version 1.201, 2015/09/15 17:34:58
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version 1.206, 2015/10/24 07:14:11
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/* $Id$ |
/* $Id$ |
$State$ |
$State$ |
$Log$ |
$Log$ |
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Revision 1.206 2015/10/24 07:14:11 brouard |
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*** empty log message *** |
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Revision 1.205 2015/10/23 15:50:53 brouard |
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Summary: 0.98r3 some clarification for graphs on likelihood contributions |
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Revision 1.204 2015/10/01 16:20:26 brouard |
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Summary: Some new graphs of contribution to likelihood |
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Revision 1.203 2015/09/30 17:45:14 brouard |
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Summary: looking at better estimation of the hessian |
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Also a better criteria for convergence to the period prevalence And |
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therefore adding the number of years needed to converge. (The |
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prevalence in any alive state shold sum to one |
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Revision 1.202 2015/09/22 19:45:16 brouard |
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Summary: Adding some overall graph on contribution to likelihood. Might change |
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Revision 1.201 2015/09/15 17:34:58 brouard |
Revision 1.201 2015/09/15 17:34:58 brouard |
Summary: 0.98r0 |
Summary: 0.98r0 |
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Line 644
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Line 663
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/* #define DEBUG */ |
/* #define DEBUG */ |
/* #define DEBUGBRENT */ |
/* #define DEBUGBRENT */ |
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/* #define DEBUGLINMIN */ |
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/* #define DEBUGHESS */ |
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#define DEBUGHESSIJ |
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/* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan)*\/ */ |
#define POWELL /* Instead of NLOPT */ |
#define POWELL /* Instead of NLOPT */ |
#define POWELLF1F3 /* Skip test */ |
#define POWELLF1F3 /* Skip test */ |
/* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */ |
/* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */ |
Line 735 typedef struct {
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Line 758 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 802 char command[FILENAMELENGTH];
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Line 825 char command[FILENAMELENGTH];
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int outcmd=0; |
int outcmd=0; |
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char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH]; |
char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH]; |
char fileresu[FILENAMELENGTH]; /* Without r in front */ |
char fileresu[FILENAMELENGTH]; /* fileres without r in front */ |
char filelog[FILENAMELENGTH]; /* Log file */ |
char filelog[FILENAMELENGTH]; /* Log file */ |
char filerest[FILENAMELENGTH]; |
char filerest[FILENAMELENGTH]; |
char fileregp[FILENAMELENGTH]; |
char fileregp[FILENAMELENGTH]; |
Line 926 static int split( char *path, char *dirc
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Line 949 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 1598 void linmin(double p[], double xi[], int
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Line 1621 void linmin(double p[], double xi[], int
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double xx,xmin,bx,ax; |
double xx,xmin,bx,ax; |
double fx,fb,fa; |
double fx,fb,fa; |
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double scale=10., axs, xxs, xxss; /* Scale added for infinity */ |
#ifdef LINMINORIGINAL |
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#else |
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double scale=10., axs, xxs; /* Scale added for infinity */ |
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#endif |
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ncom=n; |
ncom=n; |
pcom=vector(1,n); |
pcom=vector(1,n); |
xicom=vector(1,n); |
