version 1.165, 2014/12/16 11:20:36
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version 1.204, 2015/10/01 16:20:26
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/* $Id$ |
/* $Id$ |
$State$ |
$State$ |
$Log$ |
$Log$ |
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Revision 1.204 2015/10/01 16:20:26 brouard |
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Summary: Some new graphs of contribution to likelihood |
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Revision 1.203 2015/09/30 17:45:14 brouard |
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Summary: looking at better estimation of the hessian |
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Also a better criteria for convergence to the period prevalence And |
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therefore adding the number of years needed to converge. (The |
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prevalence in any alive state shold sum to one |
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Revision 1.202 2015/09/22 19:45:16 brouard |
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Summary: Adding some overall graph on contribution to likelihood. Might change |
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Revision 1.201 2015/09/15 17:34:58 brouard |
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Summary: 0.98r0 |
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- Some new graphs like suvival functions |
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- Some bugs fixed like model=1+age+V2. |
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Revision 1.200 2015/09/09 16:53:55 brouard |
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Summary: Big bug thanks to Flavia |
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Even model=1+age+V2. did not work anymore |
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Revision 1.199 2015/09/07 14:09:23 brouard |
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Summary: 0.98q6 changing default small png format for graph to vectorized svg. |
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Revision 1.198 2015/09/03 07:14:39 brouard |
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Summary: 0.98q5 Flavia |
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Revision 1.197 2015/09/01 18:24:39 brouard |
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*** empty log message *** |
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Revision 1.196 2015/08/18 23:17:52 brouard |
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Summary: 0.98q5 |
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Revision 1.195 2015/08/18 16:28:39 brouard |
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Summary: Adding a hack for testing purpose |
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After reading the title, ftol and model lines, if the comment line has |
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a q, starting with #q, the answer at the end of the run is quit. It |
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permits to run test files in batch with ctest. The former workaround was |
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$ echo q | imach foo.imach |
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Revision 1.194 2015/08/18 13:32:00 brouard |
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Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line. |
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Revision 1.193 2015/08/04 07:17:42 brouard |
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Summary: 0.98q4 |
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Revision 1.192 2015/07/16 16:49:02 brouard |
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Summary: Fixing some outputs |
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Revision 1.191 2015/07/14 10:00:33 brouard |
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Summary: Some fixes |
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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) |
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Fix 1+age+. |
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Revision 1.189 2015/04/30 14:45:16 brouard |
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Summary: 0.98q2 |
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Revision 1.188 2015/04/30 08:27:53 brouard |
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*** empty log message *** |
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Revision 1.187 2015/04/29 09:11:15 brouard |
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*** empty log message *** |
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Revision 1.186 2015/04/23 12:01:52 brouard |
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Summary: V1*age is working now, version 0.98q1 |
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Some codes had been disabled in order to simplify and Vn*age was |
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working in the optimization phase, ie, giving correct MLE parameters, |
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but, as usual, outputs were not correct and program core dumped. |
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Revision 1.185 2015/03/11 13:26:42 brouard |
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Summary: Inclusion of compile and links command line for Intel Compiler |
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Revision 1.184 2015/03/11 11:52:39 brouard |
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Summary: Back from Windows 8. Intel Compiler |
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Revision 1.183 2015/03/10 20:34:32 brouard |
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Summary: 0.98q0, trying with directest, mnbrak fixed |
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We use directest instead of original Powell test; probably no |
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incidence on the results, but better justifications; |
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We fixed Numerical Recipes mnbrak routine which was wrong and gave |
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wrong results. |
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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 |
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Author: Nicolas Brouard |
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Revision 1.181 2015/02/11 23:22:24 brouard |
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Summary: Comments on Powell added |
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Author: |
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Revision 1.180 2015/02/11 17:33:45 brouard |
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Summary: Finishing move from main to function (hpijx and prevalence_limit) |
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Revision 1.179 2015/01/04 09:57:06 brouard |
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Summary: back to OS/X |
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Revision 1.178 2015/01/04 09:35:48 brouard |
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*** empty log message *** |
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Revision 1.177 2015/01/03 18:40:56 brouard |
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Summary: Still testing ilc32 on OSX |
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Revision 1.176 2015/01/03 16:45:04 brouard |
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*** empty log message *** |
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Revision 1.175 2015/01/03 16:33:42 brouard |
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*** empty log message *** |
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Revision 1.174 2015/01/03 16:15:49 brouard |
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Summary: Still in cross-compilation |
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Revision 1.173 2015/01/03 12:06:26 brouard |
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Summary: trying to detect cross-compilation |
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Revision 1.172 2014/12/27 12:07:47 brouard |
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Summary: Back from Visual Studio and Intel, options for compiling for Windows XP |
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Revision 1.171 2014/12/23 13:26:59 brouard |
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Summary: Back from Visual C |
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Still problem with utsname.h on Windows |
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Revision 1.170 2014/12/23 11:17:12 brouard |
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Summary: Cleaning some \%% back to %% |
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The escape was mandatory for a specific compiler (which one?), but too many warnings. |
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Revision 1.169 2014/12/22 23:08:31 brouard |
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Summary: 0.98p |
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Outputs some informations on compiler used, OS etc. Testing on different platforms. |
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Revision 1.168 2014/12/22 15:17:42 brouard |
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Summary: update |
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Revision 1.167 2014/12/22 13:50:56 brouard |
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Summary: Testing uname and compiler version and if compiled 32 or 64 |
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Testing on Linux 64 |
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Revision 1.166 2014/12/22 11:40:47 brouard |
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*** empty log message *** |
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Revision 1.165 2014/12/16 11:20:36 brouard |
Revision 1.165 2014/12/16 11:20:36 brouard |
Summary: After compiling on Visual C |
Summary: After compiling on Visual C |
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Line 502
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Line 655
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end |
end |
*/ |
*/ |
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/* #define DEBUG */ |
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/* #define DEBUGBRENT */ |
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/* #define DEBUGLINMIN */ |
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/* #define DEBUGHESS */ |
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#define DEBUGHESSIJ |
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/* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan)*\/ */ |
#define POWELL /* Instead of NLOPT */ |
#define POWELL /* Instead of NLOPT */ |
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#define POWELLF1F3 /* Skip test */ |
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/* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */ |
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/* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */ |
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#include <math.h> |
#include <math.h> |
#include <stdio.h> |
#include <stdio.h> |
Line 511
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Line 673
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#ifdef _WIN32 |
#ifdef _WIN32 |
#include <io.h> |
#include <io.h> |
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#include <windows.h> |
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#include <tchar.h> |
#else |
#else |
#include <unistd.h> |
#include <unistd.h> |
#endif |
#endif |
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#include <limits.h> |
#include <limits.h> |
#include <sys/types.h> |
#include <sys/types.h> |
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#if defined(__GNUC__) |
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#include <sys/utsname.h> /* Doesn't work on Windows */ |
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#endif |
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#include <sys/stat.h> |
#include <sys/stat.h> |
#include <errno.h> |
#include <errno.h> |
/* extern int errno; */ |
/* extern int errno; */ |
Line 535
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Line 704
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#include <gsl/gsl_multimin.h> |
#include <gsl/gsl_multimin.h> |
#endif |
#endif |
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#ifdef NLOPT |
#ifdef NLOPT |
#include <nlopt.h> |
#include <nlopt.h> |
typedef struct { |
typedef struct { |
Line 561 typedef struct {
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Line 731 typedef struct {
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#define NLSTATEMAX 8 /**< Maximum number of live states (for func) */ |
#define NLSTATEMAX 8 /**< Maximum number of live states (for func) */ |
#define NDEATHMAX 8 /**< Maximum number of dead states (for func) */ |
#define NDEATHMAX 8 /**< Maximum number of dead states (for func) */ |
#define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */ |
#define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */ |
#define codtabm(h,k) 1 & (h-1) >> (k-1) ; |
#define codtabm(h,k) (1 & (h-1) >> (k-1))+1 |
#define MAXN 20000 |
#define MAXN 20000 |
#define YEARM 12. /**< Number of months per year */ |
#define YEARM 12. /**< Number of months per year */ |
#define AGESUP 130 |
#define AGESUP 130 |
#define AGEBASE 40 |
#define AGEBASE 40 |
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#define AGEOVERFLOW 1.e20 |
#define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */ |
#define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */ |
#ifdef _WIN32 |
#ifdef _WIN32 |
#define DIRSEPARATOR '\\' |
#define DIRSEPARATOR '\\' |
Line 579 typedef struct {
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Line 750 typedef struct {
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/* $Id$ */ |
/* $Id$ */ |
/* $State$ */ |
/* $State$ */ |
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#include "version.h" |
char version[]="Imach version 0.99, September 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)"; |
char version[]=__IMACH_VERSION__; |
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char copyright[]="October 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015"; |
char fullversion[]="$Revision$ $Date$"; |
char fullversion[]="$Revision$ $Date$"; |
char strstart[80]; |
char strstart[80]; |
char optionfilext[10], optionfilefiname[FILENAMELENGTH]; |
char optionfilext[10], optionfilefiname[FILENAMELENGTH]; |
int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */ |
int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */ |
int nvar=0, nforce=0; /* Number of variables, number of forces */ |
int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */ |
/* Number of covariates model=V2+V1+ V3*age+V2*V4 */ |
/* Number of covariates model=V2+V1+ V3*age+V2*V4 */ |
int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */ |
int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */ |
int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */ |
int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */ |
Line 647 char command[FILENAMELENGTH];
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Line 819 char command[FILENAMELENGTH];
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int outcmd=0; |
int outcmd=0; |
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char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH]; |
char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH]; |
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char fileresu[FILENAMELENGTH]; /* fileres without r in front */ |
char filelog[FILENAMELENGTH]; /* Log file */ |
char filelog[FILENAMELENGTH]; /* Log file */ |
char filerest[FILENAMELENGTH]; |
char filerest[FILENAMELENGTH]; |
char fileregp[FILENAMELENGTH]; |
char fileregp[FILENAMELENGTH]; |
Line 695 static double maxarg1,maxarg2;
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Line 867 static double maxarg1,maxarg2;
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#define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a)) |
#define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a)) |
#define rint(a) floor(a+0.5) |
#define rint(a) floor(a+0.5) |
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/* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */ |
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#define mytinydouble 1.0e-16 |
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/* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */ |
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/* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */ |
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/* static double dsqrarg; */ |
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/* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */ |
static double sqrarg; |
static double sqrarg; |
#define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg) |
#define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg) |
#define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} |
#define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} |
Line 710 int estepm;
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Line 887 int estepm;
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int m,nb; |
int m,nb; |
long *num; |
long *num; |
int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens; |
int firstpass=0, lastpass=4,*cod, *cens; |
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int *ncodemax; /* ncodemax[j]= Number of modalities of the j th |
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covariate for which somebody answered excluding |
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undefined. Usually 2: 0 and 1. */ |
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int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th |
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covariate for which somebody answered including |
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undefined. Usually 3: -1, 0 and 1. */ |
double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint; |
double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint; |
double **pmmij, ***probs; |
double **pmmij, ***probs; |
double *ageexmed,*agecens; |
double *ageexmed,*agecens; |
Line 721 int **s; /* Status */
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Line 904 int **s; /* Status */
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double *agedc; |
double *agedc; |
double **covar; /**< covar[j,i], value of jth covariate for individual i, |
double **covar; /**< covar[j,i], value of jth covariate for individual i, |
* covar=matrix(0,NCOVMAX,1,n); |
* covar=matrix(0,NCOVMAX,1,n); |
* cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */ |
* cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */ |
double idx; |
double idx; |
int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */ |
int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */ |
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int *Tage; |
int *Ndum; /** Freq of modality (tricode */ |
int *Ndum; /** Freq of modality (tricode */ |
int **codtab; /**< codtab=imatrix(1,100,1,10); */ |
/* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */ |
int **Tvard, *Tprod, cptcovprod, *Tvaraff; |
int **Tvard, *Tprod, cptcovprod, *Tvaraff; |
double *lsurv, *lpop, *tpop; |
double *lsurv, *lpop, *tpop; |
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Line 739 static int split( char *path, char *dirc
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Line 923 static int split( char *path, char *dirc
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the name of the file (name), its extension only (ext) and its first part of the name (finame) |
the name of the file (name), its extension only (ext) and its first part of the name (finame) |
*/ |
*/ |
char *ss; /* pointer */ |
char *ss; /* pointer */ |
int l1, l2; /* length counters */ |
int l1=0, l2=0; /* length counters */ |
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l1 = strlen(path ); /* length of path */ |
l1 = strlen(path ); /* length of path */ |
if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH ); |
if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH ); |
Line 750 static int split( char *path, char *dirc
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Line 934 static int split( char *path, char *dirc
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printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/ |
printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/ |
/* get current working directory */ |
/* get current working directory */ |
/* extern char* getcwd ( char *buf , int len);*/ |
/* extern char* getcwd ( char *buf , int len);*/ |
if ( getcwd( dirc, FILENAME_MAX ) == NULL ) { |
#ifdef WIN32 |
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if (_getcwd( dirc, FILENAME_MAX ) == NULL ) { |
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#else |
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if (getcwd(dirc, FILENAME_MAX) == NULL) { |
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#endif |
return( GLOCK_ERROR_GETCWD ); |
return( GLOCK_ERROR_GETCWD ); |
} |
} |
/* got dirc from getcwd*/ |
/* got dirc from getcwd*/ |
Line 761 static int split( char *path, char *dirc
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Line 949 static int split( char *path, char *dirc
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if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH ); |
if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH ); |
strcpy( name, ss ); /* save file name */ |
strcpy( name, ss ); /* save file name */ |
strncpy( dirc, path, l1 - l2 ); /* now the directory */ |
strncpy( dirc, path, l1 - l2 ); /* now the directory */ |
dirc[l1-l2] = 0; /* add zero */ |
dirc[l1-l2] = '\0'; /* add zero */ |
printf(" DIRC2 = %s \n",dirc); |
printf(" DIRC2 = %s \n",dirc); |
} |
} |
/* We add a separator at the end of dirc if not exists */ |
/* We add a separator at the end of dirc if not exists */ |
Line 813 char *trimbb(char *out, char *in)
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Line 1001 char *trimbb(char *out, char *in)
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return s; |
return s; |
} |
} |
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/* char *substrchaine(char *out, char *in, char *chain) */ |
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/* { */ |
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/* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */ |
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/* char *s, *t; */ |
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/* t=in;s=out; */ |
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/* while ((*in != *chain) && (*in != '\0')){ */ |
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/* *out++ = *in++; */ |
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/* } */ |
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/* /\* *in matches *chain *\/ */ |
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/* while ((*in++ == *chain++) && (*in != '\0')){ */ |
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/* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */ |
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/* } */ |
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/* in--; chain--; */ |
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/* while ( (*in != '\0')){ */ |
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/* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */ |
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/* *out++ = *in++; */ |
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/* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */ |
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/* } */ |
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/* *out='\0'; */ |
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/* out=s; */ |
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/* return out; */ |
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/* } */ |
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char *substrchaine(char *out, char *in, char *chain) |
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{ |
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/* Substract chain 'chain' from 'in', return and output 'out' */ |
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/* in="V1+V1*age+age*age+V2", chain="age*age" */ |
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char *strloc; |
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strcpy (out, in); |
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strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */ |
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printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out); |
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if(strloc != NULL){ |
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/* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */ |
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memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1); |
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/* strcpy (strloc, strloc +strlen(chain));*/ |
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} |
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printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out); |
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return out; |
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} |
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char *cutl(char *blocc, char *alocc, char *in, char occ) |
char *cutl(char *blocc, char *alocc, char *in, char occ) |
{ |
{ |
/* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' |
/* 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') |
and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2') |
gives blocc="abcdef2ghi" and alocc="j". |
gives blocc="abcdef" and alocc="ghi2j". |
If occ is not found blocc is null and alocc is equal to in. Returns blocc |
If occ is not found blocc is null and alocc is equal to in. Returns blocc |
*/ |
*/ |
char *s, *t; |
char *s, *t; |
