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Diff for /imach/src/imach.c between versions 1.303 and 1.321

version 1.303, 2021/02/11 19:50:15	version 1.321, 2022/07/22 12:04:24
Line 1	Line 1
/* $Id$	/* $Id$
$State$	$State$
$Log$	$Log$
	Revision 1.321 2022/07/22 12:04:24 brouard
	Summary: r28

	* imach.c (Module): Output of Wald test in the htm file and not only in the log.

	Revision 1.320 2022/06/02 05:10:11 brouard
	* empty log message *

	Revision 1.319 2022/06/02 04:45:11 brouard
	* imach.c (Module): Adding the Wald tests from the log to the main
	htm for better display of the maximum likelihood estimators.

	Revision 1.318 2022/05/24 08:10:59 brouard
	* imach.c (Module): Some attempts to find a bug of wrong estimates
	of confidencce intervals with product in the equation modelC

	Revision 1.317 2022/05/15 15:06:23 brouard
	* imach.c (Module): Some minor improvements

	Revision 1.316 2022/05/11 15:11:31 brouard
	Summary: r27

	Revision 1.315 2022/05/11 15:06:32 brouard
	* empty log message *

	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	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.	* (Module): imach.c Someone entered 'results:' instead of 'result:'. Now it is an error which is printed.

Line 1039 Important routines	Line 1112 Important routines
#define POWELLNOF3INFF1TEST /* Skip test */	#define POWELLNOF3INFF1TEST /* Skip test */
/* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test \/ /	/* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test \/ /
/* #define MNBRAKORIGINAL /\* Don't use mnbrak fix \/ /	/* #define MNBRAKORIGINAL /\* Don't use mnbrak fix \/ /
	/* #define FLATSUP // Suppresses directions where likelihood is flat */

#include <math.h>	#include <math.h>
#include <stdio.h>	#include <stdio.h>
Line 1105 typedef struct {	Line 1179 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 30 /*< 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
Line 1133 typedef struct {	Line 1207 typedef struct {
/* $State$ */	/* $State$ */
#include "version.h"	#include "version.h"
char version[]=__IMACH_VERSION__;	char version[]=__IMACH_VERSION__;
char copyright[]="May 2019,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2020";	char copyright[]="May 2022,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 2021-202, INED 2000-2022";
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 1315 double **cotvar; / Time varying covari	Line 1389 double **cotvar; / Time varying covari
double **cotqvar; / Time varying quantitative covariate itqv */	double **cotqvar; / Time varying quantitative covariate itqv */
double idx;	double idx;
int *nbcode, Tvar; /*< model=V2 => Tvar[1]= 2 /	int *nbcode, Tvar; /*< model=V2 => Tvar[1]= 2 /
/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */	/* Some documentation */
/k 1 2 3 4 5 6 7 8 9 /	/* Design original data
/Tvar[k]= 5 4 3 6 5 2 7 1 1 /	* V1 V2 V3 V4 V5 V6 V7 V8 Weight ddb ddth d1st s1 V9 V10 V11 V12 s2 V9 V10 V11 V12
/* Tndvar[k] 1 2 3 4 5 */	* < ncovcol=6 > nqv=2 (V7 V8) dv dv dv qtv dv dv dvv qtv
/TDvar 4 3 6 7 1 / /* For outputs only; combination of dummies fixed or varying */	* ntv=3 nqtv=1
/* Tns[k] 1 2 2 4 5 / / Number of single cova */	* cptcovn number of covariates (not including constant and age) = # of + plus 1 = 10+1=11
/* TvarsD[k] 1 2 3 / / Number of single dummy cova */	* For time varying covariate, quanti or dummies
/* TvarsDind 2 3 9 / / position K of single dummy cova */	* cotqvar[wav][iv(1 to nqtv)][i]= [1][12][i]=(V12) quanti
/* TvarsQ[k] 1 2 / / Number of single quantitative cova */	* cotvar[wav][ntv+iv][i]= [3+(1 to nqtv)][i]=(V12) quanti
/* TvarsQind 1 6 / / position K of single quantitative cova */	* cotvar[wav][iv(1 to ntv)][i]= [1][1][i]=(V9) dummies at wav 1
/* Tprod[i]=k 4 7 */	* cotvar[wav][iv(1 to ntv)][i]= [1][2][i]=(V10) dummies at wav 1
/* Tage[i]=k 5 8 */	* covar[k,i], value of kth fixed covariate dummy or quanti :
/* */	* covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
	* Model V2 + V1 + V3age + V3 + V5V6 + V7V8 + V8age + V8 + V9 + V9*age + V10
	* k= 1 2 3 4 5 6 7 8 9 10 11
	*/
	/* According to the model, more columns can be added to covar by the product of covariates */
	/* ncovcol=1(Males=0 Females=1) nqv=1(raedyrs) ntv=2(withoutiadl=0 withiadl=1, witoutadl=0 withoutadl=1) nqtv=1(bmi) nlstate=3 ndeath=1
	# States 1=Coresidence, 2 Living alone, 3 Institution
	# V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi
	*/
	/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
	/* k 1 2 3 4 5 6 7 8 9 */
	/Typevar[k]= 0 0 0 2 1 0 2 1 0 //0 for simple covariate (dummy, quantitative,/
	/* fixed or varying), 1 for age product, 2 for*/
	/* product */
	/Dummy[k]= 1 0 0 1 3 1 1 2 0 //Dummy[k] 0=dummy (0 1), 1 quantitative /
	/(single or product without age), 2 dummy/
	/* with age product, 3 quant with age product*/
	/Tvar[k]= 5 4 3 6 5 2 7 1 1 /
	/* nsd 1 2 3 / / Counting single dummies covar fixed or tv */
	/TvarsD[nsd] 4 3 1 / /* ID of single dummy cova fixed or timevary*/
	/TvarsDind[k] 2 3 9 / /* position K of single dummy cova */
	/* nsq 1 2 / / Counting single quantit tv */
	/* TvarsQ[k] 5 2 / / Number of single quantitative cova */
	/* TvarsQind 1 6 / / position K of single quantitative cova */
	/* Tprod[i]=k 1 2 / / Position in model of the ith prod without age */
	/* cptcovage 1 2 / / Counting covage in the model equation /
	/* Tage[cptcovage]=k 5 8 / / Position in the model of ith covage /
	/* Tvard[1][1]@4={4,3,1,2} V4V3 V1V2 / / Position in model of the ith prod without age */
	/* TvarF TvarF[1]=Tvar[6]=2, TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1 ID of fixed covariates or product V2, V1V2, V1 /
	/* TvarFind; TvarFind[1]=6, TvarFind[2]=7, TvarFind[3]=9 // Inverse V2(6) is first fixed (single or prod) */
/* Type */	/* Type */
/* V 1 2 3 4 5 */	/* V 1 2 3 4 5 */
/* F F V V V */	/* F F V V V */
Line 1338 int *TvarsDind;	Line 1441 int *TvarsDind;
int *TvarsQ;	int *TvarsQ;
int *TvarsQind;	int *TvarsQind;

#define MAXRESULTLINES 10	#define MAXRESULTLINESPONE 10+1
int nresult=0;	int nresult=0;
int parameterline=0; /* # of the parameter (type) line */	int parameterline=0; /* # of the parameter (type) line */
int TKresult[MAXRESULTLINES];	int TKresult[MAXRESULTLINESPONE];
int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */	int Tresult[MAXRESULTLINESPONE][NCOVMAX];/* For dummy variable , value (output) */
int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */	int Tinvresult[MAXRESULTLINESPONE][NCOVMAX];/* For dummy variable , value (output) */
int Tvresult[MAXRESULTLINES][NCOVMAX]; /* For dummy variable , variable # (output) */	int Tvresult[MAXRESULTLINESPONE][NCOVMAX]; /* For dummy variable , variable # (output) */
double Tqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */	double Tqresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , value (output) */
double Tqinvresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */	double Tqinvresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , value (output) */
int Tvqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , variable # (output) */	int Tvqresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , variable # (output) */

	/* ncovcol=1(Males=0 Females=1) nqv=1(raedyrs) ntv=2(withoutiadl=0 withiadl=1, witoutadl=0 withoutadl=1) nqtv=1(bmi) nlstate=3 ndeath=1
	# States 1=Coresidence, 2 Living alone, 3 Institution
	# V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi
	*/
/* int TDvar; /\< TDvar[1]=4, TDvarF[2]=3, TDvar[3]=6 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 \/ */	/* int TDvar; /\< TDvar[1]=4, TDvarF[2]=3, TDvar[3]=6 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 \/ */
int TvarF; /< TvarF[1]=Tvar[6]=2, TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 /	int TvarF; /< TvarF[1]=Tvar[6]=2, TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 /
int TvarFind; /< TvarFind[1]=6, TvarFind[2]=7, Tvarind[3]=9 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 /	int TvarFind; /< TvarFind[1]=6, TvarFind[2]=7, Tvarind[3]=9 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 /
Line 1550 char cutl(char blocc, char *alocc, cha	Line 1657 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 1832 char *subdirf(char fileres[])	Line 1939 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 2203 void linmin(double p[], double xi[], int	Line 2312 void linmin(double p[], double xi[], int
#endif	#endif
#ifdef LINMINORIGINAL	#ifdef LINMINORIGINAL
#else	#else
if(fb == fx){ /* Flat function in the direction */	if(fb == fx){ /* Flat function in the direction */
xmin=xx;	xmin=xx;
*flat=1;	*flat=1;
}else{	}else{
*flat=0;	*flat=0;
#endif	#endif
/Flat mnbrak2 shift (ax=0.000000000000, fa=51626.272983130431), (bx=-1.618034000000, fb=51590.149499362531), (cx=-4.236068025156, fc=51590.149499362531) /	/Flat mnbrak2 shift (ax=0.000000000000, fa=51626.272983130431), (bx=-1.618034000000, fb=51590.149499362531), (cx=-4.236068025156, fc=51590.149499362531) /
Line 2264 void linmin(double p[], double xi[], int	Line 2373 void linmin(double p[], double xi[], int