xicom=vector(1,n); |
nrfunc=func; |
nrfunc=func; |
for (j=1;j<=n;j++) { |
for (j=1;j<=n;j++) { |
pcom[j]=p[j]; |
pcom[j]=p[j]; |
xicom[j]=xi[j]; |
xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */ |
} |
} |
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/* axs=0.0; */ |
#ifdef LINMINORIGINAL |
/* xxss=1; /\* 1 and using scale *\/ */ |
xx=1.; |
xxs=1; |
#else |
/* do{ */ |
axs=0.0; |
ax=0.; |
xxs=1.; |
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do{ |
xx= xxs; |
xx= xxs; |
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#endif |
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ax=0.; |
mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */ |
mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */ |
/* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */ |
/* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */ |
/* xt[x,j]=pcom[j]+x*xicom[j] f(ax) = f(xt(a,j=1,n)) = f(p(j) + 0 * xi(j)) and f(xx) = f(xt(x, j=1,n)) = f(p(j) + 1 * xi(j)) */ |
/* xt[x,j]=pcom[j]+x*xicom[j] f(ax) = f(xt(a,j=1,n)) = f(p(j) + 0 * xi(j)) and f(xx) = f(xt(x, j=1,n)) = f(p(j) + 1 * xi(j)) */ |
Line 1622 void linmin(double p[], double xi[], int
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Line 1651 void linmin(double p[], double xi[], int
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/* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */ |
/* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */ |
/* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */ |
/* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */ |
/* Find a bracket a,x,b in direction n=xi ie xicom, order may change. Scale is [0:xxs*xi[j]] et non plus [0:xi[j]]*/ |
/* Find a bracket a,x,b in direction n=xi ie xicom, order may change. Scale is [0:xxs*xi[j]] et non plus [0:xi[j]]*/ |
/* if (fx != fx){ */ |
#ifdef LINMINORIGINAL |
/* xxs=xxs/scale; /\* Trying a smaller xx, closer to initial ax=0 *\/ */ |
#else |
/* printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n", axs, xxs, fx,fb, fa, xx, ax, bx); */ |
if (fx != fx){ |
/* } */ |
xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */ |
/* }while(fx != fx); */ |
printf("|"); |
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fprintf(ficlog,"|"); |
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#ifdef DEBUGLINMIN |
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printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n", axs, xxs, fx,fb, fa, xx, ax, bx); |
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#endif |
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} |
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}while(fx != fx); |
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#endif |
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#ifdef DEBUGLINMIN |
#ifdef DEBUGLINMIN |
printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n", ax,xx,bx,fa,fx,fb); |
printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n", ax,xx,bx,fa,fx,fb); |
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fprintf(ficlog,"\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n", ax,xx,bx,fa,fx,fb); |
#endif |
#endif |
*fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/ |
*fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/ |
/* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */ |
/* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */ |
Line 1642 void linmin(double p[], double xi[], int
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Line 1679 void linmin(double p[], double xi[], int
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#endif |
#endif |
#ifdef DEBUGLINMIN |
#ifdef DEBUGLINMIN |
printf("linmin end "); |
printf("linmin end "); |
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fprintf(ficlog,"linmin end "); |
#endif |
#endif |
for (j=1;j<=n;j++) { |
for (j=1;j<=n;j++) { |
/* printf(" before xi[%d]=%12.8f", j,xi[j]); */ |
#ifdef LINMINORIGINAL |
xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */ |
xi[j] *= xmin; |
/* if(xxs <1.0) */ |
#else |
/* printf(" after xi[%d]=%12.8f, xmin=%12.8f, ax=%12.8f, xx=%12.8f, bx=%12.8f, xxs=%12.8f", j,xi[j], xmin, ax, xx, bx,xxs ); */ |
#ifdef DEBUGLINMIN |
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if(xxs <1.0) |
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printf(" before xi[%d]=%12.8f", j,xi[j]); |
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#endif |
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xi[j] *= xmin*xxs; /* xi rescaled by xmin and number of loops: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */ |
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#ifdef DEBUGLINMIN |
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if(xxs <1.0) |
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printf(" after xi[%d]=%12.8f, xmin=%12.8f, ax=%12.8f, xx=%12.8f, bx=%12.8f, xxs=%12.8f", j,xi[j], xmin, ax, xx, bx,xxs ); |
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#endif |
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#endif |
p[j] += xi[j]; /* Parameters values are updated accordingly */ |
p[j] += xi[j]; /* Parameters values are updated accordingly */ |
} |
} |
/* printf("\n"); */ |
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#ifdef DEBUGLINMIN |
#ifdef DEBUGLINMIN |
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printf("\n"); |
printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p)); |
printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p)); |
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fprintf(ficlog,"Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p)); |
for (j=1;j<=n;j++) { |
for (j=1;j<=n;j++) { |
printf(" xi[%d]= %12.7f p[%d]= %12.7f",j,xi[j],j,p[j]); |
printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]); |
if(j % ncovmodel == 0) |
fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]); |
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if(j % ncovmodel == 0){ |
printf("\n"); |
printf("\n"); |
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fprintf(ficlog,"\n"); |
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} |
} |
} |
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#else |
#endif |
#endif |
free_vector(xicom,1,n); |
free_vector(xicom,1,n); |
free_vector(pcom,1,n); |
free_vector(pcom,1,n); |
Line 1691 void powell(double p[], double **xi, int
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Line 1743 void powell(double p[], double **xi, int
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xits=vector(1,n); |
xits=vector(1,n); |
*fret=(*func)(p); |
*fret=(*func)(p); |
for (j=1;j<=n;j++) pt[j]=p[j]; |
for (j=1;j<=n;j++) pt[j]=p[j]; |
rcurr_time = time(NULL); |
rcurr_time = time(NULL); |
for (*iter=1;;++(*iter)) { |
for (*iter=1;;++(*iter)) { |
fp=(*fret); /* From former iteration or initial value */ |
fp=(*fret); /* From former iteration or initial value */ |
ibig=0; |
ibig=0; |
Line 1735 void powell(double p[], double **xi, int
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Line 1787 void powell(double p[], double **xi, int
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for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */ |
for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */ |
fptt=(*fret); |
fptt=(*fret); |
#ifdef DEBUG |
#ifdef DEBUG |
printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret); |
printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret); |
fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret); |
fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret); |
#endif |
#endif |
printf("%d",i);fflush(stdout); /* print direction (parameter) i */ |
printf("%d",i);fflush(stdout); /* print direction (parameter) i */ |
fprintf(ficlog,"%d",i);fflush(ficlog); |
fprintf(ficlog,"%d",i);fflush(ficlog); |
linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/ |
linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/ |
/* Outputs are fret(new point p) p is updated and xit rescaled */ |
/* Outputs are fret(new point p) p is updated and xit rescaled */ |
Line 1836 void powell(double p[], double **xi, int
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Line 1888 void powell(double p[], double **xi, int
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t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */ |
t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */ |
t= t- del*SQR(fp-fptt); |
t= t- del*SQR(fp-fptt); |
#endif |
#endif |
directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */ |
directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */ |
#ifdef DEBUG |
#ifdef DEBUG |
printf("t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest); |
printf("t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest); |
fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest); |
fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest); |
Line 1851 void powell(double p[], double **xi, int
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Line 1903 void powell(double p[], double **xi, int
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if (t < 0.0) { /* Then we use it for new direction */ |
