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version 1.1.1.1, 2000/12/28 18:49:56
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version 1.49, 2002/06/20 14:03:39
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/* $Id$
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| /*********************** Imach ************************************** |
Interpolated Markov Chain
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| This program computes Healthy Life Expectancies from cross-longitudinal |
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| data. Cross-longitudinal consist in a first survey ("cross") where |
Short summary of the programme:
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| individuals from different ages are interviewed on their health status |
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| or degree of disability. At least a second wave of interviews |
This program computes Healthy Life Expectancies from
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| ("longitudinal") should measure each new individual health status. |
cross-longitudinal data. Cross-longitudinal data consist in: -1- a
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| Health expectancies are computed from the transistions observed between |
first survey ("cross") where individuals from different ages are
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| waves and are computed for each degree of severity of disability (number |
interviewed on their health status or degree of disability (in the
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| of life states). More degrees you consider, more time is necessary to |
case of a health survey which is our main interest) -2- at least a
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| reach the Maximum Likekilhood of the parameters involved in the model. |
second wave of interviews ("longitudinal") which measure each change
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| The simplest model is the multinomial logistic model where pij is |
(if any) in individual health status. Health expectancies are
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| the probabibility to be observed in state j at the second wave conditional |
computed from the time spent in each health state according to a
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| to be observed in state i at the first wave. Therefore the model is: |
model. More health states you consider, more time is necessary to reach the
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| log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex' |
Maximum Likelihood of the parameters involved in the model. The
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| is a covariate. If you want to have a more complex model than "constant and |
simplest model is the multinomial logistic model where pij is the
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| age", you should modify the program where the markup |
probability to be observed in state j at the second wave
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| *Covariates have to be included here again* invites you to do it. |
conditional to be observed in state i at the first wave. Therefore
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| More covariates you add, less is the speed of the convergence. |
the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
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| |
'age' is age and 'sex' is a covariate. If you want to have a more
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| The advantage that this computer programme claims, comes from that if the |
complex model than "constant and age", you should modify the program
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| delay between waves is not identical for each individual, or if some |
where the markup *Covariates have to be included here again* invites
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| individual missed an interview, the information is not rounded or lost, but |
you to do it. More covariates you add, slower the
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| taken into account using an interpolation or extrapolation. |
convergence.
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| hPijx is the probability to be |
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| observed in state i at age x+h conditional to the observed state i at age |
The advantage of this computer programme, compared to a simple
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| x. The delay 'h' can be split into an exact number (nh*stepm) of |
multinomial logistic model, is clear when the delay between waves is not
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| unobserved intermediate states. This elementary transition (by month or |
identical for each individual. Also, if a individual missed an
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| quarter trimester, semester or year) is model as a multinomial logistic. |
intermediate interview, the information is lost, but taken into
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| The hPx matrix is simply the matrix product of nh*stepm elementary matrices |
account using an interpolation or extrapolation.
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| and the contribution of each individual to the likelihood is simply hPijx. |
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| |
hPijx is the probability to be observed in state i at age x+h
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| Also this programme outputs the covariance matrix of the parameters but also |
conditional to the observed state i at age x. The delay 'h' can be
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| of the life expectancies. It also computes the prevalence limits. |
split into an exact number (nh*stepm) of unobserved intermediate
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| |
states. This elementary transition (by month or quarter trimester,
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| Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr). |
semester or year) is model as a multinomial logistic. The hPx
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| Institut national d'études démographiques, Paris. |
matrix is simply the matrix product of nh*stepm elementary matrices
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| This software have been partly granted by Euro-REVES, a concerted action |
and the contribution of each individual to the likelihood is simply
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| from the European Union. |
hPijx.
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| It is copyrighted identically to a GNU software product, ie programme and |
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| software can be distributed freely for non commercial use. Latest version |
Also this programme outputs the covariance matrix of the parameters but also
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| can be accessed at http://euroreves.ined.fr/imach . |
of the life expectancies. It also computes the prevalence limits.
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| **********************************************************************/ |
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| |
Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
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| #include <math.h> |
Institut national d'études démographiques, Paris.
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| #include <stdio.h> |
This software have been partly granted by Euro-REVES, a concerted action
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| #include <stdlib.h> |
from the European Union.
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| #include <unistd.h> |
It is copyrighted identically to a GNU software product, ie programme and
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| |
software can be distributed freely for non commercial use. Latest version
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| #define MAXLINE 256 |
can be accessed at http://euroreves.ined.fr/imach .
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| #define FILENAMELENGTH 80 |
**********************************************************************/
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| /*#define DEBUG*/ |
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| /*#define win*/ |
#include <math.h>
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| |
#include <stdio.h>
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| #define MAXPARM 30 /* Maximum number of parameters for the optimization */ |
#include <stdlib.h>
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| #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncov */ |
#include <unistd.h>
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| |
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| #define NINTERVMAX 8 |
#define MAXLINE 256
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| #define NLSTATEMAX 8 /* Maximum number of live states (for func) */ |
#define GNUPLOTPROGRAM "gnuplot"
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| #define NDEATHMAX 8 /* Maximum number of dead states (for func) */ |
/*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
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| #define NCOVMAX 8 /* Maximum number of covariates */ |
#define FILENAMELENGTH 80
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| #define MAXN 20000 |
/*#define DEBUG*/
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| #define YEARM 12. /* Number of months per year */ |
#define windows
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| #define AGESUP 130 |
#define GLOCK_ERROR_NOPATH -1 /* empty path */
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| #define AGEBASE 40 |
#define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
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| |
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| |
#define MAXPARM 30 /* Maximum number of parameters for the optimization */
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| int nvar; |
#define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
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| |
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| int npar=NPARMAX; |
#define NINTERVMAX 8
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| int nlstate=2; /* Number of live states */ |
#define NLSTATEMAX 8 /* Maximum number of live states (for func) */
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| int ndeath=1; /* Number of dead states */ |
#define NDEATHMAX 8 /* Maximum number of dead states (for func) */
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| int ncov; /* Total number of covariables including constant a12*1 +b12*x ncov=2 */ |
#define NCOVMAX 8 /* Maximum number of covariates */
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| |
#define MAXN 20000
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| int *wav; /* Number of waves for this individuual 0 is possible */ |
#define YEARM 12. /* Number of months per year */
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| int maxwav; /* Maxim number of waves */ |
#define AGESUP 130
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| int mle, weightopt; |
#define AGEBASE 40
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| int **mw; /* mw[mi][i] is number of the mi wave for this individual */ |
#ifdef windows
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| int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */ |
#define DIRSEPARATOR '\\'
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| double **oldm, **newm, **savm; /* Working pointers to matrices */ |
#else
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| double **oldms, **newms, **savms; /* Fixed working pointers to matrices */ |
#define DIRSEPARATOR '/'
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| FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest; |
#endif
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| FILE *ficgp, *fichtm; |
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| |
char version[80]="Imach version 0.8h, May 2002, INED-EUROREVES ";
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| #define NR_END 1 |
int erreur; /* Error number */
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| #define FREE_ARG char* |
int nvar;
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| #define FTOL 1.0e-10 |
int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
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| |
int npar=NPARMAX;
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| #define NRANSI |
int nlstate=2; /* Number of live states */
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| #define ITMAX 200 |
int ndeath=1; /* Number of dead states */
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| |
int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
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| #define TOL 2.0e-4 |
int popbased=0;
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| |
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| #define CGOLD 0.3819660 |
int *wav; /* Number of waves for this individuual 0 is possible */
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| #define ZEPS 1.0e-10 |
int maxwav; /* Maxim number of waves */
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| #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); |
int jmin, jmax; /* min, max spacing between 2 waves */
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| |
int mle, weightopt;
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| #define GOLD 1.618034 |
int **mw; /* mw[mi][i] is number of the mi wave for this individual */
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| #define GLIMIT 100.0 |
int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
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| #define TINY 1.0e-20 |
double jmean; /* Mean space between 2 waves */
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| |
double **oldm, **newm, **savm; /* Working pointers to matrices */
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| static double maxarg1,maxarg2; |
double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
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| #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2)) |
FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
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| #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2)) |
FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
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| |
FILE *fichtm; /* Html File */
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| #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a)) |
FILE *ficreseij;
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| #define rint(a) floor(a+0.5) |
char filerese[FILENAMELENGTH];
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| |
FILE *ficresvij;
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| static double sqrarg; |
char fileresv[FILENAMELENGTH];
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| #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg) |
FILE *ficresvpl;
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| #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} |
char fileresvpl[FILENAMELENGTH];
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| |
char title[MAXLINE];
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| int imx; |
char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
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| int stepm; |
char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
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| /* Stepm, step in month: minimum step interpolation*/ |
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| |
char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
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| int m,nb; |
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| int *num, firstpass=0, lastpass=2,*cod; |
char filerest[FILENAMELENGTH];
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| double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint; |
char fileregp[FILENAMELENGTH];
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| double **pmmij; |
char popfile[FILENAMELENGTH];
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| |
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| double *weight; |
char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
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| int **s; /* Status */ |
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| double *agedc, **covar, idx; |
#define NR_END 1
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| |
#define FREE_ARG char*
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| |
#define FTOL 1.0e-10
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| double ftol=FTOL; /* Tolerance for computing Max Likelihood */ |
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| double ftolhess; /* Tolerance for computing hessian */ |
#define NRANSI
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| |
#define ITMAX 200
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| |
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| /******************************************/ |
#define TOL 2.0e-4
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| |
|
| void replace(char *s, char*t) |
#define CGOLD 0.3819660
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| { |
#define ZEPS 1.0e-10
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| int i; |
#define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
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| int lg=20; |
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| i=0; |
#define GOLD 1.618034
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| lg=strlen(t); |
#define GLIMIT 100.0
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| for(i=0; i<= lg; i++) { |
#define TINY 1.0e-20
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| (s[i] = t[i]); |
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| if (t[i]== '\\') s[i]='/'; |
static double maxarg1,maxarg2;
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| } |
#define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
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| } |
#define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
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| void cut(char *u,char *v, char*t) |
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| { |
#define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
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| int i,lg,j,p; |
#define rint(a) floor(a+0.5)
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| i=0; |
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| for(j=0; j<=strlen(t); j++) { |
static double sqrarg;
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| if(t[j]=='\\') p=j; |
#define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
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| } |
#define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
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| |
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| lg=strlen(t); |
int imx;
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| for(j=0; j<p; j++) { |
int stepm;
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| (u[j] = t[j]); |
/* Stepm, step in month: minimum step interpolation*/
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| u[p]='\0'; |
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| } |
int estepm;
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| |
/* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
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| for(j=0; j<= lg; j++) { |
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| if (j>=(p+1))(v[j-p-1] = t[j]); |
int m,nb;
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| } |
int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
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| } |
double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
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| |
double **pmmij, ***probs, ***mobaverage;
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| /********************** nrerror ********************/ |
double dateintmean=0;
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| |
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| void nrerror(char error_text[]) |
double *weight;
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| { |
int **s; /* Status */
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| fprintf(stderr,"ERREUR ...\n"); |
double *agedc, **covar, idx;
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| fprintf(stderr,"%s\n",error_text); |
int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
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| exit(1); |
|
| } |
double ftol=FTOL; /* Tolerance for computing Max Likelihood */
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| /*********************** vector *******************/ |
double ftolhess; /* Tolerance for computing hessian */
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| double *vector(int nl, int nh) |
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| { |
/**************** split *************************/
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| double *v; |
static int split( char *path, char *dirc, char *name, char *ext, char *finame )
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| v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double))); |
{
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| if (!v) nrerror("allocation failure in vector"); |
char *s; /* pointer */
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| return v-nl+NR_END; |
int l1, l2; /* length counters */
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| } |
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l1 = strlen( path ); /* length of path */
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| /************************ free vector ******************/ |
if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
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| void free_vector(double*v, int nl, int nh) |
s = strrchr( path, DIRSEPARATOR ); /* find last / */
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| { |
if ( s == NULL ) { /* no directory, so use current */
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| free((FREE_ARG)(v+nl-NR_END)); |
#if defined(__bsd__) /* get current working directory */
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| } |
extern char *getwd( );
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| |
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| /************************ivector *******************************/ |
if ( getwd( dirc ) == NULL ) {
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| int *ivector(long nl,long nh) |
#else
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| { |
extern char *getcwd( );
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| int *v; |
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| v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int))); |
if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
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| if (!v) nrerror("allocation failure in ivector"); |
#endif
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| return v-nl+NR_END; |
return( GLOCK_ERROR_GETCWD );
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| } |
}
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| |
strcpy( name, path ); /* we've got it */
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| /******************free ivector **************************/ |
} else { /* strip direcotry from path */
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| void free_ivector(int *v, long nl, long nh) |
s++; /* after this, the filename */
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| { |
l2 = strlen( s ); /* length of filename */
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| free((FREE_ARG)(v+nl-NR_END)); |
if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
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| } |
strcpy( name, s ); /* save file name */
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| |
strncpy( dirc, path, l1 - l2 ); /* now the directory */
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| /******************* imatrix *******************************/ |
dirc[l1-l2] = 0; /* add zero */
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| int **imatrix(long nrl, long nrh, long ncl, long nch) |
}
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| /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ |
l1 = strlen( dirc ); /* length of directory */
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| { |
#ifdef windows
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| long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; |
if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
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| int **m; |
#else
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| |
if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
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| /* allocate pointers to rows */ |
#endif
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| m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); |
s = strrchr( name, '.' ); /* find last / */
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| if (!m) nrerror("allocation failure 1 in matrix()"); |
s++;
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| m += NR_END; |
strcpy(ext,s); /* save extension */
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| m -= nrl; |
l1= strlen( name);
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| |
l2= strlen( s)+1;
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| |
strncpy( finame, name, l1-l2);
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| /* allocate rows and set pointers to them */ |
finame[l1-l2]= 0;
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| m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); |
return( 0 ); /* we're done */
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| if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); |
}
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| m[nrl] += NR_END; |
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| m[nrl] -= ncl; |
|
| |
/******************************************/
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| for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; |
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| |
void replace(char *s, char*t)
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| /* return pointer to array of pointers to rows */ |
{
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| return m; |
int i;
|
| } |
int lg=20;
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| |
i=0;
|
| /****************** free_imatrix *************************/ |
lg=strlen(t);
|
| void free_imatrix(m,nrl,nrh,ncl,nch) |
for(i=0; i<= lg; i++) {
|
| int **m; |
(s[i] = t[i]);
|
| long nch,ncl,nrh,nrl; |
if (t[i]== '\\') s[i]='/';
|
| /* free an int matrix allocated by imatrix() */ |
}
|
| { |
}
|
| free((FREE_ARG) (m[nrl]+ncl-NR_END)); |
|
| free((FREE_ARG) (m+nrl-NR_END)); |
int nbocc(char *s, char occ)
|
| } |
{
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| |
int i,j=0;
|
| /******************* matrix *******************************/ |
int lg=20;
|
| double **matrix(long nrl, long nrh, long ncl, long nch) |
i=0;
|
| { |
lg=strlen(s);
|
| long i, nrow=nrh-nrl+1, ncol=nch-ncl+1; |
for(i=0; i<= lg; i++) {
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| double **m; |
if (s[i] == occ ) j++;
|
| |
}
|
| m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*))); |
return j;
|
| if (!m) nrerror("allocation failure 1 in matrix()"); |
}
|
| m += NR_END; |
|
| m -= nrl; |
void cutv(char *u,char *v, char*t, char occ)
|
| |
{
|
| m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double))); |
int i,lg,j,p=0;
|
| if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); |
i=0;
|
| m[nrl] += NR_END; |
for(j=0; j<=strlen(t)-1; j++) {
|
| m[nrl] -= ncl; |
if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
|
| |
}
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| for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol; |
|
| return m; |
lg=strlen(t);
|
| } |
for(j=0; j<p; j++) {
|
| |
(u[j] = t[j]);
|
| /*************************free matrix ************************/ |
}
|
| void free_matrix(double **m, long nrl, long nrh, long ncl, long nch) |
u[p]='\0';
|
| { |
|
| free((FREE_ARG)(m[nrl]+ncl-NR_END)); |
for(j=0; j<= lg; j++) {
|
| free((FREE_ARG)(m+nrl-NR_END)); |
if (j>=(p+1))(v[j-p-1] = t[j]);
|
| } |
}
|
| |
}
|
| /******************* ma3x *******************************/ |
|
| double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh) |