/************* powell **********************/	/************* powell **********************/
/*	/*
Minimization of a function func of n variables. Input consists of an initial starting point	Minimization of a function func of n variables. Input consists in an initial starting point
p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-	p[1..n] ; an initial matrix xi[1..n][1..n] whose columns contain the initial set of di-
rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value	rections (usually the n unit vectors); and ftol, the fractional tolerance in the function value
such that failure to decrease by more than this amount on one iteration signals doneness. On	such that failure to decrease by more than this amount in one iteration signals doneness. On
output, p is set to the best point found, xi is the then-current direction set, fret is the returned	output, p is set to the best point found, xi is the then-current direction set, fret is the returned
function value at p , and iter is the number of iterations taken. The routine linmin is used.	function value at p , and iter is the number of iterations taken. The routine linmin is used.
*/	*/
Line 2292 void powell(double p[], double **xi, int	Line 2401 void powell(double p[], double **xi, int
double fp,fptt;	double fp,fptt;
double *xits;	double *xits;
int niterf, itmp;	int niterf, itmp;
#ifdef LINMINORIGINAL
#else

flatdir=ivector(1,n);
for (j=1;j<=n;j++) flatdir[j]=0;
#endif

pt=vector(1,n);	pt=vector(1,n);
ptt=vector(1,n);	ptt=vector(1,n);
Line 2421 void powell(double p[], double **xi, int	Line 2524 void powell(double p[], double **xi, int
/* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */	/* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
/* 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"); */
/* fprintf(ficlog,"\n"); */
}	}
	/* printf("\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 2466 void powell(double p[], double **xi, int	Line 2569 void powell(double p[], double **xi, int
}	}
#endif	#endif

#ifdef LINMINORIGINAL
#else
free_ivector(flatdir,1,n);
#endif
free_vector(xit,1,n);	free_vector(xit,1,n);
free_vector(xits,1,n);	free_vector(xits,1,n);
free_vector(ptt,1,n);	free_vector(ptt,1,n);
Line 2583 void powell(double p[], double **xi, int	Line 2682 void powell(double p[], double **xi, int
}	}
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
	#ifdef FLATSUP
	free_vector(xit,1,n);
	free_vector(xits,1,n);
	free_vector(ptt,1,n);
	free_vector(pt,1,n);
	return;
	#endif
}	}
#endif	#endif
printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);	printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
Line 2667 void powell(double p[], double **xi, int	Line 2773 void powell(double p[], double **xi, int
newm=savm;	newm=savm;
/* Covariates have to be included here again */	/* Covariates have to be included here again */
cov[2]=agefin;	cov[2]=agefin;
if(nagesqr==1)	if(nagesqr==1){
cov[3]= agefin*agefin;;	cov[3]= agefin*agefin;
	}
for (k=1; k<=nsd;k++) { /* For single dummy covariates only */	for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
/* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */	/* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];	cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
	/* cov[++k1]=nbcode[TvarsD[k]][codtabm(ij,k)]; */
/* printf("prevalim Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */	/* printf("prevalim Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
}	}
for (k=1; k<=nsq;k++) { /* For single varying covariates only */	for (k=1; k<=nsq;k++) { /* For single varying covariates only */
/* Here comes the value of quantitative after renumbering k with single quantitative covariates */	/* Here comes the value of quantitative after renumbering k with single quantitative covariates */
cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];	cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
	/* cov[++k1]=Tqresult[nres][k]; */
/* printf("prevalim Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */	/* printf("prevalim Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
}	}
for (k=1; k<=cptcovage;k++){ /* For product with age */	for (k=1; k<=cptcovage;k++){ /* For product with age */
if(Dummy[Tvar[Tage[k]]]){	if(Dummy[Tage[k]]==2){ /* dummy with age */
cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];	cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
} else{	/* cov[++k1]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]cov[2]; /
cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];	} else if(Dummy[Tage[k]]==3){ /* quantitative with age */
	cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
	/* cov[++k1]=Tqresult[nres][k]; */
}	}
/* printf("prevalim Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */	/* printf("prevalim Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
}	}
Line 2692 void powell(double p[], double **xi, int	Line 2803 void powell(double p[], double **xi, int
if(Dummy[Tvard[k][1]==0]){	if(Dummy[Tvard[k][1]==0]){
if(Dummy[Tvard[k][2]==0]){	if(Dummy[Tvard[k][2]==0]){
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
	/* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
}else{	}else{
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
	/* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k]; */
}	}
}else{	}else{
if(Dummy[Tvard[k][2]==0]){	if(Dummy[Tvard[k][2]==0]){
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
	/* cov[++k1]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]]; */
}else{	}else{
cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];	cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
	/* cov[++k1]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]]; */
}	}
}	}
}	}
Line 2708 void powell(double p[], double **xi, int	Line 2823 void powell(double p[], double **xi, int
/printf("ij=%d cov[3]=%lf \n",ij, cov[3]);/	/printf("ij=%d cov[3]=%lf \n",ij, cov[3]);/
/* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */	/* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
/* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind \/ /	/* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind \/ /
/* age and covariate values of ij are in 'cov' */	/* age and covariate values of ij are in 'cov' */
out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */	out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */

savm=oldm;	savm=oldm;
Line 2748 void powell(double p[], double **xi, int	Line 2863 void powell(double p[], double **xi, int
if(!first){	if(!first){
first=1;	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);	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);
	}else if (first >=1 && first <10){
	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);
	first++;
	}else if (first ==10){
	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);
	printf("Warning: the stable prevalence dit not converge. This warning came too often, IMaCh will stop notifying, even in its log file. Look at the graphs to appreciate the non convergence.\n");
	fprintf(ficlog,"Warning: the stable prevalence no convergence; too many cases, giving up noticing, even in log file\n");
	first++;
}	}
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);
Line 2823 void powell(double p[], double **xi, int	Line 2946 void powell(double p[], double **xi, int
/* 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 */
/* Covariates have to be included here again */	/* Covariates have to be included here again */
cov[2]=agefin;	cov[2]=agefin;
if(nagesqr==1)	if(nagesqr==1){
cov[3]= agefin*agefin;;	cov[3]= agefin*agefin;;
	}
for (k=1; k<=nsd;k++) { /* For single dummy covariates only */	for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
/* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */	/* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];	cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
Line 2845 void powell(double p[], double **xi, int	Line 2969 void powell(double p[], double **xi, int
/* /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; \/ /	/* /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; \/ /
/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */	/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
for (k=1; k<=cptcovage;k++){ /* For product with age */	for (k=1; k<=cptcovage;k++){ /* For product with age */
if(Dummy[Tvar[Tage[k]]]){	/* if(Dummy[Tvar[Tage[k]]]== 2){ /\* dummy with age \/ ERROR ???/
	if(Dummy[Tage[k]]== 2){ /* dummy with age */
cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];	cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
} else{	} else if(Dummy[Tage[k]]== 3){ /* quantitative with age */
cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];	cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
}	}
/* printf("prevalim Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */	/* printf("prevalim Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
}	}
Line 2918 void powell(double p[], double **xi, int	Line 3043 void powell(double p[], double **xi, int

maxmax=0.;	maxmax=0.;
for(i=1; i<=nlstate; i++){	for(i=1; i<=nlstate; i++){
meandiff[i]=(max[i]-min[i])/(max[i]+min[i])2.; / mean difference for each column */	meandiff[i]=(max[i]-min[i])/(max[i]+min[i])2.; / mean difference for each column, could be nan! */
maxmax=FMAX(maxmax,meandiff[i]);	maxmax=FMAX(maxmax,meandiff[i]);
/* printf("Back age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, i, meandiff[i],(int)agefin, i, max[i], i, min[i],maxmax); */	/* printf("Back age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, i, meandiff[i],(int)agefin, i, max[i], i, min[i],maxmax); */
} /* i loop */	} /* i loop */
Line 3052 double pmij(double ps, double *cov,	Line 3177 double pmij(double ps, double *cov,
doldm=ddoldms; /* global pointers */	doldm=ddoldms; /* global pointers */
dnewm=ddnewms;	dnewm=ddnewms;
dsavm=ddsavms;	dsavm=ddsavms;

