version 1.186, 2015/04/23 12:01:52
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version 1.197, 2015/09/01 18:24:39
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/* $Id$ |
/* $Id$ |
$State$ |
$State$ |
$Log$ |
$Log$ |
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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 |
Revision 1.186 2015/04/23 12:01:52 brouard |
Summary: V1*age is working now, version 0.98q1 |
Summary: V1*age is working now, version 0.98q1 |
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Line 585
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Line 625
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end |
end |
*/ |
*/ |
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/* #define DEBUG */ |
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/* #define DEBUGBRENT */ |
#define POWELL /* Instead of NLOPT */ |
#define POWELL /* Instead of NLOPT */ |
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#define POWELLF1F3 /* Skip test */ |
/* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */ |
/* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */ |
/* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */ |
/* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */ |
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Line 654 typedef struct {
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Line 697 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 672 typedef struct {
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Line 716 typedef struct {
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/* $Id$ */ |
/* $Id$ */ |
/* $State$ */ |
/* $State$ */ |
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#include "version.h" |
char version[]="Imach version 0.98q1, April 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015"; |
char version[]=__IMACH_VERSION__; |
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char copyright[]="September 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 808 int estepm;
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Line 853 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 819 int **s; /* Status */
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Line 870 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; |
Line 915 char *trimbb(char *out, char *in)
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Line 967 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 945 char *cutl(char *blocc, char *alocc, cha
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Line 1040 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 1256 double f1dim(double x)
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Line 1351 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 1339 values at the three points, fa, fb , and
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Line 1440 values at the three points, fa, fb , and
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*/ |
*/ |
double ulim,u,r,q, dum; |
double ulim,u,r,q, dum; |
double fu; |
double fu; |
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*fa=(*func)(*ax); |
double scale=10.; |
*fb=(*func)(*bx); |
int iterscale=0; |
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*fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/ |
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*fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */ |
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/* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */ |
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/* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */ |
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/* *bx = *ax - (*ax - *bx)/scale; */ |
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/* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */ |
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/* } */ |
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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) |
Line 1374 values at the three points, fa, fb , and
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Line 1486 values at the three points, fa, fb , and
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#endif |
#endif |
#ifdef MNBRAKORIGINAL |
#ifdef MNBRAKORIGINAL |
#else |
#else |
if (fu > *fc) { |
/* if (fu > *fc) { */ |
#ifdef DEBUG |
/* #ifdef DEBUG */ |
printf("mnbrak4 fu > fc \n"); |
/* printf("mnbrak4 fu > fc \n"); */ |
fprintf(ficlog, "mnbrak4 fu > fc\n"); |
/* fprintf(ficlog, "mnbrak4 fu > fc\n"); */ |
#endif |
/* #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(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 *\/ */ |
/* /\* 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 */ |
/* dum=u; /\* Shifting c and u *\/ */ |
u = *cx; |
/* u = *cx; */ |
*cx = dum; |
/* *cx = dum; */ |
dum = fu; |
/* dum = fu; */ |
fu = *fc; |
/* fu = *fc; */ |
*fc =dum; |
/* *fc =dum; */ |
} else { /* end */ |
/* } else { /\* end *\/ */ |
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/* #ifdef DEBUG */ |
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/* printf("mnbrak3 fu < fc \n"); */ |
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/* fprintf(ficlog, "mnbrak3 fu < fc\n"); */ |
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/* #endif */ |
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/* dum=u; /\* Shifting c and u *\/ */ |
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/* u = *cx; */ |
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/* *cx = dum; */ |
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/* dum = fu; */ |
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/* fu = *fc; */ |
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/* *fc =dum; */ |
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/* } */ |
#ifdef DEBUG |
#ifdef DEBUG |
printf("mnbrak3 fu < fc \n"); |
printf("mnbrak34 fu < or >= fc \n"); |
fprintf(ficlog, "mnbrak3 fu < fc\n"); |
fprintf(ficlog, "mnbrak34 fu < fc\n"); |
#endif |
#endif |
dum=u; /* Shifting c and u */ |
dum=u; /* Shifting c and u */ |
u = *cx; |
u = *cx; |
*cx = dum; |
*cx = dum; |
dum = fu; |
dum = fu; |
fu = *fc; |
fu = *fc; |
*fc =dum; |
*fc =dum; |
} |
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#endif |
#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 |