if (t < 0.0) { /* Then we use it for new direction */ |
#else |
#else |
if (directest*t < 0.0) { /* Contradiction between both tests */ |
if (directest*t < 0.0) { /* Contradiction between both tests */ |
printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del); |
printf("directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del); |
printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt); |
printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt); |
fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del); |
fprintf(ficlog,"directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del); |
fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt); |
fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt); |
} |
} |
if (directest < 0.0) { /* Then we use it for new direction */ |
if (directest < 0.0) { /* Then we use it for new direction */ |
Line 1861 void powell(double p[], double **xi, int
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Line 1913 void powell(double p[], double **xi, int
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#ifdef DEBUGLINMIN |
#ifdef DEBUGLINMIN |
printf("Before linmin in direction P%d-P0\n",n); |
printf("Before linmin in direction P%d-P0\n",n); |
for (j=1;j<=n;j++) { |
for (j=1;j<=n;j++) { |
printf("Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]); |
printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]); |
if(j % ncovmodel == 0) |
fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]); |
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if(j % ncovmodel == 0){ |
printf("\n"); |
printf("\n"); |
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fprintf(ficlog,"\n"); |
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} |
} |
} |
#endif |
#endif |
linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/ |
linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/ |
#ifdef DEBUGLINMIN |
#ifdef DEBUGLINMIN |
for (j=1;j<=n;j++) { |
for (j=1;j<=n;j++) { |
printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]); |
printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]); |
if(j % ncovmodel == 0) |
fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]); |
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if(j % ncovmodel == 0){ |
printf("\n"); |
printf("\n"); |
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fprintf(ficlog,"\n"); |
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} |
} |
} |
#endif |
#endif |
for (j=1;j<=n;j++) { |
for (j=1;j<=n;j++) { |
Line 1901 void powell(double p[], double **xi, int
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Line 1959 void powell(double p[], double **xi, int
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/**** Prevalence limit (stable or period prevalence) ****************/ |
/**** Prevalence limit (stable or period prevalence) ****************/ |
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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 */ |
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/* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */ |
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/* Wx is row vector: population in state 1, population in state 2, population dead */ |
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/* or prevalence in state 1, prevalence in state 2, 0 */ |
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/* newm is the matrix after multiplications, its rows are identical at a factor */ |
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/* 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, */ |
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/* 0.51326036147820708, 0.48673963852179264} */ |
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/* If we start from prlim again, prlim tends to a constant matrix */ |
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int i, ii,j,k; |
int i, ii,j,k; |
double min, max, maxmin, maxmax,sumnew=0.; |
double min, max, maxmin, maxmax,sumnew=0.; |
/* double **matprod2(); */ /* test */ |
/* double **matprod2(); */ /* test */ |
double **out, cov[NCOVMAX+1], **pmij(); |
double **out, cov[NCOVMAX+1], **pmij(); |
double **newm; |
double **newm; |
double agefin, delaymax=50 ; /* Max number of years to converge */ |
double agefin, delaymax=100 ; /* Max number of years to converge */ |
|
int ncvloop=0; |
|
|
for (ii=1;ii<=nlstate+ndeath;ii++) |
for (ii=1;ii<=nlstate+ndeath;ii++) |
for (j=1;j<=nlstate+ndeath;j++){ |
for (j=1;j<=nlstate+ndeath;j++){ |
Line 1921 double **prevalim(double **prlim, int nl
|
