--- imach/src/imach.c 2005/09/30 15:54:49 1.103
+++ imach/src/imach.c 2010/04/30 18:19:40 1.138
@@ -1,6 +1,172 @@
-/* $Id: imach.c,v 1.103 2005/09/30 15:54:49 lievre Exp $
+/* $Id: imach.c,v 1.138 2010/04/30 18:19:40 brouard Exp $
$State: Exp $
$Log: imach.c,v $
+ Revision 1.138 2010/04/30 18:19:40 brouard
+ *** empty log message ***
+
+ Revision 1.137 2010/04/29 18:11:38 brouard
+ (Module): Checking covariates for more complex models
+ than V1+V2. A lot of change to be done. Unstable.
+
+ Revision 1.136 2010/04/26 20:30:53 brouard
+ (Module): merging some libgsl code. Fixing computation
+ of likelione (using inter/intrapolation if mle = 0) in order to
+ get same likelihood as if mle=1.
+ Some cleaning of code and comments added.
+
+ Revision 1.135 2009/10/29 15:33:14 brouard
+ (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
+
+ Revision 1.134 2009/10/29 13:18:53 brouard
+ (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
+
+ Revision 1.133 2009/07/06 10:21:25 brouard
+ just nforces
+
+ Revision 1.132 2009/07/06 08:22:05 brouard
+ Many tings
+
+ Revision 1.131 2009/06/20 16:22:47 brouard
+ Some dimensions resccaled
+
+ Revision 1.130 2009/05/26 06:44:34 brouard
+ (Module): Max Covariate is now set to 20 instead of 8. A
+ lot of cleaning with variables initialized to 0. Trying to make
+ V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
+
+ Revision 1.129 2007/08/31 13:49:27 lievre
+ Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
+
+ Revision 1.128 2006/06/30 13:02:05 brouard
+ (Module): Clarifications on computing e.j
+
+ Revision 1.127 2006/04/28 18:11:50 brouard
+ (Module): Yes the sum of survivors was wrong since
+ imach-114 because nhstepm was no more computed in the age
+ loop. Now we define nhstepma in the age loop.
+ (Module): In order to speed up (in case of numerous covariates) we
+ compute health expectancies (without variances) in a first step
+ and then all the health expectancies with variances or standard
+ deviation (needs data from the Hessian matrices) which slows the
+ computation.
+ In the future we should be able to stop the program is only health
+ expectancies and graph are needed without standard deviations.
+
+ Revision 1.126 2006/04/28 17:23:28 brouard
+ (Module): Yes the sum of survivors was wrong since
+ imach-114 because nhstepm was no more computed in the age
+ loop. Now we define nhstepma in the age loop.
+ Version 0.98h
+
+ Revision 1.125 2006/04/04 15:20:31 lievre
+ Errors in calculation of health expectancies. Age was not initialized.
+ Forecasting file added.
+
+ Revision 1.124 2006/03/22 17:13:53 lievre
+ Parameters are printed with %lf instead of %f (more numbers after the comma).
+ The log-likelihood is printed in the log file
+
+ Revision 1.123 2006/03/20 10:52:43 brouard
+ * imach.c (Module): changed, corresponds to .htm file
+ name. <head> headers where missing.
+
+ * imach.c (Module): Weights can have a decimal point as for
+ English (a comma might work with a correct LC_NUMERIC environment,
+ otherwise the weight is truncated).
+ Modification of warning when the covariates values are not 0 or
+ 1.
+ Version 0.98g
+
+ Revision 1.122 2006/03/20 09:45:41 brouard
+ (Module): Weights can have a decimal point as for
+ English (a comma might work with a correct LC_NUMERIC environment,
+ otherwise the weight is truncated).
+ Modification of warning when the covariates values are not 0 or
+ 1.
+ Version 0.98g
+
+ Revision 1.121 2006/03/16 17:45:01 lievre
+ * imach.c (Module): Comments concerning covariates added
+
+ * imach.c (Module): refinements in the computation of lli if
+ status=-2 in order to have more reliable computation if stepm is
+ not 1 month. Version 0.98f
+
+ Revision 1.120 2006/03/16 15:10:38 lievre
+ (Module): refinements in the computation of lli if
+ status=-2 in order to have more reliable computation if stepm is
+ not 1 month. Version 0.98f
+
+ Revision 1.119 2006/03/15 17:42:26 brouard
+ (Module): Bug if status = -2, the loglikelihood was
+ computed as likelihood omitting the logarithm. Version O.98e
+
+ Revision 1.118 2006/03/14 18:20:07 brouard
+ (Module): varevsij Comments added explaining the second
+ table of variances if popbased=1 .
+ (Module): Covariances of eij, ekl added, graphs fixed, new html link.
+ (Module): Function pstamp added
+ (Module): Version 0.98d
+
+ Revision 1.117 2006/03/14 17:16:22 brouard
+ (Module): varevsij Comments added explaining the second
+ table of variances if popbased=1 .
+ (Module): Covariances of eij, ekl added, graphs fixed, new html link.
+ (Module): Function pstamp added
+ (Module): Version 0.98d
+
+ Revision 1.116 2006/03/06 10:29:27 brouard
+ (Module): Variance-covariance wrong links and
+ varian-covariance of ej. is needed (Saito).
+
+ Revision 1.115 2006/02/27 12:17:45 brouard
+ (Module): One freematrix added in mlikeli! 0.98c
+
+ Revision 1.114 2006/02/26 12:57:58 brouard
+ (Module): Some improvements in processing parameter
+ filename with strsep.
+
+ Revision 1.113 2006/02/24 14:20:24 brouard
+ (Module): Memory leaks checks with valgrind and:
+ datafile was not closed, some imatrix were not freed and on matrix
+ allocation too.
+
+ Revision 1.112 2006/01/30 09:55:26 brouard
+ (Module): Back to gnuplot.exe instead of wgnuplot.exe
+
+ Revision 1.111 2006/01/25 20:38:18 brouard
+ (Module): Lots of cleaning and bugs added (Gompertz)
+ (Module): Comments can be added in data file. Missing date values
+ can be a simple dot '.'.
+
+ Revision 1.110 2006/01/25 00:51:50 brouard
+ (Module): Lots of cleaning and bugs added (Gompertz)
+
+ Revision 1.109 2006/01/24 19:37:15 brouard
+ (Module): Comments (lines starting with a #) are allowed in data.
+
+ Revision 1.108 2006/01/19 18:05:42 lievre
+ Gnuplot problem appeared...
+ To be fixed
+
+ Revision 1.107 2006/01/19 16:20:37 brouard
+ Test existence of gnuplot in imach path
+
+ Revision 1.106 2006/01/19 13:24:36 brouard
+ Some cleaning and links added in html output
+
+ Revision 1.105 2006/01/05 20:23:19 lievre
+ *** empty log message ***
+
+ Revision 1.104 2005/09/30 16:11:43 lievre
+ (Module): sump fixed, loop imx fixed, and simplifications.
+ (Module): If the status is missing at the last wave but we know
+ that the person is alive, then we can code his/her status as -2
+ (instead of missing=-1 in earlier versions) and his/her
+ contributions to the likelihood is 1 - Prob of dying from last
+ health status (= 1-p13= p11+p12 in the easiest case of somebody in
+ the healthy state at last known wave). Version is 0.98
+
Revision 1.103 2005/09/30 15:54:49 lievre
(Module): sump fixed, loop imx fixed, and simplifications.
@@ -27,7 +193,7 @@
The same imach parameter file can be used but the option for mle should be -3.
- Agnès, who wrote this part of the code, tried to keep most of the
+ Agnès, who wrote this part of the code, tried to keep most of the
former routines in order to include the new code within the former code.
The output is very simple: only an estimate of the intercept and of
@@ -158,10 +324,10 @@
hPijx.
Also this programme outputs the covariance matrix of the parameters but also
- of the life expectancies. It also computes the stable prevalence.
+ of the life expectancies. It also computes the period (stable) prevalence.
- Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
- Institut national d'études démographiques, Paris.
+ Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
+ Institut national d'études démographiques, Paris.
This software have been partly granted by Euro-REVES, a concerted action
from the European Union.
It is copyrighted identically to a GNU software product, ie programme and
@@ -187,7 +353,7 @@
begin-prev-date,...
open gnuplot file
open html file
- stable prevalence
+ period (stable) prevalence
for age prevalim()
h Pij x
variance of p varprob
@@ -199,7 +365,7 @@
varevsij()
if popbased==1 varevsij(,popbased)
total life expectancies
- Variance of stable prevalence
+ Variance of period (stable) prevalence
end
*/
@@ -209,31 +375,43 @@
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
+#include <string.h>
#include <unistd.h>
+#include <limits.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <errno.h>
+extern int errno;
+
/* #include <sys/time.h> */
#include <time.h>
#include "timeval.h"
+#ifdef GSL
+#include <gsl/gsl_errno.h>
+#include <gsl/gsl_multimin.h>
+#endif
+
/* #include <libintl.h> */
/* #define _(String) gettext (String) */
#define MAXLINE 256
+
#define GNUPLOTPROGRAM "gnuplot"
/*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
#define FILENAMELENGTH 132
-/*#define DEBUG*/
-/*#define windows*/
+
#define GLOCK_ERROR_NOPATH -1 /* empty path */
#define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
-#define MAXPARM 30 /* Maximum number of parameters for the optimization */
+#define MAXPARM 128 /* Maximum number of parameters for the optimization */
#define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
#define NINTERVMAX 8
#define NLSTATEMAX 8 /* Maximum number of live states (for func) */
#define NDEATHMAX 8 /* Maximum number of dead states (for func) */
-#define NCOVMAX 8 /* Maximum number of covariates */
+#define NCOVMAX 20 /* Maximum number of covariates */
#define MAXN 20000
#define YEARM 12. /* Number of months per year */
#define AGESUP 130
@@ -241,44 +419,50 @@
#define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
#ifdef UNIX
#define DIRSEPARATOR '/'
+#define CHARSEPARATOR "/"
#define ODIRSEPARATOR '\\'
#else
#define DIRSEPARATOR '\\'
+#define CHARSEPARATOR "\\"
#define ODIRSEPARATOR '/'
#endif
-/* $Id: imach.c,v 1.103 2005/09/30 15:54:49 lievre Exp $ */
+/* $Id: imach.c,v 1.138 2010/04/30 18:19:40 brouard Exp $ */
/* $State: Exp $ */
-char version[]="Imach version 0.97c, September 2004, INED-EUROREVES ";
-char fullversion[]="$Revision: 1.103 $ $Date: 2005/09/30 15:54:49 $";
-int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
-int nvar;
-int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
+char version[]="Imach version 0.98m, April 2010, INED-EUROREVES-Institut de longevite ";
+char fullversion[]="$Revision: 1.138 $ $Date: 2010/04/30 18:19:40 $";
+char strstart[80];
+char optionfilext[10], optionfilefiname[FILENAMELENGTH];
+int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
+int nvar=0, nforce=0; /* Number of variables, number of forces */
+int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
int npar=NPARMAX;
int nlstate=2; /* Number of live states */
int ndeath=1; /* Number of dead states */
-int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
+int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
int popbased=0;
int *wav; /* Number of waves for this individuual 0 is possible */
-int maxwav; /* Maxim number of waves */
-int jmin, jmax; /* min, max spacing between 2 waves */
-int gipmx, gsw; /* Global variables on the number of contributions
+int maxwav=0; /* Maxim number of waves */
+int jmin=0, jmax=0; /* min, max spacing between 2 waves */
+int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
+int gipmx=0, gsw=0; /* Global variables on the number of contributions
to the likelihood and the sum of weights (done by funcone)*/
-int mle, weightopt;
+int mle=1, weightopt=0;
int **mw; /* mw[mi][i] is number of the mi wave for this individual */
int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
* wave mi and wave mi+1 is not an exact multiple of stepm. */
-double jmean; /* Mean space between 2 waves */
+double jmean=1; /* Mean space between 2 waves */
double **oldm, **newm, **savm; /* Working pointers to matrices */
double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
-FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+/*FILE *fic ; */ /* Used in readdata only */
+FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
FILE *ficlog, *ficrespow;
-int globpr; /* Global variable for printing or not */
+int globpr=0; /* Global variable for printing or not */
double fretone; /* Only one call to likelihood */
-long ipmx; /* Number of contributions */
+long ipmx=0; /* Number of contributions */
double sw; /* Sum of weights */
char filerespow[FILENAMELENGTH];
char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
@@ -288,13 +472,17 @@ FILE *ficresprobmorprev;
FILE *fichtm, *fichtmcov; /* Html File */
FILE *ficreseij;
char filerese[FILENAMELENGTH];
+FILE *ficresstdeij;
+char fileresstde[FILENAMELENGTH];
+FILE *ficrescveij;
+char filerescve[FILENAMELENGTH];
FILE *ficresvij;
char fileresv[FILENAMELENGTH];
FILE *ficresvpl;
char fileresvpl[FILENAMELENGTH];
char title[MAXLINE];
char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
-char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
+char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
char command[FILENAMELENGTH];
int outcmd=0;
@@ -316,6 +504,10 @@ long time_value;
extern long time();
char strcurr[80], strfor[80];
+char *endptr;
+long lval;
+double dval;
+
#define NR_END 1
#define FREE_ARG char*
#define FTOL 1.0e-10
@@ -363,7 +555,8 @@ double dateintmean=0;
double *weight;
int **s; /* Status */
double *agedc, **covar, idx;
-int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
+int **nbcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
+double *lsurv, *lpop, *tpop;
double ftol=FTOL; /* Tolerance for computing Max Likelihood */
double ftolhess; /* Tolerance for computing hessian */
@@ -371,7 +564,7 @@ double ftolhess; /* Tolerance for comput
/**************** split *************************/
static int split( char *path, char *dirc, char *name, char *ext, char *finame )
{
- /* From a file name with full path (either Unix or Windows) we extract the directory (dirc)
+ /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
the name of the file (name), its extension only (ext) and its first part of the name (finame)
*/
char *ss; /* pointer */
@@ -380,7 +573,8 @@ static int split( char *path, char *dirc
l1 = strlen(path ); /* length of path */
if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
ss= strrchr( path, DIRSEPARATOR ); /* find last / */
- if ( ss == NULL ) { /* no directory, so use current */
+ if ( ss == NULL ) { /* no directory, so determine current directory */
+ strcpy( name, path ); /* we got the fullname name because no directory */
/*if(strrchr(path, ODIRSEPARATOR )==NULL)
printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
/* get current working directory */
@@ -388,7 +582,8 @@ static int split( char *path, char *dirc
if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
return( GLOCK_ERROR_GETCWD );
}
- strcpy( name, path ); /* we've got it */
+ /* got dirc from getcwd*/
+ printf(" DIRC = %s \n",dirc);
} else { /* strip direcotry from path */
ss++; /* after this, the filename */
l2 = strlen( ss ); /* length of filename */
@@ -396,14 +591,15 @@ static int split( char *path, char *dirc
strcpy( name, ss ); /* save file name */
strncpy( dirc, path, l1 - l2 ); /* now the directory */
dirc[l1-l2] = 0; /* add zero */
+ printf(" DIRC2 = %s \n",dirc);
}
+ /* We add a separator at the end of dirc if not exists */
l1 = strlen( dirc ); /* length of directory */
- /*#ifdef windows
- if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
-#else
- if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
-#endif
- */
+ if( dirc[l1-1] != DIRSEPARATOR ){
+ dirc[l1] = DIRSEPARATOR;
+ dirc[l1+1] = 0;
+ printf(" DIRC3 = %s \n",dirc);
+ }
ss = strrchr( name, '.' ); /* find last / */
if (ss >0){
ss++;
@@ -413,6 +609,7 @@ static int split( char *path, char *dirc
strncpy( finame, name, l1-l2);
finame[l1-l2]= 0;
}
+
return( 0 ); /* we're done */
}
@@ -431,6 +628,49 @@ void replace_back_to_slash(char *s, char
}
}
+char *trimbb(char *out, char *in)
+{ /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
+ char *s;
+ s=out;
+ while (*in != '\0'){
+ while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
+ in++;
+ }
+ *out++ = *in++;
+ }
+ *out='\0';
+ return s;
+}
+
+char *cutv(char *blocc, char *alocc, char *in, char occ)
+{
+ /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
+ and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
+ gives blocc="abcdef2ghi" and alocc="j".
