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Diff for /imach/src/imach.c between versions 1.285 and 1.314

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

Line 1037 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 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
Line 1064 typedef struct {	Line 1181 typedef struct {
/* $State$ */	/* $State$ */
#include "version.h"	#include "version.h"
char version[]=__IMACH_VERSION__;	char version[]=__IMACH_VERSION__;
char copyright[]="April 2018,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 1088 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 1228 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;
Line 1475 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 1757 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 2347 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 2571 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 2667 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 2736 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 2850 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 */
if(first){	if(!first){
first=1;	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\	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);	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);
Line 2935 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 2956 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 combination ij. In fact cov is already filled and x too.	/* Computes the backward probability at age agefin, cov[2], and covariate combination 'ij'. In fact cov is already filled and x too.
* Call to pmij(cov and x), call to cross prevalence, sums and inverses, left multiply, 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;
Line 2964 double pmij(double ps, double *cov,	Line 3095 double pmij(double ps, double *cov,
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 matrixe (in order for B to sum to 1 even for death state) */	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 2983 double pmij(double ps, double *cov,	Line 3114 double pmij(double ps, double *cov,
/* outputs pmmij which is a stochastic matrix in row */	/* outputs pmmij which is a stochastic matrix in row */

/* Diag(w_x) */	/* Diag(w_x) */
/* Problem with prevacurrent which can be zero */	/* Rescaling the cross-sectional prevalence: Problem with prevacurrent which can be zero */
sumnew=0.;	sumnew=0.;
/for (ii=1;ii<=nlstate+ndeath;ii++){/	/for (ii=1;ii<=nlstate+ndeath;ii++){/
for (ii=1;ii<=nlstate;ii++){ /* Only on live states */	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]); */	/* 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];	sumnew+=prevacurrent[(int)agefin][ii][ij];
}	}
if(sumnew >0.01){ /* At least some value in the prevalence */	if(sumnew >0.01){ /* At least some value in the prevalence */
Line 3010 double pmij(double ps, double *cov,	Line 3141 double pmij(double ps, double *cov,
}	}
/* End doldm, At the end doldm is diag[(w_i)] */	/* End doldm, At the end doldm is diag[(w_i)] */

/* left Product of this diag matrix by pmmij=Px (dnewm=dsavmdoldm) /	/* 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); /* Bug Valgrind */	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 */	/* 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.. */	/* 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.;	sumnew=0.;
Line 3031 double pmij(double ps, double *cov,	Line 3162 double pmij(double ps, double *cov,
} /End ii /	} /End ii /
} /* 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 */	} /* 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 */

ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* Bug Valgrind */	ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* was a Bug Valgrind */
/* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */	/* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
/* end bmij */	/* end bmij */
return ps; /pointer is unchanged /	return ps; /pointer is unchanged /
Line 3103 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 3736 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 3863 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 3887 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 4362 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 ******************/
Line 4577 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4722 Title=%s <br>Datafile=%s Firstpass=%d La
if(s[m][iind]==-1)	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.));	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 */	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 */	for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean on known values only */
idq[z1]=idq[z1]+weight[iind];	if(!isnan(covar[ncovcol+z1][iind])){
meanq[z1]+=covar[ncovcol+z1][iind]weight[iind]; / Computes mean of quantitative with selected filter */	idq[z1]=idq[z1]+weight[iind];
stdq[z1]+=covar[ncovcol+z1][iind]covar[ncovcol+z1][iind]weight[iind]weight[iind]; / weight[iind];/ /* Computes mean of quantitative with selected filter */	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) */	/* 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); */	/* printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */
Line 4643 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4791 Title=%s <br>Datafile=%s Firstpass=%d La
Printing means of quantitative variables if any	Printing means of quantitative variables if any
*/	*/
for (z1=1; z1<= nqfveff; z1++) {	for (z1=1; z1<= nqfveff; z1++) {
fprintf(ficlog,"Mean of fixed quantitative variable V%d on %.0f individuals sum=%f", ncovcol+z1, idq[z1], meanq[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]);	fprintf(ficlog,", mean=%.3g\n",meanq[z1]/idq[z1]);
if(weightopt==1){	if(weightopt==1){
printf(" Weighted mean and standard deviation of");	printf(" Weighted mean and standard deviation of");
fprintf(ficlog," Weighted mean and standard deviation of");	fprintf(ficlog," Weighted mean and standard deviation of");
fprintf(ficresphtmfr," Weighted mean and standard deviation of");	fprintf(ficresphtmfr," Weighted mean and standard deviation of");
}	}
printf(" fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));	/* mu = \frac{w x}{\sum w}
fprintf(ficlog," fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));	var = \frac{\sum w (x-mu)^2}{\sum w} = \frac{w x^2}{\sum w} - mu^2
fprintf(ficresphtmfr," fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)<p>\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));	*/
	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 (z1=1; z1<= nqtveff; z1++) { */
/* for(m=1;m<=lastpass;m++){ */	/* for(m=1;m<=lastpass;m++){ */
Line 4936 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5087 Title=%s <br>Datafile=%s Firstpass=%d La
}	}
} /* end mle=-2 */	} /* end mle=-2 */
dateintmean=dateintsum/k2cpt;	dateintmean=dateintsum/k2cpt;
	date2dmy(dateintmean,&jintmean,&mintmean,&aintmean);

