version 1.191, 2015/07/14 10:00:33
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version 1.198, 2015/09/03 07:14:39
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/* $Id$ |
/* $Id$ |
$State$ |
$State$ |
$Log$ |
$Log$ |
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Revision 1.198 2015/09/03 07:14:39 brouard |
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Summary: 0.98q5 Flavia |
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Revision 1.197 2015/09/01 18:24:39 brouard |
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*** empty log message *** |
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Revision 1.196 2015/08/18 23:17:52 brouard |
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Summary: 0.98q5 |
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Revision 1.195 2015/08/18 16:28:39 brouard |
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Summary: Adding a hack for testing purpose |
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After reading the title, ftol and model lines, if the comment line has |
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a q, starting with #q, the answer at the end of the run is quit. It |
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permits to run test files in batch with ctest. The former workaround was |
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$ echo q | imach foo.imach |
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Revision 1.194 2015/08/18 13:32:00 brouard |
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Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line. |
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Revision 1.193 2015/08/04 07:17:42 brouard |
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Summary: 0.98q4 |
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Revision 1.192 2015/07/16 16:49:02 brouard |
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Summary: Fixing some outputs |
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Revision 1.191 2015/07/14 10:00:33 brouard |
Revision 1.191 2015/07/14 10:00:33 brouard |
Summary: Some fixes |
Summary: Some fixes |
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Line 605
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Line 631
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/* #define DEBUG */ |
/* #define DEBUG */ |
/* #define DEBUGBRENT */ |
/* #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 673 typedef struct {
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Line 700 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 691 typedef struct {
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Line 719 typedef struct {
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/* $Id$ */ |
/* $Id$ */ |
/* $State$ */ |
/* $State$ */ |
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#include "version.h" |
char version[]="Imach version 0.98q2, April 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015"; |
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]; |
Line 827 int estepm;
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Line 856 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 841 double **covar; /**< covar[j,i], value
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Line 876 double **covar; /**< covar[j,i], value
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* cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */ |
* 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 1559 void linmin(double p[], double xi[], int
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Line 1595 void linmin(double p[], double xi[], int
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xicom[j]=xi[j]; |
xicom[j]=xi[j]; |
} |
} |
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axs=0.0; |
/* axs=0.0; */ |
xxss=1; /* 1 and using scale */ |
/* xxss=1; /\* 1 and using scale *\/ */ |
xxs=1; |
xxs=1; |
do{ |
/* do{ */ |
ax=0.; |
ax=0.; |
xx= xxs; |
xx= xxs; |
mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */ |
mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */ |
Line 1572 void linmin(double p[], double xi[], int
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Line 1608 void linmin(double p[], double xi[], int
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/* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */ |
/* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */ |
/* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */ |
/* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */ |
/* Find a bracket a,x,b in direction n=xi ie xicom, order may change. Scale is [0:xxs*xi[j]] et non plus [0:xi[j]]*/ |