+ If occ is not found blocc is null and alocc is equal to in. Returns alocc
+ */
+ char *s, *t;
+ t=in;s=in;
+ while (*in != '\0'){
+ while( *in == occ){
+ *blocc++ = *in++;
+ s=in;
+ }
+ *blocc++ = *in++;
+ }
+ if (s == t) /* occ not found */
+ *(blocc-(in-s))='\0';
+ else
+ *(blocc-(in-s)-1)='\0';
+ in=s;
+ while ( *in != '\0'){
+ *alocc++ = *in++;
+ }
+
+ *alocc='\0';
+ return s;
+}
+
int nbocc(char *s, char occ)
{
int i,j=0;
@@ -443,27 +683,27 @@ int nbocc(char *s, char occ)
return j;
}
-void cutv(char *u,char *v, char*t, char occ)
-{
- /* cuts string t into u and v where u ends before first occurence of char 'occ'
- and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
- gives u="abcedf" and v="ghi2j" */
- int i,lg,j,p=0;
- i=0;
- for(j=0; j<=strlen(t)-1; j++) {
- if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
- }
+/* void cutv(char *u,char *v, char*t, char occ) */
+/* { */
+/* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
+/* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
+/* gives u="abcdef2ghi" and v="j" *\/ */
+/* int i,lg,j,p=0; */
+/* i=0; */
+/* lg=strlen(t); */
+/* for(j=0; j<=lg-1; j++) { */
+/* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
+/* } */
- lg=strlen(t);
- for(j=0; j<p; j++) {
- (u[j] = t[j]);
- }
- u[p]='\0';
+/* for(j=0; j<p; j++) { */
+/* (u[j] = t[j]); */
+/* } */
+/* u[p]='\0'; */
- for(j=0; j<= lg; j++) {
- if (j>=(p+1))(v[j-p-1] = t[j]);
- }
-}
+/* for(j=0; j<= lg; j++) { */
+/* if (j>=(p+1))(v[j-p-1] = t[j]); */
+/* } */
+/* } */
/********************** nrerror ********************/
@@ -875,9 +1115,8 @@ void powell(double p[], double **xi, int
last_time=curr_time;
(void) gettimeofday(&curr_time,&tzp);
printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
- /* fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
- fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
- */
+ fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
+/* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
for (i=1;i<=n;i++) {
printf(" %d %.12f",i, p[i]);
fprintf(ficlog," %d %.12lf",i, p[i]);
@@ -999,7 +1238,7 @@ void powell(double p[], double **xi, int
}
}
-/**** Prevalence limit (stable prevalence) ****************/
+/**** Prevalence limit (stable or period prevalence) ****************/
double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
{
@@ -1009,7 +1248,7 @@ double **prevalim(double **prlim, int nl
int i, ii,j,k;
double min, max, maxmin, maxmax,sumnew=0.;
double **matprod2();
- double **out, cov[NCOVMAX], **pmij();
+ double **out, cov[NCOVMAX+1], **pmij();
double **newm;
double agefin, delaymax=50 ; /* Max number of years to converge */
@@ -1024,21 +1263,21 @@ double **prevalim(double **prlim, int nl
for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
newm=savm;
/* Covariates have to be included here again */
- cov[2]=agefin;
-
- for (k=1; k<=cptcovn;k++) {
- cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
- /* printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
- }
- for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
- for (k=1; k<=cptcovprod;k++)
- cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-
- /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
- /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
- /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
+ cov[2]=agefin;
+
+ for (k=1; k<=cptcovn;k++) {
+ cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+ /* printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
+ }
+ for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+ for (k=1; k<=cptcovprod;k++)
+ cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+
+ /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
+ /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
+ /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
-
+
savm=oldm;
oldm=newm;
maxmax=0.;
@@ -1065,37 +1304,56 @@ double **prevalim(double **prlim, int nl
double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
{
- double s1, s2;
+ /* According to parameters values stored in x and the covariate's values stored in cov,
+ computes the probability to be observed in state j being in state i by appying the
+ model to the ncovmodel covariates (including constant and age).
+ lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
+ and, according on how parameters are entered, the position of the coefficient xij(nc) of the
+ ncth covariate in the global vector x is given by the formula:
+ j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
+ j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
+ Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
+ sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
+ Outputs ps[i][j] the probability to be observed in j being in j according to
+ the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
+ */
+ double s1, lnpijopii;
/*double t34;*/
int i,j,j1, nc, ii, jj;
for(i=1; i<= nlstate; i++){
for(j=1; j<i;j++){
- for (nc=1, s2=0.;nc <=ncovmodel; nc++){
- /*s2 += param[i][j][nc]*cov[nc];*/
- s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
-/* printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
+ for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
+ /*lnpijopii += param[i][j][nc]*cov[nc];*/
+ lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
+/* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
}
- ps[i][j]=s2;
-/* printf("s1=%.17e, s2=%.17e\n",s1,s2); */
+ ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
+/* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
}
for(j=i+1; j<=nlstate+ndeath;j++){
- for (nc=1, s2=0.;nc <=ncovmodel; nc++){
- s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
-/* printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
+ for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
+ /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
+ lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
+/* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
}
- ps[i][j]=s2;
+ ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
}
}
- /*ps[3][2]=1;*/
for(i=1; i<= nlstate; i++){
s1=0;
- for(j=1; j<i; j++)
- s1+=exp(ps[i][j]);
- for(j=i+1; j<=nlstate+ndeath; j++)
- s1+=exp(ps[i][j]);
+ for(j=1; j<i; j++){
+ s1+=exp(ps[i][j]); /* In fact sums pij/pii */
+ /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
+ }
+ for(j=i+1; j<=nlstate+ndeath; j++){
+ s1+=exp(ps[i][j]); /* In fact sums pij/pii */
+ /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
+ }
+ /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
ps[i][i]=1./(s1+1.);
+ /* Computing other pijs */
for(j=1; j<i; j++)
ps[i][j]= exp(ps[i][j])*ps[i][i];
for(j=i+1; j<=nlstate+ndeath; j++)
@@ -1160,7 +1418,7 @@ double ***hpxij(double ***po, int nhstep
*/
int i, j, d, h, k;
- double **out, cov[NCOVMAX];
+ double **out, cov[NCOVMAX+1];
double **newm;
/* Hstepm could be zero and should return the unit matrix */
@@ -1176,7 +1434,8 @@ double ***hpxij(double ***po, int nhstep
/* Covariates have to be included here again */
cov[1]=1.;
cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
- for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+ for (k=1; k<=cptcovn;k++)
+ cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
for (k=1; k<=cptcovage;k++)
cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
for (k=1; k<=cptcovprod;k++)
@@ -1193,10 +1452,11 @@ double ***hpxij(double ***po, int nhstep
for(i=1; i<=nlstate+ndeath; i++)
for(j=1;j<=nlstate+ndeath;j++) {
po[i][j][h]=newm[i][j];
- /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
- */
+ /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
}
+ /*printf("h=%d ",h);*/
} /* end h */
+/* printf("\n H=%d \n",h); */
return po;
}
@@ -1205,7 +1465,7 @@ double ***hpxij(double ***po, int nhstep
double func( double *x)
{
int i, ii, j, k, mi, d, kk;
- double l, ll[NLSTATEMAX], cov[NCOVMAX];
+ double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
double **out;
double sw; /* Sum of weights */
double lli; /* Individual log likelihood */
@@ -1224,7 +1484,15 @@ double func( double *x)
if(mle==1){
for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+ /* Computes the values of the ncovmodel covariates of the model
+ depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
+ Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
+ to be observed in j being in i according to the model.
+ */
for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+ /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
+ is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
+ has been calculated etc */
for(mi=1; mi<= wav[i]-1; mi++){
for (ii=1;ii<=nlstate+ndeath;ii++)
for (j=1;j<=nlstate+ndeath;j++){
@@ -1235,7 +1503,7 @@ double func( double *x)
newm=savm;
cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
for (kk=1; kk<=cptcovage;kk++) {
- cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+ cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
}
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
@@ -1264,9 +1532,10 @@ double func( double *x)
*/
/* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
if( s2 > nlstate){
- /* i.e. if s2 is a death state and if the date of death is known then the contribution
- to the likelihood is the probability to die between last step unit time and current
- step unit time, which is also equal to probability to die before dh
+ /* i.e. if s2 is a death state and if the date of death is known
+ then the contribution to the likelihood is the probability to
+ die between last step unit time and current step unit time,
+ which is also equal to probability to die before dh
minus probability to die before dh-stepm .
In version up to 0.92 likelihood was computed
as if date of death was unknown. Death was treated as any other
@@ -1287,7 +1556,28 @@ double func( double *x)
lower mortality.
