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version 1.63, 2002/11/20 17:35:59
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version 1.125, 2006/04/04 15:20:31
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| /* $Id$ |
/* $Id$
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| Interpolated Markov Chain |
$State$
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| |
$Log$ |
| Short summary of the programme: |
Revision 1.125 2006/04/04 15:20:31 lievre |
| |
Errors in calculation of health expectancies. Age was not initialized. |
| This program computes Healthy Life Expectancies from |
Forecasting file added. |
| cross-longitudinal data. Cross-longitudinal data consist in: -1- a |
|
| first survey ("cross") where individuals from different ages are |
Revision 1.124 2006/03/22 17:13:53 lievre
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| interviewed on their health status or degree of disability (in the |
Parameters are printed with %lf instead of %f (more numbers after the comma).
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| case of a health survey which is our main interest) -2- at least a |
The log-likelihood is printed in the log file
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| second wave of interviews ("longitudinal") which measure each change |
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| (if any) in individual health status. Health expectancies are |
Revision 1.123 2006/03/20 10:52:43 brouard
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| computed from the time spent in each health state according to a |
* imach.c (Module): <title> changed, corresponds to .htm file
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| model. More health states you consider, more time is necessary to reach the |
name. <head> headers where missing.
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| Maximum Likelihood of the parameters involved in the model. The |
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| simplest model is the multinomial logistic model where pij is the |
* imach.c (Module): Weights can have a decimal point as for
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| probability to be observed in state j at the second wave |
English (a comma might work with a correct LC_NUMERIC environment,
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| conditional to be observed in state i at the first wave. Therefore |
otherwise the weight is truncated).
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| the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where |
Modification of warning when the covariates values are not 0 or
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| 'age' is age and 'sex' is a covariate. If you want to have a more |
1.
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| complex model than "constant and age", you should modify the program |
Version 0.98g
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| where the markup *Covariates have to be included here again* invites |
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| you to do it. More covariates you add, slower the |
Revision 1.122 2006/03/20 09:45:41 brouard
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| convergence. |
(Module): Weights can have a decimal point as for
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| |
English (a comma might work with a correct LC_NUMERIC environment,
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| The advantage of this computer programme, compared to a simple |
otherwise the weight is truncated).
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| multinomial logistic model, is clear when the delay between waves is not |
Modification of warning when the covariates values are not 0 or
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| identical for each individual. Also, if a individual missed an |
1.
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| intermediate interview, the information is lost, but taken into |
Version 0.98g
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| account using an interpolation or extrapolation. |
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| |
Revision 1.121 2006/03/16 17:45:01 lievre
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| hPijx is the probability to be observed in state i at age x+h |
* imach.c (Module): Comments concerning covariates added
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| conditional to the observed state i at age x. The delay 'h' can be |
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| split into an exact number (nh*stepm) of unobserved intermediate |
* imach.c (Module): refinements in the computation of lli if
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| states. This elementary transition (by month or quarter trimester, |
status=-2 in order to have more reliable computation if stepm is
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| semester or year) is model as a multinomial logistic. The hPx |
not 1 month. Version 0.98f
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| matrix is simply the matrix product of nh*stepm elementary matrices |
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| and the contribution of each individual to the likelihood is simply |
Revision 1.120 2006/03/16 15:10:38 lievre
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| hPijx. |
(Module): refinements in the computation of lli if
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| |
status=-2 in order to have more reliable computation if stepm is
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| Also this programme outputs the covariance matrix of the parameters but also |
not 1 month. Version 0.98f
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| of the life expectancies. It also computes the stable prevalence. |
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| |
Revision 1.119 2006/03/15 17:42:26 brouard
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| Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr). |
(Module): Bug if status = -2, the loglikelihood was
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| Institut national d'études démographiques, Paris. |
computed as likelihood omitting the logarithm. Version O.98e
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| This software have been partly granted by Euro-REVES, a concerted action |
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| from the European Union. |
Revision 1.118 2006/03/14 18:20:07 brouard
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| It is copyrighted identically to a GNU software product, ie programme and |
(Module): varevsij Comments added explaining the second
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| software can be distributed freely for non commercial use. Latest version |
table of variances if popbased=1 .
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| can be accessed at http://euroreves.ined.fr/imach . |
(Module): Covariances of eij, ekl added, graphs fixed, new html link.
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| **********************************************************************/ |
(Module): Function pstamp added
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| |
(Module): Version 0.98d
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| #include <math.h> |
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| #include <stdio.h> |
Revision 1.117 2006/03/14 17:16:22 brouard
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| #include <stdlib.h> |
(Module): varevsij Comments added explaining the second
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| #include <unistd.h> |
table of variances if popbased=1 .
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| |
(Module): Covariances of eij, ekl added, graphs fixed, new html link.
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| #define MAXLINE 256 |
(Module): Function pstamp added
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| #define GNUPLOTPROGRAM "gnuplot" |
(Module): Version 0.98d
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| /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/ |
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| #define FILENAMELENGTH 80 |
Revision 1.116 2006/03/06 10:29:27 brouard
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| /*#define DEBUG*/ |
(Module): Variance-covariance wrong links and
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| #define windows |
varian-covariance of ej. is needed (Saito).
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| #define GLOCK_ERROR_NOPATH -1 /* empty path */ |
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| #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */ |
Revision 1.115 2006/02/27 12:17:45 brouard
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| |
(Module): One freematrix added in mlikeli! 0.98c
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| #define MAXPARM 30 /* Maximum number of parameters for the optimization */ |
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| #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */ |
Revision 1.114 2006/02/26 12:57:58 brouard
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| |
(Module): Some improvements in processing parameter
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| #define NINTERVMAX 8 |
filename with strsep.
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| #define NLSTATEMAX 8 /* Maximum number of live states (for func) */ |
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| #define NDEATHMAX 8 /* Maximum number of dead states (for func) */ |
Revision 1.113 2006/02/24 14:20:24 brouard
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| #define NCOVMAX 8 /* Maximum number of covariates */ |
(Module): Memory leaks checks with valgrind and:
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| #define MAXN 20000 |
datafile was not closed, some imatrix were not freed and on matrix
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| #define YEARM 12. /* Number of months per year */ |
allocation too.
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| #define AGESUP 130 |
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| #define AGEBASE 40 |
Revision 1.112 2006/01/30 09:55:26 brouard
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| #ifdef windows |
(Module): Back to gnuplot.exe instead of wgnuplot.exe
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| #define DIRSEPARATOR '\\' |
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| #define ODIRSEPARATOR '/' |
Revision 1.111 2006/01/25 20:38:18 brouard
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| #else |
(Module): Lots of cleaning and bugs added (Gompertz)
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| #define DIRSEPARATOR '/' |
(Module): Comments can be added in data file. Missing date values
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| #define ODIRSEPARATOR '\\' |
can be a simple dot '.'.
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| #endif |
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| |
Revision 1.110 2006/01/25 00:51:50 brouard
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| char version[80]="Imach version 0.9, November 2002, INED-EUROREVES "; |
(Module): Lots of cleaning and bugs added (Gompertz)
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| int erreur; /* Error number */ |
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| int nvar; |
Revision 1.109 2006/01/24 19:37:15 brouard
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| int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov; |
(Module): Comments (lines starting with a #) are allowed in data.
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| int npar=NPARMAX; |
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| int nlstate=2; /* Number of live states */ |
Revision 1.108 2006/01/19 18:05:42 lievre
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| int ndeath=1; /* Number of dead states */ |
Gnuplot problem appeared...
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| int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */ |
To be fixed
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| int popbased=0; |
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| |
Revision 1.107 2006/01/19 16:20:37 brouard
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| int *wav; /* Number of waves for this individuual 0 is possible */ |
Test existence of gnuplot in imach path
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| int maxwav; /* Maxim number of waves */ |
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| int jmin, jmax; /* min, max spacing between 2 waves */ |
Revision 1.106 2006/01/19 13:24:36 brouard
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| int mle, weightopt; |
Some cleaning and links added in html output
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| int **mw; /* mw[mi][i] is number of the mi wave for this individual */ |
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| int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */ |
Revision 1.105 2006/01/05 20:23:19 lievre
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| int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between |
*** empty log message ***
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| * wave mi and wave mi+1 is not an exact multiple of stepm. */ |
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| double jmean; /* Mean space between 2 waves */ |
Revision 1.104 2005/09/30 16:11:43 lievre
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| double **oldm, **newm, **savm; /* Working pointers to matrices */ |
(Module): sump fixed, loop imx fixed, and simplifications.
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| double **oldms, **newms, **savms; /* Fixed working pointers to matrices */ |
(Module): If the status is missing at the last wave but we know
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| FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop; |
that the person is alive, then we can code his/her status as -2
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| FILE *ficlog; |
(instead of missing=-1 in earlier versions) and his/her
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| FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor; |
contributions to the likelihood is 1 - Prob of dying from last
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| FILE *ficresprobmorprev; |
health status (= 1-p13= p11+p12 in the easiest case of somebody in
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| FILE *fichtm; /* Html File */ |
the healthy state at last known wave). Version is 0.98
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| FILE *ficreseij; |
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| char filerese[FILENAMELENGTH]; |
Revision 1.103 2005/09/30 15:54:49 lievre
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| FILE *ficresvij; |
(Module): sump fixed, loop imx fixed, and simplifications.
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| char fileresv[FILENAMELENGTH]; |
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| FILE *ficresvpl; |
Revision 1.102 2004/09/15 17:31:30 brouard
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| char fileresvpl[FILENAMELENGTH]; |
Add the possibility to read data file including tab characters.
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| char title[MAXLINE]; |
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| char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH]; |
Revision 1.101 2004/09/15 10:38:38 brouard
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| char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH]; |
Fix on curr_time
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| |
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| char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH]; |
Revision 1.100 2004/07/12 18:29:06 brouard
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| char filelog[FILENAMELENGTH]; /* Log file */ |
Add version for Mac OS X. Just define UNIX in Makefile
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| char filerest[FILENAMELENGTH]; |
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| char fileregp[FILENAMELENGTH]; |
Revision 1.99 2004/06/05 08:57:40 brouard
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| char popfile[FILENAMELENGTH]; |
*** empty log message ***
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| |
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| char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH]; |
Revision 1.98 2004/05/16 15:05:56 brouard
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| |
New version 0.97 . First attempt to estimate force of mortality
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| #define NR_END 1 |
directly from the data i.e. without the need of knowing the health
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| #define FREE_ARG char* |
state at each age, but using a Gompertz model: log u =a + b*age .
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| #define FTOL 1.0e-10 |
This is the basic analysis of mortality and should be done before any
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| |
other analysis, in order to test if the mortality estimated from the
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| #define NRANSI |
cross-longitudinal survey is different from the mortality estimated
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| #define ITMAX 200 |
from other sources like vital statistic data.
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| |
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| #define TOL 2.0e-4 |
The same imach parameter file can be used but the option for mle should be -3.
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| |
|
| #define CGOLD 0.3819660 |
Agnès, who wrote this part of the code, tried to keep most of the
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| #define ZEPS 1.0e-10 |
former routines in order to include the new code within the former code.
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| #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); |
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| |
The output is very simple: only an estimate of the intercept and of
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| #define GOLD 1.618034 |
the slope with 95% confident intervals.
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| #define GLIMIT 100.0 |
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| #define TINY 1.0e-20 |
Current limitations:
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| |
A) Even if you enter covariates, i.e. with the
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| static double maxarg1,maxarg2; |
model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
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| #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2)) |
B) There is no computation of Life Expectancy nor Life Table.
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| #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2)) |
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| |
Revision 1.97 2004/02/20 13:25:42 lievre
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| #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a)) |
Version 0.96d. Population forecasting command line is (temporarily)
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| #define rint(a) floor(a+0.5) |
suppressed.
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| |
|
| static double sqrarg; |
Revision 1.96 2003/07/15 15:38:55 brouard
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| #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg) |
* imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
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| #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} |
rewritten within the same printf. Workaround: many printfs.
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| |
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| int imx; |
Revision 1.95 2003/07/08 07:54:34 brouard
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| int stepm; |
* imach.c (Repository):
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| /* Stepm, step in month: minimum step interpolation*/ |
(Repository): Using imachwizard code to output a more meaningful covariance
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| |
matrix (cov(a12,c31) instead of numbers.
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| int estepm; |
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| /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/ |
Revision 1.94 2003/06/27 13:00:02 brouard
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| |
Just cleaning
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| int m,nb; |
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| int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage; |
Revision 1.93 2003/06/25 16:33:55 brouard
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| double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint; |
(Module): On windows (cygwin) function asctime_r doesn't
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| double **pmmij, ***probs; |
exist so I changed back to asctime which exists.
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| double dateintmean=0; |
(Module): Version 0.96b
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| |
|
| double *weight; |
Revision 1.92 2003/06/25 16:30:45 brouard
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| int **s; /* Status */ |
(Module): On windows (cygwin) function asctime_r doesn't
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| double *agedc, **covar, idx; |
exist so I changed back to asctime which exists.
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| int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff; |
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| |
Revision 1.91 2003/06/25 15:30:29 brouard
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| double ftol=FTOL; /* Tolerance for computing Max Likelihood */ |
* imach.c (Repository): Duplicated warning errors corrected.
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| double ftolhess; /* Tolerance for computing hessian */ |
(Repository): Elapsed time after each iteration is now output. It
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| |
helps to forecast when convergence will be reached. Elapsed time
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| /**************** split *************************/ |
is stamped in powell. We created a new html file for the graphs
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| static int split( char *path, char *dirc, char *name, char *ext, char *finame ) |
concerning matrix of covariance. It has extension -cov.htm.
|
| { |
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| char *ss; /* pointer */ |
Revision 1.90 2003/06/24 12:34:15 brouard
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| int l1, l2; /* length counters */ |
(Module): Some bugs corrected for windows. Also, when
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| |
mle=-1 a template is output in file "or"mypar.txt with the design
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| l1 = strlen(path ); /* length of path */ |
of the covariance matrix to be input.
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| if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH ); |
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| ss= strrchr( path, DIRSEPARATOR ); /* find last / */ |
Revision 1.89 2003/06/24 12:30:52 brouard
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| if ( ss == NULL ) { /* no directory, so use current */ |
(Module): Some bugs corrected for windows. Also, when
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| /*if(strrchr(path, ODIRSEPARATOR )==NULL) |
mle=-1 a template is output in file "or"mypar.txt with the design
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| printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/ |
of the covariance matrix to be input.
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| #if defined(__bsd__) /* get current working directory */ |
|
| extern char *getwd( ); |
Revision 1.88 2003/06/23 17:54:56 brouard
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| |
* imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
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| if ( getwd( dirc ) == NULL ) { |
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| #else |
Revision 1.87 2003/06/18 12:26:01 brouard
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| extern char *getcwd( ); |
Version 0.96
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| |
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| if ( getcwd( dirc, FILENAME_MAX ) == NULL ) { |
Revision 1.86 2003/06/17 20:04:08 brouard
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| #endif |
(Module): Change position of html and gnuplot routines and added
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| return( GLOCK_ERROR_GETCWD ); |
routine fileappend.
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| } |
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| strcpy( name, path ); /* we've got it */ |
Revision 1.85 2003/06/17 13:12:43 brouard
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| } else { /* strip direcotry from path */ |
* imach.c (Repository): Check when date of death was earlier that
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| ss++; /* after this, the filename */ |
current date of interview. It may happen when the death was just
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| l2 = strlen( ss ); /* length of filename */ |
prior to the death. In this case, dh was negative and likelihood
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| if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH ); |
was wrong (infinity). We still send an "Error" but patch by
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| strcpy( name, ss ); /* save file name */ |
assuming that the date of death was just one stepm after the
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| strncpy( dirc, path, l1 - l2 ); /* now the directory */ |
interview.
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| dirc[l1-l2] = 0; /* add zero */ |
(Repository): Because some people have very long ID (first column)
|
| } |
we changed int to long in num[] and we added a new lvector for
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| l1 = strlen( dirc ); /* length of directory */ |
memory allocation. But we also truncated to 8 characters (left
|
| #ifdef windows |
truncation)
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| if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; } |
(Repository): No more line truncation errors.
|
| #else |
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| if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; } |
Revision 1.84 2003/06/13 21:44:43 brouard
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| #endif |
* imach.c (Repository): Replace "freqsummary" at a correct
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| ss = strrchr( name, '.' ); /* find last / */ |
place. It differs from routine "prevalence" which may be called
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| ss++; |
many times. Probs is memory consuming and must be used with
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| strcpy(ext,ss); /* save extension */ |
parcimony.
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| l1= strlen( name); |
Version 0.95a3 (should output exactly the same maximization than 0.8a2)
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| l2= strlen(ss)+1; |
|
| strncpy( finame, name, l1-l2); |
Revision 1.83 2003/06/10 13:39:11 lievre
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| finame[l1-l2]= 0; |
*** empty log message ***
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| return( 0 ); /* we're done */ |
|
| } |
Revision 1.82 2003/06/05 15:57:20 brouard
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| |
Add log in imach.c and fullversion number is now printed.
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| |
|
| /******************************************/ |
*/
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| |
/*
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| void replace(char *s, char*t) |
Interpolated Markov Chain
|
| { |
|
| int i; |
Short summary of the programme:
|
| int lg=20; |
|
| i=0; |
This program computes Healthy Life Expectancies from
|
| lg=strlen(t); |
cross-longitudinal data. Cross-longitudinal data consist in: -1- a
|
| for(i=0; i<= lg; i++) { |
first survey ("cross") where individuals from different ages are
|
| (s[i] = t[i]); |
interviewed on their health status or degree of disability (in the
|
| if (t[i]== '\\') s[i]='/'; |
case of a health survey which is our main interest) -2- at least a
|
| } |
second wave of interviews ("longitudinal") which measure each change
|
| } |
(if any) in individual health status. Health expectancies are
|
| |
computed from the time spent in each health state according to a
|
| int nbocc(char *s, char occ) |
model. More health states you consider, more time is necessary to reach the
|
| { |
Maximum Likelihood of the parameters involved in the model. The
|
| int i,j=0; |
simplest model is the multinomial logistic model where pij is the
|
| int lg=20; |
probability to be observed in state j at the second wave
|
| i=0; |
conditional to be observed in state i at the first wave. Therefore
|
| lg=strlen(s); |
the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
|
| for(i=0; i<= lg; i++) { |
'age' is age and 'sex' is a covariate. If you want to have a more
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| if (s[i] == occ ) j++; |
complex model than "constant and age", you should modify the program
|
| } |
where the markup *Covariates have to be included here again* invites
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| return j; |
you to do it. More covariates you add, slower the
|
| } |
convergence.
|
| |
|
| void cutv(char *u,char *v, char*t, char occ) |
The advantage of this computer programme, compared to a simple
|
| { |
multinomial logistic model, is clear when the delay between waves is not
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| /* cuts string t into u and v where u is ended by char occ excluding it |
identical for each individual. Also, if a individual missed an
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| and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2) |
intermediate interview, the information is lost, but taken into
|
| gives u="abcedf" and v="ghi2j" */ |
account using an interpolation or extrapolation.
|
| int i,lg,j,p=0; |
|
| i=0; |
hPijx is the probability to be observed in state i at age x+h
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| for(j=0; j<=strlen(t)-1; j++) { |
conditional to the observed state i at age x. The delay 'h' can be
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| if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; |
split into an exact number (nh*stepm) of unobserved intermediate
|
| } |
states. This elementary transition (by month, quarter,
|
| |
semester or year) is modelled as a multinomial logistic. The hPx
|
| lg=strlen(t); |
matrix is simply the matrix product of nh*stepm elementary matrices
|
| for(j=0; j<p; j++) { |
and the contribution of each individual to the likelihood is simply
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| (u[j] = t[j]); |
hPijx.
|
| } |
|
| u[p]='\0'; |
Also this programme outputs the covariance matrix of the parameters but also
|
| |
of the life expectancies. It also computes the period (stable) prevalence.
|
| for(j=0; j<= lg; j++) { |
|
| if (j>=(p+1))(v[j-p-1] = t[j]); |
Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
|
| } |
Institut national d'études démographiques, Paris.
|
| } |
This software have been partly granted by Euro-REVES, a concerted action
|
| |
from the European Union.
|
| /********************** nrerror ********************/ |
It is copyrighted identically to a GNU software product, ie programme and
|
| |
software can be distributed freely for non commercial use. Latest version
|
| void nrerror(char error_text[]) |
can be accessed at http://euroreves.ined.fr/imach .
|
| { |
|
| fprintf(stderr,"ERREUR ...\n"); |
Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
|
| fprintf(stderr,"%s\n",error_text); |
or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
|
| exit(EXIT_FAILURE); |
|
| } |
**********************************************************************/
|
| /*********************** vector *******************/ |
/*
|
| double *vector(int nl, int nh) |
main
|
| { |
read parameterfile
|
| double *v; |
read datafile
|
| v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double))); |
concatwav
|
| if (!v) nrerror("allocation failure in vector"); |
freqsummary
|
| return v-nl+NR_END; |
if (mle >= 1)
|
| } |
mlikeli
|
| |
print results files
|
| /************************ free vector ******************/ |
if mle==1
|
| void free_vector(double*v, int nl, int nh) |
computes hessian
|
| { |
read end of parameter file: agemin, agemax, bage, fage, estepm
|
| free((FREE_ARG)(v+nl-NR_END)); |
begin-prev-date,...
|
| } |
open gnuplot file
|
| |
open html file
|
| /************************ivector *******************************/ |
period (stable) prevalence
|
| int *ivector(long nl,long nh) |
for age prevalim()
|
| { |
h Pij x
|
| int *v; |
variance of p varprob
|
| v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int))); |
forecasting if prevfcast==1 prevforecast call prevalence()
|
| if (!v) nrerror("allocation failure in ivector"); |
health expectancies
|
| return v-nl+NR_END; |
Variance-covariance of DFLE
|
| } |
prevalence()
|
| |
movingaverage()
|
| /******************free ivector **************************/ |
varevsij()
|
| void free_ivector(int *v, long nl, long nh) |
if popbased==1 varevsij(,popbased)
|
| { |
total life expectancies
|
| free((FREE_ARG)(v+nl-NR_END)); |
Variance of period (stable) prevalence
|
| } |
end
|
| |
*/
|
| /******************* imatrix *******************************/ |
|
| int **imatrix(long nrl, long nrh, long ncl, long nch) |
|
| /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ |
|
| { |
|
| long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; |
#include <math.h>
|
| int **m; |
#include <stdio.h>
|
| |
#include <stdlib.h>
|
| /* allocate pointers to rows */ |
#include <string.h>
|
| m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); |
#include <unistd.h>
|
| if (!m) nrerror("allocation failure 1 in matrix()"); |
|
| m += NR_END; |
#include <limits.h>
|
| m -= nrl; |
#include <sys/types.h>
|
| |
#include <sys/stat.h>
|
| |
#include <errno.h>
|
| /* allocate rows and set pointers to them */ |
extern int errno;
|
| m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); |
|
| if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); |
/* #include <sys/time.h> */
|
| m[nrl] += NR_END; |
#include <time.h>
|
| m[nrl] -= ncl; |
#include "timeval.h"
|
| |
|
| for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; |
/* #include <libintl.h> */
|
| |
/* #define _(String) gettext (String) */
|
| /* return pointer to array of pointers to rows */ |
|
| return m; |
#define MAXLINE 256
|
| } |
|
| |
#define GNUPLOTPROGRAM "gnuplot"
|
| /****************** free_imatrix *************************/ |
/*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
|
| void free_imatrix(m,nrl,nrh,ncl,nch) |
#define FILENAMELENGTH 132
|
| int **m; |
|
| long nch,ncl,nrh,nrl; |
#define GLOCK_ERROR_NOPATH -1 /* empty path */
|
| /* free an int matrix allocated by imatrix() */ |
#define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
|
| { |
|
| free((FREE_ARG) (m[nrl]+ncl-NR_END)); |
#define MAXPARM 30 /* Maximum number of parameters for the optimization */
|
| free((FREE_ARG) (m+nrl-NR_END)); |
#define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
|
| } |
|
| |
#define NINTERVMAX 8
|
| /******************* matrix *******************************/ |
#define NLSTATEMAX 8 /* Maximum number of live states (for func) */
|
| double **matrix(long nrl, long nrh, long ncl, long nch) |
#define NDEATHMAX 8 /* Maximum number of dead states (for func) */
|
| { |
#define NCOVMAX 8 /* Maximum number of covariates */
|
| long i, nrow=nrh-nrl+1, ncol=nch-ncl+1; |
#define MAXN 20000
|
| double **m; |
#define YEARM 12. /* Number of months per year */
|
| |
#define AGESUP 130
|
| m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*))); |
#define AGEBASE 40
|
| if (!m) nrerror("allocation failure 1 in matrix()"); |
#define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
|
| m += NR_END; |
#ifdef UNIX
|
| m -= nrl; |
#define DIRSEPARATOR '/'
|
| |
#define CHARSEPARATOR "/"
|
| m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double))); |
#define ODIRSEPARATOR '\\'
|
| if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); |
#else
|
| m[nrl] += NR_END; |
#define DIRSEPARATOR '\\'
|
| m[nrl] -= ncl; |
#define CHARSEPARATOR "\\"
|
| |
#define ODIRSEPARATOR '/'
|
| for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol; |
#endif
|
| return m; |
|
| } |
/* $Id$ */
|
| |
/* $State$ */
|
| /*************************free matrix ************************/ |
|
| void free_matrix(double **m, long nrl, long nrh, long ncl, long nch) |
char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite ";
|
| { |
char fullversion[]="$Revision$ $Date$";
|
| free((FREE_ARG)(m[nrl]+ncl-NR_END)); |
char strstart[80];
|
| free((FREE_ARG)(m+nrl-NR_END)); |
char optionfilext[10], optionfilefiname[FILENAMELENGTH];
|
| } |
int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
|
| |
int nvar;
|
| /******************* ma3x *******************************/ |
int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
|
| double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh) |
int npar=NPARMAX;
|
| { |
int nlstate=2; /* Number of live states */
|
| long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1; |
int ndeath=1; /* Number of dead states */
|
| double ***m; |
int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
|
| |
int popbased=0;
|
| m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*))); |
|
| if (!m) nrerror("allocation failure 1 in matrix()"); |
int *wav; /* Number of waves for this individuual 0 is possible */
|
| m += NR_END; |
int maxwav; /* Maxim number of waves */
|
| m -= nrl; |
int jmin, jmax; /* min, max spacing between 2 waves */
|
| |
int ijmin, ijmax; /* Individuals having jmin and jmax */
|
| m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double))); |
int gipmx, gsw; /* Global variables on the number of contributions
|
| if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); |
to the likelihood and the sum of weights (done by funcone)*/
|
| m[nrl] += NR_END; |
int mle, weightopt;
|
| m[nrl] -= ncl; |
int **mw; /* mw[mi][i] is number of the mi wave for this individual */
|
| |
int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
|
| for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol; |
int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
|
| |
* wave mi and wave mi+1 is not an exact multiple of stepm. */
|
| m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double))); |
double jmean; /* Mean space between 2 waves */
|
| if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()"); |
double **oldm, **newm, **savm; /* Working pointers to matrices */
|
| m[nrl][ncl] += NR_END; |
double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
|
| m[nrl][ncl] -= nll; |
FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
|
| for (j=ncl+1; j<=nch; j++) |
FILE *ficlog, *ficrespow;
|
| m[nrl][j]=m[nrl][j-1]+nlay; |
int globpr; /* Global variable for printing or not */
|
| |
double fretone; /* Only one call to likelihood */
|
| for (i=nrl+1; i<=nrh; i++) { |
long ipmx; /* Number of contributions */
|
| m[i][ncl]=m[i-1l][ncl]+ncol*nlay; |
double sw; /* Sum of weights */
|
| for (j=ncl+1; j<=nch; j++) |
char filerespow[FILENAMELENGTH];
|
| m[i][j]=m[i][j-1]+nlay; |
char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
|
| } |
FILE *ficresilk;
|
| return m; |
FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
|
| } |
FILE *ficresprobmorprev;
|
| |
FILE *fichtm, *fichtmcov; /* Html File */
|
| /*************************free ma3x ************************/ |
FILE *ficreseij;
|
| void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh) |
char filerese[FILENAMELENGTH];
|
| { |
FILE *ficresstdeij;
|
| free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END)); |
char fileresstde[FILENAMELENGTH];
|
| free((FREE_ARG)(m[nrl]+ncl-NR_END)); |
FILE *ficrescveij;
|
| free((FREE_ARG)(m+nrl-NR_END)); |
char filerescve[FILENAMELENGTH];
|
| } |
FILE *ficresvij;
|
| |
char fileresv[FILENAMELENGTH];
|
| /***************** f1dim *************************/ |
FILE *ficresvpl;
|
| extern int ncom; |
char fileresvpl[FILENAMELENGTH];
|
| extern double *pcom,*xicom; |
char title[MAXLINE];
|
| extern double (*nrfunc)(double []); |
char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
|
| |
char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
|
| double f1dim(double x) |
char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
|
| { |
char command[FILENAMELENGTH];
|
| int j; |
int outcmd=0;
|
| double f; |
|
| double *xt; |
char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
|
| |
|
| xt=vector(1,ncom); |
char filelog[FILENAMELENGTH]; /* Log file */
|
| for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; |
char filerest[FILENAMELENGTH];
|
| f=(*nrfunc)(xt); |
char fileregp[FILENAMELENGTH];
|
| free_vector(xt,1,ncom); |
char popfile[FILENAMELENGTH];
|
| return f; |
|
| } |
char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
|
| |
|
| /*****************brent *************************/ |
struct timeval start_time, end_time, curr_time, last_time, forecast_time;
|
| double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin) |
struct timezone tzp;
|
| { |
extern int gettimeofday();
|
| int iter; |
struct tm tmg, tm, tmf, *gmtime(), *localtime();
|
| double a,b,d,etemp; |
long time_value;
|
| double fu,fv,fw,fx; |
extern long time();
|
| double ftemp; |
char strcurr[80], strfor[80];
|
| double p,q,r,tol1,tol2,u,v,w,x,xm; |
|
| double e=0.0; |
char *endptr;
|
| |
long lval;
|
| a=(ax < cx ? ax : cx); |
double dval;
|
| b=(ax > cx ? ax : cx); |
|
| x=w=v=bx; |
#define NR_END 1
|
| fw=fv=fx=(*f)(x); |
#define FREE_ARG char*
|
| for (iter=1;iter<=ITMAX;iter++) { |
#define FTOL 1.0e-10
|
| xm=0.5*(a+b); |
|
| tol2=2.0*(tol1=tol*fabs(x)+ZEPS); |
#define NRANSI
|
| /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/ |
#define ITMAX 200
|
| printf(".");fflush(stdout); |
|
| fprintf(ficlog,".");fflush(ficlog); |
#define TOL 2.0e-4
|
| #ifdef DEBUG |
|
| 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); |
#define CGOLD 0.3819660
|
| fprintf(ficlog,"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); |
#define ZEPS 1.0e-10
|
| /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */ |
#define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
|
| #endif |
|
| if (fabs(x-xm) <= (tol2-0.5*(b-a))){ |
#define GOLD 1.618034
|
| *xmin=x; |
#define GLIMIT 100.0
|
| return fx; |
#define TINY 1.0e-20
|
| } |
|
| ftemp=fu; |
static double maxarg1,maxarg2;
|
| if (fabs(e) > tol1) { |
#define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
|
| r=(x-w)*(fx-fv); |
#define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
|
| q=(x-v)*(fx-fw); |
|
| p=(x-v)*q-(x-w)*r; |