/********************** nrerror ********************/
|
| { |
|
| long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1; |
void nrerror(char error_text[])
|
| double ***m; |
{
|
| |
fprintf(stderr,"ERREUR ...\n");
|
| m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*))); |
fprintf(stderr,"%s\n",error_text);
|
| if (!m) nrerror("allocation failure 1 in matrix()"); |
exit(1);
|
| m += NR_END; |
}
|
| m -= nrl; |
/*********************** vector *******************/
|
| |
double *vector(int nl, int nh)
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| m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double))); |
{
|
| if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); |
double *v;
|
| m[nrl] += NR_END; |
v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
|
| m[nrl] -= ncl; |
if (!v) nrerror("allocation failure in vector");
|
| |
return v-nl+NR_END;
|
| for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol; |
}
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| |
|
| m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double))); |
/************************ free vector ******************/
|
| if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()"); |
void free_vector(double*v, int nl, int nh)
|
| m[nrl][ncl] += NR_END; |
{
|
| m[nrl][ncl] -= nll; |
free((FREE_ARG)(v+nl-NR_END));
|
| for (j=ncl+1; j<=nch; j++) |
}
|
| m[nrl][j]=m[nrl][j-1]+nlay; |
|
| |
/************************ivector *******************************/
|
| for (i=nrl+1; i<=nrh; i++) { |
int *ivector(long nl,long nh)
|
| m[i][ncl]=m[i-1l][ncl]+ncol*nlay; |
{
|
| for (j=ncl+1; j<=nch; j++) |
int *v;
|
| m[i][j]=m[i][j-1]+nlay; |
v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
|
| } |
if (!v) nrerror("allocation failure in ivector");
|
| return m; |
return v-nl+NR_END;
|
| } |
}
|
| |
|
| /*************************free ma3x ************************/ |
/******************free ivector **************************/
|
| void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh) |
void free_ivector(int *v, long nl, long nh)
|
| { |
{
|
| free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END)); |
free((FREE_ARG)(v+nl-NR_END));
|
| free((FREE_ARG)(m[nrl]+ncl-NR_END)); |
}
|
| free((FREE_ARG)(m+nrl-NR_END)); |
|
| } |
/******************* imatrix *******************************/
|
| |
int **imatrix(long nrl, long nrh, long ncl, long nch)
|
| /***************** f1dim *************************/ |
/* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
|
| extern int ncom; |
{
|
| extern double *pcom,*xicom; |
long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
|
| extern double (*nrfunc)(double []); |
int **m;
|
| |
|
| double f1dim(double x) |
/* allocate pointers to rows */
|
| { |
m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
|
| int j; |
if (!m) nrerror("allocation failure 1 in matrix()");
|
| double f; |
m += NR_END;
|
| double *xt; |
m -= nrl;
|
| |
|
| xt=vector(1,ncom); |
|
| for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; |
/* allocate rows and set pointers to them */
|
| f=(*nrfunc)(xt); |
m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
|
| free_vector(xt,1,ncom); |
if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
|
| return f; |
m[nrl] += NR_END;
|
| } |
m[nrl] -= ncl;
|
| |
|
| /*****************brent *************************/ |
for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
|
| double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin) |
|
| { |
/* return pointer to array of pointers to rows */
|
| int iter; |
return m;
|
| double a,b,d,etemp; |
}
|
| double fu,fv,fw,fx; |
|
| double ftemp; |
/****************** free_imatrix *************************/
|
| double p,q,r,tol1,tol2,u,v,w,x,xm; |
void free_imatrix(m,nrl,nrh,ncl,nch)
|
| double e=0.0; |
int **m;
|
| |
long nch,ncl,nrh,nrl;
|
| a=(ax < cx ? ax : cx); |
/* free an int matrix allocated by imatrix() */
|
| b=(ax > cx ? ax : cx); |
{
|
| x=w=v=bx; |
free((FREE_ARG) (m[nrl]+ncl-NR_END));
|
| fw=fv=fx=(*f)(x); |
free((FREE_ARG) (m+nrl-NR_END));
|
| for (iter=1;iter<=ITMAX;iter++) { |
}
|
| xm=0.5*(a+b); |
|
| tol2=2.0*(tol1=tol*fabs(x)+ZEPS); |
/******************* matrix *******************************/
|
| /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/ |
double **matrix(long nrl, long nrh, long ncl, long nch)
|
| printf(".");fflush(stdout); |
{
|
| #ifdef DEBUG |
long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
|
| printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol); |
double **m;
|
| /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */ |
|
| #endif |
m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
|
| if (fabs(x-xm) <= (tol2-0.5*(b-a))){ |
if (!m) nrerror("allocation failure 1 in matrix()");
|
| *xmin=x; |
m += NR_END;
|
| return fx; |
m -= nrl;
|
| } |
|
| ftemp=fu; |
m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
|
| if (fabs(e) > tol1) { |
if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
|
| r=(x-w)*(fx-fv); |
m[nrl] += NR_END;
|
| q=(x-v)*(fx-fw); |
m[nrl] -= ncl;
|
| p=(x-v)*q-(x-w)*r; |
|
| q=2.0*(q-r); |
for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
|
| if (q > 0.0) p = -p; |
return m;
|
| q=fabs(q); |
}
|
| etemp=e; |
|
| e=d; |
/*************************free matrix ************************/
|
| if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) |
void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
|
| d=CGOLD*(e=(x >= xm ? a-x : b-x)); |
{
|
| else { |
free((FREE_ARG)(m[nrl]+ncl-NR_END));
|
| d=p/q; |
free((FREE_ARG)(m+nrl-NR_END));
|
| u=x+d; |
}
|
| if (u-a < tol2 || b-u < tol2) |
|
| d=SIGN(tol1,xm-x); |
/******************* ma3x *******************************/
|
| } |
double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
|
| } else { |
{
|
| d=CGOLD*(e=(x >= xm ? a-x : b-x)); |
long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
|
| } |
double ***m;
|
| u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); |
|
| fu=(*f)(u); |
m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
|
| if (fu <= fx) { |
if (!m) nrerror("allocation failure 1 in matrix()");
|
| if (u >= x) a=x; else b=x; |
m += NR_END;
|
| SHFT(v,w,x,u) |
m -= nrl;
|
| SHFT(fv,fw,fx,fu) |
|
| } else { |
m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
|
| if (u < x) a=u; else b=u; |
if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
|
| if (fu <= fw || w == x) { |
m[nrl] += NR_END;
|
| v=w; |
m[nrl] -= ncl;
|
| w=u; |
|
| fv=fw; |
for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
|
| fw=fu; |
|
| } else if (fu <= fv || v == x || v == w) { |
m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
|
| v=u; |
if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
|
| fv=fu; |
m[nrl][ncl] += NR_END;
|
| } |
m[nrl][ncl] -= nll;
|
| } |
for (j=ncl+1; j<=nch; j++)
|
| } |
m[nrl][j]=m[nrl][j-1]+nlay;
|
| nrerror("Too many iterations in brent"); |
|
| *xmin=x; |
for (i=nrl+1; i<=nrh; i++) {
|
| return fx; |
m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
|
| } |
for (j=ncl+1; j<=nch; j++)
|
| |
m[i][j]=m[i][j-1]+nlay;
|
| /****************** mnbrak ***********************/ |
}
|
| |
return m;
|
| void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, |
}
|
| double (*func)(double)) |
|
| { |
/*************************free ma3x ************************/
|
| double ulim,u,r,q, dum; |
void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
|
| double fu; |
{
|
| |
free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
|
| *fa=(*func)(*ax); |
free((FREE_ARG)(m[nrl]+ncl-NR_END));
|
| *fb=(*func)(*bx); |
free((FREE_ARG)(m+nrl-NR_END));
|
| if (*fb > *fa) { |
}
|
| SHFT(dum,*ax,*bx,dum) |
|
| SHFT(dum,*fb,*fa,dum) |
/***************** f1dim *************************/
|
| } |
extern int ncom;
|
| *cx=(*bx)+GOLD*(*bx-*ax); |
extern double *pcom,*xicom;
|
| *fc=(*func)(*cx); |
extern double (*nrfunc)(double []);
|
| while (*fb > *fc) { |
|
| r=(*bx-*ax)*(*fb-*fc); |
double f1dim(double x)
|
| q=(*bx-*cx)*(*fb-*fa); |
{
|
| u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ |
int j;
|
| (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); |
double f;
|
| ulim=(*bx)+GLIMIT*(*cx-*bx); |
double *xt;
|
| if ((*bx-u)*(u-*cx) > 0.0) { |
|
| fu=(*func)(u); |
xt=vector(1,ncom);
|
| } else if ((*cx-u)*(u-ulim) > 0.0) { |
for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
|
| fu=(*func)(u); |
f=(*nrfunc)(xt);
|
| if (fu < *fc) { |
free_vector(xt,1,ncom);
|
| SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) |
return f;
|
| SHFT(*fb,*fc,fu,(*func)(u)) |
}
|
| } |
|
| } else if ((u-ulim)*(ulim-*cx) >= 0.0) { |
/*****************brent *************************/
|
| u=ulim; |
double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
|
| fu=(*func)(u); |
{
|
| } else { |
int iter;
|
| u=(*cx)+GOLD*(*cx-*bx); |
double a,b,d,etemp;
|
| fu=(*func)(u); |
double fu,fv,fw,fx;
|
| } |
double ftemp;
|
| SHFT(*ax,*bx,*cx,u) |
double p,q,r,tol1,tol2,u,v,w,x,xm;
|
| SHFT(*fa,*fb,*fc,fu) |
double e=0.0;
|
| } |
|
| } |
a=(ax < cx ? ax : cx);
|
| |
b=(ax > cx ? ax : cx);
|
| /*************** linmin ************************/ |
x=w=v=bx;
|
| |
fw=fv=fx=(*f)(x);
|
| int ncom; |
for (iter=1;iter<=ITMAX;iter++) {
|
| double *pcom,*xicom; |
xm=0.5*(a+b);
|
| double (*nrfunc)(double []); |
tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
|
| |
/* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
|
| void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) |
printf(".");fflush(stdout);
|
| { |
#ifdef DEBUG
|
| double brent(double ax, double bx, double cx, |
printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
|
| double (*f)(double), double tol, double *xmin); |
/* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
|
| double f1dim(double x); |
#endif
|
| void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, |
if (fabs(x-xm) <= (tol2-0.5*(b-a))){
|
| double *fc, double (*func)(double)); |
*xmin=x;
|
| int j; |
return fx;
|
| double xx,xmin,bx,ax; |
}
|
| double fx,fb,fa; |
ftemp=fu;
|
| |
if (fabs(e) > tol1) {
|
| ncom=n; |
r=(x-w)*(fx-fv);
|
| pcom=vector(1,n); |
q=(x-v)*(fx-fw);
|
| xicom=vector(1,n); |
p=(x-v)*q-(x-w)*r;
|
| nrfunc=func; |
q=2.0*(q-r);
|
| for (j=1;j<=n;j++) { |
if (q > 0.0) p = -p;
|
| pcom[j]=p[j]; |
q=fabs(q);
|
| xicom[j]=xi[j]; |
etemp=e;
|
| } |
e=d;
|
| ax=0.0; |
if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
|
| xx=1.0; |
d=CGOLD*(e=(x >= xm ? a-x : b-x));
|
| mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); |
else {
|
| *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); |
d=p/q;
|
| #ifdef DEBUG |
u=x+d;
|
| printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin); |
if (u-a < tol2 || b-u < tol2)
|
| #endif |
d=SIGN(tol1,xm-x);
|
| for (j=1;j<=n;j++) { |
}
|
| xi[j] *= xmin; |
} else {
|
| p[j] += xi[j]; |
d=CGOLD*(e=(x >= xm ? a-x : b-x));
|
| } |
}
|
| free_vector(xicom,1,n); |
u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
|
| free_vector(pcom,1,n); |
fu=(*f)(u);
|
| } |
if (fu <= fx) {
|
| |
if (u >= x) a=x; else b=x;
|
| /*************** powell ************************/ |
SHFT(v,w,x,u)
|
| void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, |
SHFT(fv,fw,fx,fu)
|
| double (*func)(double [])) |
} else {
|
| |
if (u < x) a=u; else b=u;
|
| { |
if (fu <= fw || w == x) {
|
| |
v=w;
|
| |
w=u;
|
| void linmin(double p[], double xi[], int n, double *fret, |
fv=fw;
|
| double (*func)(double [])); |
fw=fu;
|
| int i,ibig,j; |
} else if (fu <= fv || v == x || v == w) {
|
| double del,t,*pt,*ptt,*xit; |
v=u;
|
| double fp,fptt; |
fv=fu;
|
| double *xits; |
}
|
| pt=vector(1,n); |
}
|
| ptt=vector(1,n); |
}
|
| xit=vector(1,n); |
nrerror("Too many iterations in brent");
|
| xits=vector(1,n); |
*xmin=x;
|
| *fret=(*func)(p); |
return fx;
|
| for (j=1;j<=n;j++) pt[j]=p[j]; |
}
|
| for (*iter=1;;++(*iter)) { |
|
| fp=(*fret); |
/****************** mnbrak ***********************/
|
| ibig=0; |
|
| del=0.0; |
void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
|
| printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret); |
double (*func)(double))
|
| for (i=1;i<=n;i++) |
{
|
| printf(" %d %.12f",i, p[i]); |
double ulim,u,r,q, dum;
|
| printf("\n"); |
double fu;
|
| for (i=1;i<=n;i++) { |
|
| for (j=1;j<=n;j++) xit[j]=xi[j][i]; |
*fa=(*func)(*ax);
|
| fptt=(*fret); |
*fb=(*func)(*bx);
|
| #ifdef DEBUG |
if (*fb > *fa) {
|
| printf("fret=%lf \n",*fret); |
SHFT(dum,*ax,*bx,dum)
|
| #endif |
SHFT(dum,*fb,*fa,dum)
|
| printf("%d",i);fflush(stdout); |
}
|
| linmin(p,xit,n,fret,func); |
*cx=(*bx)+GOLD*(*bx-*ax);
|
| if (fabs(fptt-(*fret)) > del) { |
*fc=(*func)(*cx);
|
| del=fabs(fptt-(*fret)); |
while (*fb > *fc) {
|
| ibig=i; |
r=(*bx-*ax)*(*fb-*fc);
|
| } |
q=(*bx-*cx)*(*fb-*fa);
|
| #ifdef DEBUG |
u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
|
| printf("%d %.12e",i,(*fret)); |
(2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
|
| for (j=1;j<=n;j++) { |
ulim=(*bx)+GLIMIT*(*cx-*bx);
|
| xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5); |
if ((*bx-u)*(u-*cx) > 0.0) {
|
| printf(" x(%d)=%.12e",j,xit[j]); |
fu=(*func)(u);
|
| } |
} else if ((*cx-u)*(u-ulim) > 0.0) {
|
| for(j=1;j<=n;j++) |
fu=(*func)(u);
|
| printf(" p=%.12e",p[j]); |
if (fu < *fc) {
|
| printf("\n"); |
SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
|
| #endif |
SHFT(*fb,*fc,fu,(*func)(u))
|
| } |
}
|
| if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { |
} else if ((u-ulim)*(ulim-*cx) >= 0.0) {
|
| #ifdef DEBUG |
u=ulim;
|
| int k[2],l; |
fu=(*func)(u);
|
| k[0]=1; |
} else {
|
| k[1]=-1; |
u=(*cx)+GOLD*(*cx-*bx);
|
| printf("Max: %.12e",(*func)(p)); |
fu=(*func)(u);
|
| for (j=1;j<=n;j++) |
}
|
| printf(" %.12e",p[j]); |
SHFT(*ax,*bx,*cx,u)
|
| printf("\n"); |
SHFT(*fa,*fb,*fc,fu)
|
| for(l=0;l<=1;l++) { |
}
|
| for (j=1;j<=n;j++) { |
}
|
| ptt[j]=p[j]+(p[j]-pt[j])*k[l]; |
|
| printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]); |
/*************** linmin ************************/
|
| } |
|
| printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p))); |
int ncom;
|
| } |
double *pcom,*xicom;
|
| #endif |
double (*nrfunc)(double []);
|
| |
|
| |
void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
|
| free_vector(xit,1,n); |
{
|
| free_vector(xits,1,n); |
double brent(double ax, double bx, double cx,
|
| free_vector(ptt,1,n); |
double (*f)(double), double tol, double *xmin);
|
| free_vector(pt,1,n); |
double f1dim(double x);
|
| return; |
void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
|
| } |
double *fc, double (*func)(double));
|
| if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); |
int j;
|
| for (j=1;j<=n;j++) { |
double xx,xmin,bx,ax;
|
| ptt[j]=2.0*p[j]-pt[j]; |
double fx,fb,fa;
|
| xit[j]=p[j]-pt[j]; |
|
| pt[j]=p[j]; |
ncom=n;
|
| } |
pcom=vector(1,n);
|
| fptt=(*func)(ptt); |
xicom=vector(1,n);
|
| if (fptt < fp) { |
nrfunc=func;
|
| t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); |
for (j=1;j<=n;j++) {
|
| if (t < 0.0) { |
pcom[j]=p[j];
|
| linmin(p,xit,n,fret,func); |
xicom[j]=xi[j];
|
| for (j=1;j<=n;j++) { |
}
|
| xi[j][ibig]=xi[j][n]; |
ax=0.0;
|
| xi[j][n]=xit[j]; |
xx=1.0;
|
| } |
mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
|
| #ifdef DEBUG |
*fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
|
| printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig); |
#ifdef DEBUG
|
| for(j=1;j<=n;j++) |
printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
|
| printf(" %.12e",xit[j]); |
#endif
|
| printf("\n"); |
for (j=1;j<=n;j++) {
|
| #endif |
xi[j] *= xmin;
|
| } |
p[j] += xi[j];
|
| } |
}
|
| } |
free_vector(xicom,1,n);
|
| } |
free_vector(pcom,1,n);
|
| |
}
|
| /**** Prevalence limit ****************/ |
|
| |
/*************** powell ************************/
|
| double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl) |
void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
|
| { |
double (*func)(double []))
|
| /* Computes the prevalence limit in each live state at age x by left multiplying the unit |
{
|
| matrix by transitions matrix until convergence is reached */ |
void linmin(double p[], double xi[], int n, double *fret,
|
| |
double (*func)(double []));
|
| int i, ii,j,k; |
int i,ibig,j;
|
| double min, max, maxmin, maxmax,sumnew=0.; |
double del,t,*pt,*ptt,*xit;
|
| double **matprod2(); |
double fp,fptt;
|
| double **out, cov[NCOVMAX], **pmij(); |
double *xits;
|
| double **newm; |
pt=vector(1,n);
|
| double agefin, delaymax=50 ; /* Max number of years to converge */ |
ptt=vector(1,n);
|
| |
xit=vector(1,n);
|
| for (ii=1;ii<=nlstate+ndeath;ii++) |
xits=vector(1,n);
|
| for (j=1;j<=nlstate+ndeath;j++){ |
*fret=(*func)(p);
|
| oldm[ii][j]=(ii==j ? 1.0 : 0.0); |
for (j=1;j<=n;j++) pt[j]=p[j];
|
| } |
for (*iter=1;;++(*iter)) {
|
| /* Even if hstepm = 1, at least one multiplication by the unit matrix */ |
fp=(*fret);
|
| for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){ |
ibig=0;
|
| newm=savm; |
del=0.0;
|
| /* Covariates have to be included here again */ |
printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
|
| cov[1]=1.; |
for (i=1;i<=n;i++)
|
| cov[2]=agefin; |
printf(" %d %.12f",i, p[i]);
|
| out=matprod2(newm, pmij(pmmij,cov,ncov,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); |
printf("\n");
|
| /* printf("age=%f agefin=%f po=%f pn=%f\n",age,agefin,oldm[1][1],newm[1][1]);*/ |
for (i=1;i<=n;i++) {
|
| |
for (j=1;j<=n;j++) xit[j]=xi[j][i];
|
| savm=oldm; |
fptt=(*fret);
|
| oldm=newm; |
#ifdef DEBUG
|
| maxmax=0.; |
printf("fret=%lf \n",*fret);
|
| for(j=1;j<=nlstate;j++){ |
#endif
|
| min=1.; |
printf("%d",i);fflush(stdout);
|
| max=0.; |
linmin(p,xit,n,fret,func);
|
| for(i=1; i<=nlstate; i++) { |
if (fabs(fptt-(*fret)) > del) {
|
| sumnew=0; |
del=fabs(fptt-(*fret));
|
| for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k]; |
ibig=i;
|
| prlim[i][j]= newm[i][j]/(1-sumnew); |
}
|
| max=FMAX(max,prlim[i][j]); |
#ifdef DEBUG
|
| min=FMIN(min,prlim[i][j]); |
printf("%d %.12e",i,(*fret));
|
| } |
for (j=1;j<=n;j++) {
|
| maxmin=max-min; |
xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
|
| maxmax=FMAX(maxmax,maxmin); |
printf(" x(%d)=%.12e",j,xit[j]);
|
| } |
}
|
| if(maxmax < ftolpl){ |
for(j=1;j<=n;j++)
|
| return prlim; |
printf(" p=%.12e",p[j]);
|
| } |
printf("\n");
|
| } |
#endif
|
| } |
}
|
| |
if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
|
| /*************** transition probabilities **********/ |
#ifdef DEBUG
|
| |
int k[2],l;
|
| double **pmij(double **ps, double *cov, int ncov, double *x, int nlstate ) |
k[0]=1;
|
| { |
k[1]=-1;
|
| double s1, s2; |
printf("Max: %.12e",(*func)(p));
|
| /*double t34;*/ |
for (j=1;j<=n;j++)
|
| int i,j,j1, nc, ii, jj; |
printf(" %.12e",p[j]);
|
| |
printf("\n");
|
| for(i=1; i<= nlstate; i++){ |
for(l=0;l<=1;l++) {
|
| for(j=1; j<i;j++){ |
for (j=1;j<=n;j++) {
|
| for (nc=1, s2=0.;nc <=ncov; nc++){ |
ptt[j]=p[j]+(p[j]-pt[j])*k[l];
|
| /*s2 += param[i][j][nc]*cov[nc];*/ |
printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
|
| s2 += x[(i-1)*nlstate*ncov+(j-1)*ncov+nc+(i-1)*(ndeath-1)*ncov]*cov[nc]; |
}
|
| /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/ |
printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
|
| } |
}
|
| ps[i][j]=s2; |
#endif
|
| /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/ |
|
| } |
|
| for(j=i+1; j<=nlstate+ndeath;j++){ |
free_vector(xit,1,n);
|
| for (nc=1, s2=0.;nc <=ncov; nc++){ |
free_vector(xits,1,n);
|
| s2 += x[(i-1)*nlstate*ncov+(j-2)*ncov+nc+(i-1)*(ndeath-1)*ncov]*cov[nc]; |
free_vector(ptt,1,n);
|
| /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/ |
free_vector(pt,1,n);
|
| } |
return;
|
| ps[i][j]=s2; |
}
|
| } |
if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
|
| } |
for (j=1;j<=n;j++) {
|
| for(i=1; i<= nlstate; i++){ |
ptt[j]=2.0*p[j]-pt[j];
|
| s1=0; |
xit[j]=p[j]-pt[j];
|
| for(j=1; j<i; j++) |
pt[j]=p[j];
|
| s1+=exp(ps[i][j]); |
}
|
| for(j=i+1; j<=nlstate+ndeath; j++) |
fptt=(*func)(ptt);
|
| s1+=exp(ps[i][j]); |
if (fptt < fp) {
|
| ps[i][i]=1./(s1+1.); |
t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
|
| for(j=1; j<i; j++) |
if (t < 0.0) {
|
| ps[i][j]= exp(ps[i][j])*ps[i][i]; |
linmin(p,xit,n,fret,func);
|
| for(j=i+1; j<=nlstate+ndeath; j++) |
for (j=1;j<=n;j++) {
|
| ps[i][j]= exp(ps[i][j])*ps[i][i]; |
xi[j][ibig]=xi[j][n];
|
| /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */ |
xi[j][n]=xit[j];
|
| } /* end i */ |
}
|
| |
#ifdef DEBUG
|
| for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){ |
printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
|
| for(jj=1; jj<= nlstate+ndeath; jj++){ |
for(j=1;j<=n;j++)
|
| ps[ii][jj]=0; |
printf(" %.12e",xit[j]);
|
| ps[ii][ii]=1; |
printf("\n");
|
| } |
#endif
|
| } |
}
|
| |
}
|
| /* for(ii=1; ii<= nlstate+ndeath; ii++){ |
}
|
| for(jj=1; jj<= nlstate+ndeath; jj++){ |
}
|
| printf("%lf ",ps[ii][jj]); |
|
| } |
/**** Prevalence limit ****************/
|
| printf("\n "); |
|
| } |
double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
|
| printf("\n ");printf("%lf ",cov[2]);*/ |
{
|
| /* |
/* Computes the prevalence limit in each live state at age x by left multiplying the unit
|
| for(i=1; i<= npar; i++) printf("%f ",x[i]); |
matrix by transitions matrix until convergence is reached */
|
| goto end;*/ |
|
| return ps; |
int i, ii,j,k;
|
| } |
double min, max, maxmin, maxmax,sumnew=0.;
|
| |
double **matprod2();
|
| /**************** Product of 2 matrices ******************/ |
double **out, cov[NCOVMAX], **pmij();
|
| |
double **newm;
|
| double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b) |
double agefin, delaymax=50 ; /* Max number of years to converge */
|
| { |
|
| /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times |
for (ii=1;ii<=nlstate+ndeath;ii++)
|
| b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */ |
for (j=1;j<=nlstate+ndeath;j++){
|
| /* in, b, out are matrice of pointers which should have been initialized |
oldm[ii][j]=(ii==j ? 1.0 : 0.0);
|
| before: only the contents of out is modified. The function returns |
}
|
| a pointer to pointers identical to out */ |
|
| long i, j, k; |
cov[1]=1.;
|
| for(i=nrl; i<= nrh; i++) |
|
| for(k=ncolol; k<=ncoloh; k++) |
/* Even if hstepm = 1, at least one multiplication by the unit matrix */
|
| for(j=ncl,out[i][k]=0.; j<=nch; j++) |
for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
|
| out[i][k] +=in[i][j]*b[j][k]; |
newm=savm;
|
| |
/* Covariates have to be included here again */
|
| return out; |
cov[2]=agefin;
|
| } |
|
| |
for (k=1; k<=cptcovn;k++) {
|
| |
cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
|
| /************* Higher Matrix Product ***************/ |
/* 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]]);*/
|
| |
}
|
| double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm ) |
for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
|
| { |
for (k=1; k<=cptcovprod;k++)
|
| /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month |
cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
|
| duration (i.e. until |
|
| age (in years) age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices. |
/*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
|
| Output is stored in matrix po[i][j][h] for h every 'hstepm' step |
/*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
|
| (typically every 2 years instead of every month which is too big). |
/*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
|
| Model is determined by parameters x and covariates have to be |
out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
|
| included manually here. |
|
| |
savm=oldm;
|
| */ |
oldm=newm;
|
| |
maxmax=0.;
|
| int i, j, d, h; |
for(j=1;j<=nlstate;j++){
|
| double **out, cov[NCOVMAX]; |
min=1.;
|
| double **newm; |
max=0.;
|
| |
for(i=1; i<=nlstate; i++) {
|
| /* Hstepm could be zero and should return the unit matrix */ |
sumnew=0;
|
| for (i=1;i<=nlstate+ndeath;i++) |
for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
|
| for (j=1;j<=nlstate+ndeath;j++){ |
prlim[i][j]= newm[i][j]/(1-sumnew);
|
| oldm[i][j]=(i==j ? 1.0 : 0.0); |
max=FMAX(max,prlim[i][j]);
|
| po[i][j][0]=(i==j ? 1.0 : 0.0); |
min=FMIN(min,prlim[i][j]);
|
| } |
}
|
| /* Even if hstepm = 1, at least one multiplication by the unit matrix */ |
maxmin=max-min;
|
| for(h=1; h <=nhstepm; h++){ |
maxmax=FMAX(maxmax,maxmin);
|
| for(d=1; d <=hstepm; d++){ |
}
|
| newm=savm; |
if(maxmax < ftolpl){
|
| /* Covariates have to be included here again */ |
return prlim;
|
| cov[1]=1.; |
}
|
| cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM; |
}
|
| /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/ |
}
|
| out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, |
|
| pmij(pmmij,cov,ncov,x,nlstate)); |
/*************** transition probabilities ***************/
|
| savm=oldm; |
|
| oldm=newm; |
double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
|
| } |
{
|
| for(i=1; i<=nlstate+ndeath; i++) |
double s1, s2;
|
| for(j=1;j<=nlstate+ndeath;j++) { |
/*double t34;*/
|
| po[i][j][h]=newm[i][j]; |
int i,j,j1, nc, ii, jj;
|
| /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]); |
|
| */ |
for(i=1; i<= nlstate; i++){
|
| } |
for(j=1; j<i;j++){
|
| } /* end h */ |
for (nc=1, s2=0.;nc <=ncovmodel; nc++){
|
| return po; |
/*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);*/
|
| |
}
|
| /*************** log-likelihood *************/ |
ps[i][j]=s2;
|
| double func( double *x) |
/*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
|
| { |
}
|
| int i, ii, j, k, mi, d; |
for(j=i+1; j<=nlstate+ndeath;j++){
|
| double l, ll[NLSTATEMAX], cov[NCOVMAX]; |
for (nc=1, s2=0.;nc <=ncovmodel; nc++){
|
| double **out; |
s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
|
| double sw; /* Sum of weights */ |
/*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
|
| double lli; /* Individual log likelihood */ |
}
|
| long ipmx; |
ps[i][j]=s2;
|
| /*extern weight */ |
}
|
| /* We are differentiating ll according to initial status */ |
}
|
| /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/ |
/*ps[3][2]=1;*/
|
| /*for(i=1;i<imx;i++) |
|
| printf(" %d\n",s[4][i]); |
for(i=1; i<= nlstate; i++){
|
| */ |
s1=0;
|
| |
for(j=1; j<i; j++)
|
| for(k=1; k<=nlstate; k++) ll[k]=0.; |
s1+=exp(ps[i][j]);
|
| for (i=1,ipmx=0, sw=0.; i<=imx; i++){ |
for(j=i+1; j<=nlstate+ndeath; j++)
|
| for(mi=1; mi<= wav[i]-1; mi++){ |
s1+=exp(ps[i][j]);
|
| for (ii=1;ii<=nlstate+ndeath;ii++) |
ps[i][i]=1./(s1+1.);
|
| for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0); |
for(j=1; j<i; j++)
|
| for(d=0; d<dh[mi][i]; d++){ |
ps[i][j]= exp(ps[i][j])*ps[i][i];
|
| newm=savm; |
for(j=i+1; j<=nlstate+ndeath; j++)
|
| cov[1]=1.; |
ps[i][j]= exp(ps[i][j])*ps[i][i];
|
| cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM; |
/* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
|
| out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, |
} /* end i */
|
| 1,nlstate+ndeath,pmij(pmmij,cov,ncov,x,nlstate)); |
|
| savm=oldm; |
for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
|
| oldm=newm; |
for(jj=1; jj<= nlstate+ndeath; jj++){
|
| |
ps[ii][jj]=0;
|
| |
ps[ii][ii]=1;
|
| } /* end mult */ |
}
|
| |
}
|
| lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); |
|
| /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ |
|
| ipmx +=1; |
/* for(ii=1; ii<= nlstate+ndeath; ii++){
|
| sw += weight[i]; |
for(jj=1; jj<= nlstate+ndeath; jj++){
|
| ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; |
printf("%lf ",ps[ii][jj]);
|
| } /* end of wave */ |
}
|
| } /* end of individual */ |
printf("\n ");
|
| |
}
|
| for(k=1,l=0.; k<=nlstate; k++) l += ll[k]; |
printf("\n ");printf("%lf ",cov[2]);*/
|
| /* printf("l1=%f l2=%f ",ll[1],ll[2]); */ |
/*
|
| l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */ |
for(i=1; i<= npar; i++) printf("%f ",x[i]);
|
| return -l; |
goto end;*/
|
| } |
return ps;
|
| |
}
|
| |
|
| /*********** Maximum Likelihood Estimation ***************/ |
/**************** Product of 2 matrices ******************/
|
| |
|
| void mlikeli(FILE *ficres,double p[], int npar, int ncov, int nlstate, double ftol, double (*func)(double [])) |
double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
|
| { |
{
|
| int i,j, iter; |
/* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
|
| double **xi,*delti; |
b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
|
| double fret; |
/* in, b, out are matrice of pointers which should have been initialized
|
| xi=matrix(1,npar,1,npar); |
before: only the contents of out is modified. The function returns
|
| for (i=1;i<=npar;i++) |
a pointer to pointers identical to out */
|
| for (j=1;j<=npar;j++) |
long i, j, k;
|
| xi[i][j]=(i==j ? 1.0 : 0.0); |
for(i=nrl; i<= nrh; i++)
|
| printf("Powell\n"); |
for(k=ncolol; k<=ncoloh; k++)
|
| powell(p,xi,npar,ftol,&iter,&fret,func); |
for(j=ncl,out[i][k]=0.; j<=nch; j++)
|
| |
out[i][k] +=in[i][j]*b[j][k];
|
| printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p)); |
|
| fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p)); |
return out;
|
| |
}
|
| } |
|
| |
|
| /**** Computes Hessian and covariance matrix ***/ |
/************* Higher Matrix Product ***************/
|
| void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double [])) |
|
| { |
double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
|
| double **a,**y,*x,pd; |
{
|
| double **hess; |
/* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month
|
| int i, j,jk; |
duration (i.e. until
|
| int *indx; |
age (in years) age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.