Line 843 char *cutl(char *blocc, char *alocc, cha
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Line 1074 char *cutl(char *blocc, char *alocc, cha
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} |
} |
char *cutv(char *blocc, char *alocc, char *in, char occ) |
char *cutv(char *blocc, char *alocc, char *in, char occ) |
{ |
{ |
/* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' |
/* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ' |
and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2') |
and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2') |
gives blocc="abcdef2ghi" and alocc="j". |
gives blocc="abcdef2ghi" and alocc="j". |
If occ is not found blocc is null and alocc is equal to in. Returns alocc |
If occ is not found blocc is null and alocc is equal to in. Returns alocc |
Line 1154 double f1dim(double x)
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Line 1385 double f1dim(double x)
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/*****************brent *************************/ |
/*****************brent *************************/ |
double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin) |
double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin) |
{ |
{ |
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/* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is |
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* between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates |
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* the minimum to a fractional precision of about tol using Brent’s method. The abscissa of |
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* the minimum is returned as xmin, and the minimum function value is returned as brent , the |
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* returned function value. |
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*/ |
int iter; |
int iter; |
double a,b,d,etemp; |
double a,b,d,etemp; |
double fu=0,fv,fw,fx; |
double fu=0,fv,fw,fx; |
Line 1207 double brent(double ax, double bx, doubl
|
Line 1444 double brent(double ax, double bx, doubl
|
if (fu <= fx) { |
if (fu <= fx) { |
if (u >= x) a=x; else b=x; |
if (u >= x) a=x; else b=x; |
SHFT(v,w,x,u) |
SHFT(v,w,x,u) |
SHFT(fv,fw,fx,fu) |
SHFT(fv,fw,fx,fu) |
} else { |
} else { |
if (u < x) a=u; else b=u; |
if (u < x) a=u; else b=u; |
if (fu <= fw || w == x) { |
if (fu <= fw || w == x) { |
v=w; |
v=w; |
w=u; |
w=u; |
fv=fw; |
fv=fw; |
fw=fu; |
fw=fu; |
} else if (fu <= fv || v == x || v == w) { |
} else if (fu <= fv || v == x || v == w) { |
v=u; |
v=u; |
fv=fu; |
fv=fu; |
} |
} |
} |
} |
} |
} |
nrerror("Too many iterations in brent"); |
nrerror("Too many iterations in brent"); |
*xmin=x; |
*xmin=x; |
Line 1230 double brent(double ax, double bx, doubl
|
Line 1467 double brent(double ax, double bx, doubl
|
|
|
void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, |
void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, |
double (*func)(double)) |
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 ulim,u,r,q, dum; |
double fu; |
double fu; |
|
|
*fa=(*func)(*ax); |
double scale=10.; |
*fb=(*func)(*bx); |
int iterscale=0; |
|
|
|
*fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/ |
|
*fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */ |
|
|
|
|
|
/* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */ |
|
/* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */ |
|
/* *bx = *ax - (*ax - *bx)/scale; */ |
|
/* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */ |
|
/* } */ |
|
|
if (*fb > *fa) { |
if (*fb > *fa) { |
SHFT(dum,*ax,*bx,dum) |
SHFT(dum,*ax,*bx,dum) |
SHFT(dum,*fb,*fa,dum) |
SHFT(dum,*fb,*fa,dum) |
} |
} |
*cx=(*bx)+GOLD*(*bx-*ax); |
*cx=(*bx)+GOLD*(*bx-*ax); |
*fc=(*func)(*cx); |
*fc=(*func)(*cx); |
while (*fb > *fc) { /* Declining fa, fb, fc */ |
#ifdef DEBUG |
|
printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc); |
|
fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc); |
|
#endif |
|
while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */ |
r=(*bx-*ax)*(*fb-*fc); |
r=(*bx-*ax)*(*fb-*fc); |
q=(*bx-*cx)*(*fb-*fa); |
q=(*bx-*cx)*(*fb-*fa); |
u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ |
u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ |
(2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */ |
(2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */ |
ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */ |
ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */ |
if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */ |
if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */ |
fu=(*func)(u); |
fu=(*func)(u); |
#ifdef DEBUG |
#ifdef DEBUG |
/* f(x)=A(x-u)**2+f(u) */ |
/* f(x)=A(x-u)**2+f(u) */ |
Line 1257 void mnbrak(double *ax, double *bx, doub
|
Line 1513 void mnbrak(double *ax, double *bx, doub
|
fparabu= *fa - A*(*ax-u)*(*ax-u); |
fparabu= *fa - A*(*ax-u)*(*ax-u); |
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); |
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); |
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); |
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); |
|
/* And thus,it can be that fu > *fc even if fparabu < *fc */ |
|
/* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489), |
|
(*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */ |
|
/* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/ |
#endif |
#endif |
|
#ifdef MNBRAKORIGINAL |
|
#else |
|
/* if (fu > *fc) { */ |
|
/* #ifdef DEBUG */ |
|
/* printf("mnbrak4 fu > fc \n"); */ |
|
/* fprintf(ficlog, "mnbrak4 fu > fc\n"); */ |
|
/* #endif */ |
|
/* /\* 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 *\\/ *\/ */ |
|
/* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */ |
|
/* dum=u; /\* Shifting c and u *\/ */ |
|
/* u = *cx; */ |
|
/* *cx = dum; */ |
|
/* dum = fu; */ |
|
/* fu = *fc; */ |
|
/* *fc =dum; */ |
|
/* } else { /\* end *\/ */ |
|
/* #ifdef DEBUG */ |
|
/* printf("mnbrak3 fu < fc \n"); */ |
|
/* fprintf(ficlog, "mnbrak3 fu < fc\n"); */ |
|
/* #endif */ |
|
/* dum=u; /\* Shifting c and u *\/ */ |
|
/* u = *cx; */ |
|
/* *cx = dum; */ |
|
/* dum = fu; */ |
|
/* fu = *fc; */ |
|
/* *fc =dum; */ |
|
/* } */ |
|
#ifdef DEBUG |
|
printf("mnbrak34 fu < or >= fc \n"); |
|
fprintf(ficlog, "mnbrak34 fu < fc\n"); |
|
#endif |
|
dum=u; /* Shifting c and u */ |
|
u = *cx; |
|
*cx = dum; |
|
dum = fu; |
|
fu = *fc; |
|
*fc =dum; |
|
#endif |
} else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */ |
} else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */ |
|
#ifdef DEBUG |
|
printf("mnbrak2 u after c but before ulim\n"); |
|
fprintf(ficlog, "mnbrak2 u after c but before ulim\n"); |
|
#endif |
fu=(*func)(u); |
fu=(*func)(u); |
if (fu < *fc) { |
if (fu < *fc) { |
|
#ifdef DEBUG |
|
printf("mnbrak2 u after c but before ulim AND fu < fc\n"); |
|
fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n"); |
|
#endif |
SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) |
SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) |
SHFT(*fb,*fc,fu,(*func)(u)) |
SHFT(*fb,*fc,fu,(*func)(u)) |
} |
} |
} else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */ |
} else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */ |
|
#ifdef DEBUG |
|
printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n"); |
|
fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n"); |
|
#endif |
u=ulim; |
u=ulim; |
fu=(*func)(u); |
fu=(*func)(u); |
} else { |
} else { /* u could be left to b (if r > q parabola has a maximum) */ |
|
#ifdef DEBUG |
|
printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n"); |
|
fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n"); |
|
#endif |
u=(*cx)+GOLD*(*cx-*bx); |
u=(*cx)+GOLD*(*cx-*bx); |
fu=(*func)(u); |
fu=(*func)(u); |
} |
} /* end tests */ |
SHFT(*ax,*bx,*cx,u) |
SHFT(*ax,*bx,*cx,u) |
SHFT(*fa,*fb,*fc,fu) |
SHFT(*fa,*fb,*fc,fu) |
} |
#ifdef DEBUG |
|
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 |
|
} /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */ |
} |
} |
|
|
/*************** linmin ************************/ |
/*************** linmin ************************/ |
Line 1296 void linmin(double p[], double xi[], int
|
Line 1614 void linmin(double p[], double xi[], int
|
int j; |
int j; |
double xx,xmin,bx,ax; |
double xx,xmin,bx,ax; |
double fx,fb,fa; |
double fx,fb,fa; |
|
|
|
#ifdef LINMINORIGINAL |
|
#else |
|
double scale=10., axs, xxs; /* Scale added for infinity */ |
|
#endif |
|
|
ncom=n; |
ncom=n; |
pcom=vector(1,n); |
pcom=vector(1,n); |
xicom=vector(1,n); |
xicom=vector(1,n); |
nrfunc=func; |
nrfunc=func; |
for (j=1;j<=n;j++) { |
for (j=1;j<=n;j++) { |
pcom[j]=p[j]; |
pcom[j]=p[j]; |
xicom[j]=xi[j]; |
xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */ |
} |
} |
ax=0.0; |
|
xx=1.0; |
#ifdef LINMINORIGINAL |
mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */ |
xx=1.; |
*fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */ |
#else |
|
axs=0.0; |
|
xxs=1.; |
|
do{ |
|
xx= xxs; |
|
#endif |
|
ax=0.; |
|
mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */ |
|
/* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */ |
|
/* 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)) */ |
|
/* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */ |
|
/* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */ |
|
/* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */ |
|
/* 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]]*/ |
|
#ifdef LINMINORIGINAL |
|
#else |
|
if (fx != fx){ |
|
xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */ |
|
printf("|"); |
|
fprintf(ficlog,"|"); |
|
#ifdef DEBUGLINMIN |
|
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); |
|
#endif |
|
} |
|
}while(fx != fx); |
|
#endif |
|
|
|
#ifdef DEBUGLINMIN |
|
printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n", ax,xx,bx,fa,fx,fb); |
|
fprintf(ficlog,"\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n", ax,xx,bx,fa,fx,fb); |
|
#endif |
|
*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]) */ |
|
/* fmin = f(p[j] + xmin * xi[j]) */ |
|
/* P+lambda n in that direction (lambdamin), with TOL between abscisses */ |
|
/* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */ |
#ifdef DEBUG |
#ifdef DEBUG |
printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin); |
printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin); |
fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin); |
fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin); |
#endif |
#endif |
|
#ifdef DEBUGLINMIN |
|
printf("linmin end "); |
|
fprintf(ficlog,"linmin end "); |
|
#endif |
for (j=1;j<=n;j++) { |
for (j=1;j<=n;j++) { |
|
#ifdef LINMINORIGINAL |
xi[j] *= xmin; |
xi[j] *= xmin; |
p[j] += xi[j]; |
#else |
|
#ifdef DEBUGLINMIN |
|
if(xxs <1.0) |
|
printf(" before xi[%d]=%12.8f", j,xi[j]); |
|
#endif |
|
xi[j] *= xmin*xxs; /* xi rescaled by xmin and number of loops: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */ |
|
#ifdef DEBUGLINMIN |
|
if(xxs <1.0) |
|
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 ); |
|
#endif |
|
#endif |
|
p[j] += xi[j]; /* Parameters values are updated accordingly */ |
} |
} |
|
#ifdef DEBUGLINMIN |
|
printf("\n"); |
|
printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p)); |
|
fprintf(ficlog,"Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p)); |
|
for (j=1;j<=n;j++) { |
|
printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]); |
|
fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]); |
|
if(j % ncovmodel == 0){ |
|
printf("\n"); |
|
fprintf(ficlog,"\n"); |
|
} |
|
} |
|
#else |
|
#endif |
free_vector(xicom,1,n); |
free_vector(xicom,1,n); |
free_vector(pcom,1,n); |
free_vector(pcom,1,n); |
} |
} |
Line 1338 void powell(double p[], double **xi, int
|
Line 1726 void powell(double p[], double **xi, int
|
double (*func)(double [])); |
double (*func)(double [])); |
int i,ibig,j; |
int i,ibig,j; |
double del,t,*pt,*ptt,*xit; |
double del,t,*pt,*ptt,*xit; |
|
double directest; |
double fp,fptt; |
double fp,fptt; |
double *xits; |
double *xits; |
int niterf, itmp; |
int niterf, itmp; |
Line 1348 void powell(double p[], double **xi, int
|
Line 1737 void powell(double p[], double **xi, int
|
xits=vector(1,n); |
xits=vector(1,n); |
*fret=(*func)(p); |
*fret=(*func)(p); |
for (j=1;j<=n;j++) pt[j]=p[j]; |
for (j=1;j<=n;j++) pt[j]=p[j]; |
rcurr_time = time(NULL); |
rcurr_time = time(NULL); |
for (*iter=1;;++(*iter)) { |
for (*iter=1;;++(*iter)) { |
fp=(*fret); |
fp=(*fret); /* From former iteration or initial value */ |
ibig=0; |
ibig=0; |
del=0.0; |
del=0.0; |
rlast_time=rcurr_time; |
rlast_time=rcurr_time; |
Line 1360 void powell(double p[], double **xi, int
|
Line 1749 void powell(double p[], double **xi, int
|
printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout); |
printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout); |
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(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); */ |
/* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */ |
for (i=1;i<=n;i++) { |
for (i=1;i<=n;i++) { |
printf(" %d %.12f",i, p[i]); |
printf(" %d %.12f",i, p[i]); |
fprintf(ficlog," %d %.12lf",i, p[i]); |
fprintf(ficlog," %d %.12lf",i, p[i]); |
fprintf(ficrespow," %.12lf", p[i]); |
fprintf(ficrespow," %.12lf", p[i]); |
Line 1388 void powell(double p[], double **xi, int
|
Line 1777 void powell(double p[], double **xi, int
|
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); |
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 (i=1;i<=n;i++) { |
for (i=1;i<=n;i++) { /* For each direction i */ |
for (j=1;j<=n;j++) xit[j]=xi[j][i]; |
for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */ |
fptt=(*fret); |
fptt=(*fret); |
#ifdef DEBUG |
#ifdef DEBUG |
printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret); |
printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret); |
fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret); |
fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret); |
#endif |
#endif |
printf("%d",i);fflush(stdout); |
printf("%d",i);fflush(stdout); /* print direction (parameter) i */ |
fprintf(ficlog,"%d",i);fflush(ficlog); |
fprintf(ficlog,"%d",i);fflush(ficlog); |
linmin(p,xit,n,fret,func); |
linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/ |
if (fabs(fptt-(*fret)) > del) { |
/* Outputs are fret(new point p) p is updated and xit rescaled */ |
|
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. */ |
|
/* Unless the n directions are conjugate some gain in the determinant may be obtained */ |
|
/* with the new direction. */ |
del=fabs(fptt-(*fret)); |
del=fabs(fptt-(*fret)); |
ibig=i; |
ibig=i; |
} |
} |
Line 1417 void powell(double p[], double **xi, int
|
Line 1811 void powell(double p[], double **xi, int
|
printf("\n"); |
printf("\n"); |
fprintf(ficlog,"\n"); |
fprintf(ficlog,"\n"); |
#endif |
#endif |
} /* end i */ |
} /* end loop on each direction i */ |
if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { |
/* 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) */ |
|
if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */ |
|
/* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */ |
|
/* By adding age*age in a model, the new -2LL should be lower and the difference follows a */ |
|
/* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */ |
|
/* decreased of more than 3.84 */ |
|
/* 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. */ |
|
/* By adding 10 parameters more the gain should be 18.31 */ |
|
|
|
/* Starting the program with initial values given by a former maximization will simply change */ |
|
/* the scales of the directions and the directions, because the are reset to canonical directions */ |
|
/* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */ |
|
/* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */ |
#ifdef DEBUG |
#ifdef DEBUG |
int k[2],l; |
int k[2],l; |
k[0]=1; |
k[0]=1; |
Line 1448 void powell(double p[], double **xi, int
|
Line 1857 void powell(double p[], double **xi, int
|
free_vector(ptt,1,n); |
free_vector(ptt,1,n); |
free_vector(pt,1,n); |
free_vector(pt,1,n); |
return; |
return; |
} |
} /* enough precision */ |
if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); |
if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); |
for (j=1;j<=n;j++) { /* Computes an extrapolated point */ |
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]; |
ptt[j]=2.0*p[j]-pt[j]; |
xit[j]=p[j]-pt[j]; |
xit[j]=p[j]-pt[j]; |
pt[j]=p[j]; |
pt[j]=p[j]; |
} |
} |
fptt=(*func)(ptt); |
fptt=(*func)(ptt); /* f_3 */ |
|
#ifdef POWELLF1F3 |
|
#else |
if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */ |
if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */ |
|
#endif |
/* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */ |
/* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */ |
/* From x1 (P0) distance of x2 is at h and x3 is 2h */ |
/* From x1 (P0) distance of x2 is at h and x3 is 2h */ |
/* Let f"(x2) be the 2nd derivative equal everywhere. */ |
/* Let f"(x2) be the 2nd derivative equal everywhere. */ |
/* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */ |
/* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */ |
/* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */ |
/* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */ |
/* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */ |
/* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */ |
/* Thus we compare delta(2h) with observed f1-f3 */ |
|
/* or best gain on one ancient line 'del' with total */ |
|
/* gain f1-f2 = f1 - f2 - 'del' with del */ |
|
/* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */ |
/* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */ |
|
#ifdef NRCORIGINAL |
t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); |
t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/ |
|
#else |
|
t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */ |
t= t- del*SQR(fp-fptt); |
t= t- del*SQR(fp-fptt); |
printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t); |
#endif |
fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t); |
directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */ |
#ifdef DEBUG |
#ifdef DEBUG |
|
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); |
|
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); |
printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt), |
printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt), |
(fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt)); |
(fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt)); |
fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt), |
fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt), |
Line 1480 void powell(double p[], double **xi, int
|
Line 1893 void powell(double p[], double **xi, int
|
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); |
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); |
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); |
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); |
#endif |
#endif |
if (t < 0.0) { /* Then we use it for last direction */ |
#ifdef POWELLORIGINAL |
linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/ |
if (t < 0.0) { /* Then we use it for new direction */ |
|
#else |
|
if (directest*t < 0.0) { /* Contradiction between both tests */ |
|
printf("directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del); |
|
printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt); |
|
fprintf(ficlog,"directest= %.12lf (if <0 we include P0 Pn as new direction), 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 (directest < 0.0) { /* Then we use it for new direction */ |
|
#endif |
|
#ifdef DEBUGLINMIN |
|
printf("Before linmin in direction P%d-P0\n",n); |
|
for (j=1;j<=n;j++) { |
|
printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]); |
|
fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]); |
|
if(j % ncovmodel == 0){ |
|
printf("\n"); |
|
fprintf(ficlog,"\n"); |
|
} |
|
} |
|
#endif |
|
linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/ |
|
#ifdef DEBUGLINMIN |
for (j=1;j<=n;j++) { |
for (j=1;j<=n;j++) { |
xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */ |
printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]); |
xi[j][n]=xit[j]; /* and nth direction by the extrapolated */ |
fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]); |
|
if(j % ncovmodel == 0){ |
|
printf("\n"); |
|
fprintf(ficlog,"\n"); |
|
} |
} |
} |
printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig); |
#endif |
fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction :\n",n,ibig); |
for (j=1;j<=n;j++) { |
|
xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */ |
|
xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */ |
|
} |
|
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 |
#ifdef DEBUG |
printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig); |
printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig); |
Line 1499 void powell(double p[], double **xi, int
|
Line 1943 void powell(double p[], double **xi, int
|
printf("\n"); |
printf("\n"); |
fprintf(ficlog,"\n"); |
fprintf(ficlog,"\n"); |
#endif |
#endif |
} /* end of t negative */ |
} /* end of t or directest negative */ |
|
#ifdef POWELLF1F3 |
|
#else |
} /* end if (fptt < fp) */ |
} /* end if (fptt < fp) */ |
} |
#endif |
|
} /* loop iteration */ |
} |
} |
|
|
/**** Prevalence limit (stable or period prevalence) ****************/ |
/**** Prevalence limit (stable or period prevalence) ****************/ |
|
|
double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij) |
double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij) |
{ |
{ |
/* Computes the prevalence limit in each live state at age x by left multiplying the unit |
/* Computes the prevalence limit in each live state at age x by left multiplying the unit |
matrix by transitions matrix until convergence is reached */ |
matrix by transitions matrix until convergence is reached with precision ftolpl */ |
|
|
int i, ii,j,k; |
int i, ii,j,k; |
double min, max, maxmin, maxmax,sumnew=0.; |
double min, max, maxmin, maxmax,sumnew=0.; |
/* double **matprod2(); */ /* test */ |
/* double **matprod2(); */ /* test */ |
double **out, cov[NCOVMAX+1], **pmij(); |
double **out, cov[NCOVMAX+1], **pmij(); |
double **newm; |
double **newm; |
double agefin, delaymax=50 ; /* Max number of years to converge */ |
double agefin, delaymax=100 ; /* Max number of years to converge */ |
|
int ncvloop=0; |
|
|
for (ii=1;ii<=nlstate+ndeath;ii++) |
for (ii=1;ii<=nlstate+ndeath;ii++) |
for (j=1;j<=nlstate+ndeath;j++){ |
for (j=1;j<=nlstate+ndeath;j++){ |
oldm[ii][j]=(ii==j ? 1.0 : 0.0); |
oldm[ii][j]=(ii==j ? 1.0 : 0.0); |
} |
} |
|
|
cov[1]=1.; |
cov[1]=1.; |
|
|
/* Even if hstepm = 1, at least one multiplication by the unit matrix */ |
/* Even if hstepm = 1, at least one multiplication by the unit matrix */ |
|
/* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */ |
for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){ |
for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){ |
|
ncvloop++; |
newm=savm; |
newm=savm; |
/* Covariates have to be included here again */ |
/* Covariates have to be included here again */ |
cov[2]=agefin; |
cov[2]=agefin; |
|
if(nagesqr==1) |
|
cov[3]= agefin*agefin;; |
for (k=1; k<=cptcovn;k++) { |
for (k=1; k<=cptcovn;k++) { |
cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; |
/* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(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]]);*/ |
cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; |
} |
/* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); */ |
/* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ |
} |
/* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */ |
/*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ |
/* cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */ |
/* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */ |
|
for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2]; |
|
for (k=1; k<=cptcovprod;k++) /* Useless */ |
|
/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */ |
|
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; |
|
|
/*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/ |
/*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/ |
/*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/ |
/*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/ |
Line 1556 double **prevalim(double **prlim, int nl
|
Line 2011 double **prevalim(double **prlim, int nl
|
sumnew=0; |
sumnew=0; |
for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k]; |
for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k]; |
prlim[i][j]= newm[i][j]/(1-sumnew); |
prlim[i][j]= newm[i][j]/(1-sumnew); |
/*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/ |
|
max=FMAX(max,prlim[i][j]); |
max=FMAX(max,prlim[i][j]); |
min=FMIN(min,prlim[i][j]); |
min=FMIN(min,prlim[i][j]); |
|
/* printf(" age= %d prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d max=%f min=%f\n", (int)age, i, j, i, j, prlim[i][j],(int)agefin, max, min); */ |
} |
} |
maxmin=max-min; |
maxmin=(max-min)/(max+min)*2; |
maxmax=FMAX(maxmax,maxmin); |
maxmax=FMAX(maxmax,maxmin); |
} |
} /* j loop */ |
|
*ncvyear= (int)age- (int)agefin; |
|
/* printf("maxmax=%lf maxmin=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */ |
if(maxmax < ftolpl){ |
if(maxmax < ftolpl){ |
|
/* printf("maxmax=%lf maxmin=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */ |
return prlim; |
return prlim; |
} |
} |
} |
} /* age loop */ |
|
printf("Warning: the stable prevalence at age %d did not converge with the required precision %g > ftolpl=%g. \n\ |
|
Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear); |
|
/* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */ |
|
return prlim; /* should not reach here */ |
} |
} |
|
|
/*************** transition probabilities ***************/ |
/*************** transition probabilities ***************/ |
Line 1690 double ***hpxij(double ***po, int nhstep
|
Line 2152 double ***hpxij(double ***po, int nhstep
|
int i, j, d, h, k; |
int i, j, d, h, k; |
double **out, cov[NCOVMAX+1]; |
double **out, cov[NCOVMAX+1]; |
double **newm; |
double **newm; |
|
double agexact; |
|
|
/* Hstepm could be zero and should return the unit matrix */ |
/* Hstepm could be zero and should return the unit matrix */ |
for (i=1;i<=nlstate+ndeath;i++) |
for (i=1;i<=nlstate+ndeath;i++) |
Line 1703 double ***hpxij(double ***po, int nhstep
|
Line 2166 double ***hpxij(double ***po, int nhstep
|
newm=savm; |
newm=savm; |
/* Covariates have to be included here again */ |
/* Covariates have to be included here again */ |
cov[1]=1.; |
