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version 1.202, 2015/09/22 19:45:16
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version 1.213, 2015/12/11 18:22:17
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| /* $Id$ |
/* $Id$ |
| $State$ |
$State$ |
| $Log$ |
$Log$ |
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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 |
Revision 1.202 2015/09/22 19:45:16 brouard |
| Summary: Adding some overall graph on contribution to likelihood. Might change |
Summary: Adding some overall graph on contribution to likelihood. Might change |
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Line 647
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Line 693
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| /* #define DEBUG */ |
/* #define DEBUG */ |
| /* #define DEBUGBRENT */ |
/* #define DEBUGBRENT */ |
| #define DEBUGLINMIN |
/* #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 *\/ */ |
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Line 719 typedef struct {
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Line 768 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 739 typedef struct {
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Line 790 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 776 double **matprod2(); /* test */
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Line 827 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, *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 930 static int split( char *path, char *dirc
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Line 981 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 1338 char *subdirf3(char fileres[], char *pre
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Line 1389 char *subdirf3(char fileres[], char *pre
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| strcat(tmpout,fileres); |
strcat(tmpout,fileres); |
| return tmpout; |
return tmpout; |
| } |
} |
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|
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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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|
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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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|
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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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|
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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 1602 void linmin(double p[], double xi[], int
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Line 1676 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; |
| |
|
| 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); |
|
Line 1613 void linmin(double p[], double xi[], int
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Line 1690 void linmin(double p[], double xi[], int
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| xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */ |
xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */ |
| } |
} |
| |
|
| /* 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 1626 void linmin(double p[], double xi[], int
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Line 1706 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); |
| 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); |
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); |
|
Line 1650 void linmin(double p[], double xi[], int
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Line 1737 void linmin(double p[], double xi[], int
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| fprintf(ficlog,"linmin end "); |
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) */ |
| |
#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 ); |
| |
#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"); */ |
|
| #ifdef DEBUGLINMIN |
#ifdef DEBUGLINMIN |
| |
printf("\n"); |
| printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p)); |
printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p)); |
| fprintf(ficlog,"Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p)); |
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++) { |
|
Line 1668 void linmin(double p[], double xi[], int
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Line 1764 void linmin(double p[], double xi[], int
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| fprintf(ficlog,"\n"); |
fprintf(ficlog,"\n"); |
| } |
} |
| } |
} |
| |
#else |
| #endif |
#endif |
| free_vector(xicom,1,n); |
free_vector(xicom,1,n); |
| free_vector(pcom,1,n); |
free_vector(pcom,1,n); |
|
Line 1745 void powell(double p[], double **xi, int
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Line 1842 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 1917 void powell(double p[], double **xi, int
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Line 2014 void powell(double p[], double **xi, int
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| |
|
| /**** 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 */ |
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/* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */ |
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/* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */ |
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/* 0, 0 , 1} */ |
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/* |
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* and after some iteration: */ |
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/* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */ |
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/* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */ |
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/* 0, 0 , 1} */ |