*/
lli=log(out[s1][s2] - savm[s1][s2]);
- }else{
+
+
+ } else if (s2==-2) {
+ for (j=1,survp=0. ; j<=nlstate; j++)
+ survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+ /*survp += out[s1][j]; */
+ lli= log(survp);
+ }
+
+ else if (s2==-4) {
+ for (j=3,survp=0. ; j<=nlstate; j++)
+ survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+ lli= log(survp);
+ }
+
+ else if (s2==-5) {
+ for (j=1,survp=0. ; j<=2; j++)
+ survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+ lli= log(survp);
+ }
+
+ else{
lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
/* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
}
@@ -1437,7 +1727,7 @@ double funcone( double *x)
{
/* Same as likeli but slower because of a lot of printf and if */
int i, ii, j, k, mi, d, kk;
- double l, ll[NLSTATEMAX], cov[NCOVMAX];
+ double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
double **out;
double lli; /* Individual log likelihood */
double llt;
@@ -1481,7 +1771,11 @@ double funcone( double *x)
*/
if( s2 > nlstate && (mle <5) ){ /* Jackson */
lli=log(out[s1][s2] - savm[s1][s2]);
- } else if (mle==1){
+ } else if (s2==-2) {
+ for (j=1,survp=0. ; j<=nlstate; j++)
+ survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+ lli= log(survp);
+ }else if (mle==1){
lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
} else if(mle==2){
lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
@@ -1489,16 +1783,17 @@ double funcone( double *x)
lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
} else if (mle==4){ /* mle=4 no inter-extrapolation */
lli=log(out[s1][s2]); /* Original formula */
- } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
- lli=log(out[s1][s2]); /* Original formula */
+ } else{ /* mle=0 back to 1 */
+ lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+ /*lli=log(out[s1][s2]); */ /* Original formula */
} /* End of if */
ipmx +=1;
sw += weight[i];
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-/* printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
+ /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
if(globpr){
- fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
- %10.6f %10.6f %10.6f ", \
+ fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
+ %11.6f %11.6f %11.6f ", \
num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
for(k=1,llt=0.,l=0.; k<=nlstate; k++){
@@ -1583,6 +1878,7 @@ void mlikeli(FILE *ficres,double p[], in
powell(p,xi,npar,ftol,&iter,&fret,func);
+ free_matrix(xi,1,npar,1,npar);
fclose(ficrespow);
printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
@@ -1699,7 +1995,7 @@ double hessii(double x[], double delta,
int i;
int l=1, lmax=20;
double k1,k2;
- double p2[NPARMAX+1];
+ double p2[MAXPARM+1]; /* identical to x */
double res;
double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
double fx;
@@ -1720,7 +2016,7 @@ double hessii(double x[], double delta,
/*res= (k1-2.0*fx+k2)/delt/delt; */
res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
-#ifdef DEBUG
+#ifdef DEBUGHESS
printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
#endif
@@ -1746,7 +2042,7 @@ double hessij( double x[], double delti[
int i;
int l=1, l1, lmax=20;
double k1,k2,k3,k4,res,fx;
- double p2[NPARMAX+1];
+ double p2[MAXPARM+1];
int k;
fx=func(x);
@@ -1850,16 +2146,20 @@ void lubksb(double **a, int n, int *indx
}
}
+void pstamp(FILE *fichier)
+{
+ fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
+}
+
/************ Frequencies ********************/
-void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint)
+void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
{ /* Some frequencies */
- int i, m, jk, k1,i1, j1, bool, z1,z2,j;
+ int i, m, jk, k1,i1, j1, bool, z1,j;
int first;
double ***freq; /* Frequencies */
double *pp, **prop;
double pos,posprop, k2, dateintsum=0,k2cpt=0;
- FILE *ficresp;
char fileresp[FILENAMELENGTH];
pp=vector(1,nlstate);
@@ -1871,7 +2171,7 @@ void freqsummary(char fileres[], int ia
fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
exit(0);
}
- freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
+ freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
j1=0;
j=cptcoveff;
@@ -1884,8 +2184,8 @@ void freqsummary(char fileres[], int ia
j1++;
/*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
scanf("%d", i);*/
- for (i=-1; i<=nlstate+ndeath; i++)
- for (jk=-1; jk<=nlstate+ndeath; jk++)
+ for (i=-5; i<=nlstate+ndeath; i++)
+ for (jk=-5; jk<=nlstate+ndeath; jk++)
for(m=iagemin; m <= iagemax+3; m++)
freq[i][jk][m]=0;
@@ -1924,7 +2224,7 @@ void freqsummary(char fileres[], int ia
}
/* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-
+ pstamp(ficresp);
if (cptcovn>0) {
fprintf(ficresp, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
@@ -1953,7 +2253,7 @@ void freqsummary(char fileres[], int ia
pos += freq[jk][m][i];
if(pp[jk]>=1.e-10){
if(first==1){
- printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+ printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
}
fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
}else{
@@ -2010,7 +2310,7 @@ void freqsummary(char fileres[], int ia
dateintmean=dateintsum/k2cpt;
fclose(ficresp);
- free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
+ free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
free_vector(pp,1,nlstate);
free_matrix(prop,1,nlstate,iagemin, iagemax+3);
/* End of Freq */
@@ -2024,7 +2324,7 @@ void prevalence(double ***probs, double
We still use firstpass and lastpass as another selection.
*/
- int i, m, jk, k1, i1, j1, bool, z1,z2,j;
+ int i, m, jk, k1, i1, j1, bool, z1,j;
double ***freq; /* Frequencies */
double *pp, **prop;
double pos,posprop;
@@ -2082,7 +2382,8 @@ void prevalence(double ***probs, double
if( i <= iagemax){
if(posprop>=1.e-5){
probs[i][jk][j1]= prop[jk][i]/posprop;
- }
+ } else
+ printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
}
}/* end jk */
}/* end i */
@@ -2119,7 +2420,7 @@ void concatwav(int wav[], int **dh, int
mi=0;
m=firstpass;
while(s[m][i] <= nlstate){
- if(s[m][i]>=1)
+ if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
mw[++mi][i]=m;
if(m >=lastpass)
break;
@@ -2137,11 +2438,11 @@ void concatwav(int wav[], int **dh, int
if(mi==0){
nbwarn++;
if(first==0){
- printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
+ printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
first=1;
}
if(first==1){
- fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
+ fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
}
} /* end mi==0 */
} /* End individuals */
@@ -2159,13 +2460,19 @@ void concatwav(int wav[], int **dh, int
nberr++;
printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
j=1; /* Temporary Dangerous patch */
- printf(" We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n You MUST fix the contradiction between dates.\n",stepm);
+ printf(" We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
- fprintf(ficlog," We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n You MUST fix the contradiction between dates.\n",stepm);
+ fprintf(ficlog," We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
}
k=k+1;
- if (j >= jmax) jmax=j;
- if (j <= jmin) jmin=j;
+ if (j >= jmax){
+ jmax=j;
+ ijmax=i;
+ }
+ if (j <= jmin){
+ jmin=j;
+ ijmin=i;
+ }
sum=sum+j;
/*if (j<0) printf("j=%d num=%d \n",j,i);*/
/* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
@@ -2173,10 +2480,17 @@ void concatwav(int wav[], int **dh, int
}
else{
j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
- /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
+/* if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
+
k=k+1;
- if (j >= jmax) jmax=j;
- else if (j <= jmin)jmin=j;
+ if (j >= jmax) {
+ jmax=j;
+ ijmax=i;
+ }
+ else if (j <= jmin){
+ jmin=j;
+ ijmin=i;
+ }
/* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
/*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
if(j<0){
@@ -2194,7 +2508,7 @@ void concatwav(int wav[], int **dh, int
dh[mi][i]=jk;
bh[mi][i]=0;
}else{ /* We want a negative bias in order to only have interpolation ie
- * at the price of an extra matrix product in likelihood */
+ * to avoid the price of an extra matrix product in likelihood */
dh[mi][i]=jk+1;
bh[mi][i]=ju;
}
@@ -2219,96 +2533,237 @@ void concatwav(int wav[], int **dh, int
} /* end wave */
}
jmean=sum/k;
- printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
- fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
+ printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
+ fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
}
/*********** Tricode ****************************/
void tricode(int *Tvar, int **nbcode, int imx)
{
-
- int Ndum[20],ij=1, k, j, i, maxncov=19;
- int cptcode=0;
+ /* Uses cptcovn+2*cptcovprod as the number of covariates */
+ /* Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
+
+ int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
+ int modmaxcovj=0; /* Modality max of covariates j */
cptcoveff=0;
for (k=0; k<maxncov; k++) Ndum[k]=0;
- for (k=1; k<=7; k++) ncodemax[k]=0;
+ for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
- for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
- for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
- modality*/
- ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
- Ndum[ij]++; /*store the modality */
+ for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate j */
+ for (i=1; i<=imx; i++) { /*reads the data file to get the maximum value of the
+ modality of this covariate Vj*/
+ ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Finds for covariate j, n=Tvar[j] of Vn . ij is the
+ modality of the nth covariate of individual i. */
+ Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
/*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
- if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
- Tvar[j]. If V=sex and male is 0 and
- female is 1, then cptcode=1.*/
- }
-
- for (i=0; i<=cptcode; i++) {
- if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
- }
+ if (ij > modmaxcovj) modmaxcovj=ij;
+ /* getting the maximum value of the modality of the covariate
+ (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
+ female is 1, then modmaxcovj=1.*/
+ }
+ /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
+ for (i=0; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each modality of model-cov j */
+ if( Ndum[i] != 0 )
+ ncodemax[j]++;
+ /* Number of modalities of the j th covariate. In fact
+ ncodemax[j]=2 (dichotom. variables only) but it could be more for
+ historical reasons */
+ } /* Ndum[-1] number of undefined modalities */
+ /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
ij=1;
- for (i=1; i<=ncodemax[j]; i++) {
- for (k=0; k<= maxncov; k++) {
- if (Ndum[k] != 0) {
- nbcode[Tvar[j]][ij]=k;
- /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
-
+ for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 for dichotomous */
+ for (k=0; k<= modmaxcovj; k++) { /* k=-1 ? NCOVMAX*//* maxncov or modmaxcovj */
+ if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
+ nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
+ k is a modality. If we have model=V1+V1*sex
+ then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
ij++;
}
if (ij > ncodemax[j]) break;
- }
- }
- }
-
- for (k=0; k< maxncov; k++) Ndum[k]=0;
-
- for (i=1; i<=ncovmodel-2; i++) {
- /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
- ij=Tvar[i];
+ } /* end of loop on */
+ } /* end of loop on modality */
+ } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
+
+ for (k=0; k< maxncov; k++) Ndum[k]=0;
+
+ for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
+ /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
+ ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
Ndum[ij]++;
}
ij=1;
- for (i=1; i<= maxncov; i++) {
+ for (i=1; i<= maxncov; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
if((Ndum[i]!=0) && (i<=ncovcol)){
Tvaraff[ij]=i; /*For printing */
ij++;
}
}
-
- cptcoveff=ij-1; /*Number of simple covariates*/
+ ij--;
+ cptcoveff=ij; /*Number of simple covariates*/
}
/*********** Health Expectancies ****************/
-void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
+void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
+
+{
+ /* Health expectancies, no variances */
+ int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
+ int nhstepma, nstepma; /* Decreasing with age */
+ double age, agelim, hf;
+ double ***p3mat;
+ double eip;
+
+ pstamp(ficreseij);
+ fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
+ fprintf(ficreseij,"# Age");
+ for(i=1; i<=nlstate;i++){
+ for(j=1; j<=nlstate;j++){
+ fprintf(ficreseij," e%1d%1d ",i,j);
+ }
+ fprintf(ficreseij," e%1d. ",i);
+ }
+ fprintf(ficreseij,"\n");
+
+
+ if(estepm < stepm){
+ printf ("Problem %d lower than %d\n",estepm, stepm);
+ }
+ else hstepm=estepm;
+ /* We compute the life expectancy from trapezoids spaced every estepm months
+ * This is mainly to measure the difference between two models: for example
+ * if stepm=24 months pijx are given only every 2 years and by summing them
+ * we are calculating an estimate of the Life Expectancy assuming a linear
+ * progression in between and thus overestimating or underestimating according
+ * to the curvature of the survival function. If, for the same date, we
+ * estimate the model with stepm=1 month, we can keep estepm to 24 months
+ * to compare the new estimate of Life expectancy with the same linear
+ * hypothesis. A more precise result, taking into account a more precise
+ * curvature will be obtained if estepm is as small as stepm. */
+
+ /* For example we decided to compute the life expectancy with the smallest unit */
+ /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+ nhstepm is the number of hstepm from age to agelim
+ nstepm is the number of stepm from age to agelin.
+ Look at hpijx to understand the reason of that which relies in memory size
+ and note for a fixed period like estepm months */
+ /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+ survival function given by stepm (the optimization length). Unfortunately it
+ means that if the survival funtion is printed only each two years of age and if
+ you sum them up and add 1 year (area under the trapezoids) you won't get the same
+ results. So we changed our mind and took the option of the best precision.
+ */
+ hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+
+ agelim=AGESUP;
+ /* If stepm=6 months */
+ /* Computed by stepm unit matrices, product of hstepm matrices, stored
+ in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+
+/* nhstepm age range expressed in number of stepm */
+ nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
+ /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+ /* if (stepm >= YEARM) hstepm=1;*/
+ nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+ p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+
+ for (age=bage; age<=fage; age ++){
+ nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
+ /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+ /* if (stepm >= YEARM) hstepm=1;*/
+ nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
+
+ /* If stepm=6 months */
+ /* Computed by stepm unit matrices, product of hstepma matrices, stored
+ in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
+
+ hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+
+ hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
+
+ printf("%d|",(int)age);fflush(stdout);
+ fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+
+ /* Computing expectancies */
+ for(i=1; i<=nlstate;i++)
+ for(j=1; j<=nlstate;j++)
+ for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+ eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
+
+ /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
+
+ }
+
+ fprintf(ficreseij,"%3.0f",age );
+ for(i=1; i<=nlstate;i++){
+ eip=0;
+ for(j=1; j<=nlstate;j++){
+ eip +=eij[i][j][(int)age];
+ fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
+ }
+ fprintf(ficreseij,"%9.4f", eip );
+ }
+ fprintf(ficreseij,"\n");
+
+ }
+ free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ printf("\n");
+ fprintf(ficlog,"\n");
+
+}
+
+void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
{
- /* Health expectancies */
- int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
+ /* Covariances of health expectancies eij and of total life expectancies according
+ to initial status i, ei. .