cov[1]=1.; |
cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM; |
agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; |
|
cov[2]=agexact; |
|
if(nagesqr==1) |
|
cov[3]= agexact*agexact; |
for (k=1; k<=cptcovn;k++) |
for (k=1; k<=cptcovn;k++) |
cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; |
cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; |
for (k=1; k<=cptcovage;k++) |
/* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */ |
cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; |
for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */ |
|
/* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ |
|
cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; |
|
/* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */ |
for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */ |
for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */ |
cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; |
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; |
|
/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */ |
|
|
|
|
/*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/ |
/*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/ |
Line 1761 double func( double *x)
|
Line 2231 double func( double *x)
|
int s1, s2; |
int s1, s2; |
double bbh, survp; |
double bbh, survp; |
long ipmx; |
long ipmx; |
|
double agexact; |
/*extern weight */ |
/*extern weight */ |
/* We are differentiating ll according to initial status */ |
/* We are differentiating ll according to initial status */ |
/* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/ |
/* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/ |
Line 1782 double func( double *x)
|
Line 2253 double func( double *x)
|
to be observed in j being in i according to the model. |
to be observed in j being in i according to the model. |
*/ |
*/ |
for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */ |
for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */ |
cov[2+k]=covar[Tvar[k]][i]; |
cov[2+nagesqr+k]=covar[Tvar[k]][i]; |
} |
} |
/* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] |
/* 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] |
is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] |
Line 1795 double func( double *x)
|
Line 2266 double func( double *x)
|
} |
} |
for(d=0; d<dh[mi][i]; d++){ |
for(d=0; d<dh[mi][i]; d++){ |
newm=savm; |
newm=savm; |
cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM; |
agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; |
|
cov[2]=agexact; |
|
if(nagesqr==1) |
|
cov[3]= agexact*agexact; |
for (kk=1; kk<=cptcovage;kk++) { |
for (kk=1; kk<=cptcovage;kk++) { |
cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */ |
cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */ |
} |
} |
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, |
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, |
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); |
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); |
Line 1849 double func( double *x)
|
Line 2323 double func( double *x)
|
which slows down the processing. The difference can be up to 10% |
which slows down the processing. The difference can be up to 10% |
lower mortality. |
lower mortality. |
*/ |
*/ |
lli=log(out[s1][s2] - savm[s1][s2]); |
/* If, at the beginning of the maximization mostly, the |
|
cumulative probability or probability to be dead is |
|
constant (ie = 1) over time d, the difference is equal to |
|
0. out[s1][3] = savm[s1][3]: probability, being at state |
|
s1 at precedent wave, to be dead a month before current |
|
wave is equal to probability, being at state s1 at |
|
precedent wave, to be dead at mont of the current |
|
wave. Then the observed probability (that this person died) |
|
is null according to current estimated parameter. In fact, |
|
it should be very low but not zero otherwise the log go to |
|
infinity. |
|
*/ |
|
/* #ifdef INFINITYORIGINAL */ |
|
/* lli=log(out[s1][s2] - savm[s1][s2]); */ |
|
/* #else */ |
|
/* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */ |
|
/* lli=log(mytinydouble); */ |
|
/* else */ |
|
/* lli=log(out[s1][s2] - savm[s1][s2]); */ |
|
/* #endif */ |
|
lli=log(out[s1][s2] - savm[s1][s2]); |
|
|
} else if (s2==-2) { |
} else if (s2==-2) { |
for (j=1,survp=0. ; j<=nlstate; j++) |
for (j=1,survp=0. ; j<=nlstate; j++) |
Line 1881 double func( double *x)
|
Line 2374 double func( double *x)
|
ipmx +=1; |
ipmx +=1; |
sw += weight[i]; |
sw += weight[i]; |
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; |
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; |
|
/* if (lli < log(mytinydouble)){ */ |
|
/* 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); */ |
|
/* 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]); */ |
|
/* } */ |
} /* end of wave */ |
} /* end of wave */ |
} /* end of individual */ |
} /* end of individual */ |
} else if(mle==2){ |
} else if(mle==2){ |
for (i=1,ipmx=0, sw=0.; i<=imx; i++){ |
for (i=1,ipmx=0, sw=0.; i<=imx; i++){ |
for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; |
for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; |
for(mi=1; mi<= wav[i]-1; mi++){ |
for(mi=1; mi<= wav[i]-1; mi++){ |
for (ii=1;ii<=nlstate+ndeath;ii++) |
for (ii=1;ii<=nlstate+ndeath;ii++) |
for (j=1;j<=nlstate+ndeath;j++){ |
for (j=1;j<=nlstate+ndeath;j++){ |
Line 1894 double func( double *x)
|
Line 2391 double func( double *x)
|
} |
} |
for(d=0; d<=dh[mi][i]; d++){ |
for(d=0; d<=dh[mi][i]; d++){ |
newm=savm; |
newm=savm; |
cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM; |
agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; |
|
cov[2]=agexact; |
|
if(nagesqr==1) |
|
cov[3]= agexact*agexact; |
for (kk=1; kk<=cptcovage;kk++) { |
for (kk=1; kk<=cptcovage;kk++) { |
cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; |
cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; |
} |
} |
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, |
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, |
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); |
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); |
Line 1915 double func( double *x)
|
Line 2415 double func( double *x)
|
} /* end of individual */ |
} /* end of individual */ |
} else if(mle==3){ /* exponential inter-extrapolation */ |
} else if(mle==3){ /* exponential inter-extrapolation */ |
for (i=1,ipmx=0, sw=0.; i<=imx; i++){ |
for (i=1,ipmx=0, sw=0.; i<=imx; i++){ |
for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; |
for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; |
for(mi=1; mi<= wav[i]-1; mi++){ |
for(mi=1; mi<= wav[i]-1; mi++){ |
for (ii=1;ii<=nlstate+ndeath;ii++) |
for (ii=1;ii<=nlstate+ndeath;ii++) |
for (j=1;j<=nlstate+ndeath;j++){ |
for (j=1;j<=nlstate+ndeath;j++){ |
Line 1924 double func( double *x)
|
Line 2424 double func( double *x)
|
} |
} |
for(d=0; d<dh[mi][i]; d++){ |
for(d=0; d<dh[mi][i]; d++){ |
newm=savm; |
newm=savm; |
cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM; |
agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; |
|
cov[2]=agexact; |
|
if(nagesqr==1) |
|
cov[3]= agexact*agexact; |
for (kk=1; kk<=cptcovage;kk++) { |
for (kk=1; kk<=cptcovage;kk++) { |
cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; |
cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; |
} |
} |
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, |
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, |
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); |
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); |
Line 1945 double func( double *x)
|
Line 2448 double func( double *x)
|
} /* end of individual */ |
} /* end of individual */ |
}else if (mle==4){ /* ml=4 no inter-extrapolation */ |
}else if (mle==4){ /* ml=4 no inter-extrapolation */ |
for (i=1,ipmx=0, sw=0.; i<=imx; i++){ |
for (i=1,ipmx=0, sw=0.; i<=imx; i++){ |
for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; |
for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; |
for(mi=1; mi<= wav[i]-1; mi++){ |
for(mi=1; mi<= wav[i]-1; mi++){ |
for (ii=1;ii<=nlstate+ndeath;ii++) |
for (ii=1;ii<=nlstate+ndeath;ii++) |
for (j=1;j<=nlstate+ndeath;j++){ |
for (j=1;j<=nlstate+ndeath;j++){ |
Line 1954 double func( double *x)
|
Line 2457 double func( double *x)
|
} |
} |
for(d=0; d<dh[mi][i]; d++){ |
for(d=0; d<dh[mi][i]; d++){ |
newm=savm; |
newm=savm; |
cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM; |
agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; |
|
cov[2]=agexact; |
|
if(nagesqr==1) |
|
cov[3]= agexact*agexact; |
for (kk=1; kk<=cptcovage;kk++) { |
for (kk=1; kk<=cptcovage;kk++) { |
cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; |
cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; |
} |
} |
|
|
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, |
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, |
Line 1980 double func( double *x)
|
Line 2486 double func( double *x)
|
} /* end of individual */ |
} /* end of individual */ |
}else{ /* ml=5 no inter-extrapolation no jackson =0.8a */ |
}else{ /* ml=5 no inter-extrapolation no jackson =0.8a */ |
for (i=1,ipmx=0, sw=0.; i<=imx; i++){ |
for (i=1,ipmx=0, sw=0.; i<=imx; i++){ |
for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; |
for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; |
for(mi=1; mi<= wav[i]-1; mi++){ |
for(mi=1; mi<= wav[i]-1; mi++){ |
for (ii=1;ii<=nlstate+ndeath;ii++) |
for (ii=1;ii<=nlstate+ndeath;ii++) |
for (j=1;j<=nlstate+ndeath;j++){ |
for (j=1;j<=nlstate+ndeath;j++){ |
Line 1989 double func( double *x)
|
Line 2495 double func( double *x)
|
} |
} |
for(d=0; d<dh[mi][i]; d++){ |
for(d=0; d<dh[mi][i]; d++){ |
newm=savm; |
newm=savm; |
cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM; |
agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; |
|
cov[2]=agexact; |
|
if(nagesqr==1) |
|
cov[3]= agexact*agexact; |
for (kk=1; kk<=cptcovage;kk++) { |
for (kk=1; kk<=cptcovage;kk++) { |
cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; |
cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; |
} |
} |
|
|
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, |
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, |
Line 2027 double funcone( double *x)
|
Line 2536 double funcone( double *x)
|
double llt; |
double llt; |
int s1, s2; |
int s1, s2; |
double bbh, survp; |
double bbh, survp; |
|
double agexact; |
/*extern weight */ |
/*extern weight */ |
/* We are differentiating ll according to initial status */ |
/* We are differentiating ll according to initial status */ |
/* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/ |
/* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/ |
Line 2038 double funcone( double *x)
|
Line 2548 double funcone( double *x)
|
for(k=1; k<=nlstate; k++) ll[k]=0.; |
for(k=1; k<=nlstate; k++) ll[k]=0.; |
|
|
for (i=1,ipmx=0, sw=0.; i<=imx; i++){ |
for (i=1,ipmx=0, sw=0.; i<=imx; i++){ |
for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; |
for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; |
for(mi=1; mi<= wav[i]-1; mi++){ |
for(mi=1; mi<= wav[i]-1; mi++){ |
for (ii=1;ii<=nlstate+ndeath;ii++) |
for (ii=1;ii<=nlstate+ndeath;ii++) |
for (j=1;j<=nlstate+ndeath;j++){ |
for (j=1;j<=nlstate+ndeath;j++){ |
Line 2047 double funcone( double *x)
|
Line 2557 double funcone( double *x)
|
} |
} |
for(d=0; d<dh[mi][i]; d++){ |
for(d=0; d<dh[mi][i]; d++){ |
newm=savm; |
newm=savm; |
cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM; |
agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; |
|
cov[2]=agexact; |
|
if(nagesqr==1) |
|
cov[3]= agexact*agexact; |
for (kk=1; kk<=cptcovage;kk++) { |
for (kk=1; kk<=cptcovage;kk++) { |
cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; |
cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; |
} |
} |
|
|
/* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */ |
/* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */ |
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, |
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, |
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); |
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); |
Line 2089 double funcone( double *x)
|
Line 2603 double funcone( double *x)
|
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; |
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; |
/*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */ |
/*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */ |
if(globpr){ |
if(globpr){ |
fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\ |
fprintf(ficresilk,"%9ld %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f\ |
%11.6f %11.6f %11.6f ", \ |
%11.6f %11.6f %11.6f ", \ |
num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i], |
num[i], agexact, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i], |
2*weight[i]*lli,out[s1][s2],savm[s1][s2]); |
2*weight[i]*lli,out[s1][s2],savm[s1][s2]); |
for(k=1,llt=0.,l=0.; k<=nlstate; k++){ |
for(k=1,llt=0.,l=0.; k<=nlstate; k++){ |
llt +=ll[k]*gipmx/gsw; |
llt +=ll[k]*gipmx/gsw; |
Line 2123 void likelione(FILE *ficres,double p[],
|
Line 2637 void likelione(FILE *ficres,double p[],
|
int k; |
int k; |
|
|
if(*globpri !=0){ /* Just counts and sums, no printings */ |
if(*globpri !=0){ /* Just counts and sums, no printings */ |
strcpy(fileresilk,"ilk"); |
strcpy(fileresilk,"ILK_"); |
strcat(fileresilk,fileres); |
strcat(fileresilk,fileresu); |
if((ficresilk=fopen(fileresilk,"w"))==NULL) { |
if((ficresilk=fopen(fileresilk,"w"))==NULL) { |
printf("Problem with resultfile: %s\n", fileresilk); |
printf("Problem with resultfile: %s\n", fileresilk); |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk); |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk); |
} |
} |
fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n"); |
fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n"); |
fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav "); |
fprintf(ficresilk, "#num_i age i s1 s2 mi mw dh likeli weight 2wlli out sav "); |
/* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */ |
/* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */ |
for(k=1; k<=nlstate; k++) |
for(k=1; k<=nlstate; k++) |
fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k); |
fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k); |
Line 2140 void likelione(FILE *ficres,double p[],
|
Line 2654 void likelione(FILE *ficres,double p[],
|
*fretone=(*funcone)(p); |
*fretone=(*funcone)(p); |
if(*globpri !=0){ |
if(*globpri !=0){ |
fclose(ficresilk); |
fclose(ficresilk); |
fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk)); |
fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle >= 1. You should at least run with mle >= 1 and starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk)); |
fflush(fichtm); |
fprintf(fichtm,"<br>- The function drawn is -2Log(L) in Log scale: by state of origin <a href=\"%s-ori.png\">%s-ori.png</a><br> \ |
|
<img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_")); |
|
fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \ |
|
<img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_")); |
|
fflush(fichtm); |
|
|
|
for (k=1; k<= nlstate ; k++) { |
|
fprintf(fichtm,"<br>- Probability p%dj by origin %d and destination j <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \ |
|
<img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k); |
|
|
|
} |
} |
} |
return; |
return; |
} |
} |
Line 2173 void mlikeli(FILE *ficres,double p[], in
|
Line 2697 void mlikeli(FILE *ficres,double p[], in
|
for (j=1;j<=npar;j++) |
for (j=1;j<=npar;j++) |
xi[i][j]=(i==j ? 1.0 : 0.0); |
xi[i][j]=(i==j ? 1.0 : 0.0); |
printf("Powell\n"); fprintf(ficlog,"Powell\n"); |
printf("Powell\n"); fprintf(ficlog,"Powell\n"); |
strcpy(filerespow,"pow"); |
strcpy(filerespow,"POW_"); |
strcat(filerespow,fileres); |
strcat(filerespow,fileres); |
if((ficrespow=fopen(filerespow,"w"))==NULL) { |
if((ficrespow=fopen(filerespow,"w"))==NULL) { |
printf("Problem with resultfile: %s\n", filerespow); |
printf("Problem with resultfile: %s\n", filerespow); |
Line 2218 void mlikeli(FILE *ficres,double p[], in
|
Line 2742 void mlikeli(FILE *ficres,double p[], in
|
fclose(ficrespow); |
fclose(ficrespow); |
printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); |
printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); |
fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); |
fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); |
fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); |
fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); |
|
|
} |
} |
|
|
/**** Computes Hessian and covariance matrix ***/ |
/**** Computes Hessian and covariance matrix ***/ |
void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double [])) |
void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double [])) |
{ |
{ |
double **a,**y,*x,pd; |
double **a,**y,*x,pd; |
double **hess; |
/* double **hess; */ |
int i, j; |
int i, j; |
int *indx; |
int *indx; |
|
|
double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar); |
double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar); |
double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar); |
double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar); |
void lubksb(double **a, int npar, int *indx, double b[]) ; |
void lubksb(double **a, int npar, int *indx, double b[]) ; |
void ludcmp(double **a, int npar, int *indx, double *d) ; |
void ludcmp(double **a, int npar, int *indx, double *d) ; |
double gompertz(double p[]); |
double gompertz(double p[]); |
hess=matrix(1,npar,1,npar); |
/* hess=matrix(1,npar,1,npar); */ |
|
|
printf("\nCalculation of the hessian matrix. Wait...\n"); |
printf("\nCalculation of the hessian matrix. Wait...\n"); |
fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n"); |
fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n"); |
for (i=1;i<=npar;i++){ |
for (i=1;i<=npar;i++){ |
printf("%d",i);fflush(stdout); |
printf("%d-",i);fflush(stdout); |
fprintf(ficlog,"%d",i);fflush(ficlog); |
fprintf(ficlog,"%d-",i);fflush(ficlog); |
|
|
hess[i][i]=hessii(p,ftolhess,i,delti,func,npar); |
hess[i][i]=hessii(p,ftolhess,i,delti,func,npar); |
|
|
Line 2252 void hesscov(double **matcov, double p[]
|
Line 2776 void hesscov(double **matcov, double p[]
|
for (i=1;i<=npar;i++) { |
for (i=1;i<=npar;i++) { |
for (j=1;j<=npar;j++) { |
for (j=1;j<=npar;j++) { |
if (j>i) { |
if (j>i) { |
printf(".%d%d",i,j);fflush(stdout); |
printf(".%d-%d",i,j);fflush(stdout); |
fprintf(ficlog,".%d%d",i,j);fflush(ficlog); |
fprintf(ficlog,".%d-%d",i,j);fflush(ficlog); |
hess[i][j]=hessij(p,delti,i,j,func,npar); |
hess[i][j]=hessij(p,hess, delti,i,j,func,npar); |
|
|
hess[j][i]=hess[i][j]; |
hess[j][i]=hess[i][j]; |
/*printf(" %lf ",hess[i][j]);*/ |
/*printf(" %lf ",hess[i][j]);*/ |
Line 2288 void hesscov(double **matcov, double p[]
|
Line 2812 void hesscov(double **matcov, double p[]
|
fprintf(ficlog,"\n#Hessian matrix#\n"); |
fprintf(ficlog,"\n#Hessian matrix#\n"); |
for (i=1;i<=npar;i++) { |
for (i=1;i<=npar;i++) { |
for (j=1;j<=npar;j++) { |
for (j=1;j<=npar;j++) { |
printf("%.3e ",hess[i][j]); |
printf("%.6e ",hess[i][j]); |
fprintf(ficlog,"%.3e ",hess[i][j]); |
fprintf(ficlog,"%.6e ",hess[i][j]); |
} |
} |
printf("\n"); |
printf("\n"); |
fprintf(ficlog,"\n"); |
fprintf(ficlog,"\n"); |
} |
} |
|
|
|
/* printf("\n#Covariance matrix#\n"); */ |
|
/* fprintf(ficlog,"\n#Covariance matrix#\n"); */ |
|
/* for (i=1;i<=npar;i++) { */ |
|
/* for (j=1;j<=npar;j++) { */ |
|
/* printf("%.6e ",matcov[i][j]); */ |
|
/* fprintf(ficlog,"%.6e ",matcov[i][j]); */ |
|
/* } */ |
|
/* printf("\n"); */ |
|
/* fprintf(ficlog,"\n"); */ |
|
/* } */ |
|
|
/* Recompute Inverse */ |
/* Recompute Inverse */ |
for (i=1;i<=npar;i++) |
/* for (i=1;i<=npar;i++) */ |
for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; |
/* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */ |
ludcmp(a,npar,indx,&pd); |
/* ludcmp(a,npar,indx,&pd); */ |
|
|
|
/* printf("\n#Hessian matrix recomputed#\n"); */ |
|
|
|
/* for (j=1;j<=npar;j++) { */ |
|
/* for (i=1;i<=npar;i++) x[i]=0; */ |
|
/* x[j]=1; */ |
|
/* lubksb(a,npar,indx,x); */ |
|
/* for (i=1;i<=npar;i++){ */ |
|
/* y[i][j]=x[i]; */ |
|
/* printf("%.3e ",y[i][j]); */ |
|
/* fprintf(ficlog,"%.3e ",y[i][j]); */ |
|
/* } */ |
|
/* printf("\n"); */ |
|
/* fprintf(ficlog,"\n"); */ |
|
/* } */ |
|
|
/* printf("\n#Hessian matrix recomputed#\n"); |
/* Verifying the inverse matrix */ |
|
#ifdef DEBUGHESS |
|
y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov); |
|
|
|
printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n"); |
|
fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n"); |
|
|
for (j=1;j<=npar;j++) { |
for (j=1;j<=npar;j++) { |
for (i=1;i<=npar;i++) x[i]=0; |
|
x[j]=1; |
|
lubksb(a,npar,indx,x); |
|
for (i=1;i<=npar;i++){ |
for (i=1;i<=npar;i++){ |
y[i][j]=x[i]; |
printf("%.2f ",y[i][j]); |
printf("%.3e ",y[i][j]); |
fprintf(ficlog,"%.2f ",y[i][j]); |
fprintf(ficlog,"%.3e ",y[i][j]); |
|
} |
} |
printf("\n"); |
printf("\n"); |
fprintf(ficlog,"\n"); |
fprintf(ficlog,"\n"); |
} |
} |
*/ |
#endif |
|
|
free_matrix(a,1,npar,1,npar); |
free_matrix(a,1,npar,1,npar); |
free_matrix(y,1,npar,1,npar); |
free_matrix(y,1,npar,1,npar); |
free_vector(x,1,npar); |
free_vector(x,1,npar); |
free_ivector(indx,1,npar); |
free_ivector(indx,1,npar); |
free_matrix(hess,1,npar,1,npar); |
/* free_matrix(hess,1,npar,1,npar); */ |
|
|
|
|
} |
} |
|
|
/*************** hessian matrix ****************/ |
/*************** hessian matrix ****************/ |
double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar) |
double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar) |
{ |
{ /* Around values of x, computes the function func and returns the scales delti and hessian */ |
int i; |
int i; |
int l=1, lmax=20; |
int l=1, lmax=20; |
double k1,k2; |
double k1,k2, res, fx; |
double p2[MAXPARM+1]; /* identical to x */ |
double p2[MAXPARM+1]; /* identical to x */ |
double res; |
|
double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; |
double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; |
double fx; |
|
int k=0,kmax=10; |
int k=0,kmax=10; |
double l1; |
double l1; |
|
|
Line 2350 double hessii(double x[], double delta,
|
Line 2899 double hessii(double x[], double delta,
|
p2[theta]=x[theta]-delt; |
p2[theta]=x[theta]-delt; |
k2=func(p2)-fx; |
k2=func(p2)-fx; |
/*res= (k1-2.0*fx+k2)/delt/delt; */ |
/*res= (k1-2.0*fx+k2)/delt/delt; */ |
res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */ |
res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */ |
|
|
#ifdef DEBUGHESS |
#ifdef DEBUGHESSII |
printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx); |
printf("%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); |
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 |
#endif |
Line 2366 double hessii(double x[], double delta,
|
Line 2915 double hessii(double x[], double delta,
|
else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ |
else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ |
delts=delt; |
delts=delt; |
} |
} |
} |
} /* End loop k */ |
} |
} |
delti[theta]=delts; |
delti[theta]=delts; |
return res; |
return res; |
|
|
} |
} |
|
|
double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) |
double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar) |
{ |
{ |
int i; |
int i; |
int l=1, lmax=20; |
int l=1, lmax=20; |
double k1,k2,k3,k4,res,fx; |
double k1,k2,k3,k4,res,fx; |
double p2[MAXPARM+1]; |
double p2[MAXPARM+1]; |
int k; |
int k, kmax=1; |
|
double v1, v2, cv12, lc1, lc2; |
|
|
fx=func(x); |
fx=func(x); |
for (k=1; k<=2; k++) { |
for (k=1; k<=kmax; k=k+10) { |
for (i=1;i<=npar;i++) p2[i]=x[i]; |
for (i=1;i<=npar;i++) p2[i]=x[i]; |
p2[thetai]=x[thetai]+delti[thetai]/k; |
p2[thetai]=x[thetai]+delti[thetai]*k; |
p2[thetaj]=x[thetaj]+delti[thetaj]/k; |
p2[thetaj]=x[thetaj]+delti[thetaj]*k; |
k1=func(p2)-fx; |
k1=func(p2)-fx; |
|
|
p2[thetai]=x[thetai]+delti[thetai]/k; |
p2[thetai]=x[thetai]+delti[thetai]*k; |
p2[thetaj]=x[thetaj]-delti[thetaj]/k; |
p2[thetaj]=x[thetaj]-delti[thetaj]*k; |
k2=func(p2)-fx; |
k2=func(p2)-fx; |
|
|
p2[thetai]=x[thetai]-delti[thetai]/k; |
p2[thetai]=x[thetai]-delti[thetai]*k; |
p2[thetaj]=x[thetaj]+delti[thetaj]/k; |
p2[thetaj]=x[thetaj]+delti[thetaj]*k; |
k3=func(p2)-fx; |
k3=func(p2)-fx; |
|
|
p2[thetai]=x[thetai]-delti[thetai]/k; |
p2[thetai]=x[thetai]-delti[thetai]*k; |
p2[thetaj]=x[thetaj]-delti[thetaj]/k; |
p2[thetaj]=x[thetaj]-delti[thetaj]*k; |
k4=func(p2)-fx; |
k4=func(p2)-fx; |
res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */ |
res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */ |
#ifdef DEBUG |
if(k1*k2*k3*k4 <0.){ |
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); |
kmax=kmax+10; |
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); |
if(kmax >=10){ |
|
printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol); |
|
fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol); |
|
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); |
|
} |
|
} |
|
#ifdef DEBUGHESSIJ |
|
v1=hess[thetai][thetai]; |
|
v2=hess[thetaj][thetaj]; |
|
cv12=res; |
|
/* Computing eigen value of Hessian matrix */ |
|
lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; |
|
lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; |
|
if ((lc2 <0) || (lc1 <0) ){ |
|
printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj); |
|
fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj); |
|
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 |
#endif |
} |
} |
return res; |
return res; |
} |
} |
|
|
|
/* Not done yet: Was supposed to fix if not exactly at the maximum */ |
|
/* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */ |
|
/* { */ |
|
/* int i; */ |
|
/* int l=1, lmax=20; */ |
|
/* double k1,k2,k3,k4,res,fx; */ |
|
/* double p2[MAXPARM+1]; */ |
|
/* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */ |
|
/* int k=0,kmax=10; */ |
|
/* double l1; */ |
|
|
|
/* fx=func(x); */ |
|
/* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */ |
|
/* l1=pow(10,l); */ |
|
/* delts=delt; */ |
|
/* for(k=1 ; k <kmax; k=k+1){ */ |
|
/* delt = delti*(l1*k); */ |
|
/* for (i=1;i<=npar;i++) p2[i]=x[i]; */ |
|
/* p2[thetai]=x[thetai]+delti[thetai]/k; */ |
|
/* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */ |
|
/* k1=func(p2)-fx; */ |
|
|
|
/* p2[thetai]=x[thetai]+delti[thetai]/k; */ |
|
/* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */ |
|
/* k2=func(p2)-fx; */ |
|
|
|
/* p2[thetai]=x[thetai]-delti[thetai]/k; */ |
|
/* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */ |
|
/* k3=func(p2)-fx; */ |
|
|
|
/* p2[thetai]=x[thetai]-delti[thetai]/k; */ |
|
/* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */ |
|