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/* And prevalence by suppressing the deaths are close to identical rows in prlim: */ |
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/* {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=100 ; /* Max number of years to converge */ |
double agefin, delaymax=200. ; /* 100 Max number of years to converge */ |
| long int ncvyear=0, ncvloop=0; |
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 1967 double **prevalim(double **prlim, int nl
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Line 2085 double **prevalim(double **prlim, int nl
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| |
|
| 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); |
| max=FMAX(max,prlim[i][j]); |
max[j]=FMAX(max[j],prlim[i][j]); |
| min=FMIN(min,prlim[i][j]); |
min[j]=FMIN(min[j],prlim[i][j]); |
| /* printf(" age= %d prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d max=%f min=%f\n", (int)age, i, j, i, j, prlim[i][j],(int)agefin, max, min); */ |
|
| } |
} |
| maxmin=max-min; |
} |
| 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 maxmin=%lf ncvloop=%ld, ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age-(int)agefin); */ |
/* 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 */ |
| printf("Warning: the stable prevalence did not converge with the required precision ftolpl=6*10^5*ftol=%g. \n\ |
/* After some age loop it doesn't converge */ |
| Earliest age to start was %d-%d=%d, ncvloop=%ld, ncvyear=%d\n\ |
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\ |
| 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); |
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 2565 double funcone( double *x)
|
Line 2699 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 %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f\ |
fprintf(ficresilk,"%9ld %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], agexact, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i], |
num[i], agexact, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],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 2605 void likelione(FILE *ficres,double p[],
|
Line 2739 void likelione(FILE *ficres,double p[],
|
| 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 age 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 age i s1 s2 mi mw dh likeli weight 2wlli out sav "); |
fprintf(ficresilk, "#num_i age 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 2616 void likelione(FILE *ficres,double p[],
|
Line 2750 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 computed with initial parameters and mle >= 1. You should at least run with mle >= 1 and starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk)); |
if (mle ==0) |
| fprintf(fichtm,"<br>- The first 3 individuals are drawn with lines. The function drawn is -2Log(L) in log scale: <a href=\"%s.png\">%s.png</a><br> \ |
fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle); |
| <img src=\"%s.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_")); |
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); |
fflush(fichtm); |
| } |
} |
| return; |
return; |
| } |
} |
| |
|
|
Line 2694 void mlikeli(FILE *ficres,double p[], in
|
Line 2840 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 2730 void hesscov(double **matcov, double p[]
|
Line 2876 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 2766 void hesscov(double **matcov, double p[]
|
Line 2912 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"); */ |
| |
/* } */ |
| |
|
| |
/* Verifying the inverse matrix */ |
| |
#ifdef DEBUGHESS |
| |
y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov); |
| |
|
| /* printf("\n#Hessian matrix recomputed#\n"); |
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 2828 double hessii(double x[], double delta,
|
Line 2999 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 2844 double hessii(double x[], double delta,
|
Line 3015 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 2974 void freqsummary(char fileres[], int ia
|
Line 3222 void freqsummary(char fileres[], int ia
|
| 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]; |
| |
|
| 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); |
| } |
} |
| |
printf("Problem with prevalence resultfile: %s\n", fileresp); |
| |
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); |
| |
} |
| 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 3012 void freqsummary(char fileres[], int ia
|
Line 3269 void freqsummary(char fileres[], int ia
|
| k2cpt=0; |
k2cpt=0; |
| for (i=1; i<=imx; i++) { |
for (i=1; i<=imx; 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 3022 void freqsummary(char fileres[], int ia
|
Line 3279 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++){ |
|
Line 3030 void freqsummary(char fileres[], int ia
|
Line 3287 void freqsummary(char fileres[], int ia
|
| /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/ |
/*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/ |
| 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 (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i]; |
if (s[m][i]>0 && s[m][i]<=nlstate) |
| |
prop[s[m][i]][(int)agev[m][i]] += weight[i]; |
| if (m<lastpass) { |
if (m<lastpass) { |
| freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; |
freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; |
| freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i]; |
freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i]; |
| } |
} |
| |
|
| 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 bool */ |
| } /* end i */ |
} /* 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<h3>********** Variable "); |
| fprintf(ficresp, "**********\n#"); |
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(ficresp, "**********\n#"); |
| |
fprintf(ficresphtm, "**********</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\"><th></th>"); |