fclose(ficresp);	fclose(ficresp);
fclose(ficresphtm);	fclose(ficresphtm);
Line 5049 void prevalence(double ***probs, double	Line 5201 void prevalence(double ***probs, double
/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+4+AGEMARGE; iage++)	for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)
Line 5107 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 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]);	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]);
fprintf(ficlog,"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{	}else{
fprintf(ficlog,"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]);	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 5130 void prevalence(double ***probs, double	Line 5281 void prevalence(double ***probs, double

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 5155 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 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);	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 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);	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 5206 void concatwav(int wav[], int **dh, int	Line 5357 void concatwav(int wav[], int **dh, int
#ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE	#ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
else if ((int) andc[i] != 9999) { /* Date of death is known */	else if ((int) andc[i] != 9999) { /* Date of death is known */
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. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). 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], 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. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\n\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{ /* if date of interview is unknown */	}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 5363 void concatwav(int wav[], int **dh, int	Line 5515 void concatwav(int wav[], int **dh, int
nbcode[k][j]=0; /* Valgrind */	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 5381 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 5427 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 5448 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 5846 void concatwav(int wav[], int **dh, int	Line 6007 void concatwav(int wav[], int **dh, int
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 /
Line 5970 void concatwav(int wav[], int **dh, int	Line 6132 void concatwav(int wav[], int **dh, int
}	}
/**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and	/**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and
* returns into prlim .	* 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 we use crossection prevalences. Previous step is useless but prlim is created */
Line 5983 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.	/**< 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=0 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$, which are the probability	/**< And for each alive state j, sums over i \f$ w^i_x {}{h}_p^{ij}x\f$, which are the probability
* at horizon h in state j including mortality.	* at horizon h in state j including mortality.
*/	*/
for(j=1; j<= nlstate; j++){	for(j=1; j<= nlstate; j++){
Line 6008 void concatwav(int wav[], int **dh, int	Line 6170 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);

