstate;i++)	for(i=1;i<=nlstate;i++)
for(j=1;j<=nlstate;j++)	for(j=1;j<=nlstate;j++)
vareij[i][j][(int)age] =0.;	vareij[i][j][(int)age] =0.;

	/* Computing trgradg by matcov by gradg at age and summing over h
	* and k (nhstepm) formula 15 of article
	* Lievre-Brouard-Heathcote
	*/

for(h=0;h<=nhstepm;h++){	for(h=0;h<=nhstepm;h++){
for(k=0;k<=nhstepm;k++){	for(k=0;k<=nhstepm;k++){
matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);	matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
Line 5574 void concatwav(int wav[], int **dh, int	Line 6249 void concatwav(int wav[], int **dh, int
}	}
}	}

/* pptj */	/* pptj is p.3 or p.j = trgradgp by cov by gradgp, variance of
	* p.j overall mortality formula 49 but computed directly because
	* we compute the grad (wix pijx) instead of grad (pijx),even if
	* wix is independent of theta.
	*/
matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);	matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);	matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
for(j=nlstate+1;j<=nlstate+ndeath;j++)	for(j=nlstate+1;j<=nlstate+ndeath;j++)
Line 5662 void concatwav(int wav[], int **dh, int	Line 6341 void concatwav(int wav[], int **dh, int
} /* 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 ncvyearp, int ij, char strstart[], int nres)	void varprevlim(char fileresvpl[], FILE ficresvpl, 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[], int nres)
{	{
/* 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);/

double dnewm,doldm;	double dnewmpar,doldm;
int i, j, nhstepm, hstepm;	int i, j, nhstepm, hstepm;
double *xp;	double *xp;
double gp, gm;	double gp, gm;
Line 5677 void concatwav(int wav[], int **dh, int	Line 6356 void concatwav(int wav[], int **dh, int
int theta;	int theta;

pstamp(ficresvpl);	pstamp(ficresvpl);
fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");	fprintf(ficresvpl,"# Standard deviation of period (forward stable) prevalences \n");
fprintf(ficresvpl,"# Age ");	fprintf(ficresvpl,"# Age ");
if(nresult >=1)	if(nresult >=1)
fprintf(ficresvpl," Result# ");	fprintf(ficresvpl," Result# ");
Line 5686 void concatwav(int wav[], int **dh, int	Line 6365 void concatwav(int wav[], int **dh, int
fprintf(ficresvpl,"\n");	fprintf(ficresvpl,"\n");

xp=vector(1,npar);	xp=vector(1,npar);
dnewm=matrix(1,nlstate,1,npar);	dnewmpar=matrix(1,nlstate,1,npar);
doldm=matrix(1,nlstate,1,nlstate);	doldm=matrix(1,nlstate,1,nlstate);

hstepm=1YEARM; / Every year of age */	hstepm=1YEARM; / Every year of age */
Line 5706 void concatwav(int wav[], int **dh, int	Line 6385 void concatwav(int wav[], int **dh, int
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);
}	}
if((int)age==79 \|\|(int)age== 80 \|\|(int)age== 81 )	/* if((int)age==79 \|\|(int)age== 80 \|\|(int)age== 81 ) */
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);	/* prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
else	/* else */
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);	prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
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);
if((int)age==79 \|\|(int)age== 80 \|\|(int)age== 81 )	/* if((int)age==79 \|\|(int)age== 80 \|\|(int)age== 81 ) */
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);	/* prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
else	/* else */
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);	prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
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];
Line 5756 void concatwav(int wav[], int **dh, int	Line 6435 void concatwav(int wav[], int **dh, int
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==79 \|\|(int)age== 80 \|\|(int)age== 81){	if((int)age==79 \|\|(int)age== 80 \|\|(int)age== 81){
matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);	matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);	matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
}else{	}else{
matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);	matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);	matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
}	}
for(i=1;i<=nlstate;i++)	for(i=1;i<=nlstate;i++)
varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */	varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
Line 5768 void concatwav(int wav[], int **dh, int	Line 6447 void concatwav(int wav[], int **dh, int
fprintf(ficresvpl,"%.0f ",age );	fprintf(ficresvpl,"%.0f ",age );
if(nresult >=1)	if(nresult >=1)
fprintf(ficresvpl,"%d ",nres );	fprintf(ficresvpl,"%d ",nres );
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++){
fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));	fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
	/* for(j=1;j<=nlstate;j++) */
	/* fprintf(ficresvpl," %d %.5f ",j,prlim[j][i]); */
	}
fprintf(ficresvpl,"\n");	fprintf(ficresvpl,"\n");
free_vector(gp,1,nlstate);	free_vector(gp,1,nlstate);
free_vector(gm,1,nlstate);	free_vector(gm,1,nlstate);
Line 5781 void concatwav(int wav[], int **dh, int	Line 6463 void concatwav(int wav[], int **dh, int

free_vector(xp,1,npar);	free_vector(xp,1,npar);
free_matrix(doldm,1,nlstate,1,npar);	free_matrix(doldm,1,nlstate,1,npar);
free_matrix(dnewm,1,nlstate,1,nlstate);	free_matrix(dnewmpar,1,nlstate,1,nlstate);

	}


	/********** Variance of backprevalence limit ****************/
	void varbrevlim(char fileresvbl[], FILE ficresvbl, double varbpl, double matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double oldm, double savm, double bprlim, double ftolpl, int mobilavproj, int ncvyearp, int ij, char strstart[], int nres)
	{
	/* Variance of backward 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 dnewmpar,doldm;
	int i, j, nhstepm, hstepm;
	double *xp;
	double gp, gm;
	double gradg, trgradg;
	double mgm, mgp;
	double age,agelim;
	int theta;

	pstamp(ficresvbl);
	fprintf(ficresvbl,"# Standard deviation of back (stable) prevalences \n");
	fprintf(ficresvbl,"# Age ");
	if(nresult >=1)
	fprintf(ficresvbl," Result# ");
	for(i=1; i<=nlstate;i++)
	fprintf(ficresvbl," %1d-%1d",i,i);
	fprintf(ficresvbl,"\n");

	xp=vector(1,npar);
	dnewmpar=matrix(1,nlstate,1,npar);
	doldm=matrix(1,nlstate,1,nlstate);

	hstepm=1YEARM; / Every year of age */
	hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
	agelim = AGEINF;
	for (age=fage; age>=bage; age --){ /* If stepm=6 months */
	nhstepm=(int) rint((age-agelim)YEARM/stepm); / Typically 20 years = 2012/6=40 /
	if (stepm >= YEARM) hstepm=1;
	nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
	gradg=matrix(1,npar,1,nlstate);
	mgp=matrix(1,npar,1,nlstate);
	mgm=matrix(1,npar,1,nlstate);
	gp=vector(1,nlstate);
	gm=vector(1,nlstate);

	for(theta=1; theta <=npar; theta++){
	for(i=1; i<=npar; i++){ /* Computes gradient */
	xp[i] = x[i] + (i==theta ?delti[theta]:0);
	}
	if(mobilavproj > 0 )
	bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
	else
	bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
	for(i=1;i<=nlstate;i++){
	gp[i] = bprlim[i][i];
	mgp[theta][i] = bprlim[i][i];
	}
	for(i=1; i<=npar; i++) /* Computes gradient */
	xp[i] = x[i] - (i==theta ?delti[theta]:0);
	if(mobilavproj > 0 )
	bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
	else
	bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
	for(i=1;i<=nlstate;i++){
	gm[i] = bprlim[i][i];
	mgm[theta][i] = bprlim[i][i];
	}
	for(i=1;i<=nlstate;i++)
	gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
	/* gradg[theta][2]= -gradg[theta][1]; / / For testing if nlstate=2 */
	} /* End theta */

	trgradg =matrix(1,nlstate,1,npar);

	for(j=1; j<=nlstate;j++)
	for(theta=1; theta <=npar; theta++)
	trgradg[j][theta]=gradg[theta][j];
	/* if((int)age==79 \|\|(int)age== 80 \|\|(int)age== 81 ){ */
	/* printf("\nmgm mgp %d ",(int)age); */
	/* for(j=1; j<=nlstate;j++){ */
	/* printf(" %d ",j); */
	/* for(theta=1; theta <=npar; theta++) */
	/* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
	/* printf("\n "); */
	/* } */
	/* } */
	/* if((int)age==79 \|\|(int)age== 80 \|\|(int)age== 81 ){ */
	/* printf("\n gradg %d ",(int)age); */
	/* for(j=1; j<=nlstate;j++){ */
	/* printf("%d ",j); */
	/* for(theta=1; theta <=npar; theta++) */
	/* printf("%d %lf ",theta,gradg[theta][j]); */
	/* printf("\n "); */
	/* } */
	/* } */

	for(i=1;i<=nlstate;i++)
	varbpl[i][(int)age] =0.;
	if((int)age==79 \|\|(int)age== 80 \|\|(int)age== 81){
	matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
	matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
	}else{
	matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
	matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
	}
	for(i=1;i<=nlstate;i++)
	varbpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */

	fprintf(ficresvbl,"%.0f ",age );
	if(nresult >=1)
	fprintf(ficresvbl,"%d ",nres );
	for(i=1; i<=nlstate;i++)
	fprintf(ficresvbl," %.5f (%.5f)",bprlim[i][i],sqrt(varbpl[i][(int)age]));
	fprintf(ficresvbl,"\n");
	free_vector(gp,1,nlstate);
	free_vector(gm,1,nlstate);
	free_matrix(mgm,1,npar,1,nlstate);
	free_matrix(mgp,1,npar,1,nlstate);
	free_matrix(gradg,1,npar,1,nlstate);
	free_matrix(trgradg,1,nlstate,1,npar);
	} /* End age */

	free_vector(xp,1,npar);
	free_matrix(doldm,1,nlstate,1,npar);
	free_matrix(dnewmpar,1,nlstate,1,nlstate);

}	}

Line 5861 void varprob(char optionfilefiname[], do	Line 6668 void varprob(char optionfilefiname[], do
fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");	fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
fprintf(fichtm,"\n");	fprintf(fichtm,"\n");

fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back.</li>\n",optionfilehtmcov);	fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back. File %s</li>\n",optionfilehtmcov,optionfilehtmcov);
fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);	fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);
fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \	fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
and drawn. It helps understanding how is the covariance between two incidences.\	and drawn. It helps understanding how is the covariance between two incidences.\
Line 6058 To be simple, these graphs help to under	Line 6865 To be simple, these graphs help to under
}	}

/* Eigen vectors */	/* Eigen vectors */
v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));	if(1+(v1-lc1)*(v1-lc1)/cv12/cv12 <1.e-5){
	printf(" Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
	fprintf(ficlog," Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
	v11=(1./sqrt(fabs(1+(v1-lc1)*(v1-lc1)/cv12/cv12)));
	}else
	v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
/v21=sqrt(1.-v11v11); // error */	/v21=sqrt(1.-v11v11); // error */
v21=(lc1-v1)/cv12*v11;	v21=(lc1-v1)/cv12*v11;
v12=-v21;	v12=-v21;
Line 6078 To be simple, these graphs help to under	Line 6890 To be simple, these graphs help to under
fprintf(ficgp,"\nset parametric;unset label");	fprintf(ficgp,"\nset parametric;unset label");
fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);	fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
fprintf(ficgp,"\nset ter svg size 640, 480");	fprintf(ficgp,"\nset ter svg size 640, 480");
fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\	fprintf(fichtmcov,"\n<p><br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
:<a href=\"%s_%d%1d%1d-%1d%1d.svg\"> \	:<a href=\"%s_%d%1d%1d-%1d%1d.svg\"> \
%s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\	%s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \	subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \
Line 6089 To be simple, these graphs help to under	Line 6901 To be simple, these graphs help to under
fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);	fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);	fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)), %11.3e +%.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)) not", \	fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)), %11.3e +%.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)) not", \
mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \	mu1,std,v11,sqrt(fabs(lc1)),v12,sqrt(fabs(lc2)), \
mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));	mu2,std,v21,sqrt(fabs(lc1)),v22,sqrt(fabs(lc2))); /* For gnuplot only */
}else{	}else{
first=0;	first=0;
fprintf(fichtmcov," %d (%.3f),",(int) age, c12);	fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);	fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);	fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
fprintf(ficgp,"\nreplot %11.3e+ %.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)), %11.3e +%.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)) not", \	fprintf(ficgp,"\nreplot %11.3e+ %.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)), %11.3e +%.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)) not", \
mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \	mu1,std,v11,sqrt(lc1),v12,sqrt(fabs(lc2)), \
mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));	mu2,std,v21,sqrt(lc1),v22,sqrt(fabs(lc2)));
}/* if first */	}/* if first */
} /* age mod 5 */	} /* age mod 5 */
} /* end loop age */	} /* end loop age */
Line 6126 To be simple, these graphs help to under	Line 6938 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 prevfcast, int backcast, int estepm , \	int popforecast, int mobilav, int prevfcast, int mobilavproj, int prevbcast, int estepm , \
double jprev1, double mprev1,double anprev1, double dateprev1, \	double jprev1, double mprev1,double anprev1, double dateprev1, double dateprojd, double dateback1, \
double jprev2, double mprev2,double anprev2, double dateprev2){	double jprev2, double mprev2,double anprev2, double dateprev2, double dateprojf, double dateback2){
int jj1, k1, i1, cpt, k4, nres;	int jj1, k1, i1, cpt, k4, nres;

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 \
Line 6149 void printinghtml(char fileresu[], char	Line 6961 void printinghtml(char fileresu[], char
- Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",	- Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));	stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",	- Period (forward) 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,"\
- Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",	- Backward prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));	subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- (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) 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): \
Line 6164 void printinghtml(char fileresu[], char	Line 6976 void printinghtml(char fileresu[], char
<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>");

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

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

jj1=0;	jj1=0;

	fprintf(fichtm," \n<ul>");
for(nres=1; nres <= nresult; nres++) /* For each resultline */	for(nres=1; nres <= nresult; nres++) /* For each resultline */
for(k1=1; k1<=m;k1++){ /* For each combination of covariate */	for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
if(TKresult[nres]!= k1)	if(m != 1 && TKresult[nres]!= k1)
	continue;
	jj1++;
	if (cptcovn > 0) {
	fprintf(fichtm,"\n<li><a size=\"1\" color=\"#EC5E5E\" href=\"#rescov");
	for (cpt=1; cpt<=cptcoveff;cpt++){
	fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
	}
	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
	fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
	}
	fprintf(fichtm,"\">");

	/* if(nqfveff+nqtveff 0) / / Test to be done */
	fprintf(fichtm,"************ Results for covariates");
	for (cpt=1; cpt<=cptcoveff;cpt++){
	fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
	}
	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
	fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	}
	if(invalidvarcomb[k1]){
	fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1);
	continue;
	}
	fprintf(fichtm,"</a></li>");
	} /* cptcovn >0 */
	}
	fprintf(fichtm," \n</ul>");

	jj1=0;

	for(nres=1; nres <= nresult; nres++) /* For each resultline */
	for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
	if(m != 1 && TKresult[nres]!= k1)
continue;	continue;

/* for(i1=1; i1<=ncodemax[k1];i1++){ */	/* for(i1=1; i1<=ncodemax[k1];i1++){ */
jj1++;	jj1++;
if (cptcovn > 0) {	if (cptcovn > 0) {
	fprintf(fichtm,"\n<p><a name=\"rescov");
	for (cpt=1; cpt<=cptcoveff;cpt++){
	fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
	}
	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
	fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
	}
	fprintf(fichtm,"\"</a>");

fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");	fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
for (cpt=1; cpt<=cptcoveff;cpt++){	for (cpt=1; cpt<=cptcoveff;cpt++){
fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);	fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
Line 6200 void printinghtml(char fileresu[], char	Line 7057 void printinghtml(char fileresu[], char
}	}
}	}
/* aij, bij */	/* aij, bij */
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-%d.svg\">%s_%d-1-%d.svg</a><br> \	fprintf(fichtm,"<br>- Logit model (yours is: logit(pij)=log(pij/pii)= aij+ bij age+%s) as a function of age: <a href=\"%s_%d-1-%d.svg\">%s_%d-1-%d.svg</a><br> \
<img src=\"%s_%d-1-%d.svg\">",model,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);	<img src=\"%s_%d-1-%d.svg\">",model,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);
/* Pij */	/* Pij */
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-%d.svg\">%s_%d-2-%d.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-%d.svg\">%s_%d-2-%d.svg</a><br> \
Line 6213 divided by h: <sub>h</sub>P<sub>ij</sub>	Line 7070 divided by h: <sub>h</sub>P<sub>ij</sub>
<img src=\"%s_%d-3-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);	<img src=\"%s_%d-3-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);
/* Survival functions (period) in state j */	/* Survival functions (period) in state j */
for(cpt=1; cpt<=nlstate;cpt++){	for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"<br>\n- Survival functions in state %d. Or probability to survive in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \	fprintf(fichtm,"<br>\n- Survival functions in state %d. And probability to be observed in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
<img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);	<img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
}	}
/* State specific survival functions (period) */	/* State specific survival functions (period) */
for(cpt=1; cpt<=nlstate;cpt++){	for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\	fprintf(fichtm,"<br>\n- Survival functions in state %d and in any other live state (total).\
Or probability to survive in various states (1 to %d) being in state %d at different ages. \	And probability to be observed in various states (up to %d) being in state %d at different ages. \
<a href=\"%s_%d-%d-%d.svg\">%s_%d%d-%d.svg</a><br> <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);	<a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
}	}
/* Period (stable) prevalence in each health state */	/* Period (forward stable) prevalence in each health state */
for(cpt=1; cpt<=nlstate;cpt++){	for(cpt=1; cpt<=nlstate;cpt++){
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-%d.svg\">%s_%d-%d-%d.svg</a><br> \	fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability for a person being in state (1 to %d) at different ages, to be in state %d some years after. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
<img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);	<img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
}	}
if(backcast==1){	if(prevbcast==1){
/* Period (stable) back prevalence in each health state */	/* Backward prevalence in each health state */
for(cpt=1; cpt<=nlstate;cpt++){	for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"<br>\n- Convergence to period (stable) back 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-%d.svg\">%s_%d-%d-%d.svg</a><br> \	fprintf(fichtm,"<br>\n- Convergence to mixed (stable) back prevalence in state %d. Or probability for a person to be in state %d at a younger age, knowing that she/he was in state (1 to %d) at different older ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
<img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);	<img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
}	}
}	}
if(prevfcast==1){	if(prevfcast==1){
/* Projection of prevalence up to period (stable) prevalence in each health state */	/* Projection of prevalence up to period (forward stable) prevalence in each health state */
for(cpt=1; cpt<=nlstate;cpt++){	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-%d.svg\">%s_%d-%d-%d.svg</a><br> \	fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), from year %.1f up to year %.1f tending to period (stable) forward prevalence in state %d. Or probability to be in state %d being in an observed weighted state (from 1 to %d). <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a>", dateprev1, dateprev2, mobilavproj, dateprojd, dateprojf, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
<img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);	fprintf(fichtm," (data from text file <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"F_"),subdirf2(optionfilefiname,"F_"));
	fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",
	subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
	}
	}
	if(prevbcast==1){
	/* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */
	for(cpt=1; cpt<=nlstate;cpt++){
	fprintf(fichtm,"<br>\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \
	from year %.1f up to year %.1f (probably close to stable [mixed] back prevalence in state %d (randomness in cross-sectional prevalence is not taken into \
	account but can visually be appreciated). Or probability to have been in an state %d, knowing that the person was in either state (1 or %d) \
	with weights corresponding to observed prevalence at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a>", dateprev1, dateprev2, mobilavproj, dateback1, dateback2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
	fprintf(fichtm," (data from text file <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"FB_"),subdirf2(optionfilefiname,"FB_"));
	fprintf(fichtm," <img src=\"%s_%d-%d-%d.svg\">", subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
}	}
}	}

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-%d.svg\">%s_%d-%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-%d.svg\">%s_%d-%d-%d.svg</a>",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
<img src=\"%s_%d-%d-%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);	fprintf(fichtm," (data from text file <a href=\"%s.txt\"> %s.txt</a>)\n<br>",subdirf2(optionfilefiname,"E_"),subdirf2(optionfilefiname,"E_"));
	fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">", subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres );
}	}
/* } /\* end i1 \/ /	/* } /\* end i1 \/ /
}/* End k1 */	}/* End k1 */
Line 6280 See page 'Matrix of variance-covariance	Line 7151 See page 'Matrix of variance-covariance
<a href=\"%s\">%s</a> <br>\n</li>",	<a href=\"%s\">%s</a> <br>\n</li>",
estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));	estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",	- Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the forward (period) prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));	estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",	- Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));	estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\	- Standard deviation of forward (period) prevalences: <a href=\"%s\">%s</a> <br>\n",\
subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));	subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));