| |
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"); |
| |
|
| for(i=iagemin; i <= iagemax+3; i++){ |
for(i=iagemin; i <= iagemax+3; i++){ |
| |
fprintf(ficresphtm,"<tr>"); |
| if(i==iagemax+3){ |
if(i==iagemax+3){ |
| fprintf(ficlog,"Total"); |
fprintf(ficlog,"Total"); |
| }else{ |
}else{ |
|
Line 3109 void freqsummary(char fileres[], int ia
|
Line 3378 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); |
| |
} |
| } |
} |
| } |
} |
| |
|
|
Line 3124 void freqsummary(char fileres[], int ia
|
Line 3396 void freqsummary(char fileres[], int ia
|
| 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(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"); |
| /*}*/ |
/*}*/ |
| } |
} /* end j1 */ |
| dateintmean=dateintsum/k2cpt; |
dateintmean=dateintsum/k2cpt; |
| |
|
| fclose(ficresp); |
fclose(ficresp); |
| |
fclose(ficresphtm); |
| 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 3818 void cvevsij(double ***eij, double x[],
|
Line 4094 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 3872 void varevsij(char optionfilefiname[], d
|
Line 4148 void varevsij(char optionfilefiname[], d
|
| 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 3883 void varevsij(char optionfilefiname[], d
|
Line 4158 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 3920 void varevsij(char optionfilefiname[], d
|
Line 4196 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 3943 void varevsij(char optionfilefiname[], d
|
Line 4219 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 3956 void varevsij(char optionfilefiname[], d
|
Line 4232 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 3974 void varevsij(char optionfilefiname[], d
|
Line 4251 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 3987 void varevsij(char optionfilefiname[], d
|
Line 4264 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 4049 void varevsij(char optionfilefiname[], d
|
Line 4328 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 4066 void varevsij(char optionfilefiname[], d
|
Line 4345 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 4128 void varevsij(char optionfilefiname[], d
|
Line 4408 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 4138 void varprevlim(char fileres[], double *
|
Line 4418 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 4160 void varprevlim(char fileres[], double *
|
Line 4441 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 4167 void varprevlim(char fileres[], double *
|
Line 4450 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 4186 void varprevlim(char fileres[], double *
|
Line 4478 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 4200 void varprevlim(char fileres[], double *
|
Line 4515 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 4550 To be simple, these graphs help to under
|
Line 4867 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 ", |
- 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,subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_")); |
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 4568 void printinghtml(char fileresu[], char
|
Line 4886 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 4593 fprintf(fichtm," \n<ul><li><b>Graphs</b>
|
Line 4913 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 4611 divided by h: hPij/h : <a href=\"%s_%d-3
|
Line 4931 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 4620 divided by h: hPij/h : <a href=\"%s_%d-3
|
Line 4940 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 %f to %f) 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 4631 divided by h: hPij/h : <a href=\"%s_%d-3
|
Line 4959 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 4691 See page 'Matrix of variance-covariance
|
Line 5019 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 4707 true period expectancies (those weighted
|
Line 5035 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 4728 void printinggnuplot(char fileresu[], ch
|
Line 5057 void printinggnuplot(char fileresu[], ch
|
| fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n"); |
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,"\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 svg size 640, 480"); */ /* Too big for svg */ |
| fprintf(ficgp,"\nset ter png size 640, 480"); |
fprintf(ficgp,"\nset ter pngcairo size 640, 480"); |
| /* good for mle=4 plot by number of matrix products. |
/* 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 "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)" */ |
/* 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.svg\";",subdirf2(optionfilefiname,"ILK_")); */ |
| fprintf(ficgp,"\nset out \"%s.png\";",subdirf2(optionfilefiname,"ILK_")); |
fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_")); |
| fprintf(ficgp,"\nplot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); |
fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$12):5 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",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 \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_")); |
| fprintf(ficgp,"\nset out\n"); |
fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$12):4 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk)); |
| |
for (i=1; i<= nlstate ; i ++) { |
| |
fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i); |
| |
fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk)); |
| |
fprintf(ficgp," u 2:($4 == %d && $5==%d ? $9 : 1/0):($11/4.):5 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:($4 == %d && $5==%d ? $9 : 1/0):($11/4.):5 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_")); */ |
/* 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 4771 plot [%.f:%.f] \"%s\" every :::%d::%d u
|
Line 5124 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 4805 plot [%.f:%.f] \"%s\" every :::%d::%d u
|