#ifdef DEBUG |
Line 1458 void linmin(double p[], double xi[], int
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Line 1580 void linmin(double p[], double xi[], int
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int j; |
int j; |
double xx,xmin,bx,ax; |
double xx,xmin,bx,ax; |
double fx,fb,fa; |
double fx,fb,fa; |
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double scale=10., axs, xxs, xxss; /* Scale added for infinity */ |
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ncom=n; |
ncom=n; |
pcom=vector(1,n); |
pcom=vector(1,n); |
Line 1467 void linmin(double p[], double xi[], int
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Line 1591 void linmin(double p[], double xi[], int
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pcom[j]=p[j]; |
pcom[j]=p[j]; |
xicom[j]=xi[j]; |
xicom[j]=xi[j]; |
} |
} |
ax=0.0; |
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xx=1.0; |
/* axs=0.0; */ |
mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */ |
/* xxss=1; /\* 1 and using scale *\/ */ |
*fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */ |
xxs=1; |
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/* do{ */ |
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ax=0.; |
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xx= xxs; |
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mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */ |
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/* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */ |
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/* 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)) */ |
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/* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */ |
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/* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */ |
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/* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */ |
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/* 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]]*/ |
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/* if (fx != fx){ */ |
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/* xxs=xxs/scale; /\* Trying a smaller xx, closer to initial ax=0 *\/ */ |
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/* 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); */ |
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/* } */ |
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/* }while(fx != fx); */ |
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#ifdef DEBUGLINMIN |
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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); |
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#endif |
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*fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/ |
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/* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */ |
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/* fmin = f(p[j] + xmin * xi[j]) */ |
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/* P+lambda n in that direction (lambdamin), with TOL between abscisses */ |
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/* 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 |
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#ifdef DEBUGLINMIN |
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printf("linmin end "); |
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#endif |
for (j=1;j<=n;j++) { |
for (j=1;j<=n;j++) { |
xi[j] *= xmin; |
/* printf(" before xi[%d]=%12.8f", j,xi[j]); */ |
p[j] += xi[j]; |
xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */ |
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/* if(xxs <1.0) */ |
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/* 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 ); */ |
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p[j] += xi[j]; /* Parameters values are updated accordingly */ |
} |
} |
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/* printf("\n"); */ |
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#ifdef DEBUGLINMIN |
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printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p)); |
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for (j=1;j<=n;j++) { |
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printf(" xi[%d]= %12.7f p[%d]= %12.7f",j,xi[j],j,p[j]); |
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if(j % ncovmodel == 0) |
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printf("\n"); |
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} |
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#endif |
free_vector(xicom,1,n); |
free_vector(xicom,1,n); |
free_vector(pcom,1,n); |
free_vector(pcom,1,n); |
} |
} |
Line 1513 void powell(double p[], double **xi, int
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Line 1676 void powell(double p[], double **xi, int
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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 1523 void powell(double p[], double **xi, int
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Line 1686 void powell(double p[], double **xi, int
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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 1551 void powell(double p[], double **xi, int
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Line 1714 void powell(double p[], double **xi, int
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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); /* xit[n] has been loaded for direction i */ |
linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/ |
if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions |
/* Outputs are fret(new point p) p is updated and xit rescaled */ |
because that direction will be replaced unless the gain del is small |
if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */ |
in comparison with the 'probable' gain, mu^2, with the last average direction. |
/* because that direction will be replaced unless the gain del is small */ |
Unless the n directions are conjugate some gain in the determinant may be obtained |