/* 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]]*/ |
if (fx != fx){ |
/* if (fx != fx){ */ |
xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */ |
/* xxs=xxs/scale; /\* Trying a smaller xx, closer to initial ax=0 *\/ */ |
printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n", axs, xxs, fx,fb, fa, xx, ax, bx); |
/* 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); */ |
} |
/* } */ |
}while(fx != fx); |
/* }while(fx != fx); */ |
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#ifdef DEBUGLINMIN |
#ifdef DEBUGLINMIN |
printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n", ax,xx,bx,fa,fx,fb); |
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); |
Line 1653 void powell(double p[], double **xi, int
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Line 1689 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 1761 void powell(double p[], double **xi, int
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Line 1797 void powell(double p[], double **xi, int
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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 1769 void powell(double p[], double **xi, int
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Line 1805 void powell(double p[], double **xi, int
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pt[j]=p[j]; |
pt[j]=p[j]; |
} |
} |
fptt=(*func)(ptt); /* f_3 */ |
fptt=(*func)(ptt); /* f_3 */ |
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#ifdef POWELLF1F3 |
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#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 */ |
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#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 1798 void powell(double p[], double **xi, int
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Line 1837 void powell(double p[], double **xi, int
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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 |
#ifdef DEBUGLINMIN |
#ifdef DEBUGLINMIN |
Line 1838 void powell(double p[], double **xi, int
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Line 1877 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 */ |
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#ifdef POWELLF1F3 |
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#else |
} /* end if (fptt < fp) */ |
} /* end if (fptt < fp) */ |
} |
#endif |
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} /* loop iteration */ |
} |
} |
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/**** Prevalence limit (stable or period prevalence) ****************/ |
/**** Prevalence limit (stable or period prevalence) ****************/ |
Line 1872 double **prevalim(double **prlim, int nl
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Line 1914 double **prevalim(double **prlim, int nl
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if(nagesqr==1) |
if(nagesqr==1) |
cov[3]= agefin*agefin;; |
cov[3]= agefin*agefin;; |
for (k=1; k<=cptcovn;k++) { |
for (k=1; k<=cptcovn;k++) { |
cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; |
cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; |
/*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/ |
/* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); */ |
} |
} |
/*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+nagesqr+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]][codtabm(ij,Tvar[k])]*cov[2]; |
for (k=1; k<=cptcovprod;k++) /* Useless */ |
for (k=1; k<=cptcovprod;k++) /* Useless */ |
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; |
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; |
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/*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 2051 double ***hpxij(double ***po, int nhstep
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Line 2093 double ***hpxij(double ***po, int nhstep
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if(nagesqr==1) |
if(nagesqr==1) |
cov[3]= agexact*agexact; |
cov[3]= agexact*agexact; |
for (k=1; k<=cptcovn;k++) |
for (k=1; k<=cptcovn;k++) |
cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; |
cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(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+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; |
cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; |
for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */ |
for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */ |
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; |
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; |