|
| |
Output is stored in matrix po[i][j][h] for h every 'hstepm' step
|
| double hessii(double p[], double delta, int theta, double delti[]); |
(typically every 2 years instead of every month which is too big).
|
| double hessij(double p[], double delti[], int i, int j); |
Model is determined by parameters x and covariates have to be
|
| void lubksb(double **a, int npar, int *indx, double b[]) ; |
included manually here.
|
| void ludcmp(double **a, int npar, int *indx, double *d) ; |
|
| |
*/
|
| |
|
| hess=matrix(1,npar,1,npar); |
int i, j, d, h, k;
|
| |
double **out, cov[NCOVMAX];
|
| printf("\nCalculation of the hessian matrix. Wait...\n"); |
double **newm;
|
| for (i=1;i<=npar;i++){ |
|
| printf("%d",i);fflush(stdout); |
/* Hstepm could be zero and should return the unit matrix */
|
| hess[i][i]=hessii(p,ftolhess,i,delti); |
for (i=1;i<=nlstate+ndeath;i++)
|
| /*printf(" %f ",p[i]);*/ |
for (j=1;j<=nlstate+ndeath;j++){
|
| } |
oldm[i][j]=(i==j ? 1.0 : 0.0);
|
| |
po[i][j][0]=(i==j ? 1.0 : 0.0);
|
| for (i=1;i<=npar;i++) { |
}
|
| for (j=1;j<=npar;j++) { |
/* Even if hstepm = 1, at least one multiplication by the unit matrix */
|
| if (j>i) { |
for(h=1; h <=nhstepm; h++){
|
| printf(".%d%d",i,j);fflush(stdout); |
for(d=1; d <=hstepm; d++){
|
| hess[i][j]=hessij(p,delti,i,j); |
newm=savm;
|
| hess[j][i]=hess[i][j]; |
/* 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]]];
|
| printf("\n"); |
for (k=1; k<=cptcovage;k++)
|
| |
cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
|
| printf("\nInverting the hessian to get the covariance matrix. Wait...\n"); |
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]]];
|
| a=matrix(1,npar,1,npar); |
|
| y=matrix(1,npar,1,npar); |
|
| x=vector(1,npar); |
/*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
|
| indx=ivector(1,npar); |
/*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
|
| for (i=1;i<=npar;i++) |
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
|
| for (j=1;j<=npar;j++) a[i][j]=hess[i][j]; |
pmij(pmmij,cov,ncovmodel,x,nlstate));
|
| ludcmp(a,npar,indx,&pd); |
savm=oldm;
|
| |
oldm=newm;
|
| for (j=1;j<=npar;j++) { |
}
|
| for (i=1;i<=npar;i++) x[i]=0; |
for(i=1; i<=nlstate+ndeath; i++)
|
| x[j]=1; |
for(j=1;j<=nlstate+ndeath;j++) {
|
| lubksb(a,npar,indx,x); |
po[i][j][h]=newm[i][j];
|
| for (i=1;i<=npar;i++){ |
/*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
|
| matcov[i][j]=x[i]; |
*/
|
| } |
}
|
| } |
} /* end h */
|
| |
return po;
|
| printf("\n#Hessian matrix#\n"); |
}
|
| for (i=1;i<=npar;i++) { |
|
| for (j=1;j<=npar;j++) { |
|
| printf("%.3e ",hess[i][j]); |
/*************** log-likelihood *************/
|
| } |
double func( double *x)
|
| printf("\n"); |
{
|
| } |
int i, ii, j, k, mi, d, kk;
|
| |
double l, ll[NLSTATEMAX], cov[NCOVMAX];
|
| /* Recompute Inverse */ |
double **out;
|
| for (i=1;i<=npar;i++) |
double sw; /* Sum of weights */
|
| for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; |
double lli; /* Individual log likelihood */
|
| ludcmp(a,npar,indx,&pd); |
long ipmx;
|
| |
/*extern weight */
|
| /* printf("\n#Hessian matrix recomputed#\n"); |
/* We are differentiating ll according to initial status */
|
| |
/* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
|
| for (j=1;j<=npar;j++) { |
/*for(i=1;i<imx;i++)
|
| for (i=1;i<=npar;i++) x[i]=0; |
printf(" %d\n",s[4][i]);
|
| x[j]=1; |
*/
|
| lubksb(a,npar,indx,x); |
cov[1]=1.;
|
| for (i=1;i<=npar;i++){ |
|
| y[i][j]=x[i]; |
for(k=1; k<=nlstate; k++) ll[k]=0.;
|
| printf("%.3e ",y[i][j]); |
for (i=1,ipmx=0, sw=0.; i<=imx; i++){
|
| } |
for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
|
| printf("\n"); |
for(mi=1; mi<= wav[i]-1; mi++){
|
| } |
for (ii=1;ii<=nlstate+ndeath;ii++)
|
| */ |
for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
|
| |
for(d=0; d<dh[mi][i]; d++){
|
| free_matrix(a,1,npar,1,npar); |
newm=savm;
|
| free_matrix(y,1,npar,1,npar); |
cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
|
| free_vector(x,1,npar); |
for (kk=1; kk<=cptcovage;kk++) {
|
| free_ivector(indx,1,npar); |
cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
|
| free_matrix(hess,1,npar,1,npar); |
}
|
| |
|
| |
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
|
| } |
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
|
| |
savm=oldm;
|
| /*************** hessian matrix ****************/ |
oldm=newm;
|
| double hessii( double x[], double delta, int theta, double delti[]) |
|
| { |
|
| int i; |
} /* end mult */
|
| int l=1, lmax=20; |
|
| double k1,k2; |
lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);
|
| double p2[NPARMAX+1]; |
/* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
|
| double res; |
ipmx +=1;
|
| double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4; |
sw += weight[i];
|
| double fx; |
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
|
| int k=0,kmax=10; |
} /* end of wave */
|
| double l1; |
} /* end of individual */
|
| |
|
| fx=func(x); |
for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
|
| for (i=1;i<=npar;i++) p2[i]=x[i]; |
/* printf("l1=%f l2=%f ",ll[1],ll[2]); */
|
| for(l=0 ; l <=lmax; l++){ |
l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
|
| l1=pow(10,l); |
return -l;
|
| delts=delt; |
}
|
| for(k=1 ; k <kmax; k=k+1){ |
|
| delt = delta*(l1*k); |
|
| p2[theta]=x[theta] +delt; |
/*********** Maximum Likelihood Estimation ***************/
|
| k1=func(p2)-fx; |
|
| p2[theta]=x[theta]-delt; |
void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
|
| k2=func(p2)-fx; |
{
|
| /*res= (k1-2.0*fx+k2)/delt/delt; */ |
int i,j, iter;
|
| res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */ |
double **xi,*delti;
|
| |
double fret;
|
| #ifdef DEBUG |
xi=matrix(1,npar,1,npar);
|
| 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); |
for (i=1;i<=npar;i++)
|
| #endif |
for (j=1;j<=npar;j++)
|
| /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */ |
xi[i][j]=(i==j ? 1.0 : 0.0);
|
| if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){ |
printf("Powell\n");
|
| k=kmax; |
powell(p,xi,npar,ftol,&iter,&fret,func);
|
| } |
|
| else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */ |
printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
|
| k=kmax; l=lmax*10.; |
fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
|
| } |
|
| else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ |
}
|
| delts=delt; |
|
| } |
/**** Computes Hessian and covariance matrix ***/
|
| } |
void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
|
| } |
{
|
| delti[theta]=delts; |
double **a,**y,*x,pd;
|
| return res; |
double **hess;
|
| |
int i, j,jk;
|
| } |
int *indx;
|
| |
|
| double hessij( double x[], double delti[], int thetai,int thetaj) |
double hessii(double p[], double delta, int theta, double delti[]);
|
| { |
double hessij(double p[], double delti[], int i, int j);
|
| int i; |
void lubksb(double **a, int npar, int *indx, double b[]) ;
|
| int l=1, l1, lmax=20; |
void ludcmp(double **a, int npar, int *indx, double *d) ;
|
| double k1,k2,k3,k4,res,fx; |
|
| double p2[NPARMAX+1]; |
hess=matrix(1,npar,1,npar);
|
| int k; |
|
| |
printf("\nCalculation of the hessian matrix. Wait...\n");
|
| fx=func(x); |
for (i=1;i<=npar;i++){
|
| for (k=1; k<=2; k++) { |
printf("%d",i);fflush(stdout);
|
| for (i=1;i<=npar;i++) p2[i]=x[i]; |
hess[i][i]=hessii(p,ftolhess,i,delti);
|
| p2[thetai]=x[thetai]+delti[thetai]/k; |
/*printf(" %f ",p[i]);*/
|
| p2[thetaj]=x[thetaj]+delti[thetaj]/k; |
/*printf(" %lf ",hess[i][i]);*/
|
| k1=func(p2)-fx; |
}
|
| |
|
| p2[thetai]=x[thetai]+delti[thetai]/k; |
for (i=1;i<=npar;i++) {
|
| p2[thetaj]=x[thetaj]-delti[thetaj]/k; |
for (j=1;j<=npar;j++) {
|
| k2=func(p2)-fx; |
if (j>i) {
|
| |
printf(".%d%d",i,j);fflush(stdout);
|
| p2[thetai]=x[thetai]-delti[thetai]/k; |
hess[i][j]=hessij(p,delti,i,j);
|
| p2[thetaj]=x[thetaj]+delti[thetaj]/k; |
hess[j][i]=hess[i][j];
|
| k3=func(p2)-fx; |
/*printf(" %lf ",hess[i][j]);*/
|
| |
}
|
| p2[thetai]=x[thetai]-delti[thetai]/k; |
}
|
| p2[thetaj]=x[thetaj]-delti[thetaj]/k; |
}
|
| k4=func(p2)-fx; |
printf("\n");
|
| res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */ |
|
| #ifdef DEBUG |
printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
|
| printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); |
|
| #endif |
a=matrix(1,npar,1,npar);
|
| } |
y=matrix(1,npar,1,npar);
|
| return res; |
x=vector(1,npar);
|
| } |
indx=ivector(1,npar);
|
| |
for (i=1;i<=npar;i++)
|
| /************** Inverse of matrix **************/ |
for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
|
| void ludcmp(double **a, int n, int *indx, double *d) |
ludcmp(a,npar,indx,&pd);
|
| { |
|
| int i,imax,j,k; |
for (j=1;j<=npar;j++) {
|
| double big,dum,sum,temp; |
for (i=1;i<=npar;i++) x[i]=0;
|
| double *vv; |
x[j]=1;
|
| |
lubksb(a,npar,indx,x);
|
| vv=vector(1,n); |
for (i=1;i<=npar;i++){
|
| *d=1.0; |
matcov[i][j]=x[i];
|
| for (i=1;i<=n;i++) { |
}
|
| big=0.0; |
}
|
| for (j=1;j<=n;j++) |
|
| if ((temp=fabs(a[i][j])) > big) big=temp; |
printf("\n#Hessian matrix#\n");
|
| if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); |
for (i=1;i<=npar;i++) {
|
| vv[i]=1.0/big; |
for (j=1;j<=npar;j++) {
|
| } |
printf("%.3e ",hess[i][j]);
|
| for (j=1;j<=n;j++) { |
}
|
| for (i=1;i<j;i++) { |
printf("\n");
|
| sum=a[i][j]; |
}
|
| for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; |
|
| a[i][j]=sum; |
/* Recompute Inverse */
|
| } |
for (i=1;i<=npar;i++)
|
| big=0.0; |
for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
|
| for (i=j;i<=n;i++) { |
ludcmp(a,npar,indx,&pd);
|
| sum=a[i][j]; |
|
| for (k=1;k<j;k++) |
/* printf("\n#Hessian matrix recomputed#\n");
|
| sum -= a[i][k]*a[k][j]; |
|
| a[i][j]=sum; |
for (j=1;j<=npar;j++) {
|
| if ( (dum=vv[i]*fabs(sum)) >= big) { |
for (i=1;i<=npar;i++) x[i]=0;
|
| big=dum; |
x[j]=1;
|
| imax=i; |
lubksb(a,npar,indx,x);
|
| } |
for (i=1;i<=npar;i++){
|
| } |
y[i][j]=x[i];
|
| if (j != imax) { |
printf("%.3e ",y[i][j]);
|
| for (k=1;k<=n;k++) { |
}
|
| dum=a[imax][k]; |
printf("\n");
|
| a[imax][k]=a[j][k]; |
}
|
| a[j][k]=dum; |
*/
|
| } |
|
| *d = -(*d); |
free_matrix(a,1,npar,1,npar);
|
| vv[imax]=vv[j]; |
free_matrix(y,1,npar,1,npar);
|
| } |
free_vector(x,1,npar);
|
| indx[j]=imax; |
free_ivector(indx,1,npar);
|
| if (a[j][j] == 0.0) a[j][j]=TINY; |
free_matrix(hess,1,npar,1,npar);
|
| if (j != n) { |
|
| dum=1.0/(a[j][j]); |
|
| for (i=j+1;i<=n;i++) a[i][j] *= dum; |
}
|
| } |
|
| } |
/*************** hessian matrix ****************/
|
| free_vector(vv,1,n); /* Doesn't work */ |
double hessii( double x[], double delta, int theta, double delti[])
|
| ; |
{
|
| } |
int i;
|
| |
int l=1, lmax=20;
|
| void lubksb(double **a, int n, int *indx, double b[]) |
double k1,k2;
|
| { |
double p2[NPARMAX+1];
|
| int i,ii=0,ip,j; |
double res;
|
| double sum; |
double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
|
| |
double fx;
|
| for (i=1;i<=n;i++) { |
int k=0,kmax=10;
|
| ip=indx[i]; |
double l1;
|
| sum=b[ip]; |
|
| b[ip]=b[i]; |
fx=func(x);
|
| if (ii) |
for (i=1;i<=npar;i++) p2[i]=x[i];
|
| for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; |
for(l=0 ; l <=lmax; l++){
|
| else if (sum) ii=i; |
l1=pow(10,l);
|
| b[i]=sum; |
delts=delt;
|
| } |
for(k=1 ; k <kmax; k=k+1){
|
| for (i=n;i>=1;i--) { |
delt = delta*(l1*k);
|
| sum=b[i]; |
p2[theta]=x[theta] +delt;
|
| for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; |
k1=func(p2)-fx;
|
| b[i]=sum/a[i][i]; |
p2[theta]=x[theta]-delt;
|
| } |
k2=func(p2)-fx;
|
| } |
/*res= (k1-2.0*fx+k2)/delt/delt; */
|
| |
res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
|
| /************ Frequencies ********************/ |
|
| void freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx) |
#ifdef DEBUG
|
| { /* Some frequencies */ |
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);
|
| |
#endif
|
| int i, m, jk; |
/*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
|
| double ***freq; /* Frequencies */ |
if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
|
| double *pp; |
k=kmax;
|
| double pos; |
}
|
| FILE *ficresp; |
else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
|
| char fileresp[FILENAMELENGTH]; |
k=kmax; l=lmax*10.;
|
| |
}
|
| pp=vector(1,nlstate); |
else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
|
| |
delts=delt;
|
| strcpy(fileresp,"p"); |
}
|
| strcat(fileresp,fileres); |
}
|
| if((ficresp=fopen(fileresp,"w"))==NULL) { |
}
|
| printf("Problem with prevalence resultfile: %s\n", fileresp); |
delti[theta]=delts;
|
| exit(0); |
return res;
|
| } |
|
| |
}
|
| freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3); |
|
| for (i=-1; i<=nlstate+ndeath; i++) |
double hessij( double x[], double delti[], int thetai,int thetaj)
|
| for (jk=-1; jk<=nlstate+ndeath; jk++) |
{
|
| for(m=agemin; m <= agemax+3; m++) |
int i;
|
| freq[i][jk][m]=0; |
int l=1, l1, lmax=20;
|
| |
double k1,k2,k3,k4,res,fx;
|
| for (i=1; i<=imx; i++) { |
double p2[NPARMAX+1];
|
| for(m=firstpass; m<= lastpass-1; m++){ |
int k;
|
| if(agev[m][i]==0) agev[m][i]=agemax+1; |
|
| if(agev[m][i]==1) agev[m][i]=agemax+2; |
fx=func(x);
|
| freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; |
for (k=1; k<=2; k++) {
|
| freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i]; |
for (i=1;i<=npar;i++) p2[i]=x[i];
|
| } |
p2[thetai]=x[thetai]+delti[thetai]/k;
|
| } |
p2[thetaj]=x[thetaj]+delti[thetaj]/k;
|
| |
k1=func(p2)-fx;
|
| fprintf(ficresp, "#"); |
|
| for(i=1; i<=nlstate;i++) |
p2[thetai]=x[thetai]+delti[thetai]/k;
|
| fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i); |
p2[thetaj]=x[thetaj]-delti[thetaj]/k;
|
| fprintf(ficresp, "\n"); |
k2=func(p2)-fx;
|
| |
|
| for(i=(int)agemin; i <= (int)agemax+3; i++){ |
p2[thetai]=x[thetai]-delti[thetai]/k;
|
| if(i==(int)agemax+3) |
p2[thetaj]=x[thetaj]+delti[thetaj]/k;
|
| printf("Total"); |
k3=func(p2)-fx;
|
| else |
|
| printf("Age %d", i); |
p2[thetai]=x[thetai]-delti[thetai]/k;
|
| for(jk=1; jk <=nlstate ; jk++){ |
p2[thetaj]=x[thetaj]-delti[thetaj]/k;
|
| for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++) |
k4=func(p2)-fx;
|
| pp[jk] += freq[jk][m][i]; |
res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
|
| } |
#ifdef DEBUG
|
| for(jk=1; jk <=nlstate ; jk++){ |
printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
|
| for(m=-1, pos=0; m <=0 ; m++) |
#endif
|
| pos += freq[jk][m][i]; |
}
|
| if(pp[jk]>=1.e-10) |
return res;
|
| printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); |
}
|
| else |
|
| printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk); |
/************** Inverse of matrix **************/
|
| } |
void ludcmp(double **a, int n, int *indx, double *d)
|
| for(jk=1; jk <=nlstate ; jk++){ |
{
|
| for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++) |
int i,imax,j,k;
|
| pp[jk] += freq[jk][m][i]; |
double big,dum,sum,temp;
|
| } |
double *vv;
|
| for(jk=1,pos=0; jk <=nlstate ; jk++) |
|
| pos += pp[jk]; |
vv=vector(1,n);
|
| for(jk=1; jk <=nlstate ; jk++){ |
*d=1.0;
|
| if(pos>=1.e-5) |
for (i=1;i<=n;i++) {
|
| printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); |
big=0.0;
|
| else |
for (j=1;j<=n;j++)
|
| printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); |
if ((temp=fabs(a[i][j])) > big) big=temp;
|
| if( i <= (int) agemax){ |
if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
|
| if(pos>=1.e-5) |
vv[i]=1.0/big;
|
| fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos); |
}
|
| else |
for (j=1;j<=n;j++) {
|
| fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos); |
for (i=1;i<j;i++) {
|
| } |
sum=a[i][j];
|
| } |
for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
|
| for(jk=-1; jk <=nlstate+ndeath; jk++) |
a[i][j]=sum;
|
| for(m=-1; m <=nlstate+ndeath; m++) |
}
|
| if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]); |
big=0.0;
|
| if(i <= (int) agemax) |
for (i=j;i<=n;i++) {
|
| fprintf(ficresp,"\n"); |
sum=a[i][j];
|
| printf("\n"); |
for (k=1;k<j;k++)
|
| } |
sum -= a[i][k]*a[k][j];
|
| |
a[i][j]=sum;
|
| fclose(ficresp); |
if ( (dum=vv[i]*fabs(sum)) >= big) {
|
| free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3); |
big=dum;
|
| free_vector(pp,1,nlstate); |
imax=i;
|
| |
}
|
| } /* End of Freq */ |
}
|
| |
if (j != imax) {
|
| /************* Waves Concatenation ***************/ |
for (k=1;k<=n;k++) {
|
| |
dum=a[imax][k];
|
| void concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm) |
a[imax][k]=a[j][k];
|
| { |
a[j][k]=dum;
|
| /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i. |
}
|
| Death is a valid wave (if date is known). |
*d = -(*d);
|
| mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i |
vv[imax]=vv[j];
|
| dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i] |
}
|
| and mw[mi+1][i]. dh depends on stepm. |
indx[j]=imax;
|
| */ |
if (a[j][j] == 0.0) a[j][j]=TINY;
|
| |
if (j != n) {
|
| int i, mi, m; |
dum=1.0/(a[j][j]);
|
| int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1; |
for (i=j+1;i<=n;i++) a[i][j] *= dum;
|
| float sum=0.; |
}
|
| |
}
|
| for(i=1; i<=imx; i++){ |
free_vector(vv,1,n); /* Doesn't work */
|
| mi=0; |
;
|
| m=firstpass; |
}
|
| while(s[m][i] <= nlstate){ |
|
| if(s[m][i]>=1) |
void lubksb(double **a, int n, int *indx, double b[])
|
| mw[++mi][i]=m; |
{
|
| if(m >=lastpass) |
int i,ii=0,ip,j;
|
| break; |
double sum;
|
| else |
|
| m++; |
for (i=1;i<=n;i++) {
|
| }/* end while */ |
ip=indx[i];
|
| if (s[m][i] > nlstate){ |
sum=b[ip];
|
| mi++; /* Death is another wave */ |
b[ip]=b[i];
|
| /* if(mi==0) never been interviewed correctly before death */ |
if (ii)
|
| /* Only death is a correct wave */ |
for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
|
| mw[mi][i]=m; |
else if (sum) ii=i;
|
| } |
b[i]=sum;
|
| |
}
|
| wav[i]=mi; |
for (i=n;i>=1;i--) {
|
| if(mi==0) |
sum=b[i];
|
| printf("Warning, no any valid information for:%d line=%d\n",num[i],i); |
for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
|
| } |
b[i]=sum/a[i][i];
|
| |
}
|
| for(i=1; i<=imx; i++){ |
}
|
| for(mi=1; mi<wav[i];mi++){ |
|
| if (stepm <=0) |
/************ Frequencies ********************/
|
| dh[mi][i]=1; |
void freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
|
| else{ |
{ /* Some frequencies */
|
| if (s[mw[mi+1][i]][i] > nlstate) { |
|
| j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); |
int i, m, jk, k1,i1, j1, bool, z1,z2,j;
|
| if(j=0) j=1; /* Survives at least one month after exam */ |
double ***freq; /* Frequencies */
|
| } |
double *pp;
|
| else{ |
double pos, k2, dateintsum=0,k2cpt=0;
|
| j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12)); |
FILE *ficresp;
|
| k=k+1; |
char fileresp[FILENAMELENGTH];
|
| if (j >= jmax) jmax=j; |
|
| else if (j <= jmin)jmin=j; |
pp=vector(1,nlstate);
|
| sum=sum+j; |
probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
|
| } |
strcpy(fileresp,"p");
|
| jk= j/stepm; |
strcat(fileresp,fileres);
|
| jl= j -jk*stepm; |
if((ficresp=fopen(fileresp,"w"))==NULL) {
|
| ju= j -(jk+1)*stepm; |
printf("Problem with prevalence resultfile: %s\n", fileresp);
|
| if(jl <= -ju) |
exit(0);
|
| dh[mi][i]=jk; |
}
|
| else |
freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
|
| dh[mi][i]=jk+1; |
j1=0;
|
| if(dh[mi][i]==0) |
|
| dh[mi][i]=1; /* At least one step */ |
j=cptcoveff;
|
| } |
if (cptcovn<1) {j=1;ncodemax[1]=1;}
|
| } |
|
| } |
for(k1=1; k1<=j;k1++){
|
| printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k); |
for(i1=1; i1<=ncodemax[k1];i1++){
|
| } |
j1++;
|
| |
/*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
|
| /*********** Health Expectancies ****************/ |
scanf("%d", i);*/
|
| |
for (i=-1; i<=nlstate+ndeath; i++)
|
| void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm) |
for (jk=-1; jk<=nlstate+ndeath; jk++)
|
| { |
for(m=agemin; m <= agemax+3; m++)
|
| /* Health expectancies */ |
freq[i][jk][m]=0;
|
| int i, j, nhstepm, hstepm, h; |
|
| double age, agelim,hf; |
dateintsum=0;
|
| double ***p3mat; |
k2cpt=0;
|
| |
for (i=1; i<=imx; i++) {
|
| FILE *ficreseij; |
bool=1;
|
| char filerese[FILENAMELENGTH]; |
if (cptcovn>0) {
|
| |
for (z1=1; z1<=cptcoveff; z1++)
|
| strcpy(filerese,"e"); |
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
|
| strcat(filerese,fileres); |
bool=0;
|
| if((ficreseij=fopen(filerese,"w"))==NULL) { |
}
|
| printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0); |