/* if(popforecast==1) fprintf(fichtm,"\n */	/* if(popforecast==1) fprintf(fichtm,"\n */
Line 6305 See page 'Matrix of variance-covariance	Line 7176 See page 'Matrix of variance-covariance

for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
for(k1=1; k1<=m;k1++){	for(k1=1; k1<=m;k1++){
if(TKresult[nres]!= k1)	if(m != 1 && TKresult[nres]!= k1)
continue;	continue;
/* for(i1=1; i1<=ncodemax[k1];i1++){ */	/* for(i1=1; i1<=ncodemax[k1];i1++){ */
jj1++;	jj1++;
Line 6326 See page 'Matrix of variance-covariance	Line 7197 See page 'Matrix of variance-covariance
}	}
}	}
for(cpt=1; cpt<=nlstate;cpt++) {	for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \	fprintf(fichtm,"\n<br>- Observed (cross-sectional with mov_average=%d) and period (incidence based) \
prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d-%d.svg\"> %s_%d-%d-%d.svg</a>\n <br>\	prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d-%d.svg\"> %s_%d-%d-%d.svg</a>",mobilav,cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
<img src=\"%s_%d-%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);	fprintf(fichtm," (data from text file <a href=\"%s\">%s</a>)\n <br>",subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
	fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",subdirf2(optionfilefiname,"V_"), cpt,k1,nres);
}	}
fprintf(fichtm,"\n<br>- Total life expectancy by age and \	fprintf(fichtm,"\n<br>- Total life expectancy by age and \
health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \	health expectancies in each live states (1 to %d). If popbased=1 the smooth (due to the model) \
true period expectancies (those weighted with period prevalences are also\	true period expectancies (those weighted with period prevalences are also\
drawn in addition to the population based expectancies computed using\	drawn in addition to the population based expectancies computed using\
observed and cahotic prevalences: <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>\n<br>\	observed and cahotic prevalences: <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>",nlstate, subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);
<img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);	fprintf(fichtm," (data from text file <a href=\"%s.txt\">%s.txt</a>) \n<br>",subdirf2(optionfilefiname,"T_"),subdirf2(optionfilefiname,"T_"));
	fprintf(fichtm,"<img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres);
/* } /\* end i1 \/ /	/* } /\* end i1 \/ /
}/* End k1 */	}/* End k1 */
}/* End nres */	}/* End nres */
Line 6344 true period expectancies (those weighted	Line 7217 true period expectancies (those weighted
}	}

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

char dirfileres[132],optfileres[132];	char dirfileres[132],optfileres[132];
char gplotcondition[132];	char gplotcondition[132], gplotlabel[132];
int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,k4=0,ij=0, ijp=0, l=0;	int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,k4=0,ij=0, ijp=0, l=0;
int lv=0, vlv=0, kl=0;	int lv=0, vlv=0, kl=0;
int ng=0;	int ng=0;
int vpopbased;	int vpopbased;
int ioffset; /* variable offset for columns */	int ioffset; /* variable offset for columns */
	int iyearc=1; /* variable column for year of projection */
	int iagec=1; /* variable column for age of projection */
int nres=0; /* Index of resultline */	int nres=0; /* Index of resultline */
	int istart=1; /* For starting graphs in projections */

/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */	/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
/* printf("Problem with file %s",optionfilegnuplot); */	/* printf("Problem with file %s",optionfilegnuplot); */
Line 6365 void printinggnuplot(char fileresu[], ch	Line 7241 void printinggnuplot(char fileresu[], ch
/#endif /	/#endif /
m=pow(2,cptcoveff);	m=pow(2,cptcoveff);

	/* diagram of the model */
	fprintf(ficgp,"\n#Diagram of the model \n");
	fprintf(ficgp,"\ndelta=0.03;delta2=0.07;unset arrow;\n");
	fprintf(ficgp,"yoff=(%d > 2? 0:1);\n",nlstate);
	fprintf(ficgp,"\n#Peripheral arrows\nset for [i=1:%d] for [j=1:%d] arrow i10+j from cos(pi((1-(%d/2)2./%d)/2+(i-1)2./%d))-(i!=j?(i-j)/abs(i-j)delta:0), yoff +sin(pi((1-(%d/2)2./%d)/2+(i-1)2./%d)) + (i!=j?(i-j)/abs(i-j)delta:0) rto -0.95(cos(pi((1-(%d/2)2./%d)/2+(i-1)2./%d))+(i!=j?(i-j)/abs(i-j)delta:0) - cos(pi((1-(%d/2)2./%d)/2+(j-1)2./%d)) + (i!=j?(i-j)/abs(i-j)delta2:0)), -0.95(sin(pi((1-(%d/2)2./%d)/2+(i-1)2./%d)) + (i!=j?(i-j)/abs(i-j)delta:0) - sin(pi((1-(%d/2)2./%d)/2+(j-1)2./%d))+( i!=j?(i-j)/abs(i-j)*delta2:0)) ls (i < j? 1:2)\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);

	fprintf(ficgp,"\n#Centripete arrows (turning in other direction (1-i) instead of (i-1)) \nset for [i=1:%d] arrow (%d+1)10+i from cos(pi((1-(%d/2)2./%d)/2+(1-i)2./%d))-(i!=j?(i-j)/abs(i-j)delta:0), yoff +sin(pi((1-(%d/2)2./%d)/2+(1-i)2./%d)) + (i!=j?(i-j)/abs(i-j)delta:0) rto -0.80(cos(pi((1-(%d/2)2./%d)/2+(1-i)2./%d))+(i!=j?(i-j)/abs(i-j)delta:0) ), -0.80(sin(pi((1-(%d/2)2./%d)/2+(1-i)2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) + yoff ) ls 4\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
	fprintf(ficgp,"\n#show arrow\nunset label\n");
	fprintf(ficgp,"\n#States labels, starting from 2 (2-i) instead of (1-i), was (i-1)\nset for [i=1:%d] label i sprintf(\"State %%d\",i) center at cos(pi((1-(%d/2)2./%d)/2+(2-i)2./%d)), yoff+sin(pi((1-(%d/2)2./%d)/2+(2-i)2./%d)) font \"helvetica, 16\" tc rgbcolor \"blue\"\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
	fprintf(ficgp,"\nset label %d+1 sprintf(\"State %%d\",%d+1) center at 0.,0. font \"helvetica, 16\" tc rgbcolor \"red\"\n",nlstate,nlstate);
	fprintf(ficgp,"\n#show label\nunset border;unset xtics; unset ytics;\n");
	fprintf(ficgp,"\n\nset ter svg size 640, 480;set out \"%s_.svg\" \n",subdirf2(optionfilefiname,"D_"));
	fprintf(ficgp,"unset log y; plot [-1.2:1.2][yoff-1.2:1.2] 1/0 not; set out;reset;\n");

/* Contribution to likelihood */	/* Contribution to likelihood */
/* Plot the probability implied in the likelihood */	/* Plot the probability implied in the likelihood */
fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");	fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
Line 6401 void printinggnuplot(char fileresu[], ch	Line 7291 void printinggnuplot(char fileresu[], ch
for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */	for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
/* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */	/* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
if(TKresult[nres]!= k1)	if(m != 1 && TKresult[nres]!= k1)
continue;	continue;
/* We are interested in selected combination by the resultline */	/* We are interested in selected combination by the resultline */
/* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */	/* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt);	fprintf(ficgp,"\n# 1st: Forward (stable period) prevalence with CI: 'VPL_' files and live state =%d ", cpt);
	strcpy(gplotlabel,"(");
for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */	for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */
lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */	lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
Line 6415 void printinggnuplot(char fileresu[], ch	Line 7306 void printinggnuplot(char fileresu[], ch
/* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */	/* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
/* printf(" V%d=%d ",Tvaraff[k],vlv); */	/* printf(" V%d=%d ",Tvaraff[k],vlv); */
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
/* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */	/* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	}
	strcpy(gplotlabel+strlen(gplotlabel),")");
/* printf("\n#\n"); */	/* printf("\n#\n"); */
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
	/k1=k1-1;/ /* To be checked */
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
continue;	continue;
}	}

fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);	fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres);	/* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */
	fprintf(ficgp,"set title \"Alive state %d %s\" font \"Helvetica,12\"\n",cpt,gplotlabel);
	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
	/* fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */
	/* k1-1 error should be nres-1*/
for (i=1; i<= nlstate ; i ++) {	for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," %%lf (%%lf)");	if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%lf (%%lf)");	else fprintf(ficgp," %%lf (%%lf)");
}	}
fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres);	fprintf(ficgp,"\" t\"Forward prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
for (i=1; i<= nlstate ; i ++) {	for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," %%lf (%%lf)");	if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%lf (%%lf)");	else fprintf(ficgp," %%lf (%%lf)");
}	}
fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres);	fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
for (i=1; i<= nlstate ; i ++) {	for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," %%lf (%%lf)");	if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%lf (%%lf)");	else fprintf(ficgp," %%lf (%%lf)");
}	}
fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));	/* fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4(cpt-1)); /
if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
	fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" u 1:((",subdirf2(fileresu,"P_"));
	if(cptcoveff ==0){
	fprintf(ficgp,"$%d)) t 'Observed prevalence in state %d' with line lt 3", 2+3*(cpt-1), cpt );
	}else{
	kl=0;
	for (k=1; k<=cptcoveff; k++){ /* For each combination of 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[k]][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):($5==2000? 3:2) t 'p.1' with line lc variable*/
	if(k==cptcoveff){
	fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Observed prevalence in state %d' w l lt 2",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
	2+cptcoveff2+3(cpt-1), cpt ); /* 4 or 6 ?*/
	}else{
	fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
	kl++;
	}
	} /* end covariate */
	} /* end if no covariate */

	if(prevbcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
/* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */	/* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */	fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */
if(cptcoveff ==0){	if(cptcoveff ==0){
Line 6473 void printinggnuplot(char fileresu[], ch	Line 7398 void printinggnuplot(char fileresu[], ch
}	}
} /* end covariate */	} /* end covariate */
} /* end if no covariate */	} /* end if no covariate */
} /* end if backcast */	if(prevbcast == 1){
fprintf(ficgp,"\nset out \n");	fprintf(ficgp,", \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
	/* k1-1 error should be nres-1*/
	for (i=1; i<= nlstate ; i ++) {
	if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
	else fprintf(ficgp," %%lf (%%lf)");
	}
	fprintf(ficgp,"\" t\"Backward (stable) prevalence\" w l lt 6 dt 3,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
	for (i=1; i<= nlstate ; i ++) {
	if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
	else fprintf(ficgp," %%lf (%%lf)");
	}
	fprintf(ficgp,"\" t\"95%% CI\" w l lt 4,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
	for (i=1; i<= nlstate ; i ++) {
	if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
	else fprintf(ficgp," %%lf (%%lf)");
	}
	fprintf(ficgp,"\" t\"\" w l lt 4");
	} /* end if backprojcast */
	} /* end if prevbcast */
	/* fprintf(ficgp,"\nset out ;unset label;\n"); */
	fprintf(ficgp,"\nset out ;unset title;\n");
} /* nres */	} /* nres */
} /* k1 */	} /* k1 */
} /* cpt */	} /* cpt */
Line 6483 void printinggnuplot(char fileresu[], ch	Line 7428 void printinggnuplot(char fileresu[], ch
/2 eme/	/2 eme/
for (k1=1; k1<= m ; k1 ++){	for (k1=1; k1<= m ; k1 ++){
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
if(TKresult[nres]!= k1)	if(m != 1 && TKresult[nres]!= k1)
continue;	continue;
fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");	fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
	strcpy(gplotlabel,"(");
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */	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 */	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(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
Line 6493 void printinggnuplot(char fileresu[], ch	Line 7439 void printinggnuplot(char fileresu[], ch
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];	vlv= nbcode[Tvaraff[k]][lv];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
}	}
/* for(k=1; k <= ncovds; k++){ */	/* for(k=1; k <= ncovds; k++){ */
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	}
	strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
Line 6507 void printinggnuplot(char fileresu[], ch	Line 7456 void printinggnuplot(char fileresu[], ch

fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres);	fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres);
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)	fprintf(ficgp,"\nset label \"popbased %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",vpopbased,gplotlabel);
	if(vpopbased==0){
fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);	fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
else	}else
fprintf(ficgp,"\nreplot ");	fprintf(ficgp,"\nreplot ");
for (i=1; i<= nlstate+1 ; i ++) {	for (i=1; i<= nlstate+1 ; i ++) {
k=2*i;	k=2*i;
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);	fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1, vpopbased);
for (j=1; j<= nlstate+1 ; j ++) {	for (j=1; j<= nlstate+1 ; j ++) {
if (j==i) fprintf(ficgp," %%lf (%%lf)");	if (j==i) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%lf (%%lf)");	else fprintf(ficgp," %%lf (%%lf)");
}	}
if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);	if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);	else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);	fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);
for (j=1; j<= nlstate+1 ; j ++) {	for (j=1; j<= nlstate+1 ; j ++) {
if (j==i) fprintf(ficgp," %%lf (%%lf)");	if (j==i) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%lf (%%lf)");	else fprintf(ficgp," %%lf (%%lf)");
}	}
fprintf(ficgp,"\" t\"\" w l lt 0,");	fprintf(ficgp,"\" t\"\" w l lt 0,");
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);	fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);
for (j=1; j<= nlstate+1 ; j ++) {	for (j=1; j<= nlstate+1 ; j ++) {
if (j==i) fprintf(ficgp," %%lf (%%lf)");	if (j==i) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%lf (%%lf)");	else fprintf(ficgp," %%lf (%%lf)");
Line 6535 void printinggnuplot(char fileresu[], ch	Line 7485 void printinggnuplot(char fileresu[], ch
else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");	else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
} /* state */	} /* state */
} /* vpopbased */	} /* vpopbased */
fprintf(ficgp,"\nset out;set out \"%s_%d-%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1,nres); /* Buggy gnuplot */	fprintf(ficgp,"\nset out;set out \"%s_%d-%d.svg\"; replot; set out; unset label;\n",subdirf2(optionfilefiname,"E_"),k1,nres); /* Buggy gnuplot */
} /* end nres */	} /* end nres */
} /* k1 end 2 eme*/	} /* k1 end 2 eme*/

Line 6543 void printinggnuplot(char fileresu[], ch	Line 7493 void printinggnuplot(char fileresu[], ch
/3eme/	/3eme/
for (k1=1; k1<= m ; k1 ++){	for (k1=1; k1<= m ; k1 ++){
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
if(TKresult[nres]!= k1)	if(m != 1 && TKresult[nres]!= k1)
continue;	continue;

for (cpt=1; cpt<= nlstate ; cpt ++) {	for (cpt=1; cpt<= nlstate ; cpt ++) {
fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: combination=%d state=%d",k1, cpt);	fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files: combination=%d state=%d",k1, cpt);
	strcpy(gplotlabel,"(");
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */	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 */	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(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
Line 6555 void printinggnuplot(char fileresu[], ch	Line 7506 void printinggnuplot(char fileresu[], ch
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];	vlv= nbcode[Tvaraff[k]][lv];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	}
	strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
Line 6568 void printinggnuplot(char fileresu[], ch	Line 7522 void printinggnuplot(char fileresu[], ch
/* 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-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
	fprintf(ficgp,"set label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel);
fprintf(ficgp,"set ter svg size 640, 480\n\	fprintf(ficgp,"set ter svg size 640, 480\n\
plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);	plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),nres-1,nres-1,k,cpt);
/fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);	/fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");	for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
fprintf(ficgp,"\" t \"e%d1\" w l",cpt);	fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
Line 6579 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 7534 plot [%.f:%.f] \"%s\" every :::%d::%d u

*/	*/
for (i=1; i< nlstate ; i ++) {	for (i=1; i< nlstate ; i ++) {
fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+i,cpt,i+1);	fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),nres-1,nres-1,k+i,cpt,i+1);
/* fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2i,cpt,i+1);/	/* fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2i,cpt,i+1);/

}	}
fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt);	fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),nres-1,nres-1,k+nlstate,cpt);
}	}
	fprintf(ficgp,"\nunset label;\n");
} /* end nres */	} /* end nres */
} /* end kl 3eme */	} /* end kl 3eme */

Line 6592 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 7548 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 covariate and each value */	for (k1=1; k1<=m; k1++){ /* For each covariate and each value */
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
if(TKresult[nres]!= k1)	if(m != 1 && TKresult[nres]!= k1)
continue;	continue;
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
	strcpy(gplotlabel,"(");
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 */	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 */	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
Line 6603 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 7560 plot [%.f:%.f] \"%s\" every :::%d::%d u
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];	vlv= nbcode[Tvaraff[k]][lv];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	}
	strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
Line 6614 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 7574 plot [%.f:%.f] \"%s\" every :::%d::%d u
}	}

fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
	fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
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\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);	set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
k=3;	k=3;
Line 6629 set ter svg size 640, 480\nunset log y\n	Line 7590 set ter svg size 640, 480\nunset log y\n
fprintf(ficgp,"+$%d",k+l+j-1);	fprintf(ficgp,"+$%d",k+l+j-1);
fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);	fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
} /* nlstate */	} /* nlstate */
fprintf(ficgp,"\nset out\n");	fprintf(ficgp,"\nset out; unset label;\n");
} /* end cpt state*/	} /* end cpt state*/
} /* end nres */	} /* end nres */
} /* end covariate k1 */	} /* end covariate k1 */
Line 6638 set ter svg size 640, 480\nunset log y\n	Line 7599 set ter svg size 640, 480\nunset log y\n
/* 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 combination if any */	for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
if(TKresult[nres]!= k1)	if(m != 1 && TKresult[nres]!= k1)
continue;	continue;
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
	strcpy(gplotlabel,"(");
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 */	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 */	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
Line 6649 set ter svg size 640, 480\nunset log y\n	Line 7611 set ter svg size 640, 480\nunset log y\n
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];	vlv= nbcode[Tvaraff[k]][lv];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	}
	strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
Line 6660 set ter svg size 640, 480\nunset log y\n	Line 7625 set ter svg size 640, 480\nunset log y\n
}	}

fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
	fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
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\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);	set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
k=3;	k=3;
Line 6683 set ter svg size 640, 480\nunset log y\n	Line 7649 set ter svg size 640, 480\nunset log y\n
else	else
fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);	fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
}	}
fprintf(ficgp,"\nset out\n");	fprintf(ficgp,"\nset out; unset label;\n");
} /* end cpt state*/	} /* end cpt state*/
} /* end covariate */	} /* end covariate */
} /* end nres */	} /* end nres */
Line 6692 set ter svg size 640, 480\nunset log y\n	Line 7658 set ter svg size 640, 480\nunset log y\n
/* CV preval stable (period) for each covariate */	/* CV preval stable (period) for each covariate */
for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */	for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
if(TKresult[nres]!= k1)	if(m != 1 && TKresult[nres]!= k1)
continue;	continue;
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */
	strcpy(gplotlabel,"(");
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 (forward): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */	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 */	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(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
Line 6704 set ter svg size 640, 480\nunset log y\n	Line 7670 set ter svg size 640, 480\nunset log y\n
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];	vlv= nbcode[Tvaraff[k]][lv];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	}
	strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
Line 6715 set ter svg size 640, 480\nunset log y\n	Line 7684 set ter svg size 640, 480\nunset log y\n
}	}

fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1,nres);	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
	fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);	set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
k=3; /* Offset */	k=3; /* Offset */
for (i=1; i<= nlstate ; i ++){	for (i=1; i<= nlstate ; i ++){ /* State of origin */
if(i==1)	if(i==1)
fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));	fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
else	else
fprintf(ficgp,", '' ");	fprintf(ficgp,", '' ");
l=(nlstate+ndeath)*(i-1)+1;	l=(nlstate+ndeath)(i-1)+1; / 1, 1+ nlstate+ndeath, 1+2(nlstate+ndeath) /
fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);	fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
for (j=2; j<= nlstate ; j ++)	for (j=2; j<= nlstate ; j ++)
fprintf(ficgp,"+$%d",k+l+j-1);	fprintf(ficgp,"+$%d",k+l+j-1);
fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);	fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
} /* nlstate */	} /* nlstate */
fprintf(ficgp,"\nset out\n");	fprintf(ficgp,"\nset out; unset label;\n");
} /* end cpt state*/	} /* end cpt state*/
} /* end covariate */	} /* end covariate */