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/*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/ |
/*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/ |
Line 2875 void lubksb(double **a, int n, int *indx
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Line 2917 void lubksb(double **a, int n, int *indx
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void pstamp(FILE *fichier) |
void pstamp(FILE *fichier) |
{ |
{ |
fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart); |
fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart); |
} |
} |
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/************ Frequencies ********************/ |
/************ Frequencies ********************/ |
Line 2927 void freqsummary(char fileres[], int ia
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Line 2969 void freqsummary(char fileres[], int ia
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bool=1; |
bool=1; |
if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */ |
if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */ |
for (z1=1; z1<=cptcoveff; z1++) |
for (z1=1; z1<=cptcoveff; z1++) |
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){ |
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ |
/* Tests if the value of each of the covariates of i is equal to filter j1 */ |
/* Tests if the value of each of the covariates of i is equal to filter j1 */ |
bool=0; |
bool=0; |
/* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n", |
/* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n", |
bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1], |
bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1), |
j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/ |
j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/ |
/* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/ |
/* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/ |
} |
} |
} |
} |
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Line 2962 void freqsummary(char fileres[], int ia
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Line 3004 void freqsummary(char fileres[], int ia
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pstamp(ficresp); |
pstamp(ficresp); |
if (cptcovn>0) { |
if (cptcovn>0) { |
fprintf(ficresp, "\n#********** Variable "); |
fprintf(ficresp, "\n#********** Variable "); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); |
fprintf(ficresp, "**********\n#"); |
fprintf(ficresp, "**********\n#"); |
fprintf(ficlog, "\n#********** Variable "); |
fprintf(ficlog, "\n#********** Variable "); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); |
fprintf(ficlog, "**********\n#"); |
fprintf(ficlog, "**********\n#"); |
} |
} |
for(i=1; i<=nlstate;i++) |
for(i=1; i<=nlstate;i++) |
Line 3093 void prevalence(double ***probs, double
|
Line 3135 void prevalence(double ***probs, double
|
bool=1; |
bool=1; |
if (cptcovn>0) { |
if (cptcovn>0) { |
for (z1=1; z1<=cptcoveff; z1++) |
for (z1=1; z1<=cptcoveff; z1++) |
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) |
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) |
bool=0; |
bool=0; |
} |
} |
if (bool==1) { |
if (bool==1) { |
Line 3298 void tricode(int *Tvar, int **nbcode, in
|
Line 3340 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 3325 void tricode(int *Tvar, int **nbcode, in
|
Line 3367 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 */ |
} /* 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 ie V%d with value %d: %d\n", j, Tvar[j], i, 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 3350 void tricode(int *Tvar, int **nbcode, in
|
Line 3401 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; |
Line 3374 void tricode(int *Tvar, int **nbcode, in
|
Line 3436 void tricode(int *Tvar, int **nbcode, in
|
Ndum[ij]++; /* Might be supersed V1 + V1*age */ |
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 4175 void varprob(char optionfilefiname[], do
|
Line 4238 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 4199 To be simple, these graphs help to under
|
Line 4261 To be simple, these graphs help to under
|
/*j1++;*/ |
/*j1++;*/ |
if (cptcovn>0) { |
if (cptcovn>0) { |
fprintf(ficresprob, "\n#********** Variable "); |
fprintf(ficresprob, "\n#********** Variable "); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); |
fprintf(ficresprob, "**********\n#\n"); |
fprintf(ficresprob, "**********\n#\n"); |
fprintf(ficresprobcov, "\n#********** Variable "); |
fprintf(ficresprobcov, "\n#********** Variable "); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); |
fprintf(ficresprobcov, "**********\n#\n"); |
fprintf(ficresprobcov, "**********\n#\n"); |
|
|