if (bool==1) {
|
| } |
for(m=firstpass; m<=lastpass; m++){
|
| printf("Computing Health Expectancies: result on file '%s' \n", filerese); |
k2=anint[m][i]+(mint[m][i]/12.);
|
| |
if ((k2>=dateprev1) && (k2<=dateprev2)) {
|
| fprintf(ficreseij,"# Health expectancies\n"); |
if(agev[m][i]==0) agev[m][i]=agemax+1;
|
| fprintf(ficreseij,"# Age"); |
if(agev[m][i]==1) agev[m][i]=agemax+2;
|
| for(i=1; i<=nlstate;i++) |
if (m<lastpass) {
|
| for(j=1; j<=nlstate;j++) |
freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
|
| fprintf(ficreseij," %1d-%1d",i,j); |
freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
|
| fprintf(ficreseij,"\n"); |
}
|
| |
|
| hstepm=1*YEARM; /* Every j years of age (in month) */ |
if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
|
| hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ |
dateintsum=dateintsum+k2;
|
| |
k2cpt++;
|
| agelim=AGESUP; |
}
|
| for (age=bage; age<=fage; age ++){ /* If stepm=6 months */ |
}
|
| /* nhstepm age range expressed in number of stepm */ |
}
|
| nhstepm=(int) rint((agelim-age)*YEARM/stepm); |
}
|
| /* Typically if 20 years = 20*12/6=40 stepm */ |
}
|
| if (stepm >= YEARM) hstepm=1; |
|
| nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */ |
fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
|
| p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
|
| /* Computed by stepm unit matrices, product of hstepm matrices, stored |
if (cptcovn>0) {
|
| in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */ |
fprintf(ficresp, "\n#********** Variable ");
|
| hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
|
| |
fprintf(ficresp, "**********\n#");
|
| |
}
|
| for(i=1; i<=nlstate;i++) |
for(i=1; i<=nlstate;i++)
|
| for(j=1; j<=nlstate;j++) |
fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
|
| for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){ |
fprintf(ficresp, "\n");
|
| eij[i][j][(int)age] +=p3mat[i][j][h]; |
|
| } |
for(i=(int)agemin; i <= (int)agemax+3; i++){
|
| |
if(i==(int)agemax+3)
|
| hf=1; |
printf("Total");
|
| if (stepm >= YEARM) hf=stepm/YEARM; |
else
|
| fprintf(ficreseij,"%.0f",age ); |
printf("Age %d", i);
|
| for(i=1; i<=nlstate;i++) |
for(jk=1; jk <=nlstate ; jk++){
|
| for(j=1; j<=nlstate;j++){ |
for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
|
| fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]); |
pp[jk] += freq[jk][m][i];
|
| } |
}
|
| fprintf(ficreseij,"\n"); |
for(jk=1; jk <=nlstate ; jk++){
|
| free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
for(m=-1, pos=0; m <=0 ; m++)
|
| } |
pos += freq[jk][m][i];
|
| fclose(ficreseij); |
if(pp[jk]>=1.e-10)
|
| } |
printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
|
| |
else
|
| /************ Variance ******************/ |
printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
|
| void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl) |
}
|
| { |
|
| /* Variance of health expectancies */ |
for(jk=1; jk <=nlstate ; jk++){
|
| /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/ |
for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
|
| double **newm; |
pp[jk] += freq[jk][m][i];
|
| double **dnewm,**doldm; |
}
|
| int i, j, nhstepm, hstepm, h; |
|
| int k; |
for(jk=1,pos=0; jk <=nlstate ; jk++)
|
| FILE *ficresvij; |
pos += pp[jk];
|
| char fileresv[FILENAMELENGTH]; |
for(jk=1; jk <=nlstate ; jk++){
|
| double *xp; |
if(pos>=1.e-5)
|
| double **gp, **gm; |
printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
|
| double ***gradg, ***trgradg; |
else
|
| double ***p3mat; |
printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
|
| double age,agelim; |
if( i <= (int) agemax){
|
| int theta; |
if(pos>=1.e-5){
|
| |
fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
|
| strcpy(fileresv,"v"); |
probs[i][jk][j1]= pp[jk]/pos;
|
| strcat(fileresv,fileres); |
/*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
|
| if((ficresvij=fopen(fileresv,"w"))==NULL) { |
}
|
| printf("Problem with variance resultfile: %s\n", fileresv);exit(0); |
else
|
| } |
fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
|
| printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); |
}
|
| |
}
|
| |
|
| fprintf(ficresvij,"# Covariances of life expectancies\n"); |
for(jk=-1; jk <=nlstate+ndeath; jk++)
|
| fprintf(ficresvij,"# Age"); |
for(m=-1; m <=nlstate+ndeath; m++)
|
| for(i=1; i<=nlstate;i++) |
if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
|
| for(j=1; j<=nlstate;j++) |
if(i <= (int) agemax)
|
| fprintf(ficresvij," Cov(e%1d, e%1d)",i,j); |
fprintf(ficresp,"\n");
|
| fprintf(ficresvij,"\n"); |
printf("\n");
|
| |
}
|
| xp=vector(1,npar); |
}
|
| dnewm=matrix(1,nlstate,1,npar); |
}
|
| doldm=matrix(1,nlstate,1,nlstate); |
dateintmean=dateintsum/k2cpt;
|
| |
|
| hstepm=1*YEARM; /* Every year of age */ |
fclose(ficresp);
|
| hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ |
free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
|
| agelim = AGESUP; |
free_vector(pp,1,nlstate);
|
| for (age=bage; age<=fage; age ++){ /* If stepm=6 months */ |
|
| nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ |
/* End of Freq */
|
| if (stepm >= YEARM) hstepm=1; |
}
|
| nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */ |
|
| p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
/************ Prevalence ********************/
|
| gradg=ma3x(0,nhstepm,1,npar,1,nlstate); |
void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)
|
| gp=matrix(0,nhstepm,1,nlstate); |
{ /* Some frequencies */
|
| gm=matrix(0,nhstepm,1,nlstate); |
|
| |
int i, m, jk, k1, i1, j1, bool, z1,z2,j;
|
| for(theta=1; theta <=npar; theta++){ |
double ***freq; /* Frequencies */
|
| for(i=1; i<=npar; i++){ /* Computes gradient */ |
double *pp;
|
| xp[i] = x[i] + (i==theta ?delti[theta]:0); |
double pos, k2;
|
| } |
|
| hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm); |
pp=vector(1,nlstate);
|
| prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl); |
probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
|
| for(j=1; j<= nlstate; j++){ |
|
| for(h=0; h<=nhstepm; h++){ |
freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
|
| for(i=1, gp[h][j]=0.;i<=nlstate;i++) |
j1=0;
|
| gp[h][j] += prlim[i][i]*p3mat[i][j][h]; |
|
| } |
j=cptcoveff;
|
| } |
if (cptcovn<1) {j=1;ncodemax[1]=1;}
|
| |
|
| for(i=1; i<=npar; i++) /* Computes gradient */ |
for(k1=1; k1<=j;k1++){
|
| xp[i] = x[i] - (i==theta ?delti[theta]:0); |
for(i1=1; i1<=ncodemax[k1];i1++){
|
| hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm); |
j1++;
|
| prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl); |
|
| for(j=1; j<= nlstate; j++){ |
for (i=-1; i<=nlstate+ndeath; i++)
|
| for(h=0; h<=nhstepm; h++){ |
for (jk=-1; jk<=nlstate+ndeath; jk++)
|
| for(i=1, gm[h][j]=0.;i<=nlstate;i++) |
for(m=agemin; m <= agemax+3; m++)
|
| gm[h][j] += prlim[i][i]*p3mat[i][j][h]; |
freq[i][jk][m]=0;
|
| } |
|
| } |
for (i=1; i<=imx; i++) {
|
| for(j=1; j<= nlstate; j++) |
bool=1;
|
| for(h=0; h<=nhstepm; h++){ |
if (cptcovn>0) {
|
| gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta]; |
for (z1=1; z1<=cptcoveff; z1++)
|
| } |
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
|
| } /* End theta */ |
bool=0;
|
| |
}
|
| trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); |
if (bool==1) {
|
| |
for(m=firstpass; m<=lastpass; m++){
|
| for(h=0; h<=nhstepm; h++) |
k2=anint[m][i]+(mint[m][i]/12.);
|
| for(j=1; j<=nlstate;j++) |
if ((k2>=dateprev1) && (k2<=dateprev2)) {
|
| for(theta=1; theta <=npar; theta++) |
if(agev[m][i]==0) agev[m][i]=agemax+1;
|
| trgradg[h][j][theta]=gradg[h][theta][j]; |
if(agev[m][i]==1) agev[m][i]=agemax+2;
|
| |
if (m<lastpass) {
|
| for(i=1;i<=nlstate;i++) |
if (calagedate>0)
|
| for(j=1;j<=nlstate;j++) |
freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
|
| vareij[i][j][(int)age] =0.; |
else
|
| for(h=0;h<=nhstepm;h++){ |
freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
|
| for(k=0;k<=nhstepm;k++){ |
freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];
|
| matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov); |
}
|
| matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]); |
}
|
| for(i=1;i<=nlstate;i++) |
}
|
| for(j=1;j<=nlstate;j++) |
}
|
| vareij[i][j][(int)age] += doldm[i][j]; |
}
|
| } |
for(i=(int)agemin; i <= (int)agemax+3; i++){
|
| } |
for(jk=1; jk <=nlstate ; jk++){
|
| h=1; |
for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
|
| if (stepm >= YEARM) h=stepm/YEARM; |
pp[jk] += freq[jk][m][i];
|
| fprintf(ficresvij,"%.0f ",age ); |
}
|
| for(i=1; i<=nlstate;i++) |
for(jk=1; jk <=nlstate ; jk++){
|
| for(j=1; j<=nlstate;j++){ |
for(m=-1, pos=0; m <=0 ; m++)
|
| fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]); |
pos += freq[jk][m][i];
|
| } |
}
|
| fprintf(ficresvij,"\n"); |
|
| free_matrix(gp,0,nhstepm,1,nlstate); |
for(jk=1; jk <=nlstate ; jk++){
|
| free_matrix(gm,0,nhstepm,1,nlstate); |
for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
|
| free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate); |
pp[jk] += freq[jk][m][i];
|
| free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar); |
}
|
| free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
|
| } /* End age */ |
for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
|
| fclose(ficresvij); |
|
| free_vector(xp,1,npar); |
for(jk=1; jk <=nlstate ; jk++){
|
| free_matrix(doldm,1,nlstate,1,npar); |
if( i <= (int) agemax){
|
| free_matrix(dnewm,1,nlstate,1,nlstate); |
if(pos>=1.e-5){
|
| |
probs[i][jk][j1]= pp[jk]/pos;
|
| } |
}
|
| |
}
|
| /************ Variance of prevlim ******************/ |
}
|
| void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl) |
|
| { |
}
|
| /* Variance of health expectancies */ |
}
|
| /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/ |
}
|
| double **newm; |
|
| double **dnewm,**doldm; |
|
| int i, j, nhstepm, hstepm; |
free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
|
| int k; |
free_vector(pp,1,nlstate);
|
| FILE *ficresvpl; |
|
| char fileresvpl[FILENAMELENGTH]; |
} /* End of Freq */
|
| double *xp; |
|
| double *gp, *gm; |
/************* Waves Concatenation ***************/
|
| double **gradg, **trgradg; |
|
| double age,agelim; |
void concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)
|
| int theta; |
{
|
| |
/* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
|
| strcpy(fileresvpl,"vpl"); |
Death is a valid wave (if date is known).
|
| strcat(fileresvpl,fileres); |
mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
|
| if((ficresvpl=fopen(fileresvpl,"w"))==NULL) { |
dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]
|
| printf("Problem with variance prev lim resultfile: %s\n", fileresvpl); |
and mw[mi+1][i]. dh depends on stepm.
|
| exit(0); |
*/
|
| } |
|
| printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl); |
int i, mi, m;
|
| |
/* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
|
| |
double sum=0., jmean=0.;*/
|
| fprintf(ficresvpl,"# Standard deviation of prevalences limit\n"); |
|
| fprintf(ficresvpl,"# Age"); |
int j, k=0,jk, ju, jl;
|
| for(i=1; i<=nlstate;i++) |
double sum=0.;
|
| fprintf(ficresvpl," %1d-%1d",i,i); |
jmin=1e+5;
|
| fprintf(ficresvpl,"\n"); |
jmax=-1;
|
| |
jmean=0.;
|
| xp=vector(1,npar); |
for(i=1; i<=imx; i++){
|
| dnewm=matrix(1,nlstate,1,npar); |
mi=0;
|
| doldm=matrix(1,nlstate,1,nlstate); |
m=firstpass;
|
| |
while(s[m][i] <= nlstate){
|
| hstepm=1*YEARM; /* Every year of age */ |
if(s[m][i]>=1)
|
| hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ |
mw[++mi][i]=m;
|
| agelim = AGESUP; |
if(m >=lastpass)
|
| for (age=bage; age<=fage; age ++){ /* If stepm=6 months */ |
break;
|
| nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ |
else
|
| if (stepm >= YEARM) hstepm=1; |
m++;
|
| nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */ |
}/* end while */
|
| gradg=matrix(1,npar,1,nlstate); |
if (s[m][i] > nlstate){
|
| gp=vector(1,nlstate); |
mi++; /* Death is another wave */
|
| gm=vector(1,nlstate); |
/* if(mi==0) never been interviewed correctly before death */
|
| |
/* Only death is a correct wave */
|
| for(theta=1; theta <=npar; theta++){ |
mw[mi][i]=m;
|
| for(i=1; i<=npar; i++){ /* Computes gradient */ |
}
|
| xp[i] = x[i] + (i==theta ?delti[theta]:0); |
|
| } |
wav[i]=mi;
|
| prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl); |
if(mi==0)
|
| for(i=1;i<=nlstate;i++) |
printf("Warning, no any valid information for:%d line=%d\n",num[i],i);
|
| gp[i] = prlim[i][i]; |
}
|
| |
|
| for(i=1; i<=npar; i++) /* Computes gradient */ |
for(i=1; i<=imx; i++){
|
| xp[i] = x[i] - (i==theta ?delti[theta]:0); |
for(mi=1; mi<wav[i];mi++){
|
| prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl); |
if (stepm <=0)
|
| for(i=1;i<=nlstate;i++) |
dh[mi][i]=1;
|
| gm[i] = prlim[i][i]; |
else{
|
| |
if (s[mw[mi+1][i]][i] > nlstate) {
|
| for(i=1;i<=nlstate;i++) |
if (agedc[i] < 2*AGESUP) {
|
| gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta]; |
j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
|
| } /* End theta */ |
if(j==0) j=1; /* Survives at least one month after exam */
|
| |
k=k+1;
|
| trgradg =matrix(1,nlstate,1,npar); |
if (j >= jmax) jmax=j;
|
| |
if (j <= jmin) jmin=j;
|
| for(j=1; j<=nlstate;j++) |
sum=sum+j;
|
| for(theta=1; theta <=npar; theta++) |
/*if (j<0) printf("j=%d num=%d \n",j,i); */
|
| trgradg[j][theta]=gradg[theta][j]; |
}
|
| |
}
|
| for(i=1;i<=nlstate;i++) |
else{
|
| varpl[i][(int)age] =0.; |
j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
|
| matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov); |
k=k+1;
|
| matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg); |
if (j >= jmax) jmax=j;
|
| for(i=1;i<=nlstate;i++) |
else if (j <= jmin)jmin=j;
|
| varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */ |
/* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
|
| |
sum=sum+j;
|
| fprintf(ficresvpl,"%.0f ",age ); |
}
|
| for(i=1; i<=nlstate;i++) |
jk= j/stepm;
|
| fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age])); |
jl= j -jk*stepm;
|
| fprintf(ficresvpl,"\n"); |
ju= j -(jk+1)*stepm;
|
| free_vector(gp,1,nlstate); |
if(jl <= -ju)
|
| free_vector(gm,1,nlstate); |
dh[mi][i]=jk;
|
| free_matrix(gradg,1,npar,1,nlstate); |
else
|
| free_matrix(trgradg,1,nlstate,1,npar); |
dh[mi][i]=jk+1;
|
| } /* End age */ |
if(dh[mi][i]==0)
|
| fclose(ficresvpl); |
dh[mi][i]=1; /* At least one step */
|
| free_vector(xp,1,npar); |
}
|
| free_matrix(doldm,1,nlstate,1,npar); |
}
|
| free_matrix(dnewm,1,nlstate,1,nlstate); |
}
|
| |
jmean=sum/k;
|
| } |
printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
|
| |
}
|
| |
/*********** Tricode ****************************/
|
| |
void tricode(int *Tvar, int **nbcode, int imx)
|
| /***********************************************/ |
{
|
| /**************** Main Program *****************/ |
int Ndum[20],ij=1, k, j, i;
|
| /***********************************************/ |
int cptcode=0;
|
| |
cptcoveff=0;
|
| /*int main(int argc, char *argv[])*/ |
|
| int main() |
for (k=0; k<19; k++) Ndum[k]=0;
|
| { |
for (k=1; k<=7; k++) ncodemax[k]=0;
|
| |
|
| int i,j, k, n=MAXN,iter,m,size; |
for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
|
| double agedeb, agefin,hf; |
for (i=1; i<=imx; i++) {
|
| double agemin=1.e20, agemax=-1.e20; |
ij=(int)(covar[Tvar[j]][i]);
|
| |
Ndum[ij]++;
|
| double fret; |
/*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
|
| double **xi,tmp,delta; |
if (ij > cptcode) cptcode=ij;
|
| |
}
|
| double dum; /* Dummy variable */ |
|
| double ***p3mat; |
for (i=0; i<=cptcode; i++) {
|
| int *indx; |
if(Ndum[i]!=0) ncodemax[j]++;
|
| char line[MAXLINE], linepar[MAXLINE]; |
}
|
| char title[MAXLINE]; |
ij=1;
|
| char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH]; |
|
| char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH]; |
|
| char filerest[FILENAMELENGTH]; |
for (i=1; i<=ncodemax[j]; i++) {
|
| char fileregp[FILENAMELENGTH]; |
for (k=0; k<=19; k++) {
|
| char path[80],pathc[80],pathcd[80],pathtot[80]; |
if (Ndum[k] != 0) {
|
| int firstobs=1, lastobs=10; |
nbcode[Tvar[j]][ij]=k;
|
| int sdeb, sfin; /* Status at beginning and end */ |
|
| int c, h , cpt,l; |
ij++;
|
| int ju,jl, mi; |
}
|
| int i1,j1, k1,jk,aa,bb, stepsize; |
if (ij > ncodemax[j]) break;
|
| int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab; |
}
|
| |
}
|
| int hstepm, nhstepm; |
}
|
| double bage, fage, age, agelim, agebase; |
|
| double ftolpl=FTOL; |
for (k=0; k<19; k++) Ndum[k]=0;
|
| double **prlim; |
|
| double *severity; |
for (i=1; i<=ncovmodel-2; i++) {
|
| double ***param; /* Matrix of parameters */ |
ij=Tvar[i];
|
| double *p; |
Ndum[ij]++;
|
| double **matcov; /* Matrix of covariance */ |
}
|
| double ***delti3; /* Scale */ |
|
| double *delti; /* Scale */ |
ij=1;
|
| double ***eij, ***vareij; |
for (i=1; i<=10; i++) {
|
| double **varpl; /* Variances of prevalence limits by age */ |
if((Ndum[i]!=0) && (i<=ncovcol)){
|
| double *epj, vepp; |
Tvaraff[ij]=i;
|
| char version[80]="Imach version 0.64, May 2000, INED-EUROREVES "; |
ij++;
|
| char *alph[]={"a","a","b","c","d","e"}, str[4]; |
}
|
| char z[1]="c"; |
}
|
| #include <sys/time.h> |
|
| #include <time.h> |
cptcoveff=ij-1;
|
| |
}
|
| /* long total_usecs; |
|
| struct timeval start_time, end_time; |
/*********** Health Expectancies ****************/
|
| |
|
| gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */ |
void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
|
| |
|
| |
{
|
| printf("\nIMACH, Version 0.64"); |
/* Health expectancies */
|
| printf("\nEnter the parameter file name: "); |
int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
|
| #define windows 1 |
double age, agelim, hf;
|
| #ifdef windows |
double ***p3mat,***varhe;
|
| scanf("%s",pathtot); |
double **dnewm,**doldm;
|
| getcwd(pathcd, size); |
double *xp;
|
| cut(path,optionfile,pathtot); |
double **gp, **gm;
|
| chdir(path); |
double ***gradg, ***trgradg;
|
| replace(pathc,path); |
int theta;
|
| #endif |
|
| #ifdef unix |
varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
|
| scanf("%s",optionfile); |
xp=vector(1,npar);
|
| #endif |
dnewm=matrix(1,nlstate*2,1,npar);
|
| |
doldm=matrix(1,nlstate*2,1,nlstate*2);
|
| /*-------- arguments in the command line --------*/ |
|
| |
fprintf(ficreseij,"# Health expectancies\n");
|
| strcpy(fileres,"r"); |
fprintf(ficreseij,"# Age");
|
| strcat(fileres, optionfile); |
for(i=1; i<=nlstate;i++)
|
| |
for(j=1; j<=nlstate;j++)
|
| /*---------arguments file --------*/ |
fprintf(ficreseij," %1d-%1d (SE)",i,j);
|
| |
fprintf(ficreseij,"\n");
|
| if((ficpar=fopen(optionfile,"r"))==NULL) { |
|
| printf("Problem with optionfile %s\n",optionfile); |
if(estepm < stepm){
|
| goto end; |
printf ("Problem %d lower than %d\n",estepm, stepm);
|
| } |
}
|
| |
else hstepm=estepm;
|
| strcpy(filereso,"o"); |
/* We compute the life expectancy from trapezoids spaced every estepm months
|
| strcat(filereso,fileres); |
* This is mainly to measure the difference between two models: for example
|
| if((ficparo=fopen(filereso,"w"))==NULL) { |
* if stepm=24 months pijx are given only every 2 years and by summing them
|
| printf("Problem with Output resultfile: %s\n", filereso);goto end; |
* we are calculating an estimate of the Life Expectancy assuming a linear
|
| } |
* progression inbetween and thus overestimating or underestimating according
|
| |
* to the curvature of the survival function. If, for the same date, we
|
| /*--------- index.htm --------*/ |
* estimate the model with stepm=1 month, we can keep estepm to 24 months
|
| |
* to compare the new estimate of Life expectancy with the same linear
|
| if((fichtm=fopen("index.htm","w"))==NULL) { |
* hypothesis. A more precise result, taking into account a more precise
|
| printf("Problem with index.htm \n");goto end; |
* curvature will be obtained if estepm is as small as stepm. */
|
| } |
|
| |
/* For example we decided to compute the life expectancy with the smallest unit */
|
| fprintf(fichtm,"<body><ul><li>Outputs files<br><br>\n |
/* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
|
| - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n |
nhstepm is the number of hstepm from age to agelim
|
| - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br> |
nstepm is the number of stepm from age to agelin.
