version 1.201, 2015/09/15 17:34:58
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version 1.215, 2015/12/16 08:52:24
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/* $Id$ |
/* $Id$ |
$State$ |
$State$ |
$Log$ |
$Log$ |
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Revision 1.215 2015/12/16 08:52:24 brouard |
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Summary: 0.98r4 working |
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Revision 1.214 2015/12/16 06:57:54 brouard |
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Summary: temporary not working |
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Revision 1.213 2015/12/11 18:22:17 brouard |
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Summary: 0.98r4 |
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Revision 1.212 2015/11/21 12:47:24 brouard |
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Summary: minor typo |
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Revision 1.211 2015/11/21 12:41:11 brouard |
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Summary: 0.98r3 with some graph of projected cross-sectional |
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Author: Nicolas Brouard |
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Revision 1.210 2015/11/18 17:41:20 brouard |
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Summary: Start working on projected prevalences |
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Revision 1.209 2015/11/17 22:12:03 brouard |
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Summary: Adding ftolpl parameter |
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Author: N Brouard |
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We had difficulties to get smoothed confidence intervals. It was due |
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to the period prevalence which wasn't computed accurately. The inner |
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parameter ftolpl is now an outer parameter of the .imach parameter |
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file after estepm. If ftolpl is small 1.e-4 and estepm too, |
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computation are long. |
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Revision 1.208 2015/11/17 14:31:57 brouard |
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Summary: temporary |
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Revision 1.207 2015/10/27 17:36:57 brouard |
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*** empty log message *** |
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Revision 1.206 2015/10/24 07:14:11 brouard |
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*** empty log message *** |
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Revision 1.205 2015/10/23 15:50:53 brouard |
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Summary: 0.98r3 some clarification for graphs on likelihood contributions |
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Revision 1.204 2015/10/01 16:20:26 brouard |
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Summary: Some new graphs of contribution to likelihood |
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Revision 1.203 2015/09/30 17:45:14 brouard |
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Summary: looking at better estimation of the hessian |
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Also a better criteria for convergence to the period prevalence And |
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therefore adding the number of years needed to converge. (The |
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prevalence in any alive state shold sum to one |
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Revision 1.202 2015/09/22 19:45:16 brouard |
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Summary: Adding some overall graph on contribution to likelihood. Might change |
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Revision 1.201 2015/09/15 17:34:58 brouard |
Revision 1.201 2015/09/15 17:34:58 brouard |
Summary: 0.98r0 |
Summary: 0.98r0 |
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Line 644
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Line 699
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/* #define DEBUG */ |
/* #define DEBUG */ |
/* #define DEBUGBRENT */ |
/* #define DEBUGBRENT */ |
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/* #define DEBUGLINMIN */ |
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/* #define DEBUGHESS */ |
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#define DEBUGHESSIJ |
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/* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan)*\/ */ |
#define POWELL /* Instead of NLOPT */ |
#define POWELL /* Instead of NLOPT */ |
#define POWELLF1F3 /* Skip test */ |
#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 *\/ */ |
Line 715 typedef struct {
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Line 774 typedef struct {
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#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))+1 |
#define codtabm(h,k) (1 & (h-1) >> (k-1))+1 |
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/*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/ |
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#define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 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 |
Line 735 typedef struct {
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Line 796 typedef struct {
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/* $State$ */ |
/* $State$ */ |
#include "version.h" |
#include "version.h" |
char version[]=__IMACH_VERSION__; |
char version[]=__IMACH_VERSION__; |
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 copyright[]="October 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015"; |
char fullversion[]="$Revision$ $Date$"; |
char fullversion[]="$Revision$ $Date$"; |
char strstart[80]; |
char strstart[80]; |
char optionfilext[10], optionfilefiname[FILENAMELENGTH]; |
char optionfilext[10], optionfilefiname[FILENAMELENGTH]; |
Line 772 double **matprod2(); /* test */
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Line 833 double **matprod2(); /* test */
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double **oldm, **newm, **savm; /* Working pointers to matrices */ |
double **oldm, **newm, **savm; /* Working pointers to matrices */ |
double **oldms, **newms, **savms; /* Fixed working pointers to matrices */ |
double **oldms, **newms, **savms; /* Fixed working pointers to matrices */ |
/*FILE *fic ; */ /* Used in readdata only */ |
/*FILE *fic ; */ /* Used in readdata only */ |
FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop; |
FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop; |
FILE *ficlog, *ficrespow; |
FILE *ficlog, *ficrespow; |
int globpr=0; /* Global variable for printing or not */ |
int globpr=0; /* Global variable for printing or not */ |
double fretone; /* Only one call to likelihood */ |
double fretone; /* Only one call to likelihood */ |
Line 802 char command[FILENAMELENGTH];
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Line 863 char command[FILENAMELENGTH];
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int outcmd=0; |
int outcmd=0; |
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char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH]; |
char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH]; |
char fileresu[FILENAMELENGTH]; /* Without r in front */ |
char fileresu[FILENAMELENGTH]; /* fileres without r in front */ |
char filelog[FILENAMELENGTH]; /* Log file */ |
char filelog[FILENAMELENGTH]; /* Log file */ |
char filerest[FILENAMELENGTH]; |
char filerest[FILENAMELENGTH]; |
char fileregp[FILENAMELENGTH]; |
char fileregp[FILENAMELENGTH]; |
Line 926 static int split( char *path, char *dirc
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Line 987 static int split( char *path, char *dirc
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} |
} |
/* got dirc from getcwd*/ |
/* got dirc from getcwd*/ |
printf(" DIRC = %s \n",dirc); |
printf(" DIRC = %s \n",dirc); |
} else { /* strip direcotry from path */ |
} else { /* strip directory from path */ |
ss++; /* after this, the filename */ |
ss++; /* after this, the filename */ |
l2 = strlen( ss ); /* length of filename */ |
l2 = strlen( ss ); /* length of filename */ |
if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH ); |
if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH ); |
Line 1334 char *subdirf3(char fileres[], char *pre
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Line 1395 char *subdirf3(char fileres[], char *pre
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strcat(tmpout,fileres); |
strcat(tmpout,fileres); |
return tmpout; |
return tmpout; |
} |
} |
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/*************** function subdirfext ***********/ |
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char *subdirfext(char fileres[], char *preop, char *postop) |
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{ |
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strcpy(tmpout,preop); |
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strcat(tmpout,fileres); |
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strcat(tmpout,postop); |
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return tmpout; |
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} |
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/*************** function subdirfext3 ***********/ |
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char *subdirfext3(char fileres[], char *preop, char *postop) |
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{ |
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/* Caution optionfilefiname is hidden */ |
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strcpy(tmpout,optionfilefiname); |
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strcat(tmpout,"/"); |
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strcat(tmpout,preop); |
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strcat(tmpout,fileres); |
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strcat(tmpout,postop); |
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return tmpout; |
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} |
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char *asc_diff_time(long time_sec, char ascdiff[]) |
char *asc_diff_time(long time_sec, char ascdiff[]) |
{ |
{ |
long sec_left, days, hours, minutes; |
long sec_left, days, hours, minutes; |
Line 1598 void linmin(double p[], double xi[], int
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Line 1682 void linmin(double p[], double xi[], int
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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 */ |
#ifdef LINMINORIGINAL |
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#else |
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double scale=10., axs, xxs; /* Scale added for infinity */ |
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#endif |
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ncom=n; |
ncom=n; |
pcom=vector(1,n); |
pcom=vector(1,n); |
xicom=vector(1,n); |
xicom=vector(1,n); |
nrfunc=func; |
nrfunc=func; |
for (j=1;j<=n;j++) { |
for (j=1;j<=n;j++) { |
pcom[j]=p[j]; |
pcom[j]=p[j]; |
xicom[j]=xi[j]; |
xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */ |
} |
} |
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/* axs=0.0; */ |
#ifdef LINMINORIGINAL |
/* xxss=1; /\* 1 and using scale *\/ */ |
xx=1.; |
xxs=1; |
#else |
/* do{ */ |
axs=0.0; |
ax=0.; |
xxs=1.; |
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do{ |
xx= xxs; |
xx= xxs; |
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#endif |
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ax=0.; |
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]) */ |
/* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */ |
/* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */ |
/* xt[x,j]=pcom[j]+x*xicom[j] f(ax) = f(xt(a,j=1,n)) = f(p(j) + 0 * xi(j)) and f(xx) = f(xt(x, j=1,n)) = f(p(j) + 1 * xi(j)) */ |
/* 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)) */ |
Line 1622 void linmin(double p[], double xi[], int
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Line 1712 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){ */ |
#ifdef LINMINORIGINAL |
/* xxs=xxs/scale; /\* Trying a smaller xx, closer to initial ax=0 *\/ */ |
#else |
/* 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); */ |
if (fx != fx){ |
/* } */ |
xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */ |
/* }while(fx != fx); */ |
printf("|"); |
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fprintf(ficlog,"|"); |
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#ifdef DEBUGLINMIN |
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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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#endif |
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} |
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}while(fx != fx); |
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#endif |
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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); |
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fprintf(ficlog,"\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n", ax,xx,bx,fa,fx,fb); |
#endif |
#endif |
*fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/ |
*fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/ |
/* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */ |
/* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */ |
Line 1642 void linmin(double p[], double xi[], int
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Line 1740 void linmin(double p[], double xi[], int
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#endif |
#endif |
#ifdef DEBUGLINMIN |
#ifdef DEBUGLINMIN |
printf("linmin end "); |
printf("linmin end "); |
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fprintf(ficlog,"linmin end "); |
#endif |
#endif |
for (j=1;j<=n;j++) { |
for (j=1;j<=n;j++) { |
/* printf(" before xi[%d]=%12.8f", j,xi[j]); */ |
#ifdef LINMINORIGINAL |
xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */ |
xi[j] *= xmin; |
/* if(xxs <1.0) */ |
#else |
/* 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 ); */ |
#ifdef DEBUGLINMIN |
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if(xxs <1.0) |
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printf(" before xi[%d]=%12.8f", j,xi[j]); |
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#endif |
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xi[j] *= xmin*xxs; /* xi rescaled by xmin and number of loops: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */ |
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#ifdef DEBUGLINMIN |
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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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#endif |
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#endif |
p[j] += xi[j]; /* Parameters values are updated accordingly */ |
p[j] += xi[j]; /* Parameters values are updated accordingly */ |
} |
} |
/* printf("\n"); */ |
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#ifdef DEBUGLINMIN |
#ifdef DEBUGLINMIN |
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printf("\n"); |
printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p)); |
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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fprintf(ficlog,"Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p)); |
for (j=1;j<=n;j++) { |
for (j=1;j<=n;j++) { |
printf(" xi[%d]= %12.7f p[%d]= %12.7f",j,xi[j],j,p[j]); |
printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]); |
if(j % ncovmodel == 0) |
fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]); |
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if(j % ncovmodel == 0){ |
printf("\n"); |
printf("\n"); |
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fprintf(ficlog,"\n"); |
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} |
} |
} |
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#else |
#endif |
#endif |
free_vector(xicom,1,n); |
free_vector(xicom,1,n); |
free_vector(pcom,1,n); |
free_vector(pcom,1,n); |
Line 1691 void powell(double p[], double **xi, int
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Line 1804 void powell(double p[], double **xi, int
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xits=vector(1,n); |
xits=vector(1,n); |
*fret=(*func)(p); |
*fret=(*func)(p); |
for (j=1;j<=n;j++) pt[j]=p[j]; |
for (j=1;j<=n;j++) pt[j]=p[j]; |
rcurr_time = time(NULL); |
rcurr_time = time(NULL); |
for (*iter=1;;++(*iter)) { |
for (*iter=1;;++(*iter)) { |
fp=(*fret); /* From former iteration or initial value */ |
fp=(*fret); /* From former iteration or initial value */ |
ibig=0; |
ibig=0; |
Line 1735 void powell(double p[], double **xi, int
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Line 1848 void powell(double p[], double **xi, int
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for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */ |
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); /* print direction (parameter) i */ |
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); /* Point p[n]. xit[n] has been loaded for direction i as input.*/ |
linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/ |
/* Outputs are fret(new point p) p is updated and xit rescaled */ |
/* Outputs are fret(new point p) p is updated and xit rescaled */ |
Line 1836 void powell(double p[], double **xi, int
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Line 1949 void powell(double p[], double **xi, int
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t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */ |
t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */ |
t= t- del*SQR(fp-fptt); |
t= t- del*SQR(fp-fptt); |
#endif |
#endif |
directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */ |
directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */ |
#ifdef DEBUG |
#ifdef DEBUG |
printf("t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest); |
printf("t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest); |
fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest); |
fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest); |
Line 1851 void powell(double p[], double **xi, int
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Line 1964 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 (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del); |
printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt); |
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 (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del); |
fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt); |
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 */ |
Line 1861 void powell(double p[], double **xi, int
|
Line 1974 void powell(double p[], double **xi, int
|
#ifdef DEBUGLINMIN |
#ifdef DEBUGLINMIN |
printf("Before linmin in direction P%d-P0\n",n); |
printf("Before linmin in direction P%d-P0\n",n); |
for (j=1;j<=n;j++) { |
for (j=1;j<=n;j++) { |
printf("Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]); |
printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]); |
if(j % ncovmodel == 0) |
fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]); |
|
if(j % ncovmodel == 0){ |
printf("\n"); |
printf("\n"); |
|
fprintf(ficlog,"\n"); |
|
} |
} |
} |
#endif |
#endif |
linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/ |
linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/ |
#ifdef DEBUGLINMIN |
#ifdef DEBUGLINMIN |
for (j=1;j<=n;j++) { |
for (j=1;j<=n;j++) { |
printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]); |
printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]); |
if(j % ncovmodel == 0) |
fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]); |
|
if(j % ncovmodel == 0){ |
printf("\n"); |
printf("\n"); |
|
fprintf(ficlog,"\n"); |
|
} |
} |
} |
#endif |
#endif |
for (j=1;j<=n;j++) { |
for (j=1;j<=n;j++) { |
Line 1901 void powell(double p[], double **xi, int
|
Line 2020 void powell(double p[], double **xi, int
|
|
|
/**** Prevalence limit (stable or period prevalence) ****************/ |
/**** Prevalence limit (stable or period prevalence) ****************/ |
|
|
double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij) |
double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij) |
{ |
{ |
/* Computes the prevalence limit in each live state at age x by left multiplying the unit |
/* Computes the prevalence limit in each live state at age x by left multiplying the unit |
matrix by transitions matrix until convergence is reached */ |
matrix by transitions matrix until convergence is reached with precision ftolpl */ |
|
/* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */ |
|
/* Wx is row vector: population in state 1, population in state 2, population dead */ |
|
/* or prevalence in state 1, prevalence in state 2, 0 */ |
|
/* newm is the matrix after multiplications, its rows are identical at a factor */ |
|
/* Initial matrix pimij */ |
|
/* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */ |
|
/* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */ |
|
/* 0, 0 , 1} */ |
|
/* |
|
* and after some iteration: */ |
|
/* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */ |
|
/* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */ |
|
/* 0, 0 , 1} */ |
|
/* And prevalence by suppressing the deaths are close to identical rows in prlim: */ |
|
/* {0.51571254859325999, 0.4842874514067399, */ |
|
/* 0.51326036147820708, 0.48673963852179264} */ |
|
/* If we start from prlim again, prlim tends to a constant matrix */ |
|
|
int i, ii,j,k; |
int i, ii,j,k; |
double min, max, maxmin, maxmax,sumnew=0.; |
double *min, *max, *meandiff, maxmax,sumnew=0.; |
/* double **matprod2(); */ /* test */ |
/* double **matprod2(); */ /* test */ |
double **out, cov[NCOVMAX+1], **pmij(); |
double **out, cov[NCOVMAX+1], **pmij(); |
double **newm; |
double **newm; |
double agefin, delaymax=50 ; /* Max number of years to converge */ |
double agefin, delaymax=200. ; /* 100 Max number of years to converge */ |
|
int ncvloop=0; |
|
|
|
min=vector(1,nlstate); |
|
max=vector(1,nlstate); |
|
meandiff=vector(1,nlstate); |
|
|
for (ii=1;ii<=nlstate+ndeath;ii++) |
for (ii=1;ii<=nlstate+ndeath;ii++) |
for (j=1;j<=nlstate+ndeath;j++){ |
for (j=1;j<=nlstate+ndeath;j++){ |
oldm[ii][j]=(ii==j ? 1.0 : 0.0); |
oldm[ii][j]=(ii==j ? 1.0 : 0.0); |
Line 1921 double **prevalim(double **prlim, int nl
|
Line 2062 double **prevalim(double **prlim, int nl
|
cov[1]=1.; |
cov[1]=1.; |
|
|
/* Even if hstepm = 1, at least one multiplication by the unit matrix */ |
/* Even if hstepm = 1, at least one multiplication by the unit matrix */ |
|
/* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */ |
for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){ |
for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){ |
|
ncvloop++; |
newm=savm; |
newm=savm; |
/* Covariates have to be included here again */ |
/* Covariates have to be included here again */ |
cov[2]=agefin; |
cov[2]=agefin; |
Line 1948 double **prevalim(double **prlim, int nl
|
Line 2091 double **prevalim(double **prlim, int nl
|
|
|
savm=oldm; |
savm=oldm; |
oldm=newm; |
oldm=newm; |
maxmax=0.; |
|
for(j=1;j<=nlstate;j++){ |
for(j=1; j<=nlstate; j++){ |
min=1.; |
max[j]=0.; |
max=0.; |
min[j]=1.; |
for(i=1; i<=nlstate; i++) { |
} |
sumnew=0; |
for(i=1;i<=nlstate;i++){ |
for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k]; |
sumnew=0; |
|
for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k]; |
|
for(j=1; j<=nlstate; j++){ |
prlim[i][j]= newm[i][j]/(1-sumnew); |
prlim[i][j]= newm[i][j]/(1-sumnew); |
/*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/ |
max[j]=FMAX(max[j],prlim[i][j]); |
max=FMAX(max,prlim[i][j]); |
min[j]=FMIN(min[j],prlim[i][j]); |
min=FMIN(min,prlim[i][j]); |
|
} |
} |
maxmin=max-min; |
} |
maxmax=FMAX(maxmax,maxmin); |
|
|
maxmax=0.; |
|
for(j=1; j<=nlstate; j++){ |
|
meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */ |
|
maxmax=FMAX(maxmax,meandiff[j]); |
|
/* printf(" age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, j, meandiff[j],(int)agefin, j, max[j], j, min[j],maxmax); */ |
} /* j loop */ |
} /* j loop */ |
|
*ncvyear= (int)age- (int)agefin; |
|
/* printf("maxmax=%lf maxmin=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */ |
if(maxmax < ftolpl){ |
if(maxmax < ftolpl){ |
|
/* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */ |
|
free_vector(min,1,nlstate); |
|
free_vector(max,1,nlstate); |
|
free_vector(meandiff,1,nlstate); |
return prlim; |
return prlim; |
} |
} |
} /* age loop */ |
} /* age loop */ |
|
/* After some age loop it doesn't converge */ |
|
printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\ |
|
Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear); |
|
/* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */ |
|
free_vector(min,1,nlstate); |
|
free_vector(max,1,nlstate); |
|
free_vector(meandiff,1,nlstate); |
|
|
return prlim; /* should not reach here */ |
return prlim; /* should not reach here */ |
} |
} |
|
|
Line 2092 double ***hpxij(double ***po, int nhstep
|
Line 2255 double ***hpxij(double ***po, int nhstep
|
double **out, cov[NCOVMAX+1]; |
double **out, cov[NCOVMAX+1]; |
double **newm; |
double **newm; |
double agexact; |
double agexact; |
|
double agebegin, ageend; |
|
|
/* 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 2105 double ***hpxij(double ***po, int nhstep
|
Line 2269 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.; |
agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; |
agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */ |
cov[2]=agexact; |
cov[2]=agexact; |
if(nagesqr==1) |
if(nagesqr==1) |
cov[3]= agexact*agexact; |
cov[3]= agexact*agexact; |
Line 2476 double funcone( double *x)
|
Line 2640 double funcone( double *x)
|
int s1, s2; |
int s1, s2; |
double bbh, survp; |
double bbh, survp; |
double agexact; |
double agexact; |
|
double agebegin, ageend; |
/*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 2494 double funcone( double *x)
|
Line 2659 double funcone( double *x)
|
oldm[ii][j]=(ii==j ? 1.0 : 0.0); |
oldm[ii][j]=(ii==j ? 1.0 : 0.0); |
savm[ii][j]=(ii==j ? 1.0 : 0.0); |
savm[ii][j]=(ii==j ? 1.0 : 0.0); |
} |
} |
for(d=0; d<dh[mi][i]; d++){ |
|
|
agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */ |
|
ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */ |
|
for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */ |
|
/*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i] |
|
and mw[mi+1][i]. dh depends on stepm.*/ |
newm=savm; |
newm=savm; |
agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; |
agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; |
cov[2]=agexact; |
cov[2]=agexact; |
Line 2542 double funcone( double *x)
|
Line 2712 double funcone( double *x)
|
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; |
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; |
/*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */ |
/*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */ |
if(globpr){ |
if(globpr){ |
fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\ |
fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f %8.3f\ |
%11.6f %11.6f %11.6f ", \ |
%11.6f %11.6f %11.6f ", \ |
num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i], |
num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw, |
2*weight[i]*lli,out[s1][s2],savm[s1][s2]); |
2*weight[i]*lli,out[s1][s2],savm[s1][s2]); |
for(k=1,llt=0.,l=0.; k<=nlstate; k++){ |
for(k=1,llt=0.,l=0.; k<=nlstate; k++){ |
llt +=ll[k]*gipmx/gsw; |
llt +=ll[k]*gipmx/gsw; |
Line 2577 void likelione(FILE *ficres,double p[],
|
Line 2747 void likelione(FILE *ficres,double p[],
|
|
|
if(*globpri !=0){ /* Just counts and sums, no printings */ |
if(*globpri !=0){ /* Just counts and sums, no printings */ |
strcpy(fileresilk,"ILK_"); |
strcpy(fileresilk,"ILK_"); |
strcat(fileresilk,fileres); |
strcat(fileresilk,fileresu); |
if((ficresilk=fopen(fileresilk,"w"))==NULL) { |
if((ficresilk=fopen(fileresilk,"w"))==NULL) { |
printf("Problem with resultfile: %s\n", fileresilk); |
printf("Problem with resultfile: %s\n", fileresilk); |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk); |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk); |
} |
} |
fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n"); |
fprintf(ficresilk, "#individual(line's_record) count ageb ageend s1 s2 wave# effective_wave# number_of_matrices_product pij weight weight/gpw -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n"); |
fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav "); |
fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav "); |
/* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */ |
/* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */ |
for(k=1; k<=nlstate; k++) |
for(k=1; k<=nlstate; k++) |
fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k); |
fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k); |
Line 2593 void likelione(FILE *ficres,double p[],
|
Line 2763 void likelione(FILE *ficres,double p[],
|
*fretone=(*funcone)(p); |
*fretone=(*funcone)(p); |
if(*globpri !=0){ |
if(*globpri !=0){ |
fclose(ficresilk); |
fclose(ficresilk); |
fprintf(fichtm,"\n<br>File of contributions to the likelihood (if mle=1): <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk)); |
if (mle ==0) |
fflush(fichtm); |
fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle); |
} |
else if(mle >=1) |
|
fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle); |
|
fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk)); |
|
|
|
|
|
for (k=1; k<= nlstate ; k++) { |
|
fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Dot's sizes are related to corresponding weight: <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \ |
|
<img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k); |
|
} |
|
fprintf(fichtm,"<br>- The function drawn is -2Log(L) in Log scale: by state of origin <a href=\"%s-ori.png\">%s-ori.png</a><br> \ |
|
<img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_")); |
|
fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \ |
|
<img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_")); |
|
fflush(fichtm); |
|
} |
return; |
return; |
} |
} |
|
|
Line 2669 void mlikeli(FILE *ficres,double p[], in
|
Line 2853 void mlikeli(FILE *ficres,double p[], in
|
#endif |
#endif |
free_matrix(xi,1,npar,1,npar); |
free_matrix(xi,1,npar,1,npar); |
fclose(ficrespow); |
fclose(ficrespow); |
printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); |
printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); |
fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); |
fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); |
fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); |
fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); |
|
|
} |
} |
|
|
/**** Computes Hessian and covariance matrix ***/ |
/**** Computes Hessian and covariance matrix ***/ |
void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double [])) |
void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double [])) |
{ |
{ |
double **a,**y,*x,pd; |
double **a,**y,*x,pd; |
double **hess; |
/* double **hess; */ |
int i, j; |
int i, j; |
int *indx; |
int *indx; |
|
|
double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar); |
double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar); |
double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar); |
double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar); |
void lubksb(double **a, int npar, int *indx, double b[]) ; |
void lubksb(double **a, int npar, int *indx, double b[]) ; |
void ludcmp(double **a, int npar, int *indx, double *d) ; |
void ludcmp(double **a, int npar, int *indx, double *d) ; |
double gompertz(double p[]); |
double gompertz(double p[]); |
hess=matrix(1,npar,1,npar); |
/* hess=matrix(1,npar,1,npar); */ |
|
|
printf("\nCalculation of the hessian matrix. Wait...\n"); |
printf("\nCalculation of the hessian matrix. Wait...\n"); |
fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n"); |
fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n"); |
for (i=1;i<=npar;i++){ |
for (i=1;i<=npar;i++){ |
printf("%d",i);fflush(stdout); |
printf("%d-",i);fflush(stdout); |
fprintf(ficlog,"%d",i);fflush(ficlog); |
fprintf(ficlog,"%d-",i);fflush(ficlog); |
|
|
hess[i][i]=hessii(p,ftolhess,i,delti,func,npar); |
hess[i][i]=hessii(p,ftolhess,i,delti,func,npar); |
|
|
Line 2705 void hesscov(double **matcov, double p[]
|
Line 2889 void hesscov(double **matcov, double p[]
|
for (i=1;i<=npar;i++) { |
for (i=1;i<=npar;i++) { |
for (j=1;j<=npar;j++) { |
for (j=1;j<=npar;j++) { |
if (j>i) { |
if (j>i) { |
printf(".%d%d",i,j);fflush(stdout); |
printf(".%d-%d",i,j);fflush(stdout); |
fprintf(ficlog,".%d%d",i,j);fflush(ficlog); |
fprintf(ficlog,".%d-%d",i,j);fflush(ficlog); |
hess[i][j]=hessij(p,delti,i,j,func,npar); |
hess[i][j]=hessij(p,hess, delti,i,j,func,npar); |
|
|
hess[j][i]=hess[i][j]; |
hess[j][i]=hess[i][j]; |
/*printf(" %lf ",hess[i][j]);*/ |
/*printf(" %lf ",hess[i][j]);*/ |
Line 2741 void hesscov(double **matcov, double p[]
|
Line 2925 void hesscov(double **matcov, double p[]
|
fprintf(ficlog,"\n#Hessian matrix#\n"); |
fprintf(ficlog,"\n#Hessian matrix#\n"); |
for (i=1;i<=npar;i++) { |
for (i=1;i<=npar;i++) { |
for (j=1;j<=npar;j++) { |
for (j=1;j<=npar;j++) { |
printf("%.3e ",hess[i][j]); |
printf("%.6e ",hess[i][j]); |
fprintf(ficlog,"%.3e ",hess[i][j]); |
fprintf(ficlog,"%.6e ",hess[i][j]); |
} |
} |
printf("\n"); |
printf("\n"); |
fprintf(ficlog,"\n"); |
fprintf(ficlog,"\n"); |
} |
} |
|
|
|
/* printf("\n#Covariance matrix#\n"); */ |
|
/* fprintf(ficlog,"\n#Covariance matrix#\n"); */ |
|
/* for (i=1;i<=npar;i++) { */ |
|
/* for (j=1;j<=npar;j++) { */ |
|
/* printf("%.6e ",matcov[i][j]); */ |
|
/* fprintf(ficlog,"%.6e ",matcov[i][j]); */ |
|
/* } */ |
|
/* printf("\n"); */ |
|
/* fprintf(ficlog,"\n"); */ |
|
/* } */ |
|
|
/* Recompute Inverse */ |
/* Recompute Inverse */ |
for (i=1;i<=npar;i++) |
/* for (i=1;i<=npar;i++) */ |
for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; |
/* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */ |
ludcmp(a,npar,indx,&pd); |
/* ludcmp(a,npar,indx,&pd); */ |
|
|
|
/* printf("\n#Hessian matrix recomputed#\n"); */ |
|
|
|
/* for (j=1;j<=npar;j++) { */ |
|
/* for (i=1;i<=npar;i++) x[i]=0; */ |
|
/* x[j]=1; */ |
|
/* lubksb(a,npar,indx,x); */ |
|
/* for (i=1;i<=npar;i++){ */ |
|
/* y[i][j]=x[i]; */ |
|
/* printf("%.3e ",y[i][j]); */ |
|
/* fprintf(ficlog,"%.3e ",y[i][j]); */ |
|
/* } */ |
|
/* printf("\n"); */ |
|
/* fprintf(ficlog,"\n"); */ |
|
/* } */ |
|
|
/* printf("\n#Hessian matrix recomputed#\n"); |
/* Verifying the inverse matrix */ |
|
#ifdef DEBUGHESS |
|
y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov); |
|
|
|
printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n"); |
|
fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n"); |
|
|
for (j=1;j<=npar;j++) { |
for (j=1;j<=npar;j++) { |
for (i=1;i<=npar;i++) x[i]=0; |
|
x[j]=1; |
|
lubksb(a,npar,indx,x); |
|
for (i=1;i<=npar;i++){ |
for (i=1;i<=npar;i++){ |
y[i][j]=x[i]; |
printf("%.2f ",y[i][j]); |
printf("%.3e ",y[i][j]); |
fprintf(ficlog,"%.2f ",y[i][j]); |
fprintf(ficlog,"%.3e ",y[i][j]); |
|
} |
} |
printf("\n"); |
printf("\n"); |
fprintf(ficlog,"\n"); |
fprintf(ficlog,"\n"); |
} |
} |
*/ |
#endif |
|
|
free_matrix(a,1,npar,1,npar); |
free_matrix(a,1,npar,1,npar); |
free_matrix(y,1,npar,1,npar); |
free_matrix(y,1,npar,1,npar); |
free_vector(x,1,npar); |
free_vector(x,1,npar); |
free_ivector(indx,1,npar); |
free_ivector(indx,1,npar); |
free_matrix(hess,1,npar,1,npar); |
/* free_matrix(hess,1,npar,1,npar); */ |
|
|
|
|
} |
} |
|
|
/*************** hessian matrix ****************/ |
/*************** hessian matrix ****************/ |
double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar) |
