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version 1.47, 2002/06/10 13:12:01
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version 1.190, 2015/05/05 08:51:13
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| /* $Id$
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/* $Id$ |
| Interpolated Markov Chain
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$State$ |
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$Log$ |
| Short summary of the programme:
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Revision 1.190 2015/05/05 08:51:13 brouard |
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Summary: Adding digits in output parameters (7 digits instead of 6) |
| This program computes Healthy Life Expectancies from
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| cross-longitudinal data. Cross-longitudinal data consist in: -1- a
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Fix 1+age+. |
| first survey ("cross") where individuals from different ages are
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| interviewed on their health status or degree of disability (in the
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Revision 1.189 2015/04/30 14:45:16 brouard |
| case of a health survey which is our main interest) -2- at least a
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Summary: 0.98q2 |
| second wave of interviews ("longitudinal") which measure each change
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| (if any) in individual health status. Health expectancies are
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Revision 1.188 2015/04/30 08:27:53 brouard |
| computed from the time spent in each health state according to a
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*** empty log message *** |
| model. More health states you consider, more time is necessary to reach the
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| Maximum Likelihood of the parameters involved in the model. The
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Revision 1.187 2015/04/29 09:11:15 brouard |
| simplest model is the multinomial logistic model where pij is the
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*** empty log message *** |
| probability to be observed in state j at the second wave
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| conditional to be observed in state i at the first wave. Therefore
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Revision 1.186 2015/04/23 12:01:52 brouard |
| the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
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Summary: V1*age is working now, version 0.98q1 |
| 'age' is age and 'sex' is a covariate. If you want to have a more
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| complex model than "constant and age", you should modify the program
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Some codes had been disabled in order to simplify and Vn*age was |
| where the markup *Covariates have to be included here again* invites
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working in the optimization phase, ie, giving correct MLE parameters, |
| you to do it. More covariates you add, slower the
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but, as usual, outputs were not correct and program core dumped. |
| convergence.
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Revision 1.185 2015/03/11 13:26:42 brouard |
| The advantage of this computer programme, compared to a simple
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Summary: Inclusion of compile and links command line for Intel Compiler |
| multinomial logistic model, is clear when the delay between waves is not
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| identical for each individual. Also, if a individual missed an
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Revision 1.184 2015/03/11 11:52:39 brouard |
| intermediate interview, the information is lost, but taken into
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Summary: Back from Windows 8. Intel Compiler |
| account using an interpolation or extrapolation.
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Revision 1.183 2015/03/10 20:34:32 brouard |
| hPijx is the probability to be observed in state i at age x+h
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Summary: 0.98q0, trying with directest, mnbrak fixed |
| 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
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We use directest instead of original Powell test; probably no |
| states. This elementary transition (by month or quarter trimester,
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incidence on the results, but better justifications; |
| semester or year) is model as a multinomial logistic. The hPx
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We fixed Numerical Recipes mnbrak routine which was wrong and gave |
| matrix is simply the matrix product of nh*stepm elementary matrices
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wrong results. |
| and the contribution of each individual to the likelihood is simply
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| hPijx.
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Revision 1.182 2015/02/12 08:19:57 brouard |
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Summary: Trying to keep directest which seems simpler and more general |
| Also this programme outputs the covariance matrix of the parameters but also
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Author: Nicolas Brouard |
| of the life expectancies. It also computes the prevalence limits.
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Revision 1.181 2015/02/11 23:22:24 brouard |
| Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
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Summary: Comments on Powell added |
| Institut national d'études démographiques, Paris.
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| This software have been partly granted by Euro-REVES, a concerted action
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Author: |
| from the European Union.
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| It is copyrighted identically to a GNU software product, ie programme and
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Revision 1.180 2015/02/11 17:33:45 brouard |
| software can be distributed freely for non commercial use. Latest version
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Summary: Finishing move from main to function (hpijx and prevalence_limit) |
| can be accessed at http://euroreves.ined.fr/imach .
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| **********************************************************************/
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Revision 1.179 2015/01/04 09:57:06 brouard |
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Summary: back to OS/X |
| #include <math.h>
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| #include <stdio.h>
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Revision 1.178 2015/01/04 09:35:48 brouard |
| #include <stdlib.h>
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*** empty log message *** |
| #include <unistd.h>
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Revision 1.177 2015/01/03 18:40:56 brouard |
| #define MAXLINE 256
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Summary: Still testing ilc32 on OSX |
| #define GNUPLOTPROGRAM "gnuplot"
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| /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
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Revision 1.176 2015/01/03 16:45:04 brouard |
| #define FILENAMELENGTH 80
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*** empty log message *** |
| /*#define DEBUG*/
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| #define windows
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Revision 1.175 2015/01/03 16:33:42 brouard |
| #define GLOCK_ERROR_NOPATH -1 /* empty path */
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*** empty log message *** |
| #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
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Revision 1.174 2015/01/03 16:15:49 brouard |
| #define MAXPARM 30 /* Maximum number of parameters for the optimization */
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Summary: Still in cross-compilation |
| #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
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Revision 1.173 2015/01/03 12:06:26 brouard |
| #define NINTERVMAX 8
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Summary: trying to detect cross-compilation |
| #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
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| #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
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Revision 1.172 2014/12/27 12:07:47 brouard |
| #define NCOVMAX 8 /* Maximum number of covariates */
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Summary: Back from Visual Studio and Intel, options for compiling for Windows XP |
| #define MAXN 20000
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| #define YEARM 12. /* Number of months per year */
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Revision 1.171 2014/12/23 13:26:59 brouard |
| #define AGESUP 130
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Summary: Back from Visual C |
| #define AGEBASE 40
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| #ifdef windows
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Still problem with utsname.h on Windows |
| #define DIRSEPARATOR '\\'
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| #else
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Revision 1.170 2014/12/23 11:17:12 brouard |
| #define DIRSEPARATOR '/'
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Summary: Cleaning some \%% back to %% |
| #endif
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The escape was mandatory for a specific compiler (which one?), but too many warnings. |
| char version[80]="Imach version 0.8g, May 2002, INED-EUROREVES ";
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| int erreur; /* Error number */
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Revision 1.169 2014/12/22 23:08:31 brouard |
| int nvar;
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Summary: 0.98p |
| int cptcovn, cptcovage=0, cptcoveff=0,cptcov;
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| int npar=NPARMAX;
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Outputs some informations on compiler used, OS etc. Testing on different platforms. |
| int nlstate=2; /* Number of live states */
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| int ndeath=1; /* Number of dead states */
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Revision 1.168 2014/12/22 15:17:42 brouard |
| int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
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Summary: update |
| int popbased=0;
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Revision 1.167 2014/12/22 13:50:56 brouard |
| int *wav; /* Number of waves for this individuual 0 is possible */
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Summary: Testing uname and compiler version and if compiled 32 or 64 |
| int maxwav; /* Maxim number of waves */
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| int jmin, jmax; /* min, max spacing between 2 waves */
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Testing on Linux 64 |
| int mle, weightopt;
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| int **mw; /* mw[mi][i] is number of the mi wave for this individual */
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Revision 1.166 2014/12/22 11:40:47 brouard |
| int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
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*** empty log message *** |
| double jmean; /* Mean space between 2 waves */
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| double **oldm, **newm, **savm; /* Working pointers to matrices */
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Revision 1.165 2014/12/16 11:20:36 brouard |
| double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
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Summary: After compiling on Visual C |
| FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
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| FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
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* imach.c (Module): Merging 1.61 to 1.162 |
| FILE *fichtm; /* Html File */
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| FILE *ficreseij;
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Revision 1.164 2014/12/16 10:52:11 brouard |
| char filerese[FILENAMELENGTH];
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Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn |
| FILE *ficresvij;
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| char fileresv[FILENAMELENGTH];
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* imach.c (Module): Merging 1.61 to 1.162 |
| FILE *ficresvpl;
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| char fileresvpl[FILENAMELENGTH];
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Revision 1.163 2014/12/16 10:30:11 brouard |
| char title[MAXLINE];
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* imach.c (Module): Merging 1.61 to 1.162 |
| char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
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| char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
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Revision 1.162 2014/09/25 11:43:39 brouard |
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Summary: temporary backup 0.99! |
| char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
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Revision 1.1 2014/09/16 11:06:58 brouard |
| char filerest[FILENAMELENGTH];
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Summary: With some code (wrong) for nlopt |
| char fileregp[FILENAMELENGTH];
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| char popfile[FILENAMELENGTH];
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Author: |
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| char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
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Revision 1.161 2014/09/15 20:41:41 brouard |
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Summary: Problem with macro SQR on Intel compiler |
| #define NR_END 1
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| #define FREE_ARG char*
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Revision 1.160 2014/09/02 09:24:05 brouard |
| #define FTOL 1.0e-10
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*** empty log message *** |
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| #define NRANSI
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Revision 1.159 2014/09/01 10:34:10 brouard |
| #define ITMAX 200
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Summary: WIN32 |
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Author: Brouard |
| #define TOL 2.0e-4
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Revision 1.158 2014/08/27 17:11:51 brouard |
| #define CGOLD 0.3819660
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*** empty log message *** |
| #define ZEPS 1.0e-10
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| #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
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Revision 1.157 2014/08/27 16:26:55 brouard |
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Summary: Preparing windows Visual studio version |
| #define GOLD 1.618034
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Author: Brouard |
| #define GLIMIT 100.0
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| #define TINY 1.0e-20
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In order to compile on Visual studio, time.h is now correct and time_t |
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and tm struct should be used. difftime should be used but sometimes I |
| static double maxarg1,maxarg2;
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just make the differences in raw time format (time(&now). |
| #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
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Trying to suppress #ifdef LINUX |
| #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
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Add xdg-open for __linux in order to open default browser. |
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| #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
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Revision 1.156 2014/08/25 20:10:10 brouard |
| #define rint(a) floor(a+0.5)
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*** empty log message *** |
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| static double sqrarg;
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Revision 1.155 2014/08/25 18:32:34 brouard |
| #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
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Summary: New compile, minor changes |
| #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
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Author: Brouard |
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| int imx;
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Revision 1.154 2014/06/20 17:32:08 brouard |
| int stepm;
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Summary: Outputs now all graphs of convergence to period prevalence |
| /* Stepm, step in month: minimum step interpolation*/
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Revision 1.153 2014/06/20 16:45:46 brouard |
| int estepm;
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Summary: If 3 live state, convergence to period prevalence on same graph |
| /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
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Author: Brouard |
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| int m,nb;
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Revision 1.152 2014/06/18 17:54:09 brouard |
| int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
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Summary: open browser, use gnuplot on same dir than imach if not found in the path |
| double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
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| double **pmmij, ***probs, ***mobaverage;
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Revision 1.151 2014/06/18 16:43:30 brouard |
| double dateintmean=0;
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*** empty log message *** |
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| double *weight;
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Revision 1.150 2014/06/18 16:42:35 brouard |
| int **s; /* Status */
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Summary: If gnuplot is not in the path try on same directory than imach binary (OSX) |
| double *agedc, **covar, idx;
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Author: brouard |
| int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
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Revision 1.149 2014/06/18 15:51:14 brouard |
| double ftol=FTOL; /* Tolerance for computing Max Likelihood */
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Summary: Some fixes in parameter files errors |
| double ftolhess; /* Tolerance for computing hessian */
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Author: Nicolas Brouard |
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| /**************** split *************************/
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Revision 1.148 2014/06/17 17:38:48 brouard |
| static int split( char *path, char *dirc, char *name, char *ext, char *finame )
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Summary: Nothing new |
| {
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Author: Brouard |
| char *s; /* pointer */
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| int l1, l2; /* length counters */
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Just a new packaging for OS/X version 0.98nS |
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| l1 = strlen( path ); /* length of path */
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Revision 1.147 2014/06/16 10:33:11 brouard |
| if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
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*** empty log message *** |
| s = strrchr( path, DIRSEPARATOR ); /* find last / */
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| if ( s == NULL ) { /* no directory, so use current */
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Revision 1.146 2014/06/16 10:20:28 brouard |
| #if defined(__bsd__) /* get current working directory */
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Summary: Merge |
| extern char *getwd( );
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Author: Brouard |
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| if ( getwd( dirc ) == NULL ) {
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Merge, before building revised version. |
| #else
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| extern char *getcwd( );
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Revision 1.145 2014/06/10 21:23:15 brouard |
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Summary: Debugging with valgrind |
| if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
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Author: Nicolas Brouard |
| #endif
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| return( GLOCK_ERROR_GETCWD );
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Lot of changes in order to output the results with some covariates |
| }
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After the Edimburgh REVES conference 2014, it seems mandatory to |
| strcpy( name, path ); /* we've got it */
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improve the code. |
| } else { /* strip direcotry from path */
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No more memory valgrind error but a lot has to be done in order to |
| s++; /* after this, the filename */
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continue the work of splitting the code into subroutines. |
| l2 = strlen( s ); /* length of filename */
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Also, decodemodel has been improved. Tricode is still not |
| if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
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optimal. nbcode should be improved. Documentation has been added in |
| strcpy( name, s ); /* save file name */
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the source code. |
| strncpy( dirc, path, l1 - l2 ); /* now the directory */
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| dirc[l1-l2] = 0; /* add zero */
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Revision 1.143 2014/01/26 09:45:38 brouard |
| }
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Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising |
| l1 = strlen( dirc ); /* length of directory */
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|
| #ifdef windows
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* imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested... |
| if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
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(Module): Version 0.98nR Running ok, but output format still only works for three covariates. |
| #else
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| if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
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Revision 1.142 2014/01/26 03:57:36 brouard |
| #endif
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Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2 |
| s = strrchr( name, '.' ); /* find last / */
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| s++;
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* imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested... |
| strcpy(ext,s); /* save extension */
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| l1= strlen( name);
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Revision 1.141 2014/01/26 02:42:01 brouard |
| l2= strlen( s)+1;
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* imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested... |
| strncpy( finame, name, l1-l2);
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| finame[l1-l2]= 0;
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Revision 1.140 2011/09/02 10:37:54 brouard |
| return( 0 ); /* we're done */
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Summary: times.h is ok with mingw32 now. |
| }
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Revision 1.139 2010/06/14 07:50:17 brouard |
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After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree. |
| /******************************************/
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I remember having already fixed agemin agemax which are pointers now but not cvs saved. |
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| void replace(char *s, char*t)
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Revision 1.138 2010/04/30 18:19:40 brouard |
| {
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*** empty log message *** |
| int i;
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| int lg=20;
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Revision 1.137 2010/04/29 18:11:38 brouard |
| i=0;
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(Module): Checking covariates for more complex models |
| lg=strlen(t);
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than V1+V2. A lot of change to be done. Unstable. |
| for(i=0; i<= lg; i++) {
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| (s[i] = t[i]);
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Revision 1.136 2010/04/26 20:30:53 brouard |
| if (t[i]== '\\') s[i]='/';
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(Module): merging some libgsl code. Fixing computation |
| }
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of likelione (using inter/intrapolation if mle = 0) in order to |
| }
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get same likelihood as if mle=1. |
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Some cleaning of code and comments added. |
| int nbocc(char *s, char occ)
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| {
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Revision 1.135 2009/10/29 15:33:14 brouard |
| int i,j=0;
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(Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code. |
| int lg=20;
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| i=0;
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Revision 1.134 2009/10/29 13:18:53 brouard |
| lg=strlen(s);
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(Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code. |
| for(i=0; i<= lg; i++) {
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| if (s[i] == occ ) j++;
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Revision 1.133 2009/07/06 10:21:25 brouard |
| }
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just nforces |
| return j;
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| }
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Revision 1.132 2009/07/06 08:22:05 brouard |
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Many tings |
| void cutv(char *u,char *v, char*t, char occ)
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| {
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Revision 1.131 2009/06/20 16:22:47 brouard |
| int i,lg,j,p=0;
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Some dimensions resccaled |
| i=0;
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| for(j=0; j<=strlen(t)-1; j++) {
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Revision 1.130 2009/05/26 06:44:34 brouard |
| if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
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(Module): Max Covariate is now set to 20 instead of 8. A |
| }
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lot of cleaning with variables initialized to 0. Trying to make |
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V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better. |
| lg=strlen(t);
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| for(j=0; j<p; j++) {
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Revision 1.129 2007/08/31 13:49:27 lievre |
| (u[j] = t[j]);
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Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting |
| }
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| u[p]='\0';
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Revision 1.128 2006/06/30 13:02:05 brouard |
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(Module): Clarifications on computing e.j |
| for(j=0; j<= lg; j++) {
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| if (j>=(p+1))(v[j-p-1] = t[j]);
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Revision 1.127 2006/04/28 18:11:50 brouard |
| }
|
(Module): Yes the sum of survivors was wrong since |
| }
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imach-114 because nhstepm was no more computed in the age |
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loop. Now we define nhstepma in the age loop. |
| /********************** nrerror ********************/
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(Module): In order to speed up (in case of numerous covariates) we |
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compute health expectancies (without variances) in a first step |
| void nrerror(char error_text[])
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and then all the health expectancies with variances or standard |
| {
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deviation (needs data from the Hessian matrices) which slows the |
| fprintf(stderr,"ERREUR ...\n");
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computation. |
| fprintf(stderr,"%s\n",error_text);
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In the future we should be able to stop the program is only health |
| exit(1);
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expectancies and graph are needed without standard deviations. |
| }
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|
| /*********************** vector *******************/
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Revision 1.126 2006/04/28 17:23:28 brouard |
| double *vector(int nl, int nh)
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(Module): Yes the sum of survivors was wrong since |
| {
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imach-114 because nhstepm was no more computed in the age |
| double *v;
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loop. Now we define nhstepma in the age loop. |
| v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
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Version 0.98h |
| if (!v) nrerror("allocation failure in vector");
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| return v-nl+NR_END;
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Revision 1.125 2006/04/04 15:20:31 lievre |
| }
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Errors in calculation of health expectancies. Age was not initialized. |
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Forecasting file added. |
| /************************ free vector ******************/
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| void free_vector(double*v, int nl, int nh)
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Revision 1.124 2006/03/22 17:13:53 lievre |
| {
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Parameters are printed with %lf instead of %f (more numbers after the comma). |
| free((FREE_ARG)(v+nl-NR_END));
|
The log-likelihood is printed in the log file |
| }
|
|
|
|
Revision 1.123 2006/03/20 10:52:43 brouard |
| /************************ivector *******************************/
|
* imach.c (Module): <title> changed, corresponds to .htm file |
| int *ivector(long nl,long nh)
|
name. <head> headers where missing. |
| {
|
|
| int *v;
|
* imach.c (Module): Weights can have a decimal point as for |
| v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
|
English (a comma might work with a correct LC_NUMERIC environment, |
| if (!v) nrerror("allocation failure in ivector");
|
otherwise the weight is truncated). |
| return v-nl+NR_END;
|
Modification of warning when the covariates values are not 0 or |
| }
|
1. |
|
|
Version 0.98g |
| /******************free ivector **************************/
|
|
| void free_ivector(int *v, long nl, long nh)
|
Revision 1.122 2006/03/20 09:45:41 brouard |
| {
|
(Module): Weights can have a decimal point as for |
| free((FREE_ARG)(v+nl-NR_END));
|
English (a comma might work with a correct LC_NUMERIC environment, |
| }
|
otherwise the weight is truncated). |
|
|
Modification of warning when the covariates values are not 0 or |
| /******************* imatrix *******************************/
|
1. |
| int **imatrix(long nrl, long nrh, long ncl, long nch)
|
Version 0.98g |
| /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
|
|
| {
|
Revision 1.121 2006/03/16 17:45:01 lievre |
| long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
|
* imach.c (Module): Comments concerning covariates added |
| int **m;
|
|
|
|
* imach.c (Module): refinements in the computation of lli if |
| /* allocate pointers to rows */
|
status=-2 in order to have more reliable computation if stepm is |
| m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
|
not 1 month. Version 0.98f |
| if (!m) nrerror("allocation failure 1 in matrix()");
|
|
| m += NR_END;
|
Revision 1.120 2006/03/16 15:10:38 lievre |
| m -= nrl;
|
(Module): refinements in the computation of lli if |
|
|
status=-2 in order to have more reliable computation if stepm is |
|
|
not 1 month. Version 0.98f |
| /* allocate rows and set pointers to them */
|
|
| m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
|
Revision 1.119 2006/03/15 17:42:26 brouard |
| if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
|
(Module): Bug if status = -2, the loglikelihood was |
| m[nrl] += NR_END;
|
computed as likelihood omitting the logarithm. Version O.98e |
| m[nrl] -= ncl;
|
|
|
|
Revision 1.118 2006/03/14 18:20:07 brouard |
| for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
|
(Module): varevsij Comments added explaining the second |
|
|
table of variances if popbased=1 . |
| /* return pointer to array of pointers to rows */
|
(Module): Covariances of eij, ekl added, graphs fixed, new html link. |
| return m;
|
(Module): Function pstamp added |
| }
|
(Module): Version 0.98d |
|
|
|
| /****************** free_imatrix *************************/
|
Revision 1.117 2006/03/14 17:16:22 brouard |
| void free_imatrix(m,nrl,nrh,ncl,nch)
|
(Module): varevsij Comments added explaining the second |
| int **m;
|
table of variances if popbased=1 . |
| long nch,ncl,nrh,nrl;
|
(Module): Covariances of eij, ekl added, graphs fixed, new html link. |
| /* free an int matrix allocated by imatrix() */
|
(Module): Function pstamp added |
| {
|
(Module): Version 0.98d |
| free((FREE_ARG) (m[nrl]+ncl-NR_END));
|
|
| free((FREE_ARG) (m+nrl-NR_END));
|
Revision 1.116 2006/03/06 10:29:27 brouard |
| }
|
(Module): Variance-covariance wrong links and |
|
|
varian-covariance of ej. is needed (Saito). |
| /******************* matrix *******************************/
|
|
| double **matrix(long nrl, long nrh, long ncl, long nch)
|
Revision 1.115 2006/02/27 12:17:45 brouard |
| {
|
(Module): One freematrix added in mlikeli! 0.98c |
| long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
|
|
| double **m;
|
Revision 1.114 2006/02/26 12:57:58 brouard |
|
|
(Module): Some improvements in processing parameter |
| m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
|
filename with strsep. |
| if (!m) nrerror("allocation failure 1 in matrix()");
|
|
| m += NR_END;
|
Revision 1.113 2006/02/24 14:20:24 brouard |
| m -= nrl;
|
(Module): Memory leaks checks with valgrind and: |
|
|
datafile was not closed, some imatrix were not freed and on matrix |
| m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
|
allocation too. |
| if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
|
|
| m[nrl] += NR_END;
|
Revision 1.112 2006/01/30 09:55:26 brouard |
| m[nrl] -= ncl;
|
(Module): Back to gnuplot.exe instead of wgnuplot.exe |
|
|
|
| for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
|
Revision 1.111 2006/01/25 20:38:18 brouard |
| return m;
|
(Module): Lots of cleaning and bugs added (Gompertz) |
| }
|
(Module): Comments can be added in data file. Missing date values |
|
|
can be a simple dot '.'. |
| /*************************free matrix ************************/
|
|
| void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
|
Revision 1.110 2006/01/25 00:51:50 brouard |
| {
|
(Module): Lots of cleaning and bugs added (Gompertz) |
| free((FREE_ARG)(m[nrl]+ncl-NR_END));
|
|
| free((FREE_ARG)(m+nrl-NR_END));
|
Revision 1.109 2006/01/24 19:37:15 brouard |
| }
|
(Module): Comments (lines starting with a #) are allowed in data. |
|
|
|
| /******************* ma3x *******************************/
|
Revision 1.108 2006/01/19 18:05:42 lievre |
| double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
|
Gnuplot problem appeared... |
| {
|
To be fixed |
| long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
|
|
| double ***m;
|
Revision 1.107 2006/01/19 16:20:37 brouard |
|
|
Test existence of gnuplot in imach path |
| m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
|
|
| if (!m) nrerror("allocation failure 1 in matrix()");
|
Revision 1.106 2006/01/19 13:24:36 brouard |
| m += NR_END;
|
Some cleaning and links added in html output |
| m -= nrl;
|
|
|
|
Revision 1.105 2006/01/05 20:23:19 lievre |
| m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
|
*** empty log message *** |
| if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
|
|
| m[nrl] += NR_END;
|
Revision 1.104 2005/09/30 16:11:43 lievre |
| m[nrl] -= ncl;
|
(Module): sump fixed, loop imx fixed, and simplifications. |
|
|
(Module): If the status is missing at the last wave but we know |
| for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
|
that the person is alive, then we can code his/her status as -2 |
|
|
(instead of missing=-1 in earlier versions) and his/her |
| m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
|
contributions to the likelihood is 1 - Prob of dying from last |
| if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
|
health status (= 1-p13= p11+p12 in the easiest case of somebody in |
| m[nrl][ncl] += NR_END;
|
the healthy state at last known wave). Version is 0.98 |
| m[nrl][ncl] -= nll;
|
|
| for (j=ncl+1; j<=nch; j++)
|
Revision 1.103 2005/09/30 15:54:49 lievre |
| m[nrl][j]=m[nrl][j-1]+nlay;
|
(Module): sump fixed, loop imx fixed, and simplifications. |
|
|
|
| for (i=nrl+1; i<=nrh; i++) {
|
Revision 1.102 2004/09/15 17:31:30 brouard |
| m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
|
Add the possibility to read data file including tab characters. |
| for (j=ncl+1; j<=nch; j++)
|
|
| m[i][j]=m[i][j-1]+nlay;
|
Revision 1.101 2004/09/15 10:38:38 brouard |
| }
|
Fix on curr_time |
| return m;
|
|
| }
|
Revision 1.100 2004/07/12 18:29:06 brouard |
|
|
Add version for Mac OS X. Just define UNIX in Makefile |
| /*************************free ma3x ************************/
|
|
| void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
|
Revision 1.99 2004/06/05 08:57:40 brouard |
| {
|
*** empty log message *** |
| free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
|
|
| free((FREE_ARG)(m[nrl]+ncl-NR_END));
|
Revision 1.98 2004/05/16 15:05:56 brouard |
| free((FREE_ARG)(m+nrl-NR_END));
|
New version 0.97 . First attempt to estimate force of mortality |
| }
|
directly from the data i.e. without the need of knowing the health |
|
|
state at each age, but using a Gompertz model: log u =a + b*age . |
| /***************** f1dim *************************/
|
This is the basic analysis of mortality and should be done before any |
| extern int ncom;
|
other analysis, in order to test if the mortality estimated from the |
| extern double *pcom,*xicom;
|
cross-longitudinal survey is different from the mortality estimated |
| extern double (*nrfunc)(double []);
|
from other sources like vital statistic data. |
|
|
|
| double f1dim(double x)
|
The same imach parameter file can be used but the option for mle should be -3. |
| {
|
|
| int j;
|
Agnès, who wrote this part of the code, tried to keep most of the |
| double f;
|
former routines in order to include the new code within the former code. |
| double *xt;
|
|
|
|
The output is very simple: only an estimate of the intercept and of |
| xt=vector(1,ncom);
|
the slope with 95% confident intervals. |
| for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
|
|
| f=(*nrfunc)(xt);
|
Current limitations: |
| free_vector(xt,1,ncom);
|
A) Even if you enter covariates, i.e. with the |
| return f;
|
model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates. |
| }
|
B) There is no computation of Life Expectancy nor Life Table. |
|
|
|
| /*****************brent *************************/
|
Revision 1.97 2004/02/20 13:25:42 lievre |
| double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
|
Version 0.96d. Population forecasting command line is (temporarily) |
| {
|
suppressed. |
| int iter;
|
|
| double a,b,d,etemp;
|
Revision 1.96 2003/07/15 15:38:55 brouard |
| double fu,fv,fw,fx;
|
* imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is |
| double ftemp;
|
rewritten within the same printf. Workaround: many printfs. |
| double p,q,r,tol1,tol2,u,v,w,x,xm;
|
|
| double e=0.0;
|
Revision 1.95 2003/07/08 07:54:34 brouard |
|
|
* imach.c (Repository): |
| a=(ax < cx ? ax : cx);
|
(Repository): Using imachwizard code to output a more meaningful covariance |
| b=(ax > cx ? ax : cx);
|
matrix (cov(a12,c31) instead of numbers. |
| x=w=v=bx;
|
|
| fw=fv=fx=(*f)(x);
|
Revision 1.94 2003/06/27 13:00:02 brouard |
| for (iter=1;iter<=ITMAX;iter++) {
|
Just cleaning |
| xm=0.5*(a+b);
|
|
| tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
|
Revision 1.93 2003/06/25 16:33:55 brouard |
| /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
|
(Module): On windows (cygwin) function asctime_r doesn't |
| printf(".");fflush(stdout);
|
exist so I changed back to asctime which exists. |
| #ifdef DEBUG
|
(Module): Version 0.96b |
| 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);
|
|
| /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
|
Revision 1.92 2003/06/25 16:30:45 brouard |
| #endif
|
(Module): On windows (cygwin) function asctime_r doesn't |
| if (fabs(x-xm) <= (tol2-0.5*(b-a))){
|
exist so I changed back to asctime which exists. |
| *xmin=x;
|
|
| return fx;
|
Revision 1.91 2003/06/25 15:30:29 brouard |
| }
|
* imach.c (Repository): Duplicated warning errors corrected. |
| ftemp=fu;
|
(Repository): Elapsed time after each iteration is now output. It |
| if (fabs(e) > tol1) {
|
helps to forecast when convergence will be reached. Elapsed time |
| r=(x-w)*(fx-fv);
|
is stamped in powell. We created a new html file for the graphs |
| q=(x-v)*(fx-fw);
|
concerning matrix of covariance. It has extension -cov.htm. |
| p=(x-v)*q-(x-w)*r;
|
|
| q=2.0*(q-r);
|
Revision 1.90 2003/06/24 12:34:15 brouard |
| if (q > 0.0) p = -p;
|
(Module): Some bugs corrected for windows. Also, when |
| q=fabs(q);
|
mle=-1 a template is output in file "or"mypar.txt with the design |
| etemp=e;
|
of the covariance matrix to be input. |
| e=d;
|
|
| if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
|
Revision 1.89 2003/06/24 12:30:52 brouard |
| d=CGOLD*(e=(x >= xm ? a-x : b-x));
|
(Module): Some bugs corrected for windows. Also, when |
| else {
|
mle=-1 a template is output in file "or"mypar.txt with the design |
| d=p/q;
|
of the covariance matrix to be input. |
| u=x+d;
|
|
| if (u-a < tol2 || b-u < tol2)
|
Revision 1.88 2003/06/23 17:54:56 brouard |
| d=SIGN(tol1,xm-x);
|
* 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. |
| }
|
|
| } else {
|
Revision 1.87 2003/06/18 12:26:01 brouard |
| d=CGOLD*(e=(x >= xm ? a-x : b-x));
|
Version 0.96 |
| }
|
|
| u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
|
Revision 1.86 2003/06/17 20:04:08 brouard |
| fu=(*f)(u);
|
(Module): Change position of html and gnuplot routines and added |
| if (fu <= fx) {
|
routine fileappend. |
| if (u >= x) a=x; else b=x;
|
|
| SHFT(v,w,x,u)
|
Revision 1.85 2003/06/17 13:12:43 brouard |
| SHFT(fv,fw,fx,fu)
|
* imach.c (Repository): Check when date of death was earlier that |
| } else {
|
current date of interview. It may happen when the death was just |
| if (u < x) a=u; else b=u;
|
prior to the death. In this case, dh was negative and likelihood |
| if (fu <= fw || w == x) {
|
was wrong (infinity). We still send an "Error" but patch by |
| v=w;
|
assuming that the date of death was just one stepm after the |
| w=u;
|
interview. |
| fv=fw;
|
(Repository): Because some people have very long ID (first column) |
| fw=fu;
|
we changed int to long in num[] and we added a new lvector for |
| } else if (fu <= fv || v == x || v == w) {
|
memory allocation. But we also truncated to 8 characters (left |
| v=u;
|
truncation) |
| fv=fu;
|
(Repository): No more line truncation errors. |
| }
|
|
| }
|
Revision 1.84 2003/06/13 21:44:43 brouard |
| }
|
* imach.c (Repository): Replace "freqsummary" at a correct |
| nrerror("Too many iterations in brent");
|
place. It differs from routine "prevalence" which may be called |
| *xmin=x;
|
many times. Probs is memory consuming and must be used with |
| return fx;
|
parcimony. |
| }
|
Version 0.95a3 (should output exactly the same maximization than 0.8a2) |
|
|
|
| /****************** mnbrak ***********************/
|
Revision 1.83 2003/06/10 13:39:11 lievre |
|
|
*** empty log message *** |
| void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
|
|
| double (*func)(double))
|
Revision 1.82 2003/06/05 15:57:20 brouard |
| {
|
Add log in imach.c and fullversion number is now printed. |
| double ulim,u,r,q, dum;
|
|
| double fu;
|
*/ |
|
|
/* |
| *fa=(*func)(*ax);
|
Interpolated Markov Chain |
| *fb=(*func)(*bx);
|
|
| if (*fb > *fa) {
|
Short summary of the programme: |
| SHFT(dum,*ax,*bx,dum)
|
|
| SHFT(dum,*fb,*fa,dum)
|
This program computes Healthy Life Expectancies from |
| }
|
cross-longitudinal data. Cross-longitudinal data consist in: -1- a |
| *cx=(*bx)+GOLD*(*bx-*ax);
|
first survey ("cross") where individuals from different ages are |
| *fc=(*func)(*cx);
|
interviewed on their health status or degree of disability (in the |
| while (*fb > *fc) {
|
case of a health survey which is our main interest) -2- at least a |
| r=(*bx-*ax)*(*fb-*fc);
|
second wave of interviews ("longitudinal") which measure each change |
| q=(*bx-*cx)*(*fb-*fa);
|
(if any) in individual health status. Health expectancies are |
| u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
|
computed from the time spent in each health state according to a |
| (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
|
model. More health states you consider, more time is necessary to reach the |
| ulim=(*bx)+GLIMIT*(*cx-*bx);
|
Maximum Likelihood of the parameters involved in the model. The |
| if ((*bx-u)*(u-*cx) > 0.0) {
|
simplest model is the multinomial logistic model where pij is the |
| fu=(*func)(u);
|
probability to be observed in state j at the second wave |
| } else if ((*cx-u)*(u-ulim) > 0.0) {
|
conditional to be observed in state i at the first wave. Therefore |
| fu=(*func)(u);
|
the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where |
| if (fu < *fc) {
|
'age' is age and 'sex' is a covariate. If you want to have a more |
| SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
|
complex model than "constant and age", you should modify the program |
| SHFT(*fb,*fc,fu,(*func)(u))
|
where the markup *Covariates have to be included here again* invites |
| }
|
you to do it. More covariates you add, slower the |
| } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
|
convergence. |
| u=ulim;
|
|
| fu=(*func)(u);
|
The advantage of this computer programme, compared to a simple |
| } else {
|
multinomial logistic model, is clear when the delay between waves is not |
| u=(*cx)+GOLD*(*cx-*bx);
|
identical for each individual. Also, if a individual missed an |
| fu=(*func)(u);
|
intermediate interview, the information is lost, but taken into |
| }
|
account using an interpolation or extrapolation. |
| SHFT(*ax,*bx,*cx,u)
|
|
| SHFT(*fa,*fb,*fc,fu)
|
hPijx is the probability to be observed in state i at age x+h |
| }
|
conditional to the observed state i at age x. The delay 'h' can be |
| }
|
split into an exact number (nh*stepm) of unobserved intermediate |
|
|
states. This elementary transition (by month, quarter, |
| /*************** linmin ************************/
|
semester or year) is modelled as a multinomial logistic. The hPx |
|
|
matrix is simply the matrix product of nh*stepm elementary matrices |
| int ncom;
|
and the contribution of each individual to the likelihood is simply |
| double *pcom,*xicom;
|
hPijx. |
| double (*nrfunc)(double []);
|
|
|
|
Also this programme outputs the covariance matrix of the parameters but also |
| void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
|
of the life expectancies. It also computes the period (stable) prevalence. |
| {
|
|
| double brent(double ax, double bx, double cx,
|
Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr). |
| double (*f)(double), double tol, double *xmin);
|
Institut national d'études démographiques, Paris. |
| double f1dim(double x);
|
This software have been partly granted by Euro-REVES, a concerted action |
| void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
|
from the European Union. |
| double *fc, double (*func)(double));
|
It is copyrighted identically to a GNU software product, ie programme and |
| int j;
|
software can be distributed freely for non commercial use. Latest version |
| double xx,xmin,bx,ax;
|
can be accessed at http://euroreves.ined.fr/imach . |
| double fx,fb,fa;
|
|
|
|
Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach |
| ncom=n;
|
or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so |
| pcom=vector(1,n);
|
|
| xicom=vector(1,n);
|
**********************************************************************/ |
| nrfunc=func;
|
/* |
| for (j=1;j<=n;j++) {
|
main |
| pcom[j]=p[j];
|
read parameterfile |
| xicom[j]=xi[j];
|
read datafile |
| }
|
concatwav |
| ax=0.0;
|
freqsummary |
| xx=1.0;
|
if (mle >= 1) |
| mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
|
mlikeli |
| *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
|
print results files |
| #ifdef DEBUG
|
if mle==1 |
| printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
|
computes hessian |
| #endif
|
read end of parameter file: agemin, agemax, bage, fage, estepm |
| for (j=1;j<=n;j++) {
|
begin-prev-date,... |
| xi[j] *= xmin;
|
open gnuplot file |
| p[j] += xi[j];
|
open html file |
| }
|
period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate |
| free_vector(xicom,1,n);
|
for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ****** |
| free_vector(pcom,1,n);
|
| 65 1 0 2 1 3 1 4 0 0.96326 0.03674 |
| }
|
freexexit2 possible for memory heap. |
|
|
|
| /*************** powell ************************/
|
h Pij x | pij_nom ficrestpij |
| void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
|
# Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3 |
| double (*func)(double []))
|
1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000 |
| {
|
1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907 |
| void linmin(double p[], double xi[], int n, double *fret,
|
|
| double (*func)(double []));
|
1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340 |
| int i,ibig,j;
|
1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597 |
| double del,t,*pt,*ptt,*xit;
|
variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in () |
| double fp,fptt;
|
Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix |
| double *xits;
|
Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix |
| pt=vector(1,n);
|
|
| ptt=vector(1,n);
|
forecasting if prevfcast==1 prevforecast call prevalence() |
| xit=vector(1,n);
|
health expectancies |
| xits=vector(1,n);
|
Variance-covariance of DFLE |
| *fret=(*func)(p);
|
prevalence() |
| for (j=1;j<=n;j++) pt[j]=p[j];
|
movingaverage() |
| for (*iter=1;;++(*iter)) {
|
varevsij() |
| fp=(*fret);
|
if popbased==1 varevsij(,popbased) |
| ibig=0;
|
total life expectancies |
| del=0.0;
|
Variance of period (stable) prevalence |
| printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
|
end |
| for (i=1;i<=n;i++)
|
*/ |
| printf(" %d %.12f",i, p[i]);
|
|
| printf("\n");
|
/* #define DEBUG */ |
| for (i=1;i<=n;i++) {
|
/* #define DEBUGBRENT */ |
| for (j=1;j<=n;j++) xit[j]=xi[j][i];
|
#define POWELL /* Instead of NLOPT */ |
| fptt=(*fret);
|
/* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */ |
| #ifdef DEBUG
|
/* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */ |
| printf("fret=%lf \n",*fret);
|
|
| #endif
|
#include <math.h> |
| printf("%d",i);fflush(stdout);
|
#include <stdio.h> |
| linmin(p,xit,n,fret,func);
|
#include <stdlib.h> |
| if (fabs(fptt-(*fret)) > del) {
|
#include <string.h> |
| del=fabs(fptt-(*fret));
|
|
| ibig=i;
|
#ifdef _WIN32 |
| }
|
#include <io.h> |
| #ifdef DEBUG
|
#include <windows.h> |
| printf("%d %.12e",i,(*fret));
|
#include <tchar.h> |
| for (j=1;j<=n;j++) {
|
#else |
| xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
|
#include <unistd.h> |
| printf(" x(%d)=%.12e",j,xit[j]);
|
#endif |
| }
|
|
| for(j=1;j<=n;j++)
|
#include <limits.h> |
| printf(" p=%.12e",p[j]);
|
#include <sys/types.h> |
| printf("\n");
|
|
| #endif
|
#if defined(__GNUC__) |
| }
|
#include <sys/utsname.h> /* Doesn't work on Windows */ |
| if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
|
#endif |
| #ifdef DEBUG
|
|
| int k[2],l;
|
#include <sys/stat.h> |
| k[0]=1;
|
#include <errno.h> |
| k[1]=-1;
|
/* extern int errno; */ |
| printf("Max: %.12e",(*func)(p));
|
|
| for (j=1;j<=n;j++)
|
/* #ifdef LINUX */ |
| printf(" %.12e",p[j]);
|
/* #include <time.h> */ |
| printf("\n");
|
/* #include "timeval.h" */ |
| for(l=0;l<=1;l++) {
|
/* #else */ |
| for (j=1;j<=n;j++) {
|
/* #include <sys/time.h> */ |
| ptt[j]=p[j]+(p[j]-pt[j])*k[l];
|
/* #endif */ |
| printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
|
|
| }
|
#include <time.h> |
| printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
|
|
| }
|
#ifdef GSL |
| #endif
|
#include <gsl/gsl_errno.h> |
|
|
#include <gsl/gsl_multimin.h> |
|
|
#endif |
| free_vector(xit,1,n);
|
|
| free_vector(xits,1,n);
|
|
| free_vector(ptt,1,n);
|
#ifdef NLOPT |
| free_vector(pt,1,n);
|
#include <nlopt.h> |
| return;
|
typedef struct { |
| }
|
double (* function)(double [] ); |
| if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
|
} myfunc_data ; |
| for (j=1;j<=n;j++) {
|
#endif |
| ptt[j]=2.0*p[j]-pt[j];
|
|
| xit[j]=p[j]-pt[j];
|
/* #include <libintl.h> */ |
| pt[j]=p[j];
|
/* #define _(String) gettext (String) */ |
| }
|
|
| fptt=(*func)(ptt);
|
#define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */ |
| if (fptt < fp) {
|
|
| t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
|
#define GNUPLOTPROGRAM "gnuplot" |
| if (t < 0.0) {
|
/*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/ |
| linmin(p,xit,n,fret,func);
|
#define FILENAMELENGTH 132 |
| for (j=1;j<=n;j++) {
|
|
| xi[j][ibig]=xi[j][n];
|
#define GLOCK_ERROR_NOPATH -1 /* empty path */ |
| xi[j][n]=xit[j];
|
#define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */ |
| }
|
|
| #ifdef DEBUG
|
#define MAXPARM 128 /**< Maximum number of parameters for the optimization */ |
| printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
|
#define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */ |
| for(j=1;j<=n;j++)
|
|
| printf(" %.12e",xit[j]);
|
#define NINTERVMAX 8 |
| printf("\n");
|
#define NLSTATEMAX 8 /**< Maximum number of live states (for func) */ |
| #endif
|
#define NDEATHMAX 8 /**< Maximum number of dead states (for func) */ |
| }
|
#define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */ |
| }
|
#define codtabm(h,k) 1 & (h-1) >> (k-1) ; |
| }
|
#define MAXN 20000 |
| }
|
#define YEARM 12. /**< Number of months per year */ |
|
|
#define AGESUP 130 |
| /**** Prevalence limit ****************/
|
#define AGEBASE 40 |
|
|
#define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */ |
| double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
|
#ifdef _WIN32 |
| {
|
#define DIRSEPARATOR '\\' |
| /* Computes the prevalence limit in each live state at age x by left multiplying the unit
|
#define CHARSEPARATOR "\\" |
| matrix by transitions matrix until convergence is reached */
|
#define ODIRSEPARATOR '/' |
|
|
#else |
| int i, ii,j,k;
|
#define DIRSEPARATOR '/' |
| double min, max, maxmin, maxmax,sumnew=0.;
|
#define CHARSEPARATOR "/" |
| double **matprod2();
|
#define ODIRSEPARATOR '\\' |
| double **out, cov[NCOVMAX], **pmij();
|
#endif |
| double **newm;
|
|
| double agefin, delaymax=50 ; /* Max number of years to converge */
|
/* $Id$ */ |
|
|
/* $State$ */ |
| for (ii=1;ii<=nlstate+ndeath;ii++)
|
|
| for (j=1;j<=nlstate+ndeath;j++){
|
char version[]="Imach version 0.98q2, April 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015"; |
| oldm[ii][j]=(ii==j ? 1.0 : 0.0);
|
char fullversion[]="$Revision$ $Date$"; |
| }
|
char strstart[80]; |
|
|
char optionfilext[10], optionfilefiname[FILENAMELENGTH]; |
| cov[1]=1.;
|
int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */ |
|
|
int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */ |
| /* Even if hstepm = 1, at least one multiplication by the unit matrix */
|
/* Number of covariates model=V2+V1+ V3*age+V2*V4 */ |
| for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
|
int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */ |
| newm=savm;
|
int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */ |
| /* Covariates have to be included here again */
|
int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */ |
| cov[2]=agefin;
|
int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */ |
|
|
int cptcovprodnoage=0; /**< Number of covariate products without age */ |
| for (k=1; k<=cptcovn;k++) {
|
int cptcoveff=0; /* Total number of covariates to vary for printing results */ |
| cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
|
int cptcov=0; /* Working variable */ |
| /* 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]]);*/
|
int npar=NPARMAX; |
| }
|
int nlstate=2; /* Number of live states */ |
| for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
|
int ndeath=1; /* Number of dead states */ |
| for (k=1; k<=cptcovprod;k++)
|
int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */ |
| cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
|
int popbased=0; |
|
|
|
| /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
|
int *wav; /* Number of waves for this individuual 0 is possible */ |
| /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
|
int maxwav=0; /* Maxim number of waves */ |
| /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
|
int jmin=0, jmax=0; /* min, max spacing between 2 waves */ |
| out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
|
int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ |
|
|
int gipmx=0, gsw=0; /* Global variables on the number of contributions |
| savm=oldm;
|
to the likelihood and the sum of weights (done by funcone)*/ |
| oldm=newm;
|
int mle=1, weightopt=0; |
| maxmax=0.;
|
int **mw; /* mw[mi][i] is number of the mi wave for this individual */ |
| for(j=1;j<=nlstate;j++){
|
int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */ |
| min=1.;
|
int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between |
| max=0.;
|
* wave mi and wave mi+1 is not an exact multiple of stepm. */ |
| for(i=1; i<=nlstate; i++) {
|
int countcallfunc=0; /* Count the number of calls to func */ |
| sumnew=0;
|
double jmean=1; /* Mean space between 2 waves */ |
| for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
|
double **matprod2(); /* test */ |
| prlim[i][j]= newm[i][j]/(1-sumnew);
|
double **oldm, **newm, **savm; /* Working pointers to matrices */ |
| max=FMAX(max,prlim[i][j]);
|
double **oldms, **newms, **savms; /* Fixed working pointers to matrices */ |
| min=FMIN(min,prlim[i][j]);
|
/*FILE *fic ; */ /* Used in readdata only */ |
| }
|
FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop; |
| maxmin=max-min;
|
FILE *ficlog, *ficrespow; |
| maxmax=FMAX(maxmax,maxmin);
|
int globpr=0; /* Global variable for printing or not */ |
| }
|
double fretone; /* Only one call to likelihood */ |
| if(maxmax < ftolpl){
|
long ipmx=0; /* Number of contributions */ |
| return prlim;
|
double sw; /* Sum of weights */ |
| }
|
char filerespow[FILENAMELENGTH]; |
| }
|
char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */ |
| }
|
FILE *ficresilk; |
|
|
FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor; |
| /*************** transition probabilities ***************/
|
FILE *ficresprobmorprev; |
|
|
FILE *fichtm, *fichtmcov; /* Html File */ |
| double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
|
FILE *ficreseij; |
| {
|
char filerese[FILENAMELENGTH]; |
| double s1, s2;
|
FILE *ficresstdeij; |
| /*double t34;*/
|
char fileresstde[FILENAMELENGTH]; |
| int i,j,j1, nc, ii, jj;
|
FILE *ficrescveij; |
|
|
char filerescve[FILENAMELENGTH]; |
| for(i=1; i<= nlstate; i++){
|
FILE *ficresvij; |
| for(j=1; j<i;j++){
|
char fileresv[FILENAMELENGTH]; |
| for (nc=1, s2=0.;nc <=ncovmodel; nc++){
|
FILE *ficresvpl; |
| /*s2 += param[i][j][nc]*cov[nc];*/
|
char fileresvpl[FILENAMELENGTH]; |
| s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
|
char title[MAXLINE]; |
| /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
|
char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH]; |
| }
|
char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH]; |
| ps[i][j]=s2;
|
char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH]; |
| /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
|
char command[FILENAMELENGTH]; |
| }
|
int outcmd=0; |
| for(j=i+1; j<=nlstate+ndeath;j++){
|
|
| for (nc=1, s2=0.;nc <=ncovmodel; nc++){
|
char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH]; |
| s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
|
|
| /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
|
char filelog[FILENAMELENGTH]; /* Log file */ |
| }
|
char filerest[FILENAMELENGTH]; |
| ps[i][j]=s2;
|
char fileregp[FILENAMELENGTH]; |
| }
|
char popfile[FILENAMELENGTH]; |
| }
|
|
| /*ps[3][2]=1;*/
|
char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ; |
|
|
|
| for(i=1; i<= nlstate; i++){
|
/* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */ |
| s1=0;
|
/* struct timezone tzp; */ |
| for(j=1; j<i; j++)
|
/* extern int gettimeofday(); */ |
| s1+=exp(ps[i][j]);
|
struct tm tml, *gmtime(), *localtime(); |
| for(j=i+1; j<=nlstate+ndeath; j++)
|
|
| s1+=exp(ps[i][j]);
|
extern time_t time(); |
| ps[i][i]=1./(s1+1.);
|
|
| for(j=1; j<i; j++)
|
struct tm start_time, end_time, curr_time, last_time, forecast_time; |
| ps[i][j]= exp(ps[i][j])*ps[i][i];
|
time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */ |
| for(j=i+1; j<=nlstate+ndeath; j++)
|
struct tm tm; |
| ps[i][j]= exp(ps[i][j])*ps[i][i];
|
|
| /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
|
char strcurr[80], strfor[80]; |
| } /* end i */
|
|
|
|
char *endptr; |
| for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
|
long lval; |
| for(jj=1; jj<= nlstate+ndeath; jj++){
|
double dval; |
| ps[ii][jj]=0;
|
|
| ps[ii][ii]=1;
|
#define NR_END 1 |
| }
|
#define FREE_ARG char* |
| }
|
#define FTOL 1.0e-10 |
|
|
|
|
|
#define NRANSI |
| /* for(ii=1; ii<= nlstate+ndeath; ii++){
|
#define ITMAX 200 |
| for(jj=1; jj<= nlstate+ndeath; jj++){
|
|
| printf("%lf ",ps[ii][jj]);
|
#define TOL 2.0e-4 |
| }
|
|
| printf("\n ");
|
#define CGOLD 0.3819660 |
| }
|
#define ZEPS 1.0e-10 |
| printf("\n ");printf("%lf ",cov[2]);*/
|
#define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); |
| /*
|
|
| for(i=1; i<= npar; i++) printf("%f ",x[i]);
|
#define GOLD 1.618034 |
| goto end;*/
|
#define GLIMIT 100.0 |
| return ps;
|
#define TINY 1.0e-20 |
| }
|
|
|
|
static double maxarg1,maxarg2; |
| /**************** Product of 2 matrices ******************/
|
#define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2)) |
|
|
#define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2)) |
| double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
|
|
| {
|
#define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a)) |
| /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
|
#define rint(a) floor(a+0.5) |
| b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
|
/* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */ |
| /* in, b, out are matrice of pointers which should have been initialized
|
#define mytinydouble 1.0e-16 |
| before: only the contents of out is modified. The function returns
|
/* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */ |
| a pointer to pointers identical to out */
|
/* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */ |
| long i, j, k;
|
/* static double dsqrarg; */ |
| for(i=nrl; i<= nrh; i++)
|
/* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */ |
| for(k=ncolol; k<=ncoloh; k++)
|
static double sqrarg; |
| for(j=ncl,out[i][k]=0.; j<=nch; j++)
|
#define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg) |
| out[i][k] +=in[i][j]*b[j][k];
|
#define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} |
|
|
int agegomp= AGEGOMP; |
| return out;
|
|
| }
|
int imx; |
|
|
int stepm=1; |
|
|
/* Stepm, step in month: minimum step interpolation*/ |
| /************* Higher Matrix Product ***************/
|
|
|
|
int estepm; |
| double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
|
/* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/ |
| {
|
|
| /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month
|
int m,nb; |
| duration (i.e. until
|
long *num; |
| age (in years) age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.