/* in comparison with the 'probable' gain, mu^2, with the last average direction. */ |
with the new 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 1585 void powell(double p[], double **xi, int
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Line 1748 void powell(double p[], double **xi, int
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printf("\n"); |
printf("\n"); |
fprintf(ficlog,"\n"); |
fprintf(ficlog,"\n"); |
#endif |
#endif |
} /* end i */ |
} /* end loop on each direction i */ |
|
/* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */ |
|
/* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */ |
|
/* New value of last point Pn is not computed, P(n-1) */ |
if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */ |
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 1616 void powell(double p[], double **xi, int
|
Line 1794 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 the extrapolated point P_0 + 2 (P_n-P_0) */ |
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]; |
Line 1624 void powell(double p[], double **xi, int
|
Line 1802 void powell(double p[], double **xi, int
|
pt[j]=p[j]; |
pt[j]=p[j]; |
} |
} |
fptt=(*func)(ptt); /* f_3 */ |
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. */ |
Line 1653 void powell(double p[], double **xi, int
|
Line 1834 void powell(double p[], double **xi, int
|
if (t < 0.0) { /* Then we use it for new direction */ |
if (t < 0.0) { /* Then we use it for new direction */ |
#else |
#else |
if (directest*t < 0.0) { /* Contradiction between both tests */ |
if (directest*t < 0.0) { /* Contradiction between both tests */ |
printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del); |
printf("directest= %.12lf, 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); |
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, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del); |
fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del); |
fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt); |
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 */ |
if (directest < 0.0) { /* Then we use it for new direction */ |
#endif |
#endif |
linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction.*/ |
#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]); |
|
if(j % ncovmodel == 0) |
|
printf("\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++) { |
|
printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]); |
|
if(j % ncovmodel == 0) |
|
printf("\n"); |
|
} |
|
#endif |
for (j=1;j<=n;j++) { |
for (j=1;j<=n;j++) { |
xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */ |
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 */ |
xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */ |
Line 1678 void powell(double p[], double **xi, int
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Line 1874 void powell(double p[], double **xi, int
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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) ****************/ |
Line 1709 double **prevalim(double **prlim, int nl
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Line 1908 double **prevalim(double **prlim, int nl
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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]][codtab[ij][Tvar[k]]]; |
/*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/ |
/* 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]]);*/ |
} |
} |
/*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ |
/*wrong? 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[k]][codtab[ij][Tvar[k]]]*cov[2]; |
for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2]; |
for (k=1; k<=cptcovprod;k++) /* Useless */ |
for (k=1; k<=cptcovprod;k++) /* Useless */ |
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]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; |
|
|
/*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/ |
/*printf("ij=%d 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 1871 double ***hpxij(double ***po, int nhstep
|
Line 2071 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 1884 double ***hpxij(double ***po, int nhstep
|
Line 2085 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]][codtab[ij][Tvar[k]]]; |
for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */ |
for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */ |
/* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ |
/* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ |
cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; |
cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; |
for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */ |
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]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; |
|
|
|
|
/*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/ |
/*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/ |
Line 1943 double func( double *x)
|
Line 2147 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 1964 double func( double *x)
|
Line 2169 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 1977 double func( double *x)
|
Line 2182 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 2090 double func( double *x)
|
Line 2298 double func( double *x)
|
} /* 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 2099 double func( double *x)
|
Line 2307 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 2120 double func( double *x)
|
Line 2331 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 2129 double func( double *x)
|
Line 2340 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 2150 double func( double *x)
|
Line 2364 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 2159 double func( double *x)
|
Line 2373 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 2185 double func( double *x)
|
Line 2402 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 2194 double func( double *x)
|
Line 2411 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 2232 double funcone( double *x)
|
Line 2452 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 2243 double funcone( double *x)
|
Line 2464 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 2252 double funcone( double *x)
|
Line 2473 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 2689 void lubksb(double **a, int n, int *indx
|
Line 2914 void lubksb(double **a, int n, int *indx