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 6194 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 6223 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 6285 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 6503 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. %s</li>\n",optionfilehtmcov,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 6773 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 mobilav, int prevfcast, int mobilavproj, 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 dateproj1, double dateback1, \	double jprev1, double mprev1,double anprev1, double dateprev1, double dateprojd, double dateback1, \
double jprev2, double mprev2,double anprev2, double dateprev2, double dateproj2, double dateback2){	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 6796 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 6905 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 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> \	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, nlstate, cpt, 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 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> \	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 and mobil_average=%d), from year %.1f up to year %.1f tending to period (stable) 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><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, mobilavproj, dateproj1, dateproj2, 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(backcast==1){	if(prevbcast==1){
/* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */	/* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */
for(cpt=1; cpt<=nlstate;cpt++){	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), \	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 \	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) \	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><br> \	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);
<img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, dateback1, dateback2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,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 6982 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 7029 See page 'Matrix of variance-covariance	Line 7198 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 with mov_average=%d) 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\">",mobilav,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 7046 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 bage, double fage , int prevfcast, int backcast, char pathc[], double p[], int offyear, int offbyear){	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], gplotlabel[132];	char gplotcondition[132], gplotlabel[132];
Line 7124 void printinggnuplot(char fileresu[], ch	Line 7295 void printinggnuplot(char fileresu[], ch
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,"(");	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 */
Line 7162 void printinggnuplot(char fileresu[], ch	Line 7333 void printinggnuplot(char fileresu[], ch
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_"),nres-1,nres-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)");
Line 7200 void printinggnuplot(char fileresu[], ch	Line 7371 void printinggnuplot(char fileresu[], ch
} /* end covariate */	} /* end covariate */
} /* end if no covariate */	} /* end if no covariate */

if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */	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 7227 void printinggnuplot(char fileresu[], ch	Line 7398 void printinggnuplot(char fileresu[], ch
}	}
} /* end covariate */	} /* end covariate */
} /* end if no covariate */	} /* end if no covariate */
if(backcast == 1){	if(prevbcast == 1){
fprintf(ficgp,", \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);	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*/	/* k1-1 error should be nres-1*/
for (i=1; i<= nlstate ; i ++) {	for (i=1; i<= nlstate ; i ++) {
Line 7246 void printinggnuplot(char fileresu[], ch	Line 7417 void printinggnuplot(char fileresu[], ch
}	}
fprintf(ficgp,"\" t\"\" w l lt 4");	fprintf(ficgp,"\" t\"\" w l lt 4");
} /* end if backprojcast */	} /* end if backprojcast */
} /* end if backcast */	} /* end if prevbcast */
/* fprintf(ficgp,"\nset out ;unset label;\n"); */	/* fprintf(ficgp,"\nset out ;unset label;\n"); */
fprintf(ficgp,"\nset out ;unset title;\n");	fprintf(ficgp,"\nset out ;unset title;\n");
} /* nres */	} /* nres */
Line 7491 set ter svg size 640, 480\nunset log y\n	Line 7662 set ter svg size 640, 480\nunset log y\n
continue;	continue;
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */
strcpy(gplotlabel,"(");	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 7534 set ter svg size 640, 480\nunset log y\n	Line 7705 set ter svg size 640, 480\nunset log y\n


/* 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(m != 1 && TKresult[nres]!= k1)	if(m != 1 && TKresult[nres]!= k1)
continue;	continue;
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */
strcpy(gplotlabel,"(");	strcpy(gplotlabel,"(");
fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);	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 7586 set ter svg size 640, 480\nunset log y\n	Line 7757 set ter svg size 640, 480\nunset log y\n
fprintf(ficgp,"\nset out; unset label;\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 */
Line 7598 set ter svg size 640, 480\nunset log y\n	Line 7769 set ter svg size 640, 480\nunset log y\n
continue;	continue;
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
strcpy(gplotlabel,"(");	strcpy(gplotlabel,"(");
fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);	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 7702 set ter svg size 640, 480\nunset log y\n	Line 7873 set ter svg size 640, 480\nunset log y\n
} /* end covariate */	} /* end covariate */
} /* End if prevfcast */	} /* End if prevfcast */

if(backcast==1){	if(prevbcast==1){
/* Back projection from cross-sectional to stable (mixed) for each covariate */	/* Back projection from cross-sectional to stable (mixed) 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 */
Line 7815 set ter svg size 640, 480\nunset log y\n	Line 7986 set ter svg size 640, 480\nunset log y\n
fprintf(ficgp,"\nset out; unset label;\n");	fprintf(ficgp,"\nset out; unset label;\n");
} /* end cpt state*/	} /* end cpt state*/
} /* end covariate */	} /* end covariate */
} /* End if backcast */	} /* End if prevbcast */