#define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
|
| q=2.0*(q-r); |
#define rint(a) floor(a+0.5)
|
| if (q > 0.0) p = -p; |
|
| q=fabs(q); |
static double sqrarg;
|
| etemp=e; |
#define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
|
| e=d; |
#define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
|
| if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) |
int agegomp= AGEGOMP;
|
| d=CGOLD*(e=(x >= xm ? a-x : b-x)); |
|
| else { |
int imx;
|
| d=p/q; |
int stepm=1;
|
| u=x+d; |
/* Stepm, step in month: minimum step interpolation*/
|
| if (u-a < tol2 || b-u < tol2) |
|
| d=SIGN(tol1,xm-x); |
int estepm;
|
| } |
/* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
|
| } else { |
|
| d=CGOLD*(e=(x >= xm ? a-x : b-x)); |
int m,nb;
|
| } |
long *num;
|
| u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); |
int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
|
| fu=(*f)(u); |
double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
|
| if (fu <= fx) { |
double **pmmij, ***probs;
|
| if (u >= x) a=x; else b=x; |
double *ageexmed,*agecens;
|
| SHFT(v,w,x,u) |
double dateintmean=0;
|
| SHFT(fv,fw,fx,fu) |
|
| } else { |
double *weight;
|
| if (u < x) a=u; else b=u; |
int **s; /* Status */
|
| if (fu <= fw || w == x) { |
double *agedc, **covar, idx;
|
| v=w; |
int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
|
| w=u; |
double *lsurv, *lpop, *tpop;
|
| fv=fw; |
|
| fw=fu; |
double ftol=FTOL; /* Tolerance for computing Max Likelihood */
|
| } else if (fu <= fv || v == x || v == w) { |
double ftolhess; /* Tolerance for computing hessian */
|
| v=u; |
|
| fv=fu; |
/**************** split *************************/
|
| } |
static int split( char *path, char *dirc, char *name, char *ext, char *finame )
|
| } |
{
|
| } |
/* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
|
| nrerror("Too many iterations in brent"); |
the name of the file (name), its extension only (ext) and its first part of the name (finame)
|
| *xmin=x; |
*/
|
| return fx; |
char *ss; /* pointer */
|
| } |
int l1, l2; /* length counters */
|
| |
|
| /****************** mnbrak ***********************/ |
l1 = strlen(path ); /* length of path */
|
| |
if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
|
| void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, |
ss= strrchr( path, DIRSEPARATOR ); /* find last / */
|
| double (*func)(double)) |
if ( ss == NULL ) { /* no directory, so determine current directory */
|
| { |
strcpy( name, path ); /* we got the fullname name because no directory */
|
| double ulim,u,r,q, dum; |
/*if(strrchr(path, ODIRSEPARATOR )==NULL)
|
| double fu; |
printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
|
| |
/* get current working directory */
|
| *fa=(*func)(*ax); |
/* extern char* getcwd ( char *buf , int len);*/
|
| *fb=(*func)(*bx); |
if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
|
| if (*fb > *fa) { |
return( GLOCK_ERROR_GETCWD );
|
| SHFT(dum,*ax,*bx,dum) |
}
|
| SHFT(dum,*fb,*fa,dum) |
/* got dirc from getcwd*/
|
| } |
printf(" DIRC = %s \n",dirc);
|
| *cx=(*bx)+GOLD*(*bx-*ax); |
} else { /* strip direcotry from path */
|
| *fc=(*func)(*cx); |
ss++; /* after this, the filename */
|
| while (*fb > *fc) { |
l2 = strlen( ss ); /* length of filename */
|
| r=(*bx-*ax)*(*fb-*fc); |
if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
|
| q=(*bx-*cx)*(*fb-*fa); |
strcpy( name, ss ); /* save file name */
|
| u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ |
strncpy( dirc, path, l1 - l2 ); /* now the directory */
|
| (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); |
dirc[l1-l2] = 0; /* add zero */
|
| ulim=(*bx)+GLIMIT*(*cx-*bx); |
printf(" DIRC2 = %s \n",dirc);
|
| if ((*bx-u)*(u-*cx) > 0.0) { |
}
|
| fu=(*func)(u); |
/* We add a separator at the end of dirc if not exists */
|
| } else if ((*cx-u)*(u-ulim) > 0.0) { |
l1 = strlen( dirc ); /* length of directory */
|
| fu=(*func)(u); |
if( dirc[l1-1] != DIRSEPARATOR ){
|
| if (fu < *fc) { |
dirc[l1] = DIRSEPARATOR;
|
| SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) |
dirc[l1+1] = 0;
|
| SHFT(*fb,*fc,fu,(*func)(u)) |
printf(" DIRC3 = %s \n",dirc);
|
| } |
}
|
| } else if ((u-ulim)*(ulim-*cx) >= 0.0) { |
ss = strrchr( name, '.' ); /* find last / */
|
| u=ulim; |
if (ss >0){
|
| fu=(*func)(u); |
ss++;
|
| } else { |
strcpy(ext,ss); /* save extension */
|
| u=(*cx)+GOLD*(*cx-*bx); |
l1= strlen( name);
|
| fu=(*func)(u); |
l2= strlen(ss)+1;
|
| } |
strncpy( finame, name, l1-l2);
|
| SHFT(*ax,*bx,*cx,u) |
finame[l1-l2]= 0;
|
| SHFT(*fa,*fb,*fc,fu) |
}
|
| } |
|
| } |
return( 0 ); /* we're done */
|
| |
}
|
| /*************** linmin ************************/ |
|
| |
|
| int ncom; |
/******************************************/
|
| double *pcom,*xicom; |
|
| double (*nrfunc)(double []); |
void replace_back_to_slash(char *s, char*t)
|
| |
{
|
| void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) |
int i;
|
| { |
int lg=0;
|
| double brent(double ax, double bx, double cx, |
i=0;
|
| double (*f)(double), double tol, double *xmin); |
lg=strlen(t);
|
| double f1dim(double x); |
for(i=0; i<= lg; i++) {
|
| void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, |
(s[i] = t[i]);
|
| double *fc, double (*func)(double)); |
if (t[i]== '\\') s[i]='/';
|
| int j; |
}
|
| double xx,xmin,bx,ax; |
}
|
| double fx,fb,fa; |
|
| |
int nbocc(char *s, char occ)
|
| ncom=n; |
{
|
| pcom=vector(1,n); |
int i,j=0;
|
| xicom=vector(1,n); |
int lg=20;
|
| nrfunc=func; |
i=0;
|
| for (j=1;j<=n;j++) { |
lg=strlen(s);
|
| pcom[j]=p[j]; |
for(i=0; i<= lg; i++) {
|
| xicom[j]=xi[j]; |
if (s[i] == occ ) j++;
|
| } |
}
|
| ax=0.0; |
return j;
|
| xx=1.0; |
}
|
| mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); |
|
| *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); |
void cutv(char *u,char *v, char*t, char occ)
|
| #ifdef DEBUG |
{
|
| printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin); |
/* cuts string t into u and v where u ends before first occurence of char 'occ'
|
| fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin); |
and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
|
| #endif |
gives u="abcedf" and v="ghi2j" */
|
| for (j=1;j<=n;j++) { |
int i,lg,j,p=0;
|
| xi[j] *= xmin; |
i=0;
|
| p[j] += xi[j]; |
for(j=0; j<=strlen(t)-1; j++) {
|
| } |
if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
|
| free_vector(xicom,1,n); |
}
|
| free_vector(pcom,1,n); |
|
| } |
lg=strlen(t);
|
| |
for(j=0; j<p; j++) {
|
| /*************** powell ************************/ |
(u[j] = t[j]);
|
| void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, |
}
|
| double (*func)(double [])) |
u[p]='\0';
|
| { |
|
| void linmin(double p[], double xi[], int n, double *fret, |
for(j=0; j<= lg; j++) {
|
| double (*func)(double [])); |
if (j>=(p+1))(v[j-p-1] = t[j]);
|
| int i,ibig,j; |
}
|
| double del,t,*pt,*ptt,*xit; |
}
|
| double fp,fptt; |
|
| double *xits; |
/********************** nrerror ********************/
|
| pt=vector(1,n); |
|
| ptt=vector(1,n); |
void nrerror(char error_text[])
|
| xit=vector(1,n); |
{
|
| xits=vector(1,n); |
fprintf(stderr,"ERREUR ...\n");
|
| *fret=(*func)(p); |
fprintf(stderr,"%s\n",error_text);
|
| for (j=1;j<=n;j++) pt[j]=p[j]; |
exit(EXIT_FAILURE);
|
| for (*iter=1;;++(*iter)) { |
}
|
| fp=(*fret); |
/*********************** vector *******************/
|
| ibig=0; |
double *vector(int nl, int nh)
|
| del=0.0; |
{
|
| printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret); |
double *v;
|
| fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret); |
v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
|
| for (i=1;i<=n;i++) |
if (!v) nrerror("allocation failure in vector");
|
| printf(" %d %.12f",i, p[i]); |
return v-nl+NR_END;
|
| fprintf(ficlog," %d %.12f",i, p[i]); |
}
|
| printf("\n"); |
|
| fprintf(ficlog,"\n"); |
/************************ free vector ******************/
|
| for (i=1;i<=n;i++) { |
void free_vector(double*v, int nl, int nh)
|
| for (j=1;j<=n;j++) xit[j]=xi[j][i]; |
{
|
| fptt=(*fret); |
free((FREE_ARG)(v+nl-NR_END));
|
| #ifdef DEBUG |
}
|
| printf("fret=%lf \n",*fret); |
|
| fprintf(ficlog,"fret=%lf \n",*fret); |
/************************ivector *******************************/
|
| #endif |
int *ivector(long nl,long nh)
|
| printf("%d",i);fflush(stdout); |
{
|
| fprintf(ficlog,"%d",i);fflush(ficlog); |
int *v;
|
| linmin(p,xit,n,fret,func); |
v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
|
| if (fabs(fptt-(*fret)) > del) { |
if (!v) nrerror("allocation failure in ivector");
|
| del=fabs(fptt-(*fret)); |
return v-nl+NR_END;
|
| ibig=i; |
}
|
| } |
|
| #ifdef DEBUG |
/******************free ivector **************************/
|
| printf("%d %.12e",i,(*fret)); |
void free_ivector(int *v, long nl, long nh)
|
| fprintf(ficlog,"%d %.12e",i,(*fret)); |
{
|
| for (j=1;j<=n;j++) { |
free((FREE_ARG)(v+nl-NR_END));
|
| xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5); |
}
|
| printf(" x(%d)=%.12e",j,xit[j]); |
|
| fprintf(ficlog," x(%d)=%.12e",j,xit[j]); |
/************************lvector *******************************/
|
| } |
long *lvector(long nl,long nh)
|
| for(j=1;j<=n;j++) { |
{
|
| printf(" p=%.12e",p[j]); |
long *v;
|
| fprintf(ficlog," p=%.12e",p[j]); |
v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
|
| } |
if (!v) nrerror("allocation failure in ivector");
|
| printf("\n"); |
return v-nl+NR_END;
|
| fprintf(ficlog,"\n"); |
}
|
| #endif |
|
| } |
/******************free lvector **************************/
|
| if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { |
void free_lvector(long *v, long nl, long nh)
|
| #ifdef DEBUG |
{
|
| int k[2],l; |
free((FREE_ARG)(v+nl-NR_END));
|
| k[0]=1; |
}
|
| k[1]=-1; |
|
| printf("Max: %.12e",(*func)(p)); |
/******************* imatrix *******************************/
|
| fprintf(ficlog,"Max: %.12e",(*func)(p)); |
int **imatrix(long nrl, long nrh, long ncl, long nch)
|
| for (j=1;j<=n;j++) { |
/* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
|
| printf(" %.12e",p[j]); |
{
|
| fprintf(ficlog," %.12e",p[j]); |
long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
|
| } |
int **m;
|
| printf("\n"); |
|
| fprintf(ficlog,"\n"); |
/* allocate pointers to rows */
|
| for(l=0;l<=1;l++) { |
m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
|
| for (j=1;j<=n;j++) { |
if (!m) nrerror("allocation failure 1 in matrix()");
|
| ptt[j]=p[j]+(p[j]-pt[j])*k[l]; |
m += NR_END;
|
| printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]); |
m -= nrl;
|
| fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]); |
|
| } |
|
| printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p))); |
/* allocate rows and set pointers to them */
|
| fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p))); |
m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
|
| } |
if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
|
| #endif |
m[nrl] += NR_END;
|
| |
m[nrl] -= ncl;
|
| |
|
| free_vector(xit,1,n); |
for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
|
| free_vector(xits,1,n); |
|
| free_vector(ptt,1,n); |
/* return pointer to array of pointers to rows */
|
| free_vector(pt,1,n); |
return m;
|
| return; |
}
|
| } |
|
| if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); |
/****************** free_imatrix *************************/
|
| for (j=1;j<=n;j++) { |
void free_imatrix(m,nrl,nrh,ncl,nch)
|
| ptt[j]=2.0*p[j]-pt[j]; |
int **m;
|
| xit[j]=p[j]-pt[j]; |
long nch,ncl,nrh,nrl;
|
| pt[j]=p[j]; |
/* free an int matrix allocated by imatrix() */
|
| } |
{
|
| fptt=(*func)(ptt); |
free((FREE_ARG) (m[nrl]+ncl-NR_END));
|
| if (fptt < fp) { |
free((FREE_ARG) (m+nrl-NR_END));
|
| t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); |
}
|
| if (t < 0.0) { |
|
| linmin(p,xit,n,fret,func); |
/******************* matrix *******************************/
|
| for (j=1;j<=n;j++) { |
double **matrix(long nrl, long nrh, long ncl, long nch)
|
| xi[j][ibig]=xi[j][n]; |
{
|
| xi[j][n]=xit[j]; |
long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
|
| } |
double **m;
|
| #ifdef DEBUG |
|
| printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig); |
m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
|
| fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig); |
if (!m) nrerror("allocation failure 1 in matrix()");
|
| for(j=1;j<=n;j++){ |
m += NR_END;
|
| printf(" %.12e",xit[j]); |
m -= nrl;
|
| fprintf(ficlog," %.12e",xit[j]); |
|
| } |
m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
|
| printf("\n"); |
if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
|
| fprintf(ficlog,"\n"); |
m[nrl] += NR_END;
|
| #endif |
m[nrl] -= ncl;
|
| } |
|
| } |
for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
|
| } |
return m;
|
| } |
/* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
|
| |
*/
|
| /**** Prevalence limit (stable prevalence) ****************/ |
}
|
| |
|
| double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij) |
/*************************free matrix ************************/
|
| { |
void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
|
| /* Computes the prevalence limit in each live state at age x by left multiplying the unit |
{
|
| matrix by transitions matrix until convergence is reached */ |
free((FREE_ARG)(m[nrl]+ncl-NR_END));
|
| |
free((FREE_ARG)(m+nrl-NR_END));
|
| int i, ii,j,k; |
}
|
| double min, max, maxmin, maxmax,sumnew=0.; |
|
| double **matprod2(); |
/******************* ma3x *******************************/
|
| double **out, cov[NCOVMAX], **pmij(); |
double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
|
| double **newm; |
{
|
| double agefin, delaymax=50 ; /* Max number of years to converge */ |
long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
|
| |
double ***m;
|
| for (ii=1;ii<=nlstate+ndeath;ii++) |
|
| for (j=1;j<=nlstate+ndeath;j++){ |
m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
|
| oldm[ii][j]=(ii==j ? 1.0 : 0.0); |
if (!m) nrerror("allocation failure 1 in matrix()");
|
| } |
m += NR_END;
|
| |
m -= nrl;
|
| cov[1]=1.; |
|
| |
m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
|
| /* Even if hstepm = 1, at least one multiplication by the unit matrix */ |
if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
|
| for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){ |
m[nrl] += NR_END;
|
| newm=savm; |
m[nrl] -= ncl;
|
| /* Covariates have to be included here again */ |
|
| cov[2]=agefin; |
for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
|
| |
|
| for (k=1; k<=cptcovn;k++) { |
m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
|
| cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; |
if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
|
| /* 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]]);*/ |
m[nrl][ncl] += NR_END;
|
| } |
m[nrl][ncl] -= nll;
|
| for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; |
for (j=ncl+1; j<=nch; j++)
|
| for (k=1; k<=cptcovprod;k++) |
m[nrl][j]=m[nrl][j-1]+nlay;
|
| cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; |
|
| |
for (i=nrl+1; i<=nrh; i++) {
|
| /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/ |
m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
|
| /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/ |
for (j=ncl+1; j<=nch; j++)
|
| /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/ |
m[i][j]=m[i][j-1]+nlay;
|
| out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); |
}
|
| |
return m;
|
| savm=oldm; |
/* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
|
| oldm=newm; |
&(m[i][j][k]) <=> *((*(m+i) + j)+k)
|
| maxmax=0.; |
*/
|
| for(j=1;j<=nlstate;j++){ |
}
|
| min=1.; |
|
| max=0.; |
/*************************free ma3x ************************/
|
| for(i=1; i<=nlstate; i++) { |
void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
|
| sumnew=0; |
{
|
| for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k]; |
free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
|
| prlim[i][j]= newm[i][j]/(1-sumnew); |
free((FREE_ARG)(m[nrl]+ncl-NR_END));
|
| max=FMAX(max,prlim[i][j]); |
free((FREE_ARG)(m+nrl-NR_END));
|
| min=FMIN(min,prlim[i][j]); |
}
|
| } |
|
| maxmin=max-min; |
/*************** function subdirf ***********/
|
| maxmax=FMAX(maxmax,maxmin); |
char *subdirf(char fileres[])
|
| } |
{
|
| if(maxmax < ftolpl){ |
/* Caution optionfilefiname is hidden */
|
| return prlim; |
strcpy(tmpout,optionfilefiname);
|
| } |
strcat(tmpout,"/"); /* Add to the right */
|
| } |
strcat(tmpout,fileres);
|
| } |
return tmpout;
|
| |
}
|
| /*************** transition probabilities ***************/ |
|
| |
/*************** function subdirf2 ***********/
|
| double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate ) |
char *subdirf2(char fileres[], char *preop)
|
| { |
{
|
| double s1, s2; |
|
| /*double t34;*/ |
/* Caution optionfilefiname is hidden */
|
| int i,j,j1, nc, ii, jj; |
strcpy(tmpout,optionfilefiname);
|
| |
strcat(tmpout,"/");
|
| for(i=1; i<= nlstate; i++){ |
strcat(tmpout,preop);
|
| for(j=1; j<i;j++){ |
strcat(tmpout,fileres);
|
| for (nc=1, s2=0.;nc <=ncovmodel; nc++){ |
return tmpout;
|
| /*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);*/ |
/*************** function subdirf3 ***********/
|
| } |
char *subdirf3(char fileres[], char *preop, char *preop2)
|
| ps[i][j]=s2; |
{
|
| /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/ |
|
| } |
/* Caution optionfilefiname is hidden */
|
| for(j=i+1; j<=nlstate+ndeath;j++){ |
strcpy(tmpout,optionfilefiname);
|
| for (nc=1, s2=0.;nc <=ncovmodel; nc++){ |
strcat(tmpout,"/");
|
| s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc]; |
strcat(tmpout,preop);
|
| /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/ |
strcat(tmpout,preop2);
|
| } |
strcat(tmpout,fileres);
|
| ps[i][j]=s2; |
return tmpout;
|
| } |
}
|
| } |
|
| /*ps[3][2]=1;*/ |
/***************** f1dim *************************/
|
| |
extern int ncom;
|
| for(i=1; i<= nlstate; i++){ |
extern double *pcom,*xicom;
|
| s1=0; |
extern double (*nrfunc)(double []);
|
| for(j=1; j<i; j++) |
|
| s1+=exp(ps[i][j]); |
double f1dim(double x)
|
| for(j=i+1; j<=nlstate+ndeath; j++) |
{
|
| s1+=exp(ps[i][j]); |
int j;
|
| ps[i][i]=1./(s1+1.); |
double f;
|
| for(j=1; j<i; j++) |
double *xt;
|
| ps[i][j]= exp(ps[i][j])*ps[i][i]; |
|
| for(j=i+1; j<=nlstate+ndeath; j++) |
xt=vector(1,ncom);
|
| ps[i][j]= exp(ps[i][j])*ps[i][i]; |
for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
|
| /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */ |
f=(*nrfunc)(xt);
|
| } /* end i */ |
free_vector(xt,1,ncom);
|
| |
return f;
|
| for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){ |
}
|
| for(jj=1; jj<= nlstate+ndeath; jj++){ |
|
| ps[ii][jj]=0; |
/*****************brent *************************/
|
| ps[ii][ii]=1; |
double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
|
| } |
{
|
| } |
int iter;
|
| |
double a,b,d,etemp;
|
| |
double fu,fv,fw,fx;
|
| /* for(ii=1; ii<= nlstate+ndeath; ii++){ |
double ftemp;
|
| for(jj=1; jj<= nlstate+ndeath; jj++){ |
double p,q,r,tol1,tol2,u,v,w,x,xm;
|
| printf("%lf ",ps[ii][jj]); |
double e=0.0;
|
| } |
|
| printf("\n "); |
a=(ax < cx ? ax : cx);
|
| } |
b=(ax > cx ? ax : cx);
|
| printf("\n ");printf("%lf ",cov[2]);*/ |
x=w=v=bx;
|
| /* |
fw=fv=fx=(*f)(x);
|
| for(i=1; i<= npar; i++) printf("%f ",x[i]); |
for (iter=1;iter<=ITMAX;iter++) {
|
| goto end;*/ |
xm=0.5*(a+b);
|
| return ps; |
tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
|
| } |
/* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
|
| |
printf(".");fflush(stdout);
|
| /**************** Product of 2 matrices ******************/ |
fprintf(ficlog,".");fflush(ficlog);
|
| |
#ifdef DEBUG
|
| double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b) |
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);
|
| { |
fprintf(ficlog,"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);
|
| /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times |
/* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
|
| b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */ |
#endif
|
| /* in, b, out are matrice of pointers which should have been initialized |
if (fabs(x-xm) <= (tol2-0.5*(b-a))){
|
| before: only the contents of out is modified. The function returns |
*xmin=x;
|
| a pointer to pointers identical to out */ |
return fx;
|
| long i, j, k; |
}
|
| for(i=nrl; i<= nrh; i++) |
ftemp=fu;
|
| for(k=ncolol; k<=ncoloh; k++) |
if (fabs(e) > tol1) {
|
| for(j=ncl,out[i][k]=0.; j<=nch; j++) |
r=(x-w)*(fx-fv);
|
| out[i][k] +=in[i][j]*b[j][k]; |
q=(x-v)*(fx-fw);
|
| |
p=(x-v)*q-(x-w)*r;
|
| return out; |
q=2.0*(q-r);
|
| } |
if (q > 0.0) p = -p;
|
| |
q=fabs(q);
|
| |
etemp=e;
|
| /************* Higher Matrix Product ***************/ |
e=d;
|
| |
if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
|
| double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij ) |
d=CGOLD*(e=(x >= xm ? a-x : b-x));
|
| { |
else {
|
| /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month |
d=p/q;
|
| duration (i.e. until |
u=x+d;
|
| age (in years) age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices. |
if (u-a < tol2 || b-u < tol2)
|
| Output is stored in matrix po[i][j][h] for h every 'hstepm' step |
d=SIGN(tol1,xm-x);
|
| (typically every 2 years instead of every month which is too big). |
}
|
| Model is determined by parameters x and covariates have to be |
} else {
|
| included manually here. |
d=CGOLD*(e=(x >= xm ? a-x : b-x));
|
| |
}
|
| */ |
u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
|
| |
fu=(*f)(u);
|
| int i, j, d, h, k; |
if (fu <= fx) {
|
| double **out, cov[NCOVMAX]; |
if (u >= x) a=x; else b=x;
|
| double **newm; |
SHFT(v,w,x,u)
|
| |
SHFT(fv,fw,fx,fu)
|
| /* Hstepm could be zero and should return the unit matrix */ |
} else {
|
| for (i=1;i<=nlstate+ndeath;i++) |
if (u < x) a=u; else b=u;
|
| for (j=1;j<=nlstate+ndeath;j++){ |
if (fu <= fw || w == x) {
|
| oldm[i][j]=(i==j ? 1.0 : 0.0); |
v=w;
|
| po[i][j][0]=(i==j ? 1.0 : 0.0); |
w=u;
|
| } |
fv=fw;
|
| /* Even if hstepm = 1, at least one multiplication by the unit matrix */ |
fw=fu;
|
| for(h=1; h <=nhstepm; h++){ |
} else if (fu <= fv || v == x || v == w) {
|
| for(d=1; d <=hstepm; d++){ |
v=u;
|
| newm=savm; |
fv=fu;
|
| /* 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]]]; |
nrerror("Too many iterations in brent");
|
| for (k=1; k<=cptcovage;k++) |
*xmin=x;
|
| cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; |
return fx;
|
| 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]]]; |
|
| |
/****************** mnbrak ***********************/
|
| |
|
| /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/ |
void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
|
| /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/ |
double (*func)(double))
|
| out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, |
{
|
| pmij(pmmij,cov,ncovmodel,x,nlstate)); |
double ulim,u,r,q, dum;
|
| savm=oldm; |
double fu;
|
| oldm=newm; |
|
| } |
*fa=(*func)(*ax);
|
| for(i=1; i<=nlstate+ndeath; i++) |
*fb=(*func)(*bx);
|
| for(j=1;j<=nlstate+ndeath;j++) { |
if (*fb > *fa) {
|
| po[i][j][h]=newm[i][j]; |
SHFT(dum,*ax,*bx,dum)
|
| /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]); |
SHFT(dum,*fb,*fa,dum)
|
| */ |
}
|
| } |
*cx=(*bx)+GOLD*(*bx-*ax);
|
| } /* end h */ |
*fc=(*func)(*cx);
|
| return po; |
while (*fb > *fc) {
|
| } |
r=(*bx-*ax)*(*fb-*fc);
|
| |
q=(*bx-*cx)*(*fb-*fa);
|
| |
u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
|
| /*************** log-likelihood *************/ |
(2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
|
| double func( double *x) |
ulim=(*bx)+GLIMIT*(*cx-*bx);
|
| { |
if ((*bx-u)*(u-*cx) > 0.0) {
|
| int i, ii, j, k, mi, d, kk; |
fu=(*func)(u);
|
| double l, ll[NLSTATEMAX], cov[NCOVMAX]; |
} else if ((*cx-u)*(u-ulim) > 0.0) {
|
| double **out; |
fu=(*func)(u);
|
| double sw; /* Sum of weights */ |
if (fu < *fc) {
|
| double lli; /* Individual log likelihood */ |
SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
|
| int s1, s2; |
SHFT(*fb,*fc,fu,(*func)(u))
|
| double bbh; |
}
|
| long ipmx; |
} else if ((u-ulim)*(ulim-*cx) >= 0.0) {
|
| /*extern weight */ |
u=ulim;
|
| /* We are differentiating ll according to initial status */ |
fu=(*func)(u);
|
| /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/ |
} else {
|
| /*for(i=1;i<imx;i++) |
u=(*cx)+GOLD*(*cx-*bx);
|
| printf(" %d\n",s[4][i]); |
fu=(*func)(u);
|
| */ |
}
|
| cov[1]=1.; |
SHFT(*ax,*bx,*cx,u)
|
| |
SHFT(*fa,*fb,*fc,fu)
|
| for(k=1; k<=nlstate; k++) ll[k]=0.; |
}
|
| |
}
|
| if(mle==1){ |
|
| for (i=1,ipmx=0, sw=0.; i<=imx; i++){ |
/*************** linmin ************************/
|
| for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; |
|
| for(mi=1; mi<= wav[i]-1; mi++){ |
int ncom;
|
| for (ii=1;ii<=nlstate+ndeath;ii++) |
double *pcom,*xicom;
|
| for (j=1;j<=nlstate+ndeath;j++){ |
double (*nrfunc)(double []);
|
| oldm[ii][j]=(ii==j ? 1.0 : 0.0); |
|
| savm[ii][j]=(ii==j ? 1.0 : 0.0); |
void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
|
| } |
{
|
| for(d=0; d<dh[mi][i]; d++){ |
double brent(double ax, double bx, double cx,
|
| newm=savm; |
double (*f)(double), double tol, double *xmin);
|
| cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM; |
double f1dim(double x);
|
| for (kk=1; kk<=cptcovage;kk++) { |
void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
|
| cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; |
double *fc, double (*func)(double));
|
| } |
int j;
|
| |
double xx,xmin,bx,ax;
|
| out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, |
double fx,fb,fa;
|
| 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); |
|
| savm=oldm; |
ncom=n;
|
| oldm=newm; |
pcom=vector(1,n);
|
| |
xicom=vector(1,n);
|
| |
nrfunc=func;
|
| } /* end mult */ |
for (j=1;j<=n;j++) {
|
| |
pcom[j]=p[j];
|
| /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */ |
xicom[j]=xi[j];
|
| /* But now since version 0.9 we anticipate for bias and large stepm. |
}
|
| * If stepm is larger than one month (smallest stepm) and if the exact delay |
ax=0.0;
|
| * (in months) between two waves is not a multiple of stepm, we rounded to |
xx=1.0;
|
| * the nearest (and in case of equal distance, to the lowest) interval but now |
mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
|
| * we keep into memory the bias bh[mi][i] and also the previous matrix product |
*fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
|
| * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the |
#ifdef DEBUG
|
| * probability in order to take into account the bias as a fraction of the way |
printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
|
| * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies |
fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
|
| * -stepm/2 to stepm/2 . |
#endif
|
| * For stepm=1 the results are the same as for previous versions of Imach. |
for (j=1;j<=n;j++) {
|
| * For stepm > 1 the results are less biased than in previous versions. |
xi[j] *= xmin;
|
| */ |
p[j] += xi[j];
|
| s1=s[mw[mi][i]][i]; |
}
|
| s2=s[mw[mi+1][i]][i]; |
free_vector(xicom,1,n);
|
| bbh=(double)bh[mi][i]/(double)stepm; |
free_vector(pcom,1,n);
|
| |
}
|
| /* lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/ |
|
| |
char *asc_diff_time(long time_sec, char ascdiff[])
|
| lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */ |
{
|
| |
long sec_left, days, hours, minutes;
|
| /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-bbh)*out[s1][s2]));*/ |
days = (time_sec) / (60*60*24);
|
| /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/ |
sec_left = (time_sec) % (60*60*24);
|
| /*if(lli ==000.0)*/ |
hours = (sec_left) / (60*60) ;
|
| /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */ |
sec_left = (sec_left) %(60*60);
|
| ipmx +=1; |
minutes = (sec_left) /60;
|
| sw += weight[i]; |
sec_left = (sec_left) % (60);
|
| ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; |
sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
|
| } /* end of wave */ |
return ascdiff;
|
| } /* end of individual */ |
}
|
| } else{ |
|
| for (i=1,ipmx=0, sw=0.; i<=imx; i++){ |
/*************** powell ************************/
|
| for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; |
void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
|
| for(mi=1; mi<= wav[i]-1; mi++){ |
double (*func)(double []))
|
| for (ii=1;ii<=nlstate+ndeath;ii++) |
{
|
| for (j=1;j<=nlstate+ndeath;j++){ |
void linmin(double p[], double xi[], int n, double *fret,
|
| oldm[ii][j]=(ii==j ? 1.0 : 0.0); |
double (*func)(double []));
|
| savm[ii][j]=(ii==j ? 1.0 : 0.0); |
int i,ibig,j;
|
| } |
double del,t,*pt,*ptt,*xit;
|
| for(d=0; d<dh[mi][i]; d++){ |
double fp,fptt;
|
| newm=savm; |
double *xits;
|
| cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM; |
int niterf, itmp;
|
| for (kk=1; kk<=cptcovage;kk++) { |
|
| cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; |
pt=vector(1,n);
|
| } |
ptt=vector(1,n);
|
| |
xit=vector(1,n);
|
| out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, |
xits=vector(1,n);
|
| 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); |
*fret=(*func)(p);
|
| savm=oldm; |
for (j=1;j<=n;j++) pt[j]=p[j];
|
| oldm=newm; |
for (*iter=1;;++(*iter)) {
|
| } /* end mult */ |
fp=(*fret);
|
| |
ibig=0;
|
| lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */ |
del=0.0;
|
| ipmx +=1; |
last_time=curr_time;
|
| sw += weight[i]; |
(void) gettimeofday(&curr_time,&tzp);
|
| ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; |
printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
|
| } /* end of wave */ |
fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
|
| } /* end of individual */ |
/* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
|
| } /* End of if */ |
for (i=1;i<=n;i++) {
|
| for(k=1,l=0.; k<=nlstate; k++) l += ll[k]; |
printf(" %d %.12f",i, p[i]);
|
| /* printf("l1=%f l2=%f ",ll[1],ll[2]); */ |
fprintf(ficlog," %d %.12lf",i, p[i]);
|
| l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */ |
fprintf(ficrespow," %.12lf", p[i]);
|
| return -l; |
}
|
| } |
printf("\n");
|
| |
fprintf(ficlog,"\n");
|
| |
fprintf(ficrespow,"\n");fflush(ficrespow);
|
| /*********** Maximum Likelihood Estimation ***************/ |
if(*iter <=3){
|
| |
tm = *localtime(&curr_time.tv_sec);
|
| void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double [])) |
strcpy(strcurr,asctime(&tm));
|
| { |
/* asctime_r(&tm,strcurr); */
|
| int i,j, iter; |
forecast_time=curr_time;
|
| double **xi,*delti; |
itmp = strlen(strcurr);
|
| double fret; |
if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
|
| xi=matrix(1,npar,1,npar); |
strcurr[itmp-1]='\0';
|
| for (i=1;i<=npar;i++) |
printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
|
| for (j=1;j<=npar;j++) |
fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
|
| xi[i][j]=(i==j ? 1.0 : 0.0); |
for(niterf=10;niterf<=30;niterf+=10){
|
| printf("Powell\n"); fprintf(ficlog,"Powell\n"); |
forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
|
| powell(p,xi,npar,ftol,&iter,&fret,func); |
tmf = *localtime(&forecast_time.tv_sec);
|
| |
/* asctime_r(&tmf,strfor); */
|
| printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p)); |
strcpy(strfor,asctime(&tmf));
|
| fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p)); |
itmp = strlen(strfor);
|
| fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p)); |
if(strfor[itmp-1]=='\n')
|
| |
strfor[itmp-1]='\0';
|
| } |
printf(" - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
|
| |
fprintf(ficlog," - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
|
| /**** Computes Hessian and covariance matrix ***/ |
}
|
| void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double [])) |
}
|
| { |
for (i=1;i<=n;i++) {
|
| double **a,**y,*x,pd; |
for (j=1;j<=n;j++) xit[j]=xi[j][i];
|
| double **hess; |
fptt=(*fret);
|
| int i, j,jk; |
#ifdef DEBUG
|
| int *indx; |
printf("fret=%lf \n",*fret);
|
| |
fprintf(ficlog,"fret=%lf \n",*fret);
|
| double hessii(double p[], double delta, int theta, double delti[]); |
#endif
|
| double hessij(double p[], double delti[], int i, int j); |
printf("%d",i);fflush(stdout);
|
| void lubksb(double **a, int npar, int *indx, double b[]) ; |
fprintf(ficlog,"%d",i);fflush(ficlog);
|
| void ludcmp(double **a, int npar, int *indx, double *d) ; |
linmin(p,xit,n,fret,func);
|
| |
if (fabs(fptt-(*fret)) > del) {
|
| hess=matrix(1,npar,1,npar); |
del=fabs(fptt-(*fret));
|
| |
ibig=i;
|
| printf("\nCalculation of the hessian matrix. Wait...\n"); |
}
|
| fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n"); |
#ifdef DEBUG
|
| for (i=1;i<=npar;i++){ |
printf("%d %.12e",i,(*fret));
|
| printf("%d",i);fflush(stdout); |
fprintf(ficlog,"%d %.12e",i,(*fret));
|
| fprintf(ficlog,"%d",i);fflush(ficlog); |
for (j=1;j<=n;j++) {
|
| hess[i][i]=hessii(p,ftolhess,i,delti); |
xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
|
| /*printf(" %f ",p[i]);*/ |
printf(" x(%d)=%.12e",j,xit[j]);
|
| /*printf(" %lf ",hess[i][i]);*/ |
fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
|
| } |
}
|
| |
for(j=1;j<=n;j++) {
|
| for (i=1;i<=npar;i++) { |
printf(" p=%.12e",p[j]);
|
| for (j=1;j<=npar;j++) { |
fprintf(ficlog," p=%.12e",p[j]);
|
| if (j>i) { |
}
|
| printf(".%d%d",i,j);fflush(stdout); |
printf("\n");
|
| fprintf(ficlog,".%d%d",i,j);fflush(ficlog); |
fprintf(ficlog,"\n");
|
| hess[i][j]=hessij(p,delti,i,j); |
#endif
|
| hess[j][i]=hess[i][j]; |
}
|
| /*printf(" %lf ",hess[i][j]);*/ |
if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
|
| } |
#ifdef DEBUG
|
| } |
int k[2],l;
|
| } |
k[0]=1;
|
| printf("\n"); |
k[1]=-1;
|
| fprintf(ficlog,"\n"); |
printf("Max: %.12e",(*func)(p));
|
| |
fprintf(ficlog,"Max: %.12e",(*func)(p));
|
| printf("\nInverting the hessian to get the covariance matrix. Wait...\n"); |
for (j=1;j<=n;j++) {
|
| fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n"); |
printf(" %.12e",p[j]);
|
| |
fprintf(ficlog," %.12e",p[j]);
|
| a=matrix(1,npar,1,npar); |
}
|
| y=matrix(1,npar,1,npar); |
printf("\n");
|
| x=vector(1,npar); |
fprintf(ficlog,"\n");
|
| indx=ivector(1,npar); |
for(l=0;l<=1;l++) {
|
| for (i=1;i<=npar;i++) |
for (j=1;j<=n;j++) {
|
| for (j=1;j<=npar;j++) a[i][j]=hess[i][j]; |
ptt[j]=p[j]+(p[j]-pt[j])*k[l];
|
| ludcmp(a,npar,indx,&pd); |
printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
|
| |
fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
|
| for (j=1;j<=npar;j++) { |
}
|
| for (i=1;i<=npar;i++) x[i]=0; |
printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
|
| x[j]=1; |
fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
|
| lubksb(a,npar,indx,x); |
}
|
| for (i=1;i<=npar;i++){ |
#endif
|
| matcov[i][j]=x[i]; |
|
| } |
|
| } |
free_vector(xit,1,n);
|
| |
free_vector(xits,1,n);
|
| printf("\n#Hessian matrix#\n"); |
free_vector(ptt,1,n);
|
| fprintf(ficlog,"\n#Hessian matrix#\n"); |
free_vector(pt,1,n);
|
| for (i=1;i<=npar;i++) { |
return;
|
| for (j=1;j<=npar;j++) { |
}
|
| printf("%.3e ",hess[i][j]); |
if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
|
| fprintf(ficlog,"%.3e ",hess[i][j]); |
for (j=1;j<=n;j++) {
|
| } |
ptt[j]=2.0*p[j]-pt[j];
|
| printf("\n"); |
xit[j]=p[j]-pt[j];
|
| fprintf(ficlog,"\n"); |
pt[j]=p[j];
|
| } |
}
|
| |
fptt=(*func)(ptt);
|
| /* Recompute Inverse */ |
if (fptt < fp) {
|
| for (i=1;i<=npar;i++) |
t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
|
| for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; |
if (t < 0.0) {
|
| ludcmp(a,npar,indx,&pd); |
linmin(p,xit,n,fret,func);
|
| |
for (j=1;j<=n;j++) {
|
| /* printf("\n#Hessian matrix recomputed#\n"); |
xi[j][ibig]=xi[j][n];
|
| |
xi[j][n]=xit[j];
|
| for (j=1;j<=npar;j++) { |
}
|
| for (i=1;i<=npar;i++) x[i]=0; |
#ifdef DEBUG
|
| x[j]=1; |
printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
|
| lubksb(a,npar,indx,x); |
fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
|
| for (i=1;i<=npar;i++){ |
for(j=1;j<=n;j++){
|
| y[i][j]=x[i]; |
printf(" %.12e",xit[j]);
|
| printf("%.3e ",y[i][j]); |
fprintf(ficlog," %.12e",xit[j]);
|
| fprintf(ficlog,"%.3e ",y[i][j]); |
}
|
| } |
printf("\n");
|
| printf("\n"); |
fprintf(ficlog,"\n");
|
| fprintf(ficlog,"\n"); |
#endif
|
| } |
}
|
| */ |
}
|
| |
}
|
| free_matrix(a,1,npar,1,npar); |
}
|
| free_matrix(y,1,npar,1,npar); |
|
| free_vector(x,1,npar); |
/**** Prevalence limit (stable or period prevalence) ****************/
|
| free_ivector(indx,1,npar); |
|
| free_matrix(hess,1,npar,1,npar); |
double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
|
| |
{
|
| |
/* Computes the prevalence limit in each live state at age x by left multiplying the unit
|
| } |
matrix by transitions matrix until convergence is reached */
|
| |
|
| /*************** hessian matrix ****************/ |
int i, ii,j,k;
|
| double hessii( double x[], double delta, int theta, double delti[]) |
double min, max, maxmin, maxmax,sumnew=0.;
|
| { |
double **matprod2();
|
| int i; |
double **out, cov[NCOVMAX], **pmij();
|
| int l=1, lmax=20; |
double **newm;
|
| double k1,k2; |
double agefin, delaymax=50 ; /* Max number of years to converge */
|
| double p2[NPARMAX+1]; |
|
| double res; |
for (ii=1;ii<=nlstate+ndeath;ii++)
|
| double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4; |
for (j=1;j<=nlstate+ndeath;j++){
|
| double fx; |
oldm[ii][j]=(ii==j ? 1.0 : 0.0);
|
| int k=0,kmax=10; |
}
|
| double l1; |
|
| |
cov[1]=1.;
|
| fx=func(x); |
|
| for (i=1;i<=npar;i++) p2[i]=x[i]; |
/* Even if hstepm = 1, at least one multiplication by the unit matrix */
|
| for(l=0 ; l <=lmax; l++){ |
for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
|
| l1=pow(10,l); |
newm=savm;
|
| delts=delt; |
/* Covariates have to be included here again */
|
| for(k=1 ; k <kmax; k=k+1){ |
cov[2]=agefin;
|
| delt = delta*(l1*k); |
|
| p2[theta]=x[theta] +delt; |
for (k=1; k<=cptcovn;k++) {
|
| k1=func(p2)-fx; |
cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
|
| p2[theta]=x[theta]-delt; |
/* 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]]);*/
|
| k2=func(p2)-fx; |
}
|
| /*res= (k1-2.0*fx+k2)/delt/delt; */ |
for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
|
| res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */ |
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]]];
|
| #ifdef DEBUG |
|
| 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); |
/*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
|
| fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx); |
/*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
|
| #endif |
/*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
|
| /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */ |
out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
|
| if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){ |
|
| k=kmax; |
savm=oldm;
|
| } |
oldm=newm;
|
| else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */ |
maxmax=0.;
|
| k=kmax; l=lmax*10.; |
for(j=1;j<=nlstate;j++){
|
| } |
min=1.;
|
| else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ |
max=0.;
|
| delts=delt; |
for(i=1; i<=nlstate; i++) {
|
| } |
sumnew=0;
|
| } |
for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
|
| } |
prlim[i][j]= newm[i][j]/(1-sumnew);
|
| delti[theta]=delts; |
max=FMAX(max,prlim[i][j]);
|
| return res; |
min=FMIN(min,prlim[i][j]);
|
| |
}
|
| } |
maxmin=max-min;
|
| |
maxmax=FMAX(maxmax,maxmin);
|
| double hessij( double x[], double delti[], int thetai,int thetaj) |
}
|
| { |
if(maxmax < ftolpl){
|
| int i; |
return prlim;
|
| int l=1, l1, lmax=20; |
}
|
| double k1,k2,k3,k4,res,fx; |
}
|
| double p2[NPARMAX+1]; |
}
|
| int k; |
|
| |
/*************** transition probabilities ***************/
|
| fx=func(x); |
|
| for (k=1; k<=2; k++) { |
double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
|
| for (i=1;i<=npar;i++) p2[i]=x[i]; |
{
|
| p2[thetai]=x[thetai]+delti[thetai]/k; |
double s1, s2;
|
| p2[thetaj]=x[thetaj]+delti[thetaj]/k; |
/*double t34;*/
|
| k1=func(p2)-fx; |
int i,j,j1, nc, ii, jj;
|
| |
|
| p2[thetai]=x[thetai]+delti[thetai]/k; |
for(i=1; i<= nlstate; i++){
|
| p2[thetaj]=x[thetaj]-delti[thetaj]/k; |
for(j=1; j<i;j++){
|
| k2=func(p2)-fx; |
for (nc=1, s2=0.;nc <=ncovmodel; nc++){
|
| |
/*s2 += param[i][j][nc]*cov[nc];*/
|
| p2[thetai]=x[thetai]-delti[thetai]/k; |
s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
|
| p2[thetaj]=x[thetaj]+delti[thetaj]/k; |
/* printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
|
| k3=func(p2)-fx; |
}
|
| |
ps[i][j]=s2;
|
| p2[thetai]=x[thetai]-delti[thetai]/k; |
/* printf("s1=%.17e, s2=%.17e\n",s1,s2); */
|
| p2[thetaj]=x[thetaj]-delti[thetaj]/k; |
}
|
| k4=func(p2)-fx; |
for(j=i+1; j<=nlstate+ndeath;j++){
|
| res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */ |
for (nc=1, s2=0.;nc <=ncovmodel; nc++){
|
| #ifdef DEBUG |
s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
|
| 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); |
/* printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
|
| fprintf(ficlog,"%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 |
ps[i][j]=s2;
|
| } |
}
|
| return res; |
}
|
| } |
/*ps[3][2]=1;*/
|
| |
|
| /************** Inverse of matrix **************/ |
for(i=1; i<= nlstate; i++){
|
| void ludcmp(double **a, int n, int *indx, double *d) |
s1=0;
|
| { |
for(j=1; j<i; j++)
|
| int i,imax,j,k; |
s1+=exp(ps[i][j]);
|
| double big,dum,sum,temp; |
for(j=i+1; j<=nlstate+ndeath; j++)
|
| double *vv; |
s1+=exp(ps[i][j]);
|
| |
ps[i][i]=1./(s1+1.);
|
| vv=vector(1,n); |
for(j=1; j<i; j++)
|
| *d=1.0; |
ps[i][j]= exp(ps[i][j])*ps[i][i];
|
| for (i=1;i<=n;i++) { |
for(j=i+1; j<=nlstate+ndeath; j++)
|
| big=0.0; |
ps[i][j]= exp(ps[i][j])*ps[i][i];
|
| for (j=1;j<=n;j++) |
/* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
|
| if ((temp=fabs(a[i][j])) > big) big=temp; |
} /* end i */
|
| if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); |
|
| vv[i]=1.0/big; |
for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
|
| } |
for(jj=1; jj<= nlstate+ndeath; jj++){
|
| for (j=1;j<=n;j++) { |
ps[ii][jj]=0;
|
| for (i=1;i<j;i++) { |
ps[ii][ii]=1;
|
| sum=a[i][j]; |
}
|
| for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; |
}
|
| a[i][j]=sum; |
|
| } |
|
| big=0.0; |
/* for(ii=1; ii<= nlstate+ndeath; ii++){ */
|
| for (i=j;i<=n;i++) { |
/* for(jj=1; jj<= nlstate+ndeath; jj++){ */
|
| sum=a[i][j]; |
/* printf("ddd %lf ",ps[ii][jj]); */
|
| for (k=1;k<j;k++) |
/* } */
|
| sum -= a[i][k]*a[k][j]; |
/* printf("\n "); */
|
| a[i][j]=sum; |
/* } */
|
| if ( (dum=vv[i]*fabs(sum)) >= big) { |
/* printf("\n ");printf("%lf ",cov[2]); */
|
| big=dum; |
/*
|
| imax=i; |
for(i=1; i<= npar; i++) printf("%f ",x[i]);
|
| } |
goto end;*/
|
| } |
return ps;
|
| if (j != imax) { |
}
|
| for (k=1;k<=n;k++) { |
|
| dum=a[imax][k]; |
/**************** Product of 2 matrices ******************/
|
| a[imax][k]=a[j][k]; |
|
| a[j][k]=dum; |
double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
|
| } |
{
|
| *d = -(*d); |
/* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
|
| vv[imax]=vv[j]; |
b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
|
| } |
/* in, b, out are matrice of pointers which should have been initialized
|
| indx[j]=imax; |
before: only the contents of out is modified. The function returns
|
| if (a[j][j] == 0.0) a[j][j]=TINY; |
a pointer to pointers identical to out */
|
| if (j != n) { |
long i, j, k;
|
| dum=1.0/(a[j][j]); |
for(i=nrl; i<= nrh; i++)
|
| for (i=j+1;i<=n;i++) a[i][j] *= dum; |
for(k=ncolol; k<=ncoloh; k++)
|
| } |
for(j=ncl,out[i][k]=0.; j<=nch; j++)
|
| } |
out[i][k] +=in[i][j]*b[j][k];
|
| free_vector(vv,1,n); /* Doesn't work */ |
|
| ; |
return out;
|
| } |
}
|
| |
|
| void lubksb(double **a, int n, int *indx, double b[]) |
|
| { |
/************* Higher Matrix Product ***************/
|
| int i,ii=0,ip,j; |
|
| double sum; |
double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
|
| |
{
|
| for (i=1;i<=n;i++) { |
/* Computes the transition matrix starting at age 'age' over
|
| ip=indx[i]; |
'nhstepm*hstepm*stepm' months (i.e. until
|
| sum=b[ip]; |
age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
|
| b[ip]=b[i]; |
nhstepm*hstepm matrices.