	/* Debug */
	/* printf("Bmij ij=%d, cov[2}=%f\n", ij, cov[2]); */
agefin=cov[2];	agefin=cov[2];
/* Bx = Diag(w_x) P_x Diag(Sum_i w^i_x p^ij_x */	/* Bx = Diag(w_x) P_x Diag(Sum_i w^i_x p^ij_x */
/* bmij // age is cov[2], ij is included in cov, but we need for	/* bmij // age is cov[2], ij is included in cov, but we need for
Line 3272 double *hpxij(double *po, int nhstep	Line 3399 double *hpxij(double *po, int nhstep
cov[1]=1.;	cov[1]=1.;
agexact=age+((h-1)hstepm + (d-1))stepm/YEARM; /* age just before transition */	agexact=age+((h-1)hstepm + (d-1))stepm/YEARM; /* age just before transition */
cov[2]=agexact;	cov[2]=agexact;
if(nagesqr==1)	if(nagesqr==1){
cov[3]= agexact*agexact;	cov[3]= agexact*agexact;
	}
for (k=1; k<=nsd;k++) { /* For single dummy covariates only */	for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
/* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */	/* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
	/* codtabm(ij,k) (1 & (ij-1) >> (k-1))+1 */
	/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
	/* k 1 2 3 4 5 6 7 8 9 */
	/Tvar[k]= 5 4 3 6 5 2 7 1 1 /
	/* nsd 1 2 3 / / Counting single dummies covar fixed or tv */
	/TvarsD[nsd] 4 3 1 / /* ID of single dummy cova fixed or timevary*/
	/TvarsDind[k] 2 3 9 / /* position K of single dummy cova */
cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];	cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
/* printf("hpxij Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */	/* printf("hpxij Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
}	}
for (k=1; k<=nsq;k++) { /* For single varying covariates only */	for (k=1; k<=nsq;k++) { /* For single varying covariates only */
/* Here comes the value of quantitative after renumbering k with single quantitative covariates */	/* Here comes the value of quantitative after renumbering k with single quantitative covariates */
cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];	cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
/* printf("hPxij Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */	/* printf("hPxij Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
}	}
for (k=1; k<=cptcovage;k++){	for (k=1; k<=cptcovage;k++){ /* For product with age V1+V1age +V4 +ageV3 */
if(Dummy[Tvar[Tage[k]]]){	/* 1+2 Tage[1]=2 TVar[2]=1 Dummy[2]=2, Tage[2]=4 TVar[4]=3 Dummy[4]=3 quant*/
	/* */
	if(Dummy[Tage[k]]== 2){ /* dummy with age */
	/* if(Dummy[Tvar[Tage[k]]]== 2){ /\* dummy with age \/ /
cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];	cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
} else{	} else if(Dummy[Tage[k]]== 3){ /* quantitative with age */
cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];	cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
}	}
/* printf("hPxij Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */	/* printf("hPxij Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
}	}
for (k=1; k<=cptcovprod;k++){ /* */	for (k=1; k<=cptcovprod;k++){ /* For product without age */
/* printf("hPxij Prod ij=%d k=%d Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */	/* printf("hPxij Prod ij=%d k=%d Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];	/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
	if(Dummy[Tvard[k][1]==0]){
	if(Dummy[Tvard[k][2]==0]){
	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
	}else{
	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
	}
	}else{
	if(Dummy[Tvard[k][2]==0]){
	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
	}else{
	cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
	}
	}
}	}
/* for (k=1; k<=cptcovn;k++) */	/* for (k=1; k<=cptcovn;k++) */
/* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */	/* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
Line 3306 double *hpxij(double *po, int nhstep	Line 3457 double *hpxij(double *po, int nhstep

/printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);/	/printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);/
/printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);/	/printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);/
/* right multiplication of oldm by the current matrix */	/* right multiplication of oldm by the current matrix */
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
pmij(pmmij,cov,ncovmodel,x,nlstate));	pmij(pmmij,cov,ncovmodel,x,nlstate));
/* if((int)age == 70){ */	/* if((int)age == 70){ */
Line 3376 double *hbxij(double *po, int nhstep	Line 3527 double *hbxij(double *po, int nhstep
cov[1]=1.;	cov[1]=1.;
agexact=age-( (h-1)hstepm + (d) )stepm/YEARM; /* age just before transition, d or d-1? */	agexact=age-( (h-1)hstepm + (d) )stepm/YEARM; /* age just before transition, d or d-1? */
/* agexact=age+((h-1)hstepm + (d-1))stepm/YEARM; /\* age just before transition \/ /	/* agexact=age+((h-1)hstepm + (d-1))stepm/YEARM; /\* age just before transition \/ /
	/* Debug */
	/* printf("hBxij age=%lf, agexact=%lf\n", age, agexact); */
cov[2]=agexact;	cov[2]=agexact;
if(nagesqr==1)	if(nagesqr==1)
cov[3]= agexact*agexact;	cov[3]= agexact*agexact;
Line 3390 double *hbxij(double *po, int nhstep	Line 3543 double *hbxij(double *po, int nhstep
cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];	cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
/* printf("hPxij Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */	/* printf("hPxij Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
}	}
for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 */	for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 // For product with age */
if(Dummy[Tvar[Tage[k]]]){	/* if(Dummy[Tvar[Tage[k]]]== 2){ /\* dummy with age error!!!\/ /
	if(Dummy[Tage[k]]== 2){ /* dummy with age */
cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];	cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
} else{	} else if(Dummy[Tage[k]]== 3){ /* quantitative with age */
cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];	cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
}	}
/* printf("hBxij Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */	/* printf("hBxij Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
Line 3495 double func( double *x)	Line 3649 double func( double *x)
*/	*/
ioffset=2+nagesqr ;	ioffset=2+nagesqr ;
/* Fixed */	/* Fixed */
for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */	for (k=1; k<=ncovf;k++){ /* For each fixed covariate dummu or quant or prod */
cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, only V1 is fixed (k=6)*/	/* # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi */
	/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
	/* TvarF[1]=Tvar[6]=2, TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1 ID of fixed covariates or product V2, V1V2, V1 /
	/* TvarFind; TvarFind[1]=6, TvarFind[2]=7, TvarFind[3]=9 // Inverse V2(6) is first fixed (single or prod) */
	cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, only V1 is fixed (TvarFind[1]=6)*/
	/* V1V2 (7) TvarFind[2]=7, TvarFind[3]=9 /
}	}
/* In model V2+V1V4+ageV3+V3V2 Tvar[1] is V2, Tvar[2=V1V4]	/* In model V2+V1V4+ageV3+V3V2 Tvar[1] is V2, Tvar[2=V1V4]
is 6, Tvar[3=ageV3] should not be computed because of age Tvar[4=V3V2]	is 5, Tvar[3=ageV3] should not be computed because of age Tvar[4=V3V2]=6
has been calculated etc */	has been calculated etc */
/* For an individual i, wav[i] gives the number of effective waves */	/* For an individual i, wav[i] gives the number of effective waves */
/* We compute the contribution to Likelihood of each effective transition	/* We compute the contribution to Likelihood of each effective transition
Line 3511 double func( double *x)	Line 3670 double func( double *x)
meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]	meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
*/	*/
for(mi=1; mi<= wav[i]-1; mi++){	for(mi=1; mi<= wav[i]-1; mi++){
for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/	for(k=1; k <= ncovv ; k++){ /* Varying covariates in the model (single and product but no age )"V5+V4+V3+V4V3+V5age+V1age+V1" +TvarVind 1,2,3,4(V4V3) Tvar[1]@7{5, 4, 3, 6, 5, 1, 1 ; 6 because the created covar is after V5 and is 6, minus 1+1, 3,2,1,4 positions in cotvar*/
/* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */	/* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; but where is the crossproduct? */
cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];	cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
}	}
for (ii=1;ii<=nlstate+ndeath;ii++)	for (ii=1;ii<=nlstate+ndeath;ii++)
Line 3527 double func( double *x)	Line 3686 double func( double *x)
if(nagesqr==1)	if(nagesqr==1)
cov[3]= agexactagexact; / Should be changed here */	cov[3]= agexactagexact; / Should be changed here */
for (kk=1; kk<=cptcovage;kk++) {	for (kk=1; kk<=cptcovage;kk++) {
if(!FixedV[Tvar[Tage[kk]]])	if(!FixedV[Tvar[Tage[kk]]])
cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]agexact; / Tage[kk] gives the data-covariate associated with age */	cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]agexact; / Tage[kk] gives the data-covariate associated with age */
else	else
cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;	cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
}	}
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));	1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
Line 3638 double func( double *x)	Line 3797 double func( double *x)
} /* end of individual */	} /* end of individual */
} else if(mle==2){	} else if(mle==2){
for (i=1,ipmx=0, sw=0.; i<=imx; i++){	for (i=1,ipmx=0, sw=0.; i<=imx; i++){
for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];	ioffset=2+nagesqr ;
	for (k=1; k<=ncovf;k++)
	cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];
for(mi=1; mi<= wav[i]-1; mi++){	for(mi=1; mi<= wav[i]-1; mi++){
	for(k=1; k <= ncovv ; k++){
	cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
	}
for (ii=1;ii<=nlstate+ndeath;ii++)	for (ii=1;ii<=nlstate+ndeath;ii++)
for (j=1;j<=nlstate+ndeath;j++){	for (j=1;j<=nlstate+ndeath;j++){
oldm[ii][j]=(ii==j ? 1.0 : 0.0);	oldm[ii][j]=(ii==j ? 1.0 : 0.0);
Line 3817 double funcone( double *x)	Line 3981 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 3996 void likelione(FILE *ficres,double p[],	Line 4160 void likelione(FILE *ficres,double p[],

void mlikeli(FILE ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (func)(double []))	void mlikeli(FILE ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (func)(double []))
{	{
int i,j, iter=0;	int i,j,k, jk, jkk=0, iter=0;
double **xi;	double **xi;
double fret;	double fret;
double fretone; /* Only one call to likelihood */	double fretone; /* Only one call to likelihood */
Line 4030 void mlikeli(FILE *ficres,double p[], in	Line 4194 void mlikeli(FILE *ficres,double p[], in
if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);	if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
fprintf(ficrespow,"\n");	fprintf(ficrespow,"\n");
#ifdef POWELL	#ifdef POWELL
	#ifdef LINMINORIGINAL
	#else /* LINMINORIGINAL */

	flatdir=ivector(1,npar);
	for (j=1;j<=npar;j++) flatdir[j]=0;
	#endif /LINMINORIGINAL /