fprintf(ficgp, "\n#********** Variable "); |
fprintf(ficgp, "\n#********** Variable "); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); |
fprintf(ficgp, "**********\n#\n"); |
fprintf(ficgp, "**********\n#\n"); |
|
|
|
|
fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable "); |
fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable "); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); |
fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">"); |
fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">"); |
|
|
fprintf(ficresprobcor, "\n#********** Variable "); |
fprintf(ficresprobcor, "\n#********** Variable "); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); |
fprintf(ficresprobcor, "**********\n#"); |
fprintf(ficresprobcor, "**********\n#"); |
} |
} |
|
|
Line 4228 To be simple, these graphs help to under
|
Line 4290 To be simple, these graphs help to under
|
if(nagesqr==1) |
if(nagesqr==1) |
cov[3]= age*age; |
cov[3]= age*age; |
for (k=1; k<=cptcovn;k++) { |
for (k=1; k<=cptcovn;k++) { |
cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4 |
cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];/* j1 1 2 3 4 |
* 1 1 1 1 1 |
* 1 1 1 1 1 |
* 2 2 1 1 1 |
* 2 2 1 1 1 |
* 3 1 2 1 1 |
* 3 1 2 1 1 |
Line 4236 To be simple, these graphs help to under
|
Line 4298 To be simple, these graphs help to under
|
/* nbcode[1][1]=0 nbcode[1][2]=1;*/ |
/* nbcode[1][1]=0 nbcode[1][2]=1;*/ |
} |
} |
/* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ |
/* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ |
for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; |
for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; |
for (k=1; k<=cptcovprod;k++) |
for (k=1; k<=cptcovprod;k++) |
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; |
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; |
|
|
|
|
for(theta=1; theta <=npar; theta++){ |
for(theta=1; theta <=npar; theta++){ |
Line 4470 fprintf(fichtm," \n<ul><li><b>Graphs</b>
|
Line 4532 fprintf(fichtm," \n<ul><li><b>Graphs</b>
|
|
|
jj1=0; |
jj1=0; |
for(k1=1; k1<=m;k1++){ |
for(k1=1; k1<=m;k1++){ |
for(i1=1; i1<=ncodemax[k1];i1++){ |
/* for(i1=1; i1<=ncodemax[k1];i1++){ */ |
jj1++; |
jj1++; |
if (cptcovn > 0) { |
if (cptcovn > 0) { |
fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates"); |
fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates"); |
for (cpt=1; cpt<=cptcoveff;cpt++) |
for (cpt=1; cpt<=cptcoveff;cpt++){ |
fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]); |
fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); |
|
printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout); |
|
} |
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">"); |
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">"); |
} |
} |
/* Pij */ |
/* Pij */ |
Line 4494 fprintf(fichtm," \n<ul><li><b>Graphs</b>
|
Line 4558 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 4544 fprintf(fichtm," \n<ul><li><b>Graphs</b>
|
Line 4615 fprintf(fichtm," \n<ul><li><b>Graphs</b>
|
|
|
jj1=0; |
jj1=0; |
for(k1=1; k1<=m;k1++){ |
for(k1=1; k1<=m;k1++){ |
for(i1=1; i1<=ncodemax[k1];i1++){ |
/* for(i1=1; i1<=ncodemax[k1];i1++){ */ |
jj1++; |
jj1++; |
if (cptcovn > 0) { |
if (cptcovn > 0) { |
fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates"); |
fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates"); |
for (cpt=1; cpt<=cptcoveff;cpt++) |
for (cpt=1; cpt<=cptcoveff;cpt++) |
fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]); |
fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); |
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">"); |
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">"); |
} |
} |
for(cpt=1; cpt<=nlstate;cpt++) { |
for(cpt=1; cpt<=nlstate;cpt++) { |
Line 4563 true period expectancies (those weighted
|
Line 4634 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 4757 plot [%.f:%.f] ", ageminpar, agemaxpar)
|
Line 4828 plot [%.f:%.f] ", ageminpar, agemaxpar)
|
fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr); |
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-nagesqr; 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+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); |
if(ij <=cptcovage) { /* Bug valgrind */ |
ij++; |
if((j-2)==Tage[ij]) { /* Bug valgrind */ |
|
fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); |
|
ij++; |
|
} |
} |
} |
else |
else |
fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]); |
fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]); |
} |
} |
fprintf(ficgp,")/(1"); |
fprintf(ficgp,")/(1"); |
|
|
Line 4774 plot [%.f:%.f] ", ageminpar, agemaxpar)
|