|
|
|
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); |
} |
} |
|
|
/************ Frequencies ********************/ |
/************ Frequencies ********************/ |
Line 3112 void tricode(int *Tvar, int **nbcode, in
|
Line 3337 void tricode(int *Tvar, int **nbcode, in
|
|
|
cptcoveff=0; |
cptcoveff=0; |
|
|
for (k=-1; k < maxncov; k++) Ndum[k]=0; |
|
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 */ |
|
|
/* Loop on covariates without age and products */ |
/* Loop on covariates without age and products */ |
for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */ |
for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */ |
|
for (k=-1; k < maxncov; k++) Ndum[k]=0; |
for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the |
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 |
Line 3139 void tricode(int *Tvar, int **nbcode, in
|
Line 3364 void tricode(int *Tvar, int **nbcode, in
|
/* 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); |
|
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 */ |
|
if( k != -1){ |
|
ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th |
|
covariate for which somebody answered excluding |
|
undefined. Usually 2: 0 and 1. */ |
|
} |
|
ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th |
|
covariate for which somebody answered including |
|
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 */ |
Line 3164 void tricode(int *Tvar, int **nbcode, in
|
Line 3398 void tricode(int *Tvar, int **nbcode, in
|
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; |
|
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 k 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 */ |
} |
|
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 */ |
|
/* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */ |
|
/* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */ |
|
/* } */ |
|
/* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */ |
|
/* if (ij > ncodemax[j]) { */ |
|
/* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */ |
|
/* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */ |
|
/* break; */ |
|
/* } */ |
|
/* } /\* 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*/ |
|
|
for (k=-1; k< maxncov; k++) Ndum[k]=0; |
for (k=-1; k< maxncov; k++) Ndum[k]=0; |
|
|
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 */ |
} |
} |
|
|
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)){ |
|
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*/ |
|
|
} |
} |
Line 3989 void varprob(char optionfilefiname[], do
|
Line 4235 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></br>this page is important in order to visualize confidence intervals and especially correlation between disability and recovery</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 4039 To be simple, these graphs help to under
|
Line 4284 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]][codtab[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 |
Line 4050 To be simple, these graphs help to under
|
Line 4297 To be simple, these graphs help to under
|
/* 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]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; |
for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; |
for (k=1; k<=cptcovprod;k++) |
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]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; |
|
|
|
|
for(theta=1; theta <=npar; theta++){ |
for(theta=1; theta <=npar; theta++){ |
Line 4282 fprintf(fichtm," \n<ul><li><b>Graphs</b>
|
Line 4529 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]][codtab[jj1][cpt]]); |
|
printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);fflush(stdout); |
|
} |
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">"); |
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">"); |
} |
} |
/* Pij */ |
/* Pij */ |
Line 4306 fprintf(fichtm," \n<ul><li><b>Graphs</b>
|
Line 4555 fprintf(fichtm," \n<ul><li><b>Graphs</b>
|
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) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \ |
<img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1); |
<img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1); |
} |
} |
} /* end i1 */ |
/* } /\* end 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.<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(fileres,"prob"),subdirf2(fileres,"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", |
Line 4356 fprintf(fichtm," \n<ul><li><b>Graphs</b>
|
Line 4612 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"); |
Line 4375 true period expectancies (those weighted
|
Line 4631 true period expectancies (those weighted
|
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.png<br>\ |
<img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1); |
<img src=\"%s%d.png\">",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); |
Line 4510 plot [%.f:%.f] ", ageminpar, agemaxpar)
|
Line 4766 plot [%.f:%.f] ", ageminpar, agemaxpar)
|
} /* 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;*/ |
|
fprintf(ficgp,"\n##############\n#Graphics of of probabilities or incidences\n#############\n"); |
|
fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n"); |
|
fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n"); |
|
fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n"); |
|
fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n"); |
|
fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n"); |
|
fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n"); |
|
fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n"); |
|
fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n"); |
|
fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n"); |
|
fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n"); |
|
fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n"); |
|
fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n"); |
|
fprintf(ficgp,"#\n"); |
for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/ |
for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/ |
|
fprintf(ficgp,"# ng=%d\n",ng); |
|
fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m); |
for(jk=1; jk <=m; jk++) { |
for(jk=1; jk <=m; jk++) { |
|
fprintf(ficgp,"# jk=%d\n",jk); |
fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); |
fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); |
if (ng==2) |
if (ng==2) |
fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n"); |
fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n"); |
Line 4536 plot [%.f:%.f] ", ageminpar, agemaxpar)
|
Line 4814 plot [%.f:%.f] ", ageminpar, agemaxpar)
|
for(k=1; k<=(nlstate+ndeath); k++) { |
for(k=1; k<=(nlstate+ndeath); k++) { |
if (k != k2){ |
if (k != k2){ |
if(ng==2) |
if(ng==2) |
fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1); |
if(nagesqr==0) |
|
fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1); |
|
else /* nagesqr =1 */ |
|
fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr); |
else |
else |
fprintf(ficgp," exp(p%d+p%d*x",i,i+1); |
if(nagesqr==0) |
|
fprintf(ficgp," exp(p%d+p%d*x",i,i+1); |
|
else /* nagesqr =1 */ |
|
fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr); |
ij=1;/* To be checked else nbcode[0][0] wrong */ |
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]][codtab[jk][Tvar[j-2]]]); |
|
ij++; |
|
} |
} |
} |
else |
else |
fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]); |
fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]); |
} |
} |
fprintf(ficgp,")/(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) |
|
fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1); |
|
else /* nagesqr =1 */ |
|
fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr); |
|
|
ij=1; |
ij=1; |
for(j=3; j <=ncovmodel; j++){ |
for(j=3; j <=ncovmodel-nagesqr; j++){ |
if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { |
if(ij <=cptcovage) { /* Bug valgrind */ |
fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); |
if((j-2)==Tage[ij]) { /* Bug valgrind */ |
ij++; |
fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); |
|
ij++; |
|
} |
} |
} |
else |
else |
fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]); |
fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][j-2]]); |
} |
} |
fprintf(ficgp,")"); |
fprintf(ficgp,")"); |
} |
} |
Line 5175 int readdata(char datafile[], int firsto
|
Line 5468 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 5353 void removespace(char *str) {
|
Line 5646 void removespace(char *str) {
|
} |
} |
|
|
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 5370 int decodemodel ( char model[], int last
|
Line 5664 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 5393 int decodemodel ( char model[], int last
|
Line 5679 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]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[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]][codtab[ij][Tvar[k]]]; */ |
|
/* } */ |
|
/* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; */ |
|
/* |
|
* Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */ |
|
for(k=cptcovt; k>=1;k--) /**< Number of covariates */ |
Tvar[k]=0; |
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; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */ |
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 5656 BOOL IsWow64()
|
Line 5978 BOOL IsWow64()
|
} |
} |
#endif |
#endif |
|
|
void syscompilerinfo() |
void syscompilerinfo(int logged) |
{ |
{ |
/* #include "syscompilerinfo.h"*/ |
/* #include "syscompilerinfo.h"*/ |
/* command line Intel compiler 32bit windows, XP compatible:*/ |
/* command line Intel compiler 32bit windows, XP compatible:*/ |
Line 5705 void syscompilerinfo()
|
Line 6027 void syscompilerinfo()
|
int cross = CROSS; |
int cross = CROSS; |
if (cross){ |
if (cross){ |
printf("Cross-"); |
printf("Cross-"); |
fprintf(ficlog, "Cross-"); |
if(logged) fprintf(ficlog, "Cross-"); |
} |
} |
#endif |
#endif |
|
|
#include <stdint.h> |
#include <stdint.h> |
|
|
printf("Compiled with:");fprintf(ficlog,"Compiled with:"); |
printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:"); |
#if defined(__clang__) |
#if defined(__clang__) |
printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */ |
printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */ |
#endif |
#endif |
#if defined(__ICC) || defined(__INTEL_COMPILER) |
#if defined(__ICC) || defined(__INTEL_COMPILER) |
printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */ |
printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */ |
#endif |
#endif |
#if defined(__GNUC__) || defined(__GNUG__) |
#if defined(__GNUC__) || defined(__GNUG__) |
printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */ |
printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */ |
#endif |
#endif |
#if defined(__HP_cc) || defined(__HP_aCC) |
#if defined(__HP_cc) || defined(__HP_aCC) |
printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */ |
printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */ |
#endif |
#endif |
#if defined(__IBMC__) || defined(__IBMCPP__) |
#if defined(__IBMC__) || defined(__IBMCPP__) |
printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */ |
printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */ |
#endif |
#endif |
#if defined(_MSC_VER) |
#if defined(_MSC_VER) |
printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */ |
printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */ |
#endif |
#endif |
#if defined(__PGI) |
#if defined(__PGI) |
printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */ |
printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */ |
#endif |
#endif |
#if defined(__SUNPRO_C) || defined(__SUNPRO_CC) |
#if defined(__SUNPRO_C) || defined(__SUNPRO_CC) |
printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */ |
printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */ |
#endif |
#endif |
printf(" for ");fprintf(ficlog," for "); |
printf(" for "); if (logged) fprintf(ficlog, " for "); |
|
|
// http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros |
// 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! |
#ifdef _WIN32 // note the underscore: without it, it's not msdn official! |
// Windows (x64 and x86) |
// Windows (x64 and x86) |
printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) "); |
printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) "); |
#elif __unix__ // all unices, not all compilers |
#elif __unix__ // all unices, not all compilers |
// Unix |
// Unix |
printf("Unix ");fprintf(ficlog,"Unix "); |
printf("Unix ");if(logged) fprintf(ficlog,"Unix "); |
#elif __linux__ |
#elif __linux__ |
// linux |
// linux |