/* k4=func(p2)-fx; */ |
|
/* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */ |
|
/* #ifdef DEBUGHESSIJ */ |
|
/* 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); */ |
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/* 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); */ |
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/* #endif */ |
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/* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */ |
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/* k=kmax; */ |
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/* } */ |
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/* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */ |
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/* k=kmax; l=lmax*10; */ |
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/* } */ |
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/* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */ |
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/* delts=delt; */ |
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/* } */ |
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/* } /\* End loop k *\/ */ |
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/* } */ |
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/* delti[theta]=delts; */ |
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/* return res; */ |
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/* } */ |
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/************** Inverse of matrix **************/ |
/************** Inverse of matrix **************/ |
void ludcmp(double **a, int n, int *indx, double *d) |
void ludcmp(double **a, int n, int *indx, double *d) |
{ |
{ |
Line 2484 void lubksb(double **a, int n, int *indx
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Line 3107 void lubksb(double **a, int n, int *indx
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void pstamp(FILE *fichier) |
void pstamp(FILE *fichier) |
{ |
{ |
fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart); |
fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart); |
} |
} |
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/************ Frequencies ********************/ |
/************ Frequencies ********************/ |
Line 2500 void freqsummary(char fileres[], int ia
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Line 3123 void freqsummary(char fileres[], int ia
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pp=vector(1,nlstate); |
pp=vector(1,nlstate); |
prop=matrix(1,nlstate,iagemin,iagemax+3); |
prop=matrix(1,nlstate,iagemin,iagemax+3); |
strcpy(fileresp,"p"); |
strcpy(fileresp,"P_"); |
strcat(fileresp,fileres); |
strcat(fileresp,fileresu); |
if((ficresp=fopen(fileresp,"w"))==NULL) { |
if((ficresp=fopen(fileresp,"w"))==NULL) { |
printf("Problem with prevalence resultfile: %s\n", fileresp); |
printf("Problem with prevalence resultfile: %s\n", fileresp); |
fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp); |
fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp); |
Line 2515 void freqsummary(char fileres[], int ia
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Line 3138 void freqsummary(char fileres[], int ia
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first=1; |
first=1; |
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/* for(k1=1; k1<=j ; k1++){ /* Loop on covariates */ |
/* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */ |
/* for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */ |
/* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */ |
/* j1++; |
/* j1++; */ |
*/ |
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for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ |
for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ |
/*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]); |
/*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]); |
scanf("%d", i);*/ |
scanf("%d", i);*/ |
Line 2537 void freqsummary(char fileres[], int ia
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Line 3159 void freqsummary(char fileres[], int ia
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bool=1; |
bool=1; |
if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */ |
if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */ |
for (z1=1; z1<=cptcoveff; z1++) |
for (z1=1; z1<=cptcoveff; z1++) |
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){ |
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ |
/* Tests if the value of each of the covariates of i is equal to filter j1 */ |
/* Tests if the value of each of the covariates of i is equal to filter j1 */ |
bool=0; |
bool=0; |
/* 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", |
/* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n", |
bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1], |
bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1), |
j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/ |
j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/ |
/* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/ |
/* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/ |
} |
} |
} |
} |
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Line 2572 void freqsummary(char fileres[], int ia
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Line 3194 void freqsummary(char fileres[], int ia
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pstamp(ficresp); |
pstamp(ficresp); |
if (cptcovn>0) { |
if (cptcovn>0) { |
fprintf(ficresp, "\n#********** Variable "); |
fprintf(ficresp, "\n#********** Variable "); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); |
fprintf(ficresp, "**********\n#"); |
fprintf(ficresp, "**********\n#"); |
fprintf(ficlog, "\n#********** Variable "); |
fprintf(ficlog, "\n#********** Variable "); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); |
fprintf(ficlog, "**********\n#"); |
fprintf(ficlog, "**********\n#"); |
} |
} |
for(i=1; i<=nlstate;i++) |
for(i=1; i<=nlstate;i++) |
Line 2703 void prevalence(double ***probs, double
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Line 3325 void prevalence(double ***probs, double
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bool=1; |
bool=1; |
if (cptcovn>0) { |
if (cptcovn>0) { |
for (z1=1; z1<=cptcoveff; z1++) |
for (z1=1; z1<=cptcoveff; z1++) |
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) |
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) |
bool=0; |
bool=0; |
} |
} |
if (bool==1) { |
if (bool==1) { |
Line 2895 void tricode(int *Tvar, int **nbcode, in
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Line 3517 void tricode(int *Tvar, int **nbcode, in
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{ |
{ |
/**< Uses cptcovn+2*cptcovprod as the number of covariates */ |
/**< Uses cptcovn+2*cptcovprod as the number of covariates */ |
/* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 |
/* 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] |
* Boring subroutine which should only output nbcode[Tvar[j]][k] |
* Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2) |
* Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2) |
/* nbcode[Tvar[j]][1]= |
* nbcode[Tvar[j]][1]= |
*/ |
*/ |
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int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX; |
int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX; |
Line 2908 void tricode(int *Tvar, int **nbcode, in
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Line 3530 void tricode(int *Tvar, int **nbcode, in
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cptcoveff=0; |
cptcoveff=0; |
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for (k=-1; k < maxncov; k++) Ndum[k]=0; |
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for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */ |
for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */ |
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/* Loop on covariates without age and products */ |
/* Loop on covariates without age and products */ |
for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */ |
for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */ |
for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the |
for (k=-1; k < maxncov; k++) Ndum[k]=0; |
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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*/ |
modality of this covariate Vj*/ |
ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i |
ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i |
* If product of Vn*Vm, still boolean *: |
* If product of Vn*Vm, still boolean *: |
Line 2935 void tricode(int *Tvar, int **nbcode, in
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Line 3557 void tricode(int *Tvar, int **nbcode, in
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/* getting the maximum value of the modality of the covariate |
/* getting the maximum value of the modality of the covariate |
(should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and |
(should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and |
female is 1, then modmaxcovj=1.*/ |
female is 1, then modmaxcovj=1.*/ |
} |
} /* end for loop on individuals i */ |
printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj); |
printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj); |
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fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj); |
cptcode=modmaxcovj; |
cptcode=modmaxcovj; |
/* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */ |
/* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */ |
/*for (i=0; i<=cptcode; i++) {*/ |
/*for (i=0; i<=cptcode; i++) {*/ |
for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */ |
for (k=modmincovj; k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */ |
printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]); |
printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]); |
if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */ |
fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]); |
ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */ |
if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */ |
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if( k != -1){ |
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ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th |
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covariate for which somebody answered excluding |
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undefined. Usually 2: 0 and 1. */ |
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} |
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ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th |
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covariate for which somebody answered including |
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undefined. Usually 3: -1, 0 and 1. */ |
} |
} |
/* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for |
/* 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 */ |
historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */ |
} /* Ndum[-1] number of undefined modalities */ |
} /* Ndum[-1] number of undefined modalities */ |
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/* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */ |
/* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */ |
/* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */ |
/* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. |
/* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125; |
If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; |
modmincovj=3; modmaxcovj = 7; |
modmincovj=3; modmaxcovj = 7; |
There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3; |
There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; |
which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy |
which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; |
variables V1_1 and V1_2. |
defining two dummy variables: variables V1_1 and V1_2. |
nbcode[Tvar[j]][ij]=k; |
nbcode[Tvar[j]][ij]=k; |
nbcode[Tvar[j]][1]=0; |
nbcode[Tvar[j]][1]=0; |
nbcode[Tvar[j]][2]=1; |
nbcode[Tvar[j]][2]=1; |
nbcode[Tvar[j]][3]=2; |
nbcode[Tvar[j]][3]=2; |
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To be continued (not working yet). |
*/ |
*/ |
ij=1; /* ij is similar to i but can jumps over null modalities */ |
ij=0; /* ij is similar to i but can jump over null modalities */ |
for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */ |
for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/ |
for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */ |
if (Ndum[i] == 0) { /* If nobody responded to this modality k */ |
/*recode from 0 */ |
break; |
if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */ |
} |
nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode. |
ij++; |
k is a modality. If we have model=V1+V1*sex |
nbcode[Tvar[j]][ij]=i; /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/ |
then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */ |
cptcode = ij; /* New max modality for covar j */ |
ij++; |
} /* end of loop on modality i=-1 to 1 or more */ |
} |
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if (ij > ncodemax[j]) break; |
/* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */ |
} /* end of loop on */ |
/* /\*recode from 0 *\/ */ |
} /* end of loop on modality */ |
/* k is a modality. If we have model=V1+V1*sex */ |
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/* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */ |
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/* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */ |
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/* } */ |
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/* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */ |
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/* if (ij > ncodemax[j]) { */ |
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/* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */ |
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/* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */ |
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/* break; */ |
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/* } */ |
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/* } /\* end of loop on modality k *\/ */ |
} /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/ |
} /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/ |
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for (k=-1; k< maxncov; k++) Ndum[k]=0; |
for (k=-1; k< maxncov; k++) Ndum[k]=0; |
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for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ |
for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */ |
/* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ |
/* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ |
ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ |
ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ |
Ndum[ij]++; |
Ndum[ij]++; /* Might be supersed V1 + V1*age */ |
} |
} |
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ij=1; |
ij=0; |
for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */ |
for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */ |
/*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/ |
/*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/ |
if((Ndum[i]!=0) && (i<=ncovcol)){ |
if((Ndum[i]!=0) && (i<=ncovcol)){ |
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ij++; |
/*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/ |
/*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/ |
Tvaraff[ij]=i; /*For printing (unclear) */ |
Tvaraff[ij]=i; /*For printing (unclear) */ |
ij++; |
}else{ |
}else |
/* Tvaraff[ij]=0; */ |
Tvaraff[ij]=0; |
} |
} |
} |
ij--; |
/* ij--; */ |
cptcoveff=ij; /*Number of total covariates*/ |
cptcoveff=ij; /*Number of total covariates*/ |
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} |
} |
Line 3320 void cvevsij(double ***eij, double x[],
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Line 3963 void cvevsij(double ***eij, double x[],
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} |
} |
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/************ Variance ******************/ |
/************ 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[]) |
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 *ncvyear, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[]) |
{ |
{ |
/* Variance of health expectancies */ |
/* Variance of health expectancies */ |
/* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/ |
/* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/ |
/* double **newm;*/ |
/* double **newm;*/ |
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/* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/ |
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|
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int movingaverage(); |
double **dnewm,**doldm; |
double **dnewm,**doldm; |
double **dnewmp,**doldmp; |
double **dnewmp,**doldmp; |
int i, j, nhstepm, hstepm, h, nstepm ; |
int i, j, nhstepm, hstepm, h, nstepm ; |
Line 3346 void varevsij(char optionfilefiname[], d
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Line 3992 void varevsij(char optionfilefiname[], d
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if(popbased==1){ |
if(popbased==1){ |
if(mobilav!=0) |
if(mobilav!=0) |
strcpy(digitp,"-populbased-mobilav-"); |
strcpy(digitp,"-POPULBASED-MOBILAV_"); |
else strcpy(digitp,"-populbased-nomobil-"); |
else strcpy(digitp,"-POPULBASED-NOMOBIL_"); |
} |
} |
else |
else |
strcpy(digitp,"-stablbased-"); |
strcpy(digitp,"-STABLBASED_"); |
|
|
if (mobilav!=0) { |
if (mobilav!=0) { |
mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
Line 3360 void varevsij(char optionfilefiname[], d
|
Line 4006 void varevsij(char optionfilefiname[], d
|
} |
} |
} |
} |
|
|
strcpy(fileresprobmorprev,"prmorprev"); |
strcpy(fileresprobmorprev,"PRMORPREV-"); |
sprintf(digit,"%-d",ij); |
sprintf(digit,"%-d",ij); |
/*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/ |
/*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/ |
strcat(fileresprobmorprev,digit); /* Tvar to be done */ |
strcat(fileresprobmorprev,digit); /* Tvar to be done */ |
strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */ |
strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */ |
strcat(fileresprobmorprev,fileres); |
strcat(fileresprobmorprev,fileresu); |
if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) { |
if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) { |
printf("Problem with resultfile: %s\n", fileresprobmorprev); |
printf("Problem with resultfile: %s\n", fileresprobmorprev); |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev); |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev); |
Line 3383 void varevsij(char optionfilefiname[], d
|
Line 4029 void varevsij(char optionfilefiname[], d
|
} |
} |
fprintf(ficresprobmorprev,"\n"); |
fprintf(ficresprobmorprev,"\n"); |
fprintf(ficgp,"\n# Routine varevsij"); |
fprintf(ficgp,"\n# Routine varevsij"); |
/* fprintf(fichtm, "#Local time at start: %s", strstart);*/ |
fprintf(ficgp,"\nunset title \n"); |
|
/* 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<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); |
fprintf(fichtm,"\n<br>%s <br>\n",digitp); |
/* } */ |
/* } */ |
Line 3442 void varevsij(char optionfilefiname[], d
|
Line 4089 void varevsij(char optionfilefiname[], d
|
xp[i] = x[i] + (i==theta ?delti[theta]:0); |
xp[i] = x[i] + (i==theta ?delti[theta]:0); |
} |
} |
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); |
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij); |
|
|
if (popbased==1) { |
if (popbased==1) { |
if(mobilav ==0){ |
if(mobilav ==0){ |
Line 3473 void varevsij(char optionfilefiname[], d
|
Line 4120 void varevsij(char optionfilefiname[], d
|
for(i=1; i<=npar; i++) /* Computes gradient x - delta */ |
for(i=1; i<=npar; i++) /* Computes gradient x - delta */ |
xp[i] = x[i] - (i==theta ?delti[theta]:0); |
xp[i] = x[i] - (i==theta ?delti[theta]:0); |
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); |
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear, ij); |
|
|
if (popbased==1) { |
if (popbased==1) { |
if(mobilav ==0){ |
if(mobilav ==0){ |
Line 3548 void varevsij(char optionfilefiname[], d
|
Line 4195 void varevsij(char optionfilefiname[], d
|
/* end ppptj */ |
/* end ppptj */ |
/* x centered again */ |
/* x centered again */ |
hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij); |
hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij); |
prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij); |
prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyear,ij); |
|
|
if (popbased==1) { |
if (popbased==1) { |
if(mobilav ==0){ |
if(mobilav ==0){ |
Line 3595 void varevsij(char optionfilefiname[], d
|
Line 4242 void varevsij(char optionfilefiname[], d
|
free_vector(gmp,nlstate+1,nlstate+ndeath); |
free_vector(gmp,nlstate+1,nlstate+ndeath); |
free_matrix(gradgp,1,npar,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*/ |
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"); |
/* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */ |
|
fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480"); |
/* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */ |
/* 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 set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";"); |
|
fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit); |
/* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */ |
/* 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) 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 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 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)) 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(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> 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. <br> <img src=\"%s%s.svg\"> <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(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.svg\"> <br>\n", stepm,YEARM,digitp,digit); |
*/ |
*/ |
/* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */ |
/* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */ |
fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit); |
fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit); |
|
|
free_vector(xp,1,npar); |
free_vector(xp,1,npar); |
free_matrix(doldm,1,nlstate,1,nlstate); |
free_matrix(doldm,1,nlstate,1,nlstate); |
Line 3624 void varevsij(char optionfilefiname[], d
|
Line 4273 void varevsij(char optionfilefiname[], d
|
} /* end varevsij */ |
} /* end varevsij */ |
|
|
/************ Variance of prevlim ******************/ |
/************ 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[]) |
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 *ncvyear, int ij, char strstart[]) |
{ |
{ |
/* Variance of prevalence limit */ |
/* Variance of prevalence limit */ |
/* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/ |
/* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/ |
Line 3663 void varprevlim(char fileres[], double *
|
Line 4312 void varprevlim(char fileres[], double *
|
for(i=1; i<=npar; i++){ /* Computes gradient */ |
for(i=1; i<=npar; i++){ /* Computes gradient */ |
xp[i] = x[i] + (i==theta ?delti[theta]:0); |
xp[i] = x[i] + (i==theta ?delti[theta]:0); |
} |
} |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij); |
for(i=1;i<=nlstate;i++) |
for(i=1;i<=nlstate;i++) |
gp[i] = prlim[i][i]; |
gp[i] = prlim[i][i]; |
|
|
for(i=1; i<=npar; i++) /* Computes gradient */ |
for(i=1; i<=npar; i++) /* Computes gradient */ |
xp[i] = x[i] - (i==theta ?delti[theta]:0); |
xp[i] = x[i] - (i==theta ?delti[theta]:0); |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij); |
for(i=1;i<=nlstate;i++) |
for(i=1;i<=nlstate;i++) |
gm[i] = prlim[i][i]; |
gm[i] = prlim[i][i]; |
|
|
Line 3727 void varprob(char optionfilefiname[], do
|
Line 4376 void varprob(char optionfilefiname[], do
|
char fileresprobcor[FILENAMELENGTH]; |
char fileresprobcor[FILENAMELENGTH]; |
double ***varpij; |
double ***varpij; |
|
|
strcpy(fileresprob,"prob"); |
strcpy(fileresprob,"PROB_"); |
strcat(fileresprob,fileres); |
strcat(fileresprob,fileres); |
if((ficresprob=fopen(fileresprob,"w"))==NULL) { |
if((ficresprob=fopen(fileresprob,"w"))==NULL) { |
printf("Problem with resultfile: %s\n", fileresprob); |
printf("Problem with resultfile: %s\n", fileresprob); |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob); |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob); |
} |
} |
strcpy(fileresprobcov,"probcov"); |
strcpy(fileresprobcov,"PROBCOV_"); |
strcat(fileresprobcov,fileres); |
strcat(fileresprobcov,fileresu); |
if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) { |
if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) { |
printf("Problem with resultfile: %s\n", fileresprobcov); |
printf("Problem with resultfile: %s\n", fileresprobcov); |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov); |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov); |
} |
} |
strcpy(fileresprobcor,"probcor"); |
strcpy(fileresprobcor,"PROBCOR_"); |
strcat(fileresprobcor,fileres); |
strcat(fileresprobcor,fileresu); |
if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) { |
if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) { |
printf("Problem with resultfile: %s\n", fileresprobcor); |
printf("Problem with resultfile: %s\n", fileresprobcor); |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor); |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor); |
Line 3782 void varprob(char optionfilefiname[], do
|
Line 4431 void varprob(char optionfilefiname[], do
|
fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n"); |
fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n"); |
fprintf(fichtm,"\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(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back.</li>\n",optionfilehtmcov); |
fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\ |
fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov); |
file %s<br>\n",optionfilehtmcov); |
fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \ |
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.\ |
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"); |
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. \ |
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. \ |
Line 3806 To be simple, these graphs help to under
|
Line 4454 To be simple, these graphs help to under
|
/*j1++;*/ |
/*j1++;*/ |