Line 4848 plot [%.f:%.f] ", ageminpar, agemaxpar)
|
|
|
ij=1; |
ij=1; |
for(j=3; j <=ncovmodel-nagesqr; 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+nagesqr,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]][codtabm(jk,Tvar[j-2])]); |
|
ij++; |
|
} |
} |
} |
else |
else |
fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,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]][codtabm(jk,j-2)]); |
} |
} |
fprintf(ficgp,")"); |
fprintf(ficgp,")"); |
} |
} |
Line 4906 void prevforecast(char fileres[], double
|
Line 4982 void prevforecast(char fileres[], double
|
k=k+1; |
k=k+1; |
fprintf(ficresf,"\n#******"); |
fprintf(ficresf,"\n#******"); |
for(j=1;j<=cptcoveff;j++) { |
for(j=1;j<=cptcoveff;j++) { |
fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); |
} |
} |
fprintf(ficresf,"******\n"); |
fprintf(ficresf,"******\n"); |
fprintf(ficresf,"# Covariate valuofcovar yearproj age"); |
fprintf(ficresf,"# Covariate valuofcovar yearproj age"); |
Line 4930 void prevforecast(char fileres[], double
|
Line 5006 void prevforecast(char fileres[], double
|
if (h*hstepm/YEARM*stepm ==yearp) { |
if (h*hstepm/YEARM*stepm ==yearp) { |
fprintf(ficresf,"\n"); |
fprintf(ficresf,"\n"); |
for(j=1;j<=cptcoveff;j++) |
for(j=1;j<=cptcoveff;j++) |
fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); |
fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm); |
fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm); |
} |
} |
for(j=1; j<=nlstate+ndeath;j++) { |
for(j=1; j<=nlstate+ndeath;j++) { |
Line 5028 void populforecast(char fileres[], doubl
|
Line 5104 void populforecast(char fileres[], doubl
|
k=k+1; |
k=k+1; |
fprintf(ficrespop,"\n#******"); |
fprintf(ficrespop,"\n#******"); |
for(j=1;j<=cptcoveff;j++) { |
for(j=1;j<=cptcoveff;j++) { |
fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); |
} |
} |
fprintf(ficrespop,"******\n"); |
fprintf(ficrespop,"******\n"); |
fprintf(ficrespop,"# Age"); |
fprintf(ficrespop,"# Age"); |
Line 5395 int readdata(char datafile[], int firsto
|
Line 5471 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 5597 int decodemodel ( char model[], int last
|
Line 5673 int decodemodel ( char model[], int last
|
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; |
if (strstr(model,"AGE") !=0){ |
if (strstr(model,"AGE") !=0){ |
printf("Error. AGE must be in lower case 'age' model=1+age+%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=1+age+%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 5611 int decodemodel ( char model[], int last
|
Line 5687 int decodemodel ( char model[], int last
|
printf(" strpt=%s, model=%s\n",strpt, model); |
printf(" strpt=%s, model=%s\n",strpt, model); |
if(strpt != model){ |
if(strpt != model){ |
printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \ |
printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \ |
'model=1+age+age*age+V1' or 'model=1+age+age*age+V1+V1*age', please swap as well as \n \ |
'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \ |
corresponding column of parameters.\n",model); |
corresponding column of parameters.\n",model); |
fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \ |
fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \ |
'model=1+age+age*age+V1' or 'model=1+age+age*age+V1+V1*age', please swap as well as \n \ |
'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \ |
corresponding column of parameters.\n",model); fflush(ficlog); |
corresponding column of parameters.\n",model); fflush(ficlog); |
return 1; |
return 1; |
} |
} |
Line 5685 int decodemodel ( char model[], int last
|
Line 5761 int decodemodel ( char model[], int last
|
/* k=1 Tvar[1]=2 (from V2) */ |
/* k=1 Tvar[1]=2 (from V2) */ |
/* k=5 Tvar[5] */ |
/* k=5 Tvar[5] */ |
/* for (k=1; k<=cptcovn;k++) { */ |
/* for (k=1; k<=cptcovn;k++) { */ |
/* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */ |
/* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */ |
/* } */ |
/* } */ |
/* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; */ |
/* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */ |
/* |
/* |
* Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */ |
* 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 */ |
for(k=cptcovt; k>=1;k--) /**< Number of covariates */ |
Line 6098 int prevalence_limit(double *p, double *
|
Line 6174 int prevalence_limit(double *p, double *
|
//for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ |
//for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ |
k=k+1; |
k=k+1; |
/* to clean */ |
/* to clean */ |
//printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]); |
//printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov)); |