double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar) |
{ |
{ /* Around values of x, computes the function func and returns the scales delti and hessian */ |
int i; |
int i; |
int l=1, lmax=20; |
int l=1, lmax=20; |
double k1,k2; |
double k1,k2, res, fx; |
double p2[MAXPARM+1]; /* identical to x */ |
double p2[MAXPARM+1]; /* identical to x */ |
double res; |
|
double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; |
double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; |
double fx; |
|
int k=0,kmax=10; |
int k=0,kmax=10; |
double l1; |
double l1; |
|
|
Line 2803 double hessii(double x[], double delta,
|
Line 3012 double hessii(double x[], double delta,
|
p2[theta]=x[theta]-delt; |
p2[theta]=x[theta]-delt; |
k2=func(p2)-fx; |
k2=func(p2)-fx; |
/*res= (k1-2.0*fx+k2)/delt/delt; */ |
/*res= (k1-2.0*fx+k2)/delt/delt; */ |
res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */ |
res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */ |
|
|
#ifdef DEBUGHESS |
#ifdef DEBUGHESSII |
printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx); |
printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx); |
fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx); |
fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx); |
#endif |
#endif |
Line 2819 double hessii(double x[], double delta,
|
Line 3028 double hessii(double x[], double delta,
|
else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ |
else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ |
delts=delt; |
delts=delt; |
} |
} |
} |
} /* End loop k */ |
} |
} |
delti[theta]=delts; |
delti[theta]=delts; |
return res; |
return res; |
|
|
} |
} |
|
|
double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) |
double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar) |
{ |
{ |
int i; |
int i; |
int l=1, lmax=20; |
int l=1, lmax=20; |
double k1,k2,k3,k4,res,fx; |
double k1,k2,k3,k4,res,fx; |
double p2[MAXPARM+1]; |
double p2[MAXPARM+1]; |
int k; |
int k, kmax=1; |
|
double v1, v2, cv12, lc1, lc2; |
|
|
|
int firstime=0; |
|
|
fx=func(x); |
fx=func(x); |
for (k=1; k<=2; k++) { |
for (k=1; k<=kmax; k=k+10) { |
for (i=1;i<=npar;i++) p2[i]=x[i]; |
for (i=1;i<=npar;i++) p2[i]=x[i]; |
p2[thetai]=x[thetai]+delti[thetai]/k; |
p2[thetai]=x[thetai]+delti[thetai]*k; |
p2[thetaj]=x[thetaj]+delti[thetaj]/k; |
p2[thetaj]=x[thetaj]+delti[thetaj]*k; |
k1=func(p2)-fx; |
k1=func(p2)-fx; |
|
|
p2[thetai]=x[thetai]+delti[thetai]/k; |
p2[thetai]=x[thetai]+delti[thetai]*k; |
p2[thetaj]=x[thetaj]-delti[thetaj]/k; |
p2[thetaj]=x[thetaj]-delti[thetaj]*k; |
k2=func(p2)-fx; |
k2=func(p2)-fx; |
|
|
p2[thetai]=x[thetai]-delti[thetai]/k; |
p2[thetai]=x[thetai]-delti[thetai]*k; |
p2[thetaj]=x[thetaj]+delti[thetaj]/k; |
p2[thetaj]=x[thetaj]+delti[thetaj]*k; |
k3=func(p2)-fx; |
k3=func(p2)-fx; |
|
|
p2[thetai]=x[thetai]-delti[thetai]/k; |
p2[thetai]=x[thetai]-delti[thetai]*k; |
p2[thetaj]=x[thetaj]-delti[thetaj]/k; |
p2[thetaj]=x[thetaj]-delti[thetaj]*k; |
k4=func(p2)-fx; |
k4=func(p2)-fx; |
res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */ |
res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */ |
#ifdef DEBUG |
if(k1*k2*k3*k4 <0.){ |
printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); |
firstime=1; |
fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); |
kmax=kmax+10; |
|
} |
|
if(kmax >=10 || firstime ==1){ |
|
printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol); |
|
fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol); |
|
printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); |
|
fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); |
|
} |
|
#ifdef DEBUGHESSIJ |
|
v1=hess[thetai][thetai]; |
|
v2=hess[thetaj][thetaj]; |
|
cv12=res; |
|
/* Computing eigen value of Hessian matrix */ |
|
lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; |
|
lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; |
|
if ((lc2 <0) || (lc1 <0) ){ |
|
printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj); |
|
fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj); |
|
printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); |
|
fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); |
|
} |
#endif |
#endif |
} |
} |
return res; |
return res; |
} |
} |
|
|
|
/* Not done yet: Was supposed to fix if not exactly at the maximum */ |
|
/* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */ |
|
/* { */ |
|
/* int i; */ |
|
/* int l=1, lmax=20; */ |
|
/* double k1,k2,k3,k4,res,fx; */ |
|
/* double p2[MAXPARM+1]; */ |
|
/* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */ |
|
/* int k=0,kmax=10; */ |
|
/* double l1; */ |
|
|
|
/* fx=func(x); */ |
|
/* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */ |
|
/* l1=pow(10,l); */ |
|
/* delts=delt; */ |
|
/* for(k=1 ; k <kmax; k=k+1){ */ |
|
/* delt = delti*(l1*k); */ |
|
/* for (i=1;i<=npar;i++) p2[i]=x[i]; */ |
|
/* p2[thetai]=x[thetai]+delti[thetai]/k; */ |
|
/* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */ |
|
/* k1=func(p2)-fx; */ |
|
|
|
/* p2[thetai]=x[thetai]+delti[thetai]/k; */ |
|
/* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */ |
|
/* k2=func(p2)-fx; */ |
|
|
|
/* p2[thetai]=x[thetai]-delti[thetai]/k; */ |
|
/* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */ |
|
/* k3=func(p2)-fx; */ |
|
|
|
/* p2[thetai]=x[thetai]-delti[thetai]/k; */ |
|
/* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */ |
|
/* k4=func(p2)-fx; */ |
|
/* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */ |
|
/* #ifdef DEBUGHESSIJ */ |
|
/* printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); */ |
|
/* fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); */ |
|
/* #endif */ |
|
/* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */ |
|
/* k=kmax; */ |
|
/* } */ |
|
/* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */ |
|
/* k=kmax; l=lmax*10; */ |
|
/* } */ |
|
/* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */ |
|
/* delts=delt; */ |
|
/* } */ |
|
/* } /\* End loop k *\/ */ |
|
/* } */ |
|
/* delti[theta]=delts; */ |
|
/* return res; */ |
|
/* } */ |
|
|
|
|
/************** Inverse of matrix **************/ |
/************** Inverse of matrix **************/ |
void ludcmp(double **a, int n, int *indx, double *d) |
void ludcmp(double **a, int n, int *indx, double *d) |
{ |
{ |
Line 2941 void pstamp(FILE *fichier)
|
Line 3227 void pstamp(FILE *fichier)
|
} |
} |
|
|
/************ Frequencies ********************/ |
/************ Frequencies ********************/ |
void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[]) |
void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \ |
|
int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[],\ |
|
int firstpass, int lastpass, int stepm, int weightopt, char model[]) |
{ /* Some frequencies */ |
{ /* Some frequencies */ |
|
|
int i, m, jk, j1, bool, z1,j; |
int i, m, jk, j1, bool, z1,j; |
|
int mi; /* Effective wave */ |
int first; |
int first; |
double ***freq; /* Frequencies */ |
double ***freq; /* Frequencies */ |
double *pp, **prop; |
double *pp, **prop; |
double pos,posprop, k2, dateintsum=0,k2cpt=0; |
double pos,posprop, k2, dateintsum=0,k2cpt=0; |
char fileresp[FILENAMELENGTH]; |
char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH]; |
|
double agebegin, ageend; |
|
|
pp=vector(1,nlstate); |
pp=vector(1,nlstate); |
prop=matrix(1,nlstate,iagemin,iagemax+3); |
prop=matrix(1,nlstate,iagemin,iagemax+3); |
strcpy(fileresp,"P_"); |
strcpy(fileresp,"P_"); |
strcat(fileresp,fileresu); |
strcat(fileresp,fileresu); |
|
/*strcat(fileresphtm,fileresu);*/ |
if((ficresp=fopen(fileresp,"w"))==NULL) { |
if((ficresp=fopen(fileresp,"w"))==NULL) { |
printf("Problem with prevalence resultfile: %s\n", fileresp); |
printf("Problem with prevalence resultfile: %s\n", fileresp); |
fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp); |
fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp); |
exit(0); |
exit(0); |
} |
} |
|
|
|
strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm")); |
|
if((ficresphtm=fopen(fileresphtm,"w"))==NULL) { |
|
printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno)); |
|
fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno)); |
|
fflush(ficlog); |
|
exit(70); |
|
} |
|
else{ |
|
fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \ |
|
<hr size=\"2\" color=\"#EC5E5E\"> \n\ |
|
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\ |
|
fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model); |
|
} |
|
fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition</h4>\n",fileresphtm, fileresphtm); |
|
|
|
strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm")); |
|
if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) { |
|
printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno)); |
|
fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno)); |
|
fflush(ficlog); |
|
exit(70); |
|
} |
|
else{ |
|
fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \ |
|
<hr size=\"2\" color=\"#EC5E5E\"> \n\ |
|
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\ |
|
fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model); |
|
} |
|
fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions by age at begin of transition </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr); |
|
|
freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3); |
freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3); |
j1=0; |
j1=0; |
|
|
Line 2968 void freqsummary(char fileres[], int ia
|
Line 3290 void freqsummary(char fileres[], int ia
|
|
|
first=1; |
first=1; |
|
|
/* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */ |
for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ /* Loop on covariates combination */ |
/* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */ |
|
/* j1++; */ |
|
for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ |
|
/*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]); |
/*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]); |
scanf("%d", i);*/ |
scanf("%d", i);*/ |
for (i=-5; i<=nlstate+ndeath; i++) |
for (i=-5; i<=nlstate+ndeath; i++) |
Line 2985 void freqsummary(char fileres[], int ia
|
Line 3304 void freqsummary(char fileres[], int ia
|
|
|
dateintsum=0; |
dateintsum=0; |
k2cpt=0; |
k2cpt=0; |
for (i=1; i<=imx; i++) { |
for (i=1; i<=imx; i++) { /* For each individual i */ |
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]][codtabm(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 */ |
Line 2997 void freqsummary(char fileres[], int ia
|
Line 3316 void freqsummary(char fileres[], int ia
|
j1,z1,nbcode[Tvaraff[z1]][codtabm(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 codtabm(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*/ |
} |
} |
} |
} /* cptcovn > 0 */ |
|
|
if (bool==1){ |
if (bool==1){ |
for(m=firstpass; m<=lastpass; m++){ |
/* for(m=firstpass; m<=lastpass; m++){ */ |
k2=anint[m][i]+(mint[m][i]/12.); |
for(mi=1; mi<wav[i];mi++){ |
/*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/ |
m=mw[mi][i]; |
if(agev[m][i]==0) agev[m][i]=iagemax+1; |
/* dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective (mi) waves m=mw[mi][i] |
if(agev[m][i]==1) agev[m][i]=iagemax+2; |
and mw[mi+1][i]. dh depends on stepm. */ |
if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i]; |
agebegin=agev[m][i]; /* Age at beginning of wave before transition*/ |
|
ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /* Age at end of wave and transition */ |
|
if(m >=firstpass && m <=lastpass){ |
|
k2=anint[m][i]+(mint[m][i]/12.); |
|
/*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/ |
|
if(agev[m][i]==0) agev[m][i]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */ |
|
if(agev[m][i]==1) agev[m][i]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */ |
|
if (s[m][i]>0 && s[m][i]<=nlstate) /* If status at wave m is known and a live state */ |
|
prop[s[m][i]][(int)agev[m][i]] += weight[i]; /* At age of beginning of transition, where status is known */ |
if (m<lastpass) { |
if (m<lastpass) { |
freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; |
/* if(s[m][i]==4 && s[m+1][i]==4) */ |
freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i]; |
/* printf(" num=%ld m=%d, i=%d s1=%d s2=%d agev at m=%d\n", num[i], m, i,s[m][i],s[m+1][i], (int)agev[m][i]); */ |
|
if(s[m][i]==-1) |
|
printf(" num=%ld m=%d, i=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[i], m, i,s[m][i],s[m+1][i], (int)agev[m][i],agebegin, ageend, (int)((agebegin+ageend)/2.)); |
|
freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; /* At age of beginning of transition, where status is known */ |
|
/* freq[s[m][i]][s[m+1][i]][(int)((agebegin+ageend)/2.)] += weight[i]; */ |
|
freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */ |
} |
} |
|
} |
if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) { |
if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3)) && (anint[m][i]!=9999) && (mint[m][i]!=99)) { |
dateintsum=dateintsum+k2; |
dateintsum=dateintsum+k2; |
k2cpt++; |
k2cpt++; |
} |
/* printf("i=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",i, dateintsum/k2cpt, dateintsum,k2cpt, k2); */ |
/*}*/ |
} |
} |
/*}*/ |
} |
} /* end m */ |
} /* end i */ |
} /* end bool */ |
|
} /* end i = 1 to imx */ |
|
|
/* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/ |
/* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/ |
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]][codtabm(j1,z1)]); |
fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable "); |
fprintf(ficresp, "**********\n#"); |
fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable "); |
|
for (z1=1; z1<=cptcoveff; z1++){ |
|
fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); |
|
fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); |
|
fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); |
|
} |
|
fprintf(ficresp, "**********\n#"); |
|
fprintf(ficresphtm, "**********</h3>\n"); |
|
fprintf(ficresphtmfr, "**********</h3>\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]][codtabm(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++) |
fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">"); |
|
for(i=1; i<=nlstate;i++) { |
fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i); |
fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i); |
|
fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i); |
|
} |
fprintf(ficresp, "\n"); |
fprintf(ficresp, "\n"); |
|
fprintf(ficresphtm, "\n"); |
|
|
|
/* Header of frequency table by age */ |
|
fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">"); |
|
fprintf(ficresphtmfr,"<th>Age</th> "); |
|
for(jk=-1; jk <=nlstate+ndeath; jk++){ |
|
for(m=-1; m <=nlstate+ndeath; m++){ |
|
if(jk!=0 && m!=0) |
|
fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m); |
|
} |
|
} |
|
fprintf(ficresphtmfr, "\n"); |
|
|
|
/* For each age */ |
for(i=iagemin; i <= iagemax+3; i++){ |
for(i=iagemin; i <= iagemax+3; i++){ |
if(i==iagemax+3){ |
fprintf(ficresphtm,"<tr>"); |
|
if(i==iagemax+1){ |
|
fprintf(ficlog,"1"); |
|
fprintf(ficresphtmfr,"<tr><th>0</th> "); |
|
}else if(i==iagemax+2){ |
|
fprintf(ficlog,"0"); |
|
fprintf(ficresphtmfr,"<tr><th>Unknown</th> "); |
|
}else if(i==iagemax+3){ |
fprintf(ficlog,"Total"); |
fprintf(ficlog,"Total"); |
|
fprintf(ficresphtmfr,"<tr><th>Total</th> "); |
}else{ |
}else{ |
if(first==1){ |
if(first==1){ |
first=0; |
first=0; |
printf("See log file for details...\n"); |
printf("See log file for details...\n"); |
} |
} |
|
fprintf(ficresphtmfr,"<tr><th>%d</th> ",i); |
fprintf(ficlog,"Age %d", i); |
fprintf(ficlog,"Age %d", i); |
} |
} |
for(jk=1; jk <=nlstate ; jk++){ |
for(jk=1; jk <=nlstate ; jk++){ |
Line 3084 void freqsummary(char fileres[], int ia
|
Line 3450 void freqsummary(char fileres[], int ia
|
if( i <= iagemax){ |
if( i <= iagemax){ |
if(pos>=1.e-5){ |
if(pos>=1.e-5){ |
fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop); |
fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop); |
|
fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",i,prop[jk][i]/posprop, prop[jk][i],posprop); |
/*probs[i][jk][j1]= pp[jk]/pos;*/ |
/*probs[i][jk][j1]= pp[jk]/pos;*/ |
/*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/ |
/*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/ |
} |
} |
else |
else{ |
fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop); |
fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop); |
|
fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",i, prop[jk][i],posprop); |
|
} |
} |
} |
} |
} |
|
|
for(jk=-1; jk <=nlstate+ndeath; jk++) |
for(jk=-1; jk <=nlstate+ndeath; jk++){ |
for(m=-1; m <=nlstate+ndeath; m++) |
for(m=-1; m <=nlstate+ndeath; m++){ |
if(freq[jk][m][i] !=0 ) { |
if(freq[jk][m][i] !=0 ) { /* minimizing output */ |
if(first==1) |
if(first==1){ |
printf(" %d%d=%.0f",jk,m,freq[jk][m][i]); |
printf(" %d%d=%.0f",jk,m,freq[jk][m][i]); |
|
} |
fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]); |
fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]); |
} |
} |
if(i <= iagemax) |
if(jk!=0 && m!=0) |
|
fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][i]); |
|
} |
|
} |
|
fprintf(ficresphtmfr,"</tr>\n "); |
|
if(i <= iagemax){ |
fprintf(ficresp,"\n"); |
fprintf(ficresp,"\n"); |
|
fprintf(ficresphtm,"</tr>\n"); |
|
} |
if(first==1) |
if(first==1) |
printf("Others in log...\n"); |
printf("Others in log...\n"); |
fprintf(ficlog,"\n"); |
fprintf(ficlog,"\n"); |
} |
} /* end loop i */ |
|
fprintf(ficresphtm,"</table>\n"); |
|
fprintf(ficresphtmfr,"</table>\n"); |
/*}*/ |
/*}*/ |
} |
} /* end j1 */ |
dateintmean=dateintsum/k2cpt; |
dateintmean=dateintsum/k2cpt; |
|
|
fclose(ficresp); |
fclose(ficresp); |
|
fclose(ficresphtm); |
|
fclose(ficresphtmfr); |
free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3); |
free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3); |
free_vector(pp,1,nlstate); |
free_vector(pp,1,nlstate); |
free_matrix(prop,1,nlstate,iagemin, iagemax+3); |
free_matrix(prop,1,nlstate,iagemin, iagemax+3); |
Line 3125 void prevalence(double ***probs, double
|
Line 3506 void prevalence(double ***probs, double
|
*/ |
*/ |
|
|
int i, m, jk, j1, bool, z1,j; |
int i, m, jk, j1, bool, z1,j; |
|
int mi; /* Effective wave */ |
|
int iage; |
|
double agebegin, ageend; |
|
|
double **prop; |