|
| if (ii) |
Output is stored in matrix po[i][j][h] for h every 'hstepm' step
|
| for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; |
(typically every 2 years instead of every month which is too big
|
| else if (sum) ii=i; |
for the memory).
|
| b[i]=sum; |
Model is determined by parameters x and covariates have to be
|
| } |
included manually here.
|
| for (i=n;i>=1;i--) { |
|
| sum=b[i]; |
*/
|
| for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; |
|
| b[i]=sum/a[i][i]; |
int i, j, d, h, k;
|
| } |
double **out, cov[NCOVMAX];
|
| } |
double **newm;
|
| |
|
| /************ Frequencies ********************/ |
/* Hstepm could be zero and should return the unit matrix */
|
| void freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2) |
for (i=1;i<=nlstate+ndeath;i++)
|
| { /* Some frequencies */ |
for (j=1;j<=nlstate+ndeath;j++){
|
| |
oldm[i][j]=(i==j ? 1.0 : 0.0);
|
| int i, m, jk, k1,i1, j1, bool, z1,z2,j; |
po[i][j][0]=(i==j ? 1.0 : 0.0);
|
| int first; |
}
|
| double ***freq; /* Frequencies */ |
/* Even if hstepm = 1, at least one multiplication by the unit matrix */
|
| double *pp; |
for(h=1; h <=nhstepm; h++){
|
| double pos, k2, dateintsum=0,k2cpt=0; |
for(d=1; d <=hstepm; d++){
|
| FILE *ficresp; |
newm=savm;
|
| char fileresp[FILENAMELENGTH]; |
/* Covariates have to be included here again */
|
| |
cov[1]=1.;
|
| pp=vector(1,nlstate); |
cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
|
| probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX); |
for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
|
| strcpy(fileresp,"p"); |
for (k=1; k<=cptcovage;k++)
|
| strcat(fileresp,fileres); |
cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
|
| if((ficresp=fopen(fileresp,"w"))==NULL) { |
for (k=1; k<=cptcovprod;k++)
|
| printf("Problem with prevalence resultfile: %s\n", fileresp); |
cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
|
| fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp); |
|
| exit(0); |
|
| } |
/*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
|
| freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3); |
/*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
|
| j1=0; |
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
|
| |
pmij(pmmij,cov,ncovmodel,x,nlstate));
|
| j=cptcoveff; |
savm=oldm;
|
| if (cptcovn<1) {j=1;ncodemax[1]=1;} |
oldm=newm;
|
| |
}
|
| first=1; |
for(i=1; i<=nlstate+ndeath; i++)
|
| |
for(j=1;j<=nlstate+ndeath;j++) {
|
| for(k1=1; k1<=j;k1++){ |
po[i][j][h]=newm[i][j];
|
| for(i1=1; i1<=ncodemax[k1];i1++){ |
/*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
|
| j1++; |
*/
|
| /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]); |
}
|
| scanf("%d", i);*/ |
} /* end h */
|
| for (i=-1; i<=nlstate+ndeath; i++) |
return po;
|
| for (jk=-1; jk<=nlstate+ndeath; jk++) |
}
|
| for(m=agemin; m <= agemax+3; m++) |
|
| freq[i][jk][m]=0; |
|
| |
/*************** log-likelihood *************/
|
| dateintsum=0; |
double func( double *x)
|
| k2cpt=0; |
{
|
| for (i=1; i<=imx; i++) { |
int i, ii, j, k, mi, d, kk;
|
| bool=1; |
double l, ll[NLSTATEMAX], cov[NCOVMAX];
|
| if (cptcovn>0) { |
double **out;
|
| for (z1=1; z1<=cptcoveff; z1++) |
double sw; /* Sum of weights */
|
| if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) |
double lli; /* Individual log likelihood */
|
| bool=0; |
int s1, s2;
|
| } |
double bbh, survp;
|
| if (bool==1){ |
long ipmx;
|
| for(m=firstpass; m<=lastpass; m++){ |
/*extern weight */
|
| k2=anint[m][i]+(mint[m][i]/12.); |
/* We are differentiating ll according to initial status */
|
| if ((k2>=dateprev1) && (k2<=dateprev2)) { |
/* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
|
| if(agev[m][i]==0) agev[m][i]=agemax+1; |
/*for(i=1;i<imx;i++)
|
| if(agev[m][i]==1) agev[m][i]=agemax+2; |
printf(" %d\n",s[4][i]);
|
| if (m<lastpass) { |
*/
|
| freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; |
cov[1]=1.;
|
| freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i]; |
|
| } |
for(k=1; k<=nlstate; k++) ll[k]=0.;
|
| |
|
| if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) { |
if(mle==1){
|
| dateintsum=dateintsum+k2; |
for (i=1,ipmx=0, sw=0.; i<=imx; i++){
|
| k2cpt++; |
for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
|
| } |
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);
|
| } |
savm[ii][j]=(ii==j ? 1.0 : 0.0);
|
| |
}
|
| fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); |
for(d=0; d<dh[mi][i]; d++){
|
| |
newm=savm;
|
| if (cptcovn>0) { |
cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
|
| fprintf(ficresp, "\n#********** Variable "); |
for (kk=1; kk<=cptcovage;kk++) {
|
| for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); |
cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
|
| fprintf(ficresp, "**********\n#"); |
}
|
| } |
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
|
| for(i=1; i<=nlstate;i++) |
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
|
| fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i); |
savm=oldm;
|
| fprintf(ficresp, "\n"); |
oldm=newm;
|
| |
} /* end mult */
|
| for(i=(int)agemin; i <= (int)agemax+3; i++){ |
|
| if(i==(int)agemax+3){ |
/*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
|
| fprintf(ficlog,"Total"); |
/* But now since version 0.9 we anticipate for bias at large stepm.
|
| }else{ |
* If stepm is larger than one month (smallest stepm) and if the exact delay
|
| if(first==1){ |
* (in months) between two waves is not a multiple of stepm, we rounded to
|
| first=0; |
* the nearest (and in case of equal distance, to the lowest) interval but now
|
| printf("See log file for details...\n"); |
* we keep into memory the bias bh[mi][i] and also the previous matrix product
|
| } |
* (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
|
| fprintf(ficlog,"Age %d", i); |
* probability in order to take into account the bias as a fraction of the way
|
| } |
* from savm to out if bh is negative or even beyond if bh is positive. bh varies
|
| for(jk=1; jk <=nlstate ; jk++){ |
* -stepm/2 to stepm/2 .
|
| for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++) |
* For stepm=1 the results are the same as for previous versions of Imach.
|
| pp[jk] += freq[jk][m][i]; |
* For stepm > 1 the results are less biased than in previous versions.
|
| } |
*/
|
| for(jk=1; jk <=nlstate ; jk++){ |
s1=s[mw[mi][i]][i];
|
| for(m=-1, pos=0; m <=0 ; m++) |
s2=s[mw[mi+1][i]][i];
|
| pos += freq[jk][m][i]; |
bbh=(double)bh[mi][i]/(double)stepm;
|
| if(pp[jk]>=1.e-10){ |
/* bias bh is positive if real duration
|
| if(first==1){ |
* is higher than the multiple of stepm and negative otherwise.
|
| printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); |
*/
|
| } |
/* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
|
| fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); |
if( s2 > nlstate){
|
| }else{ |
/* i.e. if s2 is a death state and if the date of death is known
|
| if(first==1) |
then the contribution to the likelihood is the probability to
|
| printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk); |
die between last step unit time and current step unit time,
|
| fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk); |
which is also equal to probability to die before dh
|
| } |
minus probability to die before dh-stepm .
|
| } |
In version up to 0.92 likelihood was computed
|
| |
as if date of death was unknown. Death was treated as any other
|
| for(jk=1; jk <=nlstate ; jk++){ |
health state: the date of the interview describes the actual state
|
| for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++) |
and not the date of a change in health state. The former idea was
|
| pp[jk] += freq[jk][m][i]; |
to consider that at each interview the state was recorded
|
| } |
(healthy, disable or death) and IMaCh was corrected; but when we
|
| |
introduced the exact date of death then we should have modified
|
| for(jk=1,pos=0; jk <=nlstate ; jk++) |
the contribution of an exact death to the likelihood. This new
|
| pos += pp[jk]; |
contribution is smaller and very dependent of the step unit
|
| for(jk=1; jk <=nlstate ; jk++){ |
stepm. It is no more the probability to die between last interview
|
| if(pos>=1.e-5){ |
and month of death but the probability to survive from last
|
| if(first==1) |
interview up to one month before death multiplied by the
|
| printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); |
probability to die within a month. Thanks to Chris
|
| fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); |
Jackson for correcting this bug. Former versions increased
|
| }else{ |
mortality artificially. The bad side is that we add another loop
|
| if(first==1) |
which slows down the processing. The difference can be up to 10%
|
| printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); |
lower mortality.
|
| fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); |
*/
|
| } |
lli=log(out[s1][s2] - savm[s1][s2]);
|
| if( i <= (int) agemax){ |
|
| if(pos>=1.e-5){ |
|
| fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos); |
} else if (s2==-2) {
|
| probs[i][jk][j1]= pp[jk]/pos; |
for (j=1,survp=0. ; j<=nlstate; j++)
|
| /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/ |
survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
|
| } |
/*survp += out[s1][j]; */
|
| else |
lli= log(survp);
|
| fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos); |
}
|
| } |
|
| } |
else if (s2==-4) {
|
| |
for (j=3,survp=0. ; j<=nlstate; j++)
|
| for(jk=-1; jk <=nlstate+ndeath; jk++) |
survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
|
| for(m=-1; m <=nlstate+ndeath; m++) |
lli= log(survp);
|
| if(freq[jk][m][i] !=0 ) { |
}
|
| if(first==1) |
|
| printf(" %d%d=%.0f",jk,m,freq[jk][m][i]); |
else if (s2==-5) {
|
| fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]); |
for (j=1,survp=0. ; j<=2; j++)
|
| } |
survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
|
| if(i <= (int) agemax) |
lli= log(survp);
|
| fprintf(ficresp,"\n"); |
}
|
| if(first==1) |
|
| printf("Others in log...\n"); |
else{
|
| fprintf(ficlog,"\n"); |
lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
|
| } |
/* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
|
| } |
}
|
| } |
/*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
|
| dateintmean=dateintsum/k2cpt; |
/*if(lli ==000.0)*/
|
| |
/*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
|
| fclose(ficresp); |
ipmx +=1;
|
| free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3); |
sw += weight[i];
|
| free_vector(pp,1,nlstate); |
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
|
| |
} /* end of wave */
|
| /* End of Freq */ |
} /* end of individual */
|
| } |
} else if(mle==2){
|
| |
for (i=1,ipmx=0, sw=0.; i<=imx; i++){
|
| /************ Prevalence ********************/ |
for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
|
| 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) |
for(mi=1; mi<= wav[i]-1; mi++){
|
| { /* Some frequencies */ |
for (ii=1;ii<=nlstate+ndeath;ii++)
|
| |
for (j=1;j<=nlstate+ndeath;j++){
|
| int i, m, jk, k1, i1, j1, bool, z1,z2,j; |
oldm[ii][j]=(ii==j ? 1.0 : 0.0);
|
| double ***freq; /* Frequencies */ |
savm[ii][j]=(ii==j ? 1.0 : 0.0);
|
| double *pp; |
}
|
| double pos, k2; |
for(d=0; d<=dh[mi][i]; d++){
|
| |
newm=savm;
|
| pp=vector(1,nlstate); |
cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
|
| |
for (kk=1; kk<=cptcovage;kk++) {
|
| freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3); |
cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
|
| j1=0; |
}
|
| |
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
|
| j=cptcoveff; |
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
|
| if (cptcovn<1) {j=1;ncodemax[1]=1;} |
savm=oldm;
|
| |
oldm=newm;
|
| for(k1=1; k1<=j;k1++){ |
} /* end mult */
|
| for(i1=1; i1<=ncodemax[k1];i1++){ |
|
| j1++; |
s1=s[mw[mi][i]][i];
|
| |
s2=s[mw[mi+1][i]][i];
|
| for (i=-1; i<=nlstate+ndeath; i++) |
bbh=(double)bh[mi][i]/(double)stepm;
|
| for (jk=-1; jk<=nlstate+ndeath; jk++) |
lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
|
| for(m=agemin; m <= agemax+3; m++) |
ipmx +=1;
|
| freq[i][jk][m]=0; |
sw += weight[i];
|
| |
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
|
| for (i=1; i<=imx; i++) { |
} /* end of wave */
|
| bool=1; |
} /* end of individual */
|
| if (cptcovn>0) { |
} else if(mle==3){ /* exponential inter-extrapolation */
|
| for (z1=1; z1<=cptcoveff; z1++) |
for (i=1,ipmx=0, sw=0.; i<=imx; i++){
|
| if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) |
for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
|
| bool=0; |
for(mi=1; mi<= wav[i]-1; mi++){
|
| } |
for (ii=1;ii<=nlstate+ndeath;ii++)
|
| if (bool==1) { |
for (j=1;j<=nlstate+ndeath;j++){
|
| for(m=firstpass; m<=lastpass; m++){ |
oldm[ii][j]=(ii==j ? 1.0 : 0.0);
|
| k2=anint[m][i]+(mint[m][i]/12.); |
savm[ii][j]=(ii==j ? 1.0 : 0.0);
|
| if ((k2>=dateprev1) && (k2<=dateprev2)) { |
}
|
| if(agev[m][i]==0) agev[m][i]=agemax+1; |
for(d=0; d<dh[mi][i]; d++){
|
| if(agev[m][i]==1) agev[m][i]=agemax+2; |
newm=savm;
|
| if (m<lastpass) { |
cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
|
| if (calagedate>0) |
for (kk=1; kk<=cptcovage;kk++) {
|
| freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i]; |
cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
|
| else |
}
|
| freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; |
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
|
| freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i]; |
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
|
| } |
savm=oldm;
|
| } |
oldm=newm;
|
| } |
} /* end mult */
|
| } |
|
| } |
s1=s[mw[mi][i]][i];
|
| for(i=(int)agemin; i <= (int)agemax+3; i++){ |
s2=s[mw[mi+1][i]][i];
|
| for(jk=1; jk <=nlstate ; jk++){ |
bbh=(double)bh[mi][i]/(double)stepm;
|
| for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++) |
lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
|
| pp[jk] += freq[jk][m][i]; |
ipmx +=1;
|
| } |
sw += weight[i];
|
| for(jk=1; jk <=nlstate ; jk++){ |
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
|
| for(m=-1, pos=0; m <=0 ; m++) |
} /* end of wave */
|
| pos += freq[jk][m][i]; |
} /* end of individual */
|
| } |
}else if (mle==4){ /* ml=4 no inter-extrapolation */
|
| |
for (i=1,ipmx=0, sw=0.; i<=imx; i++){
|
| for(jk=1; jk <=nlstate ; jk++){ |
for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
|
| for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++) |
for(mi=1; mi<= wav[i]-1; mi++){
|
| pp[jk] += freq[jk][m][i]; |
for (ii=1;ii<=nlstate+ndeath;ii++)
|
| } |
for (j=1;j<=nlstate+ndeath;j++){
|
| |
oldm[ii][j]=(ii==j ? 1.0 : 0.0);
|
| for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk]; |
savm[ii][j]=(ii==j ? 1.0 : 0.0);
|
| |
}
|
| for(jk=1; jk <=nlstate ; jk++){ |
for(d=0; d<dh[mi][i]; d++){
|
| if( i <= (int) agemax){ |
newm=savm;
|
| if(pos>=1.e-5){ |
cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
|
| probs[i][jk][j1]= pp[jk]/pos; |
for (kk=1; kk<=cptcovage;kk++) {
|
| } |
cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
|
| } |
}
|
| }/* end jk */ |
|
| }/* end i */ |
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
|
| } /* end i1 */ |
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
|
| } /* end k1 */ |
savm=oldm;
|
| |
oldm=newm;
|
| |
} /* end mult */
|
| free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3); |
|
| free_vector(pp,1,nlstate); |
s1=s[mw[mi][i]][i];
|
| |
s2=s[mw[mi+1][i]][i];
|
| } /* End of Freq */ |
if( s2 > nlstate){
|
| |
lli=log(out[s1][s2] - savm[s1][s2]);
|
| /************* Waves Concatenation ***************/ |
}else{
|
| |
lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
|
| void concatwav(int wav[], int **dh, int **bh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm) |
}
|
| { |
ipmx +=1;
|
| /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i. |
sw += weight[i];
|
| Death is a valid wave (if date is known). |
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
|
| mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i |
/* printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
|
| dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i] |
} /* end of wave */
|
| and mw[mi+1][i]. dh depends on stepm. |
} /* end of individual */
|
| */ |
}else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
|
| |
for (i=1,ipmx=0, sw=0.; i<=imx; i++){
|
| int i, mi, m; |
for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
|
| /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1; |
for(mi=1; mi<= wav[i]-1; mi++){
|
| double sum=0., jmean=0.;*/ |
for (ii=1;ii<=nlstate+ndeath;ii++)
|
| int first; |
for (j=1;j<=nlstate+ndeath;j++){
|
| int j, k=0,jk, ju, jl; |
oldm[ii][j]=(ii==j ? 1.0 : 0.0);
|
| double sum=0.; |
savm[ii][j]=(ii==j ? 1.0 : 0.0);
|
| first=0; |
}
|
| jmin=1e+5; |
for(d=0; d<dh[mi][i]; d++){
|
| jmax=-1; |
newm=savm;
|
| jmean=0.; |
cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
|
| for(i=1; i<=imx; i++){ |
for (kk=1; kk<=cptcovage;kk++) {
|
| mi=0; |
cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
|
| m=firstpass; |
}
|
| while(s[m][i] <= nlstate){ |
|
| if(s[m][i]>=1) |
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
|
| mw[++mi][i]=m; |
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
|
| if(m >=lastpass) |
savm=oldm;
|
| break; |
oldm=newm;
|
| else |
} /* end mult */
|
| m++; |
|
| }/* end while */ |
s1=s[mw[mi][i]][i];
|
| if (s[m][i] > nlstate){ |
s2=s[mw[mi+1][i]][i];
|
| mi++; /* Death is another wave */ |
lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
|
| /* if(mi==0) never been interviewed correctly before death */ |
ipmx +=1;
|
| /* Only death is a correct wave */ |
sw += weight[i];
|
| mw[mi][i]=m; |
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
|
| } |
/*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
|
| |
} /* end of wave */
|
| wav[i]=mi; |
} /* end of individual */
|
| if(mi==0){ |
} /* End of if */
|
| if(first==0){ |
for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
|
| printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i); |
/* printf("l1=%f l2=%f ",ll[1],ll[2]); */
|
| first=1; |
l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
|
| } |
return -l;
|
| if(first==1){ |
}
|
| fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i); |
|
| } |
/*************** log-likelihood *************/
|
| } /* end mi==0 */ |
double funcone( double *x)
|
| } |
{
|
| |
/* Same as likeli but slower because of a lot of printf and if */
|
| for(i=1; i<=imx; i++){ |
int i, ii, j, k, mi, d, kk;
|
| for(mi=1; mi<wav[i];mi++){ |
double l, ll[NLSTATEMAX], cov[NCOVMAX];
|
| if (stepm <=0) |
double **out;
|
| dh[mi][i]=1; |
double lli; /* Individual log likelihood */
|
| else{ |
double llt;
|
| if (s[mw[mi+1][i]][i] > nlstate) { |
int s1, s2;
|
| if (agedc[i] < 2*AGESUP) { |
double bbh, survp;
|
| j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); |
/*extern weight */
|
| if(j==0) j=1; /* Survives at least one month after exam */ |
/* We are differentiating ll according to initial status */
|
| k=k+1; |
/* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
|
| if (j >= jmax) jmax=j; |
/*for(i=1;i<imx;i++)
|
| if (j <= jmin) jmin=j; |
printf(" %d\n",s[4][i]);
|
| sum=sum+j; |
*/
|
| /*if (j<0) printf("j=%d num=%d \n",j,i); */ |
cov[1]=1.;
|
| } |
|
| } |
for(k=1; k<=nlstate; k++) ll[k]=0.;
|
| else{ |
|
| j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12)); |
for (i=1,ipmx=0, sw=0.; i<=imx; i++){
|
| k=k+1; |
for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
|
| if (j >= jmax) jmax=j; |
for(mi=1; mi<= wav[i]-1; mi++){
|
| else if (j <= jmin)jmin=j; |
for (ii=1;ii<=nlstate+ndeath;ii++)
|
| /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */ |
for (j=1;j<=nlstate+ndeath;j++){
|
| sum=sum+j; |
oldm[ii][j]=(ii==j ? 1.0 : 0.0);
|
| } |
savm[ii][j]=(ii==j ? 1.0 : 0.0);
|
| jk= j/stepm; |
}
|
| jl= j -jk*stepm; |
for(d=0; d<dh[mi][i]; d++){
|
| ju= j -(jk+1)*stepm; |
newm=savm;
|
| if(jl <= -ju){ |
cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
|
| dh[mi][i]=jk; |
for (kk=1; kk<=cptcovage;kk++) {
|
| bh[mi][i]=jl; |
cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
|
| } |
}
|
| else{ |
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
|
| dh[mi][i]=jk+1; |
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
|
| bh[mi][i]=ju; |
savm=oldm;
|
| } |
oldm=newm;
|
| if(dh[mi][i]==0){ |
} /* end mult */
|
| dh[mi][i]=1; /* At least one step */ |
|
| bh[mi][i]=ju; /* At least one step */ |
s1=s[mw[mi][i]][i];
|
| printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i); |
s2=s[mw[mi+1][i]][i];
|
| } |
bbh=(double)bh[mi][i]/(double)stepm;
|
| if(i==298 || i==287 || i==763 ||i==1061)printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d",bh[mi][i],ju,jl,dh[mi][i],jk,stepm); |
/* bias is positive if real duration
|
| } |
* is higher than the multiple of stepm and negative otherwise.
|
| } |
*/
|
| } |
if( s2 > nlstate && (mle <5) ){ /* Jackson */
|
| jmean=sum/k; |
lli=log(out[s1][s2] - savm[s1][s2]);
|
| printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean); |
} else if (s2==-2) {
|
| fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean); |
for (j=1,survp=0. ; j<=nlstate; j++)
|
| } |
survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
|
| |
lli= log(survp);
|
| /*********** Tricode ****************************/ |
}else if (mle==1){
|
| void tricode(int *Tvar, int **nbcode, int imx) |
lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
|
| { |
} else if(mle==2){
|
| |
lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
|
| int Ndum[20],ij=1, k, j, i, maxncov=19; |
} else if(mle==3){ /* exponential inter-extrapolation */
|
| int cptcode=0; |
lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
|
| cptcoveff=0; |
} else if (mle==4){ /* mle=4 no inter-extrapolation */
|
| |
lli=log(out[s1][s2]); /* Original formula */
|
| for (k=0; k<maxncov; k++) Ndum[k]=0; |
} else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
|
| for (k=1; k<=7; k++) ncodemax[k]=0; |
lli=log(out[s1][s2]); /* Original formula */
|
| |
} /* End of if */
|
| for (j=1; j<=(cptcovn+2*cptcovprod); j++) { |
ipmx +=1;
|
| for (i=1; i<=imx; i++) { /*reads the data file to get the maximum |
sw += weight[i];
|
| modality*/ |
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
|
| ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/ |
/* printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
|
| Ndum[ij]++; /*store the modality */ |
if(globpr){
|
| /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/ |
fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
|
| if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable |
%11.6f %11.6f %11.6f ", \
|
| Tvar[j]. If V=sex and male is 0 and |
num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
|
| female is 1, then cptcode=1.*/ |
2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
|
| } |
for(k=1,llt=0.,l=0.; k<=nlstate; k++){
|
| |
llt +=ll[k]*gipmx/gsw;
|
| for (i=0; i<=cptcode; i++) { |
fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
|
| if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */ |
}
|
| } |
fprintf(ficresilk," %10.6f\n", -llt);
|
| |
}
|
| ij=1; |
} /* end of wave */
|
| for (i=1; i<=ncodemax[j]; i++) { |
} /* end of individual */
|
| for (k=0; k<= maxncov; k++) { |
for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
|
| if (Ndum[k] != 0) { |
/* printf("l1=%f l2=%f ",ll[1],ll[2]); */
|
| nbcode[Tvar[j]][ij]=k; |
l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
|
| /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */ |
if(globpr==0){ /* First time we count the contributions and weights */
|
| |
gipmx=ipmx;
|
| ij++; |
gsw=sw;
|
| } |
}
|
| if (ij > ncodemax[j]) break; |
return -l;
|
| } |
}
|
| } |
|
| } |
|
| |
/*************** function likelione ***********/
|
| for (k=0; k< maxncov; k++) Ndum[k]=0; |
void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
|
| |
{
|
| for (i=1; i<=ncovmodel-2; i++) { |
/* This routine should help understanding what is done with
|
| /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ |
the selection of individuals/waves and
|
| ij=Tvar[i]; |
to check the exact contribution to the likelihood.
|
| Ndum[ij]++; |
Plotting could be done.
|
| } |
*/
|
| |
int k;
|
| ij=1; |
|
| for (i=1; i<= maxncov; i++) { |
if(*globpri !=0){ /* Just counts and sums, no printings */
|
| if((Ndum[i]!=0) && (i<=ncovcol)){ |
strcpy(fileresilk,"ilk");
|
| Tvaraff[ij]=i; /*For printing */ |
strcat(fileresilk,fileres);
|
| ij++; |
if((ficresilk=fopen(fileresilk,"w"))==NULL) {
|
| } |
printf("Problem with resultfile: %s\n", fileresilk);
|
| } |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
|
| |
}
|
| cptcoveff=ij-1; /*Number of simple covariates*/ |
fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
|
| } |
fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
|
| |
/* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
|
| /*********** Health Expectancies ****************/ |
for(k=1; k<=nlstate; k++)
|
| |
fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
|
| 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 ) |
fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
|
| |
}
|
| { |
|
| /* Health expectancies */ |
*fretone=(*funcone)(p);
|
| int i, j, nhstepm, hstepm, h, nstepm, k, cptj; |
if(*globpri !=0){
|
| double age, agelim, hf; |
fclose(ficresilk);
|
| double ***p3mat,***varhe; |
fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
|
| double **dnewm,**doldm; |
fflush(fichtm);
|
| double *xp; |
}
|
| double **gp, **gm; |
return;
|
| double ***gradg, ***trgradg; |
}
|
| int theta; |
|
| |
|
| varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage); |
/*********** Maximum Likelihood Estimation ***************/
|
| xp=vector(1,npar); |
|
| dnewm=matrix(1,nlstate*2,1,npar); |
void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
|
| doldm=matrix(1,nlstate*2,1,nlstate*2); |
{
|
| |
int i,j, iter;
|
| fprintf(ficreseij,"# Health expectancies\n"); |
double **xi;
|
| fprintf(ficreseij,"# Age"); |
double fret;
|
| for(i=1; i<=nlstate;i++) |
double fretone; /* Only one call to likelihood */
|
| for(j=1; j<=nlstate;j++) |
/* char filerespow[FILENAMELENGTH];*/
|
| fprintf(ficreseij," %1d-%1d (SE)",i,j); |
xi=matrix(1,npar,1,npar);
|
| fprintf(ficreseij,"\n"); |
for (i=1;i<=npar;i++)
|
| |
for (j=1;j<=npar;j++)
|
| if(estepm < stepm){ |
xi[i][j]=(i==j ? 1.0 : 0.0);
|
| printf ("Problem %d lower than %d\n",estepm, stepm); |
printf("Powell\n"); fprintf(ficlog,"Powell\n");
|
| } |
strcpy(filerespow,"pow");
|
| else hstepm=estepm; |
strcat(filerespow,fileres);
|
| /* We compute the life expectancy from trapezoids spaced every estepm months |
if((ficrespow=fopen(filerespow,"w"))==NULL) {
|
| * This is mainly to measure the difference between two models: for example |
printf("Problem with resultfile: %s\n", filerespow);
|
| * if stepm=24 months pijx are given only every 2 years and by summing them |
fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
|
| * we are calculating an estimate of the Life Expectancy assuming a linear |
}
|
| * progression inbetween and thus overestimating or underestimating according |
fprintf(ficrespow,"# Powell\n# iter -2*LL");
|
| * to the curvature of the survival function. If, for the same date, we |
for (i=1;i<=nlstate;i++)
|
| * estimate the model with stepm=1 month, we can keep estepm to 24 months |
for(j=1;j<=nlstate+ndeath;j++)
|
| * to compare the new estimate of Life expectancy with the same linear |
if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
|
| * hypothesis. A more precise result, taking into account a more precise |
fprintf(ficrespow,"\n");
|
| * curvature will be obtained if estepm is as small as stepm. */ |
|
| |
powell(p,xi,npar,ftol,&iter,&fret,func);
|
| /* For example we decided to compute the life expectancy with the smallest unit */ |
|
| /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. |
free_matrix(xi,1,npar,1,npar);
|
| nhstepm is the number of hstepm from age to agelim |
fclose(ficrespow);
|
| nstepm is the number of stepm from age to agelin. |
printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
|
| Look at hpijx to understand the reason of that which relies in memory size |
fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
|
| and note for a fixed period like estepm months */ |
fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
|
| /* We decided (b) to get a life expectancy respecting the most precise curvature of the |
|
| survival function given by stepm (the optimization length). Unfortunately it |
}
|
| means that if the survival funtion is printed only each two years of age and if |
|
| you sum them up and add 1 year (area under the trapezoids) you won't get the same |
/**** Computes Hessian and covariance matrix ***/
|
| results. So we changed our mind and took the option of the best precision. |
void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
|
| */ |
{
|
| hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ |
double **a,**y,*x,pd;
|
| |
double **hess;
|
| agelim=AGESUP; |
int i, j,jk;
|
| for (age=bage; age<=fage; age ++){ /* If stepm=6 months */ |
int *indx;
|
| /* nhstepm age range expressed in number of stepm */ |
|
| nstepm=(int) rint((agelim-age)*YEARM/stepm); |
double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
|
| /* Typically if 20 years nstepm = 20*12/6=40 stepm */ |
double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
|
| /* if (stepm >= YEARM) hstepm=1;*/ |
void lubksb(double **a, int npar, int *indx, double b[]) ;
|
| nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ |
void ludcmp(double **a, int npar, int *indx, double *d) ;
|
| p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
double gompertz(double p[]);
|
| gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2); |
hess=matrix(1,npar,1,npar);
|
| gp=matrix(0,nhstepm,1,nlstate*2); |
|
| gm=matrix(0,nhstepm,1,nlstate*2); |
printf("\nCalculation of the hessian matrix. Wait...\n");
|
| |
fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
|
| /* Computed by stepm unit matrices, product of hstepm matrices, stored |
for (i=1;i<=npar;i++){
|
| in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */ |
printf("%d",i);fflush(stdout);
|
| hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij); |
fprintf(ficlog,"%d",i);fflush(ficlog);
|
| |
|
| |
hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
|
| hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ |
|
| |
/* printf(" %f ",p[i]);
|
| /* Computing Variances of health expectancies */ |
printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
|
| |
}
|
| for(theta=1; theta <=npar; theta++){ |
|
| for(i=1; i<=npar; i++){ |
for (i=1;i<=npar;i++) {
|
| xp[i] = x[i] + (i==theta ?delti[theta]:0); |
for (j=1;j<=npar;j++) {
|
| } |
if (j>i) {
|
| hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); |
printf(".%d%d",i,j);fflush(stdout);
|
| |
fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
|
| cptj=0; |
hess[i][j]=hessij(p,delti,i,j,func,npar);
|
| for(j=1; j<= nlstate; j++){ |
|
| for(i=1; i<=nlstate; i++){ |
hess[j][i]=hess[i][j];
|
| cptj=cptj+1; |
/*printf(" %lf ",hess[i][j]);*/
|
| for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){ |
}
|
| gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.; |
}
|
| } |
}
|
| } |
printf("\n");
|
| } |
fprintf(ficlog,"\n");
|
| |
|
| |
printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
|
| for(i=1; i<=npar; i++) |
fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
|
| xp[i] = x[i] - (i==theta ?delti[theta]:0); |
|
| hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); |
a=matrix(1,npar,1,npar);
|
| |
y=matrix(1,npar,1,npar);
|
| cptj=0; |
x=vector(1,npar);
|
| for(j=1; j<= nlstate; j++){ |
indx=ivector(1,npar);
|
| for(i=1;i<=nlstate;i++){ |
for (i=1;i<=npar;i++)
|
| cptj=cptj+1; |
for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
|
| for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){ |
ludcmp(a,npar,indx,&pd);
|
| gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.; |
|
| } |
for (j=1;j<=npar;j++) {
|
| } |
for (i=1;i<=npar;i++) x[i]=0;
|
| } |
x[j]=1;
|
| for(j=1; j<= nlstate*2; j++) |
lubksb(a,npar,indx,x);
|
| for(h=0; h<=nhstepm-1; h++){ |
for (i=1;i<=npar;i++){
|
| gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta]; |
matcov[i][j]=x[i];
|
| } |
}
|
| } |
}
|
| |
|
| /* End theta */ |
printf("\n#Hessian matrix#\n");
|
| |
fprintf(ficlog,"\n#Hessian matrix#\n");
|
| trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar); |
for (i=1;i<=npar;i++) {
|
| |
for (j=1;j<=npar;j++) {
|
| for(h=0; h<=nhstepm-1; h++) |
printf("%.3e ",hess[i][j]);
|
| for(j=1; j<=nlstate*2;j++) |
fprintf(ficlog,"%.3e ",hess[i][j]);
|
| for(theta=1; theta <=npar; theta++) |
}
|
| trgradg[h][j][theta]=gradg[h][theta][j]; |
printf("\n");
|
| |
fprintf(ficlog,"\n");
|
| |
}
|
| for(i=1;i<=nlstate*2;i++) |
|
| for(j=1;j<=nlstate*2;j++) |
/* Recompute Inverse */
|
| varhe[i][j][(int)age] =0.; |
for (i=1;i<=npar;i++)
|
| |
for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
|
| printf("%d|",(int)age);fflush(stdout); |
ludcmp(a,npar,indx,&pd);
|
| fprintf(ficlog,"%d|",(int)age);fflush(ficlog); |
|
| for(h=0;h<=nhstepm-1;h++){ |
/* printf("\n#Hessian matrix recomputed#\n");
|
| for(k=0;k<=nhstepm-1;k++){ |
|
| matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov); |
for (j=1;j<=npar;j++) {
|
| matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]); |
for (i=1;i<=npar;i++) x[i]=0;
|
| for(i=1;i<=nlstate*2;i++) |
x[j]=1;
|
| for(j=1;j<=nlstate*2;j++) |
lubksb(a,npar,indx,x);
|
| varhe[i][j][(int)age] += doldm[i][j]*hf*hf; |
for (i=1;i<=npar;i++){
|
| } |
y[i][j]=x[i];
|
| } |
printf("%.3e ",y[i][j]);
|
| /* Computing expectancies */ |
fprintf(ficlog,"%.3e ",y[i][j]);
|
| for(i=1; i<=nlstate;i++) |
}
|
| for(j=1; j<=nlstate;j++) |
printf("\n");
|
| for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){ |
fprintf(ficlog,"\n");
|
| eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf; |
}
|
| |
*/
|
| /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/ |
|
| |
free_matrix(a,1,npar,1,npar);
|
| } |
free_matrix(y,1,npar,1,npar);
|
| |
free_vector(x,1,npar);
|
| fprintf(ficreseij,"%3.0f",age ); |
free_ivector(indx,1,npar);
|
| cptj=0; |
free_matrix(hess,1,npar,1,npar);
|
| for(i=1; i<=nlstate;i++) |
|
| for(j=1; j<=nlstate;j++){ |
|
| cptj++; |
}
|
| fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) ); |
|
| } |
/*************** hessian matrix ****************/
|
| fprintf(ficreseij,"\n"); |
double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
|
| |
{
|
| free_matrix(gm,0,nhstepm,1,nlstate*2); |
int i;
|
| free_matrix(gp,0,nhstepm,1,nlstate*2); |
int l=1, lmax=20;
|
| free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2); |
double k1,k2;
|
| free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar); |
double p2[NPARMAX+1];
|
| free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
double res;
|
| } |
double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
|
| printf("\n"); |
double fx;
|
| fprintf(ficlog,"\n"); |
int k=0,kmax=10;
|
| |
double l1;
|
| free_vector(xp,1,npar); |
|
| free_matrix(dnewm,1,nlstate*2,1,npar); |
fx=func(x);
|
| free_matrix(doldm,1,nlstate*2,1,nlstate*2); |
for (i=1;i<=npar;i++) p2[i]=x[i];
|
| free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage); |
for(l=0 ; l <=lmax; l++){
|
| } |
l1=pow(10,l);
|
| |
delts=delt;
|
| /************ Variance ******************/ |
for(k=1 ; k <kmax; k=k+1){
|
| void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav) |
delt = delta*(l1*k);
|
| { |
p2[theta]=x[theta] +delt;
|
| /* Variance of health expectancies */ |
k1=func(p2)-fx;
|
| /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/ |
p2[theta]=x[theta]-delt;
|
| /* double **newm;*/ |
k2=func(p2)-fx;
|
| double **dnewm,**doldm; |
/*res= (k1-2.0*fx+k2)/delt/delt; */
|
| double **dnewmp,**doldmp; |
res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
|
| int i, j, nhstepm, hstepm, h, nstepm ; |
|
| int k, cptcode; |
#ifdef DEBUG
|
| double *xp; |
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);
|
| double **gp, **gm; /* for var eij */ |
fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
|
| double ***gradg, ***trgradg; /*for var eij */ |
#endif
|
| double **gradgp, **trgradgp; /* for var p point j */ |
/*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
|
| double *gpp, *gmp; /* for var p point j */ |
if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
|
| double **varppt; /* for var p point j nlstate to nlstate+ndeath */ |
k=kmax;
|
| double ***p3mat; |
}
|
| double age,agelim, hf; |
else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
|
| double ***mobaverage; |
k=kmax; l=lmax*10.;
|
| int theta; |
}
|
| char digit[4]; |
else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
|
| char digitp[25]; |
delts=delt;
|
| |
}
|
| char fileresprobmorprev[FILENAMELENGTH]; |
}
|
| |
}
|
| if(popbased==1){ |
delti[theta]=delts;
|
| if(mobilav!=0) |
return res;
|
| strcpy(digitp,"-populbased-mobilav-"); |
|
| else strcpy(digitp,"-populbased-nomobil-"); |
}
|
| } |
|
| else |
double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
|
| strcpy(digitp,"-stablbased-"); |
{
|
| |
int i;
|
| if (mobilav!=0) { |
int l=1, l1, lmax=20;
|
| mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
double k1,k2,k3,k4,res,fx;