|
int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens; |
| Output is stored in matrix po[i][j][h] for h every 'hstepm' step
|
double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint; |
| (typically every 2 years instead of every month which is too big).
|
double **pmmij, ***probs; |
| Model is determined by parameters x and covariates have to be
|
double *ageexmed,*agecens; |
| included manually here.
|
double dateintmean=0; |
|
|
|
| */
|
double *weight; |
|
|
int **s; /* Status */ |
| int i, j, d, h, k;
|
double *agedc; |
| double **out, cov[NCOVMAX];
|
double **covar; /**< covar[j,i], value of jth covariate for individual i, |
| double **newm;
|
* covar=matrix(0,NCOVMAX,1,n); |
|
|
* cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */ |
| /* Hstepm could be zero and should return the unit matrix */
|
double idx; |
| for (i=1;i<=nlstate+ndeath;i++)
|
int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */ |
| for (j=1;j<=nlstate+ndeath;j++){
|
int *Ndum; /** Freq of modality (tricode */ |
| oldm[i][j]=(i==j ? 1.0 : 0.0);
|
int **codtab; /**< codtab=imatrix(1,100,1,10); */ |
| po[i][j][0]=(i==j ? 1.0 : 0.0);
|
int **Tvard, *Tprod, cptcovprod, *Tvaraff; |
| }
|
double *lsurv, *lpop, *tpop; |
| /* Even if hstepm = 1, at least one multiplication by the unit matrix */
|
|
| for(h=1; h <=nhstepm; h++){
|
double ftol=FTOL; /**< Tolerance for computing Max Likelihood */ |
| for(d=1; d <=hstepm; d++){
|
double ftolhess; /**< Tolerance for computing hessian */ |
| newm=savm;
|
|
| /* Covariates have to be included here again */
|
/**************** split *************************/ |
| cov[1]=1.;
|
static int split( char *path, char *dirc, char *name, char *ext, char *finame ) |
| 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]]];
|
/* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc) |
| for (k=1; k<=cptcovage;k++)
|
the name of the file (name), its extension only (ext) and its first part of the name (finame) |
| cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
|
*/ |
| for (k=1; k<=cptcovprod;k++)
|
char *ss; /* pointer */ |
| cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
|
int l1=0, l2=0; /* length counters */ |
|
|
|
|
|
l1 = strlen(path ); /* length of path */ |
| /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
|
if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH ); |
| /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
|
ss= strrchr( path, DIRSEPARATOR ); /* find last / */ |
| out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
|
if ( ss == NULL ) { /* no directory, so determine current directory */ |
| pmij(pmmij,cov,ncovmodel,x,nlstate));
|
strcpy( name, path ); /* we got the fullname name because no directory */ |
| savm=oldm;
|
/*if(strrchr(path, ODIRSEPARATOR )==NULL) |
| oldm=newm;
|
printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/ |
| }
|
/* get current working directory */ |
| for(i=1; i<=nlstate+ndeath; i++)
|
/* extern char* getcwd ( char *buf , int len);*/ |
| for(j=1;j<=nlstate+ndeath;j++) {
|
#ifdef WIN32 |
| po[i][j][h]=newm[i][j];
|
if (_getcwd( dirc, FILENAME_MAX ) == NULL ) { |
| /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
|
#else |
| */
|
if (getcwd(dirc, FILENAME_MAX) == NULL) { |
| }
|
#endif |
| } /* end h */
|
return( GLOCK_ERROR_GETCWD ); |
| return po;
|
} |
| }
|
/* got dirc from getcwd*/ |
|
|
printf(" DIRC = %s \n",dirc); |
|
|
} else { /* strip direcotry from path */ |
| /*************** log-likelihood *************/
|
ss++; /* after this, the filename */ |
| double func( double *x)
|
l2 = strlen( ss ); /* length of filename */ |
| {
|
if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH ); |
| int i, ii, j, k, mi, d, kk;
|
strcpy( name, ss ); /* save file name */ |
| double l, ll[NLSTATEMAX], cov[NCOVMAX];
|
strncpy( dirc, path, l1 - l2 ); /* now the directory */ |
| double **out;
|
dirc[l1-l2] = '\0'; /* add zero */ |
| double sw; /* Sum of weights */
|
printf(" DIRC2 = %s \n",dirc); |
| double lli; /* Individual log likelihood */
|
} |
| long ipmx;
|
/* We add a separator at the end of dirc if not exists */ |
| /*extern weight */
|
l1 = strlen( dirc ); /* length of directory */ |
| /* We are differentiating ll according to initial status */
|
if( dirc[l1-1] != DIRSEPARATOR ){ |
| /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
|
dirc[l1] = DIRSEPARATOR; |
| /*for(i=1;i<imx;i++)
|
dirc[l1+1] = 0; |
| printf(" %d\n",s[4][i]);
|
printf(" DIRC3 = %s \n",dirc); |
| */
|
} |
| cov[1]=1.;
|
ss = strrchr( name, '.' ); /* find last / */ |
|
|
if (ss >0){ |
| for(k=1; k<=nlstate; k++) ll[k]=0.;
|
ss++; |
| for (i=1,ipmx=0, sw=0.; i<=imx; i++){
|
strcpy(ext,ss); /* save extension */ |
| for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
|
l1= strlen( name); |
| for(mi=1; mi<= wav[i]-1; mi++){
|
l2= strlen(ss)+1; |
| for (ii=1;ii<=nlstate+ndeath;ii++)
|
strncpy( finame, name, l1-l2); |
| for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
|
finame[l1-l2]= 0; |
| for(d=0; d<dh[mi][i]; d++){
|
} |
| newm=savm;
|
|
| cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
|
return( 0 ); /* we're done */ |
| for (kk=1; kk<=cptcovage;kk++) {
|
} |
| cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
|
|
| }
|
|
|
|
/******************************************/ |
| out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
|
|
| 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
|
void replace_back_to_slash(char *s, char*t) |
| savm=oldm;
|
{ |
| oldm=newm;
|
int i; |
|
|
int lg=0; |
|
|
i=0; |
| } /* end mult */
|
lg=strlen(t); |
|
|
for(i=0; i<= lg; i++) { |
| lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);
|
(s[i] = t[i]); |
| /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
|
if (t[i]== '\\') s[i]='/'; |
| ipmx +=1;
|
} |
| sw += weight[i];
|
} |
| ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
|
|
| } /* end of wave */
|
char *trimbb(char *out, char *in) |
| } /* end of individual */
|
{ /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */ |
|
|
char *s; |
| for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
|
s=out; |
| /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
|
while (*in != '\0'){ |
| l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
|
while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/ |
| return -l;
|
in++; |
| }
|
} |
|
|
*out++ = *in++; |
|
|
} |
| /*********** Maximum Likelihood Estimation ***************/
|
*out='\0'; |
|
|
return s; |
| void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
|
} |
| {
|
|
| int i,j, iter;
|
/* char *substrchaine(char *out, char *in, char *chain) */ |
| double **xi,*delti;
|
/* { */ |
| double fret;
|
/* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */ |
| xi=matrix(1,npar,1,npar);
|
/* char *s, *t; */ |
| for (i=1;i<=npar;i++)
|
/* t=in;s=out; */ |
| for (j=1;j<=npar;j++)
|
/* while ((*in != *chain) && (*in != '\0')){ */ |
| xi[i][j]=(i==j ? 1.0 : 0.0);
|
/* *out++ = *in++; */ |
| printf("Powell\n");
|
/* } */ |
| powell(p,xi,npar,ftol,&iter,&fret,func);
|
|
|
|
/* /\* *in matches *chain *\/ */ |
| printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
|
/* while ((*in++ == *chain++) && (*in != '\0')){ */ |
| fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
|
/* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */ |
|
|
/* } */ |
| }
|
/* in--; chain--; */ |
|
|
/* while ( (*in != '\0')){ */ |
| /**** Computes Hessian and covariance matrix ***/
|
/* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */ |
| void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
|
/* *out++ = *in++; */ |
| {
|
/* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */ |
| double **a,**y,*x,pd;
|
/* } */ |
| double **hess;
|
/* *out='\0'; */ |
| int i, j,jk;
|
/* out=s; */ |
| int *indx;
|
/* return out; */ |
|
|
/* } */ |
| double hessii(double p[], double delta, int theta, double delti[]);
|
char *substrchaine(char *out, char *in, char *chain) |
| double hessij(double p[], double delti[], int i, int j);
|
{ |
| void lubksb(double **a, int npar, int *indx, double b[]) ;
|
/* Substract chain 'chain' from 'in', return and output 'out' */ |
| void ludcmp(double **a, int npar, int *indx, double *d) ;
|
/* in="V1+V1*age+age*age+V2", chain="age*age" */ |
|
|
|
| hess=matrix(1,npar,1,npar);
|
char *strloc; |
|
|
|
| printf("\nCalculation of the hessian matrix. Wait...\n");
|
strcpy (out, in); |
| for (i=1;i<=npar;i++){
|
strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */ |
| printf("%d",i);fflush(stdout);
|
printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out); |
| hess[i][i]=hessii(p,ftolhess,i,delti);
|
if(strloc != NULL){ |
| /*printf(" %f ",p[i]);*/
|
/* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */ |
| /*printf(" %lf ",hess[i][i]);*/
|
memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1); |
| }
|
/* strcpy (strloc, strloc +strlen(chain));*/ |
|
|
} |
| for (i=1;i<=npar;i++) {
|
printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out); |
| for (j=1;j<=npar;j++) {
|
return out; |
| if (j>i) {
|
} |
| printf(".%d%d",i,j);fflush(stdout);
|
|
| hess[i][j]=hessij(p,delti,i,j);
|
|
| hess[j][i]=hess[i][j];
|
char *cutl(char *blocc, char *alocc, char *in, char occ) |
| /*printf(" %lf ",hess[i][j]);*/
|
{ |
| }
|
/* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ' |
| }
|
and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2') |
| }
|
gives blocc="abcdef" and alocc="ghi2j". |
| printf("\n");
|
If occ is not found blocc is null and alocc is equal to in. Returns blocc |
|
|
*/ |
| printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
|
char *s, *t; |
|
|
t=in;s=in; |
| a=matrix(1,npar,1,npar);
|
while ((*in != occ) && (*in != '\0')){ |
| y=matrix(1,npar,1,npar);
|
*alocc++ = *in++; |
| x=vector(1,npar);
|
} |
| indx=ivector(1,npar);
|
if( *in == occ){ |
| for (i=1;i<=npar;i++)
|
*(alocc)='\0'; |
| for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
|
s=++in; |
| ludcmp(a,npar,indx,&pd);
|
} |
|
|
|
| for (j=1;j<=npar;j++) {
|
if (s == t) {/* occ not found */ |
| for (i=1;i<=npar;i++) x[i]=0;
|
*(alocc-(in-s))='\0'; |
| x[j]=1;
|
in=s; |
| lubksb(a,npar,indx,x);
|
} |
| for (i=1;i<=npar;i++){
|
while ( *in != '\0'){ |
| matcov[i][j]=x[i];
|
*blocc++ = *in++; |
| }
|
} |
| }
|
|
|
|
*blocc='\0'; |
| printf("\n#Hessian matrix#\n");
|
return t; |
| for (i=1;i<=npar;i++) {
|
} |
| for (j=1;j<=npar;j++) {
|
char *cutv(char *blocc, char *alocc, char *in, char occ) |
| printf("%.3e ",hess[i][j]);
|
{ |
| }
|
/* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ' |
| printf("\n");
|
and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2') |
| }
|
gives blocc="abcdef2ghi" and alocc="j". |
|
|
If occ is not found blocc is null and alocc is equal to in. Returns alocc |
| /* Recompute Inverse */
|
*/ |
| for (i=1;i<=npar;i++)
|
char *s, *t; |
| for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
|
t=in;s=in; |
| ludcmp(a,npar,indx,&pd);
|
while (*in != '\0'){ |
|
|
while( *in == occ){ |
| /* printf("\n#Hessian matrix recomputed#\n");
|
*blocc++ = *in++; |
|
|
s=in; |
| for (j=1;j<=npar;j++) {
|
} |
| for (i=1;i<=npar;i++) x[i]=0;
|
*blocc++ = *in++; |
| x[j]=1;
|
} |
| lubksb(a,npar,indx,x);
|
if (s == t) /* occ not found */ |
| for (i=1;i<=npar;i++){
|
*(blocc-(in-s))='\0'; |
| y[i][j]=x[i];
|
else |
| printf("%.3e ",y[i][j]);
|
*(blocc-(in-s)-1)='\0'; |
| }
|
in=s; |
| printf("\n");
|
while ( *in != '\0'){ |
| }
|
*alocc++ = *in++; |
| */
|
} |
|
|
|
| free_matrix(a,1,npar,1,npar);
|
*alocc='\0'; |
| free_matrix(y,1,npar,1,npar);
|
return s; |
| free_vector(x,1,npar);
|
} |
| free_ivector(indx,1,npar);
|
|
| free_matrix(hess,1,npar,1,npar);
|
int nbocc(char *s, char occ) |
|
|
{ |
|
|
int i,j=0; |
| }
|
int lg=20; |
|
|
i=0; |
| /*************** hessian matrix ****************/
|
lg=strlen(s); |
| double hessii( double x[], double delta, int theta, double delti[])
|
for(i=0; i<= lg; i++) { |
| {
|
if (s[i] == occ ) j++; |
| int i;
|
} |
| int l=1, lmax=20;
|
return j; |
| double k1,k2;
|
} |
| double p2[NPARMAX+1];
|
|
| double res;
|
/* void cutv(char *u,char *v, char*t, char occ) */ |
| double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
|
/* { */ |
| double fx;
|
/* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */ |
| int k=0,kmax=10;
|
/* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */ |
| double l1;
|
/* gives u="abcdef2ghi" and v="j" *\/ */ |
|
|
/* int i,lg,j,p=0; */ |
| fx=func(x);
|
/* i=0; */ |
| for (i=1;i<=npar;i++) p2[i]=x[i];
|
/* lg=strlen(t); */ |
| for(l=0 ; l <=lmax; l++){
|
/* for(j=0; j<=lg-1; j++) { */ |
| l1=pow(10,l);
|
/* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */ |
| delts=delt;
|
/* } */ |
| for(k=1 ; k <kmax; k=k+1){
|
|
| delt = delta*(l1*k);
|
/* for(j=0; j<p; j++) { */ |
| p2[theta]=x[theta] +delt;
|
/* (u[j] = t[j]); */ |
| k1=func(p2)-fx;
|
/* } */ |
| p2[theta]=x[theta]-delt;
|
/* u[p]='\0'; */ |
| k2=func(p2)-fx;
|
|
| /*res= (k1-2.0*fx+k2)/delt/delt; */
|
/* for(j=0; j<= lg; j++) { */ |
| res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
|
/* if (j>=(p+1))(v[j-p-1] = t[j]); */ |
|
|
/* } */ |
| #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);
|
|
| #endif
|
#ifdef _WIN32 |
| /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
|
char * strsep(char **pp, const char *delim) |
| if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
|
{ |
| k=kmax;
|
char *p, *q; |
| }
|
|
| else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
|
if ((p = *pp) == NULL) |
| k=kmax; l=lmax*10.;
|
return 0; |
| }
|
if ((q = strpbrk (p, delim)) != NULL) |
| else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
|
{ |
| delts=delt;
|
*pp = q + 1; |
| }
|
*q = '\0'; |
| }
|
} |
| }
|
else |
| delti[theta]=delts;
|
*pp = 0; |
| return res;
|
return p; |
|
|
} |
| }
|
#endif |
|
|
|
| double hessij( double x[], double delti[], int thetai,int thetaj)
|
/********************** nrerror ********************/ |
| {
|
|
| int i;
|
void nrerror(char error_text[]) |
| int l=1, l1, lmax=20;
|
{ |
| double k1,k2,k3,k4,res,fx;
|
fprintf(stderr,"ERREUR ...\n"); |
| double p2[NPARMAX+1];
|
fprintf(stderr,"%s\n",error_text); |
| int k;
|
exit(EXIT_FAILURE); |
|
|
} |
| fx=func(x);
|
/*********************** vector *******************/ |
| for (k=1; k<=2; k++) {
|
double *vector(int nl, int nh) |
| for (i=1;i<=npar;i++) p2[i]=x[i];
|
{ |
| p2[thetai]=x[thetai]+delti[thetai]/k;
|
double *v; |
| p2[thetaj]=x[thetaj]+delti[thetaj]/k;
|
v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double))); |
| k1=func(p2)-fx;
|
if (!v) nrerror("allocation failure in vector"); |
|
|
return v-nl+NR_END; |
| p2[thetai]=x[thetai]+delti[thetai]/k;
|
} |
| p2[thetaj]=x[thetaj]-delti[thetaj]/k;
|
|
| k2=func(p2)-fx;
|
/************************ free vector ******************/ |
|
|
void free_vector(double*v, int nl, int nh) |
| p2[thetai]=x[thetai]-delti[thetai]/k;
|
{ |
| p2[thetaj]=x[thetaj]+delti[thetaj]/k;
|
free((FREE_ARG)(v+nl-NR_END)); |
| k3=func(p2)-fx;
|
} |
|
|
|
| p2[thetai]=x[thetai]-delti[thetai]/k;
|
/************************ivector *******************************/ |
| p2[thetaj]=x[thetaj]-delti[thetaj]/k;
|
int *ivector(long nl,long nh) |
| k4=func(p2)-fx;
|
{ |
| res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
|
int *v; |
| #ifdef DEBUG
|
v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int))); |
| 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);
|
if (!v) nrerror("allocation failure in ivector"); |
| #endif
|
return v-nl+NR_END; |
| }
|
} |
| return res;
|
|
| }
|
/******************free ivector **************************/ |
|
|
void free_ivector(int *v, long nl, long nh) |
| /************** Inverse of matrix **************/
|
{ |
| void ludcmp(double **a, int n, int *indx, double *d)
|
free((FREE_ARG)(v+nl-NR_END)); |
| {
|
} |
| int i,imax,j,k;
|
|
| double big,dum,sum,temp;
|
/************************lvector *******************************/ |
| double *vv;
|
long *lvector(long nl,long nh) |
|
|
{ |
| vv=vector(1,n);
|
long *v; |
| *d=1.0;
|
v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long))); |
| for (i=1;i<=n;i++) {
|
if (!v) nrerror("allocation failure in ivector"); |
| big=0.0;
|
return v-nl+NR_END; |
| for (j=1;j<=n;j++)
|
} |
| if ((temp=fabs(a[i][j])) > big) big=temp;
|
|
| if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
|
/******************free lvector **************************/ |
| vv[i]=1.0/big;
|
void free_lvector(long *v, long nl, long nh) |
| }
|
{ |
| for (j=1;j<=n;j++) {
|
free((FREE_ARG)(v+nl-NR_END)); |
| for (i=1;i<j;i++) {
|
} |
| sum=a[i][j];
|
|
| for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
|
/******************* imatrix *******************************/ |
| a[i][j]=sum;
|
int **imatrix(long nrl, long nrh, long ncl, long nch) |
| }
|
/* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ |
| big=0.0;
|
{ |
| for (i=j;i<=n;i++) {
|
long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; |
| sum=a[i][j];
|
int **m; |
| for (k=1;k<j;k++)
|
|
| sum -= a[i][k]*a[k][j];
|
/* allocate pointers to rows */ |
| a[i][j]=sum;
|
m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); |
| if ( (dum=vv[i]*fabs(sum)) >= big) {
|
if (!m) nrerror("allocation failure 1 in matrix()"); |
| big=dum;
|
m += NR_END; |
| imax=i;
|
m -= nrl; |
| }
|
|
| }
|
|
| if (j != imax) {
|
/* allocate rows and set pointers to them */ |
| for (k=1;k<=n;k++) {
|
m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); |
| dum=a[imax][k];
|
if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); |
| a[imax][k]=a[j][k];
|
m[nrl] += NR_END; |
| a[j][k]=dum;
|
m[nrl] -= ncl; |
| }
|
|
| *d = -(*d);
|
for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; |
| vv[imax]=vv[j];
|
|
| }
|
/* return pointer to array of pointers to rows */ |
| indx[j]=imax;
|
return m; |
| if (a[j][j] == 0.0) a[j][j]=TINY;
|
} |
| if (j != n) {
|
|
| dum=1.0/(a[j][j]);
|
/****************** free_imatrix *************************/ |
| for (i=j+1;i<=n;i++) a[i][j] *= dum;
|
void free_imatrix(m,nrl,nrh,ncl,nch) |
| }
|
int **m; |
| }
|
long nch,ncl,nrh,nrl; |
| free_vector(vv,1,n); /* Doesn't work */
|
/* free an int matrix allocated by imatrix() */ |
| ;
|
{ |
| }
|
free((FREE_ARG) (m[nrl]+ncl-NR_END)); |
|
|
free((FREE_ARG) (m+nrl-NR_END)); |
| void lubksb(double **a, int n, int *indx, double b[])
|
} |
| {
|
|
| int i,ii=0,ip,j;
|
/******************* matrix *******************************/ |
| double sum;
|
double **matrix(long nrl, long nrh, long ncl, long nch) |
|
|
{ |
| for (i=1;i<=n;i++) {
|
long i, nrow=nrh-nrl+1, ncol=nch-ncl+1; |
| ip=indx[i];
|
double **m; |
| sum=b[ip];
|
|
| b[ip]=b[i];
|
m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*))); |
| if (ii)
|
if (!m) nrerror("allocation failure 1 in matrix()"); |
| for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
|
m += NR_END; |
| else if (sum) ii=i;
|
m -= nrl; |
| b[i]=sum;
|
|
| }
|
m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double))); |
| for (i=n;i>=1;i--) {
|
if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); |
| sum=b[i];
|
m[nrl] += NR_END; |
| for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
|
m[nrl] -= ncl; |
| b[i]=sum/a[i][i];
|
|
| }
|
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]) or &(m[1][0]) |
| /************ Frequencies ********************/
|
m[i] = address of ith row of the table. &(m[i]) is its value which is another adress |
| void freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
|
that of m[i][0]. In order to get the value p m[i][0] but it is unitialized. |
| { /* Some frequencies */
|
*/ |
|
|
} |
| int i, m, jk, k1,i1, j1, bool, z1,z2,j;
|
|
| double ***freq; /* Frequencies */
|
/*************************free matrix ************************/ |
| double *pp;
|
void free_matrix(double **m, long nrl, long nrh, long ncl, long nch) |
| double pos, k2, dateintsum=0,k2cpt=0;
|
{ |
| FILE *ficresp;
|
free((FREE_ARG)(m[nrl]+ncl-NR_END)); |
| char fileresp[FILENAMELENGTH];
|
free((FREE_ARG)(m+nrl-NR_END)); |
|
|
} |
| pp=vector(1,nlstate);
|
|
| probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
|
/******************* ma3x *******************************/ |
| strcpy(fileresp,"p");
|
double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh) |
| strcat(fileresp,fileres);
|
{ |
| if((ficresp=fopen(fileresp,"w"))==NULL) {
|
long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1; |
| printf("Problem with prevalence resultfile: %s\n", fileresp);
|
double ***m; |
| exit(0);
|
|
| }
|
m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*))); |
| freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
|
if (!m) nrerror("allocation failure 1 in matrix()"); |
| j1=0;
|
m += NR_END; |
|
|
m -= nrl; |
| j=cptcoveff;
|
|
| if (cptcovn<1) {j=1;ncodemax[1]=1;}
|
m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double))); |
|
|
if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); |
| for(k1=1; k1<=j;k1++){
|
m[nrl] += NR_END; |
| for(i1=1; i1<=ncodemax[k1];i1++){
|
m[nrl] -= ncl; |
| j1++;
|
|
| /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
|
for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol; |
| scanf("%d", i);*/
|
|
| for (i=-1; i<=nlstate+ndeath; i++)
|
m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double))); |
| for (jk=-1; jk<=nlstate+ndeath; jk++)
|
if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()"); |
| for(m=agemin; m <= agemax+3; m++)
|
m[nrl][ncl] += NR_END; |
| freq[i][jk][m]=0;
|
m[nrl][ncl] -= nll; |
|
|
for (j=ncl+1; j<=nch; j++) |
| dateintsum=0;
|
m[nrl][j]=m[nrl][j-1]+nlay; |
| k2cpt=0;
|
|
| for (i=1; i<=imx; i++) {
|
for (i=nrl+1; i<=nrh; i++) { |
| bool=1;
|
m[i][ncl]=m[i-1l][ncl]+ncol*nlay; |
| if (cptcovn>0) {
|
for (j=ncl+1; j<=nch; j++) |
| for (z1=1; z1<=cptcoveff; z1++)
|
m[i][j]=m[i][j-1]+nlay; |
| if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
|
} |
| bool=0;
|
return m; |
| }
|
/* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1]) |
| if (bool==1) {
|
&(m[i][j][k]) <=> *((*(m+i) + j)+k) |
| for(m=firstpass; m<=lastpass; m++){
|
*/ |
| k2=anint[m][i]+(mint[m][i]/12.);
|
} |
| if ((k2>=dateprev1) && (k2<=dateprev2)) {
|
|
| if(agev[m][i]==0) agev[m][i]=agemax+1;
|
/*************************free ma3x ************************/ |
| if(agev[m][i]==1) agev[m][i]=agemax+2;
|
void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh) |
| if (m<lastpass) {
|
{ |
| freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
|
free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END)); |
| freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
|
free((FREE_ARG)(m[nrl]+ncl-NR_END)); |
| }
|
free((FREE_ARG)(m+nrl-NR_END)); |
|
|
} |
| if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
|
|
| dateintsum=dateintsum+k2;
|
/*************** function subdirf ***********/ |
| k2cpt++;
|
char *subdirf(char fileres[]) |
| }
|
{ |
| }
|
/* Caution optionfilefiname is hidden */ |
| }
|
strcpy(tmpout,optionfilefiname); |
| }
|
strcat(tmpout,"/"); /* Add to the right */ |
| }
|
strcat(tmpout,fileres); |
|
|
return tmpout; |
| fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
|
} |
|
|
|
| if (cptcovn>0) {
|
/*************** function subdirf2 ***********/ |
| fprintf(ficresp, "\n#********** Variable ");
|
char *subdirf2(char fileres[], char *preop) |
| for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
|
{ |
| fprintf(ficresp, "**********\n#");
|
|
| }
|
/* Caution optionfilefiname is hidden */ |
| for(i=1; i<=nlstate;i++)
|
strcpy(tmpout,optionfilefiname); |
| fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
|
strcat(tmpout,"/"); |
| fprintf(ficresp, "\n");
|
strcat(tmpout,preop); |
|
|
strcat(tmpout,fileres); |
| for(i=(int)agemin; i <= (int)agemax+3; i++){
|
return tmpout; |
| if(i==(int)agemax+3)
|
} |
| printf("Total");
|
|
| else
|
/*************** function subdirf3 ***********/ |
| printf("Age %d", i);
|
char *subdirf3(char fileres[], char *preop, char *preop2) |
| for(jk=1; jk <=nlstate ; jk++){
|
{ |
| for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
|
|
| pp[jk] += freq[jk][m][i];
|
/* Caution optionfilefiname is hidden */ |
| }
|
strcpy(tmpout,optionfilefiname); |
| for(jk=1; jk <=nlstate ; jk++){
|
strcat(tmpout,"/"); |
| for(m=-1, pos=0; m <=0 ; m++)
|
strcat(tmpout,preop); |
| pos += freq[jk][m][i];
|
strcat(tmpout,preop2); |
| if(pp[jk]>=1.e-10)
|
strcat(tmpout,fileres); |
| printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
|
return tmpout; |
| else
|
} |
| printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
|
|
| }
|
char *asc_diff_time(long time_sec, char ascdiff[]) |
|
|
{ |
| for(jk=1; jk <=nlstate ; jk++){
|
long sec_left, days, hours, minutes; |
| for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
|
days = (time_sec) / (60*60*24); |
| pp[jk] += freq[jk][m][i];
|
sec_left = (time_sec) % (60*60*24); |
| }
|
hours = (sec_left) / (60*60) ; |
|
|
sec_left = (sec_left) %(60*60); |
| for(jk=1,pos=0; jk <=nlstate ; jk++)
|
minutes = (sec_left) /60; |
| pos += pp[jk];
|
sec_left = (sec_left) % (60); |
| for(jk=1; jk <=nlstate ; jk++){
|
sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left); |
| if(pos>=1.e-5)
|
return ascdiff; |
| printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
|
} |
| else
|
|
| printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
|
/***************** f1dim *************************/ |
| if( i <= (int) agemax){
|
extern int ncom; |
| if(pos>=1.e-5){
|
extern double *pcom,*xicom; |
| fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
|
extern double (*nrfunc)(double []); |
| probs[i][jk][j1]= pp[jk]/pos;
|
|
| /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
|
double f1dim(double x) |
| }
|
{ |
| else
|
int j; |
| fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
|
double f; |
| }
|
double *xt; |
| }
|
|
|
|
xt=vector(1,ncom); |
| for(jk=-1; jk <=nlstate+ndeath; jk++)
|
for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; |
| for(m=-1; m <=nlstate+ndeath; m++)
|
f=(*nrfunc)(xt); |
| if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
|
free_vector(xt,1,ncom); |
| if(i <= (int) agemax)
|
return f; |
| fprintf(ficresp,"\n");
|
} |
| printf("\n");
|
|
| }
|
/*****************brent *************************/ |
| }
|
double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin) |
| }
|
{ |
| dateintmean=dateintsum/k2cpt;
|
/* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is |
|
|
* between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates |
| fclose(ficresp);
|
* the minimum to a fractional precision of about tol using Brent’s method. The abscissa of |
| free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
|
* the minimum is returned as xmin, and the minimum function value is returned as brent , the |
| free_vector(pp,1,nlstate);
|
* returned function value. |
|
|
*/ |
| /* End of Freq */
|
int iter; |
| }
|
double a,b,d,etemp; |
|
|
double fu=0,fv,fw,fx; |
| /************ Prevalence ********************/
|
double ftemp=0.; |
| 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)
|
double p,q,r,tol1,tol2,u,v,w,x,xm; |
| { /* Some frequencies */
|
double e=0.0; |
|
|
|
| int i, m, jk, k1, i1, j1, bool, z1,z2,j;
|
a=(ax < cx ? ax : cx); |
| double ***freq; /* Frequencies */
|
b=(ax > cx ? ax : cx); |
| double *pp;
|
x=w=v=bx; |
| double pos, k2;
|
fw=fv=fx=(*f)(x); |
|
|
for (iter=1;iter<=ITMAX;iter++) { |
| pp=vector(1,nlstate);
|
xm=0.5*(a+b); |
| probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
|
tol2=2.0*(tol1=tol*fabs(x)+ZEPS); |
|
|
/* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/ |
| freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
|
printf(".");fflush(stdout); |
| j1=0;
|
fprintf(ficlog,".");fflush(ficlog); |
|
|
#ifdef DEBUGBRENT |
| j=cptcoveff;
|
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); |
| if (cptcovn<1) {j=1;ncodemax[1]=1;}
|
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); |
|
|
/* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */ |
| for(k1=1; k1<=j;k1++){
|
#endif |
| for(i1=1; i1<=ncodemax[k1];i1++){
|
if (fabs(x-xm) <= (tol2-0.5*(b-a))){ |
| j1++;
|
*xmin=x; |
|
|
return fx; |
| for (i=-1; i<=nlstate+ndeath; i++)
|
} |
| for (jk=-1; jk<=nlstate+ndeath; jk++)
|
ftemp=fu; |
| for(m=agemin; m <= agemax+3; m++)
|
if (fabs(e) > tol1) { |
| freq[i][jk][m]=0;
|
r=(x-w)*(fx-fv); |
|
|
q=(x-v)*(fx-fw); |
| for (i=1; i<=imx; i++) {
|
p=(x-v)*q-(x-w)*r; |
| bool=1;
|
q=2.0*(q-r); |
| if (cptcovn>0) {
|
if (q > 0.0) p = -p; |
| for (z1=1; z1<=cptcoveff; z1++)
|
q=fabs(q); |
| if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
|
etemp=e; |
| bool=0;
|
e=d; |
| }
|
if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) |
| if (bool==1) {
|
d=CGOLD*(e=(x >= xm ? a-x : b-x)); |
| for(m=firstpass; m<=lastpass; m++){
|
else { |
| k2=anint[m][i]+(mint[m][i]/12.);
|
d=p/q; |
| if ((k2>=dateprev1) && (k2<=dateprev2)) {
|
u=x+d; |
| if(agev[m][i]==0) agev[m][i]=agemax+1;
|
if (u-a < tol2 || b-u < tol2) |
| if(agev[m][i]==1) agev[m][i]=agemax+2;
|
d=SIGN(tol1,xm-x); |
| if (m<lastpass) {
|
} |
| if (calagedate>0)
|
} else { |
| freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
|
d=CGOLD*(e=(x >= xm ? a-x : b-x)); |
| else
|
} |
| freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
|
u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); |
| freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];
|
fu=(*f)(u); |
| }
|
if (fu <= fx) { |
| }
|
if (u >= x) a=x; else b=x; |
| }
|
SHFT(v,w,x,u) |
| }
|
SHFT(fv,fw,fx,fu) |
| }
|
} else { |
| for(i=(int)agemin; i <= (int)agemax+3; i++){
|
if (u < x) a=u; else b=u; |
| for(jk=1; jk <=nlstate ; jk++){
|
if (fu <= fw || w == x) { |
| for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
|
v=w; |
| pp[jk] += freq[jk][m][i];
|
w=u; |
| }
|
fv=fw; |
| for(jk=1; jk <=nlstate ; jk++){
|
fw=fu; |
| for(m=-1, pos=0; m <=0 ; m++)
|
} else if (fu <= fv || v == x || v == w) { |
| pos += freq[jk][m][i];
|
v=u; |
| }
|
fv=fu; |
|
|
} |
| for(jk=1; jk <=nlstate ; jk++){
|
} |
| for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
|
} |
| pp[jk] += freq[jk][m][i];
|
nrerror("Too many iterations in brent"); |
| }
|
*xmin=x; |
|
|
return fx; |
| for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
|
} |
|
|
|
| for(jk=1; jk <=nlstate ; jk++){
|
/****************** mnbrak ***********************/ |
| if( i <= (int) agemax){
|
|
| if(pos>=1.e-5){
|
void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, |
| probs[i][jk][j1]= pp[jk]/pos;
|
double (*func)(double)) |
| }
|
{ /* Given a function func , and given distinct initial points ax and bx , this routine searches in |
| }
|
the downhill direction (defined by the function as evaluated at the initial points) and returns |
| }
|
new points ax , bx , cx that bracket a minimum of the function. Also returned are the function |
|
|
values at the three points, fa, fb , and fc such that fa > fb and fb < fc. |
| }
|
*/ |
| }
|
double ulim,u,r,q, dum; |
| }
|
double fu; |
|
|
|
|
|
double scale=10.; |
| free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
|
int iterscale=0; |
| free_vector(pp,1,nlstate);
|
|
|
|
*fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/ |
| } /* End of Freq */
|
*fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */ |
|
|
|
| /************* Waves Concatenation ***************/
|
|
|
|
/* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */ |
| void concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)
|
/* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */ |
| {
|
/* *bx = *ax - (*ax - *bx)/scale; */ |
| /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
|
/* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */ |
| Death is a valid wave (if date is known).