Line 1997 double **prevalim(double **prlim, int nl
|
cov[1]=1.; |
cov[1]=1.; |
|
|
/* Even if hstepm = 1, at least one multiplication by the unit matrix */ |
/* Even if hstepm = 1, at least one multiplication by the unit matrix */ |
|
/* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */ |
for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){ |
for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){ |
|
ncvloop++; |
newm=savm; |
newm=savm; |
/* Covariates have to be included here again */ |
/* Covariates have to be included here again */ |
cov[2]=agefin; |
cov[2]=agefin; |
Line 1956 double **prevalim(double **prlim, int nl
|
Line 2034 double **prevalim(double **prlim, int nl
|
sumnew=0; |
sumnew=0; |
for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k]; |
for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k]; |
prlim[i][j]= newm[i][j]/(1-sumnew); |
prlim[i][j]= newm[i][j]/(1-sumnew); |
/*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/ |
|
max=FMAX(max,prlim[i][j]); |
max=FMAX(max,prlim[i][j]); |
min=FMIN(min,prlim[i][j]); |
min=FMIN(min,prlim[i][j]); |
|
printf(" age= %d prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d max=%f min=%f\n", (int)age, i, j, i, j, prlim[i][j],(int)agefin, max, min); |
} |
} |
maxmin=max-min; |
maxmin=(max-min)/(max+min)*2; |
maxmax=FMAX(maxmax,maxmin); |
maxmax=FMAX(maxmax,maxmin); |
} /* j loop */ |
} /* j loop */ |
|
*ncvyear= (int)age- (int)agefin; |
|
printf("maxmax=%lf maxmin=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); |
if(maxmax < ftolpl){ |
if(maxmax < ftolpl){ |
|
/* printf("maxmax=%lf maxmin=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */ |
return prlim; |
return prlim; |
} |
} |
} /* age loop */ |
} /* age loop */ |
|
printf("Warning: the stable prevalence at age %d did not converge with the required precision %g > ftolpl=%g. \n\ |
|
Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear); |
|
/* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */ |
return prlim; /* should not reach here */ |
return prlim; /* should not reach here */ |
} |
} |
|
|
Line 2542 double funcone( double *x)
|
Line 2626 double funcone( double *x)
|
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; |
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; |
/*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */ |
/*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */ |
if(globpr){ |
if(globpr){ |
fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\ |
fprintf(ficresilk,"%9ld %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f %8.3f\ |
%11.6f %11.6f %11.6f ", \ |
%11.6f %11.6f %11.6f ", \ |
num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i], |
num[i], 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 2577 void likelione(FILE *ficres,double p[],
|
Line 2661 void likelione(FILE *ficres,double p[],
|
|
|
if(*globpri !=0){ /* Just counts and sums, no printings */ |
if(*globpri !=0){ /* Just counts and sums, no printings */ |
strcpy(fileresilk,"ILK_"); |
strcpy(fileresilk,"ILK_"); |
strcat(fileresilk,fileres); |
strcat(fileresilk,fileresu); |
if((ficresilk=fopen(fileresilk,"w"))==NULL) { |
if((ficresilk=fopen(fileresilk,"w"))==NULL) { |
printf("Problem with resultfile: %s\n", fileresilk); |
printf("Problem with resultfile: %s\n", fileresilk); |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk); |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk); |
} |
} |
fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n"); |
fprintf(ficresilk, "#individual(line's_record) count 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 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 2593 void likelione(FILE *ficres,double p[],
|
Line 2677 void likelione(FILE *ficres,double p[],
|
*fretone=(*funcone)(p); |
*fretone=(*funcone)(p); |
if(*globpri !=0){ |
if(*globpri !=0){ |
fclose(ficresilk); |
fclose(ficresilk); |
fprintf(fichtm,"\n<br>File of contributions to the likelihood (if mle=1): <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk)); |
if (mle ==0) |
fflush(fichtm); |
fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle); |
} |
else if(mle >=1) |
|
fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle); |
|
fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk)); |
|
|
|
fprintf(fichtm,"<br>- The function drawn is -2Log(L) in Log scale: by state of origin <a href=\"%s-ori.png\">%s-ori.png</a><br> \ |
|
<img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_")); |
|
fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \ |
|
<img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_")); |