|
| if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ |
double p2[NPARMAX+1];
|
| fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); |
int k;
|
| printf(" Error in movingaverage mobilav=%d\n",mobilav); |
|
| } |
fx=func(x);
|
| } |
for (k=1; k<=2; k++) {
|
| |
for (i=1;i<=npar;i++) p2[i]=x[i];
|
| strcpy(fileresprobmorprev,"prmorprev"); |
p2[thetai]=x[thetai]+delti[thetai]/k;
|
| sprintf(digit,"%-d",ij); |
p2[thetaj]=x[thetaj]+delti[thetaj]/k;
|
| /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/ |
k1=func(p2)-fx;
|
| strcat(fileresprobmorprev,digit); /* Tvar to be done */ |
|
| strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */ |
p2[thetai]=x[thetai]+delti[thetai]/k;
|
| strcat(fileresprobmorprev,fileres); |
p2[thetaj]=x[thetaj]-delti[thetaj]/k;
|
| if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) { |
k2=func(p2)-fx;
|
| printf("Problem with resultfile: %s\n", fileresprobmorprev); |
|
| fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev); |
p2[thetai]=x[thetai]-delti[thetai]/k;
|
| } |
p2[thetaj]=x[thetaj]+delti[thetaj]/k;
|
| printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); |
k3=func(p2)-fx;
|
| fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); |
|
| fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n"); |
p2[thetai]=x[thetai]-delti[thetai]/k;
|
| fprintf(ficresprobmorprev,"# Age cov=%-d",ij); |
p2[thetaj]=x[thetaj]-delti[thetaj]/k;
|
| for(j=nlstate+1; j<=(nlstate+ndeath);j++){ |
k4=func(p2)-fx;
|
| fprintf(ficresprobmorprev," p.%-d SE",j); |
res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
|
| for(i=1; i<=nlstate;i++) |
#ifdef DEBUG
|
| fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j); |
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);
|
| } |
fprintf(ficlog,"%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);
|
| fprintf(ficresprobmorprev,"\n"); |
#endif
|
| if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { |
}
|
| printf("Problem with gnuplot file: %s\n", optionfilegnuplot); |
return res;
|
| fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot); |
}
|
| exit(0); |
|
| } |
/************** Inverse of matrix **************/
|
| else{ |
void ludcmp(double **a, int n, int *indx, double *d)
|
| fprintf(ficgp,"\n# Routine varevsij"); |
{
|
| } |
int i,imax,j,k;
|
| if((fichtm=fopen(optionfilehtm,"a"))==NULL) { |
double big,dum,sum,temp;
|
| printf("Problem with html file: %s\n", optionfilehtm); |
double *vv;
|
| fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm); |
|
| exit(0); |
vv=vector(1,n);
|
| } |
*d=1.0;
|
| else{ |
for (i=1;i<=n;i++) {
|
| fprintf(fichtm,"\n<li><h4> Computing probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n"); |
big=0.0;
|
| fprintf(fichtm,"\n<br>%s (à revoir) <br>\n",digitp); |
for (j=1;j<=n;j++)
|
| } |
if ((temp=fabs(a[i][j])) > big) big=temp;
|
| varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); |
if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
|
| |
vv[i]=1.0/big;
|
| 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"); |
for (j=1;j<=n;j++) {
|
| for(i=1; i<=nlstate;i++) |
for (i=1;i<j;i++) {
|
| for(j=1; j<=nlstate;j++) |
sum=a[i][j];
|
| fprintf(ficresvij," Cov(e%1d, e%1d)",i,j); |
for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
|
| fprintf(ficresvij,"\n"); |
a[i][j]=sum;
|
| |
}
|
| xp=vector(1,npar); |
big=0.0;
|
| dnewm=matrix(1,nlstate,1,npar); |
for (i=j;i<=n;i++) {
|
| doldm=matrix(1,nlstate,1,nlstate); |
sum=a[i][j];
|
| dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar); |
for (k=1;k<j;k++)
|
| doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); |
sum -= a[i][k]*a[k][j];
|
| |
a[i][j]=sum;
|
| gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath); |
if ( (dum=vv[i]*fabs(sum)) >= big) {
|
| gpp=vector(nlstate+1,nlstate+ndeath); |
big=dum;
|
| gmp=vector(nlstate+1,nlstate+ndeath); |
imax=i;
|
| trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/ |
}
|
| |
}
|
| if(estepm < stepm){ |
if (j != imax) {
|
| printf ("Problem %d lower than %d\n",estepm, stepm); |
for (k=1;k<=n;k++) {
|
| } |
dum=a[imax][k];
|
| else hstepm=estepm; |
a[imax][k]=a[j][k];
|
| /* For example we decided to compute the life expectancy with the smallest unit */ |
a[j][k]=dum;
|
| /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. |
}
|
| nhstepm is the number of hstepm from age to agelim |
*d = -(*d);
|
| nstepm is the number of stepm from age to agelin. |
vv[imax]=vv[j];
|
| Look at hpijx to understand the reason of that which relies in memory size |
}
|
| and note for a fixed period like k years */ |
indx[j]=imax;
|
| /* We decided (b) to get a life expectancy respecting the most precise curvature of the |
if (a[j][j] == 0.0) a[j][j]=TINY;
|
| survival function given by stepm (the optimization length). Unfortunately it |
if (j != n) {
|
| means that if the survival funtion is printed only each two years of age and if |
dum=1.0/(a[j][j]);
|
| you sum them up and add 1 year (area under the trapezoids) you won't get the same |
for (i=j+1;i<=n;i++) a[i][j] *= dum;
|
| results. So we changed our mind and took the option of the best precision. |
}
|
| */ |
}
|
| hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ |
free_vector(vv,1,n); /* Doesn't work */
|
| agelim = AGESUP; |
;
|
| for (age=bage; age<=fage; age ++){ /* If stepm=6 months */ |
}
|
| nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ |
|
| nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ |
void lubksb(double **a, int n, int *indx, double b[])
|
| p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
{
|
| gradg=ma3x(0,nhstepm,1,npar,1,nlstate); |
int i,ii=0,ip,j;
|
| gp=matrix(0,nhstepm,1,nlstate); |
double sum;
|
| gm=matrix(0,nhstepm,1,nlstate); |
|
| |
for (i=1;i<=n;i++) {
|
| |
ip=indx[i];
|
| for(theta=1; theta <=npar; theta++){ |
sum=b[ip];
|
| for(i=1; i<=npar; i++){ /* Computes gradient */ |
b[ip]=b[i];
|
| xp[i] = x[i] + (i==theta ?delti[theta]:0); |
if (ii)
|
| } |
for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
|
| hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); |
else if (sum) ii=i;
|
| prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); |
b[i]=sum;
|
| |
}
|
| if (popbased==1) { |
for (i=n;i>=1;i--) {
|
| if(mobilav ==0){ |
sum=b[i];
|
| for(i=1; i<=nlstate;i++) |
for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
|
| prlim[i][i]=probs[(int)age][i][ij]; |
b[i]=sum/a[i][i];
|
| }else{ /* mobilav */ |
}
|
| for(i=1; i<=nlstate;i++) |
}
|
| prlim[i][i]=mobaverage[(int)age][i][ij]; |
|
| } |
void pstamp(FILE *fichier)
|
| } |
{
|
| |
fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
|
| for(j=1; j<= nlstate; j++){ |
}
|
| for(h=0; h<=nhstepm; h++){ |
|
| for(i=1, gp[h][j]=0.;i<=nlstate;i++) |
/************ Frequencies ********************/
|
| gp[h][j] += prlim[i][i]*p3mat[i][j][h]; |
void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
|
| } |
{ /* Some frequencies */
|
| } |
|
| /* This for computing forces of mortality (h=1)as a weighted average */ |
int i, m, jk, k1,i1, j1, bool, z1,z2,j;
|
| for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){ |
int first;
|
| for(i=1; i<= nlstate; i++) |
double ***freq; /* Frequencies */
|
| gpp[j] += prlim[i][i]*p3mat[i][j][1]; |
double *pp, **prop;
|
| } |
double pos,posprop, k2, dateintsum=0,k2cpt=0;
|
| /* end force of mortality */ |
char fileresp[FILENAMELENGTH];
|
| |
|
| for(i=1; i<=npar; i++) /* Computes gradient */ |
pp=vector(1,nlstate);
|
| xp[i] = x[i] - (i==theta ?delti[theta]:0); |
prop=matrix(1,nlstate,iagemin,iagemax+3);
|
| hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); |
strcpy(fileresp,"p");
|
| prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); |
strcat(fileresp,fileres);
|
| |
if((ficresp=fopen(fileresp,"w"))==NULL) {
|
| if (popbased==1) { |
printf("Problem with prevalence resultfile: %s\n", fileresp);
|
| if(mobilav ==0){ |
fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
|
| for(i=1; i<=nlstate;i++) |
exit(0);
|
| prlim[i][i]=probs[(int)age][i][ij]; |
}
|
| }else{ /* mobilav */ |
freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
|
| for(i=1; i<=nlstate;i++) |
j1=0;
|
| prlim[i][i]=mobaverage[(int)age][i][ij]; |
|
| } |
j=cptcoveff;
|
| } |
if (cptcovn<1) {j=1;ncodemax[1]=1;}
|
| |
|
| for(j=1; j<= nlstate; j++){ |
first=1;
|
| for(h=0; h<=nhstepm; h++){ |
|
| for(i=1, gm[h][j]=0.;i<=nlstate;i++) |
for(k1=1; k1<=j;k1++){
|
| gm[h][j] += prlim[i][i]*p3mat[i][j][h]; |
for(i1=1; i1<=ncodemax[k1];i1++){
|
| } |
j1++;
|
| } |
/*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
|
| /* This for computing force of mortality (h=1)as a weighted average */ |
scanf("%d", i);*/
|
| for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){ |
for (i=-5; i<=nlstate+ndeath; i++)
|
| for(i=1; i<= nlstate; i++) |
for (jk=-5; jk<=nlstate+ndeath; jk++)
|
| gmp[j] += prlim[i][i]*p3mat[i][j][1]; |
for(m=iagemin; m <= iagemax+3; m++)
|
| } |
freq[i][jk][m]=0;
|
| /* end force of mortality */ |
|
| |
for (i=1; i<=nlstate; i++)
|
| for(j=1; j<= nlstate; j++) /* vareij */ |
for(m=iagemin; m <= iagemax+3; m++)
|
| for(h=0; h<=nhstepm; h++){ |
prop[i][m]=0;
|
| gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta]; |
|
| } |
dateintsum=0;
|
| for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */ |
k2cpt=0;
|
| gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta]; |
for (i=1; i<=imx; i++) {
|
| } |
bool=1;
|
| |
if (cptcovn>0) {
|
| } /* End theta */ |
for (z1=1; z1<=cptcoveff; z1++)
|
| |
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
|
| trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */ |
bool=0;
|
| |
}
|
| for(h=0; h<=nhstepm; h++) /* veij */ |
if (bool==1){
|
| for(j=1; j<=nlstate;j++) |
for(m=firstpass; m<=lastpass; m++){
|
| for(theta=1; theta <=npar; theta++) |
k2=anint[m][i]+(mint[m][i]/12.);
|
| trgradg[h][j][theta]=gradg[h][theta][j]; |
/*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
|
| |
if(agev[m][i]==0) agev[m][i]=iagemax+1;
|
| for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */ |
if(agev[m][i]==1) agev[m][i]=iagemax+2;
|
| for(theta=1; theta <=npar; theta++) |
if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
|
| trgradgp[j][theta]=gradgp[theta][j]; |
if (m<lastpass) {
|
| |
freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
|
| hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ |
freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
|
| for(i=1;i<=nlstate;i++) |
}
|
| for(j=1;j<=nlstate;j++) |
|
| vareij[i][j][(int)age] =0.; |
if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
|
| |
dateintsum=dateintsum+k2;
|
| for(h=0;h<=nhstepm;h++){ |
k2cpt++;
|
| 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]); |
}
|
| for(i=1;i<=nlstate;i++) |
}
|
| for(j=1;j<=nlstate;j++) |
}
|
| vareij[i][j][(int)age] += doldm[i][j]*hf*hf; |
|
| } |
/* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
|
| } |
pstamp(ficresp);
|
| |
if (cptcovn>0) {
|
| /* pptj */ |
fprintf(ficresp, "\n#********** Variable ");
|
| matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
|
| matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp); |
fprintf(ficresp, "**********\n#");
|
| for(j=nlstate+1;j<=nlstate+ndeath;j++) |
}
|
| for(i=nlstate+1;i<=nlstate+ndeath;i++) |
for(i=1; i<=nlstate;i++)
|
| varppt[j][i]=doldmp[j][i]; |
fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
|
| /* end ppptj */ |
fprintf(ficresp, "\n");
|
| hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij); |
|
| prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij); |
for(i=iagemin; i <= iagemax+3; i++){
|
| |
if(i==iagemax+3){
|
| if (popbased==1) { |
fprintf(ficlog,"Total");
|
| if(mobilav ==0){ |
}else{
|
| for(i=1; i<=nlstate;i++) |
if(first==1){
|
| prlim[i][i]=probs[(int)age][i][ij]; |
first=0;
|
| }else{ /* mobilav */ |
printf("See log file for details...\n");
|
| for(i=1; i<=nlstate;i++) |
}
|
| prlim[i][i]=mobaverage[(int)age][i][ij]; |
fprintf(ficlog,"Age %d", i);
|
| } |
}
|
| } |
for(jk=1; jk <=nlstate ; jk++){
|
| |
for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
|
| /* This for computing force of mortality (h=1)as a weighted average */ |
pp[jk] += freq[jk][m][i];
|
| for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){ |
}
|
| for(i=1; i<= nlstate; i++) |
for(jk=1; jk <=nlstate ; jk++){
|
| gmp[j] += prlim[i][i]*p3mat[i][j][1]; |
for(m=-1, pos=0; m <=0 ; m++)
|
| } |
pos += freq[jk][m][i];
|
| /* end force of mortality */ |
if(pp[jk]>=1.e-10){
|
| |
if(first==1){
|
| fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij); |
printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
|
| for(j=nlstate+1; j<=(nlstate+ndeath);j++){ |
}
|
| fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j])); |
fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
|
| for(i=1; i<=nlstate;i++){ |
}else{
|
| fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]); |
if(first==1)
|
| } |
printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
|
| } |
fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
|
| fprintf(ficresprobmorprev,"\n"); |
}
|
| |
}
|
| fprintf(ficresvij,"%.0f ",age ); |
|
| for(i=1; i<=nlstate;i++) |
for(jk=1; jk <=nlstate ; jk++){
|
| for(j=1; j<=nlstate;j++){ |
for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
|
| fprintf(ficresvij," %.4f", vareij[i][j][(int)age]); |
pp[jk] += freq[jk][m][i];
|
| } |
}
|
| fprintf(ficresvij,"\n"); |
for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
|
| free_matrix(gp,0,nhstepm,1,nlstate); |
pos += pp[jk];
|
| free_matrix(gm,0,nhstepm,1,nlstate); |
posprop += prop[jk][i];
|
| free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate); |
}
|
| free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar); |
for(jk=1; jk <=nlstate ; jk++){
|
| free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
if(pos>=1.e-5){
|
| } /* End age */ |
if(first==1)
|
| free_vector(gpp,nlstate+1,nlstate+ndeath); |
printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
|
| free_vector(gmp,nlstate+1,nlstate+ndeath); |
fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
|
| free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath); |
}else{
|
| free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/ |
if(first==1)
|
| fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65"); |
printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
|
| /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */ |
fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
|
| fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";"); |
}
|
| fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); |
if( i <= iagemax){
|
| fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); |
if(pos>=1.e-5){
|
| fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); |
fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
|
| fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev); |
/*probs[i][jk][j1]= pp[jk]/pos;*/
|
| fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit); |
/*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
|
| /* fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit); |
}
|
| */ |
else
|
| fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit); |
fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
|
| |
}
|
| free_vector(xp,1,npar); |
}
|
| free_matrix(doldm,1,nlstate,1,nlstate); |
|
| free_matrix(dnewm,1,nlstate,1,npar); |
for(jk=-1; jk <=nlstate+ndeath; jk++)
|
| free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); |
for(m=-1; m <=nlstate+ndeath; m++)
|
| free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar); |
if(freq[jk][m][i] !=0 ) {
|
| free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); |
if(first==1)
|
| if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
|
| fclose(ficresprobmorprev); |
fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
|
| fclose(ficgp); |
}
|
| fclose(fichtm); |
if(i <= iagemax)
|
| } |
fprintf(ficresp,"\n");
|
| |
if(first==1)
|
| /************ Variance of prevlim ******************/ |
printf("Others in log...\n");
|
| 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) |
fprintf(ficlog,"\n");
|
| { |
}
|
| /* Variance of prevalence limit */ |
}
|
| /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/ |
}
|
| double **newm; |
dateintmean=dateintsum/k2cpt;
|
| double **dnewm,**doldm; |
|
| int i, j, nhstepm, hstepm; |
fclose(ficresp);
|
| int k, cptcode; |
free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
|
| double *xp; |
free_vector(pp,1,nlstate);
|
| double *gp, *gm; |
free_matrix(prop,1,nlstate,iagemin, iagemax+3);
|
| double **gradg, **trgradg; |
/* End of Freq */
|
| double age,agelim; |
}
|
| int theta; |
|
| |
/************ Prevalence ********************/
|
| fprintf(ficresvpl,"# Standard deviation of stable prevalences \n"); |
void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
|
| fprintf(ficresvpl,"# Age"); |
{
|
| for(i=1; i<=nlstate;i++) |
/* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
|
| fprintf(ficresvpl," %1d-%1d",i,i); |
in each health status at the date of interview (if between dateprev1 and dateprev2).
|
| fprintf(ficresvpl,"\n"); |
We still use firstpass and lastpass as another selection.
|
| |
*/
|
| xp=vector(1,npar); |
|
| dnewm=matrix(1,nlstate,1,npar); |
int i, m, jk, k1, i1, j1, bool, z1,z2,j;
|
| doldm=matrix(1,nlstate,1,nlstate); |
double ***freq; /* Frequencies */
|
| |
double *pp, **prop;
|
| hstepm=1*YEARM; /* Every year of age */ |
double pos,posprop;
|
| hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ |
double y2; /* in fractional years */
|
| agelim = AGESUP; |
int iagemin, iagemax;
|
| for (age=bage; age<=fage; age ++){ /* If stepm=6 months */ |
|
| nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ |
iagemin= (int) agemin;
|
| if (stepm >= YEARM) hstepm=1; |
iagemax= (int) agemax;
|
| nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */ |
/*pp=vector(1,nlstate);*/
|
| gradg=matrix(1,npar,1,nlstate); |
prop=matrix(1,nlstate,iagemin,iagemax+3);
|
| gp=vector(1,nlstate); |
/* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
|
| gm=vector(1,nlstate); |
j1=0;
|
| |
|
| for(theta=1; theta <=npar; theta++){ |
j=cptcoveff;
|
| for(i=1; i<=npar; i++){ /* Computes gradient */ |
if (cptcovn<1) {j=1;ncodemax[1]=1;}
|
| xp[i] = x[i] + (i==theta ?delti[theta]:0); |
|
| } |
for(k1=1; k1<=j;k1++){
|
| prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); |
for(i1=1; i1<=ncodemax[k1];i1++){
|
| for(i=1;i<=nlstate;i++) |
j1++;
|
| gp[i] = prlim[i][i]; |
|
| |
for (i=1; i<=nlstate; i++)
|
| for(i=1; i<=npar; i++) /* Computes gradient */ |
for(m=iagemin; m <= iagemax+3; m++)
|
| xp[i] = x[i] - (i==theta ?delti[theta]:0); |
prop[i][m]=0.0;
|
| prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); |
|
| for(i=1;i<=nlstate;i++) |
for (i=1; i<=imx; i++) { /* Each individual */
|
| gm[i] = prlim[i][i]; |
bool=1;
|
| |
if (cptcovn>0) {
|
| for(i=1;i<=nlstate;i++) |
for (z1=1; z1<=cptcoveff; z1++)
|
| gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta]; |
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
|
| } /* End theta */ |
bool=0;
|
| |
}
|
| trgradg =matrix(1,nlstate,1,npar); |
if (bool==1) {
|
| |
for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
|
| for(j=1; j<=nlstate;j++) |
y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
|
| for(theta=1; theta <=npar; theta++) |
if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
|
| trgradg[j][theta]=gradg[theta][j]; |
if(agev[m][i]==0) agev[m][i]=iagemax+1;
|
| |
if(agev[m][i]==1) agev[m][i]=iagemax+2;
|
| for(i=1;i<=nlstate;i++) |
if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m);
|
| varpl[i][(int)age] =0.; |
if (s[m][i]>0 && s[m][i]<=nlstate) {
|
| matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov); |
/*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
|
| matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg); |
prop[s[m][i]][(int)agev[m][i]] += weight[i];
|
| for(i=1;i<=nlstate;i++) |
prop[s[m][i]][iagemax+3] += weight[i];
|
| varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */ |
}
|
| |
}
|
| fprintf(ficresvpl,"%.0f ",age ); |
} /* end selection of waves */
|
| for(i=1; i<=nlstate;i++) |
}
|
| fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age])); |
}
|
| fprintf(ficresvpl,"\n"); |
for(i=iagemin; i <= iagemax+3; i++){
|
| free_vector(gp,1,nlstate); |
|
| free_vector(gm,1,nlstate); |
for(jk=1,posprop=0; jk <=nlstate ; jk++) {
|
| free_matrix(gradg,1,npar,1,nlstate); |
posprop += prop[jk][i];
|
| free_matrix(trgradg,1,nlstate,1,npar); |
}
|
| } /* End age */ |
|
| |
for(jk=1; jk <=nlstate ; jk++){
|
| free_vector(xp,1,npar); |
if( i <= iagemax){
|
| free_matrix(doldm,1,nlstate,1,npar); |
if(posprop>=1.e-5){
|
| free_matrix(dnewm,1,nlstate,1,nlstate); |
probs[i][jk][j1]= prop[jk][i]/posprop;
|
| |
}
|
| } |
}
|
| |
}/* end jk */
|
| /************ Variance of one-step probabilities ******************/ |
}/* end i */
|
| void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax) |
} /* end i1 */
|
| { |
} /* end k1 */
|
| int i, j=0, i1, k1, l1, t, tj; |
|
| int k2, l2, j1, z1; |
/* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
|
| int k=0,l, cptcode; |
/*free_vector(pp,1,nlstate);*/
|
| int first=1, first1; |
free_matrix(prop,1,nlstate, iagemin,iagemax+3);
|
| double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp; |
} /* End of prevalence */
|
| double **dnewm,**doldm; |
|
| double *xp; |
/************* Waves Concatenation ***************/
|
| double *gp, *gm; |
|
| double **gradg, **trgradg; |
void concatwav(int wav[], int **dh, int **bh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)
|
| double **mu; |
{
|
| double age,agelim, cov[NCOVMAX]; |
/* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
|
| double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */ |
Death is a valid wave (if date is known).
|
| int theta; |
mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
|
| char fileresprob[FILENAMELENGTH]; |
dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
|
| char fileresprobcov[FILENAMELENGTH]; |
and mw[mi+1][i]. dh depends on stepm.
|
| char fileresprobcor[FILENAMELENGTH]; |
*/
|
| |
|
| double ***varpij; |
int i, mi, m;
|
| |
/* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
|
| strcpy(fileresprob,"prob"); |
double sum=0., jmean=0.;*/
|
| strcat(fileresprob,fileres); |
int first;
|
| if((ficresprob=fopen(fileresprob,"w"))==NULL) { |
int j, k=0,jk, ju, jl;
|
| printf("Problem with resultfile: %s\n", fileresprob); |
double sum=0.;
|
| fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob); |
first=0;
|
| } |
jmin=1e+5;
|
| strcpy(fileresprobcov,"probcov"); |
jmax=-1;
|
| strcat(fileresprobcov,fileres); |
jmean=0.;
|
| if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) { |
for(i=1; i<=imx; i++){
|
| printf("Problem with resultfile: %s\n", fileresprobcov); |
mi=0;
|
| fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov); |
m=firstpass;
|
| } |
while(s[m][i] <= nlstate){
|
| strcpy(fileresprobcor,"probcor"); |
if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
|
| strcat(fileresprobcor,fileres); |
mw[++mi][i]=m;
|
| if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) { |
if(m >=lastpass)
|
| printf("Problem with resultfile: %s\n", fileresprobcor); |
break;
|
| fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor); |
else
|
| } |
m++;
|
| printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob); |
}/* end while */
|
| fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob); |
if (s[m][i] > nlstate){
|
| printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov); |
mi++; /* Death is another wave */
|
| fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov); |
/* if(mi==0) never been interviewed correctly before death */
|
| printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); |
/* Only death is a correct wave */
|
| fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); |
mw[mi][i]=m;
|
| |
}
|
| fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n"); |
|
| fprintf(ficresprob,"# Age"); |
wav[i]=mi;
|
| fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n"); |
if(mi==0){
|
| fprintf(ficresprobcov,"# Age"); |
nbwarn++;
|
| fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n"); |
if(first==0){
|
| fprintf(ficresprobcov,"# Age"); |
printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
|
| |
first=1;
|
| |
}
|
| for(i=1; i<=nlstate;i++) |
if(first==1){
|
| for(j=1; j<=(nlstate+ndeath);j++){ |
fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
|
| fprintf(ficresprob," p%1d-%1d (SE)",i,j); |
}
|
| fprintf(ficresprobcov," p%1d-%1d ",i,j); |
} /* end mi==0 */
|
| fprintf(ficresprobcor," p%1d-%1d ",i,j); |
} /* End individuals */
|
| } |
|
| fprintf(ficresprob,"\n"); |
for(i=1; i<=imx; i++){
|
| fprintf(ficresprobcov,"\n"); |
for(mi=1; mi<wav[i];mi++){
|
| fprintf(ficresprobcor,"\n"); |
if (stepm <=0)
|
| xp=vector(1,npar); |
dh[mi][i]=1;
|
| dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); |
else{
|
| doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath)); |
if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
|
| mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage); |
if (agedc[i] < 2*AGESUP) {
|
| varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage); |
j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
|
| first=1; |
if(j==0) j=1; /* Survives at least one month after exam */
|
| if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { |
else if(j<0){
|
| printf("Problem with gnuplot file: %s\n", optionfilegnuplot); |
nberr++;
|
| fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot); |
printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
|
| exit(0); |
j=1; /* Temporary Dangerous patch */
|
| } |
printf(" We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
|
| else{ |
fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
|
| fprintf(ficgp,"\n# Routine varprob"); |
fprintf(ficlog," We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
|
| } |
}
|
| if((fichtm=fopen(optionfilehtm,"a"))==NULL) { |
k=k+1;
|
| printf("Problem with html file: %s\n", optionfilehtm); |
if (j >= jmax){
|
| fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm); |
jmax=j;
|
| exit(0); |
ijmax=i;
|
| } |
}
|
| else{ |
if (j <= jmin){
|
| fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n"); |
jmin=j;
|
| fprintf(fichtm,"\n"); |
ijmin=i;
|
| |
}
|
| fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n"); |
sum=sum+j;
|
| 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"); |
/*if (j<0) printf("j=%d num=%d \n",j,i);*/
|
| 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"); |
/* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
|
| |
}
|
| } |
}
|
| |
else{
|
| cov[1]=1; |
j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
|
| tj=cptcoveff; |
/* if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
|
| if (cptcovn<1) {tj=1;ncodemax[1]=1;} |
|
| j1=0; |
k=k+1;
|
| for(t=1; t<=tj;t++){ |
if (j >= jmax) {
|
| for(i1=1; i1<=ncodemax[t];i1++){ |
jmax=j;
|
| j1++; |
ijmax=i;
|
| if (cptcovn>0) { |
}
|
| fprintf(ficresprob, "\n#********** Variable "); |
else if (j <= jmin){
|
| for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); |
jmin=j;
|
| fprintf(ficresprob, "**********\n#"); |
ijmin=i;
|
| fprintf(ficresprobcov, "\n#********** Variable "); |
}
|
| for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); |
/* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
|
| fprintf(ficresprobcov, "**********\n#"); |
/*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
|
| |
if(j<0){
|
| fprintf(ficgp, "\n#********** Variable "); |
nberr++;
|
| for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); |
printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
|
| fprintf(ficgp, "**********\n#"); |
fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
|
| |
}
|
| |
sum=sum+j;
|
| fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable "); |
}
|
| for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); |
jk= j/stepm;
|
| fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">"); |
jl= j -jk*stepm;
|
| |
ju= j -(jk+1)*stepm;
|
| fprintf(ficresprobcor, "\n#********** Variable "); |
if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
|
| for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); |
if(jl==0){
|
| fprintf(ficgp, "**********\n#"); |
dh[mi][i]=jk;
|
| } |
bh[mi][i]=0;
|
| |
}else{ /* We want a negative bias in order to only have interpolation ie
|
| for (age=bage; age<=fage; age ++){ |
* at the price of an extra matrix product in likelihood */
|
| cov[2]=age; |
dh[mi][i]=jk+1;
|
| for (k=1; k<=cptcovn;k++) { |
bh[mi][i]=ju;
|
| cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]]; |
}
|
| } |
}else{
|
| for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; |
if(jl <= -ju){
|
| for (k=1; k<=cptcovprod;k++) |
dh[mi][i]=jk;
|
| cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; |
bh[mi][i]=jl; /* bias is positive if real duration
|
| |
* is higher than the multiple of stepm and negative otherwise.
|
| gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath)); |
*/
|
| trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); |
}
|
| gp=vector(1,(nlstate)*(nlstate+ndeath)); |
else{
|
| gm=vector(1,(nlstate)*(nlstate+ndeath)); |
dh[mi][i]=jk+1;
|
| |
bh[mi][i]=ju;
|
| for(theta=1; theta <=npar; theta++){ |
}
|
| for(i=1; i<=npar; i++) |
if(dh[mi][i]==0){
|
| xp[i] = x[i] + (i==theta ?delti[theta]:0); |
dh[mi][i]=1; /* At least one step */
|
| |
bh[mi][i]=ju; /* At least one step */
|
| pmij(pmmij,cov,ncovmodel,xp,nlstate); |
/* printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
|
| |
}
|
| k=0; |
} /* end if mle */
|
| for(i=1; i<= (nlstate); i++){ |
}
|
| for(j=1; j<=(nlstate+ndeath);j++){ |
} /* end wave */
|
| k=k+1; |
}
|
| gp[k]=pmmij[i][j]; |
jmean=sum/k;
|
| } |
printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
|
| } |
fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
|
| |
}
|
| for(i=1; i<=npar; i++) |
|
| xp[i] = x[i] - (i==theta ?delti[theta]:0); |
/*********** Tricode ****************************/
|
| |
void tricode(int *Tvar, int **nbcode, int imx)
|
| pmij(pmmij,cov,ncovmodel,xp,nlstate); |
{
|
| k=0; |
|
| for(i=1; i<=(nlstate); i++){ |
int Ndum[20],ij=1, k, j, i, maxncov=19;
|
| for(j=1; j<=(nlstate+ndeath);j++){ |
int cptcode=0;
|
| k=k+1; |
cptcoveff=0;
|
| gm[k]=pmmij[i][j]; |
|
| } |
for (k=0; k<maxncov; k++) Ndum[k]=0;
|
| } |
for (k=1; k<=7; k++) ncodemax[k]=0;
|
| |
|
| for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) |
for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
|
| gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta]; |
for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
|
| } |
modality*/
|
| |
ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
|
| for(j=1; j<=(nlstate)*(nlstate+ndeath);j++) |
Ndum[ij]++; /*store the modality */
|
| for(theta=1; theta <=npar; theta++) |
/*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
|
| trgradg[j][theta]=gradg[theta][j]; |
if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
|
| |
Tvar[j]. If V=sex and male is 0 and
|
| matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); |
female is 1, then cptcode=1.*/
|
| matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg); |
}
|
| free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath)); |
|
| free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath)); |
for (i=0; i<=cptcode; i++) {
|
| free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); |
if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
|
| free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); |
}
|
| |
|
| pmij(pmmij,cov,ncovmodel,x,nlstate); |
ij=1;
|
| |
for (i=1; i<=ncodemax[j]; i++) {
|
| k=0; |
for (k=0; k<= maxncov; k++) {
|
| for(i=1; i<=(nlstate); i++){ |
if (Ndum[k] != 0) {
|
| for(j=1; j<=(nlstate+ndeath);j++){ |
nbcode[Tvar[j]][ij]=k;
|
| k=k+1; |
/* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
|
| mu[k][(int) age]=pmmij[i][j]; |
|
| } |
ij++;
|
| } |
}
|
| for(i=1;i<=(nlstate)*(nlstate+ndeath);i++) |
if (ij > ncodemax[j]) break;
|
| for(j=1;j<=(nlstate)*(nlstate+ndeath);j++) |
}
|
| varpij[i][j][(int)age] = doldm[i][j]; |
}
|
| |
}
|
| /*printf("\n%d ",(int)age); |
|
| for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){ |
for (k=0; k< maxncov; k++) Ndum[k]=0;
|
| printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i])); |
|
| fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i])); |
for (i=1; i<=ncovmodel-2; i++) {
|
| }*/ |
/* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
|
| |
ij=Tvar[i];
|
| fprintf(ficresprob,"\n%d ",(int)age); |
Ndum[ij]++;
|
| fprintf(ficresprobcov,"\n%d ",(int)age); |
}
|
| fprintf(ficresprobcor,"\n%d ",(int)age); |
|
| |
ij=1;
|
| for (i=1; i<=(nlstate)*(nlstate+ndeath);i++) |
for (i=1; i<= maxncov; i++) {
|
| fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age])); |
if((Ndum[i]!=0) && (i<=ncovcol)){
|
| for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){ |
Tvaraff[ij]=i; /*For printing */
|
| fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]); |
ij++;
|
| fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]); |
}
|
| } |
}
|
| i=0; |
|
| for (k=1; k<=(nlstate);k++){ |
cptcoveff=ij-1; /*Number of simple covariates*/
|
| for (l=1; l<=(nlstate+ndeath);l++){ |
}
|
| i=i++; |
|
| fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l); |
/*********** Health Expectancies ****************/
|
| fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l); |
|
| for (j=1; j<=i;j++){ |
void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
|
| 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])); |
{
|
| } |
/* Health expectancies, no variances */
|
| } |
int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
|
| }/* end of loop for state */ |
double age, agelim, hf;
|
| } /* end of loop for age */ |
double ***p3mat;
|
| |
double eip;
|
| /* Confidence intervalle of pij */ |
|
| /* |
pstamp(ficreseij);
|
| fprintf(ficgp,"\nset noparametric;unset label"); |
fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
|
| fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\""); |
fprintf(ficreseij,"# Age");
|
| fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65"); |
for(i=1; i<=nlstate;i++){
|
| fprintf(fichtm,"\n<br>Probability with confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname); |
for(j=1; j<=nlstate;j++){
|
| fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname); |
fprintf(ficreseij," e%1d%1d ",i,j);
|
| fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname); |
}
|
| fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob); |
fprintf(ficreseij," e%1d. ",i);
|
| */ |
}
|
| |
fprintf(ficreseij,"\n");
|
| /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/ |
|
| first1=1; |
|
| for (k2=1; k2<=(nlstate);k2++){ |
if(estepm < stepm){
|
| for (l2=1; l2<=(nlstate+ndeath);l2++){ |
printf ("Problem %d lower than %d\n",estepm, stepm);
|
| if(l2==k2) continue; |
}
|
| j=(k2-1)*(nlstate+ndeath)+l2; |
else hstepm=estepm;
|
| for (k1=1; k1<=(nlstate);k1++){ |
/* We compute the life expectancy from trapezoids spaced every estepm months
|
| for (l1=1; l1<=(nlstate+ndeath);l1++){ |
* This is mainly to measure the difference between two models: for example
|
| if(l1==k1) continue; |
* if stepm=24 months pijx are given only every 2 years and by summing them
|
| i=(k1-1)*(nlstate+ndeath)+l1; |
* we are calculating an estimate of the Life Expectancy assuming a linear
|
| if(i<=j) continue; |
* progression in between and thus overestimating or underestimating according
|
| for (age=bage; age<=fage; age ++){ |
* to the curvature of the survival function. If, for the same date, we
|
| if ((int)age %5==0){ |
* estimate the model with stepm=1 month, we can keep estepm to 24 months
|
| v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM; |
* to compare the new estimate of Life expectancy with the same linear
|
| v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM; |
* hypothesis. A more precise result, taking into account a more precise
|
| cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM; |
* curvature will be obtained if estepm is as small as stepm. */
|
| mu1=mu[i][(int) age]/stepm*YEARM ; |
|
| mu2=mu[j][(int) age]/stepm*YEARM; |
/* For example we decided to compute the life expectancy with the smallest unit */
|
| c12=cv12/sqrt(v1*v2); |
/* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
|
| /* Computing eigen value of matrix of covariance */ |
nhstepm is the number of hstepm from age to agelim
|
| lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; |
nstepm is the number of stepm from age to agelin.
|
| lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; |
Look at hpijx to understand the reason of that which relies in memory size
|
| /* Eigen vectors */ |
and note for a fixed period like estepm months */
|
| v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12)); |
/* We decided (b) to get a life expectancy respecting the most precise curvature of the
|
| /*v21=sqrt(1.-v11*v11); *//* error */ |
survival function given by stepm (the optimization length). Unfortunately it
|
| v21=(lc1-v1)/cv12*v11; |
means that if the survival funtion is printed only each two years of age and if
|
| v12=-v21; |
you sum them up and add 1 year (area under the trapezoids) you won't get the same
|
| v22=v11; |
results. So we changed our mind and took the option of the best precision.