|
/* } */ |
| mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
|
|
| dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]
|
if (*fb > *fa) { |
| and mw[mi+1][i]. dh depends on stepm.
|
SHFT(dum,*ax,*bx,dum) |
| */
|
SHFT(dum,*fb,*fa,dum) |
|
|
} |
| int i, mi, m;
|
*cx=(*bx)+GOLD*(*bx-*ax); |
| /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
|
*fc=(*func)(*cx); |
| double sum=0., jmean=0.;*/
|
#ifdef DEBUG |
|
|
printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc); |
| int j, k=0,jk, ju, jl;
|
fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc); |
| double sum=0.;
|
#endif |
| jmin=1e+5;
|
while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */ |
| jmax=-1;
|
r=(*bx-*ax)*(*fb-*fc); |
| jmean=0.;
|
q=(*bx-*cx)*(*fb-*fa); |
| for(i=1; i<=imx; i++){
|
u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ |
| mi=0;
|
(2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */ |
| m=firstpass;
|
ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */ |
| while(s[m][i] <= nlstate){
|
if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */ |
| if(s[m][i]>=1)
|
fu=(*func)(u); |
| mw[++mi][i]=m;
|
#ifdef DEBUG |
| if(m >=lastpass)
|
/* f(x)=A(x-u)**2+f(u) */ |
| break;
|
double A, fparabu; |
| else
|
A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u); |
| m++;
|
fparabu= *fa - A*(*ax-u)*(*ax-u); |
| }/* end while */
|
printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu); |
| if (s[m][i] > nlstate){
|
fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu); |
| mi++; /* Death is another wave */
|
/* And thus,it can be that fu > *fc even if fparabu < *fc */ |
| /* if(mi==0) never been interviewed correctly before death */
|
/* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489), |
| /* Only death is a correct wave */
|
(*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */ |
| mw[mi][i]=m;
|
/* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/ |
| }
|
#endif |
|
|
#ifdef MNBRAKORIGINAL |
| wav[i]=mi;
|
#else |
| if(mi==0)
|
if (fu > *fc) { |
| printf("Warning, no any valid information for:%d line=%d\n",num[i],i);
|
#ifdef DEBUG |
| }
|
printf("mnbrak4 fu > fc \n"); |
|
|
fprintf(ficlog, "mnbrak4 fu > fc\n"); |
| for(i=1; i<=imx; i++){
|
#endif |
| for(mi=1; mi<wav[i];mi++){
|
/* SHFT(u,*cx,*cx,u) /\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\/ */ |
| if (stepm <=0)
|
/* SHFT(*fa,*fc,fu,*fc) /\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\/ */ |
| dh[mi][i]=1;
|
dum=u; /* Shifting c and u */ |
| else{
|
u = *cx; |
| if (s[mw[mi+1][i]][i] > nlstate) {
|
*cx = dum; |
| if (agedc[i] < 2*AGESUP) {
|
dum = fu; |
| j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
|
fu = *fc; |
| if(j==0) j=1; /* Survives at least one month after exam */
|
*fc =dum; |
| k=k+1;
|
} else { /* end */ |
| if (j >= jmax) jmax=j;
|
#ifdef DEBUG |
| if (j <= jmin) jmin=j;
|
printf("mnbrak3 fu < fc \n"); |
| sum=sum+j;
|
fprintf(ficlog, "mnbrak3 fu < fc\n"); |
| /*if (j<0) printf("j=%d num=%d \n",j,i); */
|
#endif |
| }
|
dum=u; /* Shifting c and u */ |
| }
|
u = *cx; |
| else{
|
*cx = dum; |
| j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
|
dum = fu; |
| k=k+1;
|
fu = *fc; |
| if (j >= jmax) jmax=j;
|
*fc =dum; |
| else if (j <= jmin)jmin=j;
|
} |
| /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
|
#endif |
| sum=sum+j;
|
} else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */ |
| }
|
#ifdef DEBUG |
| jk= j/stepm;
|
printf("mnbrak2 u after c but before ulim\n"); |
| jl= j -jk*stepm;
|
fprintf(ficlog, "mnbrak2 u after c but before ulim\n"); |
| ju= j -(jk+1)*stepm;
|
#endif |
| if(jl <= -ju)
|
fu=(*func)(u); |
| dh[mi][i]=jk;
|
if (fu < *fc) { |
| else
|
#ifdef DEBUG |
| dh[mi][i]=jk+1;
|
printf("mnbrak2 u after c but before ulim AND fu < fc\n"); |
| if(dh[mi][i]==0)
|
fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n"); |
| dh[mi][i]=1; /* At least one step */
|
#endif |
| }
|
SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) |
| }
|
SHFT(*fb,*fc,fu,(*func)(u)) |
| }
|
} |
| jmean=sum/k;
|
} else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */ |
| printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
|
#ifdef DEBUG |
| }
|
printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n"); |
| /*********** Tricode ****************************/
|
fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n"); |
| void tricode(int *Tvar, int **nbcode, int imx)
|
#endif |
| {
|
u=ulim; |
| int Ndum[20],ij=1, k, j, i;
|
fu=(*func)(u); |
| int cptcode=0;
|
} else { /* u could be left to b (if r > q parabola has a maximum) */ |
| cptcoveff=0;
|
#ifdef DEBUG |
|
|
printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n"); |
| for (k=0; k<19; k++) Ndum[k]=0;
|
fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n"); |
| for (k=1; k<=7; k++) ncodemax[k]=0;
|
#endif |
|
|
u=(*cx)+GOLD*(*cx-*bx); |
| for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
|
fu=(*func)(u); |
| for (i=1; i<=imx; i++) {
|
} /* end tests */ |
| ij=(int)(covar[Tvar[j]][i]);
|
SHFT(*ax,*bx,*cx,u) |
| Ndum[ij]++;
|
SHFT(*fa,*fb,*fc,fu) |
| /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
|
#ifdef DEBUG |
| if (ij > cptcode) cptcode=ij;
|
printf("mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu); |
| }
|
fprintf(ficlog, "mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu); |
|
|
#endif |
| for (i=0; i<=cptcode; i++) {
|
} /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */ |
| if(Ndum[i]!=0) ncodemax[j]++;
|
} |
| }
|
|
| ij=1;
|
/*************** linmin ************************/ |
|
|
/* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and |
|
|
resets p to where the function func(p) takes on a minimum along the direction xi from p , |
| for (i=1; i<=ncodemax[j]; i++) {
|
and replaces xi by the actual vector displacement that p was moved. Also returns as fret |
| for (k=0; k<=19; k++) {
|
the value of func at the returned location p . This is actually all accomplished by calling the |
| if (Ndum[k] != 0) {
|
routines mnbrak and brent .*/ |
| nbcode[Tvar[j]][ij]=k;
|
int ncom; |
|
|
double *pcom,*xicom; |
| ij++;
|
double (*nrfunc)(double []); |
| }
|
|
| if (ij > ncodemax[j]) break;
|
void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) |
| }
|
{ |
| }
|
double brent(double ax, double bx, double cx, |
| }
|
double (*f)(double), double tol, double *xmin); |
|
|
double f1dim(double x); |
| for (k=0; k<19; k++) Ndum[k]=0;
|
void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, |
|
|
double *fc, double (*func)(double)); |
| for (i=1; i<=ncovmodel-2; i++) {
|
int j; |
| ij=Tvar[i];
|
double xx,xmin,bx,ax; |
| Ndum[ij]++;
|
double fx,fb,fa; |
| }
|
|
|
|
double scale=10., axs, xxs, xxss; /* Scale added for infinity */ |
| ij=1;
|
|
| for (i=1; i<=10; i++) {
|
ncom=n; |
| if((Ndum[i]!=0) && (i<=ncovcol)){
|
pcom=vector(1,n); |
| Tvaraff[ij]=i;
|
xicom=vector(1,n); |
| ij++;
|
nrfunc=func; |
| }
|
for (j=1;j<=n;j++) { |
| }
|
pcom[j]=p[j]; |
|
|
xicom[j]=xi[j]; |
| cptcoveff=ij-1;
|
} |
| }
|
|
|
|
axs=0.0; |
| /*********** Health Expectancies ****************/
|
xxss=1; /* 1 and using scale */ |
|
|
xxs=1; |
| 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 )
|
do{ |
|
|
ax=0.; |
| {
|
xx= xxs; |
| /* Health expectancies */
|
mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */ |
| int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
|
/* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */ |
| double age, agelim, hf;
|
/* xt[x,j]=pcom[j]+x*xicom[j] f(ax) = f(xt(a,j=1,n)) = f(p(j) + 0 * xi(j)) and f(xx) = f(xt(x, j=1,n)) = f(p(j) + 1 * xi(j)) */ |
| double ***p3mat,***varhe;
|
/* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */ |
| double **dnewm,**doldm;
|
/* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */ |
| double *xp;
|
/* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */ |
| double **gp, **gm;
|
/* Find a bracket a,x,b in direction n=xi ie xicom, order may change. Scale is [0:xxs*xi[j]] et non plus [0:xi[j]]*/ |
| double ***gradg, ***trgradg;
|
if (fx != fx){ |
| int theta;
|
xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */ |
|
|
printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n", axs, xxs, fx,fb, fa, xx, ax, bx); |
| varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
|
} |
| xp=vector(1,npar);
|
}while(fx != fx); |
| dnewm=matrix(1,nlstate*2,1,npar);
|
|
| doldm=matrix(1,nlstate*2,1,nlstate*2);
|
*fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/ |
|
|
/* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */ |
| fprintf(ficreseij,"# Health expectancies\n");
|
/* fmin = f(p[j] + xmin * xi[j]) */ |
| fprintf(ficreseij,"# Age");
|
/* P+lambda n in that direction (lambdamin), with TOL between abscisses */ |
| for(i=1; i<=nlstate;i++)
|
/* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */ |
| for(j=1; j<=nlstate;j++)
|
#ifdef DEBUG |
| fprintf(ficreseij," %1d-%1d (SE)",i,j);
|
printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin); |
| fprintf(ficreseij,"\n");
|
fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin); |
|
|
#endif |
| if(estepm < stepm){
|
/* printf("linmin end "); */ |
| printf ("Problem %d lower than %d\n",estepm, stepm);
|
for (j=1;j<=n;j++) { |
| }
|
/* printf(" before xi[%d]=%12.8f", j,xi[j]); */ |
| else hstepm=estepm;
|
xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */ |
| /* We compute the life expectancy from trapezoids spaced every estepm months
|
/* if(xxs <1.0) */ |
| * This is mainly to measure the difference between two models: for example
|
/* printf(" after xi[%d]=%12.8f, xmin=%12.8f, ax=%12.8f, xx=%12.8f, bx=%12.8f, xxs=%12.8f", j,xi[j], xmin, ax, xx, bx,xxs ); */ |
| * if stepm=24 months pijx are given only every 2 years and by summing them
|
p[j] += xi[j]; /* Parameters values are updated accordingly */ |
| * we are calculating an estimate of the Life Expectancy assuming a linear
|
} |
| * progression inbetween and thus overestimating or underestimating according
|
/* printf("\n"); */ |
| * to the curvature of the survival function. If, for the same date, we
|
/* printf("Comparing last *frec(xmin)=%12.8f from Brent and frec(0.)=%12.8f \n", *fret, (*func)(p)); */ |
| * estimate the model with stepm=1 month, we can keep estepm to 24 months
|
free_vector(xicom,1,n); |
| * to compare the new estimate of Life expectancy with the same linear
|
free_vector(pcom,1,n); |
| * hypothesis. A more precise result, taking into account a more precise
|
} |
| * curvature will be obtained if estepm is as small as stepm. */
|
|
|
|
|
| /* For example we decided to compute the life expectancy with the smallest unit */
|
/*************** powell ************************/ |
| /* 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
|
Minimization of a function func of n variables. Input consists of an initial starting point |
| nstepm is the number of stepm from age to agelin.
|
p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di- |
| Look at hpijx to understand the reason of that which relies in memory size
|
rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value |
| and note for a fixed period like estepm months */
|
such that failure to decrease by more than this amount on one iteration signals doneness. On |
| /* We decided (b) to get a life expectancy respecting the most precise curvature of the
|
output, p is set to the best point found, xi is the then-current direction set, fret is the returned |
| survival function given by stepm (the optimization length). Unfortunately it
|
function value at p , and iter is the number of iterations taken. The routine linmin is used. |
| 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
|
void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, |
| results. So we changed our mind and took the option of the best precision.
|
double (*func)(double [])) |
| */
|
{ |
| hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
|
void linmin(double p[], double xi[], int n, double *fret, |
|
|
double (*func)(double [])); |
| agelim=AGESUP;
|
int i,ibig,j; |
| for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
|
double del,t,*pt,*ptt,*xit; |
| /* nhstepm age range expressed in number of stepm */
|
double directest; |
| nstepm=(int) rint((agelim-age)*YEARM/stepm);
|
double fp,fptt; |
| /* Typically if 20 years nstepm = 20*12/6=40 stepm */
|
double *xits; |
| /* if (stepm >= YEARM) hstepm=1;*/
|
int niterf, itmp; |
| nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
|
|
| p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
pt=vector(1,n); |
| gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
|
ptt=vector(1,n); |
| gp=matrix(0,nhstepm,1,nlstate*2);
|
xit=vector(1,n); |
| gm=matrix(0,nhstepm,1,nlstate*2);
|
xits=vector(1,n); |
|
|
*fret=(*func)(p); |
| /* Computed by stepm unit matrices, product of hstepm matrices, stored
|
for (j=1;j<=n;j++) pt[j]=p[j]; |
| in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
|
rcurr_time = time(NULL); |
| hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
|
for (*iter=1;;++(*iter)) { |
|
|
fp=(*fret); /* From former iteration or initial value */ |
|
|
ibig=0; |
| hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
|
del=0.0; |
|
|
rlast_time=rcurr_time; |
| /* Computing Variances of health expectancies */
|
/* (void) gettimeofday(&curr_time,&tzp); */ |
|
|
rcurr_time = time(NULL); |
| for(theta=1; theta <=npar; theta++){
|
curr_time = *localtime(&rcurr_time); |
| for(i=1; i<=npar; i++){
|
printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout); |
| xp[i] = x[i] + (i==theta ?delti[theta]:0);
|
fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog); |
| }
|
/* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */ |
| hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
|
for (i=1;i<=n;i++) { |
|
|
printf(" %d %.12f",i, p[i]); |
| cptj=0;
|
fprintf(ficlog," %d %.12lf",i, p[i]); |
| for(j=1; j<= nlstate; j++){
|
fprintf(ficrespow," %.12lf", p[i]); |
| for(i=1; i<=nlstate; i++){
|
} |
| cptj=cptj+1;
|
printf("\n"); |
| for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
|
fprintf(ficlog,"\n"); |
| gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
|
fprintf(ficrespow,"\n");fflush(ficrespow); |
| }
|
if(*iter <=3){ |
| }
|
tml = *localtime(&rcurr_time); |
| }
|
strcpy(strcurr,asctime(&tml)); |
|
|
rforecast_time=rcurr_time; |
|
|
itmp = strlen(strcurr); |
| for(i=1; i<=npar; i++)
|
if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */ |
| xp[i] = x[i] - (i==theta ?delti[theta]:0);
|
strcurr[itmp-1]='\0'; |
| hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
|
printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time); |
|
|
fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time); |
| cptj=0;
|
for(niterf=10;niterf<=30;niterf+=10){ |
| for(j=1; j<= nlstate; j++){
|
rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time); |
| for(i=1;i<=nlstate;i++){
|
forecast_time = *localtime(&rforecast_time); |
| cptj=cptj+1;
|
strcpy(strfor,asctime(&forecast_time)); |
| for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
|
itmp = strlen(strfor); |
| gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
|
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(rforecast_time-rcurr_time,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(rforecast_time-rcurr_time,tmpout),strfor,strcurr); |
| for(j=1; j<= nlstate*2; j++)
|
} |
| for(h=0; h<=nhstepm-1; h++){
|
} |
| gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
|
for (i=1;i<=n;i++) { /* For each direction i */ |
| }
|
for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */ |
| }
|
fptt=(*fret); |
|
|
#ifdef DEBUG |
| /* End theta */
|
printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret); |
|
|
fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret); |
| trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
|
#endif |
|
|
printf("%d",i);fflush(stdout); /* print direction (parameter) i */ |
| for(h=0; h<=nhstepm-1; h++)
|
fprintf(ficlog,"%d",i);fflush(ficlog); |
| for(j=1; j<=nlstate*2;j++)
|
linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/ |
| for(theta=1; theta <=npar; theta++)
|
/* Outputs are fret(new point p) p is updated and xit rescaled */ |
| trgradg[h][j][theta]=gradg[h][theta][j];
|
if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */ |
|
|
/* because that direction will be replaced unless the gain del is small */ |
|
|
/* in comparison with the 'probable' gain, mu^2, with the last average direction. */ |
| for(i=1;i<=nlstate*2;i++)
|
/* Unless the n directions are conjugate some gain in the determinant may be obtained */ |
| for(j=1;j<=nlstate*2;j++)
|
/* with the new direction. */ |
| varhe[i][j][(int)age] =0.;
|
del=fabs(fptt-(*fret)); |
|
|
ibig=i; |
| printf("%d|",(int)age);fflush(stdout);
|
} |
| for(h=0;h<=nhstepm-1;h++){
|
#ifdef DEBUG |
| for(k=0;k<=nhstepm-1;k++){
|
printf("%d %.12e",i,(*fret)); |
| matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
|
fprintf(ficlog,"%d %.12e",i,(*fret)); |
| matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
|
for (j=1;j<=n;j++) { |
| for(i=1;i<=nlstate*2;i++)
|
xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5); |
| for(j=1;j<=nlstate*2;j++)
|
printf(" x(%d)=%.12e",j,xit[j]); |
| varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
|
fprintf(ficlog," x(%d)=%.12e",j,xit[j]); |
| }
|
} |
| }
|
for(j=1;j<=n;j++) { |
| /* Computing expectancies */
|
printf(" p(%d)=%.12e",j,p[j]); |
| for(i=1; i<=nlstate;i++)
|
fprintf(ficlog," p(%d)=%.12e",j,p[j]); |
| for(j=1; j<=nlstate;j++)
|
} |
| for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
|
printf("\n"); |
| eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
|
fprintf(ficlog,"\n"); |
|
|
#endif |
| /* 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 on each direction i */ |
|
|
/* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */ |
| }
|
/* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */ |
|
|
/* New value of last point Pn is not computed, P(n-1) */ |
| fprintf(ficreseij,"%3.0f",age );
|
if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */ |
| cptj=0;
|
/* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */ |
| for(i=1; i<=nlstate;i++)
|
/* By adding age*age in a model, the new -2LL should be lower and the difference follows a */ |
| for(j=1; j<=nlstate;j++){
|
/* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */ |
| cptj++;
|
/* decreased of more than 3.84 */ |
| fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
|
/* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */ |
| }
|
/* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */ |
| fprintf(ficreseij,"\n");
|
/* By adding 10 parameters more the gain should be 18.31 */ |
|
|
|
| free_matrix(gm,0,nhstepm,1,nlstate*2);
|
/* Starting the program with initial values given by a former maximization will simply change */ |
| free_matrix(gp,0,nhstepm,1,nlstate*2);
|
/* the scales of the directions and the directions, because the are reset to canonical directions */ |
| free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
|
/* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */ |
| free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
|
/* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */ |
| free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
#ifdef DEBUG |
| }
|
int k[2],l; |
| printf("\n");
|
k[0]=1; |
|
|
k[1]=-1; |
| free_vector(xp,1,npar);
|
printf("Max: %.12e",(*func)(p)); |
| free_matrix(dnewm,1,nlstate*2,1,npar);
|
fprintf(ficlog,"Max: %.12e",(*func)(p)); |
| free_matrix(doldm,1,nlstate*2,1,nlstate*2);
|
for (j=1;j<=n;j++) { |
| free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
|
printf(" %.12e",p[j]); |
| }
|
fprintf(ficlog," %.12e",p[j]); |
|
|
} |
| /************ Variance ******************/
|
printf("\n"); |
| void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)
|
fprintf(ficlog,"\n"); |
| {
|
for(l=0;l<=1;l++) { |
| /* Variance of health expectancies */
|
for (j=1;j<=n;j++) { |
| /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
|
ptt[j]=p[j]+(p[j]-pt[j])*k[l]; |
| double **newm;
|
printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]); |
| double **dnewm,**doldm;
|
fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]); |
| int i, j, nhstepm, hstepm, h, nstepm ;
|
} |
| int k, cptcode;
|
printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p))); |
| double *xp;
|
fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p))); |
| double **gp, **gm;
|
} |
| double ***gradg, ***trgradg;
|
#endif |
| double ***p3mat;
|
|
| double age,agelim, hf;
|
|
| int theta;
|
free_vector(xit,1,n); |
|
|
free_vector(xits,1,n); |
| 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");
|
free_vector(ptt,1,n); |
| fprintf(ficresvij,"# Age");
|
free_vector(pt,1,n); |
| for(i=1; i<=nlstate;i++)
|
return; |
| for(j=1; j<=nlstate;j++)
|
} |
| fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
|
if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); |
| fprintf(ficresvij,"\n");
|
for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */ |
|
|
ptt[j]=2.0*p[j]-pt[j]; |
| xp=vector(1,npar);
|
xit[j]=p[j]-pt[j]; |
| dnewm=matrix(1,nlstate,1,npar);
|
pt[j]=p[j]; |
| doldm=matrix(1,nlstate,1,nlstate);
|
} |
|
|
fptt=(*func)(ptt); /* f_3 */ |
| if(estepm < stepm){
|
if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */ |
| printf ("Problem %d lower than %d\n",estepm, stepm);
|
/* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */ |
| }
|
/* From x1 (P0) distance of x2 is at h and x3 is 2h */ |
| else hstepm=estepm;
|
/* Let f"(x2) be the 2nd derivative equal everywhere. */ |
| /* For example we decided to compute the life expectancy with the smallest unit */
|
/* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */ |
| /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
|
/* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */ |
| nhstepm is the number of hstepm from age to agelim
|
/* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */ |
| nstepm is the number of stepm from age to agelin.
|
/* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */ |
| Look at hpijx to understand the reason of that which relies in memory size
|
#ifdef NRCORIGINAL |
| and note for a fixed period like k years */
|
t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/ |
| /* We decided (b) to get a life expectancy respecting the most precise curvature of the
|
#else |
| survival function given by stepm (the optimization length). Unfortunately it
|
t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */ |
| means that if the survival funtion is printed only each two years of age and if
|
t= t- del*SQR(fp-fptt); |
| you sum them up and add 1 year (area under the trapezoids) you won't get the same
|
#endif |
| results. So we changed our mind and took the option of the best precision.
|
directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */ |
| */
|
#ifdef DEBUG |
| hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
|
printf("t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest); |
| agelim = AGESUP;
|
fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest); |
| for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
|
printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt), |
| nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
|
(fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt)); |
| nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
|
fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt), |
| p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
(fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt)); |
| gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
|
printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t); |
| gp=matrix(0,nhstepm,1,nlstate);
|
fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t); |
| gm=matrix(0,nhstepm,1,nlstate);
|
#endif |
|
|
#ifdef POWELLORIGINAL |
| for(theta=1; theta <=npar; theta++){
|
if (t < 0.0) { /* Then we use it for new direction */ |
| for(i=1; i<=npar; i++){ /* Computes gradient */
|
#else |
| xp[i] = x[i] + (i==theta ?delti[theta]:0);
|
if (directest*t < 0.0) { /* Contradiction between both tests */ |
| }
|
printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del); |
| hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
|
printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt); |
| prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
|
fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del); |
|
|
fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt); |
| if (popbased==1) {
|
} |
| for(i=1; i<=nlstate;i++)
|
if (directest < 0.0) { /* Then we use it for new direction */ |
| prlim[i][i]=probs[(int)age][i][ij];
|
#endif |
| }
|
linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/ |
|
|
for (j=1;j<=n;j++) { |
| for(j=1; j<= nlstate; j++){
|
xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */ |
| for(h=0; h<=nhstepm; h++){
|
xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */ |
| for(i=1, gp[h][j]=0.;i<=nlstate;i++)
|
} |
| gp[h][j] += prlim[i][i]*p3mat[i][j][h];
|
printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig); |
| }
|
fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig); |
| }
|
|
|
|
#ifdef DEBUG |
| for(i=1; i<=npar; i++) /* Computes gradient */
|
printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig); |
| xp[i] = x[i] - (i==theta ?delti[theta]:0);
|
fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig); |
| hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
|
for(j=1;j<=n;j++){ |
| prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
|
printf(" %.12e",xit[j]); |
|
|
fprintf(ficlog," %.12e",xit[j]); |
| if (popbased==1) {
|
} |
| for(i=1; i<=nlstate;i++)
|
printf("\n"); |
| prlim[i][i]=probs[(int)age][i][ij];
|
fprintf(ficlog,"\n"); |
| }
|
#endif |
|
|
} /* end of t negative */ |
| for(j=1; j<= nlstate; j++){
|
} /* end if (fptt < fp) */ |
| for(h=0; h<=nhstepm; h++){
|
} |
| for(i=1, gm[h][j]=0.;i<=nlstate;i++)
|
} |
| gm[h][j] += prlim[i][i]*p3mat[i][j][h];
|
|
| }
|
/**** Prevalence limit (stable or period prevalence) ****************/ |
| }
|
|
|
|
double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij) |
| for(j=1; j<= nlstate; j++)
|
{ |
| for(h=0; h<=nhstepm; h++){
|
/* Computes the prevalence limit in each live state at age x by left multiplying the unit |
| gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
|
matrix by transitions matrix until convergence is reached */ |
| }
|
|
| } /* End theta */
|
int i, ii,j,k; |
|
|
double min, max, maxmin, maxmax,sumnew=0.; |
| trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);
|
/* double **matprod2(); */ /* test */ |
|
|
double **out, cov[NCOVMAX+1], **pmij(); |
| for(h=0; h<=nhstepm; h++)
|
double **newm; |
| for(j=1; j<=nlstate;j++)
|
double agefin, delaymax=50 ; /* Max number of years to converge */ |
| for(theta=1; theta <=npar; theta++)
|
|
| trgradg[h][j][theta]=gradg[h][theta][j];
|
for (ii=1;ii<=nlstate+ndeath;ii++) |
|
|
for (j=1;j<=nlstate+ndeath;j++){ |
| hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
|
oldm[ii][j]=(ii==j ? 1.0 : 0.0); |
| for(i=1;i<=nlstate;i++)
|
} |
| for(j=1;j<=nlstate;j++)
|
|
| vareij[i][j][(int)age] =0.;
|
cov[1]=1.; |
|
|
|
| for(h=0;h<=nhstepm;h++){
|
/* Even if hstepm = 1, at least one multiplication by the unit matrix */ |
| for(k=0;k<=nhstepm;k++){
|
for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){ |
| matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
|
newm=savm; |
| matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
|
/* Covariates have to be included here again */ |
| for(i=1;i<=nlstate;i++)
|
cov[2]=agefin; |
| for(j=1;j<=nlstate;j++)
|
if(nagesqr==1) |
| vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
|
cov[3]= agefin*agefin;; |
| }
|
for (k=1; k<=cptcovn;k++) { |
| }
|
cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; |
|
|
/*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/ |
| fprintf(ficresvij,"%.0f ",age );
|
} |
| for(i=1; i<=nlstate;i++)
|
/*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ |
| for(j=1; j<=nlstate;j++){
|
for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2]; |
| fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
|
for (k=1; k<=cptcovprod;k++) /* Useless */ |
| }
|
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; |
| fprintf(ficresvij,"\n");
|
|
| free_matrix(gp,0,nhstepm,1,nlstate);
|
/*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/ |
| free_matrix(gm,0,nhstepm,1,nlstate);
|
/*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/ |
| free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
|
/*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/ |
| free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
|
/* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */ |
| free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
/* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */ |
| } /* End age */
|
out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */ |
|
|
|
| free_vector(xp,1,npar);
|
savm=oldm; |
| free_matrix(doldm,1,nlstate,1,npar);
|
oldm=newm; |
| free_matrix(dnewm,1,nlstate,1,nlstate);
|
maxmax=0.; |
|
|
for(j=1;j<=nlstate;j++){ |
| }
|
min=1.; |
|
|
max=0.; |
| /************ Variance of prevlim ******************/
|
for(i=1; i<=nlstate; i++) { |
| 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)
|
sumnew=0; |
| {
|
for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k]; |
| /* Variance of prevalence limit */
|
prlim[i][j]= newm[i][j]/(1-sumnew); |
| /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
|
/*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/ |
| double **newm;
|
max=FMAX(max,prlim[i][j]); |
| double **dnewm,**doldm;
|
min=FMIN(min,prlim[i][j]); |
| int i, j, nhstepm, hstepm;
|
} |
| int k, cptcode;
|
maxmin=max-min; |
| double *xp;
|
maxmax=FMAX(maxmax,maxmin); |
| double *gp, *gm;
|
} /* j loop */ |
| double **gradg, **trgradg;
|
if(maxmax < ftolpl){ |
| double age,agelim;
|
return prlim; |
| int theta;
|
} |
|
|
} /* age loop */ |
| fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");
|
return prlim; /* should not reach here */ |
| fprintf(ficresvpl,"# Age");
|
} |
| for(i=1; i<=nlstate;i++)
|
|
| fprintf(ficresvpl," %1d-%1d",i,i);
|
/*************** transition probabilities ***************/ |
| fprintf(ficresvpl,"\n");
|
|
|
|
double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate ) |
| xp=vector(1,npar);
|
{ |
| dnewm=matrix(1,nlstate,1,npar);
|
/* According to parameters values stored in x and the covariate's values stored in cov, |
| doldm=matrix(1,nlstate,1,nlstate);
|
computes the probability to be observed in state j being in state i by appying the |
|
|
model to the ncovmodel covariates (including constant and age). |
| hstepm=1*YEARM; /* Every year of age */
|
lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc] |
| hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
|
and, according on how parameters are entered, the position of the coefficient xij(nc) of the |
| agelim = AGESUP;
|
ncth covariate in the global vector x is given by the formula: |
| for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
|
j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel |
| nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
|
j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel |
| if (stepm >= YEARM) hstepm=1;
|
Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation, |
| nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
|
sums on j different of i to get 1-pii/pii, deduces pii, and then all pij. |
| gradg=matrix(1,npar,1,nlstate);
|
Outputs ps[i][j] the probability to be observed in j being in j according to |
| gp=vector(1,nlstate);
|
the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij] |
| gm=vector(1,nlstate);
|
*/ |
|
|
double s1, lnpijopii; |
| for(theta=1; theta <=npar; theta++){
|
/*double t34;*/ |
| for(i=1; i<=npar; i++){ /* Computes gradient */
|
int i,j, nc, ii, jj; |
| xp[i] = x[i] + (i==theta ?delti[theta]:0);
|
|
| }
|
for(i=1; i<= nlstate; i++){ |
| prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
|
for(j=1; j<i;j++){ |
| for(i=1;i<=nlstate;i++)
|
for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){ |
| gp[i] = prlim[i][i];
|
/*lnpijopii += param[i][j][nc]*cov[nc];*/ |
|
|
lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc]; |
| for(i=1; i<=npar; i++) /* Computes gradient */
|
/* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */ |
| xp[i] = x[i] - (i==theta ?delti[theta]:0);
|
} |
| prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
|
ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */ |
| for(i=1;i<=nlstate;i++)
|
/* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */ |
| gm[i] = prlim[i][i];
|
} |
|
|
for(j=i+1; j<=nlstate+ndeath;j++){ |
| for(i=1;i<=nlstate;i++)
|
for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){ |
| gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
|
/*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/ |
| } /* End theta */
|
lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc]; |
|
|
/* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */ |
| trgradg =matrix(1,nlstate,1,npar);
|
} |
|
|
ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */ |
| for(j=1; j<=nlstate;j++)
|
} |
| for(theta=1; theta <=npar; theta++)
|
} |
| trgradg[j][theta]=gradg[theta][j];
|
|
|
|
for(i=1; i<= nlstate; i++){ |
| for(i=1;i<=nlstate;i++)
|
s1=0; |
| varpl[i][(int)age] =0.;
|
for(j=1; j<i; j++){ |
| matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
|
s1+=exp(ps[i][j]); /* In fact sums pij/pii */ |
| matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
|
/*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */ |
| for(i=1;i<=nlstate;i++)
|
} |
| varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
|
for(j=i+1; j<=nlstate+ndeath; j++){ |
|
|
s1+=exp(ps[i][j]); /* In fact sums pij/pii */ |
| fprintf(ficresvpl,"%.0f ",age );
|
/*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */ |
| for(i=1; i<=nlstate;i++)
|
} |
| fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
|
/* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */ |
| fprintf(ficresvpl,"\n");
|
ps[i][i]=1./(s1+1.); |
| free_vector(gp,1,nlstate);
|
/* Computing other pijs */ |
| free_vector(gm,1,nlstate);
|
for(j=1; j<i; j++) |
| free_matrix(gradg,1,npar,1,nlstate);
|
ps[i][j]= exp(ps[i][j])*ps[i][i]; |
| free_matrix(trgradg,1,nlstate,1,npar);
|
for(j=i+1; j<=nlstate+ndeath; j++) |
| } /* End age */
|
ps[i][j]= exp(ps[i][j])*ps[i][i]; |
|
|
/* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */ |
| free_vector(xp,1,npar);
|
} /* end i */ |
| free_matrix(doldm,1,nlstate,1,npar);
|
|
| free_matrix(dnewm,1,nlstate,1,nlstate);
|
for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){ |
|
|
for(jj=1; jj<= nlstate+ndeath; jj++){ |
| }
|
ps[ii][jj]=0; |
|
|
ps[ii][ii]=1; |
| /************ 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)
|
} |
| {
|
|
| int i, j, i1, k1, l1;
|
|
| int k2, l2, j1, z1;
|
/* for(ii=1; ii<= nlstate+ndeath; ii++){ */ |
| int k=0,l, cptcode;
|
/* for(jj=1; jj<= nlstate+ndeath; jj++){ */ |
| int first=1;
|
/* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */ |
| double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;
|
/* } */ |
| double **dnewm,**doldm;
|
/* printf("\n "); */ |
| double *xp;
|
/* } */ |
| double *gp, *gm;
|
/* printf("\n ");printf("%lf ",cov[2]);*/ |
| double **gradg, **trgradg;
|
/* |
| double **mu;
|
for(i=1; i<= npar; i++) printf("%f ",x[i]); |
| double age,agelim, cov[NCOVMAX];
|
goto end;*/ |
| double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
|
return ps; |
| int theta;
|
} |
| char fileresprob[FILENAMELENGTH];
|
|
| char fileresprobcov[FILENAMELENGTH];
|
/**************** Product of 2 matrices ******************/ |
| char fileresprobcor[FILENAMELENGTH];
|
|
|
|
double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b) |
| double ***varpij;
|
{ |
|
|
/* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times |
| strcpy(fileresprob,"prob");
|
b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */ |
| strcat(fileresprob,fileres);
|
/* in, b, out are matrice of pointers which should have been initialized |
| if((ficresprob=fopen(fileresprob,"w"))==NULL) {
|
before: only the contents of out is modified. The function returns |
| printf("Problem with resultfile: %s\n", fileresprob);
|
a pointer to pointers identical to out */ |
| }
|
int i, j, k; |
| strcpy(fileresprobcov,"probcov");
|
for(i=nrl; i<= nrh; i++) |
| strcat(fileresprobcov,fileres);
|
for(k=ncolol; k<=ncoloh; k++){ |
| if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
|
out[i][k]=0.; |
| printf("Problem with resultfile: %s\n", fileresprobcov);
|
for(j=ncl; j<=nch; j++) |
| }
|
out[i][k] +=in[i][j]*b[j][k]; |
| strcpy(fileresprobcor,"probcor");
|
} |
| strcat(fileresprobcor,fileres);
|
return out; |
| if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
|
} |
| printf("Problem with resultfile: %s\n", fileresprobcor);
|
|
| }
|
|
| printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
|
/************* Higher Matrix Product ***************/ |
| printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
|
|
| printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
|
double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij ) |
|
|
{ |
| fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
|
/* Computes the transition matrix starting at age 'age' over |
| fprintf(ficresprob,"# Age");
|
'nhstepm*hstepm*stepm' months (i.e. until |
| fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
|
age (in years) age+nhstepm*hstepm*stepm/12) by multiplying |
| fprintf(ficresprobcov,"# Age");
|
nhstepm*hstepm matrices. |
| fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
|
Output is stored in matrix po[i][j][h] for h every 'hstepm' step |
| fprintf(ficresprobcov,"# Age");
|
(typically every 2 years instead of every month which is too big |
|
|
for the memory). |
|
|
Model is determined by parameters x and covariates have to be |
| for(i=1; i<=nlstate;i++)
|
included manually here. |
| for(j=1; j<=(nlstate+ndeath);j++){
|
|
| fprintf(ficresprob," p%1d-%1d (SE)",i,j);
|
*/ |
| fprintf(ficresprobcov," p%1d-%1d ",i,j);
|
|
| fprintf(ficresprobcor," p%1d-%1d ",i,j);
|
int i, j, d, h, k; |
| }
|
double **out, cov[NCOVMAX+1]; |
| fprintf(ficresprob,"\n");
|
double **newm; |
| fprintf(ficresprobcov,"\n");
|
double agexact; |
| fprintf(ficresprobcor,"\n");
|
|
| xp=vector(1,npar);
|
/* Hstepm could be zero and should return the unit matrix */ |
| dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
|
for (i=1;i<=nlstate+ndeath;i++) |
| doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
|
for (j=1;j<=nlstate+ndeath;j++){ |
| mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
|
oldm[i][j]=(i==j ? 1.0 : 0.0); |
| varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
|
po[i][j][0]=(i==j ? 1.0 : 0.0); |
| first=1;
|
} |
| if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
|
/* Even if hstepm = 1, at least one multiplication by the unit matrix */ |
| printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
|
for(h=1; h <=nhstepm; h++){ |
| exit(0);
|
for(d=1; d <=hstepm; d++){ |
| }
|
newm=savm; |
| else{
|
/* Covariates have to be included here again */ |
| fprintf(ficgp,"\n# Routine varprob");
|
cov[1]=1.; |
| }
|
agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; |
| if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
|
cov[2]=agexact; |
| printf("Problem with html file: %s\n", optionfilehtm);
|
if(nagesqr==1) |
| exit(0);
|
cov[3]= agexact*agexact; |
| }
|
for (k=1; k<=cptcovn;k++) |
| else{
|
cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; |
| fprintf(fichtm,"\n<H2> Computing matrix of variance-covariance of step probabilities</h2>\n");
|
for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */ |
| fprintf(fichtm,"\n<br> We 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");
|
/* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ |
| 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");
|
cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; |
|
|
for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */ |
| }
|
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; |
| cov[1]=1;
|
|
| j=cptcoveff;
|
|
| if (cptcovn<1) {j=1;ncodemax[1]=1;}
|
/*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/ |
| j1=0;
|
/*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/ |
| for(k1=1; k1<=1;k1++){
|
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, |
| for(i1=1; i1<=ncodemax[k1];i1++){
|
pmij(pmmij,cov,ncovmodel,x,nlstate)); |
| j1++;
|
savm=oldm; |
|
|
oldm=newm; |
| if (cptcovn>0) {
|
} |
| fprintf(ficresprob, "\n#********** Variable ");
|
for(i=1; i<=nlstate+ndeath; i++) |
| fprintf(ficresprobcov, "\n#********** Variable ");
|
for(j=1;j<=nlstate+ndeath;j++) { |
| fprintf(ficgp, "\n#********** Variable ");
|
po[i][j][h]=newm[i][j]; |
| fprintf(fichtm, "\n<h4>********** Variable</h4>\n ");
|
/*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/ |
| fprintf(ficresprobcor, "\n#********** Variable ");
|
} |
| for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
|
/*printf("h=%d ",h);*/ |
| fprintf(ficresprob, "**********\n#");
|
} /* end h */ |
| for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
|
/* printf("\n H=%d \n",h); */ |
| fprintf(ficresprobcov, "**********\n#");
|
return po; |
| for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
|
} |
| fprintf(ficgp, "**********\n#");
|
|
| for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
|
#ifdef NLOPT |
| fprintf(ficgp, "**********\n#");
|
double myfunc(unsigned n, const double *p1, double *grad, void *pd){ |
| for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
|
double fret; |
| fprintf(fichtm, "**********\n#");
|
double *xt; |
| }
|
int j; |
|
|
myfunc_data *d2 = (myfunc_data *) pd; |
| for (age=bage; age<=fage; age ++){
|
/* xt = (p1-1); */ |