|
fflush(fichtm); |
|
|
|
for (k=1; k<= nlstate ; k++) { |
|
fprintf(fichtm,"<br>- Probability p%dj by origin %d and destination j <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \ |
|
<img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k); |
|
} |
|
} |
return; |
return; |
} |
} |
|
|
Line 2669 void mlikeli(FILE *ficres,double p[], in
|
Line 2767 void mlikeli(FILE *ficres,double p[], in
|
#endif |
#endif |
free_matrix(xi,1,npar,1,npar); |
free_matrix(xi,1,npar,1,npar); |
fclose(ficrespow); |
fclose(ficrespow); |
printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); |
printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); |
fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); |
fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); |
fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); |
fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); |
|
|
} |
} |
|
|
/**** Computes Hessian and covariance matrix ***/ |
/**** Computes Hessian and covariance matrix ***/ |
void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double [])) |
void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double [])) |
{ |
{ |
double **a,**y,*x,pd; |
double **a,**y,*x,pd; |
double **hess; |
/* double **hess; */ |
int i, j; |
int i, j; |
int *indx; |
int *indx; |
|
|
double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar); |
double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar); |
double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar); |
double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar); |
void lubksb(double **a, int npar, int *indx, double b[]) ; |
void lubksb(double **a, int npar, int *indx, double b[]) ; |
void ludcmp(double **a, int npar, int *indx, double *d) ; |
void ludcmp(double **a, int npar, int *indx, double *d) ; |
double gompertz(double p[]); |
double gompertz(double p[]); |
hess=matrix(1,npar,1,npar); |
/* hess=matrix(1,npar,1,npar); */ |
|
|
printf("\nCalculation of the hessian matrix. Wait...\n"); |
printf("\nCalculation of the hessian matrix. Wait...\n"); |
fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n"); |
fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n"); |
for (i=1;i<=npar;i++){ |
for (i=1;i<=npar;i++){ |
printf("%d",i);fflush(stdout); |
printf("%d-",i);fflush(stdout); |
fprintf(ficlog,"%d",i);fflush(ficlog); |
fprintf(ficlog,"%d-",i);fflush(ficlog); |
|
|
hess[i][i]=hessii(p,ftolhess,i,delti,func,npar); |
hess[i][i]=hessii(p,ftolhess,i,delti,func,npar); |
|
|
Line 2705 void hesscov(double **matcov, double p[]
|
Line 2803 void hesscov(double **matcov, double p[]
|
for (i=1;i<=npar;i++) { |
for (i=1;i<=npar;i++) { |
for (j=1;j<=npar;j++) { |
for (j=1;j<=npar;j++) { |
if (j>i) { |
if (j>i) { |
printf(".%d%d",i,j);fflush(stdout); |
printf(".%d-%d",i,j);fflush(stdout); |
fprintf(ficlog,".%d%d",i,j);fflush(ficlog); |
fprintf(ficlog,".%d-%d",i,j);fflush(ficlog); |
hess[i][j]=hessij(p,delti,i,j,func,npar); |
hess[i][j]=hessij(p,hess, delti,i,j,func,npar); |
|
|
hess[j][i]=hess[i][j]; |
hess[j][i]=hess[i][j]; |
/*printf(" %lf ",hess[i][j]);*/ |
/*printf(" %lf ",hess[i][j]);*/ |
Line 2741 void hesscov(double **matcov, double p[]
|
Line 2839 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 2803 double hessii(double x[], double delta,
|
Line 2926 double hessii(double x[], double delta,
|
p2[theta]=x[theta]-delt; |
p2[theta]=x[theta]-delt; |
k2=func(p2)-fx; |
k2=func(p2)-fx; |
/*res= (k1-2.0*fx+k2)/delt/delt; */ |
/*res= (k1-2.0*fx+k2)/delt/delt; */ |
res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */ |
res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */ |
|
|
#ifdef DEBUGHESS |
#ifdef DEBUGHESSII |
printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx); |
printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx); |
fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx); |
fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx); |
#endif |
#endif |
Line 2819 double hessii(double x[], double delta,
|
Line 2942 double hessii(double x[], double delta,
|
else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ |
else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ |
delts=delt; |
delts=delt; |
} |
} |
} |
} /* End loop k */ |
} |
} |
delti[theta]=delts; |
delti[theta]=delts; |
return res; |
return res; |
|
|
} |
} |
|
|
double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) |
double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar) |
{ |
{ |
int i; |
int i; |
int l=1, lmax=20; |
int l=1, lmax=20; |
double k1,k2,k3,k4,res,fx; |
double k1,k2,k3,k4,res,fx; |