double **prop; |
double posprop; |
double posprop; |
Line 3144 void prevalence(double ***probs, double
|
Line 3528 void prevalence(double ***probs, double
|
|
|
first=1; |
first=1; |
for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ |
for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ |
/*for(i1=1; i1<=ncodemax[k1];i1++){ |
for (i=1; i<=nlstate; i++) |
j1++;*/ |
for(iage=iagemin; iage <= iagemax+3; iage++) |
|
prop[i][iage]=0.0; |
for (i=1; i<=nlstate; i++) |
|
for(m=iagemin; m <= iagemax+3; m++) |
for (i=1; i<=imx; i++) { /* Each individual */ |
prop[i][m]=0.0; |
bool=1; |
|
if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */ |
for (i=1; i<=imx; i++) { /* Each individual */ |
for (z1=1; z1<=cptcoveff; z1++) |
bool=1; |
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) |
if (cptcovn>0) { |
bool=0; |
for (z1=1; z1<=cptcoveff; z1++) |
} |
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) |
if (bool==1) { |
bool=0; |
/* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */ |
} |
for(mi=1; mi<wav[i];mi++){ |
if (bool==1) { |
m=mw[mi][i]; |
for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/ |
agebegin=agev[m][i]; /* Age at beginning of wave before transition*/ |
|
/* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */ |
|
if(m >=firstpass && m <=lastpass){ |
y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */ |
y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */ |
if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */ |
if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */ |
if(agev[m][i]==0) agev[m][i]=iagemax+1; |
if(agev[m][i]==0) agev[m][i]=iagemax+1; |
if(agev[m][i]==1) agev[m][i]=iagemax+2; |
if(agev[m][i]==1) agev[m][i]=iagemax+2; |
if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); |
if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); |
if (s[m][i]>0 && s[m][i]<=nlstate) { |
if (s[m][i]>0 && s[m][i]<=nlstate) { |
/*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/ |
/*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/ |
prop[s[m][i]][(int)agev[m][i]] += weight[i]; |
prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */ |
prop[s[m][i]][iagemax+3] += weight[i]; |
prop[s[m][i]][iagemax+3] += weight[i]; |
} |
} /* end valid statuses */ |
} |
} /* end selection of dates */ |
} /* end selection of waves */ |
} /* end selection of waves */ |
} |
} /* end effective waves */ |
} |
} /* end bool */ |
for(i=iagemin; i <= iagemax+3; i++){ |
} |
for(jk=1,posprop=0; jk <=nlstate ; jk++) { |
for(i=iagemin; i <= iagemax+3; i++){ |
posprop += prop[jk][i]; |
for(jk=1,posprop=0; jk <=nlstate ; jk++) { |
} |
posprop += prop[jk][i]; |
|
} |
for(jk=1; jk <=nlstate ; jk++){ |
|
if( i <= iagemax){ |
for(jk=1; jk <=nlstate ; jk++){ |
if(posprop>=1.e-5){ |
if( i <= iagemax){ |
probs[i][jk][j1]= prop[jk][i]/posprop; |
if(posprop>=1.e-5){ |
} else{ |
probs[i][jk][j1]= prop[jk][i]/posprop; |
if(first==1){ |
} else{ |
first=0; |
if(first==1){ |
printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]); |
first=0; |
} |
printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]); |
} |
} |
} |
} |
}/* end jk */ |
} |
}/* end i */ |
}/* end jk */ |
|
}/* end i */ |
/*} *//* end i1 */ |
/*} *//* end i1 */ |
} /* end j1 */ |
} /* end j1 */ |
|
|
Line 3214 void concatwav(int wav[], int **dh, int
|
Line 3601 void concatwav(int wav[], int **dh, int
|
int i, mi, m; |
int i, mi, m; |
/* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1; |
/* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1; |
double sum=0., jmean=0.;*/ |
double sum=0., jmean=0.;*/ |
int first; |
int first, firstwo; |
int j, k=0,jk, ju, jl; |
int j, k=0,jk, ju, jl; |
double sum=0.; |
double sum=0.; |
first=0; |
first=0; |
|
firstwo=0; |
jmin=100000; |
jmin=100000; |
jmax=-1; |
jmax=-1; |
jmean=0.; |
jmean=0.; |
for(i=1; i<=imx; i++){ |
for(i=1; i<=imx; i++){ /* For simple cases and if state is death */ |
mi=0; |
mi=0; |
m=firstpass; |
m=firstpass; |
while(s[m][i] <= nlstate){ |
while(s[m][i] <= nlstate){ /* a live state */ |
if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5) |
if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5) |
mw[++mi][i]=m; |
mw[++mi][i]=m; |
if(m >=lastpass) |
if(m >=lastpass) |
Line 3232 void concatwav(int wav[], int **dh, int
|
Line 3620 void concatwav(int wav[], int **dh, int
|
else |
else |
m++; |
m++; |
}/* end while */ |
}/* end while */ |
if (s[m][i] > nlstate){ |
if (s[m][i] > nlstate){ /* In a death state */ |
mi++; /* Death is another wave */ |
mi++; /* Death is another wave */ |
/* if(mi==0) never been interviewed correctly before death */ |
/* if(mi==0) never been interviewed correctly before death */ |
/* Only death is a correct wave */ |
/* Only death is a correct wave */ |
mw[mi][i]=m; |
mw[mi][i]=m; |
|
}else if (andc[i] != 9999) { /* A death occured after lastpass */ |
|
m++; |
|
mi++; |
|
s[m][i]=nlstate+1; /* We are setting the status to the last of non live state */ |
|
mw[mi][i]=m; |
|
nbwarn++; |
|
if(firstwo==0){ |
|
printf("Warning! Death for individual %ld line=%d occurred after last wave %d. Since 0.98r4 we considered a status %d at wave %d\nOthers in log file only\n",num[i],i,lastpass,nlstate+1, m); |
|
fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred after last wave %d. Since 0.98r4 we considered a status %d at wave %d\n",num[i],i,lastpass,nlstate+1, m); |
|
firstwo=1; |
|
} |
|
if(firstwo==1){ |
|
fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred after last wave %d. Since 0.98r4 we considered a status %d at wave %d\n",num[i],i,lastpass,nlstate+1, m); |
|
} |
} |
} |
|
|
wav[i]=mi; |
wav[i]=mi; |
if(mi==0){ |
if(mi==0){ |
nbwarn++; |
nbwarn++; |
Line 3251 void concatwav(int wav[], int **dh, int
|
Line 3652 void concatwav(int wav[], int **dh, int
|
} |
} |
} /* end mi==0 */ |
} /* end mi==0 */ |
} /* End individuals */ |
} /* End individuals */ |
|
/* wav and mw are no more changed */ |
|
|
|
|
for(i=1; i<=imx; i++){ |
for(i=1; i<=imx; i++){ |
for(mi=1; mi<wav[i];mi++){ |
for(mi=1; mi<wav[i];mi++){ |
if (stepm <=0) |
if (stepm <=0) |
Line 3793 void cvevsij(double ***eij, double x[],
|
Line 4196 void cvevsij(double ***eij, double x[],
|
} |
} |
|
|
/************ Variance ******************/ |
/************ Variance ******************/ |
void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[]) |
void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[]) |
{ |
{ |
/* Variance of health expectancies */ |
/* Variance of health expectancies */ |
/* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/ |
/* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/ |
Line 3841 void varevsij(char optionfilefiname[], d
|
Line 4244 void varevsij(char optionfilefiname[], d
|
/*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/ |
/*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/ |
strcat(fileresprobmorprev,digit); /* Tvar to be done */ |
strcat(fileresprobmorprev,digit); /* Tvar to be done */ |
strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */ |
strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */ |
strcat(fileresprobmorprev,fileres); |
strcat(fileresprobmorprev,fileresu); |
if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) { |
if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) { |
printf("Problem with resultfile: %s\n", fileresprobmorprev); |
printf("Problem with resultfile: %s\n", fileresprobmorprev); |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev); |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev); |
} |
} |
printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); |
printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); |
|
|
fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); |
fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); |
pstamp(ficresprobmorprev); |
pstamp(ficresprobmorprev); |
fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm); |
fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm); |
Line 3858 void varevsij(char optionfilefiname[], d
|
Line 4260 void varevsij(char optionfilefiname[], d
|
fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j); |
fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j); |
} |
} |
fprintf(ficresprobmorprev,"\n"); |
fprintf(ficresprobmorprev,"\n"); |
|
|
fprintf(ficgp,"\n# Routine varevsij"); |
fprintf(ficgp,"\n# Routine varevsij"); |
fprintf(ficgp,"\nunset title \n"); |
fprintf(ficgp,"\nunset title \n"); |
/* fprintf(fichtm, "#Local time at start: %s", strstart);*/ |
/* fprintf(fichtm, "#Local time at start: %s", strstart);*/ |
Line 3895 void varevsij(char optionfilefiname[], d
|
Line 4298 void varevsij(char optionfilefiname[], d
|
/* For example we decided to compute the life expectancy with the smallest unit */ |
/* For example we decided to compute the life expectancy with the smallest unit */ |
/* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. |
/* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. |
nhstepm is the number of hstepm from age to agelim |
nhstepm is the number of hstepm from age to agelim |
nstepm is the number of stepm from age to agelin. |
nstepm is the number of stepm from age to agelim. |
Look at function hpijx to understand why (it is linked to memory size questions) */ |
Look at function hpijx to understand why because of memory size limitations, |
/* We decided (b) to get a life expectancy respecting the most precise curvature of the |
we decided (b) to get a life expectancy respecting the most precise curvature of the |
survival function given by stepm (the optimization length). Unfortunately it |
survival function given by stepm (the optimization length). Unfortunately it |
means that if the survival funtion is printed every two years of age and if |
means that if the survival funtion is printed every two years of age and if |
you sum them up and add 1 year (area under the trapezoids) you won't get the same |
you sum them up and add 1 year (area under the trapezoids) you won't get the same |
Line 3918 void varevsij(char optionfilefiname[], d
|
Line 4321 void varevsij(char optionfilefiname[], d
|
for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/ |
for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/ |
xp[i] = x[i] + (i==theta ?delti[theta]:0); |
xp[i] = x[i] + (i==theta ?delti[theta]:0); |
} |
} |
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); |
|
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij); |
|
|
if (popbased==1) { |
if (popbased==1) { |
if(mobilav ==0){ |
if(mobilav ==0){ |
Line 3931 void varevsij(char optionfilefiname[], d
|
Line 4334 void varevsij(char optionfilefiname[], d
|
} |
} |
} |
} |
|
|
|
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); /* Returns p3mat[i][j][h] for h=1 to nhstepm */ |
for(j=1; j<= nlstate; j++){ |
for(j=1; j<= nlstate; j++){ |
for(h=0; h<=nhstepm; h++){ |
for(h=0; h<=nhstepm; h++){ |
for(i=1, gp[h][j]=0.;i<=nlstate;i++) |
for(i=1, gp[h][j]=0.;i<=nlstate;i++) |
gp[h][j] += prlim[i][i]*p3mat[i][j][h]; |
gp[h][j] += prlim[i][i]*p3mat[i][j][h]; |
} |
} |
} |
} |
/* This for computing probability of death (h=1 means |
/* Next for computing probability of death (h=1 means |
computed over hstepm matrices product = hstepm*stepm months) |
computed over hstepm matrices product = hstepm*stepm months) |
as a weighted average of prlim. |
as a weighted average of prlim. |
*/ |
*/ |
Line 3949 void varevsij(char optionfilefiname[], d
|
Line 4353 void varevsij(char optionfilefiname[], d
|
|
|
for(i=1; i<=npar; i++) /* Computes gradient x - delta */ |
for(i=1; i<=npar; i++) /* Computes gradient x - delta */ |
xp[i] = x[i] - (i==theta ?delti[theta]:0); |
xp[i] = x[i] - (i==theta ?delti[theta]:0); |
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); |
|
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij); |
|
|
if (popbased==1) { |
if (popbased==1) { |
if(mobilav ==0){ |
if(mobilav ==0){ |
Line 3962 void varevsij(char optionfilefiname[], d
|
Line 4366 void varevsij(char optionfilefiname[], d
|
} |
} |
} |
} |
|
|
|
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); |
|
|
for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */ |
for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */ |
for(h=0; h<=nhstepm; h++){ |
for(h=0; h<=nhstepm; h++){ |
for(i=1, gm[h][j]=0.;i<=nlstate;i++) |
for(i=1, gm[h][j]=0.;i<=nlstate;i++) |
Line 4024 void varevsij(char optionfilefiname[], d
|
Line 4430 void varevsij(char optionfilefiname[], d
|
varppt[j][i]=doldmp[j][i]; |
varppt[j][i]=doldmp[j][i]; |
/* end ppptj */ |
/* end ppptj */ |
/* x centered again */ |
/* x centered again */ |
hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij); |
|
prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij); |
prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij); |
|
|
if (popbased==1) { |
if (popbased==1) { |
if(mobilav ==0){ |
if(mobilav ==0){ |
Line 4041 void varevsij(char optionfilefiname[], d
|
Line 4447 void varevsij(char optionfilefiname[], d
|
computed over hstepm (estepm) matrices product = hstepm*stepm months) |
computed over hstepm (estepm) matrices product = hstepm*stepm months) |
as a weighted average of prlim. |
as a weighted average of prlim. |
*/ |
*/ |
|
hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij); |
for(j=nlstate+1;j<=nlstate+ndeath;j++){ |
for(j=nlstate+1;j<=nlstate+ndeath;j++){ |
for(i=1,gmp[j]=0.;i<= nlstate; i++) |
for(i=1,gmp[j]=0.;i<= nlstate; i++) |
gmp[j] += prlim[i][i]*p3mat[i][j][1]; |
gmp[j] += prlim[i][i]*p3mat[i][j][1]; |
Line 4103 void varevsij(char optionfilefiname[], d
|
Line 4510 void varevsij(char optionfilefiname[], d
|
} /* end varevsij */ |
} /* end varevsij */ |
|
|
/************ Variance of prevlim ******************/ |
/************ Variance of prevlim ******************/ |
void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[]) |
void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, char strstart[]) |
{ |
{ |
/* Variance of prevalence limit */ |
/* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/ |
/* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/ |
/* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/ |
|
|
double **dnewm,**doldm; |
double **dnewm,**doldm; |
Line 4113 void varprevlim(char fileres[], double *
|
Line 4520 void varprevlim(char fileres[], double *
|
double *xp; |
double *xp; |
double *gp, *gm; |
double *gp, *gm; |
double **gradg, **trgradg; |
double **gradg, **trgradg; |
|
double **mgm, **mgp; |
double age,agelim; |
double age,agelim; |
int theta; |
int theta; |
|
|
Line 4135 void varprevlim(char fileres[], double *
|
Line 4543 void varprevlim(char fileres[], double *
|
if (stepm >= YEARM) hstepm=1; |
if (stepm >= YEARM) hstepm=1; |
nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */ |
nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */ |
gradg=matrix(1,npar,1,nlstate); |
gradg=matrix(1,npar,1,nlstate); |
|
mgp=matrix(1,npar,1,nlstate); |
|
mgm=matrix(1,npar,1,nlstate); |
gp=vector(1,nlstate); |
gp=vector(1,nlstate); |
gm=vector(1,nlstate); |
gm=vector(1,nlstate); |
|
|
Line 4142 void varprevlim(char fileres[], double *
|
Line 4552 void varprevlim(char fileres[], double *
|
for(i=1; i<=npar; i++){ /* Computes gradient */ |
for(i=1; i<=npar; i++){ /* Computes gradient */ |
xp[i] = x[i] + (i==theta ?delti[theta]:0); |
xp[i] = x[i] + (i==theta ?delti[theta]:0); |
} |
} |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); |
if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) |
for(i=1;i<=nlstate;i++) |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij); |
|
else |
|
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij); |
|
for(i=1;i<=nlstate;i++){ |
gp[i] = prlim[i][i]; |
gp[i] = prlim[i][i]; |
|
mgp[theta][i] = prlim[i][i]; |
|
} |
for(i=1; i<=npar; i++) /* Computes gradient */ |
for(i=1; i<=npar; i++) /* Computes gradient */ |
xp[i] = x[i] - (i==theta ?delti[theta]:0); |
xp[i] = x[i] - (i==theta ?delti[theta]:0); |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); |
if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) |
for(i=1;i<=nlstate;i++) |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij); |
|
else |
|
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij); |
|
for(i=1;i<=nlstate;i++){ |
gm[i] = prlim[i][i]; |
gm[i] = prlim[i][i]; |
|
mgm[theta][i] = prlim[i][i]; |
|
} |
for(i=1;i<=nlstate;i++) |
for(i=1;i<=nlstate;i++) |
gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta]; |
gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta]; |
|
/* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */ |
} /* End theta */ |
} /* End theta */ |
|
|
trgradg =matrix(1,nlstate,1,npar); |
trgradg =matrix(1,nlstate,1,npar); |
Line 4161 void varprevlim(char fileres[], double *
|
Line 4580 void varprevlim(char fileres[], double *
|
for(j=1; j<=nlstate;j++) |
for(j=1; j<=nlstate;j++) |
for(theta=1; theta <=npar; theta++) |
for(theta=1; theta <=npar; theta++) |
trgradg[j][theta]=gradg[theta][j]; |
trgradg[j][theta]=gradg[theta][j]; |
|
/* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */ |
|
/* printf("\nmgm mgp %d ",(int)age); */ |
|
/* for(j=1; j<=nlstate;j++){ */ |
|
/* printf(" %d ",j); */ |
|
/* for(theta=1; theta <=npar; theta++) */ |
|
/* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */ |
|
/* printf("\n "); */ |
|
/* } */ |
|
/* } */ |
|
/* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */ |
|
/* printf("\n gradg %d ",(int)age); */ |
|
/* for(j=1; j<=nlstate;j++){ */ |
|
/* printf("%d ",j); */ |
|
/* for(theta=1; theta <=npar; theta++) */ |
|
/* printf("%d %lf ",theta,gradg[theta][j]); */ |
|
/* printf("\n "); */ |
|
/* } */ |
|
/* } */ |
|
|
for(i=1;i<=nlstate;i++) |
for(i=1;i<=nlstate;i++) |
varpl[i][(int)age] =0.; |
varpl[i][(int)age] =0.; |
|
if((int)age==79 ||(int)age== 80 ||(int)age== 81){ |
|
matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov); |
|
matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg); |
|
}else{ |
matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov); |
matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov); |
matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg); |
matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg); |
|
} |
for(i=1;i<=nlstate;i++) |
for(i=1;i<=nlstate;i++) |
varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */ |
varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */ |
|
|
Line 4175 void varprevlim(char fileres[], double *
|
Line 4617 void varprevlim(char fileres[], double *
|
fprintf(ficresvpl,"\n"); |
fprintf(ficresvpl,"\n"); |
free_vector(gp,1,nlstate); |
free_vector(gp,1,nlstate); |
free_vector(gm,1,nlstate); |
free_vector(gm,1,nlstate); |
|
free_matrix(mgm,1,npar,1,nlstate); |
|
free_matrix(mgp,1,npar,1,nlstate); |
free_matrix(gradg,1,npar,1,nlstate); |
free_matrix(gradg,1,npar,1,nlstate); |
free_matrix(trgradg,1,nlstate,1,npar); |
free_matrix(trgradg,1,nlstate,1,npar); |
} /* End age */ |
} /* End age */ |
Line 4213 void varprob(char optionfilefiname[], do
|
Line 4657 void varprob(char optionfilefiname[], do
|
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob); |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob); |
} |
} |
strcpy(fileresprobcov,"PROBCOV_"); |
strcpy(fileresprobcov,"PROBCOV_"); |
strcat(fileresprobcov,fileres); |
strcat(fileresprobcov,fileresu); |
if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) { |
if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) { |
printf("Problem with resultfile: %s\n", fileresprobcov); |
printf("Problem with resultfile: %s\n", fileresprobcov); |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov); |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov); |
} |
} |
strcpy(fileresprobcor,"PROBCOR_"); |
strcpy(fileresprobcor,"PROBCOR_"); |
strcat(fileresprobcor,fileres); |
strcat(fileresprobcor,fileresu); |
if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) { |
if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) { |
printf("Problem with resultfile: %s\n", fileresprobcor); |
printf("Problem with resultfile: %s\n", fileresprobcor); |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor); |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor); |
Line 4525 To be simple, these graphs help to under
|
Line 4969 To be simple, these graphs help to under
|
void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \ |
void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \ |
int lastpass, int stepm, int weightopt, char model[],\ |
int lastpass, int stepm, int weightopt, char model[],\ |
int imx,int jmin, int jmax, double jmeanint,char rfileres[],\ |
int imx,int jmin, int jmax, double jmeanint,char rfileres[],\ |
int popforecast, int estepm ,\ |
int popforecast, int prevfcast, int estepm , \ |
double jprev1, double mprev1,double anprev1, \ |
double jprev1, double mprev1,double anprev1, double dateprev1, \ |
double jprev2, double mprev2,double anprev2){ |
double jprev2, double mprev2,double anprev2, double dateprev2){ |
int jj1, k1, i1, cpt; |
int jj1, k1, i1, cpt; |
|
|
fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \ |
fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \ |
<li><a href='#secondorder'>Result files (second order (variance)</a>\n \ |
<li><a href='#secondorder'>Result files (second order (variance)</a>\n \ |
</ul>"); |
</ul>"); |
fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \ |
fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n"); |
- Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ", |
fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n", |
jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_")); |
jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm")); |
|
fprintf(fichtm,"<li> - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file) ", |
|
jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm")); |
|
fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_")); |
fprintf(fichtm,"\ |
fprintf(fichtm,"\ |
- Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ", |
- Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ", |
stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_")); |
stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_")); |
Line 4543 void printinghtml(char fileresu[], char
|
Line 4990 void printinghtml(char fileresu[], char
|
- Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n", |
- Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n", |
subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_")); |
subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_")); |
fprintf(fichtm,"\ |
fprintf(fichtm,"\ |
- (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \ |
- (a) Life expectancies by health status at initial age, e<sub>i.</sub> (b) health expectancies by health status at initial age, e<sub>ij</sub> . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \ |
<a href=\"%s\">%s</a> <br>\n", |
<a href=\"%s\">%s</a> <br>\n", |
estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_")); |
estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_")); |
fprintf(fichtm,"\ |
if(prevfcast==1){ |
- Population projections by age and states: \ |
fprintf(fichtm,"\ |
|
- Prevalence projections by age and states: \ |
<a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_")); |
<a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_")); |
|
} |
|
|
fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>"); |
fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>"); |
|
|
Line 4568 fprintf(fichtm," \n<ul><li><b>Graphs</b>
|
Line 5017 fprintf(fichtm," \n<ul><li><b>Graphs</b>
|
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">"); |
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">"); |
} |
} |
/* aij, bij */ |
/* aij, bij */ |
fprintf(fichtm,"<br>- Logit model, for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1.svg\">%s_%d-1.svg</a><br> \ |
fprintf(fichtm,"<br>- Logit model (yours is: 1+age+%s), for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1.svg\">%s_%d-1.svg</a><br> \ |
<img src=\"%s_%d-1.svg\">",subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1); |
<img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1); |
/* Pij */ |
/* Pij */ |
fprintf(fichtm,"<br>\n- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2.svg\">%s_%d-2.svg</a><br> \ |
fprintf(fichtm,"<br>\n- P<sub>ij</sub> or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2.svg\">%s_%d-2.svg</a><br> \ |
<img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1); |
<img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1); |
/* Quasi-incidences */ |
/* Quasi-incidences */ |
fprintf(fichtm,"<br>\n- Iij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\ |
fprintf(fichtm,"<br>\n- I<sub>ij</sub> or Conditional probabilities to be observed in state j being in state i %d (stepm) months\ |
before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too,\ |
before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too,\ |
incidence (rates) are the limit when h tends to zero of the ratio of the probability hPij \ |
incidence (rates) are the limit when h tends to zero of the ratio of the probability <sub>h</sub>P<sub>ij</sub> \ |
divided by h: hPij/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \ |
divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \ |
<img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1); |
<img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1); |
/* Survival functions (period) in state j */ |
/* Survival functions (period) in state j */ |
for(cpt=1; cpt<=nlstate;cpt++){ |
for(cpt=1; cpt<=nlstate;cpt++){ |
Line 4586 divided by h: hPij/h : <a href=\"%s_%d-3
|
Line 5035 divided by h: hPij/h : <a href=\"%s_%d-3
|
} |
} |
/* State specific survival functions (period) */ |
/* State specific survival functions (period) */ |
for(cpt=1; cpt<=nlstate;cpt++){ |
for(cpt=1; cpt<=nlstate;cpt++){ |
fprintf(fichtm,"<br>\n- Survival functions from state %d in any different live states and total.\ |
fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\ |
Or probability to survive in various states (1 to %d) being in state %d at different ages.\ |
Or probability to survive in various states (1 to %d) being in state %d at different ages.\ |
<a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> <img src=\"%s_%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1); |
<a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> <img src=\"%s_%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1); |
} |
} |
Line 4595 divided by h: hPij/h : <a href=\"%s_%d-3
|
Line 5044 divided by h: hPij/h : <a href=\"%s_%d-3
|
fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \ |
fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \ |
<img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1); |
<img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1); |
} |
} |
|
if(prevfcast==1){ |
|
/* Projection of prevalence up to period (stable) prevalence in each health state */ |
|
for(cpt=1; cpt<=nlstate;cpt++){ |
|
fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \ |
|
<img src=\"%s_%d-%d.svg\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1); |
|
} |
|
} |
|
|
for(cpt=1; cpt<=nlstate;cpt++) { |
for(cpt=1; cpt<=nlstate;cpt++) { |
fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s%d%d.svg\">%s%d%d.svg</a> <br> \ |
fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d%d.svg\">%s_%d%d.svg</a> <br> \ |
<img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1); |
<img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1); |
} |
} |
/* } /\* end i1 *\/ */ |
/* } /\* end i1 *\/ */ |
Line 4606 divided by h: hPij/h : <a href=\"%s_%d-3
|
Line 5063 divided by h: hPij/h : <a href=\"%s_%d-3
|
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> \ |
- 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> \ |
- 95%% confidence intervals and Wald tests of the estimated parameters are in the log file if optimization has been done (mle != 0).<br> \ |
But because parameters are usually highly correlated (a higher incidence of disability \ |
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 \ |
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 \ |
be very useful to look not only at linear confidence intervals estimated from the \ |
Line 4666 See page 'Matrix of variance-covariance
|
Line 5123 See page 'Matrix of variance-covariance
|
} |
} |
for(cpt=1; cpt<=nlstate;cpt++) { |
for(cpt=1; cpt<=nlstate;cpt++) { |
fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \ |
fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \ |
prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.svg <br>\ |
prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d%d.svg\"> %s_%d-%d.svg <br>\ |
<img src=\"%s_%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1); |
<img src=\"%s_%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1); |
} |
} |
fprintf(fichtm,"\n<br>- Total life expectancy by age and \ |
fprintf(fichtm,"\n<br>- Total life expectancy by age and \ |
health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \ |
health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \ |
true period expectancies (those weighted with period prevalences are also\ |
true period expectancies (those weighted with period prevalences are also\ |
drawn in addition to the population based expectancies computed using\ |
drawn in addition to the population based expectancies computed using\ |
observed and cahotic prevalences: %s_%d.svg<br>\ |
observed and cahotic prevalences: <a href=\"%s_%d.svg\">%s_%d.svg<br>\ |
<img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1); |
<img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1); |
/* } /\* end i1 *\/ */ |
/* } /\* end i1 *\/ */ |
}/* End k1 */ |
}/* End k1 */ |
fprintf(fichtm,"</ul>"); |
fprintf(fichtm,"</ul>"); |
Line 4682 true period expectancies (those weighted
|
Line 5139 true period expectancies (those weighted
|
} |
} |
|
|
/******************* Gnuplot file **************/ |
/******************* Gnuplot file **************/ |
void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){ |
void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, char pathc[], double p[]){ |
|
|
char dirfileres[132],optfileres[132]; |
char dirfileres[132],optfileres[132]; |
int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0; |
int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0; |
|
int lv=0, vlv=0, kl=0; |
int ng=0; |
int ng=0; |
int vpopbased; |
int vpopbased; |
/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */ |
/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */ |
Line 4698 void printinggnuplot(char fileresu[], ch
|
Line 5156 void printinggnuplot(char fileresu[], ch
|
/*#endif */ |
/*#endif */ |
m=pow(2,cptcoveff); |
m=pow(2,cptcoveff); |
|
|
|
/* Contribution to likelihood */ |
|
/* Plot the probability implied in the likelihood */ |
|
fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n"); |
|
fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";"); |
|
/* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */ |
|
fprintf(ficgp,"\nset ter pngcairo size 640, 480"); |
|
/* nice for mle=4 plot by number of matrix products. |
|
replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */ |
|
/* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */ |
|
/* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */ |
|
fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_")); |
|
fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$13):6 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk)); |
|
fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_")); |
|
fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$13):5 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk)); |
|
for (i=1; i<= nlstate ; i ++) { |
|
fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i); |
|
fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk)); |
|
fprintf(ficgp," u 2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1); |
|
for (j=2; j<= nlstate+ndeath ; j ++) { |
|
fprintf(ficgp,",\\\n \"\" u 2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j); |
|
} |
|
fprintf(ficgp,";\nset out; unset ylabel;\n"); |
|
} |
|
/* unset log; plot "rrtest1_sorted_4/ILK_rrtest1_sorted_4.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with points lc variable */ |
|
/* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */ |
|
/* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */ |
|
fprintf(ficgp,"\nset out;unset log\n"); |
|
/* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */ |
|
|
strcpy(dirfileres,optionfilefiname); |
strcpy(dirfileres,optionfilefiname); |
strcpy(optfileres,"vpl"); |
strcpy(optfileres,"vpl"); |
/* 1eme*/ |
/* 1eme*/ |
fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files\n"); |
for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */ |
for (cpt=1; cpt<= nlstate ; cpt ++) { |
for (k1=1; k1<= m ; k1 ++) { /* For each combination of covariate */ |
for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */ |
/* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */ |
|
fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files "); |
|
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */ |
|
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */ |
|
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ |
|
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ |
|
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ |
|
vlv= nbcode[Tvaraff[lv]][lv]; |
|
fprintf(ficgp," V%d=%d ",k,vlv); |
|
} |
|
fprintf(ficgp,"\n#\n"); |
|
|
fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1); |
fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1); |
fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1); |
fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1); |
fprintf(ficgp,"set xlabel \"Age\" \n\ |
fprintf(ficgp,"set xlabel \"Age\" \n\ |
Line 4730 plot [%.f:%.f] \"%s\" every :::%d::%d u
|
Line 5228 plot [%.f:%.f] \"%s\" every :::%d::%d u
|
} /* k1 */ |
} /* k1 */ |
} /* cpt */ |
} /* cpt */ |
/*2 eme*/ |
/*2 eme*/ |
fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n"); |
|
for (k1=1; k1<= m ; k1 ++) { |
for (k1=1; k1<= m ; k1 ++) { |
|
fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files "); |
|
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */ |
|
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */ |
|
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ |
|
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ |
|
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ |
|
vlv= nbcode[Tvaraff[lv]][lv]; |
|
fprintf(ficgp," V%d=%d ",k,vlv); |
|
} |
|
fprintf(ficgp,"\n#\n"); |
|
|
fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1); |
fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1); |
for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/ |
for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/ |
if(vpopbased==0) |
if(vpopbased==0) |
Line 4764 plot [%.f:%.f] \"%s\" every :::%d::%d u
|
Line 5272 plot [%.f:%.f] \"%s\" every :::%d::%d u
|
} /* vpopbased */ |
} /* vpopbased */ |
fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */ |
fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */ |
} /* k1 */ |
} /* k1 */ |
|
|
|
|
/*3eme*/ |
/*3eme*/ |
|
|
for (k1=1; k1<= m ; k1 ++) { |
for (k1=1; k1<= m ; k1 ++) { |
for (cpt=1; cpt<= nlstate ; cpt ++) { |
for (cpt=1; cpt<= nlstate ; cpt ++) { |
|
fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: cov=%d state=%d",k1, cpt); |
|
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */ |
|
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */ |
|
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ |
|
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ |
|
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ |
|
vlv= nbcode[Tvaraff[lv]][lv]; |
|
fprintf(ficgp," V%d=%d ",k,vlv); |
|
} |
|
fprintf(ficgp,"\n#\n"); |
|
|
/* k=2+nlstate*(2*cpt-2); */ |
/* k=2+nlstate*(2*cpt-2); */ |
k=2+(nlstate+1)*(cpt-1); |
k=2+(nlstate+1)*(cpt-1); |
fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1); |
fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1); |
Line 4793 plot [%.f:%.f] \"%s\" every :::%d::%d u
|
Line 5313 plot [%.f:%.f] \"%s\" every :::%d::%d u
|
/* Survival functions (period) from state i in state j by initial state i */ |
/* Survival functions (period) from state i in state j by initial state i */ |
for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */ |
for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */ |
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */ |
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */ |
k=3; |
fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt); |
fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'lij' files, cov=%d state=%d",k1, cpt); |
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */ |
|
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */ |
|
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ |
|
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ |
|
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ |
|
vlv= nbcode[Tvaraff[lv]][lv]; |
|
fprintf(ficgp," V%d=%d ",k,vlv); |
|
} |
|
fprintf(ficgp,"\n#\n"); |
|
|
fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1); |
fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1); |
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\ |
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\ |
set ter svg size 640, 480\n\ |
set ter svg size 640, 480\n\ |
unset log y\n\ |
unset log y\n\ |
plot [%.f:%.f] ", ageminpar, agemaxpar); |
plot [%.f:%.f] ", ageminpar, agemaxpar); |
|
k=3; |
for (i=1; i<= nlstate ; i ++){ |
for (i=1; i<= nlstate ; i ++){ |
if(i==1) |
if(i==1) |
fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_")); |
fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_")); |
Line 4816 plot [%.f:%.f] ", ageminpar, agemaxpar)
|
Line 5346 plot [%.f:%.f] ", ageminpar, agemaxpar)
|
} /* end covariate */ |
} /* end covariate */ |
|
|
/* Survival functions (period) from state i in state j by final state j */ |
/* Survival functions (period) from state i in state j by final state j */ |
for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */ |
for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */ |
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */ |
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */ |
k=3; |
|
fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt); |
fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt); |
|
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */ |
|
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */ |
|
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ |
|
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ |
|
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ |
|
vlv= nbcode[Tvaraff[lv]][lv]; |
|
fprintf(ficgp," V%d=%d ",k,vlv); |
|
} |
|
fprintf(ficgp,"\n#\n"); |
|
|
fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1); |
fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1); |
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\ |
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\ |
set ter svg size 640, 480\n\ |
set ter svg size 640, 480\n\ |
unset log y\n\ |
unset log y\n\ |
plot [%.f:%.f] ", ageminpar, agemaxpar); |
plot [%.f:%.f] ", ageminpar, agemaxpar); |
|
k=3; |
for (j=1; j<= nlstate ; j ++){ /* Lived in state j */ |
for (j=1; j<= nlstate ; j ++){ /* Lived in state j */ |
if(j==1) |
if(j==1) |
fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_")); |
fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_")); |
Line 4849 plot [%.f:%.f] ", ageminpar, agemaxpar)
|
Line 5389 plot [%.f:%.f] ", ageminpar, agemaxpar)
|
} /* end cpt state*/ |
} /* end cpt state*/ |
} /* end covariate */ |
} /* end covariate */ |
|
|
/* CV preval stable (period) */ |
/* CV preval stable (period) for each covariate */ |
for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */ |
for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */ |
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */ |
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */ |
k=3; |
fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt); |
fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt); |
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */ |
|
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */ |
|
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ |
|
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ |
|
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ |
|
vlv= nbcode[Tvaraff[lv]][lv]; |
|
fprintf(ficgp," V%d=%d ",k,vlv); |
|
} |
|
fprintf(ficgp,"\n#\n"); |
|
|
fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1); |
fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1); |
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\ |
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\ |
set ter svg size 640, 480\n\ |
set ter svg size 640, 480\n\ |
unset log y\n\ |
unset log y\n\ |
plot [%.f:%.f] ", ageminpar, agemaxpar); |
plot [%.f:%.f] ", ageminpar, agemaxpar); |
|
k=3; /* Offset */ |
for (i=1; i<= nlstate ; i ++){ |
for (i=1; i<= nlstate ; i ++){ |
if(i==1) |
if(i==1) |
fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_")); |
fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_")); |
Line 4874 plot [%.f:%.f] ", ageminpar, agemaxpar)
|
Line 5424 plot [%.f:%.f] ", ageminpar, agemaxpar)
|
} /* end cpt state*/ |
} /* end cpt state*/ |
} /* end covariate */ |
} /* end covariate */ |
|
|
|
if(prevfcast==1){ |
|
/* Projection from cross-sectional to stable (period) for each covariate */ |
|
|
|
for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */ |
|
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */ |
|
fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt); |
|
for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */ |
|
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */ |
|
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ |
|
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ |
|
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ |
|
vlv= nbcode[Tvaraff[lv]][lv]; |
|
fprintf(ficgp," V%d=%d ",k,vlv); |
|
} |
|
fprintf(ficgp,"\n#\n"); |
|
|
|
fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n "); |
|
fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1); |
|
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\ |
|
set ter svg size 640, 480\n\ |
|
unset log y\n\ |
|
plot [%.f:%.f] ", ageminpar, agemaxpar); |
|
for (i=1; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */ |
|
/*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/ |
|
/*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */ |
|
/*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/ |
|
/*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */ |
|
if(i==1){ |
|
fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_")); |
|
}else{ |
|
fprintf(ficgp,",\\\n '' "); |
|
} |
|
if(cptcoveff ==0){ /* No covariate */ |
|
fprintf(ficgp," u 2:("); /* Age is in 2 */ |
|
/*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/ |
|
/*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */ |
|
if(i==nlstate+1) |
|
fprintf(ficgp," $%d/(1.-$%d)) t 'p.%d' with line ", \ |
|
2+(cpt-1)*(nlstate+1)+1+(i-1), 2+1+(i-1)+(nlstate+1)*nlstate,cpt ); |
|
else |
|
fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \ |
|
2+(cpt-1)*(nlstate+1)+1+(i-1), 2+1+(i-1)+(nlstate+1)*nlstate,i,cpt ); |
|
}else{ |
|
fprintf(ficgp,"u 6:(("); /* Age is in 6 */ |
|
/*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/ |
|
/*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */ |
|
kl=0; |
|
for (k=1; k<=cptcoveff; k++){ /* For each covariate */ |
|
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */ |
|
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ |
|
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ |
|
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ |
|
vlv= nbcode[Tvaraff[lv]][lv]; |
|
kl++; |
|
/* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */ |
|
/*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */ |
|
/*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ |
|
/* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/ |
|
if(k==cptcoveff) |
|
if(i==nlstate+1) |
|
fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv], \ |
|
6+(cpt-1)*(nlstate+1)+1+(i-1), 6+1+(i-1)+(nlstate+1)*nlstate,cpt ); |
|
else |
|
fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv], \ |
|
6+(cpt-1)*(nlstate+1)+1+(i-1), 6+1+(i-1)+(nlstate+1)*nlstate,i,cpt ); |
|
else{ |
|
fprintf(ficgp,"$%d==%d && $%d==%d && ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv]); |
|
kl++; |
|
} |
|
} /* end covariate */ |
|
} /* end if covariate */ |
|
} /* nlstate */ |
|
fprintf(ficgp,"\nset out\n"); |
|
} /* end cpt state*/ |
|
} /* end covariate */ |
|
} /* End if prevfcast */ |
|
|
|
|
/* proba elementaires */ |
/* proba elementaires */ |
fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n"); |
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++){ |
Line 5065 void prevforecast(char fileres[], double
|
Line 5693 void prevforecast(char fileres[], double
|
char fileresf[FILENAMELENGTH]; |
char fileresf[FILENAMELENGTH]; |
|
|
agelim=AGESUP; |
agelim=AGESUP; |
|
/* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people |
|
in each health status at the date of interview (if between dateprev1 and dateprev2). |
|
We still use firstpass and lastpass as another selection. |
|
*/ |
|
/* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */ |
|
/* firstpass, lastpass, stepm, weightopt, model); */ |
prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); |
prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); |
|
|
strcpy(fileresf,"F_"); |
strcpy(fileresf,"F_"); |
Line 5073 void prevforecast(char fileres[], double
|
Line 5707 void prevforecast(char fileres[], double
|
printf("Problem with forecast resultfile: %s\n", fileresf); |
printf("Problem with forecast resultfile: %s\n", fileresf); |
fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf); |
fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf); |
} |
} |
printf("Computing forecasting: result on file '%s' \n", fileresf); |
printf("Computing forecasting: result on file '%s', please wait... \n", fileresf); |
fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf); |
fprintf(ficlog,"Computing forecasting: result on file '%s', please wait... \n", fileresf); |
|
|
if (cptcoveff==0) ncodemax[cptcoveff]=1; |
if (cptcoveff==0) ncodemax[cptcoveff]=1; |
|
|
Line 5115 void prevforecast(char fileres[], double
|
Line 5749 void prevforecast(char fileres[], double
|
for(cptcov=1, k=0;cptcov<=i1;cptcov++){ |
for(cptcov=1, k=0;cptcov<=i1;cptcov++){ |
for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ |
for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ |
k=k+1; |
k=k+1; |
fprintf(ficresf,"\n#******"); |
fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \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]][codtabm(k,j)]); |
fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); |
} |
} |
fprintf(ficresf,"******\n"); |
fprintf(ficresf," yearproj age"); |
fprintf(ficresf,"# Covariate valuofcovar yearproj age"); |
|
for(j=1; j<=nlstate+ndeath;j++){ |
for(j=1; j<=nlstate+ndeath;j++){ |
for(i=1; i<=nlstate;i++) |
for(i=1; i<=nlstate;i++) |
fprintf(ficresf," p%d%d",i,j); |
fprintf(ficresf," p%d%d",i,j); |
Line 5170 void prevforecast(char fileres[], double
|
Line 5803 void prevforecast(char fileres[], double
|
if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
|
|
fclose(ficresf); |
fclose(ficresf); |
|
printf("End of Computing forecasting \n"); |
|
fprintf(ficlog,"End of Computing forecasting\n"); |
|
|
} |
} |
|
|
/************** Forecasting *****not tested NB*************/ |
/************** Forecasting *****not tested NB*************/ |
Line 6009 int calandcheckages(int imx, int maxwav,
|
Line 6645 int calandcheckages(int imx, int maxwav,
|
for (i=1; i<=imx; i++) { |
for (i=1; i<=imx; i++) { |
agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]); |
agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]); |
for(m=firstpass; (m<= lastpass); m++){ |
for(m=firstpass; (m<= lastpass); m++){ |
if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){ |
if(s[m][i] >0 || s[m][i]==-1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){ /* What if s[m][i]=-1 */ |
if (s[m][i] >= nlstate+1) { |
if (s[m][i] >= nlstate+1) { |
if(agedc[i]>0){ |
if(agedc[i]>0){ |
if((int)moisdc[i]!=99 && (int)andc[i]!=9999){ |
if((int)moisdc[i]!=99 && (int)andc[i]!=9999){ |
agev[m][i]=agedc[i]; |
agev[m][i]=agedc[i]; |
/*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/ |
/*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/ |
}else { |
}else { |
if ((int)andc[i]!=9999){ |
if ((int)andc[i]!=9999){ |
nbwarn++; |
nbwarn++; |
Line 6024 int calandcheckages(int imx, int maxwav,
|
Line 6660 int calandcheckages(int imx, int maxwav,
|
} |
} |
} |
} |
} /* agedc > 0 */ |
} /* agedc > 0 */ |
} |
} /* end if */ |
else if(s[m][i] !=9){ /* Standard case, age in fractional |
else if(s[m][i] !=9){ /* Standard case, age in fractional |
years but with the precision of a month */ |
years but with the precision of a month */ |
agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]); |
agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]); |
Line 6040 int calandcheckages(int imx, int maxwav,
|
Line 6676 int calandcheckages(int imx, int maxwav,
|
} |
} |
/*agev[m][i]=anint[m][i]-annais[i];*/ |
/*agev[m][i]=anint[m][i]-annais[i];*/ |
/* agev[m][i] = age[i]+2*m;*/ |
/* agev[m][i] = age[i]+2*m;*/ |
} |
} /* en if 9*/ |
else { /* =9 */ |
else { /* =9 */ |
|
/* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */ |
agev[m][i]=1; |
agev[m][i]=1; |
s[m][i]=-1; |
s[m][i]=-1; |
} |
} |
} |
} |
else /*= 0 Unknown */ |
else if(s[m][i]==0) /*= 0 Unknown */ |
agev[m][i]=1; |
agev[m][i]=1; |
} |
else{ |
|
printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]); |
|
fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]); |
|
agev[m][i]=0; |
|
} |
|
} /* End for lastpass */ |
} |
} |
|
|
for (i=1; i<=imx; i++) { |
for (i=1; i<=imx; i++) { |
for(m=firstpass; (m<=lastpass); m++){ |
for(m=firstpass; (m<=lastpass); m++){ |
if (s[m][i] > (nlstate+ndeath)) { |
if (s[m][i] > (nlstate+ndeath)) { |
Line 6276 void syscompilerinfo(int logged)
|
Line 6918 void syscompilerinfo(int logged)
|
|
|
} |
} |
|
|
int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){ |
int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){ |
/*--------------- Prevalence limit (period or stable prevalence) --------------*/ |
/*--------------- Prevalence limit (period or stable prevalence) --------------*/ |
int i, j, k, i1 ; |
int i, j, k, i1 ; |
double ftolpl = 1.e-10; |
/* double ftolpl = 1.e-10; */ |
double age, agebase, agelim; |
double age, agebase, agelim; |
|
double tot; |
|
|
strcpy(filerespl,"PL_"); |
strcpy(filerespl,"PL_"); |
strcat(filerespl,fileresu); |
strcat(filerespl,fileresu); |
if((ficrespl=fopen(filerespl,"w"))==NULL) { |
if((ficrespl=fopen(filerespl,"w"))==NULL) { |
printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1; |
printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1; |
fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1; |
fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1; |
} |
} |
printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl); |
printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl); |
fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl); |
fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl); |
pstamp(ficrespl); |
pstamp(ficrespl); |
fprintf(ficrespl,"# Period (stable) prevalence \n"); |
fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl); |
fprintf(ficrespl,"#Age "); |
fprintf(ficrespl,"#Age "); |
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"); |
|
|
/* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */ |
/* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */ |
|
|
Line 6326 int prevalence_limit(double *p, double *
|
Line 6969 int prevalence_limit(double *p, double *
|
for(j=1;j<=cptcoveff;j++) { |
for(j=1;j<=cptcoveff;j++) { |
fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(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,"Total Years_to_converge\n"); |
|
|
for (age=agebase; age<=agelim; age++){ |
for (age=agebase; age<=agelim; age++){ |
/* for (age=agebase; age<=agebase; age++){ */ |
/* for (age=agebase; age<=agebase; age++){ */ |
prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); |
prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, 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]][codtabm(k,j)]); |
fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); |
for(i=1; i<=nlstate;i++) |
tot=0.; |
|
for(i=1; i<=nlstate;i++){ |
|
tot += prlim[i][i]; |
fprintf(ficrespl," %.5f", prlim[i][i]); |
fprintf(ficrespl," %.5f", prlim[i][i]); |
fprintf(ficrespl,"\n"); |
} |
|
fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp); |
} /* Age */ |
} /* Age */ |
/* was end of cptcod */ |
/* was end of cptcod */ |
} /* cptcov */ |
} /* cptcov */ |
Line 6430 int main(int argc, char *argv[])
|
Line 7076 int main(int argc, char *argv[])
|
#endif |
#endif |
int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav); |
int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav); |
int i,j, k, n=MAXN,iter=0,m,size=100, cptcod; |
int i,j, k, n=MAXN,iter=0,m,size=100, cptcod; |
|
int ncvyear=0; /* Number of years needed for the period prevalence to converge */ |
int jj, ll, li, lj, lk; |
int jj, ll, li, lj, lk; |
int numlinepar=0; /* Current linenumber of parameter file */ |
int numlinepar=0; /* Current linenumber of parameter file */ |
int num_filled; |
int num_filled; |
Line 6478 int main(int argc, char *argv[])
|
Line 7124 int main(int argc, char *argv[])
|
double ***param; /* Matrix of parameters */ |
double ***param; /* Matrix of parameters */ |
double *p; |
double *p; |
double **matcov; /* Matrix of covariance */ |
double **matcov; /* Matrix of covariance */ |
|
double **hess; /* Hessian matrix */ |
double ***delti3; /* Scale */ |
double ***delti3; /* Scale */ |
double *delti; /* Scale */ |
double *delti; /* Scale */ |
double ***eij, ***vareij; |
double ***eij, ***vareij; |
Line 6537 int main(int argc, char *argv[])
|
Line 7184 int main(int argc, char *argv[])
|
printf("\nIMaCh version %s, %s\n%s",version, copyright, 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); |
if(!fgets(pathr,FILENAMELENGTH,stdin)){ |
|
printf("ERROR Empty parameter file name\n"); |
|
goto end; |
|
} |
i=strlen(pathr); |
i=strlen(pathr); |
if(pathr[i-1]=='\n') |
if(pathr[i-1]=='\n') |
pathr[i-1]='\0'; |
pathr[i-1]='\0'; |
i=strlen(pathr); |
i=strlen(pathr); |
if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */ |
if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */ |
pathr[i-1]='\0'; |
pathr[i-1]='\0'; |
for (tok = pathr; tok != NULL; ){ |
} |
|
i=strlen(pathr); |
|
if( i==0 ){ |
|
printf("ERROR Empty parameter file name\n"); |
|
goto end; |
|
} |
|
for (tok = pathr; tok != NULL; ){ |
printf("Pathr |%s|\n",pathr); |
printf("Pathr |%s|\n",pathr); |
while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0'); |
while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0'); |
printf("val= |%s| pathr=%s\n",val,pathr); |
printf("val= |%s| pathr=%s\n",val,pathr); |
Line 6680 int main(int argc, char *argv[])
|
Line 7336 int main(int argc, char *argv[])
|
if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \ |
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){ |
&ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){ |
if (num_filled != 8) { |
if (num_filled != 8) { |
printf("Not 8\n"); |
printf("Not 8 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n"); |
|
printf("but line=%s\n",line); |
} |
} |
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); |
printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt); |
} |
} |
|
/* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */ |
|
/*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */ |
/* Third parameter line */ |
/* Third parameter line */ |
while(fgets(line, MAXLINE, ficpar)) { |
while(fgets(line, MAXLINE, ficpar)) { |
/* If line starts with a # it is a comment */ |
/* If line starts with a # it is a comment */ |
Line 6714 int main(int argc, char *argv[])
|
Line 7372 int main(int argc, char *argv[])
|
} |
} |
} |
} |
/* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */ |
/* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */ |
|
printf("model=1+age+%s\n",model);fflush(stdout); |
} |
} |
/* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */ |
/* 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 *\/ */ |
/* 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); */ |
/* 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 */ |
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); |
model[strlen(model)-1]='\0'; |
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(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]=='#'|| model[0]== '\0'){ */ |
if(model[0]=='#'){ |
if(model[0]=='#'){ |
Line 6786 int main(int argc, char *argv[])
|
Line 7443 int main(int argc, char *argv[])
|
fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso); |
fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso); |
param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); |
param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); |
matcov=matrix(1,npar,1,npar); |
matcov=matrix(1,npar,1,npar); |
|
hess=matrix(1,npar,1,npar); |
} |
} |
else{ |
else{ |
/* Read guessed parameters */ |
/* Read guessed parameters */ |
Line 6894 run imach with mle=-1 to get a correct t
|
Line 7552 run imach with mle=-1 to get a correct t
|
ungetc(c,ficpar); |
ungetc(c,ficpar); |
|
|
matcov=matrix(1,npar,1,npar); |
matcov=matrix(1,npar,1,npar); |
|
hess=matrix(1,npar,1,npar); |
for(i=1; i <=npar; i++) |
for(i=1; i <=npar; i++) |
for(j=1; j <=npar; j++) matcov[i][j]=0.; |
for(j=1; j <=npar; j++) matcov[i][j]=0.; |
|
|
Line 7032 Please run with mle=-1 to get a correct
|
Line 7691 Please run with mle=-1 to get a correct
|
free_vector(annais,1,n); |
free_vector(annais,1,n); |
/* free_matrix(mint,1,maxwav,1,n); |
/* free_matrix(mint,1,maxwav,1,n); |
free_matrix(anint,1,maxwav,1,n);*/ |
free_matrix(anint,1,maxwav,1,n);*/ |
free_vector(moisdc,1,n); |
/* free_vector(moisdc,1,n); */ |
free_vector(andc,1,n); |
/* free_vector(andc,1,n); */ |
/* */ |
/* */ |
|
|
wav=ivector(1,imx); |
wav=ivector(1,imx); |
dh=imatrix(1,lastpass-firstpass+1,1,imx); |
/* dh=imatrix(1,lastpass-firstpass+1,1,imx); */ |
bh=imatrix(1,lastpass-firstpass+1,1,imx); |
/* bh=imatrix(1,lastpass-firstpass+1,1,imx); */ |
mw=imatrix(1,lastpass-firstpass+1,1,imx); |
/* mw=imatrix(1,lastpass-firstpass+1,1,imx); */ |
|
dh=imatrix(1,lastpass-firstpass+2,1,imx); /* We are adding a wave if status is unknown at last wave but death occurs after last wave.*/ |
|
bh=imatrix(1,lastpass-firstpass+2,1,imx); |
|
mw=imatrix(1,lastpass-firstpass+2,1,imx); |
|
|
/* Concatenates waves */ |
/* Concatenates waves */ |
|
/* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i. |
|
Death is a valid wave (if date is known). |
|
mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i |
|
dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i] |
|
and mw[mi+1][i]. dh depends on stepm. |
|
*/ |
|
|
concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm); |
concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm); |
/* */ |
/* */ |
|
|
|
free_vector(moisdc,1,n); |
|
free_vector(andc,1,n); |
|
|
/* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */ |
/* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */ |
|
|
nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); |
nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); |
Line 7052 Please run with mle=-1 to get a correct
|
Line 7724 Please run with mle=-1 to get a correct
|
Ndum =ivector(-1,NCOVMAX); |
Ndum =ivector(-1,NCOVMAX); |
if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */ |
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 (currently 1 to 2) 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).*/ |
/* 1 to ncodemax[j] is the maximum value of this jth covariate */ |
/* 1 to ncodemax[j] which 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],codtabm(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).*/ |
|
/* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j, |
|
* codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded |
|
* (currently 0 or 1) in the data. |
|
* In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of |
|
* corresponding modality (h,j). |
|
*/ |
|
|
h=0; |
h=0; |
|
|
|
|
Line 7068 Please run with mle=-1 to get a correct
|
Line 7747 Please run with mle=-1 to get a correct
|
m=pow(2,cptcoveff); |
m=pow(2,cptcoveff); |
|
|
/**< 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 m=2**k |
* codtabm(h,k)= 1 & (h-1) >> (k-1) ; |
* codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1; |
|
* #define codtabm(h,k) (1 & (h-1) >> (k-1))+1 |
* h\k 1 2 3 4 |
* h\k 1 2 3 4 |
*______________________________ |
*______________________________ |
* 1 i=1 1 i=1 1 i=1 1 i=1 1 |
* 1 i=1 1 i=1 1 i=1 1 i=1 1 |
Line 7089 Please run with mle=-1 to get a correct
|
Line 7769 Please run with mle=-1 to get a correct
|
* 15 i=8 1 2 2 2 |
* 15 i=8 1 2 2 2 |
* 16 2 2 2 2 |
* 16 2 2 2 2 |
*/ |
*/ |
for(h=1; h <=100 ;h++){ |
/* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */ |
/* printf("h=%2d ", h); */ |
/* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4 |
/* for(k=1; k <=10; k++){ */ |
* and the value of each covariate? |
/* printf("k=%d %d ",k,codtabm(h,k)); */ |
* V1=1, V2=1, V3=2, V4=1 ? |
/* codtab[h][k]=codtabm(h,k); */ |
* h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok. |
/* } */ |
* h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st. |
/* printf("\n"); */ |
* In order to get the real value in the data, we use nbcode |
} |
* nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0 |
|
* We are keeping this crazy system in order to be able (in the future?) |
|
* to have more than 2 values (0 or 1) for a covariate. |
|
* #define codtabm(h,k) (1 & (h-1) >> (k-1))+1 |
|
* h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1 |
|
* bbbbbbbb |
|
* 76543210 |
|
* h-1 00000101 (6-1=5) |
|
*(h-1)>>(k-1)= 00000001 >> (2-1) = 1 right shift |
|
* & |
|
* 1 00000001 (1) |
|
* 00000001 = 1 & ((h-1) >> (k-1)) |
|
* +1= 00000010 =2 |
|
* |
|
* h=14, k=3 => h'=h-1=13, k'=k-1=2 |
|
* h' 1101 =2^3+2^2+0x2^1+2^0 |
|
* >>k' 11 |
|
* & 00000001 |
|
* = 00000001 |
|
* +1 = 00000010=2 = codtabm(14,3) |
|
* Reverse h=6 and m=16? |
|
* cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1. |
|
* for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff) |
|
* decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1 |
|
* decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1) |
|
* V3=decodtabm(14,3,2**4)=2 |
|
* h'=13 1101 =2^3+2^2+0x2^1+2^0 |
|
*(h-1) >> (j-1) 0011 =13 >> 2 |
|
* &1 000000001 |
|
* = 000000001 |
|
* +1= 000000010 =2 |
|
* 2211 |
|
* V1=1+1, V2=0+1, V3=1+1, V4=1+1 |
|
* V3=2 |
|
*/ |
|
|
|
/* /\* for(h=1; h <=100 ;h++){ *\/ */ |
|
/* /\* printf("h=%2d ", h); *\/ */ |
|
/* /\* for(k=1; k <=10; k++){ *\/ */ |
|
/* /\* printf("k=%d %d ",k,codtabm(h,k)); *\/ */ |
|
/* /\* codtab[h][k]=codtabm(h,k); *\/ */ |
|
/* /\* } *\/ */ |
|
/* /\* printf("\n"); *\/ */ |
|
/* } */ |
/* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */ |
/* for(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(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(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */ |
Line 7136 Please run with mle=-1 to get a correct
|
Line 7859 Please run with mle=-1 to get a correct
|
printf("Problem with file %s",optionfilegnuplot); |
printf("Problem with file %s",optionfilegnuplot); |
} |
} |
else{ |
else{ |
fprintf(ficgp,"\n# %s\n", version); |
fprintf(ficgp,"\n# IMaCh-%s\n", version); |
fprintf(ficgp,"# %s\n", optionfilegnuplot); |
fprintf(ficgp,"# %s\n", optionfilegnuplot); |
//fprintf(ficgp,"set missing 'NaNq'\n"); |
//fprintf(ficgp,"set missing 'NaNq'\n"); |
fprintf(ficgp,"set datafile missing 'NaNq'\n"); |
fprintf(ficgp,"set datafile missing 'NaNq'\n"); |
Line 7163 Please run with mle=-1 to get a correct
|
Line 7886 Please run with mle=-1 to get a correct
|
else{ |
else{ |
fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \ |
fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \ |
<hr size=\"2\" color=\"#EC5E5E\"> \n\ |
<hr size=\"2\" color=\"#EC5E5E\"> \n\ |
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\ |
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\ |
optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model); |
optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model); |
} |
} |
|
|
fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \ |
fprintf(fichtm,"<html><head>\n<head>\n<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n<title>IMaCh %s</title></head>\n <body><font size=\"7\"><a href=http:/euroreves.ined.fr/imach>IMaCh for Interpolated Markov Chain</a> </font><br>\n<font size=\"3\">Sponsored by Copyright (C) 2002-2015 <a href=http://www.ined.fr>INED</a>-EUROREVES-Institut de longévité-2013-2016-Japan Society for the Promotion of Sciences 日本å¦è¡“振興会 (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - <a href=https://software.intel.com/en-us>Intel Software 2015-2018</a></font><br> \ |
<hr size=\"2\" color=\"#EC5E5E\"> \n\ |
<hr size=\"2\" color=\"#EC5E5E\"> \n\ |
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\ |
<font size=\"2\">IMaCh-%s <br> %s</font> \ |
|
<hr size=\"2\" color=\"#EC5E5E\"> \n\ |
|
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\ |
\n\ |
\n\ |
<hr size=\"2\" color=\"#EC5E5E\">\ |
<hr size=\"2\" color=\"#EC5E5E\">\ |
<ul><li><h4>Parameter files</h4>\n\ |
<ul><li><h4>Parameter files</h4>\n\ |
Line 7195 Title=%s <br>Datafile=%s Firstpass=%d La
|
Line 7920 Title=%s <br>Datafile=%s Firstpass=%d La
|
|
|
/* Calculates basic frequencies. Computes observed prevalence at single age |
/* Calculates basic frequencies. Computes observed prevalence at single age |
and prints on file fileres'p'. */ |
and prints on file fileres'p'. */ |
freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart); |
freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ |
|
firstpass, lastpass, stepm, weightopt, model); |
|
|
fprintf(fichtm,"\n"); |
fprintf(fichtm,"\n"); |
fprintf(fichtm,"<br>Total number of observations=%d <br>\n\ |
fprintf(fichtm,"<br>Total number of observations=%d <br>\n\ |
Line 7361 Interval (in months) between two waves:
|
Line 8087 Interval (in months) between two waves:
|
#endif |
#endif |
fclose(ficrespow); |
fclose(ficrespow); |
|
|
hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); |
hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz); |
|
|
for(i=1; i <=NDIM; i++) |
for(i=1; i <=NDIM; i++) |
for(j=i+1;j<=NDIM;j++) |
for(j=i+1;j<=NDIM;j++) |
matcov[i][j]=matcov[j][i]; |
matcov[i][j]=matcov[j][i]; |
|
|
printf("\nCovariance matrix\n "); |
printf("\nCovariance matrix\n "); |
|
fprintf(ficlog,"\nCovariance matrix\n "); |
for(i=1; i <=NDIM; i++) { |
for(i=1; i <=NDIM; i++) { |
for(j=1;j<=NDIM;j++){ |
for(j=1;j<=NDIM;j++){ |
printf("%f ",matcov[i][j]); |
printf("%f ",matcov[i][j]); |
|
fprintf(ficlog,"%f ",matcov[i][j]); |
} |
} |
printf("\n "); |
printf("\n "); fprintf(ficlog,"\n "); |
} |
} |
|
|
printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp); |
printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp); |
Line 7434 Please run with mle=-1 to get a correct
|
Line 8162 Please run with mle=-1 to get a correct
|
free_matrix(ximort,1,NDIM,1,NDIM); |
free_matrix(ximort,1,NDIM,1,NDIM); |
#endif |
#endif |
} /* Endof if mle==-3 mortality only */ |
} /* Endof if mle==-3 mortality only */ |
/* Standard maximisation */ |
/* Standard */ |
else{ /* For mle >=1 */ |
else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */ |
globpr=0;/* debug */ |
globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */ |
/* Computes likelihood for initial parameters */ |
/* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */ |
likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */ |
likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */ |
printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw); |
printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw); |
for (k=1; k<=npar;k++) |
for (k=1; k<=npar;k++) |
printf(" %d %8.5f",k,p[k]); |
printf(" %d %8.5f",k,p[k]); |
printf("\n"); |
printf("\n"); |
globpr=1; /* again, to print the contributions */ |
if(mle>=1){ /* Could be 1 or 2, Real Maximization */ |
|
/* mlikeli uses func not funcone */ |
|
mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func); |
|
} |
|
if(mle==0) {/* No optimization, will print the likelihoods for the datafile */ |
|
globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */ |
|
/* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */ |
|
likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */ |
|
} |
|
globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */ |
likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */ |
likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */ |
printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw); |
printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw); |
for (k=1; k<=npar;k++) |
for (k=1; k<=npar;k++) |
printf(" %d %8.5f",k,p[k]); |
printf(" %d %8.5f",k,p[k]); |
printf("\n"); |
printf("\n"); |
if(mle>=1){ /* Could be 1 or 2, Real Maximisation */ |
|
mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func); |
|
} |
|
|
|
/*--------- results files --------------*/ |
/*--------- results files --------------*/ |
fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=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); |
Line 7478 Please run with mle=-1 to get a correct
|
Line 8212 Please run with mle=-1 to get a correct
|
} |
} |
} |
} |
} |
} |
if(mle!=0){ |
if(mle != 0){ |
/* Computing hessian and covariance matrix */ |
/* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */ |
ftolhess=ftol; /* Usually correct */ |
ftolhess=ftol; /* Usually correct */ |
hesscov(matcov, p, npar, delti, ftolhess, func); |
hesscov(matcov, hess, p, npar, delti, ftolhess, func); |
} |
printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n"); |
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"); |
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(i=1,jk=1; i <=nlstate; i++){ |
for(k=1; k <=(nlstate+ndeath); k++){ |
for(k=1; k <=(nlstate+ndeath); k++){ |
if (k != i) { |
if (k != i) { |
printf("%d%d ",i,k); |
printf("%d%d ",i,k); |
fprintf(ficlog,"%d%d ",i,k); |
fprintf(ficlog,"%d%d ",i,k); |
for(j=1; j <=ncovmodel; j++){ |
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])); |
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])); |
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++; |
jk++; |
} |
|
printf("\n"); |
|
fprintf(ficlog,"\n"); |
} |
} |
printf("\n"); |
|
fprintf(ficlog,"\n"); |
|
} |
} |
} |
} |
} |
} /* end of hesscov and Wald tests */ |
|
|
|
/* */ |
fprintf(ficres,"# Scales (for hessian or gradient estimation)\n"); |
fprintf(ficres,"# Scales (for hessian or gradient estimation)\n"); |
printf("# Scales (for hessian or gradient estimation)\n"); |
printf("# Scales (for hessian or gradient estimation)\n"); |
fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n"); |
fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n"); |
Line 7524 Please run with mle=-1 to get a correct
|
Line 8259 Please run with mle=-1 to get a correct
|
} |
} |
|
|
fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); |
fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); |
if(mle>=1) |
if(mle >= 1) /* To big for the screen */ |
printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); |
printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); |
fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); |
fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); |
/* # 121 Var(a12)\n\ */ |
/* # 121 Var(a12)\n\ */ |
Line 7587 Please run with mle=-1 to get a correct
|
Line 8322 Please run with mle=-1 to get a correct
|
fprintf(ficres," Var(%s%1d%1d)",ca,i,j); |
fprintf(ficres," Var(%s%1d%1d)",ca,i,j); |
}else{ |
}else{ |
if(mle>=1) |
if(mle>=1) |
printf(" %.5e",matcov[jj][ll]); |
printf(" %.7e",matcov[jj][ll]); |
fprintf(ficlog," %.5e",matcov[jj][ll]); |
fprintf(ficlog," %.7e",matcov[jj][ll]); |
fprintf(ficres," %.5e",matcov[jj][ll]); |
fprintf(ficres," %.7e",matcov[jj][ll]); |
} |
} |
} |
} |
} |
} |
Line 7608 Please run with mle=-1 to get a correct
|
Line 8343 Please run with mle=-1 to get a correct
|
|
|
fflush(ficlog); |
fflush(ficlog); |
fflush(ficres); |
fflush(ficres); |
|
while(fgets(line, MAXLINE, ficpar)) { |
while((c=getc(ficpar))=='#' && c!= EOF){ |
/* If line starts with a # it is a comment */ |
ungetc(c,ficpar); |
if (line[0] == '#') { |
fgets(line, MAXLINE, ficpar); |
numlinepar++; |
fputs(line,stdout); |
