--- imach/src/imach.c 2006/03/14 18:20:07 1.118
+++ imach/src/imach.c 2010/04/30 18:19:40 1.138
@@ -1,6 +1,106 @@
-/* $Id: imach.c,v 1.118 2006/03/14 18:20:07 brouard 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 .
@@ -93,7 +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
@@ -226,8 +326,8 @@
Also this programme outputs the covariance matrix of the parameters but also
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
@@ -288,6 +388,11 @@ extern int errno;
#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) */
@@ -300,13 +405,13 @@ extern int errno;
#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
@@ -322,41 +427,42 @@ extern int errno;
#define ODIRSEPARATOR '/'
#endif
-/* $Id: imach.c,v 1.118 2006/03/14 18:20:07 brouard Exp $ */
+/* $Id: imach.c,v 1.138 2010/04/30 18:19:40 brouard Exp $ */
/* $State: Exp $ */
-char version[]="Imach version 0.98d, March 2006, INED-EUROREVES-Institut de longevite ";
-char fullversion[]="$Revision: 1.118 $ $Date: 2006/03/14 18:20:07 $";
+char version[]="Imach version 0.98m, April 2010, INED-EUROREVES-Institut de longevite ";
+char fullversion[]="$Revision: 1.138 $ $Date: 2010/04/30 18:19:40 $";
char strstart[80];
char optionfilext[10], optionfilefiname[FILENAMELENGTH];
-int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
-int nvar;
-int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
+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 ijmin, ijmax; /* Individuals having jmin and jmax */
-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, *ficresp, *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 */
@@ -400,6 +506,7 @@ char strcurr[80], strfor[80];
char *endptr;
long lval;
+double dval;
#define NR_END 1
#define FREE_ARG char*
@@ -448,7 +555,7 @@ 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 */
@@ -521,6 +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;
@@ -533,27 +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 ********************/
@@ -965,9 +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]);
@@ -1099,7 +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 */
@@ -1114,21 +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.;
@@ -1155,37 +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++)
@@ -1250,7 +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 */
@@ -1266,7 +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++)
@@ -1283,10 +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;
}
@@ -1295,7 +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 */
@@ -1314,7 +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++){
@@ -1325,7 +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));
@@ -1382,23 +1560,23 @@ double func( double *x)
} else if (s2==-2) {
for (j=1,survp=0. ; j<=nlstate; j++)
- survp += out[s1][j];
- lli= survp;
- }
-
- else if (s2==-4) {
- for (j=3,survp=0. ; j<=nlstate; j++)
- survp += out[s1][j];
- lli= survp;
+ survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+ /*survp += out[s1][j]; */
+ lli= log(survp);
}
- else if (s2==-5) {
- for (j=1,survp=0. ; j<=2; j++)
- survp += out[s1][j];
- lli= 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 */
@@ -1549,7 +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;
@@ -1593,7 +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 */
@@ -1601,16 +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++){
@@ -1812,7 +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;
@@ -1833,7 +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
@@ -1859,7 +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);
@@ -1972,7 +2155,7 @@ void pstamp(FILE *fichier)
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;
@@ -2070,7 +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{
@@ -2141,7 +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;
@@ -2199,7 +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 */
@@ -2324,7 +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;
}
@@ -2356,69 +2540,79 @@ void concatwav(int wav[], int **dh, int
/*********** 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++) {
+ } /* 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];
+ 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 cij, int estepm,char strstart[] )
+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;
@@ -2465,33 +2659,41 @@ void evsij(char fileres[], double ***eij
hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
agelim=AGESUP;
- /* nhstepm age range expressed in number of stepm */
- nstepm=(int) rint((agelim-age)*YEARM/stepm);
+ /* 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 ++){ /* 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 */
-
- hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-
+ 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. */
-
- /* Computing Variances of health expectancies */
- /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
- decrease memory allocation */
- printf("%d|",(int)age);fflush(stdout);
- fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+
+ 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]);*/
+ /* 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]);*/
}
@@ -2505,21 +2707,22 @@ void evsij(char fileres[], double ***eij
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(char fileres[], 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[] )
+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[] )
{
/* 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 ***p3matp, ***p3matm, ***varhe;
double **dnewm,**doldm;
@@ -2593,7 +2796,7 @@ void cvevsij(char fileres[], double ***e
/* If stepm=6 months */