+ */
+ int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
+ int nhstepma, nstepma; /* Decreasing with age */
double age, agelim, hf;
- double ***p3mat,***varhe;
+ double ***p3matp, ***p3matm, ***varhe;
double **dnewm,**doldm;
- double *xp;
+ double *xp, *xm;
double **gp, **gm;
double ***gradg, ***trgradg;
int theta;
+ double eip, vip;
+
varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
xp=vector(1,npar);
+ xm=vector(1,npar);
dnewm=matrix(1,nlstate*nlstate,1,npar);
doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
- fprintf(ficreseij,"# Health expectancies\n");
- fprintf(ficreseij,"# Age");
- for(i=1; i<=nlstate;i++)
+ pstamp(ficresstdeij);
+ fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
+ fprintf(ficresstdeij,"# Age");
+ for(i=1; i<=nlstate;i++){
for(j=1; j<=nlstate;j++)
- fprintf(ficreseij," %1d-%1d (SE)",i,j);
- fprintf(ficreseij,"\n");
+ fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
+ fprintf(ficresstdeij," e%1d. ",i);
+ }
+ fprintf(ficresstdeij,"\n");
+ pstamp(ficrescveij);
+ fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
+ fprintf(ficrescveij,"# Age");
+ for(i=1; i<=nlstate;i++)
+ for(j=1; j<=nlstate;j++){
+ cptj= (j-1)*nlstate+i;
+ for(i2=1; i2<=nlstate;i2++)
+ for(j2=1; j2<=nlstate;j2++){
+ cptj2= (j2-1)*nlstate+i2;
+ if(cptj2 <= cptj)
+ fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
+ }
+ }
+ fprintf(ficrescveij,"\n");
+
if(estepm < stepm){
printf ("Problem %d lower than %d\n",estepm, stepm);
}
@@ -2338,77 +2793,69 @@ void evsij(char fileres[], double ***eij
*/
hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+ /* If stepm=6 months */
+ /* nhstepm age range expressed in number of stepm */
agelim=AGESUP;
- for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
- /* nhstepm age range expressed in number of stepm */
- nstepm=(int) rint((agelim-age)*YEARM/stepm);
+ nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+ /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+ /* if (stepm >= YEARM) hstepm=1;*/
+ nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+
+ p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
+ trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
+ gp=matrix(0,nhstepm,1,nlstate*nlstate);
+ gm=matrix(0,nhstepm,1,nlstate*nlstate);
+
+ for (age=bage; age<=fage; age ++){
+ nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
/* Typically if 20 years nstepm = 20*12/6=40 stepm */
/* if (stepm >= YEARM) hstepm=1;*/
- nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
- p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
- gp=matrix(0,nhstepm,1,nlstate*nlstate);
- gm=matrix(0,nhstepm,1,nlstate*nlstate);
-
- /* Computed by stepm unit matrices, product of hstepm matrices, stored
- in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
- hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
-
+ nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
+ /* If stepm=6 months */
+ /* Computed by stepm unit matrices, product of hstepma matrices, stored
+ in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
+
hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
/* Computing Variances of health expectancies */
-
- for(theta=1; theta <=npar; theta++){
+ /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
+ decrease memory allocation */
+ for(theta=1; theta <=npar; theta++){
for(i=1; i<=npar; i++){
xp[i] = x[i] + (i==theta ?delti[theta]:0);
+ xm[i] = x[i] - (i==theta ?delti[theta]:0);
}
- hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+ hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
+ hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
- cptj=0;
for(j=1; j<= nlstate; j++){
for(i=1; i<=nlstate; i++){
- cptj=cptj+1;
- for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
- gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
+ for(h=0; h<=nhstepm-1; h++){
+ gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
+ gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
}
}
}
-
- for(i=1; i<=npar; i++)
- xp[i] = x[i] - (i==theta ?delti[theta]:0);
- hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-
- cptj=0;
- for(j=1; j<= nlstate; j++){
- for(i=1;i<=nlstate;i++){
- cptj=cptj+1;
- for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
-
- gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
- }
- }
- }
- for(j=1; j<= nlstate*nlstate; j++)
+ for(ij=1; ij<= nlstate*nlstate; ij++)
for(h=0; h<=nhstepm-1; h++){
- gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+ gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
}
- }
-
-/* End theta */
-
- trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
-
- for(h=0; h<=nhstepm-1; h++)
+ }/* End theta */
+
+
+ for(h=0; h<=nhstepm-1; h++)
for(j=1; j<=nlstate*nlstate;j++)
for(theta=1; theta <=npar; theta++)
trgradg[h][j][theta]=gradg[h][theta][j];
-
+
- for(i=1;i<=nlstate*nlstate;i++)
- for(j=1;j<=nlstate*nlstate;j++)
- varhe[i][j][(int)age] =0.;
+ for(ij=1;ij<=nlstate*nlstate;ij++)
+ for(ji=1;ji<=nlstate*nlstate;ji++)
+ varhe[ij][ji][(int)age] =0.;
printf("%d|",(int)age);fflush(stdout);
fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
@@ -2416,39 +2863,61 @@ void evsij(char fileres[], double ***eij
for(k=0;k<=nhstepm-1;k++){
matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
- for(i=1;i<=nlstate*nlstate;i++)
- for(j=1;j<=nlstate*nlstate;j++)
- varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
+ for(ij=1;ij<=nlstate*nlstate;ij++)
+ for(ji=1;ji<=nlstate*nlstate;ji++)
+ varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
}
}
+
/* Computing expectancies */
+ hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++)
for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
- eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
+ eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
-/* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
+ /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
}
- fprintf(ficreseij,"%3.0f",age );
- cptj=0;
+ fprintf(ficresstdeij,"%3.0f",age );
+ for(i=1; i<=nlstate;i++){
+ eip=0.;
+ vip=0.;
+ for(j=1; j<=nlstate;j++){
+ eip += eij[i][j][(int)age];
+ for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
+ vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
+ fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
+ }
+ fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
+ }
+ fprintf(ficresstdeij,"\n");
+
+ fprintf(ficrescveij,"%3.0f",age );
for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++){
- cptj++;
- fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
+ cptj= (j-1)*nlstate+i;
+ for(i2=1; i2<=nlstate;i2++)
+ for(j2=1; j2<=nlstate;j2++){
+ cptj2= (j2-1)*nlstate+i2;
+ if(cptj2 <= cptj)
+ fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
+ }
}
- fprintf(ficreseij,"\n");
+ fprintf(ficrescveij,"\n");
- free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
- free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
- free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
- free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
- free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
}
+ free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
+ free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
+ free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
+ free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
+ free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
printf("\n");
fprintf(ficlog,"\n");
+ free_vector(xm,1,npar);
free_vector(xp,1,npar);
free_matrix(dnewm,1,nlstate*nlstate,1,npar);
free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
@@ -2456,7 +2925,7 @@ void evsij(char fileres[], double ***eij
}
/************ Variance ******************/
-void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
+void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
{
/* Variance of health expectancies */
/* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
@@ -2507,7 +2976,9 @@ void varevsij(char optionfilefiname[], d
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
}
printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+
fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+ pstamp(ficresprobmorprev);
fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
for(j=nlstate+1; j<=(nlstate+ndeath);j++){
@@ -2517,16 +2988,21 @@ void varevsij(char optionfilefiname[], d
}
fprintf(ficresprobmorprev,"\n");
fprintf(ficgp,"\n# Routine varevsij");
+ /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
fprintf(fichtm,"\n<br>%s <br>\n",digitp);
/* } */
varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-
- fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are the stable prevalence in health states i\n");
+ pstamp(ficresvij);
+ fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
+ if(popbased==1)
+ fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
+ else
+ fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
fprintf(ficresvij,"# Age");
for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++)
- fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
+ fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
fprintf(ficresvij,"\n");
xp=vector(1,npar);
@@ -2548,8 +3024,7 @@ void varevsij(char optionfilefiname[], d
/* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
nhstepm is the number of hstepm from age to agelim
nstepm is the number of stepm from age to agelin.
- Look at hpijx to understand the reason of that which relies in memory size
- and note for a fixed period like k years */
+ Look at function hpijx to understand why (it is linked to memory size questions) */
/* We decided (b) to get a life expectancy respecting the most precise curvature of the
survival function given by stepm (the optimization length). Unfortunately it
means that if the survival funtion is printed every two years of age and if
@@ -2615,7 +3090,7 @@ void varevsij(char optionfilefiname[], d
}
}
- for(j=1; j<= nlstate; j++){
+ for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
for(h=0; h<=nhstepm; h++){
for(i=1, gm[h][j]=0.;i<=nlstate;i++)
gm[h][j] += prlim[i][i]*p3mat[i][j][h];
@@ -2725,9 +3200,9 @@ void varevsij(char optionfilefiname[], d
free_vector(gmp,nlstate+1,nlstate+ndeath);
free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
- fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
+ fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
/* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
- fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
+ fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
/* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
@@ -2754,7 +3229,7 @@ void varevsij(char optionfilefiname[], d
} /* end varevsij */
/************ Variance of prevlim ******************/
-void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
+void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
{
/* Variance of prevalence limit */
/* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
@@ -2767,8 +3242,9 @@ void varprevlim(char fileres[], double *
double **gradg, **trgradg;
double age,agelim;
int theta;
-
- fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
+
+ pstamp(ficresvpl);
+ fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
fprintf(ficresvpl,"# Age");
for(i=1; i<=nlstate;i++)
fprintf(ficresvpl," %1d-%1d",i,i);
@@ -2837,7 +3313,7 @@ void varprevlim(char fileres[], double *
}
/************ Variance of one-step probabilities ******************/
-void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
+void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
{
int i, j=0, i1, k1, l1, t, tj;
int k2, l2, j1, z1;
@@ -2882,13 +3358,15 @@ void varprob(char optionfilefiname[], do
fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-
+ pstamp(ficresprob);
fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
fprintf(ficresprob,"# Age");
+ pstamp(ficresprobcov);
fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
fprintf(ficresprobcov,"# Age");
+ pstamp(ficresprobcor);
fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
- fprintf(ficresprobcov,"# Age");
+ fprintf(ficresprobcor,"# Age");
for(i=1; i<=nlstate;i++)
@@ -2901,7 +3379,7 @@ void varprob(char optionfilefiname[], do
fprintf(ficresprobcov,"\n");
fprintf(ficresprobcor,"\n");
*/
- xp=vector(1,npar);
+ xp=vector(1,npar);
dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
@@ -3054,7 +3532,7 @@ To be simple, these graphs help to under
/* Confidence intervalle of pij */
/*
- fprintf(ficgp,"\nset noparametric;unset label");
+ fprintf(ficgp,"\nunset parametric;unset label");
fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
fprintf(fichtm,"\n<br>Probability with confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
@@ -3085,6 +3563,13 @@ To be simple, these graphs help to under
/* Computing eigen value of matrix of covariance */
lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+ if ((lc2 <0) || (lc1 <0) ){
+ printf("Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Continuing by making them positive: WRONG RESULTS.\n", lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
+ fprintf(ficlog,"Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e\n", lc1, lc2, v1, v2, cv12);fflush(ficlog);
+ lc1=fabs(lc1);
+ lc2=fabs(lc2);
+ }
+
/* Eigen vectors */
v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
/*v21=sqrt(1.-v11*v11); *//* error */
@@ -3139,6 +3624,8 @@ To be simple, these graphs help to under
}
free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
+ free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+ free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
free_vector(xp,1,npar);
fclose(ficresprob);
fclose(ficresprobcov);
@@ -3157,19 +3644,25 @@ void printinghtml(char fileres[], char t
double jprev2, double mprev2,double anprev2){
int jj1, k1, i1, cpt;
- fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\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 \
+</ul>");
+ fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
- Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
fprintf(fichtm,"\
- Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
fprintf(fichtm,"\
- - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+ - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
fprintf(fichtm,"\
- - Life expectancies by age and initial health status (estepm=%2d months): \
- <a href=\"%s\">%s</a> <br>\n</li>",
+ - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
+ <a href=\"%s\">%s</a> <br>\n",
estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
+ fprintf(fichtm,"\
+ - Population projections by age and states: \
+ <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
@@ -3187,20 +3680,20 @@ fprintf(fichtm," \n<ul><li><b>Graphs</b>
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
}
/* Pij */
- fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
-<img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+ fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
+<img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
/* Quasi-incidences */
fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
- before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
-<img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
- /* Stable prevalence in each health state */
+ before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
+<img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+ /* Period (stable) prevalence in each health state */
for(cpt=1; cpt<nlstate;cpt++){
- fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
-<img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
+ fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
+<img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
}
for(cpt=1; cpt<=nlstate;cpt++) {
- fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
-<img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
+ fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
+<img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
}
} /* end i1 */
}/* End k1 */
@@ -3208,7 +3701,7 @@ fprintf(fichtm," \n<ul><li><b>Graphs</b>
fprintf(fichtm,"\
-\n<br><li><h4> Result files (second order: variances)</h4>\n\
+\n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
- Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
@@ -3221,13 +3714,21 @@ fprintf(fichtm," \n<ul><li><b>Graphs</b>
- Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
fprintf(fichtm,"\
- - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
+ - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
+ <a href=\"%s\">%s</a> <br>\n</li>",
+ estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
+ fprintf(fichtm,"\
+ - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
+ <a href=\"%s\">%s</a> <br>\n</li>",
+ estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
+ fprintf(fichtm,"\
+ - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
fprintf(fichtm,"\
- - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
- subdirf2(fileres,"t"),subdirf2(fileres,"t"));
+ - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
+ estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
fprintf(fichtm,"\
- - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
+ - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
/* if(popforecast==1) fprintf(fichtm,"\n */
@@ -3258,7 +3759,10 @@ prevalence (with 95%% confidence interva
<img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
}
fprintf(fichtm,"\n<br>- Total life expectancy by age and \
-health expectancies in states (1) and (2): %s%d.png<br>\
+health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
+true period expectancies (those weighted with period prevalences are also\
+ drawn in addition to the population based expectancies computed using\
+ observed and cahotic prevalences: %s%d.png<br>\
<img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
} /* end i1 */
}/* End k1 */
@@ -3270,8 +3774,8 @@ health expectancies in states (1) and (2
void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
char dirfileres[132],optfileres[132];
- int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
- int ng;
+ int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
+ int ng=0;
/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
/* printf("Problem with file %s",optionfilegnuplot); */
/* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
@@ -3297,9 +3801,9 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u
for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
- else fprintf(ficgp," \%%*lf (\%%*lf)");
+ else fprintf(ficgp," \%%*lf (\%%*lf)");
}
- fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+ fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
else fprintf(ficgp," \%%*lf (\%%*lf)");
@@ -3347,7 +3851,8 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u
for (k1=1; k1<= m ; k1 ++) {
for (cpt=1; cpt<= nlstate ; cpt ++) {
- k=2+nlstate*(2*cpt-2);
+ /* k=2+nlstate*(2*cpt-2); */
+ k=2+(nlstate+1)*(cpt-1);
fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
fprintf(ficgp,"set ter png small\n\
set size 0.65,0.65\n\
@@ -3361,9 +3866,11 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u
*/
for (i=1; i< nlstate ; i ++) {
- fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
+ fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
+ /* fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
}
+ fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
}
}
@@ -3922,6 +4429,7 @@ double gompertz(double x[])
{
double A,B,L=0.0,sump=0.,num=0.;
int i,n=0; /* n is the size of the sample */
+
for (i=0;i<=imx-1 ; i++) {
sump=sump+weight[i];
/* sump=sump+1;*/
@@ -3934,14 +4442,15 @@ double gompertz(double x[])
for (i=1;i<=imx ; i++)
{
- if (cens[i]==1 & wav[i]>1)
+ if (cens[i] == 1 && wav[i]>1)
A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
- if (cens[i]==0 & wav[i]>1)
+ if (cens[i] == 0 && wav[i]>1)
A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
+log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
- if (wav[i]>1 & agecens[i]>15) {
+ /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+ if (wav[i] > 1 ) { /* ??? */
L=L+A*weight[i];
/* printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
}
@@ -3952,25 +4461,75 @@ double gompertz(double x[])
return -2*L*num/sump;
}
-/******************* Printing html file ***********/
-void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
- int lastpass, int stepm, int weightopt, char model[],\
- int imx, double p[],double **matcov){
- int i;
-
- fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
- fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
- for (i=1;i<=2;i++)
- fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
- fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
- fprintf(fichtm,"</ul>");
- fflush(fichtm);
-}
-
-/******************* Gnuplot file **************/
-void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+#ifdef GSL
+/******************* Gompertz_f Likelihood ******************************/
+double gompertz_f(const gsl_vector *v, void *params)
+{
+ double A,B,LL=0.0,sump=0.,num=0.;
+ double *x= (double *) v->data;
+ int i,n=0; /* n is the size of the sample */
- char dirfileres[132],optfileres[132];
+ for (i=0;i<=imx-1 ; i++) {
+ sump=sump+weight[i];
+ /* sump=sump+1;*/
+ num=num+1;
+ }
+
+
+ /* for (i=0; i<=imx; i++)
+ if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
+ printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
+ for (i=1;i<=imx ; i++)
+ {
+ if (cens[i] == 1 && wav[i]>1)
+ A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
+
+ if (cens[i] == 0 && wav[i]>1)
+ A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
+ +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
+
+ /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+ if (wav[i] > 1 ) { /* ??? */
+ LL=LL+A*weight[i];
+ /* printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
+ }
+ }
+
+ /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+ printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
+
+ return -2*LL*num/sump;
+}
+#endif
+
+/******************* Printing html file ***********/
+void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
+ int lastpass, int stepm, int weightopt, char model[],\
+ int imx, double p[],double **matcov,double agemortsup){
+ int i,k;
+
+ fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
+ fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
+ for (i=1;i<=2;i++)
+ fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+ fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
+ fprintf(fichtm,"</ul>");
+
+fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
+
+ fprintf(fichtm,"\nAge l<inf>x</inf> q<inf>x</inf> d(x,x+1) L<inf>x</inf> T<inf>x</inf> e<infx</inf><br>");
+
+ for (k=agegomp;k<(agemortsup-2);k++)
+ fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
+
+
+ fflush(fichtm);
+}
+
+/******************* Gnuplot file **************/
+void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+
+ char dirfileres[132],optfileres[132];
int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
int ng;
@@ -3990,7 +4549,396 @@ void printinggnuplotmort(char fileres[],
}
+int readdata(char datafile[], int firstobs, int lastobs, int *imax)
+{
+
+ /*-------- data file ----------*/
+ FILE *fic;
+ char dummy[]=" ";
+ int i, j, n;
+ int linei, month, year,iout;
+ char line[MAXLINE], linetmp[MAXLINE];
+ char stra[80], strb[80];
+ char *stratrunc;
+ int lstra;
+
+
+ if((fic=fopen(datafile,"r"))==NULL) {
+ printf("Problem while opening datafile: %s\n", datafile);return 1;
+ fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
+ }
+
+ i=1;
+ linei=0;
+ while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
+ linei=linei+1;
+ for(j=strlen(line); j>=0;j--){ /* Untabifies line */
+ if(line[j] == '\t')
+ line[j] = ' ';
+ }
+ for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
+ ;
+ };
+ line[j+1]=0; /* Trims blanks at end of line */
+ if(line[0]=='#'){
+ fprintf(ficlog,"Comment line\n%s\n",line);
+ printf("Comment line\n%s\n",line);
+ continue;
+ }
+ trimbb(linetmp,line); /* Trims multiple blanks in line */
+ for (j=0; line[j]!='\0';j++){
+ line[j]=linetmp[j];
+ }
+
+
+ for (j=maxwav;j>=1;j--){
+ cutv(stra, strb, line, ' ');
+ if(strb[0]=='.') { /* Missing status */
+ lval=-1;
+ }else{
+ errno=0;
+ lval=strtol(strb,&endptr,10);
+ /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+ if( strb[0]=='\0' || (*endptr != '\0')){
+ printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);
+ fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
+ return 1;
+ }
+ }
+ s[j][i]=lval;
+
+ strcpy(line,stra);
+ cutv(stra, strb,line,' ');
+ if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+ }
+ else if(iout=sscanf(strb,"%s.") != 0){
+ month=99;
+ year=9999;
+ }else{
+ printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);
+ fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
+ return 1;
+ }
+ anint[j][i]= (double) year;
+ mint[j][i]= (double)month;
+ strcpy(line,stra);
+ } /* ENd Waves */
+
+ cutv(stra, strb,line,' ');
+ if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+ }
+ else if(iout=sscanf(strb,"%s.",dummy) != 0){
+ month=99;
+ year=9999;
+ }else{
+ printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
+ fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
+ return 1;
+ }
+ andc[i]=(double) year;
+ moisdc[i]=(double) month;
+ strcpy(line,stra);
+
+ cutv(stra, strb,line,' ');
+ if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+ }
+ else if(iout=sscanf(strb,"%s.") != 0){
+ month=99;
+ year=9999;
+ }else{
+ printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
+ fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
+ return 1;
+ }
+ if (year==9999) {
+ printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);
+ fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
+ return 1;
+
+ }
+ annais[i]=(double)(year);
+ moisnais[i]=(double)(month);
+ strcpy(line,stra);
+
+ cutv(stra, strb,line,' ');
+ errno=0;
+ dval=strtod(strb,&endptr);
+ if( strb[0]=='\0' || (*endptr != '\0')){
+ printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
+ fprintf(ficlog,"Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
+ fflush(ficlog);
+ return 1;
+ }
+ weight[i]=dval;
+ strcpy(line,stra);
+
+ for (j=ncovcol;j>=1;j--){
+ cutv(stra, strb,line,' ');
+ if(strb[0]=='.') { /* Missing status */
+ lval=-1;
+ }else{
+ errno=0;
+ lval=strtol(strb,&endptr,10);
+ if( strb[0]=='\0' || (*endptr != '\0')){
+ printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);
+ fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);fflush(ficlog);
+ return 1;
+ }
+ }
+ if(lval <-1 || lval >1){
+ printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
+ Should be a value of %d(nth) covariate (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 example, for multinomial values like 1, 2 and 3,\n \
+ build V1=0 V2=0 for the reference value (1),\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 \
+ output of IMaCh is often meaningless.\n \
+ Exiting.\n",lval,linei, i,line,j);
+ fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
+ Should be a value of %d(nth) covariate (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 example, for multinomial values like 1, 2 and 3,\n \
+ build V1=0 V2=0 for the reference value (1),\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 \
+ output of IMaCh is often meaningless.\n \
+ Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
+ return 1;
+ }
+ covar[j][i]=(double)(lval);
+ strcpy(line,stra);
+ }
+ lstra=strlen(stra);
+
+ if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
+ stratrunc = &(stra[lstra-9]);
+ num[i]=atol(stratrunc);
+ }
+ else
+ num[i]=atol(stra);
+ /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
+ printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
+
+ i=i+1;
+ } /* End loop reading data */
+
+ *imax=i-1; /* Number of individuals */
+ fclose(fic);
+
+ return (0);
+ endread:
+ printf("Exiting readdata: ");
+ fclose(fic);
+ return (1);
+
+
+
+}
+
+int decodemodel ( char model[], int lastobs)
+{
+ int i, j, k;
+ int i1, j1, k1, k2;
+ char modelsav[80];
+ char stra[80], strb[80], strc[80], strd[80],stre[80];
+
+ if (strlen(model) >1){ /* If there is at least 1 covariate */
+ j=0, j1=0, k1=1, k2=1;
+ j=nbocc(model,'+'); /* j=Number of '+' */
+ j1=nbocc(model,'*'); /* j1=Number of '*' */
+ cptcovn=j+1; /* Number of covariates V1+V2*age+V3 =>(2 plus signs) + 1=3
+ but the covariates which are product must be computed and stored. */
+ cptcovprod=j1; /*Number of products V1*V2 +v3*age = 2 */
+
+ strcpy(modelsav,model);
+ if (strstr(model,"AGE") !=0){
+ printf("Error. AGE must be in lower case 'age' model=%s ",model);
+ fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
+ return 1;
+ }
+