/* 9eme writing MLE parameters */	/* 9eme writing MLE parameters */
Line 8032 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., sumr=0.;	double sum=0., sumr=0.;
double age;	double age;
Line 8129 set ter svg size 640, 480\nunset log y\n	Line 8301 set ter svg size 640, 480\nunset log y\n
} /* age */	} /* age */
/* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */	/* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */
/* but they will change */	/* 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 */	for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */
sumnewm[cptcod]=0.;	sumnewm[cptcod]=0.;
sumnewmr[cptcod]=0.;	sumnewmr[cptcod]=0.;
Line 8161 set ter svg size 640, 480\nunset log y\n	Line 8334 set ter svg size 640, 480\nunset log y\n
sumr+=probs[(int)age][i][cptcod];	sumr+=probs[(int)age][i][cptcod];
}	}
if(fabs(sum - 1.) > 1.e-3) { /* bad */	if(fabs(sum - 1.) > 1.e-3) { /* bad */
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\n",cptcod,sumr, (int)age, (int)bage);	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 */	} /* end bad */
/* else{ /\* We found some ages summing to one, we will smooth the oldest \/ /	/* else{ /\* We found some ages summing to one, we will smooth the oldest \/ /
if(fabs(sumr - 1.) > 1.e-3) { /* bad */	if(fabs(sumr - 1.) > 1.e-3) { /* bad */
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\n",cptcod,sumr, (int)age, (int)bage);	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 */

Line 8253 set ter svg size 640, 480\nunset log y\n	Line 8434 set ter svg size 640, 480\nunset log y\n
}/* 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 ***prev, 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).
*/	*/
	/* double anprojd, mprojd, jprojd; */
	/* double anprojf, mprojf, jprojf; */
int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;	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 8299 set ter svg size 640, 480\nunset log y\n	Line 8485 set ter svg size 640, 480\nunset log y\n
if(estepm > stepm){ /* Yes every two year */	if(estepm > stepm){ /* Yes every two year */
stepsize=2;	stepsize=2;
}	}
	hstepm=hstepm/stepm;

hstepm=hstepm/stepm;
yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and	/* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
fractional in yp1 */	/* fractional in yp1 \/ /
anprojmean=yp;	/* aintmean=yp; */
yp2=modf((yp1*12),&yp);	/* yp2=modf((yp112),&yp); /
mprojmean=yp;	/* mintmean=yp; */
yp1=modf((yp2*30.5),&yp);	/* yp1=modf((yp230.5),&yp); /
jprojmean=yp;	/* jintmean=yp; */
if(jprojmean==0) jprojmean=1;	/* if(jintmean==0) jintmean=1; */
if(mprojmean==0) jprojmean=1;	/* if(mintmean==0) mintmean=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");

Line 8340 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--){	for (agec=fage; agec>=(bage); agec--){
nhstepm=(int) rint((agelim-agec)*YEARM/stepm);	nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
Line 8360 set ter svg size 640, 480\nunset log y\n	Line 8551 set ter svg size 640, 480\nunset log y\n
fprintf(ficresf,"\n");	fprintf(ficresf,"\n");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+hhstepm/YEARMstepm);	fprintf(ficresf,"%.f %.f ",anprojd+yearp,agec+hhstepm/YEARMstepm);

for(j=1; j<=nlstate+ndeath;j++) {	for(j=1; j<=nlstate+ndeath;j++) {
ppij=0.;	ppij=0.;
Line 8388 set ter svg size 640, 480\nunset log y\n	Line 8579 set ter svg size 640, 480\nunset log y\n
}	}