	#ifdef FLATSUP
	powell(p,xi,npar,ftol,&iter,&fret,flatdir,func);
	/* reorganizing p by suppressing flat directions */
	for(i=1, jk=1; i <=nlstate; i++){
	for(k=1; k <=(nlstate+ndeath); k++){
	if (k != i) {
	printf("%d%d flatdir[%d]=%d",i,k,jk, flatdir[jk]);
	if(flatdir[jk]==1){
	printf(" To be skipped %d%d flatdir[%d]=%d ",i,k,jk, flatdir[jk]);
	}
	for(j=1; j <=ncovmodel; j++){
	printf("%12.7f ",p[jk]);
	jk++;
	}
	printf("\n");
	}
	}
	}
	/* skipping */
	/* for(i=1, jk=1, jkk=1;(flatdir[jk]==0)&& (i <=nlstate); i++){ */
	for(i=1, jk=1, jkk=1;i <=nlstate; i++){
	for(k=1; k <=(nlstate+ndeath); k++){
	if (k != i) {
	printf("%d%d flatdir[%d]=%d",i,k,jk, flatdir[jk]);
	if(flatdir[jk]==1){
	printf(" To be skipped %d%d flatdir[%d]=%d jk=%d p[%d] ",i,k,jk, flatdir[jk],jk, jk);
	for(j=1; j <=ncovmodel; jk++,j++){
	printf(" p[%d]=%12.7f",jk, p[jk]);
	/q[jjk]=p[jk];/
	}
	}else{
	printf(" To be kept %d%d flatdir[%d]=%d jk=%d q[%d]=p[%d] ",i,k,jk, flatdir[jk],jk, jkk, jk);
	for(j=1; j <=ncovmodel; jk++,jkk++,j++){
	printf(" p[%d]=%12.7f=q[%d]",jk, p[jk],jkk);
	/q[jjk]=p[jk];/
	}
	}
	printf("\n");
	}
	fflush(stdout);
	}
	}
	powell(p,xi,npar,ftol,&iter,&fret,flatdir,func);
	#else /* FLATSUP */
powell(p,xi,npar,ftol,&iter,&fret,func);	powell(p,xi,npar,ftol,&iter,&fret,func);
#endif	#endif /* FLATSUP */

	#ifdef LINMINORIGINAL
	#else
	free_ivector(flatdir,1,npar);
	#endif /* LINMINORIGINAL*/
	#endif /* POWELL */

#ifdef NLOPT	#ifdef NLOPT
#ifdef NEWUOA	#ifdef NEWUOA
Line 4059 void mlikeli(FILE *ficres,double p[], in	Line 4280 void mlikeli(FILE *ficres,double p[], in
}	}
nlopt_destroy(opt);	nlopt_destroy(opt);
#endif	#endif
	#ifdef FLATSUP
	/* npared = npar -flatd/ncovmodel; */
	/* xired= matrix(1,npared,1,npared); */
	/* paramred= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */
	/* powell(pred,xired,npared,ftol,&iter,&fret,flatdir,func); */
	/* free_matrix(xire,1,npared,1,npared); */
	#else /* FLATSUP */
	#endif /* FLATSUP */
free_matrix(xi,1,npar,1,npar);	free_matrix(xi,1,npar,1,npar);
fclose(ficrespow);	fclose(ficrespow);
printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));	printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
Line 4510 void freqsummary(char fileres[], double	Line 4739 void freqsummary(char fileres[], double
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\	Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);	fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
}	}
fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition and dummy covariate value at beginning of transition</h4>\n",fileresphtm, fileresphtm);	fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies (weight=%d) and prevalence by age at begin of transition and dummy covariate value at beginning of transition</h4>\n",fileresphtm, fileresphtm, weightopt);

strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));	strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {	if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
Line 4520 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4749 Title=%s <br>Datafile=%s Firstpass=%d La
exit(70);	exit(70);
} else{	} else{
fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \	fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
<hr size=\"2\" color=\"#EC5E5E\"> \n \	,<hr size=\"2\" color=\"#EC5E5E\"> \n \
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\	Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);	fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
}	}
fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions of the model, by age at begin of transition, and covariate value at the begin of transition (if the covariate is a varying covariate) </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);	fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>(weight=%d) frequencies of all effective transitions of the model, by age at begin of transition, and covariate value at the begin of transition (if the covariate is a varying covariate) </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr,weightopt);

y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);	y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);	x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
Line 4672 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4901 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 4699 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4931 Title=%s <br>Datafile=%s Firstpass=%d La
/* } */	/* } */
} /* end bool */	} /* end bool */
} /* end iind = 1 to imx */	} /* end iind = 1 to imx */
/* prop[s][age] is feeded for any initial and valid live state as well as	/* prop[s][age] is fed for any initial and valid live state as well as
freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */	freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */


Line 4738 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4970 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 5250 void concatwav(int wav[], int **dh, int	Line 5485 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){ /* no death date and known date of interview, 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;
	}else if(firsthree >=1 && firsthree < 10){
	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);
	firsthree++;
	}else if(firsthree == 10){
	printf("Information, too many Information flags: no more reported to log either\n");
	fprintf(ficlog,"Information, too many Information flags: no more reported to log either\n");
	firsthree++;
	}else{
	firsthree++;
}	}
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; /* Valid transition with unknown status */
mw[++mi][i]=m;
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 5301 void concatwav(int wav[], int **dh, int	Line 5544 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 5342 void concatwav(int wav[], int **dh, int	Line 5586 void concatwav(int wav[], int **dh, int
} /* End individuals */	} /* End individuals */
/* wav and mw are no more changed */	/* wav and mw are no more changed */

	printf("Information, you have to check %d informations which haven't been logged!\n",firsthree);
	fprintf(ficlog,"Information, you have to check %d informations which haven't been logged!\n",firsthree);


for(i=1; i<=imx; i++){	for(i=1; i<=imx; i++){
for(mi=1; mi<wav[i];mi++){	for(mi=1; mi<wav[i];mi++){
if (stepm <=0)	if (stepm <=0)
Line 5463 void concatwav(int wav[], int **dh, int	Line 5710 void concatwav(int wav[], int **dh, int
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 5476 void concatwav(int wav[], int **dh, int	Line 5725 void concatwav(int wav[], int **dh, int
else if (ij < modmincovj)	else if (ij < modmincovj)
modmincovj=ij;	modmincovj=ij;
if (ij <0 \|\| ij >1 ){	if (ij <0 \|\| ij >1 ){
printf("Information, IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);	printf("ERROR, IMaCh doesn't treat covariate with missing values V%d=-1, individual %d will be skipped.\n",Tvar[k],i);
fprintf(ficlog,"Information, currently IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",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)){	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 );
Line 5552 void concatwav(int wav[], int **dh, int	Line 5803 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 (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the modality of this covariate Vj*/
	if(isnan(covar[Tvar[k]][i])){
	printf("ERROR, IMaCh doesn't treat fixed quantitative covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i);
	fprintf(ficlog,"ERROR, currently IMaCh doesn't treat covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i);
	fflush(ficlog);
	exit(1);
	}
	}
	}
} /* 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*/	} /* 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*/

for (k=-1; k< maxncov; k++) Ndum[k]=0;	for (k=-1; k< maxncov; k++) Ndum[k]=0;
Line 5865 void concatwav(int wav[], int **dh, int	Line 6126 void concatwav(int wav[], int **dh, int
varhe[ij][ji][(int)age] += doldm[ij][ji]hfhf;	varhe[ij][ji][(int)age] += doldm[ij][ji]hfhf;
}	}
}	}
	/* if((int)age ==50){ */
	/* printf(" age=%d cij=%d nres=%d varhe[%d][%d]=%f ",(int)age, cij, nres, 1,2,varhe[1][2]); */
	/* } */
/* Computing expectancies */	/* Computing expectancies */
hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);	hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
Line 6630 To be simple, these graphs help to under	Line 6893 To be simple, these graphs help to under