/* 7eme */	/* 7eme */
if(backcast == 1){	if(prevbcast == 1){
/* CV back preval stable (period) for each covariate */	/* CV backward prevalence for each covariate */
for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */	for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
if(TKresult[nres]!= k1)	if(m != 1 && TKresult[nres]!= k1)
continue;	continue;
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */
fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);	strcpy(gplotlabel,"(");
	fprintf(ficgp,"\n#\n#\n#CV Backward stable prevalence: 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */	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 */	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(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
Line 6750 set ter svg size 640, 480\nunset log y\n	Line 7721 set ter svg size 640, 480\nunset log y\n
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];	vlv= nbcode[Tvaraff[k]][lv];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	}
	strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
Line 6761 set ter svg size 640, 480\nunset log y\n	Line 7735 set ter svg size 640, 480\nunset log y\n
}	}

fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
	fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);	set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
k=3; /* Offset */	k=3; /* Offset */
for (i=1; i<= nlstate ; i ++){	for (i=1; i<= nlstate ; i ++){ /* State of arrival */
if(i==1)	if(i==1)
fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));	fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
else	else
fprintf(ficgp,", '' ");	fprintf(ficgp,", '' ");
/* l=(nlstate+ndeath)(i-1)+1; /	/* l=(nlstate+ndeath)(i-1)+1; /
l=(nlstate+ndeath)*(cpt-1)+1;	l=(nlstate+ndeath)(cpt-1)+1; / fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2(nlstate+ndeath) /
/* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier \/ /	/* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier \/ /
/* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier \/ /	/* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier \/ /
fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+(cpt-1)+i-1); /* a vérifier */	fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+i-1); /* To be verified */
/* for (j=2; j<= nlstate ; j ++) */	/* for (j=2; j<= nlstate ; j ++) */
/* fprintf(ficgp,"+$%d",k+l+j-1); */	/* fprintf(ficgp,"+$%d",k+l+j-1); */
/* /\* fprintf(ficgp,"+$%d",k+l+j-1); \/ /	/* /\* fprintf(ficgp,"+$%d",k+l+j-1); \/ /
fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);	fprintf(ficgp,") t \"bprev(%d,%d)\" w l",cpt,i);
} /* nlstate */	} /* nlstate */
fprintf(ficgp,"\nset out\n");	fprintf(ficgp,"\nset out; unset label;\n");
} /* end cpt state*/	} /* end cpt state*/
} /* end covariate */	} /* end covariate */
} /* End if backcast */	} /* End if prevbcast */

/* 8eme */	/* 8eme */
if(prevfcast==1){	if(prevfcast==1){
/* Projection from cross-sectional to stable (period) for each covariate */	/* Projection from cross-sectional to forward stable (period) prevalence for each covariate */

for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */	for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
if(TKresult[nres]!= k1)	if(m != 1 && TKresult[nres]!= k1)
continue;	continue;
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */	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);	strcpy(gplotlabel,"(");
	fprintf(ficgp,"\n#\n#\n#Projection of prevalence to forward stable prevalence (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */	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 */	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(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
Line 6801 set ter svg size 640, 480\nunset log y\n	Line 7777 set ter svg size 640, 480\nunset log y\n
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];	vlv= nbcode[Tvaraff[k]][lv];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	}
	strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
Line 6813 set ter svg size 640, 480\nunset log y\n	Line 7792 set ter svg size 640, 480\nunset log y\n

fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");	fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
	fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);	set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
for (i=1; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
	/* for (i=1; i<= nlstate+1 ; i ++){ /\* nlstate +1 p11 p21 p.1 \/ /
	istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
	/istart=1;/ /* Could be one if by state, but nlstate+1 is w.i projection only */
	for (i=istart; 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/	/# 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 /	/# 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/	/# 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 /	/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 /
if(i==1){	if(i==istart){
fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));	fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
}else{	}else{
fprintf(ficgp,",\\\n '' ");	fprintf(ficgp,",\\\n '' ");
Line 6832 set ter svg size 640, 480\nunset log y\n	Line 7816 set ter svg size 640, 480\nunset log y\n
/# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4/	/# V1 = 1 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 /	/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 /
fprintf(ficgp," u %d:(", ioffset);	fprintf(ficgp," u %d:(", ioffset);
if(i==nlstate+1)	if(i==nlstate+1){
fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ", \	fprintf(ficgp," $%d/(1.-$%d)):1 t 'pw.%d' with line lc variable ", \
ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)nlstate,cpt );	ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)nlstate,cpt );
else	fprintf(ficgp,",\\\n '' ");
	fprintf(ficgp," u %d:(",ioffset);
	fprintf(ficgp," (($1-$2) == %d ) ? $%d/(1.-$%d) : 1/0):1 with labels center not ", \
	offyear, \
	ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)nlstate );
	}else
fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \	fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)nlstate,i,cpt );	ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)nlstate,i,cpt );
}else{ /* more than 2 covariates */	}else{ /* more than 2 covariates */
if(cptcoveff ==1){	ioffset=2cptcoveff+2; / Age is in 4 or 6 or etc.*/
ioffset=4; /* Age is in 4 */	/# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3/
}else{	/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 /
ioffset=6; /* Age is in 6 */	iyearc=ioffset-1;
/# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3/	iagec=ioffset;
/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 /
}
fprintf(ficgp," u %d:(",ioffset);	fprintf(ficgp," u %d:(",ioffset);
kl=0;	kl=0;
strcpy(gplotcondition,"(");	strcpy(gplotcondition,"(");
Line 6867 set ter svg size 640, 480\nunset log y\n	Line 7854 set ter svg size 640, 480\nunset log y\n
/6+1+(i-1)+(nlstate+1)nlstate; 6+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*/	/* '' 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(i==nlstate+1){	if(i==nlstate+1){
fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \	fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0):%d t 'p.%d' with line lc variable", gplotcondition, \
ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)nlstate,cpt );	ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)nlstate,iyearc, cpt );
	fprintf(ficgp,",\\\n '' ");
	fprintf(ficgp," u %d:(",iagec);
	fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d/(1.-$%d) : 1/0):%d with labels center not ", gplotcondition, \
	iyearc, iagec, offyear, \
	ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)nlstate, iyearc );
	/* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
}else{	}else{
fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \	fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)nlstate,i,cpt );	ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)nlstate,i,cpt );
}	}
} /* end if covariate */	} /* end if covariate */
} /* nlstate */	} /* nlstate */
fprintf(ficgp,"\nset out\n");	fprintf(ficgp,"\nset out; unset label;\n");
} /* end cpt state*/	} /* end cpt state*/
} /* end covariate */	} /* end covariate */
} /* End if prevfcast */	} /* End if prevfcast */

	if(prevbcast==1){
/* 9eme writing MLE parameters */	/* Back projection from cross-sectional to stable (mixed) for each covariate */
fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");
for(i=1,jk=1; i <=nlstate; i++){	for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
fprintf(ficgp,"# initial state %d\n",i);	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
for(k=1; k <=(nlstate+ndeath); k++){	if(m != 1 && TKresult[nres]!= k1)
if (k != i) {	continue;
fprintf(ficgp,"# current state %d\n",k);	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
	strcpy(gplotlabel,"(");
	fprintf(ficgp,"\n#\n#\n#Back projection of prevalence to stable (mixed) back prevalence: 'BPROJ_' files, covariatecombination#=%d originstate=%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[k]][lv];
	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
	}
	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	}
	strcpy(gplotlabel+strlen(gplotlabel),")");
	fprintf(ficgp,"\n#\n");
	if(invalidvarcomb[k1]){
	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
	continue;
	}

	fprintf(ficgp,"# hbijx=backprobability over h years, hb.jx is weighted by observed prev at destination state\n ");
	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
	fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
	set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);

	/* for (i=1; i<= nlstate+1 ; i ++){ /\* nlstate +1 p11 p21 p.1 \/ /
	istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
	/istart=1;/ /* Could be one if by state, but nlstate+1 is w.i projection only */
	for (i=istart; 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==istart){
	fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"FB_"));
	}else{
	fprintf(ficgp,",\\\n '' ");
	}
	if(cptcoveff ==0){ /* No covariate */
	ioffset=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 /
	/# V1 = 1 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 /
	fprintf(ficgp," u %d:(", ioffset);
	if(i==nlstate+1){
	fprintf(ficgp," $%d/(1.-$%d)):1 t 'bw%d' with line lc variable ", \
	ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)nlstate,cpt );
	fprintf(ficgp,",\\\n '' ");
	fprintf(ficgp," u %d:(",ioffset);
	fprintf(ficgp," (($1-$2) == %d ) ? $%d : 1/0):1 with labels center not ", \
	offbyear, \
	ioffset+(cpt-1)*(nlstate+1)+1+(i-1) );
	}else
	fprintf(ficgp," $%d/(1.-$%d)) t 'b%d%d' with line ", \
	ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)nlstate,cpt,i );
	}else{ /* more than 2 covariates */
	ioffset=2cptcoveff+2; / Age is in 4 or 6 or etc.*/
	/# 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 /
	iyearc=ioffset-1;
	iagec=ioffset;
	fprintf(ficgp," u %d:(",ioffset);
	kl=0;
	strcpy(gplotcondition,"(");
	for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
	/* 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[k]][lv]; /* Value of the modality of Tvaraff[k] */
	kl++;
	sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
	kl++;
	if(k <cptcoveff && cptcoveff>1)
	sprintf(gplotcondition+strlen(gplotcondition)," && ");
	}
	strcpy(gplotcondition+strlen(gplotcondition),")");
	/* 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(i==nlstate+1){
	fprintf(ficgp,"%s ? $%d : 1/0):%d t 'bw%d' with line lc variable", gplotcondition, \
	ioffset+(cpt-1)*(nlstate+1)+1+(i-1),iyearc,cpt );
	fprintf(ficgp,",\\\n '' ");
	fprintf(ficgp," u %d:(",iagec);
	/* fprintf(ficgp,"%s && (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", gplotcondition, \ */
	fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d : 1/0):%d with labels center not ", gplotcondition, \
	iyearc,iagec,offbyear, \
	ioffset+(cpt-1)*(nlstate+1)+1+(i-1), iyearc );
	/* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
	}else{
	/* fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \ */
	fprintf(ficgp,"%s ? $%d : 1/0) t 'b%d%d' with line ", gplotcondition, \
	ioffset+(cpt-1)*(nlstate+1)+1+(i-1), cpt,i );
	}
	} /* end if covariate */
	} /* nlstate */
	fprintf(ficgp,"\nset out; unset label;\n");
	} /* end cpt state*/
	} /* end covariate */
	} /* End if prevbcast */


	/* 9eme writing MLE parameters */
	fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");
	for(i=1,jk=1; i <=nlstate; i++){
	fprintf(ficgp,"# initial state %d\n",i);
	for(k=1; k <=(nlstate+ndeath); k++){
	if (k != i) {
	fprintf(ficgp,"# current state %d\n",k);
for(j=1; j <=ncovmodel; j++){	for(j=1; j <=ncovmodel; j++){
fprintf(ficgp,"p%d=%f; ",jk,p[jk]);	fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
jk++;	jk++;
Line 6918 set ter svg size 640, 480\nunset log y\n	Line 8026 set ter svg size 640, 480\nunset log y\n
fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");	fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
fprintf(ficgp,"#model=%s \n",model);	fprintf(ficgp,"#model=%s \n",model);
fprintf(ficgp,"# Type of graphic ng=%d\n",ng);	fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */	fprintf(ficgp,"# k1=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
for(jk=1; jk <=m; jk++) /* For each combination of covariate */	for(k1=1; k1 <=m; k1++) /* For each combination of covariate */
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
if(TKresult[nres]!= jk)	if(m != 1 && TKresult[nres]!= k1)
continue;	continue;
fprintf(ficgp,"# Combination of dummy jk=%d and ",jk);	fprintf(ficgp,"\n\n# Combination of dummy k1=%d which is ",k1);
	strcpy(gplotlabel,"(");
	/sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);/
	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[k]][lv];
	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	}
	strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng,nres);	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);
	fprintf(ficgp,"\nset key outside ");
	/* fprintf(ficgp,"\nset label \"%s\" at graph 1.2,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel); */
	fprintf(ficgp,"\nset title \"%s\" font \"Helvetica,12\"\n",gplotlabel);
fprintf(ficgp,"\nset ter svg size 640, 480 ");	fprintf(ficgp,"\nset ter svg size 640, 480 ");
if (ng==1){	if (ng==1){
fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12x) could be nice /	fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12x) could be nice /
Line 6972 set ter svg size 640, 480\nunset log y\n	Line 8096 set ter svg size 640, 480\nunset log y\n
/* for(j=3; j <=ncovmodel-nagesqr; j++) { */	/* for(j=3; j <=ncovmodel-nagesqr; j++) { */
for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */	for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
/* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */	/* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
if(j==Tage[ij]) { /* Product by age */	if(cptcovage >0){ /* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, 2 V5 and V1 */
if(ij <=cptcovage) { /* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, 2 V5 and V1 */	if(j==Tage[ij]) { /* Product by age To be looked at!!*/
if(DummyV[j]==0){	if(ij <=cptcovage) { /* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, 2 V5 and V1 */
fprintf(ficgp,"+p%d%dx",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;	if(DummyV[j]==0){
}else{ /* quantitative */	fprintf(ficgp,"+p%d%dx",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
fprintf(ficgp,"+p%d%fx",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */	}else{ /* quantitative */
/* fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */	fprintf(ficgp,"+p%d%fx",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
}	/* fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
ij++;
}
}else if(j==Tprod[ijp]) { /* */
/* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
if(ijp <=cptcovprod) { /* Product */
if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
/* fprintf(ficgp,"+p%d%d%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(jk,j)],nbcode[Tvard[ijp][2]][codtabm(jk,j)]); */
fprintf(ficgp,"+p%d%d%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
}else{ /* Vn is dummy and Vm is quanti */
/* fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(jk,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
}	}
}else{ /* VnVm Vn is quanti /	ij++;
if(DummyV[Tvard[ijp][2]]==0){	}
fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);	}
}else{ /* Both quanti */	}else if(cptcovprod >0){
fprintf(ficgp,"+p%d%f%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);	if(j==Tprod[ijp]) { /* */
	/* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
	if(ijp <=cptcovprod) { /* Product */
	if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
	if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
	/* fprintf(ficgp,"+p%d%d%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */
	fprintf(ficgp,"+p%d%d%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
	}else{ /* Vn is dummy and Vm is quanti */
	/* fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
	fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
	}
	}else{ /* VnVm Vn is quanti /
	if(DummyV[Tvard[ijp][2]]==0){
	fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
	}else{ /* Both quanti */
	fprintf(ficgp,"+p%d%f%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
	}
}	}
	ijp++;
}	}
ijp++;	} /* end Tprod */
}
} else{ /* simple covariate */	} else{ /* simple covariate */
/* fprintf(ficgp,"+p%d%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(jk,j)]); /\ Valgrind bug nbcode \/ /	/* fprintf(ficgp,"+p%d%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\ Valgrind bug nbcode \/ /
if(Dummy[j]==0){	if(Dummy[j]==0){
fprintf(ficgp,"+p%d%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); / */	fprintf(ficgp,"+p%d%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); / */
}else{ /* quantitative */	}else{ /* quantitative */
fprintf(ficgp,"+p%d%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); / */	fprintf(ficgp,"+p%d%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); / */
/* fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */	/* fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
}	}
} /* end simple */	} /* end simple */
} /* end j */	} /* end j */
Line 7021 set ter svg size 640, 480\nunset log y\n	Line 8149 set ter svg size 640, 480\nunset log y\n
if(ng != 1){	if(ng != 1){
fprintf(ficgp,")/(1");	fprintf(ficgp,")/(1");

for(k1=1; k1 <=nlstate; k1++){	for(cpt=1; cpt <=nlstate; cpt++){
if(nagesqr==0)	if(nagesqr==0)
fprintf(ficgp,"+exp(p%d+p%dx",k3+(k1-1)ncovmodel,k3+(k1-1)*ncovmodel+1);	fprintf(ficgp,"+exp(p%d+p%dx",k3+(cpt-1)ncovmodel,k3+(cpt-1)*ncovmodel+1);
else /* nagesqr =1 */	else /* nagesqr =1 */
fprintf(ficgp,"+exp(p%d+p%dx+p%dxx",k3+(k1-1)ncovmodel,k3+(k1-1)ncovmodel+1,k3+(k1-1)ncovmodel+1+nagesqr);	fprintf(ficgp,"+exp(p%d+p%dx+p%dxx",k3+(cpt-1)ncovmodel,k3+(cpt-1)ncovmodel+1,k3+(cpt-1)ncovmodel+1+nagesqr);

ij=1;	ij=1;
for(j=3; j <=ncovmodel-nagesqr; j++){	for(j=3; j <=ncovmodel-nagesqr; j++){
if((j-2)==Tage[ij]) { /* Bug valgrind */	if(cptcovage >0){
if(ij <=cptcovage) { /* Bug valgrind */	if((j-2)==Tage[ij]) { /* Bug valgrind */
fprintf(ficgp,"+p%d%dx",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);	if(ij <=cptcovage) { /* Bug valgrind */
/* fprintf(ficgp,"+p%d%dx",k3+(k1-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); /	fprintf(ficgp,"+p%d%dx",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);
ij++;	/* fprintf(ficgp,"+p%d%dx",k3+(cpt-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); /
}	ij++;
}	}
else	}
fprintf(ficgp,"+p%d%d",k3+(k1-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);/* Valgrind bug nbcode */	}else
	fprintf(ficgp,"+p%d%d",k3+(cpt-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);/* Valgrind bug nbcode */
}	}
fprintf(ficgp,")");	fprintf(ficgp,")");
}	}
fprintf(ficgp,")");	fprintf(ficgp,")");
if(ng ==2)	if(ng ==2)
fprintf(ficgp," t \"p%d%d\" ", k2,k);	fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"p%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
else /* ng= 3 */	else /* ng= 3 */
fprintf(ficgp," t \"i%d%d\" ", k2,k);	fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"i%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
}else{ /* end ng <> 1 */	}else{ /* end ng <> 1 */
if( k !=k2) /* logit p11 is hard to draw */	if( k !=k2) /* logit p11 is hard to draw */
fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);	fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"logit(p%d%d)\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
}	}
if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)	if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
fprintf(ficgp,",");	fprintf(ficgp,",");
Line 7057 set ter svg size 640, 480\nunset log y\n	Line 8186 set ter svg size 640, 480\nunset log y\n
i=i+ncovmodel;	i=i+ncovmodel;
} /* end k */	} /* end k */
} /* end k2 */	} /* end k2 */
fprintf(ficgp,"\n set out\n");	/* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */
} /* end jk */	fprintf(ficgp,"\n set out; unset title;set key default;\n");
	} /* end k1 */
} /* end ng */	} /* end ng */
/* avoid: */	/* avoid: */
fflush(ficgp);	fflush(ficgp);
Line 7073 set ter svg size 640, 480\nunset log y\n	Line 8203 set ter svg size 640, 480\nunset log y\n
int modcovmax =1;	int modcovmax =1;
int mobilavrange, mob;	int mobilavrange, mob;
int iage=0;	int iage=0;
	int firstA1=0, firstA2=0;

double sum=0.;	double sum=0., sumr=0.;
double age;	double age;
double sumnewp, sumnewm;	double sumnewp, sumnewm, *sumnewmr;
double agemingood, agemaxgood; /* Currently identical for all covariates */	double agemingood, agemaxgood;
	double agemingoodr, agemaxgoodr;