/* nhstepm age range expressed in number of stepm */
agelim=AGESUP;
- 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 */
@@ -2606,10 +2809,15 @@ void cvevsij(char fileres[], double ***e
gm=matrix(0,nhstepm,1,nlstate*nlstate);
for (age=bage; age<=fage; age ++){
-
- /* Computed by stepm unit matrices, product of hstepm matrices, stored
- in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
-
+ 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 */
+
hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
/* Computing Variances of health expectancies */
@@ -2660,6 +2868,7 @@ void cvevsij(char fileres[], double ***e
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++)
@@ -2787,7 +2996,7 @@ void varevsij(char optionfilefiname[], d
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 in the population i.e cross-sectionally\n in each health state (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");
@@ -2815,8 +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
@@ -2882,7 +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];
@@ -2992,9 +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); */
@@ -3171,7 +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);
@@ -3324,7 +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);
@@ -3355,6 +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 */
@@ -3442,10 +3657,12 @@ void printinghtml(char fileres[], char t
- Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
fprintf(fichtm,"\
- - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age: ei., eij (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>");
@@ -3505,11 +3722,11 @@ fprintf(fichtm," \n<ul><li><b>Graphs</b>
<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), eij are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences (i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
+ - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the 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,"\
- - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors: <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 period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
@@ -3542,7 +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 */
@@ -3554,8 +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); */
@@ -3581,7 +3801,7 @@ 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\"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 ++) {
@@ -4241,6 +4461,47 @@ double gompertz(double x[])
return -2*L*num/sump;
}
+#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 */
+
+ 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[],\
@@ -4288,116 +4549,508 @@ void printinggnuplotmort(char fileres[],
}
-
-
-
-
-/***********************************************/
-/**************** Main Program *****************/
-/***********************************************/
-
-int main(int argc, char *argv[])
+int readdata(char datafile[], int firstobs, int lastobs, int *imax)
{
- 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;
- char ca[32], cb[32], cc[32];
+ /*-------- data file ----------*/
+ FILE *fic;
char dummy[]=" ";
- /* 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;
-
- double fret;
- double **xi,tmp,delta;
-
- double dum; /* Dummy variable */
- double ***p3mat;
- double ***mobaverage;
- int *indx;
- 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 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 */
- double ***delti3; /* Scale */
- double *delti; /* Scale */
- double ***eij, ***vareij;
- double **varpl; /* Variances of prevalence limits by age */
- double *epj, vepp;
- double kk1, kk2;
- double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
- double **ximort;
- char *alph[]={"a","a","b","c","d","e"}, str[4];
- int *dcwave;
-
- char z[1]="c", occ;
-
- char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
- char *strt, strtend[80];
+ int i, j, n;
+ int linei, month, year,iout;
+ char line[MAXLINE], linetmp[MAXLINE];
+ char stra[80], strb[80];
char *stratrunc;
int lstra;
- long total_usecs;
-
-/* setlocale (LC_ALL, ""); */
-/* bindtextdomain (PACKAGE, LOCALEDIR); */
-/* textdomain (PACKAGE); */
-/* setlocale (LC_CTYPE, ""); */
-/* setlocale (LC_MESSAGES, ""); */
-
- /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
- (void) gettimeofday(&start_time,&tzp);
- curr_time=start_time;
- tm = *localtime(&start_time.tv_sec);
- tmg = *gmtime(&start_time.tv_sec);
- strcpy(strstart,asctime(&tm));
-/* printf("Localtime (at start)=%s",strstart); */
-/* tp.tv_sec = tp.tv_sec +86400; */
-/* tm = *localtime(&start_time.tv_sec); */
-/* tmg.tm_year=tmg.tm_year +dsign*dyear; */
-/* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
-/* tmg.tm_hour=tmg.tm_hour + 1; */
-/* tp.tv_sec = mktime(&tmg); */
-/* strt=asctime(&tmg); */
-/* printf("Time(after) =%s",strstart); */
-/* (void) time (&time_value);
-* printf("time=%d,t-=%d\n",time_value,time_value-86400);
-* tm = *localtime(&time_value);
-* strstart=asctime(&tm);
-* printf("tim_value=%d,asctime=%s\n",time_value,strstart);
-*/
+ 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;
+ }
- nberr=0; /* Number of errors and warnings */
- nbwarn=0;
- getcwd(pathcd, size);
+ 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);
+}
+
+
+/***********************************************/
+/**************** Main Program *****************/
+/***********************************************/
+
+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;
+
+ double fret;
+ double **xi,tmp,delta;
+
+ double dum; /* Dummy variable */
+ double ***p3mat;
+ double ***mobaverage;
+ int *indx;