/************ Back Forecasting ****************/	/************ Back Forecasting ****************/
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){	/* 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){
	/* back1, year, month, day of starting backprojection
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
anback2 year of end of backprojection (same day and month as back1).	anback2 year of end of backprojection (same day and month as back1).
Line 8397 set ter svg size 640, 480\nunset log y\n	Line 8589 set ter svg size 640, 480\nunset log y\n
*/	*/
int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;	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, ppi, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;	double agelim, ppij, ppi, yp,yp1,yp2; /* ,jintmean,mintmean,aintmean;*/
double popeffectif,popcount;	double popeffectif,popcount;
double ***p3mat;	double ***p3mat;
/* double **mobaverage; /	/* double **mobaverage; /
Line 8440 set ter svg size 640, 480\nunset log y\n	Line 8632 set ter svg size 640, 480\nunset log y\n
}	}

hstepm=hstepm/stepm;	hstepm=hstepm/stepm;
yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and	/* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
fractional in yp1 */	/* fractional in yp1 \/ /
anprojmean=yp;	/* aintmean=yp; */
yp2=modf((yp1*12),&yp);	/* yp2=modf((yp112),&yp); /
mprojmean=yp;	/* mintmean=yp; */
yp1=modf((yp2*30.5),&yp);	/* yp1=modf((yp230.5),&yp); /
jprojmean=yp;	/* jintmean=yp; */
if(jprojmean==0) jprojmean=1;	/* if(jintmean==0) jintmean=1; */
if(mprojmean==0) jprojmean=1;	/* if(mintmean==0) jintmean=1; */

i1=pow(2,cptcoveff);	i1=pow(2,cptcoveff);
if (cptcovn < 1){i1=1;}	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);	fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);	printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);

fprintf(ficresfb,"#**** Routine prevbackforecast \n");	fprintf(ficresfb,"#**** Routine prevbackforecast \n");

Line 8479 set ter svg size 640, 480\nunset log y\n	Line 8671 set ter svg size 640, 480\nunset log y\n
fprintf(ficresfb," b%d%d",i,j);	fprintf(ficresfb," b%d%d",i,j);
fprintf(ficresfb," b.%d",j);	fprintf(ficresfb," b.%d",j);
}	}
for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {	for (yearp=0; yearp>=(anbackf-anbackd);yearp -=stepsize) {
/* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { */	/* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { */
fprintf(ficresfb,"\n");	fprintf(ficresfb,"\n");
fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);	fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jbackd,mbackd,anbackd+yearp);
/* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */	/* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
/* for (agec=bage; agec<=agemax-1; agec++){ /\* testing \/ /	/* for (agec=bage; agec<=agemax-1; agec++){ /\* testing \/ /
for (agec=bage; agec<=fage; agec++){ /* testing */	for (agec=bage; agec<=fage; agec++){ /* testing */
Line 8505 set ter svg size 640, 480\nunset log y\n	Line 8697 set ter svg size 640, 480\nunset log y\n
fprintf(ficresfb,"\n");	fprintf(ficresfb,"\n");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec-hhstepm/YEARMstepm);	fprintf(ficresfb,"%.f %.f ",anbackd+yearp,agec-hhstepm/YEARMstepm);
for(i=1; i<=nlstate+ndeath;i++) {	for(i=1; i<=nlstate+ndeath;i++) {
ppij=0.;ppi=0.;	ppij=0.;ppi=0.;
for(j=1; j<=nlstate;j++) {	for(j=1; j<=nlstate;j++) {
Line 8540 set ter svg size 640, 480\nunset log y\n	Line 8732 set ter svg size 640, 480\nunset log y\n

/* Variance of prevalence limit: varprlim */	/* 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){	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 period (stable) prevalence------/	/------- Variance of forward period (stable) prevalence------/

char fileresvpl[FILENAMELENGTH];	char fileresvpl[FILENAMELENGTH];
FILE *ficresvpl;	FILE *ficresvpl;
Line 8551 set ter svg size 640, 480\nunset log y\n	Line 8743 set ter svg size 640, 480\nunset log y\n
strcpy(fileresvpl,"VPL_");	strcpy(fileresvpl,"VPL_");
strcat(fileresvpl,fileresu);	strcat(fileresvpl,fileresu);
if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {	if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);	printf("Problem with variance of forward period (stable) prevalence resultfile: %s\n", fileresvpl);
exit(0);	exit(0);
}	}
printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);	printf("Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);	fprintf(ficlog, "Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);

/*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++){*/
Line 8592 set ter svg size 640, 480\nunset log y\n	Line 8784 set ter svg size 640, 480\nunset log y\n
}	}