| cov[2]=age;
|
xt=vector(1,n); |
| for (k=1; k<=cptcovn;k++) {
|
for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */ |
| cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
|
|
| }
|
fret=(d2->function)(xt); /* p xt[1]@8 is fine */ |
| for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
|
/* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */ |
| for (k=1; k<=cptcovprod;k++)
|
printf("Function = %.12lf ",fret); |
| cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
|
for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); |
|
|
printf("\n"); |
| gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
|
free_vector(xt,1,n); |
| trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
|
return fret; |
| gp=vector(1,(nlstate)*(nlstate+ndeath));
|
} |
| gm=vector(1,(nlstate)*(nlstate+ndeath));
|
#endif |
|
|
|
| for(theta=1; theta <=npar; theta++){
|
/*************** log-likelihood *************/ |
| for(i=1; i<=npar; i++)
|
double func( double *x) |
| xp[i] = x[i] + (i==theta ?delti[theta]:0);
|
{ |
|
|
int i, ii, j, k, mi, d, kk; |
| pmij(pmmij,cov,ncovmodel,xp,nlstate);
|
double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1]; |
|
|
double **out; |
| k=0;
|
double sw; /* Sum of weights */ |
| for(i=1; i<= (nlstate); i++){
|
double lli; /* Individual log likelihood */ |
| for(j=1; j<=(nlstate+ndeath);j++){
|
int s1, s2; |
| k=k+1;
|
double bbh, survp; |
| gp[k]=pmmij[i][j];
|
long ipmx; |
| }
|
double agexact; |
| }
|
/*extern weight */ |
|
|
/* We are differentiating ll according to initial status */ |
| for(i=1; i<=npar; i++)
|
/* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/ |
| xp[i] = x[i] - (i==theta ?delti[theta]:0);
|
/*for(i=1;i<imx;i++) |
|
|
printf(" %d\n",s[4][i]); |
| pmij(pmmij,cov,ncovmodel,xp,nlstate);
|
*/ |
| k=0;
|
|
| for(i=1; i<=(nlstate); i++){
|
++countcallfunc; |
| for(j=1; j<=(nlstate+ndeath);j++){
|
|
| k=k+1;
|
cov[1]=1.; |
| gm[k]=pmmij[i][j];
|
|
| }
|
for(k=1; k<=nlstate; k++) ll[k]=0.; |
| }
|
|
|
|
if(mle==1){ |
| for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
|
for (i=1,ipmx=0, sw=0.; i<=imx; i++){ |
| gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];
|
/* Computes the values of the ncovmodel covariates of the model |
| }
|
depending if the covariates are fixed or variying (age dependent) and stores them in cov[] |
|
|
Then computes with function pmij which return a matrix p[i][j] giving the elementary probability |
| for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
|
to be observed in j being in i according to the model. |
| for(theta=1; theta <=npar; theta++)
|
*/ |
| trgradg[j][theta]=gradg[theta][j];
|
for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */ |
|
|
cov[2+nagesqr+k]=covar[Tvar[k]][i]; |
| matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
|
} |
| matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
|
/* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] |
|
|
is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] |
| pmij(pmmij,cov,ncovmodel,x,nlstate);
|
has been calculated etc */ |
|
|
for(mi=1; mi<= wav[i]-1; mi++){ |
| k=0;
|
for (ii=1;ii<=nlstate+ndeath;ii++) |
| for(i=1; i<=(nlstate); i++){
|
for (j=1;j<=nlstate+ndeath;j++){ |
| for(j=1; j<=(nlstate+ndeath);j++){
|
oldm[ii][j]=(ii==j ? 1.0 : 0.0); |
| k=k+1;
|
savm[ii][j]=(ii==j ? 1.0 : 0.0); |
| mu[k][(int) age]=pmmij[i][j];
|
} |
| }
|
for(d=0; d<dh[mi][i]; d++){ |
| }
|
newm=savm; |
| for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
|
agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; |
| for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
|
cov[2]=agexact; |
| varpij[i][j][(int)age] = doldm[i][j];
|
if(nagesqr==1) |
|
|
cov[3]= agexact*agexact; |
| /*printf("\n%d ",(int)age);
|
for (kk=1; kk<=cptcovage;kk++) { |
| for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
|
cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */ |
| printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
|
} |
| }*/
|
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, |
|
|
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); |
| fprintf(ficresprob,"\n%d ",(int)age);
|
savm=oldm; |
| fprintf(ficresprobcov,"\n%d ",(int)age);
|
oldm=newm; |
| fprintf(ficresprobcor,"\n%d ",(int)age);
|
} /* end mult */ |
|
|
|
| for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
|
/*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */ |
| fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
|
/* But now since version 0.9 we anticipate for bias at large stepm. |
| for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
|
* If stepm is larger than one month (smallest stepm) and if the exact delay |
| fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
|
* (in months) between two waves is not a multiple of stepm, we rounded to |
| fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
|
* the nearest (and in case of equal distance, to the lowest) interval but now |
| }
|
* we keep into memory the bias bh[mi][i] and also the previous matrix product |
| i=0;
|
* (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the |
| for (k=1; k<=(nlstate);k++){
|
* probability in order to take into account the bias as a fraction of the way |
| for (l=1; l<=(nlstate+ndeath);l++){
|
* from savm to out if bh is negative or even beyond if bh is positive. bh varies |
| i=i++;
|
* -stepm/2 to stepm/2 . |
| fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
|
* For stepm=1 the results are the same as for previous versions of Imach. |
| fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
|
* For stepm > 1 the results are less biased than in previous versions. |
| for (j=1; j<=i;j++){
|
*/ |
| fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
|
s1=s[mw[mi][i]][i]; |
| fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
|
s2=s[mw[mi+1][i]][i]; |
| }
|
bbh=(double)bh[mi][i]/(double)stepm; |
| }
|
/* bias bh is positive if real duration |
| }/* end of loop for state */
|
* is higher than the multiple of stepm and negative otherwise. |
| } /* end of loop for age */
|
*/ |
| /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
|
/* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/ |
| for (k1=1; k1<=(nlstate);k1++){
|
if( s2 > nlstate){ |
| for (l1=1; l1<=(nlstate+ndeath);l1++){
|
/* i.e. if s2 is a death state and if the date of death is known |
| if(l1==k1) continue;
|
then the contribution to the likelihood is the probability to |
| i=(k1-1)*(nlstate+ndeath)+l1;
|
die between last step unit time and current step unit time, |
| for (k2=1; k2<=(nlstate);k2++){
|
which is also equal to probability to die before dh |
| for (l2=1; l2<=(nlstate+ndeath);l2++){
|
minus probability to die before dh-stepm . |
| if(l2==k2) continue;
|
In version up to 0.92 likelihood was computed |
| j=(k2-1)*(nlstate+ndeath)+l2;
|
as if date of death was unknown. Death was treated as any other |
| if(j<=i) continue;
|
health state: the date of the interview describes the actual state |
| for (age=bage; age<=fage; age ++){
|
and not the date of a change in health state. The former idea was |
| if ((int)age %5==0){
|
to consider that at each interview the state was recorded |
| v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
|
(healthy, disable or death) and IMaCh was corrected; but when we |
| v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
|
introduced the exact date of death then we should have modified |
| cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
|
the contribution of an exact death to the likelihood. This new |
| mu1=mu[i][(int) age]/stepm*YEARM ;
|
contribution is smaller and very dependent of the step unit |
| mu2=mu[j][(int) age]/stepm*YEARM;
|
stepm. It is no more the probability to die between last interview |
| /* Computing eigen value of matrix of covariance */
|
and month of death but the probability to survive from last |
| lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));
|
interview up to one month before death multiplied by the |
| lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));
|
probability to die within a month. Thanks to Chris |
| printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);
|
Jackson for correcting this bug. Former versions increased |
| /* Eigen vectors */
|
mortality artificially. The bad side is that we add another loop |
| v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
|
which slows down the processing. The difference can be up to 10% |
| v21=sqrt(1.-v11*v11);
|
lower mortality. |
| v12=-v21;
|
*/ |
| v22=v11;
|
/* If, at the beginning of the maximization mostly, the |
| /*printf(fignu*/
|
cumulative probability or probability to be dead is |
| /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
|
constant (ie = 1) over time d, the difference is equal to |
| /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */
|
0. out[s1][3] = savm[s1][3]: probability, being at state |
| if(first==1){
|
s1 at precedent wave, to be dead a month before current |
| first=0;
|
wave is equal to probability, being at state s1 at |
| fprintf(ficgp,"\nset parametric;set nolabel");
|
precedent wave, to be dead at mont of the current |
| fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);
|
wave. Then the observed probability (that this person died) |
| fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
|
is null according to current estimated parameter. In fact, |
| fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%1d%1d-%1d%1d.png\">varpijgr%s%1d%1d-%1d%1d.png</A>, ",k2,l2,k1,l1,optionfilefiname,k2,l2,k1,l1,optionfilefiname,k2,l2,k1,l1);
|
it should be very low but not zero otherwise the log go to |
| fprintf(fichtm,"\n<br><img src=\"varpijgr%s%1d%1d-%1d%1d.png\">, ",optionfilefiname,k2,l2,k1,l1);
|
infinity. |
| fprintf(ficgp,"\nset out \"varpijgr%s%1d%1d-%1d%1d.png\"",optionfilefiname,k2,l2,k1,l1);
|
*/ |
| fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);
|
/* #ifdef INFINITYORIGINAL */ |
| fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);
|
/* lli=log(out[s1][s2] - savm[s1][s2]); */ |
| fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\
|
/* #else */ |
| mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \
|
/* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */ |
| mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);
|
/* lli=log(mytinydouble); */ |
| }else{
|
/* else */ |
| first=0;
|
/* lli=log(out[s1][s2] - savm[s1][s2]); */ |
| fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);
|
/* #endif */ |
| fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);
|
lli=log(out[s1][s2] - savm[s1][s2]); |
| fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\
|
|
| mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \
|
} else if (s2==-2) { |
| mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);
|
for (j=1,survp=0. ; j<=nlstate; j++) |
| }/* if first */
|
survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; |
| } /* age mod 5 */
|
/*survp += out[s1][j]; */ |
| } /* end loop age */
|
lli= log(survp); |
| fprintf(ficgp,"\nset out \"varpijgr%s%1d%1d-%1d%1d.png\";replot;",optionfilefiname,k2,l2,k1,l1);
|
} |
| first=1;
|
|
| } /*l12 */
|
else if (s2==-4) { |
| } /* k12 */
|
for (j=3,survp=0. ; j<=nlstate; j++) |
| } /*l1 */
|
survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; |
| }/* k1 */
|
lli= log(survp); |
| } /* loop covariates */
|
} |
| free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
|
|
| free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
|
else if (s2==-5) { |
| free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
|
for (j=1,survp=0. ; j<=2; j++) |
| free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
|
survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; |
| free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
|
lli= log(survp); |
| free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
|
} |
| }
|
|
| free_vector(xp,1,npar);
|
else{ |
| fclose(ficresprob);
|
lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ |
| fclose(ficresprobcov);
|
/* 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 */ |
| fclose(ficresprobcor);
|
} |
| fclose(ficgp);
|
/*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/ |
| fclose(fichtm);
|
/*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); */ |
|
|
ipmx +=1; |
|
|
sw += weight[i]; |
| /******************* Printing html file ***********/
|
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; |
| void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
|
/* if (lli < log(mytinydouble)){ */ |
| int lastpass, int stepm, int weightopt, char model[],\
|
/* printf("Close to inf lli = %.10lf < %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */ |
| int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
|
/* fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */ |
| int popforecast, int estepm ,\
|
/* } */ |
| double jprev1, double mprev1,double anprev1, \
|
} /* end of wave */ |
| double jprev2, double mprev2,double anprev2){
|
} /* end of individual */ |
| int jj1, k1, i1, cpt;
|
} else if(mle==2){ |
| /*char optionfilehtm[FILENAMELENGTH];*/
|
for (i=1,ipmx=0, sw=0.; i<=imx; i++){ |
| if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
|
for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; |
| printf("Problem with %s \n",optionfilehtm), exit(0);
|
for(mi=1; mi<= wav[i]-1; mi++){ |
| }
|
for (ii=1;ii<=nlstate+ndeath;ii++) |
|
|
for (j=1;j<=nlstate+ndeath;j++){ |
| fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n
|
oldm[ii][j]=(ii==j ? 1.0 : 0.0); |
| - 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
|
savm[ii][j]=(ii==j ? 1.0 : 0.0); |
| - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
|
} |
| - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
|
for(d=0; d<=dh[mi][i]; d++){ |
| - Life expectancies by age and initial health status (estepm=%2d months):
|
newm=savm; |
| <a href=\"e%s\">e%s</a> <br>\n</li>", \
|
agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; |
| jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
|
cov[2]=agexact; |
|
|
if(nagesqr==1) |
| fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n
|
cov[3]= agexact*agexact; |
| - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
|
for (kk=1; kk<=cptcovage;kk++) { |
| - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
|
cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; |
| - 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
|
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, |
| - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
|
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); |
| - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
|
savm=oldm; |
| - 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);
|
oldm=newm; |
|
|
} /* end mult */ |
| if(popforecast==1) fprintf(fichtm,"\n
|
|
| - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
|
s1=s[mw[mi][i]][i]; |
| - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
|
s2=s[mw[mi+1][i]][i]; |
| <br>",fileres,fileres,fileres,fileres);
|
bbh=(double)bh[mi][i]/(double)stepm; |
| else
|
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 */ |
| 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);
|
ipmx +=1; |
| fprintf(fichtm," <li>Graphs</li><p>");
|
sw += weight[i]; |
|
|
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; |
| m=cptcoveff;
|
} /* end of wave */ |
| if (cptcovn < 1) {m=1;ncodemax[1]=1;}
|
} /* end of individual */ |
|
|
} else if(mle==3){ /* exponential inter-extrapolation */ |
| jj1=0;
|
for (i=1,ipmx=0, sw=0.; i<=imx; i++){ |
| for(k1=1; k1<=m;k1++){
|
for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; |
| for(i1=1; i1<=ncodemax[k1];i1++){
|
for(mi=1; mi<= wav[i]-1; mi++){ |
| jj1++;
|
for (ii=1;ii<=nlstate+ndeath;ii++) |
| if (cptcovn > 0) {
|
for (j=1;j<=nlstate+ndeath;j++){ |
| fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
|
oldm[ii][j]=(ii==j ? 1.0 : 0.0); |
| for (cpt=1; cpt<=cptcoveff;cpt++)
|
savm[ii][j]=(ii==j ? 1.0 : 0.0); |
| fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
|
} |
| fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
|
for(d=0; d<dh[mi][i]; d++){ |
| }
|
newm=savm; |
| /* Pij */
|
agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; |
| 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>
|
cov[2]=agexact; |
| <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
|
if(nagesqr==1) |
| /* Quasi-incidences */
|
cov[3]= agexact*agexact; |
| 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 (kk=1; kk<=cptcovage;kk++) { |
| <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
|
cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; |
| /* Stable prevalence in each health state */
|
} |
| for(cpt=1; cpt<nlstate;cpt++){
|
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, |
| fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
|
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); |
| <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
|
savm=oldm; |
| }
|
oldm=newm; |
| for(cpt=1; cpt<=nlstate;cpt++) {
|
} /* end mult */ |
| fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
|
|
| interval) in state (%d): v%s%d%d.png <br>
|
s1=s[mw[mi][i]][i]; |
| <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
|
s2=s[mw[mi+1][i]][i]; |
| }
|
bbh=(double)bh[mi][i]/(double)stepm; |
| for(cpt=1; cpt<=nlstate;cpt++) {
|
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 */ |
| fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
|
ipmx +=1; |
| <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
|
sw += weight[i]; |
| }
|
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; |
| fprintf(fichtm,"\n<br>- Total life expectancy by age and
|
} /* end of wave */ |
| health expectancies in states (1) and (2): e%s%d.png<br>
|
} /* end of individual */ |
| <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
|
}else if (mle==4){ /* ml=4 no inter-extrapolation */ |
| }
|
for (i=1,ipmx=0, sw=0.; i<=imx; i++){ |
| }
|
for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; |
| fclose(fichtm);
|
for(mi=1; mi<= wav[i]-1; mi++){ |
| }
|
for (ii=1;ii<=nlstate+ndeath;ii++) |
|
|
for (j=1;j<=nlstate+ndeath;j++){ |
| /******************* Gnuplot file **************/
|
oldm[ii][j]=(ii==j ? 1.0 : 0.0); |
| void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
|
savm[ii][j]=(ii==j ? 1.0 : 0.0); |
|
|
} |
| int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
|
for(d=0; d<dh[mi][i]; d++){ |
| int ng;
|
newm=savm; |
| if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
|
agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; |
| printf("Problem with file %s",optionfilegnuplot);
|
cov[2]=agexact; |
| }
|
if(nagesqr==1) |
|
|
cov[3]= agexact*agexact; |
| #ifdef windows
|
for (kk=1; kk<=cptcovage;kk++) { |
| fprintf(ficgp,"cd \"%s\" \n",pathc);
|
cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; |
| #endif
|
} |
| m=pow(2,cptcoveff);
|
|
|
|
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, |
| /* 1eme*/
|
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); |
| for (cpt=1; cpt<= nlstate ; cpt ++) {
|
savm=oldm; |
| for (k1=1; k1<= m ; k1 ++) {
|
oldm=newm; |
|
|
} /* end mult */ |
| #ifdef windows
|
|
| fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
|
s1=s[mw[mi][i]][i]; |
| 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);
|
s2=s[mw[mi+1][i]][i]; |
| #endif
|
if( s2 > nlstate){ |
| #ifdef unix
|
lli=log(out[s1][s2] - savm[s1][s2]); |
| fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
|
}else{ |
| fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);
|
lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */ |
| #endif
|
} |
|
|
ipmx +=1; |
| for (i=1; i<= nlstate ; i ++) {
|
sw += weight[i]; |
| if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
|
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; |
| else fprintf(ficgp," \%%*lf (\%%*lf)");
|
/* 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 */ |
| fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
|
} /* end of individual */ |
| for (i=1; i<= nlstate ; i ++) {
|
}else{ /* ml=5 no inter-extrapolation no jackson =0.8a */ |
| if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
|
for (i=1,ipmx=0, sw=0.; i<=imx; i++){ |
| else fprintf(ficgp," \%%*lf (\%%*lf)");
|
for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; |
| }
|
for(mi=1; mi<= wav[i]-1; mi++){ |
| fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);
|
for (ii=1;ii<=nlstate+ndeath;ii++) |
| for (i=1; i<= nlstate ; i ++) {
|
for (j=1;j<=nlstate+ndeath;j++){ |
| if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
|
oldm[ii][j]=(ii==j ? 1.0 : 0.0); |
| else fprintf(ficgp," \%%*lf (\%%*lf)");
|
savm[ii][j]=(ii==j ? 1.0 : 0.0); |
| }
|
} |
| fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
|
for(d=0; d<dh[mi][i]; d++){ |
| #ifdef unix
|
newm=savm; |
| fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");
|
agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; |
| #endif
|
cov[2]=agexact; |
| }
|
if(nagesqr==1) |
| }
|
cov[3]= agexact*agexact; |
| /*2 eme*/
|
for (kk=1; kk<=cptcovage;kk++) { |
|
|
cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; |
| for (k1=1; k1<= m ; k1 ++) {
|
} |
| fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
|
|
| fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
|
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, |
|
|
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); |
| for (i=1; i<= nlstate+1 ; i ++) {
|
savm=oldm; |
| k=2*i;
|
oldm=newm; |
| fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
|
} /* end mult */ |
| for (j=1; j<= nlstate+1 ; j ++) {
|
|
| if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
|
s1=s[mw[mi][i]][i]; |
| else fprintf(ficgp," \%%*lf (\%%*lf)");
|
s2=s[mw[mi+1][i]][i]; |
| }
|
lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */ |
| if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
|
ipmx +=1; |
| else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
|
sw += weight[i]; |
| fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
|
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; |
| for (j=1; j<= nlstate+1 ; j ++) {
|
/*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/ |
| if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
|
} /* end of wave */ |
| else fprintf(ficgp," \%%*lf (\%%*lf)");
|
} /* end of individual */ |
| }
|
} /* End of if */ |
| fprintf(ficgp,"\" t\"\" w l 0,");
|
for(k=1,l=0.; k<=nlstate; k++) l += ll[k]; |
| fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
|
/* printf("l1=%f l2=%f ",ll[1],ll[2]); */ |
| for (j=1; j<= nlstate+1 ; j ++) {
|
l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */ |
| if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
|
return -l; |
| else fprintf(ficgp," \%%*lf (\%%*lf)");
|
} |
| }
|
|
| if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
|
/*************** log-likelihood *************/ |
| else fprintf(ficgp,"\" t\"\" w l 0,");
|
double funcone( double *x) |
| }
|
{ |
| }
|
/* Same as likeli but slower because of a lot of printf and if */ |
|
|
int i, ii, j, k, mi, d, kk; |
| /*3eme*/
|
double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1]; |
|
|
double **out; |
| for (k1=1; k1<= m ; k1 ++) {
|
double lli; /* Individual log likelihood */ |
| for (cpt=1; cpt<= nlstate ; cpt ++) {
|
double llt; |
| k=2+nlstate*(2*cpt-2);
|
int s1, s2; |
| fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
|
double bbh, survp; |
| fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
|
double agexact; |
| /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
|
/*extern weight */ |
| for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
|
/* We are differentiating ll according to initial status */ |
| fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
|
/* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/ |
| fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
|
/*for(i=1;i<imx;i++) |
| for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
|
printf(" %d\n",s[4][i]); |
| fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
|
*/ |
|
|
cov[1]=1.; |
| */
|
|
| for (i=1; i< nlstate ; i ++) {
|
for(k=1; k<=nlstate; k++) ll[k]=0.; |
| 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);
|
|
|
|
for (i=1,ipmx=0, sw=0.; i<=imx; i++){ |
| }
|
for (k=1; k<=cptcovn;k++) cov[2+nagesqr+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++){ |
| /* CV preval stat */
|
oldm[ii][j]=(ii==j ? 1.0 : 0.0); |
| for (k1=1; k1<= m ; k1 ++) {
|
savm[ii][j]=(ii==j ? 1.0 : 0.0); |
| for (cpt=1; cpt<nlstate ; cpt ++) {
|
} |
| k=3;
|
for(d=0; d<dh[mi][i]; d++){ |
| fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
|
newm=savm; |
| 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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
|
agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; |
|
|
cov[2]=agexact; |
| for (i=1; i< nlstate ; i ++)
|
if(nagesqr==1) |
| fprintf(ficgp,"+$%d",k+i+1);
|
cov[3]= agexact*agexact; |
| fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
|
for (kk=1; kk<=cptcovage;kk++) { |
|
|
cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; |
| l=3+(nlstate+ndeath)*cpt;
|
} |
| fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
|
|
| for (i=1; i< nlstate ; i ++) {
|
/* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */ |
| l=3+(nlstate+ndeath)*cpt;
|
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, |
| fprintf(ficgp,"+$%d",l+i+1);
|
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); |
| }
|
/* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */ |
| fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
|
/* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */ |
| }
|
savm=oldm; |
| }
|
oldm=newm; |
|
|
} /* end mult */ |
| /* proba elementaires */
|
|
| for(i=1,jk=1; i <=nlstate; i++){
|
s1=s[mw[mi][i]][i]; |
| for(k=1; k <=(nlstate+ndeath); k++){
|
s2=s[mw[mi+1][i]][i]; |
| if (k != i) {
|
bbh=(double)bh[mi][i]/(double)stepm; |
| for(j=1; j <=ncovmodel; j++){
|
/* bias is positive if real duration |
|
|
* is higher than the multiple of stepm and negative otherwise. |
| fprintf(ficgp,"p%d=%f ",jk,p[jk]);
|
*/ |
| jk++;
|
if( s2 > nlstate && (mle <5) ){ /* Jackson */ |
| fprintf(ficgp,"\n");
|
lli=log(out[s1][s2] - savm[s1][s2]); |
| }
|
} else if (s2==-2) { |
| }
|
for (j=1,survp=0. ; j<=nlstate; j++) |
| }
|
survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; |
| }
|
lli= log(survp); |
|
|
}else if (mle==1){ |
| for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
|
lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ |
| for(jk=1; jk <=m; jk++) {
|
} else if(mle==2){ |
| fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
|
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 */ |
| if (ng==2)
|
} else if(mle==3){ /* exponential inter-extrapolation */ |
| fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\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])); /* exponential inter-extrapolation */ |
| else
|
} else if (mle==4){ /* mle=4 no inter-extrapolation */ |
| fprintf(ficgp,"\nset title \"Probability\"\n");
|
lli=log(out[s1][s2]); /* Original formula */ |
| fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
|
} else{ /* mle=0 back to 1 */ |
| i=1;
|
lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ |
| for(k2=1; k2<=nlstate; k2++) {
|
/*lli=log(out[s1][s2]); */ /* Original formula */ |
| k3=i;
|
} /* End of if */ |
| for(k=1; k<=(nlstate+ndeath); k++) {
|
ipmx +=1; |
| if (k != k2){
|
sw += weight[i]; |
| if(ng==2)
|
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; |
| fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
|
/*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]); */ |
| else
|
if(globpr){ |
| fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
|
fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\ |
| ij=1;
|
%11.6f %11.6f %11.6f ", \ |
| for(j=3; j <=ncovmodel; j++) {
|
num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i], |
| if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
|
2*weight[i]*lli,out[s1][s2],savm[s1][s2]); |
| fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
|
for(k=1,llt=0.,l=0.; k<=nlstate; k++){ |
| ij++;
|
llt +=ll[k]*gipmx/gsw; |
| }
|
fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw); |
| else
|
} |
| fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
|
fprintf(ficresilk," %10.6f\n", -llt); |
| }
|
} |
| fprintf(ficgp,")/(1");
|
} /* end of wave */ |
|
|
} /* end of individual */ |
| for(k1=1; k1 <=nlstate; k1++){
|
for(k=1,l=0.; k<=nlstate; k++) l += ll[k]; |
| fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
|
/* printf("l1=%f l2=%f ",ll[1],ll[2]); */ |
| ij=1;
|
l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */ |
| for(j=3; j <=ncovmodel; j++){
|
if(globpr==0){ /* First time we count the contributions and weights */ |
| if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
|
gipmx=ipmx; |
| fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
|
gsw=sw; |
| ij++;
|
} |
| }
|
return -l; |
| else
|
} |
| fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
|
|
| }
|
|
| fprintf(ficgp,")");
|
/*************** function likelione ***********/ |
| }
|
void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double [])) |
| fprintf(ficgp,") t \"p%d%d\" ", k2,k);
|
{ |
| if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
|
/* This routine should help understanding what is done with |
| i=i+ncovmodel;
|
the selection of individuals/waves and |
| }
|
to check the exact contribution to the likelihood. |
| }
|
Plotting could be done. |
| }
|
*/ |
| }
|
int k; |
| }
|
|
| fclose(ficgp);
|
if(*globpri !=0){ /* Just counts and sums, no printings */ |
| } /* end gnuplot */
|
strcpy(fileresilk,"ilk"); |
|
|
strcat(fileresilk,fileres); |
|
|
if((ficresilk=fopen(fileresilk,"w"))==NULL) { |
| /*************** Moving average **************/
|
printf("Problem with resultfile: %s\n", fileresilk); |
| void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){
|
fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk); |
|
|
} |
| int i, cpt, cptcod;
|
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"); |
| for (agedeb=ageminpar; agedeb<=fage; agedeb++)
|
fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav "); |
| for (i=1; i<=nlstate;i++)
|
/* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */ |
| for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
|
for(k=1; k<=nlstate; k++) |
| mobaverage[(int)agedeb][i][cptcod]=0.;
|
fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k); |
|
|
fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n"); |
| for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){
|
} |
| for (i=1; i<=nlstate;i++){
|
|
| for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
|
*fretone=(*funcone)(p); |
| for (cpt=0;cpt<=4;cpt++){
|
if(*globpri !=0){ |
| mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];
|
fclose(ficresilk); |
| }
|
fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk)); |
| mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;
|
fflush(fichtm); |
| }
|
} |
| }
|
return; |
| }
|
} |
|
|
|
| }
|
|
|
|
/*********** Maximum Likelihood Estimation ***************/ |
|
|
|
| /************** Forecasting ******************/
|
void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double [])) |
| prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){
|
{ |
|
|
int i,j, iter=0; |
| int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
|
double **xi; |
| int *popage;
|
double fret; |
| double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
|
double fretone; /* Only one call to likelihood */ |
| double *popeffectif,*popcount;
|
/* char filerespow[FILENAMELENGTH];*/ |
| double ***p3mat;
|
|
| char fileresf[FILENAMELENGTH];
|
#ifdef NLOPT |
|
|
int creturn; |
| agelim=AGESUP;
|
nlopt_opt opt; |
| calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
|
/* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */ |
|
|
double *lb; |
| prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
|
double minf; /* the minimum objective value, upon return */ |
|
|
double * p1; /* Shifted parameters from 0 instead of 1 */ |
|
|
myfunc_data dinst, *d = &dinst; |
| strcpy(fileresf,"f");
|
#endif |
| strcat(fileresf,fileres);
|
|
| if((ficresf=fopen(fileresf,"w"))==NULL) {
|
|
| printf("Problem with forecast resultfile: %s\n", fileresf);
|
xi=matrix(1,npar,1,npar); |
| }
|
for (i=1;i<=npar;i++) |
| printf("Computing forecasting: result on file '%s' \n", fileresf);
|
for (j=1;j<=npar;j++) |
|
|
xi[i][j]=(i==j ? 1.0 : 0.0); |
| if (cptcoveff==0) ncodemax[cptcoveff]=1;
|
printf("Powell\n"); fprintf(ficlog,"Powell\n"); |
|
|
strcpy(filerespow,"pow"); |
| if (mobilav==1) {
|
strcat(filerespow,fileres); |
| mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
|
if((ficrespow=fopen(filerespow,"w"))==NULL) { |
| movingaverage(agedeb, fage, ageminpar, mobaverage);
|
printf("Problem with resultfile: %s\n", filerespow); |
| }
|
fprintf(ficlog,"Problem with resultfile: %s\n", filerespow); |
|
|
} |
| stepsize=(int) (stepm+YEARM-1)/YEARM;
|
fprintf(ficrespow,"# Powell\n# iter -2*LL"); |
| if (stepm<=12) stepsize=1;
|
for (i=1;i<=nlstate;i++) |
|
|
for(j=1;j<=nlstate+ndeath;j++) |
| agelim=AGESUP;
|
if(j!=i)fprintf(ficrespow," p%1d%1d",i,j); |
|
|
fprintf(ficrespow,"\n"); |
| hstepm=1;
|
#ifdef POWELL |
| hstepm=hstepm/stepm;
|
powell(p,xi,npar,ftol,&iter,&fret,func); |
| yp1=modf(dateintmean,&yp);
|
#endif |
| anprojmean=yp;
|
|
| yp2=modf((yp1*12),&yp);
|
#ifdef NLOPT |
| mprojmean=yp;
|
#ifdef NEWUOA |
| yp1=modf((yp2*30.5),&yp);
|
opt = nlopt_create(NLOPT_LN_NEWUOA,npar); |
| jprojmean=yp;
|
#else |
| if(jprojmean==0) jprojmean=1;
|
opt = nlopt_create(NLOPT_LN_BOBYQA,npar); |
| if(mprojmean==0) jprojmean=1;
|
#endif |
|
|
lb=vector(0,npar-1); |
| fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);
|
for (i=0;i<npar;i++) lb[i]= -HUGE_VAL; |
|
|
nlopt_set_lower_bounds(opt, lb); |
| for(cptcov=1;cptcov<=i2;cptcov++){
|
nlopt_set_initial_step1(opt, 0.1); |
| for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
|
|
| k=k+1;
|
p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */ |
| fprintf(ficresf,"\n#******");
|
d->function = func; |
| for(j=1;j<=cptcoveff;j++) {
|
printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d)); |
| fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
|
nlopt_set_min_objective(opt, myfunc, d); |
| }
|
nlopt_set_xtol_rel(opt, ftol); |
| fprintf(ficresf,"******\n");
|
if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) { |
| fprintf(ficresf,"# StartingAge FinalAge");
|
printf("nlopt failed! %d\n",creturn); |
| for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
|
} |
|
|
else { |
|
|
printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT); |
| for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {
|
printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf); |
| fprintf(ficresf,"\n");
|
iter=1; /* not equal */ |
| fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);
|
} |
|
|
nlopt_destroy(opt); |
| for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
|
#endif |
| nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
|
free_matrix(xi,1,npar,1,npar); |
| nhstepm = nhstepm/hstepm;
|
fclose(ficrespow); |
|
|
printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); |
| p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); |
| oldm=oldms;savm=savms;
|
fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); |
| hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
|
|
|
|
} |
| for (h=0; h<=nhstepm; h++){
|
|
| if (h==(int) (calagedate+YEARM*cpt)) {
|
/**** Computes Hessian and covariance matrix ***/ |
| fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
|
void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double [])) |
| }
|
{ |
| for(j=1; j<=nlstate+ndeath;j++) {
|
double **a,**y,*x,pd; |
| kk1=0.;kk2=0;
|
double **hess; |
| for(i=1; i<=nlstate;i++) {
|
int i, j; |
| if (mobilav==1)
|
int *indx; |
| kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
|
|
| else {
|
double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar); |
| kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
|
double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar); |
| }
|
void lubksb(double **a, int npar, int *indx, double b[]) ; |
|
|
void ludcmp(double **a, int npar, int *indx, double *d) ; |
| }
|
double gompertz(double p[]); |
| if (h==(int)(calagedate+12*cpt)){
|
hess=matrix(1,npar,1,npar); |
| fprintf(ficresf," %.3f", kk1);
|
|
|
|
printf("\nCalculation of the hessian matrix. Wait...\n"); |
| }
|
fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n"); |
| }
|
for (i=1;i<=npar;i++){ |
| }
|
printf("%d",i);fflush(stdout); |
| free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
fprintf(ficlog,"%d",i);fflush(ficlog); |
| }
|
|
| }
|
hess[i][i]=hessii(p,ftolhess,i,delti,func,npar); |
| }
|
|
| }
|
/* printf(" %f ",p[i]); |
|
|
printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/ |
| if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
|
} |
|
|
|
| fclose(ficresf);
|
for (i=1;i<=npar;i++) { |
| }
|
for (j=1;j<=npar;j++) { |
| /************** Forecasting ******************/
|
if (j>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){
|
printf(".%d%d",i,j);fflush(stdout); |
|
|
fprintf(ficlog,".%d%d",i,j);fflush(ficlog); |
| int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
|
hess[i][j]=hessij(p,delti,i,j,func,npar); |
| int *popage;
|
|
| double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
|
hess[j][i]=hess[i][j]; |
| double *popeffectif,*popcount;
|
/*printf(" %lf ",hess[i][j]);*/ |
| double ***p3mat,***tabpop,***tabpopprev;
|
} |
| char filerespop[FILENAMELENGTH];
|
} |
|
|
} |
| tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
|
printf("\n"); |
| tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
|
fprintf(ficlog,"\n"); |
| agelim=AGESUP;
|
|
| calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
|
printf("\nInverting the hessian to get the covariance matrix. Wait...\n"); |
|
|
fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n"); |
| prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
|
|
|
|
a=matrix(1,npar,1,npar); |
|
|
y=matrix(1,npar,1,npar); |
| strcpy(filerespop,"pop");
|
x=vector(1,npar); |
| strcat(filerespop,fileres);
|
indx=ivector(1,npar); |
| if((ficrespop=fopen(filerespop,"w"))==NULL) {
|
for (i=1;i<=npar;i++) |
| printf("Problem with forecast resultfile: %s\n", filerespop);
|
for (j=1;j<=npar;j++) a[i][j]=hess[i][j]; |
| }
|
ludcmp(a,npar,indx,&pd); |
| printf("Computing forecasting: result on file '%s' \n", filerespop);
|
|
|
|
for (j=1;j<=npar;j++) { |
| if (cptcoveff==0) ncodemax[cptcoveff]=1;
|
for (i=1;i<=npar;i++) x[i]=0; |
|
|
x[j]=1; |
| if (mobilav==1) {
|
lubksb(a,npar,indx,x); |
| mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
|
for (i=1;i<=npar;i++){ |
| movingaverage(agedeb, fage, ageminpar, mobaverage);
|
matcov[i][j]=x[i]; |
| }
|
} |
|
|
} |
| stepsize=(int) (stepm+YEARM-1)/YEARM;
|
|
| if (stepm<=12) stepsize=1;
|
printf("\n#Hessian matrix#\n"); |
|
|
fprintf(ficlog,"\n#Hessian matrix#\n"); |
| agelim=AGESUP;
|
for (i=1;i<=npar;i++) { |
|
|
for (j=1;j<=npar;j++) { |
| hstepm=1;
|
printf("%.3e ",hess[i][j]); |
| hstepm=hstepm/stepm;
|
fprintf(ficlog,"%.3e ",hess[i][j]); |
|
|
} |
| if (popforecast==1) {
|
printf("\n"); |
| if((ficpop=fopen(popfile,"r"))==NULL) {
|
fprintf(ficlog,"\n"); |
| printf("Problem with population file : %s\n",popfile);exit(0);
|
} |
| }
|
|
| popage=ivector(0,AGESUP);
|
/* Recompute Inverse */ |
| popeffectif=vector(0,AGESUP);
|
for (i=1;i<=npar;i++) |
| popcount=vector(0,AGESUP);
|
for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; |
|
|
ludcmp(a,npar,indx,&pd); |
| i=1;
|
|
| while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
|
/* printf("\n#Hessian matrix recomputed#\n"); |
|
|
|
| imx=i;
|
for (j=1;j<=npar;j++) { |
| for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
|
for (i=1;i<=npar;i++) x[i]=0; |
| }
|
x[j]=1; |
|
|
lubksb(a,npar,indx,x); |
| for(cptcov=1;cptcov<=i2;cptcov++){
|
for (i=1;i<=npar;i++){ |
| for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
|
y[i][j]=x[i]; |
| k=k+1;
|
printf("%.3e ",y[i][j]); |
| fprintf(ficrespop,"\n#******");
|
fprintf(ficlog,"%.3e ",y[i][j]); |
| for(j=1;j<=cptcoveff;j++) {
|
} |
| fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
|
printf("\n"); |
| }
|
fprintf(ficlog,"\n"); |
| fprintf(ficrespop,"******\n");
|
} |
| fprintf(ficrespop,"# Age");
|
*/ |
| for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
|
|
| if (popforecast==1) fprintf(ficrespop," [Population]");
|
free_matrix(a,1,npar,1,npar); |
|
|
free_matrix(y,1,npar,1,npar); |
| for (cpt=0; cpt<=0;cpt++) {
|
free_vector(x,1,npar); |
| fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
|
free_ivector(indx,1,npar); |
|
|
free_matrix(hess,1,npar,1,npar); |
| for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
|
|
| nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
|
|
| nhstepm = nhstepm/hstepm;
|
} |
|
|
|
| p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
/*************** hessian matrix ****************/ |
| oldm=oldms;savm=savms;
|
double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar) |
| hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
|
{ |
|
|
int i; |
| for (h=0; h<=nhstepm; h++){
|
int l=1, lmax=20; |
| if (h==(int) (calagedate+YEARM*cpt)) {
|
double k1,k2; |
| fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
|
double p2[MAXPARM+1]; /* identical to x */ |
| }
|
double res; |
| for(j=1; j<=nlstate+ndeath;j++) {
|
double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; |
| kk1=0.;kk2=0;
|
double fx; |
| for(i=1; i<=nlstate;i++) {
|
int k=0,kmax=10; |
| if (mobilav==1)
|
double l1; |
| kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
|
|
| else {
|
fx=func(x); |
| kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
|