if (cptcovn>0) { |
if (cptcovn>0) { |
fprintf(ficresprob, "\n#********** Variable "); |
fprintf(ficresprob, "\n#********** Variable "); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); |
fprintf(ficresprob, "**********\n#\n"); |
fprintf(ficresprob, "**********\n#\n"); |
fprintf(ficresprobcov, "\n#********** Variable "); |
fprintf(ficresprobcov, "\n#********** Variable "); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); |
fprintf(ficresprobcov, "**********\n#\n"); |
fprintf(ficresprobcov, "**********\n#\n"); |
|
|
fprintf(ficgp, "\n#********** Variable "); |
fprintf(ficgp, "\n#********** Variable "); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); |
fprintf(ficgp, "**********\n#\n"); |
fprintf(ficgp, "**********\n#\n"); |
|
|
|
|
fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable "); |
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]]); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); |
fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">"); |
fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">"); |
|
|
fprintf(ficresprobcor, "\n#********** Variable "); |
fprintf(ficresprobcor, "\n#********** Variable "); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); |
fprintf(ficresprobcor, "**********\n#"); |
fprintf(ficresprobcor, "**********\n#"); |
} |
} |
|
|
Line 3832 To be simple, these graphs help to under
|
Line 4480 To be simple, these graphs help to under
|
gm=vector(1,(nlstate)*(nlstate+ndeath)); |
gm=vector(1,(nlstate)*(nlstate+ndeath)); |
for (age=bage; age<=fage; age ++){ |
for (age=bage; age<=fage; age ++){ |
cov[2]=age; |
cov[2]=age; |
|
if(nagesqr==1) |
|
cov[3]= age*age; |
for (k=1; k<=cptcovn;k++) { |
for (k=1; k<=cptcovn;k++) { |
cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4 |
cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)]; |
|
/*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4 |
* 1 1 1 1 1 |
* 1 1 1 1 1 |
* 2 2 1 1 1 |
* 2 2 1 1 1 |
* 3 1 2 1 1 |
* 3 1 2 1 1 |
*/ |
*/ |
/* nbcode[1][1]=0 nbcode[1][2]=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]]=cov[2+Tage[k]]*cov[2]; */ |
|
for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; |
for (k=1; k<=cptcovprod;k++) |
for (k=1; k<=cptcovprod;k++) |
cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; |
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; |
|
|
|
|
for(theta=1; theta <=npar; theta++){ |
for(theta=1; theta <=npar; theta++){ |
Line 3990 To be simple, these graphs help to under
|
Line 4642 To be simple, these graphs help to under
|
/* mu2+ v21*lc1*cost + v22*lc2*sin(t) */ |
/* mu2+ v21*lc1*cost + v22*lc2*sin(t) */ |
if(first==1){ |
if(first==1){ |
first=0; |
first=0; |
|
fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n"); |
fprintf(ficgp,"\nset parametric;unset label"); |
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 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(ficgp,"\nset ter svg size 640, 480"); |
fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\ |
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\">\ |
:<a href=\"%s_%d%1d%1d-%1d%1d.svg\">\ |
%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\ |
%s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\ |
subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\ |
subdirf2(optionfilefiname,"VARPIJGR_"), j1,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><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2); |
fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12); |
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 out \"%s_%d%1d%1d-%1d%1d.svg\"",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,"\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,"\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",\ |
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",\ |
Line 4017 To be simple, these graphs help to under
|
Line 4670 To be simple, these graphs help to under
|
}/* if first */ |
}/* if first */ |
} /* age mod 5 */ |
} /* age mod 5 */ |
} /* end loop age */ |
} /* end loop age */ |
fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2); |
fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2); |
first=1; |
first=1; |
} /*l12 */ |
} /*l12 */ |
} /* k12 */ |
} /* k12 */ |
} /*l1 */ |
} /*l1 */ |
}/* k1 */ |
}/* k1 */ |
/* } /* loop covariates */ |
/* } */ /* loop covariates */ |
} |
} |
free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage); |
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(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage); |
Line 4039 To be simple, these graphs help to under
|
Line 4692 To be simple, these graphs help to under
|
|
|
|
|
/******************* Printing html file ***********/ |
/******************* Printing html file ***********/ |
void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \ |
void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \ |
int lastpass, int stepm, int weightopt, char model[],\ |
int lastpass, int stepm, int weightopt, char model[],\ |
int imx,int jmin, int jmax, double jmeanint,char rfileres[],\ |
int imx,int jmin, int jmax, double jmeanint,char rfileres[],\ |
int popforecast, int estepm ,\ |
int popforecast, int estepm ,\ |
Line 4052 void printinghtml(char fileres[], char t
|
Line 4705 void printinghtml(char fileres[], char t
|
</ul>"); |
</ul>"); |
fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \ |
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 ", |
- 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")); |
jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_")); |
fprintf(fichtm,"\ |
fprintf(fichtm,"\ |
- Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ", |
- Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ", |
stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij")); |
stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_")); |
fprintf(fichtm,"\ |
fprintf(fichtm,"\ |
- Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n", |
- Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n", |
subdirf2(fileres,"pl"),subdirf2(fileres,"pl")); |
subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_")); |
fprintf(fichtm,"\ |
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) 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", |
<a href=\"%s\">%s</a> <br>\n", |
estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e")); |
estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_")); |
fprintf(fichtm,"\ |
fprintf(fichtm,"\ |
- Population projections by age and states: \ |
- Population projections by age and states: \ |
<a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f")); |
<a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_")); |
|
|
fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>"); |
fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>"); |
|
|
Line 4074 fprintf(fichtm," \n<ul><li><b>Graphs</b>
|
Line 4727 fprintf(fichtm," \n<ul><li><b>Graphs</b>
|
|
|
jj1=0; |
jj1=0; |
for(k1=1; k1<=m;k1++){ |
for(k1=1; k1<=m;k1++){ |
for(i1=1; i1<=ncodemax[k1];i1++){ |
/* for(i1=1; i1<=ncodemax[k1];i1++){ */ |
jj1++; |
jj1++; |
if (cptcovn > 0) { |
if (cptcovn > 0) { |
fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates"); |
fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates"); |
for (cpt=1; cpt<=cptcoveff;cpt++) |
for (cpt=1; cpt<=cptcoveff;cpt++){ |
fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]); |
fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); |
|
printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout); |
|
} |
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">"); |
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">"); |
} |
} |
|
/* aij, bij */ |
|
fprintf(fichtm,"<br>- Logit model, for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1.svg\">%s_%d-1.svg</a><br> \ |
|
<img src=\"%s_%d-1.svg\">",subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1); |
/* Pij */ |
/* 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> \ |
fprintf(fichtm,"<br>\n- Pij or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2.svg\">%s_%d-2.svg</a><br> \ |
<img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); |
<img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1); |
/* Quasi-incidences */ |
/* Quasi-incidences */ |
fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\ |
fprintf(fichtm,"<br>\n- Iij 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> \ |
before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too,\ |
<img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); |
incidence (rates) are the limit when h tends to zero of the ratio of the probability hPij \ |
/* Period (stable) prevalence in each health state */ |
divided by h: hPij/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \ |
for(cpt=1; cpt<=nlstate;cpt++){ |
<img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1); |
fprintf(fichtm,"<br>- Convergence from cross-sectional prevalence in each state (1 to %d) to period (stable) prevalence in specific state %d <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \ |
/* Survival functions (period) in state j */ |
<img src=\"%s%d_%d.png\">",nlstate, cpt, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1); |
for(cpt=1; cpt<=nlstate;cpt++){ |
} |
fprintf(fichtm,"<br>\n- Survival functions in state %d. Or probability to survive in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \ |
|
<img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1); |
|
} |
|
/* State specific survival functions (period) */ |
|
for(cpt=1; cpt<=nlstate;cpt++){ |
|
fprintf(fichtm,"<br>\n- Survival functions from state %d in any different live states and total.\ |
|
Or probability to survive in various states (1 to %d) being in state %d at different ages.\ |
|
<a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> <img src=\"%s_%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1); |
|
} |
|
/* Period (stable) prevalence in each health state */ |
|
for(cpt=1; cpt<=nlstate;cpt++){ |
|
fprintf(fichtm,"<br>\n- 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.svg\">%s%d_%d.svg</a><br> \ |
|
<img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1); |
|
} |
for(cpt=1; cpt<=nlstate;cpt++) { |
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> \ |
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) (or area under each survival functions): <a href=\"%s%d%d.svg\">%s%d%d.svg</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); |
<img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1); |
} |
} |
} /* end i1 */ |
/* } /\* end i1 *\/ */ |
}/* End k1 */ |
}/* End k1 */ |
fprintf(fichtm,"</ul>"); |
fprintf(fichtm,"</ul>"); |
|
|
|
|
fprintf(fichtm,"\ |
fprintf(fichtm,"\ |
\n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\ |
\n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\ |
- Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres); |
- Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \ |
|
- 95%% confidence intervals and Wald tests of the estimated parameters are in the log file if optimization has been done (mle != 0).<br> \ |
|
But because parameters are usually highly correlated (a higher incidence of disability \ |
|
and a higher incidence of recovery can give very close observed transition) it might \ |
|
be very useful to look not only at linear confidence intervals estimated from the \ |
|
variances but at the covariance matrix. And instead of looking at the estimated coefficients \ |
|
(parameters) of the logistic regression, it might be more meaningful to visualize the \ |
|
covariance matrix of the one-step probabilities. \ |
|
See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres); |
|
|
fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n", |
fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n", |
subdirf2(fileres,"prob"),subdirf2(fileres,"prob")); |
subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_")); |
fprintf(fichtm,"\ |
fprintf(fichtm,"\ |
- Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n", |
- Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n", |
subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov")); |
subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_")); |
|
|
fprintf(fichtm,"\ |
fprintf(fichtm,"\ |
- Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n", |
- Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n", |
subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor")); |
subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_")); |
fprintf(fichtm,"\ |
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): \ |
- 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>", |
<a href=\"%s\">%s</a> <br>\n</li>", |
estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve")); |
estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_")); |
fprintf(fichtm,"\ |
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) 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>", |
<a href=\"%s\">%s</a> <br>\n</li>", |
estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde")); |
estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_")); |
fprintf(fichtm,"\ |
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", |
- 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")); |
estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_")); |
fprintf(fichtm,"\ |
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", |
- 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")); |
estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_")); |
fprintf(fichtm,"\ |
fprintf(fichtm,"\ |
- Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\ |
- Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\ |
subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl")); |
subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_")); |
|
|
/* if(popforecast==1) fprintf(fichtm,"\n */ |
/* if(popforecast==1) fprintf(fichtm,"\n */ |
/* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */ |
/* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */ |
Line 4148 fprintf(fichtm," \n<ul><li><b>Graphs</b>
|
Line 4826 fprintf(fichtm," \n<ul><li><b>Graphs</b>
|
|
|
jj1=0; |
jj1=0; |
for(k1=1; k1<=m;k1++){ |
for(k1=1; k1<=m;k1++){ |
for(i1=1; i1<=ncodemax[k1];i1++){ |
/* for(i1=1; i1<=ncodemax[k1];i1++){ */ |
jj1++; |
jj1++; |
if (cptcovn > 0) { |
if (cptcovn > 0) { |
fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates"); |
fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates"); |
for (cpt=1; cpt<=cptcoveff;cpt++) |
for (cpt=1; cpt<=cptcoveff;cpt++) |
fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]); |
fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); |
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">"); |
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">"); |
} |
} |
for(cpt=1; cpt<=nlstate;cpt++) { |
for(cpt=1; cpt<=nlstate;cpt++) { |
fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \ |
fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \ |
prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\ |
prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.svg <br>\ |
<img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1); |
<img src=\"%s_%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1); |
} |
} |
fprintf(fichtm,"\n<br>- Total life expectancy by age and \ |
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) \ |
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\ |
true period expectancies (those weighted with period prevalences are also\ |
drawn in addition to the population based expectancies computed using\ |
drawn in addition to the population based expectancies computed using\ |
observed and cahotic prevalences: %s%d.png<br>\ |
observed and cahotic prevalences: %s_%d.svg<br>\ |
<img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1); |
<img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1); |
} /* end i1 */ |
/* } /\* end i1 *\/ */ |
}/* End k1 */ |
}/* End k1 */ |
fprintf(fichtm,"</ul>"); |
fprintf(fichtm,"</ul>"); |
fflush(fichtm); |
fflush(fichtm); |
} |
} |
|
|
/******************* Gnuplot file **************/ |
/******************* Gnuplot file **************/ |
void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){ |
void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){ |
|
|
char dirfileres[132],optfileres[132]; |
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 cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0; |
int ng=0; |
int ng=0; |
|
int vpopbased; |
/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */ |
/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */ |
/* printf("Problem with file %s",optionfilegnuplot); */ |
/* printf("Problem with file %s",optionfilegnuplot); */ |
/* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */ |
/* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */ |
Line 4189 void printinggnuplot(char fileres[], cha
|
Line 4868 void printinggnuplot(char fileres[], cha
|
/*#endif */ |
/*#endif */ |
m=pow(2,cptcoveff); |
m=pow(2,cptcoveff); |
|
|
|
/* Contribution to likelihood */ |
|
/* Plot the probability implied in the likelihood */ |
|
fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n"); |
|
fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";"); |
|
/* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */ |
|
fprintf(ficgp,"\nset ter png size 640, 480"); |
|
/* nice for mle=4 plot by number of matrix products. |
|
replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */ |
|
/* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */ |
|
/* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */ |
|
fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_")); |
|
fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):5 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk)); |
|
fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_")); |
|
fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):4 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk)); |
|
for (i=1; i<= nlstate ; i ++) { |
|
fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i); |
|
fprintf(ficgp,"unset log;\n plot \"%s\"",subdirf(fileresilk)); |
|
fprintf(ficgp," u 2:($4 == %d && $5==%d ? $9 : 1/0):5 t \"p%d%d\" with points lc variable \\\n",i,1,i,1); |
|
for (j=2; j<= nlstate+ndeath ; j ++) { |
|
fprintf(ficgp,", \"\" u 2:($4 == %d && $5==%d ? $9 : 1/0):5 t \"p%d%d\" with points lc variable ",i,j,i,j); |
|
} |
|
fprintf(ficgp,";\nset out; unset ylabel;\n"); |
|
} |
|
/* unset log; plot "rrtest1_sorted_4/ILK_rrtest1_sorted_4.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with points lc variable */ |
|
/* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */ |
|
/* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */ |
|
fprintf(ficgp,"\nset out;unset log\n"); |
|
/* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */ |
|
|
strcpy(dirfileres,optionfilefiname); |
strcpy(dirfileres,optionfilefiname); |
strcpy(optfileres,"vpl"); |
strcpy(optfileres,"vpl"); |
/* 1eme*/ |
/* 1eme*/ |
fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n"); |
fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files\n"); |
for (cpt=1; cpt<= nlstate ; cpt ++) { |
for (cpt=1; cpt<= nlstate ; cpt ++) { |
for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */ |
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,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1); |
fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1); |
fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1); |
fprintf(ficgp,"set xlabel \"Age\" \n\ |
fprintf(ficgp,"set xlabel \"Age\" \n\ |
set ylabel \"Probability\" \n\ |
set ylabel \"Probability\" \n\ |
set ter png small size 320, 240\n\ |
set ter svg size 640, 480\n\ |
plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1); |
plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1); |
|
|
for (i=1; i<= nlstate ; i ++) { |
for (i=1; i<= nlstate ; i ++) { |
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)"); |
if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); |
else fprintf(ficgp," \%%*lf (\%%*lf)"); |
else fprintf(ficgp," %%*lf (%%*lf)"); |
} |
} |
fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); |
fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1); |
for (i=1; i<= nlstate ; i ++) { |
for (i=1; i<= nlstate ; i ++) { |
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)"); |
if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); |
else 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); |
fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1); |
for (i=1; i<= nlstate ; i ++) { |
for (i=1; i<= nlstate ; i ++) { |
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)"); |
if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); |
else fprintf(ficgp," \%%*lf (\%%*lf)"); |
else fprintf(ficgp," %%*lf (%%*lf)"); |
} |
} |
fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1)); |
fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1)); |
} |
fprintf(ficgp,"\nset out \n"); |
} |
} /* k1 */ |
|
} /* cpt */ |
/*2 eme*/ |
/*2 eme*/ |
fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n"); |
fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n"); |
for (k1=1; k1<= m ; k1 ++) { |
for (k1=1; k1<= m ; k1 ++) { |
fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1); |
fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1); |
fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage); |
for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/ |
|
if(vpopbased==0) |
for (i=1; i<= nlstate+1 ; i ++) { |
fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage); |
k=2*i; |
else |
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1); |
fprintf(ficgp,"\nreplot "); |
for (j=1; j<= nlstate+1 ; j ++) { |
for (i=1; i<= nlstate+1 ; i ++) { |
if (j==i) fprintf(ficgp," \%%lf (\%%lf)"); |
k=2*i; |
else fprintf(ficgp," \%%*lf (\%%*lf)"); |
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased); |
} |
for (j=1; j<= nlstate+1 ; j ++) { |
if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,"); |
if (j==i) fprintf(ficgp," %%lf (%%lf)"); |
else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1); |
else fprintf(ficgp," %%*lf (%%*lf)"); |
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 (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i); |
if (j==i) fprintf(ficgp," \%%lf (\%%lf)"); |
else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1); |
else fprintf(ficgp," \%%*lf (\%%*lf)"); |
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased); |
} |
for (j=1; j<= nlstate+1 ; j ++) { |
fprintf(ficgp,"\" t\"\" w l lt 0,"); |
if (j==i) fprintf(ficgp," %%lf (%%lf)"); |
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1); |
else fprintf(ficgp," %%*lf (%%*lf)"); |
for (j=1; j<= nlstate+1 ; j ++) { |
} |
if (j==i) fprintf(ficgp," \%%lf (\%%lf)"); |
fprintf(ficgp,"\" t\"\" w l lt 0,"); |
else fprintf(ficgp," \%%*lf (\%%*lf)"); |
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased); |
} |
for (j=1; j<= nlstate+1 ; j ++) { |
if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0"); |
if (j==i) fprintf(ficgp," %%lf (%%lf)"); |
else fprintf(ficgp,"\" t\"\" w l lt 0,"); |
else fprintf(ficgp," %%*lf (%%*lf)"); |
} |
} |
} |
if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0"); |
|
else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n"); |
|
} /* state */ |
|
} /* vpopbased */ |
|
fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */ |
|
} /* k1 */ |
/*3eme*/ |
/*3eme*/ |
|
|
for (k1=1; k1<= m ; k1 ++) { |
for (k1=1; k1<= m ; k1 ++) { |
for (cpt=1; cpt<= nlstate ; cpt ++) { |
for (cpt=1; cpt<= nlstate ; cpt ++) { |
/* k=2+nlstate*(2*cpt-2); */ |
/* k=2+nlstate*(2*cpt-2); */ |
k=2+(nlstate+1)*(cpt-1); |
k=2+(nlstate+1)*(cpt-1); |
fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1); |
fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1); |
fprintf(ficgp,"set ter png small size 320, 240\n\ |
fprintf(ficgp,"set ter svg size 640, 480\n\ |
plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt); |
plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt); |
/*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); |
/*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); |
for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); |
for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); |
fprintf(ficgp,"\" t \"e%d1\" w l",cpt); |
fprintf(ficgp,"\" t \"e%d1\" w l",cpt); |
Line 4268 plot [%.f:%.f] \"%s\" every :::%d::%d u
|
Line 4981 plot [%.f:%.f] \"%s\" every :::%d::%d u
|
|
|
*/ |
*/ |
for (i=1; i< nlstate ; i ++) { |
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(fileresu,"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%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); |
fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt); |
} |
} |
} |
} |
|
|
/* CV preval stable (period) */ |
/* Survival functions (period) from state i in state j by initial state i */ |
for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */ |
for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */ |
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */ |
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */ |
k=3; |
k=3; |
|
fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'lij' files, cov=%d state=%d",k1, cpt); |
|
fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1); |
|
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\ |
|
set ter svg size 640, 480\n\ |
|
unset log y\n\ |
|
plot [%.f:%.f] ", ageminpar, agemaxpar); |
|
for (i=1; i<= nlstate ; i ++){ |
|
if(i==1) |
|
fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_")); |
|
else |
|
fprintf(ficgp,", '' "); |
|
l=(nlstate+ndeath)*(i-1)+1; |
|
fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); |
|
for (j=2; j<= nlstate+ndeath ; j ++) |
|
fprintf(ficgp,"+$%d",k+l+j-1); |
|
fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt); |
|
} /* nlstate */ |
|
fprintf(ficgp,"\nset out\n"); |
|
} /* end cpt state*/ |
|
} /* end covariate */ |
|
|
|
/* Survival functions (period) from state i in state j by final state j */ |
|
for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */ |
|
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */ |
|
k=3; |
|
fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt); |
|
fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1); |
|
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\ |
|
set ter svg size 640, 480\n\ |
|
unset log y\n\ |
|
plot [%.f:%.f] ", ageminpar, agemaxpar); |
|
for (j=1; j<= nlstate ; j ++){ /* Lived in state j */ |
|
if(j==1) |
|
fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_")); |
|
else |
|
fprintf(ficgp,", '' "); |
|
l=(nlstate+ndeath)*(cpt-1) +j; |
|
fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l); |
|
/* for (i=2; i<= nlstate+ndeath ; i ++) */ |
|
/* fprintf(ficgp,"+$%d",k+l+i-1); */ |