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

}	}
/* Variance of back prevalence: varbprlim */	/* Variance of back prevalence: varbprlim */
Line 8953 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 8961 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 8991 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 9084 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 9117 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 9239 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 9278 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 9298 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 9401 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 9416 int decoderesult ( char resultline[], in	Line 9672 int decoderesult ( char resultline[], in
TKresult[nres]=0; /* Combination for the nresult and the model */	TKresult[nres]=0; /* Combination for the nresult and the model */
return (0);	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 9449 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 9466 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 10163 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 10199 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 10215 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 10302 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 10323 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 10332 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 10413 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 10428 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 10623 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 */

Line 10653 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/

Line 10702 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 10737 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 10745 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 10770 int main(int argc, char *argv[])	Line 11041 int main(int argc, char *argv[])
double *epj, vepp;	double *epj, vepp;

double dateprev1, dateprev2;	double dateprev1, dateprev2;
double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0;	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;	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 10966 int main(int argc, char *argv[])	Line 11238 int main(int argc, char *argv[])
noffset=noffset+3;	noffset=noffset+3;
printf("# File is an UTF8 Bom.\n"); // 0xBF	printf("# File is an UTF8 Bom.\n"); // 0xBF
}	}
else if( line[0] == (char)0xFE && line[1] == (char)0xFF)	/* else if( line[0] == (char)0xFE && line[1] == (char)0xFF)*/
	else if( line[0] == (char)0xFF && line[1] == (char)0xFE)
{	{
noffset=noffset+2;	noffset=noffset+2;
printf("# File is an UTF16BE BOM file\n");	printf("# File is an UTF16BE BOM file\n");
Line 11026 int main(int argc, char *argv[])	Line 11299 int main(int argc, char *argv[])
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,"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);	fprintf(ficlog,"but line=%s\n",line);
}	}
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);	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);
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(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, 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);	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 \/ /
Line 11048 int main(int argc, char *argv[])	Line 11327 int main(int argc, char *argv[])
}	}
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 != 1){	if (num_filled != 1){
printf("ERROR %d: Model should be at minimum 'model=1+age' %s\n",num_filled, line);	printf("ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
fprintf(ficlog,"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+' instead of '%s'\n",num_filled, line);
model[0]='\0';	model[0]='\0';
goto end;	goto end;
}	}
Line 11098 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 /
if(nqv>=1)coqvar=matrix(1,nqv,1,n); /*< Fixed quantitative covariate /	if(nqv>=1)coqvar=matrix(1,nqv,firstobs,lastobs); /*< Fixed quantitative covariate /
if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,1,n); /*< Time varying quantitative covariate /	if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,firstobs,lastobs); /*< Time varying quantitative covariate /
if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,1,n); /*< Time varying covariate (dummy and quantitative)/	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 11164 int main(int argc, char *argv[])	Line 11443 int main(int argc, char *argv[])
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 11304 Please run with mle=-1 to get a correct	Line 11592 Please run with mle=-1 to get a correct

/* 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 11323 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 11427 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 11454 Please run with mle=-1 to get a correct	Line 11751 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 */	/* 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 11637 Title=%s <br>Datafile=%s Firstpass=%d La	Line 11934 Title=%s <br>Datafile=%s Firstpass=%d La
firstpass, lastpass, stepm, weightopt, model);	firstpass, lastpass, stepm, weightopt, model);