+ 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, 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 ***param; /* Matrix of parameters */
+ double *p;
+ double **matcov; /* Matrix of covariance */
+ double ***delti3; /* Scale */
+ double *delti; /* Scale */
+ double ***eij, ***vareij;
+ double **varpl; /* Variances of prevalence limits by age */
+ double *epj, vepp;
+ double kk1, kk2;
+ double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+ double **ximort;
+ char *alph[]={"a","a","b","c","d","e"}, str[4];
+ int *dcwave;
+
+ char z[1]="c", occ;
+
+ /*char *strt;*/
+ char strtend[80];
+
+ long total_usecs;
+
+/* setlocale (LC_ALL, ""); */
+/* bindtextdomain (PACKAGE, LOCALEDIR); */
+/* textdomain (PACKAGE); */
+/* setlocale (LC_CTYPE, ""); */
+/* setlocale (LC_MESSAGES, ""); */
+
+ /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+ (void) gettimeofday(&start_time,&tzp);
+ curr_time=start_time;
+ tm = *localtime(&start_time.tv_sec);
+ tmg = *gmtime(&start_time.tv_sec);
+ strcpy(strstart,asctime(&tm));
+
+/* printf("Localtime (at start)=%s",strstart); */
+/* tp.tv_sec = tp.tv_sec +86400; */
+/* tm = *localtime(&start_time.tv_sec); */
+/* tmg.tm_year=tmg.tm_year +dsign*dyear; */
+/* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
+/* tmg.tm_hour=tmg.tm_hour + 1; */
+/* tp.tv_sec = mktime(&tmg); */
+/* strt=asctime(&tmg); */
+/* printf("Time(after) =%s",strstart); */
+/* (void) time (&time_value);
+* printf("time=%d,t-=%d\n",time_value,time_value-86400);
+* tm = *localtime(&time_value);
+* strstart=asctime(&tm);
+* printf("tim_value=%d,asctime=%s\n",time_value,strstart);
+*/
+
+ nberr=0; /* Number of errors and warnings */
+ nbwarn=0;
+ getcwd(pathcd, size);
printf("\n%s\n%s",version,fullversion);
if(argc <=1){
@@ -4411,7 +5064,7 @@ int main(int argc, char *argv[])
while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
printf("val= |%s| pathr=%s\n",val,pathr);
strcpy (pathtot, val);
- if(pathr[0] == '\0') break; /* Un peu sale */
+ if(pathr[0] == '\0') break; /* Dirty */
}
}
else{
@@ -4430,7 +5083,9 @@ int main(int argc, char *argv[])
/* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
split(pathtot,path,optionfile,optionfilext,optionfilefiname);
printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
- chdir(path);
+ 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){
@@ -4522,13 +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)*/
@@ -4539,6 +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) {
@@ -4569,7 +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);
@@ -4651,6 +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)
@@ -4680,352 +5352,90 @@ int main(int argc, char *argv[])
printf("\n");
fprintf(ficlog,"\n");
- fflush(ficlog);
-
- /*-------- Rewriting parameter file ----------*/
- strcpy(rfileres,"r"); /* "Rparameterfile */
- strcat(rfileres,optionfilefiname); /* Parameter file first name*/
- strcat(rfileres,"."); /* */
- strcat(rfileres,optionfilext); /* Other files have txt extension */
- if((ficres =fopen(rfileres,"w"))==NULL) {
- printf("Problem writing new parameter file: %s\n", fileres);goto end;
- fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
- }
- fprintf(ficres,"#%s\n",version);
- } /* End of mle != -3 */
-
- /*-------- data file ----------*/
- if((fic=fopen(datafile,"r"))==NULL) {
- printf("Problem while opening datafile: %s\n", datafile);goto end;
- fprintf(ficlog,"Problem while opening 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);
- moisdc=vector(1,n);
- andc=vector(1,n);
- agedc=vector(1,n);
- cod=ivector(1,n);
- weight=vector(1,n);
- 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);
- tab=ivector(1,NCOVMAX);
- ncodemax=ivector(1,8);
-
- 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;
- }
-
- for (j=maxwav;j>=1;j--){
- cutv(stra, strb,line,' ');
- 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 '%d' at line number %d %s 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);
- exit(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 %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);
- exit(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 %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
- exit(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 %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line,j);
- exit(1);
- }
- annais[i]=(double)(year);
- moisnais[i]=(double)(month);
- strcpy(line,stra);
-
- cutv(stra, strb,line,' ');
- errno=0;
- lval=strtol(strb,&endptr,10);
- if( strb[0]=='\0' || (*endptr != '\0')){
- printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight. Exiting.\n",lval, i,line,linei);
- exit(1);
- }
- weight[i]=(double)(lval);
- strcpy(line,stra);
-
- for (j=ncovcol;j>=1;j--){
- cutv(stra, strb,line,' ');
- errno=0;
- lval=strtol(strb,&endptr,10);
- if( strb[0]=='\0' || (*endptr != '\0')){
- printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1). Exiting.\n",lval, linei,i, line);
- exit(1);
- }
- if(lval <-1 || lval >1){
- printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a value of the %d covar (meaning 0 for the reference or 1. IMaCh does not build design variables, do it your self). Exiting.\n",lval,linei, i,line,j);
- exit(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 */
- fclose(fic);
- /* 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;*/
-
- /* Calculation of the number of parameters from char model */
- Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
- Tprod=ivector(1,15);
- 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 */
+ fflush(ficlog);
- 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;
+ /*-------- Rewriting parameter file ----------*/