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

fprintf(ficresprobcor, "\n#********** Variable ");	fprintf(ficresprobcor, "\n#********** Variable ");
Line 6659 To be simple, these graphs help to under	Line 6923 To be simple, these graphs help to under
*/	*/
/* nbcode[1][1]=0 nbcode[1][2]=1;*/	/* nbcode[1][1]=0 nbcode[1][2]=1;*/
}	}
/* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]cov[2]; /	/* V2+V1+V4+V3age Tvar[4]=3 ; V1+V2age Tvar[2]=2; V1+V1age Tvar[2]=1, Tage[1]=2 /
for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];	/* ) p nbcode[Tvar[Tage[k]]][(1 & (ij-1) >> (k-1))+1] */
	/for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]cov[2]; */
	for (k=1; k<=cptcovage;k++)
	cov[2+Tage[k]+nagesqr]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
for (k=1; k<=cptcovprod;k++)	for (k=1; k<=cptcovprod;k++)
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];

Line 6871 void printinghtml(char fileresu[], char	Line 7138 void printinghtml(char fileresu[], char
double jprev1, double mprev1,double anprev1, double dateprev1, double dateprojd, double dateback1, \	double jprev1, double mprev1,double anprev1, double dateprev1, double dateprojd, double dateback1, \
double jprev2, double mprev2,double anprev2, double dateprev2, double dateprojf, 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;
	/* In fact some results are already printed in fichtm which is open */
fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \	fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
<li><a href='#secondorder'>Result files (second order (variance)</a>\n \	<li><a href='#secondorder'>Result files (second order (variance)</a>\n \
</ul>");	</ul>");
fprintf(fichtm,"<ul><li> model=1+age+%s\n \	/* fprintf(fichtm,"<ul><li> model=1+age+%s\n \ */
</ul>", model);	/* </ul>", model); */
fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");	fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",	fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",
jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));	jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
Line 6909 void printinghtml(char fileresu[], char	Line 7176 void printinghtml(char fileresu[], char
m=pow(2,cptcoveff);	m=pow(2,cptcoveff);
if (cptcovn < 1) {m=1;ncodemax[1]=1;}	if (cptcovn < 1) {m=1;ncodemax[1]=1;}

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

jj1=0;	jj1=0;

Line 6944 void printinghtml(char fileresu[], char	Line 7211 void printinghtml(char fileresu[], char
fprintf(fichtm,"</a></li>");	fprintf(fichtm,"</a></li>");
} /* cptcovn >0 */	} /* cptcovn >0 */
}	}
fprintf(fichtm," \n</ul>");	fprintf(fichtm," \n</ul>");

jj1=0;	jj1=0;

Line 6978 void printinghtml(char fileresu[], char	Line 7245 void printinghtml(char fileresu[], char
}	}

/* if(nqfveff+nqtveff 0) / / Test to be done */	/* if(nqfveff+nqtveff 0) / / Test to be done */
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");	fprintf(fichtm," (model=%s) ************\n<hr size=\"2\" color=\"#EC5E5E\">",model);
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);	fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
printf("\nCombination (%d) ignored because no cases \n",k1);	printf("\nCombination (%d) ignored because no cases \n",k1);
Line 7023 divided by h: <sub>h</sub>P<sub>ij</sub>	Line 7290 divided by h: <sub>h</sub>P<sub>ij</sub>
if(prevfcast==1){	if(prevfcast==1){
/* Projection of prevalence up to period (forward 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) 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><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, dateprojd, dateprojf, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);	fprintf(fichtm," (data from text file <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"F_"),subdirf2(optionfilefiname,"F_"));
	fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",
	subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
}	}
}	}
if(prevbcast==1){	if(prevbcast==1){
Line 7033 divided by h: <sub>h</sub>P<sub>ij</sub>	Line 7302 divided by h: <sub>h</sub>P<sub>ij</sub>
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 7092 See page 'Matrix of variance-covariance	Line 7363 See page 'Matrix of variance-covariance
/* else */	/* else */
/* fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */	/* fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
fflush(fichtm);	fflush(fichtm);
fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");

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

	fprintf(fichtm," <ul><li><b>Graphs (second order)</b></li><p>");

	jj1=0;

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

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

jj1=0;	jj1=0;

for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
Line 7106 See page 'Matrix of variance-covariance	Line 7413 See page 'Matrix of variance-covariance
/* for(i1=1; i1<=ncodemax[k1];i1++){ */	/* for(i1=1; i1<=ncodemax[k1];i1++){ */
jj1++;	jj1++;
if (cptcovn > 0) {	if (cptcovn > 0) {
	fprintf(fichtm,"\n<p><a name=\"rescovsecond");
	for (cpt=1; cpt<=cptcoveff;cpt++){
	fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
	}
	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
	fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
	}
	fprintf(fichtm,"\"</a>");

fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");	fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
for (cpt=1; cpt<=cptcoveff;cpt++) /*< cptcoveff number of variables /	for (cpt=1; cpt<=cptcoveff;cpt++){ /*< cptcoveff number of variables /
fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);	fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);
	printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
/* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */	/* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	}

fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");	fprintf(fichtm," (model=%s) ************\n<hr size=\"2\" color=\"#EC5E5E\">",model);

if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);	fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
Line 7123 See page 'Matrix of variance-covariance	Line 7441 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 7248 void printinggnuplot(char fileresu[], ch	Line 7568 void printinggnuplot(char fileresu[], ch
fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);	fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
/* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */	/* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */
fprintf(ficgp,"set title \"Alive state %d %s\" font \"Helvetica,12\"\n",cpt,gplotlabel);	fprintf(ficgp,"set title \"Alive state %d %s model=%s\" font \"Helvetica,12\"\n",cpt,gplotlabel,model);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
/* fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */	/* fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */
/* k1-1 error should be nres-1*/	/* k1-1 error should be nres-1*/
Line 9255 int readdata(char datafile[], int firsto	Line 9575 int readdata(char datafile[], int firsto
else if( line[0] == (char)0xFF && line[1] == (char)0xFE)	else if( line[0] == (char)0xFF && line[1] == (char)0xFE)
{	{
noffset=noffset+2;	noffset=noffset+2;
printf("# 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);	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,"# Data file '%s' is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);	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;	fflush(ficlog); return 1;
}	}
else if( line[0] == 0 && line[1] == 0)	else if( line[0] == 0 && line[1] == 0)
{	{
if( line[2] == (char)0xFE && line[3] == (char)0xFF){	if( line[2] == (char)0xFE && line[3] == (char)0xFF){
noffset=noffset+4;	noffset=noffset+4;
printf("# 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);	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,"# Data file '%s' is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);	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;	fflush(ficlog); return 1;
}	}
} else{	} else{
Line 9352 int readdata(char datafile[], int firsto	Line 9672 int readdata(char datafile[], int firsto
}	}
if(lval <-1 \|\| lval >1){	if(lval <-1 \|\| lval >1){
printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \	printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \	Should be a value of %d(nth) covariate of wave %d (0 should be the value for the reference and 1\n \
for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \	for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
For example, for multinomial values like 1, 2 and 3,\n \	For example, for multinomial values like 1, 2 and 3,\n \
build V1=0 V2=0 for the reference value (1),\n \	build V1=0 V2=0 for the reference value (1),\n \
V1=1 V2=0 for (2) \n \	V1=1 V2=0 for (2) \n \
and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \	and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
output of IMaCh is often meaningless.\n \	output of IMaCh is often meaningless.\n \
Exiting.\n",lval,linei, i,line,j);	Exiting.\n",lval,linei, i,line,iv,j);
fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \	fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \	Should be a value of %d(nth) covariate of wave %d (0 should be the value for the reference and 1\n \
for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \	for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
For example, for multinomial values like 1, 2 and 3,\n \	For example, for multinomial values like 1, 2 and 3,\n \
build V1=0 V2=0 for the reference value (1),\n \	build V1=0 V2=0 for the reference value (1),\n \
V1=1 V2=0 for (2) \n \	V1=1 V2=0 for (2) \n \
and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \	and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
output of IMaCh is often meaningless.\n \	output of IMaCh is often meaningless.\n \
Exiting.\n",lval,linei, i,line,j);fflush(ficlog);	Exiting.\n",lval,linei, i,line,iv,j);fflush(ficlog);
return 1;	return 1;
}	}
cotvar[j][iv][i]=(double)(lval);	cotvar[j][iv][i]=(double)(lval);
Line 9476 int readdata(char datafile[], int firsto	Line 9796 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 9579 int decoderesult ( char resultline[], in	Line 9901 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 9594 int decoderesult ( char resultline[], in	Line 9915 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 this result line, %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 ' ' (stra is the rest of the resultline to be analyzed in the next loop // resultsav= "V4=1 V5=25.1 V3=0" stra= "V5=25.1 V3=0" strb= "V4=1" */
resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */	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,'=');
Tvalsel[k]=atof(strc); /* 1 */	Tvalsel[k]=atof(strc); /* 1 / / Tvalsel of k is the float value of the kth covariate appearing in this result line */

cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;	cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
Tvarsel[k]=atoi(strc);	Tvarsel[k]=atoi(strc); /* 4 / / Tvarsel is the id of the kth covariate in the result line Tvarsel[1] in "V4=1.." is 4.*/
/* Typevarsel[k]=1; /\* 1 for age product \/ /	/* Typevarsel[k]=1; /\* 1 for age product \/ /
/* cptcovsel++; */	/* cptcovsel++; */
if (nbocc(stra,'=') >0)	if (nbocc(stra,'=') >0)
strcpy(resultsav,stra); /* and analyzes it */	strcpy(resultsav,stra); /* and analyzes it */
}	}
/* Checking for missing or useless values in comparison of current model needs */	/* Checking for missing or useless values in comparison of current model needs */
for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */	for(k1=1; k1<= cptcovt ;k1++){ /* Loop on model. model line V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
if(Typevar[k1]==0){ /* Single covariate in model */	if(Typevar[k1]==0){ /* Single covariate in model //0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product */
match=0;	match=0;
for(k2=1; k2 <=j;k2++){/* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */	for(k2=1; k2 <=j;k2++){/* Loop on resultline. In result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
if(Tvar[k1]==Tvarsel[k2]) {/* Tvar[1]=5 == Tvarsel[2]=5 */	if(Tvar[k1]==Tvarsel[k2]) {/* Tvar is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5 */
modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2 modelresult[3]=3 modelresult[6]=4 modelresult[9]=5 */	modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2 modelresult[3]=3 modelresult[6]=4 modelresult[9]=5 */
match=1;	match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
break;	break;
}	}
}	}
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;
}	}
}	}
}	}
/* Checking for missing or useless values in comparison of current model needs */	/* Checking for missing or useless values in comparison of current model needs */
for(k2=1; k2 <=j;k2++){ /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */	for(k2=1; k2 <=j;k2++){ /* Loop on resultline variables: result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
match=0;	match=0;
for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */	for(k1=1; k1<= cptcovt ;k1++){ /* loop on model: model line V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
if(Typevar[k1]==0){ /* Single */	if(Typevar[k1]==0){ /* Single */
if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4 */	if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4 */
resultmodel[k1]=k2; /* resultmodel[2]=1 resultmodel[1]=2 resultmodel[3]=3 resultmodel[6]=4 resultmodel[9]=5 */	resultmodel[k1]=k2; /* k2th variable of the model corresponds to k1 variable of the model. resultmodel[2]=1 resultmodel[1]=2 resultmodel[3]=3 resultmodel[6]=4 resultmodel[9]=5 */
++match;	++match;
}	}
}	}
}	}
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 9667 int decoderesult ( char resultline[], in	Line 9992 int decoderesult ( char resultline[], in
/* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */	/* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */
/* V5age V5 known which value for nres? /	/* V5age V5 known which value for nres? /
/* Tqinvresult[2]=8 Tqinvresult[1]=25.1 */	/* Tqinvresult[2]=8 Tqinvresult[1]=25.1 */
for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* model line */	for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* loop on model line */
if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */	if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */
k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */	k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */
k2=(int)Tvarsel[k3]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */	k2=(int)Tvarsel[k3]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
Line 9678 int decoderesult ( char resultline[], in	Line 10003 int decoderesult ( char resultline[], in
printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);	printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);
k4++;;	k4++;;
} else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */	} else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */
k3q= resultmodel[k1]; /* resultmodel[2] = 1=k3 */	k3q= resultmodel[k1]; /* resultmodel[1(V5)] = 25.1=k3q */
k2q=(int)Tvarsel[k3q]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */	k2q=(int)Tvarsel[k3q]; /* Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */
Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */	Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */	Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */	Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
Line 9702 int decodemodel( char model[], int lasto	Line 10027 int decodemodel( char model[], int lasto
* - cptcovs number of simple covariates	* - cptcovs number of simple covariates
* - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10	* - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
* which is a new column after the 9 (ncovcol) variables.	* which is a new column after the 9 (ncovcol) variables.
* - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual	* - if k is a product Vn*Vm, covar[k][i] is filled with correct values for each individual
* - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage	* - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
* Tprod[1]@2 {5, 6}: position of first product V7V8 is 5, and second V5V6 is 6.	* Tprod[1]@2 {5, 6}: position of first product V7V8 is 5, and second V5V6 is 6.
* - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7V8 and V5V6 .	* - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7V8 and V5V6 .
*/	*/
	/* V2+V1+V4+V3age Tvar[4]=3 ; V1+V2age Tvar[2]=2; V1+V1age Tvar[2]=1, Tage[1]=2 /
{	{
int i, j, k, ks, v;	int i, j, k, ks, v;
int j1, k1, k2, k3, k4;	int j1, k1, k2, k3, k4;
Line 9784 int decodemodel( char model[], int lasto	Line 10110 int decodemodel( char model[], int lasto
* Model V2 + V1 + V3age + V3 + V5V6 + V7V8 + V8age + V8 d1 d1 d2 d2	* Model V2 + V1 + V3age + V3 + V5V6 + V7V8 + V8age + V8 d1 d1 d2 d2
* k= 1 2 3 4 5 6 7 8 9 10 11 12	* k= 1 2 3 4 5 6 7 8 9 10 11 12
* Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8	* Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
* p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}	* p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
* p Tprod[1]@2={ 6, 5}	* p Tprod[1]@2={ 6, 5}
*p Tvard[1][1]@4= {7, 8, 5, 6}	*p Tvard[1][1]@4= {7, 8, 5, 6}
* covar[k][i]= V2 V1 ? V3 V5V6? V7V8? ? V8	* covar[k][i]= V2 V1 ? V3 V5V6? V7V8? ? V8
* cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];	* cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
*How to reorganize?	*How to reorganize? Tvars(orted)
* Model V1 + V2 + V3 + V8 + V5V6 + V7V8 + V3age + V8age	* Model V1 + V2 + V3 + V8 + V5V6 + V7V8 + V3age + V8age
* Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}	* Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
* {2, 1, 4, 8, 5, 6, 3, 7}	* {2, 1, 4, 8, 5, 6, 3, 7}
Line 9814 int decodemodel( char model[], int lasto	Line 10140 int decodemodel( char model[], int lasto
Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;	Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
}	}
cptcovage=0;	cptcovage=0;
for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */	for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model line */
cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'	cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' cutl from left to right
modelsav==V2+V1+V4+V3age strb=V3age stra=V2+V1+V4 */	modelsav==V2+V1+V5age+V4+V3age strb=V3age stra=V2+V1V5age+V4 / / <model> "V5+V4+V3+V4V3+V5age+V1age+V1" strb="V5" stra="V4+V3+V4V3+V5age+V1age+V1" */
if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */	if (nbocc(modelsav,'+')==0)
	strcpy(strb,modelsav); /* and analyzes it */
/* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/	/* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
/scanf("%d",i);/	/scanf("%d",i);/
if (strchr(strb,'')) { /< Model includes a product V2+V1+V4+V3age strb=V3age /	if (strchr(strb,'')) { /< Model includes a product V2+V1+V5age+ V4+V3age strb=V3age */
cutl(strc,strd,strb,''); /< strdstrc VmVn: strb=V3age(input) strc=age strd=V3 ; V3V2 strc=V2, strd=V3 /	cutl(strc,strd,strb,''); /< k=1 strdstrc VmVn: strb=V3age(input) strc=age strd=V3 ; V3V2 strc=V2, strd=V3 /
if (strcmp(strc,"age")==0) { /*< Model includes age: Vnage */	if (strcmp(strc,"age")==0) { /*< Model includes age: Vnage */
/* covar is not filled and then is empty */	/* covar is not filled and then is empty */
cptcovprod--;	cptcovprod--;
cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */	cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
Tvar[k]=atoi(stre); /* V2+V1+V4+V3age Tvar[4]=3 ; V1+V2age Tvar[2]=2; V1+V1age Tvar[2]=1 /	Tvar[k]=atoi(stre); /* V2+V1+V5age+V4+V3age Tvar[5]=3 ; V1+V2age Tvar[2]=2; V1+V1age Tvar[2]=1 */
Typevar[k]=1; /* 1 for age product */	Typevar[k]=1; /* 1 for age product */
cptcovage++; /* Sums the number of covariates which include age as a product */	cptcovage++; /* Counts the number of covariates which include age as a product */
Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1age Tvar[2]=1, Tage[1]=2 /	Tage[cptcovage]=k; /* V2+V1+V4+V3age Tvar[4]=3, Tage[1] = 4 or V1+V1age Tvar[2]=1, Tage[1]=2 */
/printf("stre=%s ", stre);/	/printf("stre=%s ", stre);/
} else if (strcmp(strd,"age")==0) { /* or ageVn /	} else if (strcmp(strd,"age")==0) { /* or ageVn /
cptcovprod--;	cptcovprod--;
Line 9846 int decodemodel( char model[], int lasto	Line 10173 int decodemodel( char model[], int lasto
Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but	Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
because this model-covariate is a construction we invent a new column	because this model-covariate is a construction we invent a new column
which is after existing variables ncovcol+nqv+ntv+nqtv + k1	which is after existing variables ncovcol+nqv+ntv+nqtv + k1
If already ncovcol=4 and model=V2+V1+V1V4+ageV3+V3*V2	If already ncovcol=4 and model=V2 + V1 +V1V4 +ageV3 +V3*V2
Tvar[3=V1V4]=4+1 Tvar[5=V3V2]=4 + 2= 6, etc */	thus after V4 we invent V5 and V6 because age*V3 will be computed in 4
	Tvar[3=V1V4]=4+1=5 Tvar[5=V3V2]=4 + 2= 6, Tvar[4=ageV3]=4 etc /
Typevar[k]=2; /* 2 for double fixed dummy covariates */	Typevar[k]=2; /* 2 for double fixed dummy covariates */
cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */	cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
Tprod[k1]=k; /* Tprod[1]=3(=V1V4) for V2+V1+V1V4+ageV3+V3V2 */	Tprod[k1]=k; /* Tprod[1]=3(=V1V4) for V2+V1+V1V4+ageV3+V3V2 */
Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */	Tposprod[k]=k1; /* Tposprod[3]=1, Tposprod[2]=5 */
Tvard[k1][1] =atoi(strc); /* m 1 for V1*/	Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
Tvard[k1][2] =atoi(stre); /* n 4 for V4*/	Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
k2=k2+2; /* k2 is initialize to -1, We want to store the n and m in VnVm at the end of Tvar /	k2=k2+2; /* k2 is initialize to -1, We want to store the n and m in VnVm at the end of Tvar /
Line 9866 int decodemodel( char model[], int lasto	Line 10194 int decodemodel( char model[], int lasto
}	}
} /* End age is not in the model */	} /* End age is not in the model */
} /* End if model includes a product */	} /* End if model includes a product */
else { /* no more sum */	else { /* not a product */
/printf("d=%s c=%s b=%s\n", strd,strc,strb);/	/printf("d=%s c=%s b=%s\n", strd,strc,strb);/
/* scanf("%d",i);*/	/* scanf("%d",i);*/
cutl(strd,strc,strb,'V');	cutl(strd,strc,strb,'V');
Line 9897 int decodemodel( char model[], int lasto	Line 10225 int decodemodel( char model[], int lasto
model= V5 + V4 +V3 + V4V3 + V5age + V2 + V1V2 + V1age + V5*age, V1 is not used saving its place	model= V5 + V4 +V3 + V4V3 + V5age + V2 + V1V2 + V1age + V5*age, V1 is not used saving its place
k = 1 2 3 4 5 6 7 8 9	k = 1 2 3 4 5 6 7 8 9
Tvar[k]= 5 4 3 1+1+2+1+1=6 5 2 7 1 5	Tvar[k]= 5 4 3 1+1+2+1+1=6 5 2 7 1 5
Typevar[k]= 0 0 0 2 1 0 2 1 1	Typevar[k]= 0 0 0 2 1 0 2 1 0
Fixed[k] 1 1 1 1 3 0 0 or 2 2 3	Fixed[k] 1 1 1 1 3 0 0 or 2 2 3
Dummy[k] 1 0 0 0 3 1 1 2 3	Dummy[k] 1 0 0 0 3 1 1 2 3
Tmodelind[combination of covar]=k;	Tmodelind[combination of covar]=k;
Line 9906 int decodemodel( char model[], int lasto	Line 10234 int decodemodel( char model[], int lasto
/* If Tvar[k] >ncovcol it is a product */	/* If Tvar[k] >ncovcol it is a product */
/* Tvar[k] is the value n of Vn with n varying for 1 to nvcol, or p Vp=VnVm for product /	/* Tvar[k] is the value n of Vn with n varying for 1 to nvcol, or p Vp=VnVm for product /
/* Computing effective variables, ie used by the model, that is from the cptcovt variables */	/* Computing effective variables, ie used by the model, that is from the cptcovt variables */
printf("Model=%s\n\	printf("Model=1+age+%s\n\
Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\	Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\	Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);	Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
fprintf(ficlog,"Model=%s\n\	fprintf(ficlog,"Model=1+age+%s\n\
Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\	Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\	Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);	Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
Line 9977 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 10305 Dummy[k] 0=dummy (0 1), 1 quantitative (
modell[k].subtype= VQ;	modell[k].subtype= VQ;
ncovv++; /* Only simple time varying variables */	ncovv++; /* Only simple time varying variables */
nsq++;	nsq++;
TvarsQ[nsq]=Tvar[k];	TvarsQ[nsq]=Tvar[k]; /* k=1 Tvar=5 nsq=1 TvarsQ[1]=5 */
TvarsQind[nsq]=k;	TvarsQind[nsq]=k;
TvarV[ncovv]=Tvar[k];	TvarV[ncovv]=Tvar[k];
TvarVind[ncovv]=k; /* TvarVind[1]=1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Any time varying singele */	TvarVind[ncovv]=k; /* TvarVind[1]=1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Any time varying singele */
Line 10909 int main(int argc, char *argv[])	Line 11237 int main(int argc, char *argv[])
double dum=0.; /* Dummy variable */	double dum=0.; /* Dummy variable */
double ***p3mat;	double ***p3mat;
/* double **mobaverage; /	/* double **mobaverage; /
	double wald;