fprintf(ficrespl,"\n#******"); |
fprintf(ficrespl,"\n#******"); |
printf("\n#******"); |
printf("\n#******"); |
fprintf(ficlog,"\n#******"); |
fprintf(ficlog,"\n#******"); |
for(j=1;j<=cptcoveff;j++) { |
for(j=1;j<=cptcoveff;j++) { |
fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); |
printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); |
fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); |
} |
} |
fprintf(ficrespl,"******\n"); |
fprintf(ficrespl,"******\n"); |
printf("******\n"); |
printf("******\n"); |
Line 6113 int prevalence_limit(double *p, double *
|
Line 6189 int prevalence_limit(double *p, double *
|
|
|
fprintf(ficrespl,"#Age "); |
fprintf(ficrespl,"#Age "); |
for(j=1;j<=cptcoveff;j++) { |
for(j=1;j<=cptcoveff;j++) { |
fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); |
} |
} |
for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i); |
for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i); |
fprintf(ficrespl,"\n"); |
fprintf(ficrespl,"\n"); |
Line 6123 int prevalence_limit(double *p, double *
|
Line 6199 int prevalence_limit(double *p, double *
|
prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); |
prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); |
fprintf(ficrespl,"%.0f ",age ); |
fprintf(ficrespl,"%.0f ",age ); |
for(j=1;j<=cptcoveff;j++) |
for(j=1;j<=cptcoveff;j++) |
fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); |
for(i=1; i<=nlstate;i++) |
for(i=1; i<=nlstate;i++) |
fprintf(ficrespl," %.5f", prlim[i][i]); |
fprintf(ficrespl," %.5f", prlim[i][i]); |
fprintf(ficrespl,"\n"); |
fprintf(ficrespl,"\n"); |
Line 6170 int hPijx(double *p, int bage, int fage)
|
Line 6246 int hPijx(double *p, int bage, int fage)
|
for (k=1; k <= (int) pow(2,cptcoveff); k++){ |
for (k=1; k <= (int) pow(2,cptcoveff); k++){ |
fprintf(ficrespij,"\n#****** "); |
fprintf(ficrespij,"\n#****** "); |
for(j=1;j<=cptcoveff;j++) |
for(j=1;j<=cptcoveff;j++) |
fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); |
fprintf(ficrespij,"******\n"); |
fprintf(ficrespij,"******\n"); |
|
|
for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */ |
for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */ |
Line 6222 int main(int argc, char *argv[])
|
Line 6298 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 6231 int main(int argc, char *argv[])
|
Line 6308 int main(int argc, char *argv[])
|
/* FILE *ficgp;*/ /*Gnuplot File */ |
/* FILE *ficgp;*/ /*Gnuplot File */ |
struct stat info; |
struct stat info; |
double agedeb=0.; |
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=0.; /* Dummy variable */ |
double dum=0.; /* Dummy variable */ |
Line 6239 int main(int argc, char *argv[])
|
Line 6317 int main(int argc, char *argv[])
|
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=0; |
int jl=0; |
int i1, j1, jk, stepsize=0; |
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; |
Line 6317 int main(int argc, char *argv[])
|
Line 6399 int main(int argc, char *argv[])
|
getcwd(pathcd, size); |
getcwd(pathcd, size); |
#endif |
#endif |
syscompilerinfo(0); |
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 6381 int main(int argc, char *argv[])
|
Line 6463 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 6389 int main(int argc, char *argv[])
|
Line 6471 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(0); |
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 6425 int main(int argc, char *argv[])
|
Line 6507 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=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); |
/* Third parameter line */ |
numlinepar++; |
while(fgets(line, MAXLINE, ficpar)) { |
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 line starts with a # it is a comment */ |
|
if (line[0] == '#') { |
|
numlinepar++; |
|
fputs(line,stdout); |
|
fputs(line,ficparo); |
|
fputs(line,ficlog); |
|
continue; |
|
}else |
|
break; |
|
} |
|
if((num_filled=sscanf(line,"model=1+age%[^.\n]\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 */ |
if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */ |
model[strlen(model)-1]='\0'; |
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(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); |
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]=='#'|| model[0]== '\0'){ */ |
if(model[0]=='#'){ |
if(model[0]=='#'){ |
Line 6457 int main(int argc, char *argv[])
|
Line 6598 int main(int argc, char *argv[])
|
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 6498 int main(int argc, char *argv[])
|
Line 6643 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 6523 int main(int argc, char *argv[])
|