printf("linux ");fprintf(ficlog,"linux "); |
printf("linux ");if(logged) fprintf(ficlog,"linux "); |
#elif __APPLE__ |
#elif __APPLE__ |
// Mac OS, not sure if this is covered by __posix__ and/or __unix__ though.. |
// Mac OS, not sure if this is covered by __posix__ and/or __unix__ though.. |
printf("Mac OS ");fprintf(ficlog,"Mac OS "); |
printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS "); |
#endif |
#endif |
|
|
/* __MINGW32__ */ |
/* __MINGW32__ */ |
Line 5764 void syscompilerinfo()
|
Line 6086 void syscompilerinfo()
|
/* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */ |
/* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */ |
|
|
#if UINTPTR_MAX == 0xffffffff |
#if UINTPTR_MAX == 0xffffffff |
printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */ |
printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */ |
#elif UINTPTR_MAX == 0xffffffffffffffff |
#elif UINTPTR_MAX == 0xffffffffffffffff |
printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */ |
printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */ |
#else |
#else |
printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */ |
printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */ |
#endif |
#endif |
|
|
#if defined(__GNUC__) |
#if defined(__GNUC__) |
Line 5781 void syscompilerinfo()
|
Line 6103 void syscompilerinfo()
|
+ __GNUC_MINOR__ * 100) |
+ __GNUC_MINOR__ * 100) |
# endif |
# endif |
printf(" using GNU C version %d.\n", __GNUC_VERSION__); |
printf(" using GNU C version %d.\n", __GNUC_VERSION__); |
fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__); |
if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__); |
|
|
if (uname(&sysInfo) != -1) { |
if (uname(&sysInfo) != -1) { |
printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine); |
printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine); |
fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine); |
if(logged) fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine); |
} |
} |
else |
else |
perror("uname() error"); |
perror("uname() error"); |
//#ifndef __INTEL_COMPILER |
//#ifndef __INTEL_COMPILER |
#if !defined (__INTEL_COMPILER) && !defined(__APPLE__) |
#if !defined (__INTEL_COMPILER) && !defined(__APPLE__) |
printf("GNU libc version: %s\n", gnu_get_libc_version()); |
printf("GNU libc version: %s\n", gnu_get_libc_version()); |
fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version()); |
if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version()); |
#endif |
#endif |
#endif |
#endif |
|
|
Line 5800 void syscompilerinfo()
|
Line 6122 void syscompilerinfo()
|
// { |
// { |
#if defined(_MSC_VER) |
#if defined(_MSC_VER) |
if (IsWow64()){ |
if (IsWow64()){ |
printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n"); |
printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n"); |
fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n"); |
if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n"); |
} |
} |
else{ |
else{ |
printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n"); |
printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n"); |
fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n"); |
if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n"); |
} |
} |
// printf("\nPress Enter to continue..."); |
// printf("\nPress Enter to continue..."); |
// getchar(); |
// getchar(); |
Line 5973 int main(int argc, char *argv[])
|
Line 6295 int main(int argc, char *argv[])
|
|
|
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 5981 int main(int argc, char *argv[])
|
Line 6304 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 */ |
Line 6067 int main(int argc, char *argv[])
|
Line 6395 int main(int argc, char *argv[])
|
#else |
#else |
getcwd(pathcd, size); |
getcwd(pathcd, size); |
#endif |
#endif |
|
syscompilerinfo(0); |
printf("\n%s\n%s",version,fullversion); |
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 6132 int main(int argc, char *argv[])
|
Line 6460 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 6140 int main(int argc, char *argv[])
|
Line 6468 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(); |
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); |
Line 6176 int main(int argc, char *argv[])
|
Line 6504 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); |
/* Second 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,"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); |
} |
} |
ungetc(c,ficpar); |
|
|
|
fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); |
|
numlinepar++; |
|
/* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */ |
|
printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n",title, datafile, lastobs, firstpass,lastpass); |
|
/* |
|
|
|
|
|
|
|
*/ |
/* Third parameter line */ |
printf("\nftol=%e \n", ftol); |
while(fgets(line, MAXLINE, ficpar)) { |
printf("stepm=%d \n", stepm); |
/* If line starts with a # it is a comment */ |
printf("ncovcol=%d nlstate=%d \n", ncovcol, nlstate); |
if (line[0] == '#') { |
printf("ndeath=%d maxwav=%d mle=%d weight=%d\n", ndeath, maxwav, mle, weightopt); |
numlinepar++; |
printf("model=%s\n",model); |
fputs(line,stdout); |
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,ficparo); |
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,ficlog); |
|
continue; |
|
}else |
|
break; |
|
} |
|
if((num_filled=sscanf(line,"model=1+age%[^.\n]\n", model)) !=EOF){ |
|
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); |
|
} |
|
/* 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); */ |
|
if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */ |
|
model[strlen(model)-1]='\0'; |
|
fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); |
|
fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); |
fflush(ficlog); |
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 6221 int main(int argc, char *argv[])
|
Line 6613 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 6239 int main(int argc, char *argv[])
|
Line 6630 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); |
Line 6249 int main(int argc, char *argv[])
|
Line 6640 int main(int argc, char *argv[])
|
} |
} |
else if(mle==-3) { /* Main Wizard */ |
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); |
} |
} |
Line 6274 int main(int argc, char *argv[])
|