/* modcovmax=2cptcoveff;/\ Max number of modalities. We suppose */	/* modcovmax=2cptcoveff; Max number of modalities. We suppose /
/* a covariate has 2 modalities, should be equal to ncovcombmax \/ /	/* a covariate has 2 modalities, should be equal to ncovcombmax */

sumnewp = vector(1,ncovcombmax);	sumnewp = vector(1,ncovcombmax);
sumnewm = vector(1,ncovcombmax);	sumnewm = vector(1,ncovcombmax);
	sumnewmr = vector(1,ncovcombmax);
agemingood = vector(1,ncovcombmax);	agemingood = vector(1,ncovcombmax);
	agemingoodr = vector(1,ncovcombmax);
agemaxgood = vector(1,ncovcombmax);	agemaxgood = vector(1,ncovcombmax);
	agemaxgoodr = vector(1,ncovcombmax);

for (cptcod=1;cptcod<=ncovcombmax;cptcod++){	for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
sumnewm[cptcod]=0.;	sumnewm[cptcod]=0.; sumnewmr[cptcod]=0.;
sumnewp[cptcod]=0.;	sumnewp[cptcod]=0.;
agemingood[cptcod]=0;	agemingood[cptcod]=0, agemingoodr[cptcod]=0;
agemaxgood[cptcod]=0;	agemaxgood[cptcod]=0, agemaxgoodr[cptcod]=0;
}	}
if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */	if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */

if(mobilav==1\|\|mobilav ==3 \|\|mobilav==5 \|\|mobilav== 7){	if(mobilav==-1 \|\| mobilav==1\|\|mobilav ==3 \|\|mobilav==5 \|\|mobilav== 7){
if(mobilav==1) mobilavrange=5; /* default */	if(mobilav==1 \|\| mobilav==-1) mobilavrange=5; /* default */
else mobilavrange=mobilav;	else mobilavrange=mobilav;
for (age=bage; age<=fage; age++)	for (age=bage; age<=fage; age++)
for (i=1; i<=nlstate;i++)	for (i=1; i<=nlstate;i++)
Line 7109 set ter svg size 640, 480\nunset log y\n	Line 8244 set ter svg size 640, 480\nunset log y\n
*/	*/
for (mob=3;mob <=mobilavrange;mob=mob+2){	for (mob=3;mob <=mobilavrange;mob=mob+2){
for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){	for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
for (i=1; i<=nlstate;i++){	for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
for (cptcod=1;cptcod<=ncovcombmax;cptcod++){	sumnewm[cptcod]=0.;
	for (i=1; i<=nlstate;i++){
mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];	mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
for (cpt=1;cpt<=(mob-1)/2;cpt++){	for (cpt=1;cpt<=(mob-1)/2;cpt++){
mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];	mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];	mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
}	}
mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;	mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
}	sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
}	} /* end i */
	if(sumnewm[cptcod] >1.e-3) mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/sumnewm[cptcod]; /* Rescaling to sum one */
	} /* end cptcod */
}/* end age */	}/* end age */
}/* end mob */	}/* end mob */
}else	}else{
	printf("Error internal in movingaverage, mobilav=%d.\n",mobilav);
return -1;	return -1;
for (cptcod=1;cptcod<=ncovcombmax;cptcod++){	}

	for (cptcod=1;cptcod<=ncovcombmax;cptcod++){ /* for each combination */
/* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */	/* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
if(invalidvarcomb[cptcod]){	if(invalidvarcomb[cptcod]){
printf("\nCombination (%d) ignored because no cases \n",cptcod);	printf("\nCombination (%d) ignored because no cases \n",cptcod);
continue;	continue;
}	}

agemingood[cptcod]=fage-(mob-1)/2;	for (age=fage-(mob-1)/2; age>=bage+(mob-1)/2; age--){ /looking for the youngest and oldest good age /
for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */
sumnewm[cptcod]=0.;	sumnewm[cptcod]=0.;
	sumnewmr[cptcod]=0.;
for (i=1; i<=nlstate;i++){	for (i=1; i<=nlstate;i++){
sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];	sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
	sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
	}
	if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
	agemingoodr[cptcod]=age;
}	}
if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */	if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
agemingood[cptcod]=age;	agemingood[cptcod]=age;
}else{ /* bad */	}
for (i=1; i<=nlstate;i++){	} /* age */
mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];	for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ /looking for the youngest and oldest good age /
} /* i */
} /* end bad */
}/* age */
sum=0.;
for (i=1; i<=nlstate;i++){
sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];
}
if(fabs(sum - 1.) > 1.e-3) { /* bad */
printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any descending age!\n",cptcod);
/* for (i=1; i<=nlstate;i++){ */
/* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
/* } /\* i \/ /
} /* end bad */
/* else{ /\* We found some ages summing to one, we will smooth the oldest \/ /
/* From youngest, finding the oldest wrong */
agemaxgood[cptcod]=bage+(mob-1)/2;
for (age=bage+(mob-1)/2; age<=fage; age++){
sumnewm[cptcod]=0.;	sumnewm[cptcod]=0.;
	sumnewmr[cptcod]=0.;
for (i=1; i<=nlstate;i++){	for (i=1; i<=nlstate;i++){
sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];	sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
	sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
	}
	if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
	agemaxgoodr[cptcod]=age;
}	}
if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */	if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
agemaxgood[cptcod]=age;	agemaxgood[cptcod]=age;
}else{ /* bad */	}
for (i=1; i<=nlstate;i++){	} /* age */
mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];	/* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */
} /* i */	/* but they will change */
	firstA1=0;firstA2=0;
	for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */
	sumnewm[cptcod]=0.;
	sumnewmr[cptcod]=0.;
	for (i=1; i<=nlstate;i++){
	sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
	sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
	}
	if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
	if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
	agemaxgoodr[cptcod]=age; /* age min */
	for (i=1; i<=nlstate;i++)
	mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
	}else{ /* bad we change the value with the values of good ages */
	for (i=1; i<=nlstate;i++){
	mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgoodr[cptcod]][i][cptcod];
	} /* i */
	} /* end bad */
	}else{
	if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
	agemaxgood[cptcod]=age;
	}else{ /* bad we change the value with the values of good ages */
	for (i=1; i<=nlstate;i++){
	mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
	} /* i */
	} /* end bad */
	}/* end else */
	sum=0.;sumr=0.;
	for (i=1; i<=nlstate;i++){
	sum+=mobaverage[(int)age][i][cptcod];
	sumr+=probs[(int)age][i][cptcod];
	}
	if(fabs(sum - 1.) > 1.e-3) { /* bad */
	if(!firstA1){
	firstA1=1;
	printf("Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d. Others in log file...\n",cptcod,sumr, (int)age, (int)bage);
	}
	fprintf(ficlog,"Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage);
	} /* end bad */
	/* else{ /\* We found some ages summing to one, we will smooth the oldest \/ /
	if(fabs(sumr - 1.) > 1.e-3) { /* bad */
	if(!firstA2){
	firstA2=1;
	printf("Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d. Others in log file...\n",cptcod,sumr, (int)age, (int)bage);
	}
	fprintf(ficlog,"Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage);
} /* end bad */	} /* end bad */
}/* age */	}/* age */
sum=0.;
for (i=1; i<=nlstate;i++){	for (age=bage+(mob-1)/2; age<=fage; age++){/* From youngest, finding the oldest wrong */
sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];	sumnewm[cptcod]=0.;
}	sumnewmr[cptcod]=0.;
if(fabs(sum - 1.) > 1.e-3) { /* bad */	for (i=1; i<=nlstate;i++){
printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any ascending age!\n",cptcod);	sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
/* for (i=1; i<=nlstate;i++){ */	sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
/* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */	}
/* } /\* i \/ /	if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
} /* end bad */	if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good */
	agemingoodr[cptcod]=age;
	for (i=1; i<=nlstate;i++)
	mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
	}else{ /* bad we change the value with the values of good ages */
	for (i=1; i<=nlstate;i++){
	mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingoodr[cptcod]][i][cptcod];
	} /* i */
	} /* end bad */
	}else{
	if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
	agemingood[cptcod]=age;
	}else{ /* bad */
	for (i=1; i<=nlstate;i++){
	mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
	} /* i */
	} /* end bad */
	}/* end else */
	sum=0.;sumr=0.;
	for (i=1; i<=nlstate;i++){
	sum+=mobaverage[(int)age][i][cptcod];
	sumr+=mobaverage[(int)age][i][cptcod];
	}
	if(fabs(sum - 1.) > 1.e-3) { /* bad */
	printf("Moving average B1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you decrease fage=%d?\n",cptcod, sum, (int) age, (int)fage);
	} /* end bad */
	/* else{ /\* We found some ages summing to one, we will smooth the oldest \/ /
	if(fabs(sumr - 1.) > 1.e-3) { /* bad */
	printf("Moving average B2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase fage=%d\n",cptcod,sumr, (int)age, (int)fage);
	} /* end bad */
	}/* age */


for (age=bage; age<=fage; age++){	for (age=bage; age<=fage; age++){
/* printf("%d %d ", cptcod, (int)age); */	/* printf("%d %d ", cptcod, (int)age); */
Line 7194 set ter svg size 640, 480\nunset log y\n	Line 8404 set ter svg size 640, 480\nunset log y\n
}	}
/* printf("\n"); */	/* printf("\n"); */
/* } */	/* } */

/* brutal averaging */	/* brutal averaging */
for (i=1; i<=nlstate;i++){	/* for (i=1; i<=nlstate;i++){ */
for (age=1; age<=bage; age++){	/* for (age=1; age<=bage; age++){ */
mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];	/* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
/* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */	/* /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); \/ /
}	/* } */
for (age=fage; age<=AGESUP; age++){	/* for (age=fage; age<=AGESUP; age++){ */
mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];	/* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod]; */
/* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */	/* /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); \/ /
}	/* } */
} /* end i status */	/* } /\* end i status \/ /
for (i=nlstate+1; i<=nlstate+ndeath;i++){	/* for (i=nlstate+1; i<=nlstate+ndeath;i++){ */
for (age=1; age<=AGESUP; age++){	/* for (age=1; age<=AGESUP; age++){ */
/printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);/	/* /\printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);\/ */
mobaverage[(int)age][i][cptcod]=0.;	/* mobaverage[(int)age][i][cptcod]=0.; */
}	/* } */
}	/* } */
}/* end cptcod */	}/* end cptcod */
free_vector(sumnewm,1, ncovcombmax);	free_vector(agemaxgoodr,1, ncovcombmax);
free_vector(sumnewp,1, ncovcombmax);
free_vector(agemaxgood,1, ncovcombmax);	free_vector(agemaxgood,1, ncovcombmax);
free_vector(agemingood,1, ncovcombmax);	free_vector(agemingood,1, ncovcombmax);
	free_vector(agemingoodr,1, ncovcombmax);
	free_vector(sumnewmr,1, ncovcombmax);
	free_vector(sumnewm,1, ncovcombmax);
	free_vector(sumnewp,1, ncovcombmax);
return 0;	return 0;
}/* End movingaverage */	}/* End movingaverage */



/************ Forecasting ****************/	/************ Forecasting ****************/
void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){	/* void prevforecast(char fileres[], double dateintmean, double anprojd, double mprojd, double jprojd, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double **prev, double bage, double fage, int firstpass, int lastpass, double anprojf, double p[], int cptcoveff)/
/* proj1, year, month, day of starting projection	void prevforecast(char fileres[], double dateintmean, double dateprojd, double dateprojf, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double ***prev, double bage, double fage, int firstpass, int lastpass, double p[], int cptcoveff){
	/* dateintemean, mean date of interviews
	dateprojd, year, month, day of starting projection
	dateprojf date of end of projection;year of end of projection (same day and month as proj1).
agemin, agemax range of age	agemin, agemax range of age
dateprev1 dateprev2 range of dates during which prevalence is computed	dateprev1 dateprev2 range of dates during which prevalence is computed
anproj2 year of en of projection (same day and month as proj1).
*/	*/
int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;	/* double anprojd, mprojd, jprojd; */
	/* double anprojf, mprojf, jprojf; */
	int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
double agec; /* generic age */	double agec; /* generic age */
double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;	double agelim, ppij, yp,yp1,yp2;
double popeffectif,popcount;	double popeffectif,popcount;
double ***p3mat;	double ***p3mat;
/* double **mobaverage; /	/* double **mobaverage; /
Line 7260 set ter svg size 640, 480\nunset log y\n	Line 8479 set ter svg size 640, 480\nunset log y\n
if(estepm < stepm){	if(estepm < stepm){
printf ("Problem %d lower than %d\n",estepm, stepm);	printf ("Problem %d lower than %d\n",estepm, stepm);
}	}
else hstepm=estepm;	else{
	hstepm=estepm;
	}
	if(estepm > stepm){ /* Yes every two year */
	stepsize=2;
	}
	hstepm=hstepm/stepm;


	/* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
	/* fractional in yp1 \/ /
	/* aintmean=yp; */
	/* yp2=modf((yp112),&yp); /
	/* mintmean=yp; */
	/* yp1=modf((yp230.5),&yp); /
	/* jintmean=yp; */
	/* if(jintmean==0) jintmean=1; */
	/* if(mintmean==0) mintmean=1; */

hstepm=hstepm/stepm;
yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
fractional in yp1 */
anprojmean=yp;
yp2=modf((yp1*12),&yp);
mprojmean=yp;
yp1=modf((yp2*30.5),&yp);
jprojmean=yp;
if(jprojmean==0) jprojmean=1;
if(mprojmean==0) jprojmean=1;

	/* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */
	/* date2dmy(dateprojd,&jprojd, &mprojd, &anprojd); */
	/* date2dmy(dateprojf,&jprojf, &mprojf, &anprojf); */
i1=pow(2,cptcoveff);	i1=pow(2,cptcoveff);
if (cptcovn < 1){i1=1;}	if (cptcovn < 1){i1=1;}

fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);	fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);

fprintf(ficresf,"#**** Routine prevforecast \n");	fprintf(ficresf,"#**** Routine prevforecast \n");

/* if (h==(int)(YEARMyearp)){ /	/* if (h==(int)(YEARMyearp)){ /
for(nres=1; nres <= nresult; nres++) /* For each resultline */	for(nres=1; nres <= nresult; nres++) /* For each resultline */
for(k=1; k<=i1;k++){	for(k=1; k<=i1;k++){
if(TKresult[nres]!= k)	if(i1 != 1 && TKresult[nres]!= k)
continue;	continue;
if(invalidvarcomb[k]){	if(invalidvarcomb[k]){
printf("\nCombination (%d) projection ignored because no cases \n",k);	printf("\nCombination (%d) projection ignored because no cases \n",k);
Line 7302 set ter svg size 640, 480\nunset log y\n	Line 8531 set ter svg size 640, 480\nunset log y\n
fprintf(ficresf," p%d%d",i,j);	fprintf(ficresf," p%d%d",i,j);
fprintf(ficresf," wp.%d",j);	fprintf(ficresf," wp.%d",j);
}	}
for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {	for (yearp=0; yearp<=(anprojf-anprojd);yearp +=stepsize) {
fprintf(ficresf,"\n");	fprintf(ficresf,"\n");
fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);	fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jprojd,mprojd,anprojd+yearp);
for (agec=fage; agec>=(ageminpar-1); agec--){	/* for (agec=fage; agec>=(ageminpar-1); agec--){ */
	for (agec=fage; agec>=(bage); agec--){
nhstepm=(int) rint((agelim-agec)*YEARM/stepm);	nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
nhstepm = nhstepm/hstepm;	nhstepm = nhstepm/hstepm;
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
oldm=oldms;savm=savms;	oldm=oldms;savm=savms;
	/* We compute pii at age agec over nhstepm);*/
hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);	hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);
	/* Then we print p3mat for h corresponding to the right agec+hstepms=yearp /
for (h=0; h<=nhstepm; h++){	for (h=0; h<=nhstepm; h++){
if (hhstepm/YEARMstepm ==yearp) {	if (hhstepm/YEARMstepm ==yearp) {
fprintf(ficresf,"\n");	break;
for(j=1;j<=cptcoveff;j++)	}
fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	}
fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+hhstepm/YEARMstepm);	fprintf(ficresf,"\n");
}	for(j=1;j<=cptcoveff;j++)
for(j=1; j<=nlstate+ndeath;j++) {	fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
ppij=0.;	fprintf(ficresf,"%.f %.f ",anprojd+yearp,agec+hhstepm/YEARMstepm);
for(i=1; i<=nlstate;i++) {
if (mobilav==1)	for(j=1; j<=nlstate+ndeath;j++) {
ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][k];	ppij=0.;
else {	for(i=1; i<=nlstate;i++) {
ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];	if (mobilav>=1)
}	ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];
if (hhstepm/YEARMstepm== yearp) {	else { /* even if mobilav==-1 we use mobaverage, probs may not sums to 1 */
fprintf(ficresf," %.3f", p3mat[i][j][h]);	ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
}
} /* end i */
if (hhstepm/YEARMstepm==yearp) {
fprintf(ficresf," %.3f", ppij);
}	}
}/* end j */	fprintf(ficresf," %.3f", p3mat[i][j][h]);
} /* end h */	} /* end i */
	fprintf(ficresf," %.3f", ppij);
	}/* end j */
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
} /* end agec */	} /* end agec */
	/* diffyear=(int) anproj1+yearp-ageminpar-1; */
	/printf("Prevforecast %d+%d-%d=diffyear=%d\n",(int) anproj1, (int)yearp,(int)ageminpar,(int) anproj1-(int)ageminpar);/
} /* end yearp */	} /* end yearp */
} /* end k */	} /* end k */

Line 7347 set ter svg size 640, 480\nunset log y\n	Line 8578 set ter svg size 640, 480\nunset log y\n

}	}

/* /\************ Back Forecasting ***************\/ /	/************ Back Forecasting ****************/
/* void prevbackforecast(char fileres[], double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){ */	/* void prevbackforecast(char fileres[], double **prevacurrent, double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){ /
/* /\* back1, year, month, day of starting backection */	void prevbackforecast(char fileres[], double ***prevacurrent, double dateintmean, double dateprojd, double dateprojf, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double p[], int cptcoveff){
/* agemin, agemax range of age */	/* back1, year, month, day of starting backprojection
/* dateprev1 dateprev2 range of dates during which prevalence is computed */	agemin, agemax range of age
/* anback2 year of en of backection (same day and month as back1). */	dateprev1 dateprev2 range of dates during which prevalence is computed
/* \/ /	anback2 year of end of backprojection (same day and month as back1).
/* int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; */	prevacurrent and prev are prevalences.
/* double agec; /\* generic age \/ /	*/
/* double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; */	int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
/* double popeffectif,popcount; */	double agec; /* generic age */
/* double **p3mat; /	double agelim, ppij, ppi, yp,yp1,yp2; /* ,jintmean,mintmean,aintmean;*/
/* /\* double **mobaverage; \/ */	double popeffectif,popcount;
/* char fileresfb[FILENAMELENGTH]; */	double ***p3mat;
	/* double **mobaverage; /
/* agelim=AGESUP; */	char fileresfb[FILENAMELENGTH];
/* /\* 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). */	agelim=AGEINF;
/* We still use firstpass and lastpass as another selection. */	/* 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).
/* /\* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ \/ /	We still use firstpass and lastpass as another selection.
/* /\* firstpass, lastpass, stepm, weightopt, model); \/ /	*/
/* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */	/* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
	/* firstpass, lastpass, stepm, weightopt, model); */
/* strcpy(fileresfb,"FB_"); */
/* strcat(fileresfb,fileresu); */	/Do we need to compute prevalence again?/
/* if((ficresfb=fopen(fileresfb,"w"))==NULL) { */
/* printf("Problem with back forecast resultfile: %s\n", fileresfb); */	/* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
/* fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb); */
/* } */
/* printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
/* fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */

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

/* /\* if (mobilav!=0) { \/ /
/* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); \/ /
/* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ \/ /
/* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); \/ /
/* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); \/ /
/* /\* } \/ /
/* /\* } \/ /

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

/* hstepm=hstepm/stepm; */
/* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
/* fractional in yp1 \/ /
/* anprojmean=yp; */
/* yp2=modf((yp112),&yp); /
/* mprojmean=yp; */
/* yp1=modf((yp230.5),&yp); /
/* jprojmean=yp; */
/* if(jprojmean==0) jprojmean=1; */
/* if(mprojmean==0) jprojmean=1; */

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

/* fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); */	strcpy(fileresfb,"FB_");
	strcat(fileresfb,fileresu);
	if((ficresfb=fopen(fileresfb,"w"))==NULL) {
	printf("Problem with back forecast resultfile: %s\n", fileresfb);
	fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb);
	}
	printf("\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
	fprintf(ficlog,"\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);

/* fprintf(ficresfb,"#**** Routine prevbackforecast \n"); */	if (cptcoveff==0) ncodemax[cptcoveff]=1;