fputs(line,stdout); |
fputs(line,ficparo); |
fputs(line,ficparo); |
} |
fputs(line,ficlog); |
ungetc(c,ficpar); |
continue; |
|
}else |
|
break; |
|
} |
|
|
|
/* while((c=getc(ficpar))=='#' && c!= EOF){ */ |
|
/* ungetc(c,ficpar); */ |
|
/* fgets(line, MAXLINE, ficpar); */ |
|
/* fputs(line,stdout); */ |
|
/* fputs(line,ficparo); */ |
|
/* } */ |
|
/* ungetc(c,ficpar); */ |
|
|
estepm=0; |
estepm=0; |
fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); |
if((num_filled=sscanf(line,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm, &ftolpl)) !=EOF){ |
|
|
|
if (num_filled != 6) { |
|
printf("Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n"); |
|
printf("but line=%s\n",line); |
|
goto end; |
|
} |
|
printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl); |
|
} |
|
/* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */ |
|
/*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */ |
|
|
|
/* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */ |
if (estepm==0 || estepm < stepm) estepm=stepm; |
if (estepm==0 || estepm < stepm) estepm=stepm; |
if (fage <= 2) { |
if (fage <= 2) { |
bage = ageminpar; |
bage = ageminpar; |
Line 7626 Please run with mle=-1 to get a correct
|
Line 8384 Please run with mle=-1 to get a correct
|
} |
} |
|
|
fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n"); |
fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n"); |
fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); |
fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl); |
fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); |
fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl); |
|
|
/* Other stuffs, more or less useful */ |
/* Other stuffs, more or less useful */ |
while((c=getc(ficpar))=='#' && c!= EOF){ |
while((c=getc(ficpar))=='#' && c!= EOF){ |
Line 7690 Please run with mle=-1 to get a correct
|
Line 8448 Please run with mle=-1 to get a correct
|
This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\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); |
Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar); |
}else |
}else |
printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p); |
printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, pathc,p); |
|
|
printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt,\ |
printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt,\ |
model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\ |
model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,estepm, \ |
jprev1,mprev1,anprev1,jprev2,mprev2,anprev2); |
jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2); |
|
|
/*------------ free_vector -------------*/ |
/*------------ free_vector -------------*/ |
/* chdir(path); */ |
/* chdir(path); */ |
|
|
free_ivector(wav,1,imx); |
/* free_ivector(wav,1,imx); */ /* Moved after last prevalence call */ |
free_imatrix(dh,1,lastpass-firstpass+1,1,imx); |
/* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */ |
free_imatrix(bh,1,lastpass-firstpass+1,1,imx); |
/* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */ |
free_imatrix(mw,1,lastpass-firstpass+1,1,imx); |
/* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */ |
free_lvector(num,1,n); |
free_lvector(num,1,n); |
free_vector(agedc,1,n); |
free_vector(agedc,1,n); |
/*free_matrix(covar,0,NCOVMAX,1,n);*/ |
/*free_matrix(covar,0,NCOVMAX,1,n);*/ |
Line 7717 Please run with mle=-1 to get a correct
|
Line 8475 Please run with mle=-1 to get a correct
|
/*--------------- Prevalence limit (period or stable prevalence) --------------*/ |
/*--------------- Prevalence limit (period or stable prevalence) --------------*/ |
/*#include "prevlim.h"*/ /* Use ficrespl, ficlog */ |
/*#include "prevlim.h"*/ /* Use ficrespl, ficlog */ |
prlim=matrix(1,nlstate,1,nlstate); |
prlim=matrix(1,nlstate,1,nlstate); |
prevalence_limit(p, prlim, ageminpar, agemaxpar); |
prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear); |
fclose(ficrespl); |
fclose(ficrespl); |
|
|
#ifdef FREEEXIT2 |
#ifdef FREEEXIT2 |
Line 7762 Please run with mle=-1 to get a correct
|
Line 8520 Please run with mle=-1 to get a correct
|
/* printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d, mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\ |
/* printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d, mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\ |
ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass); |
ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass); |
*/ |
*/ |
|
free_ivector(wav,1,imx); |
|
free_imatrix(dh,1,lastpass-firstpass+2,1,imx); |
|
free_imatrix(bh,1,lastpass-firstpass+2,1,imx); |
|
free_imatrix(mw,1,lastpass-firstpass+2,1,imx); |
|
|
|
|
if (mobilav!=0) { |
if (mobilav!=0) { |
mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
Line 7780 Please run with mle=-1 to get a correct
|
Line 8543 Please run with mle=-1 to get a correct
|
printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0); |
printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0); |
fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0); |
fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0); |
} |
} |
printf("Computing Health Expectancies: result on file '%s' \n", filerese); |
printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout); |
fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese); |
fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog); |
/*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ |
/*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ |
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ |
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ |
|
|
Line 7800 Please run with mle=-1 to get a correct
|
Line 8563 Please run with mle=-1 to get a correct
|
/*}*/ |
/*}*/ |
} |
} |
fclose(ficreseij); |
fclose(ficreseij); |
|
printf("done evsij\n");fflush(stdout); |
|
fprintf(ficlog,"done evsij\n");fflush(ficlog); |
|
|
/*---------- Health expectancies and variances ------------*/ |
/*---------- Health expectancies and variances ------------*/ |
|
|
Line 7811 Please run with mle=-1 to get a correct
|
Line 8575 Please run with mle=-1 to get a correct
|
printf("Problem with total LE resultfile: %s\n", filerest);goto end; |
printf("Problem with total LE resultfile: %s\n", filerest);goto end; |
fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end; |
fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end; |
} |
} |
printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); |
printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout); |
fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); |
fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog); |
|
|
|
|
strcpy(fileresstde,"STDE_"); |
strcpy(fileresstde,"STDE_"); |
Line 7821 Please run with mle=-1 to get a correct
|
Line 8585 Please run with mle=-1 to get a correct
|
printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0); |
printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0); |
fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0); |
fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0); |
} |
} |
printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde); |
printf(" Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde); |
fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde); |
fprintf(ficlog," Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde); |
|
|
strcpy(filerescve,"CVE_"); |
strcpy(filerescve,"CVE_"); |
strcat(filerescve,fileresu); |
strcat(filerescve,fileresu); |
Line 7830 Please run with mle=-1 to get a correct
|
Line 8594 Please run with mle=-1 to get a correct
|
printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0); |
printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0); |
fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0); |
fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0); |
} |
} |
printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve); |
printf(" Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve); |
fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve); |
fprintf(ficlog," Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve); |
|
|
strcpy(fileresv,"V_"); |
strcpy(fileresv,"V_"); |
strcat(fileresv,fileresu); |
strcat(fileresv,fileresu); |
Line 7839 Please run with mle=-1 to get a correct
|
Line 8603 Please run with mle=-1 to get a correct
|
printf("Problem with variance resultfile: %s\n", fileresv);exit(0); |
printf("Problem with variance resultfile: %s\n", fileresv);exit(0); |
fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0); |
fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0); |
} |
} |
printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); |
printf(" Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(stdout); |
fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); |
fprintf(ficlog," Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(ficlog); |
|
|
/*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ |
/*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ |
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ |
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ |
|
|
for (k=1; k <= (int) pow(2,cptcoveff); k++){ |
for (k=1; k <= (int) pow(2,cptcoveff); k++){ |
fprintf(ficrest,"\n#****** "); |
fprintf(ficrest,"\n#****** "); |
for(j=1;j<=cptcoveff;j++) |
for(j=1;j<=cptcoveff;j++) |
fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); |
fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); |
fprintf(ficrest,"******\n"); |
fprintf(ficrest,"******\n"); |
|
|
fprintf(ficresstdeij,"\n#****** "); |
fprintf(ficresstdeij,"\n#****** "); |
fprintf(ficrescveij,"\n#****** "); |
fprintf(ficrescveij,"\n#****** "); |
for(j=1;j<=cptcoveff;j++) { |
for(j=1;j<=cptcoveff;j++) { |
fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); |
fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); |
fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); |
fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); |
} |
} |
fprintf(ficresstdeij,"******\n"); |
fprintf(ficresstdeij,"******\n"); |
fprintf(ficrescveij,"******\n"); |
fprintf(ficrescveij,"******\n"); |
|
|
fprintf(ficresvij,"\n#****** "); |
fprintf(ficresvij,"\n#****** "); |
for(j=1;j<=cptcoveff;j++) |
for(j=1;j<=cptcoveff;j++) |
fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); |
fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); |
fprintf(ficresvij,"******\n"); |
fprintf(ficresvij,"******\n"); |
|
|
eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); |
eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); |
oldm=oldms;savm=savms; |
oldm=oldms;savm=savms; |
cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart); |
printf(" cvevsij %d, ",k); |
/* |
fprintf(ficlog, " cvevsij %d, ",k); |
*/ |
cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart); |
/* goto endfree; */ |
printf(" end cvevsij \n "); |
|
fprintf(ficlog, " end cvevsij \n "); |
vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); |
|
pstamp(ficrest); |
/* |
|
*/ |
|
/* goto endfree; */ |
for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/ |
|
oldm=oldms;savm=savms; /* ZZ Segmentation fault */ |
vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); |
cptcod= 0; /* To be deleted */ |
pstamp(ficrest); |
varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */ |
|
fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are "); |
|
if(vpopbased==1) |
for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/ |
fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav); |
oldm=oldms;savm=savms; /* ZZ Segmentation fault */ |
else |
cptcod= 0; /* To be deleted */ |
fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n"); |
printf("varevsij %d \n",vpopbased); |
fprintf(ficrest,"# Age popbased mobilav e.. (std) "); |
fprintf(ficlog, "varevsij %d \n",vpopbased); |
for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i); |
varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */ |
fprintf(ficrest,"\n"); |
fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are "); |
/* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */ |
if(vpopbased==1) |
epj=vector(1,nlstate+1); |
fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav); |
for(age=bage; age <=fage ;age++){ |
else |
prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); /*ZZ Is it the correct prevalim */ |
fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n"); |
if (vpopbased==1) { |
fprintf(ficrest,"# Age popbased mobilav e.. (std) "); |
if(mobilav ==0){ |
for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i); |
for(i=1; i<=nlstate;i++) |
fprintf(ficrest,"\n"); |
prlim[i][i]=probs[(int)age][i][k]; |
/* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */ |
}else{ /* mobilav */ |
epj=vector(1,nlstate+1); |
for(i=1; i<=nlstate;i++) |
printf("Computing age specific period (stable) prevalences in each health state \n"); |
prlim[i][i]=mobaverage[(int)age][i][k]; |
fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n"); |
} |
for(age=bage; age <=fage ;age++){ |
} |
prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */ |
|
if (vpopbased==1) { |
fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav); |
if(mobilav ==0){ |
/* printf(" age %4.0f ",age); */ |
for(i=1; i<=nlstate;i++) |
for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){ |
prlim[i][i]=probs[(int)age][i][k]; |
for(i=1, epj[j]=0.;i <=nlstate;i++) { |
}else{ /* mobilav */ |
epj[j] += prlim[i][i]*eij[i][j][(int)age]; |
for(i=1; i<=nlstate;i++) |
/*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/ |
prlim[i][i]=mobaverage[(int)age][i][k]; |
/* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */ |
|
} |
|
epj[nlstate+1] +=epj[j]; |
|
} |
} |
/* printf(" age %4.0f \n",age); */ |
} |
|
|
for(i=1, vepp=0.;i <=nlstate;i++) |
fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav); |
for(j=1;j <=nlstate;j++) |
/* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */ |
vepp += vareij[i][j][(int)age]; |
/* printf(" age %4.0f ",age); */ |
fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp)); |
for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){ |
for(j=1;j <=nlstate;j++){ |
for(i=1, epj[j]=0.;i <=nlstate;i++) { |
fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age])); |
epj[j] += prlim[i][i]*eij[i][j][(int)age]; |
|
/*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/ |
|
/* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */ |
} |
} |
fprintf(ficrest,"\n"); |
epj[nlstate+1] +=epj[j]; |
} |
} |
|
/* printf(" age %4.0f \n",age); */ |
|
|
|
for(i=1, vepp=0.;i <=nlstate;i++) |
|
for(j=1;j <=nlstate;j++) |
|
vepp += vareij[i][j][(int)age]; |
|
fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp)); |
|
for(j=1;j <=nlstate;j++){ |
|
fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age])); |
|
} |
|
fprintf(ficrest,"\n"); |
} |
} |
free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage); |
} /* End vpopbased */ |
free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage); |
free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage); |
free_vector(epj,1,nlstate+1); |
free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage); |
|
free_vector(epj,1,nlstate+1); |
|
printf("done \n");fflush(stdout); |
|
fprintf(ficlog,"done\n");fflush(ficlog); |
|
|
/*}*/ |
/*}*/ |
} |
} /* End k */ |
free_vector(weight,1,n); |
free_vector(weight,1,n); |
free_imatrix(Tvard,1,NCOVMAX,1,2); |
free_imatrix(Tvard,1,NCOVMAX,1,2); |
free_imatrix(s,1,maxwav+1,1,n); |
free_imatrix(s,1,maxwav+1,1,n); |
Line 7940 Please run with mle=-1 to get a correct
|
Line 8717 Please run with mle=-1 to get a correct
|
fclose(ficrescveij); |
fclose(ficrescveij); |
fclose(ficresvij); |
fclose(ficresvij); |
fclose(ficrest); |
fclose(ficrest); |
|
printf("done Health expectancies\n");fflush(stdout); |
|
fprintf(ficlog,"done Health expectancies\n");fflush(ficlog); |
fclose(ficpar); |
fclose(ficpar); |
|
|
/*------- Variance of period (stable) prevalence------*/ |
/*------- Variance of period (stable) prevalence------*/ |
Line 7950 Please run with mle=-1 to get a correct
|
Line 8729 Please run with mle=-1 to get a correct
|
printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl); |
printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl); |
exit(0); |
exit(0); |
} |
} |
printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl); |
printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout); |
|
fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog); |
|
|
/*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ |
/*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ |
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ |
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ |
Line 7963 Please run with mle=-1 to get a correct
|
Line 8743 Please run with mle=-1 to get a correct
|
|
|
varpl=matrix(1,nlstate,(int) bage, (int) fage); |
varpl=matrix(1,nlstate,(int) bage, (int) fage); |
oldm=oldms;savm=savms; |
oldm=oldms;savm=savms; |
varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart); |
varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart); |
free_matrix(varpl,1,nlstate,(int) bage, (int)fage); |
free_matrix(varpl,1,nlstate,(int) bage, (int)fage); |
/*}*/ |
/*}*/ |
} |
} |
|
|
fclose(ficresvpl); |
fclose(ficresvpl); |
|
printf("done variance-covariance of period prevalence\n");fflush(stdout); |
|
fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog); |
|
|
/*---------- End : free ----------------*/ |
/*---------- End : free ----------------*/ |
if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
Line 7982 Please run with mle=-1 to get a correct
|
Line 8764 Please run with mle=-1 to get a correct
|
free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath); |
free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath); |
free_matrix(covar,0,NCOVMAX,1,n); |
free_matrix(covar,0,NCOVMAX,1,n); |
free_matrix(matcov,1,npar,1,npar); |
free_matrix(matcov,1,npar,1,npar); |
|
free_matrix(hess,1,npar,1,npar); |
/*free_vector(delti,1,npar);*/ |
/*free_vector(delti,1,npar);*/ |
free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); |
free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); |
free_matrix(agev,1,maxwav,1,imx); |
free_matrix(agev,1,maxwav,1,imx); |