|
| - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br> |
Look at hpijx to understand the reason of that which relies in memory size
|
| - Transition probabilities: <a href=\"pij%s\">pij%s</a><br> |
and note for a fixed period like estepm months */
|
| - Copy of the parameter file: <a href=\"o%s\">o%s</a><br> |
/* We decided (b) to get a life expectancy respecting the most precise curvature of the
|
| - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br> |
survival function given by stepm (the optimization length). Unfortunately it
|
| - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br> |
means that if the survival funtion is printed only each two years of age and if
|
| - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br> |
you sum them up and add 1 year (area under the trapezoids) you won't get the same
|
| - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><br>",fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres); |
results. So we changed our mind and took the option of the best precision.
|
| |
*/
|
| fprintf(fichtm," <li>Graphs<br> <br>"); |
hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
|
| |
|
| for(cpt=1; cpt<nlstate;cpt++) |
agelim=AGESUP;
|
| fprintf(fichtm,"- Prevalence of disability: p%s1.gif<br> |
for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
|
| <img src=\"p%s1.gif\"><br>",strtok(optionfile, "."),strtok(optionfile, "."),cpt); |
/* nhstepm age range expressed in number of stepm */
|
| for(cpt=1; cpt<=nlstate;cpt++) |
nstepm=(int) rint((agelim-age)*YEARM/stepm);
|
| fprintf(fichtm,"- Observed and stationary prevalence (with confident |
/* Typically if 20 years nstepm = 20*12/6=40 stepm */
|
| interval) in state (%d): v%s%d.gif <br> |
/* if (stepm >= YEARM) hstepm=1;*/
|
| <img src=\"v%s%d.gif\"><br>",cpt,strtok(optionfile, "."),cpt,strtok(optionfile, "."),cpt); |
nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
|
| |
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
| for(cpt=1; cpt<=nlstate;cpt++) |
gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
|
| fprintf(fichtm,"- Health life expectancies by age and initial health state (%d): exp%s%d.gif <br> |
gp=matrix(0,nhstepm,1,nlstate*2);
|
| <img src=\"ex%s%d.gif\"><br>",cpt,strtok(optionfile, "."),cpt,strtok(optionfile, "."),cpt); |
gm=matrix(0,nhstepm,1,nlstate*2);
|
| |
|
| fprintf(fichtm,"- Total life expectancy by age and |
/* Computed by stepm unit matrices, product of hstepm matrices, stored
|
| health expectancies in states (1) and (2): e%s.gif<br> |
in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
|
| <img src=\"e%s.gif\"></li> </ul></body>",strtok(optionfile, "."),strtok(optionfile, ".")); |
hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
|
| |
|
| |
|
| fclose(fichtm); |
hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
|
| |
|
| /* Reads comments: lines beginning with '#' */ |
/* Computing Variances of health expectancies */
|
| while((c=getc(ficpar))=='#' && c!= EOF){ |
|
| ungetc(c,ficpar); |
for(theta=1; theta <=npar; theta++){
|
| fgets(line, MAXLINE, ficpar); |
for(i=1; i<=npar; i++){
|
| puts(line); |
xp[i] = x[i] + (i==theta ?delti[theta]:0);
|
| fputs(line,ficparo); |
}
|
| } |
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
|
| ungetc(c,ficpar); |
|
| |
cptj=0;
|
| fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt); |
for(j=1; j<= nlstate; j++){
|
| printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt); |
for(i=1; i<=nlstate; i++){
|
| fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt); |
cptj=cptj+1;
|
| |
for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
|
| nvar=ncov-1; /* Suppressing age as a basic covariate */ |
gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
|
| |
}
|
| /* Read guess parameters */ |
}
|
| /* Reads comments: lines beginning with '#' */ |
}
|
| while((c=getc(ficpar))=='#' && c!= EOF){ |
|
| ungetc(c,ficpar); |
|
| fgets(line, MAXLINE, ficpar); |
for(i=1; i<=npar; i++)
|
| puts(line); |
xp[i] = x[i] - (i==theta ?delti[theta]:0);
|
| fputs(line,ficparo); |
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
|
| } |
|
| ungetc(c,ficpar); |
cptj=0;
|
| |
for(j=1; j<= nlstate; j++){
|
| param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncov); |
for(i=1;i<=nlstate;i++){
|
| for(i=1; i <=nlstate; i++) |
cptj=cptj+1;
|
| for(j=1; j <=nlstate+ndeath-1; j++){ |
for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
|
| fscanf(ficpar,"%1d%1d",&i1,&j1); |
gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
|
| fprintf(ficparo,"%1d%1d",i1,j1); |
}
|
| printf("%1d%1d",i,j); |
}
|
| for(k=1; k<=ncov;k++){ |
}
|
| fscanf(ficpar," %lf",¶m[i][j][k]); |
for(j=1; j<= nlstate*2; j++)
|
| printf(" %lf",param[i][j][k]); |
for(h=0; h<=nhstepm-1; h++){
|
| fprintf(ficparo," %lf",param[i][j][k]); |
gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
|
| } |
}
|
| fscanf(ficpar,"\n"); |
}
|
| printf("\n"); |
|
| fprintf(ficparo,"\n"); |
/* End theta */
|
| } |
|
| |
trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
|
| npar= (nlstate+ndeath-1)*nlstate*ncov; |
|
| p=param[1][1]; |
for(h=0; h<=nhstepm-1; h++)
|
| |
for(j=1; j<=nlstate*2;j++)
|
| /* Reads comments: lines beginning with '#' */ |
for(theta=1; theta <=npar; theta++)
|
| while((c=getc(ficpar))=='#' && c!= EOF){ |
trgradg[h][j][theta]=gradg[h][theta][j];
|
| ungetc(c,ficpar); |
|
| fgets(line, MAXLINE, ficpar); |
|
| puts(line); |
for(i=1;i<=nlstate*2;i++)
|
| fputs(line,ficparo); |
for(j=1;j<=nlstate*2;j++)
|
| } |
varhe[i][j][(int)age] =0.;
|
| ungetc(c,ficpar); |
|
| |
printf("%d|",(int)age);fflush(stdout);
|
| delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncov); |
for(h=0;h<=nhstepm-1;h++){
|
| delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */ |
for(k=0;k<=nhstepm-1;k++){
|
| for(i=1; i <=nlstate; i++){ |
matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
|
| for(j=1; j <=nlstate+ndeath-1; j++){ |
matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
|
| fscanf(ficpar,"%1d%1d",&i1,&j1); |
for(i=1;i<=nlstate*2;i++)
|
| printf("%1d%1d",i,j); |
for(j=1;j<=nlstate*2;j++)
|
| fprintf(ficparo,"%1d%1d",i1,j1); |
varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
|
| for(k=1; k<=ncov;k++){ |
}
|
| fscanf(ficpar,"%le",&delti3[i][j][k]); |
}
|
| printf(" %le",delti3[i][j][k]); |
/* Computing expectancies */
|
| fprintf(ficparo," %le",delti3[i][j][k]); |
for(i=1; i<=nlstate;i++)
|
| } |
for(j=1; j<=nlstate;j++)
|
| fscanf(ficpar,"\n"); |
for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
|
| printf("\n"); |
eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
|
| fprintf(ficparo,"\n"); |
|
| } |
/* 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]);*/
|
| } |
|
| delti=delti3[1][1]; |
}
|
| |
|
| /* Reads comments: lines beginning with '#' */ |
fprintf(ficreseij,"%3.0f",age );
|
| while((c=getc(ficpar))=='#' && c!= EOF){ |
cptj=0;
|
| ungetc(c,ficpar); |
for(i=1; i<=nlstate;i++)
|
| fgets(line, MAXLINE, ficpar); |
for(j=1; j<=nlstate;j++){
|
| puts(line); |
cptj++;
|
| fputs(line,ficparo); |
fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
|
| } |
}
|
| ungetc(c,ficpar); |
fprintf(ficreseij,"\n");
|
| |
|
| matcov=matrix(1,npar,1,npar); |
free_matrix(gm,0,nhstepm,1,nlstate*2);
|
| for(i=1; i <=npar; i++){ |
free_matrix(gp,0,nhstepm,1,nlstate*2);
|
| fscanf(ficpar,"%s",&str); |
free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
|
| printf("%s",str); |
free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
|
| fprintf(ficparo,"%s",str); |
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
| for(j=1; j <=i; j++){ |
}
|
| fscanf(ficpar," %le",&matcov[i][j]); |
printf("\n");
|
| printf(" %.5le",matcov[i][j]); |
|
| fprintf(ficparo," %.5le",matcov[i][j]); |
free_vector(xp,1,npar);
|
| } |
free_matrix(dnewm,1,nlstate*2,1,npar);
|
| fscanf(ficpar,"\n"); |
free_matrix(doldm,1,nlstate*2,1,nlstate*2);
|
| printf("\n"); |
free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
|
| fprintf(ficparo,"\n"); |
}
|
| } |
|
| for(i=1; i <=npar; i++) |
/************ Variance ******************/
|
| for(j=i+1;j<=npar;j++) |
void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)
|
| matcov[i][j]=matcov[j][i]; |
{
|
| |
/* Variance of health expectancies */
|
| printf("\n"); |
/* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
|
| |
double **newm;
|
| |
double **dnewm,**doldm;
|
| if(mle==1){ |
int i, j, nhstepm, hstepm, h, nstepm ;
|
| /*-------- data file ----------*/ |
int k, cptcode;
|
| if((ficres =fopen(fileres,"w"))==NULL) { |
double *xp;
|
| printf("Problem with resultfile: %s\n", fileres);goto end; |
double **gp, **gm;
|
| } |
double ***gradg, ***trgradg;
|
| fprintf(ficres,"#%s\n",version); |
double ***p3mat;
|
| |
double age,agelim, hf;
|
| if((fic=fopen(datafile,"r"))==NULL) { |
int theta;
|
| printf("Problem with datafile: %s\n", datafile);goto end; |
|
| } |
fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are the stable prevalence in health states i\n");
|
| |
fprintf(ficresvij,"# Age");
|
| n= lastobs; |
for(i=1; i<=nlstate;i++)
|
| severity = vector(1,maxwav); |
for(j=1; j<=nlstate;j++)
|
| outcome=imatrix(1,maxwav+1,1,n); |
fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
|
| num=ivector(1,n); |
fprintf(ficresvij,"\n");
|
| moisnais=vector(1,n); |
|
| annais=vector(1,n); |
xp=vector(1,npar);
|
| moisdc=vector(1,n); |
dnewm=matrix(1,nlstate,1,npar);
|
| andc=vector(1,n); |
doldm=matrix(1,nlstate,1,nlstate);
|
| agedc=vector(1,n); |
|
| cod=ivector(1,n); |
if(estepm < stepm){
|
| weight=vector(1,n); |
printf ("Problem %d lower than %d\n",estepm, stepm);
|
| for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */ |
}
|
| mint=matrix(1,maxwav,1,n); |
else hstepm=estepm;
|
| anint=matrix(1,maxwav,1,n); |
/* For example we decided to compute the life expectancy with the smallest unit */
|
| covar=matrix(1,NCOVMAX,1,n); |
/* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
|
| s=imatrix(1,maxwav+1,1,n); |
nhstepm is the number of hstepm from age to agelim
|
| adl=imatrix(1,maxwav+1,1,n); |
nstepm is the number of stepm from age to agelin.
|
| tab=ivector(1,NCOVMAX); |
Look at hpijx to understand the reason of that which relies in memory size
|
| i=1; |
and note for a fixed period like k years */
|
| while (fgets(line, MAXLINE, fic) != NULL) { |
/* We decided (b) to get a life expectancy respecting the most precise curvature of the
|
| if ((i >= firstobs) && (i <lastobs)) { |
survival function given by stepm (the optimization length). Unfortunately it
|
| sscanf(line,"%d %lf %lf %lf %lf/%lf %lf/%lf %lf/%lf %d %lf/%lf %d %lf/%lf %d %lf/%lf %d", &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]); |
means that if the survival funtion is printed only each two years of age and if
|
| i=i+1; |
you sum them up and add 1 year (area under the trapezoids) you won't get the same
|
| } |
results. So we changed our mind and took the option of the best precision.
|
| } |
*/
|
| imx=i-1; /* Number of individuals */ |
hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
|
| |
agelim = AGESUP;
|
| fclose(fic); |
for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
|
| |
nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
|
| if (weightopt != 1) { /* Maximisation without weights*/ |
nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
|
| for(i=1;i<=n;i++) weight[i]=1.0; |
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
| } |
gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
|
| /*-calculation of age at interview from date of interview and age at death -*/ |
gp=matrix(0,nhstepm,1,nlstate);
|
| agev=matrix(1,maxwav,1,imx); |
gm=matrix(0,nhstepm,1,nlstate);
|
| |
|
| for (i=1; i<=imx; i++) { |
for(theta=1; theta <=npar; theta++){
|
| agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]); |
for(i=1; i<=npar; i++){ /* Computes gradient */
|
| for(m=1; (m<= maxwav); m++){ |
xp[i] = x[i] + (i==theta ?delti[theta]:0);
|
| if(s[m][i] >0){ |
}
|
| if (s[m][i] == nlstate+1) { |
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
|
| if(agedc[i]>0) |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
|
| agev[m][i]=agedc[i]; |
|
| else{ |
if (popbased==1) {
|
| printf("Warning negative age at death: %d line:%d\n",num[i],i); |
for(i=1; i<=nlstate;i++)
|
| agev[m][i]=-1; |
prlim[i][i]=probs[(int)age][i][ij];
|
| } |
}
|
| } |
|
| else if(s[m][i] !=9){ /* Should no more exist */ |
for(j=1; j<= nlstate; j++){
|
| agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]); |
for(h=0; h<=nhstepm; h++){
|
| if(mint[m][i]==99 || anint[m][i]==9999) |
for(i=1, gp[h][j]=0.;i<=nlstate;i++)
|
| agev[m][i]=1; |
gp[h][j] += prlim[i][i]*p3mat[i][j][h];
|
| 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);*/ |
|
| } |
for(i=1; i<=npar; i++) /* Computes gradient */
|
| else if(agev[m][i] >agemax){ |
xp[i] = x[i] - (i==theta ?delti[theta]:0);
|
| agemax=agev[m][i]; |
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
|
| /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/ |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
|
| } |
|
| /*agev[m][i]=anint[m][i]-annais[i];*/ |
if (popbased==1) {
|
| /* agev[m][i] = age[i]+2*m;*/ |
for(i=1; i<=nlstate;i++)
|
| } |
prlim[i][i]=probs[(int)age][i][ij];
|
| else { /* =9 */ |
}
|
| agev[m][i]=1; |
|
| s[m][i]=-1; |
for(j=1; j<= nlstate; j++){
|
| } |
for(h=0; h<=nhstepm; h++){
|
| } |
for(i=1, gm[h][j]=0.;i<=nlstate;i++)
|
| else /*= 0 Unknown */ |
gm[h][j] += prlim[i][i]*p3mat[i][j][h];
|
| agev[m][i]=1; |
}
|
| } |
}
|
| |
|
| } |
for(j=1; j<= nlstate; j++)
|
| for (i=1; i<=imx; i++) { |
for(h=0; h<=nhstepm; h++){
|
| for(m=1; (m<= maxwav); m++){ |
gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
|
| if (s[m][i] > (nlstate+ndeath)) { |
}
|
| printf("Error: Wrong value in nlstate or ndeath\n"); |
} /* End theta */
|
| goto end; |
|
| } |
trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);
|
| } |
|
| } |
for(h=0; h<=nhstepm; h++)
|
| |
for(j=1; j<=nlstate;j++)
|
| printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); |
for(theta=1; theta <=npar; theta++)
|
| |
trgradg[h][j][theta]=gradg[h][theta][j];
|
| free_vector(severity,1,maxwav); |
|
| free_imatrix(outcome,1,maxwav+1,1,n); |
hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
|
| free_vector(moisnais,1,n); |
for(i=1;i<=nlstate;i++)
|
| free_vector(annais,1,n); |
for(j=1;j<=nlstate;j++)
|
| free_matrix(mint,1,maxwav,1,n); |
vareij[i][j][(int)age] =0.;
|
| free_matrix(anint,1,maxwav,1,n); |
|
| free_vector(moisdc,1,n); |
for(h=0;h<=nhstepm;h++){
|
| free_vector(andc,1,n); |
for(k=0;k<=nhstepm;k++){
|
| |
matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
|
| |
matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
|
| wav=ivector(1,imx); |
for(i=1;i<=nlstate;i++)
|
| dh=imatrix(1,lastpass-firstpass+1,1,imx); |
for(j=1;j<=nlstate;j++)
|
| mw=imatrix(1,lastpass-firstpass+1,1,imx); |
vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
|
| |
}
|
| /* Concatenates waves */ |
}
|
| concatwav(wav, dh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm); |
|
| |
fprintf(ficresvij,"%.0f ",age );
|
| /* Calculates basic frequencies. Computes observed prevalence at single age |
for(i=1; i<=nlstate;i++)
|
| and prints on file fileres'p'. */ |
for(j=1; j<=nlstate;j++){
|
| freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx); |
fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
|
| |
}
|
| pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ |
fprintf(ficresvij,"\n");
|
| oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ |
free_matrix(gp,0,nhstepm,1,nlstate);
|
| newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ |
free_matrix(gm,0,nhstepm,1,nlstate);
|
| savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ |
free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
|
| oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */ |
free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
|
| |
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
| /* For Powell, parameters are in a vector p[] starting at p[1] |
} /* End age */
|
| so we point p on param[1][1] so that p[1] maps on param[1][1][1] */ |
|
| p=param[1][1]; /* *(*(*(param +1)+1)+0) */ |
free_vector(xp,1,npar);
|
| |
free_matrix(doldm,1,nlstate,1,npar);
|
| mlikeli(ficres,p, npar, ncov, nlstate, ftol, func); |
free_matrix(dnewm,1,nlstate,1,nlstate);
|
| |
|
| |
}
|
| /*--------- results files --------------*/ |
|
| fprintf(ficres,"\ntitle=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt); |
/************ Variance of prevlim ******************/
|
| |
void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
|
| jk=1; |
{
|
| fprintf(ficres,"# Parameters\n"); |
/* Variance of prevalence limit */
|
| printf("# Parameters\n"); |
/* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
|
| for(i=1,jk=1; i <=nlstate; i++){ |
double **newm;
|
| for(k=1; k <=(nlstate+ndeath); k++){ |
double **dnewm,**doldm;
|
| if (k != i) |
int i, j, nhstepm, hstepm;
|
| { |
int k, cptcode;
|
| printf("%d%d ",i,k); |
double *xp;
|
| fprintf(ficres,"%1d%1d ",i,k); |
double *gp, *gm;
|
| for(j=1; j <=ncov; j++){ |
double **gradg, **trgradg;
|
| printf("%f ",p[jk]); |
double age,agelim;
|
| fprintf(ficres,"%f ",p[jk]); |
int theta;
|
| jk++; |
|
| } |
fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");
|
| printf("\n"); |
fprintf(ficresvpl,"# Age");
|
| fprintf(ficres,"\n"); |
for(i=1; i<=nlstate;i++)
|
| } |
fprintf(ficresvpl," %1d-%1d",i,i);
|
| } |
fprintf(ficresvpl,"\n");
|
| } |
|
| |
xp=vector(1,npar);
|
| /* Computing hessian and covariance matrix */ |
dnewm=matrix(1,nlstate,1,npar);
|
| ftolhess=ftol; /* Usually correct */ |
doldm=matrix(1,nlstate,1,nlstate);
|
| hesscov(matcov, p, npar, delti, ftolhess, func); |
|
| fprintf(ficres,"# Scales\n"); |
hstepm=1*YEARM; /* Every year of age */
|
| printf("# Scales\n"); |
hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
|
| for(i=1,jk=1; i <=nlstate; i++){ |
agelim = AGESUP;
|
| for(j=1; j <=nlstate+ndeath; j++){ |
for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
|
| if (j!=i) { |
nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
|
| fprintf(ficres,"%1d%1d",i,j); |
if (stepm >= YEARM) hstepm=1;
|
| printf("%1d%1d",i,j); |
nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
|
| for(k=1; k<=ncov;k++){ |
gradg=matrix(1,npar,1,nlstate);
|
| printf(" %.5e",delti[jk]); |
gp=vector(1,nlstate);
|
| fprintf(ficres," %.5e",delti[jk]); |
gm=vector(1,nlstate);
|
| jk++; |
|
| } |
for(theta=1; theta <=npar; theta++){
|
| printf("\n"); |
for(i=1; i<=npar; i++){ /* Computes gradient */
|
| fprintf(ficres,"\n"); |
xp[i] = x[i] + (i==theta ?delti[theta]:0);
|
| } |
}
|
| } |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
|
| } |
for(i=1;i<=nlstate;i++)
|
| |
gp[i] = prlim[i][i];
|
| k=1; |
|
| fprintf(ficres,"# Covariance\n"); |
for(i=1; i<=npar; i++) /* Computes gradient */
|
| printf("# Covariance\n"); |
xp[i] = x[i] - (i==theta ?delti[theta]:0);
|
| for(i=1;i<=npar;i++){ |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
|
| /* if (k>nlstate) k=1; |
for(i=1;i<=nlstate;i++)
|
| i1=(i-1)/(ncov*nlstate)+1; |
gm[i] = prlim[i][i];
|
| fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]); |
|
| printf("%s%d%d",alph[k],i1,tab[i]);*/ |
for(i=1;i<=nlstate;i++)
|
| fprintf(ficres,"%3d",i); |
gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
|
| printf("%3d",i); |
} /* End theta */
|
| for(j=1; j<=i;j++){ |
|
| fprintf(ficres," %.5e",matcov[i][j]); |
trgradg =matrix(1,nlstate,1,npar);
|
| printf(" %.5e",matcov[i][j]); |
|
| } |
for(j=1; j<=nlstate;j++)
|
| fprintf(ficres,"\n"); |
for(theta=1; theta <=npar; theta++)
|
| printf("\n"); |
trgradg[j][theta]=gradg[theta][j];
|
| k++; |
|
| } |
for(i=1;i<=nlstate;i++)
|
| |
varpl[i][(int)age] =0.;
|
| while((c=getc(ficpar))=='#' && c!= EOF){ |
matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
|
| ungetc(c,ficpar); |
matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
|
| fgets(line, MAXLINE, ficpar); |
for(i=1;i<=nlstate;i++)
|
| puts(line); |
varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
|
| fputs(line,ficparo); |
|
| } |
fprintf(ficresvpl,"%.0f ",age );
|
| ungetc(c,ficpar); |
for(i=1; i<=nlstate;i++)
|
| |
fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
|
| fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage); |
fprintf(ficresvpl,"\n");
|
| |
free_vector(gp,1,nlstate);
|
| if (fage <= 2) { |
free_vector(gm,1,nlstate);
|
| bage = agemin; |
free_matrix(gradg,1,npar,1,nlstate);
|
| fage = agemax; |
free_matrix(trgradg,1,nlstate,1,npar);
|
| } |
} /* End age */
|
| |
|
| fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n"); |
free_vector(xp,1,npar);
|
| fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage); |
free_matrix(doldm,1,nlstate,1,npar);
|
| /*------------ gnuplot -------------*/ |
free_matrix(dnewm,1,nlstate,1,nlstate);
|
| chdir(pathcd); |
|
| if((ficgp=fopen("graph.gp","w"))==NULL) { |
}
|
| printf("Problem with file graph.gp");goto end; |
|
| } |
/************ Variance of one-step probabilities ******************/
|
| #ifdef windows |
void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
|
| fprintf(ficgp,"cd \"%s\" \n",pathc); |
{
|
| #endif |
int i, j=0, i1, k1, l1, t, tj;
|
| /* 1eme*/ |
int k2, l2, j1, z1;
|
| |
int k=0,l, cptcode;
|
| for (cpt=1; cpt<= nlstate ; cpt ++) { |
int first=1;
|
| #ifdef windows |
double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;
|
| fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" u 1:%d \"\%%lf",agemin,fage,fileres,cpt*2); |