fprintf(fichtm,"\n");	fprintf(fichtm,"\n");
fprintf(fichtm,"<h4>Parameter line 2</h4><ul><li>Tolerance for the convergence of the likelihood: ftol=%f \n<li>Interval for the elementary matrix (in month): stepm=%d",\	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);	ftol, stepm);
fprintf(fichtm,"\n<li>Number of fixed dummy covariates: ncovcol=%d ", ncovcol);	fprintf(fichtm,"\n<li>Number of fixed dummy covariates: ncovcol=%d ", ncovcol);
ncurrv=1;	ncurrv=1;
Line 11645 Title=%s <br>Datafile=%s Firstpass=%d La	Line 11942 Title=%s <br>Datafile=%s Firstpass=%d La
fprintf(fichtm,"\n<li> Number of fixed quantitative variables: nqv=%d ", nqv);	fprintf(fichtm,"\n<li> Number of fixed quantitative variables: nqv=%d ", nqv);
ncurrv=i;	ncurrv=i;
for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i);	for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i);
fprintf(fichtm,"\n<li> Number of time varying (wave varying) covariates: ntv=%d ", ntv);	fprintf(fichtm,"\n<li> Number of time varying (wave varying) dummy covariates: ntv=%d ", ntv);
ncurrv=i;	ncurrv=i;
for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i);	for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i);
fprintf(fichtm,"\n<li>Number of quantitative time varying covariates: nqtv=%d ", nqtv);	fprintf(fichtm,"\n<li>Number of time varying quantitative covariates: nqtv=%d ", nqtv);
ncurrv=i;	ncurrv=i;
for(i=ncurrv; i <=ncurrv-1+nqtv; i++) fprintf(fichtm,"V%d ", 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", \	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", \
Line 11680 Interval (in months) between two waves:	Line 11977 Interval (in months) between two waves:
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 11717 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 11844 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 11893 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 12095 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 12140 Please run with mle=-1 to get a correct	Line 12439 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 12165 Please run with mle=-1 to get a correct	Line 12465 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 12187 Please run with mle=-1 to get a correct	Line 12488 Please run with mle=-1 to get a correct
}	}

/* Results */	/* Results */
	endishere=0;
nresult=0;	nresult=0;
	parameterline=0;
do{	do{
if(!fgets(line, MAXLINE, ficpar)){	if(!fgets(line, MAXLINE, ficpar)){
endishere=1;	endishere=1;
parameterline=14;	parameterline=15;
}else if (line[0] == '#') {	}else if (line[0] == '#') {
/* If line starts with a # it is a comment */	/* If line starts with a # it is a comment */
numlinepar++;	numlinepar++;
fputs(line,stdout);	fputs(line,stdout);
fputs(line,ficparo);	fputs(line,ficparo);
fputs(line,ficlog);	fputs(line,ficlog);
	fputs(line,ficres);
continue;	continue;
}else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))	}else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))
parameterline=11;	parameterline=11;
else if(sscanf(line,"backcast=%[^\n]\n",modeltemp))	else if(sscanf(line,"prevbackcast=%[^\n]\n",modeltemp))
parameterline=12;	parameterline=12;
else if(sscanf(line,"result:%[^\n]\n",modeltemp))	else if(sscanf(line,"result:%[^\n]\n",modeltemp)){
parameterline=13;	parameterline=13;
	}
else{	else{
parameterline=14;	parameterline=14;
}	}
switch (parameterline){	switch (parameterline){ /* =0 only if only comments */
case 11:	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){	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)){
if (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("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\n, your line=%s . Probably you are running 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 mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
goto end;
}
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);	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(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);	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.*/	/* day and month of proj2 are not used but only year anproj2.*/
dateproj1=anproj1+(mproj1-1)/12.+(jproj1-1)/365.;	dateproj1=anproj1+(mproj1-1)/12.+(jproj1-1)/365.;
dateproj2=anproj2+(mproj2-1)/12.+(jproj2-1)/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;
case 12:	case 12:
/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);/	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)){
if((num_filled=sscanf(line,"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)) !=EOF){	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);
if (num_filled != 8) {	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);
printf("Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 final-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);	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(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 final-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);	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);
goto end;	/* day and month of back2 are not used but only year anback2.*/
}
printf("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.*/
dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;	dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;
dateback2=anback2+(mback2-1)/12.+(jback2-1)/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;	break;
case 13:	case 13:
if((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){	num_filled=sscanf(line,"result:%[^\n]\n",resultline);
if (num_filled == 0){	nresult++; /* Sum of resultlines */
resultline[0]='\0';	printf("Result %d: result:%s\n",nresult, resultline);
printf("Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);	if(nresult > MAXRESULTLINES){
fprintf(ficlog,"Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);	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);
break;	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);
} else if (num_filled != 1){	goto end;
printf("ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);	}
fprintf(ficlog,"ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);	if(!decoderesult(resultline, nresult)){ /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
}
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\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;
}
decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
fprintf(ficparo,"result: %s\n",resultline);	fprintf(ficparo,"result: %s\n",resultline);
fprintf(ficres,"result: %s\n",resultline);	fprintf(ficres,"result: %s\n",resultline);
fprintf(ficlog,"result: %s\n",resultline);	fprintf(ficlog,"result: %s\n",resultline);
break;	} else
case 14:	goto end;
if(ncovmodel >2 && nresult==0 ){	break;
printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);	case 14:
goto end;	printf("Error: Unknown command '%s'\n",line);
}	fprintf(ficlog,"Error: Unknown command '%s'\n",line);
break;	if(line[0] == ' ' \|\| line[0] == '\n'){
default:	printf("It should not be an empty line '%s'\n",line);
nresult=1;	fprintf(ficlog,"It should not be an empty line '%s'\n",line);
decoderesult(".",nresult ); /* No covariate */	}
	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 */	} /* End switch parameterline */
}while(endishere==0); /* End do */	}while(endishere==0); /* End do */