+ /* This loop fills the array Tvar from the string 'model'.*/
+ /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
+ /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
+ /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
+ /* k=3 V4 Tvar[k=3]= 4 (from V4) */
+ /* k=2 V1 Tvar[k=2]= 1 (from V1) */
+ /* k=1 Tvar[1]=2 (from V2) */
+ /* k=5 Tvar[5] */
+ /* for (k=1; k<=cptcovn;k++) { */
+ /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
+ /* } */
+ /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
+ for(k=cptcovn; k>=1;k--){
+ cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
+ modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4
+ */
+ if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+ /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+ /*scanf("%d",i);*/
+ if (strchr(strb,'*')) { /* Model includes a product V2+V1+V4+V3*age strb=V3*age */
+ cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn: strb=V3*age strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
+ if (strcmp(strc,"age")==0) { /* Vn*age */
+ cptcovprod--;
+ cutv(strb,stre,strd,'V'); /* stre="V3" */
+ Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=2 ; V1+V2*age Tvar[2]=2 */
+ cptcovage++; /* Sums the number of covariates which include age as a product */
+ Tage[cptcovage]=k; /* Tage[1] = 4 */
+ /*printf("stre=%s ", stre);*/
+ } else if (strcmp(strd,"age")==0) { /* or age*Vn */
+ cptcovprod--;
+ cutv(strb,stre,strc,'V');
+ Tvar[k]=atoi(stre);
+ cptcovage++;
+ Tage[cptcovage]=k;
+ } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
+ /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
+ cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
+ Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
+ because this model-covariate is a construction we invent a new column
+ ncovcol + k1
+ If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
+ Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
+ cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
+ Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
+ Tvard[k1][1]=atoi(strc); /* m 1 for V1*/
+ Tvard[k1][2]=atoi(stre); /* n 4 for V4*/
+ Tvar[cptcovn+k2]=Tvard[k1][1]; /* Tvar[(cptcovn=4+k2=1)=5]= 1 (V1) */
+ Tvar[cptcovn+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovn=4+(k2=1)+1)=6]= 4 (V4) */
+ for (i=1; i<=lastobs;i++){
+ /* Computes the new covariate which is a product of
+ covar[n][i]* covar[m][i] and stores it at ncovol+k1 */
+ covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
+ }
+ k1++;
+ k2=k2+2;
+ } /* End age is not in the model */
+ } /* End if model includes a product */
+ else { /* no more sum */
+ /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+ /* scanf("%d",i);*/
+ cutv(strd,strc,strb,'V');
+ Tvar[k]=atoi(strc);
+ }
+ strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
+ /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+ scanf("%d",i);*/
+ } /* end of loop + */
+ } /* end model */
+
+ /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
+ If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
+
+ /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
+ printf("cptcovprod=%d ", cptcovprod);
+ fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+
+ scanf("%d ",i);*/
+
+
+ return (0); /* with covar[new additional covariate if product] and Tage if age */
+ endread:
+ printf("Exiting decodemodel: ");
+ return (1);
+}
+
+calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
+{
+ int i, m;
+
+ for (i=1; i<=imx; i++) {
+ for(m=2; (m<= maxwav); m++) {
+ if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
+ anint[m][i]=9999;
+ s[m][i]=-1;
+ }
+ if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
+ *nberr++;
+ printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
+ fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
+ s[m][i]=-1;
+ }
+ if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
+ *nberr++;
+ printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
+ fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
+ s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
+ }
+ }
+ }
+
+ for (i=1; i<=imx; i++) {
+ agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
+ for(m=firstpass; (m<= lastpass); m++){
+ if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
+ if (s[m][i] >= nlstate+1) {
+ if(agedc[i]>0)
+ if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
+ agev[m][i]=agedc[i];
+ /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
+ else {
+ if ((int)andc[i]!=9999){
+ nbwarn++;
+ printf("Warning negative age at death: %ld line:%d\n",num[i],i);
+ fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
+ agev[m][i]=-1;
+ }
+ }
+ }
+ else if(s[m][i] !=9){ /* Standard case, age in fractional
+ years but with the precision of a month */
+ agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
+ if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
+ agev[m][i]=1;
+ else if(agev[m][i] < *agemin){
+ *agemin=agev[m][i];
+ printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
+ }
+ else if(agev[m][i] >*agemax){
+ *agemax=agev[m][i];
+ /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
+ }
+ /*agev[m][i]=anint[m][i]-annais[i];*/
+ /* agev[m][i] = age[i]+2*m;*/
+ }
+ else { /* =9 */
+ agev[m][i]=1;
+ s[m][i]=-1;
+ }
+ }
+ else /*= 0 Unknown */
+ agev[m][i]=1;
+ }
+
+ }
+ for (i=1; i<=imx; i++) {
+ for(m=firstpass; (m<=lastpass); m++){
+ if (s[m][i] > (nlstate+ndeath)) {
+ *nberr++;
+ printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
+ fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
+ return 1;
+ }
+ }
+ }
+
+ /*for (i=1; i<=imx; i++){
+ for (m=firstpass; (m<lastpass); m++){
+ printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
+}
+
+}*/
+
+ printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+ fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+
+ return (0);
+ endread:
+ printf("Exiting calandcheckages: ");
+ return (1);
+}
/***********************************************/
@@ -3999,16 +4947,26 @@ void printinggnuplotmort(char fileres[],
int main(int argc, char *argv[])
{
+#ifdef GSL
+ const gsl_multimin_fminimizer_type *T;
+ size_t iteri = 0, it;
+ int rval = GSL_CONTINUE;
+ int status = GSL_SUCCESS;
+ double ssval;
+#endif
int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
+ int linei, month, year,iout;
int jj, ll, li, lj, lk, imk;
int numlinepar=0; /* Current linenumber of parameter file */
int itimes;
int NDIM=2;
+ int vpopbased=0;
char ca[32], cb[32], cc[32];
/* FILE *fichtm; *//* Html File */
/* FILE *ficgp;*/ /*Gnuplot File */
+ struct stat info;
double agedeb, agefin,hf;
double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
@@ -4022,22 +4980,24 @@ int main(int argc, char *argv[])
char line[MAXLINE], linepar[MAXLINE];
char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
char pathr[MAXLINE], pathimach[MAXLINE];
+ char **bp, *tok, *val; /* pathtot */
int firstobs=1, lastobs=10;
int sdeb, sfin; /* Status at beginning and end */
int c, h , cpt,l;
int ju,jl, mi;
- int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
- int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
+ int i1,j1, jk,aa,bb, stepsize, ij;
+ int jnais,jdc,jint4,jint1,jint2,jint3,*tab;
int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
int mobilav=0,popforecast=0;
int hstepm, nhstepm;
+ int agemortsup;
+ float sumlpop=0.;
double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
double bage, fage, age, agelim, agebase;
double ftolpl=FTOL;
double **prlim;
- double *severity;
double ***param; /* Matrix of parameters */
double *p;
double **matcov; /* Matrix of covariance */
@@ -4054,10 +5014,8 @@ int main(int argc, char *argv[])
char z[1]="c", occ;
- char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
- char strstart[80], *strt, strtend[80];
- char *stratrunc;
- int lstra;
+ /*char *strt;*/
+ char strtend[80];
long total_usecs;
@@ -4097,7 +5055,17 @@ int main(int argc, char *argv[])
printf("\n%s\n%s",version,fullversion);
if(argc <=1){
printf("\nEnter the parameter file name: ");
- scanf("%s",pathtot);
+ fgets(pathr,FILENAMELENGTH,stdin);
+ i=strlen(pathr);
+ if(pathr[i-1]=='\n')
+ pathr[i-1]='\0';
+ for (tok = pathr; tok != NULL; ){
+ printf("Pathr |%s|\n",pathr);
+ while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
+ printf("val= |%s| pathr=%s\n",val,pathr);
+ strcpy (pathtot, val);
+ if(pathr[0] == '\0') break; /* Dirty */
+ }
}
else{
strcpy(pathtot,argv[1]);
@@ -4107,11 +5075,17 @@ int main(int argc, char *argv[])
printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
/* cutv(path,optionfile,pathtot,'\\');*/
+ /* Split argv[0], imach program to get pathimach */
+ printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+ printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
/* strcpy(pathimach,argv[0]); */
+ /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
split(pathtot,path,optionfile,optionfilext,optionfilefiname);
- printf("pathimach=%s, pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
- chdir(path);
+ printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+ chdir(path); /* Can be a relative path */
+ if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+ printf("Current directory %s!\n",pathcd);
strcpy(command,"mkdir ");
strcat(command,optionfilefiname);
if((outcmd=system(command)) != 0){
@@ -4203,13 +5177,24 @@ int main(int argc, char *argv[])
covar=matrix(0,NCOVMAX,1,n);
- cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
- if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
-
- ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
+ cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
+ /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
+ v1+v2*age+v2*v3 makes cptcovn = 3
+ */
+ if (strlen(model)>1)
+ cptcovn=nbocc(model,'+')+1;
+ /* ncovprod */
+ ncovmodel=2+cptcovn; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
- npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
-
+ nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
+ npar= nforce*ncovmodel; /* Number of parameters like aij*/
+ if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
+ printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
+ fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
+ fflush(stdout);
+ fclose (ficlog);
+ goto end;
+ }
delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
delti=delti3[1][1];
/*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
@@ -4220,6 +5205,7 @@ int main(int argc, char *argv[])
free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
fclose (ficparo);
fclose (ficlog);
+ goto end;
exit(0);
}
else if(mle==-3) {
@@ -4250,7 +5236,9 @@ int main(int argc, char *argv[])
j++;
fscanf(ficpar,"%1d%1d",&i1,&j1);
if ((i1 != i) && (j1 != j)){
- printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+ printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
+It might be a problem of design; if ncovcol and the model are correct\n \
+run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
exit(1);
}
fprintf(ficparo,"%1d%1d",i1,j1);
@@ -4277,7 +5265,6 @@ int main(int argc, char *argv[])
}
fflush(ficlog);
-
p=param[1][1];
/* Reads comments: lines beginning with '#' */
@@ -4333,6 +5320,9 @@ int main(int argc, char *argv[])
ungetc(c,ficpar);
matcov=matrix(1,npar,1,npar);
+ for(i=1; i <=npar; i++)
+ for(j=1; j <=npar; j++) matcov[i][j]=0.;
+
for(i=1; i <=npar; i++){
fscanf(ficpar,"%s",&str);
if(mle==1)
@@ -4376,15 +5366,8 @@ int main(int argc, char *argv[])
fprintf(ficres,"#%s\n",version);
} /* End of mle != -3 */
- /*-------- data file ----------*/
- if((fic=fopen(datafile,"r"))==NULL) {
- printf("Problem with datafile: %s\n", datafile);goto end;
- fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
- }
n= lastobs;
- severity = vector(1,maxwav);
- outcome=imatrix(1,maxwav+1,1,n);
num=lvector(1,n);
moisnais=vector(1,n);
annais=vector(1,n);
@@ -4396,246 +5379,63 @@ int main(int argc, char *argv[])
for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
mint=matrix(1,maxwav,1,n);
anint=matrix(1,maxwav,1,n);
- s=imatrix(1,maxwav+1,1,n);
+ s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
tab=ivector(1,NCOVMAX);
- ncodemax=ivector(1,8);
-
- i=1;
- while (fgets(line, MAXLINE, fic) != NULL) {
- if ((i >= firstobs) && (i <=lastobs)) {
- for(j=0; line[j] != '\n';j++){ /* Untabifies line */
- if(line[j] == '\t')
- line[j] = ' ';
- }
- for (j=maxwav;j>=1;j--){
- cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
- strcpy(line,stra);
- cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
- cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
- }
-
- cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
- cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
-
- cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
- cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
-
- cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
- for (j=ncovcol;j>=1;j--){
- cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
- }
- lstra=strlen(stra);
- if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
- stratrunc = &(stra[lstra-9]);
- num[i]=atol(stratrunc);
- }
- else
- num[i]=atol(stra);
-
- /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
- printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
+ ncodemax=ivector(1,8); /* hard coded ? */
- i=i+1;
- }
- }
- /* printf("ii=%d", ij);
- scanf("%d",i);*/
- imx=i-1; /* Number of individuals */
-
- /* for (i=1; i<=imx; i++){
- if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
- if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
- if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
- }*/
- /* for (i=1; i<=imx; i++){
- if (s[4][i]==9) s[4][i]=-1;
- printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
-
- for (i=1; i<=imx; i++)
-
- /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
- else weight[i]=1;*/
+ /* Reads data from file datafile */
+ if (readdata(datafile, firstobs, lastobs, &imx)==1)
+ goto end;
- /* Calculation of the number of parameter from char model*/
- Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
+ /* Calculation of the number of parameters from char model */
+ /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
+ k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
+ k=3 V4 Tvar[k=3]= 4 (from V4)
+ k=2 V1 Tvar[k=2]= 1 (from V1)
+ k=1 Tvar[1]=2 (from V2)
+ */
+ Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