double **dnewm,**doldm;
|
| #endif |
double *xp;
|
| #ifdef unix |
double *gp, *gm;
|
| fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:%d \"\%%lf",agemin,fage,fileres,cpt*2); |
double **gradg, **trgradg;
|
| #endif |
double **mu;
|
| for (i=1; i<= nlstate ; i ++) fprintf(ficgp," \%%lf (\%%lf)"); |
double age,agelim, cov[NCOVMAX];
|
| fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" u 1:($%d+2*$%d) \"\%%lf",fileres,2*cpt,cpt*2+1); |
double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
|
| for (i=1; i<= nlstate ; i ++) fprintf(ficgp," \%%lf (\%%lf)"); |
int theta;
|
| fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" u 1:($%d-2*$%d) \"\%%lf",fileres,2*cpt,2*cpt+1); |
char fileresprob[FILENAMELENGTH];
|
| for (i=1; i<= nlstate ; i ++) fprintf(ficgp," \%%lf (\%%lf)"); |
char fileresprobcov[FILENAMELENGTH];
|
| fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" u 1:($%d) t\"Observed prevalence \" w l 2",fileres,2+4*(cpt-1)); |
char fileresprobcor[FILENAMELENGTH];
|
| #ifdef unix |
|
| fprintf(ficgp,"\nset ter gif small size 400,300"); |
double ***varpij;
|
| #endif |
|
| fprintf(ficgp,"\nset out \"v%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt); |
strcpy(fileresprob,"prob");
|
| |
strcat(fileresprob,fileres);
|
| } |
if((ficresprob=fopen(fileresprob,"w"))==NULL) {
|
| /*2 eme*/ |
printf("Problem with resultfile: %s\n", fileresprob);
|
| |
}
|
| fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage); |
strcpy(fileresprobcov,"probcov");
|
| for (i=1; i<= nlstate+1 ; i ++) { |
strcat(fileresprobcov,fileres);
|
| k=2*i; |
if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
|
| fprintf(ficgp,"\"t%s\" u 1:%d \"\%%lf \%%lf (\%%lf) \%%lf (\%%lf)",fileres,k); |
printf("Problem with resultfile: %s\n", fileresprobcov);
|
| for (j=1; j< nlstate ; j ++) fprintf(ficgp," \%%lf (\%%lf)"); |
}
|
| if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,"); |
strcpy(fileresprobcor,"probcor");
|
| else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1); |
strcat(fileresprobcor,fileres);
|
| fprintf(ficgp,"\"t%s\" u 1:($%d-2*$%d) \"\%%lf \%%lf (\%%lf) \%%lf (\%%lf)",fileres,k,k+1); |
if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
|
| for (j=1; j< nlstate ; j ++) fprintf(ficgp," \%%lf (\%%lf)"); |
printf("Problem with resultfile: %s\n", fileresprobcor);
|
| fprintf(ficgp,"\" t\"\" w l 0,"); |
}
|
| fprintf(ficgp,"\"t%s\" u 1:($%d+2*$%d) \"\%%lf \%%lf (\%%lf) \%%lf (\%%lf)",fileres,k,k+1); |
printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
|
| for (j=1; j< nlstate ; j ++) fprintf(ficgp," \%%lf (\%%lf)"); |
printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
|
| if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0"); |
printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
|
| else fprintf(ficgp,"\" t\"\" w l 0,"); |
|
| } |
fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
|
| fprintf(ficgp,"\nset out \"e%s.gif\" \nreplot\n\n",strtok(optionfile, ".")); |
fprintf(ficresprob,"# Age");
|
| |
fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
|
| /*3eme*/ |
fprintf(ficresprobcov,"# Age");
|
| for (cpt=1; cpt<= nlstate ; cpt ++) { |
fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
|
| k=2+nlstate*(cpt-1); |
fprintf(ficresprobcov,"# Age");
|
| fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k,cpt); |
|
| for (i=1; i< nlstate ; i ++) { |
|
| fprintf(ficgp,",\"e%s\" u 1:%d t \"e%d%d\" w l",fileres,k+1,cpt,i+1); |
for(i=1; i<=nlstate;i++)
|
| } |
for(j=1; j<=(nlstate+ndeath);j++){
|
| fprintf(ficgp,"\nset out \"ex%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt); |
fprintf(ficresprob," p%1d-%1d (SE)",i,j);
|
| } |
fprintf(ficresprobcov," p%1d-%1d ",i,j);
|
| |
fprintf(ficresprobcor," p%1d-%1d ",i,j);
|
| /* CV preval stat */ |
}
|
| for (cpt=1; cpt<nlstate ; cpt ++) { |
fprintf(ficresprob,"\n");
|
| k=3; |
fprintf(ficresprobcov,"\n");
|
| fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u 2:($%d/($%d",agemin,agemax,fileres,k+cpt,k); |
fprintf(ficresprobcor,"\n");
|
| for (i=1; i< nlstate ; i ++) |
xp=vector(1,npar);
|
| fprintf(ficgp,"+$%d",k+i); |
dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
|
| fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1); |
doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
|
| |
mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
|
| l=3+(nlstate+ndeath)*cpt; |
varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
|
| fprintf(ficgp,",\"pij%s\" u 2:($%d/($%d",fileres,l+cpt,l); |
first=1;
|
| |
if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
|
| for (i=1; i< nlstate ; i ++) { |
printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
|
| l=3+(nlstate+ndeath)*cpt; |
exit(0);
|
| fprintf(ficgp,"+$%d",l+i); |
}
|
| } |
else{
|
| fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1); |
fprintf(ficgp,"\n# Routine varprob");
|
| |
}
|
| |
if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
|
| fprintf(ficgp,"set out \"p%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt); |
printf("Problem with html file: %s\n", optionfilehtm);
|
| } |
exit(0);
|
| |
}
|
| |
else{
|
| fclose(ficgp); |
fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
|
| |
fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
|
| chdir(path); |
fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
|
| free_matrix(agev,1,maxwav,1,imx); |
|
| free_ivector(wav,1,imx); |
}
|
| free_imatrix(dh,1,lastpass-firstpass+1,1,imx); |
|
| free_imatrix(mw,1,lastpass-firstpass+1,1,imx); |
|
| |
cov[1]=1;
|
| free_imatrix(s,1,maxwav+1,1,n); |
tj=cptcoveff;
|
| |
if (cptcovn<1) {tj=1;ncodemax[1]=1;}
|
| |
j1=0;
|
| free_ivector(num,1,n); |
for(t=1; t<=tj;t++){
|
| free_vector(agedc,1,n); |
for(i1=1; i1<=ncodemax[t];i1++){
|
| free_vector(weight,1,n); |
j1++;
|
| free_matrix(covar,1,NCOVMAX,1,n); |
|
| fclose(ficparo); |
if (cptcovn>0) {
|
| fclose(ficres); |
fprintf(ficresprob, "\n#********** Variable ");
|
| } |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
|
| |
fprintf(ficresprob, "**********\n#");
|
| /*________fin mle=1_________*/ |
fprintf(ficresprobcov, "\n#********** Variable ");
|
| |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
|
| |
fprintf(ficresprobcov, "**********\n#");
|
| |
|
| /* No more information from the sample is required now */ |
fprintf(ficgp, "\n#********** Variable ");
|
| /* Reads comments: lines beginning with '#' */ |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
|
| while((c=getc(ficpar))=='#' && c!= EOF){ |
fprintf(ficgp, "**********\n#");
|
| ungetc(c,ficpar); |
|
| fgets(line, MAXLINE, ficpar); |
|
| puts(line); |
fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
|
| fputs(line,ficparo); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
|
| } |
fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
|
| ungetc(c,ficpar); |
|
| |
fprintf(ficresprobcor, "\n#********** Variable ");
|
| fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
|
| printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage); |
fprintf(ficgp, "**********\n#");
|
| fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage); |
}
|
| |
|
| /*--------------- Prevalence limit --------------*/ |
for (age=bage; age<=fage; age ++){
|
| |
cov[2]=age;
|
| strcpy(filerespl,"pl"); |
for (k=1; k<=cptcovn;k++) {
|
| strcat(filerespl,fileres); |
cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
|
| if((ficrespl=fopen(filerespl,"w"))==NULL) { |
}
|
| printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end; |
for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
|
| } |
for (k=1; k<=cptcovprod;k++)
|
| printf("Computing prevalence limit: result on file '%s' \n", filerespl); |
cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
|
| fprintf(ficrespl,"#Prevalence limit\n"); |
|
| fprintf(ficrespl,"#Age "); |
gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
|
| for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i); |
trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
|
| fprintf(ficrespl,"\n"); |
gp=vector(1,(nlstate)*(nlstate+ndeath));
|
| |
gm=vector(1,(nlstate)*(nlstate+ndeath));
|
| prlim=matrix(1,nlstate,1,nlstate); |
|
| pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ |
for(theta=1; theta <=npar; theta++){
|
| oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ |
for(i=1; i<=npar; i++)
|
| newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ |
xp[i] = x[i] + (i==theta ?delti[theta]:0);
|
| savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ |
|
| oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */ |
pmij(pmmij,cov,ncovmodel,xp,nlstate);
|
| |
|
| agebase=agemin; |
k=0;
|
| agelim=agemax; |
for(i=1; i<= (nlstate); i++){
|
| ftolpl=1.e-10; |
for(j=1; j<=(nlstate+ndeath);j++){
|
| for (age=agebase; age<=agelim; age++){ |
k=k+1;
|
| prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl); |
gp[k]=pmmij[i][j];
|
| fprintf(ficrespl,"%.0f",age ); |
}
|
| for(i=1; i<=nlstate;i++) |
}
|
| fprintf(ficrespl," %.5f", prlim[i][i]); |
|
| fprintf(ficrespl,"\n"); |
for(i=1; i<=npar; i++)
|
| } |
xp[i] = x[i] - (i==theta ?delti[theta]:0);
|
| fclose(ficrespl); |
|
| |
pmij(pmmij,cov,ncovmodel,xp,nlstate);
|
| /*------------- h Pij x at various ages ------------*/ |
k=0;
|
| |
for(i=1; i<=(nlstate); i++){
|
| strcpy(filerespij,"pij"); strcat(filerespij,fileres); |
for(j=1; j<=(nlstate+ndeath);j++){
|
| if((ficrespij=fopen(filerespij,"w"))==NULL) { |
k=k+1;
|
| printf("Problem with Pij resultfile: %s\n", filerespij);goto end; |
gm[k]=pmmij[i][j];
|
| } |
}
|
| printf("Computing pij: result on file '%s' \n", filerespij); |
}
|
| stepsize=(int) (stepm+YEARM-1)/YEARM; |
|
| if (stepm<=24) stepsize=2; |
for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
|
| |
gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];
|
| agelim=AGESUP; |
}
|
| hstepm=stepsize*YEARM; /* Every year of age */ |
|
| hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ |
for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
|
| for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */ |
for(theta=1; theta <=npar; theta++)
|
| nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ |
trgradg[j][theta]=gradg[theta][j];
|
| nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */ |
|
| p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
|
| oldm=oldms;savm=savms; |
matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
|
| hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm); |
|
| fprintf(ficrespij,"# Age"); |
pmij(pmmij,cov,ncovmodel,x,nlstate);
|
| for(i=1; i<=nlstate;i++) |
|
| for(j=1; j<=nlstate+ndeath;j++) |
k=0;
|
| fprintf(ficrespij," %1d-%1d",i,j); |
for(i=1; i<=(nlstate); i++){
|
| fprintf(ficrespij,"\n"); |
for(j=1; j<=(nlstate+ndeath);j++){
|
| for (h=0; h<=nhstepm; h++){ |
k=k+1;
|
| fprintf(ficrespij,"%.0f %.0f",agedeb, agedeb+ h*hstepm/YEARM*stepm ); |
mu[k][(int) age]=pmmij[i][j];
|
| for(i=1; i<=nlstate;i++) |
}
|
| for(j=1; j<=nlstate+ndeath;j++) |
}
|
| fprintf(ficrespij," %.5f", p3mat[i][j][h]); |
for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
|
| fprintf(ficrespij,"\n"); |
for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
|
| } |
varpij[i][j][(int)age] = doldm[i][j];
|
| free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
|
| fprintf(ficrespij,"\n"); |
/*printf("\n%d ",(int)age);
|
| } |
for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
|
| fclose(ficrespij); |
printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
|
| |
}*/
|
| /*---------- Health expectancies and variances ------------*/ |
|
| |
fprintf(ficresprob,"\n%d ",(int)age);
|
| eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); |
fprintf(ficresprobcov,"\n%d ",(int)age);
|
| oldm=oldms;savm=savms; |
fprintf(ficresprobcor,"\n%d ",(int)age);
|
| evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm); |
|
| |
for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
|
| vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); |
fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
|
| oldm=oldms;savm=savms; |
for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
|
| varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl); |
fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
|
| |
fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
|
| strcpy(filerest,"t"); |
}
|
| strcat(filerest,fileres); |
i=0;
|
| if((ficrest=fopen(filerest,"w"))==NULL) { |
for (k=1; k<=(nlstate);k++){
|
| printf("Problem with total LE resultfile: %s\n", filerest);goto end; |
for (l=1; l<=(nlstate+ndeath);l++){
|
| } |
i=i++;
|
| printf("Computing Total LEs with variances: file '%s' \n", filerest); |
fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
|
| fprintf(ficrest,"#Total LEs with variances: e.. (std) "); |
fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
|
| for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i); |
for (j=1; j<=i;j++){
|
| fprintf(ficrest,"\n"); |
fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
|
| |
fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
|
| hf=1; |
}
|
| if (stepm >= YEARM) hf=stepm/YEARM; |
}
|
| epj=vector(1,nlstate+1); |
}/* end of loop for state */
|
| for(age=bage; age <=fage ;age++){ |
} /* end of loop for age */
|
| prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl); |
/* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
|
| fprintf(ficrest," %.0f",age); |
for (k1=1; k1<=(nlstate);k1++){
|
| for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){ |
for (l1=1; l1<=(nlstate+ndeath);l1++){
|
| for(i=1, epj[j]=0.;i <=nlstate;i++) { |
if(l1==k1) continue;
|
| epj[j] += prlim[i][i]*hf*eij[i][j][(int)age]; |
i=(k1-1)*(nlstate+ndeath)+l1;
|
| } |
for (k2=1; k2<=(nlstate);k2++){
|
| epj[nlstate+1] +=epj[j]; |
for (l2=1; l2<=(nlstate+ndeath);l2++){
|
| } |
if(l2==k2) continue;
|
| for(i=1, vepp=0.;i <=nlstate;i++) |
j=(k2-1)*(nlstate+ndeath)+l2;
|
| for(j=1;j <=nlstate;j++) |
if(j<=i) continue;
|
| vepp += vareij[i][j][(int)age]; |
for (age=bage; age<=fage; age ++){
|
| fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp)); |
if ((int)age %5==0){
|
| for(j=1;j <=nlstate;j++){ |
v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
|
| fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age])); |
v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
|
| } |
cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
|
| fprintf(ficrest,"\n"); |
mu1=mu[i][(int) age]/stepm*YEARM ;
|
| } |
mu2=mu[j][(int) age]/stepm*YEARM;
|
| fclose(ficrest); |
/* Computing eigen value of matrix of covariance */
|
| fclose(ficpar); |
lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));
|
| free_vector(epj,1,nlstate+1); |
lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));
|
| |
printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);
|
| /*------- Variance limit prevalence------*/ |
/* Eigen vectors */
|
| |
v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
|
| varpl=matrix(1,nlstate,(int) bage, (int) fage); |
v21=sqrt(1.-v11*v11);
|
| oldm=oldms;savm=savms; |
v12=-v21;
|
| varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl); |
v22=v11;
|
| |
/*printf(fignu*/
|
| |
/* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
|
| free_matrix(varpl,1,nlstate,(int) bage, (int)fage); |
/* mu2+ v21*lc1*cost + v21*lc2*sin(t) */
|
| |
if(first==1){
|
| free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage); |
first=0;
|
| free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage); |
fprintf(ficgp,"\nset parametric;set nolabel");
|
| |
fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);
|
| |
fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
|
| free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath); |
fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1);
|
| free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath); |
fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k2,l2,k1,l1);
|
| free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath); |
fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k2,l2,k1,l1);
|
| free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath); |
fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);
|
| |
fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);
|
| free_matrix(matcov,1,npar,1,npar); |
fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\
|
| free_vector(delti,1,npar); |
mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \
|
| |
mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);
|
| free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncov); |
}else{
|
| |
first=0;
|
| printf("End of Imach\n"); |
fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);
|
| /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */ |
fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);
|
| |
fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\
|
| /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/ |
mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \
|
| /*printf("Total time was %d uSec.\n", total_usecs);*/ |
mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);
|
| /*------ End -----------*/ |
}/* if first */
|
| |
} /* age mod 5 */
|
| end: |
} /* end loop age */
|
| #ifdef windows |
fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k2,l2,k1,l1);
|
| chdir(pathcd); |
first=1;
|
| #endif |
} /*l12 */
|
| system("gnuplot graph.gp"); |
} /* k12 */
|
| |
} /*l1 */
|
| #ifdef windows |
}/* k1 */
|
| while (z[0] != 'q') { |
} /* loop covariates */
|
| chdir(pathcd); |
free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
|
| printf("\nType e to edit output files, c to start again, and q for exiting: "); |
free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
|
| scanf("%s",z); |
free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
|
| if (z[0] == 'c') system("./imach"); |
free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
|
| else if (z[0] == 'e') { |
free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
|
| chdir(path); |
free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
|
| system("index.htm"); |
}
|
| } |
free_vector(xp,1,npar);
|
| else if (z[0] == 'q') exit(0); |
fclose(ficresprob);
|
| } |
fclose(ficresprobcov);
|
| #endif |
fclose(ficresprobcor);
|
| } |
fclose(ficgp);
|
| |
fclose(fichtm);
|
| |
}
|
| |
|
| |
|
| |
/******************* Printing html file ***********/
|
| |
void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
|
| |
int lastpass, int stepm, int weightopt, char model[],\
|
| |
int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
|
| |
int popforecast, int estepm ,\
|
| |
double jprev1, double mprev1,double anprev1, \
|
| |
double jprev2, double mprev2,double anprev2){
|
| |
int jj1, k1, i1, cpt;
|
| |
/*char optionfilehtm[FILENAMELENGTH];*/
|
| |
if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
|
| |
printf("Problem with %s \n",optionfilehtm), exit(0);
|
| |
}
|
| |
|
| |
fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
|
| |
- Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
|
| |
- Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
|
| |
- Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
|
| |
- Life expectancies by age and initial health status (estepm=%2d months):
|
| |
<a href=\"e%s\">e%s</a> <br>\n</li>", \
|
| |
jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
|
| |
|
| |
fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
|
| |
- Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
|
| |
- Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
|
| |
- Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
|
| |
- Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
|
| |
- Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
|
| |
- Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
|
| |
- Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
|
| |
|
| |
if(popforecast==1) fprintf(fichtm,"\n
|
| |
- Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
|
| |
- Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
|
| |
<br>",fileres,fileres,fileres,fileres);
|
| |
else
|
| |
fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);
|
| |
fprintf(fichtm," <li><b>Graphs</b></li><p>");
|
| |
|
| |
m=cptcoveff;
|
| |
if (cptcovn < 1) {m=1;ncodemax[1]=1;}
|
| |
|
| |
jj1=0;
|
| |
for(k1=1; k1<=m;k1++){
|
| |
for(i1=1; i1<=ncodemax[k1];i1++){
|
| |
jj1++;
|
| |
if (cptcovn > 0) {
|
| |
fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
|
| |
for (cpt=1; cpt<=cptcoveff;cpt++)
|
| |
fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
|
| |
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
|
| |
}
|
| |
/* Pij */
|
| |
fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>
|
| |
<img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
|
| |
/* Quasi-incidences */
|
| |
fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
|
| |
<img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
|
| |
/* Stable prevalence in each health state */
|
| |
for(cpt=1; cpt<nlstate;cpt++){
|
| |
fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
|
| |
<img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
|
| |
}
|
| |
for(cpt=1; cpt<=nlstate;cpt++) {
|
| |
fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
|
| |
interval) in state (%d): v%s%d%d.png <br>
|
| |
<img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
|
| |
}
|
| |
for(cpt=1; cpt<=nlstate;cpt++) {
|
| |
fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
|
| |
<img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
|
| |
}
|
| |
fprintf(fichtm,"\n<br>- Total life expectancy by age and
|
| |