|
| tnalp=v21/v11; |
*/
|
| if(first1==1){ |
hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
|
| first1=0; |
|
| printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp); |
agelim=AGESUP;
|
| } |
/* If stepm=6 months */
|
| fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp); |
/* Computed by stepm unit matrices, product of hstepm matrices, stored
|
| /*printf(fignu*/ |
in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
|
| /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */ |
|
| /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */ |
/* nhstepm age range expressed in number of stepm */
|
| if(first==1){ |
nstepm=(int) rint((agelim-bage)*YEARM/stepm);
|
| first=0; |
/* Typically if 20 years nstepm = 20*12/6=40 stepm */
|
| fprintf(ficgp,"\nset parametric;unset label"); |
/* if (stepm >= YEARM) hstepm=1;*/
|
| fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2); |
nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
|
| fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65"); |
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
| 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>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2); |
|
| fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2); |
for (age=bage; age<=fage; age ++){
|
| fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12); |
|
| fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2); |
|
| fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2); |
hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
|
| fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2); |
|
| 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)) not",\ |
hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
|
| mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\ |
|
| mu2,std,v21,sqrt(lc1),v22,sqrt(lc2)); |
printf("%d|",(int)age);fflush(stdout);
|
| }else{ |
fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
|
| first=0; |
|
| fprintf(fichtm," %d (%.3f),",(int) age, c12); |
|
| fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2); |
/* Computing expectancies */
|
| fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2); |
for(i=1; i<=nlstate;i++)
|
| 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)) not",\ |
for(j=1; j<=nlstate;j++)
|
| mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\ |
for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
|
| mu2,std,v21,sqrt(lc1),v22,sqrt(lc2)); |
eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
|
| }/* if first */ |
|
| } /* age mod 5 */ |
/*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]);*/
|
| } /* end loop age */ |
|
| fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2); |
}
|
| first=1; |
|
| } /*l12 */ |
fprintf(ficreseij,"%3.0f",age );
|
| } /* k12 */ |
for(i=1; i<=nlstate;i++){
|
| } /*l1 */ |
eip=0;
|
| }/* k1 */ |
for(j=1; j<=nlstate;j++){
|
| } /* loop covariates */ |
eip +=eij[i][j][(int)age];
|
| } |
fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
|
| free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage); |
}
|
| free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage); |
fprintf(ficreseij,"%9.4f", eip );
|
| free_vector(xp,1,npar); |
}
|
| fclose(ficresprob); |
fprintf(ficreseij,"\n");
|
| fclose(ficresprobcov); |
|
| fclose(ficresprobcor); |
}
|
| fclose(ficgp); |
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
| fclose(fichtm); |
printf("\n");
|
| } |
fprintf(ficlog,"\n");
|
| |
|
| |
}
|
| /******************* Printing html file ***********/ |
|
| void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \ |
void cvevsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
|
| int lastpass, int stepm, int weightopt, char model[],\ |
|
| int imx,int jmin, int jmax, double jmeanint,char rfileres[],\ |
{
|
| int popforecast, int estepm ,\ |
/* Covariances of health expectancies eij and of total life expectancies according
|
| double jprev1, double mprev1,double anprev1, \ |
to initial status i, ei. .
|
| double jprev2, double mprev2,double anprev2){ |
*/
|
| int jj1, k1, i1, cpt; |
int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
|
| /*char optionfilehtm[FILENAMELENGTH];*/ |
double age, agelim, hf;
|
| if((fichtm=fopen(optionfilehtm,"a"))==NULL) { |
double ***p3matp, ***p3matm, ***varhe;
|
| printf("Problem with %s \n",optionfilehtm), exit(0); |
double **dnewm,**doldm;
|
| fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); |
double *xp, *xm;
|
| } |
double **gp, **gm;
|
| |
double ***gradg, ***trgradg;
|
| fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n |
int theta;
|
| - 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 |
double eip, vip;
|
| - 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): |
varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
|
| <a href=\"e%s\">e%s</a> <br>\n</li>", \ |
xp=vector(1,npar);
|
| jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres); |
xm=vector(1,npar);
|
| |
dnewm=matrix(1,nlstate*nlstate,1,npar);
|
| fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>"); |
doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
|
| |
|
| m=cptcoveff; |
pstamp(ficresstdeij);
|
| if (cptcovn < 1) {m=1;ncodemax[1]=1;} |
fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
|
| |
fprintf(ficresstdeij,"# Age");
|
| jj1=0; |
for(i=1; i<=nlstate;i++){
|
| for(k1=1; k1<=m;k1++){ |
for(j=1; j<=nlstate;j++)
|
| for(i1=1; i1<=ncodemax[k1];i1++){ |
fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
|
| jj1++; |
fprintf(ficresstdeij," e%1d. ",i);
|
| if (cptcovn > 0) { |
}
|
| fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates"); |
fprintf(ficresstdeij,"\n");
|
| for (cpt=1; cpt<=cptcoveff;cpt++) |
|
| fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]); |
pstamp(ficrescveij);
|
| fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">"); |
fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
|
| } |
fprintf(ficrescveij,"# Age");
|
| /* Pij */ |
for(i=1; i<=nlstate;i++)
|
| 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> |
for(j=1; j<=nlstate;j++){
|
| <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); |
cptj= (j-1)*nlstate+i;
|
| /* Quasi-incidences */ |
for(i2=1; i2<=nlstate;i2++)
|
| 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> |
for(j2=1; j2<=nlstate;j2++){
|
| <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); |
cptj2= (j2-1)*nlstate+i2;
|
| /* Stable prevalence in each health state */ |
if(cptj2 <= cptj)
|
| for(cpt=1; cpt<nlstate;cpt++){ |
fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
|
| 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); |
}
|
| } |
fprintf(ficrescveij,"\n");
|
| 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> |
if(estepm < stepm){
|
| <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1); |
printf ("Problem %d lower than %d\n",estepm, stepm);
|
| } |
}
|
| fprintf(fichtm,"\n<br>- Total life expectancy by age and |
else hstepm=estepm;
|
| health expectancies in states (1) and (2): e%s%d.png<br> |
/* We compute the life expectancy from trapezoids spaced every estepm months
|
| <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); |
* This is mainly to measure the difference between two models: for example
|
| } /* end i1 */ |
* if stepm=24 months pijx are given only every 2 years and by summing them
|
| }/* End k1 */ |
* we are calculating an estimate of the Life Expectancy assuming a linear
|
| fprintf(fichtm,"</ul>"); |
* progression in between and thus overestimating or underestimating according
|
| |
* to the curvature of the survival function. If, for the same date, we
|
| |
* estimate the model with stepm=1 month, we can keep estepm to 24 months
|
| fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n |
* to compare the new estimate of Life expectancy with the same linear
|
| - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n |
* hypothesis. A more precise result, taking into account a more precise
|
| - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n |
* curvature will be obtained if estepm is as small as stepm. */
|
| - 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 |
/* For example we decided to compute the life expectancy with the smallest unit */
|
| - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n |
/* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
|
| - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n |
nhstepm is the number of hstepm from age to agelim
|
| - 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); |
nstepm is the number of stepm from age to agelin.
|
| |
Look at hpijx to understand the reason of that which relies in memory size
|
| if(popforecast==1) fprintf(fichtm,"\n |
and note for a fixed period like estepm months */
|
| - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n |
/* We decided (b) to get a life expectancy respecting the most precise curvature of the
|
| - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n |
survival function given by stepm (the optimization length). Unfortunately it
|
| <br>",fileres,fileres,fileres,fileres); |
means that if the survival funtion is printed only each two years of age and if
|
| else |
you sum them up and add 1 year (area under the trapezoids) you won't get the same
|
| 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); |
results. So we changed our mind and took the option of the best precision.
|
| fprintf(fichtm," <ul><li><b>Graphs</b></li><p>"); |
*/
|
| |
hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
|
| m=cptcoveff; |
|
| if (cptcovn < 1) {m=1;ncodemax[1]=1;} |
/* If stepm=6 months */
|
| |
/* nhstepm age range expressed in number of stepm */
|
| jj1=0; |
agelim=AGESUP;
|
| for(k1=1; k1<=m;k1++){ |
nstepm=(int) rint((agelim-bage)*YEARM/stepm);
|
| for(i1=1; i1<=ncodemax[k1];i1++){ |
/* Typically if 20 years nstepm = 20*12/6=40 stepm */
|
| jj1++; |
/* if (stepm >= YEARM) hstepm=1;*/
|
| if (cptcovn > 0) { |
nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
|
| fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates"); |
|
| for (cpt=1; cpt<=cptcoveff;cpt++) |
p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
| fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]); |
p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
| fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">"); |
gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
|
| } |
trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
|
| for(cpt=1; cpt<=nlstate;cpt++) { |
gp=matrix(0,nhstepm,1,nlstate*nlstate);
|
| fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident |
gm=matrix(0,nhstepm,1,nlstate*nlstate);
|
| 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 (age=bage; age<=fage; age ++){
|
| } |
|
| } /* end i1 */ |
/* Computed by stepm unit matrices, product of hstepm matrices, stored
|
| }/* End k1 */ |
in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
|
| fprintf(fichtm,"</ul>"); |
|
| fclose(fichtm); |
hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
|
| } |
|
| |
/* Computing Variances of health expectancies */
|
| /******************* Gnuplot file **************/ |
/* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
|
| void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){ |
decrease memory allocation */
|
| |
for(theta=1; theta <=npar; theta++){
|
| int m,cpt,k1,i,k,j,jk,k2,k3,ij,l; |
for(i=1; i<=npar; i++){
|
| int ng; |
xp[i] = x[i] + (i==theta ?delti[theta]:0);
|
| if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { |
xm[i] = x[i] - (i==theta ?delti[theta]:0);
|
| printf("Problem with file %s",optionfilegnuplot); |
}
|
| fprintf(ficlog,"Problem with file %s",optionfilegnuplot); |
hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
|
| } |
hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
|
| |
|
| /*#ifdef windows */ |
for(j=1; j<= nlstate; j++){
|
| fprintf(ficgp,"cd \"%s\" \n",pathc); |
for(i=1; i<=nlstate; i++){
|
| /*#endif */ |
for(h=0; h<=nhstepm-1; h++){
|
| m=pow(2,cptcoveff); |
gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
|
| |
gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
|
| /* 1eme*/ |
}
|
| for (cpt=1; cpt<= nlstate ; cpt ++) { |
}
|
| for (k1=1; k1<= m ; k1 ++) { |
}
|
| 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); |
for(ij=1; ij<= nlstate*nlstate; ij++)
|
| |
for(h=0; h<=nhstepm-1; h++){
|
| for (i=1; i<= nlstate ; i ++) { |
gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
|
| if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)"); |
}
|
| else fprintf(ficgp," \%%*lf (\%%*lf)"); |
}/* End theta */
|
| } |
|
| fprintf(ficgp,"\" t\"Stable 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 ++) { |
for(h=0; h<=nhstepm-1; h++)
|
| if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)"); |
for(j=1; j<=nlstate*nlstate;j++)
|
| else fprintf(ficgp," \%%*lf (\%%*lf)"); |
for(theta=1; theta <=npar; theta++)
|
| } |
trgradg[h][j][theta]=gradg[h][theta][j];
|
| fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1); |
|
| for (i=1; i<= nlstate ; i ++) { |
|
| if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)"); |
for(ij=1;ij<=nlstate*nlstate;ij++)
|
| else fprintf(ficgp," \%%*lf (\%%*lf)"); |
for(ji=1;ji<=nlstate*nlstate;ji++)
|
| } |
varhe[ij][ji][(int)age] =0.;
|
| fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1)); |
|
| } |
printf("%d|",(int)age);fflush(stdout);
|
| } |
fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
|
| /*2 eme*/ |
for(h=0;h<=nhstepm-1;h++){
|
| |
for(k=0;k<=nhstepm-1;k++){
|
| for (k1=1; k1<= m ; k1 ++) { |
matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
|
| fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1); |
matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
|
| fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage); |
for(ij=1;ij<=nlstate*nlstate;ij++)
|
| |
for(ji=1;ji<=nlstate*nlstate;ji++)
|
| for (i=1; i<= nlstate+1 ; i ++) { |
varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
|
| 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)"); |
/* Computing expectancies */
|
| else fprintf(ficgp," \%%*lf (\%%*lf)"); |
hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
|
| } |
for(i=1; i<=nlstate;i++)
|
| if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,"); |
for(j=1; j<=nlstate;j++)
|
| else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1); |
for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
|
| fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1); |
eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
|
| for (j=1; j<= nlstate+1 ; j ++) { |
|
| if (j==i) fprintf(ficgp," \%%lf (\%%lf)"); |
/* 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]);*/
|
| else fprintf(ficgp," \%%*lf (\%%*lf)"); |
|
| } |
}
|
| fprintf(ficgp,"\" t\"\" w l 0,"); |
|
| fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1); |
fprintf(ficresstdeij,"%3.0f",age );
|
| for (j=1; j<= nlstate+1 ; j ++) { |
for(i=1; i<=nlstate;i++){
|
| if (j==i) fprintf(ficgp," \%%lf (\%%lf)"); |
eip=0.;
|
| else fprintf(ficgp," \%%*lf (\%%*lf)"); |
vip=0.;
|
| } |
for(j=1; j<=nlstate;j++){
|
| if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0"); |
eip += eij[i][j][(int)age];
|
| else fprintf(ficgp,"\" t\"\" w l 0,"); |
for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
|
| } |
vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
|
| } |
fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
|
| |
}
|
| /*3eme*/ |
fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
|
| |
}
|
| for (k1=1; k1<= m ; k1 ++) { |
fprintf(ficresstdeij,"\n");
|
| for (cpt=1; cpt<= nlstate ; cpt ++) { |
|
| k=2+nlstate*(2*cpt-2); |
fprintf(ficrescveij,"%3.0f",age );
|
| fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1); |
for(i=1; i<=nlstate;i++)
|
| fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt); |
for(j=1; j<=nlstate;j++){
|
| /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); |
cptj= (j-1)*nlstate+i;
|
| for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); |
for(i2=1; i2<=nlstate;i2++)
|
| fprintf(ficgp,"\" t \"e%d1\" w l",cpt); |
for(j2=1; j2<=nlstate;j2++){
|
| fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); |
cptj2= (j2-1)*nlstate+i2;
|
| for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); |
if(cptj2 <= cptj)
|
| fprintf(ficgp,"\" t \"e%d1\" w l",cpt); |
fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
|
| |
}
|
| */ |
}
|
| for (i=1; i< nlstate ; i ++) { |
fprintf(ficrescveij,"\n");
|
| 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); |
|
| |
}
|
| } |
free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
|
| } |
free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
|
| } |
free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
|
| |
free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
|
| /* CV preval stat */ |
free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
| for (k1=1; k1<= m ; k1 ++) { |
free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
| for (cpt=1; cpt<nlstate ; cpt ++) { |
printf("\n");
|
| k=3; |
fprintf(ficlog,"\n");
|
| 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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1); |
free_vector(xm,1,npar);
|
| |
free_vector(xp,1,npar);
|
| for (i=1; i< nlstate ; i ++) |
free_matrix(dnewm,1,nlstate*nlstate,1,npar);
|
| fprintf(ficgp,"+$%d",k+i+1); |
free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
|
| fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1); |
free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
|
| |
}
|
| l=3+(nlstate+ndeath)*cpt; |
|
| fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1); |
/************ Variance ******************/
|
| for (i=1; i< nlstate ; i ++) { |
void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
|
| l=3+(nlstate+ndeath)*cpt; |
{
|
| fprintf(ficgp,"+$%d",l+i+1); |
/* Variance of health expectancies */
|
| } |
/* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
|
| fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1); |
/* double **newm;*/
|
| } |
double **dnewm,**doldm;
|
| } |
double **dnewmp,**doldmp;
|
| |
int i, j, nhstepm, hstepm, h, nstepm ;
|
| /* proba elementaires */ |
int k, cptcode;
|
| for(i=1,jk=1; i <=nlstate; i++){ |
double *xp;
|
| for(k=1; k <=(nlstate+ndeath); k++){ |
double **gp, **gm; /* for var eij */
|
| if (k != i) { |
double ***gradg, ***trgradg; /*for var eij */
|
| for(j=1; j <=ncovmodel; j++){ |
double **gradgp, **trgradgp; /* for var p point j */
|
| fprintf(ficgp,"p%d=%f ",jk,p[jk]); |
double *gpp, *gmp; /* for var p point j */
|
| jk++; |
double **varppt; /* for var p point j nlstate to nlstate+ndeath */
|
| fprintf(ficgp,"\n"); |
double ***p3mat;
|
| } |
double age,agelim, hf;
|
| } |
double ***mobaverage;
|
| } |
int theta;
|
| } |
char digit[4];
|
| |
char digitp[25];
|
| for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/ |
|
| for(jk=1; jk <=m; jk++) { |
char fileresprobmorprev[FILENAMELENGTH];
|
| fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); |
|
| if (ng==2) |
if(popbased==1){
|
| fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n"); |
if(mobilav!=0)
|
| else |
strcpy(digitp,"-populbased-mobilav-");
|
| fprintf(ficgp,"\nset title \"Probability\"\n"); |
else strcpy(digitp,"-populbased-nomobil-");
|
| fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar); |
}
|
| i=1; |
else
|
| for(k2=1; k2<=nlstate; k2++) { |
strcpy(digitp,"-stablbased-");
|
| k3=i; |
|
| for(k=1; k<=(nlstate+ndeath); k++) { |
if (mobilav!=0) {
|
| if (k != k2){ |
mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
|
| if(ng==2) |
if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
|
| fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1); |
fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
|
| else |
printf(" Error in movingaverage mobilav=%d\n",mobilav);
|
| 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)) { |
strcpy(fileresprobmorprev,"prmorprev");
|
| fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); |
sprintf(digit,"%-d",ij);
|
| ij++; |
/*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
|
| } |
strcat(fileresprobmorprev,digit); /* Tvar to be done */
|
| else |
strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
|
| fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]); |
strcat(fileresprobmorprev,fileres);
|
| } |
if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
|
| fprintf(ficgp,")/(1"); |
printf("Problem with resultfile: %s\n", fileresprobmorprev);
|
| |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
|
| for(k1=1; k1 <=nlstate; k1++){ |
}
|
| fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1); |
printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
|
| ij=1; |
|
| for(j=3; j <=ncovmodel; j++){ |
fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
|
| if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { |
pstamp(ficresprobmorprev);
|
| fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); |
fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
|
| ij++; |
fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
|
| } |
for(j=nlstate+1; j<=(nlstate+ndeath);j++){
|
| else |
fprintf(ficresprobmorprev," p.%-d SE",j);
|
| fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]); |
for(i=1; i<=nlstate;i++)
|
| } |
fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
|
| fprintf(ficgp,")"); |
}
|
| } |
fprintf(ficresprobmorprev,"\n");
|
| fprintf(ficgp,") t \"p%d%d\" ", k2,k); |
fprintf(ficgp,"\n# Routine varevsij");
|
| if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,","); |
/* fprintf(fichtm, "#Local time at start: %s", strstart);*/
|
| i=i+ncovmodel; |
fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
|
| } |
fprintf(fichtm,"\n<br>%s <br>\n",digitp);
|
| } /* end k */ |
/* } */
|
| } /* end k2 */ |
varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
|
| } /* end jk */ |
pstamp(ficresvij);
|
| } /* end ng */ |
fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
|
| fclose(ficgp); |
if(popbased==1)
|
| } /* end gnuplot */ |
fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
|
| |
else
|
| |
fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
|
| /*************** Moving average **************/ |
fprintf(ficresvij,"# Age");
|
| int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){ |
for(i=1; i<=nlstate;i++)
|
| |
for(j=1; j<=nlstate;j++)
|
| int i, cpt, cptcod; |
fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
|
| int modcovmax =1; |
fprintf(ficresvij,"\n");
|
| int mobilavrange, mob; |
|
| double age; |
xp=vector(1,npar);
|
| |
dnewm=matrix(1,nlstate,1,npar);
|
| modcovmax=2*cptcoveff;/* Max number of modalities. We suppose |
doldm=matrix(1,nlstate,1,nlstate);
|
| a covariate has 2 modalities */ |
dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
|
| if (cptcovn<1) modcovmax=1; /* At least 1 pass */ |
doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
|
| |
|
| if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){ |
gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
|
| if(mobilav==1) mobilavrange=5; /* default */ |
gpp=vector(nlstate+1,nlstate+ndeath);
|
| else mobilavrange=mobilav; |
gmp=vector(nlstate+1,nlstate+ndeath);
|
| for (age=bage; age<=fage; age++) |
trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
|
| for (i=1; i<=nlstate;i++) |
|
| for (cptcod=1;cptcod<=modcovmax;cptcod++) |
if(estepm < stepm){
|
| mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod]; |
printf ("Problem %d lower than %d\n",estepm, stepm);
|
| /* We keep the original values on the extreme ages bage, fage and for |
}
|
| fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2 |
else hstepm=estepm;
|
| we use a 5 terms etc. until the borders are no more concerned. |
/* For example we decided to compute the life expectancy with the smallest unit */
|
| */ |
/* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
|
| for (mob=3;mob <=mobilavrange;mob=mob+2){ |
nhstepm is the number of hstepm from age to agelim
|
| for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ |
nstepm is the number of stepm from age to agelin.
|
| for (i=1; i<=nlstate;i++){ |
Look at hpijx to understand the reason of that which relies in memory size
|
| for (cptcod=1;cptcod<=modcovmax;cptcod++){ |
and note for a fixed period like k years */
|
| mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod]; |
/* We decided (b) to get a life expectancy respecting the most precise curvature of the
|
| for (cpt=1;cpt<=(mob-1)/2;cpt++){ |
survival function given by stepm (the optimization length). Unfortunately it
|
| mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod]; |
means that if the survival funtion is printed every two years of age and if
|
| mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod]; |
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.
|
| mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob; |
*/
|
| } |
hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
|
| } |
agelim = AGESUP;
|
| }/* end age */ |
for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
|
| }/* end mob */ |
nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
|
| }else return -1; |
nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
|
| return 0; |
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
| }/* End movingaverage */ |
gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
|
| |
gp=matrix(0,nhstepm,1,nlstate);
|
| |
gm=matrix(0,nhstepm,1,nlstate);
|
| /************** 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){ |
|
| |
for(theta=1; theta <=npar; theta++){
|
| int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; |
for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
|
| int *popage; |
xp[i] = x[i] + (i==theta ?delti[theta]:0);
|
| double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; |
}
|
| double *popeffectif,*popcount; |
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
|
| double ***p3mat; |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
|
| double ***mobaverage; |
|
| char fileresf[FILENAMELENGTH]; |
if (popbased==1) {
|
| |
if(mobilav ==0){
|
| agelim=AGESUP; |
for(i=1; i<=nlstate;i++)
|
| calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM; |
prlim[i][i]=probs[(int)age][i][ij];
|
| |
}else{ /* mobilav */
|
| prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate); |
for(i=1; i<=nlstate;i++)
|
| |
prlim[i][i]=mobaverage[(int)age][i][ij];
|
| |
}
|
| strcpy(fileresf,"f"); |
}
|
| strcat(fileresf,fileres); |
|
| if((ficresf=fopen(fileresf,"w"))==NULL) { |
for(j=1; j<= nlstate; j++){
|
| printf("Problem with forecast resultfile: %s\n", fileresf); |
for(h=0; h<=nhstepm; h++){
|
| fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf); |
for(i=1, gp[h][j]=0.;i<=nlstate;i++)
|
| } |
gp[h][j] += prlim[i][i]*p3mat[i][j][h];
|
| printf("Computing forecasting: result on file '%s' \n", fileresf); |
}
|
| fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf); |
}
|
| |
/* This for computing probability of death (h=1 means
|
| if (cptcoveff==0) ncodemax[cptcoveff]=1; |
computed over hstepm matrices product = hstepm*stepm months)
|
| |
as a weighted average of prlim.
|
| if (mobilav!=0) { |
*/
|
| mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
for(j=nlstate+1;j<=nlstate+ndeath;j++){
|
| if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ |
for(i=1,gpp[j]=0.; i<= nlstate; i++)
|
| fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); |
gpp[j] += prlim[i][i]*p3mat[i][j][1];
|
| printf(" Error in movingaverage mobilav=%d\n",mobilav); |
}
|
| } |
/* end probability of death */
|
| } |
|
| |
for(i=1; i<=npar; i++) /* Computes gradient x - delta */
|
| stepsize=(int) (stepm+YEARM-1)/YEARM; |
xp[i] = x[i] - (i==theta ?delti[theta]:0);
|
| if (stepm<=12) stepsize=1; |
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
|
| |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
|
| agelim=AGESUP; |
|
| |
if (popbased==1) {
|
| hstepm=1; |
if(mobilav ==0){
|
| hstepm=hstepm/stepm; |
for(i=1; i<=nlstate;i++)
|
| yp1=modf(dateintmean,&yp); |
prlim[i][i]=probs[(int)age][i][ij];
|
| anprojmean=yp; |
}else{ /* mobilav */
|
| yp2=modf((yp1*12),&yp); |
for(i=1; i<=nlstate;i++)
|
| mprojmean=yp; |
prlim[i][i]=mobaverage[(int)age][i][ij];
|
| yp1=modf((yp2*30.5),&yp); |
}
|
| jprojmean=yp; |
}
|
| if(jprojmean==0) jprojmean=1; |
|
| if(mprojmean==0) jprojmean=1; |
for(j=1; j<= nlstate; j++){
|
| |
for(h=0; h<=nhstepm; h++){
|
| fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean); |
for(i=1, gm[h][j]=0.;i<=nlstate;i++)
|
| |
gm[h][j] += prlim[i][i]*p3mat[i][j][h];
|
| for(cptcov=1;cptcov<=i2;cptcov++){ |
}
|
| for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ |
}
|
| k=k+1; |
/* This for computing probability of death (h=1 means
|
| fprintf(ficresf,"\n#******"); |
computed over hstepm matrices product = hstepm*stepm months)
|
| for(j=1;j<=cptcoveff;j++) { |
as a weighted average of prlim.
|
| fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
*/
|
| } |
for(j=nlstate+1;j<=nlstate+ndeath;j++){
|
| fprintf(ficresf,"******\n"); |
for(i=1,gmp[j]=0.; i<= nlstate; i++)
|
| fprintf(ficresf,"# StartingAge FinalAge"); |
gmp[j] += prlim[i][i]*p3mat[i][j][1];
|
| for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j); |
}
|
| |
/* end probability of death */
|
| |
|
| for (cpt=0; cpt<=(anproj2-anproj1);cpt++) { |
for(j=1; j<= nlstate; j++) /* vareij */
|
| fprintf(ficresf,"\n"); |
for(h=0; h<=nhstepm; h++){
|
| fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt); |
gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
|
| |
}
|
| for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ |
|
| nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); |
for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
|
| nhstepm = nhstepm/hstepm; |
gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
|
| |
}
|
| p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
|
| oldm=oldms;savm=savms; |
} /* End theta */
|
| hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); |
|
| |
trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
|
| for (h=0; h<=nhstepm; h++){ |
|
| if (h==(int) (calagedate+YEARM*cpt)) { |
for(h=0; h<=nhstepm; h++) /* veij */
|
| fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm); |
for(j=1; j<=nlstate;j++)
|
| } |
for(theta=1; theta <=npar; theta++)
|
| for(j=1; j<=nlstate+ndeath;j++) { |
trgradg[h][j][theta]=gradg[h][theta][j];
|
| kk1=0.;kk2=0; |
|
| for(i=1; i<=nlstate;i++) { |
for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
|
| if (mobilav==1) |
for(theta=1; theta <=npar; theta++)
|
| kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; |
trgradgp[j][theta]=gradgp[theta][j];
|
| else { |
|
| kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; |
|
| } |
hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
|
| |
for(i=1;i<=nlstate;i++)
|
| } |
for(j=1;j<=nlstate;j++)
|
| if (h==(int)(calagedate+12*cpt)){ |
vareij[i][j][(int)age] =0.;
|
| fprintf(ficresf," %.3f", kk1); |
|
| |
for(h=0;h<=nhstepm;h++){
|
| } |
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]);
|
| free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
for(i=1;i<=nlstate;i++)
|
| } |
for(j=1;j<=nlstate;j++)
|
| } |
vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
|
| } |
}
|
| } |
}
|
| |
|
| if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
/* pptj */
|
| |
matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
|
| fclose(ficresf); |
matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
|
| } |
for(j=nlstate+1;j<=nlstate+ndeath;j++)
|
| /************** Forecasting ******************/ |
for(i=nlstate+1;i<=nlstate+ndeath;i++)
|
| 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){ |
varppt[j][i]=doldmp[j][i];
|
| |
/* end ppptj */
|
| int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; |
/* x centered again */
|
| int *popage; |
hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
|
| double calagedate, agelim, kk1, kk2; |
prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
|
| double *popeffectif,*popcount; |
|
| double ***p3mat,***tabpop,***tabpopprev; |
if (popbased==1) {
|
| double ***mobaverage; |
if(mobilav ==0){
|
| char filerespop[FILENAMELENGTH]; |
for(i=1; i<=nlstate;i++)
|
| |
prlim[i][i]=probs[(int)age][i][ij];
|
| tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
}else{ /* mobilav */
|
| tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
for(i=1; i<=nlstate;i++)
|
| agelim=AGESUP; |
prlim[i][i]=mobaverage[(int)age][i][ij];
|
| calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; |
}
|
| |
}
|
| prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate); |
|
| |
/* This for computing probability of death (h=1 means
|
| |
computed over hstepm (estepm) matrices product = hstepm*stepm months)
|
| strcpy(filerespop,"pop"); |
as a weighted average of prlim.