/* /\* if (h==(int)(YEARMyearp)){ \/ */
/* for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */	stepsize=(int) (stepm+YEARM-1)/YEARM;
/* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */	if (stepm<=12) stepsize=1;
/* k=k+1; */	if(estepm < stepm){
/* fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */	printf ("Problem %d lower than %d\n",estepm, stepm);
/* for(j=1;j<=cptcoveff;j++) { */	}
/* fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */	else{
/* } */	hstepm=estepm;
/* fprintf(ficresfb," yearbproj age"); */	}
/* for(j=1; j<=nlstate+ndeath;j++){ */	if(estepm >= stepm){ /* Yes every two year */
/* for(i=1; i<=nlstate;i++) */	stepsize=2;
/* fprintf(ficresfb," p%d%d",i,j); */	}
/* fprintf(ficresfb," p.%d",j); */
/* } */	hstepm=hstepm/stepm;
/* for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) { */	/* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
/* /\* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { \/ /	/* fractional in yp1 \/ /
/* fprintf(ficresfb,"\n"); */	/* aintmean=yp; */
/* fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */	/* yp2=modf((yp112),&yp); /
/* for (agec=fage; agec>=(ageminpar-1); agec--){ */	/* mintmean=yp; */
/* nhstepm=(int) rint((agelim-agec)YEARM/stepm); /	/* yp1=modf((yp230.5),&yp); /
/* nhstepm = nhstepm/hstepm; */	/* jintmean=yp; */
/* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */	/* if(jintmean==0) jintmean=1; */
/* oldm=oldms;savm=savms; */	/* if(mintmean==0) jintmean=1; */
/* hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm,oldm,savm, dnewm, doldm, dsavm, k); */
/* for (h=0; h<=nhstepm; h++){ */	i1=pow(2,cptcoveff);
/* if (hhstepm/YEARMstepm ==yearp) { */	if (cptcovn < 1){i1=1;}
/* fprintf(ficresfb,"\n"); */
/* for(j=1;j<=cptcoveff;j++) */	fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
/* fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */	printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
/* fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+hhstepm/YEARMstepm); */
/* } */	fprintf(ficresfb,"#**** Routine prevbackforecast \n");
/* for(j=1; j<=nlstate+ndeath;j++) { */
/* ppij=0.; */	for(nres=1; nres <= nresult; nres++) /* For each resultline */
/* for(i=1; i<=nlstate;i++) { */	for(k=1; k<=i1;k++){
/* if (mobilav==1) */	if(i1 != 1 && TKresult[nres]!= k)
/* ppij=ppij+p3mat[i][j][h]mobaverage[(int)agec][i][cptcod]; /	continue;
/* else { */	if(invalidvarcomb[k]){
/* ppij=ppij+p3mat[i][j][h]probs[(int)(agec)][i][cptcod]; /	printf("\nCombination (%d) projection ignored because no cases \n",k);
/* } */	continue;
/* if (hhstepm/YEARMstepm== yearp) { */	}
/* fprintf(ficresfb," %.3f", p3mat[i][j][h]); */	fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
/* } */	for(j=1;j<=cptcoveff;j++) {
/* } /\* end i \/ /	fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
/* if (hhstepm/YEARMstepm==yearp) { */	}
/* fprintf(ficresfb," %.3f", ppij); */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
/* } */	fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
/* }/\* end j \/ /	}
/* } /\* end h \/ /	fprintf(ficresfb," yearbproj age");
/* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */	for(j=1; j<=nlstate+ndeath;j++){
/* } /\* end agec \/ /	for(i=1; i<=nlstate;i++)
/* } /\* end yearp \/ /	fprintf(ficresfb," b%d%d",i,j);
/* } /\* end cptcod \/ /	fprintf(ficresfb," b.%d",j);
/* } /\* end cptcov \/ /	}
	for (yearp=0; yearp>=(anbackf-anbackd);yearp -=stepsize) {
/* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); \/ /	/* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { */
	fprintf(ficresfb,"\n");
/* fclose(ficresfb); */	fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jbackd,mbackd,anbackd+yearp);
/* printf("End of Computing Back forecasting \n"); */	/* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
/* fprintf(ficlog,"End of Computing Back forecasting\n"); */	/* for (agec=bage; agec<=agemax-1; agec++){ /\* testing \/ /
	for (agec=bage; agec<=fage; agec++){ /* testing */
	/* We compute bij at age agec over nhstepm, nhstepm decreases when agec increases because of agemax;*/
	nhstepm=(int) (agec-agelim) YEARM/stepm;/ nhstepm=(int) rint((agec-agelim)YEARM/stepm);/
	nhstepm = nhstepm/hstepm;
	p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
	oldm=oldms;savm=savms;
	/* computes hbxij at age agec over 1 to nhstepm */
	/* printf("####prevbackforecast debug agec=%.2f nhstepm=%d\n",agec, nhstepm);fflush(stdout); */
	hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
	/* hpxij(p3mat,nhstepm,agec,hstepm,p, nlstate,stepm,oldm,savm, k,nres); */
	/* Then we print p3mat for h corresponding to the right agec+hstepms=yearp /
	/* printf(" agec=%.2f\n",agec);fflush(stdout); */
	for (h=0; h<=nhstepm; h++){
	if (hhstepm/YEARMstepm ==-yearp) {
	break;
	}
	}
	fprintf(ficresfb,"\n");
	for(j=1;j<=cptcoveff;j++)
	fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
	fprintf(ficresfb,"%.f %.f ",anbackd+yearp,agec-hhstepm/YEARMstepm);
	for(i=1; i<=nlstate+ndeath;i++) {
	ppij=0.;ppi=0.;
	for(j=1; j<=nlstate;j++) {
	/* if (mobilav==1) */
	ppij=ppij+p3mat[i][j][h]*prevacurrent[(int)agec][j][k];
	ppi=ppi+prevacurrent[(int)agec][j][k];
	/* ppij=ppij+p3mat[i][j][h]mobaverage[(int)agec][j][k]; /
	/* ppi=ppi+mobaverage[(int)agec][j][k]; */
	/* else { */
	/* ppij=ppij+p3mat[i][j][h]probs[(int)(agec)][i][k]; /
	/* } */
	fprintf(ficresfb," %.3f", p3mat[i][j][h]);
	} /* end j */
	if(ppi <0.99){
	printf("Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
	fprintf(ficlog,"Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
	}
	fprintf(ficresfb," %.3f", ppij);
	}/* end j */
	free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
	} /* end agec */
	} /* end yearp */
	} /* end k */

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

	fclose(ficresfb);
	printf("End of Computing Back forecasting \n");
	fprintf(ficlog,"End of Computing Back forecasting\n");

/* } */	}

	/* Variance of prevalence limit: varprlim */
	void varprlim(char fileresu[], int nresult, double *prevacurrent, int mobilavproj, double bage, double fage, double prlim, int ncvyearp, double ftolpl, double p[], double matcov, double delti, int stepm, int cptcoveff){
	/------- Variance of forward period (stable) prevalence------/

	char fileresvpl[FILENAMELENGTH];
	FILE *ficresvpl;
	double oldm, savm;
	double *varpl; / Variances of prevalence limits by age */
	int i1, k, nres, j ;

	strcpy(fileresvpl,"VPL_");
	strcat(fileresvpl,fileresu);
	if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
	printf("Problem with variance of forward period (stable) prevalence resultfile: %s\n", fileresvpl);
	exit(0);
	}
	printf("Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
	fprintf(ficlog, "Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);

	/*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
	for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/

	i1=pow(2,cptcoveff);
	if (cptcovn < 1){i1=1;}

	for(nres=1; nres <= nresult; nres++) /* For each resultline */
	for(k=1; k<=i1;k++){
	if(i1 != 1 && TKresult[nres]!= k)
	continue;
	fprintf(ficresvpl,"\n#****** ");
	printf("\n#****** ");
	fprintf(ficlog,"\n#****** ");
	for(j=1;j<=cptcoveff;j++) {
	fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
	fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
	printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
	}
	for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
	printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
	fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
	fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
	}
	fprintf(ficresvpl,"******\n");
	printf("******\n");
	fprintf(ficlog,"******\n");

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

	fclose(ficresvpl);
	printf("done variance-covariance of forward period prevalence\n");fflush(stdout);
	fprintf(ficlog,"done variance-covariance of forward period prevalence\n");fflush(ficlog);

	}
	/* Variance of back prevalence: varbprlim */
	void varbprlim(char fileresu[], int nresult, double *prevacurrent, int mobilavproj, double bage, double fage, double bprlim, int ncvyearp, double ftolpl, double p[], double matcov, double delti, int stepm, int cptcoveff){
	/------- Variance of back (stable) prevalence------/

	char fileresvbl[FILENAMELENGTH];
	FILE *ficresvbl;

	double oldm, savm;
	double *varbpl; / Variances of back prevalence limits by age */
	int i1, k, nres, j ;

	strcpy(fileresvbl,"VBL_");
	strcat(fileresvbl,fileresu);
	if((ficresvbl=fopen(fileresvbl,"w"))==NULL) {
	printf("Problem with variance of back (stable) prevalence resultfile: %s\n", fileresvbl);
	exit(0);
	}
	printf("Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(stdout);
	fprintf(ficlog, "Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(ficlog);


	i1=pow(2,cptcoveff);
	if (cptcovn < 1){i1=1;}

	for(nres=1; nres <= nresult; nres++) /* For each resultline */
	for(k=1; k<=i1;k++){
	if(i1 != 1 && TKresult[nres]!= k)
	continue;
	fprintf(ficresvbl,"\n#****** ");
	printf("\n#****** ");
	fprintf(ficlog,"\n#****** ");
	for(j=1;j<=cptcoveff;j++) {
	fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
	fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
	printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
	}
	for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
	printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
	fprintf(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
	fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
	}
	fprintf(ficresvbl,"******\n");
	printf("******\n");
	fprintf(ficlog,"******\n");

	varbpl=matrix(1,nlstate,(int) bage, (int) fage);
	oldm=oldms;savm=savms;

	varbrevlim(fileresvbl, ficresvbl, varbpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, bprlim, ftolpl, mobilavproj, ncvyearp, k, strstart, nres);
	free_matrix(varbpl,1,nlstate,(int) bage, (int)fage);
	/}/
	}

	fclose(ficresvbl);
	printf("done variance-covariance of back prevalence\n");fflush(stdout);
	fprintf(ficlog,"done variance-covariance of back prevalence\n");fflush(ficlog);

	} /* End of varbprlim */

/************ Forecasting *not tested NB***********/	/************ Forecasting *not tested NB***********/
/* void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2s, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ */	/* void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2s, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ */
Line 7775 void prwizard(int ncovmodel, int nlstate	Line 9145 void prwizard(int ncovmodel, int nlstate
/***************** Gompertz Likelihood ****************************/	/***************** Gompertz Likelihood ****************************/
double gompertz(double x[])	double gompertz(double x[])
{	{
double A,B,L=0.0,sump=0.,num=0.;	double A=0.0,B=0.,L=0.0,sump=0.,num=0.;
int i,n=0; /* n is the size of the sample */	int i,n=0; /* n is the size of the sample */

for (i=1;i<=imx ; i++) {	for (i=1;i<=imx ; i++) {
Line 7783 double gompertz(double x[])	Line 9153 double gompertz(double x[])
/* sump=sump+1;*/	/* sump=sump+1;*/
num=num+1;	num=num+1;
}	}
	L=0.0;
	/* agegomp=AGEGOMP; */
/* for (i=0; i<=imx; i++)	/* for (i=0; i<=imx; i++)
if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/	if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/

for (i=1;i<=imx ; i++)	for (i=1;i<=imx ; i++) {
{	/* mu(a)=mu(agecomp)exp(teta(age-agegomp))
if (cens[i] == 1 && wav[i]>1)	mu(a)=x[1]exp(x[2](age-agegomp)); x[1] and x[2] are per year.
A=-x[1]/(x[2])(exp(x[2](agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));	* L= Product mu(agedeces)exp(-\int_ageexam^agedc mu(u) du ) for a death between agedc (in month)
	* and agedc +1 month, cens[i]=0: log(x[1]/YEARM)
if (cens[i] == 0 && wav[i]>1)	* +
	* exp(-\int_ageexam^agecens mu(u) du ) when censored, cens[i]=1
	*/
	if (wav[i] > 1 \|\| agedc[i] < AGESUP) {
	if (cens[i] == 1){
	A=-x[1]/(x[2])(exp(x[2](agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
	} else if (cens[i] == 0){
A=-x[1]/(x[2])(exp(x[2](agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))	A=-x[1]/(x[2])(exp(x[2](agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
+log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);	+log(x[1]/YEARM) +x[2]*(agedc[i]-agegomp)+log(YEARM);
	} else
	printf("Gompertz cens[%d] neither 1 nor 0\n",i);
/if (wav[i] > 1 && agecens[i] > 15) {/ /* ??? */	/if (wav[i] > 1 && agecens[i] > 15) {/ /* ??? */
if (wav[i] > 1 ) { /* ??? */	L=L+A*weight[i];
L=L+A*weight[i];
/* printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]12,agecens[i]12,cens[i],agedc[i]12,weight[i]);/	/* printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]12,agecens[i]12,cens[i],agedc[i]12,weight[i]);/
}	}
}	}

/printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);/	/printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);/

return -2Lnum/sump;	return -2Lnum/sump;
}	}
Line 7813 double gompertz(double x[])	Line 9189 double gompertz(double x[])
/***************** Gompertz_f Likelihood ****************************/	/***************** Gompertz_f Likelihood ****************************/
double gompertz_f(const gsl_vector v, void params)	double gompertz_f(const gsl_vector v, void params)
{	{
double A,B,LL=0.0,sump=0.,num=0.;	double A=0.,B=0.,LL=0.0,sump=0.,num=0.;
double x= (double ) v->data;	double x= (double ) v->data;
int i,n=0; /* n is the size of the sample */	int i,n=0; /* n is the size of the sample */

Line 7906 int readdata(char datafile[], int firsto	Line 9282 int readdata(char datafile[], int firsto
int i=0, j=0, n=0, iv=0, v;	int i=0, j=0, n=0, iv=0, v;
int lstra;	int lstra;
int linei, month, year,iout;	int linei, month, year,iout;
	int noffset=0; /* This is the offset if BOM data file */
char line[MAXLINE], linetmp[MAXLINE];	char line[MAXLINE], linetmp[MAXLINE];
char stra[MAXLINE], strb[MAXLINE];	char stra[MAXLINE], strb[MAXLINE];
char *stratrunc;	char *stratrunc;
Line 7939 int readdata(char datafile[], int firsto	Line 9316 int readdata(char datafile[], int firsto
fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;	fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
}	}

i=1;	/* Is it a BOM UTF-8 Windows file? */
	/* First data line */
linei=0;	linei=0;
	while(fgets(line, MAXLINE, fic)) {
	noffset=0;
	if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
	{
	noffset=noffset+3;
	printf("# Data file '%s' is an UTF8 BOM file, please convert to UTF8 or ascii file and rerun.\n",datafile);fflush(stdout);
	fprintf(ficlog,"# Data file '%s' is an UTF8 BOM file, please convert to UTF8 or ascii file and rerun.\n",datafile);
	fflush(ficlog); return 1;
	}
	/* else if( line[0] == (char)0xFE && line[1] == (char)0xFF)*/
	else if( line[0] == (char)0xFF && line[1] == (char)0xFE)
	{
	noffset=noffset+2;
	printf("# Error Data file '%s' is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);fflush(stdout);
	fprintf(ficlog,"# Error Data file '%s' is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);
	fflush(ficlog); return 1;
	}
	else if( line[0] == 0 && line[1] == 0)
	{
	if( line[2] == (char)0xFE && line[3] == (char)0xFF){
	noffset=noffset+4;
	printf("# Error Data file '%s' is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);fflush(stdout);
	fprintf(ficlog,"# Error Data file '%s' is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);
	fflush(ficlog); return 1;
	}
	} else{
	;/printf(" Not a BOM file\n");/
	}
	/* If line starts with a # it is a comment */
	if (line[noffset] == '#') {
	linei=linei+1;
	break;
	}else{
	break;
	}
	}
	fclose(fic);
	if((fic=fopen(datafile,"r"))==NULL) {
	printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
	fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
	}
	/* Not a Bom file */

	i=1;
while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {	while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
linei=linei+1;	linei=linei+1;
for(j=strlen(line); j>=0;j--){ /* Untabifies line */	for(j=strlen(line); j>=0;j--){ /* Untabifies line */
Line 8061 int readdata(char datafile[], int firsto	Line 9483 int readdata(char datafile[], int firsto
return 1;	return 1;
}	}
anint[j][i]= (double) year;	anint[j][i]= (double) year;
mint[j][i]= (double)month;	mint[j][i]= (double)month;
	/* if( (int)anint[j][i]+ (int)(mint[j][i])/12. < (int) (moisnais[i]/12.+annais[i])){ */
	/* printf("Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, mint[j][i],anint[j][i], moisnais[i],annais[i]); */
	/* fprintf(ficlog,"Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, mint[j][i],anint[j][i], moisnais[i],annais[i]); */
	/* } */
strcpy(line,stra);	strcpy(line,stra);
} /* End loop on waves */	} /* End loop on waves */

Line 8100 int readdata(char datafile[], int firsto	Line 9526 int readdata(char datafile[], int firsto

}	}
annais[i]=(double)(year);	annais[i]=(double)(year);
moisnais[i]=(double)(month);	moisnais[i]=(double)(month);
	for (j=1;j<=maxwav;j++){
	if( (int)anint[j][i]+ (int)(mint[j][i])/12. < (int) (moisnais[i]/12.+annais[i])){
	printf("Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, (int)mint[j][i],(int)anint[j][i], j,(int)moisnais[i],(int)annais[i]);
	fprintf(ficlog,"Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, (int)mint[j][i],(int)anint[j][i], j, (int)moisnais[i],(int)annais[i]);
	}
	}

strcpy(line,stra);	strcpy(line,stra);

/* Sample weight */	/* Sample weight */
Line 8120 int readdata(char datafile[], int firsto	Line 9553 int readdata(char datafile[], int firsto
cutv(stra, strb, line, ' ');	cutv(stra, strb, line, ' ');
if(strb[0]=='.') { /* Missing value */	if(strb[0]=='.') { /* Missing value */
lval=-1;	lval=-1;
	coqvar[iv][i]=NAN;
	covar[ncovcol+iv][i]=NAN; /* including qvar in standard covar for performance reasons */
}else{	}else{
errno=0;	errno=0;
/* what_kind_of_number(strb); */	/* what_kind_of_number(strb); */
Line 8223 int decoderesult ( char resultline[], in	Line 9658 int decoderesult ( char resultline[], in
char stra[80], strb[80], strc[80], strd[80],stre[80];	char stra[80], strb[80], strc[80], strd[80],stre[80];

removefirstspace(&resultline);	removefirstspace(&resultline);
printf("decoderesult:%s\n",resultline);

if (strstr(resultline,"v") !=0){	if (strstr(resultline,"v") !=0){
printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);	printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
Line 8234 int decoderesult ( char resultline[], in	Line 9668 int decoderesult ( char resultline[], in
if (strlen(resultsav) >1){	if (strlen(resultsav) >1){
j=nbocc(resultsav,'='); /*< j=Number of covariate values'=' /	j=nbocc(resultsav,'='); /*< j=Number of covariate values'=' /
}	}
	if(j == 0){ /* Resultline but no = */
	TKresult[nres]=0; /* Combination for the nresult and the model */
	return (0);
	}
if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */	if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
printf("ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);	printf("ERROR: the number of variables in the resultline, %d, differs from the number of variables used in the model line, %d.\n",j, cptcovs);
fprintf(ficlog,"ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);	fprintf(ficlog,"ERROR: the number of variables in the resultline, %d, differs from the number of variables used in the model line, %d.\n",j, cptcovs);
}	}
for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */	for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */
if(nbocc(resultsav,'=') >1){	if(nbocc(resultsav,'=') >1){
cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' '	cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' '
resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */	resultsav= V4=1 V5=25.1 V3=0 stra= V5=25.1 V3=0 strb= V4=1 */
cutl(strc,strd,strb,'='); /* strb:V4=1 strc=1 strd=V4 */	cutl(strc,strd,strb,'='); /* strb:V4=1 strc=1 strd=V4 */
}else	}else
cutl(strc,strd,resultsav,'=');	cutl(strc,strd,resultsav,'=');
Line 8266 int decoderesult ( char resultline[], in	Line 9704 int decoderesult ( char resultline[], in
}	}
}	}
if(match == 0){	if(match == 0){
printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);	printf("Error in result line: V%d is missing in result: %s according to model=%s\n",k1, resultline, model);
	fprintf(ficlog,"Error in result line: V%d is missing in result: %s according to model=%s\n",k1, resultline, model);
	return 1;
}	}
}	}
}	}
Line 8283 int decoderesult ( char resultline[], in	Line 9723 int decoderesult ( char resultline[], in
}	}
if(match == 0){	if(match == 0){
printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);	printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
	fprintf(ficlog,"Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
	return 1;
}else if(match > 1){	}else if(match > 1){
printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);	printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
	fprintf(ficlog,"Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
	return 1;
}	}
}	}