Line 6668 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 6531 run imach with mle=-1 to get a correct t
|
Line 6676 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 6613 run imach with mle=-1 to get a correct t
|
Line 6758 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 6634 run imach with mle=-1 to get a correct t
|
Line 6789 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 6673 run imach with mle=-1 to get a correct t
|
Line 6829 run imach with mle=-1 to get a correct t
|
s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ |
s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ |
tab=ivector(1,NCOVMAX); |
tab=ivector(1,NCOVMAX); |
ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */ |
ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */ |
|
ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */ |
|
|
/* Reads data from file datafile */ |
/* Reads data from file datafile */ |
if (readdata(datafile, firstobs, lastobs, &imx)==1) |
if (readdata(datafile, firstobs, lastobs, &imx)==1) |
Line 6761 run imach with mle=-1 to get a correct t
|
Line 6918 run imach with mle=-1 to get a correct t
|
/* 1 to ncodemax[j] is the maximum value of this jth covariate */ |
/* 1 to ncodemax[j] is the maximum value of this jth covariate */ |
|
|
codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */ |
codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */ |
/*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/ |
/*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/ |
/* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/ |
/* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/ |
h=0; |
h=0; |
|
|
Line 6771 run imach with mle=-1 to get a correct t
|
Line 6928 run imach with mle=-1 to get a correct t
|
|
|
m=pow(2,cptcoveff); |
m=pow(2,cptcoveff); |
|
|
for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */ |
|
for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ |
|
for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/ |
|
for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ |
|
h++; |
|
if (h>m) |
|
h=1; |
|
/**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1 |
/**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1 |
* 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 6791 run imach with mle=-1 to get a correct t
|
Line 6941 run imach with mle=-1 to get a correct t
|
* 6 2 1 2 1 |
* 6 2 1 2 1 |
* 7 i=4 1 2 2 1 |
* 7 i=4 1 2 2 1 |
* 8 2 2 2 1 |
* 8 2 2 2 1 |
* 9 i=5 1 i=3 1 i=2 1 1 |
* 9 i=5 1 i=3 1 i=2 1 2 |
* 10 2 1 1 1 |
* 10 2 1 1 2 |
* 11 i=6 1 2 1 1 |
* 11 i=6 1 2 1 2 |
* 12 2 2 1 1 |
* 12 2 2 1 2 |
* 13 i=7 1 i=4 1 2 1 |
* 13 i=7 1 i=4 1 2 2 |
* 14 2 1 2 1 |
* 14 2 1 2 2 |
* 15 i=8 1 2 2 1 |
* 15 i=8 1 2 2 2 |
* 16 2 2 2 1 |
* 16 2 2 2 2 |
*/ |
*/ |
codtab[h][k]=j; |
for(h=1; h <=100 ;h++){ |
/* codtab[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"); */ |
} |
} |
|
/* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */ |
|
/* for(i=1; i <=pow(2,cptcoveff-k);i++){ /\* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 *\/ */ |
|
/* for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */ |
|
/* for(cpt=1; cpt <=pow(2,k-1); cpt++){ /\* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 *\/ */ |
|
/* h++; */ |
|
/* if (h>m) */ |
|
/* h=1; */ |
|
/* codtab[h][k]=j; */ |
|
/* /\* codtab[12][3]=1; *\/ */ |
|
/* /\*codtab[h][Tvar[k]]=j;*\/ */ |
|
/* /\* printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]); *\/ */ |
|
/* } */ |
|
/* } */ |
|
/* } */ |
|
/* } */ |
/* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); |
/* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); |
codtab[1][2]=1;codtab[2][2]=2; */ |
codtab[1][2]=1;codtab[2][2]=2; */ |
/* for(i=1; i <=m ;i++){ |
/* for(i=1; i <=m ;i++){ */ |
for(k=1; k <=cptcovn; k++){ |
/* for(k=1; k <=cptcovn; k++){ */ |
printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); |
/* printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); */ |
} |
/* } */ |
printf("\n"); |
/* printf("\n"); */ |
} |
/* } */ |
scanf("%d",i);*/ |
/* scanf("%d",i);*/ |
|
|
free_ivector(Ndum,-1,NCOVMAX); |
free_ivector(Ndum,-1,NCOVMAX); |
|
|
Line 7072 Interval (in months) between two waves:
|
Line 7237 Interval (in months) between two waves:
|
} |
} |
|
|
printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp); |
printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp); |
for (i=1;i<=NDIM;i++) |
for (i=1;i<=NDIM;i++) { |
printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i])); |
printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i])); |
|
fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i])); |
|
} |
lsurv=vector(1,AGESUP); |
lsurv=vector(1,AGESUP); |
lpop=vector(1,AGESUP); |