|
| strcat(filerespop,fileres); |
*/
|
| if((ficrespop=fopen(filerespop,"w"))==NULL) { |
for(j=nlstate+1;j<=nlstate+ndeath;j++){
|
| printf("Problem with forecast resultfile: %s\n", filerespop); |
for(i=1,gmp[j]=0.;i<= nlstate; i++)
|
| fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); |
gmp[j] += prlim[i][i]*p3mat[i][j][1];
|
| } |
}
|
| printf("Computing forecasting: result on file '%s' \n", filerespop); |
/* end probability of death */
|
| fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); |
|
| |
fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
|
| if (cptcoveff==0) ncodemax[cptcoveff]=1; |
for(j=nlstate+1; j<=(nlstate+ndeath);j++){
|
| |
fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
|
| if (mobilav!=0) { |
for(i=1; i<=nlstate;i++){
|
| mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
|
| if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ |
}
|
| fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); |
}
|
| printf(" Error in movingaverage mobilav=%d\n",mobilav); |
fprintf(ficresprobmorprev,"\n");
|
| } |
|
| } |
fprintf(ficresvij,"%.0f ",age );
|
| |
for(i=1; i<=nlstate;i++)
|
| stepsize=(int) (stepm+YEARM-1)/YEARM; |
for(j=1; j<=nlstate;j++){
|
| if (stepm<=12) stepsize=1; |
fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
|
| |
}
|
| agelim=AGESUP; |
fprintf(ficresvij,"\n");
|
| |
free_matrix(gp,0,nhstepm,1,nlstate);
|
| hstepm=1; |
free_matrix(gm,0,nhstepm,1,nlstate);
|
| hstepm=hstepm/stepm; |
free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
|
| |
free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
|
| if (popforecast==1) { |
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
| if((ficpop=fopen(popfile,"r"))==NULL) { |
} /* End age */
|
| printf("Problem with population file : %s\n",popfile);exit(0); |
free_vector(gpp,nlstate+1,nlstate+ndeath);
|
| fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); |
free_vector(gmp,nlstate+1,nlstate+ndeath);
|
| } |
free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
|
| popage=ivector(0,AGESUP); |
free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
|
| popeffectif=vector(0,AGESUP); |
fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
|
| popcount=vector(0,AGESUP); |
/* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
|
| |
fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
|
| i=1; |
/* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
|
| while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; |
/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
|
| |
/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
|
| imx=i; |
fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
|
| for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; |
fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
|
| } |
fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
|
| |
fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
|
| for(cptcov=1;cptcov<=i2;cptcov++){ |
fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
|
| for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ |
/* fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
|
| k=k+1; |
*/
|
| fprintf(ficrespop,"\n#******"); |
/* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
|
| for(j=1;j<=cptcoveff;j++) { |
fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
|
| fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
|
| } |
free_vector(xp,1,npar);
|
| fprintf(ficrespop,"******\n"); |
free_matrix(doldm,1,nlstate,1,nlstate);
|
| fprintf(ficrespop,"# Age"); |
free_matrix(dnewm,1,nlstate,1,npar);
|
| for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); |
free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
|
| if (popforecast==1) fprintf(ficrespop," [Population]"); |
free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
|
| |
free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
|
| for (cpt=0; cpt<=0;cpt++) { |
if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
|
| fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); |
fclose(ficresprobmorprev);
|
| |
fflush(ficgp);
|
| for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ |
fflush(fichtm);
|
| nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); |
} /* end varevsij */
|
| nhstepm = nhstepm/hstepm; |
|
| |
/************ Variance of prevlim ******************/
|
| p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
|
| oldm=oldms;savm=savms; |
{
|
| hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); |
/* Variance of prevalence limit */
|
| |
/* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
|
| for (h=0; h<=nhstepm; h++){ |
double **newm;
|
| if (h==(int) (calagedate+YEARM*cpt)) { |
double **dnewm,**doldm;
|
| fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); |
int i, j, nhstepm, hstepm;
|
| } |
int k, cptcode;
|
| for(j=1; j<=nlstate+ndeath;j++) { |
double *xp;
|
| kk1=0.;kk2=0; |
double *gp, *gm;
|
| for(i=1; i<=nlstate;i++) { |
double **gradg, **trgradg;
|
| if (mobilav==1) |
double age,agelim;
|
| kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; |
int theta;
|
| else { |
|
| kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; |
pstamp(ficresvpl);
|
| } |
fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
|
| } |
fprintf(ficresvpl,"# Age");
|
| if (h==(int)(calagedate+12*cpt)){ |
for(i=1; i<=nlstate;i++)
|
| tabpop[(int)(agedeb)][j][cptcod]=kk1; |
fprintf(ficresvpl," %1d-%1d",i,i);
|
| /*fprintf(ficrespop," %.3f", kk1); |
fprintf(ficresvpl,"\n");
|
| if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/ |
|
| } |
xp=vector(1,npar);
|
| } |
dnewm=matrix(1,nlstate,1,npar);
|
| for(i=1; i<=nlstate;i++){ |
doldm=matrix(1,nlstate,1,nlstate);
|
| kk1=0.; |
|
| for(j=1; j<=nlstate;j++){ |
hstepm=1*YEARM; /* Every year of age */
|
| kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; |
hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
|
| } |
agelim = AGESUP;
|
| tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)]; |
for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
|
| } |
nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
|
| |
if (stepm >= YEARM) hstepm=1;
|
| if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++) |
nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
|
| fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); |
gradg=matrix(1,npar,1,nlstate);
|
| } |
gp=vector(1,nlstate);
|
| free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
gm=vector(1,nlstate);
|
| } |
|
| } |
for(theta=1; theta <=npar; theta++){
|
| |
for(i=1; i<=npar; i++){ /* Computes gradient */
|
| /******/ |
xp[i] = x[i] + (i==theta ?delti[theta]:0);
|
| |
}
|
| for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
|
| fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); |
for(i=1;i<=nlstate;i++)
|
| for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ |
gp[i] = prlim[i][i];
|
| nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); |
|
| nhstepm = nhstepm/hstepm; |
for(i=1; i<=npar; i++) /* Computes gradient */
|
| |
xp[i] = x[i] - (i==theta ?delti[theta]:0);
|
| p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
|
| oldm=oldms;savm=savms; |
for(i=1;i<=nlstate;i++)
|
| hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); |
gm[i] = prlim[i][i];
|
| for (h=0; h<=nhstepm; h++){ |
|
| if (h==(int) (calagedate+YEARM*cpt)) { |
for(i=1;i<=nlstate;i++)
|
| fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); |
gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
|
| } |
} /* End theta */
|
| for(j=1; j<=nlstate+ndeath;j++) { |
|
| kk1=0.;kk2=0; |
trgradg =matrix(1,nlstate,1,npar);
|
| for(i=1; i<=nlstate;i++) { |
|
| kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; |
for(j=1; j<=nlstate;j++)
|
| } |
for(theta=1; theta <=npar; theta++)
|
| if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1); |
trgradg[j][theta]=gradg[theta][j];
|
| } |
|
| } |
for(i=1;i<=nlstate;i++)
|
| free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
varpl[i][(int)age] =0.;
|
| } |
matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
|
| } |
matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
|
| } |
for(i=1;i<=nlstate;i++)
|
| } |
varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
|
| |
|
| if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
fprintf(ficresvpl,"%.0f ",age );
|
| |
for(i=1; i<=nlstate;i++)
|
| if (popforecast==1) { |
fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
|
| free_ivector(popage,0,AGESUP); |
fprintf(ficresvpl,"\n");
|
| free_vector(popeffectif,0,AGESUP); |
free_vector(gp,1,nlstate);
|
| free_vector(popcount,0,AGESUP); |
free_vector(gm,1,nlstate);
|
| } |
free_matrix(gradg,1,npar,1,nlstate);
|
| free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
free_matrix(trgradg,1,nlstate,1,npar);
|
| free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
} /* End age */
|
| fclose(ficrespop); |
|
| } |
free_vector(xp,1,npar);
|
| |
free_matrix(doldm,1,nlstate,1,npar);
|
| /***********************************************/ |
free_matrix(dnewm,1,nlstate,1,nlstate);
|
| /**************** Main Program *****************/ |
|
| /***********************************************/ |
}
|
| |
|
| int main(int argc, char *argv[]) |
/************ Variance of one-step probabilities ******************/
|
| { |
void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
|
| int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav); |
{
|
| int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod; |
int i, j=0, i1, k1, l1, t, tj;
|
| double agedeb, agefin,hf; |
int k2, l2, j1, z1;
|
| double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20; |
int k=0,l, cptcode;
|
| |
int first=1, first1;
|
| double fret; |
double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
|
| double **xi,tmp,delta; |
double **dnewm,**doldm;
|
| |
double *xp;
|
| double dum; /* Dummy variable */ |
double *gp, *gm;
|
| double ***p3mat; |
double **gradg, **trgradg;
|
| double ***mobaverage; |
double **mu;
|
| int *indx; |
double age,agelim, cov[NCOVMAX];
|
| char line[MAXLINE], linepar[MAXLINE]; |
double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
|
| char path[80],pathc[80],pathcd[80],pathtot[80],model[80]; |
int theta;
|
| int firstobs=1, lastobs=10; |
char fileresprob[FILENAMELENGTH];
|
| int sdeb, sfin; /* Status at beginning and end */ |
char fileresprobcov[FILENAMELENGTH];
|
| int c, h , cpt,l; |
char fileresprobcor[FILENAMELENGTH];
|
| int ju,jl, mi; |
|
| int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij; |
double ***varpij;
|
| int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; |
|
| int mobilav=0,popforecast=0; |
strcpy(fileresprob,"prob");
|
| int hstepm, nhstepm; |
strcat(fileresprob,fileres);
|
| double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate; |
if((ficresprob=fopen(fileresprob,"w"))==NULL) {
|
| |
printf("Problem with resultfile: %s\n", fileresprob);
|
| double bage, fage, age, agelim, agebase; |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
|
| double ftolpl=FTOL; |
}
|
| double **prlim; |
strcpy(fileresprobcov,"probcov");
|
| double *severity; |
strcat(fileresprobcov,fileres);
|
| double ***param; /* Matrix of parameters */ |
if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
|
| double *p; |
printf("Problem with resultfile: %s\n", fileresprobcov);
|
| double **matcov; /* Matrix of covariance */ |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
|
| double ***delti3; /* Scale */ |
}
|
| double *delti; /* Scale */ |
strcpy(fileresprobcor,"probcor");
|
| double ***eij, ***vareij; |
strcat(fileresprobcor,fileres);
|
| double **varpl; /* Variances of prevalence limits by age */ |
if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
|
| double *epj, vepp; |
printf("Problem with resultfile: %s\n", fileresprobcor);
|
| double kk1, kk2; |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
|
| double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2; |
}
|
| |
printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
|
| char *alph[]={"a","a","b","c","d","e"}, str[4]; |
fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
|
| |
printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
|
| |
fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
|
| char z[1]="c", occ; |
printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
|
| #include <sys/time.h> |
fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
|
| #include <time.h> |
pstamp(ficresprob);
|
| char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80]; |
fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
|
| |
fprintf(ficresprob,"# Age");
|
| /* long total_usecs; |
pstamp(ficresprobcov);
|
| struct timeval start_time, end_time; |
fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
|
| |
fprintf(ficresprobcov,"# Age");
|
| gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */ |
pstamp(ficresprobcor);
|
| getcwd(pathcd, size); |
fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
|
| |
fprintf(ficresprobcor,"# Age");
|
| printf("\n%s",version); |
|
| if(argc <=1){ |
|
| printf("\nEnter the parameter file name: "); |
for(i=1; i<=nlstate;i++)
|
| scanf("%s",pathtot); |
for(j=1; j<=(nlstate+ndeath);j++){
|
| } |
fprintf(ficresprob," p%1d-%1d (SE)",i,j);
|
| else{ |
fprintf(ficresprobcov," p%1d-%1d ",i,j);
|
| strcpy(pathtot,argv[1]); |
fprintf(ficresprobcor," p%1d-%1d ",i,j);
|
| } |
}
|
| /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/ |
/* fprintf(ficresprob,"\n");
|
| /*cygwin_split_path(pathtot,path,optionfile); |
fprintf(ficresprobcov,"\n");
|
| printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/ |
fprintf(ficresprobcor,"\n");
|
| /* cutv(path,optionfile,pathtot,'\\');*/ |
*/
|
| |
xp=vector(1,npar);
|
| split(pathtot,path,optionfile,optionfilext,optionfilefiname); |
dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
|
| printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname); |
doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
|
| chdir(path); |
mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
|
| replace(pathc,path); |
varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
|
| |
first=1;
|
| /*-------- arguments in the command line --------*/ |
fprintf(ficgp,"\n# Routine varprob");
|
| |
fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
|
| /* Log file */ |
fprintf(fichtm,"\n");
|
| strcat(filelog, optionfilefiname); |
|
| strcat(filelog,".log"); /* */ |
fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
|
| if((ficlog=fopen(filelog,"w"))==NULL) { |
fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
|
| printf("Problem with logfile %s\n",filelog); |
file %s<br>\n",optionfilehtmcov);
|
| goto end; |
fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
|
| } |
and drawn. It helps understanding how is the covariance between two incidences.\
|
| fprintf(ficlog,"Log filename:%s\n",filelog); |
They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
|
| fprintf(ficlog,"\n%s",version); |
fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
|
| fprintf(ficlog,"\nEnter the parameter file name: "); |
It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
|
| fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname); |
would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
|
| fflush(ficlog); |
standard deviations wide on each axis. <br>\
|
| |
Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
|
| /* */ |
and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
|
| strcpy(fileres,"r"); |
To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
|
| strcat(fileres, optionfilefiname); |
|
| strcat(fileres,".txt"); /* Other files have txt extension */ |
cov[1]=1;
|
| |
tj=cptcoveff;
|
| /*---------arguments file --------*/ |
if (cptcovn<1) {tj=1;ncodemax[1]=1;}
|
| |
j1=0;
|
| if((ficpar=fopen(optionfile,"r"))==NULL) { |
for(t=1; t<=tj;t++){
|
| printf("Problem with optionfile %s\n",optionfile); |
for(i1=1; i1<=ncodemax[t];i1++){
|
| fprintf(ficlog,"Problem with optionfile %s\n",optionfile); |
j1++;
|
| goto end; |
if (cptcovn>0) {
|
| } |
fprintf(ficresprob, "\n#********** Variable ");
|
| |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
|
| strcpy(filereso,"o"); |
fprintf(ficresprob, "**********\n#\n");
|
| strcat(filereso,fileres); |
fprintf(ficresprobcov, "\n#********** Variable ");
|
| if((ficparo=fopen(filereso,"w"))==NULL) { |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
|
| printf("Problem with Output resultfile: %s\n", filereso); |
fprintf(ficresprobcov, "**********\n#\n");
|
| fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso); |
|
| goto end; |
fprintf(ficgp, "\n#********** Variable ");
|
| } |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
|
| |
fprintf(ficgp, "**********\n#\n");
|
| /* Reads comments: lines beginning with '#' */ |
|
| while((c=getc(ficpar))=='#' && c!= EOF){ |
|
| ungetc(c,ficpar); |
fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
|
| fgets(line, MAXLINE, ficpar); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
|
| puts(line); |
fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
|
| fputs(line,ficparo); |
|
| } |
fprintf(ficresprobcor, "\n#********** Variable ");
|
| ungetc(c,ficpar); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
|
| |
fprintf(ficresprobcor, "**********\n#");
|
| 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 model=%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); |
for (age=bage; age<=fage; age ++){
|
| while((c=getc(ficpar))=='#' && c!= EOF){ |
cov[2]=age;
|
| ungetc(c,ficpar); |
for (k=1; k<=cptcovn;k++) {
|
| fgets(line, MAXLINE, ficpar); |
cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
|
| puts(line); |
}
|
| fputs(line,ficparo); |
for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
|
| } |
for (k=1; k<=cptcovprod;k++)
|
| ungetc(c,ficpar); |
cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
|
| |
|
| |
gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
|
| covar=matrix(0,NCOVMAX,1,n); |
trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
|
| cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/ |
gp=vector(1,(nlstate)*(nlstate+ndeath));
|
| if (strlen(model)>1) cptcovn=nbocc(model,'+')+1; |
gm=vector(1,(nlstate)*(nlstate+ndeath));
|
| |
|
| ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */ |
for(theta=1; theta <=npar; theta++){
|
| nvar=ncovmodel-1; /* Suppressing age as a basic covariate */ |
for(i=1; i<=npar; i++)
|
| |
xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
|
| /* Read guess parameters */ |
|
| /* Reads comments: lines beginning with '#' */ |
pmij(pmmij,cov,ncovmodel,xp,nlstate);
|
| while((c=getc(ficpar))=='#' && c!= EOF){ |
|
| ungetc(c,ficpar); |
k=0;
|
| fgets(line, MAXLINE, ficpar); |
for(i=1; i<= (nlstate); i++){
|
| puts(line); |
for(j=1; j<=(nlstate+ndeath);j++){
|
| fputs(line,ficparo); |
k=k+1;
|
| } |
gp[k]=pmmij[i][j];
|
| ungetc(c,ficpar); |
}
|
| |
}
|
| param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); |
|
| for(i=1; i <=nlstate; i++) |
for(i=1; i<=npar; i++)
|
| for(j=1; j <=nlstate+ndeath-1; j++){ |
xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
|
| fscanf(ficpar,"%1d%1d",&i1,&j1); |
|
| fprintf(ficparo,"%1d%1d",i1,j1); |
pmij(pmmij,cov,ncovmodel,xp,nlstate);
|
| if(mle==1) |
k=0;
|
| printf("%1d%1d",i,j); |
for(i=1; i<=(nlstate); i++){
|
| fprintf(ficlog,"%1d%1d",i,j); |
for(j=1; j<=(nlstate+ndeath);j++){
|
| for(k=1; k<=ncovmodel;k++){ |
k=k+1;
|
| fscanf(ficpar," %lf",¶m[i][j][k]); |
gm[k]=pmmij[i][j];
|
| if(mle==1){ |
}
|
| printf(" %lf",param[i][j][k]); |
}
|
| fprintf(ficlog," %lf",param[i][j][k]); |
|
| } |
for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
|
| else |
gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
|
| fprintf(ficlog," %lf",param[i][j][k]); |
}
|
| fprintf(ficparo," %lf",param[i][j][k]); |
|
| } |
for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
|
| fscanf(ficpar,"\n"); |
for(theta=1; theta <=npar; theta++)
|
| if(mle==1) |
trgradg[j][theta]=gradg[theta][j];
|
| printf("\n"); |
|
| fprintf(ficlog,"\n"); |
matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
|
| fprintf(ficparo,"\n"); |
matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
|
| } |
free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
|
| |
free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
|
| npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ |
free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
|
| |
free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
|
| p=param[1][1]; |
|
| |
pmij(pmmij,cov,ncovmodel,x,nlstate);
|
| /* Reads comments: lines beginning with '#' */ |
|
| while((c=getc(ficpar))=='#' && c!= EOF){ |
k=0;
|
| ungetc(c,ficpar); |
for(i=1; i<=(nlstate); i++){
|
| fgets(line, MAXLINE, ficpar); |
for(j=1; j<=(nlstate+ndeath);j++){
|
| puts(line); |
k=k+1;
|
| fputs(line,ficparo); |
mu[k][(int) age]=pmmij[i][j];
|
| } |
}
|
| ungetc(c,ficpar); |
}
|
| |
for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
|
| delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); |
for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
|
| delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */ |
varpij[i][j][(int)age] = doldm[i][j];
|
| for(i=1; i <=nlstate; i++){ |
|
| for(j=1; j <=nlstate+ndeath-1; j++){ |
/*printf("\n%d ",(int)age);
|
| fscanf(ficpar,"%1d%1d",&i1,&j1); |
for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
|
| printf("%1d%1d",i,j); |
printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
|
| fprintf(ficparo,"%1d%1d",i1,j1); |
fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
|
| for(k=1; k<=ncovmodel;k++){ |
}*/
|
| fscanf(ficpar,"%le",&delti3[i][j][k]); |
|
| printf(" %le",delti3[i][j][k]); |
fprintf(ficresprob,"\n%d ",(int)age);
|
| fprintf(ficparo," %le",delti3[i][j][k]); |
fprintf(ficresprobcov,"\n%d ",(int)age);
|
| } |
fprintf(ficresprobcor,"\n%d ",(int)age);
|
| fscanf(ficpar,"\n"); |
|
| printf("\n"); |
for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
|
| fprintf(ficparo,"\n"); |
fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
|
| } |
for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
|
| } |
fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
|
| delti=delti3[1][1]; |
fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
|
| |
}
|
| /* Reads comments: lines beginning with '#' */ |
i=0;
|
| while((c=getc(ficpar))=='#' && c!= EOF){ |
for (k=1; k<=(nlstate);k++){
|
| ungetc(c,ficpar); |
for (l=1; l<=(nlstate+ndeath);l++){
|
| fgets(line, MAXLINE, ficpar); |
i=i++;
|
| puts(line); |
fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
|
| fputs(line,ficparo); |
fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
|
| } |
for (j=1; j<=i;j++){
|
| ungetc(c,ficpar); |
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]));
|
| matcov=matrix(1,npar,1,npar); |
}
|
| for(i=1; i <=npar; i++){ |
}
|
| fscanf(ficpar,"%s",&str); |
}/* end of loop for state */
|
| if(mle==1) |
} /* end of loop for age */
|
| printf("%s",str); |
|
| fprintf(ficlog,"%s",str); |
/* Confidence intervalle of pij */
|
| fprintf(ficparo,"%s",str); |
/*
|
| for(j=1; j <=i; j++){ |
fprintf(ficgp,"\nset noparametric;unset label");
|
| fscanf(ficpar," %le",&matcov[i][j]); |
fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
|
| if(mle==1){ |
fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
|
| printf(" %.5le",matcov[i][j]); |
fprintf(fichtm,"\n<br>Probability with confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
|
| fprintf(ficlog," %.5le",matcov[i][j]); |
fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
|
| } |
fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
|
| else |
fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
|
| fprintf(ficlog," %.5le",matcov[i][j]); |
*/
|
| fprintf(ficparo," %.5le",matcov[i][j]); |
|
| } |
/* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
|
| fscanf(ficpar,"\n"); |
first1=1;
|
| if(mle==1) |
for (k2=1; k2<=(nlstate);k2++){
|
| printf("\n"); |
for (l2=1; l2<=(nlstate+ndeath);l2++){
|
| fprintf(ficlog,"\n"); |
if(l2==k2) continue;
|
| fprintf(ficparo,"\n"); |
j=(k2-1)*(nlstate+ndeath)+l2;
|
| } |
for (k1=1; k1<=(nlstate);k1++){
|
| for(i=1; i <=npar; i++) |
for (l1=1; l1<=(nlstate+ndeath);l1++){
|
| for(j=i+1;j<=npar;j++) |
if(l1==k1) continue;
|
| matcov[i][j]=matcov[j][i]; |
i=(k1-1)*(nlstate+ndeath)+l1;
|
| |
if(i<=j) continue;
|
| if(mle==1) |
for (age=bage; age<=fage; age ++){
|
| printf("\n"); |
if ((int)age %5==0){
|
| fprintf(ficlog,"\n"); |
v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
|
| |
v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
|
| |
cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
|
| /*-------- Rewriting paramater file ----------*/ |
mu1=mu[i][(int) age]/stepm*YEARM ;
|
| strcpy(rfileres,"r"); /* "Rparameterfile */ |
mu2=mu[j][(int) age]/stepm*YEARM;
|
| strcat(rfileres,optionfilefiname); /* Parameter file first name*/ |
c12=cv12/sqrt(v1*v2);
|
| strcat(rfileres,"."); /* */ |
/* Computing eigen value of matrix of covariance */
|
| strcat(rfileres,optionfilext); /* Other files have txt extension */ |
lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
|
| if((ficres =fopen(rfileres,"w"))==NULL) { |
lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
|
| printf("Problem writing new parameter file: %s\n", fileres);goto end; |
/* Eigen vectors */
|
| fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end; |
v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
|
| } |
/*v21=sqrt(1.-v11*v11); *//* error */
|
| fprintf(ficres,"#%s\n",version); |
v21=(lc1-v1)/cv12*v11;
|
| |
v12=-v21;
|
| /*-------- data file ----------*/ |
v22=v11;
|
| if((fic=fopen(datafile,"r"))==NULL) { |
tnalp=v21/v11;
|
| printf("Problem with datafile: %s\n", datafile);goto end; |
if(first1==1){
|
| fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end; |
first1=0;
|
| } |
printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
|
| |
}
|
| n= lastobs; |
fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
|
| severity = vector(1,maxwav); |
/*printf(fignu*/
|
| outcome=imatrix(1,maxwav+1,1,n); |
/* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
|
| num=ivector(1,n); |
/* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
|
| moisnais=vector(1,n); |
if(first==1){
|
| annais=vector(1,n); |
first=0;
|
| moisdc=vector(1,n); |
fprintf(ficgp,"\nset parametric;unset label");
|
| andc=vector(1,n); |
fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
|
| agedc=vector(1,n); |
fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
|
| cod=ivector(1,n); |
fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
|
| weight=vector(1,n); |
:<a href=\"%s%d%1d%1d-%1d%1d.png\">\
|
| for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */ |
%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
|
| mint=matrix(1,maxwav,1,n); |
subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
|
| anint=matrix(1,maxwav,1,n); |
subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
|
| s=imatrix(1,maxwav+1,1,n); |
fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
|
| tab=ivector(1,NCOVMAX); |
fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
|
| ncodemax=ivector(1,8); |
fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
|
| |
fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
|
| i=1; |
fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
|
| while (fgets(line, MAXLINE, fic) != NULL) { |
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)) not",\
|
| if ((i >= firstobs) && (i <=lastobs)) { |
mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
|
| |
mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
|
| for (j=maxwav;j>=1;j--){ |
}else{
|
| cutv(stra, strb,line,' '); s[j][i]=atoi(strb); |
first=0;
|
| strcpy(line,stra); |
fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
|
| cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra); |
fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
|
| cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra); |
fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
|
| } |
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)) not",\
|
| |
mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
|
| cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra); |
mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
|
| cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra); |
}/* if first */
|
| |
} /* age mod 5 */
|
| cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra); |
} /* end loop age */
|
| cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra); |
fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
|
| |
first=1;
|
| cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra); |
} /*l12 */
|
| for (j=ncovcol;j>=1;j--){ |
} /* k12 */
|
| cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra); |
} /*l1 */
|
| } |
}/* k1 */
|
| num[i]=atol(stra); |
} /* loop covariates */
|
| |
}
|
| /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){ |
free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
|
| 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;}*/ |
free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
|
| |
free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
|
| i=i+1; |
free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
|
| } |
free_vector(xp,1,npar);
|
| } |
fclose(ficresprob);
|
| /* printf("ii=%d", ij); |
fclose(ficresprobcov);
|
| scanf("%d",i);*/ |
fclose(ficresprobcor);
|
| imx=i-1; /* Number of individuals */ |
fflush(ficgp);
|
| |
fflush(fichtmcov);
|
| /* 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; |
/******************* Printing html file ***********/
|
| }*/ |
void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
|
| /* for (i=1; i<=imx; i++){ |
int lastpass, int stepm, int weightopt, char model[],\
|
| if (s[4][i]==9) s[4][i]=-1; |
int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
|
| 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]));}*/ |
int popforecast, int estepm ,\
|
| |
double jprev1, double mprev1,double anprev1, \
|
| |
double jprev2, double mprev2,double anprev2){
|
| /* Calculation of the number of parameter from char model*/ |
int jj1, k1, i1, cpt;
|
| Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */ |
|
| Tprod=ivector(1,15); |
fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
|
| Tvaraff=ivector(1,15); |
<li><a href='#secondorder'>Result files (second order (variance)</a>\n \
|
| Tvard=imatrix(1,15,1,2); |
</ul>");
|
| Tage=ivector(1,15); |
fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
|
| |
- Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
|
| if (strlen(model) >1){ /* If there is at least 1 covariate */ |
jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
|
| j=0, j1=0, k1=1, k2=1; |
fprintf(fichtm,"\
|
| j=nbocc(model,'+'); /* j=Number of '+' */ |
- Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
|
| j1=nbocc(model,'*'); /* j1=Number of '*' */ |
stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
|
| cptcovn=j+1; |
fprintf(fichtm,"\
|
| cptcovprod=j1; /*Number of products */ |
- Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
|
| |
subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
|
| strcpy(modelsav,model); |
fprintf(fichtm,"\
|
| if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){ |
- (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age: ei., eij . If one or more covariate are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
|
| printf("Error. Non available option model=%s ",model); |
<a href=\"%s\">%s</a> <br>\n",
|
| fprintf(ficlog,"Error. Non available option model=%s ",model); |
estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
|
| goto end; |
fprintf(fichtm,"\
|
| } |
- Population projections by age and states: \
|
| |
<a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
|
| /* This loop fills the array Tvar from the string 'model'.*/ |
|
| |
fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
|
| for(i=(j+1); i>=1;i--){ |
|
| cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ |
m=cptcoveff;
|
| if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */ |
if (cptcovn < 1) {m=1;ncodemax[1]=1;}
|
| /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/ |
|
| /*scanf("%d",i);*/ |
jj1=0;
|
| if (strchr(strb,'*')) { /* Model includes a product */ |
for(k1=1; k1<=m;k1++){
|
| cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/ |
for(i1=1; i1<=ncodemax[k1];i1++){
|
| if (strcmp(strc,"age")==0) { /* Vn*age */ |
jj1++;
|
| cptcovprod--; |
if (cptcovn > 0) {
|
| cutv(strb,stre,strd,'V'); |
fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
|
| Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/ |
for (cpt=1; cpt<=cptcoveff;cpt++)
|
| cptcovage++; |
fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
|
| Tage[cptcovage]=i; |
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
|
| /*printf("stre=%s ", stre);*/ |
}
|
| } |
/* Pij */
|
| else if (strcmp(strd,"age")==0) { /* or age*Vn */ |
fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
|
| cptcovprod--; |
<img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
|
| cutv(strb,stre,strc,'V'); |
/* Quasi-incidences */
|
| Tvar[i]=atoi(stre); |
fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
|
| cptcovage++; |
before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
|
| Tage[cptcovage]=i; |
<img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
|
| } |
/* Period (stable) prevalence in each health state */
|
| else { /* Age is not in the model */ |
for(cpt=1; cpt<nlstate;cpt++){
|
| cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/ |
fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
|
| Tvar[i]=ncovcol+k1; |
<img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
|
| cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */ |
}
|
| Tprod[k1]=i; |
for(cpt=1; cpt<=nlstate;cpt++) {
|
| Tvard[k1][1]=atoi(strc); /* m*/ |
fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
|
| Tvard[k1][2]=atoi(stre); /* n */ |
<img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
|
| Tvar[cptcovn+k2]=Tvard[k1][1]; |
}
|
| Tvar[cptcovn+k2+1]=Tvard[k1][2]; |
} /* end i1 */
|
| for (k=1; k<=lastobs;k++) |
}/* End k1 */
|
| covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k]; |
fprintf(fichtm,"</ul>");
|
| k1++; |
|
| k2=k2+2; |
|
| } |
fprintf(fichtm,"\
|
| } |
\n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
|
| else { /* no more sum */ |
- Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
|
| /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/ |
|
| /* scanf("%d",i);*/ |
fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
|
| cutv(strd,strc,strb,'V'); |
subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
|
| Tvar[i]=atoi(strc); |
fprintf(fichtm,"\
|
| } |
- Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
|
| strcpy(modelsav,stra); |
subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
|
| /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav); |
|
| scanf("%d",i);*/ |
fprintf(fichtm,"\
|
| } /* end of loop + */ |
- Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
|
| } /* end model */ |
subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
|
| |
fprintf(fichtm,"\
|
| /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products. |
- Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
|
| If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/ |
<a href=\"%s\">%s</a> <br>\n</li>",
|
| |
estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
|
| /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]); |
fprintf(fichtm,"\
|
| printf("cptcovprod=%d ", cptcovprod); |
- (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
|
| fprintf(ficlog,"cptcovprod=%d ", cptcovprod); |
<a href=\"%s\">%s</a> <br>\n</li>",
|
| |
estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
|
| scanf("%d ",i); |
fprintf(fichtm,"\
|
| fclose(fic);*/ |
- Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences (i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
|
| |
estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
|
| /* if(mle==1){*/ |
fprintf(fichtm,"\
|
| if (weightopt != 1) { /* Maximisation without weights*/ |
- Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors: <a href=\"%s\">%s</a> <br>\n",
|
| for(i=1;i<=n;i++) weight[i]=1.0; |
subdirf2(fileres,"t"),subdirf2(fileres,"t"));
|
| } |
fprintf(fichtm,"\
|
| /*-calculation of age at interview from date of interview and age at death -*/ |
- Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
|
| agev=matrix(1,maxwav,1,imx); |
subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
|
| |
|
| for (i=1; i<=imx; i++) { |
/* if(popforecast==1) fprintf(fichtm,"\n */
|
| for(m=2; (m<= maxwav); m++) { |
/* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
|
| if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){ |
/* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
|
| anint[m][i]=9999; |
/* <br>",fileres,fileres,fileres,fileres); */
|
| s[m][i]=-1; |
/* 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); */
|
| if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1; |
fflush(fichtm);
|
| } |
fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
|
| } |
|
| |
m=cptcoveff;
|
| for (i=1; i<=imx; i++) { |
if (cptcovn < 1) {m=1;ncodemax[1]=1;}
|
| agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]); |
|
| for(m=1; (m<= maxwav); m++){ |
jj1=0;
|
| if(s[m][i] >0){ |
for(k1=1; k1<=m;k1++){
|
| if (s[m][i] >= nlstate+1) { |
for(i1=1; i1<=ncodemax[k1];i1++){
|
| if(agedc[i]>0) |
jj1++;
|
| if(moisdc[i]!=99 && andc[i]!=9999) |
if (cptcovn > 0) {
|
| agev[m][i]=agedc[i]; |
fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
|
| /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/ |
for (cpt=1; cpt<=cptcoveff;cpt++)
|
| else { |
fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
|
| if (andc[i]!=9999){ |
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
|
| printf("Warning negative age at death: %d line:%d\n",num[i],i); |
}
|
| fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i); |
for(cpt=1; cpt<=nlstate;cpt++) {
|
| agev[m][i]=-1; |
fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
|
| } |
prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
|
| } |
<img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
|
| } |
}
|
| else if(s[m][i] !=9){ /* Should no more exist */ |
fprintf(fichtm,"\n<br>- Total life expectancy by age and \
|
| agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]); |
health expectancies in states (1) and (2): %s%d.png<br>\
|
| if(mint[m][i]==99 || anint[m][i]==9999) |
<img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
|
| agev[m][i]=1; |
} /* end i1 */
|
| else if(agev[m][i] <agemin){ |
}/* End k1 */
|
| agemin=agev[m][i]; |
fprintf(fichtm,"</ul>");
|
| /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/ |
fflush(fichtm);
|
| } |
}
|
| else if(agev[m][i] >agemax){ |
|
| agemax=agev[m][i]; |
/******************* Gnuplot file **************/
|
| /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/ |
void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
|
| } |
|
| /*agev[m][i]=anint[m][i]-annais[i];*/ |
char dirfileres[132],optfileres[132];
|
| /* agev[m][i] = age[i]+2*m;*/ |
int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
|
| } |
int ng;
|
| else { /* =9 */ |
/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
|
| agev[m][i]=1; |
/* printf("Problem with file %s",optionfilegnuplot); */
|
| s[m][i]=-1; |
/* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
|
| } |
/* } */
|
| } |
|
| else /*= 0 Unknown */ |
/*#ifdef windows */
|
| agev[m][i]=1; |
fprintf(ficgp,"cd \"%s\" \n",pathc);
|
| } |
/*#endif */
|
| |
m=pow(2,cptcoveff);
|
| } |
|
| for (i=1; i<=imx; i++) { |
strcpy(dirfileres,optionfilefiname);
|
| for(m=1; (m<= maxwav); m++){ |
strcpy(optfileres,"vpl");
|
| if (s[m][i] > (nlstate+ndeath)) { |
/* 1eme*/
|
| printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath); |
for (cpt=1; cpt<= nlstate ; cpt ++) {
|
| fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath); |
for (k1=1; k1<= m ; k1 ++) {
|
| goto end; |
fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
|
| } |
fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
|
| } |
fprintf(ficgp,"set xlabel \"Age\" \n\
|
| } |
set ylabel \"Probability\" \n\
|
| |
set ter png small\n\
|
| printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); |
set size 0.65,0.65\n\
|
| fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); |
plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
|
| |
|
| free_vector(severity,1,maxwav); |
for (i=1; i<= nlstate ; i ++) {
|
| free_imatrix(outcome,1,maxwav+1,1,n); |
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
|
| free_vector(moisnais,1,n); |
else fprintf(ficgp," \%%*lf (\%%*lf)");
|
| free_vector(annais,1,n); |
}
|
| /* free_matrix(mint,1,maxwav,1,n); |
fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
|
| free_matrix(anint,1,maxwav,1,n);*/ |
for (i=1; i<= nlstate ; i ++) {
|
| free_vector(moisdc,1,n); |
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
|
| free_vector(andc,1,n); |
else fprintf(ficgp," \%%*lf (\%%*lf)");
|
| |
}
|
| |
fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
|
| wav=ivector(1,imx); |
for (i=1; i<= nlstate ; i ++) {
|
| dh=imatrix(1,lastpass-firstpass+1,1,imx); |
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
|
| bh=imatrix(1,lastpass-firstpass+1,1,imx); |
else fprintf(ficgp," \%%*lf (\%%*lf)");
|
| mw=imatrix(1,lastpass-firstpass+1,1,imx); |
}
|
| |
fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
|
| /* Concatenates waves */ |
}
|
| concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm); |
}
|
| |
/*2 eme*/
|
| /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */ |
|
| |
for (k1=1; k1<= m ; k1 ++) {
|
| Tcode=ivector(1,100); |
fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
|
| nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); |
fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
|
| ncodemax[1]=1; |
|
| if (cptcovn > 0) tricode(Tvar,nbcode,imx); |
for (i=1; i<= nlstate+1 ; i ++) {
|
| |
k=2*i;
|
| codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of |
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
|
| the estimations*/ |
for (j=1; j<= nlstate+1 ; j ++) {
|
| h=0; |
if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
|
| m=pow(2,cptcoveff); |
else fprintf(ficgp," \%%*lf (\%%*lf)");
|
| |
}
|
| for(k=1;k<=cptcoveff; k++){ |
if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
|
| for(i=1; i <=(m/pow(2,k));i++){ |
else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
|
| for(j=1; j <= ncodemax[k]; j++){ |
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
|
| for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){ |
for (j=1; j<= nlstate+1 ; j ++) {
|
| h++; |
if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
|
| if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j; |
else fprintf(ficgp," \%%*lf (\%%*lf)");
|
| /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/ |
}
|
| } |
fprintf(ficgp,"\" t\"\" w l 0,");
|
| } |
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
|
| } |
for (j=1; j<= nlstate+1 ; j ++) {
|
| } |
if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
|
| /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); |
else fprintf(ficgp," \%%*lf (\%%*lf)");
|
| codtab[1][2]=1;codtab[2][2]=2; */ |
}
|
| /* for(i=1; i <=m ;i++){ |
if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
|
| for(k=1; k <=cptcovn; k++){ |
else fprintf(ficgp,"\" t\"\" w l 0,");
|
| printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); |
}
|
| } |
}
|
| printf("\n"); |
|
| } |
/*3eme*/
|
| scanf("%d",i);*/ |
|
| |
for (k1=1; k1<= m ; k1 ++) {
|
| /* Calculates basic frequencies. Computes observed prevalence at single age |
for (cpt=1; cpt<= nlstate ; cpt ++) {
|
| and prints on file fileres'p'. */ |
/* k=2+nlstate*(2*cpt-2); */
|
| |
k=2+(nlstate+1)*(cpt-1);
|
| pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ |
fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
|
| oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ |
fprintf(ficgp,"set ter png small\n\
|
| newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ |
set size 0.65,0.65\n\
|
| savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ |
plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
|
| oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */ |
/*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
|
| |
for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
|
| |
fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
|
| /* For Powell, parameters are in a vector p[] starting at p[1] |
fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
|
| so we point p on param[1][1] so that p[1] maps on param[1][1][1] */ |
for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
|
| p=param[1][1]; /* *(*(*(param +1)+1)+0) */ |
fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
|
| |
|
| if(mle>=1){ /* Could be 1 or 2 */ |
*/
|
| mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func); |
for (i=1; i< nlstate ; i ++) {
|
| } |
fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
|
| |
/* fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
|
| /*--------- 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); |
}
|
| |
fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
|
| |
}
|
| jk=1; |
}
|
| fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); |
|
| printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); |
/* CV preval stable (period) */
|
| fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); |
for (k1=1; k1<= m ; k1 ++) {
|
| for(i=1,jk=1; i <=nlstate; i++){ |
for (cpt=1; cpt<=nlstate ; cpt ++) {
|
| for(k=1; k <=(nlstate+ndeath); k++){ |
k=3;
|
| if (k != i) |
fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
|
| { |
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
|
| printf("%d%d ",i,k); |
set ter png small\nset size 0.65,0.65\n\
|
| fprintf(ficlog,"%d%d ",i,k); |
unset log y\n\
|
| fprintf(ficres,"%1d%1d ",i,k); |
plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
|
| for(j=1; j <=ncovmodel; j++){ |
|
| printf("%f ",p[jk]); |
for (i=1; i< nlstate ; i ++)
|
| fprintf(ficlog,"%f ",p[jk]); |
fprintf(ficgp,"+$%d",k+i+1);
|
| fprintf(ficres,"%f ",p[jk]); |
fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
|
| jk++; |
|
| } |
l=3+(nlstate+ndeath)*cpt;
|
| printf("\n"); |
fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
|
| fprintf(ficlog,"\n"); |
for (i=1; i< nlstate ; i ++) {
|
| fprintf(ficres,"\n"); |
l=3+(nlstate+ndeath)*cpt;
|
| } |
fprintf(ficgp,"+$%d",l+i+1);
|
| } |
}
|
| } |
fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
|
| if(mle==1){ |
}
|
| /* Computing hessian and covariance matrix */ |
}
|
| ftolhess=ftol; /* Usually correct */ |
|
| hesscov(matcov, p, npar, delti, ftolhess, func); |
/* proba elementaires */
|
| } |
for(i=1,jk=1; i <=nlstate; i++){
|
| fprintf(ficres,"# Scales (for hessian or gradient estimation)\n"); |
for(k=1; k <=(nlstate+ndeath); k++){
|
| printf("# Scales (for hessian or gradient estimation)\n"); |
if (k != i) {
|
| fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n"); |
for(j=1; j <=ncovmodel; j++){
|
| for(i=1,jk=1; i <=nlstate; i++){ |
fprintf(ficgp,"p%d=%f ",jk,p[jk]);
|
| for(j=1; j <=nlstate+ndeath; j++){ |
jk++;
|
| if (j!=i) { |
fprintf(ficgp,"\n");
|
| fprintf(ficres,"%1d%1d",i,j); |
}
|
| printf("%1d%1d",i,j); |
}
|
| fprintf(ficlog,"%1d%1d",i,j); |
}
|
| for(k=1; k<=ncovmodel;k++){ |
}
|
| printf(" %.5e",delti[jk]); |
|
| fprintf(ficlog," %.5e",delti[jk]); |
for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
|
| fprintf(ficres," %.5e",delti[jk]); |
for(jk=1; jk <=m; jk++) {
|
| jk++; |
fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
|
| } |
if (ng==2)
|
| printf("\n"); |
fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
|
| fprintf(ficlog,"\n"); |
else
|
| fprintf(ficres,"\n"); |
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;
|
| 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"); |
for(k=1; k<=(nlstate+ndeath); k++) {
|
| if(mle==1) |
if (k != k2){
|
| 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"); |
if(ng==2)
|
| fprintf(ficlog,"# 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"); |
fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
|
| for(i=1,k=1;i<=npar;i++){ |
else
|
| /* if (k>nlstate) k=1; |
fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
|
| i1=(i-1)/(ncovmodel*nlstate)+1; |
ij=1;
|
| fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]); |
for(j=3; j <=ncovmodel; j++) {
|
| printf("%s%d%d",alph[k],i1,tab[i]); |
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]]]);
|
| fprintf(ficres,"%3d",i); |
ij++;
|
| if(mle==1) |
}
|
| printf("%3d",i); |
else
|
| fprintf(ficlog,"%3d",i); |
fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
|
| for(j=1; j<=i;j++){ |
}
|
| fprintf(ficres," %.5e",matcov[i][j]); |
fprintf(ficgp,")/(1");
|
| if(mle==1) |
|
| printf(" %.5e",matcov[i][j]); |
for(k1=1; k1 <=nlstate; k1++){
|
| fprintf(ficlog," %.5e",matcov[i][j]); |
fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
|
| } |
ij=1;
|
| fprintf(ficres,"\n"); |
for(j=3; j <=ncovmodel; j++){
|
| if(mle==1) |
if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
|
| printf("\n"); |
fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
|
| fprintf(ficlog,"\n"); |
ij++;
|
| k++; |
}
|
| } |
else
|
| |
fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
|
| while((c=getc(ficpar))=='#' && c!= EOF){ |
}
|
| ungetc(c,ficpar); |
fprintf(ficgp,")");
|
| fgets(line, MAXLINE, ficpar); |
}
|
| puts(line); |
fprintf(ficgp,") t \"p%d%d\" ", k2,k);
|
| fputs(line,ficparo); |
if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
|
| } |
i=i+ncovmodel;
|
| ungetc(c,ficpar); |
}
|
| |
} /* end k */
|
| estepm=0; |
} /* end k2 */
|
| fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); |
} /* end jk */
|
| if (estepm==0 || estepm < stepm) estepm=stepm; |
} /* end ng */
|
| if (fage <= 2) { |
fflush(ficgp);
|
| bage = ageminpar; |
} /* end gnuplot */
|
| fage = agemaxpar; |
|
| } |
|
| |
/*************** Moving average **************/
|
| fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n"); |
int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
|
| 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); |
int i, cpt, cptcod;
|
| |
int modcovmax =1;
|
| while((c=getc(ficpar))=='#' && c!= EOF){ |
int mobilavrange, mob;
|
| ungetc(c,ficpar); |
double age;
|
| fgets(line, MAXLINE, ficpar); |
|
| puts(line); |
modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
|
| fputs(line,ficparo); |
a covariate has 2 modalities */
|
| } |
if (cptcovn<1) modcovmax=1; /* At least 1 pass */
|
| ungetc(c,ficpar); |
|
| |
if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
|
| fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav); |
if(mobilav==1) mobilavrange=5; /* default */
|
| fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav); |
else mobilavrange=mobilav;
|
| fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav); |
for (age=bage; age<=fage; age++)
|
| |
for (i=1; i<=nlstate;i++)
|
| while((c=getc(ficpar))=='#' && c!= EOF){ |
for (cptcod=1;cptcod<=modcovmax;cptcod++)
|
| ungetc(c,ficpar); |
mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
|
| fgets(line, MAXLINE, ficpar); |
/* We keep the original values on the extreme ages bage, fage and for
|
| puts(line); |
fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
|
| fputs(line,ficparo); |
we use a 5 terms etc. until the borders are no more concerned.
|
| } |
*/
|
| ungetc(c,ficpar); |
for (mob=3;mob <=mobilavrange;mob=mob+2){
|
| |
for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
|
| |
for (i=1; i<=nlstate;i++){
|
| dateprev1=anprev1+mprev1/12.+jprev1/365.; |
for (cptcod=1;cptcod<=modcovmax;cptcod++){
|
| dateprev2=anprev2+mprev2/12.+jprev2/365.; |
mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
|
| |
for (cpt=1;cpt<=(mob-1)/2;cpt++){
|
| fscanf(ficpar,"pop_based=%d\n",&popbased); |
mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
|
| fprintf(ficparo,"pop_based=%d\n",popbased); |
mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
|
| fprintf(ficres,"pop_based=%d\n",popbased); |
}
|
| |
mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
|
| while((c=getc(ficpar))=='#' && c!= EOF){ |
}
|
| ungetc(c,ficpar); |
}
|
| fgets(line, MAXLINE, ficpar); |
}/* end age */
|
| puts(line); |
}/* end mob */
|
| fputs(line,ficparo); |
}else return -1;
|
| } |
return 0;
|
| ungetc(c,ficpar); |
}/* End movingaverage */
|
| |
|
| fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2); |
|
| fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2); |
/************** Forecasting ******************/
|
| fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2); |
prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
|
| |
/* proj1, year, month, day of starting projection
|
| |
agemin, agemax range of age
|
| while((c=getc(ficpar))=='#' && c!= EOF){ |
dateprev1 dateprev2 range of dates during which prevalence is computed
|
| ungetc(c,ficpar); |
anproj2 year of en of projection (same day and month as proj1).