+ strcpy(rfileres,"r"); /* "Rparameterfile */
+ strcat(rfileres,optionfilefiname); /* Parameter file first name*/
+ strcat(rfileres,"."); /* */
+ strcat(rfileres,optionfilext); /* Other files have txt extension */
+ if((ficres =fopen(rfileres,"w"))==NULL) {
+ printf("Problem writing new parameter file: %s\n", fileres);goto end;
+ fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
}
-
- /* This loop fills the array Tvar from the string 'model'.*/
+ fprintf(ficres,"#%s\n",version);
+ } /* End of mle != -3 */
- 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);
+ n= lastobs;
+ num=lvector(1,n);
+ moisnais=vector(1,n);
+ annais=vector(1,n);
+ moisdc=vector(1,n);
+ andc=vector(1,n);
+ agedc=vector(1,n);
+ cod=ivector(1,n);
+ weight=vector(1,n);
+ 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[i][j] health state for wave i and individual j */
+ tab=ivector(1,NCOVMAX);
+ ncodemax=ivector(1,8); /* hard coded ? */
- scanf("%d ",i);*/
+ /* Reads data from file datafile */
+ if (readdata(datafile, firstobs, lastobs, &imx)==1)
+ goto end;
- /* if(mle==1){*/
- if (weightopt != 1) { /* Maximisation without weights*/
- for(i=1;i<=n;i++) weight[i]=1.0;
- }
- /*-calculation of age at interview from date of interview and age at death -*/
- agev=matrix(1,maxwav,1,imx);
+ /* 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); /* 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
+ */
- 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 */
- }
- }
- }
+ if(decodemodel(model, lastobs) == 1)
+ goto end;
- 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;
- }
-
+ 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);
}
- 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;
- }
- }
+ /* if(mle==1){*/
+ 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 */
}
- /*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]);
-}
-
-}*/
+ /*-calculation of age at interview from date of interview and age at death -*/
+ agev=matrix(1,maxwav,1,imx);
+ 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);
@@ -5044,7 +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);
@@ -5054,13 +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]]);
}
}
}
@@ -5069,7 +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");
}
@@ -5097,7 +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 */
@@ -5106,13 +5520,13 @@ 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\
@@ -5123,7 +5537,7 @@ Title=%s
Datafile=%s Firstpass=%d La
- 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);
@@ -5156,7 +5570,8 @@ Interval (in months) between two waves:
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);
@@ -5198,21 +5613,106 @@ Interval (in months) between two waves:
/*printf("%lf %lf", p[1], p[2]);*/
+#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");
+
+ 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);
+ }
- powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+ 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);
@@ -5263,7 +5763,7 @@ Interval (in months) between two waves:
printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\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]);
- replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
+ replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
@@ -5273,10 +5773,16 @@ Interval (in months) between two waves:
free_vector(lsurv,1,AGESUP);
free_vector(lpop,1,AGESUP);
free_vector(tpop,1,AGESUP);
+#ifdef GSL
+ free_ivector(cens,1,n);
+ free_vector(agecens,1,n);
+ free_ivector(dcwave,1,n);
+ free_matrix(ximort,1,NDIM,1,NDIM);
+#endif
} /* Endof if mle==-3 */
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++)
@@ -5306,9 +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");
@@ -5500,7 +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,\
@@ -5549,7 +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#******");
@@ -5655,18 +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 Life expectancies with their standard errors: file '%s' \n", filerest);
- fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+ /*---------- Health expectancies, no variances ------------*/
+
strcpy(filerese,"e");
strcat(filerese,fileres);
if((ficreseij=fopen(filerese,"w"))==NULL) {
@@ -5675,6 +6188,37 @@ 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);
@@ -5703,20 +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;
@@ -5725,15 +6255,12 @@ 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#****** ");
fprintf(ficresstdeij,"\n#****** ");
fprintf(ficrescveij,"\n#****** ");
for(j=1;j<=cptcoveff;j++) {
- fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][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(ficreseij,"******\n");
fprintf(ficresstdeij,"******\n");
fprintf(ficrescveij,"******\n");
@@ -5744,51 +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, strstart);
- cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+ 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, strstart);
- 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, strstart);
- }
-
pstamp(ficrest);
- fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
- for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
- fprintf(ficrest,"\n");
+ 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);
@@ -5802,7 +6330,6 @@ 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);
@@ -5841,6 +6368,7 @@ 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);
@@ -5858,7 +6386,6 @@ 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);
@@ -5888,14 +6415,20 @@ 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);
+
+ 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