lpop=vector(1,AGESUP); |
tpop=vector(1,AGESUP); |
tpop=vector(1,AGESUP); |
Line 7106 Interval (in months) between two waves:
|
Line 7272 Interval (in months) between two waves:
|
|
|
|
|
replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */ |
replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */ |
printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p); |
if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){ |
|
printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\ |
|
This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\ |
|
Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar); |
|
fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\ |
|
This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\ |
|
Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar); |
|
}else |
|
printinggnuplotmort(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 7142 Interval (in months) between two waves:
|
Line 7315 Interval (in months) between two waves:
|
} |
} |
|
|
/*--------- 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=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model); |
fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model); |
|
|
|
|
fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); |
fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); |
Line 7171 Interval (in months) between two waves:
|
Line 7344 Interval (in months) between two waves:
|
ftolhess=ftol; /* Usually correct */ |
ftolhess=ftol; /* Usually correct */ |
hesscov(matcov, p, npar, delti, ftolhess, func); |
hesscov(matcov, p, npar, delti, ftolhess, func); |
} |
} |
|
printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n"); |
|
fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n"); |
|
for(i=1,jk=1; i <=nlstate; i++){ |
|
for(k=1; k <=(nlstate+ndeath); k++){ |
|
if (k != i) { |
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printf("%d%d ",i,k); |
|
fprintf(ficlog,"%d%d ",i,k); |
|
for(j=1; j <=ncovmodel; j++){ |
|
printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk])); |
|
fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk])); |
|
jk++; |
|
} |
|
printf("\n"); |
|
fprintf(ficlog,"\n"); |
|
} |
|
} |
|
} |
|
|
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 7327 Interval (in months) between two waves:
|
Line 7518 Interval (in months) between two waves:
|
dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.; |
dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.; |
|
|
fscanf(ficpar,"pop_based=%d\n",&popbased); |
fscanf(ficpar,"pop_based=%d\n",&popbased); |
|
fprintf(ficlog,"pop_based=%d\n",popbased); |
fprintf(ficparo,"pop_based=%d\n",popbased); |
fprintf(ficparo,"pop_based=%d\n",popbased); |
fprintf(ficres,"pop_based=%d\n",popbased); |
fprintf(ficres,"pop_based=%d\n",popbased); |
|
|
Line 7351 Interval (in months) between two waves:
|
Line 7543 Interval (in months) between two waves:
|
/* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */ |
/* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */ |
|
|
replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */ |
replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */ |
printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p); |
if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){ |
|
printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\ |
|
This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\ |
|
Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar); |
|
fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\ |
|
This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\ |
|
Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar); |
|
}else |
|
printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p); |
|
|
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 7646 Interval (in months) between two waves:
|
Line 7846 Interval (in months) between two waves:
|
free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); |
free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); |
|
|
free_ivector(ncodemax,1,NCOVMAX); |
free_ivector(ncodemax,1,NCOVMAX); |
|
free_ivector(ncodemaxwundef,1,NCOVMAX); |
free_ivector(Tvar,1,NCOVMAX); |
free_ivector(Tvar,1,NCOVMAX); |
free_ivector(Tprod,1,NCOVMAX); |
free_ivector(Tprod,1,NCOVMAX); |
free_ivector(Tvaraff,1,NCOVMAX); |
free_ivector(Tvaraff,1,NCOVMAX); |
Line 7753 Interval (in months) between two waves:
|
Line 7954 Interval (in months) between two waves:
|
} |
} |
end: |
end: |
while (z[0] != 'q') { |
while (z[0] != 'q') { |
printf("\nType q for exiting: "); |
printf("\nType q for exiting: "); fflush(stdout); |
scanf("%s",z); |
scanf("%s",z); |
} |
} |
} |
} |