|
| fgets(line, MAXLINE, ficpar); |
*/
|
| puts(line); |
int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
|
| fputs(line,ficparo); |
int *popage;
|
| } |
double agec; /* generic age */
|
| ungetc(c,ficpar); |
double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
|
| |
double *popeffectif,*popcount;
|
| fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1); |
double ***p3mat;
|
| fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1); |
double ***mobaverage;
|
| fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1); |
char fileresf[FILENAMELENGTH];
|
| |
|
| freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); |
agelim=AGESUP;
|
| |
prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
|
| /*------------ gnuplot -------------*/ |
|
| strcpy(optionfilegnuplot,optionfilefiname); |
strcpy(fileresf,"f");
|
| strcat(optionfilegnuplot,".gp"); |
strcat(fileresf,fileres);
|
| if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) { |
if((ficresf=fopen(fileresf,"w"))==NULL) {
|
| printf("Problem with file %s",optionfilegnuplot); |
printf("Problem with forecast resultfile: %s\n", fileresf);
|
| } |
fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
|
| else{ |
}
|
| fprintf(ficgp,"\n# %s\n", version); |
printf("Computing forecasting: result on file '%s' \n", fileresf);
|
| fprintf(ficgp,"# %s\n", optionfilegnuplot); |
fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
|
| fprintf(ficgp,"set missing 'NaNq'\n"); |
|
| } |
if (cptcoveff==0) ncodemax[cptcoveff]=1;
|
| fclose(ficgp); |
|
| printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p); |
if (mobilav!=0) {
|
| /*--------- index.htm --------*/ |
mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
|
| |
if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
|
| strcpy(optionfilehtm,optionfile); |
fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
|
| strcat(optionfilehtm,".htm"); |
printf(" Error in movingaverage mobilav=%d\n",mobilav);
|
| if((fichtm=fopen(optionfilehtm,"w"))==NULL) { |
}
|
| printf("Problem with %s \n",optionfilehtm), exit(0); |
}
|
| } |
|
| |
stepsize=(int) (stepm+YEARM-1)/YEARM;
|
| fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n |
if (stepm<=12) stepsize=1;
|
| Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n |
if(estepm < stepm){
|
| \n |
printf ("Problem %d lower than %d\n",estepm, stepm);
|
| Total number of observations=%d <br>\n |
}
|
| Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n |
else hstepm=estepm;
|
| <hr size=\"2\" color=\"#EC5E5E\"> |
|
| <ul><li><h4>Parameter files</h4>\n |
hstepm=hstepm/stepm;
|
| - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n |
yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
|
| - Log file of the run: <a href=\"%s\">%s</a><br>\n |
fractional in yp1 */
|
| - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot); |
anprojmean=yp;
|
| fclose(fichtm); |
yp2=modf((yp1*12),&yp);
|
| |
mprojmean=yp;
|
| printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2); |
yp1=modf((yp2*30.5),&yp);
|
| |
jprojmean=yp;
|
| /*------------ free_vector -------------*/ |
if(jprojmean==0) jprojmean=1;
|
| chdir(path); |
if(mprojmean==0) jprojmean=1;
|
| |
|
| free_ivector(wav,1,imx); |
i1=cptcoveff;
|
| free_imatrix(dh,1,lastpass-firstpass+1,1,imx); |
if (cptcovn < 1){i1=1;}
|
| free_imatrix(bh,1,lastpass-firstpass+1,1,imx); |
|
| free_imatrix(mw,1,lastpass-firstpass+1,1,imx); |
fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
|
| free_ivector(num,1,n); |
|
| free_vector(agedc,1,n); |
fprintf(ficresf,"#****** Routine prevforecast **\n");
|
| free_matrix(covar,0,NCOVMAX,1,n); |
|
| /*free_matrix(covar,1,NCOVMAX,1,n);*/ |
/* if (h==(int)(YEARM*yearp)){ */
|
| fclose(ficparo); |
for(cptcov=1, k=0;cptcov<=i1;cptcov++){
|
| fclose(ficres); |
for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
|
| |
k=k+1;
|
| |
fprintf(ficresf,"\n#******");
|
| /*--------------- Prevalence limit (stable prevalence) --------------*/ |
for(j=1;j<=cptcoveff;j++) {
|
| |
fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
|
| strcpy(filerespl,"pl"); |
}
|
| strcat(filerespl,fileres); |
fprintf(ficresf,"******\n");
|
| if((ficrespl=fopen(filerespl,"w"))==NULL) { |
fprintf(ficresf,"# Covariate valuofcovar yearproj age");
|
| printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end; |
for(j=1; j<=nlstate+ndeath;j++){
|
| fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end; |
for(i=1; i<=nlstate;i++)
|
| } |
fprintf(ficresf," p%d%d",i,j);
|
| printf("Computing stable prevalence: result on file '%s' \n", filerespl); |
fprintf(ficresf," p.%d",j);
|
| fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl); |
}
|
| fprintf(ficrespl,"#Stable prevalence \n"); |
for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
|
| fprintf(ficrespl,"#Age "); |
fprintf(ficresf,"\n");
|
| for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i); |
fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
|
| fprintf(ficrespl,"\n"); |
|
| |
for (agec=fage; agec>=(ageminpar-1); agec--){
|
| prlim=matrix(1,nlstate,1,nlstate); |
nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
|
| |
nhstepm = nhstepm/hstepm;
|
| agebase=ageminpar; |
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
| agelim=agemaxpar; |
oldm=oldms;savm=savms;
|
| ftolpl=1.e-10; |
hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
|
| i1=cptcoveff; |
|
| if (cptcovn < 1){i1=1;} |
for (h=0; h<=nhstepm; h++){
|
| |
if (h*hstepm/YEARM*stepm ==yearp) {
|
| for(cptcov=1,k=0;cptcov<=i1;cptcov++){ |
fprintf(ficresf,"\n");
|
| for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ |
for(j=1;j<=cptcoveff;j++)
|
| k=k+1; |
fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
|
| /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/ |
fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
|
| fprintf(ficrespl,"\n#******"); |
}
|
| printf("\n#******"); |
for(j=1; j<=nlstate+ndeath;j++) {
|
| fprintf(ficlog,"\n#******"); |
ppij=0.;
|
| for(j=1;j<=cptcoveff;j++) { |
for(i=1; i<=nlstate;i++) {
|
| fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
if (mobilav==1)
|
| printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
|
| fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
else {
|
| } |
ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
|
| fprintf(ficrespl,"******\n"); |
}
|
| printf("******\n"); |
if (h*hstepm/YEARM*stepm== yearp) {
|
| fprintf(ficlog,"******\n"); |
fprintf(ficresf," %.3f", p3mat[i][j][h]);
|
| |
}
|
| for (age=agebase; age<=agelim; age++){ |
} /* end i */
|
| prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); |
if (h*hstepm/YEARM*stepm==yearp) {
|
| fprintf(ficrespl,"%.0f",age ); |
fprintf(ficresf," %.3f", ppij);
|
| for(i=1; i<=nlstate;i++) |
}
|
| fprintf(ficrespl," %.5f", prlim[i][i]); |
}/* end j */
|
| fprintf(ficrespl,"\n"); |
} /* end h */
|
| } |
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
| } |
} /* end agec */
|
| } |
} /* end yearp */
|
| fclose(ficrespl); |
} /* end cptcod */
|
| |
} /* end cptcov */
|
| /*------------- h Pij x at various ages ------------*/ |
|
| |
if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
|
| strcpy(filerespij,"pij"); strcat(filerespij,fileres); |
|
| if((ficrespij=fopen(filerespij,"w"))==NULL) { |
fclose(ficresf);
|
| printf("Problem with Pij resultfile: %s\n", filerespij);goto end; |
}
|
| fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end; |
|
| } |
/************** Forecasting *****not tested NB*************/
|
| printf("Computing pij: result on file '%s' \n", filerespij); |
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){
|
| fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij); |
|
| |
int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
|
| stepsize=(int) (stepm+YEARM-1)/YEARM; |
int *popage;
|
| /*if (stepm<=24) stepsize=2;*/ |
double calagedatem, agelim, kk1, kk2;
|
| |
double *popeffectif,*popcount;
|
| agelim=AGESUP; |
double ***p3mat,***tabpop,***tabpopprev;
|
| hstepm=stepsize*YEARM; /* Every year of age */ |
double ***mobaverage;
|
| hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ |
char filerespop[FILENAMELENGTH];
|
| |
|
| /* hstepm=1; aff par mois*/ |
tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
|
| |
tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
|
| for(cptcov=1,k=0;cptcov<=i1;cptcov++){ |
agelim=AGESUP;
|
| for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ |
calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
|
| k=k+1; |
|
| fprintf(ficrespij,"\n#****** "); |
prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
|
| for(j=1;j<=cptcoveff;j++) |
|
| fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
|
| fprintf(ficrespij,"******\n"); |
strcpy(filerespop,"pop");
|
| |
strcat(filerespop,fileres);
|
| for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */ |
if((ficrespop=fopen(filerespop,"w"))==NULL) {
|
| nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ |
printf("Problem with forecast resultfile: %s\n", filerespop);
|
| nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */ |
fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
|
| |
}
|
| /* nhstepm=nhstepm*YEARM; aff par mois*/ |
printf("Computing forecasting: result on file '%s' \n", filerespop);
|
| |
fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
|
| p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
|
| oldm=oldms;savm=savms; |
if (cptcoveff==0) ncodemax[cptcoveff]=1;
|
| hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); |
|
| fprintf(ficrespij,"# Age"); |
if (mobilav!=0) {
|
| for(i=1; i<=nlstate;i++) |
mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
|
| for(j=1; j<=nlstate+ndeath;j++) |
if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
|
| fprintf(ficrespij," %1d-%1d",i,j); |
fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
|
| fprintf(ficrespij,"\n"); |
printf(" Error in movingaverage mobilav=%d\n",mobilav);
|
| 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++) |
stepsize=(int) (stepm+YEARM-1)/YEARM;
|
| fprintf(ficrespij," %.5f", p3mat[i][j][h]); |
if (stepm<=12) stepsize=1;
|
| fprintf(ficrespij,"\n"); |
|
| } |
agelim=AGESUP;
|
| free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
|
| fprintf(ficrespij,"\n"); |
hstepm=1;
|
| } |
hstepm=hstepm/stepm;
|
| } |
|
| } |
if (popforecast==1) {
|
| |
if((ficpop=fopen(popfile,"r"))==NULL) {
|
| varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax); |
printf("Problem with population file : %s\n",popfile);exit(0);
|
| |
fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
|
| fclose(ficrespij); |
}
|
| |
popage=ivector(0,AGESUP);
|
| |
popeffectif=vector(0,AGESUP);
|
| /*---------- Forecasting ------------------*/ |
popcount=vector(0,AGESUP);
|
| if((stepm == 1) && (strcmp(model,".")==0)){ |
|
| prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1); |
i=1;
|
| if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1); |
while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
|
| } |
|
| else{ |
imx=i;
|
| erreur=108; |
for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
|
| 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); |
}
|
| fprintf(ficlog,"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); |
|
| } |
for(cptcov=1,k=0;cptcov<=i2;cptcov++){
|
| |
for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
|
| |
k=k+1;
|
| /*---------- Health expectancies and variances ------------*/ |
fprintf(ficrespop,"\n#******");
|
| |
for(j=1;j<=cptcoveff;j++) {
|
| strcpy(filerest,"t"); |
fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
|
| strcat(filerest,fileres); |
}
|
| if((ficrest=fopen(filerest,"w"))==NULL) { |
fprintf(ficrespop,"******\n");
|
| printf("Problem with total LE resultfile: %s\n", filerest);goto end; |
fprintf(ficrespop,"# Age");
|
| fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end; |
for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
|
| } |
if (popforecast==1) fprintf(ficrespop," [Population]");
|
| printf("Computing Total LEs with variances: file '%s' \n", filerest); |
|
| fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); |
for (cpt=0; cpt<=0;cpt++) {
|
| |
fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
|
| |
|
| strcpy(filerese,"e"); |
for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
|
| strcat(filerese,fileres); |
nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
|
| if((ficreseij=fopen(filerese,"w"))==NULL) { |
nhstepm = nhstepm/hstepm;
|
| printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0); |
|
| fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0); |
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
| } |
oldm=oldms;savm=savms;
|
| printf("Computing Health Expectancies: result on file '%s' \n", filerese); |
hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
|
| fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese); |
|
| |
for (h=0; h<=nhstepm; h++){
|
| strcpy(fileresv,"v"); |
if (h==(int) (calagedatem+YEARM*cpt)) {
|
| strcat(fileresv,fileres); |
fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
|
| if((ficresvij=fopen(fileresv,"w"))==NULL) { |
}
|
| printf("Problem with variance resultfile: %s\n", fileresv);exit(0); |
for(j=1; j<=nlstate+ndeath;j++) {
|
| fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0); |
kk1=0.;kk2=0;
|
| } |
for(i=1; i<=nlstate;i++) {
|
| printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); |
if (mobilav==1)
|
| fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); |
kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
|
| |
else {
|
| calagedate=-1; |
kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
|
| |
}
|
| prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate); |
}
|
| |
if (h==(int)(calagedatem+12*cpt)){
|
| if (mobilav!=0) { |
tabpop[(int)(agedeb)][j][cptcod]=kk1;
|
| mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
/*fprintf(ficrespop," %.3f", kk1);
|
| if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ |
if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
|
| fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); |
}
|
| printf(" Error in movingaverage mobilav=%d\n",mobilav); |
}
|
| } |
for(i=1; i<=nlstate;i++){
|
| } |
kk1=0.;
|
| |
for(j=1; j<=nlstate;j++){
|
| for(cptcov=1,k=0;cptcov<=i1;cptcov++){ |
kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
|
| for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ |
}
|
| k=k+1; |
tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
|
| fprintf(ficrest,"\n#****** "); |
}
|
| for(j=1;j<=cptcoveff;j++) |
|
| fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
|
| fprintf(ficrest,"******\n"); |
fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
|
| |
}
|
| fprintf(ficreseij,"\n#****** "); |
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
| 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++) |
for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
|
| fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
|
| fprintf(ficresvij,"******\n"); |
for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
|
| |
nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
|
| eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); |
nhstepm = nhstepm/hstepm;
|
| oldm=oldms;savm=savms; |
|
| evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov); |
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
| |
oldm=oldms;savm=savms;
|
| vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); |
hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
|
| oldm=oldms;savm=savms; |
for (h=0; h<=nhstepm; h++){
|
| varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav); |
if (h==(int) (calagedatem+YEARM*cpt)) {
|
| if(popbased==1){ |
fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
|
| varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav); |
}
|
| } |
for(j=1; j<=nlstate+ndeath;j++) {
|
| |
kk1=0.;kk2=0;
|
| |
for(i=1; i<=nlstate;i++) {
|
| fprintf(ficrest,"#Total LEs with variances: e.. (std) "); |
kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
|
| for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i); |
}
|
| fprintf(ficrest,"\n"); |
if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
|
| |
}
|
| epj=vector(1,nlstate+1); |
}
|
| for(age=bage; age <=fage ;age++){ |
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
| prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); |
}
|
| if (popbased==1) { |
}
|
| if(mobilav ==0){ |
}
|
| for(i=1; i<=nlstate;i++) |
}
|
| prlim[i][i]=probs[(int)age][i][k]; |
|
| }else{ /* mobilav */ |
if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
|
| for(i=1; i<=nlstate;i++) |
|
| prlim[i][i]=mobaverage[(int)age][i][k]; |
if (popforecast==1) {
|
| } |
free_ivector(popage,0,AGESUP);
|
| } |
free_vector(popeffectif,0,AGESUP);
|
| |
free_vector(popcount,0,AGESUP);
|
| fprintf(ficrest," %4.0f",age); |
}
|
| for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){ |
free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
|
| for(i=1, epj[j]=0.;i <=nlstate;i++) { |
free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
|
| epj[j] += prlim[i][i]*eij[i][j][(int)age]; |
fclose(ficrespop);
|
| /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/ |
} /* End of popforecast */
|
| } |
|
| epj[nlstate+1] +=epj[j]; |
int fileappend(FILE *fichier, char *optionfich)
|
| } |
{
|
| |
if((fichier=fopen(optionfich,"a"))==NULL) {
|
| for(i=1, vepp=0.;i <=nlstate;i++) |
printf("Problem with file: %s\n", optionfich);
|
| for(j=1;j <=nlstate;j++) |
fprintf(ficlog,"Problem with file: %s\n", optionfich);
|
| vepp += vareij[i][j][(int)age]; |
return (0);
|
| fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp)); |
}
|
| for(j=1;j <=nlstate;j++){ |
fflush(fichier);
|
| fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age])); |
return (1);
|
| } |
}
|
| fprintf(ficrest,"\n"); |
|
| } |
|
| free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage); |
/**************** function prwizard **********************/
|
| free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage); |
void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
|
| free_vector(epj,1,nlstate+1); |
{
|
| } |
|
| } |
/* Wizard to print covariance matrix template */
|
| free_vector(weight,1,n); |
|
| free_imatrix(Tvard,1,15,1,2); |
char ca[32], cb[32], cc[32];
|
| free_imatrix(s,1,maxwav+1,1,n); |
int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
|
| free_matrix(anint,1,maxwav,1,n); |
int numlinepar;
|
| free_matrix(mint,1,maxwav,1,n); |
|
| free_ivector(cod,1,n); |
printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
|
| free_ivector(tab,1,NCOVMAX); |
fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
|
| fclose(ficreseij); |
for(i=1; i <=nlstate; i++){
|
| fclose(ficresvij); |
jj=0;
|
| fclose(ficrest); |
for(j=1; j <=nlstate+ndeath; j++){
|
| fclose(ficpar); |
if(j==i) continue;
|
| |
jj++;
|
| /*------- Variance of stable prevalence------*/ |
/*ca[0]= k+'a'-1;ca[1]='\0';*/
|
| |
printf("%1d%1d",i,j);
|
| strcpy(fileresvpl,"vpl"); |
fprintf(ficparo,"%1d%1d",i,j);
|
| strcat(fileresvpl,fileres); |
for(k=1; k<=ncovmodel;k++){
|
| if((ficresvpl=fopen(fileresvpl,"w"))==NULL) { |
/* printf(" %lf",param[i][j][k]); */
|
| printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl); |
/* fprintf(ficparo," %lf",param[i][j][k]); */
|
| exit(0); |
printf(" 0.");
|
| } |
fprintf(ficparo," 0.");
|
| printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl); |
}
|
| |
printf("\n");
|
| for(cptcov=1,k=0;cptcov<=i1;cptcov++){ |
fprintf(ficparo,"\n");
|
| for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ |
}
|
| k=k+1; |
}
|
| fprintf(ficresvpl,"\n#****** "); |
printf("# Scales (for hessian or gradient estimation)\n");
|
| for(j=1;j<=cptcoveff;j++) |
fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
|
| fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
|
| fprintf(ficresvpl,"******\n"); |
for(i=1; i <=nlstate; i++){
|
| |
jj=0;
|
| varpl=matrix(1,nlstate,(int) bage, (int) fage); |
for(j=1; j <=nlstate+ndeath; j++){
|
| oldm=oldms;savm=savms; |
if(j==i) continue;
|
| varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k); |
jj++;
|
| free_matrix(varpl,1,nlstate,(int) bage, (int)fage); |
fprintf(ficparo,"%1d%1d",i,j);
|
| } |
printf("%1d%1d",i,j);
|
| } |
fflush(stdout);
|
| |
for(k=1; k<=ncovmodel;k++){
|
| fclose(ficresvpl); |
/* printf(" %le",delti3[i][j][k]); */
|
| |
/* fprintf(ficparo," %le",delti3[i][j][k]); */
|
| /*---------- End : free ----------------*/ |
printf(" 0.");
|
| free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath); |
fprintf(ficparo," 0.");
|
| free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath); |
}
|
| free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath); |
numlinepar++;
|
| free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath); |
printf("\n");
|
| |
fprintf(ficparo,"\n");
|
| free_matrix(matcov,1,npar,1,npar); |
}
|
| free_vector(delti,1,npar); |
}
|
| free_matrix(agev,1,maxwav,1,imx); |
printf("# Covariance matrix\n");
|
| free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); |
/* # 121 Var(a12)\n\ */
|
| if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
/* # 122 Cov(b12,a12) Var(b12)\n\ */
|
| free_ivector(ncodemax,1,8); |
/* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
|
| free_ivector(Tvar,1,15); |
/* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
|
| free_ivector(Tprod,1,15); |
/* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
|
| free_ivector(Tvaraff,1,15); |
/* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
|
| free_ivector(Tage,1,15); |
/* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
|
| free_ivector(Tcode,1,100); |
/* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
|
| |
fflush(stdout);
|
| fprintf(fichtm,"\n</body>"); |
fprintf(ficparo,"# Covariance matrix\n");
|
| fclose(fichtm); |
/* # 121 Var(a12)\n\ */
|
| fclose(ficgp); |
/* # 122 Cov(b12,a12) Var(b12)\n\ */
|
| |
/* # ...\n\ */
|
| |
/* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
|
| if(erreur >0){ |
|
| printf("End of Imach with error or warning %d\n",erreur); |
for(itimes=1;itimes<=2;itimes++){
|
| fprintf(ficlog,"End of Imach with error or warning %d\n",erreur); |
jj=0;
|
| }else{ |
for(i=1; i <=nlstate; i++){
|
| printf("End of Imach\n"); |
for(j=1; j <=nlstate+ndeath; j++){
|
| fprintf(ficlog,"End of Imach\n"); |
if(j==i) continue;
|
| } |
for(k=1; k<=ncovmodel;k++){
|
| printf("See log file on %s\n",filelog); |
jj++;
|
| fclose(ficlog); |
ca[0]= k+'a'-1;ca[1]='\0';
|
| /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */ |
if(itimes==1){
|
| |
printf("#%1d%1d%d",i,j,k);
|
| /* 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);*/ |
fprintf(ficparo,"#%1d%1d%d",i,j,k);
|
| /*printf("Total time was %d uSec.\n", total_usecs);*/ |
}else{
|
| /*------ End -----------*/ |
printf("%1d%1d%d",i,j,k);
|
| |
fprintf(ficparo,"%1d%1d%d",i,j,k);
|
| end: |
/* printf(" %.5le",matcov[i][j]); */
|
| #ifdef windows |
}
|
| /* chdir(pathcd);*/ |
ll=0;
|
| #endif |
for(li=1;li <=nlstate; li++){
|
| /*system("wgnuplot graph.plt");*/ |
for(lj=1;lj <=nlstate+ndeath; lj++){
|
| /*system("../gp37mgw/wgnuplot graph.plt");*/ |
if(lj==li) continue;
|
| /*system("cd ../gp37mgw");*/ |
for(lk=1;lk<=ncovmodel;lk++){
|
| /* system("..\\gp37mgw\\wgnuplot graph.plt");*/ |
ll++;
|
| strcpy(plotcmd,GNUPLOTPROGRAM); |
if(ll<=jj){
|
| strcat(plotcmd," "); |
cb[0]= lk +'a'-1;cb[1]='\0';
|
| strcat(plotcmd,optionfilegnuplot); |
if(ll<jj){
|
| printf("Starting: %s\n",plotcmd);fflush(stdout); |
if(itimes==1){
|
| system(plotcmd); |
printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
|
| |
fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
|
| /*#ifdef windows*/ |
}else{
|
| while (z[0] != 'q') { |
printf(" 0.");
|
| /* chdir(path); */ |
fprintf(ficparo," 0.");
|
| printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: "); |
}
|
| scanf("%s",z); |
}else{
|
| if (z[0] == 'c') system("./imach"); |
if(itimes==1){
|
| else if (z[0] == 'e') system(optionfilehtm); |
printf(" Var(%s%1d%1d)",ca,i,j);
|
| else if (z[0] == 'g') system(plotcmd); |
fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
|
| else if (z[0] == 'q') exit(0); |
}else{
|
| } |
printf(" 0.");
|
| /*#endif */ |
fprintf(ficparo," 0.");
|
| } |
}
|
| |
}
|
| |
}
|
| |
} /* end lk */
|
| |
} /* end lj */
|
| |
} /* end li */
|
| |
printf("\n");
|
| |
fprintf(ficparo,"\n");
|
| |
numlinepar++;
|
| |
} /* end k*/
|
| |
} /*end j */
|
| |
} /* end i */
|
| |
} /* end itimes */
|
| |
|
| |
} /* end of prwizard */
|
| |
/******************* Gompertz Likelihood ******************************/
|
| |
double gompertz(double x[])
|
| |
{
|
| |
double A,B,L=0.0,sump=0.,num=0.;
|
| |
int i,n=0; /* n is the size of the sample */
|
| |
|
| |
for (i=0;i<=imx-1 ; i++) {
|
| |
sump=sump+weight[i];
|
| |
/* sump=sump+1;*/
|
| |
num=num+1;
|
| |
}
|
| |
|
| |
|
| |
/* for (i=0; i<=imx; i++)
|
| |
if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
|
| |
|
| |
for (i=1;i<=imx ; i++)
|
| |
{
|
| |
if (cens[i] == 1 && wav[i]>1)
|
| |
A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
|
| |
|
| |
if (cens[i] == 0 && wav[i]>1)
|
| |
A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
|
| |
+log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
|
| |
|
| |
/*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
|
| |
if (wav[i] > 1 ) { /* ??? */
|
| |
L=L+A*weight[i];
|
| |
/* printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
|
| |
}
|
| |
}
|
| |
|
| |
/*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
|
| |
|
| |
return -2*L*num/sump;
|
| |
}
|
| |
|
| |
/******************* Printing html file ***********/
|
| |
void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
|
| |
int lastpass, int stepm, int weightopt, char model[],\
|
| |
int imx, double p[],double **matcov,double agemortsup){
|
| |
int i,k;
|
| |
|
| |
fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
|
| |
fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
|
| |
for (i=1;i<=2;i++)
|
| |
fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
|
| |
fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
|
| |
fprintf(fichtm,"</ul>");
|
| |
|
| |
fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
|
| |
|
| |
fprintf(fichtm,"\nAge l<inf>x</inf> q<inf>x</inf> d(x,x+1) L<inf>x</inf> T<inf>x</inf> e<infx</inf><br>");
|
| |
|
| |
for (k=agegomp;k<(agemortsup-2);k++)
|
| |
fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
|
| |
|
| |
|
| |
fflush(fichtm);
|
| |
}
|
| |
|
| |
/******************* Gnuplot file **************/
|
| |
void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
|
| |
|
| |
char dirfileres[132],optfileres[132];
|
| |
int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
|
| |
int ng;
|
| |
|
| |
|
| |
/*#ifdef windows */
|
| |
fprintf(ficgp,"cd \"%s\" \n",pathc);
|
| |
/*#endif */
|
| |
|
| |
|
| |
strcpy(dirfileres,optionfilefiname);
|
| |
strcpy(optfileres,"vpl");
|
| |
fprintf(ficgp,"set out \"graphmort.png\"\n ");
|
| |
fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
|
| |
fprintf(ficgp, "set ter png small\n set log y\n");
|
| |
fprintf(ficgp, "set size 0.65,0.65\n");
|
| |
fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
|
| |
|
| |
}
|
| |
|
| |
|
| |
|
| |
|
| |
|
| |
/***********************************************/
|
| |
/**************** Main Program *****************/
|
| |
/***********************************************/
|
| |
|
| |
int main(int argc, char *argv[])
|
| |
{
|
| |
int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
|
| |
int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
|
| |
int linei, month, year,iout;
|
| |
int jj, ll, li, lj, lk, imk;
|
| |
int numlinepar=0; /* Current linenumber of parameter file */
|
| |
int itimes;
|
| |
int NDIM=2;
|
| |
|
| |
char ca[32], cb[32], cc[32];
|
| |
char dummy[]=" ";
|
| |
/* FILE *fichtm; *//* Html File */
|
| |
/* FILE *ficgp;*/ /*Gnuplot File */
|
| |
struct stat info;
|
| |
double agedeb, agefin,hf;
|
| |
double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
|
| |
|
| |
double fret;
|
| |
double **xi,tmp,delta;
|
| |
|
| |
double dum; /* Dummy variable */
|
| |
double ***p3mat;
|
| |
double ***mobaverage;
|
| |
int *indx;
|
| |
char line[MAXLINE], linepar[MAXLINE];
|
| |
char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
|
| |
char pathr[MAXLINE], pathimach[MAXLINE];
|
| |
char **bp, *tok, *val; /* pathtot */
|
| |
int firstobs=1, lastobs=10;
|
| |
int sdeb, sfin; /* Status at beginning and end */
|
| |
int c, h , cpt,l;
|
| |
int ju,jl, mi;
|
| |
int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
|
| |
int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
|
| |
int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
|
| |
int mobilav=0,popforecast=0;
|
| |
int hstepm, nhstepm;
|
| |
int agemortsup;
|
| |
float sumlpop=0.;
|
| |
double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
|
| |
double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
|
| |
|
| |
double bage, fage, age, agelim, agebase;
|
| |
double ftolpl=FTOL;
|
| |
double **prlim;
|
| |
double *severity;
|
| |
double ***param; /* Matrix of parameters */
|
| |
double *p;
|
| |
double **matcov; /* Matrix of covariance */
|
| |
double ***delti3; /* Scale */
|
| |
double *delti; /* Scale */
|
| |
double ***eij, ***vareij;
|
| |
double **varpl; /* Variances of prevalence limits by age */
|
| |
double *epj, vepp;
|
| |
double kk1, kk2;
|
| |
double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
|
| |
double **ximort;
|
| |
char *alph[]={"a","a","b","c","d","e"}, str[4];
|
| |
int *dcwave;
|
| |
|
| |
char z[1]="c", occ;
|
| |
|
| |
char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
|
| |
char *strt, strtend[80];
|
| |
char *stratrunc;
|
| |
int lstra;
|
| |
|
| |
long total_usecs;
|
| |
|
| |
/* setlocale (LC_ALL, ""); */
|
| |
/* bindtextdomain (PACKAGE, LOCALEDIR); */
|
| |
/* textdomain (PACKAGE); */
|
| |
/* setlocale (LC_CTYPE, ""); */
|
| |
/* setlocale (LC_MESSAGES, ""); */
|
| |
|
| |
/* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
|
| |
(void) gettimeofday(&start_time,&tzp);
|
| |
curr_time=start_time;
|
| |
tm = *localtime(&start_time.tv_sec);
|
| |
tmg = *gmtime(&start_time.tv_sec);
|
| |
strcpy(strstart,asctime(&tm));
|
| |
|
| |
/* printf("Localtime (at start)=%s",strstart); */
|
| |
/* tp.tv_sec = tp.tv_sec +86400; */
|
| |
/* tm = *localtime(&start_time.tv_sec); */
|
| |
/* tmg.tm_year=tmg.tm_year +dsign*dyear; */
|
| |
/* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
|
| |
/* tmg.tm_hour=tmg.tm_hour + 1; */
|
| |
/* tp.tv_sec = mktime(&tmg); */
|
| |
/* strt=asctime(&tmg); */
|
| |
/* printf("Time(after) =%s",strstart); */
|
| |
/* (void) time (&time_value);
|
| |
* printf("time=%d,t-=%d\n",time_value,time_value-86400);
|
| |
* tm = *localtime(&time_value);
|
| |
* strstart=asctime(&tm);
|
| |
* printf("tim_value=%d,asctime=%s\n",time_value,strstart);
|
| |
*/
|
| |
|
| |
nberr=0; /* Number of errors and warnings */
|
| |
nbwarn=0;
|
| |
getcwd(pathcd, size);
|
| |
|
| |
printf("\n%s\n%s",version,fullversion);
|
| |
if(argc <=1){
|
| |
printf("\nEnter the parameter file name: ");
|
| |
fgets(pathr,FILENAMELENGTH,stdin);
|
| |
i=strlen(pathr);
|
| |
if(pathr[i-1]=='\n')
|
| |
pathr[i-1]='\0';
|
| |
for (tok = pathr; tok != NULL; ){
|
| |
printf("Pathr |%s|\n",pathr);
|
| |
while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
|
| |
printf("val= |%s| pathr=%s\n",val,pathr);
|
| |
strcpy (pathtot, val);
|
| |
if(pathr[0] == '\0') break; /* Dirty */
|
| |
}
|
| |
}
|
| |
else{
|
| |
strcpy(pathtot,argv[1]);
|
| |
}
|
| |
/*if(getcwd(pathcd, MAXLINE)!= 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 argv[0], imach program to get pathimach */
|
| |
printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
|
| |
split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
|
| |
printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
|
| |
/* strcpy(pathimach,argv[0]); */
|
| |
/* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
|
| |
split(pathtot,path,optionfile,optionfilext,optionfilefiname);
|
| |
printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
|
| |
chdir(path); /* Can be a relative path */
|
| |
if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
|
| |
printf("Current directory %s!\n",pathcd);
|
| |
strcpy(command,"mkdir ");
|
| |
strcat(command,optionfilefiname);
|
| |
if((outcmd=system(command)) != 0){
|
| |
printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
|
| |
/* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
|
| |
/* fclose(ficlog); */
|
| |
/* exit(1); */
|
| |
}
|
| |
/* if((imk=mkdir(optionfilefiname))<0){ */
|
| |
/* perror("mkdir"); */
|
| |
/* } */
|
| |
|
| |
/*-------- arguments in the command line --------*/
|
| |
|
| |
/* Log file */
|
| |
strcat(filelog, optionfilefiname);
|
| |
strcat(filelog,".log"); /* */
|
| |
if((ficlog=fopen(filelog,"w"))==NULL) {
|
| |
printf("Problem with logfile %s\n",filelog);
|
| |
goto end;
|
| |
}
|
| |
fprintf(ficlog,"Log filename:%s\n",filelog);
|
| |
fprintf(ficlog,"\n%s\n%s",version,fullversion);
|
| |
fprintf(ficlog,"\nEnter the parameter file name: \n");
|
| |
fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
|
| |
path=%s \n\
|
| |
optionfile=%s\n\
|
| |
optionfilext=%s\n\
|
| |
optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
|
| |
|
| |
printf("Local time (at start):%s",strstart);
|
| |
fprintf(ficlog,"Local time (at start): %s",strstart);
|
| |
fflush(ficlog);
|
| |
/* (void) gettimeofday(&curr_time,&tzp); */
|
| |
/* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
|
| |
|
| |
/* */
|
| |
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);
|
| |
fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
|
| |
fflush(ficlog);
|
| |
goto end;
|
| |
}
|
| |
|
| |
|
| |
|
| |
strcpy(filereso,"o");
|
| |
strcat(filereso,fileres);
|
| |
if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
|
| |
printf("Problem with Output resultfile: %s\n", filereso);
|
| |
fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
|
| |
fflush(ficlog);
|
| |
goto end;
|
| |
}
|
| |
|
| |
/* Reads comments: lines beginning with '#' */
|
| |
numlinepar=0;
|
| |
while((c=getc(ficpar))=='#' && c!= EOF){
|
| |
ungetc(c,ficpar);
|
| |
fgets(line, MAXLINE, ficpar);
|
| |
numlinepar++;
|
| |
puts(line);
|
| |
fputs(line,ficparo);
|
| |
fputs(line,ficlog);
|
| |
}
|
| |
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 model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
|
| |
numlinepar++;
|
| |
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);
|
| |
fprintf(ficlog,"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);
|
| |
fflush(ficlog);
|
| |
while((c=getc(ficpar))=='#' && c!= EOF){
|
| |
ungetc(c,ficpar);
|
| |
fgets(line, MAXLINE, ficpar);
|
| |
numlinepar++;
|
| |
puts(line);
|
| |
fputs(line,ficparo);
|
| |
fputs(line,ficlog);
|
| |
}
|
| |
ungetc(c,ficpar);
|
| |
|
| |
|
| |
covar=matrix(0,NCOVMAX,1,n);
|
| |
cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
|
| |
if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
|
| |
|
| |
ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
|
| |
nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
|
| |
npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
|
| |
|
| |
delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
|
| |
delti=delti3[1][1];
|
| |
/*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
|
| |
if(mle==-1){ /* Print a wizard for help writing covariance matrix */
|
| |
prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
|
| |
printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
|
| |
fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
|
| |
free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
|
| |
fclose (ficparo);
|
| |
fclose (ficlog);
|
| |
goto end;
|
| |
exit(0);
|
| |
}
|
| |
else if(mle==-3) {
|
| |
prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
|
| |
printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
|
| |
fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
|
| |
param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
|
| |
matcov=matrix(1,npar,1,npar);
|
| |
}
|
| |
else{
|
| |
/* Read guess parameters */
|
| |
/* Reads comments: lines beginning with '#' */
|
| |
while((c=getc(ficpar))=='#' && c!= EOF){
|
| |
ungetc(c,ficpar);
|
| |
fgets(line, MAXLINE, ficpar);
|
| |
numlinepar++;
|
| |
puts(line);
|
| |
fputs(line,ficparo);
|
| |
fputs(line,ficlog);
|
| |
}
|
| |
ungetc(c,ficpar);
|
| |
|
| |
param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
|
| |
for(i=1; i <=nlstate; i++){
|
| |
j=0;
|
| |
for(jj=1; jj <=nlstate+ndeath; jj++){
|
| |
if(jj==i) continue;
|
| |
j++;
|
| |
fscanf(ficpar,"%1d%1d",&i1,&j1);
|
| |
if ((i1 != i) && (j1 != j)){
|
| |
printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
|
| |
It might be a problem of design; if ncovcol and the model are correct\n \
|
| |
run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
|
| |
exit(1);
|
| |
}
|
| |
fprintf(ficparo,"%1d%1d",i1,j1);
|
| |
if(mle==1)
|
| |
printf("%1d%1d",i,j);
|
| |
fprintf(ficlog,"%1d%1d",i,j);
|
| |
for(k=1; k<=ncovmodel;k++){
|
| |
fscanf(ficpar," %lf",¶m[i][j][k]);
|
| |
if(mle==1){
|
| |
printf(" %lf",param[i][j][k]);
|
| |
fprintf(ficlog," %lf",param[i][j][k]);
|
| |
}
|
| |
else
|
| |
fprintf(ficlog," %lf",param[i][j][k]);
|
| |
fprintf(ficparo," %lf",param[i][j][k]);
|
| |
}
|
| |
fscanf(ficpar,"\n");
|
| |
numlinepar++;
|
| |
if(mle==1)
|
| |
printf("\n");
|
| |
fprintf(ficlog,"\n");
|
| |
fprintf(ficparo,"\n");
|
| |
}
|
| |
}
|
| |
fflush(ficlog);
|
| |
|
| |
p=param[1][1];
|
| |
|
| |
/* Reads comments: lines beginning with '#' */
|
| |
while((c=getc(ficpar))=='#' && c!= EOF){
|
| |
ungetc(c,ficpar);
|
| |
fgets(line, MAXLINE, ficpar);
|
| |
numlinepar++;
|
| |
puts(line);
|
| |
fputs(line,ficparo);
|
| |
fputs(line,ficlog);
|
| |
}
|
| |
ungetc(c,ficpar);
|
| |
|
| |
for(i=1; i <=nlstate; i++){
|
| |
for(j=1; j <=nlstate+ndeath-1; j++){
|
| |
fscanf(ficpar,"%1d%1d",&i1,&j1);
|
| |
if ((i1-i)*(j1-j)!=0){
|
| |
printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
|
| |
exit(1);
|
| |
}
|
| |
printf("%1d%1d",i,j);
|
| |