double p2[MAXPARM+1]; |
double p2[MAXPARM+1]; |
int k; |
int k, kmax=1; |
|
double v1, v2, cv12, lc1, lc2; |
|
|
fx=func(x); |
fx=func(x); |
for (k=1; k<=2; k++) { |
for (k=1; k<=kmax; k=k+10) { |
for (i=1;i<=npar;i++) p2[i]=x[i]; |
for (i=1;i<=npar;i++) p2[i]=x[i]; |
p2[thetai]=x[thetai]+delti[thetai]/k; |
p2[thetai]=x[thetai]+delti[thetai]*k; |
p2[thetaj]=x[thetaj]+delti[thetaj]/k; |
p2[thetaj]=x[thetaj]+delti[thetaj]*k; |
k1=func(p2)-fx; |
k1=func(p2)-fx; |
|
|
p2[thetai]=x[thetai]+delti[thetai]/k; |
p2[thetai]=x[thetai]+delti[thetai]*k; |
p2[thetaj]=x[thetaj]-delti[thetaj]/k; |
p2[thetaj]=x[thetaj]-delti[thetaj]*k; |
k2=func(p2)-fx; |
k2=func(p2)-fx; |
|
|
p2[thetai]=x[thetai]-delti[thetai]/k; |
p2[thetai]=x[thetai]-delti[thetai]*k; |
p2[thetaj]=x[thetaj]+delti[thetaj]/k; |
p2[thetaj]=x[thetaj]+delti[thetaj]*k; |
k3=func(p2)-fx; |
k3=func(p2)-fx; |
|
|
p2[thetai]=x[thetai]-delti[thetai]/k; |
p2[thetai]=x[thetai]-delti[thetai]*k; |
p2[thetaj]=x[thetaj]-delti[thetaj]/k; |
p2[thetaj]=x[thetaj]-delti[thetaj]*k; |
k4=func(p2)-fx; |
k4=func(p2)-fx; |
res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */ |
res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */ |
#ifdef DEBUG |
if(k1*k2*k3*k4 <0.){ |
printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); |
kmax=kmax+10; |
fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); |
if(kmax >=10){ |
|
printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol); |
|
fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol); |
|
printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); |
|
fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); |
|
} |
|
} |
|
#ifdef DEBUGHESSIJ |
|
v1=hess[thetai][thetai]; |
|
v2=hess[thetaj][thetaj]; |
|
cv12=res; |
|
/* Computing eigen value of Hessian matrix */ |
|
lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; |
|
lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; |
|
if ((lc2 <0) || (lc1 <0) ){ |
|
printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj); |
|
fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj); |
|
printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); |
|
fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); |
|
} |
#endif |
#endif |
} |
} |
return res; |
return res; |
} |
} |
|
|
|
/* Not done yet: Was supposed to fix if not exactly at the maximum */ |
|
/* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */ |
|
/* { */ |
|
/* int i; */ |
|
/* int l=1, lmax=20; */ |
|
/* double k1,k2,k3,k4,res,fx; */ |
|
/* double p2[MAXPARM+1]; */ |
|
/* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */ |
|
/* int k=0,kmax=10; */ |
|
/* double l1; */ |
|
|
|
/* fx=func(x); */ |
|
/* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */ |
|
/* l1=pow(10,l); */ |
|
/* delts=delt; */ |
|
/* for(k=1 ; k <kmax; k=k+1){ */ |
|
/* delt = delti*(l1*k); */ |
|
/* for (i=1;i<=npar;i++) p2[i]=x[i]; */ |
|
/* p2[thetai]=x[thetai]+delti[thetai]/k; */ |
|
/* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */ |
|
/* k1=func(p2)-fx; */ |
|
|
|
/* p2[thetai]=x[thetai]+delti[thetai]/k; */ |
|
/* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */ |
|
/* k2=func(p2)-fx; */ |
|
|
|
/* p2[thetai]=x[thetai]-delti[thetai]/k; */ |
|
/* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */ |
|
/* k3=func(p2)-fx; */ |
|
|
|
/* p2[thetai]=x[thetai]-delti[thetai]/k; */ |
|
/* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */ |
|
/* k4=func(p2)-fx; */ |
|
/* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */ |
|
/* #ifdef DEBUGHESSIJ */ |
|
/* printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); */ |
|
/* 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 3793 void cvevsij(double ***eij, double x[],
|
Line 3990 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 *ncvyear, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[]) |
{ |
{ |
/* Variance of health expectancies */ |
/* Variance of health expectancies */ |
/* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/ |
/* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/ |
Line 3841 void varevsij(char optionfilefiname[], d
|
Line 4038 void varevsij(char optionfilefiname[], d
|
/*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/ |
/*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/ |
strcat(fileresprobmorprev,digit); /* Tvar to be done */ |
strcat(fileresprobmorprev,digit); /* Tvar to be done */ |
strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */ |
strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */ |
strcat(fileresprobmorprev,fileres); |