+ /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
+ For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
+ Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
+ */
+ /* For model-covariate k tells which data-covariate to use but
+ because this model-covariate is a construction we invent a new column
+ ncovcol + k1
+ If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
+ Tvar[3=V1*V4]=4+1 etc */
Tprod=ivector(1,15);
+ /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
+ if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
+ */
Tvaraff=ivector(1,15);
- Tvard=imatrix(1,15,1,2);
- Tage=ivector(1,15);
-
- if (strlen(model) >1){ /* If there is at least 1 covariate */
- j=0, j1=0, k1=1, k2=1;
- j=nbocc(model,'+'); /* j=Number of '+' */
- j1=nbocc(model,'*'); /* j1=Number of '*' */
- cptcovn=j+1;
- cptcovprod=j1; /*Number of products */
-
- strcpy(modelsav,model);
- if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
- printf("Error. Non available option model=%s ",model);
- fprintf(ficlog,"Error. Non available option model=%s ",model);
- goto end;
- }
-
- /* This loop fills the array Tvar from the string 'model'.*/
-
- for(i=(j+1); i>=1;i--){
- cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
- if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
- /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
- /*scanf("%d",i);*/
- if (strchr(strb,'*')) { /* Model includes a product */
- cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
- if (strcmp(strc,"age")==0) { /* Vn*age */
- cptcovprod--;
- cutv(strb,stre,strd,'V');
- Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
- cptcovage++;
- Tage[cptcovage]=i;
- /*printf("stre=%s ", stre);*/
- }
- else if (strcmp(strd,"age")==0) { /* or age*Vn */
- cptcovprod--;
- cutv(strb,stre,strc,'V');
- Tvar[i]=atoi(stre);
- cptcovage++;
- Tage[cptcovage]=i;
- }
- else { /* Age is not in the model */
- cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
- Tvar[i]=ncovcol+k1;
- cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
- Tprod[k1]=i;
- Tvard[k1][1]=atoi(strc); /* m*/
- Tvard[k1][2]=atoi(stre); /* n */
- Tvar[cptcovn+k2]=Tvard[k1][1];
- Tvar[cptcovn+k2+1]=Tvard[k1][2];
- for (k=1; k<=lastobs;k++)
- covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
- k1++;
- k2=k2+2;
- }
- }
- else { /* no more sum */
- /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
- /* scanf("%d",i);*/
- cutv(strd,strc,strb,'V');
- Tvar[i]=atoi(strc);
- }
- strcpy(modelsav,stra);
- /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
- scanf("%d",i);*/
- } /* end of loop + */
- } /* end model */
-
- /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
- If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
-
- /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
- printf("cptcovprod=%d ", cptcovprod);
- fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+ Tvard=imatrix(1,15,1,2); /* For V3*V2 Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
+ Tage=ivector(1,15); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
+ 4 covariates (3 plus signs)
+ Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
+ */
- scanf("%d ",i);
- fclose(fic);*/
+ if(decodemodel(model, lastobs) == 1)
+ goto end;
+ if((double)(lastobs-imx)/(double)imx > 1.10){
+ nbwarn++;
+ printf("Warning: The value of parameter lastobs=%d is big compared to the \n effective number of cases imx=%d, please adjust, \n otherwise you are allocating more memory than necessary.\n",lastobs, imx);
+ fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n effective number of cases imx=%d, please adjust, \n otherwise you are allocating more memory than necessary.\n",lastobs, imx);
+ }
/* if(mle==1){*/
- if (weightopt != 1) { /* Maximisation without weights*/
- for(i=1;i<=n;i++) weight[i]=1.0;
+ if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
+ for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
}
+
/*-calculation of age at interview from date of interview and age at death -*/
agev=matrix(1,maxwav,1,imx);
- for (i=1; i<=imx; i++) {
- for(m=2; (m<= maxwav); m++) {
- if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
- anint[m][i]=9999;
- s[m][i]=-1;
- }
- if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
- nberr++;
- printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
- fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
- s[m][i]=-1;
- }
- if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
- nberr++;
- printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
- fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
- s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
- }
- }
- }
-
- for (i=1; i<=imx; i++) {
- agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
- for(m=firstpass; (m<= lastpass); m++){
- if(s[m][i] >0){
- if (s[m][i] >= nlstate+1) {
- if(agedc[i]>0)
- if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
- agev[m][i]=agedc[i];
- /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
- else {
- if ((int)andc[i]!=9999){
- nbwarn++;
- printf("Warning negative age at death: %ld line:%d\n",num[i],i);
- fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
- agev[m][i]=-1;
- }
- }
- }
- else if(s[m][i] !=9){ /* Standard case, age in fractional
- years but with the precision of a
- month */
- agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
- if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
- agev[m][i]=1;
- else if(agev[m][i] <agemin){
- agemin=agev[m][i];
- /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
- }
- else if(agev[m][i] >agemax){
- agemax=agev[m][i];
- /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
- }
- /*agev[m][i]=anint[m][i]-annais[i];*/
- /* agev[m][i] = age[i]+2*m;*/
- }
- else { /* =9 */
- agev[m][i]=1;
- s[m][i]=-1;
- }
- }
- else /*= 0 Unknown */
- agev[m][i]=1;
- }
-
- }
- for (i=1; i<=imx; i++) {
- for(m=firstpass; (m<=lastpass); m++){
- if (s[m][i] > (nlstate+ndeath)) {
- nberr++;
- printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
- fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
- goto end;
- }
- }
- }
-
- /*for (i=1; i<=imx; i++){
- for (m=firstpass; (m<lastpass); m++){
- printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
-}
-
-}*/
-
+ if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
+ goto end;
- printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
- fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
agegomp=(int)agemin;
- free_vector(severity,1,maxwav);
- free_imatrix(outcome,1,maxwav+1,1,n);
free_vector(moisnais,1,n);
free_vector(annais,1,n);
/* free_matrix(mint,1,maxwav,1,n);
@@ -4654,7 +5454,6 @@ int main(int argc, char *argv[])
/* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
- Tcode=ivector(1,100);
nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
ncodemax[1]=1;
if (cptcovn > 0) tricode(Tvar,nbcode,imx);
@@ -4664,13 +5463,17 @@ int main(int argc, char *argv[])
h=0;
m=pow(2,cptcoveff);
- for(k=1;k<=cptcoveff; k++){
- for(i=1; i <=(m/pow(2,k));i++){
- for(j=1; j <= ncodemax[k]; j++){
- for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
+ for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
+ for(i=1; i <=(m/pow(2,k));i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */
+ for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate */
+ for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
h++;
- if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
- /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
+ if (h>m) {
+ h=1;
+ codtab[h][k]=j;
+ codtab[h][Tvar[k]]=j;
+ }
+ printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
}
}
}
@@ -4679,7 +5482,7 @@ int main(int argc, char *argv[])
codtab[1][2]=1;codtab[2][2]=2; */
/* for(i=1; i <=m ;i++){
for(k=1; k <=cptcovn; k++){
- printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
+ printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
}
printf("\n");
}
@@ -4707,7 +5510,8 @@ int main(int argc, char *argv[])
strcat(optionfilehtm,"-mort");
strcat(optionfilehtm,".htm");
if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
- printf("Problem with %s \n",optionfilehtm), exit(0);
+ printf("Problem with %s \n",optionfilehtm);
+ exit(0);
}
strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
@@ -4716,23 +5520,25 @@ int main(int argc, char *argv[])
printf("Problem with %s \n",optionfilehtmcov), exit(0);
}
else{
- fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s\n %s
%s \
+ fprintf(fichtmcov,"\nIMaCh Cov %s\n %s
%s \
\n\
Title=%s
Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s
\n",\
- fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+ optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
}
- fprintf(fichtm,"\nIMaCh %s\n %s
%s \
+ fprintf(fichtm,"\nIMaCh %s\n %s
%s \
\n\
Title=%s
Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s
\n\
\n\
\
Parameter files
\n\
+ - Parameter file: %s.%s
\n\
- Copy of the parameter file: o%s
\n\
- Log file of the run: %s
\n\
- Gnuplot file name: %s
\n\
- Date and time at start: %s
\n",\
- fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+ optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+ optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
fileres,fileres,\
filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
fflush(fichtm);
@@ -4743,7 +5549,7 @@ Title=%s
Datafile=%s Firstpass=%d La
/* Calculates basic frequencies. Computes observed prevalence at single age
and prints on file fileres'p'. */
- freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
+ freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
fprintf(fichtm,"\n");
fprintf(fichtm,"
Total number of observations=%d
\n\
@@ -4762,8 +5568,10 @@ Interval (in months) between two waves:
p=param[1][1]; /* *(*(*(param +1)+1)+0) */
globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
+
if (mle==-3){
- ximort=matrix(1,NDIM,1,NDIM);
+ ximort=matrix(1,NDIM,1,NDIM);
+/* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
cens=ivector(1,n);
ageexmed=vector(1,n);
agecens=vector(1,n);
@@ -4771,9 +5579,9 @@ Interval (in months) between two waves:
for (i=1; i<=imx; i++){
dcwave[i]=-1;
- for (j=1; j<=lastpass; j++)
- if (s[j][i]>nlstate) {
- dcwave[i]=j;
+ for (m=firstpass; m<=lastpass; m++)
+ if (s[m][i]>nlstate) {
+ dcwave[i]=m;
/* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
break;
}
@@ -4782,12 +5590,16 @@ Interval (in months) between two waves:
for (i=1; i<=imx; i++) {
if (wav[i]>0){
ageexmed[i]=agev[mw[1][i]][i];
- j=wav[i];agecens[i]=1.;
- if (ageexmed[i]>1 & wav[i]>0) agecens[i]=agev[mw[j][i]][i];
- cens[i]=1;
-
- if (ageexmed[i]<1) cens[i]=-1;
- if (agedc[i]< AGESUP & agedc[i]>1 & dcwave[i]>firstpass & dcwave[i]<=lastpass) cens[i]=0 ;
+ j=wav[i];
+ agecens[i]=1.;
+
+ if (ageexmed[i]> 1 && wav[i] > 0){
+ agecens[i]=agev[mw[j][i]][i];
+ cens[i]= 1;
+ }else if (ageexmed[i]< 1)
+ cens[i]= -1;
+ if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
+ cens[i]=0 ;
}
else cens[i]=-1;
}
@@ -4796,29 +5608,114 @@ Interval (in months) between two waves:
for (j=1;j<=NDIM;j++)
ximort[i][j]=(i == j ? 1.0 : 0.0);
}
-
- p[1]=0.1; p[2]=0.1;
+
+ p[1]=0.0268; p[NDIM]=0.083;
/*printf("%lf %lf", p[1], p[2]);*/
- printf("Powell\n"); fprintf(ficlog,"Powell\n");
- strcpy(filerespow,"pow-mort");
- strcat(filerespow,fileres);
- if((ficrespow=fopen(filerespow,"w"))==NULL) {
- printf("Problem with resultfile: %s\n", filerespow);
- fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
- }
- fprintf(ficrespow,"# Powell\n# iter -2*LL");
- /* for (i=1;i<=nlstate;i++)
- for(j=1;j<=nlstate+ndeath;j++)
- if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
- */
- fprintf(ficrespow,"\n");
+#ifdef GSL
+ printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
+#elsedef
+ printf("Powell\n"); fprintf(ficlog,"Powell\n");
+#endif
+ strcpy(filerespow,"pow-mort");
+ strcat(filerespow,fileres);
+ if((ficrespow=fopen(filerespow,"w"))==NULL) {
+ printf("Problem with resultfile: %s\n", filerespow);
+ fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+ }
+#ifdef GSL
+ fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
+#elsedef
+ fprintf(ficrespow,"# Powell\n# iter -2*LL");
+#endif
+ /* for (i=1;i<=nlstate;i++)
+ for(j=1;j<=nlstate+ndeath;j++)
+ if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+ */
+ fprintf(ficrespow,"\n");
+#ifdef GSL
+ /* gsl starts here */
+ T = gsl_multimin_fminimizer_nmsimplex;
+ gsl_multimin_fminimizer *sfm = NULL;
+ gsl_vector *ss, *x;
+ gsl_multimin_function minex_func;
+
+ /* Initial vertex size vector */
+ ss = gsl_vector_alloc (NDIM);
+
+ if (ss == NULL){
+ GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
+ }
+ /* Set all step sizes to 1 */
+ gsl_vector_set_all (ss, 0.001);
+
+ /* Starting point */
+
+ x = gsl_vector_alloc (NDIM);
+
+ if (x == NULL){
+ gsl_vector_free(ss);
+ GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
+ }
+
+ /* Initialize method and iterate */
+ /* p[1]=0.0268; p[NDIM]=0.083; */
+/* gsl_vector_set(x, 0, 0.0268); */
+/* gsl_vector_set(x, 1, 0.083); */
+ gsl_vector_set(x, 0, p[1]);
+ gsl_vector_set(x, 1, p[2]);
+
+ minex_func.f = &gompertz_f;
+ minex_func.n = NDIM;
+ minex_func.params = (void *)&p; /* ??? */
+
+ sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
+ gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
+
+ printf("Iterations beginning .....\n\n");
+ printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
- powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+ iteri=0;
+ while (rval == GSL_CONTINUE){
+ iteri++;
+ status = gsl_multimin_fminimizer_iterate(sfm);
+
+ if (status) printf("error: %s\n", gsl_strerror (status));
+ fflush(0);
+
+ if (status)
+ break;
+
+ rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
+ ssval = gsl_multimin_fminimizer_size (sfm);
+
+ if (rval == GSL_SUCCESS)
+ printf ("converged to a local maximum at\n");
+
+ printf("%5d ", iteri);
+ for (it = 0; it < NDIM; it++){
+ printf ("%10.5f ", gsl_vector_get (sfm->x, it));
+ }
+ printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
+ }
+
+ printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
+
+ gsl_vector_free(x); /* initial values */
+ gsl_vector_free(ss); /* inital step size */
+ for (it=0; itx,it);
+ fprintf(ficrespow," %.12lf", p[it]);
+ }
+ gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
+#endif
+#ifdef POWELL
+ powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+#endif