fprintf(ficparo,"%1d%1d",i1,j1);
|
| |
fprintf(ficlog,"%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]);
|
| |
fprintf(ficlog," %le",delti3[i][j][k]);
|
| |
}
|
| |
fscanf(ficpar,"\n");
|
| |
numlinepar++;
|
| |
printf("\n");
|
| |
fprintf(ficparo,"\n");
|
| |
fprintf(ficlog,"\n");
|
| |
}
|
| |
}
|
| |
fflush(ficlog);
|
| |
|
| |
delti=delti3[1][1];
|
| |
|
| |
|
| |
/* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
|
| |
|
| |
/* Reads comments: lines beginning with '#' */
|
| |
while((c=getc(ficpar))=='#' && c!= EOF){
|
| |
ungetc(c,ficpar);
|
| |
fgets(line, MAXLINE, ficpar);
|
| |
numlinepar++;
|
| |
puts(line);
|
| |
fputs(line,ficparo);
|
| |
fputs(line,ficlog);
|
| |
}
|
| |
ungetc(c,ficpar);
|
| |
|
| |
matcov=matrix(1,npar,1,npar);
|
| |
for(i=1; i <=npar; i++){
|
| |
fscanf(ficpar,"%s",&str);
|
| |
if(mle==1)
|
| |
printf("%s",str);
|
| |
fprintf(ficlog,"%s",str);
|
| |
fprintf(ficparo,"%s",str);
|
| |
for(j=1; j <=i; j++){
|
| |
fscanf(ficpar," %le",&matcov[i][j]);
|
| |
if(mle==1){
|
| |
printf(" %.5le",matcov[i][j]);
|
| |
}
|
| |
fprintf(ficlog," %.5le",matcov[i][j]);
|
| |
fprintf(ficparo," %.5le",matcov[i][j]);
|
| |
}
|
| |
fscanf(ficpar,"\n");
|
| |
numlinepar++;
|
| |
if(mle==1)
|
| |
printf("\n");
|
| |
fprintf(ficlog,"\n");
|
| |
fprintf(ficparo,"\n");
|
| |
}
|
| |
for(i=1; i <=npar; i++)
|
| |
for(j=i+1;j<=npar;j++)
|
| |
matcov[i][j]=matcov[j][i];
|
| |
|
| |
if(mle==1)
|
| |
printf("\n");
|
| |
fprintf(ficlog,"\n");
|
| |
|
| |
fflush(ficlog);
|
| |
|
| |
/*-------- Rewriting parameter file ----------*/
|
| |
strcpy(rfileres,"r"); /* "Rparameterfile */
|
| |
strcat(rfileres,optionfilefiname); /* Parameter file first name*/
|
| |
strcat(rfileres,"."); /* */
|
| |
strcat(rfileres,optionfilext); /* Other files have txt extension */
|
| |
if((ficres =fopen(rfileres,"w"))==NULL) {
|
| |
printf("Problem writing new parameter file: %s\n", fileres);goto end;
|
| |
fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
|
| |
}
|
| |
fprintf(ficres,"#%s\n",version);
|
| |
} /* End of mle != -3 */
|
| |
|
| |
/*-------- data file ----------*/
|
| |
if((fic=fopen(datafile,"r"))==NULL) {
|
| |
printf("Problem while opening datafile: %s\n", datafile);goto end;
|
| |
fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
|
| |
}
|
| |
|
| |
n= lastobs;
|
| |
severity = vector(1,maxwav);
|
| |
outcome=imatrix(1,maxwav+1,1,n);
|
| |
num=lvector(1,n);
|
| |
moisnais=vector(1,n);
|
| |
annais=vector(1,n);
|
| |
moisdc=vector(1,n);
|
| |
andc=vector(1,n);
|
| |
agedc=vector(1,n);
|
| |
cod=ivector(1,n);
|
| |
weight=vector(1,n);
|
| |
for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
|
| |
mint=matrix(1,maxwav,1,n);
|
| |
anint=matrix(1,maxwav,1,n);
|
| |
s=imatrix(1,maxwav+1,1,n);
|
| |
tab=ivector(1,NCOVMAX);
|
| |
ncodemax=ivector(1,8);
|
| |
|
| |
i=1;
|
| |
linei=0;
|
| |
while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
|
| |
linei=linei+1;
|
| |
for(j=strlen(line); j>=0;j--){ /* Untabifies line */
|
| |
if(line[j] == '\t')
|
| |
line[j] = ' ';
|
| |
}
|
| |
for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
|
| |
;
|
| |
};
|
| |
line[j+1]=0; /* Trims blanks at end of line */
|
| |
if(line[0]=='#'){
|
| |
fprintf(ficlog,"Comment line\n%s\n",line);
|
| |
printf("Comment line\n%s\n",line);
|
| |
continue;
|
| |
}
|
| |
|
| |
for (j=maxwav;j>=1;j--){
|
| |
cutv(stra, strb,line,' ');
|
| |
errno=0;
|
| |
lval=strtol(strb,&endptr,10);
|
| |
/* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
|
| |
if( strb[0]=='\0' || (*endptr != '\0')){
|
| |
printf("Error reading data around '%d' at line number %d %s for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);
|
| |
exit(1);
|
| |
}
|
| |
s[j][i]=lval;
|
| |
|
| |
strcpy(line,stra);
|
| |
cutv(stra, strb,line,' ');
|
| |
if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
|
| |
}
|
| |
else if(iout=sscanf(strb,"%s.") != 0){
|
| |
month=99;
|
| |
year=9999;
|
| |
}else{
|
| |
printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);
|
| |
exit(1);
|
| |
}
|
| |
anint[j][i]= (double) year;
|
| |
mint[j][i]= (double)month;
|
| |
strcpy(line,stra);
|
| |
} /* ENd Waves */
|
| |
|
| |
cutv(stra, strb,line,' ');
|
| |
if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
|
| |
}
|
| |
else if(iout=sscanf(strb,"%s.",dummy) != 0){
|
| |
month=99;
|
| |
year=9999;
|
| |
}else{
|
| |
printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
|
| |
exit(1);
|
| |
}
|
| |
andc[i]=(double) year;
|
| |
moisdc[i]=(double) month;
|
| |
strcpy(line,stra);
|
| |
|
| |
cutv(stra, strb,line,' ');
|
| |
if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
|
| |
}
|
| |
else if(iout=sscanf(strb,"%s.") != 0){
|
| |
month=99;
|
| |
year=9999;
|
| |
}else{
|
| |
printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line,j);
|
| |
exit(1);
|
| |
}
|
| |
annais[i]=(double)(year);
|
| |
moisnais[i]=(double)(month);
|
| |
strcpy(line,stra);
|
| |
|
| |
cutv(stra, strb,line,' ');
|
| |
errno=0;
|
| |
dval=strtod(strb,&endptr);
|
| |
if( strb[0]=='\0' || (*endptr != '\0')){
|
| |
printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
|
| |
exit(1);
|
| |
}
|
| |
weight[i]=dval;
|
| |
strcpy(line,stra);
|
| |
|
| |
for (j=ncovcol;j>=1;j--){
|
| |
cutv(stra, strb,line,' ');
|
| |
errno=0;
|
| |
lval=strtol(strb,&endptr,10);
|
| |
if( strb[0]=='\0' || (*endptr != '\0')){
|
| |
printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1). Exiting.\n",lval, linei,i, line);
|
| |
exit(1);
|
| |
}
|
| |
if(lval <-1 || lval >1){
|
| |
printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
|
| |
Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
|
| |
for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
|
| |
For example, for multinomial values like 1, 2 and 3,\n \
|
| |
build V1=0 V2=0 for the reference value (1),\n \
|
| |
V1=1 V2=0 for (2) \n \
|
| |
and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
|
| |
output of IMaCh is often meaningless.\n \
|
| |
Exiting.\n",lval,linei, i,line,j);
|
| |
exit(1);
|
| |
}
|
| |
covar[j][i]=(double)(lval);
|
| |
strcpy(line,stra);
|
| |
}
|
| |
lstra=strlen(stra);
|
| |
|
| |
if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
|
| |
stratrunc = &(stra[lstra-9]);
|
| |
num[i]=atol(stratrunc);
|
| |
}
|
| |
else
|
| |
num[i]=atol(stra);
|
| |
/*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
|
| |
printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
|
| |
|
| |
i=i+1;
|
| |
} /* End loop reading data */
|
| |
fclose(fic);
|
| |
/* printf("ii=%d", ij);
|
| |
scanf("%d",i);*/
|
| |
imx=i-1; /* Number of individuals */
|
| |
|
| |
/* for (i=1; i<=imx; i++){
|
| |
if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
|
| |
if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
|
| |
if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
|
| |
}*/
|
| |
/* for (i=1; i<=imx; i++){
|
| |
if (s[4][i]==9) s[4][i]=-1;
|
| |
printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
|
| |
|
| |
/* for (i=1; i<=imx; i++) */
|
| |
|
| |
/*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
|
| |
else weight[i]=1;*/
|
| |
|
| |
/* Calculation of the number of parameters from char model */
|
| |
Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
|
| |
Tprod=ivector(1,15);
|
| |
Tvaraff=ivector(1,15);
|
| |
Tvard=imatrix(1,15,1,2);
|
| |
Tage=ivector(1,15);
|
| |
|
| |
if (strlen(model) >1){ /* If there is at least 1 covariate */
|
| |
j=0, j1=0, k1=1, k2=1;
|
| |
j=nbocc(model,'+'); /* j=Number of '+' */
|
| |
j1=nbocc(model,'*'); /* j1=Number of '*' */
|
| |
cptcovn=j+1;
|
| |
cptcovprod=j1; /*Number of products */
|
| |
|
| |
strcpy(modelsav,model);
|
| |
if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
|
| |
printf("Error. Non available option model=%s ",model);
|
| |
fprintf(ficlog,"Error. Non available option model=%s ",model);
|
| |
goto end;
|
| |
}
|
| |
|
| |
/* This loop fills the array Tvar from the string 'model'.*/
|
| |
|
| |
for(i=(j+1); i>=1;i--){
|
| |
cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
|
| |
if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
|
| |
/* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
|
| |
/*scanf("%d",i);*/
|
| |
if (strchr(strb,'*')) { /* Model includes a product */
|
| |
cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
|
| |
if (strcmp(strc,"age")==0) { /* Vn*age */
|
| |
cptcovprod--;
|
| |
cutv(strb,stre,strd,'V');
|
| |
Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
|
| |
cptcovage++;
|
| |
Tage[cptcovage]=i;
|
| |
/*printf("stre=%s ", stre);*/
|
| |
}
|
| |
else if (strcmp(strd,"age")==0) { /* or age*Vn */
|
| |
cptcovprod--;
|
| |
cutv(strb,stre,strc,'V');
|
| |
Tvar[i]=atoi(stre);
|
| |
cptcovage++;
|
| |
Tage[cptcovage]=i;
|
| |
}
|
| |
else { /* Age is not in the model */
|
| |
cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
|
| |
Tvar[i]=ncovcol+k1;
|
| |
cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
|
| |
Tprod[k1]=i;
|
| |
Tvard[k1][1]=atoi(strc); /* m*/
|
| |
Tvard[k1][2]=atoi(stre); /* n */
|
| |
Tvar[cptcovn+k2]=Tvard[k1][1];
|
| |
Tvar[cptcovn+k2+1]=Tvard[k1][2];
|
| |
for (k=1; k<=lastobs;k++)
|
| |
covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
|
| |
k1++;
|
| |
k2=k2+2;
|
| |
}
|
| |
}
|
| |
else { /* no more sum */
|
| |
/*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
|
| |
/* scanf("%d",i);*/
|
| |
cutv(strd,strc,strb,'V');
|
| |
Tvar[i]=atoi(strc);
|
| |
}
|
| |
strcpy(modelsav,stra);
|
| |
/*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
|
| |
scanf("%d",i);*/
|
| |
} /* end of loop + */
|
| |
} /* end model */
|
| |
|
| |
/*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
|
| |
If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
|
| |
|
| |
/* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
|
| |
printf("cptcovprod=%d ", cptcovprod);
|
| |
fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
|
| |
|
| |
scanf("%d ",i);*/
|
| |
|
| |
/* 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 (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
|
| |
anint[m][i]=9999;
|
| |
s[m][i]=-1;
|
| |
}
|
| |
if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
|
| |
nberr++;
|
| |
printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
|
| |
fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
|
| |
s[m][i]=-1;
|
| |
}
|
| |
if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
|
| |
nberr++;
|
| |
printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
|
| |
fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
|
| |
s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
|
| |
}
|
| |
}
|
| |
}
|
| |
|
| |
for (i=1; i<=imx; i++) {
|
| |
agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
|
| |
for(m=firstpass; (m<= lastpass); m++){
|
| |
if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
|
| |
if (s[m][i] >= nlstate+1) {
|
| |
if(agedc[i]>0)
|
| |
if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
|
| |
agev[m][i]=agedc[i];
|
| |
/*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
|
| |
else {
|
| |
if ((int)andc[i]!=9999){
|
| |
nbwarn++;
|
| |
printf("Warning negative age at death: %ld line:%d\n",num[i],i);
|
| |
fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
|
| |
agev[m][i]=-1;
|
| |
}
|
| |
}
|
| |
}
|
| |
else if(s[m][i] !=9){ /* Standard case, age in fractional
|
| |
years but with the precision of a month */
|
| |
agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
|
| |
if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
|
| |
agev[m][i]=1;
|
| |
else if(agev[m][i] <agemin){
|
| |
agemin=agev[m][i];
|
| |
/*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
|
| |
}
|
| |
else if(agev[m][i] >agemax){
|
| |
agemax=agev[m][i];
|
| |
/* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
|
| |
}
|
| |
/*agev[m][i]=anint[m][i]-annais[i];*/
|
| |
/* agev[m][i] = age[i]+2*m;*/
|
| |
}
|
| |
else { /* =9 */
|
| |
agev[m][i]=1;
|
| |
s[m][i]=-1;
|
| |
}
|
| |
}
|
| |
else /*= 0 Unknown */
|
| |
agev[m][i]=1;
|
| |
}
|
| |
|
| |
}
|
| |
for (i=1; i<=imx; i++) {
|
| |
for(m=firstpass; (m<=lastpass); m++){
|
| |
if (s[m][i] > (nlstate+ndeath)) {
|
| |
nberr++;
|
| |
printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
|
| |
fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
|
| |
goto end;
|
| |
}
|
| |
}
|
| |
}
|
| |
|
| |
/*for (i=1; i<=imx; i++){
|
| |
for (m=firstpass; (m<lastpass); m++){
|
| |
printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
|
| |
}
|
| |
|
| |
}*/
|
| |
|
| |
|
| |
printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
|
| |
fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
|
| |
|
| |
agegomp=(int)agemin;
|
| |
free_vector(severity,1,maxwav);
|
| |
free_imatrix(outcome,1,maxwav+1,1,n);
|
| |
free_vector(moisnais,1,n);
|
| |
free_vector(annais,1,n);
|
| |
/* free_matrix(mint,1,maxwav,1,n);
|
| |
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);
|
| |
bh=imatrix(1,lastpass-firstpass+1,1,imx);
|
| |
mw=imatrix(1,lastpass-firstpass+1,1,imx);
|
| |
|
| |
/* Concatenates waves */
|
| |
concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
|
| |
|
| |
/* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
|
| |
|
| |
Tcode=ivector(1,100);
|
| |
nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
|
| |
ncodemax[1]=1;
|
| |
if (cptcovn > 0) tricode(Tvar,nbcode,imx);
|
| |
|
| |
codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
|
| |
the estimations*/
|
| |
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);*/
|
| |
|
| |
/*------------ gnuplot -------------*/
|
| |
strcpy(optionfilegnuplot,optionfilefiname);
|
| |
if(mle==-3)
|
| |
strcat(optionfilegnuplot,"-mort");
|
| |
strcat(optionfilegnuplot,".gp");
|
| |
|
| |
if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
|
| |
printf("Problem with file %s",optionfilegnuplot);
|
| |
}
|
| |
else{
|
| |
fprintf(ficgp,"\n# %s\n", version);
|
| |
fprintf(ficgp,"# %s\n", optionfilegnuplot);
|
| |
fprintf(ficgp,"set missing 'NaNq'\n");
|
| |
}
|
| |
/* fclose(ficgp);*/
|
| |
/*--------- index.htm --------*/
|
| |
|
| |
strcpy(optionfilehtm,optionfilefiname); /* Main html file */
|
| |
if(mle==-3)
|
| |
strcat(optionfilehtm,"-mort");
|
| |
strcat(optionfilehtm,".htm");
|
| |
if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
|
| |
printf("Problem with %s \n",optionfilehtm), exit(0);
|
| |
}
|
| |
|
| |
strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
|
| |
strcat(optionfilehtmcov,"-cov.htm");
|
| |
if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
|
| |
printf("Problem with %s \n",optionfilehtmcov), exit(0);
|
| |
}
|
| |
else{
|
| |
fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %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",\
|
| |
optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
|
| |
}
|
| |
|
| |
fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %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\
|
| |
<hr size=\"2\" color=\"#EC5E5E\">\
|
| |
<ul><li><h4>Parameter files</h4>\n\
|
| |
- Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
|
| |
- Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
|
| |
- Log file of the run: <a href=\"%s\">%s</a><br>\n\
|
| |
- Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
|
| |
- Date and time at start: %s</ul>\n",\
|
| |
optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
|
| |
optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
|
| |
fileres,fileres,\
|
| |
filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
|
| |
fflush(fichtm);
|
| |
|
| |
strcpy(pathr,path);
|
| |
strcat(pathr,optionfilefiname);
|
| |
chdir(optionfilefiname); /* Move to directory named optionfile */
|
| |
|
| |
/* Calculates basic frequencies. Computes observed prevalence at single age
|
| |
and prints on file fileres'p'. */
|
| |
freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
|
| |
|
| |
fprintf(fichtm,"\n");
|
| |
fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
|
| |
Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
|
| |
Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
|
| |
imx,agemin,agemax,jmin,jmax,jmean);
|
| |
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) */
|
| |
|
| |
globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
|
| |
|
| |
if (mle==-3){
|
| |
ximort=matrix(1,NDIM,1,NDIM);
|
| |
cens=ivector(1,n);
|
| |
ageexmed=vector(1,n);
|
| |
agecens=vector(1,n);
|
| |
dcwave=ivector(1,n);
|
| |
|
| |
for (i=1; i<=imx; i++){
|
| |
dcwave[i]=-1;
|
| |
for (m=firstpass; m<=lastpass; m++)
|
| |
if (s[m][i]>nlstate) {
|
| |
dcwave[i]=m;
|
| |
/* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
|
| |
break;
|
| |
}
|
| |
}
|
| |
|
| |
for (i=1; i<=imx; i++) {
|
| |
if (wav[i]>0){
|
| |
ageexmed[i]=agev[mw[1][i]][i];
|
| |
j=wav[i];
|
| |
agecens[i]=1.;
|
| |
|
| |
if (ageexmed[i]> 1 && wav[i] > 0){
|
| |
agecens[i]=agev[mw[j][i]][i];
|
| |
cens[i]= 1;
|
| |
}else if (ageexmed[i]< 1)
|
| |
cens[i]= -1;
|
| |
if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
|
| |
cens[i]=0 ;
|
| |
}
|
| |
else cens[i]=-1;
|
| |
}
|
| |
|
| |
for (i=1;i<=NDIM;i++) {
|
| |
for (j=1;j<=NDIM;j++)
|
| |
ximort[i][j]=(i == j ? 1.0 : 0.0);
|
| |
}
|
| |
|
| |
p[1]=0.0268; p[NDIM]=0.083;
|
| |
/*printf("%lf %lf", p[1], p[2]);*/
|
| |
|
| |
|
| |
printf("Powell\n"); fprintf(ficlog,"Powell\n");
|
| |
strcpy(filerespow,"pow-mort");
|
| |
strcat(filerespow,fileres);
|
| |
if((ficrespow=fopen(filerespow,"w"))==NULL) {
|
| |
printf("Problem with resultfile: %s\n", filerespow);
|
| |
fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
|
| |
}
|
| |
fprintf(ficrespow,"# Powell\n# iter -2*LL");
|
| |
/* for (i=1;i<=nlstate;i++)
|
| |
for(j=1;j<=nlstate+ndeath;j++)
|
| |
if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
|
| |
*/
|
| |
fprintf(ficrespow,"\n");
|
| |
|
| |
powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
|
| |
fclose(ficrespow);
|
| |
|
| |
hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
|
| |
|
| |
for(i=1; i <=NDIM; i++)
|
| |
for(j=i+1;j<=NDIM;j++)
|
| |
matcov[i][j]=matcov[j][i];
|
| |
|
| |
printf("\nCovariance matrix\n ");
|
| |
for(i=1; i <=NDIM; i++) {
|
| |
for(j=1;j<=NDIM;j++){
|
| |
printf("%f ",matcov[i][j]);
|
| |
}
|
| |
printf("\n ");
|
| |
}
|
| |
|
| |
printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
|
| |
for (i=1;i<=NDIM;i++)
|
| |
printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
|
| |
|
| |
lsurv=vector(1,AGESUP);
|
| |
lpop=vector(1,AGESUP);
|
| |
tpop=vector(1,AGESUP);
|
| |
lsurv[agegomp]=100000;
|
| |
|
| |
for (k=agegomp;k<=AGESUP;k++) {
|
| |
agemortsup=k;
|
| |
if (p[1]*exp(p[2]*(k-agegomp))>1) break;
|
| |
}
|
| |
|
| |
for (k=agegomp;k<agemortsup;k++)
|
| |
lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
|
| |
|
| |
for (k=agegomp;k<agemortsup;k++){
|
| |
lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
|
| |
sumlpop=sumlpop+lpop[k];
|
| |
}
|
| |
|
| |
tpop[agegomp]=sumlpop;
|
| |
for (k=agegomp;k<(agemortsup-3);k++){
|
| |
/* tpop[k+1]=2;*/
|
| |
tpop[k+1]=tpop[k]-lpop[k];
|
| |
}
|
| |
|
| |
|
| |
printf("\nAge lx qx dx Lx Tx e(x)\n");
|
| |
for (k=agegomp;k<(agemortsup-2);k++)
|
| |
printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
|
| |
|
| |
|
| |
replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
|
| |
printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
|
| |
|
| |
printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
|
| |
stepm, weightopt,\
|
| |
model,imx,p,matcov,agemortsup);
|
| |
|
| |
free_vector(lsurv,1,AGESUP);
|
| |
free_vector(lpop,1,AGESUP);
|
| |
free_vector(tpop,1,AGESUP);
|
| |
} /* Endof if mle==-3 */
|
| |
|
| |
else{ /* For mle >=1 */
|
| |
|
| |
likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
|
| |
printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
|
| |
for (k=1; k<=npar;k++)
|
| |
printf(" %d %8.5f",k,p[k]);
|
| |
printf("\n");
|
| |
globpr=1; /* to print the contributions */
|
| |
likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
|
| |
printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
|
| |
for (k=1; k<=npar;k++)
|
| |
printf(" %d %8.5f",k,p[k]);
|
| |
printf("\n");
|
| |
if(mle>=1){ /* Could be 1 or 2 */
|
| |
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);
|
| |
|
| |
|
| |
fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
|
| |
printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
|
| |
fprintf(ficlog,"# 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(ficlog,"%d%d ",i,k);
|
| |
fprintf(ficres,"%1d%1d ",i,k);
|
| |
for(j=1; j <=ncovmodel; j++){
|
| |
printf("%lf ",p[jk]);
|
| |
fprintf(ficlog,"%lf ",p[jk]);
|
| |
fprintf(ficres,"%lf ",p[jk]);
|
| |
jk++;
|
| |
}
|
| |
printf("\n");
|
| |
fprintf(ficlog,"\n");
|
| |
fprintf(ficres,"\n");
|
| |
}
|
| |
}
|
| |
}
|
| |
if(mle!=0){
|
| |
/* 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");
|
| |
fprintf(ficlog,"# 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);
|
| |
fprintf(ficlog,"%1d%1d",i,j);
|
| |
for(k=1; k<=ncovmodel;k++){
|
| |
printf(" %.5e",delti[jk]);
|
| |
fprintf(ficlog," %.5e",delti[jk]);
|
| |
fprintf(ficres," %.5e",delti[jk]);
|
| |
jk++;
|
| |
}
|
| |
printf("\n");
|
| |
fprintf(ficlog,"\n");
|
| |
fprintf(ficres,"\n");
|
| |
}
|
| |
}
|
| |
}
|
| |
|
| |
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");
|
| |
if(mle>=1)
|
| |
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");
|
| |
fprintf(ficlog,"# 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");
|
| |
/* # 121 Var(a12)\n\ */
|
| |
/* # 122 Cov(b12,a12) Var(b12)\n\ */
|
| |
/* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
|
| |
/* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
|
| |
/* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
|
| |
/* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
|
| |
/* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
|
| |
/* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
|
| |
|
| |
|
| |
/* Just to have a covariance matrix which will be more understandable
|
| |
even is we still don't want to manage dictionary of variables
|
| |
*/
|
| |
for(itimes=1;itimes<=2;itimes++){
|
| |
jj=0;
|
| |
for(i=1; i <=nlstate; i++){
|
| |
for(j=1; j <=nlstate+ndeath; j++){
|
| |
if(j==i) continue;
|
| |
for(k=1; k<=ncovmodel;k++){
|
| |
jj++;
|
| |
ca[0]= k+'a'-1;ca[1]='\0';
|
| |
if(itimes==1){
|
| |
if(mle>=1)
|
| |
printf("#%1d%1d%d",i,j,k);
|
| |
fprintf(ficlog,"#%1d%1d%d",i,j,k);
|
| |
fprintf(ficres,"#%1d%1d%d",i,j,k);
|
| |
}else{
|
| |
if(mle>=1)
|
| |
printf("%1d%1d%d",i,j,k);
|
| |
fprintf(ficlog,"%1d%1d%d",i,j,k);
|
| |
fprintf(ficres,"%1d%1d%d",i,j,k);
|
| |
}
|
| |
ll=0;
|
| |
for(li=1;li <=nlstate; li++){
|
| |
for(lj=1;lj <=nlstate+ndeath; lj++){
|
| |
if(lj==li) continue;
|
| |
for(lk=1;lk<=ncovmodel;lk++){
|
| |
ll++;
|
| |
if(ll<=jj){
|
| |
cb[0]= lk +'a'-1;cb[1]='\0';
|
| |
if(ll<jj){
|
| |
if(itimes==1){
|
| |
if(mle>=1)
|
| |
printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
|
| |
fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
|
| |
fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
|
| |
}else{
|
| |
if(mle>=1)
|
| |
printf(" %.5e",matcov[jj][ll]);
|
| |
fprintf(ficlog," %.5e",matcov[jj][ll]);
|
| |
fprintf(ficres," %.5e",matcov[jj][ll]);
|
| |
}
|
| |
}else{
|
| |
if(itimes==1){
|
| |
if(mle>=1)
|
| |
printf(" Var(%s%1d%1d)",ca,i,j);
|
| |
fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
|
| |
fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
|
| |
}else{
|
| |
if(mle>=1)
|
| |
printf(" %.5e",matcov[jj][ll]);
|
| |
fprintf(ficlog," %.5e",matcov[jj][ll]);
|
| |
fprintf(ficres," %.5e",matcov[jj][ll]);
|
| |
}
|
| |
}
|
| |
}
|
| |
} /* end lk */
|
| |
} /* end lj */
|
| |
} /* end li */
|
| |
if(mle>=1)
|
| |
printf("\n");
|
| |
fprintf(ficlog,"\n");
|
| |
fprintf(ficres,"\n");
|
| |
numlinepar++;
|
| |
} /* end k*/
|
| |
} /*end j */
|
| |
} /* end i */
|
| |
} /* end itimes */
|
| |
|
| |
fflush(ficlog);
|
| |
fflush(ficres);
|
| |
|
| |
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 mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
|
| |
fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
|
| |
fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
|
| |
printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
|
| |
fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
|
| |
|
| |
while((c=getc(ficpar))=='#' && c!= EOF){
|
| |
ungetc(c,ficpar);
|
| |
fgets(line, MAXLINE, ficpar);
|
| |
puts(line);
|
| |
fputs(line,ficparo);
|
| |
}
|
| |
ungetc(c,ficpar);
|
| |
|
| |
|
| |
dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
|
| |
dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/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,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
|
| |
fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
|
| |
printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
|
| |
fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
|
| |
fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
|
| |
/* day and month of proj2 are not used but only year anproj2.*/
|
| |
|
| |
|
| |
|
| |
/* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
|
| |
/*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
|
| |
|
| |
replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
|
| |
printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
|
| |
|
| |
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(bh,1,lastpass-firstpass+1,1,imx);
|
| |
free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
|
| |
free_lvector(num,1,n);
|
| |
free_vector(agedc,1,n);
|
| |
/*free_matrix(covar,0,NCOVMAX,1,n);*/
|
| |
/*free_matrix(covar,1,NCOVMAX,1,n);*/
|
| |
fclose(ficparo);
|
| |
fclose(ficres);
|
| |
|
| |
|
| |
/*--------------- Prevalence limit (period or stable prevalence) --------------*/
|
| |
|
| |
strcpy(filerespl,"pl");
|
| |
strcat(filerespl,fileres);
|
| |
if((ficrespl=fopen(filerespl,"w"))==NULL) {
|
| |
printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
|
| |
fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
|
| |
}
|
| |
printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
|
| |
fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
|
| |
pstamp(ficrespl);
|
| |
fprintf(ficrespl,"# Period (stable) prevalence \n");
|
| |
fprintf(ficrespl,"#Age ");
|
| |
for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
|
| |
fprintf(ficrespl,"\n");
|
| |
|
| |
prlim=matrix(1,nlstate,1,nlstate);
|
| |
|
| |
agebase=ageminpar;
|
| |
agelim=agemaxpar;
|
| |
ftolpl=1.e-10;
|
| |
i1=cptcoveff;
|
| |
if (cptcovn < 1){i1=1;}
|
| |
|
| |
for(cptcov=1,k=0;cptcov<=i1;cptcov++){
|
| |
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
|
| |
k=k+1;
|
| |
/*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
|
| |
fprintf(ficrespl,"\n#******");
|
| |
printf("\n#******");
|
| |
fprintf(ficlog,"\n#******");
|
| |
for(j=1;j<=cptcoveff;j++) {
|
| |
fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
|
| |
printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
|
| |
fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
|
| |
}
|
| |
fprintf(ficrespl,"******\n");
|
| |
printf("******\n");
|
| |
fprintf(ficlog,"******\n");
|
| |
|
| |
for (age=agebase; age<=agelim; age++){
|
| |
prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
|
| |
fprintf(ficrespl,"%.0f ",age );
|
| |
for(j=1;j<=cptcoveff;j++)
|
| |
fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
|
| |
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;
|
| |
fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
|
| |
}
|
| |
printf("Computing pij: result on file '%s' \n", filerespij);
|
| |
fprintf(ficlog,"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*/
|
| |
pstamp(ficrespij);
|
| |
fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
|
| |
for(cptcov=1,k=0;cptcov<=i1;cptcov++){
|
| |
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
|
| |
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,"# Cov Agex agex+h hpijx with i,j=");
|
| |
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 %3.f %3.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, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
|
| |
|
| |
fclose(ficrespij);
|
| |
|
| |
probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
|
| |
for(i=1;i<=AGESUP;i++)
|
| |
for(j=1;j<=NCOVMAX;j++)
|
| |
for(k=1;k<=NCOVMAX;k++)
|
| |
probs[i][j][k]=0.;
|
| |
|
| |
/*---------- Forecasting ------------------*/
|
| |
/*if((stepm == 1) && (strcmp(model,".")==0)){*/
|
| |
if(prevfcast==1){
|
| |
/* if(stepm ==1){*/
|
| |
prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
|
| |
/* (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); */
|
| |
/* fprintf(ficlog,"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;
|
| |
fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
|
| |
}
|
| |
printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
|
| |
fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
|
| |
|
| |
|
| |
strcpy(filerese,"e");
|
| |
strcat(filerese,fileres);
|
| |
if((ficreseij=fopen(filerese,"w"))==NULL) {
|
| |
printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
|
| |
fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
|
| |
}
|
| |
printf("Computing Health Expectancies: result on file '%s' \n", filerese);
|
| |
fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
|
| |
|
| |
strcpy(fileresstde,"stde");
|
| |
strcat(fileresstde,fileres);
|
| |
if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
|
| |
printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
|
| |
fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
|
| |
}
|
| |
printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
|
| |
fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
|
| |
|
| |
strcpy(filerescve,"cve");
|
| |
strcat(filerescve,fileres);
|
| |
if((ficrescveij=fopen(filerescve,"w"))==NULL) {
|
| |
printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
|
| |
fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
|
| |
}
|
| |
printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
|
| |
fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
|
| |
|
| |
strcpy(fileresv,"v");
|
| |
strcat(fileresv,fileres);
|
| |
if((ficresvij=fopen(fileresv,"w"))==NULL) {
|
| |
printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
|
| |
fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
|
| |
}
|
| |
printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
|
| |
fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
|
| |
|
| |
/* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
|
| |
prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
|
| |
/* printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d, mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
|
| |
ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
|
| |
*/
|
| |
|
| |
if (mobilav!=0) {
|
| |
mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
|
| |
if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
|
| |
fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
|
| |
printf(" Error in movingaverage mobilav=%d\n",mobilav);
|
| |
}
|
| |
}
|
| |
|
| |
for(cptcov=1,k=0;cptcov<=i1;cptcov++){
|
| |
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
|
| |
k=k+1;
|
| |
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#****** ");
|
| |
fprintf(ficresstdeij,"\n#****** ");
|
| |
fprintf(ficrescveij,"\n#****** ");
|
| |
for(j=1;j<=cptcoveff;j++) {
|
| |
fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
|
| |
fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
|
| |
fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
|
| |
}
|
| |
fprintf(ficreseij,"******\n");
|
| |
fprintf(ficresstdeij,"******\n");
|
| |
fprintf(ficrescveij,"******\n");
|
| |
|
| |
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, strstart);
|
| |
cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
|
| |
|
| |
vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
|
| |
oldm=oldms;savm=savms;
|
| |
varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
|
| |
if(popbased==1){
|
| |
varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
|
| |
}
|
| |
|
| |
pstamp(ficrest);
|
| |
fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
|
| |
for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
|
| |
fprintf(ficrest,"\n");
|
| |
|
| |
epj=vector(1,nlstate+1);
|
| |
for(age=bage; age <=fage ;age++){
|
| |
prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
|
| |
if (popbased==1) {
|
| |
if(mobilav ==0){
|
| |
for(i=1; i<=nlstate;i++)
|
| |
prlim[i][i]=probs[(int)age][i][k];
|
| |
}else{ /* mobilav */
|
| |
for(i=1; i<=nlstate;i++)
|
| |
prlim[i][i]=mobaverage[(int)age][i][k];
|
| |
}
|
| |
}
|
| |
|
| |
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_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
|
| |
free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
|
| |
free_vector(epj,1,nlstate+1);
|
| |
}
|
| |
}
|
| |
free_vector(weight,1,n);
|
| |
free_imatrix(Tvard,1,15,1,2);
|
| |
free_imatrix(s,1,maxwav+1,1,n);
|
| |
free_matrix(anint,1,maxwav,1,n);
|
| |
free_matrix(mint,1,maxwav,1,n);
|
| |
free_ivector(cod,1,n);
|
| |
free_ivector(tab,1,NCOVMAX);
|
| |
fclose(ficreseij);
|
| |
fclose(ficresstdeij);
|
| |
fclose(ficrescveij);
|
| |
fclose(ficresvij);
|
| |
fclose(ficrest);
|
| |
fclose(ficpar);
|
| |
|
| |
/*------- Variance of period (stable) prevalence------*/
|
| |
|
| |
strcpy(fileresvpl,"vpl");
|
| |
strcat(fileresvpl,fileres);
|
| |
if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
|
| |
printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
|
| |
exit(0);
|
| |
}
|
| |
printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
|
| |
|
| |
for(cptcov=1,k=0;cptcov<=i1;cptcov++){
|
| |
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
|
| |
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,strstart);
|
| |
free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
|
| |
}
|
| |
}
|
| |
|
| |
fclose(ficresvpl);
|
| |
|
| |
/*---------- End : free ----------------*/
|
| |
if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
|
| |
free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
|
| |
|
| |
} /* mle==-3 arrives here for freeing */
|
| |
free_matrix(prlim,1,nlstate,1,nlstate);
|
| |
free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
|
| |
free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
|
| |
free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
|
| |
free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
|
| |
free_matrix(covar,0,NCOVMAX,1,n);
|
| |
free_matrix(matcov,1,npar,1,npar);
|
| |
/*free_vector(delti,1,npar);*/
|
| |
free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
|
| |
free_matrix(agev,1,maxwav,1,imx);
|
| |
free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
|
| |
|
| |
free_ivector(ncodemax,1,8);
|
| |
free_ivector(Tvar,1,15);
|
| |
free_ivector(Tprod,1,15);
|
| |
free_ivector(Tvaraff,1,15);
|
| |
free_ivector(Tage,1,15);
|
| |
free_ivector(Tcode,1,100);
|
| |
|
| |
free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
|
| |
free_imatrix(codtab,1,100,1,10);
|
| |
fflush(fichtm);
|
| |
fflush(ficgp);
|
| |
|
| |
|
| |
if((nberr >0) || (nbwarn>0)){
|
| |
printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
|
| |
fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
|
| |
}else{
|
| |
printf("End of Imach\n");
|
| |
fprintf(ficlog,"End of Imach\n");
|
| |
}
|
| |
printf("See log file on %s\n",filelog);
|
| |
/* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
|
| |
(void) gettimeofday(&end_time,&tzp);
|
| |
tm = *localtime(&end_time.tv_sec);
|
| |
tmg = *gmtime(&end_time.tv_sec);
|
| |
strcpy(strtend,asctime(&tm));
|
| |
printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
|
| |
fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
|
| |
printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
|
| |
|
| |
printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
|
| |
fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
|
| |
fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
|
| |
/* printf("Total time was %d uSec.\n", total_usecs);*/
|
| |
/* if(fileappend(fichtm,optionfilehtm)){ */
|
| |
fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
|
| |
fclose(fichtm);
|
| |
fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
|
| |
fclose(fichtmcov);
|
| |
fclose(ficgp);
|
| |
fclose(ficlog);
|
| |
/*------ End -----------*/
|
| |
|
| |
|
| |
printf("Before Current directory %s!\n",pathcd);
|
| |
if(chdir(pathcd) != 0)
|
| |
printf("Can't move to directory %s!\n",path);
|
| |
if(getcwd(pathcd,MAXLINE) > 0)
|
| |
printf("Current directory %s!\n",pathcd);
|
| |
/*strcat(plotcmd,CHARSEPARATOR);*/
|
| |
sprintf(plotcmd,"gnuplot");
|
| |
#ifndef UNIX
|
| |
sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
|
| |
#endif
|
| |
if(!stat(plotcmd,&info)){
|
| |
printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
|
| |
if(!stat(getenv("GNUPLOTBIN"),&info)){
|
| |
printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
|
| |
}else
|
| |
strcpy(pplotcmd,plotcmd);
|
| |
#ifdef UNIX
|
| |
strcpy(plotcmd,GNUPLOTPROGRAM);
|
| |
if(!stat(plotcmd,&info)){
|
| |
printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
|
| |
}else
|
| |
strcpy(pplotcmd,plotcmd);
|
| |
#endif
|
| |
}else
|
| |
strcpy(pplotcmd,plotcmd);
|
| |
|
| |
sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
|
| |
printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
|
| |
|
| |
if((outcmd=system(plotcmd)) != 0){
|
| |
printf("\n Problem with gnuplot\n");
|
| |
}
|
| |
printf(" Wait...");
|
| |
while (z[0] != 'q') {
|
| |
/* chdir(path); */
|
| |
printf("\nType e to edit output files, g to graph again and q for exiting: ");
|
| |
scanf("%s",z);
|
| |
/* if (z[0] == 'c') system("./imach"); */
|
| |
if (z[0] == 'e') {
|
| |
printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
|
| |
system(optionfilehtm);
|
| |
}
|
| |
else if (z[0] == 'g') system(plotcmd);
|
| |
else if (z[0] == 'q') exit(0);
|
| |
}
|
| |
end:
|
| |
while (z[0] != 'q') {
|
| |
printf("\nType q for exiting: ");
|
| |
scanf("%s",z);
|
| |
}
|
| |
}
|
| |
|
| |
|
| |
|
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