char line[MAXLINE];	char line[MAXLINE];
char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];	char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
Line 10945 int main(int argc, char *argv[])	Line 11274 int main(int argc, char *argv[])
double ftolpl=FTOL;	double ftolpl=FTOL;
double **prlim;	double **prlim;
double **bprlim;	double **bprlim;
double **param; / Matrix of parameters */	double **param; / Matrix of parameters, param[i][j][k] param=ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel)
	state of origin, state of destination including death, for each covariate: constante, age, and V1 V2 etc. */
double **paramstart; / Matrix of starting parameter values */	double **paramstart; / Matrix of starting parameter values */
double p, pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */	double p, pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */
double *matcov; / Matrix of covariance */	double *matcov; / Matrix of covariance */
Line 11872 Title=%s <br>Datafile=%s Firstpass=%d La	Line 12202 Title=%s <br>Datafile=%s Firstpass=%d La
<img src=\"%s_.svg\">", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"));	<img src=\"%s_.svg\">", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"));


fprintf(fichtm,"\n<h4>Some descriptive statistics </h4>\n<br>Total number of observations=%d <br>\n\	fprintf(fichtm,"\n<h4>Some descriptive statistics </h4>\n<br>Number of (used) observations=%d <br>\n\
Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\	Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\	Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
imx,agemin,agemax,jmin,jmax,jmean);	imx,agemin,agemax,jmin,jmax,jmean);
Line 12152 Please run with mle=-1 to get a correct	Line 12482 Please run with mle=-1 to get a correct


fprintf(ficres,"# Parameters nlstatenlstatencov a121 + b12 age + ...\n");	fprintf(ficres,"# Parameters nlstatenlstatencov a121 + b12 age + ...\n");
printf("# Parameters nlstatenlstatencov a121 + b12 age + ...\n");	printf("# Parameters nlstatenlstatencov a121 + b12 age + ...\n"); /* Printing model equation */
fprintf(ficlog,"# Parameters nlstatenlstatencov a121 + b12 age + ...\n");	fprintf(ficlog,"# Parameters nlstatenlstatencov a121 + b12 age + ...\n");

	printf("#model= 1 + age ");
	fprintf(ficres,"#model= 1 + age ");
	fprintf(ficlog,"#model= 1 + age ");
	fprintf(fichtm,"\n<ul><li> model=1+age+%s\n \
	</ul>", model);

	fprintf(fichtm,"\n<table style=\"text-align:center; border: 1px solid\">\n");
	fprintf(fichtm, "<tr><th>Model=</th><th>1</th><th>+ age</th>");
	if(nagesqr==1){
	printf(" + age*age ");
	fprintf(ficres," + age*age ");
	fprintf(ficlog," + age*age ");
	fprintf(fichtm, "<th>+ age*age</th>");
	}
	for(j=1;j <=ncovmodel-2;j++){
	if(Typevar[j]==0) {
	printf(" + V%d ",Tvar[j]);
	fprintf(ficres," + V%d ",Tvar[j]);
	fprintf(ficlog," + V%d ",Tvar[j]);
	fprintf(fichtm, "<th>+ V%d</th>",Tvar[j]);
	}else if(Typevar[j]==1) {
	printf(" + V%d*age ",Tvar[j]);
	fprintf(ficres," + V%d*age ",Tvar[j]);
	fprintf(ficlog," + V%d*age ",Tvar[j]);
	fprintf(fichtm, "<th>+ V%d*age</th>",Tvar[j]);
	}else if(Typevar[j]==2) {
	printf(" + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
	fprintf(ficres," + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
	fprintf(ficlog," + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
	fprintf(fichtm, "<th>+ V%d*V%d</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
	}
	}
	printf("\n");
	fprintf(ficres,"\n");
	fprintf(ficlog,"\n");
	fprintf(fichtm, "</tr>");
	fprintf(fichtm, "\n");