for (i=1;i<=npar;i++) p2[i]=x[i]; |
| }
|
for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */ |
| }
|
l1=pow(10,l); |
| if (h==(int)(calagedate+12*cpt)){
|
delts=delt; |
| tabpop[(int)(agedeb)][j][cptcod]=kk1;
|
for(k=1 ; k <kmax; k=k+1){ |
| /*fprintf(ficrespop," %.3f", kk1);
|
delt = delta*(l1*k); |
| if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
|
p2[theta]=x[theta] +delt; |
| }
|
k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */ |
| }
|
p2[theta]=x[theta]-delt; |
| for(i=1; i<=nlstate;i++){
|
k2=func(p2)-fx; |
| kk1=0.;
|
/*res= (k1-2.0*fx+k2)/delt/delt; */ |
| for(j=1; j<=nlstate;j++){
|
res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */ |
| kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
|
|
| }
|
#ifdef DEBUGHESS |
| tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
|
printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx); |
| }
|
fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx); |
|
|
#endif |
| if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)
|
/*if(fabs(k1-2.0*fx+k2) <1.e-13){ */ |
| fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
|
if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){ |
| }
|
k=kmax; |
| free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
} |
| }
|
else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */ |
| }
|
k=kmax; l=lmax*10; |
|
|
} |
| /******/
|
else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ |
|
|
delts=delt; |
| for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
|
} |
| fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
|
} |
| for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
|
} |
| nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
|
delti[theta]=delts; |
| nhstepm = nhstepm/hstepm;
|
return res; |
|
|
|
| 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);
|
double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) |
| for (h=0; h<=nhstepm; h++){
|
{ |
| if (h==(int) (calagedate+YEARM*cpt)) {
|
int i; |
| fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
|
int l=1, lmax=20; |
| }
|
double k1,k2,k3,k4,res,fx; |
| for(j=1; j<=nlstate+ndeath;j++) {
|
double p2[MAXPARM+1]; |
| kk1=0.;kk2=0;
|
int k; |
| for(i=1; i<=nlstate;i++) {
|
|
| kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
|
fx=func(x); |
| }
|
for (k=1; k<=2; k++) { |
| if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);
|
for (i=1;i<=npar;i++) p2[i]=x[i]; |
| }
|
p2[thetai]=x[thetai]+delti[thetai]/k; |
| }
|
p2[thetaj]=x[thetaj]+delti[thetaj]/k; |
| free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
k1=func(p2)-fx; |
| }
|
|
| }
|
p2[thetai]=x[thetai]+delti[thetai]/k; |
| }
|
p2[thetaj]=x[thetaj]-delti[thetaj]/k; |
| }
|
k2=func(p2)-fx; |
|
|
|
| if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
|
p2[thetai]=x[thetai]-delti[thetai]/k; |
|
|
p2[thetaj]=x[thetaj]+delti[thetaj]/k; |
| if (popforecast==1) {
|
k3=func(p2)-fx; |
| free_ivector(popage,0,AGESUP);
|
|
| free_vector(popeffectif,0,AGESUP);
|
p2[thetai]=x[thetai]-delti[thetai]/k; |
| free_vector(popcount,0,AGESUP);
|
p2[thetaj]=x[thetaj]-delti[thetaj]/k; |
| }
|
k4=func(p2)-fx; |
| free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
|
res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */ |
| free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
|
#ifdef DEBUG |
| fclose(ficrespop);
|
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); |
|
|
#endif |
| /***********************************************/
|
} |
| /**************** Main Program *****************/
|
return res; |
| /***********************************************/
|
} |
|
|
|
| int main(int argc, char *argv[])
|
/************** Inverse of matrix **************/ |
| {
|
void ludcmp(double **a, int n, int *indx, double *d) |
|
|
{ |
| int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
|
int i,imax,j,k; |
| double agedeb, agefin,hf;
|
double big,dum,sum,temp; |
| double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
|
double *vv; |
|
|
|
| double fret;
|
vv=vector(1,n); |
| double **xi,tmp,delta;
|
*d=1.0; |
|
|
for (i=1;i<=n;i++) { |
| double dum; /* Dummy variable */
|
big=0.0; |
| double ***p3mat;
|
for (j=1;j<=n;j++) |
| int *indx;
|
if ((temp=fabs(a[i][j])) > big) big=temp; |
| char line[MAXLINE], linepar[MAXLINE];
|
if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); |
| char path[80],pathc[80],pathcd[80],pathtot[80],model[20];
|
vv[i]=1.0/big; |
| int firstobs=1, lastobs=10;
|
} |
| int sdeb, sfin; /* Status at beginning and end */
|
for (j=1;j<=n;j++) { |
| int c, h , cpt,l;
|
for (i=1;i<j;i++) { |
| int ju,jl, mi;
|
sum=a[i][j]; |
| int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
|
for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; |
| int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
|
a[i][j]=sum; |
| int mobilav=0,popforecast=0;
|
} |
| int hstepm, nhstepm;
|
big=0.0; |
| double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
|
for (i=j;i<=n;i++) { |
|
|
sum=a[i][j]; |
| double bage, fage, age, agelim, agebase;
|
for (k=1;k<j;k++) |
| double ftolpl=FTOL;
|
sum -= a[i][k]*a[k][j]; |
| double **prlim;
|
a[i][j]=sum; |
| double *severity;
|
if ( (dum=vv[i]*fabs(sum)) >= big) { |
| double ***param; /* Matrix of parameters */
|
big=dum; |
| double *p;
|
imax=i; |
| double **matcov; /* Matrix of covariance */
|
} |
| double ***delti3; /* Scale */
|
} |
| double *delti; /* Scale */
|
if (j != imax) { |
| double ***eij, ***vareij;
|
for (k=1;k<=n;k++) { |
| double **varpl; /* Variances of prevalence limits by age */
|
dum=a[imax][k]; |
| double *epj, vepp;
|
a[imax][k]=a[j][k]; |
| double kk1, kk2;
|
a[j][k]=dum; |
| double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
|
} |
|
|
*d = -(*d); |
|
|
vv[imax]=vv[j]; |
| char *alph[]={"a","a","b","c","d","e"}, str[4];
|
} |
|
|
indx[j]=imax; |
|
|
if (a[j][j] == 0.0) a[j][j]=TINY; |
| char z[1]="c", occ;
|
if (j != n) { |
| #include <sys/time.h>
|
dum=1.0/(a[j][j]); |
| #include <time.h>
|
for (i=j+1;i<=n;i++) a[i][j] *= dum; |
| char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
|
} |
|
|
} |
| /* long total_usecs;
|
free_vector(vv,1,n); /* Doesn't work */ |
| struct timeval start_time, end_time;
|
; |
|
|
} |
| gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
|
|
| getcwd(pathcd, size);
|
void lubksb(double **a, int n, int *indx, double b[]) |
|
|
{ |
| printf("\n%s",version);
|
int i,ii=0,ip,j; |
| if(argc <=1){
|
double sum; |
| printf("\nEnter the parameter file name: ");
|
|
| scanf("%s",pathtot);
|
for (i=1;i<=n;i++) { |
| }
|
ip=indx[i]; |
| else{
|
sum=b[ip]; |
| strcpy(pathtot,argv[1]);
|
b[ip]=b[i]; |
| }
|
if (ii) |
| /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
|
for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; |
| /*cygwin_split_path(pathtot,path,optionfile);
|
else if (sum) ii=i; |
| printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
|
b[i]=sum; |
| /* cutv(path,optionfile,pathtot,'\\');*/
|
} |
|
|
for (i=n;i>=1;i--) { |
| split(pathtot,path,optionfile,optionfilext,optionfilefiname);
|
sum=b[i]; |
| printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
|
for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; |
| chdir(path);
|
b[i]=sum/a[i][i]; |
| replace(pathc,path);
|
} |
|
|
} |
| /*-------- arguments in the command line --------*/
|
|
|
|
void pstamp(FILE *fichier) |
| strcpy(fileres,"r");
|
{ |
| strcat(fileres, optionfilefiname);
|
fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart); |
| strcat(fileres,".txt"); /* Other files have txt extension */
|
} |
|
|
|
| /*---------arguments file --------*/
|
/************ Frequencies ********************/ |
|
|
void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[]) |
| if((ficpar=fopen(optionfile,"r"))==NULL) {
|
{ /* Some frequencies */ |
| printf("Problem with optionfile %s\n",optionfile);
|
|
| goto end;
|
int i, m, jk, j1, bool, z1,j; |
| }
|
int first; |
|
|
double ***freq; /* Frequencies */ |
| strcpy(filereso,"o");
|
double *pp, **prop; |
| strcat(filereso,fileres);
|
double pos,posprop, k2, dateintsum=0,k2cpt=0; |
| if((ficparo=fopen(filereso,"w"))==NULL) {
|
char fileresp[FILENAMELENGTH]; |
| printf("Problem with Output resultfile: %s\n", filereso);goto end;
|
|
| }
|
pp=vector(1,nlstate); |
|
|
prop=matrix(1,nlstate,iagemin,iagemax+3); |
| /* Reads comments: lines beginning with '#' */
|
strcpy(fileresp,"p"); |
| while((c=getc(ficpar))=='#' && c!= EOF){
|
strcat(fileresp,fileres); |
| ungetc(c,ficpar);
|
if((ficresp=fopen(fileresp,"w"))==NULL) { |
| fgets(line, MAXLINE, ficpar);
|
printf("Problem with prevalence resultfile: %s\n", fileresp); |
| puts(line);
|
fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp); |
| fputs(line,ficparo);
|
exit(0); |
| }
|
} |
| ungetc(c,ficpar);
|
freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3); |
|
|
j1=0; |
| fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
|
|
| printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
|
j=cptcoveff; |
| 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);
|
if (cptcovn<1) {j=1;ncodemax[1]=1;} |
| while((c=getc(ficpar))=='#' && c!= EOF){
|
|
| ungetc(c,ficpar);
|
first=1; |
| fgets(line, MAXLINE, ficpar);
|
|
| puts(line);
|
/* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */ |
| fputs(line,ficparo);
|
/* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */ |
| }
|
/* j1++; */ |
| ungetc(c,ficpar);
|
for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ |
|
|
/*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]); |
|
|
scanf("%d", i);*/ |
| covar=matrix(0,NCOVMAX,1,n);
|
for (i=-5; i<=nlstate+ndeath; i++) |
| cptcovn=0;
|
for (jk=-5; jk<=nlstate+ndeath; jk++) |
| if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
|
for(m=iagemin; m <= iagemax+3; m++) |
|
|
freq[i][jk][m]=0; |
| ncovmodel=2+cptcovn;
|
|
| nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
|
for (i=1; i<=nlstate; i++) |
|
|
for(m=iagemin; m <= iagemax+3; m++) |
| /* Read guess parameters */
|
prop[i][m]=0; |
| /* Reads comments: lines beginning with '#' */
|
|
| while((c=getc(ficpar))=='#' && c!= EOF){
|
dateintsum=0; |
| ungetc(c,ficpar);
|
k2cpt=0; |
| fgets(line, MAXLINE, ficpar);
|
for (i=1; i<=imx; i++) { |
| puts(line);
|
bool=1; |
| fputs(line,ficparo);
|
if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */ |
| }
|
for (z1=1; z1<=cptcoveff; z1++) |
| ungetc(c,ficpar);
|
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){ |
|
|
/* Tests if the value of each of the covariates of i is equal to filter j1 */ |
| param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
|
bool=0; |
| for(i=1; i <=nlstate; i++)
|
/* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n", |
| for(j=1; j <=nlstate+ndeath-1; j++){
|
bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1], |
| fscanf(ficpar,"%1d%1d",&i1,&j1);
|
j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/ |
| fprintf(ficparo,"%1d%1d",i1,j1);
|
/* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/ |
| printf("%1d%1d",i,j);
|
} |
| for(k=1; k<=ncovmodel;k++){
|
} |
| fscanf(ficpar," %lf",¶m[i][j][k]);
|
|
| printf(" %lf",param[i][j][k]);
|
if (bool==1){ |
| fprintf(ficparo," %lf",param[i][j][k]);
|
for(m=firstpass; m<=lastpass; m++){ |
| }
|
k2=anint[m][i]+(mint[m][i]/12.); |
| fscanf(ficpar,"\n");
|
/*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/ |
| printf("\n");
|
if(agev[m][i]==0) agev[m][i]=iagemax+1; |
| fprintf(ficparo,"\n");
|
if(agev[m][i]==1) agev[m][i]=iagemax+2; |
| }
|
if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i]; |
|
|
if (m<lastpass) { |
| npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
|
freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; |
|
|
freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i]; |
| p=param[1][1];
|
} |
|
|
|
| /* Reads comments: lines beginning with '#' */
|
if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) { |
| while((c=getc(ficpar))=='#' && c!= EOF){
|
dateintsum=dateintsum+k2; |
| ungetc(c,ficpar);
|
k2cpt++; |
| fgets(line, MAXLINE, ficpar);
|
} |
| puts(line);
|
/*}*/ |
| fputs(line,ficparo);
|
} |
| }
|
} |
| ungetc(c,ficpar);
|
} /* end i */ |
|
|
|
| delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
|
/* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/ |
| delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
|
pstamp(ficresp); |
| for(i=1; i <=nlstate; i++){
|
if (cptcovn>0) { |
| for(j=1; j <=nlstate+ndeath-1; j++){
|
fprintf(ficresp, "\n#********** Variable "); |
| fscanf(ficpar,"%1d%1d",&i1,&j1);
|
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); |
| printf("%1d%1d",i,j);
|
fprintf(ficresp, "**********\n#"); |
| fprintf(ficparo,"%1d%1d",i1,j1);
|
fprintf(ficlog, "\n#********** Variable "); |
| for(k=1; k<=ncovmodel;k++){
|
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); |
| fscanf(ficpar,"%le",&delti3[i][j][k]);
|
fprintf(ficlog, "**********\n#"); |
| printf(" %le",delti3[i][j][k]);
|
} |
| fprintf(ficparo," %le",delti3[i][j][k]);
|
for(i=1; i<=nlstate;i++) |
| }
|
fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i); |
| fscanf(ficpar,"\n");
|
fprintf(ficresp, "\n"); |
| printf("\n");
|
|
| fprintf(ficparo,"\n");
|
for(i=iagemin; i <= iagemax+3; i++){ |
| }
|
if(i==iagemax+3){ |
| }
|
fprintf(ficlog,"Total"); |
| delti=delti3[1][1];
|
}else{ |
|
|
if(first==1){ |
| /* Reads comments: lines beginning with '#' */
|
first=0; |
| while((c=getc(ficpar))=='#' && c!= EOF){
|
printf("See log file for details...\n"); |
| ungetc(c,ficpar);
|
} |
| fgets(line, MAXLINE, ficpar);
|
fprintf(ficlog,"Age %d", i); |
| puts(line);
|
} |
| fputs(line,ficparo);
|
for(jk=1; jk <=nlstate ; jk++){ |
| }
|
for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++) |
| ungetc(c,ficpar);
|
pp[jk] += freq[jk][m][i]; |
|
|
} |
| matcov=matrix(1,npar,1,npar);
|
for(jk=1; jk <=nlstate ; jk++){ |
| for(i=1; i <=npar; i++){
|
for(m=-1, pos=0; m <=0 ; m++) |
| fscanf(ficpar,"%s",&str);
|
pos += freq[jk][m][i]; |
| printf("%s",str);
|
if(pp[jk]>=1.e-10){ |
| fprintf(ficparo,"%s",str);
|
if(first==1){ |
| for(j=1; j <=i; j++){
|
printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); |
| fscanf(ficpar," %le",&matcov[i][j]);
|
} |
| printf(" %.5le",matcov[i][j]);
|
fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); |
| fprintf(ficparo," %.5le",matcov[i][j]);
|
}else{ |
| }
|
if(first==1) |
| fscanf(ficpar,"\n");
|
printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk); |
| printf("\n");
|
fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk); |
| fprintf(ficparo,"\n");
|
} |
| }
|
} |
| for(i=1; i <=npar; i++)
|
|
| for(j=i+1;j<=npar;j++)
|
for(jk=1; jk <=nlstate ; jk++){ |
| matcov[i][j]=matcov[j][i];
|
for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++) |
|
|
pp[jk] += freq[jk][m][i]; |
| printf("\n");
|
} |
|
|
for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){ |
|
|
pos += pp[jk]; |
| /*-------- Rewriting paramater file ----------*/
|
posprop += prop[jk][i]; |
| strcpy(rfileres,"r"); /* "Rparameterfile */
|
} |
| strcat(rfileres,optionfilefiname); /* Parameter file first name*/
|
for(jk=1; jk <=nlstate ; jk++){ |
| strcat(rfileres,"."); /* */
|
if(pos>=1.e-5){ |
| strcat(rfileres,optionfilext); /* Other files have txt extension */
|
if(first==1) |
| if((ficres =fopen(rfileres,"w"))==NULL) {
|
printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); |
| printf("Problem writing new parameter file: %s\n", fileres);goto end;
|
fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); |
| }
|
}else{ |
| fprintf(ficres,"#%s\n",version);
|
if(first==1) |
|
|
printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); |
| /*-------- data file ----------*/
|
fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); |
| if((fic=fopen(datafile,"r"))==NULL) {
|
} |
| printf("Problem with datafile: %s\n", datafile);goto end;
|
if( i <= iagemax){ |
| }
|
if(pos>=1.e-5){ |
|
|
fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop); |
| n= lastobs;
|
/*probs[i][jk][j1]= pp[jk]/pos;*/ |
| severity = vector(1,maxwav);
|
/*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/ |
| outcome=imatrix(1,maxwav+1,1,n);
|
} |
| num=ivector(1,n);
|
else |
| moisnais=vector(1,n);
|
fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop); |
| annais=vector(1,n);
|
} |
| moisdc=vector(1,n);
|
} |
| andc=vector(1,n);
|
|
| agedc=vector(1,n);
|
for(jk=-1; jk <=nlstate+ndeath; jk++) |
| cod=ivector(1,n);
|
for(m=-1; m <=nlstate+ndeath; m++) |
| weight=vector(1,n);
|
if(freq[jk][m][i] !=0 ) { |
| for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
|
if(first==1) |
| mint=matrix(1,maxwav,1,n);
|
printf(" %d%d=%.0f",jk,m,freq[jk][m][i]); |
| anint=matrix(1,maxwav,1,n);
|
fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]); |
| s=imatrix(1,maxwav+1,1,n);
|
} |
| adl=imatrix(1,maxwav+1,1,n);
|
if(i <= iagemax) |
| tab=ivector(1,NCOVMAX);
|
fprintf(ficresp,"\n"); |
| ncodemax=ivector(1,8);
|
if(first==1) |
|
|
printf("Others in log...\n"); |
| i=1;
|
fprintf(ficlog,"\n"); |
| while (fgets(line, MAXLINE, fic) != NULL) {
|
} |
| if ((i >= firstobs) && (i <=lastobs)) {
|
/*}*/ |
|
|
} |
| for (j=maxwav;j>=1;j--){
|
dateintmean=dateintsum/k2cpt; |
| cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
|
|
| strcpy(line,stra);
|
fclose(ficresp); |
| cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
|
free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3); |
| cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
|
free_vector(pp,1,nlstate); |
| }
|
free_matrix(prop,1,nlstate,iagemin, iagemax+3); |
|
|
/* End of Freq */ |
| cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
|
} |
| cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
|
|
|
|
/************ Prevalence ********************/ |
| cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
|
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) |
| cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
|
{ |
|
|
/* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people |
| cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
|
in each health status at the date of interview (if between dateprev1 and dateprev2). |
| for (j=ncovcol;j>=1;j--){
|
We still use firstpass and lastpass as another selection. |
| cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
|
*/ |
| }
|
|
| num[i]=atol(stra);
|
int i, m, jk, j1, bool, z1,j; |
|
|
|
| /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
|
double **prop; |
| 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;}*/
|
double posprop; |
|
|
double y2; /* in fractional years */ |
| i=i+1;
|
int iagemin, iagemax; |
| }
|
int first; /** to stop verbosity which is redirected to log file */ |
| }
|
|
| /* printf("ii=%d", ij);
|
iagemin= (int) agemin; |
| scanf("%d",i);*/
|
iagemax= (int) agemax; |
| imx=i-1; /* Number of individuals */
|
/*pp=vector(1,nlstate);*/ |
|
|
prop=matrix(1,nlstate,iagemin,iagemax+3); |
| /* for (i=1; i<=imx; i++){
|
/* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/ |
| if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
|
j1=0; |
| 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;
|
/*j=cptcoveff;*/ |
| }*/
|
if (cptcovn<1) {j=1;ncodemax[1]=1;} |
| /* for (i=1; i<=imx; i++){
|
|
| if (s[4][i]==9) s[4][i]=-1;
|
first=1; |
| printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
|
for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ |
|
|
/*for(i1=1; i1<=ncodemax[k1];i1++){ |
|
|
j1++;*/ |
| /* Calculation of the number of parameter from char model*/
|
|
| Tvar=ivector(1,15);
|
for (i=1; i<=nlstate; i++) |
| Tprod=ivector(1,15);
|
for(m=iagemin; m <= iagemax+3; m++) |
| Tvaraff=ivector(1,15);
|
prop[i][m]=0.0; |
| Tvard=imatrix(1,15,1,2);
|
|
| Tage=ivector(1,15);
|
for (i=1; i<=imx; i++) { /* Each individual */ |
|
|
bool=1; |
| if (strlen(model) >1){
|
if (cptcovn>0) { |
| j=0, j1=0, k1=1, k2=1;
|
for (z1=1; z1<=cptcoveff; z1++) |
| j=nbocc(model,'+');
|
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) |
| j1=nbocc(model,'*');
|
bool=0; |
| cptcovn=j+1;
|
} |
| cptcovprod=j1;
|
if (bool==1) { |
|
|
for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/ |
| strcpy(modelsav,model);
|
y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */ |
| if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
|
if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */ |
| printf("Error. Non available option model=%s ",model);
|
if(agev[m][i]==0) agev[m][i]=iagemax+1; |
| goto end;
|
if(agev[m][i]==1) agev[m][i]=iagemax+2; |
| }
|
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); |
|
|
if (s[m][i]>0 && s[m][i]<=nlstate) { |
| for(i=(j+1); i>=1;i--){
|
/*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]]);*/ |
| cutv(stra,strb,modelsav,'+');
|
prop[s[m][i]][(int)agev[m][i]] += weight[i]; |
| if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);
|
prop[s[m][i]][iagemax+3] += weight[i]; |
| /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
|
} |
| /*scanf("%d",i);*/
|
} |
| if (strchr(strb,'*')) {
|
} /* end selection of waves */ |
| cutv(strd,strc,strb,'*');
|
} |
| if (strcmp(strc,"age")==0) {
|
} |
| cptcovprod--;
|
for(i=iagemin; i <= iagemax+3; i++){ |
| cutv(strb,stre,strd,'V');
|
for(jk=1,posprop=0; jk <=nlstate ; jk++) { |
| Tvar[i]=atoi(stre);
|
posprop += prop[jk][i]; |
| cptcovage++;
|
} |
| Tage[cptcovage]=i;
|
|
| /*printf("stre=%s ", stre);*/
|
for(jk=1; jk <=nlstate ; jk++){ |
| }
|
if( i <= iagemax){ |
| else if (strcmp(strd,"age")==0) {
|
if(posprop>=1.e-5){ |
| cptcovprod--;
|
probs[i][jk][j1]= prop[jk][i]/posprop; |
| cutv(strb,stre,strc,'V');
|
} else{ |
| Tvar[i]=atoi(stre);
|
if(first==1){ |
| cptcovage++;
|
first=0; |
| Tage[cptcovage]=i;
|
printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]); |
| }
|
} |
| else {
|
} |
| cutv(strb,stre,strc,'V');
|
} |
| Tvar[i]=ncovcol+k1;
|
}/* end jk */ |
| cutv(strb,strc,strd,'V');
|
}/* end i */ |
| Tprod[k1]=i;
|
/*} *//* end i1 */ |
| Tvard[k1][1]=atoi(strc);
|
} /* end j1 */ |
| Tvard[k1][2]=atoi(stre);
|
|
| Tvar[cptcovn+k2]=Tvard[k1][1];
|
/* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/ |
| Tvar[cptcovn+k2+1]=Tvard[k1][2];
|
/*free_vector(pp,1,nlstate);*/ |
| for (k=1; k<=lastobs;k++)
|
free_matrix(prop,1,nlstate, iagemin,iagemax+3); |
| covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
|
} /* End of prevalence */ |
| k1++;
|
|
| k2=k2+2;
|
/************* Waves Concatenation ***************/ |
| }
|
|
| }
|
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) |
| else {
|
{ |
| /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
|
/* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i. |
| /* scanf("%d",i);*/
|
Death is a valid wave (if date is known). |
| cutv(strd,strc,strb,'V');
|
mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i |
| Tvar[i]=atoi(strc);
|
dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i] |
| }
|
and mw[mi+1][i]. dh depends on stepm. |
| strcpy(modelsav,stra);
|
*/ |
| /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
|
|
| scanf("%d",i);*/
|
int i, mi, m; |
| }
|
/* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1; |
| }
|
double sum=0., jmean=0.;*/ |
|
|
int first; |
| /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
|
int j, k=0,jk, ju, jl; |
| printf("cptcovprod=%d ", cptcovprod);
|
double sum=0.; |
| scanf("%d ",i);*/
|
first=0; |
| fclose(fic);
|
jmin=100000; |
|
|
jmax=-1; |
| /* if(mle==1){*/
|
jmean=0.; |
| if (weightopt != 1) { /* Maximisation without weights*/
|
for(i=1; i<=imx; i++){ |
| for(i=1;i<=n;i++) weight[i]=1.0;
|
mi=0; |
| }
|
m=firstpass; |
| /*-calculation of age at interview from date of interview and age at death -*/
|
while(s[m][i] <= nlstate){ |
| agev=matrix(1,maxwav,1,imx);
|
if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5) |
|
|
mw[++mi][i]=m; |
| for (i=1; i<=imx; i++) {
|
if(m >=lastpass) |
| for(m=2; (m<= maxwav); m++) {
|
break; |
| if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
|
else |
| anint[m][i]=9999;
|
m++; |
| s[m][i]=-1;
|
}/* end while */ |
| }
|
if (s[m][i] > nlstate){ |
| if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
|
mi++; /* Death is another wave */ |
| }
|
/* if(mi==0) never been interviewed correctly before death */ |
| }
|
/* Only death is a correct wave */ |
|
|
mw[mi][i]=m; |
| for (i=1; i<=imx; i++) {
|
} |
| agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
|
|
| for(m=1; (m<= maxwav); m++){
|
wav[i]=mi; |
| if(s[m][i] >0){
|
if(mi==0){ |
| if (s[m][i] >= nlstate+1) {
|
nbwarn++; |
| if(agedc[i]>0)
|
if(first==0){ |
| if(moisdc[i]!=99 && andc[i]!=9999)
|
printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i); |
| agev[m][i]=agedc[i];
|
first=1; |
| /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
|
} |
| else {
|
if(first==1){ |
| if (andc[i]!=9999){
|
fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i); |
| printf("Warning negative age at death: %d line:%d\n",num[i],i);
|
} |
| agev[m][i]=-1;
|
} /* end mi==0 */ |
| }
|
} /* End individuals */ |
| }
|
|
| }
|
for(i=1; i<=imx; i++){ |
| else if(s[m][i] !=9){ /* Should no more exist */
|
for(mi=1; mi<wav[i];mi++){ |
| agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
|
if (stepm <=0) |
| if(mint[m][i]==99 || anint[m][i]==9999)
|
dh[mi][i]=1; |
| agev[m][i]=1;
|
else{ |
| else if(agev[m][i] <agemin){
|
if (s[mw[mi+1][i]][i] > nlstate) { /* A death */ |
| agemin=agev[m][i];
|
if (agedc[i] < 2*AGESUP) { |
| /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
|
j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); |
| }
|
if(j==0) j=1; /* Survives at least one month after exam */ |
| else if(agev[m][i] >agemax){
|
else if(j<0){ |
| agemax=agev[m][i];
|
nberr++; |
| /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
|
printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); |
| }
|
j=1; /* Temporary Dangerous patch */ |
| /*agev[m][i]=anint[m][i]-annais[i];*/
|
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); |
| /* agev[m][i] = age[i]+2*m;*/
|
fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); |
| }
|
fprintf(ficlog," We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm); |
| else { /* =9 */
|
} |
| agev[m][i]=1;
|
k=k+1; |
| s[m][i]=-1;
|
if (j >= jmax){ |
| }
|
jmax=j; |
| }
|
ijmax=i; |
| else /*= 0 Unknown */
|
} |
| agev[m][i]=1;
|
if (j <= jmin){ |
| }
|
jmin=j; |
|
|
ijmin=i; |
| }
|
} |
| for (i=1; i<=imx; i++) {
|
sum=sum+j; |
| for(m=1; (m<= maxwav); m++){
|
/*if (j<0) printf("j=%d num=%d \n",j,i);*/ |
| if (s[m][i] > (nlstate+ndeath)) {
|
/* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/ |
| printf("Error: Wrong value in nlstate or ndeath\n");
|
} |
| goto end;
|
} |
| }
|
else{ |
| }
|
j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12)); |
| }
|
/* 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]); */ |
|
|
|
| printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
|
k=k+1; |
|
|
if (j >= jmax) { |
| free_vector(severity,1,maxwav);
|
jmax=j; |
| free_imatrix(outcome,1,maxwav+1,1,n);
|
ijmax=i; |
| free_vector(moisnais,1,n);
|
} |
| free_vector(annais,1,n);
|
else if (j <= jmin){ |
| /* free_matrix(mint,1,maxwav,1,n);
|
jmin=j; |
| free_matrix(anint,1,maxwav,1,n);*/
|
ijmin=i; |
| free_vector(moisdc,1,n);
|
} |
| free_vector(andc,1,n);
|
/* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */ |
|
|
/*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/ |
|
|
if(j<0){ |
| wav=ivector(1,imx);
|
nberr++; |
| dh=imatrix(1,lastpass-firstpass+1,1,imx);
|
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]); |
| mw=imatrix(1,lastpass-firstpass+1,1,imx);
|
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]); |
|
|
} |
| /* Concatenates waves */
|
sum=sum+j; |
| concatwav(wav, dh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
|
} |
|
|
jk= j/stepm; |
|
|
jl= j -jk*stepm; |
| Tcode=ivector(1,100);
|
ju= j -(jk+1)*stepm; |
| nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
|
if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */ |
| ncodemax[1]=1;
|
if(jl==0){ |
| if (cptcovn > 0) tricode(Tvar,nbcode,imx);
|
dh[mi][i]=jk; |
|
|
bh[mi][i]=0; |
| codtab=imatrix(1,100,1,10);
|
}else{ /* We want a negative bias in order to only have interpolation ie |
| h=0;
|
* to avoid the price of an extra matrix product in likelihood */ |
| m=pow(2,cptcoveff);
|
dh[mi][i]=jk+1; |
|
|
bh[mi][i]=ju; |
| for(k=1;k<=cptcoveff; k++){
|
} |
| for(i=1; i <=(m/pow(2,k));i++){
|
}else{ |
| for(j=1; j <= ncodemax[k]; j++){
|
if(jl <= -ju){ |
| for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
|
dh[mi][i]=jk; |
| h++;
|
bh[mi][i]=jl; /* bias is positive if real duration |
| if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
|
* is higher than the multiple of stepm and negative otherwise. |
| /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
|
*/ |
| }
|
} |
| }
|
else{ |
| }
|
dh[mi][i]=jk+1; |
| }
|
bh[mi][i]=ju; |
| /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
|
} |
| codtab[1][2]=1;codtab[2][2]=2; */
|
if(dh[mi][i]==0){ |
| /* for(i=1; i <=m ;i++){
|
dh[mi][i]=1; /* At least one step */ |
| for(k=1; k <=cptcovn; k++){
|
bh[mi][i]=ju; /* At least one step */ |
| printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
|
/* 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);*/ |
| }
|
} |
| printf("\n");
|
} /* end if mle */ |
| }
|
} |
| scanf("%d",i);*/
|
} /* end wave */ |
|
|
} |
| /* Calculates basic frequencies. Computes observed prevalence at single age
|
jmean=sum/k; |
| and prints on file fileres'p'. */
|
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 %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean); |
|
|
} |
|
|
|
| pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
|
/*********** Tricode ****************************/ |
| oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
|
void tricode(int *Tvar, int **nbcode, int imx, int *Ndum) |
| newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
|
{ |
| savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
|
/**< Uses cptcovn+2*cptcovprod as the number of covariates */ |
| oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
|
/* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 |
|
|
* Boring subroutine which should only output nbcode[Tvar[j]][k] |
| /* For Powell, parameters are in a vector p[] starting at p[1]
|
* Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2) |
| so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
|
* nbcode[Tvar[j]][1]= |
| p=param[1][1]; /* *(*(*(param +1)+1)+0) */
|
*/ |
|
|
|
| if(mle==1){
|
int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX; |
| mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
|
int modmaxcovj=0; /* Modality max of covariates j */ |
| }
|
int cptcode=0; /* Modality max of covariates j */ |
|
|
int modmincovj=0; /* Modality min of covariates j */ |
| /*--------- 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);
|
|
|
|
cptcoveff=0; |
|
|
|
| jk=1;
|
for (k=-1; k < maxncov; k++) Ndum[k]=0; |
| fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
|
for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */ |
| printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
|
|
| for(i=1,jk=1; i <=nlstate; i++){
|
/* Loop on covariates without age and products */ |
| for(k=1; k <=(nlstate+ndeath); k++){
|
for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */ |
| if (k != i)
|
for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the |
| {
|
modality of this covariate Vj*/ |
| printf("%d%d ",i,k);
|
ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i |
| fprintf(ficres,"%1d%1d ",i,k);
|
* If product of Vn*Vm, still boolean *: |
| for(j=1; j <=ncovmodel; j++){
|
* If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables |
| printf("%f ",p[jk]);
|
* 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */ |
| fprintf(ficres,"%f ",p[jk]);
|
/* Finds for covariate j, n=Tvar[j] of Vn . ij is the |
| jk++;
|
modality of the nth covariate of individual i. */ |
| }
|
if (ij > modmaxcovj) |
| printf("\n");
|
modmaxcovj=ij; |
| fprintf(ficres,"\n");
|
else if (ij < modmincovj) |
| }
|
modmincovj=ij; |
| }
|
if ((ij < -1) && (ij > NCOVMAX)){ |
| }
|
printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX ); |
| if(mle==1){
|
exit(1); |
| /* Computing hessian and covariance matrix */
|
}else |
| ftolhess=ftol; /* Usually correct */
|
Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/ |
| hesscov(matcov, p, npar, delti, ftolhess, func);
|
/* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */ |
| }
|
/*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/ |
| fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
|
/* getting the maximum value of the modality of the covariate |
| printf("# Scales (for hessian or gradient estimation)\n");
|
(should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and |
| for(i=1,jk=1; i <=nlstate; i++){
|
female is 1, then modmaxcovj=1.*/ |
| for(j=1; j <=nlstate+ndeath; j++){
|
} /* end for loop on individuals */ |
| if (j!=i) {
|
printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj); |
| fprintf(ficres,"%1d%1d",i,j);
|
cptcode=modmaxcovj; |
| printf("%1d%1d",i,j);
|
/* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */ |
| for(k=1; k<=ncovmodel;k++){
|
/*for (i=0; i<=cptcode; i++) {*/ |
| printf(" %.5e",delti[jk]);
|
for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */ |
| fprintf(ficres," %.5e",delti[jk]);
|
printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], i, Ndum[i]); |
| jk++;
|
if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */ |
| }
|
ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */ |
| printf("\n");
|
} |
| fprintf(ficres,"\n");
|
/* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for |
| }
|
historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */ |
| }
|
} /* Ndum[-1] number of undefined modalities */ |
| }
|
|
|
|
/* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */ |
| k=1;
|
/* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. |
| 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 Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; |
| 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");
|
modmincovj=3; modmaxcovj = 7; |
| for(i=1;i<=npar;i++){
|
There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; |
| /* if (k>nlstate) k=1;
|
which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; |
| i1=(i-1)/(ncovmodel*nlstate)+1;
|
defining two dummy variables: variables V1_1 and V1_2. |
| fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
|
nbcode[Tvar[j]][ij]=k; |
| printf("%s%d%d",alph[k],i1,tab[i]);*/
|
nbcode[Tvar[j]][1]=0; |
| fprintf(ficres,"%3d",i);
|
nbcode[Tvar[j]][2]=1; |
| printf("%3d",i);
|
nbcode[Tvar[j]][3]=2; |
| for(j=1; j<=i;j++){
|
*/ |
| fprintf(ficres," %.5e",matcov[i][j]);
|
ij=1; /* ij is similar to i but can jumps over null modalities */ |
| printf(" %.5e",matcov[i][j]);
|
for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */ |
| }
|
for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */ |
| fprintf(ficres,"\n");
|
/*recode from 0 */ |
| printf("\n");
|
if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */ |
| k++;
|
nbcode[Tvar[j]][ij]=k; /* stores the modality k in an array nbcode. |
| }
|
k is a modality. If we have model=V1+V1*sex |
|
|
then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */ |
| while((c=getc(ficpar))=='#' && c!= EOF){
|
ij++; |
| ungetc(c,ficpar);
|
} |
| fgets(line, MAXLINE, ficpar);
|
if (ij > ncodemax[j]) break; |
| puts(line);
|
} /* end of loop on */ |
| fputs(line,ficparo);
|
} /* end of loop on modality */ |
| }
|
} /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/ |
| ungetc(c,ficpar);
|
|
| estepm=0;
|
for (k=-1; k< maxncov; k++) Ndum[k]=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;
|
for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */ |
| if (fage <= 2) {
|
/* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ |
| bage = ageminpar;
|
ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ |
| fage = agemaxpar;
|
Ndum[ij]++; /* Might be supersed V1 + V1*age */ |
| }
|
} |
|
|
|
| fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
|
ij=1; |
| fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
|
for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */ |
| fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
|
/*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/ |
|
|
if((Ndum[i]!=0) && (i<=ncovcol)){ |
| while((c=getc(ficpar))=='#' && c!= EOF){
|
/*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/ |
| ungetc(c,ficpar);
|
Tvaraff[ij]=i; /*For printing (unclear) */ |
| fgets(line, MAXLINE, ficpar);
|
ij++; |
| puts(line);
|
}else |
| fputs(line,ficparo);
|
Tvaraff[ij]=0; |
| }
|
} |
| ungetc(c,ficpar);
|
ij--; |
|
|
cptcoveff=ij; /*Number of total covariates*/ |
| fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);
|
|
| fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
|
} |
| fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
|
|
|
|
|
| while((c=getc(ficpar))=='#' && c!= EOF){
|
/*********** Health Expectancies ****************/ |
| ungetc(c,ficpar);
|
|
| fgets(line, MAXLINE, ficpar);
|
void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] ) |
| puts(line);
|
|
| fputs(line,ficparo);
|
{ |
| }
|
/* Health expectancies, no variances */ |
| ungetc(c,ficpar);
|
int i, j, nhstepm, hstepm, h, nstepm; |
|
|
int nhstepma, nstepma; /* Decreasing with age */ |
|
|
double age, agelim, hf; |
| dateprev1=anprev1+mprev1/12.+jprev1/365.;
|
double ***p3mat; |
| dateprev2=anprev2+mprev2/12.+jprev2/365.;
|
double eip; |
|
|
|
| fscanf(ficpar,"pop_based=%d\n",&popbased);
|
pstamp(ficreseij); |
| fprintf(ficparo,"pop_based=%d\n",popbased);
|
fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n"); |
| fprintf(ficres,"pop_based=%d\n",popbased);
|
fprintf(ficreseij,"# Age"); |
|
|
for(i=1; i<=nlstate;i++){ |
| while((c=getc(ficpar))=='#' && c!= EOF){
|
for(j=1; j<=nlstate;j++){ |
| ungetc(c,ficpar);
|
fprintf(ficreseij," e%1d%1d ",i,j); |
| fgets(line, MAXLINE, ficpar);
|
} |
| puts(line);
|
fprintf(ficreseij," e%1d. ",i); |
| fputs(line,ficparo);
|
} |
| }
|
fprintf(ficreseij,"\n"); |
| ungetc(c,ficpar);
|
|
|
|
|
| fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);
|
if(estepm < stepm){ |
| fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);
|
printf ("Problem %d lower than %d\n",estepm, stepm); |
| fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);
|
} |
|
|
else hstepm=estepm; |
|
|
/* We compute the life expectancy from trapezoids spaced every estepm months |
| while((c=getc(ficpar))=='#' && c!= EOF){
|
* This is mainly to measure the difference between two models: for example |
| ungetc(c,ficpar);
|
* if stepm=24 months pijx are given only every 2 years and by summing them |
| fgets(line, MAXLINE, ficpar);
|
* we are calculating an estimate of the Life Expectancy assuming a linear |
| puts(line);
|
* progression in between and thus overestimating or underestimating according |
| fputs(line,ficparo);
|
* 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 |
| ungetc(c,ficpar);
|
* to compare the new estimate of Life expectancy with the same linear |
|
|
* hypothesis. A more precise result, taking into account a more precise |
| fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
|
* curvature will be obtained if estepm is as small as stepm. */ |
| fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
|
|
| fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
|
/* 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. |
| freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
|
nhstepm is the number of hstepm from age to agelim |
|
|
nstepm is the number of stepm from age to agelin. |
| /*------------ gnuplot -------------*/
|
Look at hpijx to understand the reason of that which relies in memory size |
| strcpy(optionfilegnuplot,optionfilefiname);
|
and note for a fixed period like estepm months */ |
| strcat(optionfilegnuplot,".gp");
|
/* We decided (b) to get a life expectancy respecting the most precise curvature of the |
| if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
|
survival function given by stepm (the optimization length). Unfortunately it |
| printf("Problem with file %s",optionfilegnuplot);
|
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 |
| fclose(ficgp);
|
results. So we changed our mind and took the option of the best precision. |
| printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
|
*/ |
| /*--------- index.htm --------*/
|
hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ |
|
|
|
| strcpy(optionfilehtm,optionfile);
|
agelim=AGESUP; |
| strcat(optionfilehtm,".htm");
|
/* If stepm=6 months */ |
| if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
|
/* Computed by stepm unit matrices, product of hstepm matrices, stored |
| printf("Problem with %s \n",optionfilehtm), exit(0);
|
in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */ |
| }
|
|
|
|
/* nhstepm age range expressed in number of stepm */ |
| fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
|
nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */ |
| Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
|
/* Typically if 20 years nstepm = 20*12/6=40 stepm */ |
| \n
|
/* if (stepm >= YEARM) hstepm=1;*/ |
| Total number of observations=%d <br>\n
|
nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ |
| Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
|
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
| <hr size=\"2\" color=\"#EC5E5E\">
|
|
| <ul><li>Parameter files<br>\n
|
for (age=bage; age<=fage; age ++){ |
| - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
|
nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */ |
| - Gnuplot file name: <a href=\"%s\">%s</a><br></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);
|
/* Typically if 20 years nstepm = 20*12/6=40 stepm */ |
| fclose(fichtm);
|
/* if (stepm >= YEARM) hstepm=1;*/ |
|
|
nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */ |
| printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
|
|
|
|
/* If stepm=6 months */ |
| /*------------ free_vector -------------*/
|
/* Computed by stepm unit matrices, product of hstepma matrices, stored |
| chdir(path);
|
in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */ |
|
|
|
| free_ivector(wav,1,imx);
|
hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij); |
| free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
|
|
| free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
|
hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ |
| free_ivector(num,1,n);
|
|
| free_vector(agedc,1,n);
|
printf("%d|",(int)age);fflush(stdout); |
| /*free_matrix(covar,1,NCOVMAX,1,n);*/
|
fprintf(ficlog,"%d|",(int)age);fflush(ficlog); |
| fclose(ficparo);
|
|
| fclose(ficres);
|
/* Computing expectancies */ |
|
|
for(i=1; i<=nlstate;i++) |
|
|
for(j=1; j<=nlstate;j++) |
| /*--------------- Prevalence limit --------------*/
|
for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){ |
|
|
eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf; |
| strcpy(filerespl,"pl");
|
|
| strcat(filerespl,fileres);
|
/* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/ |
| if((ficrespl=fopen(filerespl,"w"))==NULL) {
|
|
| printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;
|
} |
| }
|
|
| printf("Computing prevalence limit: result on file '%s' \n", filerespl);
|
fprintf(ficreseij,"%3.0f",age ); |
| fprintf(ficrespl,"#Prevalence limit\n");
|
for(i=1; i<=nlstate;i++){ |
| fprintf(ficrespl,"#Age ");
|
eip=0; |
| for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
|
for(j=1; j<=nlstate;j++){ |
| fprintf(ficrespl,"\n");
|
eip +=eij[i][j][(int)age]; |
|
|
fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] ); |
| prlim=matrix(1,nlstate,1,nlstate);
|
} |
| pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
|
fprintf(ficreseij,"%9.4f", eip ); |
| oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
|
} |
| newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
|
fprintf(ficreseij,"\n"); |
| savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
|
|
| oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
|
} |
| k=0;
|
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
| agebase=ageminpar;
|
printf("\n"); |
| agelim=agemaxpar;
|
fprintf(ficlog,"\n"); |
| ftolpl=1.e-10;
|
|
| i1=cptcoveff;
|
} |
| if (cptcovn < 1){i1=1;}
|
|
|
|
void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] ) |
| for(cptcov=1;cptcov<=i1;cptcov++){
|
|
| for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
|
{ |
| k=k+1;
|
/* Covariances of health expectancies eij and of total life expectancies according |
| /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
|
to initial status i, ei. . |
| fprintf(ficrespl,"\n#******");
|
*/ |
| for(j=1;j<=cptcoveff;j++)
|
int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji; |
| fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
|
int nhstepma, nstepma; /* Decreasing with age */ |
| fprintf(ficrespl,"******\n");
|
double age, agelim, hf; |
|
|
double ***p3matp, ***p3matm, ***varhe; |
| for (age=agebase; age<=agelim; age++){
|
double **dnewm,**doldm; |
| prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
|
double *xp, *xm; |
| fprintf(ficrespl,"%.0f",age );
|
double **gp, **gm; |
| for(i=1; i<=nlstate;i++)
|
double ***gradg, ***trgradg; |
| fprintf(ficrespl," %.5f", prlim[i][i]);
|
int theta; |
| fprintf(ficrespl,"\n");
|
|
| }
|
double eip, vip; |
| }
|
|
| }
|
varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage); |
| fclose(ficrespl);
|
xp=vector(1,npar); |
|
|
xm=vector(1,npar); |
| /*------------- h Pij x at various ages ------------*/
|
dnewm=matrix(1,nlstate*nlstate,1,npar); |
|
|
doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate); |
| strcpy(filerespij,"pij"); strcat(filerespij,fileres);
|
|
| if((ficrespij=fopen(filerespij,"w"))==NULL) {
|
pstamp(ficresstdeij); |
| printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
|
fprintf(ficresstdeij,"# Health expectancies with standard errors\n"); |
| }
|
fprintf(ficresstdeij,"# Age"); |
| printf("Computing pij: result on file '%s' \n", filerespij);
|
for(i=1; i<=nlstate;i++){ |
|
|
for(j=1; j<=nlstate;j++) |
| stepsize=(int) (stepm+YEARM-1)/YEARM;
|
fprintf(ficresstdeij," e%1d%1d (SE)",i,j); |
| /*if (stepm<=24) stepsize=2;*/
|
fprintf(ficresstdeij," e%1d. ",i); |
|
|
} |
| agelim=AGESUP;
|
fprintf(ficresstdeij,"\n"); |
| hstepm=stepsize*YEARM; /* Every year of age */
|
|
| hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
|
pstamp(ficrescveij); |
|
|
fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n"); |
| k=0;
|
fprintf(ficrescveij,"# Age"); |
| for(cptcov=1;cptcov<=i1;cptcov++){
|
for(i=1; i<=nlstate;i++) |
| for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
|
for(j=1; j<=nlstate;j++){ |
| k=k+1;
|
cptj= (j-1)*nlstate+i; |
| fprintf(ficrespij,"\n#****** ");
|
for(i2=1; i2<=nlstate;i2++) |
| for(j=1;j<=cptcoveff;j++)
|
for(j2=1; j2<=nlstate;j2++){ |
| fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
|
cptj2= (j2-1)*nlstate+i2; |
| fprintf(ficrespij,"******\n");
|
if(cptj2 <= cptj) |
|
|
fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2); |
| 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 */
|
fprintf(ficrescveij,"\n"); |
| p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
|
| oldm=oldms;savm=savms;
|
if(estepm < stepm){ |
| hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
|
printf ("Problem %d lower than %d\n",estepm, stepm); |
| fprintf(ficrespij,"# Age");
|
} |
| for(i=1; i<=nlstate;i++)
|
else hstepm=estepm; |
| for(j=1; j<=nlstate+ndeath;j++)
|
/* We compute the life expectancy from trapezoids spaced every estepm months |
| fprintf(ficrespij," %1d-%1d",i,j);
|
* This is mainly to measure the difference between two models: for example |
| fprintf(ficrespij,"\n");
|
* if stepm=24 months pijx are given only every 2 years and by summing them |
| for (h=0; h<=nhstepm; h++){
|
* we are calculating an estimate of the Life Expectancy assuming a linear |
| fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
|
* progression in between and thus overestimating or underestimating according |
| for(i=1; i<=nlstate;i++)
|
* to the curvature of the survival function. If, for the same date, we |
| for(j=1; j<=nlstate+ndeath;j++)
|
* estimate the model with stepm=1 month, we can keep estepm to 24 months |
| fprintf(ficrespij," %.5f", p3mat[i][j][h]);
|
* to compare the new estimate of Life expectancy with the same linear |
| fprintf(ficrespij,"\n");
|
* hypothesis. A more precise result, taking into account a more precise |
| }
|
* curvature will be obtained if estepm is as small as stepm. */ |
| free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
|
|
| fprintf(ficrespij,"\n");
|
/* For example we decided to compute the life expectancy with the smallest unit */ |
| }
|
/* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. |
| }
|
nhstepm is the number of hstepm from age to agelim |
| }
|
nstepm is the number of stepm from age to agelin. |
|
|
Look at hpijx to understand the reason of that which relies in memory size |
| varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
|
and note for a fixed period like estepm months */ |
|
|
/* We decided (b) to get a life expectancy respecting the most precise curvature of the |
| fclose(ficrespij);
|
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 |
| /*---------- Forecasting ------------------*/
|
results. So we changed our mind and took the option of the best precision. |
| if((stepm == 1) && (strcmp(model,".")==0)){
|
*/ |
| prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
|
hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ |
| if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
|
|
| }
|
/* If stepm=6 months */ |
| else{
|
/* nhstepm age range expressed in number of stepm */ |
| erreur=108;
|
agelim=AGESUP; |
| 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);
|
nstepm=(int) rint((agelim-bage)*YEARM/stepm); |
| }
|
/* Typically if 20 years nstepm = 20*12/6=40 stepm */ |
|
|
/* if (stepm >= YEARM) hstepm=1;*/ |
|
|
nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ |
| /*---------- Health expectancies and variances ------------*/
|
|
|
|
p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
| strcpy(filerest,"t");
|
p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
| strcat(filerest,fileres);
|
gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate); |
| if((ficrest=fopen(filerest,"w"))==NULL) {
|
trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar); |
| printf("Problem with total LE resultfile: %s\n", filerest);goto end;
|
gp=matrix(0,nhstepm,1,nlstate*nlstate); |
| }
|
gm=matrix(0,nhstepm,1,nlstate*nlstate); |
| printf("Computing Total LEs with variances: file '%s' \n", filerest);
|
|
|
|
for (age=bage; age<=fage; age ++){ |
|
|
nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */ |
| strcpy(filerese,"e");
|
/* Typically if 20 years nstepm = 20*12/6=40 stepm */ |
| strcat(filerese,fileres);
|
/* if (stepm >= YEARM) hstepm=1;*/ |
| if((ficreseij=fopen(filerese,"w"))==NULL) {
|
nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */ |
| printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
|
|
| }
|
/* If stepm=6 months */ |
| printf("Computing Health Expectancies: result on file '%s' \n", filerese);
|
/* Computed by stepm unit matrices, product of hstepma matrices, stored |
|
|
in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */ |
| strcpy(fileresv,"v");
|
|
| strcat(fileresv,fileres);
|
hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ |
| if((ficresvij=fopen(fileresv,"w"))==NULL) {
|
|
| printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
|
/* Computing Variances of health expectancies */ |
| }
|
/* Gradient is computed with plus gp and minus gm. Code is duplicated in order to |
| printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
|
decrease memory allocation */ |
| calagedate=-1;
|
for(theta=1; theta <=npar; theta++){ |
| prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
|
for(i=1; i<=npar; i++){ |
|
|
xp[i] = x[i] + (i==theta ?delti[theta]:0); |
| k=0;
|
xm[i] = x[i] - (i==theta ?delti[theta]:0); |
| for(cptcov=1;cptcov<=i1;cptcov++){
|
} |
| for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
|
hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij); |
| k=k+1;
|
hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij); |
| fprintf(ficrest,"\n#****** ");
|
|
| for(j=1;j<=cptcoveff;j++)
|
for(j=1; j<= nlstate; j++){ |
| fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
|
for(i=1; i<=nlstate; i++){ |
| fprintf(ficrest,"******\n");
|
for(h=0; h<=nhstepm-1; h++){ |
|
|
gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.; |
| fprintf(ficreseij,"\n#****** ");
|
gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.; |
| 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(ij=1; ij<= nlstate*nlstate; ij++) |
| for(j=1;j<=cptcoveff;j++)
|
for(h=0; h<=nhstepm-1; h++){ |
| fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
|
gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta]; |
| fprintf(ficresvij,"******\n");
|
} |
|
|
}/* End theta */ |
| eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
|
|
| oldm=oldms;savm=savms;
|
|
| evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
|
for(h=0; h<=nhstepm-1; h++) |
|
|
for(j=1; j<=nlstate*nlstate;j++) |
| vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
|
for(theta=1; theta <=npar; theta++) |
| oldm=oldms;savm=savms;
|
trgradg[h][j][theta]=gradg[h][theta][j]; |
| varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);
|
|
|
|
|
|
|
for(ij=1;ij<=nlstate*nlstate;ij++) |
|
|
for(ji=1;ji<=nlstate*nlstate;ji++) |
| fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
|
varhe[ij][ji][(int)age] =0.; |
| for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
|
|
| fprintf(ficrest,"\n");
|
printf("%d|",(int)age);fflush(stdout); |
|
|
fprintf(ficlog,"%d|",(int)age);fflush(ficlog); |
| epj=vector(1,nlstate+1);
|
for(h=0;h<=nhstepm-1;h++){ |
| for(age=bage; age <=fage ;age++){
|
for(k=0;k<=nhstepm-1;k++){ |
| prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
|
matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov); |
| if (popbased==1) {
|
matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]); |
| for(i=1; i<=nlstate;i++)
|
for(ij=1;ij<=nlstate*nlstate;ij++) |
| prlim[i][i]=probs[(int)age][i][k];
|
for(ji=1;ji<=nlstate*nlstate;ji++) |
| }
|
varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf; |
|
|
} |
| fprintf(ficrest," %4.0f",age);
|
} |
| for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
|
|
| for(i=1, epj[j]=0.;i <=nlstate;i++) {
|
/* Computing expectancies */ |
| epj[j] += prlim[i][i]*eij[i][j][(int)age];
|
hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij); |
| /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
|
for(i=1; i<=nlstate;i++) |
| }
|
for(j=1; j<=nlstate;j++) |
| epj[nlstate+1] +=epj[j];
|
for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){ |
| }
|
eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf; |
|
|
|
| for(i=1, vepp=0.;i <=nlstate;i++)
|
/* 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]);*/ |
| 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(ficresstdeij,"%3.0f",age ); |
| fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
|
for(i=1; i<=nlstate;i++){ |
| }
|
eip=0.; |
| fprintf(ficrest,"\n");
|
vip=0.; |
| }
|
for(j=1; j<=nlstate;j++){ |
| }
|
eip += eij[i][j][(int)age]; |
| }
|
for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */ |
| free_matrix(mint,1,maxwav,1,n);
|
vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age]; |
| free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);
|
fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) ); |
| free_vector(weight,1,n);
|
} |
| fclose(ficreseij);
|
fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip)); |
| fclose(ficresvij);
|
} |
| fclose(ficrest);
|
fprintf(ficresstdeij,"\n"); |
| fclose(ficpar);
|
|
| free_vector(epj,1,nlstate+1);
|
fprintf(ficrescveij,"%3.0f",age ); |
|
|
for(i=1; i<=nlstate;i++) |
| /*------- Variance limit prevalence------*/
|
for(j=1; j<=nlstate;j++){ |
|
|
cptj= (j-1)*nlstate+i; |
| strcpy(fileresvpl,"vpl");
|
for(i2=1; i2<=nlstate;i2++) |
| strcat(fileresvpl,fileres);
|
for(j2=1; j2<=nlstate;j2++){ |
| if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
|
cptj2= (j2-1)*nlstate+i2; |
| printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);
|
if(cptj2 <= cptj) |
| exit(0);
|
fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]); |
| }
|
} |
| printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);
|
} |
|
|
fprintf(ficrescveij,"\n"); |
| k=0;
|
|
| for(cptcov=1;cptcov<=i1;cptcov++){
|
} |
| for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
|
free_matrix(gm,0,nhstepm,1,nlstate*nlstate); |
| k=k+1;
|
free_matrix(gp,0,nhstepm,1,nlstate*nlstate); |
| fprintf(ficresvpl,"\n#****** ");
|
free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate); |
| for(j=1;j<=cptcoveff;j++)
|
free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar); |
| fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
|
free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
| fprintf(ficresvpl,"******\n");
|
free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
|
|
printf("\n"); |
| varpl=matrix(1,nlstate,(int) bage, (int) fage);
|
fprintf(ficlog,"\n"); |
| oldm=oldms;savm=savms;
|
|
| varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
|
free_vector(xm,1,npar); |
| }
|
free_vector(xp,1,npar); |
| }
|
free_matrix(dnewm,1,nlstate*nlstate,1,npar); |
|
|
free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate); |
| fclose(ficresvpl);
|
free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage); |
|
|
} |
| /*---------- End : free ----------------*/
|
|
| free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
|
/************ Variance ******************/ |
|
|
void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[]) |
| free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
|
{ |
| free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
|
/* Variance of health expectancies */ |
|
|
/* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/ |
|
|
/* double **newm;*/ |
| free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
|
/* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/ |
| free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
|
|
| free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
|
int movingaverage(); |
| free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
|
double **dnewm,**doldm; |
|
|
double **dnewmp,**doldmp; |
| free_matrix(matcov,1,npar,1,npar);
|
int i, j, nhstepm, hstepm, h, nstepm ; |
| free_vector(delti,1,npar);
|
int k; |
| free_matrix(agev,1,maxwav,1,imx);
|
double *xp; |
| free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
|
double **gp, **gm; /* for var eij */ |
|
|
double ***gradg, ***trgradg; /*for var eij */ |
| fprintf(fichtm,"\n</body>");
|
double **gradgp, **trgradgp; /* for var p point j */ |
| fclose(fichtm);
|
double *gpp, *gmp; /* for var p point j */ |
| fclose(ficgp);
|
double **varppt; /* for var p point j nlstate to nlstate+ndeath */ |
|
|
double ***p3mat; |
|
|
double age,agelim, hf; |
| if(erreur >0)
|
double ***mobaverage; |
| printf("End of Imach with error or warning %d\n",erreur);
|
int theta; |
| else printf("End of Imach\n");
|
char digit[4]; |
| /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
|
char digitp[25]; |
|
|
|
| /* 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);*/
|
char fileresprobmorprev[FILENAMELENGTH]; |
| /*printf("Total time was %d uSec.\n", total_usecs);*/
|
|
| /*------ End -----------*/
|
if(popbased==1){ |
|
|
if(mobilav!=0) |
|
|
strcpy(digitp,"-populbased-mobilav-"); |
| end:
|
else strcpy(digitp,"-populbased-nomobil-"); |
| #ifdef windows
|
} |
| /* chdir(pathcd);*/
|
else |
| #endif
|
strcpy(digitp,"-stablbased-"); |
| /*system("wgnuplot graph.plt");*/
|
|
| /*system("../gp37mgw/wgnuplot graph.plt");*/
|
if (mobilav!=0) { |
| /*system("cd ../gp37mgw");*/
|
mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
| /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
|
if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ |
| strcpy(plotcmd,GNUPLOTPROGRAM);
|
fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); |
| strcat(plotcmd," ");
|
printf(" Error in movingaverage mobilav=%d\n",mobilav); |
| strcat(plotcmd,optionfilegnuplot);
|
} |
| system(plotcmd);
|
} |
|
|
|
| #ifdef windows
|
strcpy(fileresprobmorprev,"prmorprev"); |
| while (z[0] != 'q') {
|
sprintf(digit,"%-d",ij); |
| /* chdir(path); */
|
/*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/ |
| printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
|
strcat(fileresprobmorprev,digit); /* Tvar to be done */ |
| scanf("%s",z);
|
strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */ |
| if (z[0] == 'c') system("./imach");
|
strcat(fileresprobmorprev,fileres); |
| else if (z[0] == 'e') system(optionfilehtm);
|
if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) { |
| else if (z[0] == 'g') system(plotcmd);
|
printf("Problem with resultfile: %s\n", fileresprobmorprev); |
| else if (z[0] == 'q') exit(0);
|
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev); |
| }
|
} |
| #endif
|
printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); |
| }
|
|
|
|
fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); |
|
|
pstamp(ficresprobmorprev); |
| |
fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm); |
| |
fprintf(ficresprobmorprev,"# Age cov=%-d",ij); |
| |
for(j=nlstate+1; j<=(nlstate+ndeath);j++){ |
| |
fprintf(ficresprobmorprev," p.%-d SE",j); |
| |
for(i=1; i<=nlstate;i++) |
| |
fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j); |
| |
} |
| |
fprintf(ficresprobmorprev,"\n"); |
| |
fprintf(ficgp,"\n# Routine varevsij"); |
| |
/* fprintf(fichtm, "#Local time at start: %s", strstart);*/ |
| |
fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n"); |
| |
fprintf(fichtm,"\n<br>%s <br>\n",digitp); |
| |
/* } */ |
| |
varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); |
| |
pstamp(ficresvij); |
| |
fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are "); |
| |
if(popbased==1) |
| |
fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav); |
| |
else |
| |
fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n"); |
| |
fprintf(ficresvij,"# Age"); |
| |
for(i=1; i<=nlstate;i++) |
| |
for(j=1; j<=nlstate;j++) |
| |
fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j); |
| |
fprintf(ficresvij,"\n"); |
| |
|
| |
xp=vector(1,npar); |
| |
dnewm=matrix(1,nlstate,1,npar); |
| |
doldm=matrix(1,nlstate,1,nlstate); |
| |
dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar); |
| |
doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); |
| |
|
| |
gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath); |
| |
gpp=vector(nlstate+1,nlstate+ndeath); |
| |
gmp=vector(nlstate+1,nlstate+ndeath); |
| |
trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/ |
| |
|
| |
if(estepm < stepm){ |
| |
printf ("Problem %d lower than %d\n",estepm, stepm); |
| |
} |
| |
else hstepm=estepm; |
| |
/* For example we decided to compute the life expectancy with the smallest unit */ |
| |
/* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. |
| |
nhstepm is the number of hstepm from age to agelim |
| |
nstepm is the number of stepm from age to agelin. |
| |
Look at function hpijx to understand why (it is linked to memory size questions) */ |
| |
/* We decided (b) to get a life expectancy respecting the most precise curvature of the |
| |
survival function given by stepm (the optimization length). Unfortunately it |
| |
means that if the survival funtion is printed every two years of age and if |
| |
you sum them up and add 1 year (area under the trapezoids) you won't get the same |
| |
results. So we changed our mind and took the option of the best precision. |
| |
*/ |
| |
hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ |
| |
agelim = AGESUP; |
| |
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 */ |
| |
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
| |
gradg=ma3x(0,nhstepm,1,npar,1,nlstate); |
| |
gp=matrix(0,nhstepm,1,nlstate); |
| |
gm=matrix(0,nhstepm,1,nlstate); |
| |
|
| |
|
| |
for(theta=1; theta <=npar; theta++){ |
| |
for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/ |
| |
xp[i] = x[i] + (i==theta ?delti[theta]:0); |
| |
} |
| |
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); |
| |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); |
| |
|
| |
if (popbased==1) { |
| |
if(mobilav ==0){ |
| |
for(i=1; i<=nlstate;i++) |
| |
prlim[i][i]=probs[(int)age][i][ij]; |
| |
}else{ /* mobilav */ |
| |
for(i=1; i<=nlstate;i++) |
| |
prlim[i][i]=mobaverage[(int)age][i][ij]; |
| |
} |
| |
} |
| |
|
| |
for(j=1; j<= nlstate; j++){ |
| |
for(h=0; h<=nhstepm; h++){ |
| |
for(i=1, gp[h][j]=0.;i<=nlstate;i++) |
| |
gp[h][j] += prlim[i][i]*p3mat[i][j][h]; |
| |
} |
| |
} |
| |
/* This for computing probability of death (h=1 means |
| |
computed over hstepm matrices product = hstepm*stepm months) |
| |
as a weighted average of prlim. |
| |
*/ |
| |
for(j=nlstate+1;j<=nlstate+ndeath;j++){ |
| |
for(i=1,gpp[j]=0.; i<= nlstate; i++) |
| |
gpp[j] += prlim[i][i]*p3mat[i][j][1]; |
| |
} |
| |
/* end probability of death */ |
| |
|
| |
for(i=1; i<=npar; i++) /* Computes gradient x - delta */ |
| |
xp[i] = x[i] - (i==theta ?delti[theta]:0); |
| |
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); |
| |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); |
| |
|
| |
if (popbased==1) { |
| |
if(mobilav ==0){ |
| |
for(i=1; i<=nlstate;i++) |
| |
prlim[i][i]=probs[(int)age][i][ij]; |
| |
}else{ /* mobilav */ |
| |
for(i=1; i<=nlstate;i++) |
| |
prlim[i][i]=mobaverage[(int)age][i][ij]; |
| |
} |
| |
} |
| |
|
| |
for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */ |
| |
for(h=0; h<=nhstepm; h++){ |
| |
for(i=1, gm[h][j]=0.;i<=nlstate;i++) |
| |
gm[h][j] += prlim[i][i]*p3mat[i][j][h]; |
| |
} |
| |
} |
| |
/* This for computing probability of death (h=1 means |
| |
computed over hstepm matrices product = hstepm*stepm months) |
| |
as a weighted average of prlim. |
| |
*/ |
| |
for(j=nlstate+1;j<=nlstate+ndeath;j++){ |
| |
for(i=1,gmp[j]=0.; i<= nlstate; i++) |
| |
gmp[j] += prlim[i][i]*p3mat[i][j][1]; |
| |
} |
| |
/* end probability of death */ |
| |
|
| |
for(j=1; j<= nlstate; j++) /* vareij */ |
| |
for(h=0; h<=nhstepm; h++){ |
| |
gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta]; |
| |
} |
| |
|
| |
for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */ |
| |
gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta]; |
| |
} |
| |
|
| |
} /* End theta */ |
| |
|
| |
trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */ |
| |
|
| |
for(h=0; h<=nhstepm; h++) /* veij */ |
| |
for(j=1; j<=nlstate;j++) |
| |
for(theta=1; theta <=npar; theta++) |
| |
trgradg[h][j][theta]=gradg[h][theta][j]; |
| |
|
| |
for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */ |
| |
for(theta=1; theta <=npar; theta++) |
| |
trgradgp[j][theta]=gradgp[theta][j]; |
| |
|
| |
|
| |
hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ |
| |
for(i=1;i<=nlstate;i++) |
| |
for(j=1;j<=nlstate;j++) |
| |
vareij[i][j][(int)age] =0.; |
| |
|
| |
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]); |
| |
for(i=1;i<=nlstate;i++) |
| |
for(j=1;j<=nlstate;j++) |
| |
vareij[i][j][(int)age] += doldm[i][j]*hf*hf; |
| |
} |
| |
} |
| |
|
| |
/* pptj */ |
| |
matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov); |
| |
matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp); |
| |
for(j=nlstate+1;j<=nlstate+ndeath;j++) |
| |
for(i=nlstate+1;i<=nlstate+ndeath;i++) |
| |
varppt[j][i]=doldmp[j][i]; |
| |
/* end ppptj */ |
| |
/* x centered again */ |
| |
hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij); |
| |
prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij); |
| |
|
| |
if (popbased==1) { |
| |
if(mobilav ==0){ |
| |
for(i=1; i<=nlstate;i++) |
| |
prlim[i][i]=probs[(int)age][i][ij]; |
| |
}else{ /* mobilav */ |
| |
for(i=1; i<=nlstate;i++) |
| |
prlim[i][i]=mobaverage[(int)age][i][ij]; |
| |
} |
| |
} |
| |
|
| |
/* This for computing probability of death (h=1 means |
| |
computed over hstepm (estepm) matrices product = hstepm*stepm months) |
| |
as a weighted average of prlim. |
| |
*/ |
| |
for(j=nlstate+1;j<=nlstate+ndeath;j++){ |
| |
for(i=1,gmp[j]=0.;i<= nlstate; i++) |
| |
gmp[j] += prlim[i][i]*p3mat[i][j][1]; |
| |
} |
| |
/* end probability of death */ |
| |
|
| |
fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij); |
| |
for(j=nlstate+1; j<=(nlstate+ndeath);j++){ |
| |
fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j])); |
| |
for(i=1; i<=nlstate;i++){ |
| |
fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]); |
| |
} |
| |
} |
| |
fprintf(ficresprobmorprev,"\n"); |
| |
|
| |
fprintf(ficresvij,"%.0f ",age ); |
| |
for(i=1; i<=nlstate;i++) |
| |
for(j=1; j<=nlstate;j++){ |
| |
fprintf(ficresvij," %.4f", vareij[i][j][(int)age]); |
| |
} |
| |
fprintf(ficresvij,"\n"); |
| |
free_matrix(gp,0,nhstepm,1,nlstate); |
| |
free_matrix(gm,0,nhstepm,1,nlstate); |
| |
free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate); |
| |
free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar); |
| |
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
| |
} /* End age */ |
| |
free_vector(gpp,nlstate+1,nlstate+ndeath); |
| |
free_vector(gmp,nlstate+1,nlstate+ndeath); |
| |
free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath); |
| |
free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/ |
| |
fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); |
| |
/* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */ |
| |
fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";"); |
| |
/* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */ |
| |
/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */ |
| |
/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */ |
| |
fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev)); |
| |
fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev)); |
| |
fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 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)); |
| |
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); |
| |
/* 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); |
| |
*/ |
| |
/* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */ |
| |
fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit); |
| |
|
| |
free_vector(xp,1,npar); |
| |
free_matrix(doldm,1,nlstate,1,nlstate); |
| |
free_matrix(dnewm,1,nlstate,1,npar); |
| |
free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); |
| |
free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar); |
| |
free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); |
| |
if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
| |
fclose(ficresprobmorprev); |
| |
fflush(ficgp); |
| |
fflush(fichtm); |
| |
} /* end varevsij */ |
| |
|
| |
/************ Variance of prevlim ******************/ |
| |
void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[]) |
| |
{ |
| |
/* Variance of prevalence limit */ |
| |
/* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/ |
| |
|
| |
double **dnewm,**doldm; |
| |
int i, j, nhstepm, hstepm; |
| |
double *xp; |
| |
double *gp, *gm; |
| |
double **gradg, **trgradg; |
| |
double age,agelim; |
| |
int theta; |
| |
|
| |
pstamp(ficresvpl); |
| |
fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n"); |
| |
fprintf(ficresvpl,"# Age"); |
| |
for(i=1; i<=nlstate;i++) |
| |
fprintf(ficresvpl," %1d-%1d",i,i); |
| |
fprintf(ficresvpl,"\n"); |
| |
|
| |
xp=vector(1,npar); |
| |
dnewm=matrix(1,nlstate,1,npar); |
| |
doldm=matrix(1,nlstate,1,nlstate); |
| |
|
| |
hstepm=1*YEARM; /* Every year of age */ |
| |
hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ |
| |
agelim = AGESUP; |
| |
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; |
| |
nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */ |
| |
gradg=matrix(1,npar,1,nlstate); |
| |
gp=vector(1,nlstate); |
| |
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); |
| |
} |
| |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); |
| |
for(i=1;i<=nlstate;i++) |
| |
gp[i] = prlim[i][i]; |
| |
|
| |
for(i=1; i<=npar; i++) /* Computes gradient */ |
| |
xp[i] = x[i] - (i==theta ?delti[theta]:0); |
| |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); |
| |
for(i=1;i<=nlstate;i++) |
| |
gm[i] = prlim[i][i]; |
| |
|
| |
for(i=1;i<=nlstate;i++) |
| |
gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta]; |
| |
} /* End theta */ |
| |
|
| |
trgradg =matrix(1,nlstate,1,npar); |
| |
|
| |
for(j=1; j<=nlstate;j++) |
| |
for(theta=1; theta <=npar; theta++) |
| |
trgradg[j][theta]=gradg[theta][j]; |
| |
|
| |
for(i=1;i<=nlstate;i++) |
| |
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 */ |
| |
|
| |
fprintf(ficresvpl,"%.0f ",age ); |
| |
for(i=1; i<=nlstate;i++) |
| |
fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age])); |
| |
fprintf(ficresvpl,"\n"); |
| |
free_vector(gp,1,nlstate); |
| |
free_vector(gm,1,nlstate); |
| |
free_matrix(gradg,1,npar,1,nlstate); |
| |
free_matrix(trgradg,1,nlstate,1,npar); |
| |
} /* End age */ |
| |
|
| |
free_vector(xp,1,npar); |
| |
free_matrix(doldm,1,nlstate,1,npar); |
| |
free_matrix(dnewm,1,nlstate,1,nlstate); |
| |
|
| |
} |
| |
|
| |
/************ 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 i, j=0, k1, l1, tj; |
| |
int k2, l2, j1, z1; |
| |
int k=0, l; |
| |
int first=1, first1, first2; |
| |
double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp; |
| |
double **dnewm,**doldm; |
| |
double *xp; |
| |
double *gp, *gm; |
| |
double **gradg, **trgradg; |
| |
double **mu; |
| |
double age, cov[NCOVMAX+1]; |
| |
double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */ |
| |
int theta; |
| |
char fileresprob[FILENAMELENGTH]; |
| |
char fileresprobcov[FILENAMELENGTH]; |
| |
char fileresprobcor[FILENAMELENGTH]; |
| |
double ***varpij; |
| |
|
| |
strcpy(fileresprob,"prob"); |
| |
strcat(fileresprob,fileres); |
| |
if((ficresprob=fopen(fileresprob,"w"))==NULL) { |
| |
printf("Problem with resultfile: %s\n", fileresprob); |
| |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob); |
| |
} |
| |
strcpy(fileresprobcov,"probcov"); |
| |
strcat(fileresprobcov,fileres); |
| |
if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) { |
| |
printf("Problem with resultfile: %s\n", fileresprobcov); |
| |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov); |
| |
} |
| |
strcpy(fileresprobcor,"probcor"); |
| |
strcat(fileresprobcor,fileres); |
| |
if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) { |
| |
printf("Problem with resultfile: %s\n", fileresprobcor); |
| |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor); |
| |
} |
| |
printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob); |
| |
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); |
| |
printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); |
| |
fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); |
| |
pstamp(ficresprob); |
| |
fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n"); |
| |
fprintf(ficresprob,"# Age"); |
| |
pstamp(ficresprobcov); |
| |
fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n"); |
| |
fprintf(ficresprobcov,"# Age"); |
| |
pstamp(ficresprobcor); |
| |
fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n"); |
| |
fprintf(ficresprobcor,"# Age"); |
| |
|
| |
|
| |
for(i=1; i<=nlstate;i++) |
| |
for(j=1; j<=(nlstate+ndeath);j++){ |
| |
fprintf(ficresprob," p%1d-%1d (SE)",i,j); |
| |
fprintf(ficresprobcov," p%1d-%1d ",i,j); |
| |
fprintf(ficresprobcor," p%1d-%1d ",i,j); |
| |
} |
| |
/* fprintf(ficresprob,"\n"); |
| |
fprintf(ficresprobcov,"\n"); |
| |
fprintf(ficresprobcor,"\n"); |
| |
*/ |
| |
xp=vector(1,npar); |
| |
dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); |
| |
doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath)); |
| |
mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage); |
| |
varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage); |
| |
first=1; |
| |
fprintf(ficgp,"\n# Routine varprob"); |
| |
fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n"); |
| |
fprintf(fichtm,"\n"); |
| |
|
| |
fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov); |
| |
fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\ |
| |
file %s<br>\n",optionfilehtmcov); |
| |
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.\ |
| |
They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n"); |
| |
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. \ |
| |
It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \ |
| |
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>\ |
| |
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>\ |
| |
To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n"); |
| |
|
| |
cov[1]=1; |
| |
/* tj=cptcoveff; */ |
| |
tj = (int) pow(2,cptcoveff); |
| |
if (cptcovn<1) {tj=1;ncodemax[1]=1;} |
| |
j1=0; |
| |
for(j1=1; j1<=tj;j1++){ |
| |
/*for(i1=1; i1<=ncodemax[t];i1++){ */ |
| |
/*j1++;*/ |
| |
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]]); |
| |
fprintf(ficresprob, "**********\n#\n"); |
| |
fprintf(ficresprobcov, "\n#********** Variable "); |
| |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); |
| |
fprintf(ficresprobcov, "**********\n#\n"); |
| |
|
| |
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"); |
| |
|
| |
|
| |
fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable "); |
| |
for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); |
| |
fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">"); |
| |
|
| |
fprintf(ficresprobcor, "\n#********** Variable "); |
| |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); |
| |
fprintf(ficresprobcor, "**********\n#"); |
| |
} |
| |
|
| |
gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath)); |
| |
trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); |
| |
gp=vector(1,(nlstate)*(nlstate+ndeath)); |
| |
gm=vector(1,(nlstate)*(nlstate+ndeath)); |
| |
for (age=bage; age<=fage; age ++){ |
| |
cov[2]=age; |
| |
if(nagesqr==1) |
| |
cov[3]= age*age; |
| |
for (k=1; k<=cptcovn;k++) { |
| |
cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4 |
| |
* 1 1 1 1 1 |
| |
* 2 2 1 1 1 |
| |
* 3 1 2 1 1 |
| |
*/ |
| |
/* nbcode[1][1]=0 nbcode[1][2]=1;*/ |
| |
} |
| |
/* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ |
| |
for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; |
| |
for (k=1; k<=cptcovprod;k++) |
| |
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; |
| |
|
| |
|
| |
for(theta=1; theta <=npar; theta++){ |
| |
for(i=1; i<=npar; i++) |
| |
xp[i] = x[i] + (i==theta ?delti[theta]:(double)0); |
| |
|
| |
pmij(pmmij,cov,ncovmodel,xp,nlstate); |
| |
|
| |
k=0; |
| |
for(i=1; i<= (nlstate); i++){ |
| |
for(j=1; j<=(nlstate+ndeath);j++){ |
| |
k=k+1; |
| |
gp[k]=pmmij[i][j]; |
| |
} |
| |
} |
| |
|
| |
for(i=1; i<=npar; i++) |
| |
xp[i] = x[i] - (i==theta ?delti[theta]:(double)0); |
| |
|
| |
pmij(pmmij,cov,ncovmodel,xp,nlstate); |
| |
k=0; |
| |
for(i=1; i<=(nlstate); i++){ |
| |
for(j=1; j<=(nlstate+ndeath);j++){ |
| |
k=k+1; |
| |
gm[k]=pmmij[i][j]; |
| |
} |
| |
} |
| |
|
| |
for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) |
| |
gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta]; |
| |
} |
| |
|
| |
for(j=1; j<=(nlstate)*(nlstate+ndeath);j++) |
| |
for(theta=1; theta <=npar; theta++) |
| |
trgradg[j][theta]=gradg[theta][j]; |
| |
|
| |
matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); |
| |
matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg); |
| |
|
| |
pmij(pmmij,cov,ncovmodel,x,nlstate); |
| |
|
| |
k=0; |
| |
for(i=1; i<=(nlstate); i++){ |
| |
for(j=1; j<=(nlstate+ndeath);j++){ |
| |
k=k+1; |
| |
mu[k][(int) age]=pmmij[i][j]; |
| |
} |
| |
} |
| |
for(i=1;i<=(nlstate)*(nlstate+ndeath);i++) |
| |
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++){ |
| |
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])); |
| |
}*/ |
| |
|
| |
fprintf(ficresprob,"\n%d ",(int)age); |
| |
fprintf(ficresprobcov,"\n%d ",(int)age); |
| |
fprintf(ficresprobcor,"\n%d ",(int)age); |
| |
|
| |
for (i=1; i<=(nlstate)*(nlstate+ndeath);i++) |
| |
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]); |
| |
fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]); |
| |
} |
| |
i=0; |
| |
for (k=1; k<=(nlstate);k++){ |
| |
for (l=1; l<=(nlstate+ndeath);l++){ |
| |
i++; |
| |
fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l); |
| |
fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l); |
| |
for (j=1; j<=i;j++){ |
| |
/* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */ |
| |
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])); |
| |
} |
| |
} |
| |
}/* end of loop for state */ |
| |
} /* end of loop for age */ |
| |
free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath)); |
| |
free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath)); |
| |
free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); |
| |
free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); |
| |
|
| |
/* Confidence intervalle of pij */ |
| |
/* |
| |
fprintf(ficgp,"\nunset parametric;unset label"); |
| |
fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\""); |
| |
fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65"); |
| |
fprintf(fichtm,"\n<br>Probability with confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname); |
| |
fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname); |
| |
fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname); |
| |
fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob); |
| |
*/ |
| |
|
| |
/* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/ |
| |
first1=1;first2=2; |
| |
for (k2=1; k2<=(nlstate);k2++){ |
| |
for (l2=1; l2<=(nlstate+ndeath);l2++){ |
| |
if(l2==k2) continue; |
| |
j=(k2-1)*(nlstate+ndeath)+l2; |
| |
for (k1=1; k1<=(nlstate);k1++){ |
| |
for (l1=1; l1<=(nlstate+ndeath);l1++){ |
| |
if(l1==k1) continue; |
| |
i=(k1-1)*(nlstate+ndeath)+l1; |
| |
if(i<=j) continue; |
| |
for (age=bage; age<=fage; age ++){ |
| |
if ((int)age %5==0){ |
| |
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; |
| |
mu1=mu[i][(int) age]/stepm*YEARM ; |
| |
mu2=mu[j][(int) age]/stepm*YEARM; |
| |
c12=cv12/sqrt(v1*v2); |
| |
/* Computing eigen value of matrix of covariance */ |
| |
lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; |
| |
lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; |
| |
if ((lc2 <0) || (lc1 <0) ){ |
| |
if(first2==1){ |
| |
first1=0; |
| |
printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor); |
| |
} |
| |
fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog); |
| |
/* lc1=fabs(lc1); */ /* If we want to have them positive */ |
| |
/* lc2=fabs(lc2); */ |
| |
} |
| |
|
| |
/* Eigen vectors */ |
| |
v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12)); |
| |
/*v21=sqrt(1.-v11*v11); *//* error */ |
| |
v21=(lc1-v1)/cv12*v11; |
| |
v12=-v21; |
| |
v22=v11; |
| |
tnalp=v21/v11; |
| |
if(first1==1){ |
| |
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); |
| |
} |
| |
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); |
| |
/*printf(fignu*/ |
| |
/* mu1+ v11*lc1*cost + v12*lc2*sin(t) */ |
| |
/* mu2+ v21*lc1*cost + v22*lc2*sin(t) */ |
| |
if(first==1){ |
| |
first=0; |
| |
fprintf(ficgp,"\nset parametric;unset label"); |
| |
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); |
| |
fprintf(ficgp,"\nset ter png small size 320, 240"); |
| |
fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\ |
| |
:<a href=\"%s%d%1d%1d-%1d%1d.png\">\ |
| |
%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\ |
| |
subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\ |
| |
subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2); |
| |
fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2); |
| |
fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12); |
| |
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); |
| |
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",\ |
| |
mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\ |
| |
mu2,std,v21,sqrt(lc1),v22,sqrt(lc2)); |
| |
}else{ |
| |
first=0; |
| |
fprintf(fichtmcov," %d (%.3f),",(int) age, c12); |
| |
fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2); |
| |
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),\ |
| |
mu2,std,v21,sqrt(lc1),v22,sqrt(lc2)); |
| |
}/* if first */ |
| |
} /* age mod 5 */ |
| |
} /* end loop age */ |
| |
fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2); |
| |
first=1; |
| |
} /*l12 */ |
| |
} /* k12 */ |
| |
} /*l1 */ |
| |
}/* k1 */ |
| |
/* } */ /* loop covariates */ |
| |
} |
| |
free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage); |
| |
free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage); |
| |
free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath)); |
| |
free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar); |
| |
free_vector(xp,1,npar); |
| |
fclose(ficresprob); |
| |
fclose(ficresprobcov); |
| |
fclose(ficresprobcor); |
| |
fflush(ficgp); |
| |
fflush(fichtmcov); |
| |
} |
| |
|
| |
|
| |
/******************* Printing html file ***********/ |
| |
void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \ |
| |
int lastpass, int stepm, int weightopt, char model[],\ |
| |
int imx,int jmin, int jmax, double jmeanint,char rfileres[],\ |
| |
int popforecast, int estepm ,\ |
| |
double jprev1, double mprev1,double anprev1, \ |
| |
double jprev2, double mprev2,double anprev2){ |
| |
int jj1, k1, i1, cpt; |
| |
|
| |
fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \ |
| |
<li><a href='#secondorder'>Result files (second order (variance)</a>\n \ |
| |
</ul>"); |
| |
fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \ |
| |
- Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ", |
| |
jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p")); |
| |
fprintf(fichtm,"\ |
| |
- Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ", |
| |
stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij")); |
| |
fprintf(fichtm,"\ |
| |
- Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n", |
| |
subdirf2(fileres,"pl"),subdirf2(fileres,"pl")); |
| |
fprintf(fichtm,"\ |
| |
- (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \ |
| |
<a href=\"%s\">%s</a> <br>\n", |
| |
estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e")); |
| |
fprintf(fichtm,"\ |
| |
- Population projections by age and states: \ |
| |
<a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f")); |
| |
|
| |
fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>"); |
| |
|
| |
m=pow(2,cptcoveff); |
| |
if (cptcovn < 1) {m=1;ncodemax[1]=1;} |
| |
|
| |
jj1=0; |
| |
for(k1=1; k1<=m;k1++){ |
| |
for(i1=1; i1<=ncodemax[k1];i1++){ |
| |
jj1++; |
| |
if (cptcovn > 0) { |
| |
fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates"); |
| |
for (cpt=1; cpt<=cptcoveff;cpt++) |
| |
fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]); |
| |
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">"); |
| |
} |
| |
/* Pij */ |
| |
fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \ |
| |
<img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); |
| |
/* Quasi-incidences */ |
| |
fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\ |
| |
before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \ |
| |
<img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); |
| |
/* Period (stable) prevalence in each health state */ |
| |
for(cpt=1; cpt<=nlstate;cpt++){ |
| |
fprintf(fichtm,"<br>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \ |
| |
<img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1); |
| |
} |
| |
for(cpt=1; cpt<=nlstate;cpt++) { |
| |
fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \ |
| |
<img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1); |
| |
} |
| |
} /* end i1 */ |
| |
}/* End k1 */ |
| |
fprintf(fichtm,"</ul>"); |
| |
|
| |
|
| |
fprintf(fichtm,"\ |
| |
\n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\ |
| |
- Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres); |
| |
|
| |
fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n", |
| |
subdirf2(fileres,"prob"),subdirf2(fileres,"prob")); |
| |
fprintf(fichtm,"\ |
| |
- Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n", |
| |
subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov")); |
| |
|
| |
fprintf(fichtm,"\ |
| |
- Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n", |
| |
subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor")); |
| |
fprintf(fichtm,"\ |
| |
- Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \ |
| |
<a href=\"%s\">%s</a> <br>\n</li>", |
| |
estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve")); |
| |
fprintf(fichtm,"\ |
| |
- (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \ |
| |
<a href=\"%s\">%s</a> <br>\n</li>", |
| |
estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde")); |
| |
fprintf(fichtm,"\ |
| |
- Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n", |
| |
estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v")); |
| |
fprintf(fichtm,"\ |
| |
- Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n", |
| |
estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t")); |
| |
fprintf(fichtm,"\ |
| |
- Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\ |
| |
subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl")); |
| |
|
| |
/* if(popforecast==1) fprintf(fichtm,"\n */ |
| |
/* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */ |
| |
/* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */ |
| |
/* <br>",fileres,fileres,fileres,fileres); */ |
| |
/* else */ |
| |
/* fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */ |
| |
fflush(fichtm); |
| |
fprintf(fichtm," <ul><li><b>Graphs</b></li><p>"); |
| |
|
| |
m=pow(2,cptcoveff); |
| |
if (cptcovn < 1) {m=1;ncodemax[1]=1;} |
| |
|
| |
jj1=0; |
| |
for(k1=1; k1<=m;k1++){ |
| |
for(i1=1; i1<=ncodemax[k1];i1++){ |
| |
jj1++; |
| |
if (cptcovn > 0) { |
| |
fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates"); |
| |
for (cpt=1; cpt<=cptcoveff;cpt++) |
| |
fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]); |
| |
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">"); |
| |
} |
| |
for(cpt=1; cpt<=nlstate;cpt++) { |
| |
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); |
| |
} |
| |
fprintf(fichtm,"\n<br>- Total life expectancy by age and \ |
| |
health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \ |
| |
true period expectancies (those weighted with period prevalences are also\ |
| |
drawn in addition to the population based expectancies computed using\ |
| |
observed and cahotic prevalences: %s%d.png<br>\ |
| |
<img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1); |
| |
} /* end i1 */ |
| |
}/* End k1 */ |
| |
fprintf(fichtm,"</ul>"); |
| |
fflush(fichtm); |
| |
} |
| |
|
| |
/******************* Gnuplot file **************/ |
| |
void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){ |
| |
|
| |
char dirfileres[132],optfileres[132]; |
| |
int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0; |
| |
int ng=0; |
| |
/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */ |
| |
/* printf("Problem with file %s",optionfilegnuplot); */ |
| |
/* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */ |
| |
/* } */ |
| |
|
| |
/*#ifdef windows */ |
| |
fprintf(ficgp,"cd \"%s\" \n",pathc); |
| |
/*#endif */ |
| |
m=pow(2,cptcoveff); |
| |
|
| |
strcpy(dirfileres,optionfilefiname); |
| |
strcpy(optfileres,"vpl"); |
| |
/* 1eme*/ |
| |
fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n"); |
| |
for (cpt=1; cpt<= nlstate ; cpt ++) { |
| |
for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */ |
| |
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 size 320, 240\n\ |
| |
plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1); |
| |
|
| |
for (i=1; i<= nlstate ; i ++) { |
| |
if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); |
| |
else fprintf(ficgp," %%*lf (%%*lf)"); |
| |
} |
| |
fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); |
| |
for (i=1; i<= nlstate ; i ++) { |
| |
if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); |
| |
else fprintf(ficgp," %%*lf (%%*lf)"); |
| |
} |
| |
fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); |
| |
for (i=1; i<= nlstate ; i ++) { |
| |
if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); |
| |
else fprintf(ficgp," %%*lf (%%*lf)"); |
| |
} |
| |
fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1)); |
| |
} |
| |
} |
| |
/*2 eme*/ |
| |
fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n"); |
| |
for (k1=1; k1<= m ; k1 ++) { |
| |
fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1); |
| |
fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage); |
| |
|
| |
for (i=1; i<= nlstate+1 ; i ++) { |
| |
k=2*i; |
| |
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1); |
| |
for (j=1; j<= nlstate+1 ; j ++) { |
| |
if (j==i) fprintf(ficgp," %%lf (%%lf)"); |
| |
else fprintf(ficgp," %%*lf (%%*lf)"); |
| |
} |
| |
if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,"); |
| |
else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1); |
| |
fprintf(ficgp,"\"%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)"); |
| |
else fprintf(ficgp," %%*lf (%%*lf)"); |
| |
} |
| |
fprintf(ficgp,"\" t\"\" w l lt 0,"); |
| |
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1); |
| |
for (j=1; j<= nlstate+1 ; j ++) { |
| |
if (j==i) fprintf(ficgp," %%lf (%%lf)"); |
| |
else fprintf(ficgp," %%*lf (%%*lf)"); |
| |
} |
| |
if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0"); |
| |
else fprintf(ficgp,"\" t\"\" w l lt 0,"); |
| |
} |
| |
} |
| |
|
| |
/*3eme*/ |
| |
|
| |
for (k1=1; k1<= m ; k1 ++) { |
| |
for (cpt=1; cpt<= nlstate ; cpt ++) { |
| |
/* k=2+nlstate*(2*cpt-2); */ |
| |
k=2+(nlstate+1)*(cpt-1); |
| |
fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1); |
| |
fprintf(ficgp,"set ter png small size 320, 240\n\ |
| |
plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt); |
| |
/*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); |
| |
for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); |
| |
fprintf(ficgp,"\" t \"e%d1\" w l",cpt); |
| |
fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); |
| |
for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); |
| |
fprintf(ficgp,"\" t \"e%d1\" w l",cpt); |
| |
|
| |
*/ |
| |
for (i=1; i< nlstate ; i ++) { |
| |
fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1); |
| |
/* fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/ |
| |
|
| |
} |
| |
fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt); |
| |
} |
| |
} |
| |
|
| |
/* CV preval stable (period) */ |
| |
for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */ |
| |
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */ |
| |
k=3; |
| |
fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt); |
| |
fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1); |
| |
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\ |
| |
set ter png small size 320, 240\n\ |
| |
unset log y\n\ |
| |
plot [%.f:%.f] ", ageminpar, agemaxpar); |
| |
for (i=1; i<= nlstate ; i ++){ |
| |
if(i==1) |
| |
fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij")); |
| |
else |
| |
fprintf(ficgp,", '' "); |
| |
l=(nlstate+ndeath)*(i-1)+1; |
| |
fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); |
| |
for (j=1; j<= (nlstate-1) ; j ++) |
| |
fprintf(ficgp,"+$%d",k+l+j); |
| |
fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt); |
| |
} /* nlstate */ |
| |
fprintf(ficgp,"\n"); |
| |
} /* end cpt state*/ |
| |
} /* end covariate */ |
| |
|
| |
/* proba elementaires */ |
| |
fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n"); |
| |
for(i=1,jk=1; i <=nlstate; i++){ |
| |
fprintf(ficgp,"# initial state %d\n",i); |
| |
for(k=1; k <=(nlstate+ndeath); k++){ |
| |
if (k != i) { |
| |
fprintf(ficgp,"# current state %d\n",k); |
| |
for(j=1; j <=ncovmodel; j++){ |
| |
fprintf(ficgp,"p%d=%f; ",jk,p[jk]); |
| |
jk++; |
| |
} |
| |
fprintf(ficgp,"\n"); |
| |
} |
| |
} |
| |
} |
| |
fprintf(ficgp,"##############\n#\n"); |
| |
|
| |
/*goto avoid;*/ |
| |
fprintf(ficgp,"\n##############\n#Graphics of of probabilities or incidences\n#############\n"); |
| |
fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n"); |
| |
fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n"); |
| |
fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n"); |
| |
fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n"); |
| |
fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n"); |
| |
fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n"); |
| |
fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n"); |
| |
fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n"); |
| |
fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n"); |
| |
fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n"); |
| |
fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n"); |
| |
fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n"); |
| |
fprintf(ficgp,"#\n"); |
| |
for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/ |
| |
fprintf(ficgp,"# ng=%d\n",ng); |
| |
fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m); |
| |
for(jk=1; jk <=m; jk++) { |
| |
fprintf(ficgp,"# jk=%d\n",jk); |
| |
fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); |
| |
if (ng==2) |
| |
fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n"); |
| |
else |
| |
fprintf(ficgp,"\nset title \"Probability\"\n"); |
| |
fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar); |
| |
i=1; |
| |
for(k2=1; k2<=nlstate; k2++) { |
| |
k3=i; |
| |
for(k=1; k<=(nlstate+ndeath); k++) { |
| |
if (k != k2){ |
| |
if(ng==2) |
| |
if(nagesqr==0) |
| |
fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1); |
| |
else /* nagesqr =1 */ |
| |
fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr); |
| |
else |
| |
if(nagesqr==0) |
| |
fprintf(ficgp," exp(p%d+p%d*x",i,i+1); |
| |
else /* nagesqr =1 */ |
| |
fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr); |
| |
ij=1;/* To be checked else nbcode[0][0] wrong */ |
| |
for(j=3; j <=ncovmodel-nagesqr; j++) { |
| |
if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */ |
| |
fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); |
| |
ij++; |
| |
} |
| |
else |
| |
fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]); |
| |
} |
| |
fprintf(ficgp,")/(1"); |
| |
|
| |
for(k1=1; k1 <=nlstate; k1++){ |
| |
if(nagesqr==0) |
| |
fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1); |
| |
else /* nagesqr =1 */ |
| |
fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr); |
| |
|
| |
ij=1; |
| |
for(j=3; j <=ncovmodel-nagesqr; j++){ |
| |
if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { |
| |
fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); |
| |
ij++; |
| |
} |
| |
else |
| |
fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][j-2]]); |
| |
} |
| |
fprintf(ficgp,")"); |
| |
} |
| |
fprintf(ficgp,") t \"p%d%d\" ", k2,k); |
| |
if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,","); |
| |
i=i+ncovmodel; |
| |
} |
| |
} /* end k */ |
| |
} /* end k2 */ |
| |
} /* end jk */ |
| |
} /* end ng */ |
| |
/* avoid: */ |
| |
fflush(ficgp); |
| |
} /* end gnuplot */ |
| |
|
| |
|
| |
/*************** Moving average **************/ |
| |
int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){ |
| |
|
| |
int i, cpt, cptcod; |
| |
int modcovmax =1; |
| |
int mobilavrange, mob; |
| |
double age; |
| |
|
| |
modcovmax=2*cptcoveff;/* Max number of modalities. We suppose |
| |
a covariate has 2 modalities */ |
| |
if (cptcovn<1) modcovmax=1; /* At least 1 pass */ |
| |
|
| |
if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){ |
| |
if(mobilav==1) mobilavrange=5; /* default */ |
| |
else mobilavrange=mobilav; |
| |
for (age=bage; age<=fage; age++) |
| |
for (i=1; i<=nlstate;i++) |
| |
for (cptcod=1;cptcod<=modcovmax;cptcod++) |
| |
mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod]; |
| |
/* 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 |
| |
we use a 5 terms etc. until the borders are no more concerned. |
| |
*/ |
| |
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++){ |
| |
for (cptcod=1;cptcod<=modcovmax;cptcod++){ |
| |
mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod]; |
| |
for (cpt=1;cpt<=(mob-1)/2;cpt++){ |
| |
mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod]; |
| |
mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod]; |
| |
} |
| |
mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob; |
| |
} |
| |
} |
| |
}/* end age */ |
| |
}/* end mob */ |
| |
}else return -1; |
| |
return 0; |
| |
}/* End movingaverage */ |
| |
|
| |
|
| |
/************** Forecasting ******************/ |
| |
void 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 |
| |
dateprev1 dateprev2 range of dates during which prevalence is computed |
| |
anproj2 year of en of projection (same day and month as proj1). |
| |
*/ |
| |
int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; |
| |
double agec; /* generic age */ |
| |
double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; |
| |
double *popeffectif,*popcount; |
| |
double ***p3mat; |
| |
double ***mobaverage; |
| |
char fileresf[FILENAMELENGTH]; |
| |
|
| |
agelim=AGESUP; |
| |
prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); |
| |
|
| |
strcpy(fileresf,"f"); |
| |
strcat(fileresf,fileres); |
| |
if((ficresf=fopen(fileresf,"w"))==NULL) { |
| |
printf("Problem with forecast resultfile: %s\n", fileresf); |
| |
fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf); |
| |
} |
| |
printf("Computing forecasting: result on file '%s' \n", fileresf); |
| |
fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf); |
| |
|
| |
if (cptcoveff==0) ncodemax[cptcoveff]=1; |
| |
|
| |
if (mobilav!=0) { |
| |
mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
| |
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); |
| |
} |
| |
} |
| |
|
| |
stepsize=(int) (stepm+YEARM-1)/YEARM; |
| |
if (stepm<=12) stepsize=1; |
| |
if(estepm < stepm){ |
| |
printf ("Problem %d lower than %d\n",estepm, stepm); |
| |
} |
| |
else hstepm=estepm; |
| |
|
| |
hstepm=hstepm/stepm; |
| |
yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and |
| |
fractional in yp1 */ |
| |
anprojmean=yp; |
| |
yp2=modf((yp1*12),&yp); |
| |
mprojmean=yp; |
| |
yp1=modf((yp2*30.5),&yp); |
| |
jprojmean=yp; |
| |
if(jprojmean==0) jprojmean=1; |
| |
if(mprojmean==0) jprojmean=1; |
| |
|
| |
i1=cptcoveff; |
| |
if (cptcovn < 1){i1=1;} |
| |
|
| |
fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); |
| |
|
| |
fprintf(ficresf,"#****** Routine prevforecast **\n"); |
| |
|
| |
/* if (h==(int)(YEARM*yearp)){ */ |
| |
for(cptcov=1, k=0;cptcov<=i1;cptcov++){ |
| |
for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ |
| |
k=k+1; |
| |
fprintf(ficresf,"\n#******"); |
| |
for(j=1;j<=cptcoveff;j++) { |
| |
fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
| |
} |
| |
fprintf(ficresf,"******\n"); |
| |
fprintf(ficresf,"# Covariate valuofcovar yearproj age"); |
| |
for(j=1; j<=nlstate+ndeath;j++){ |
| |
for(i=1; i<=nlstate;i++) |
| |
fprintf(ficresf," p%d%d",i,j); |
| |
fprintf(ficresf," p.%d",j); |
| |
} |
| |
for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { |
| |
fprintf(ficresf,"\n"); |
| |
fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp); |
| |
|
| |
for (agec=fage; agec>=(ageminpar-1); agec--){ |
| |
nhstepm=(int) rint((agelim-agec)*YEARM/stepm); |
| |
nhstepm = nhstepm/hstepm; |
| |
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
| |
oldm=oldms;savm=savms; |
| |
hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k); |
| |
|
| |
for (h=0; h<=nhstepm; h++){ |
| |
if (h*hstepm/YEARM*stepm ==yearp) { |
| |
fprintf(ficresf,"\n"); |
| |
for(j=1;j<=cptcoveff;j++) |
| |
fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
| |
fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm); |
| |
} |
| |
for(j=1; j<=nlstate+ndeath;j++) { |
| |
ppij=0.; |
| |
for(i=1; i<=nlstate;i++) { |
| |
if (mobilav==1) |
| |
ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; |
| |
else { |
| |
ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; |
| |
} |
| |
if (h*hstepm/YEARM*stepm== yearp) { |
| |
fprintf(ficresf," %.3f", p3mat[i][j][h]); |
| |
} |
| |
} /* end i */ |
| |
if (h*hstepm/YEARM*stepm==yearp) { |
| |
fprintf(ficresf," %.3f", ppij); |
| |
} |
| |
}/* end j */ |
| |
} /* end h */ |
| |
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
| |
} /* end agec */ |
| |
} /* end yearp */ |
| |
} /* end cptcod */ |
| |
} /* end cptcov */ |
| |
|
| |
if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
| |
|
| |
fclose(ficresf); |
| |
} |
| |
|
| |
/************** Forecasting *****not tested NB*************/ |
| |
void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ |
| |
|
| |
int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; |
| |
int *popage; |
| |
double calagedatem, agelim, kk1, kk2; |
| |
double *popeffectif,*popcount; |
| |
double ***p3mat,***tabpop,***tabpopprev; |
| |
double ***mobaverage; |
| |
char filerespop[FILENAMELENGTH]; |
| |
|
| |
tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
| |
tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
| |
agelim=AGESUP; |
| |
calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; |
| |
|
| |
prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); |
| |
|
| |
|
| |
strcpy(filerespop,"pop"); |
| |
strcat(filerespop,fileres); |
| |
if((ficrespop=fopen(filerespop,"w"))==NULL) { |
| |
printf("Problem with forecast resultfile: %s\n", filerespop); |
| |
fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); |
| |
} |
| |
printf("Computing forecasting: result on file '%s' \n", filerespop); |
| |
fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); |
| |
|
| |
if (cptcoveff==0) ncodemax[cptcoveff]=1; |
| |
|
| |
if (mobilav!=0) { |
| |
mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
| |
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); |
| |
} |
| |
} |
| |
|
| |
stepsize=(int) (stepm+YEARM-1)/YEARM; |
| |
if (stepm<=12) stepsize=1; |
| |
|
| |
agelim=AGESUP; |
| |
|
| |
hstepm=1; |
| |
hstepm=hstepm/stepm; |
| |
|
| |
if (popforecast==1) { |
| |
if((ficpop=fopen(popfile,"r"))==NULL) { |
| |
printf("Problem with population file : %s\n",popfile);exit(0); |
| |
fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); |
| |
} |
| |
popage=ivector(0,AGESUP); |
| |
popeffectif=vector(0,AGESUP); |
| |
popcount=vector(0,AGESUP); |
| |
|
| |
i=1; |
| |
while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; |
| |
|
| |
imx=i; |
| |
for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; |
| |
} |
| |
|
| |
for(cptcov=1,k=0;cptcov<=i2;cptcov++){ |
| |
for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ |
| |
k=k+1; |
| |
fprintf(ficrespop,"\n#******"); |
| |
for(j=1;j<=cptcoveff;j++) { |
| |
fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
| |
} |
| |
fprintf(ficrespop,"******\n"); |
| |
fprintf(ficrespop,"# Age"); |
| |
for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); |
| |
if (popforecast==1) fprintf(ficrespop," [Population]"); |
| |
|
| |
for (cpt=0; cpt<=0;cpt++) { |
| |
fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); |
| |
|
| |
for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ |
| |
nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); |
| |
nhstepm = nhstepm/hstepm; |
| |
|
| |
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
| |
oldm=oldms;savm=savms; |
| |
hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); |
| |
|
| |
for (h=0; h<=nhstepm; h++){ |
| |
if (h==(int) (calagedatem+YEARM*cpt)) { |
| |
fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); |
| |
} |
| |
for(j=1; j<=nlstate+ndeath;j++) { |
| |
kk1=0.;kk2=0; |
| |
for(i=1; i<=nlstate;i++) { |
| |
if (mobilav==1) |
| |
kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; |
| |
else { |
| |
kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; |
| |
} |
| |
} |
| |
if (h==(int)(calagedatem+12*cpt)){ |
| |
tabpop[(int)(agedeb)][j][cptcod]=kk1; |
| |
/*fprintf(ficrespop," %.3f", kk1); |
| |
if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/ |
| |
} |
| |
} |
| |
for(i=1; i<=nlstate;i++){ |
| |
kk1=0.; |
| |
for(j=1; j<=nlstate;j++){ |
| |
kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; |
| |
} |
| |
tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; |
| |
} |
| |
|
| |
if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) |
| |
fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); |
| |
} |
| |
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
| |
} |
| |
} |
| |
|
| |
/******/ |
| |
|
| |
for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { |
| |
fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); |
| |
for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ |
| |
nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); |
| |
nhstepm = nhstepm/hstepm; |
| |
|
| |
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
| |
oldm=oldms;savm=savms; |
| |
hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); |
| |
for (h=0; h<=nhstepm; h++){ |
| |
if (h==(int) (calagedatem+YEARM*cpt)) { |
| |
fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); |
| |
} |
| |
for(j=1; j<=nlstate+ndeath;j++) { |
| |
kk1=0.;kk2=0; |
| |
for(i=1; i<=nlstate;i++) { |
| |
kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; |
| |
} |
| |
if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1); |
| |
} |
| |
} |
| |
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
| |
} |
| |
} |
| |
} |
| |
} |
| |
|
| |
if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
| |
|
| |
if (popforecast==1) { |
| |
free_ivector(popage,0,AGESUP); |
| |
free_vector(popeffectif,0,AGESUP); |
| |
free_vector(popcount,0,AGESUP); |
| |
} |
| |
free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
| |
free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
| |
fclose(ficrespop); |
| |
} /* End of popforecast */ |
| |
|
| |
int fileappend(FILE *fichier, char *optionfich) |
| |
{ |
| |
if((fichier=fopen(optionfich,"a"))==NULL) { |
| |
printf("Problem with file: %s\n", optionfich); |
| |
fprintf(ficlog,"Problem with file: %s\n", optionfich); |
| |
return (0); |
| |
} |
| |
fflush(fichier); |
| |
return (1); |
| |
} |
| |
|
| |
|
| |
/**************** function prwizard **********************/ |
| |
void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo) |
| |
{ |
| |
|
| |
/* Wizard to print covariance matrix template */ |
| |
|
| |
char ca[32], cb[32]; |
| |
int i,j, k, li, lj, lk, ll, jj, npar, itimes; |
| |
int numlinepar; |
| |
|
| |
printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); |
| |
fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); |
| |
for(i=1; i <=nlstate; i++){ |
| |
jj=0; |
| |
for(j=1; j <=nlstate+ndeath; j++){ |
| |
if(j==i) continue; |
| |
jj++; |
| |
/*ca[0]= k+'a'-1;ca[1]='\0';*/ |
| |
printf("%1d%1d",i,j); |
| |
fprintf(ficparo,"%1d%1d",i,j); |
| |
for(k=1; k<=ncovmodel;k++){ |
| |
/* printf(" %lf",param[i][j][k]); */ |
| |
/* fprintf(ficparo," %lf",param[i][j][k]); */ |
| |
printf(" 0."); |
| |
fprintf(ficparo," 0."); |
| |
} |
| |
printf("\n"); |
| |
fprintf(ficparo,"\n"); |
| |
} |
| |
} |
| |
printf("# Scales (for hessian or gradient estimation)\n"); |
| |
fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n"); |
| |
npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ |
| |
for(i=1; i <=nlstate; i++){ |
| |
jj=0; |
| |
for(j=1; j <=nlstate+ndeath; j++){ |
| |
if(j==i) continue; |
| |
jj++; |
| |
fprintf(ficparo,"%1d%1d",i,j); |
| |
printf("%1d%1d",i,j); |
| |
fflush(stdout); |
| |
for(k=1; k<=ncovmodel;k++){ |
| |
/* printf(" %le",delti3[i][j][k]); */ |
| |
/* fprintf(ficparo," %le",delti3[i][j][k]); */ |
| |
printf(" 0."); |
| |
fprintf(ficparo," 0."); |
| |
} |
| |
numlinepar++; |
| |
printf("\n"); |
| |
fprintf(ficparo,"\n"); |
| |
} |
| |
} |
| |
printf("# Covariance matrix\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" */ |
| |
fflush(stdout); |
| |
fprintf(ficparo,"# 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(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){ |
| |
printf("#%1d%1d%d",i,j,k); |
| |
fprintf(ficparo,"#%1d%1d%d",i,j,k); |
| |
}else{ |
| |
printf("%1d%1d%d",i,j,k); |
| |
fprintf(ficparo,"%1d%1d%d",i,j,k); |
| |
/* printf(" %.5le",matcov[i][j]); */ |
| |
} |
| |
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){ |
| |
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); |
| |
}else{ |
| |
printf(" 0."); |
| |
fprintf(ficparo," 0."); |
| |
} |
| |
}else{ |
| |
if(itimes==1){ |
| |
printf(" Var(%s%1d%1d)",ca,i,j); |
| |
fprintf(ficparo," Var(%s%1d%1d)",ca,i,j); |
| |
}else{ |
| |
printf(" 0."); |
| |
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; |
| |
} |
| |
|
| |
#ifdef GSL |
| |
/******************* Gompertz_f Likelihood ******************************/ |
| |
double gompertz_f(const gsl_vector *v, void *params) |
| |
{ |
| |
double A,B,LL=0.0,sump=0.,num=0.; |
| |
double *x= (double *) v->data; |
| |
int i,n=0; /* n is the size of the sample */ |
| |
|
| |
for (i=0;i<=imx-1 ; i++) { |
| |
sump=sump+weight[i]; |
| |
/* sump=sump+1;*/ |
| |
num=num+1; |
| |
} |
| |
|
| |
|
| |
/* for (i=0; i<=imx; i++) |
| |
if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/ |
| |
printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]); |
| |
for (i=1;i<=imx ; i++) |
| |
{ |
| |
if (cens[i] == 1 && wav[i]>1) |
| |
A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp))); |
| |
|
| |
if (cens[i] == 0 && wav[i]>1) |
| |
A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp))) |
| |
+log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM); |
| |
|
| |
/*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */ |
| |
if (wav[i] > 1 ) { /* ??? */ |
| |
LL=LL+A*weight[i]; |
| |
/* printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/ |
| |
} |
| |
} |
| |
|
| |
/*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/ |
| |
printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump); |
| |
|
| |
return -2*LL*num/sump; |
| |
} |
| |
#endif |
| |
|
| |
/******************* Printing html file ***********/ |
| |
void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \ |
| |
int lastpass, int stepm, int weightopt, char model[],\ |
| |
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 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 size 320, 240\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); |
| |
|
| |
} |
| |
|
| |
int readdata(char datafile[], int firstobs, int lastobs, int *imax) |
| |
{ |
| |
|
| |
/*-------- data file ----------*/ |
| |
FILE *fic; |
| |
char dummy[]=" "; |
| |
int i=0, j=0, n=0; |
| |
int linei, month, year,iout; |
| |
char line[MAXLINE], linetmp[MAXLINE]; |
| |
char stra[MAXLINE], strb[MAXLINE]; |
| |
char *stratrunc; |
| |
int lstra; |
| |
|
| |
|
| |
if((fic=fopen(datafile,"r"))==NULL) { |
| |
printf("Problem while opening datafile: %s\n", datafile);return 1; |
| |
fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1; |
| |
} |
| |
|
| |
i=1; |
| |
linei=0; |
| |
while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) { |
| |
linei=linei+1; |
| |
for(j=strlen(line); j>=0;j--){ /* Untabifies line */ |
| |
if(line[j] == '\t') |
| |
line[j] = ' '; |
| |
} |
| |
for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){ |
| |
; |
| |
}; |
| |
line[j+1]=0; /* Trims blanks at end of line */ |
| |
if(line[0]=='#'){ |
| |
fprintf(ficlog,"Comment line\n%s\n",line); |
| |
printf("Comment line\n%s\n",line); |
| |
continue; |
| |
} |
| |
trimbb(linetmp,line); /* Trims multiple blanks in line */ |
| |
strcpy(line, linetmp); |
| |
|
| |
|
| |
for (j=maxwav;j>=1;j--){ |
| |
cutv(stra, strb, line, ' '); |
| |
if(strb[0]=='.') { /* Missing status */ |
| |
lval=-1; |
| |
}else{ |
| |
errno=0; |
| |
lval=strtol(strb,&endptr,10); |
| |
/* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/ |
| |
if( strb[0]=='\0' || (*endptr != '\0')){ |
| |
printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav); |
| |
fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog); |
| |
return 1; |
| |
} |
| |
} |
| |
s[j][i]=lval; |
| |
|
| |
strcpy(line,stra); |
| |
cutv(stra, strb,line,' '); |
| |
if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){ |
| |
} |
| |
else if( (iout=sscanf(strb,"%s.",dummy)) != 0){ |
| |
month=99; |
| |
year=9999; |
| |
}else{ |
| |
printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j); |
| |
fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);fflush(ficlog); |
| |
return 1; |
| |
} |
| |
anint[j][i]= (double) year; |
| |
mint[j][i]= (double)month; |
| |
strcpy(line,stra); |
| |
} /* ENd Waves */ |
| |
|
| |
cutv(stra, strb,line,' '); |
| |
if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){ |
| |
} |
| |
else if( (iout=sscanf(strb,"%s.",dummy)) != 0){ |
| |
month=99; |
| |
year=9999; |
| |
}else{ |
| |
printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line); |
| |
fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog); |
| |
return 1; |
| |
} |
| |
andc[i]=(double) year; |
| |
moisdc[i]=(double) month; |
| |
strcpy(line,stra); |
| |
|
| |
cutv(stra, strb,line,' '); |
| |
if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){ |
| |
} |
| |
else if( (iout=sscanf(strb,"%s.", dummy)) != 0){ |
| |
month=99; |
| |
year=9999; |
| |
}else{ |
| |
printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line); |
| |
fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog); |
| |
return 1; |
| |
} |
| |
if (year==9999) { |
| |
printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line); |
| |
fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog); |
| |
return 1; |
| |
|
| |
} |
| |
annais[i]=(double)(year); |
| |
moisnais[i]=(double)(month); |
| |
strcpy(line,stra); |
| |
|
| |
cutv(stra, strb,line,' '); |
| |
errno=0; |
| |
dval=strtod(strb,&endptr); |
| |
if( strb[0]=='\0' || (*endptr != '\0')){ |
| |
printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei); |
| |
fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei); |
| |
fflush(ficlog); |
| |
return 1; |
| |
} |
| |
weight[i]=dval; |
| |
strcpy(line,stra); |
| |
|
| |
for (j=ncovcol;j>=1;j--){ |
| |
cutv(stra, strb,line,' '); |
| |
if(strb[0]=='.') { /* Missing status */ |
| |
lval=-1; |
| |
}else{ |
| |
errno=0; |
| |
lval=strtol(strb,&endptr,10); |
| |
if( strb[0]=='\0' || (*endptr != '\0')){ |
| |
printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line); |
| |
fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);fflush(ficlog); |
| |
return 1; |
| |
} |
| |
} |
| |
if(lval <-1 || lval >1){ |
| |
printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \ |
| |
Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \ |
| |
for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \ |
| |
For example, for multinomial values like 1, 2 and 3,\n \ |
| |
build V1=0 V2=0 for the reference value (1),\n \ |
| |
V1=1 V2=0 for (2) \n \ |
| |
and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \ |
| |
output of IMaCh is often meaningless.\n \ |
| |
Exiting.\n",lval,linei, i,line,j); |
| |
fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \ |
| |
Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \ |
| |
for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \ |
| |
For example, for multinomial values like 1, 2 and 3,\n \ |
| |
build V1=0 V2=0 for the reference value (1),\n \ |
| |
V1=1 V2=0 for (2) \n \ |
| |
and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \ |
| |
output of IMaCh is often meaningless.\n \ |
| |
Exiting.\n",lval,linei, i,line,j);fflush(ficlog); |
| |
return 1; |
| |
} |
| |
covar[j][i]=(double)(lval); |
| |
strcpy(line,stra); |
| |
} |
| |
lstra=strlen(stra); |
| |
|
| |
if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */ |
| |
stratrunc = &(stra[lstra-9]); |
| |
num[i]=atol(stratrunc); |
| |
} |
| |
else |
| |
num[i]=atol(stra); |
| |
/*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){ |
| |
printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/ |
| |
|
| |
i=i+1; |
| |
} /* End loop reading data */ |
| |
|
| |
*imax=i-1; /* Number of individuals */ |
| |
fclose(fic); |
| |
|
| |
return (0); |
| |
/* endread: */ |
| |
printf("Exiting readdata: "); |
| |
fclose(fic); |
| |
return (1); |
| |
|
| |
|
| |
|
| |
} |
| |
void removespace(char *str) { |
| |
char *p1 = str, *p2 = str; |
| |
do |
| |
while (*p2 == ' ') |
| |
p2++; |
| |
while (*p1++ == *p2++); |
| |
} |
| |
|
| |
int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns: |
| |
* Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age |
| |
* - nagesqr = 1 if age*age in the model, otherwise 0. |
| |
* - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age |
| |
* - cptcovn or number of covariates k of the models excluding age*products =6 and age*age |
| |
* - cptcovage number of covariates with age*products =2 |
| |
* - cptcovs number of simple covariates |
| |
* - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10 |
| |
* which is a new column after the 9 (ncovcol) variables. |
| |
* - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual |
| |
* - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage |
| |
* Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6. |
| |
* - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 . |
| |
*/ |
| |
{ |
| |
int i, j, k, ks; |
| |
int j1, k1, k2; |
| |
char modelsav[80]; |
| |
char stra[80], strb[80], strc[80], strd[80],stre[80]; |
| |
char *strpt; |
| |
|
| |
/*removespace(model);*/ |
| |
if (strlen(model) >1){ /* If there is at least 1 covariate */ |
| |
j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0; |
| |
if (strstr(model,"AGE") !=0){ |
| |
printf("Error. AGE must be in lower case 'age' model=1+age+%s ",model); |
| |
fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s ",model);fflush(ficlog); |
| |
return 1; |
| |
} |
| |
if (strstr(model,"v") !=0){ |
| |
printf("Error. 'v' must be in upper case 'V' model=%s ",model); |
| |
fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog); |
| |
return 1; |
| |
} |
| |
strcpy(modelsav,model); |
| |
if ((strpt=strstr(model,"age*age")) !=0){ |
| |
printf(" strpt=%s, model=%s\n",strpt, model); |
| |
if(strpt != model){ |
| |
printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \ |
| |
'model=1+age+age*age+V1' or 'model=1+age+age*age+V1+V1*age', please swap as well as \n \ |
| |
corresponding column of parameters.\n",model); |
| |
fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \ |
| |
'model=1+age+age*age+V1' or 'model=1+age+age*age+V1+V1*age', please swap as well as \n \ |
| |
corresponding column of parameters.\n",model); fflush(ficlog); |
| |
return 1; |
| |
} |
| |
|
| |
nagesqr=1; |
| |
if (strstr(model,"+age*age") !=0) |
| |
substrchaine(modelsav, model, "+age*age"); |
| |
else if (strstr(model,"age*age+") !=0) |
| |
substrchaine(modelsav, model, "age*age+"); |
| |
else |
| |
substrchaine(modelsav, model, "age*age"); |
| |
}else |
| |
nagesqr=0; |
| |
if (strlen(modelsav) >1){ |
| |
j=nbocc(modelsav,'+'); /**< j=Number of '+' */ |
| |
j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */ |
| |
cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */ |
| |
cptcovt= j+1; /* Number of total covariates in the model, not including |
| |
* cst, age and age*age |
| |
* V1+V1*age+ V3 + V3*V4+age*age=> 4*/ |
| |
/* including age products which are counted in cptcovage. |
| |
* but the covariates which are products must be treated |
| |
* separately: ncovn=4- 2=2 (V1+V3). */ |
| |
cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */ |
| |
cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */ |
| |
|
| |
|
| |
/* Design |
| |
* V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight |
| |
* < ncovcol=8 > |
| |
* Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 |
| |
* k= 1 2 3 4 5 6 7 8 |
| |
* cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8 |
| |
* covar[k,i], value of kth covariate if not including age for individual i: |
| |
* covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8) |
| |
* Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8 |
| |
* if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and |
| |
* Tage[++cptcovage]=k |
| |
* if products, new covar are created after ncovcol with k1 |
| |
* Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11 |
| |
* Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product |
| |
* Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8 |
| |
* Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2]; |
| |
* Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted |
| |
* V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 |
| |
* < ncovcol=8 > |
| |
* Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2 |
| |
* k= 1 2 3 4 5 6 7 8 9 10 11 12 |
| |
* Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8 |
| |
* p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6} |
| |
* p Tprod[1]@2={ 6, 5} |
| |
*p Tvard[1][1]@4= {7, 8, 5, 6} |
| |
* covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8 |
| |
* cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; |
| |
*How to reorganize? |
| |
* Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age |
| |
* Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6} |
| |
* {2, 1, 4, 8, 5, 6, 3, 7} |
| |
* Struct [] |
| |
*/ |
| |
|
| |
/* This loop fills the array Tvar from the string 'model'.*/ |
| |
/* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */ |
| |
/* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */ |
| |
/* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */ |
| |
/* k=3 V4 Tvar[k=3]= 4 (from V4) */ |
| |
/* k=2 V1 Tvar[k=2]= 1 (from V1) */ |