fclose(ficrespow);
- hesscov(matcov, p, NDIM,delti, 1e-4, gompertz);
+ hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
for(i=1; i <=NDIM; i++)
for(j=i+1;j<=NDIM;j++)
@@ -4835,16 +5732,57 @@ Interval (in months) between two waves:
printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
for (i=1;i<=NDIM;i++)
printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
- replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
+
+ lsurv=vector(1,AGESUP);
+ lpop=vector(1,AGESUP);
+ tpop=vector(1,AGESUP);
+ lsurv[agegomp]=100000;
+
+ for (k=agegomp;k<=AGESUP;k++) {
+ agemortsup=k;
+ if (p[1]*exp(p[2]*(k-agegomp))>1) break;
+ }
+
+ for (k=agegomp;k=1 */
+ else{ /* For mle >=1 */
+ globpr=0;/* debug */
likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
for (k=1; k<=npar;k++)
@@ -4874,9 +5812,9 @@ Interval (in months) between two waves:
fprintf(ficlog,"%d%d ",i,k);
fprintf(ficres,"%1d%1d ",i,k);
for(j=1; j <=ncovmodel; j++){
- printf("%f ",p[jk]);
- fprintf(ficlog,"%f ",p[jk]);
- fprintf(ficres,"%f ",p[jk]);
+ printf("%lf ",p[jk]);
+ fprintf(ficlog,"%lf ",p[jk]);
+ fprintf(ficres,"%lf ",p[jk]);
jk++;
}
printf("\n");
@@ -5068,7 +6006,7 @@ Interval (in months) between two waves:
/* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
/*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
- replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
+ replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
@@ -5090,17 +6028,18 @@ Interval (in months) between two waves:
fclose(ficres);
- /*--------------- Prevalence limit (stable prevalence) --------------*/
+ /*--------------- Prevalence limit (period or stable prevalence) --------------*/
strcpy(filerespl,"pl");
strcat(filerespl,fileres);
if((ficrespl=fopen(filerespl,"w"))==NULL) {
- printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
- fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
+ printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+ fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
}
- printf("Computing stable prevalence: result on file '%s' \n", filerespl);
- fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
- fprintf(ficrespl,"#Stable prevalence \n");
+ printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+ fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+ pstamp(ficrespl);
+ fprintf(ficrespl,"# Period (stable) prevalence \n");
fprintf(ficrespl,"#Age ");
for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
fprintf(ficrespl,"\n");
@@ -5116,7 +6055,8 @@ Interval (in months) between two waves:
for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
k=k+1;
- /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
+ /* to clean */
+ printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,codtab[cptcod][cptcov],nbcode);
fprintf(ficrespl,"\n#******");
printf("\n#******");
fprintf(ficlog,"\n#******");
@@ -5160,7 +6100,7 @@ Interval (in months) between two waves:
hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
/* hstepm=1; aff par mois*/
-
+ pstamp(ficrespij);
fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
@@ -5197,7 +6137,7 @@ Interval (in months) between two waves:
}
}
- varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
+ varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
fclose(ficrespij);
@@ -5222,18 +6162,24 @@ Interval (in months) between two waves:
}
- /*---------- Health expectancies and variances ------------*/
+ /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
- strcpy(filerest,"t");
- strcat(filerest,fileres);
- if((ficrest=fopen(filerest,"w"))==NULL) {
- printf("Problem with total LE resultfile: %s\n", filerest);goto end;
- fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+ prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+ /* printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d, mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
+ ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
+ */
+
+ if (mobilav!=0) {
+ mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+ fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+ printf(" Error in movingaverage mobilav=%d\n",mobilav);
+ }
}
- printf("Computing Total LEs with variances: file '%s' \n", filerest);
- fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
+ /*---------- Health expectancies, no variances ------------*/
+
strcpy(filerese,"e");
strcat(filerese,fileres);
if((ficreseij=fopen(filerese,"w"))==NULL) {
@@ -5242,6 +6188,55 @@ Interval (in months) between two waves:
}
printf("Computing Health Expectancies: result on file '%s' \n", filerese);
fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+ for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+ for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+ k=k+1;
+ fprintf(ficreseij,"\n#****** ");
+ for(j=1;j<=cptcoveff;j++) {
+ fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+ }
+ fprintf(ficreseij,"******\n");
+
+ eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+ oldm=oldms;savm=savms;
+ evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+
+ free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+ }
+ }
+ fclose(ficreseij);
+
+
+ /*---------- Health expectancies and variances ------------*/
+
+
+ strcpy(filerest,"t");
+ strcat(filerest,fileres);
+ if((ficrest=fopen(filerest,"w"))==NULL) {
+ printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+ fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+ }
+ printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+ fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+
+
+ strcpy(fileresstde,"stde");
+ strcat(fileresstde,fileres);
+ if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
+ printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+ fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+ }
+ printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+ fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+
+ strcpy(filerescve,"cve");
+ strcat(filerescve,fileres);
+ if((ficrescveij=fopen(filerescve,"w"))==NULL) {
+ printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+ fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+ }
+ printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+ fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
strcpy(fileresv,"v");
strcat(fileresv,fileres);
@@ -5252,20 +6247,6 @@ Interval (in months) between two waves:
printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
- /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
- prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
- /* printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d, mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
- ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
- */
-
- if (mobilav!=0) {
- mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
- if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
- fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
- printf(" Error in movingaverage mobilav=%d\n",mobilav);
- }
- }
-
for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
k=k+1;
@@ -5274,10 +6255,14 @@ Interval (in months) between two waves:
fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
fprintf(ficrest,"******\n");
- fprintf(ficreseij,"\n#****** ");
- for(j=1;j<=cptcoveff;j++)
- fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- fprintf(ficreseij,"******\n");
+ fprintf(ficresstdeij,"\n#****** ");
+ fprintf(ficrescveij,"\n#****** ");
+ for(j=1;j<=cptcoveff;j++) {
+ fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+ fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+ }
+ fprintf(ficresstdeij,"******\n");
+ fprintf(ficrescveij,"******\n");
fprintf(ficresvij,"\n#****** ");
for(j=1;j<=cptcoveff;j++)
@@ -5286,50 +6271,52 @@ Interval (in months) between two waves:
eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
oldm=oldms;savm=savms;
- evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
+ cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
- oldm=oldms;savm=savms;
- varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
- if(popbased==1){
- varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
- }
-
-
- fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
- for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
- fprintf(ficrest,"\n");
+ pstamp(ficrest);
+ for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
+ oldm=oldms;savm=savms;
+ varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are ");
+ if(vpopbased==1)
+ fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
+ else
+ fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
+ fprintf(ficrest,"# Age e.. (std) ");
+ for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+ fprintf(ficrest,"\n");
- epj=vector(1,nlstate+1);
- for(age=bage; age <=fage ;age++){
- prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
- if (popbased==1) {
- if(mobilav ==0){
- for(i=1; i<=nlstate;i++)
- prlim[i][i]=probs[(int)age][i][k];
- }else{ /* mobilav */
- for(i=1; i<=nlstate;i++)
- prlim[i][i]=mobaverage[(int)age][i][k];
+ epj=vector(1,nlstate+1);
+ for(age=bage; age <=fage ;age++){
+ prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+ if (vpopbased==1) {
+ if(mobilav ==0){
+ for(i=1; i<=nlstate;i++)
+ prlim[i][i]=probs[(int)age][i][k];
+ }else{ /* mobilav */
+ for(i=1; i<=nlstate;i++)
+ prlim[i][i]=mobaverage[(int)age][i][k];
+ }
}
- }
- fprintf(ficrest," %4.0f",age);
- for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
- for(i=1, epj[j]=0.;i <=nlstate;i++) {
- epj[j] += prlim[i][i]*eij[i][j][(int)age];
- /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+ fprintf(ficrest," %4.0f",age);
+ for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+ for(i=1, epj[j]=0.;i <=nlstate;i++) {
+ epj[j] += prlim[i][i]*eij[i][j][(int)age];
+ /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+ }
+ epj[nlstate+1] +=epj[j];
}
- epj[nlstate+1] +=epj[j];
- }
- for(i=1, vepp=0.;i <=nlstate;i++)
- for(j=1;j <=nlstate;j++)
- vepp += vareij[i][j][(int)age];
- fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
- for(j=1;j <=nlstate;j++){
- fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+ for(i=1, vepp=0.;i <=nlstate;i++)
+ for(j=1;j <=nlstate;j++)
+ vepp += vareij[i][j][(int)age];
+ fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+ for(j=1;j <=nlstate;j++){
+ fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+ }
+ fprintf(ficrest,"\n");
}
- fprintf(ficrest,"\n");
}
free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
@@ -5343,20 +6330,21 @@ Interval (in months) between two waves:
free_matrix(mint,1,maxwav,1,n);
free_ivector(cod,1,n);
free_ivector(tab,1,NCOVMAX);
- fclose(ficreseij);
+ fclose(ficresstdeij);
+ fclose(ficrescveij);
fclose(ficresvij);
fclose(ficrest);
fclose(ficpar);
- /*------- Variance of stable prevalence------*/
+ /*------- Variance of period (stable) prevalence------*/
strcpy(fileresvpl,"vpl");
strcat(fileresvpl,fileres);
if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
- printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
+ printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
exit(0);
}
- printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
+ printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
@@ -5368,7 +6356,7 @@ Interval (in months) between two waves:
varpl=matrix(1,nlstate,(int) bage, (int) fage);
oldm=oldms;savm=savms;
- varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
+ varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
}
}
@@ -5380,11 +6368,12 @@ Interval (in months) between two waves:
free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
} /* mle==-3 arrives here for freeing */
+ endfree:
+ free_matrix(prlim,1,nlstate,1,nlstate);
free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
-
free_matrix(covar,0,NCOVMAX,1,n);
free_matrix(matcov,1,npar,1,npar);
/*free_vector(delti,1,npar);*/
@@ -5397,9 +6386,9 @@ Interval (in months) between two waves:
free_ivector(Tprod,1,15);
free_ivector(Tvaraff,1,15);
free_ivector(Tage,1,15);
- free_ivector(Tcode,1,100);
-
+ free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+ free_imatrix(codtab,1,100,1,10);
fflush(fichtm);
fflush(ficgp);
@@ -5417,7 +6406,7 @@ Interval (in months) between two waves:
tm = *localtime(&end_time.tv_sec);
tmg = *gmtime(&end_time.tv_sec);
strcpy(strtend,asctime(&tm));
- printf("Local time at start %s\nLocaltime at end %s",strstart, strtend);
+ printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
@@ -5426,23 +6415,46 @@ Interval (in months) between two waves:
fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
/* printf("Total time was %d uSec.\n", total_usecs);*/
/* if(fileappend(fichtm,optionfilehtm)){ */
- fprintf(fichtm,"
Local time at start %s
Local time at end %s
",strstart, strtend);
+ fprintf(fichtm,"
Local time at start %s
Local time at end %s
\n",strstart, strtend);
fclose(fichtm);
+ fprintf(fichtmcov,"
Local time at start %s
Local time at end %s
\n",strstart, strtend);
fclose(fichtmcov);
fclose(ficgp);
fclose(ficlog);
/*------ End -----------*/
- chdir(path);
- strcpy(plotcmd,"\"");
- strcat(plotcmd,pathimach);
- strcat(plotcmd,GNUPLOTPROGRAM);
- strcat(plotcmd,"\"");
- strcat(plotcmd," ");
- strcat(plotcmd,optionfilegnuplot);
- printf("Starting graphs with: %s",plotcmd);fflush(stdout);
+
+ printf("Before Current directory %s!\n",pathcd);
+ if(chdir(pathcd) != 0)
+ printf("Can't move to directory %s!\n",path);
+ if(getcwd(pathcd,MAXLINE) > 0)
+ printf("Current directory %s!\n",pathcd);
+ /*strcat(plotcmd,CHARSEPARATOR);*/
+ sprintf(plotcmd,"gnuplot");
+#ifndef UNIX
+ sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
+#endif
+ if(!stat(plotcmd,&info)){
+ printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+ if(!stat(getenv("GNUPLOTBIN"),&info)){
+ printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+ }else
+ strcpy(pplotcmd,plotcmd);
+#ifdef UNIX
+ strcpy(plotcmd,GNUPLOTPROGRAM);
+ if(!stat(plotcmd,&info)){
+ printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+ }else
+ strcpy(pplotcmd,plotcmd);
+#endif
+ }else
+ strcpy(pplotcmd,plotcmd);
+
+ sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
+ printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
+
if((outcmd=system(plotcmd)) != 0){
- printf(" Problem with gnuplot\n");
+ printf("\n Problem with gnuplot\n");
}
printf(" Wait...");
while (z[0] != 'q') {