Line 6665 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 6282 run imach with mle=-1 to get a correct t
|
Line 6673 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 6364 run imach with mle=-1 to get a correct t
|
Line 6755 run imach with mle=-1 to get a correct t
|
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 6385 run imach with mle=-1 to get a correct t
|
Line 6786 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 6424 run imach with mle=-1 to get a correct t
|
Line 6826 run imach with mle=-1 to get a correct t
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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 */ |
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ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */ |
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/* 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 6461 run imach with mle=-1 to get a correct t
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Line 6864 run imach with mle=-1 to get a correct t
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/* Main decodemodel */ |
/* Main decodemodel */ |
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if(decodemodel(model, lastobs) == 1) |
if(decodemodel(model, lastobs) == 1) |
goto end; |
goto end; |
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Line 6504 run imach with mle=-1 to get a correct t
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Line 6908 run imach with mle=-1 to get a correct t
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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 |
/* Nbcode gives the value of the lth modality of jth covariate, in |
V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/ |
V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/ |
Line 6521 run imach with mle=-1 to get a correct t
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Line 6925 run imach with mle=-1 to get a correct t
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m=pow(2,cptcoveff); |
m=pow(2,cptcoveff); |
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for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */ |
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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 */ |
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for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/ |
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for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ |
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h++; |
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if (h>m) |
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h=1; |
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/**< 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 |
* For k=4 covariates, h goes from 1 to 2**k |
* For k=4 covariates, h goes from 1 to 2**k |
* codtabm(h,k)= 1 & (h-1) >> (k-1) ; |
* codtabm(h,k)= 1 & (h-1) >> (k-1) ; |
Line 6541 run imach with mle=-1 to get a correct t
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Line 6938 run imach with mle=-1 to get a correct t
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* 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[12][3]=1; */ |
/* printf("h=%2d ", h); */ |
/*codtab[h][Tvar[k]]=j;*/ |
for(k=1; k <=10; k++){ |
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("k=%d %d ",k,codtabm(h,k)); */ |
} |
codtab[h][k]=codtabm(h,k); |
} |
} |
} |
/* printf("\n"); */ |
} |
} |
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/* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */ |
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/* 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 *\/ */ |
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/* for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */ |
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/* for(cpt=1; cpt <=pow(2,k-1); cpt++){ /\* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 *\/ */ |
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/* h++; */ |
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/* if (h>m) */ |
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/* h=1; */ |
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/* codtab[h][k]=j; */ |
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/* /\* codtab[12][3]=1; *\/ */ |
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/* /\*codtab[h][Tvar[k]]=j;*\/ */ |
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/* /\* 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]]); *\/ */ |
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/* } */ |
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/* } */ |
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/* } */ |
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/* } */ |
/* 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);*/ |
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free_ivector(Ndum,-1,NCOVMAX); |
free_ivector(Ndum,-1,NCOVMAX); |
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Line 6822 Interval (in months) between two waves:
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Line 7234 Interval (in months) between two waves:
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} |
} |
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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])); |
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fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i])); |
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} |
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 6856 Interval (in months) between two waves:
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Line 7269 Interval (in months) between two waves:
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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){ |
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printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\ |
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This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\ |
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Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar); |
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fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\ |