|
fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j); |
|
} /* nlstate */ |
|
fprintf(ficgp,", '' "); |
|
fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1); |
|
for (j=1; j<= nlstate ; j ++){ /* Lived in state j */ |
|
l=(nlstate+ndeath)*(cpt-1) +j; |
|
if(j < nlstate) |
|
fprintf(ficgp,"$%d +",k+l); |
|
else |
|
fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt); |
|
} |
|
fprintf(ficgp,"\nset out\n"); |
|
} /* end cpt state*/ |
|
} /* end covariate */ |
|
|
|
/* CV preval stable (period) for each covariate */ |
|
for (k1=1; k1<= m ; k1 ++) { /* For each covariate 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,"\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,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1); |
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\ |
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\ |
set ter png small size 320, 240\n\ |
set ter svg size 640, 480\n\ |
unset log y\n\ |
unset log y\n\ |
plot [%.f:%.f] ", ageminpar, agemaxpar); |
plot [%.f:%.f] ", ageminpar, agemaxpar); |
for (i=1; i<= nlstate ; i ++){ |
for (i=1; i<= nlstate ; i ++){ |
if(i==1) |
if(i==1) |
fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij")); |
fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_")); |
else |
else |
fprintf(ficgp,", '' "); |
fprintf(ficgp,", '' "); |
l=(nlstate+ndeath)*(i-1)+1; |
l=(nlstate+ndeath)*(i-1)+1; |
fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); |
fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); |
for (j=1; j<= (nlstate-1) ; j ++) |
for (j=2; j<= nlstate ; j ++) |
fprintf(ficgp,"+$%d",k+l+j); |
fprintf(ficgp,"+$%d",k+l+j-1); |
fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt); |
fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt); |
} /* nlstate */ |
} /* nlstate */ |
fprintf(ficgp,"\n"); |
fprintf(ficgp,"\nset out\n"); |
} /* end cpt state*/ |
} /* end cpt state*/ |
} /* end covariate */ |
} /* end covariate */ |
|
|
/* proba elementaires */ |
/* proba elementaires */ |
|
fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n"); |
for(i=1,jk=1; i <=nlstate; i++){ |
for(i=1,jk=1; i <=nlstate; i++){ |
|
fprintf(ficgp,"# initial state %d\n",i); |
for(k=1; k <=(nlstate+ndeath); k++){ |
for(k=1; k <=(nlstate+ndeath); k++){ |
if (k != i) { |
if (k != i) { |
|
fprintf(ficgp,"# current state %d\n",k); |
for(j=1; j <=ncovmodel; j++){ |
for(j=1; j <=ncovmodel; j++){ |
fprintf(ficgp,"p%d=%f ",jk,p[jk]); |
fprintf(ficgp,"p%d=%f; ",jk,p[jk]); |
jk++; |
jk++; |
fprintf(ficgp,"\n"); |
|
} |
} |
|
fprintf(ficgp,"\n"); |
} |
} |
} |
} |
} |
} |
|
fprintf(ficgp,"##############\n#\n"); |
|
|
/*goto avoid;*/ |
/*goto avoid;*/ |
for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/ |
fprintf(ficgp,"\n##############\n#Graphics 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<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences 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++) { |
for(jk=1; jk <=m; jk++) { |
fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); |
fprintf(ficgp,"# jk=%d\n",jk); |
if (ng==2) |
fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng); |
|
fprintf(ficgp,"\nset ter svg size 640, 480 "); |
|
if (ng==1){ |
|
fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */ |
|
fprintf(ficgp,"\nunset log y"); |
|
}else if (ng==2){ |
|
fprintf(ficgp,"\nset ylabel \"Probability\"\n"); |
|
fprintf(ficgp,"\nset log y"); |
|
}else if (ng==3){ |
fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n"); |
fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n"); |
else |
fprintf(ficgp,"\nset log y"); |
fprintf(ficgp,"\nset title \"Probability\"\n"); |
}else |
fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar); |
fprintf(ficgp,"\nunset title "); |
|
fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar); |
i=1; |
i=1; |
for(k2=1; k2<=nlstate; k2++) { |
for(k2=1; k2<=nlstate; k2++) { |
k3=i; |
k3=i; |
for(k=1; k<=(nlstate+ndeath); k++) { |
for(k=1; k<=(nlstate+ndeath); k++) { |
if (k != k2){ |
if (k != k2){ |
if(ng==2) |
switch( ng) { |
fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1); |
case 1: |
else |
if(nagesqr==0) |
fprintf(ficgp," exp(p%d+p%d*x",i,i+1); |
fprintf(ficgp," p%d+p%d*x",i,i+1); |
|
else /* nagesqr =1 */ |
|
fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr); |
|
break; |
|
case 2: /* ng=2 */ |
|
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); |
|
break; |
|
case 3: |
|
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); |
|
break; |
|
} |
ij=1;/* To be checked else nbcode[0][0] wrong */ |
ij=1;/* To be checked else nbcode[0][0] wrong */ |
for(j=3; j <=ncovmodel; j++) { |
for(j=3; j <=ncovmodel-nagesqr; j++) { |
/* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */ |
/* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */ |
/* /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */ |
if(ij <=cptcovage) { /* Bug valgrind */ |
/* ij++; */ |
if((j-2)==Tage[ij]) { /* Bug valgrind */ |
/* } */ |
fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]); |
/* else */ |
/* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */ |
fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]); |
ij++; |
|
} |
|
} |
|
else |
|
fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]); |
} |
} |
fprintf(ficgp,")/(1"); |
if(ng != 1){ |
|
fprintf(ficgp,")/(1"); |
|
|
for(k1=1; k1 <=nlstate; k1++){ |
for(k1=1; k1 <=nlstate; k1++){ |
fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1); |
if(nagesqr==0) |
ij=1; |
fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1); |
for(j=3; j <=ncovmodel; j++){ |
else /* nagesqr =1 */ |
/* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */ |
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); |
/* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */ |
|
/* ij++; */ |
ij=1; |
/* } */ |
for(j=3; j <=ncovmodel-nagesqr; j++){ |
/* else */ |
if(ij <=cptcovage) { /* Bug valgrind */ |
fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]); |
if((j-2)==Tage[ij]) { /* Bug valgrind */ |
|
fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]); |
|
/* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */ |
|
ij++; |
|
} |
|
} |
|
else |
|
fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]); |
|
} |
|
fprintf(ficgp,")"); |
} |
} |
fprintf(ficgp,")"); |
fprintf(ficgp,")"); |
|
if(ng ==2) |
|
fprintf(ficgp," t \"p%d%d\" ", k2,k); |
|
else /* ng= 3 */ |
|
fprintf(ficgp," t \"i%d%d\" ", k2,k); |
|
}else{ /* end ng <> 1 */ |
|
fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k); |
} |
} |
fprintf(ficgp,") t \"p%d%d\" ", k2,k); |
|
if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,","); |
if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,","); |
i=i+ncovmodel; |
i=i+ncovmodel; |
} |
} |
} /* end k */ |
} /* end k */ |
} /* end k2 */ |
} /* end k2 */ |
|
fprintf(ficgp,"\n set out\n"); |
} /* end jk */ |
} /* end jk */ |
} /* end ng */ |
} /* end ng */ |
/* avoid: */ |
/* avoid: */ |
Line 4411 int movingaverage(double ***probs, doubl
|
Line 5249 int movingaverage(double ***probs, doubl
|
|
|
|
|
/************** Forecasting ******************/ |
/************** Forecasting ******************/ |
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){ |
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 |
/* proj1, year, month, day of starting projection |
agemin, agemax range of age |
agemin, agemax range of age |
dateprev1 dateprev2 range of dates during which prevalence is computed |
dateprev1 dateprev2 range of dates during which prevalence is computed |
Line 4428 prevforecast(char fileres[], double anpr
|
Line 5266 prevforecast(char fileres[], double anpr
|
agelim=AGESUP; |
agelim=AGESUP; |
prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); |
prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); |
|
|
strcpy(fileresf,"f"); |
strcpy(fileresf,"F_"); |
strcat(fileresf,fileres); |
strcat(fileresf,fileresu); |
if((ficresf=fopen(fileresf,"w"))==NULL) { |
if((ficresf=fopen(fileresf,"w"))==NULL) { |
printf("Problem with forecast resultfile: %s\n", fileresf); |
printf("Problem with forecast resultfile: %s\n", fileresf); |
fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf); |
fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf); |
Line 4478 prevforecast(char fileres[], double anpr
|
Line 5316 prevforecast(char fileres[], double anpr
|
k=k+1; |
k=k+1; |
fprintf(ficresf,"\n#******"); |
fprintf(ficresf,"\n#******"); |
for(j=1;j<=cptcoveff;j++) { |
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," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); |
} |
} |
fprintf(ficresf,"******\n"); |
fprintf(ficresf,"******\n"); |
fprintf(ficresf,"# Covariate valuofcovar yearproj age"); |
fprintf(ficresf,"# Covariate valuofcovar yearproj age"); |
Line 4502 prevforecast(char fileres[], double anpr
|
Line 5340 prevforecast(char fileres[], double anpr
|
if (h*hstepm/YEARM*stepm ==yearp) { |
if (h*hstepm/YEARM*stepm ==yearp) { |
fprintf(ficresf,"\n"); |
fprintf(ficresf,"\n"); |
for(j=1;j<=cptcoveff;j++) |
for(j=1;j<=cptcoveff;j++) |
fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); |
fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm); |
fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm); |
} |
} |
for(j=1; j<=nlstate+ndeath;j++) { |
for(j=1; j<=nlstate+ndeath;j++) { |
Line 4534 prevforecast(char fileres[], double anpr
|
Line 5372 prevforecast(char fileres[], double anpr
|
} |
} |
|
|
/************** Forecasting *****not tested NB*************/ |
/************** Forecasting *****not tested NB*************/ |
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){ |
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 cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; |
int *popage; |
int *popage; |
Line 4552 populforecast(char fileres[], double anp
|
Line 5390 populforecast(char fileres[], double anp
|
prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); |
prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); |
|
|
|
|
strcpy(filerespop,"pop"); |
strcpy(filerespop,"POP_"); |
strcat(filerespop,fileres); |
strcat(filerespop,fileresu); |
if((ficrespop=fopen(filerespop,"w"))==NULL) { |
if((ficrespop=fopen(filerespop,"w"))==NULL) { |
printf("Problem with forecast resultfile: %s\n", filerespop); |
printf("Problem with forecast resultfile: %s\n", filerespop); |
fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); |
fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); |
Line 4600 populforecast(char fileres[], double anp
|
Line 5438 populforecast(char fileres[], double anp
|
k=k+1; |
k=k+1; |
fprintf(ficrespop,"\n#******"); |
fprintf(ficrespop,"\n#******"); |
for(j=1;j<=cptcoveff;j++) { |
for(j=1;j<=cptcoveff;j++) { |
fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); |
} |
} |
fprintf(ficrespop,"******\n"); |
fprintf(ficrespop,"******\n"); |
fprintf(ficrespop,"# Age"); |
fprintf(ficrespop,"# Age"); |
Line 4906 double gompertz_f(const gsl_vector *v, v
|
Line 5744 double gompertz_f(const gsl_vector *v, v
|
#endif |
#endif |
|
|
/******************* Printing html file ***********/ |
/******************* Printing html file ***********/ |
void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \ |
void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \ |
int lastpass, int stepm, int weightopt, char model[],\ |
int lastpass, int stepm, int weightopt, char model[],\ |
int imx, double p[],double **matcov,double agemortsup){ |
int imx, double p[],double **matcov,double agemortsup){ |
int i,k; |
int i,k; |
Line 4915 void printinghtmlmort(char fileres[], ch
|
Line 5753 void printinghtmlmort(char fileres[], ch
|
fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp); |
fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp); |
for (i=1;i<=2;i++) |
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," 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,"<br><br><img src=\"graphmort.svg\">"); |
fprintf(fichtm,"</ul>"); |
fprintf(fichtm,"</ul>"); |
|
|
fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>"); |
fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>"); |
Line 4930 fprintf(fichtm,"<ul><li><h4>Life table</
|
Line 5768 fprintf(fichtm,"<ul><li><h4>Life table</
|
} |
} |
|
|
/******************* Gnuplot file **************/ |
/******************* Gnuplot file **************/ |
void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){ |
void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){ |
|
|
char dirfileres[132],optfileres[132]; |
char dirfileres[132],optfileres[132]; |
|
|
Line 4944 void printinggnuplotmort(char fileres[],
|
Line 5782 void printinggnuplotmort(char fileres[],
|
|
|
strcpy(dirfileres,optionfilefiname); |
strcpy(dirfileres,optionfilefiname); |
strcpy(optfileres,"vpl"); |
strcpy(optfileres,"vpl"); |
fprintf(ficgp,"set out \"graphmort.png\"\n "); |
fprintf(ficgp,"set out \"graphmort.svg\"\n "); |
fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \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 ter svg size 640, 480\n set log y\n"); |
/* fprintf(ficgp, "set size 0.65,0.65\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); |
fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp); |
|
|
Line 4967 int readdata(char datafile[], int firsto
|
Line 5805 int readdata(char datafile[], int firsto
|
|
|
|
|
if((fic=fopen(datafile,"r"))==NULL) { |
if((fic=fopen(datafile,"r"))==NULL) { |
printf("Problem while opening datafile: %s\n", datafile);return 1; |
printf("Problem while opening datafile: %s\n", datafile);fflush(stdout); |
fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1; |
fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);fflush(ficlog);return 1; |
} |
} |
|
|
i=1; |
i=1; |
Line 5010 int readdata(char datafile[], int firsto
|
Line 5848 int readdata(char datafile[], int firsto
|
|
|
strcpy(line,stra); |
strcpy(line,stra); |
cutv(stra, strb,line,' '); |
cutv(stra, strb,line,' '); |
if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){ |
if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){ |
} |
} |
else if(iout=sscanf(strb,"%s.",dummy) != 0){ |
else if( (iout=sscanf(strb,"%s.",dummy)) != 0){ |
month=99; |
month=99; |
year=9999; |
year=9999; |
}else{ |
}else{ |
Line 5026 int readdata(char datafile[], int firsto
|
Line 5864 int readdata(char datafile[], int firsto
|
} /* ENd Waves */ |
} /* ENd Waves */ |
|
|
cutv(stra, strb,line,' '); |
cutv(stra, strb,line,' '); |
if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){ |
if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){ |
} |
} |
else if(iout=sscanf(strb,"%s.",dummy) != 0){ |
else if( (iout=sscanf(strb,"%s.",dummy)) != 0){ |
month=99; |
month=99; |
year=9999; |
year=9999; |
}else{ |
}else{ |
Line 5041 int readdata(char datafile[], int firsto
|
Line 5879 int readdata(char datafile[], int firsto
|
strcpy(line,stra); |
strcpy(line,stra); |
|
|
cutv(stra, strb,line,' '); |
cutv(stra, strb,line,' '); |
if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){ |
if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){ |
} |
} |
else if(iout=sscanf(strb,"%s.", dummy) != 0){ |
else if( (iout=sscanf(strb,"%s.", dummy)) != 0){ |
month=99; |
month=99; |
year=9999; |
year=9999; |
}else{ |
}else{ |
Line 5141 void removespace(char *str) {
|
Line 5979 void removespace(char *str) {
|
do |
do |
while (*p2 == ' ') |
while (*p2 == ' ') |
p2++; |
p2++; |
while (*p1++ = *p2++); |
while (*p1++ == *p2++); |
} |
} |
|
|
int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns: |
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 |
* Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age |
* - cptcovt total number of covariates of the model nbocc(+)+1 = 8 |
* - nagesqr = 1 if age*age in the model, otherwise 0. |
* - cptcovn or number of covariates k of the models excluding age*products =6 |
* - 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 |
* - cptcovage number of covariates with age*products =2 |
* - cptcovs number of simple covariates |
* - 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 |
* - 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 |
Line 5162 int decodemodel ( char model[], int last
|
Line 6001 int decodemodel ( char model[], int last
|
int j1, k1, k2; |
int j1, k1, k2; |
char modelsav[80]; |
char modelsav[80]; |
char stra[80], strb[80], strc[80], strd[80],stre[80]; |
char stra[80], strb[80], strc[80], strd[80],stre[80]; |
|
char *strpt; |
|
|
/*removespace(model);*/ |
/*removespace(model);*/ |
if (strlen(model) >1){ /* If there is at least 1 covariate */ |
if (strlen(model) >1){ /* If there is at least 1 covariate */ |
j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0; |
j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0; |
j=nbocc(model,'+'); /**< j=Number of '+' */ |
|
j1=nbocc(model,'*'); /**< j1=Number of '*' */ |
|
cptcovs=j+1-j1; /**< Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2 */ |
|
cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 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 */ |
|
strcpy(modelsav,model); |
|
if (strstr(model,"AGE") !=0){ |
if (strstr(model,"AGE") !=0){ |
printf("Error. AGE must be in lower case 'age' model=%s ",model); |
printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model); |
fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog); |
fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog); |
return 1; |
return 1; |
} |
} |
if (strstr(model,"v") !=0){ |
if (strstr(model,"v") !=0){ |
Line 5185 int decodemodel ( char model[], int last
|
Line 6016 int decodemodel ( char model[], int last
|
fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog); |
fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog); |
return 1; |
return 1; |
} |
} |
|
strcpy(modelsav,model); |
/* Design |
if ((strpt=strstr(model,"age*age")) !=0){ |
* V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight |
printf(" strpt=%s, model=%s\n",strpt, model); |
* < ncovcol=8 > |
if(strpt != model){ |
* Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 |
printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \ |
* k= 1 2 3 4 5 6 7 8 |
'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \ |
* cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8 |
corresponding column of parameters.\n",model); |
* covar[k,i], value of kth covariate if not including age for individual i: |
fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \ |
* covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8) |
'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \ |
* Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8 |
corresponding column of parameters.\n",model); fflush(ficlog); |
* if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and |
return 1; |
* 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'.*/ |
nagesqr=1; |
/* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */ |
if (strstr(model,"+age*age") !=0) |
/* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */ |
substrchaine(modelsav, model, "+age*age"); |
/* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */ |
else if (strstr(model,"age*age+") !=0) |
/* k=3 V4 Tvar[k=3]= 4 (from V4) */ |
substrchaine(modelsav, model, "age*age+"); |
/* k=2 V1 Tvar[k=2]= 1 (from V1) */ |
else |
/* k=1 Tvar[1]=2 (from V2) */ |
substrchaine(modelsav, model, "age*age"); |
/* k=5 Tvar[5] */ |
}else |
/* for (k=1; k<=cptcovn;k++) { */ |
nagesqr=0; |
/* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */ |
if (strlen(modelsav) >1){ |
/* } */ |
j=nbocc(modelsav,'+'); /**< j=Number of '+' */ |
/* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ |
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 */ |
* Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */ |
cptcovt= j+1; /* Number of total covariates in the model, not including |
for(k=cptcovt; k>=1;k--) /**< Number of covariates */ |
* 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]][codtabm(ij,Tvar[k])]; */ |
|
/* } */ |
|
/* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(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; |
Tvar[k]=0; |
cptcovage=0; |
cptcovage=0; |
for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */ |
for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */ |
cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' |
cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' |
modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ |
modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ |
if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */ |
if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */ |
/* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/ |
/* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/ |
/*scanf("%d",i);*/ |
/*scanf("%d",i);*/ |
if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */ |
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 */ |
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 */ |
if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */ |
/* covar is not filled and then is empty */ |
/* covar is not filled and then is empty */ |
cptcovprod--; |
cptcovprod--; |
cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */ |
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 */ |
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 */ |
cptcovage++; /* Sums the number of covariates which include age as a product */ |
Tage[cptcovage]=k; /* Tage[1] = 4 */ |
Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */ |
/*printf("stre=%s ", stre);*/ |
/*printf("stre=%s ", stre);*/ |
} else if (strcmp(strd,"age")==0) { /* or age*Vn */ |
} else if (strcmp(strd,"age")==0) { /* or age*Vn */ |
cptcovprod--; |
cptcovprod--; |
cutl(stre,strb,strc,'V'); |
cutl(stre,strb,strc,'V'); |
Tvar[k]=atoi(stre); |
Tvar[k]=atoi(stre); |
cptcovage++; |
cptcovage++; |
Tage[cptcovage]=k; |
Tage[cptcovage]=k; |
} else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/ |
} 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 */ |
/* 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++; |
cptcovn++; |
cptcovprodnoage++;k1++; |
Tvar[k]=atoi(strd); |
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 |
strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ |
because this model-covariate is a construction we invent a new column |
/*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav); |
ncovcol + k1 |
scanf("%d",i);*/ |
If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2 |
} /* end of loop + on total covariates */ |
Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */ |
} /* end if strlen(modelsave == 0) age*age might exist */ |
cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */ |
} /* end if strlen(model == 0) */ |
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 + */ |
|
} /* end model */ |
|
|
|
/*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products. |
/*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*/ |
If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/ |
Line 5313 int decodemodel ( char model[], int last
|
Line 6180 int decodemodel ( char model[], int last
|
return (1); |
return (1); |
} |
} |
|
|
calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn ) |
int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn ) |
{ |
{ |
int i, m; |
int i, m; |
|
|
Line 5324 calandcheckages(int imx, int maxwav, dou
|
Line 6191 calandcheckages(int imx, int maxwav, dou
|
s[m][i]=-1; |
s[m][i]=-1; |
} |
} |
if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){ |
if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){ |
*nberr++; |
*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\n",(int)moisdc[i],(int)andc[i],num[i],i); |
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\n",(int)moisdc[i],(int)andc[i],num[i],i); |
fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr); |
s[m][i]=-1; |
s[m][i]=-1; |
} |
} |
if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){ |
if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){ |
*nberr++; |
(*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]); |
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]); |
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 */ |
s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */ |
Line 5343 calandcheckages(int imx, int maxwav, dou
|
Line 6210 calandcheckages(int imx, int maxwav, dou
|
for(m=firstpass; (m<= lastpass); m++){ |
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] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){ |
if (s[m][i] >= nlstate+1) { |
if (s[m][i] >= nlstate+1) { |
if(agedc[i]>0) |
if(agedc[i]>0){ |
if((int)moisdc[i]!=99 && (int)andc[i]!=9999) |
if((int)moisdc[i]!=99 && (int)andc[i]!=9999){ |
agev[m][i]=agedc[i]; |
agev[m][i]=agedc[i]; |
/*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/ |
/*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/ |
else { |
}else { |
if ((int)andc[i]!=9999){ |
if ((int)andc[i]!=9999){ |
nbwarn++; |
nbwarn++; |
printf("Warning negative age at death: %ld line:%d\n",num[i],i); |
printf("Warning negative age at death: %ld line:%d\n",num[i],i); |
Line 5355 calandcheckages(int imx, int maxwav, dou
|
Line 6222 calandcheckages(int imx, int maxwav, dou
|
agev[m][i]=-1; |
agev[m][i]=-1; |
} |
} |
} |
} |
|
} /* agedc > 0 */ |
} |
} |
else if(s[m][i] !=9){ /* Standard case, age in fractional |
else if(s[m][i] !=9){ /* Standard case, age in fractional |
years but with the precision of a month */ |
years but with the precision of a month */ |
Line 5385 calandcheckages(int imx, int maxwav, dou
|
Line 6253 calandcheckages(int imx, int maxwav, dou
|
for (i=1; i<=imx; i++) { |
for (i=1; i<=imx; i++) { |
for(m=firstpass; (m<=lastpass); m++){ |
for(m=firstpass; (m<=lastpass); m++){ |
if (s[m][i] > (nlstate+ndeath)) { |
if (s[m][i] > (nlstate+ndeath)) { |
*nberr++; |
(*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); |
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); |
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; |
return 1; |
Line 5410 calandcheckages(int imx, int maxwav, dou
|
Line 6278 calandcheckages(int imx, int maxwav, dou
|
return (1); |
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(int logged) |
|
{ |
|
/* #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-"); |
|
if(logged) fprintf(ficlog, "Cross-"); |
|
} |
|
#endif |
|
|
|
#include <stdint.h> |
|
|
|
printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:"); |
|
#if defined(__clang__) |
|
printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */ |
|
#endif |
|
#if defined(__ICC) || defined(__INTEL_COMPILER) |
|
printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */ |
|
#endif |
|
#if defined(__GNUC__) || defined(__GNUG__) |
|
printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */ |
|
#endif |
|
#if defined(__HP_cc) || defined(__HP_aCC) |
|
printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */ |
|
#endif |
|
#if defined(__IBMC__) || defined(__IBMCPP__) |
|
printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */ |
|
#endif |
|
#if defined(_MSC_VER) |
|
printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */ |
|
#endif |
|
#if defined(__PGI) |
|
printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */ |
|
#endif |
|
#if defined(__SUNPRO_C) || defined(__SUNPRO_CC) |
|
printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */ |
|
#endif |
|
printf(" for "); if (logged) 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) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) "); |
|
#elif __unix__ // all unices, not all compilers |
|
// Unix |
|
printf("Unix ");if(logged) fprintf(ficlog,"Unix "); |
|
#elif __linux__ |
|
// linux |
|
printf("linux ");if(logged) fprintf(ficlog,"linux "); |
|
#elif __APPLE__ |
|
// Mac OS, not sure if this is covered by __posix__ and/or __unix__ though.. |
|
printf("Mac OS ");if(logged) 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"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */ |
|
#elif UINTPTR_MAX == 0xffffffffffffffff |
|
printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */ |
|
#else |
|
printf(" wtf-bit"); if(logged) 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__); |
|
if(logged) 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); |
|
if(logged) 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()); |
|
if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version()); |
|
#endif |
|
#endif |
|
|
|
// void main() |
|
// { |
|
#if defined(_MSC_VER) |
|
if (IsWow64()){ |
|
printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n"); |
|
if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n"); |
|
} |
|
else{ |
|
printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n"); |
|
if (logged) fprintf(ficlog, "\nThe 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, double ftolpl, int *ncvyear){ |
|
/*--------------- Prevalence limit (period or stable prevalence) --------------*/ |
|
int i, j, k, i1 ; |
|
/* double ftolpl = 1.e-10; */ |
|
double age, agebase, agelim; |
|
double tot; |
|
|
|
strcpy(filerespl,"PL_"); |
|
strcat(filerespl,fileresu); |
|
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. Precision given by ftolpl=%g \n", ftolpl); |
|
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,codtabm(cptcod,cptcov)); |
|
fprintf(ficrespl,"#******"); |
|
printf("#******"); |
|
fprintf(ficlog,"#******"); |
|
for(j=1;j<=cptcoveff;j++) { |
|
fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); |
|
printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); |
|
fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(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]][codtabm(k,j)]); |
|
} |
|
for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i); |
|
fprintf(ficrespl,"Total Years_to_converge\n"); |
|
|
|
for (age=agebase; age<=agelim; age++){ |
|
/* for (age=agebase; age<=agebase; age++){ */ |
|
prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyear, k); |
|
fprintf(ficrespl,"%.0f ",age ); |
|
for(j=1;j<=cptcoveff;j++) |
|
fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); |
|
tot=0.; |
|
for(i=1; i<=nlstate;i++){ |
|
tot += prlim[i][i]; |
|
fprintf(ficrespl," %.5f", prlim[i][i]); |
|
} |
|
fprintf(ficrespl," %.3f %d\n", tot, *ncvyear); |
|
} /* 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,fileresu); |
|
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]][codtabm(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 *****************/ |
/**************** Main Program *****************/ |
Line 5426 int main(int argc, char *argv[])
|
Line 6633 int main(int argc, char *argv[])
|
#endif |
#endif |
int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav); |
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 i,j, k, n=MAXN,iter=0,m,size=100, cptcod; |
|
int ncvyearnp=0; |
|
int *ncvyear=&ncvyearnp; /* Number of years needed for the period prevalence to converge */ |
int jj, ll, li, lj, lk; |
int jj, ll, li, lj, lk; |
int numlinepar=0; /* Current linenumber of parameter file */ |
int numlinepar=0; /* Current linenumber of parameter file */ |
|
int num_filled; |
int itimes; |
int itimes; |
int NDIM=2; |
int NDIM=2; |
int vpopbased=0; |
int vpopbased=0; |
Line 5437 int main(int argc, char *argv[])
|
Line 6646 int main(int argc, char *argv[])
|
/* FILE *fichtm; *//* Html File */ |
/* FILE *fichtm; *//* Html File */ |
/* FILE *ficgp;*/ /*Gnuplot File */ |
/* FILE *ficgp;*/ /*Gnuplot File */ |
struct stat info; |
struct stat info; |
double agedeb; |
double agedeb=0.; |
double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20; |
|
|
double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW; |
|
|
double fret; |
double fret; |
double dum; /* Dummy variable */ |
double dum=0.; /* Dummy variable */ |
double ***p3mat; |
double ***p3mat; |
double ***mobaverage; |
double ***mobaverage; |
|
|
char line[MAXLINE]; |
char line[MAXLINE]; |
char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE]; |
char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE]; |
|
|
|
char model[MAXLINE], modeltemp[MAXLINE]; |
char pathr[MAXLINE], pathimach[MAXLINE]; |
char pathr[MAXLINE], pathimach[MAXLINE]; |
char *tok, *val; /* pathtot */ |
char *tok, *val; /* pathtot */ |
int firstobs=1, lastobs=10; |
int firstobs=1, lastobs=10; |
int c, h , cpt; |
int c, h , cpt, c2; |
int jl; |
int jl=0; |
int i1, j1, jk, stepsize; |
int i1, j1, jk, stepsize=0; |
|
int count=0; |
|
|
int *tab; |
int *tab; |
int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */ |
int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */ |
int mobilav=0,popforecast=0; |
int mobilav=0,popforecast=0; |
int hstepm, nhstepm; |
int hstepm=0, nhstepm=0; |
int agemortsup; |
int agemortsup; |
float sumlpop=0.; |
float sumlpop=0.; |
double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000; |
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 jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000; |
|
|
double bage=0, fage=110, age, agelim, agebase; |
double bage=0, fage=110., age, agelim=0., agebase=0.; |
double ftolpl=FTOL; |
double ftolpl=FTOL; |
double **prlim; |
double **prlim; |
double ***param; /* Matrix of parameters */ |
double ***param; /* Matrix of parameters */ |
double *p; |
double *p; |
double **matcov; /* Matrix of covariance */ |
double **matcov; /* Matrix of covariance */ |
|
double **hess; /* Hessian matrix */ |
double ***delti3; /* Scale */ |
double ***delti3; /* Scale */ |
double *delti; /* Scale */ |
double *delti; /* Scale */ |
double ***eij, ***vareij; |
double ***eij, ***vareij; |
Line 5518 int main(int argc, char *argv[])
|
Line 6733 int main(int argc, char *argv[])
|
|
|
nberr=0; /* Number of errors and warnings */ |
nberr=0; /* Number of errors and warnings */ |
nbwarn=0; |
nbwarn=0; |
|
#ifdef WIN32 |
|
_getcwd(pathcd, size); |
|
#else |
getcwd(pathcd, size); |
getcwd(pathcd, size); |
|
#endif |
printf("\n%s\n%s",version,fullversion); |
syscompilerinfo(0); |
|
printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion); |
if(argc <=1){ |
if(argc <=1){ |
printf("\nEnter the parameter file name: "); |
printf("\nEnter the parameter file name: "); |
fgets(pathr,FILENAMELENGTH,stdin); |
fgets(pathr,FILENAMELENGTH,stdin); |
Line 5554 int main(int argc, char *argv[])
|
Line 6773 int main(int argc, char *argv[])
|
/* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */ |
/* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */ |
split(pathtot,path,optionfile,optionfilext,optionfilefiname); |
split(pathtot,path,optionfile,optionfilext,optionfilefiname); |
printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",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 */ |
chdir(path); /* Can be a relative path */ |
if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */ |
if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */ |
printf("Current directory %s!\n",pathcd); |
#endif |
|
printf("Current directory %s!\n",pathcd); |
strcpy(command,"mkdir "); |
strcpy(command,"mkdir "); |
strcat(command,optionfilefiname); |
strcat(command,optionfilefiname); |
if((outcmd=system(command)) != 0){ |
if((outcmd=system(command)) != 0){ |
printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd); |
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); */ |
/* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */ |
/* fclose(ficlog); */ |
/* fclose(ficlog); */ |
/* exit(1); */ |
/* exit(1); */ |
Line 5571 int main(int argc, char *argv[])
|
Line 6795 int main(int argc, char *argv[])
|
|
|
/*-------- arguments in the command line --------*/ |
/*-------- arguments in the command line --------*/ |
|
|
/* Log file */ |
/* Main Log file */ |
strcat(filelog, optionfilefiname); |
strcat(filelog, optionfilefiname); |
strcat(filelog,".log"); /* */ |
strcat(filelog,".log"); /* */ |
if((ficlog=fopen(filelog,"w"))==NULL) { |
if((ficlog=fopen(filelog,"w"))==NULL) { |
Line 5579 int main(int argc, char *argv[])
|
Line 6803 int main(int argc, char *argv[])
|
goto end; |
goto end; |
} |
} |
fprintf(ficlog,"Log filename:%s\n",filelog); |
fprintf(ficlog,"Log filename:%s\n",filelog); |
fprintf(ficlog,"\n%s\n%s",version,fullversion); |
fprintf(ficlog,"Version %s %s",version,fullversion); |
fprintf(ficlog,"\nEnter the parameter file name: \n"); |
fprintf(ficlog,"\nEnter the parameter file name: \n"); |
fprintf(ficlog,"pathimach=%s\npathtot=%s\n\ |
fprintf(ficlog,"pathimach=%s\npathtot=%s\n\ |
path=%s \n\ |
path=%s \n\ |
Line 5587 int main(int argc, char *argv[])
|
Line 6811 int main(int argc, char *argv[])
|
optionfilext=%s\n\ |
optionfilext=%s\n\ |
optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname); |
optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname); |
|
|
|
syscompilerinfo(1); |
|
|
printf("Local time (at start):%s",strstart); |
printf("Local time (at start):%s",strstart); |
fprintf(ficlog,"Local time (at start): %s",strstart); |
fprintf(ficlog,"Local time (at start): %s",strstart); |
fflush(ficlog); |
fflush(ficlog); |
Line 5596 int main(int argc, char *argv[])
|
Line 6822 int main(int argc, char *argv[])
|
/* */ |
/* */ |
strcpy(fileres,"r"); |
strcpy(fileres,"r"); |
strcat(fileres, optionfilefiname); |
strcat(fileres, optionfilefiname); |
|
strcat(fileresu, optionfilefiname); /* Without r in front */ |
strcat(fileres,".txt"); /* Other files have txt extension */ |
strcat(fileres,".txt"); /* Other files have txt extension */ |
|
strcat(fileresu,".txt"); /* Other files have txt extension */ |
|
|
/*---------arguments file --------*/ |
/* Main ---------arguments file --------*/ |
|
|
if((ficpar=fopen(optionfile,"r"))==NULL) { |
if((ficpar=fopen(optionfile,"r"))==NULL) { |
printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno)); |
printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno)); |
Line 5611 int main(int argc, char *argv[])
|
Line 6839 int main(int argc, char *argv[])
|
|
|
|
|
strcpy(filereso,"o"); |
strcpy(filereso,"o"); |
strcat(filereso,fileres); |
strcat(filereso,fileresu); |
if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */ |
if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */ |
printf("Problem with Output resultfile: %s\n", filereso); |
printf("Problem with Output resultfile: %s\n", filereso); |
fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso); |
fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso); |
Line 5621 int main(int argc, char *argv[])
|
Line 6849 int main(int argc, char *argv[])
|
|
|
/* Reads comments: lines beginning with '#' */ |
/* Reads comments: lines beginning with '#' */ |
numlinepar=0; |
numlinepar=0; |
while((c=getc(ficpar))=='#' && c!= EOF){ |
|
ungetc(c,ficpar); |
/* First parameter line */ |
fgets(line, MAXLINE, ficpar); |
while(fgets(line, MAXLINE, ficpar)) { |
|
/* If line starts with a # it is a comment */ |
|
if (line[0] == '#') { |
|
numlinepar++; |
|
fputs(line,stdout); |
|
fputs(line,ficparo); |
|
fputs(line,ficlog); |
|
continue; |
|
}else |
|
break; |
|
} |
|
if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \ |
|
title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){ |
|
if (num_filled != 5) { |
|
printf("Should be 5 parameters\n"); |
|
} |
numlinepar++; |
numlinepar++; |
fputs(line,stdout); |
printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass); |
fputs(line,ficparo); |
|
fputs(line,ficlog); |
|
} |
} |
ungetc(c,ficpar); |
/* Second parameter line */ |
|
while(fgets(line, MAXLINE, ficpar)) { |
fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); |
/* If line starts with a # it is a comment */ |
numlinepar++; |
if (line[0] == '#') { |
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); |
numlinepar++; |
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); |
fputs(line,stdout); |
fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); |
fputs(line,ficparo); |
|
fputs(line,ficlog); |
|
continue; |
|
}else |
|
break; |
|
} |
|
if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \ |
|
&ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){ |
|
if (num_filled != 8) { |
|
printf("Not 8\n"); |
|
} |
|
printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt); |
|
} |
|
/* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */ |
|
ftolpl=6.e-3; /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */ |
|
/* Third parameter line */ |
|
while(fgets(line, MAXLINE, ficpar)) { |
|
/* If line starts with a # it is a comment */ |
|
if (line[0] == '#') { |
|
numlinepar++; |
|
fputs(line,stdout); |
|
fputs(line,ficparo); |
|
fputs(line,ficlog); |
|
continue; |
|
}else |
|
break; |
|
} |
|
if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){ |
|
if (num_filled == 0) |
|
model[0]='\0'; |
|
else if (num_filled != 1){ |
|
printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line); |
|
fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line); |
|
model[0]='\0'; |
|
goto end; |
|
} |
|
else{ |
|
if (model[0]=='+'){ |
|
for(i=1; i<=strlen(model);i++) |
|
modeltemp[i-1]=model[i]; |
|
strcpy(model,modeltemp); |
|
} |
|
} |
|
/* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */ |
|
printf("model=1+age+%s\n",model);fflush(stdout); |
|
} |
|
/* 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=numlinepar+3; /\* In general *\/ */ |
|
/* 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); */ |
|
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); |
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){ |
while((c=getc(ficpar))=='#' && c!= EOF){ |
ungetc(c,ficpar); |
ungetc(c,ficpar); |
fgets(line, MAXLINE, ficpar); |
fgets(line, MAXLINE, ficpar); |
numlinepar++; |
numlinepar++; |
|
if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */ |
|
z[0]=line[1]; |
|
} |
|
/* printf("****line [1] = %c \n",line[1]); */ |
fputs(line, stdout); |
fputs(line, stdout); |
//puts(line); |
//puts(line); |
fputs(line,ficparo); |
fputs(line,ficparo); |
Line 5655 int main(int argc, char *argv[])
|
Line 6960 int main(int argc, char *argv[])
|
v1+v2*age+v2*v3 makes cptcovn = 3 |
v1+v2*age+v2*v3 makes cptcovn = 3 |
*/ |
*/ |
if (strlen(model)>1) |
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*/ |
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 |
else |
ncovmodel=2; |
ncovmodel=2; /* Constant and age */ |
nvar=ncovmodel-1; /* Suppressing age as a basic covariate */ |
|
nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */ |
nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */ |
npar= nforce*ncovmodel; /* Number of parameters like aij*/ |
npar= nforce*ncovmodel; /* Number of parameters like aij*/ |
if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){ |
if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){ |
Line 5673 int main(int argc, char *argv[])
|
Line 6977 int main(int argc, char *argv[])
|
/*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/ |
/*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/ |
if(mle==-1){ /* Print a wizard for help writing covariance matrix */ |
if(mle==-1){ /* Print a wizard for help writing covariance matrix */ |
prwizard(ncovmodel, nlstate, ndeath, model, ficparo); |
prwizard(ncovmodel, nlstate, ndeath, model, ficparo); |
printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso); |
printf(" You chose 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); |
fprintf(ficlog," You chose 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); |
free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); |
fclose (ficparo); |
fclose (ficparo); |
fclose (ficlog); |
fclose (ficlog); |
goto end; |
goto end; |
exit(0); |
exit(0); |
} |
} |
else if(mle==-3) { |
else if(mle==-3) { /* Main Wizard */ |
prwizard(ncovmodel, nlstate, ndeath, model, ficparo); |
prwizard(ncovmodel, nlstate, ndeath, model, ficparo); |
printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso); |
printf(" You chose 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); |
fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso); |
param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); |
param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); |
matcov=matrix(1,npar,1,npar); |
matcov=matrix(1,npar,1,npar); |
|
hess=matrix(1,npar,1,npar); |
} |
} |
else{ |
else{ |
/* Read guessed parameters */ |
/* Read guessed parameters */ |
Line 5708 int main(int argc, char *argv[])
|
Line 7013 int main(int argc, char *argv[])
|
if(jj==i) continue; |
if(jj==i) continue; |
j++; |
j++; |
fscanf(ficpar,"%1d%1d",&i1,&j1); |
fscanf(ficpar,"%1d%1d",&i1,&j1); |
if ((i1 != i) && (j1 != j)){ |
if ((i1 != i) || (j1 != jj)){ |
printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \ |
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 \ |
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); |
run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1); |
Line 5716 run imach with mle=-1 to get a correct t
|
Line 7021 run imach with mle=-1 to get a correct t
|
} |
} |
fprintf(ficparo,"%1d%1d",i1,j1); |
fprintf(ficparo,"%1d%1d",i1,j1); |
if(mle==1) |
if(mle==1) |
printf("%1d%1d",i,j); |
printf("%1d%1d",i,jj); |
fprintf(ficlog,"%1d%1d",i,j); |
fprintf(ficlog,"%1d%1d",i,jj); |
for(k=1; k<=ncovmodel;k++){ |
for(k=1; k<=ncovmodel;k++){ |
fscanf(ficpar," %lf",¶m[i][j][k]); |
fscanf(ficpar," %lf",¶m[i][j][k]); |
if(mle==1){ |
if(mle==1){ |
Line 5795 run imach with mle=-1 to get a correct t
|
Line 7100 run imach with mle=-1 to get a correct t
|
ungetc(c,ficpar); |
ungetc(c,ficpar); |
|
|
matcov=matrix(1,npar,1,npar); |
matcov=matrix(1,npar,1,npar); |
|
hess=matrix(1,npar,1,npar); |
for(i=1; i <=npar; i++) |
for(i=1; i <=npar; i++) |
for(j=1; j <=npar; j++) matcov[i][j]=0.; |
for(j=1; j <=npar; j++) matcov[i][j]=0.; |
|
|
|
/* Scans npar lines */ |
for(i=1; i <=npar; i++){ |
for(i=1; i <=npar; i++){ |
fscanf(ficpar,"%s",str); |
count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk); |
|
if(count != 3){ |
|
printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\ |
|
This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\ |
|
Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model); |
|
fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\ |
|
This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\ |
|
Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model); |
|
exit(1); |
|
}else |
if(mle==1) |
if(mle==1) |
printf("%s",str); |
printf("%1d%1d%1d",i1,j1,jk); |
fprintf(ficlog,"%s",str); |
fprintf(ficlog,"%1d%1d%1d",i1,j1,jk); |
fprintf(ficparo,"%s",str); |
fprintf(ficparo,"%1d%1d%1d",i1,j1,jk); |
for(j=1; j <=i; j++){ |
for(j=1; j <=i; j++){ |
fscanf(ficpar," %le",&matcov[i][j]); |
fscanf(ficpar," %le",&matcov[i][j]); |
if(mle==1){ |
if(mle==1){ |
Line 5819 run imach with mle=-1 to get a correct t
|
Line 7135 run imach with mle=-1 to get a correct t
|
fprintf(ficlog,"\n"); |
fprintf(ficlog,"\n"); |
fprintf(ficparo,"\n"); |
fprintf(ficparo,"\n"); |
} |
} |
|
/* End of read covariance matrix npar lines */ |
for(i=1; i <=npar; i++) |
for(i=1; i <=npar; i++) |
for(j=i+1;j<=npar;j++) |
for(j=i+1;j<=npar;j++) |
matcov[i][j]=matcov[j][i]; |
matcov[i][j]=matcov[j][i]; |
Line 5835 run imach with mle=-1 to get a correct t
|
Line 7152 run imach with mle=-1 to get a correct t
|
strcat(rfileres,"."); /* */ |
strcat(rfileres,"."); /* */ |
strcat(rfileres,optionfilext); /* Other files have txt extension */ |
strcat(rfileres,optionfilext); /* Other files have txt extension */ |
if((ficres =fopen(rfileres,"w"))==NULL) { |
if((ficres =fopen(rfileres,"w"))==NULL) { |
printf("Problem writing new parameter file: %s\n", fileres);goto end; |
printf("Problem writing new parameter file: %s\n", rfileres);goto end; |
fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end; |
fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end; |
} |
} |
fprintf(ficres,"#%s\n",version); |
fprintf(ficres,"#%s\n",version); |
} /* End of mle != -3 */ |
} /* End of mle != -3 */ |
|
|
|
/* Main data |
|
*/ |
n= lastobs; |
n= lastobs; |
num=lvector(1,n); |
num=lvector(1,n); |
moisnais=vector(1,n); |
moisnais=vector(1,n); |
Line 5857 run imach with mle=-1 to get a correct t
|
Line 7175 run imach with mle=-1 to get a correct t
|
s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ |
s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ |
tab=ivector(1,NCOVMAX); |
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 */ |
ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */ |
|
ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */ |
|
|
/* Reads data from file datafile */ |
/* Reads data from file datafile */ |
if (readdata(datafile, firstobs, lastobs, &imx)==1) |
if (readdata(datafile, firstobs, lastobs, &imx)==1) |
Line 5892 run imach with mle=-1 to get a correct t
|
Line 7211 run imach with mle=-1 to get a correct t
|
Tage[1=V3*age]= 4; Tage[2=age*V4] = 3 |
Tage[1=V3*age]= 4; Tage[2=age*V4] = 3 |
*/ |
*/ |
|
|
|
/* Main decodemodel */ |
|
|
|
|
if(decodemodel(model, lastobs) == 1) |
if(decodemodel(model, lastobs) == 1) |
goto end; |
goto end; |
|
|
Line 5935 run imach with mle=-1 to get a correct t
|
Line 7257 run imach with mle=-1 to get a correct t
|
nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); |
nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); |
ncodemax[1]=1; |
ncodemax[1]=1; |
Ndum =ivector(-1,NCOVMAX); |
Ndum =ivector(-1,NCOVMAX); |
if (ncovmodel > 2) |
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]; */ |
tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */ |
|
/* Nbcode gives the value of the lth modality of jth covariate, in |
codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */ |
V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/ |
/*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/ |
/* 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],codtabm(100,10));*/ |
|
/* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/ |
h=0; |
h=0; |
|
|
|
|
Line 5948 run imach with mle=-1 to get a correct t
|
Line 7274 run imach with mle=-1 to get a correct t
|
|
|
m=pow(2,cptcoveff); |
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 |
/**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1 |
* h 1 2 3 4 |
* 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 |
* 1 i=1 1 i=1 1 i=1 1 i=1 1 |
* 2 2 1 1 1 |
* 2 2 1 1 1 |
Line 5966 run imach with mle=-1 to get a correct t
|
Line 7287 run imach with mle=-1 to get a correct t
|
* 6 2 1 2 1 |
* 6 2 1 2 1 |
* 7 i=4 1 2 2 1 |
* 7 i=4 1 2 2 1 |
* 8 2 2 2 1 |
* 8 2 2 2 1 |
* 9 i=5 1 i=3 1 i=2 1 1 |
* 9 i=5 1 i=3 1 i=2 1 2 |
* 10 2 1 1 1 |
* 10 2 1 1 2 |
* 11 i=6 1 2 1 1 |
* 11 i=6 1 2 1 2 |
* 12 2 2 1 1 |
* 12 2 2 1 2 |
* 13 i=7 1 i=4 1 2 1 |
* 13 i=7 1 i=4 1 2 2 |
* 14 2 1 2 1 |
* 14 2 1 2 2 |
* 15 i=8 1 2 2 1 |
* 15 i=8 1 2 2 2 |
* 16 2 2 2 1 |
* 16 2 2 2 2 |
*/ |
*/ |
codtab[h][k]=j; |
/* /\* for(h=1; h <=100 ;h++){ *\/ */ |
/*codtab[h][Tvar[k]]=j;*/ |
/* /\* printf("h=%2d ", h); *\/ */ |
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]]); |
/* /\* for(k=1; k <=10; k++){ *\/ */ |
} |
/* /\* printf("k=%d %d ",k,codtabm(h,k)); *\/ */ |
} |
/* /\* codtab[h][k]=codtabm(h,k); *\/ */ |
} |
/* /\* } *\/ */ |
} |
/* /\* printf("\n"); *\/ */ |
|
/* } */ |
|
/* 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]=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]); |
/* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); |
codtab[1][2]=1;codtab[2][2]=2; */ |
codtab[1][2]=1;codtab[2][2]=2; */ |
/* for(i=1; i <=m ;i++){ |
/* for(i=1; i <=m ;i++){ */ |
for(k=1; k <=cptcovn; k++){ |
/* for(k=1; k <=cptcovn; k++){ */ |
printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); |
/* printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); */ |
} |
/* } */ |
printf("\n"); |
/* printf("\n"); */ |
} |
/* } */ |
scanf("%d",i);*/ |
/* scanf("%d",i);*/ |
|
|
free_ivector(Ndum,-1,NCOVMAX); |
free_ivector(Ndum,-1,NCOVMAX); |
|
|
|
|
|
|
/*------------ gnuplot -------------*/ |
/* Initialisation of ----------- gnuplot -------------*/ |
strcpy(optionfilegnuplot,optionfilefiname); |
strcpy(optionfilegnuplot,optionfilefiname); |
if(mle==-3) |
if(mle==-3) |
strcat(optionfilegnuplot,"-mort"); |
strcat(optionfilegnuplot,"-MORT_"); |
strcat(optionfilegnuplot,".gp"); |
strcat(optionfilegnuplot,".gp"); |
|
|
if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) { |
if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) { |
printf("Problem with file %s",optionfilegnuplot); |
printf("Problem with file %s",optionfilegnuplot); |
} |
} |
else{ |
else{ |
fprintf(ficgp,"\n# %s\n", version); |
fprintf(ficgp,"\n# IMaCh-%s\n", version); |
fprintf(ficgp,"# %s\n", optionfilegnuplot); |
fprintf(ficgp,"# %s\n", optionfilegnuplot); |
//fprintf(ficgp,"set missing 'NaNq'\n"); |
//fprintf(ficgp,"set missing 'NaNq'\n"); |
fprintf(ficgp,"set datafile missing 'NaNq'\n"); |
fprintf(ficgp,"set datafile missing 'NaNq'\n"); |
} |
} |
/* fclose(ficgp);*/ |
/* fclose(ficgp);*/ |
/*--------- index.htm --------*/ |
|
|
|
|
/* Initialisation of --------- index.htm --------*/ |
|
|
strcpy(optionfilehtm,optionfilefiname); /* Main html file */ |
strcpy(optionfilehtm,optionfilefiname); /* Main html file */ |
if(mle==-3) |
if(mle==-3) |
strcat(optionfilehtm,"-mort"); |
strcat(optionfilehtm,"-MORT_"); |
strcat(optionfilehtm,".htm"); |
strcat(optionfilehtm,".htm"); |
if((fichtm=fopen(optionfilehtm,"w"))==NULL) { |
if((fichtm=fopen(optionfilehtm,"w"))==NULL) { |
printf("Problem with %s \n",optionfilehtm); |
printf("Problem with %s \n",optionfilehtm); |
Line 6031 run imach with mle=-1 to get a correct t
|
Line 7370 run imach with mle=-1 to get a correct t
|
else{ |
else{ |
fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \ |
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\ |
<hr size=\"2\" color=\"#EC5E5E\"> \n\ |
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\ |