health expectancies in states (1) and (2): e%s%d.png<br>
|
| |
<img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
|
| |
}
|
| |
}
|
| |
fclose(fichtm);
|
| |
}
|
| |
|
| |
/******************* Gnuplot file **************/
|
| |
void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
|
| |
|
| |
int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
|
| |
int ng;
|
| |
if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
|
| |
printf("Problem with file %s",optionfilegnuplot);
|
| |
}
|
| |
|
| |
#ifdef windows
|
| |
fprintf(ficgp,"cd \"%s\" \n",pathc);
|
| |
#endif
|
| |
m=pow(2,cptcoveff);
|
| |
|
| |
/* 1eme*/
|
| |
for (cpt=1; cpt<= nlstate ; cpt ++) {
|
| |
for (k1=1; k1<= m ; k1 ++) {
|
| |
|
| |
#ifdef windows
|
| |
fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
|
| |
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
|
| |
#endif
|
| |
#ifdef unix
|
| |
fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
|
| |
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);
|
| |
#endif
|
| |
|
| |
for (i=1; i<= nlstate ; i ++) {
|
| |
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
|
| |
else fprintf(ficgp," \%%*lf (\%%*lf)");
|
| |
}
|
| |
fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
|
| |
for (i=1; i<= nlstate ; i ++) {
|
| |
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
|
| |
else fprintf(ficgp," \%%*lf (\%%*lf)");
|
| |
}
|
| |
fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);
|
| |
for (i=1; i<= nlstate ; i ++) {
|
| |
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
|
| |
else fprintf(ficgp," \%%*lf (\%%*lf)");
|
| |
}
|
| |
fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
|
| |
#ifdef unix
|
| |
fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");
|
| |
#endif
|
| |
}
|
| |
}
|
| |
/*2 eme*/
|
| |
|
| |
for (k1=1; k1<= m ; k1 ++) {
|
| |
fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
|
| |
fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
|
| |
|
| |
for (i=1; i<= nlstate+1 ; i ++) {
|
| |
k=2*i;
|
| |
fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
|
| |
for (j=1; j<= nlstate+1 ; j ++) {
|
| |
if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
|
| |
else fprintf(ficgp," \%%*lf (\%%*lf)");
|
| |
}
|
| |
if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
|
| |
else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
|
| |
fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
|
| |
for (j=1; j<= nlstate+1 ; j ++) {
|
| |
if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
|
| |
else fprintf(ficgp," \%%*lf (\%%*lf)");
|
| |
}
|
| |
fprintf(ficgp,"\" t\"\" w l 0,");
|
| |
fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
|
| |
for (j=1; j<= nlstate+1 ; j ++) {
|
| |
if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
|
| |
else fprintf(ficgp," \%%*lf (\%%*lf)");
|
| |
}
|
| |
if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
|
| |
else fprintf(ficgp,"\" t\"\" w l 0,");
|
| |
}
|
| |
}
|
| |
|
| |
/*3eme*/
|
| |
|
| |
for (k1=1; k1<= m ; k1 ++) {
|
| |
for (cpt=1; cpt<= nlstate ; cpt ++) {
|
| |
k=2+nlstate*(2*cpt-2);
|
| |
fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
|
| |
fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
|
| |
/*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
|
| |
for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
|
| |
fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
|
| |
fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
|
| |
for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
|
| |
fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
|
| |
|
| |
*/
|
| |
for (i=1; i< nlstate ; i ++) {
|
| |
fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
|
| |
|
| |
}
|
| |
}
|
| |
}
|
| |
|
| |
/* CV preval stat */
|
| |
for (k1=1; k1<= m ; k1 ++) {
|
| |
for (cpt=1; cpt<nlstate ; cpt ++) {
|
| |
k=3;
|
| |
fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
|
| |
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
|
| |
|
| |
for (i=1; i< nlstate ; i ++)
|
| |
fprintf(ficgp,"+$%d",k+i+1);
|
| |
fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
|
| |
|
| |
l=3+(nlstate+ndeath)*cpt;
|
| |
fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
|
| |
for (i=1; i< nlstate ; i ++) {
|
| |
l=3+(nlstate+ndeath)*cpt;
|
| |
fprintf(ficgp,"+$%d",l+i+1);
|
| |
}
|
| |
fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
|
| |
}
|
| |
}
|
| |
|
| |
/* proba elementaires */
|
| |
for(i=1,jk=1; i <=nlstate; i++){
|
| |
for(k=1; k <=(nlstate+ndeath); k++){
|
| |
if (k != i) {
|
| |
for(j=1; j <=ncovmodel; j++){
|
| |
|
| |
fprintf(ficgp,"p%d=%f ",jk,p[jk]);
|
| |
jk++;
|
| |
fprintf(ficgp,"\n");
|
| |
}
|
| |
}
|
| |
}
|
| |
}
|
| |
|
| |
for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
|
| |
for(jk=1; jk <=m; jk++) {
|
| |
fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
|
| |
if (ng==2)
|
| |
fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
|
| |
else
|
| |
fprintf(ficgp,"\nset title \"Probability\"\n");
|
| |
fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
|
| |
i=1;
|
| |
for(k2=1; k2<=nlstate; k2++) {
|
| |
k3=i;
|
| |
for(k=1; k<=(nlstate+ndeath); k++) {
|
| |
if (k != k2){
|
| |
if(ng==2)
|
| |
fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
|
| |
else
|
| |
fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
|
| |
ij=1;
|
| |
for(j=3; j <=ncovmodel; j++) {
|
| |
if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
|
| |
fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
|
| |
ij++;
|
| |
}
|
| |
else
|
| |
fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
|
| |
}
|
| |
fprintf(ficgp,")/(1");
|
| |
|
| |
for(k1=1; k1 <=nlstate; k1++){
|
| |
fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
|
| |
ij=1;
|
| |
for(j=3; j <=ncovmodel; j++){
|
| |
if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
|
| |
fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
|
| |
ij++;
|
| |
}
|
| |
else
|
| |
fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
|
| |
}
|
| |
fprintf(ficgp,")");
|
| |
}
|
| |
fprintf(ficgp,") t \"p%d%d\" ", k2,k);
|
| |
if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
|
| |
i=i+ncovmodel;
|
| |
}
|
| |
}
|
| |
}
|
| |
}
|
| |
}
|
| |
fclose(ficgp);
|
| |
} /* end gnuplot */
|
| |
|
| |
|
| |
/*************** Moving average **************/
|
| |
void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){
|
| |
|
| |
int i, cpt, cptcod;
|
| |
for (agedeb=ageminpar; agedeb<=fage; agedeb++)
|
| |
for (i=1; i<=nlstate;i++)
|
| |
for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
|
| |
mobaverage[(int)agedeb][i][cptcod]=0.;
|
| |
|
| |
for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){
|
| |
for (i=1; i<=nlstate;i++){
|
| |
for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
|
| |
for (cpt=0;cpt<=4;cpt++){
|
| |
mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];
|
| |
}
|
| |
mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;
|
| |
}
|
| |
}
|
| |
}
|
| |
|
| |
}
|
| |
|
| |
|
| |
/************** Forecasting ******************/
|
| |
prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){
|
| |
|
| |
int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
|
| |
int *popage;
|
| |
double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
|
| |
double *popeffectif,*popcount;
|
| |
double ***p3mat;
|
| |
char fileresf[FILENAMELENGTH];
|
| |
|
| |
agelim=AGESUP;
|
| |
calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
|
| |
|
| |
prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
|
| |
|
| |
|
| |
strcpy(fileresf,"f");
|
| |
strcat(fileresf,fileres);
|
| |
if((ficresf=fopen(fileresf,"w"))==NULL) {
|
| |
printf("Problem with forecast resultfile: %s\n", fileresf);
|
| |
}
|
| |
printf("Computing forecasting: result on file '%s' \n", fileresf);
|
| |
|
| |
if (cptcoveff==0) ncodemax[cptcoveff]=1;
|
| |
|
| |
if (mobilav==1) {
|
| |
mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
|
| |
movingaverage(agedeb, fage, ageminpar, mobaverage);
|
| |
}
|
| |
|
| |
stepsize=(int) (stepm+YEARM-1)/YEARM;
|
| |
if (stepm<=12) stepsize=1;
|
| |
|
| |
agelim=AGESUP;
|
| |
|
| |
hstepm=1;
|
| |
hstepm=hstepm/stepm;
|
| |
yp1=modf(dateintmean,&yp);
|
| |
anprojmean=yp;
|
| |
yp2=modf((yp1*12),&yp);
|
| |
mprojmean=yp;
|
| |
yp1=modf((yp2*30.5),&yp);
|
| |
jprojmean=yp;
|
| |
if(jprojmean==0) jprojmean=1;
|
| |
if(mprojmean==0) jprojmean=1;
|
| |
|
| |
fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);
|
| |
|
| |
for(cptcov=1;cptcov<=i2;cptcov++){
|
| |
for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
|
| |
k=k+1;
|
| |
fprintf(ficresf,"\n#******");
|
| |
for(j=1;j<=cptcoveff;j++) {
|
| |
fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
|
| |
}
|
| |
fprintf(ficresf,"******\n");
|
| |
fprintf(ficresf,"# StartingAge FinalAge");
|
| |
for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
|
| |
|
| |
|
| |
for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {
|
| |
fprintf(ficresf,"\n");
|
| |
fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);
|
| |
|
| |
for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
|
| |
nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
|
| |
nhstepm = nhstepm/hstepm;
|
| |
|
| |
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
| |
oldm=oldms;savm=savms;
|
| |
hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
|
| |
|
| |
for (h=0; h<=nhstepm; h++){
|
| |
if (h==(int) (calagedate+YEARM*cpt)) {
|
| |
fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
|
| |
}
|
| |
for(j=1; j<=nlstate+ndeath;j++) {
|
| |
kk1=0.;kk2=0;
|
| |
for(i=1; i<=nlstate;i++) {
|
| |
if (mobilav==1)
|
| |
kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
|
| |
else {
|
| |
kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
|
| |
}
|
| |
|
| |
}
|
| |
if (h==(int)(calagedate+12*cpt)){
|
| |
fprintf(ficresf," %.3f", kk1);
|
| |
|
| |
}
|
| |
}
|
| |
}
|
| |
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
| |
}
|
| |
}
|
| |
}
|
| |
}
|
| |
|
| |
if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
|
| |
|
| |
fclose(ficresf);
|
| |
}
|
| |
/************** Forecasting ******************/
|
| |
populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
|
| |
|
| |
int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
|
| |
int *popage;
|
| |
double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
|
| |
double *popeffectif,*popcount;
|
| |
double ***p3mat,***tabpop,***tabpopprev;
|
| |
char filerespop[FILENAMELENGTH];
|
| |
|
| |
tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
|
| |
tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
|
| |
agelim=AGESUP;
|
| |
calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
|
| |
|
| |
prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
|
| |
|
| |
|
| |
strcpy(filerespop,"pop");
|
| |
strcat(filerespop,fileres);
|
| |
if((ficrespop=fopen(filerespop,"w"))==NULL) {
|
| |
printf("Problem with forecast resultfile: %s\n", filerespop);
|
| |
}
|
| |
printf("Computing forecasting: result on file '%s' \n", filerespop);
|
| |
|
| |
if (cptcoveff==0) ncodemax[cptcoveff]=1;
|
| |
|
| |
if (mobilav==1) {
|
| |
mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
|
| |
movingaverage(agedeb, fage, ageminpar, mobaverage);
|
| |
}
|
| |
|
| |
stepsize=(int) (stepm+YEARM-1)/YEARM;
|
| |
if (stepm<=12) stepsize=1;
|
| |
|
| |
agelim=AGESUP;
|
| |
|
| |
hstepm=1;
|
| |
hstepm=hstepm/stepm;
|
| |
|
| |
if (popforecast==1) {
|
| |
if((ficpop=fopen(popfile,"r"))==NULL) {
|
| |
printf("Problem with population file : %s\n",popfile);exit(0);
|
| |
}
|
| |
popage=ivector(0,AGESUP);
|
| |
popeffectif=vector(0,AGESUP);
|
| |
popcount=vector(0,AGESUP);
|
| |
|
| |
i=1;
|
| |
while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
|
| |
|
| |
imx=i;
|
| |
for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
|
| |
}
|
| |
|
| |
for(cptcov=1;cptcov<=i2;cptcov++){
|
| |
for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
|
| |
k=k+1;
|
| |
fprintf(ficrespop,"\n#******");
|
| |
for(j=1;j<=cptcoveff;j++) {
|
| |
fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
|
| |
}
|
| |
fprintf(ficrespop,"******\n");
|
| |
fprintf(ficrespop,"# Age");
|
| |
for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
|
| |
if (popforecast==1) fprintf(ficrespop," [Population]");
|
| |
|
| |
for (cpt=0; cpt<=0;cpt++) {
|
| |
fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
|
| |
|
| |
for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
|
| |
nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
|
| |
nhstepm = nhstepm/hstepm;
|
| |
|
| |
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
| |
oldm=oldms;savm=savms;
|
| |
hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
|
| |
|
| |
for (h=0; h<=nhstepm; h++){
|
| |
if (h==(int) (calagedate+YEARM*cpt)) {
|
| |
fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
|
| |
}
|
| |
for(j=1; j<=nlstate+ndeath;j++) {
|
| |
kk1=0.;kk2=0;
|
| |
for(i=1; i<=nlstate;i++) {
|
| |
if (mobilav==1)
|
| |
kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
|
| |
else {
|
| |
kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
|
| |
}
|
| |
}
|
| |
if (h==(int)(calagedate+12*cpt)){
|
| |
tabpop[(int)(agedeb)][j][cptcod]=kk1;
|
| |
/*fprintf(ficrespop," %.3f", kk1);
|
| |
if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
|
| |
}
|
| |
}
|
| |
for(i=1; i<=nlstate;i++){
|
| |
kk1=0.;
|
| |
for(j=1; j<=nlstate;j++){
|
| |
kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
|
| |
}
|
| |
tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
|
| |
}
|
| |
|
| |
if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)
|
| |
fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
|
| |
}
|
| |
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
| |
}
|
| |
}
|
| |
|
| |
/******/
|
| |
|
| |
for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
|
| |
fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
|
| |
for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
|
| |
nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
|
| |
nhstepm = nhstepm/hstepm;
|
| |
|
| |
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
| |
oldm=oldms;savm=savms;
|
| |
hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
|
| |
for (h=0; h<=nhstepm; h++){
|
| |
if (h==(int) (calagedate+YEARM*cpt)) {
|
| |
fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
|
| |
}
|
| |
for(j=1; j<=nlstate+ndeath;j++) {
|
| |
kk1=0.;kk2=0;
|
| |
for(i=1; i<=nlstate;i++) {
|
| |
kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
|
| |
}
|
| |
if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);
|
| |
}
|
| |
}
|
| |
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
| |
}
|
| |
}
|
| |
}
|
| |
}
|
| |
|
| |
if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
|
| |
|
| |
if (popforecast==1) {
|
| |
free_ivector(popage,0,AGESUP);
|
| |
free_vector(popeffectif,0,AGESUP);
|
| |
free_vector(popcount,0,AGESUP);
|
| |
}
|
| |
free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
|
| |
free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
|
| |
fclose(ficrespop);
|
| |
}
|
| |
|
| |
/***********************************************/
|
| |
/**************** Main Program *****************/
|
| |
/***********************************************/
|
| |
|
| |
int main(int argc, char *argv[])
|
| |
{
|
| |
|
| |
int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
|
| |
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;
|
| |
int *indx;
|
| |
char line[MAXLINE], linepar[MAXLINE];
|
| |
char path[80],pathc[80],pathcd[80],pathtot[80],model[20];
|
| |
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,**adl,*tab;
|
| |
int mobilav=0,popforecast=0;
|
| |
int hstepm, nhstepm;
|
| |
double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
|
| |
|
| |
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,mproj1,anproj1,jproj2,mproj2,anproj2;
|
| |
|
| |
|
| |
char *alph[]={"a","a","b","c","d","e"}, str[4];
|
| |
|
| |
|
| |
char z[1]="c", occ;
|
| |
#include <sys/time.h>
|
| |
#include <time.h>
|
| |
char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
|
| |
|
| |
/* long total_usecs;
|
| |
struct timeval start_time, end_time;
|
| |
|
| |
gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
|
| |
getcwd(pathcd, size);
|
| |
|
| |
printf("\n%s",version);
|
| |
if(argc <=1){
|
| |
printf("\nEnter the parameter file name: ");
|
| |
scanf("%s",pathtot);
|
| |
}
|
| |
else{
|
| |
strcpy(pathtot,argv[1]);
|
| |
}
|
| |
/*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
|
| |
/*cygwin_split_path(pathtot,path,optionfile);
|
| |
printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
|
| |
/* cutv(path,optionfile,pathtot,'\\');*/
|
| |
|
| |
split(pathtot,path,optionfile,optionfilext,optionfilefiname);
|
| |
printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
|
| |
chdir(path);
|
| |
replace(pathc,path);
|
| |
|
| |
/*-------- arguments in the command line --------*/
|
| |
|
| |
strcpy(fileres,"r");
|
| |
strcat(fileres, optionfilefiname);
|
| |
strcat(fileres,".txt"); /* Other files have txt extension */
|
| |
|
| |
/*---------arguments file --------*/
|
| |
|
| |
if((ficpar=fopen(optionfile,"r"))==NULL) {
|
| |
printf("Problem with optionfile %s\n",optionfile);
|
| |
goto end;
|
| |
}
|
| |
|
| |
strcpy(filereso,"o");
|
| |
strcat(filereso,fileres);
|
| |
if((ficparo=fopen(filereso,"w"))==NULL) {
|
| |
printf("Problem with Output resultfile: %s\n", filereso);goto end;
|
| |
}
|
| |
|
| |
/* Reads comments: lines beginning with '#' */
|
| |
while((c=getc(ficpar))=='#' && c!= EOF){
|
| |
ungetc(c,ficpar);
|
| |
fgets(line, MAXLINE, ficpar);
|
| |
puts(line);
|
| |
fputs(line,ficparo);
|
| |
}
|
| |
ungetc(c,ficpar);
|
| |
|
| |
fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
|
| |
printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
|
| |
fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
|
| |
while((c=getc(ficpar))=='#' && c!= EOF){
|
| |
ungetc(c,ficpar);
|
| |
fgets(line, MAXLINE, ficpar);
|
| |
puts(line);
|
| |
fputs(line,ficparo);
|
| |
}
|
| |
ungetc(c,ficpar);
|
| |
|
| |
|
| |
covar=matrix(0,NCOVMAX,1,n);
|
| |
cptcovn=0;
|
| |
if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
|
| |
|
| |
ncovmodel=2+cptcovn;
|
| |
nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
|
| |
|
| |
/* Read guess parameters */
|
| |
/* Reads comments: lines beginning with '#' */
|
| |
while((c=getc(ficpar))=='#' && c!= EOF){
|
| |
ungetc(c,ficpar);
|
| |
fgets(line, MAXLINE, ficpar);
|
| |
puts(line);
|
| |
fputs(line,ficparo);
|
| |
}
|
| |
ungetc(c,ficpar);
|
| |
|
| |
param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
|
| |
for(i=1; i <=nlstate; i++)
|
| |
for(j=1; j <=nlstate+ndeath-1; j++){
|
| |
fscanf(ficpar,"%1d%1d",&i1,&j1);
|
| |
fprintf(ficparo,"%1d%1d",i1,j1);
|
| |
printf("%1d%1d",i,j);
|
| |
for(k=1; k<=ncovmodel;k++){
|
| |
fscanf(ficpar," %lf",¶m[i][j][k]);
|
| |
printf(" %lf",param[i][j][k]);
|
| |
fprintf(ficparo," %lf",param[i][j][k]);
|
| |
}
|
| |
fscanf(ficpar,"\n");
|
| |
printf("\n");
|
| |
fprintf(ficparo,"\n");
|
| |
}
|
| |
|
| |
npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
|
| |
|
| |
p=param[1][1];
|
| |
|
| |
/* Reads comments: lines beginning with '#' */
|
| |
while((c=getc(ficpar))=='#' && c!= EOF){
|
| |
ungetc(c,ficpar);
|
| |
fgets(line, MAXLINE, ficpar);
|
| |
puts(line);
|
| |
fputs(line,ficparo);
|
| |
}
|
| |
ungetc(c,ficpar);
|
| |
|
| |
delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
|
| |
delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
|
| |
for(i=1; i <=nlstate; i++){
|
| |
for(j=1; j <=nlstate+ndeath-1; j++){
|
| |
fscanf(ficpar,"%1d%1d",&i1,&j1);
|
| |
printf("%1d%1d",i,j);
|
| |
fprintf(ficparo,"%1d%1d",i1,j1);
|
| |
for(k=1; k<=ncovmodel;k++){
|
| |
fscanf(ficpar,"%le",&delti3[i][j][k]);
|
| |
printf(" %le",delti3[i][j][k]);
|
| |
fprintf(ficparo," %le",delti3[i][j][k]);
|
| |
}
|
| |
fscanf(ficpar,"\n");
|
| |
printf("\n");
|
| |
fprintf(ficparo,"\n");
|
| |
}
|
| |
}
|
| |
delti=delti3[1][1];
|
| |
|
| |
/* Reads comments: lines beginning with '#' */
|
| |
while((c=getc(ficpar))=='#' && c!= EOF){
|
| |
ungetc(c,ficpar);
|
| |
fgets(line, MAXLINE, ficpar);
|
| |
puts(line);
|
| |
fputs(line,ficparo);
|
| |
}
|
| |
ungetc(c,ficpar);
|
| |
|
| |
matcov=matrix(1,npar,1,npar);
|
| |
for(i=1; i <=npar; i++){
|
| |
fscanf(ficpar,"%s",&str);
|
| |
printf("%s",str);
|
| |
fprintf(ficparo,"%s",str);
|
| |
for(j=1; j <=i; j++){
|
| |
fscanf(ficpar," %le",&matcov[i][j]);
|
| |
printf(" %.5le",matcov[i][j]);
|
| |
fprintf(ficparo," %.5le",matcov[i][j]);
|
| |
}
|
| |
fscanf(ficpar,"\n");
|
| |
printf("\n");
|
| |
fprintf(ficparo,"\n");
|
| |
}
|
| |
for(i=1; i <=npar; i++)
|
| |
for(j=i+1;j<=npar;j++)
|
| |
matcov[i][j]=matcov[j][i];
|
| |
|
| |
printf("\n");
|
| |
|
| |
|
| |
/*-------- Rewriting paramater 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(ficres,"#%s\n",version);
|
| |
|
| |
/*-------- data file ----------*/
|
| |
if((fic=fopen(datafile,"r"))==NULL) {
|
| |
printf("Problem with datafile: %s\n", datafile);goto end;
|
| |
}
|
| |
|
| |
n= lastobs;
|
| |
severity = vector(1,maxwav);
|
| |
outcome=imatrix(1,maxwav+1,1,n);
|
| |
num=ivector(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);
|
| |
adl=imatrix(1,maxwav+1,1,n);
|
| |
tab=ivector(1,NCOVMAX);
|
| |
ncodemax=ivector(1,8);
|
| |
|
| |
i=1;
|
| |
while (fgets(line, MAXLINE, fic) != NULL) {
|
| |
if ((i >= firstobs) && (i <=lastobs)) {
|
| |
|
| |
for (j=maxwav;j>=1;j--){
|
| |
cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
|
| |
strcpy(line,stra);
|
| |
cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
|
| |
cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
|
| |
}
|
| |
|
| |
cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
|
| |
cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
|
| |
|
| |
cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
|
| |
cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
|
| |
|
| |
cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
|
| |
for (j=ncovcol;j>=1;j--){
|
| |
cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
|
| |
}
|
| |
num[i]=atol(stra);
|
| |
|
| |
/*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
|
| |
printf("%d %.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;
|
| |
}
|
| |
}
|
| |
/* 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("%d %.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]));}*/
|
| |
|
| |
|
| |
/* Calculation of the number of parameter from char model*/
|
| |
Tvar=ivector(1,15);
|
| |
Tprod=ivector(1,15);
|
| |
Tvaraff=ivector(1,15);
|
| |
Tvard=imatrix(1,15,1,2);
|
| |
Tage=ivector(1,15);
|
| |
|
| |
if (strlen(model) >1){
|
| |
j=0, j1=0, k1=1, k2=1;
|
| |
j=nbocc(model,'+');
|
| |
j1=nbocc(model,'*');
|
| |
cptcovn=j+1;
|
| |
cptcovprod=j1;
|
| |
|
| |
strcpy(modelsav,model);
|
| |
if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
|
| |
printf("Error. Non available option model=%s ",model);
|
| |
goto end;
|
| |
}
|
| |
|
| |
for(i=(j+1); i>=1;i--){
|
| |
cutv(stra,strb,modelsav,'+');
|
| |
if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);
|
| |
/* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
|
| |
/*scanf("%d",i);*/
|
| |
if (strchr(strb,'*')) {
|
| |
cutv(strd,strc,strb,'*');
|
| |
if (strcmp(strc,"age")==0) {
|
| |
cptcovprod--;
|
| |
cutv(strb,stre,strd,'V');
|
| |
Tvar[i]=atoi(stre);
|
| |
cptcovage++;
|
| |
Tage[cptcovage]=i;
|
| |
/*printf("stre=%s ", stre);*/
|
| |
}
|
| |
else if (strcmp(strd,"age")==0) {
|
| |
cptcovprod--;
|
| |
cutv(strb,stre,strc,'V');
|
| |
Tvar[i]=atoi(stre);
|
| |
cptcovage++;
|
| |
Tage[cptcovage]=i;
|
| |
}
|
| |
else {
|
| |
cutv(strb,stre,strc,'V');
|
| |
Tvar[i]=ncovcol+k1;
|
| |
cutv(strb,strc,strd,'V');
|
| |
Tprod[k1]=i;
|
| |
Tvard[k1][1]=atoi(strc);
|
| |
Tvard[k1][2]=atoi(stre);
|
| |
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 {
|
| |
/*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);*/
|
| |
}
|
| |
}
|
| |
|
| |
/* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
|
| |
printf("cptcovprod=%d ", cptcovprod);
|
| |
scanf("%d ",i);*/
|
| |
fclose(fic);
|
| |
|
| |
/* 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);
|
| |
|
| |
for (i=1; i<=imx; i++) {
|
| |
for(m=2; (m<= maxwav); m++) {
|
| |
if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
|
| |
anint[m][i]=9999;
|
| |
s[m][i]=-1;
|
| |
}
|
| |
if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
|
| |
}
|
| |
}
|
| |
|
| |
for (i=1; i<=imx; i++) {
|
| |
agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
|
| |
for(m=1; (m<= maxwav); m++){
|
| |
if(s[m][i] >0){
|
| |
if (s[m][i] >= nlstate+1) {
|
| |
if(agedc[i]>0)
|
| |
if(moisdc[i]!=99 && andc[i]!=9999)
|
| |
agev[m][i]=agedc[i];
|
| |
/*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
|
| |
else {
|
| |
if (andc[i]!=9999){
|
| |
printf("Warning negative age at death: %d line:%d\n",num[i],i);
|
| |
agev[m][i]=-1;
|
| |
}
|
| |
}
|
| |
}
|
| |
else if(s[m][i] !=9){ /* Should no more exist */
|
| |
agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
|
| |
if(mint[m][i]==99 || 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=1; (m<= maxwav); m++){
|
| |
if (s[m][i] > (nlstate+ndeath)) {
|
| |
printf("Error: Wrong value in nlstate or ndeath\n");
|
| |
goto end;
|
| |
}
|
| |
}
|
| |
}
|
| |
|
| |
printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
|
| |
|
| |
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);
|
| |
free_matrix(anint,1,maxwav,1,n);*/
|
| |
free_vector(moisdc,1,n);
|
| |
free_vector(andc,1,n);
|
| |
|
| |
|
| |
wav=ivector(1,imx);
|
| |
dh=imatrix(1,lastpass-firstpass+1,1,imx);
|
| |
mw=imatrix(1,lastpass-firstpass+1,1,imx);
|
| |
|
| |
/* Concatenates waves */
|
| |
concatwav(wav, dh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
|
| |
|
| |
|
| |
Tcode=ivector(1,100);
|
| |
nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
|
| |
ncodemax[1]=1;
|
| |
if (cptcovn > 0) tricode(Tvar,nbcode,imx);
|
| |
|
| |
codtab=imatrix(1,100,1,10);
|
| |
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++){
|
| |
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]);*/
|
| |
}
|
| |
}
|
| |
}
|
| |
}
|
| |
/* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
|
| |
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("\n");
|
| |
}
|
| |
scanf("%d",i);*/
|
| |
|
| |
/* Calculates basic frequencies. Computes observed prevalence at single age
|
| |
and prints on file fileres'p'. */
|
| |
|
| |
|
| |
|
| |
pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
|
| |
oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
|
| |
newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
|
| |
savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
|
| |
oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
|
| |
|
| |
/* For Powell, parameters are in a vector p[] starting at p[1]
|
| |
so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
|
| |
p=param[1][1]; /* *(*(*(param +1)+1)+0) */
|
| |
|
| |
if(mle==1){
|
| |
mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
|
| |
}
|
| |
|
| |
/*--------- results files --------------*/
|
| |
fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
|
| |
|
| |
|
| |
jk=1;
|
| |
fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
|
| |
printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
|
| |
for(i=1,jk=1; i <=nlstate; i++){
|
| |
for(k=1; k <=(nlstate+ndeath); k++){
|
| |
if (k != i)
|
| |
{
|
| |
printf("%d%d ",i,k);
|
| |
fprintf(ficres,"%1d%1d ",i,k);
|
| |
for(j=1; j <=ncovmodel; j++){
|
| |
printf("%f ",p[jk]);
|
| |
fprintf(ficres,"%f ",p[jk]);
|
| |
jk++;
|
| |
}
|
| |
printf("\n");
|
| |
fprintf(ficres,"\n");
|
| |
}
|
| |
}
|
| |
}
|
| |
if(mle==1){
|
| |
/* Computing hessian and covariance matrix */
|
| |
ftolhess=ftol; /* Usually correct */
|
| |
hesscov(matcov, p, npar, delti, ftolhess, func);
|
| |
}
|
| |
fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
|
| |
printf("# Scales (for hessian or gradient estimation)\n");
|
| |
for(i=1,jk=1; i <=nlstate; i++){
|
| |
for(j=1; j <=nlstate+ndeath; j++){
|
| |
if (j!=i) {
|
| |
fprintf(ficres,"%1d%1d",i,j);
|
| |
printf("%1d%1d",i,j);
|
| |
for(k=1; k<=ncovmodel;k++){
|
| |
printf(" %.5e",delti[jk]);
|
| |
fprintf(ficres," %.5e",delti[jk]);
|
| |
jk++;
|
| |
}
|
| |
printf("\n");
|
| |
fprintf(ficres,"\n");
|
| |
}
|
| |
}
|
| |
}
|
| |
|
| |
k=1;
|
| |
fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
|
| |
printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
|
| |
for(i=1;i<=npar;i++){
|
| |
/* if (k>nlstate) k=1;
|
| |
i1=(i-1)/(ncovmodel*nlstate)+1;
|
| |
fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
|
| |
printf("%s%d%d",alph[k],i1,tab[i]);*/
|
| |
fprintf(ficres,"%3d",i);
|
| |
printf("%3d",i);
|
| |
for(j=1; j<=i;j++){
|
| |
fprintf(ficres," %.5e",matcov[i][j]);
|
| |
printf(" %.5e",matcov[i][j]);
|
| |
}
|
| |
fprintf(ficres,"\n");
|
| |
printf("\n");
|
| |
k++;
|
| |
}
|
| |
|
| |
while((c=getc(ficpar))=='#' && c!= EOF){
|
| |
ungetc(c,ficpar);
|
| |
fgets(line, MAXLINE, ficpar);
|
| |
puts(line);
|
| |
fputs(line,ficparo);
|
| |
}
|
| |
ungetc(c,ficpar);
|
| |
estepm=0;
|
| |
fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
|
| |
if (estepm==0 || estepm < stepm) estepm=stepm;
|
| |
if (fage <= 2) {
|
| |
bage = ageminpar;
|
| |
fage = agemaxpar;
|
| |
}
|
| |
|
| |
fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
|
| |
fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
|
| |
fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
|
| |
|
| |
while((c=getc(ficpar))=='#' && c!= EOF){
|
| |
ungetc(c,ficpar);
|
| |
fgets(line, MAXLINE, ficpar);
|
| |
puts(line);
|
| |
fputs(line,ficparo);
|
| |
}
|
| |
ungetc(c,ficpar);
|
| |
|
| |
fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);
|
| |
fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
|
| |
fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
|
| |
|
| |
while((c=getc(ficpar))=='#' && c!= EOF){
|
| |
ungetc(c,ficpar);
|
| |
fgets(line, MAXLINE, ficpar);
|
| |
puts(line);
|
| |
fputs(line,ficparo);
|
| |
}
|
| |
ungetc(c,ficpar);
|
| |
|
| |
|
| |
dateprev1=anprev1+mprev1/12.+jprev1/365.;
|
| |
dateprev2=anprev2+mprev2/12.+jprev2/365.;
|
| |
|
| |
fscanf(ficpar,"pop_based=%d\n",&popbased);
|
| |
fprintf(ficparo,"pop_based=%d\n",popbased);
|
| |
fprintf(ficres,"pop_based=%d\n",popbased);
|
| |
|
| |
while((c=getc(ficpar))=='#' && c!= EOF){
|
| |
ungetc(c,ficpar);
|
| |
fgets(line, MAXLINE, ficpar);
|
| |
puts(line);
|
| |
fputs(line,ficparo);
|
| |
}
|
| |
ungetc(c,ficpar);
|
| |
|
| |
fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);
|
| |
fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);
|
| |
fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);
|
| |
|
| |
|
| |
while((c=getc(ficpar))=='#' && c!= EOF){
|
| |
ungetc(c,ficpar);
|
| |
fgets(line, MAXLINE, ficpar);
|
| |
puts(line);
|
| |
fputs(line,ficparo);
|
| |
}
|
| |
ungetc(c,ficpar);
|
| |
|
| |
fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
|
| |
fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
|
| |
fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
|
| |
|
| |
freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
|
| |
|
| |
/*------------ gnuplot -------------*/
|
| |
strcpy(optionfilegnuplot,optionfilefiname);
|
| |
strcat(optionfilegnuplot,".gp");
|
| |
if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
|
| |
printf("Problem with file %s",optionfilegnuplot);
|
| |
}
|
| |
fclose(ficgp);
|
| |
printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
|
| |
/*--------- index.htm --------*/
|
| |
|
| |
strcpy(optionfilehtm,optionfile);
|
| |
strcat(optionfilehtm,".htm");
|
| |
if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
|
| |
printf("Problem with %s \n",optionfilehtm), exit(0);
|
| |
}
|
| |
|
| |
fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
|
| |
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
|
| |
\n
|
| |
Total number of observations=%d <br>\n
|
| |
Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
|
| |
<hr size=\"2\" color=\"#EC5E5E\">
|
| |
<ul><li><h4>Parameter files</h4>\n
|
| |
- Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
|
| |
- Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);
|
| |
fclose(fichtm);
|
| |
|
| |
printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
|
| |
|
| |
/*------------ free_vector -------------*/
|
| |
chdir(path);
|
| |
|
| |
free_ivector(wav,1,imx);
|
| |
free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
|
| |
free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
|
| |
free_ivector(num,1,n);
|
| |
free_vector(agedc,1,n);
|
| |
/*free_matrix(covar,1,NCOVMAX,1,n);*/
|
| |
fclose(ficparo);
|
| |
fclose(ficres);
|
| |
|
| |
|
| |
/*--------------- Prevalence limit --------------*/
|
| |
|
| |
strcpy(filerespl,"pl");
|
| |
strcat(filerespl,fileres);
|
| |
if((ficrespl=fopen(filerespl,"w"))==NULL) {
|
| |
printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;
|
| |
}
|
| |
printf("Computing prevalence limit: result on file '%s' \n", filerespl);
|
| |
fprintf(ficrespl,"#Prevalence limit\n");
|
| |
fprintf(ficrespl,"#Age ");
|
| |
for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
|
| |
fprintf(ficrespl,"\n");
|
| |
|
| |
prlim=matrix(1,nlstate,1,nlstate);
|
| |
pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
|
| |
oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
|
| |
newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
|
| |
savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
|
| |
oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
|
| |
k=0;
|
| |
agebase=ageminpar;
|
| |
agelim=agemaxpar;
|
| |
ftolpl=1.e-10;
|
| |
i1=cptcoveff;
|
| |
if (cptcovn < 1){i1=1;}
|
| |
|
| |
for(cptcov=1;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]);*/
|
| |
fprintf(ficrespl,"\n#******");
|
| |
for(j=1;j<=cptcoveff;j++)
|
| |
fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
|
| |
fprintf(ficrespl,"******\n");
|
| |
|
| |
for (age=agebase; age<=agelim; age++){
|
| |
prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
|
| |
fprintf(ficrespl,"%.0f",age );
|
| |
for(i=1; i<=nlstate;i++)
|
| |
fprintf(ficrespl," %.5f", prlim[i][i]);
|
| |
fprintf(ficrespl,"\n");
|
| |
}
|
| |
}
|
| |
}
|
| |
fclose(ficrespl);
|
| |
|
| |
/*------------- h Pij x at various ages ------------*/
|
| |
|
| |
strcpy(filerespij,"pij"); strcat(filerespij,fileres);
|
| |
if((ficrespij=fopen(filerespij,"w"))==NULL) {
|
| |
printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
|
| |
}
|
| |
printf("Computing pij: result on file '%s' \n", filerespij);
|
| |
|
| |
stepsize=(int) (stepm+YEARM-1)/YEARM;
|
| |
/*if (stepm<=24) stepsize=2;*/
|
| |
|
| |
agelim=AGESUP;
|
| |
hstepm=stepsize*YEARM; /* Every year of age */
|
| |
hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
|
| |
|
| |
/* hstepm=1; aff par mois*/
|
| |
|
| |
k=0;
|
| |
for(cptcov=1;cptcov<=i1;cptcov++){
|
| |
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
|
| |
k=k+1;
|
| |
fprintf(ficrespij,"\n#****** ");
|
| |
for(j=1;j<=cptcoveff;j++)
|
| |
fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
|
| |
fprintf(ficrespij,"******\n");
|
| |
|
| |
for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
|
| |
nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
|
| |
nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
|
| |
|
| |
/* nhstepm=nhstepm*YEARM; aff par mois*/
|
| |
|
| |
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
| |
oldm=oldms;savm=savms;
|
| |
hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
|
| |
fprintf(ficrespij,"# Age");
|
| |
for(i=1; i<=nlstate;i++)
|
| |
for(j=1; j<=nlstate+ndeath;j++)
|
| |
fprintf(ficrespij," %1d-%1d",i,j);
|
| |
fprintf(ficrespij,"\n");
|
| |
for (h=0; h<=nhstepm; h++){
|
| |
fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
|
| |
for(i=1; i<=nlstate;i++)
|
| |
for(j=1; j<=nlstate+ndeath;j++)
|
| |
fprintf(ficrespij," %.5f", p3mat[i][j][h]);
|
| |
fprintf(ficrespij,"\n");
|
| |
}
|
| |
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
| |
fprintf(ficrespij,"\n");
|
| |
}
|
| |
}
|
| |
}
|
| |
|
| |
varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
|
| |
|
| |
fclose(ficrespij);
|
| |
|
| |
|
| |
/*---------- Forecasting ------------------*/
|
| |
if((stepm == 1) && (strcmp(model,".")==0)){
|
| |
prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
|
| |
if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
|
| |
}
|
| |
else{
|
| |
erreur=108;
|
| |
printf("Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
|
| |
}
|
| |
|
| |
|
| |
/*---------- 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;
|
| |
}
|
| |
printf("Computing Total LEs with variances: file '%s' \n", filerest);
|
| |
|
| |
|
| |
strcpy(filerese,"e");
|
| |
strcat(filerese,fileres);
|
| |
if((ficreseij=fopen(filerese,"w"))==NULL) {
|
| |
printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
|
| |
}
|
| |
printf("Computing Health Expectancies: result on file '%s' \n", filerese);
|
| |
|
| |
strcpy(fileresv,"v");
|
| |
strcat(fileresv,fileres);
|
| |
if((ficresvij=fopen(fileresv,"w"))==NULL) {
|
| |
printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
|
| |
}
|
| |
printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
|
| |
calagedate=-1;
|
| |
prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
|
| |
|
| |
k=0;
|
| |
for(cptcov=1;cptcov<=i1;cptcov++){
|
| |
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
|
| |
k=k+1;
|
| |
fprintf(ficrest,"\n#****** ");
|
| |
for(j=1;j<=cptcoveff;j++)
|
| |
fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
|
| |
fprintf(ficrest,"******\n");
|
| |
|
| |
fprintf(ficreseij,"\n#****** ");
|
| |
for(j=1;j<=cptcoveff;j++)
|
| |
fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
|
| |
fprintf(ficreseij,"******\n");
|
| |
|
| |
fprintf(ficresvij,"\n#****** ");
|
| |
for(j=1;j<=cptcoveff;j++)
|
| |
fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
|
| |
fprintf(ficresvij,"******\n");
|
| |
|
| |
eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
|
| |
oldm=oldms;savm=savms;
|
| |
evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
|
| |
|
| |
vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
|
| |
oldm=oldms;savm=savms;
|
| |
varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);
|
| |
|
| |
|
| |
|
| |
fprintf(ficrest,"#Total LEs with variances: 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) {
|
| |
for(i=1; i<=nlstate;i++)
|
| |
prlim[i][i]=probs[(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]);*/
|
| |
}
|
| |
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]));
|
| |
}
|
| |
fprintf(ficrest,"\n");
|
| |
}
|
| |
}
|
| |
}
|
| |
free_matrix(mint,1,maxwav,1,n);
|
| |
free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);
|
| |
free_vector(weight,1,n);
|
| |
fclose(ficreseij);
|
| |
fclose(ficresvij);
|
| |
fclose(ficrest);
|
| |
fclose(ficpar);
|
| |
free_vector(epj,1,nlstate+1);
|
| |
|
| |
/*------- Variance limit prevalence------*/
|
| |
|
| |
strcpy(fileresvpl,"vpl");
|
| |
strcat(fileresvpl,fileres);
|
| |
if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
|
| |
printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);
|
| |
exit(0);
|
| |
}
|
| |
printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);
|
| |
|
| |
k=0;
|
| |
for(cptcov=1;cptcov<=i1;cptcov++){
|
| |
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
|
| |
k=k+1;
|
| |
fprintf(ficresvpl,"\n#****** ");
|
| |
for(j=1;j<=cptcoveff;j++)
|
| |
fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
|
| |
fprintf(ficresvpl,"******\n");
|
| |
|
| |
varpl=matrix(1,nlstate,(int) bage, (int) fage);
|
| |
oldm=oldms;savm=savms;
|
| |
varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
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}
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| |
}
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| |
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| |
fclose(ficresvpl);
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| |
|
| |
/*---------- End : free ----------------*/
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| |
free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
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| |
|
| |
free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
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| |
free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
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| |
|
| |
|
| |
free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
|
| |
free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
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| |
free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
|
| |
free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
|
| |
|
| |
free_matrix(matcov,1,npar,1,npar);
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| |
free_vector(delti,1,npar);
|
| |
free_matrix(agev,1,maxwav,1,imx);
|
| |
free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
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| |
|
| |
fprintf(fichtm,"\n</body>");
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| |
fclose(fichtm);
|
| |
fclose(ficgp);
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| |
|
| |
|
| |
if(erreur >0)
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| |
printf("End of Imach with error or warning %d\n",erreur);
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| |
else printf("End of Imach\n");
|
| |
/* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
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| |
|
| |
/* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
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| |
/*printf("Total time was %d uSec.\n", total_usecs);*/
|
| |
/*------ End -----------*/
|
| |
|
| |
|
| |
end:
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| |
#ifdef windows
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| |
/* chdir(pathcd);*/
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| |
#endif
|
| |
/*system("wgnuplot graph.plt");*/
|
| |
/*system("../gp37mgw/wgnuplot graph.plt");*/
|
| |
/*system("cd ../gp37mgw");*/
|
| |
/* system("..\\gp37mgw\\wgnuplot graph.plt");*/
|
| |
strcpy(plotcmd,GNUPLOTPROGRAM);
|
| |
strcat(plotcmd," ");
|
| |
strcat(plotcmd,optionfilegnuplot);
|
| |
system(plotcmd);
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| |
|
| |
#ifdef windows
|
| |
while (z[0] != 'q') {
|
| |
/* chdir(path); */
|
| |
printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
|
| |
scanf("%s",z);
|
| |
if (z[0] == 'c') system("./imach");
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| |
else if (z[0] == 'e') system(optionfilehtm);
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| |
else if (z[0] == 'g') system(plotcmd);
|
| |
else if (z[0] == 'q') exit(0);
|
| |
}
|
| |
#endif
|
| |
}
|
| |
|
| |
|
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