Line 5168 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 4834 plot [%.f:%.f] \"%s\" every :::%d::%d u
|
Line 5209 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 4859 plot [%.f:%.f] ", ageminpar, agemaxpar)
|
Line 5244 plot [%.f:%.f] ", ageminpar, agemaxpar)
|
| /* 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 covariate 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 4891 plot [%.f:%.f] ", ageminpar, agemaxpar)
|
Line 5286 plot [%.f:%.f] ", ageminpar, agemaxpar)
|
| } /* end covariate */ |
} /* end covariate */ |
| |
|
| /* CV preval stable (period) for each covariate */ |
/* CV preval stable (period) for each covariate */ |
| for (k1=1; k1<= m ; k1 ++) { /* For each covariate 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 4915 plot [%.f:%.f] ", ageminpar, agemaxpar)
|
Line 5320 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 5106 void prevforecast(char fileres[], double
|
Line 5589 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. |
| |
*/ |
| 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 5156 void prevforecast(char fileres[], double
|
Line 5643 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 6317 void syscompilerinfo(int logged)
|
Line 6803 void syscompilerinfo(int logged)
|
| |
|
| } |
} |
| |
|
| int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl){ |
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); |
|
Line 6332 void syscompilerinfo(int logged)
|
Line 6819 void syscompilerinfo(int logged)
|
| 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"); |
|
Line 6367 void syscompilerinfo(int logged)
|
Line 6854 void syscompilerinfo(int logged)
|
| 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 6471 int main(int argc, char *argv[])
|
Line 6961 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 6519 int main(int argc, char *argv[])
|
Line 7009 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 6578 int main(int argc, char *argv[])
|
Line 7069 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 6721 int main(int argc, char *argv[])
|
Line 7221 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*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 6755 int main(int argc, char *argv[])
|
Line 7257 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 6827 int main(int argc, char *argv[])
|
Line 7328 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 6935 run imach with mle=-1 to get a correct t
|
Line 7437 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 7093 Please run with mle=-1 to get a correct
|
Line 7596 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 7109 Please run with mle=-1 to get a correct
|
Line 7619 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 7130 Please run with mle=-1 to get a correct
|
Line 7641 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 |
| */ |
*/ |
| |
/* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */ |
| |
/* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4 |
| |
* and the value of each covariate? |
| |
* V1=1, V2=1, V3=2, V4=1 ? |
| |
* 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. |
| |
* 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++){ *\/ */ |
/* /\* for(h=1; h <=100 ;h++){ *\/ */ |
| /* /\* printf("h=%2d ", h); *\/ */ |
/* /\* printf("h=%2d ", h); *\/ */ |
| /* /\* for(k=1; k <=10; k++){ *\/ */ |
/* /\* for(k=1; k <=10; k++){ *\/ */ |
|
Line 7177 Please run with mle=-1 to get a correct
|
Line 7731 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 7204 Please run with mle=-1 to get a correct
|
Line 7758 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 7402 Interval (in months) between two waves:
|
Line 7958 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 7475 Please run with mle=-1 to get a correct
|
Line 8033 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 7519 Please run with mle=-1 to get a correct
|
Line 8083 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 7565 Please run with mle=-1 to get a correct
|
Line 8130 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 7628 Please run with mle=-1 to get a correct
|
Line 8193 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 7649 Please run with mle=-1 to get a correct
|
Line 8214 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 7667 Please run with mle=-1 to get a correct
|
Line 8255 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 7731 Please run with mle=-1 to get a correct
|
Line 8319 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); */ |
|
Line 7758 Please run with mle=-1 to get a correct
|
Line 8346 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, ftolpl); |
prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear); |
| fclose(ficrespl); |
fclose(ficrespl); |
| |
|
| #ifdef FREEEXIT2 |
#ifdef FREEEXIT2 |
|
Line 7821 Please run with mle=-1 to get a correct
|
Line 8409 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 7841 Please run with mle=-1 to get a correct
|
Line 8429 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 7852 Please run with mle=-1 to get a correct
|
Line 8441 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 7862 Please run with mle=-1 to get a correct
|
Line 8451 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 7871 Please run with mle=-1 to get a correct
|
Line 8460 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 7880 Please run with mle=-1 to get a correct
|
Line 8469 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 7981 Please run with mle=-1 to get a correct
|
Line 8583 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 7991 Please run with mle=-1 to get a correct
|
Line 8595 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 8004 Please run with mle=-1 to get a correct
|
Line 8609 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 8023 Please run with mle=-1 to get a correct
|
Line 8630 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); |
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