Line 8553 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 9997 Dummy[k] 0=dummy (0 1), 1 quantitative (
Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\	Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\	Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);	Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
for(k=1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}	for(k=-1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}
for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */	for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */
if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */	if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
Fixed[k]= 0;	Fixed[k]= 0;
Line 8803 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 10247 Dummy[k] 0=dummy (0 1), 1 quantitative (
/* Searching for doublons in the model */	/* Searching for doublons in the model */
for(k1=1; k1<= cptcovt;k1++){	for(k1=1; k1<= cptcovt;k1++){
for(k2=1; k2 <k1;k2++){	for(k2=1; k2 <k1;k2++){
if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){	/* if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){ */
	if((Typevar[k1]==Typevar[k2]) && (Fixed[k1]==Fixed[k2]) && (Dummy[k1]==Dummy[k2] )){
if((Typevar[k1] == 0 \|\| Typevar[k1] == 1)){ /* Simple or age product */	if((Typevar[k1] == 0 \|\| Typevar[k1] == 1)){ /* Simple or age product */
if(Tvar[k1]==Tvar[k2]){	if(Tvar[k1]==Tvar[k2]){
printf("Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]);	printf("Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[k1],Dummy[k1]);
fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);	fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[k1],Dummy[k1]); fflush(ficlog);
return(1);	return(1);
}	}
}else if (Typevar[k1] ==2){	}else if (Typevar[k1] ==2){
Line 8833 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 10278 Dummy[k] 0=dummy (0 1), 1 quantitative (
}	}

int calandcheckages(int imx, int maxwav, double agemin, double agemax, int nberr, int nbwarn )	int calandcheckages(int imx, int maxwav, double agemin, double agemax, int nberr, int nbwarn )
{	{/* Check ages at death */
int i, m;	int i, m;
int firstone=0;	int firstone=0;

Line 8848 int calandcheckages(int imx, int maxwav,	Line 10293 int calandcheckages(int imx, int maxwav,
nberr = nberr + 1;	nberr = nberr + 1;
if(firstone == 0){	if(firstone == 0){
firstone=1;	firstone=1;
printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\nOther similar cases in log file\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);	printf("Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we do not believe in a death, skipped.\nOther similar cases in log file\n", *nberr,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m);
}	}
fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);	fprintf(ficlog,"Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we do not believe in a death, skipped.\n", *nberr,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m);
s[m][i]=-1;	s[m][i]=-1; /* Droping the death status */
}	}
if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){	if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
(*nberr)++;	(*nberr)++;
printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);	printf("Error (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\nOther similar cases in log file\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m);
fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);	fprintf(ficlog,"Error (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m);
s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */	s[m][i]=-2; /* We prefer to skip it (and to skip it in version 0.8a1 too */
}	}
}	}
}	}
Line 8979 BOOL IsWow64()	Line 10424 BOOL IsWow64()
#endif	#endif

void syscompilerinfo(int logged)	void syscompilerinfo(int logged)
{	{
/* #include "syscompilerinfo.h"*/	#include <stdint.h>

	/* #include "syscompilerinfo.h"*/
/* command line Intel compiler 32bit windows, XP compatible:*/	/* command line Intel compiler 32bit windows, XP compatible:*/
/* /GS /W3 /Gy	/* /GS /W3 /Gy
/Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D	/Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
Line 9015 void syscompilerinfo(int logged)	Line 10462 void syscompilerinfo(int logged)
/ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF	/ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
/NOLOGO /TLBID:1	/NOLOGO /TLBID:1
*/	*/


#if defined __INTEL_COMPILER	#if defined __INTEL_COMPILER
#if defined(__GNUC__)	#if defined(__GNUC__)
struct utsname sysInfo; /* For Intel on Linux and OS/X */	struct utsname sysInfo; /* For Intel on Linux and OS/X */
Line 9031 void syscompilerinfo(int logged)	Line 10480 void syscompilerinfo(int logged)
}	}
#endif	#endif

#include <stdint.h>

printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");	printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
#if defined(__clang__)	#if defined(__clang__)
printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */	printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
Line 9118 void syscompilerinfo(int logged)	Line 10565 void syscompilerinfo(int logged)
#endif	#endif
#endif	#endif

// void main()	// void main ()
// {	// {
#if defined(_MSC_VER)	#if defined(_MSC_VER)
if (IsWow64()){	if (IsWow64()){
Line 9139 void syscompilerinfo(int logged)	Line 10586 void syscompilerinfo(int logged)
}	}

int prevalence_limit(double p, double prlim, double ageminpar, double agemaxpar, double ftolpl, int ncvyearp){	int prevalence_limit(double p, double prlim, double ageminpar, double agemaxpar, double ftolpl, int ncvyearp){
/--------------- Prevalence limit (period or stable prevalence) --------------/	/--------------- Prevalence limit (forward period or forward stable prevalence) --------------/
int i, j, k, i1, k4=0, nres=0 ;	int i, j, k, i1, k4=0, nres=0 ;
/* double ftolpl = 1.e-10; */	/* double ftolpl = 1.e-10; */
double age, agebase, agelim;	double age, agebase, agelim;
Line 9148 int prevalence_limit(double p, double	Line 10595 int prevalence_limit(double p, double
strcpy(filerespl,"PL_");	strcpy(filerespl,"PL_");
strcat(filerespl,fileresu);	strcat(filerespl,fileresu);
if((ficrespl=fopen(filerespl,"w"))==NULL) {	if((ficrespl=fopen(filerespl,"w"))==NULL) {
printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;	printf("Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;	fprintf(ficlog,"Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
}	}
printf("\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);	printf("\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
fprintf(ficlog,"\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);	fprintf(ficlog,"\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
pstamp(ficrespl);	pstamp(ficrespl);
fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);	fprintf(ficrespl,"# Forward period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
fprintf(ficrespl,"#Age ");	fprintf(ficrespl,"#Age ");
for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);	for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
fprintf(ficrespl,"\n");	fprintf(ficrespl,"\n");
Line 9170 int prevalence_limit(double p, double	Line 10617 int prevalence_limit(double p, double

for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */	for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
if(TKresult[nres]!= k)	if(i1 != 1 && TKresult[nres]!= k)
continue;	continue;

/* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */	/* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
Line 9229 int prevalence_limit(double p, double	Line 10676 int prevalence_limit(double p, double
}	}

int back_prevalence_limit(double p, double bprlim, double ageminpar, double agemaxpar, double ftolpl, int ncvyearp, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj){	int back_prevalence_limit(double p, double bprlim, double ageminpar, double agemaxpar, double ftolpl, int ncvyearp, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj){
/--------------- Back Prevalence limit (period or stable prevalence) --------------/	/--------------- Back Prevalence limit (backward stable prevalence) --------------/

/* Computes the back prevalence limit for any combination of covariate values	/* Computes the back prevalence limit for any combination of covariate values
* at any age between ageminpar and agemaxpar	* at any age between ageminpar and agemaxpar
Line 9244 int back_prevalence_limit(double *p, dou	Line 10691 int back_prevalence_limit(double *p, dou
strcpy(fileresplb,"PLB_");	strcpy(fileresplb,"PLB_");
strcat(fileresplb,fileresu);	strcat(fileresplb,fileresu);
if((ficresplb=fopen(fileresplb,"w"))==NULL) {	if((ficresplb=fopen(fileresplb,"w"))==NULL) {
printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;	printf("Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;	fprintf(ficlog,"Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
}	}
printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);	printf("Computing backward prevalence: result on file '%s' \n", fileresplb);
fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);	fprintf(ficlog,"Computing backward prevalence: result on file '%s' \n", fileresplb);
pstamp(ficresplb);	pstamp(ficresplb);
fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl);	fprintf(ficresplb,"# Backward prevalence. Precision given by ftolpl=%g \n", ftolpl);
fprintf(ficresplb,"#Age ");	fprintf(ficresplb,"#Age ");
for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);	for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
fprintf(ficresplb,"\n");	fprintf(ficresplb,"\n");
Line 9267 int back_prevalence_limit(double *p, dou	Line 10714 int back_prevalence_limit(double *p, dou

for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */	for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
if(TKresult[nres]!= k)	if(i1 != 1 && TKresult[nres]!= k)
continue;	continue;
//printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));	//printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
fprintf(ficresplb,"#******");	fprintf(ficresplb,"#******");
Line 9314 int back_prevalence_limit(double *p, dou	Line 10761 int back_prevalence_limit(double *p, dou
}else{	}else{
/* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */	/* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres);	bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres);
	/* printf("TOTOT\n"); */
	/* exit(1); */
}	}
fprintf(ficresplb,"%.0f ",age );	fprintf(ficresplb,"%.0f ",age );
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
Line 9326 int back_prevalence_limit(double *p, dou	Line 10775 int back_prevalence_limit(double *p, dou
fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);	fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
} /* Age */	} /* Age */
/* was end of cptcod */	/* was end of cptcod */
	/fprintf(ficresplb,"\n");/ /* Seems to be necessary for gnuplot only if two result lines and no covariate. */
} /* end of any combination */	} /* end of any combination */
} /* end of nres */	} /* end of nres */
/* hBijx(p, bage, fage); */	/* hBijx(p, bage, fage); */
Line 9370 int hPijx(double *p, int bage, int fage)	Line 10820 int hPijx(double *p, int bage, int fage)
/* k=k+1; */	/* k=k+1; */
for(nres=1; nres <= nresult; nres++) /* For each resultline */	for(nres=1; nres <= nresult; nres++) /* For each resultline */
for(k=1; k<=i1;k++){	for(k=1; k<=i1;k++){
if(TKresult[nres]!= k)	if(i1 != 1 && TKresult[nres]!= k)
continue;	continue;
fprintf(ficrespij,"\n#****** ");	fprintf(ficrespij,"\n#****** ");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
Line 9436 int hPijx(double *p, int bage, int fage)	Line 10886 int hPijx(double *p, int bage, int fage)
/if (stepm<=24) stepsize=2;/	/if (stepm<=24) stepsize=2;/

/* agelim=AGESUP; */	/* agelim=AGESUP; */
ageminl=30;	ageminl=AGEINF; /* was 30 */
hstepm=stepsizeYEARM; / Every year of age */	hstepm=stepsizeYEARM; / Every year of age */
hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */	hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */

/* hstepm=1; aff par mois*/	/* hstepm=1; aff par mois*/
pstamp(ficrespijb);	pstamp(ficrespijb);
fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x ");	fprintf(ficrespijb,"#****** h Bij x Back probability to be in state i at age x-h being in j at x: B1j+B2j+...=1 ");
i1= pow(2,cptcoveff);	i1= pow(2,cptcoveff);
/* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */	/* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
/* /\for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){\/ */	/* /\for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){\/ */
/* k=k+1; */	/* k=k+1; */
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */	for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
if(TKresult[nres]!= k)	if(i1 != 1 && TKresult[nres]!= k)
continue;	continue;
fprintf(ficrespijb,"\n#****** ");	fprintf(ficrespijb,"\n#****** ");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
Line 9458 int hPijx(double *p, int bage, int fage)	Line 10908 int hPijx(double *p, int bage, int fage)
fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
}	}
fprintf(ficrespijb,"******\n");	fprintf(ficrespijb,"******\n");
if(invalidvarcomb[k]){	if(invalidvarcomb[k]){ /* Is it necessary here? */
fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);	fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
continue;	continue;
}	}
Line 9466 int hPijx(double *p, int bage, int fage)	Line 10916 int hPijx(double *p, int bage, int fage)
/* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months \/ /	/* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months \/ /
for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */	for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
/* nhstepm=(int) rint((agelim-agedeb)YEARM/stepm); /\ Typically 20 years = 2012/6=40 \/ */	/* nhstepm=(int) rint((agelim-agedeb)YEARM/stepm); /\ Typically 20 years = 2012/6=40 \/ */
nhstepm=(int) rint((agedeb-ageminl)YEARM/stepm); / Typically 20 years = 2012/6=40 /	nhstepm=(int) rint((agedeb-ageminl)YEARM/stepm+0.1)-1; / Typically 20 years = 2012/6=40 or 5512/24=27.5-1.1=>27 */
nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */	nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 or 28*/

/* nhstepm=nhstepmYEARM; aff par mois/	/* nhstepm=nhstepmYEARM; aff par mois/

p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */
	/* and memory limitations if stepm is small */

/* oldm=oldms;savm=savms; */	/* oldm=oldms;savm=savms; */
/* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */	/* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);	hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
/* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */	/* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");	fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate+ndeath;j++)	for(j=1; j<=nlstate+ndeath;j++)
fprintf(ficrespijb," %1d-%1d",i,j);	fprintf(ficrespijb," %1d-%1d",i,j);
Line 9513 int main(int argc, char *argv[])	Line 10965 int main(int argc, char *argv[])
double ssval;	double ssval;
#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, iter=0,m,size=100, cptcod; /* Suppressing because nobs */
	/* int i,j, k, n=MAXN,iter=0,m,size=100, cptcod; */
int ncvyear=0; /* Number of years needed for the period prevalence to converge */	int ncvyear=0; /* 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 */
Line 9522 int main(int argc, char *argv[])	Line 10975 int main(int argc, char *argv[])
int NDIM=2;	int NDIM=2;
int vpopbased=0;	int vpopbased=0;
int nres=0;	int nres=0;
	int endishere=0;
	int noffset=0;
	int ncurrv=0; /* Temporary variable */

char ca[32], cb[32];	char ca[32], cb[32];
/* FILE fichtm; //* Html File */	/* FILE fichtm; //* Html File */
/* FILE ficgp;/ /Gnuplot File /	/* FILE ficgp;/ /Gnuplot File /
Line 9545 int main(int argc, char *argv[])	Line 11001 int main(int argc, char *argv[])

char pathr[MAXLINE], pathimach[MAXLINE];	char pathr[MAXLINE], pathimach[MAXLINE];
char tok, val; /* pathtot */	char tok, val; /* pathtot */
int firstobs=1, lastobs=10;	int firstobs=1, lastobs=10; /* nobs = lastobs-firstobs declared globally ;*/
int c, h , cpt, c2;	int c, h , cpt, c2;
int jl=0;	int jl=0;
int i1, j1, jk, stepsize=0;	int i1, j1, jk, stepsize=0;
Line 9553 int main(int argc, char *argv[])	Line 11009 int main(int argc, char *argv[])

int *tab;	int *tab;
int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */	int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
int backcast=0;	/* double anprojd, mprojd, jprojd; /\* For eventual projections \/ /
	/* double anprojf, mprojf, jprojf; */
	/* double jintmean,mintmean,aintmean; */
	int prvforecast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */
	int prvbackcast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */
	double yrfproj= 10.0; /* Number of years of forward projections */
	double yrbproj= 10.0; /* Number of years of backward projections */
	int prevbcast=0; /* defined as global for mlikeli and mle, replacing backcast */
int mobilav=0,popforecast=0;	int mobilav=0,popforecast=0;
int hstepm=0, nhstepm=0;	int hstepm=0, nhstepm=0;
int agemortsup;	int agemortsup;
Line 9566 int main(int argc, char *argv[])	Line 11029 int main(int argc, char *argv[])
double **prlim;	double **prlim;
double **bprlim;	double **bprlim;
double **param; / Matrix of parameters */	double **param; / Matrix of parameters */
double *p;	double **paramstart; / Matrix of starting parameter values */
	double p, pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */
double *matcov; / Matrix of covariance */	double *matcov; / Matrix of covariance */
double *hess; / Hessian matrix */	double *hess; / Hessian matrix */
double **delti3; / Scale */	double **delti3; / Scale */
double delti; / Scale */	double delti; / Scale */
double *eij, *vareij;	double *eij, *vareij;
double *varpl; / Variances of prevalence limits by age */	double *varpl; / Variances of prevalence limits by age */

double *epj, vepp;	double *epj, vepp;

double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;	double dateprev1, dateprev2;
double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000;	double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0, dateprojd=0, dateprojf=0;
	double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000, dateback1=0, dateback2=0, datebackd=0, datebackf=0;


double **ximort;	double **ximort;
char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";	char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
Line 9654 int main(int argc, char *argv[])	Line 11121 int main(int argc, char *argv[])
if(pathr[0] == '\0') break; /* Dirty */	if(pathr[0] == '\0') break; /* Dirty */
}	}
}	}
	else if (argc<=2){
	strcpy(pathtot,argv[1]);
	}
else{	else{
strcpy(pathtot,argv[1]);	strcpy(pathtot,argv[1]);
	strcpy(z,argv[2]);
	printf("\nargv[2]=%s z=%c\n",argv[2],z[0]);
}	}
/if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");/	/if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");/
/*cygwin_split_path(pathtot,path,optionfile);	/*cygwin_split_path(pathtot,path,optionfile);
Line 9733 int main(int argc, char *argv[])	Line 11205 int main(int argc, char *argv[])
exit(70);	exit(70);
}	}



strcpy(filereso,"o");	strcpy(filereso,"o");
strcat(filereso,fileresu);	strcat(filereso,fileresu);
if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */	if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
Line 9743 int main(int argc, char *argv[])	Line 11213 int main(int argc, char *argv[])
fflush(ficlog);	fflush(ficlog);
goto end;	goto end;
}	}
	/-------- Rewriting parameter file ----------/
	strcpy(rfileres,"r"); /* "Rparameterfile */
	strcat(rfileres,optionfilefiname); /* Parameter file first name */
	strcat(rfileres,"."); /* */
	strcat(rfileres,optionfilext); /* Other files have txt extension */
	if((ficres =fopen(rfileres,"w"))==NULL) {
	printf("Problem writing new parameter file: %s\n", rfileres);goto end;
	fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
	fflush(ficlog);
	goto end;
	}
	fprintf(ficres,"#IMaCh %s\n",version);


/* Reads comments: lines beginning with '#' */	/* Reads comments: lines beginning with '#' */
numlinepar=0;	numlinepar=0;
	/* Is it a BOM UTF-8 Windows file? */
/* First parameter line */	/* First parameter line */
while(fgets(line, MAXLINE, ficpar)) {	while(fgets(line, MAXLINE, ficpar)) {
	noffset=0;
	if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
	{
	noffset=noffset+3;
	printf("# File is an UTF8 Bom.\n"); // 0xBF
	}
	/* else if( line[0] == (char)0xFE && line[1] == (char)0xFF)*/
	else if( line[0] == (char)0xFF && line[1] == (char)0xFE)
	{
	noffset=noffset+2;
	printf("# File is an UTF16BE BOM file\n");
	}
	else if( line[0] == 0 && line[1] == 0)
	{
	if( line[2] == (char)0xFE && line[3] == (char)0xFF){
	noffset=noffset+4;
	printf("# File is an UTF16BE BOM file\n");
	}
	} else{
	;/printf(" Not a BOM file\n");/
	}