Line 12292 This is probably because your parameter	Line 12612 This is probably because your parameter
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, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */	/* printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */
printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, backcast, pathc,p, (int)anproj1-bage, (int)anback1-fage);	/* 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,mobilav,prevfcast,mobilavproj,backcast, estepm, \	model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,prevbcast, estepm, \
jprev1,mprev1,anprev1,dateprev1, dateproj1, dateback1,jprev2,mprev2,anprev2,dateprev2,dateproj2, dateback2);	jprev1,mprev1,anprev1,dateprev1, dateprojd, datebackd,jprev2,mprev2,anprev2,dateprev2,dateprojf, datebackf);

/------------ free_vector -------------/	/------------ free_vector -------------/
/* chdir(path); */	/* chdir(path); */
Line 12305 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 12369 Please run with mle=-1 to get a correct	Line 12722 Please run with mle=-1 to get a correct
}/* end if moving average */	}/* end if moving average */

/---------- Forecasting ------------------/	/---------- Forecasting ------------------/
if(prevfcast==1){	if(prevfcast==1){
/* if(stepm ==1){*/	/* /\* if(stepm ==1){\/ /
prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);	/* /\* anproj1, mproj1, jproj1 either read explicitly or yrfproj \/ /
	/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);
}	}

/* Backcasting */	/* Prevbcasting */
if(backcast==1){	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 12390 Please run with mle=-1 to get a correct	Line 12753 Please run with mle=-1 to get a correct
hBijx(p, bage, fage, mobaverage);	hBijx(p, bage, fage, mobaverage);
fclose(ficrespijb);	fclose(ficrespijb);

prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2,	/* /\* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, \/ /
mobilavproj, 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);	varbprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, bprlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);


Line 12399 Please run with mle=-1 to get a correct	Line 12768 Please run with mle=-1 to get a correct
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 Backcasting */	} /* end Prevbcasting */


/* ------ Other prevalence ratios------------ */	/* ------ Other prevalence ratios------------ */
Line 12563 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"); */
printf("Computing age specific period (stable) prevalences in each health state \n");	printf("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");	fprintf(ficlog,"Computing age specific forward 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 12616 Please run with mle=-1 to get a correct	Line 12985 Please run with mle=-1 to get a correct
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-covariance of period prevalence*/	/* variance-covariance of forward period prevalence*/
varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);	varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);


free_vector(weight,1,n);	free_vector(weight,firstobs,lastobs);
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 12645 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);
if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,1,n);	if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,firstobs,lastobs);
if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);	if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,firstobs,lastobs);
if(nqv>=1)free_matrix(coqvar,1,nqv,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);/
Line 12768 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') {

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

Removed from v.1.285
changed lines
	Added in v.1.314