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\ |
optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model); |
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> \ |
fprintf(fichtm,"<html><head>\n<head>\n<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n<title>IMaCh %s</title></head>\n <body><font size=\"7\"><a href=http:/euroreves.ined.fr/imach>IMaCh for Interpolated Markov Chain</a> </font><br>\n<font size=\"3\">Sponsored by Copyright (C) 2002-2015 <a href=http://www.ined.fr>INED</a>-EUROREVES-Institut de longévité-Japan Society for the Promotion of Sciences 日本å¦è¡“振興会 (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - <a href=https://software.intel.com/en-us>Intel Software 2015</a></font><br> \ |
<hr size=\"2\" color=\"#EC5E5E\"> \n\ |
<hr size=\"2\" color=\"#EC5E5E\"> \n\ |
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\ |
<font size=\"2\">IMaCh-%s <br> %s</font> \ |
|
<hr size=\"2\" color=\"#EC5E5E\"> \n\ |
|
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\ |
\n\ |
\n\ |
<hr size=\"2\" color=\"#EC5E5E\">\ |
<hr size=\"2\" color=\"#EC5E5E\">\ |
<ul><li><h4>Parameter files</h4>\n\ |
<ul><li><h4>Parameter files</h4>\n\ |
Line 6054 Title=%s <br>Datafile=%s Firstpass=%d La
|
Line 7395 Title=%s <br>Datafile=%s Firstpass=%d La
|
|
|
strcpy(pathr,path); |
strcpy(pathr,path); |
strcat(pathr,optionfilefiname); |
strcat(pathr,optionfilefiname); |
|
#ifdef WIN32 |
|
_chdir(optionfilefiname); /* Move to directory named optionfile */ |
|
#else |
chdir(optionfilefiname); /* Move to directory named optionfile */ |
chdir(optionfilefiname); /* Move to directory named optionfile */ |
|
#endif |
|
|
|
|
/* Calculates basic frequencies. Computes observed prevalence at single age |
/* Calculates basic frequencies. Computes observed prevalence at single age |
and prints on file fileres'p'. */ |
and prints on file fileres'p'. */ |
Line 6077 Interval (in months) between two waves:
|
Line 7423 Interval (in months) between two waves:
|
p=param[1][1]; /* *(*(*(param +1)+1)+0) */ |
p=param[1][1]; /* *(*(*(param +1)+1)+0) */ |
|
|
globpr=0; /* To get the number ipmx of contributions and the sum of weights*/ |
globpr=0; /* To get the number ipmx of contributions and the sum of weights*/ |
|
/* For mortality only */ |
if (mle==-3){ |
if (mle==-3){ |
ximort=matrix(1,NDIM,1,NDIM); |
ximort=matrix(1,NDIM,1,NDIM); |
/* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */ |
/* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */ |
cens=ivector(1,n); |
cens=ivector(1,n); |
ageexmed=vector(1,n); |
ageexmed=vector(1,n); |
agecens=vector(1,n); |
agecens=vector(1,n); |
Line 6127 Interval (in months) between two waves:
|
Line 7473 Interval (in months) between two waves:
|
#else |
#else |
printf("Powell\n"); fprintf(ficlog,"Powell\n"); |
printf("Powell\n"); fprintf(ficlog,"Powell\n"); |
#endif |
#endif |
strcpy(filerespow,"pow-mort"); |
strcpy(filerespow,"POW-MORT_"); |
strcat(filerespow,fileres); |
strcat(filerespow,fileresu); |
if((ficrespow=fopen(filerespow,"w"))==NULL) { |
if((ficrespow=fopen(filerespow,"w"))==NULL) { |
printf("Problem with resultfile: %s\n", filerespow); |
printf("Problem with resultfile: %s\n", filerespow); |
fprintf(ficlog,"Problem with resultfile: %s\n", filerespow); |
fprintf(ficlog,"Problem with resultfile: %s\n", filerespow); |
Line 6170 Interval (in months) between two waves:
|
Line 7516 Interval (in months) between two waves:
|
|
|
/* Initialize method and iterate */ |
/* Initialize method and iterate */ |
/* p[1]=0.0268; p[NDIM]=0.083; */ |
/* p[1]=0.0268; p[NDIM]=0.083; */ |
/* gsl_vector_set(x, 0, 0.0268); */ |
/* gsl_vector_set(x, 0, 0.0268); */ |
/* gsl_vector_set(x, 1, 0.083); */ |
/* gsl_vector_set(x, 1, 0.083); */ |
gsl_vector_set(x, 0, p[1]); |
gsl_vector_set(x, 0, p[1]); |
gsl_vector_set(x, 1, p[2]); |
gsl_vector_set(x, 1, p[2]); |
|
|
Line 6224 Interval (in months) between two waves:
|
Line 7570 Interval (in months) between two waves:
|
#endif |
#endif |
fclose(ficrespow); |
fclose(ficrespow); |
|
|
hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); |
hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz); |
|
|
for(i=1; i <=NDIM; i++) |
for(i=1; i <=NDIM; i++) |
for(j=i+1;j<=NDIM;j++) |
for(j=i+1;j<=NDIM;j++) |
matcov[i][j]=matcov[j][i]; |
matcov[i][j]=matcov[j][i]; |
|
|
printf("\nCovariance matrix\n "); |
printf("\nCovariance matrix\n "); |
|
fprintf(ficlog,"\nCovariance matrix\n "); |
for(i=1; i <=NDIM; i++) { |
for(i=1; i <=NDIM; i++) { |
for(j=1;j<=NDIM;j++){ |
for(j=1;j<=NDIM;j++){ |
printf("%f ",matcov[i][j]); |
printf("%f ",matcov[i][j]); |
|
fprintf(ficlog,"%f ",matcov[i][j]); |
} |
} |
printf("\n "); |
printf("\n "); fprintf(ficlog,"\n "); |
} |
} |
|
|
printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp); |
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++) |
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])); |
printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i])); |
|
fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i])); |
|
} |
lsurv=vector(1,AGESUP); |
lsurv=vector(1,AGESUP); |
lpop=vector(1,AGESUP); |
lpop=vector(1,AGESUP); |
tpop=vector(1,AGESUP); |
tpop=vector(1,AGESUP); |
Line 6273 Interval (in months) between two waves:
|
Line 7622 Interval (in months) between two waves:
|
|
|
|
|
replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */ |
replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */ |
printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p); |
if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){ |
|
printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\ |
printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \ |
This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\ |
|
Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar); |
|
fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\ |
|
This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\ |
|
Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar); |
|
}else |
|
printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p); |
|
printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \ |
stepm, weightopt,\ |
stepm, weightopt,\ |
model,imx,p,matcov,agemortsup); |
model,imx,p,matcov,agemortsup); |
|
|
Line 6288 Interval (in months) between two waves:
|
Line 7644 Interval (in months) between two waves:
|
free_ivector(dcwave,1,n); |
free_ivector(dcwave,1,n); |
free_matrix(ximort,1,NDIM,1,NDIM); |
free_matrix(ximort,1,NDIM,1,NDIM); |
#endif |
#endif |
} /* Endof if mle==-3 */ |
} /* Endof if mle==-3 mortality only */ |
|
/* Standard maximisation */ |
else{ /* For mle >=1 */ |
else{ /* For mle !=- 3 */ |
globpr=0;/* debug */ |
globpr=0;/* debug */ |
|
/* Computes likelihood for initial parameters */ |
likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */ |
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); |
printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw); |
for (k=1; k<=npar;k++) |
for (k=1; k<=npar;k++) |
printf(" %d %8.5f",k,p[k]); |
printf(" %d %8.5f",k,p[k]); |
printf("\n"); |
printf("\n"); |
globpr=1; /* to print the contributions */ |
globpr=1; /* again, to print the contributions */ |
likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */ |
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); |
printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw); |
for (k=1; k<=npar;k++) |
for (k=1; k<=npar;k++) |
printf(" %d %8.5f",k,p[k]); |
printf(" %d %8.5f",k,p[k]); |
printf("\n"); |
printf("\n"); |
if(mle>=1){ /* Could be 1 or 2 */ |
if(mle>=1){ /* Could be 1 or 2, Real Maximisation */ |
mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func); |
mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func); |
} |
} |
|
|
/*--------- results files --------------*/ |
/*--------- results files --------------*/ |
fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model); |
fprintf(ficres,"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"); |
fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); |
Line 6321 Interval (in months) between two waves:
|
Line 7678 Interval (in months) between two waves:
|
fprintf(ficlog,"%d%d ",i,k); |
fprintf(ficlog,"%d%d ",i,k); |
fprintf(ficres,"%1d%1d ",i,k); |
fprintf(ficres,"%1d%1d ",i,k); |
for(j=1; j <=ncovmodel; j++){ |
for(j=1; j <=ncovmodel; j++){ |
printf("%lf ",p[jk]); |
printf("%12.7f ",p[jk]); |
fprintf(ficlog,"%lf ",p[jk]); |
fprintf(ficlog,"%12.7f ",p[jk]); |
fprintf(ficres,"%lf ",p[jk]); |
fprintf(ficres,"%12.7f ",p[jk]); |
jk++; |
jk++; |
} |
} |
printf("\n"); |
printf("\n"); |
Line 6332 Interval (in months) between two waves:
|
Line 7689 Interval (in months) between two waves:
|
} |
} |
} |
} |
} |
} |
if(mle!=0){ |
if(mle != 0){ |
/* Computing hessian and covariance matrix */ |
/* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */ |
ftolhess=ftol; /* Usually correct */ |
ftolhess=ftol; /* Usually correct */ |
hesscov(matcov, p, npar, delti, ftolhess, func); |
hesscov(matcov, hess, p, npar, delti, ftolhess, func); |
} |
printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n"); |
|
fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\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); |
|
for(j=1; j <=ncovmodel; j++){ |
|
printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk])); |
|
fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk])); |
|
jk++; |
|
} |
|
printf("\n"); |
|
fprintf(ficlog,"\n"); |
|
} |
|
} |
|
} |
|
} /* end of hesscov and Wald tests */ |
|
|
|
/* */ |
fprintf(ficres,"# Scales (for hessian or gradient estimation)\n"); |
fprintf(ficres,"# Scales (for hessian or gradient estimation)\n"); |
printf("# Scales (for hessian or gradient estimation)\n"); |
printf("# Scales (for hessian or gradient estimation)\n"); |
fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n"); |
fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n"); |
Line 6360 Interval (in months) between two waves:
|
Line 7736 Interval (in months) between two waves:
|
} |
} |
|
|
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"); |
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) |
if(mle >= 1) /* To big for the screen */ |
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"); |
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"); |
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\ */ |
/* # 121 Var(a12)\n\ */ |
Line 6423 Interval (in months) between two waves:
|
Line 7799 Interval (in months) between two waves:
|
fprintf(ficres," Var(%s%1d%1d)",ca,i,j); |
fprintf(ficres," Var(%s%1d%1d)",ca,i,j); |
}else{ |
}else{ |
if(mle>=1) |
if(mle>=1) |
printf(" %.5e",matcov[jj][ll]); |
printf(" %.7e",matcov[jj][ll]); |
fprintf(ficlog," %.5e",matcov[jj][ll]); |
fprintf(ficlog," %.7e",matcov[jj][ll]); |
fprintf(ficres," %.5e",matcov[jj][ll]); |
fprintf(ficres," %.7e",matcov[jj][ll]); |
} |
} |
} |
} |
} |
} |
Line 6464 Interval (in months) between two waves:
|
Line 7840 Interval (in months) between two waves:
|
fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n"); |
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(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); |
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){ |
while((c=getc(ficpar))=='#' && c!= EOF){ |
ungetc(c,ficpar); |
ungetc(c,ficpar); |
fgets(line, MAXLINE, ficpar); |
fgets(line, MAXLINE, ficpar); |
Line 6492 Interval (in months) between two waves:
|
Line 7869 Interval (in months) between two waves:
|
dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.; |
dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.; |
|
|
fscanf(ficpar,"pop_based=%d\n",&popbased); |
fscanf(ficpar,"pop_based=%d\n",&popbased); |
|
fprintf(ficlog,"pop_based=%d\n",popbased); |
fprintf(ficparo,"pop_based=%d\n",popbased); |
fprintf(ficparo,"pop_based=%d\n",popbased); |
fprintf(ficres,"pop_based=%d\n",popbased); |
fprintf(ficres,"pop_based=%d\n",popbased); |
|
|
Line 6516 Interval (in months) between two waves:
|
Line 7894 Interval (in months) between two waves:
|
/* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */ |
/* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */ |
|
|
replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */ |
replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */ |
printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p); |
if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){ |
|
printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\ |
|
This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\ |
|
Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar); |
|
fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\ |
|
This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\ |
|
Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar); |
|
}else |
|
printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p); |
|
|
printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\ |
printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt,\ |
model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\ |
model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\ |
jprev1,mprev1,anprev1,jprev2,mprev2,anprev2); |
jprev1,mprev1,anprev1,jprev2,mprev2,anprev2); |
|
|
Line 6537 Interval (in months) between two waves:
|
Line 7923 Interval (in months) between two waves:
|
fclose(ficres); |
fclose(ficres); |
|
|
|
|
|
/* Other results (useful)*/ |
|
|
|
|
/*--------------- Prevalence limit (period or stable prevalence) --------------*/ |
/*--------------- Prevalence limit (period or stable prevalence) --------------*/ |
#include "prevlim.h" /* Use ficrespl, ficlog */ |
/*#include "prevlim.h"*/ /* Use ficrespl, ficlog */ |
|
prlim=matrix(1,nlstate,1,nlstate); |
|
prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, ncvyear); |
fclose(ficrespl); |
fclose(ficrespl); |
|
|
#ifdef FREEEXIT2 |
#ifdef FREEEXIT2 |
Line 6546 Interval (in months) between two waves:
|
Line 7937 Interval (in months) between two waves:
|
#endif |
#endif |
|
|
/*------------- h Pij x at various ages ------------*/ |
/*------------- h Pij x at various ages ------------*/ |
#include "hpijx.h" |
/*#include "hpijx.h"*/ |
|
hPijx(p, bage, fage); |
fclose(ficrespij); |
fclose(ficrespij); |
|
|
/*-------------- Variance of one-step probabilities---*/ |
/*-------------- Variance of one-step probabilities---*/ |
Line 6564 Interval (in months) between two waves:
|
Line 7956 Interval (in months) between two waves:
|
/*if((stepm == 1) && (strcmp(model,".")==0)){*/ |
/*if((stepm == 1) && (strcmp(model,".")==0)){*/ |
if(prevfcast==1){ |
if(prevfcast==1){ |
/* if(stepm ==1){*/ |
/* if(stepm ==1){*/ |
prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff); |
prevforecast(fileresu, 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);*/ |
/* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/ |
/* } */ |
/* } */ |
/* else{ */ |
/* else{ */ |
Line 6573 Interval (in months) between two waves:
|
Line 7965 Interval (in months) between two waves:
|
/* 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); */ |
/* 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 */ |
/* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */ |
|
|
Line 6593 Interval (in months) between two waves:
|
Line 7986 Interval (in months) between two waves:
|
|
|
/*---------- Health expectancies, no variances ------------*/ |
/*---------- Health expectancies, no variances ------------*/ |
|
|
strcpy(filerese,"e"); |
strcpy(filerese,"E_"); |
strcat(filerese,fileres); |
strcat(filerese,fileresu); |
if((ficreseij=fopen(filerese,"w"))==NULL) { |
if((ficreseij=fopen(filerese,"w"))==NULL) { |
printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0); |
printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0); |
fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0); |
fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0); |
Line 6607 Interval (in months) between two waves:
|
Line 8000 Interval (in months) between two waves:
|
for (k=1; k <= (int) pow(2,cptcoveff); k++){ |
for (k=1; k <= (int) pow(2,cptcoveff); k++){ |
fprintf(ficreseij,"\n#****** "); |
fprintf(ficreseij,"\n#****** "); |
for(j=1;j<=cptcoveff;j++) { |
for(j=1;j<=cptcoveff;j++) { |
fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); |
} |
} |
fprintf(ficreseij,"******\n"); |
fprintf(ficreseij,"******\n"); |
|
|
Line 6624 Interval (in months) between two waves:
|
Line 8017 Interval (in months) between two waves:
|
/*---------- Health expectancies and variances ------------*/ |
/*---------- Health expectancies and variances ------------*/ |
|
|
|
|
strcpy(filerest,"t"); |
strcpy(filerest,"T_"); |
strcat(filerest,fileres); |
strcat(filerest,fileresu); |
if((ficrest=fopen(filerest,"w"))==NULL) { |
if((ficrest=fopen(filerest,"w"))==NULL) { |
printf("Problem with total LE resultfile: %s\n", filerest);goto end; |
printf("Problem with total LE resultfile: %s\n", filerest);goto end; |
fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end; |
fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end; |
Line 6634 Interval (in months) between two waves:
|
Line 8027 Interval (in months) between two waves:
|
fprintf(ficlog,"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"); |
strcpy(fileresstde,"STDE_"); |
strcat(fileresstde,fileres); |
strcat(fileresstde,fileresu); |
if((ficresstdeij=fopen(fileresstde,"w"))==NULL) { |
if((ficresstdeij=fopen(fileresstde,"w"))==NULL) { |
printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0); |
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); |
fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0); |
Line 6643 Interval (in months) between two waves:
|
Line 8036 Interval (in months) between two waves:
|
printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde); |
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); |
fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde); |
|
|
strcpy(filerescve,"cve"); |
strcpy(filerescve,"CVE_"); |
strcat(filerescve,fileres); |
strcat(filerescve,fileresu); |
if((ficrescveij=fopen(filerescve,"w"))==NULL) { |
if((ficrescveij=fopen(filerescve,"w"))==NULL) { |
printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0); |
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); |
fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0); |
Line 6652 Interval (in months) between two waves:
|
Line 8045 Interval (in months) between two waves:
|
printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve); |
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); |
fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve); |
|
|
strcpy(fileresv,"v"); |
strcpy(fileresv,"V_"); |
strcat(fileresv,fileres); |
strcat(fileresv,fileresu); |
if((ficresvij=fopen(fileresv,"w"))==NULL) { |
if((ficresvij=fopen(fileresv,"w"))==NULL) { |
printf("Problem with variance resultfile: %s\n", fileresv);exit(0); |
printf("Problem with variance resultfile: %s\n", fileresv);exit(0); |
fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0); |
fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0); |
Line 6667 Interval (in months) between two waves:
|
Line 8060 Interval (in months) between two waves:
|
for (k=1; k <= (int) pow(2,cptcoveff); k++){ |
for (k=1; k <= (int) pow(2,cptcoveff); k++){ |
fprintf(ficrest,"\n#****** "); |
fprintf(ficrest,"\n#****** "); |
for(j=1;j<=cptcoveff;j++) |
for(j=1;j<=cptcoveff;j++) |
fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); |
fprintf(ficrest,"******\n"); |
fprintf(ficrest,"******\n"); |
|
|
fprintf(ficresstdeij,"\n#****** "); |
fprintf(ficresstdeij,"\n#****** "); |
fprintf(ficrescveij,"\n#****** "); |
fprintf(ficrescveij,"\n#****** "); |
for(j=1;j<=cptcoveff;j++) { |
for(j=1;j<=cptcoveff;j++) { |
fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); |
fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); |
} |
} |
fprintf(ficresstdeij,"******\n"); |
fprintf(ficresstdeij,"******\n"); |
fprintf(ficrescveij,"******\n"); |
fprintf(ficrescveij,"******\n"); |
|
|
fprintf(ficresvij,"\n#****** "); |
fprintf(ficresvij,"\n#****** "); |
for(j=1;j<=cptcoveff;j++) |
for(j=1;j<=cptcoveff;j++) |
fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); |
fprintf(ficresvij,"******\n"); |
fprintf(ficresvij,"******\n"); |
|
|
eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); |
eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); |
Line 6696 Interval (in months) between two waves:
|
Line 8089 Interval (in months) between two waves:
|
|
|
|
|
for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/ |
for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/ |
oldm=oldms;savm=savms; /* Segmentation fault */ |
oldm=oldms;savm=savms; /* ZZ Segmentation fault */ |
cptcod= 0; /* To be deleted */ |
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 */ |
varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyear, 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 "); |
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) |
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); |
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 |
else |
fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n"); |
fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n"); |
fprintf(ficrest,"# Age e.. (std) "); |
fprintf(ficrest,"# Age popbased mobilav e.. (std) "); |
for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i); |
for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i); |
fprintf(ficrest,"\n"); |
fprintf(ficrest,"\n"); |
|
/* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */ |
epj=vector(1,nlstate+1); |
epj=vector(1,nlstate+1); |
for(age=bage; age <=fage ;age++){ |
for(age=bage; age <=fage ;age++){ |
prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); |
prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyear, k); /*ZZ Is it the correct prevalim */ |
if (vpopbased==1) { |
if (vpopbased==1) { |
if(mobilav ==0){ |
if(mobilav ==0){ |
for(i=1; i<=nlstate;i++) |
for(i=1; i<=nlstate;i++) |
Line 6721 Interval (in months) between two waves:
|
Line 8114 Interval (in months) between two waves:
|
} |
} |
} |
} |
|
|
fprintf(ficrest," %4.0f",age); |
fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav); |
|
/* printf(" age %4.0f ",age); */ |
for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){ |
for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){ |
for(i=1, epj[j]=0.;i <=nlstate;i++) { |
for(i=1, epj[j]=0.;i <=nlstate;i++) { |
epj[j] += prlim[i][i]*eij[i][j][(int)age]; |
epj[j] += prlim[i][i]*eij[i][j][(int)age]; |
/* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/ |
/*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/ |
|
/* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */ |
} |
} |
epj[nlstate+1] +=epj[j]; |
epj[nlstate+1] +=epj[j]; |
} |
} |
|
/* printf(" age %4.0f \n",age); */ |
|
|
for(i=1, vepp=0.;i <=nlstate;i++) |
for(i=1, vepp=0.;i <=nlstate;i++) |
for(j=1;j <=nlstate;j++) |
for(j=1;j <=nlstate;j++) |
Line 6760 Interval (in months) between two waves:
|
Line 8156 Interval (in months) between two waves:
|
|
|
/*------- Variance of period (stable) prevalence------*/ |
/*------- Variance of period (stable) prevalence------*/ |
|
|
strcpy(fileresvpl,"vpl"); |
strcpy(fileresvpl,"VPL_"); |
strcat(fileresvpl,fileres); |
strcat(fileresvpl,fileresu); |
if((ficresvpl=fopen(fileresvpl,"w"))==NULL) { |
if((ficresvpl=fopen(fileresvpl,"w"))==NULL) { |
printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl); |
printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl); |
exit(0); |
exit(0); |
Line 6774 Interval (in months) between two waves:
|
Line 8170 Interval (in months) between two waves:
|
for (k=1; k <= (int) pow(2,cptcoveff); k++){ |
for (k=1; k <= (int) pow(2,cptcoveff); k++){ |
fprintf(ficresvpl,"\n#****** "); |
fprintf(ficresvpl,"\n#****** "); |
for(j=1;j<=cptcoveff;j++) |
for(j=1;j<=cptcoveff;j++) |
fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); |
fprintf(ficresvpl,"******\n"); |
fprintf(ficresvpl,"******\n"); |
|
|
varpl=matrix(1,nlstate,(int) bage, (int) fage); |
varpl=matrix(1,nlstate,(int) bage, (int) fage); |
oldm=oldms;savm=savms; |
oldm=oldms;savm=savms; |
varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart); |
varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyear, k, strstart); |
free_matrix(varpl,1,nlstate,(int) bage, (int)fage); |
free_matrix(varpl,1,nlstate,(int) bage, (int)fage); |
/*}*/ |
/*}*/ |
} |
} |
Line 6798 Interval (in months) between two waves:
|
Line 8194 Interval (in months) between two waves:
|
free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath); |
free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath); |
free_matrix(covar,0,NCOVMAX,1,n); |
free_matrix(covar,0,NCOVMAX,1,n); |
free_matrix(matcov,1,npar,1,npar); |
free_matrix(matcov,1,npar,1,npar); |
|
free_matrix(hess,1,npar,1,npar); |
/*free_vector(delti,1,npar);*/ |
/*free_vector(delti,1,npar);*/ |
free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); |
free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); |
free_matrix(agev,1,maxwav,1,imx); |
free_matrix(agev,1,maxwav,1,imx); |
free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); |
free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); |
|
|
free_ivector(ncodemax,1,NCOVMAX); |
free_ivector(ncodemax,1,NCOVMAX); |
|
free_ivector(ncodemaxwundef,1,NCOVMAX); |
free_ivector(Tvar,1,NCOVMAX); |
free_ivector(Tvar,1,NCOVMAX); |
free_ivector(Tprod,1,NCOVMAX); |
free_ivector(Tprod,1,NCOVMAX); |
free_ivector(Tvaraff,1,NCOVMAX); |
free_ivector(Tvaraff,1,NCOVMAX); |
free_ivector(Tage,1,NCOVMAX); |
free_ivector(Tage,1,NCOVMAX); |
|
|
free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX); |
free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX); |
free_imatrix(codtab,1,100,1,10); |
/* free_imatrix(codtab,1,100,1,10); */ |
fflush(fichtm); |
fflush(fichtm); |
fflush(ficgp); |
fflush(ficgp); |
|
|
Line 6848 Interval (in months) between two waves:
|
Line 8246 Interval (in months) between two waves:
|
|
|
|
|
printf("Before Current directory %s!\n",pathcd); |
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) |
if(chdir(pathcd) != 0) |
printf("Can't move to directory %s!\n",path); |
printf("Can't move to directory %s!\n", path); |
if(getcwd(pathcd,MAXLINE) > 0) |
if (getcwd(pathcd, MAXLINE) > 0) |
|
#endif |
printf("Current directory %s!\n",pathcd); |
printf("Current directory %s!\n",pathcd); |
/*strcat(plotcmd,CHARSEPARATOR);*/ |
/*strcat(plotcmd,CHARSEPARATOR);*/ |
sprintf(plotcmd,"gnuplot"); |
sprintf(plotcmd,"gnuplot"); |
Line 6905 Interval (in months) between two waves:
|
Line 8309 Interval (in months) between two waves:
|
} |
} |
end: |
end: |
while (z[0] != 'q') { |
while (z[0] != 'q') { |
printf("\nType q for exiting: "); |
printf("\nType q for exiting: "); fflush(stdout); |
scanf("%s",z); |
scanf("%s",z); |
} |
} |
} |
} |