/* If line starts with a # it is a comment */	/* If line starts with a # it is a comment */
if (line[0] == '#') {	if (line[noffset] == '#') {
numlinepar++;	numlinepar++;
fputs(line,stdout);	fputs(line,stdout);
fputs(line,ficparo);	fputs(line,ficparo);
	fputs(line,ficres);
fputs(line,ficlog);	fputs(line,ficlog);
continue;	continue;
}else	}else
Line 9763 int main(int argc, char *argv[])	Line 11269 int main(int argc, char *argv[])
title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){	title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
if (num_filled != 5) {	if (num_filled != 5) {
printf("Should be 5 parameters\n");	printf("Should be 5 parameters\n");
	fprintf(ficlog,"Should be 5 parameters\n");
}	}
numlinepar++;	numlinepar++;
printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);	printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
	fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
	fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
	fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
}	}
/* Second parameter line */	/* Second parameter line */
while(fgets(line, MAXLINE, ficpar)) {	while(fgets(line, MAXLINE, ficpar)) {
/* If line starts with a # it is a comment */	/* while(fscanf(ficpar,"%[^\n]", line)) { */
	/* If line starts with a # it is a comment. Strangely fgets reads the EOL and fputs doesn't */
if (line[0] == '#') {	if (line[0] == '#') {
numlinepar++;	numlinepar++;
fputs(line,stdout);	printf("%s",line);
fputs(line,ficparo);	fprintf(ficres,"%s",line);
fputs(line,ficlog);	fprintf(ficparo,"%s",line);
	fprintf(ficlog,"%s",line);
continue;	continue;
}else	}else
break;	break;
Line 9784 int main(int argc, char *argv[])	Line 11296 int main(int argc, char *argv[])
if (num_filled != 11) {	if (num_filled != 11) {
printf("Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");	printf("Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
printf("but line=%s\n",line);	printf("but line=%s\n",line);
	fprintf(ficlog,"Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
	fprintf(ficlog,"but line=%s\n",line);
	}
	if( lastpass > maxwav){
	printf("Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
	fprintf(ficlog,"Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
	fflush(ficlog);
	goto end;
}	}
printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);	printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
	fprintf(ficparo,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
	fprintf(ficres,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, 0, weightopt);
	fprintf(ficlog,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, 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-4; //* 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 */
Line 9794 int main(int argc, char *argv[])	Line 11317 int main(int argc, char *argv[])
/* If line starts with a # it is a comment */	/* If line starts with a # it is a comment */
if (line[0] == '#') {	if (line[0] == '#') {
numlinepar++;	numlinepar++;
fputs(line,stdout);	printf("%s",line);
fputs(line,ficparo);	fprintf(ficres,"%s",line);
fputs(line,ficlog);	fprintf(ficparo,"%s",line);
	fprintf(ficlog,"%s",line);
continue;	continue;
}else	}else
break;	break;
}	}
if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){	if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
if (num_filled == 0)	if (num_filled != 1){
model[0]='\0';	printf("ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
else if (num_filled != 1){	fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
model[0]='\0';	model[0]='\0';
goto end;	goto end;
}	}
Line 9819 int main(int argc, char *argv[])	Line 11341 int main(int argc, char *argv[])
}	}
/* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */	/* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
printf("model=1+age+%s\n",model);fflush(stdout);	printf("model=1+age+%s\n",model);fflush(stdout);
	fprintf(ficparo,"model=1+age+%s\n",model);fflush(stdout);
	fprintf(ficres,"model=1+age+%s\n",model);fflush(stdout);
	fprintf(ficlog,"model=1+age+%s\n",model);fflush(stdout);
}	}
/* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */	/* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */
/* numlinepar=numlinepar+3; /\* In general \/ /	/* numlinepar=numlinepar+3; /\* In general \/ /
/* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */	/* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);	/* fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); */
fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);	/* fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); */
fflush(ficlog);	fflush(ficlog);
/* if(model[0]=='#'\|\| model[0]== '\0'){ */	/* if(model[0]=='#'\|\| model[0]== '\0'){ */
if(model[0]=='#'){	if(model[0]=='#'){
printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \	printf("Error in 'model' line: model should start with 'model=1+age+' and end without space \n \
'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+ageage+V1+V1age.' or \n \	'model=1+age+' or 'model=1+age+V1.' or 'model=1+age+ageage+V1+V1age' or \n \
'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \	'model=1+age+V1+V2' or 'model=1+age+V1+V2+V1*V2' etc. \n"); \
if(mle != -1){	if(mle != -1){
printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");	printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter vectors and subdiagonal covariance matrix.\n");
exit(1);	exit(1);
}	}
}	}
Line 9852 int main(int argc, char *argv[])	Line 11377 int main(int argc, char *argv[])
ungetc(c,ficpar);	ungetc(c,ficpar);


covar=matrix(0,NCOVMAX,1,n); /*< used in readdata /	covar=matrix(0,NCOVMAX,firstobs,lastobs); /*< used in readdata /
coqvar=matrix(1,nqv,1,n); /*< Fixed quantitative covariate /	if(nqv>=1)coqvar=matrix(1,nqv,firstobs,lastobs); /*< Fixed quantitative covariate /
cotvar=ma3x(1,maxwav,1,ntv+nqtv,1,n); /*< Time varying covariate (dummy and quantitative)/	if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,firstobs,lastobs); /*< Time varying quantitative covariate /
cotqvar=ma3x(1,maxwav,1,nqtv,1,n); /*< Time varying quantitative covariate /	if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,firstobs,lastobs); /*< Time varying covariate (dummy and quantitative)/
cptcovn=0; /Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn/	cptcovn=0; /Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn/
/* v1+v2+v3+v2v4+v5age makes cptcovn = 5	/* v1+v2+v3+v2v4+v5age makes cptcovn = 5
v1+v2age+v2v3 makes cptcovn = 3	v1+v2age+v2v3 makes cptcovn = 3
Line 9877 int main(int argc, char *argv[])	Line 11402 int main(int argc, char *argv[])
delti=delti3[1][1];	delti=delti3[1][1];
/delti=vector(1,npar); //* Scale of each paramater (output from hesscov)*/	/delti=vector(1,npar); //* Scale of each paramater (output from hesscov)*/
if(mle==-1){ /* Print a wizard for help writing covariance matrix */	if(mle==-1){ /* Print a wizard for help writing covariance matrix */
	/* We could also provide initial parameters values giving by simple logistic regression
	* only one way, that is without matrix product. We will have nlstate maximizations */
	/* for(i=1;i<nlstate;i++){ */
	/* /\reducing xi for 1 to npar to 1 to ncovmodel; \/ */
	/* mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
	/* } */
prwizard(ncovmodel, nlstate, ndeath, model, ficparo);	prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);	printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);	fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
Line 9906 int main(int argc, char *argv[])	Line 11437 int main(int argc, char *argv[])
ungetc(c,ficpar);	ungetc(c,ficpar);

param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);	param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
	paramstart= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
for(i=1; i <=nlstate; i++){	for(i=1; i <=nlstate; i++){
j=0;	j=0;
for(jj=1; jj <=nlstate+ndeath; jj++){	for(jj=1; jj <=nlstate+ndeath; jj++){
if(jj==i) continue;	if(jj==i) continue;
j++;	j++;
	while((c=getc(ficpar))=='#' && c!= EOF){
	ungetc(c,ficpar);
	fgets(line, MAXLINE, ficpar);
	numlinepar++;
	fputs(line,stdout);
	fputs(line,ficparo);
	fputs(line,ficlog);
	}
	ungetc(c,ficpar);
fscanf(ficpar,"%1d%1d",&i1,&j1);	fscanf(ficpar,"%1d%1d",&i1,&j1);
if ((i1 != i) \|\| (j1 != jj)){	if ((i1 != i) \|\| (j1 != jj)){
printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \	printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
Line 9942 run imach with mle=-1 to get a correct t	Line 11483 run imach with mle=-1 to get a correct t
}	}
fflush(ficlog);	fflush(ficlog);

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

/* Reads comments: lines beginning with '#' */	/* Reads comments: lines beginning with '#' */
while((c=getc(ficpar))=='#' && c!= EOF){	while((c=getc(ficpar))=='#' && c!= EOF){
Line 10046 Please run with mle=-1 to get a correct	Line 11588 Please run with mle=-1 to get a correct

fflush(ficlog);	fflush(ficlog);

/-------- Rewriting parameter file ----------/
strcpy(rfileres,"r"); /* "Rparameterfile */
strcat(rfileres,optionfilefiname); /* Parameter file first name*/
strcat(rfileres,"."); /* */
strcat(rfileres,optionfilext); /* Other files have txt extension */
if((ficres =fopen(rfileres,"w"))==NULL) {
printf("Problem writing new parameter file: %s\n", rfileres);goto end;
fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
}
fprintf(ficres,"#%s\n",version);
} /* End of mle != -3 */	} /* End of mle != -3 */

/* Main data	/* Main data
*/	*/
n= lastobs;	nobs=lastobs-firstobs+1; /* was = lastobs;*/
num=lvector(1,n);	/* num=lvector(1,n); */
moisnais=vector(1,n);	/* moisnais=vector(1,n); */
annais=vector(1,n);	/* annais=vector(1,n); */
moisdc=vector(1,n);	/* moisdc=vector(1,n); */
andc=vector(1,n);	/* andc=vector(1,n); */
weight=vector(1,n);	/* weight=vector(1,n); */
agedc=vector(1,n);	/* agedc=vector(1,n); */
cod=ivector(1,n);	/* cod=ivector(1,n); */
for(i=1;i<=n;i++){	/* for(i=1;i<=n;i++){ */
	num=lvector(firstobs,lastobs);
	moisnais=vector(firstobs,lastobs);
	annais=vector(firstobs,lastobs);
	moisdc=vector(firstobs,lastobs);
	andc=vector(firstobs,lastobs);
	weight=vector(firstobs,lastobs);
	agedc=vector(firstobs,lastobs);
	cod=ivector(firstobs,lastobs);
	for(i=firstobs;i<=lastobs;i++){
num[i]=0;	num[i]=0;
moisnais[i]=0;	moisnais[i]=0;
annais[i]=0;	annais[i]=0;
Line 10079 Please run with mle=-1 to get a correct	Line 11620 Please run with mle=-1 to get a correct
cod[i]=0;	cod[i]=0;
weight[i]=1.0; /* Equal weights, 1 by default */	weight[i]=1.0; /* Equal weights, 1 by default */
}	}
mint=matrix(1,maxwav,1,n);	mint=matrix(1,maxwav,firstobs,lastobs);
anint=matrix(1,maxwav,1,n);	anint=matrix(1,maxwav,firstobs,lastobs);
s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */	s=imatrix(1,maxwav+1,firstobs,lastobs); /* s[i][j] health state for wave i and individual j */
tab=ivector(1,NCOVMAX);	tab=ivector(1,NCOVMAX);
ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2*ncov; V1+V2+V3+V4=>16 /	ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2*ncov; V1+V2+V3+V4=>16 /
ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2*ncov; V1+V2+V3+V4=>16 /	ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2*ncov; V1+V2+V3+V4=>16 /
Line 10183 Please run with mle=-1 to get a correct	Line 11724 Please run with mle=-1 to get a correct


agegomp=(int)agemin;	agegomp=(int)agemin;
free_vector(moisnais,1,n);	free_vector(moisnais,firstobs,lastobs);
free_vector(annais,1,n);	free_vector(annais,firstobs,lastobs);
/* 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); */
Line 10208 Please run with mle=-1 to get a correct	Line 11749 Please run with mle=-1 to get a correct
*/	*/

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);
/* */	/* Concatenates waves */

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

/* 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 10389 Title=%s <br>Datafile=%s Firstpass=%d La	Line 11930 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 for any valid combination of covariates	and for any valid combination of covariates
and prints on file fileres'p'. */	and prints on file fileres'p'. */
freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \	freqsummary(fileres, p, pstart, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
firstpass, lastpass, stepm, weightopt, model);	firstpass, lastpass, stepm, weightopt, model);

fprintf(fichtm,"\n");	fprintf(fichtm,"\n");
fprintf(fichtm,"<br>Total number of observations=%d <br>\n\	fprintf(fichtm,"<h4>Parameter line 2</h4><ul><li>Tolerance for the convergence of the likelihood: ftol=%g \n<li>Interval for the elementary matrix (in month): stepm=%d",\
	ftol, stepm);
	fprintf(fichtm,"\n<li>Number of fixed dummy covariates: ncovcol=%d ", ncovcol);
	ncurrv=1;
	for(i=ncurrv; i <=ncovcol; i++) fprintf(fichtm,"V%d ", i);
	fprintf(fichtm,"\n<li> Number of fixed quantitative variables: nqv=%d ", nqv);
	ncurrv=i;
	for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i);
	fprintf(fichtm,"\n<li> Number of time varying (wave varying) dummy covariates: ntv=%d ", ntv);
	ncurrv=i;
	for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i);
	fprintf(fichtm,"\n<li>Number of time varying quantitative covariates: nqtv=%d ", nqtv);
	ncurrv=i;
	for(i=ncurrv; i <=ncurrv-1+nqtv; i++) fprintf(fichtm,"V%d ", i);
	fprintf(fichtm,"\n<li>Weights column \n<br>Number of alive states: nlstate=%d <br>Number of death states (not really implemented): ndeath=%d \n<li>Number of waves: maxwav=%d \n<li>Parameter for maximization (1), using parameter values (0), for design of parameters and variance-covariance matrix: mle=%d \n<li>Does the weight column be taken into account (1), or not (0): weight=%d</ul>\n", \
	nlstate, ndeath, maxwav, mle, weightopt);

	fprintf(fichtm,"<h4> Diagram of states <a href=\"%s_.svg\">%s_.svg</a></h4> \n\
	<img src=\"%s_.svg\">", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"));


	fprintf(fichtm,"\n<h4>Some descriptive statistics </h4>\n<br>Total number of observations=%d <br>\n\
Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\	Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\	Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
imx,agemin,agemax,jmin,jmax,jmean);	imx,agemin,agemax,jmin,jmax,jmean);
pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */	pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */	oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */	newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */	savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */	oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */

/* For Powell, parameters are in a vector p[] starting at p[1]	/* For Powell, parameters are in a vector p[] starting at p[1]
so we point p on param[1][1] so that p[1] maps on param[1][1][1] */	so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
Line 10411 Interval (in months) between two waves:	Line 11973 Interval (in months) between two waves:
/* For mortality only */	/* For mortality only */
if (mle==-3){	if (mle==-3){
ximort=matrix(1,NDIM,1,NDIM);	ximort=matrix(1,NDIM,1,NDIM);
for(i=1;i<=NDIM;i++)	for(i=1;i<=NDIM;i++)
for(j=1;j<=NDIM;j++)	for(j=1;j<=NDIM;j++)
ximort[i][j]=0.;	ximort[i][j]=0.;
/* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */	/* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
cens=ivector(1,n);	cens=ivector(firstobs,lastobs);
ageexmed=vector(1,n);	ageexmed=vector(firstobs,lastobs);
agecens=vector(1,n);	agecens=vector(firstobs,lastobs);
dcwave=ivector(1,n);	dcwave=ivector(firstobs,lastobs);

for (i=1; i<=imx; i++){	for (i=1; i<=imx; i++){
dcwave[i]=-1;	dcwave[i]=-1;
Line 10452 Interval (in months) between two waves:	Line 12014 Interval (in months) between two waves:
ximort[i][j]=(i == j ? 1.0 : 0.0);	ximort[i][j]=(i == j ? 1.0 : 0.0);
}	}

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


#ifdef GSL	#ifdef GSL
Line 10579 Interval (in months) between two waves:	Line 12141 Interval (in months) between two waves:
printf("%f [%f ; %f]\n",p[i],p[i]-2sqrt(matcov[i][i]),p[i]+2sqrt(matcov[i][i]));	printf("%f [%f ; %f]\n",p[i],p[i]-2sqrt(matcov[i][i]),p[i]+2sqrt(matcov[i][i]));
fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2sqrt(matcov[i][i]),p[i]+2sqrt(matcov[i][i]));	fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2sqrt(matcov[i][i]),p[i]+2sqrt(matcov[i][i]));
}	}
lsurv=vector(1,AGESUP);	lsurv=vector(agegomp,AGESUP);
lpop=vector(1,AGESUP);	lpop=vector(agegomp,AGESUP);
tpop=vector(1,AGESUP);	tpop=vector(agegomp,AGESUP);
lsurv[agegomp]=100000;	lsurv[agegomp]=100000;

for (k=agegomp;k<=AGESUP;k++) {	for (k=agegomp;k<=AGESUP;k++) {
Line 10628 Please run with mle=-1 to get a correct	Line 12190 Please run with mle=-1 to get a correct
stepm, weightopt,\	stepm, weightopt,\
model,imx,p,matcov,agemortsup);	model,imx,p,matcov,agemortsup);

free_vector(lsurv,1,AGESUP);	free_vector(lsurv,agegomp,AGESUP);
free_vector(lpop,1,AGESUP);	free_vector(lpop,agegomp,AGESUP);
free_vector(tpop,1,AGESUP);	free_vector(tpop,agegomp,AGESUP);
free_matrix(ximort,1,NDIM,1,NDIM);	free_matrix(ximort,1,NDIM,1,NDIM);
free_ivector(cens,1,n);	free_ivector(dcwave,firstobs,lastobs);
free_vector(agecens,1,n);	free_vector(agecens,firstobs,lastobs);
free_ivector(dcwave,1,n);	free_vector(ageexmed,firstobs,lastobs);
	free_ivector(cens,firstobs,lastobs);
#ifdef GSL	#ifdef GSL
#endif	#endif
} /* Endof if mle==-3 mortality only */	} /* Endof if mle==-3 mortality only */
Line 10649 Please run with mle=-1 to get a correct	Line 12212 Please run with mle=-1 to get a correct
printf("\n");	printf("\n");
if(mle>=1){ /* Could be 1 or 2, Real Maximization */	if(mle>=1){ /* Could be 1 or 2, Real Maximization */
/* mlikeli uses func not funcone */	/* mlikeli uses func not funcone */
	/* for(i=1;i<nlstate;i++){ */
	/* /\reducing xi for 1 to npar to 1 to ncovmodel; \/ */
	/* mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
	/* } */
mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);	mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
}	}
if(mle==0) {/* No optimization, will print the likelihoods for the datafile */	if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
Line 10664 Please run with mle=-1 to get a correct	Line 12231 Please run with mle=-1 to get a correct
printf("\n");	printf("\n");

/--------- results files --------------/	/--------- results files --------------/
fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, weightopt,model);	/* fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, weightopt,model); */


fprintf(ficres,"# Parameters nlstatenlstatencov a121 + b12 age + ...\n");	fprintf(ficres,"# Parameters nlstatenlstatencov a121 + b12 age + ...\n");
Line 10826 Please run with mle=-1 to get a correct	Line 12393 Please run with mle=-1 to get a correct
fputs(line,stdout);	fputs(line,stdout);
fputs(line,ficparo);	fputs(line,ficparo);
fputs(line,ficlog);	fputs(line,ficlog);
	fputs(line,ficres);
continue;	continue;
}else	}else
break;	break;
Line 10864 Please run with mle=-1 to get a correct	Line 12432 Please run with mle=-1 to get a correct
fprintf(ficparo,"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, 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(fgets(line, MAXLINE, ficpar)) {
ungetc(c,ficpar);	/* If line starts with a # it is a comment */
fgets(line, MAXLINE, ficpar);	if (line[0] == '#') {
fputs(line,stdout);	numlinepar++;
fputs(line,ficparo);	fputs(line,stdout);
}	fputs(line,ficparo);
ungetc(c,ficpar);	fputs(line,ficlog);
	fputs(line,ficres);
fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);	continue;
fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);	}else
fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);	break;
printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);

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


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

fscanf(ficpar,"pop_based=%d\n",&popbased);
fprintf(ficlog,"pop_based=%d\n",popbased);
fprintf(ficparo,"pop_based=%d\n",popbased);
fprintf(ficres,"pop_based=%d\n",popbased);

while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);
fputs(line,stdout);
fputs(line,ficres);
fputs(line,ficparo);
}	}
ungetc(c,ficpar);
	if((num_filled=sscanf(line,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav)) !=EOF){
fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);	if (num_filled != 7) {
printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);	printf("Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004 mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);	fprintf(ficlog,"Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004 mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);	goto end;
/* day and month of proj2 are not used but only year anproj2.*/	}
	printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
while((c=getc(ficpar))=='#' && c!= EOF){	fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
ungetc(c,ficpar);	fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
fgets(line, MAXLINE, ficpar);	fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
fputs(line,stdout);
fputs(line,ficparo);
fputs(line,ficres);
}	}
ungetc(c,ficpar);

fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);
fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
/* day and month of proj2 are not used but only year anproj2.*/

/* Results */
nresult=0;
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 */
if (line[0] == '#') {	if (line[0] == '#') {
Line 10940 Please run with mle=-1 to get a correct	Line 12470 Please run with mle=-1 to get a correct
}else	}else
break;	break;
}	}
if (!feof(ficpar))
while((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
if (num_filled == 0){	dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
resultline[0]='\0';	dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
break;
} else if (num_filled != 1){	if((num_filled=sscanf(line,"pop_based=%d\n",&popbased)) !=EOF){
printf("ERROR %d: result line should be at minimum 'result=' %s\n",num_filled, line);	if (num_filled != 1) {
}	printf("Error: Not 1 (data)parameters in line but %d, for example:pop_based=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
nresult++; /* Sum of resultlines */	fprintf(ficlog,"Error: Not 1 (data)parameters in line but %d, for example: pop_based=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
printf("Result %d: result=%s\n",nresult, resultline);
if(nresult > MAXRESULTLINES){
printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
goto end;	goto end;
}	}
decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */	printf("pop_based=%d\n",popbased);
fprintf(ficparo,"result: %s\n",resultline);	fprintf(ficlog,"pop_based=%d\n",popbased);
fprintf(ficres,"result: %s\n",resultline);	fprintf(ficparo,"pop_based=%d\n",popbased);
fprintf(ficlog,"result: %s\n",resultline);	fprintf(ficres,"pop_based=%d\n",popbased);
while(fgets(line, MAXLINE, ficpar)) {	}