| |
/* k=1 Tvar[1]=2 (from V2) */ |
| |
/* k=5 Tvar[5] */ |
| |
/* for (k=1; k<=cptcovn;k++) { */ |
| |
/* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */ |
| |
/* } */ |
| |
/* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; */ |
| |
/* |
| |
* Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */ |
| |
for(k=cptcovt; k>=1;k--) /**< Number of covariates */ |
| |
Tvar[k]=0; |
| |
cptcovage=0; |
| |
for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */ |
| |
cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' |
| |
modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ |
| |
if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */ |
| |
/* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/ |
| |
/*scanf("%d",i);*/ |
| |
if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */ |
| |
cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */ |
| |
if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */ |
| |
/* covar is not filled and then is empty */ |
| |
cptcovprod--; |
| |
cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */ |
| |
Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */ |
| |
cptcovage++; /* Sums the number of covariates which include age as a product */ |
| |
Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */ |
| |
/*printf("stre=%s ", stre);*/ |
| |
} else if (strcmp(strd,"age")==0) { /* or age*Vn */ |
| |
cptcovprod--; |
| |
cutl(stre,strb,strc,'V'); |
| |
Tvar[k]=atoi(stre); |
| |
cptcovage++; |
| |
Tage[cptcovage]=k; |
| |
} else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/ |
| |
/* loops on k1=1 (V3*V2) and k1=2 V4*V3 */ |
| |
cptcovn++; |
| |
cptcovprodnoage++;k1++; |
| |
cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/ |
| |
Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but |
| |
because this model-covariate is a construction we invent a new column |
| |
ncovcol + k1 |
| |
If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2 |
| |
Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */ |
| |
cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */ |
| |
Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */ |
| |
Tvard[k1][1] =atoi(strc); /* m 1 for V1*/ |
| |
Tvard[k1][2] =atoi(stre); /* n 4 for V4*/ |
| |
k2=k2+2; |
| |
Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */ |
| |
Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */ |
| |
for (i=1; i<=lastobs;i++){ |
| |
/* Computes the new covariate which is a product of |
| |
covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */ |
| |
covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i]; |
| |
} |
| |
} /* End age is not in the model */ |
| |
} /* End if model includes a product */ |
| |
else { /* no more sum */ |
| |
/*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/ |
| |
/* scanf("%d",i);*/ |
| |
cutl(strd,strc,strb,'V'); |
| |
ks++; /**< Number of simple covariates */ |
| |
cptcovn++; |
| |
Tvar[k]=atoi(strd); |
| |
} |
| |
strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ |
| |
/*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav); |
| |
scanf("%d",i);*/ |
| |
} /* end of loop + on total covariates */ |
| |
} /* end if strlen(modelsave == 0) age*age might exist */ |
| |
} /* end if strlen(model == 0) */ |
| |
|
| |
/*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products. |
| |
If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/ |
| |
|
| |
/* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]); |
| |
printf("cptcovprod=%d ", cptcovprod); |
| |
fprintf(ficlog,"cptcovprod=%d ", cptcovprod); |
| |
|
| |
scanf("%d ",i);*/ |
| |
|
| |
|
| |
return (0); /* with covar[new additional covariate if product] and Tage if age */ |
| |
/*endread:*/ |
| |
printf("Exiting decodemodel: "); |
| |
return (1); |
| |
} |
| |
|
| |
int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn ) |
| |
{ |
| |
int i, m; |
| |
|
| |
for (i=1; i<=imx; i++) { |
| |
for(m=2; (m<= maxwav); m++) { |
| |
if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){ |
| |
anint[m][i]=9999; |
| |
s[m][i]=-1; |
| |
} |
| |
if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){ |
| |
*nberr = *nberr + 1; |
| |
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 (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr); |
| |
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 (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr); |
| |
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; |
| |
} |
| |
} |
| |
} /* agedc > 0 */ |
| |
} |
| |
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(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/ |
| |
} |
| |
/*agev[m][i]=anint[m][i]-annais[i];*/ |
| |
/* agev[m][i] = age[i]+2*m;*/ |
| |
} |
| |
else { /* =9 */ |
| |
agev[m][i]=1; |
| |
s[m][i]=-1; |
| |
} |
| |
} |
| |
else /*= 0 Unknown */ |
| |
agev[m][i]=1; |
| |
} |
| |
|
| |
} |
| |
for (i=1; i<=imx; i++) { |
| |
for(m=firstpass; (m<=lastpass); m++){ |
| |
if (s[m][i] > (nlstate+ndeath)) { |
| |
(*nberr)++; |
| |
printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath); |
| |
fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath); |
| |
return 1; |
| |
} |
| |
} |
| |
} |
| |
|
| |
/*for (i=1; i<=imx; i++){ |
| |
for (m=firstpass; (m<lastpass); m++){ |
| |
printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]); |
| |
} |
| |
|
| |
}*/ |
| |
|
| |
|
| |
printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); |
| |
fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); |
| |
|
| |
return (0); |
| |
/* endread:*/ |
| |
printf("Exiting calandcheckages: "); |
| |
return (1); |
| |
} |
| |
|
| |
#if defined(_MSC_VER) |
| |
/*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/ |
| |
/*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/ |
| |
//#include "stdafx.h" |
| |
//#include <stdio.h> |
| |
//#include <tchar.h> |
| |
//#include <windows.h> |
| |
//#include <iostream> |
| |
typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL); |
| |
|
| |
LPFN_ISWOW64PROCESS fnIsWow64Process; |
| |
|
| |
BOOL IsWow64() |
| |
{ |
| |
BOOL bIsWow64 = FALSE; |
| |
|
| |
//typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS) |
| |
// (HANDLE, PBOOL); |
| |
|
| |
//LPFN_ISWOW64PROCESS fnIsWow64Process; |
| |
|
| |
HMODULE module = GetModuleHandle(_T("kernel32")); |
| |
const char funcName[] = "IsWow64Process"; |
| |
fnIsWow64Process = (LPFN_ISWOW64PROCESS) |
| |
GetProcAddress(module, funcName); |
| |
|
| |
if (NULL != fnIsWow64Process) |
| |
{ |
| |
if (!fnIsWow64Process(GetCurrentProcess(), |
| |
&bIsWow64)) |
| |
//throw std::exception("Unknown error"); |
| |
printf("Unknown error\n"); |
| |
} |
| |
return bIsWow64 != FALSE; |
| |
} |
| |
#endif |
| |
|
| |
void syscompilerinfo() |
| |
{ |
| |
/* #include "syscompilerinfo.h"*/ |
| |
/* command line Intel compiler 32bit windows, XP compatible:*/ |
| |
/* /GS /W3 /Gy |
| |
/Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D |
| |
"_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D |
| |
"UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo |
| |
/Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch" |
| |
*/ |
| |
/* 64 bits */ |
| |
/* |
| |
/GS /W3 /Gy |
| |
/Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG" |
| |
/D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope |
| |
/Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir |
| |
"x64\Release\" /Fp"x64\Release\IMaCh.pch" */ |
| |
/* Optimization are useless and O3 is slower than O2 */ |
| |
/* |
| |
/GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32" |
| |
/D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo |
| |
/Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel |
| |
/Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch" |
| |
*/ |
| |
/* Link is */ /* /OUT:"visual studio |
| |
2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT |
| |
/PDB:"visual studio |
| |
2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE |
| |
"kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib" |
| |
"comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib" |
| |
"oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib" |
| |
/MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO |
| |
/SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker' |
| |
uiAccess='false'" |
| |
/ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF |
| |
/NOLOGO /TLBID:1 |
| |
*/ |
| |
#if defined __INTEL_COMPILER |
| |
#if defined(__GNUC__) |
| |
struct utsname sysInfo; /* For Intel on Linux and OS/X */ |
| |
#endif |
| |
#elif defined(__GNUC__) |
| |
#ifndef __APPLE__ |
| |
#include <gnu/libc-version.h> /* Only on gnu */ |
| |
#endif |
| |
struct utsname sysInfo; |
| |
int cross = CROSS; |
| |
if (cross){ |
| |
printf("Cross-"); |
| |
fprintf(ficlog, "Cross-"); |
| |
} |
| |
#endif |
| |
|
| |
#include <stdint.h> |
| |
|
| |
printf("Compiled with:");fprintf(ficlog,"Compiled with:"); |
| |
#if defined(__clang__) |
| |
printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */ |
| |
#endif |
| |
#if defined(__ICC) || defined(__INTEL_COMPILER) |
| |
printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */ |
| |
#endif |
| |
#if defined(__GNUC__) || defined(__GNUG__) |
| |
printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */ |
| |
#endif |
| |
#if defined(__HP_cc) || defined(__HP_aCC) |
| |
printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */ |
| |
#endif |
| |
#if defined(__IBMC__) || defined(__IBMCPP__) |
| |
printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */ |
| |
#endif |
| |
#if defined(_MSC_VER) |
| |
printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */ |
| |
#endif |
| |
#if defined(__PGI) |
| |
printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */ |
| |
#endif |
| |
#if defined(__SUNPRO_C) || defined(__SUNPRO_CC) |
| |
printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */ |
| |
#endif |
| |
printf(" for ");fprintf(ficlog," for "); |
| |
|
| |
// http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros |
| |
#ifdef _WIN32 // note the underscore: without it, it's not msdn official! |
| |
// Windows (x64 and x86) |
| |
printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) "); |
| |
#elif __unix__ // all unices, not all compilers |
| |
// Unix |
| |
printf("Unix ");fprintf(ficlog,"Unix "); |
| |
#elif __linux__ |
| |
// linux |
| |
printf("linux ");fprintf(ficlog,"linux "); |
| |
#elif __APPLE__ |
| |
// Mac OS, not sure if this is covered by __posix__ and/or __unix__ though.. |
| |
printf("Mac OS ");fprintf(ficlog,"Mac OS "); |
| |
#endif |
| |
|
| |
/* __MINGW32__ */ |
| |
/* __CYGWIN__ */ |
| |
/* __MINGW64__ */ |
| |
// http://msdn.microsoft.com/en-us/library/b0084kay.aspx |
| |
/* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */ |
| |
/* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */ |
| |
/* _WIN64 // Defined for applications for Win64. */ |
| |
/* _M_X64 // Defined for compilations that target x64 processors. */ |
| |
/* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */ |
| |
|
| |
#if UINTPTR_MAX == 0xffffffff |
| |
printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */ |
| |
#elif UINTPTR_MAX == 0xffffffffffffffff |
| |
printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */ |
| |
#else |
| |
printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */ |
| |
#endif |
| |
|
| |
#if defined(__GNUC__) |
| |
# if defined(__GNUC_PATCHLEVEL__) |
| |
# define __GNUC_VERSION__ (__GNUC__ * 10000 \ |
| |
+ __GNUC_MINOR__ * 100 \ |
| |
+ __GNUC_PATCHLEVEL__) |
| |
# else |
| |
# define __GNUC_VERSION__ (__GNUC__ * 10000 \ |
| |
+ __GNUC_MINOR__ * 100) |
| |
# endif |
| |
printf(" using GNU C version %d.\n", __GNUC_VERSION__); |
| |
fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__); |
| |
|
| |
if (uname(&sysInfo) != -1) { |
| |
printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine); |
| |
fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine); |
| |
} |
| |
else |
| |
perror("uname() error"); |
| |
//#ifndef __INTEL_COMPILER |
| |
#if !defined (__INTEL_COMPILER) && !defined(__APPLE__) |
| |
printf("GNU libc version: %s\n", gnu_get_libc_version()); |
| |
fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version()); |
| |
#endif |
| |
#endif |
| |
|
| |
// void main() |
| |
// { |
| |
#if defined(_MSC_VER) |
| |
if (IsWow64()){ |
| |
printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n"); |
| |
fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n"); |
| |
} |
| |
else{ |
| |
printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n"); |
| |
fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n"); |
| |
} |
| |
// printf("\nPress Enter to continue..."); |
| |
// getchar(); |
| |
// } |
| |
|
| |
#endif |
| |
|
| |
|
| |
} |
| |
|
| |
int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){ |
| |
/*--------------- Prevalence limit (period or stable prevalence) --------------*/ |
| |
int i, j, k, i1 ; |
| |
double ftolpl = 1.e-10; |
| |
double age, agebase, agelim; |
| |
|
| |
strcpy(filerespl,"pl"); |
| |
strcat(filerespl,fileres); |
| |
if((ficrespl=fopen(filerespl,"w"))==NULL) { |
| |
printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1; |
| |
fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1; |
| |
} |
| |
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);*/ /* back in main */ |
| |
|
| |
agebase=ageminpar; |
| |
agelim=agemaxpar; |
| |
|
| |
i1=pow(2,cptcoveff); |
| |
if (cptcovn < 1){i1=1;} |
| |
|
| |
for(cptcov=1,k=0;cptcov<=i1;cptcov++){ |
| |
/* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */ |
| |
//for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ |
| |
k=k+1; |
| |
/* to clean */ |
| |
//printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,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"); |
| |
|
| |
fprintf(ficrespl,"#Age "); |
| |
for(j=1;j<=cptcoveff;j++) { |
| |
fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
| |
} |
| |
for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i); |
| |
fprintf(ficrespl,"\n"); |
| |
|
| |
for (age=agebase; age<=agelim; age++){ |
| |
/* for (age=agebase; age<=agebase; 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"); |
| |
} /* Age */ |
| |
/* was end of cptcod */ |
| |
} /* cptcov */ |
| |
return 0; |
| |
} |
| |
|
| |
int hPijx(double *p, int bage, int fage){ |
| |
/*------------- h Pij x at various ages ------------*/ |
| |
|
| |
int stepsize; |
| |
int agelim; |
| |
int hstepm; |
| |
int nhstepm; |
| |
int h, i, i1, j, k; |
| |
|
| |
double agedeb; |
| |
double ***p3mat; |
| |
|
| |
strcpy(filerespij,"pij"); strcat(filerespij,fileres); |
| |
if((ficrespij=fopen(filerespij,"w"))==NULL) { |
| |
printf("Problem with Pij resultfile: %s\n", filerespij); return 1; |
| |
fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1; |
| |
} |
| |
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 "); |
| |
i1= pow(2,cptcoveff); |
| |
/* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */ |
| |
/* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */ |
| |
/* k=k+1; */ |
| |
for (k=1; k <= (int) pow(2,cptcoveff); k++){ |
| |
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++){ |
| |
/*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/ |
| |
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"); |
| |
} |
| |
/*}*/ |
| |
} |
| |
return 0; |
| |
} |
| |
|
| |
|
| |
/***********************************************/ |
| |
/**************** Main Program *****************/ |
| |
/***********************************************/ |
| |
|
| |
int main(int argc, char *argv[]) |
| |
{ |
| |
#ifdef GSL |
| |
const gsl_multimin_fminimizer_type *T; |
| |
size_t iteri = 0, it; |
| |
int rval = GSL_CONTINUE; |
| |
int status = GSL_SUCCESS; |
| |
double ssval; |
| |
#endif |
| |
int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav); |
| |
int i,j, k, n=MAXN,iter=0,m,size=100, cptcod; |
| |
|
| |
int jj, ll, li, lj, lk; |
| |
int numlinepar=0; /* Current linenumber of parameter file */ |
| |
int itimes; |
| |
int NDIM=2; |
| |
int vpopbased=0; |
| |
|
| |
char ca[32], cb[32]; |
| |
/* FILE *fichtm; *//* Html File */ |
| |
/* FILE *ficgp;*/ /*Gnuplot File */ |
| |
struct stat info; |
| |
double agedeb; |
| |
double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20; |
| |
|
| |
double fret; |
| |
double dum; /* Dummy variable */ |
| |
double ***p3mat; |
| |
double ***mobaverage; |
| |
|
| |
char line[MAXLINE]; |
| |
char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE]; |
| |
char pathr[MAXLINE], pathimach[MAXLINE]; |
| |
char *tok, *val; /* pathtot */ |
| |
int firstobs=1, lastobs=10; |
| |
int c, h , cpt; |
| |
int jl; |
| |
int i1, j1, jk, stepsize; |
| |
int *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=0, fage=110, age, agelim, agebase; |
| |
double ftolpl=FTOL; |
| |
double **prlim; |
| |
double ***param; /* Matrix of parameters */ |
| |
double *p; |
| |
double **matcov; /* Matrix of covariance */ |
| |
double ***delti3; /* Scale */ |
| |
double *delti; /* Scale */ |
| |
double ***eij, ***vareij; |
| |
double **varpl; /* Variances of prevalence limits by age */ |
| |
double *epj, vepp; |
| |
|
| |
double 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]="1234"; |
| |
int *dcwave; |
| |
|
| |
char z[1]="c"; |
| |
|
| |
/*char *strt;*/ |
| |
char strtend[80]; |
| |
|
| |
|
| |
/* setlocale (LC_ALL, ""); */ |
| |
/* bindtextdomain (PACKAGE, LOCALEDIR); */ |
| |
/* textdomain (PACKAGE); */ |
| |
/* setlocale (LC_CTYPE, ""); */ |
| |
/* setlocale (LC_MESSAGES, ""); */ |
| |
|
| |
/* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */ |
| |
rstart_time = time(NULL); |
| |
/* (void) gettimeofday(&start_time,&tzp);*/ |
| |
start_time = *localtime(&rstart_time); |
| |
curr_time=start_time; |
| |
/*tml = *localtime(&start_time.tm_sec);*/ |
| |
/* strcpy(strstart,asctime(&tml)); */ |
| |
strcpy(strstart,asctime(&start_time)); |
| |
|
| |
/* printf("Localtime (at start)=%s",strstart); */ |
| |
/* tp.tm_sec = tp.tm_sec +86400; */ |
| |
/* tm = *localtime(&start_time.tm_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.tm_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; |
| |
#ifdef WIN32 |
| |
_getcwd(pathcd, size); |
| |
#else |
| |
getcwd(pathcd, size); |
| |
#endif |
| |
|
| |
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'; |
| |
i=strlen(pathr); |
| |
if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */ |
| |
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); |
| |
#ifdef WIN32 |
| |
_chdir(path); /* Can be a relative path */ |
| |
if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */ |
| |
#else |
| |
chdir(path); /* Can be a relative path */ |
| |
if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */ |
| |
#endif |
| |
printf("Current directory %s!\n",pathcd); |
| |
strcpy(command,"mkdir "); |
| |
strcat(command,optionfilefiname); |
| |
if((outcmd=system(command)) != 0){ |
| |
printf("Directory already exists (or can't create it) %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 --------*/ |
| |
|
| |
/* Main 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); |
| |
|
| |
syscompilerinfo(); |
| |
|
| |
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.tm_sec-start_time.tm_sec,tmpout)); */ |
| |
|
| |
/* */ |
| |
strcpy(fileres,"r"); |
| |
strcat(fileres, optionfilefiname); |
| |
strcat(fileres,".txt"); /* Other files have txt extension */ |
| |
|
| |
/* Main ---------arguments file --------*/ |
| |
|
| |
if((ficpar=fopen(optionfile,"r"))==NULL) { |
| |
printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno)); |
| |
fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno)); |
| |
fflush(ficlog); |
| |
/* goto end; */ |
| |
exit(70); |
| |
} |
| |
|
| |
|
| |
|
| |
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++; |
| |
fputs(line,stdout); |
| |
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=1+age+%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=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); |
| |
if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */ |
| |
model[strlen(model)-1]='\0'; |
| |
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=1+age+%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=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); |
| |
fflush(ficlog); |
| |
/* if(model[0]=='#'|| model[0]== '\0'){ */ |
| |
if(model[0]=='#'){ |
| |
printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \ |
| |
'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \ |
| |
'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \ |
| |
if(mle != -1){ |
| |
printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n"); |
| |
exit(1); |
| |
} |
| |
} |
| |
while((c=getc(ficpar))=='#' && c!= EOF){ |
| |
ungetc(c,ficpar); |
| |
fgets(line, MAXLINE, ficpar); |
| |
numlinepar++; |
| |
fputs(line, stdout); |
| |
//puts(line); |
| |
fputs(line,ficparo); |
| |
fputs(line,ficlog); |
| |
} |
| |
ungetc(c,ficpar); |
| |
|
| |
|
| |
covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */ |
| |
cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/ |
| |
/* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5 |
| |
v1+v2*age+v2*v3 makes cptcovn = 3 |
| |
*/ |
| |
if (strlen(model)>1) |
| |
ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7,age*age makes 3*/ |
| |
else |
| |
ncovmodel=2; /* Constant and age */ |
| |
nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */ |
| |
npar= nforce*ncovmodel; /* Number of parameters like aij*/ |
| |
if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){ |
| |
printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX); |
| |
fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX); |
| |
fflush(stdout); |
| |
fclose (ficlog); |
| |
goto end; |
| |
} |
| |
delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); |
| |
delti=delti3[1][1]; |
| |
/*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/ |
| |
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) { /* Main Wizard */ |
| |
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 guessed parameters */ |
| |
/* Reads comments: lines beginning with '#' */ |
| |
while((c=getc(ficpar))=='#' && c!= EOF){ |
| |
ungetc(c,ficpar); |
| |
fgets(line, MAXLINE, ficpar); |
| |
numlinepar++; |
| |
fputs(line,stdout); |
| |
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); |
| |
|
| |
/* Reads scales values */ |
| |
p=param[1][1]; |
| |
|
| |
/* Reads comments: lines beginning with '#' */ |
| |
while((c=getc(ficpar))=='#' && c!= EOF){ |
| |
ungetc(c,ficpar); |
| |
fgets(line, MAXLINE, ficpar); |
| |
numlinepar++; |
| |
fputs(line,stdout); |
| |
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); |
| |
|
| |
/* Reads covariance matrix */ |
| |
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++; |
| |
fputs(line,stdout); |
| |
fputs(line,ficparo); |
| |
fputs(line,ficlog); |
| |
} |
| |
ungetc(c,ficpar); |
| |
|
| |
matcov=matrix(1,npar,1,npar); |
| |
for(i=1; i <=npar; i++) |
| |
for(j=1; j <=npar; j++) matcov[i][j]=0.; |
| |
|
| |
for(i=1; i <=npar; i++){ |
| |
fscanf(ficpar,"%s",str); |
| |
if(mle==1) |
| |
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 */ |
| |
|
| |
/* Main data |
| |
*/ |
| |
n= lastobs; |
| |
num=lvector(1,n); |
| |
moisnais=vector(1,n); |
| |
annais=vector(1,n); |
| |
moisdc=vector(1,n); |
| |
andc=vector(1,n); |
| |
agedc=vector(1,n); |
| |
cod=ivector(1,n); |
| |
weight=vector(1,n); |
| |
for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */ |
| |
mint=matrix(1,maxwav,1,n); |
| |
anint=matrix(1,maxwav,1,n); |
| |
s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ |
| |
tab=ivector(1,NCOVMAX); |
| |
ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */ |
| |
|
| |
/* Reads data from file datafile */ |
| |
if (readdata(datafile, firstobs, lastobs, &imx)==1) |
| |
goto end; |
| |
|
| |
/* Calculation of the number of parameters from char model */ |
| |
/* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 |
| |
k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4 |
| |
k=3 V4 Tvar[k=3]= 4 (from V4) |
| |
k=2 V1 Tvar[k=2]= 1 (from V1) |
| |
k=1 Tvar[1]=2 (from V2) |
| |
*/ |
| |
Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */ |
| |
/* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). |
| |
For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, |
| |
Tvar[4=age*V3] is 3 and 'age' is recorded in Tage. |
| |
*/ |
| |
/* For model-covariate k tells which data-covariate to use but |
| |
because this model-covariate is a construction we invent a new column |
| |
ncovcol + k1 |
| |
If already ncovcol=4 and model=V2+V1+V1*V4+age*V3 |
| |
Tvar[3=V1*V4]=4+1 etc */ |
| |
Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */ |
| |
/* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3 |
| |
if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2) |
| |
*/ |
| |
Tvaraff=ivector(1,NCOVMAX); /* Unclear */ |
| |
Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1] and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm |
| |
* For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. |
| |
* Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */ |
| |
Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age |
| |
4 covariates (3 plus signs) |
| |
Tage[1=V3*age]= 4; Tage[2=age*V4] = 3 |
| |
*/ |
| |
|
| |
/* Main decodemodel */ |
| |
|
| |
|
| |
if(decodemodel(model, lastobs) == 1) |
| |
goto end; |
| |
|
| |
if((double)(lastobs-imx)/(double)imx > 1.10){ |
| |
nbwarn++; |
| |
printf("Warning: The value of parameter lastobs=%d is big compared to the \n effective number of cases imx=%d, please adjust, \n otherwise you are allocating more memory than necessary.\n",lastobs, imx); |
| |
fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n effective number of cases imx=%d, please adjust, \n otherwise you are allocating more memory than necessary.\n",lastobs, imx); |
| |
} |
| |
/* if(mle==1){*/ |
| |
if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/ |
| |
for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */ |
| |
} |
| |
|
| |
/*-calculation of age at interview from date of interview and age at death -*/ |
| |
agev=matrix(1,maxwav,1,imx); |
| |
|
| |
if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1) |
| |
goto end; |
| |
|
| |
|
| |
agegomp=(int)agemin; |
| |
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 */ |
| |
|
| |
nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); |
| |
ncodemax[1]=1; |
| |
Ndum =ivector(-1,NCOVMAX); |
| |
if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */ |
| |
tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */ |
| |
/* Nbcode gives the value of the lth modality of jth covariate, in |
| |
V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/ |
| |
/* 1 to ncodemax[j] is the maximum value of this jth covariate */ |
| |
|
| |
codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */ |
| |
/*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/ |
| |
/* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/ |
| |
h=0; |
| |
|
| |
|
| |
/*if (cptcovn > 0) */ |
| |
|
| |
|
| |
m=pow(2,cptcoveff); |
| |
|
| |
for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */ |
| |
for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ |
| |
for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/ |
| |
for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ |
| |
h++; |
| |
if (h>m) |
| |
h=1; |
| |
/**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1 |
| |
* For k=4 covariates, h goes from 1 to 2**k |
| |
* codtabm(h,k)= 1 & (h-1) >> (k-1) ; |
| |
* h\k 1 2 3 4 |
| |
*______________________________ |
| |
* 1 i=1 1 i=1 1 i=1 1 i=1 1 |
| |
* 2 2 1 1 1 |
| |
* 3 i=2 1 2 1 1 |
| |
* 4 2 2 1 1 |
| |
* 5 i=3 1 i=2 1 2 1 |
| |
* 6 2 1 2 1 |
| |
* 7 i=4 1 2 2 1 |
| |
* 8 2 2 2 1 |
| |
* 9 i=5 1 i=3 1 i=2 1 1 |
| |
* 10 2 1 1 1 |
| |
* 11 i=6 1 2 1 1 |
| |
* 12 2 2 1 1 |
| |
* 13 i=7 1 i=4 1 2 1 |
| |
* 14 2 1 2 1 |
| |
* 15 i=8 1 2 2 1 |
| |
* 16 2 2 2 1 |
| |
*/ |
| |
codtab[h][k]=j; |
| |
/* codtab[12][3]=1; */ |
| |
/*codtab[h][Tvar[k]]=j;*/ |
| |
printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]); |
| |
} |
| |
} |
| |
} |
| |
} |
| |
/* 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);*/ |
| |
|
| |
free_ivector(Ndum,-1,NCOVMAX); |
| |
|
| |
|
| |
|
| |
/* Initialisation of ----------- 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"); |
| |
fprintf(ficgp,"set datafile missing 'NaNq'\n"); |
| |
} |
| |
/* fclose(ficgp);*/ |
| |
|
| |
|
| |
/* Initialisation of --------- 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); |
| |
#ifdef WIN32 |
| |
_chdir(optionfilefiname); /* Move to directory named optionfile */ |
| |
#else |
| |
chdir(optionfilefiname); /* Move to directory named optionfile */ |
| |
#endif |
| |
|
| |
|
| |
/* 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*/ |
| |
/* For mortality only */ |
| |
if (mle==-3){ |
| |
ximort=matrix(1,NDIM,1,NDIM); |
| |
/* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */ |
| |
cens=ivector(1,n); |
| |
ageexmed=vector(1,n); |
| |
agecens=vector(1,n); |
| |
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]);*/ |
| |
|
| |
|
| |
#ifdef GSL |
| |
printf("GSL optimization\n"); fprintf(ficlog,"Powell\n"); |
| |
#else |
| |
printf("Powell\n"); fprintf(ficlog,"Powell\n"); |
| |
#endif |
| |
strcpy(filerespow,"pow-mort"); |
| |
strcat(filerespow,fileres); |
| |
if((ficrespow=fopen(filerespow,"w"))==NULL) { |
| |
printf("Problem with resultfile: %s\n", filerespow); |
| |
fprintf(ficlog,"Problem with resultfile: %s\n", filerespow); |
| |
} |
| |
#ifdef GSL |
| |
fprintf(ficrespow,"# GSL optimization\n# iter -2*LL"); |
| |
#else |
| |
fprintf(ficrespow,"# Powell\n# iter -2*LL"); |
| |
#endif |
| |
/* for (i=1;i<=nlstate;i++) |
| |
for(j=1;j<=nlstate+ndeath;j++) |
| |
if(j!=i)fprintf(ficrespow," p%1d%1d",i,j); |
| |
*/ |
| |
fprintf(ficrespow,"\n"); |
| |
#ifdef GSL |
| |
/* gsl starts here */ |
| |
T = gsl_multimin_fminimizer_nmsimplex; |
| |
gsl_multimin_fminimizer *sfm = NULL; |
| |
gsl_vector *ss, *x; |
| |
gsl_multimin_function minex_func; |
| |
|
| |
/* Initial vertex size vector */ |
| |
ss = gsl_vector_alloc (NDIM); |
| |
|
| |
if (ss == NULL){ |
| |
GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0); |
| |
} |
| |
/* Set all step sizes to 1 */ |
| |
gsl_vector_set_all (ss, 0.001); |
| |
|
| |
/* Starting point */ |
| |
|
| |
x = gsl_vector_alloc (NDIM); |
| |
|
| |
if (x == NULL){ |
| |
gsl_vector_free(ss); |
| |
GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0); |
| |
} |
| |
|
| |
/* Initialize method and iterate */ |
| |
/* p[1]=0.0268; p[NDIM]=0.083; */ |
| |
/* gsl_vector_set(x, 0, 0.0268); */ |
| |
/* gsl_vector_set(x, 1, 0.083); */ |
| |
gsl_vector_set(x, 0, p[1]); |
| |
gsl_vector_set(x, 1, p[2]); |
| |
|
| |
minex_func.f = &gompertz_f; |
| |
minex_func.n = NDIM; |
| |
minex_func.params = (void *)&p; /* ??? */ |
| |
|
| |
sfm = gsl_multimin_fminimizer_alloc (T, NDIM); |
| |
gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss); |
| |
|
| |
printf("Iterations beginning .....\n\n"); |
| |
printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n"); |
| |
|
| |
iteri=0; |
| |
while (rval == GSL_CONTINUE){ |
| |
iteri++; |
| |
status = gsl_multimin_fminimizer_iterate(sfm); |
| |
|
| |
if (status) printf("error: %s\n", gsl_strerror (status)); |
| |
fflush(0); |
| |
|
| |
if (status) |
| |
break; |
| |
|
| |
rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6); |
| |
ssval = gsl_multimin_fminimizer_size (sfm); |
| |
|
| |
if (rval == GSL_SUCCESS) |
| |
printf ("converged to a local maximum at\n"); |
| |
|
| |
printf("%5d ", iteri); |
| |
for (it = 0; it < NDIM; it++){ |
| |
printf ("%10.5f ", gsl_vector_get (sfm->x, it)); |
| |
} |
| |
printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval); |
| |
} |
| |
|
| |
printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n"); |
| |
|
| |
gsl_vector_free(x); /* initial values */ |
| |
gsl_vector_free(ss); /* inital step size */ |
| |
for (it=0; it<NDIM; it++){ |
| |
p[it+1]=gsl_vector_get(sfm->x,it); |
| |
fprintf(ficrespow," %.12lf", p[it]); |
| |
} |
| |
gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */ |
| |
#endif |
| |
#ifdef POWELL |
| |
powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz); |
| |
#endif |
| |
fclose(ficrespow); |
| |
|
| |
hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); |
| |
|
| |
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); |
| |
#ifdef GSL |
| |
free_ivector(cens,1,n); |
| |
free_vector(agecens,1,n); |
| |
free_ivector(dcwave,1,n); |
| |
free_matrix(ximort,1,NDIM,1,NDIM); |
| |
#endif |
| |
} /* Endof if mle==-3 mortality only */ |
| |
/* Standard maximisation */ |
| |
else{ /* For mle >=1 */ |
| |
globpr=0;/* debug */ |
| |
/* Computes likelihood for initial parameters */ |
| |
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; /* again, 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, Real Maximisation */ |
| |
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=1+age+%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("%12.7f ",p[jk]); |
| |
fprintf(ficlog,"%12.7f ",p[jk]); |
| |
fprintf(ficres,"%12.7f ",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); |
| |
fputs(line,stdout); |
| |
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); |
| |
|
| |
/* Other stuffs, more or less useful */ |
| |
while((c=getc(ficpar))=='#' && c!= EOF){ |
| |
ungetc(c,ficpar); |
| |
fgets(line, MAXLINE, ficpar); |
| |
fputs(line,stdout); |
| |
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); |
| |
fputs(line,stdout); |
| |
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); |
| |
fputs(line,stdout); |
| |
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); |
| |
|
| |
|
| |
/* Other results (useful)*/ |
| |
|
| |
|
| |
/*--------------- Prevalence limit (period or stable prevalence) --------------*/ |
| |
/*#include "prevlim.h"*/ /* Use ficrespl, ficlog */ |
| |
prlim=matrix(1,nlstate,1,nlstate); |
| |
prevalence_limit(p, prlim, ageminpar, agemaxpar); |
| |
fclose(ficrespl); |
| |
|
| |
#ifdef FREEEXIT2 |
| |
#include "freeexit2.h" |
| |
#endif |
| |
|
| |
/*------------- h Pij x at various ages ------------*/ |
| |
/*#include "hpijx.h"*/ |
| |
hPijx(p, bage, fage); |
| |
fclose(ficrespij); |
| |
|
| |
/*-------------- Variance of one-step probabilities---*/ |
| |
k=1; |
| |
varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart); |
| |
|
| |
|
| |
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); */ |
| |
/* } */ |
| |
} |
| |
|
| |
/* ------ Other prevalence ratios------------ */ |
| |
|
| |
/* 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); |
| |
} |
| |
} |
| |
|
| |
|
| |
/*---------- Health expectancies, no variances ------------*/ |
| |
|
| |
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); |
| |
/*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ |
| |
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ |
| |
|
| |
for (k=1; k <= (int) pow(2,cptcoveff); k++){ |
| |
fprintf(ficreseij,"\n#****** "); |
| |
for(j=1;j<=cptcoveff;j++) { |
| |
fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
| |
} |
| |
fprintf(ficreseij,"******\n"); |
| |
|
| |
eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); |
| |
oldm=oldms;savm=savms; |
| |
evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart); |
| |
|
| |
free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage); |
| |
/*}*/ |
| |
} |
| |
fclose(ficreseij); |
| |
|
| |
|
| |
/*---------- Health expectancies and variances ------------*/ |
| |
|
| |
|
| |
strcpy(filerest,"t"); |
| |
strcat(filerest,fileres); |
| |
if((ficrest=fopen(filerest,"w"))==NULL) { |
| |
printf("Problem with total LE resultfile: %s\n", filerest);goto end; |
| |
fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end; |
| |
} |
| |
printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); |
| |
fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); |
| |
|
| |
|
| |
strcpy(fileresstde,"stde"); |
| |
strcat(fileresstde,fileres); |
| |
if((ficresstdeij=fopen(fileresstde,"w"))==NULL) { |
| |
printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0); |
| |
fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0); |
| |
} |
| |
printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde); |
| |
fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde); |
| |
|
| |
strcpy(filerescve,"cve"); |
| |
strcat(filerescve,fileres); |
| |
if((ficrescveij=fopen(filerescve,"w"))==NULL) { |
| |
printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0); |
| |
fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0); |
| |
} |
| |
printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve); |
| |
fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve); |
| |
|
| |
strcpy(fileresv,"v"); |
| |
strcat(fileresv,fileres); |
| |
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); |
| |
|
| |
/*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ |
| |
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ |
| |
|
| |
for (k=1; k <= (int) pow(2,cptcoveff); k++){ |
| |
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(ficresstdeij,"\n#****** "); |
| |
fprintf(ficrescveij,"\n#****** "); |
| |
for(j=1;j<=cptcoveff;j++) { |
| |
fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
| |
fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
| |
} |
| |
fprintf(ficresstdeij,"******\n"); |
| |
fprintf(ficrescveij,"******\n"); |
| |
|
| |
fprintf(ficresvij,"\n#****** "); |
| |
for(j=1;j<=cptcoveff;j++) |
| |
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; |
| |
cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart); |
| |
/* |
| |
*/ |
| |
/* goto endfree; */ |
| |
|
| |
vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); |
| |
pstamp(ficrest); |
| |
|
| |
|
| |
for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/ |
| |
oldm=oldms;savm=savms; /* Segmentation fault */ |
| |
cptcod= 0; /* To be deleted */ |
| |
varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */ |
| |
fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are "); |
| |
if(vpopbased==1) |
| |
fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav); |
| |
else |
| |
fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n"); |
| |
fprintf(ficrest,"# Age e.. (std) "); |
| |
for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i); |
| |
fprintf(ficrest,"\n"); |
| |
|
| |
epj=vector(1,nlstate+1); |
| |
for(age=bage; age <=fage ;age++){ |
| |
prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); |
| |
if (vpopbased==1) { |
| |
if(mobilav ==0){ |
| |
for(i=1; i<=nlstate;i++) |
| |
prlim[i][i]=probs[(int)age][i][k]; |
| |
}else{ /* mobilav */ |
| |
for(i=1; i<=nlstate;i++) |
| |
prlim[i][i]=mobaverage[(int)age][i][k]; |
| |
} |
| |
} |
| |
|
| |
fprintf(ficrest," %4.0f",age); |
| |
for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){ |
| |
for(i=1, epj[j]=0.;i <=nlstate;i++) { |
| |
epj[j] += prlim[i][i]*eij[i][j][(int)age]; |
| |
/* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/ |
| |
} |
| |
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,NCOVMAX,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(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++){*/ |
| |
|
| |
for (k=1; k <= (int) pow(2,cptcoveff); k++){ |
| |
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 */ |
| |
/* endfree:*/ |
| |
free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */ |
| |
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,NCOVMAX); |
| |
free_ivector(Tvar,1,NCOVMAX); |
| |
free_ivector(Tprod,1,NCOVMAX); |
| |
free_ivector(Tvaraff,1,NCOVMAX); |
| |
free_ivector(Tage,1,NCOVMAX); |
| |
|
| |
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);*/ |
| |
rend_time = time(NULL); |
| |
end_time = *localtime(&rend_time); |
| |
/* tml = *localtime(&end_time.tm_sec); */ |
| |
strcpy(strtend,asctime(&end_time)); |
| |
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(rend_time -rstart_time,tmpout)); |
| |
|
| |
printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time)); |
| |
fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout)); |
| |
fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time)); |
| |
/* 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); |
| |
#ifdef WIN32 |
| |
if (_chdir(pathcd) != 0) |
| |
printf("Can't move to directory %s!\n",path); |
| |
if(_getcwd(pathcd,MAXLINE) > 0) |
| |
#else |
| |
if(chdir(pathcd) != 0) |
| |
printf("Can't move to directory %s!\n", path); |
| |
if (getcwd(pathcd, MAXLINE) > 0) |
| |
#endif |
| |
printf("Current directory %s!\n",pathcd); |
| |
/*strcat(plotcmd,CHARSEPARATOR);*/ |
| |
sprintf(plotcmd,"gnuplot"); |
| |
#ifdef _WIN32 |
| |
sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach); |
| |
#endif |
| |
if(!stat(plotcmd,&info)){ |
| |
printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout); |
| |
if(!stat(getenv("GNUPLOTBIN"),&info)){ |
| |
printf("Error or 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("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd); |
| |
printf("\n Trying if gnuplot resides on the same directory that IMaCh\n"); |
| |
sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot); |
| |
if((outcmd=system(plotcmd)) != 0) |
| |
printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd); |
| |
} |
| |
printf(" Successful, please wait..."); |
| |
while (z[0] != 'q') { |
| |
/* chdir(path); */ |
| |
printf("\nType e to edit results with your browser, g to graph again and q for exit: "); |
| |
scanf("%s",z); |
| |
/* if (z[0] == 'c') system("./imach"); */ |
| |
if (z[0] == 'e') { |
| |
#ifdef __APPLE__ |
| |
sprintf(pplotcmd, "open %s", optionfilehtm); |
| |
#elif __linux |
| |
sprintf(pplotcmd, "xdg-open %s", optionfilehtm); |
| |
#else |
| |
sprintf(pplotcmd, "%s", optionfilehtm); |
| |
#endif |
| |
printf("Starting browser with: %s",pplotcmd);fflush(stdout); |
| |
system(pplotcmd); |
| |
} |
| |
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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