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This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\ |
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Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar); |
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}else |
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printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p); |
printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \ |
printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \ |
stepm, weightopt,\ |
stepm, weightopt,\ |
model,imx,p,matcov,agemortsup); |
model,imx,p,matcov,agemortsup); |
Line 6892 Interval (in months) between two waves:
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Line 7312 Interval (in months) between two waves:
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} |
} |
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/*--------- 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); |
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fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); |
fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); |
Line 6905 Interval (in months) between two waves:
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Line 7325 Interval (in months) between two waves:
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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 6921 Interval (in months) between two waves:
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Line 7341 Interval (in months) between two waves:
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ftolhess=ftol; /* Usually correct */ |
ftolhess=ftol; /* Usually correct */ |
hesscov(matcov, p, npar, delti, ftolhess, func); |
hesscov(matcov, p, npar, delti, ftolhess, func); |
} |
} |
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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"); |
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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"); |
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for(i=1,jk=1; i <=nlstate; i++){ |
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for(k=1; k <=(nlstate+ndeath); k++){ |
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if (k != i) { |
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printf("%d%d ",i,k); |
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fprintf(ficlog,"%d%d ",i,k); |
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for(j=1; j <=ncovmodel; j++){ |
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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])); |
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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])); |
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jk++; |
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} |
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printf("\n"); |
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fprintf(ficlog,"\n"); |
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} |
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} |
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} |
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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 7077 Interval (in months) between two waves:
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Line 7515 Interval (in months) between two waves:
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dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.; |
dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.; |
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fscanf(ficpar,"pop_based=%d\n",&popbased); |
fscanf(ficpar,"pop_based=%d\n",&popbased); |
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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); |
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Line 7101 Interval (in months) between two waves:
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Line 7540 Interval (in months) between two waves:
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/* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */ |
/* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */ |
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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){ |
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printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\ |
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This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\ |
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Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar); |
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fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\ |
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This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\ |
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Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar); |
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}else |
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printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p); |
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printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\ |
printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\ |
model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\ |
model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\ |
Line 7396 Interval (in months) between two waves:
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Line 7843 Interval (in months) between two waves:
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free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); |
free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); |
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free_ivector(ncodemax,1,NCOVMAX); |
free_ivector(ncodemax,1,NCOVMAX); |
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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); |
Line 7503 Interval (in months) between two waves:
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Line 7951 Interval (in months) between two waves:
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} |
} |
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); |
} |
} |
} |
} |