	/* Results */
	endishere=0;
	nresult=0;
	parameterline=0;
	do{
	if(!fgets(line, MAXLINE, ficpar)){
	endishere=1;
	parameterline=15;
	}else if (line[0] == '#') {
/* If line starts with a # it is a comment */	/* If line starts with a # it is a comment */
if (line[0] == '#') {	numlinepar++;
numlinepar++;	fputs(line,stdout);
fputs(line,stdout);	fputs(line,ficparo);
fputs(line,ficparo);	fputs(line,ficlog);
fputs(line,ficres);	fputs(line,ficres);
fputs(line,ficlog);	continue;
continue;	}else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))
}else	parameterline=11;
break;	else if(sscanf(line,"prevbackcast=%[^\n]\n",modeltemp))
	parameterline=12;
	else if(sscanf(line,"result:%[^\n]\n",modeltemp)){
	parameterline=13;
	}
	else{
	parameterline=14;
}	}
if (feof(ficpar))	switch (parameterline){ /* =0 only if only comments */
	case 11:
	if((num_filled=sscanf(line,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj)) !=EOF && (num_filled == 8)){
	fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
	printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
	fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
	fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
	/* day and month of proj2 are not used but only year anproj2.*/
	dateproj1=anproj1+(mproj1-1)/12.+(jproj1-1)/365.;
	dateproj2=anproj2+(mproj2-1)/12.+(jproj2-1)/365.;
	prvforecast = 1;
	}
	else if((num_filled=sscanf(line,"prevforecast=%d yearsfproj=%lf mobil_average=%d\n",&prevfcast,&yrfproj,&mobilavproj)) !=EOF){/* && (num_filled == 3))*/
	printf("prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
	fprintf(ficlog,"prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
	fprintf(ficres,"prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
	prvforecast = 2;
	}
	else {
	printf("Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevforecast=1 yearsfproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
	fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevforecast=1 yearproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
	goto end;
	}
break;	break;
else{ /* Processess output results for this combination of covariate values */	case 12:
}	if((num_filled=sscanf(line,"prevbackcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&prevbcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj)) !=EOF && (num_filled == 8)){
} /* end while */	fprintf(ficparo,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
	printf("prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
	fprintf(ficlog,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
	fprintf(ficres,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
	/* day and month of back2 are not used but only year anback2.*/
	dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;
	dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.;
	prvbackcast = 1;
	}
	else if((num_filled=sscanf(line,"prevbackcast=%d yearsbproj=%lf mobil_average=%d\n",&prevbcast,&yrbproj,&mobilavproj)) ==3){/* && (num_filled == 3))*/
	printf("prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
	fprintf(ficlog,"prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
	fprintf(ficres,"prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
	prvbackcast = 2;
	}
	else {
	printf("Error: Not 8 (data)parameters in line but %d, for example:prevbackcast=1 starting-back-date=1/1/1990 final-back-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevbackcast=1 yearsbproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
	fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevbackcast=1 starting-back-date=1/1/1990 final-back-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevbackcast=1 yearbproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
	goto end;
	}
	break;
	case 13:
	num_filled=sscanf(line,"result:%[^\n]\n",resultline);
	nresult++; /* Sum of resultlines */
	printf("Result %d: result:%s\n",nresult, resultline);
	if(nresult > MAXRESULTLINES){
	printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINES,nresult,rfileres);
	fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINES,nresult,rfileres);
	goto end;
	}
	if(!decoderesult(resultline, nresult)){ /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
	fprintf(ficparo,"result: %s\n",resultline);
	fprintf(ficres,"result: %s\n",resultline);
	fprintf(ficlog,"result: %s\n",resultline);
	} else
	goto end;
	break;
	case 14:
	printf("Error: Unknown command '%s'\n",line);
	fprintf(ficlog,"Error: Unknown command '%s'\n",line);
	if(line[0] == ' ' \|\| line[0] == '\n'){
	printf("It should not be an empty line '%s'\n",line);
	fprintf(ficlog,"It should not be an empty line '%s'\n",line);
	}
	if(ncovmodel >=2 && nresult==0 ){
	printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
	fprintf(ficlog,"ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
	}
	/* goto end; */
	break;
	case 15:
	printf("End of resultlines.\n");
	fprintf(ficlog,"End of resultlines.\n");
	break;
	default: /* parameterline =0 */
	nresult=1;
	decoderesult(".",nresult ); /* No covariate */
	} /* End switch parameterline */
	}while(endishere==0); /* End do */

/* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */	/* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
/* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */	/* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
Line 10991 Please run with mle=-1 to get a correct	Line 12611 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, prevfcast, backcast, pathc,p);	/* printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */
	/* It seems that anprojd which is computed from the mean year at interview which is known yet because of freqsummary */
	/* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); / / Done in freqsummary */
	if(prvforecast==1){
	dateprojd=(jproj1+12mproj1+365anproj1)/365;
	jprojd=jproj1;
	mprojd=mproj1;
	anprojd=anproj1;
	dateprojf=(jproj2+12mproj2+365anproj2)/365;
	jprojf=jproj2;
	mprojf=mproj2;
	anprojf=anproj2;
	} else if(prvforecast == 2){
	dateprojd=dateintmean;
	date2dmy(dateprojd,&jprojd, &mprojd, &anprojd);
	dateprojf=dateintmean+yrfproj;
	date2dmy(dateprojf,&jprojf, &mprojf, &anprojf);
	}
	if(prvbackcast==1){
	datebackd=(jback1+12mback1+365anback1)/365;
	jbackd=jback1;
	mbackd=mback1;
	anbackd=anback1;
	datebackf=(jback2+12mback2+365anback2)/365;
	jbackf=jback2;
	mbackf=mback2;
	anbackf=anback2;
	} else if(prvbackcast == 2){
	datebackd=dateintmean;
	date2dmy(datebackd,&jbackd, &mbackd, &anbackd);
	datebackf=dateintmean-yrbproj;
	date2dmy(datebackf,&jbackf, &mbackf, &anbackf);
	}

	printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, prevbcast, pathc,p, (int)anprojd-bage, (int)anbackd-fage);
}	}
printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \	printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \	model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,prevbcast, estepm, \
jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);	jprev1,mprev1,anprev1,dateprev1, dateprojd, datebackd,jprev2,mprev2,anprev2,dateprev2,dateprojf, datebackf);

/------------ free_vector -------------/	/------------ free_vector -------------/
/* chdir(path); */	/* chdir(path); */
Line 11004 Please run with mle=-1 to get a correct	Line 12658 Please run with mle=-1 to get a correct
/* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */	/* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
/* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */	/* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
/* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */	/* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */
free_lvector(num,1,n);	free_lvector(num,firstobs,lastobs);
free_vector(agedc,1,n);	free_vector(agedc,firstobs,lastobs);
/free_matrix(covar,0,NCOVMAX,1,n);/	/free_matrix(covar,0,NCOVMAX,1,n);/
/free_matrix(covar,1,NCOVMAX,1,n);/	/free_matrix(covar,1,NCOVMAX,1,n);/
fclose(ficparo);	fclose(ficparo);
Line 11031 Please run with mle=-1 to get a correct	Line 12685 Please run with mle=-1 to get a correct
k=1;	k=1;
varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);	varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);

/* Prevalence for each covariates in probs[age][status][cov] */	/* Prevalence for each covariate combination in probs[age][status][cov] */
probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);	probs= ma3x(AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
for(i=1;i<=AGESUP;i++)	for(i=AGEINF;i<=AGESUP;i++)
for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */	for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
for(k=1;k<=ncovcombmax;k++)	for(k=1;k<=ncovcombmax;k++)
probs[i][j][k]=0.;	probs[i][j][k]=0.;
prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);	prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode,
	ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
if (mobilav!=0 \|\|mobilavproj !=0 ) {	if (mobilav!=0 \|\|mobilavproj !=0 ) {
mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);	mobaverages= ma3x(AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
for(i=1;i<=AGESUP;i++)	for(i=AGEINF;i<=AGESUP;i++)
for(j=1;j<=nlstate;j++)	for(j=1;j<=nlstate+ndeath;j++)
for(k=1;k<=ncovcombmax;k++)	for(k=1;k<=ncovcombmax;k++)
mobaverages[i][j][k]=0.;	mobaverages[i][j][k]=0.;
mobaverage=mobaverages;	mobaverage=mobaverages;
if (mobilav!=0) {	if (mobilav!=0) {
printf("Movingaveraging observed prevalence\n");	printf("Movingaveraging observed prevalence\n");
	fprintf(ficlog,"Movingaveraging observed prevalence\n");
if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){	if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);	fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
printf(" Error in movingaverage mobilav=%d\n",mobilav);	printf(" Error in movingaverage mobilav=%d\n",mobilav);
}	}
}	} else if (mobilavproj !=0) {
/* /\* Prevalence for each covariates in probs[age][status][cov] \/ /
/* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
else if (mobilavproj !=0) {
printf("Movingaveraging projected observed prevalence\n");	printf("Movingaveraging projected observed prevalence\n");
	fprintf(ficlog,"Movingaveraging projected observed prevalence\n");
if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){	if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);	fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);	printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
}	}
	}else{
	printf("Internal error moving average\n");
	fflush(stdout);
	exit(1);
}	}
}/* end if moving average */	}/* end if moving average */

/---------- Forecasting ------------------/	/---------- Forecasting ------------------/
/if((stepm == 1) && (strcmp(model,".")==0)){/	if(prevfcast==1){
if(prevfcast==1){	/* /\* if(stepm ==1){\/ /
/* if(stepm ==1){*/	/* /\* anproj1, mproj1, jproj1 either read explicitly or yrfproj \/ /
prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);	/This done previously after freqsummary./
	/* dateprojd=(jproj1+12mproj1+365anproj1)/365; */
	/* dateprojf=(jproj2+12mproj2+365anproj2)/365; */

	/* } else if (prvforecast==2){ */
	/* /\* if(stepm ==1){\/ /
	/* /\* anproj1, mproj1, jproj1 either read explicitly or yrfproj \/ /
	/* } */
	/prevforecast(fileresu, dateintmean, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);/
	prevforecast(fileresu,dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, p, cptcoveff);
}	}
if(backcast==1){
	/* Prevbcasting */
	if(prevbcast==1){
ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);	ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);	ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);	ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
Line 11077 Please run with mle=-1 to get a correct	Line 12746 Please run with mle=-1 to get a correct
/--------------- Back Prevalence limit (period or stable prevalence) --------------/	/--------------- Back Prevalence limit (period or stable prevalence) --------------/

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

back_prevalence_limit(p, bprlim, ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);	back_prevalence_limit(p, bprlim, ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
fclose(ficresplb);	fclose(ficresplb);

hBijx(p, bage, fage, mobaverage);	hBijx(p, bage, fage, mobaverage);
fclose(ficrespijb);	fclose(ficrespijb);
free_matrix(bprlim,1,nlstate,1,nlstate); /here or after loop ? /

/* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,	/* /\* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, \/ /
bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */	/* /\* mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); \/ /
	/* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, */
	/* mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
	prevbackforecast(fileresu, mobaverage, dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2,
	mobilavproj, bage, fage, firstpass, lastpass, p, cptcoveff);


	varbprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, bprlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);


	free_matrix(bprlim,1,nlstate,1,nlstate); /here or after loop ? /
free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);	free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);	free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);	free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
}	} /* end Prevbcasting */


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

Line 11118 Please run with mle=-1 to get a correct	Line 12797 Please run with mle=-1 to get a correct

for(nres=1; nres <= nresult; nres++) /* For each resultline */	for(nres=1; nres <= nresult; nres++) /* For each resultline */
for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */	for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
if(TKresult[nres]!= k)	if(i1 != 1 && TKresult[nres]!= k)
continue;	continue;
fprintf(ficreseij,"\n#****** ");	fprintf(ficreseij,"\n#****** ");
printf("\n#****** ");	printf("\n#****** ");
Line 11142 Please run with mle=-1 to get a correct	Line 12821 Please run with mle=-1 to get a correct
fclose(ficreseij);	fclose(ficreseij);
printf("done evsij\n");fflush(stdout);	printf("done evsij\n");fflush(stdout);
fprintf(ficlog,"done evsij\n");fflush(ficlog);	fprintf(ficlog,"done evsij\n");fflush(ficlog);


/---------- State-specific expectancies and variances ------------/	/---------- State-specific expectancies and variances ------------/


strcpy(filerest,"T_");	strcpy(filerest,"T_");
strcat(filerest,fileresu);	strcat(filerest,fileresu);
if((ficrest=fopen(filerest,"w"))==NULL) {	if((ficrest=fopen(filerest,"w"))==NULL) {
Line 11154 Please run with mle=-1 to get a correct	Line 12833 Please run with mle=-1 to get a correct
}	}
printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);	printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);	fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);


strcpy(fileresstde,"STDE_");	strcpy(fileresstde,"STDE_");
strcat(fileresstde,fileresu);	strcat(fileresstde,fileresu);
if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {	if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
Line 11183 Please run with mle=-1 to get a correct	Line 12860 Please run with mle=-1 to get a correct
printf(" Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);	printf(" Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
fprintf(ficlog," Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);	fprintf(ficlog," Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);

/*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/

i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */	i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
if (cptcovn < 1){i1=1;}	if (cptcovn < 1){i1=1;}

for(nres=1; nres <= nresult; nres++) /* For each resultline */	for(nres=1; nres <= nresult; nres++) /* For each resultline */
for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */	for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
if(TKresult[nres]!= k)	if(i1 != 1 && TKresult[nres]!= k)
continue;	continue;
printf("\n#****** Result for:");	printf("\n#****** Result for:");
fprintf(ficrest,"\n#****** Result for:");	fprintf(ficrest,"\n#****** Result for:");
Line 11247 Please run with mle=-1 to get a correct	Line 12921 Please run with mle=-1 to get a correct
vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);	vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
pstamp(ficrest);	pstamp(ficrest);

	epj=vector(1,nlstate+1);
for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/	for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
oldm=oldms;savm=savms; /* ZZ Segmentation fault */	oldm=oldms;savm=savms; /* ZZ Segmentation fault */
cptcod= 0; /* To be deleted */	cptcod= 0; /* To be deleted */
Line 11258 Please run with mle=-1 to get a correct	Line 12932 Please run with mle=-1 to get a correct
if(vpopbased==1)	if(vpopbased==1)
fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);	fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
else	else
fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");	fprintf(ficrest,"the age specific forward period (stable) prevalences in each health state \n");
fprintf(ficrest,"# Age popbased mobilav e.. (std) ");	fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);	for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
fprintf(ficrest,"\n");	fprintf(ficrest,"\n");
/* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */	/* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
epj=vector(1,nlstate+1);	printf("Computing age specific forward 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 forward 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, nres); /ZZ Is it the correct prevalim /	prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /ZZ Is it the correct prevalim /
if (vpopbased==1) {	if (vpopbased==1) {
Line 11301 Please run with mle=-1 to get a correct	Line 12974 Please run with mle=-1 to get a correct
fprintf(ficrest,"\n");	fprintf(ficrest,"\n");
}	}
} /* End vpopbased */	} /* End vpopbased */
	free_vector(epj,1,nlstate+1);
free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);	free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);	free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
free_vector(epj,1,nlstate+1);
printf("done selection\n");fflush(stdout);	printf("done selection\n");fflush(stdout);
fprintf(ficlog,"done selection\n");fflush(ficlog);	fprintf(ficlog,"done selection\n");fflush(ficlog);

/}/
} /* End k selection */	} /* End k selection */

printf("done State-specific expectancies\n");fflush(stdout);	printf("done State-specific expectancies\n");fflush(stdout);
fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);	fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);

/------- Variance of period (stable) prevalence------/	/* variance-covariance of forward period prevalence*/
	varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
strcpy(fileresvpl,"VPL_");
strcat(fileresvpl,fileresu);
if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
exit(0);
}
printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);

/*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/

i1=pow(2,cptcoveff);
if (cptcovn < 1){i1=1;}

for(nres=1; nres <= nresult; nres++) /* For each resultline */
for(k=1; k<=i1;k++){
if(TKresult[nres]!= k)
continue;
fprintf(ficresvpl,"\n#****** ");
printf("\n#****** ");
fprintf(ficlog,"\n#****** ");
for(j=1;j<=cptcoveff;j++) {
fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
}
for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
}
fprintf(ficresvpl,"******\n");
printf("******\n");
fprintf(ficlog,"******\n");

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

fclose(ficresvpl);	free_vector(weight,firstobs,lastobs);
printf("done variance-covariance of period prevalence\n");fflush(stdout);
fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);

free_vector(weight,1,n);
free_imatrix(Tvard,1,NCOVMAX,1,2);	free_imatrix(Tvard,1,NCOVMAX,1,2);
free_imatrix(s,1,maxwav+1,1,n);	free_imatrix(s,1,maxwav+1,firstobs,lastobs);
free_matrix(anint,1,maxwav,1,n);	free_matrix(anint,1,maxwav,firstobs,lastobs);
free_matrix(mint,1,maxwav,1,n);	free_matrix(mint,1,maxwav,firstobs,lastobs);
free_ivector(cod,1,n);	free_ivector(cod,firstobs,lastobs);
free_ivector(tab,1,NCOVMAX);	free_ivector(tab,1,NCOVMAX);
fclose(ficresstdeij);	fclose(ficresstdeij);
fclose(ficrescveij);	fclose(ficrescveij);
Line 11378 Please run with mle=-1 to get a correct	Line 13005 Please run with mle=-1 to get a correct

/---------- End : free ----------------/	/---------- End : free ----------------/
if (mobilav!=0 \|\|mobilavproj !=0)	if (mobilav!=0 \|\|mobilavproj !=0)
free_ma3x(mobaverages,1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */	free_ma3x(mobaverages,AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
free_ma3x(probs,1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);	free_ma3x(probs,AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
free_matrix(prlim,1,nlstate,1,nlstate); /here or after loop ? /	free_matrix(prlim,1,nlstate,1,nlstate); /here or after loop ? /
free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);	free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
} /* mle==-3 arrives here for freeing */	} /* mle==-3 arrives here for freeing */
Line 11387 Please run with mle=-1 to get a correct	Line 13014 Please run with mle=-1 to get a correct
free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);	free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);	free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);	free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);	if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,firstobs,lastobs);
free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,1,n);	if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,firstobs,lastobs);
free_matrix(coqvar,1,maxwav,1,n);	if(nqv>=1)free_matrix(coqvar,1,nqv,firstobs,lastobs);
free_matrix(covar,0,NCOVMAX,1,n);	free_matrix(covar,0,NCOVMAX,firstobs,lastobs);
free_matrix(matcov,1,npar,1,npar);	free_matrix(matcov,1,npar,1,npar);
free_matrix(hess,1,npar,1,npar);	free_matrix(hess,1,npar,1,npar);
/free_vector(delti,1,npar);/	/free_vector(delti,1,npar);/
free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);	free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
free_matrix(agev,1,maxwav,1,imx);	free_matrix(agev,1,maxwav,1,imx);
	free_ma3x(paramstart,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);	free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);

free_ivector(ncodemax,1,NCOVMAX);	free_ivector(ncodemax,1,NCOVMAX);
Line 11472 Please run with mle=-1 to get a correct	Line 13100 Please run with mle=-1 to get a correct
fclose(ficlog);	fclose(ficlog);
/------ End -----------/	/------ End -----------/


	/* Executes gnuplot */

printf("Before Current directory %s!\n",pathcd);	printf("Before Current directory %s!\n",pathcd);
#ifdef WIN32	#ifdef WIN32
Line 11507 Please run with mle=-1 to get a correct	Line 13137 Please run with mle=-1 to get a correct

sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);	sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);	printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
	strcpy(pplotcmd,plotcmd);

if((outcmd=system(plotcmd)) != 0){	if((outcmd=system(plotcmd)) != 0){
printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);	printf("Error in gnuplot, command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");	printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);	sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
if((outcmd=system(plotcmd)) != 0)	if((outcmd=system(plotcmd)) != 0){
printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);	printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
	strcpy(plotcmd,pplotcmd);
	}
}	}
printf(" Successful, please wait...");	printf(" Successful, please wait...");
while (z[0] != 'q') {	while (z[0] != 'q') {
Line 11540 end:	Line 13173 end:
printf("\nType q for exiting: "); fflush(stdout);	printf("\nType q for exiting: "); fflush(stdout);
scanf("%s",z);	scanf("%s",z);
}	}
	printf("End\n");
	exit(0);
}	}

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