for(i=1,jk=1; i <=nlstate; i++){	for(i=1,jk=1; i <=nlstate; i++){
for(k=1; k <=(nlstate+ndeath); k++){	for(k=1; k <=(nlstate+ndeath); k++){
if (k != i) {	if (k != i) {
	fprintf(fichtm, "<tr>");
printf("%d%d ",i,k);	printf("%d%d ",i,k);
fprintf(ficlog,"%d%d ",i,k);	fprintf(ficlog,"%d%d ",i,k);
fprintf(ficres,"%1d%1d ",i,k);	fprintf(ficres,"%1d%1d ",i,k);
	fprintf(fichtm, "<td>%1d%1d</td>",i,k);
for(j=1; j <=ncovmodel; j++){	for(j=1; j <=ncovmodel; j++){
printf("%12.7f ",p[jk]);	printf("%12.7f ",p[jk]);
fprintf(ficlog,"%12.7f ",p[jk]);	fprintf(ficlog,"%12.7f ",p[jk]);
fprintf(ficres,"%12.7f ",p[jk]);	fprintf(ficres,"%12.7f ",p[jk]);
	fprintf(fichtm, "<td>%12.7f</td>",p[jk]);
jk++;	jk++;
}	}
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
fprintf(ficres,"\n");	fprintf(ficres,"\n");
	fprintf(fichtm, "</tr>\n");
}	}
}	}
}	}
	/* fprintf(fichtm,"</tr>\n"); */
	fprintf(fichtm,"</table>\n");
	fprintf(fichtm, "\n");

if(mle != 0){	if(mle != 0){
/* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */	/* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
ftolhess=ftol; /* Usually correct */	ftolhess=ftol; /* Usually correct */
hesscov(matcov, hess, p, npar, delti, ftolhess, func);	hesscov(matcov, hess, p, npar, delti, ftolhess, func);
printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");	printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");	fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
	fprintf(fichtm, "\n<p>Parameters, Wald tests and Wald-based confidence intervals\n</br> W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n</br> And Wald-based confidence intervals plus and minus 1.96 * W \n </br> It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n</br>");
	fprintf(fichtm,"\n<table style=\"text-align:center; border: 1px solid\">");
	fprintf(fichtm, "\n<tr><th>Model=</th><th>1</th><th>+ age</th>");
	if(nagesqr==1){
	printf(" + age*age ");
	fprintf(ficres," + age*age ");
	fprintf(ficlog," + age*age ");
	fprintf(fichtm, "<th>+ age*age</th>");
	}
	for(j=1;j <=ncovmodel-2;j++){
	if(Typevar[j]==0) {
	printf(" + V%d ",Tvar[j]);
	fprintf(fichtm, "<th>+ V%d</th>",Tvar[j]);
	}else if(Typevar[j]==1) {
	printf(" + V%d*age ",Tvar[j]);
	fprintf(fichtm, "<th>+ V%d*age</th>",Tvar[j]);
	}else if(Typevar[j]==2) {
	fprintf(fichtm, "<th>+ V%d*V%d</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
	}
	}
	fprintf(fichtm, "</tr>\n");

for(i=1,jk=1; i <=nlstate; i++){	for(i=1,jk=1; i <=nlstate; i++){
for(k=1; k <=(nlstate+ndeath); k++){	for(k=1; k <=(nlstate+ndeath); k++){
if (k != i) {	if (k != i) {
	fprintf(fichtm, "<tr valign=top>");
printf("%d%d ",i,k);	printf("%d%d ",i,k);
fprintf(ficlog,"%d%d ",i,k);	fprintf(ficlog,"%d%d ",i,k);
	fprintf(fichtm, "<td>%1d%1d</td>",i,k);
for(j=1; j <=ncovmodel; j++){	for(j=1; j <=ncovmodel; j++){
printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96sqrt(matcov[jk][jk]),p[jk]+1.96sqrt(matcov[jk][jk]));	wald=p[jk]/sqrt(matcov[jk][jk]);
fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96sqrt(matcov[jk][jk]),p[jk]+1.96sqrt(matcov[jk][jk]));	printf("%12.7f(%12.7f) sqrt(W)=%8.3f CI=[%12.7f ; %12.7f] ",p[jk],sqrt(matcov[jk][jk]), p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96sqrt(matcov[jk][jk]),p[jk]+1.96sqrt(matcov[jk][jk]));
	fprintf(ficlog,"%12.7f(%12.7f) sqrt(W)=%8.3f CI=[%12.7f ; %12.7f] ",p[jk],sqrt(matcov[jk][jk]), p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96sqrt(matcov[jk][jk]),p[jk]+1.96sqrt(matcov[jk][jk]));
	if(fabs(wald) > 1.96){
	fprintf(fichtm, "<td><b>%12.7f</b></br> (%12.7f)</br>",p[jk],sqrt(matcov[jk][jk]));
	}else{
	fprintf(fichtm, "<td>%12.7f (%12.7f)</br>",p[jk],sqrt(matcov[jk][jk]));
	}
	fprintf(fichtm,"sqrt(W)=%8.3f</br>",wald);
	fprintf(fichtm,"[%12.7f;%12.7f]</br></td>", p[jk]-1.96sqrt(matcov[jk][jk]),p[jk]+1.96sqrt(matcov[jk][jk]));
jk++;	jk++;
}	}
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
	fprintf(fichtm, "</tr>\n");
}	}
}	}
}	}
} /* end of hesscov and Wald tests */	} /* end of hesscov and Wald tests */
	fprintf(fichtm,"</table>\n");

/* */	/* */
fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");	fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
Line 12405 Please run with mle=-1 to get a correct	Line 12817 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++;
Line 12422 Please run with mle=-1 to get a correct	Line 12836 Please run with mle=-1 to get a correct
parameterline=11;	parameterline=11;
else if(sscanf(line,"prevbackcast=%[^\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 && (num_filled == 8)){	if((num_filled=sscanf(line,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj)) !=EOF && (num_filled == 8)){
fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);	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);
Line 12440 Please run with mle=-1 to get a correct	Line 12855 Please run with mle=-1 to get a correct
prvforecast = 1;	prvforecast = 1;
}	}
else if((num_filled=sscanf(line,"prevforecast=%d yearsfproj=%lf mobil_average=%d\n",&prevfcast,&yrfproj,&mobilavproj)) !=EOF){/* && (num_filled == 3))*/	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=%lf.2 mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);	printf("prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
fprintf(ficlog,"prevforecast=%d yearsfproj=%lf.2 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=%lf.2 mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);	fprintf(ficres,"prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
prvforecast = 2;	prvforecast = 2;
}	}
else {	else {
Line 12463 Please run with mle=-1 to get a correct	Line 12878 Please run with mle=-1 to get a correct
prvbackcast = 1;	prvbackcast = 1;
}	}
else if((num_filled=sscanf(line,"prevbackcast=%d yearsbproj=%lf mobil_average=%d\n",&prevbcast,&yrbproj,&mobilavproj)) ==3){/* && (num_filled == 3))*/	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=%lf.2 mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);	printf("prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
fprintf(ficlog,"prevbackcast=%d yearsbproj=%lf.2 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=%lf.2 mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);	fprintf(ficres,"prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
prvbackcast = 2;	prvbackcast = 2;
}	}
else {	else {
Line 12475 Please run with mle=-1 to get a correct	Line 12890 Please run with mle=-1 to get a correct
}	}
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 > MAXRESULTLINESPONE-1){
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. ",MAXRESULTLINESPONE-1,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. ",MAXRESULTLINESPONE-1,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:
printf("Error: Unknown command '%s'\n",line);
fprintf(ficlog,"Error: Unknown command '%s'\n",line);
if(ncovmodel >=2 && nresult==0 ){
printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
fprintf(ficlog,"ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
}
goto end;	goto end;
break;	break;
default:	case 14:
nresult=1;	printf("Error: Unknown command '%s'\n",line);
decoderesult(".",nresult ); /* No covariate */	fprintf(ficlog,"Error: Unknown command '%s'\n",line);
	if(line[0] == ' ' \|\| line[0] == '\n'){
	printf("It should not be an empty line '%s'\n",line);
	fprintf(ficlog,"It should not be an empty line '%s'\n",line);
	}
	if(ncovmodel >=2 && nresult==0 ){
	printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
	fprintf(ficlog,"ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
}	}
	/* goto end; */
	break;
	case 15:
	printf("End of resultlines.\n");
	fprintf(ficlog,"End of resultlines.\n");
	break;
	default: /* parameterline =0 */
	nresult=1;
	decoderesult(".",nresult ); /* No covariate */
} /* End switch parameterline */	} /* End switch parameterline */
}while(endishere==0); /* End do */	}while(endishere==0); /* End do */

Line 12781 Please run with mle=-1 to get a correct	Line 13196 Please run with mle=-1 to get a correct
for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */	for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
if(i1 != 1 && TKresult[nres]!= k)	if(i1 != 1 && TKresult[nres]!= k)
continue;	continue;
printf("\n#****** Result for:");	printf("\n# model %s \n#****** Result for:", model);
fprintf(ficrest,"\n#****** Result for:");	fprintf(ficrest,"\n# model %s \n#****** Result for:", model);
fprintf(ficlog,"\n#****** Result for:");	fprintf(ficlog,"\n# model %s \n#****** Result for:", model);
for(j=1;j<=cptcoveff;j++){	for(j=1;j<=cptcoveff;j++){
printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);

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

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	Added in v.1.321