strcat(fileresprobmorprev,fileresu); |
if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) { |
if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) { |
printf("Problem with resultfile: %s\n", fileresprobmorprev); |
printf("Problem with resultfile: %s\n", fileresprobmorprev); |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev); |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev); |
Line 3919 void varevsij(char optionfilefiname[], d
|
Line 4116 void varevsij(char optionfilefiname[], d
|
xp[i] = x[i] + (i==theta ?delti[theta]:0); |
xp[i] = x[i] + (i==theta ?delti[theta]:0); |
} |
} |
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); |
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij); |
|
|
if (popbased==1) { |
if (popbased==1) { |
if(mobilav ==0){ |
if(mobilav ==0){ |
Line 3950 void varevsij(char optionfilefiname[], d
|
Line 4147 void varevsij(char optionfilefiname[], d
|
for(i=1; i<=npar; i++) /* Computes gradient x - delta */ |
for(i=1; i<=npar; i++) /* Computes gradient x - delta */ |
xp[i] = x[i] - (i==theta ?delti[theta]:0); |
xp[i] = x[i] - (i==theta ?delti[theta]:0); |
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); |
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear, ij); |
|
|
if (popbased==1) { |
if (popbased==1) { |
if(mobilav ==0){ |
if(mobilav ==0){ |
Line 4025 void varevsij(char optionfilefiname[], d
|
Line 4222 void varevsij(char optionfilefiname[], d
|
/* end ppptj */ |
/* end ppptj */ |
/* x centered again */ |
/* x centered again */ |
hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij); |
hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij); |
prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij); |
prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyear,ij); |
|
|
if (popbased==1) { |
if (popbased==1) { |
if(mobilav ==0){ |
if(mobilav ==0){ |
Line 4103 void varevsij(char optionfilefiname[], d
|
Line 4300 void varevsij(char optionfilefiname[], d
|
} /* end varevsij */ |
} /* end varevsij */ |
|
|
/************ Variance of prevlim ******************/ |
/************ Variance of prevlim ******************/ |
void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[]) |
void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyear, int ij, char strstart[]) |
{ |
{ |
/* Variance of prevalence limit */ |
/* Variance of prevalence limit 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 4142 void varprevlim(char fileres[], double *
|
Line 4339 void varprevlim(char fileres[], double *
|
for(i=1; i<=npar; i++){ /* Computes gradient */ |
for(i=1; i<=npar; i++){ /* Computes gradient */ |
xp[i] = x[i] + (i==theta ?delti[theta]:0); |
xp[i] = x[i] + (i==theta ?delti[theta]:0); |
} |
} |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij); |
for(i=1;i<=nlstate;i++) |
for(i=1;i<=nlstate;i++) |
gp[i] = prlim[i][i]; |
gp[i] = prlim[i][i]; |
|
|
for(i=1; i<=npar; i++) /* Computes gradient */ |
for(i=1; i<=npar; i++) /* Computes gradient */ |
xp[i] = x[i] - (i==theta ?delti[theta]:0); |
xp[i] = x[i] - (i==theta ?delti[theta]:0); |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij); |
for(i=1;i<=nlstate;i++) |
for(i=1;i<=nlstate;i++) |
gm[i] = prlim[i][i]; |
gm[i] = prlim[i][i]; |
|
|
Line 4164 void varprevlim(char fileres[], double *
|
Line 4361 void varprevlim(char fileres[], double *
|
|
|
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==67 ||(int)age== 66 ){ |
|
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 4213 void varprob(char optionfilefiname[], do
|
Line 4415 void varprob(char optionfilefiname[], do
|
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob); |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob); |
} |
} |
strcpy(fileresprobcov,"PROBCOV_"); |
strcpy(fileresprobcov,"PROBCOV_"); |
strcat(fileresprobcov,fileres); |
strcat(fileresprobcov,fileresu); |
if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) { |
if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) { |
printf("Problem with resultfile: %s\n", fileresprobcov); |
printf("Problem with resultfile: %s\n", fileresprobcov); |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov); |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov); |
} |
} |
strcpy(fileresprobcor,"PROBCOR_"); |
strcpy(fileresprobcor,"PROBCOR_"); |
strcat(fileresprobcor,fileres); |
strcat(fileresprobcor,fileresu); |
if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) { |
if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) { |
printf("Problem with resultfile: %s\n", fileresprobcor); |
printf("Problem with resultfile: %s\n", fileresprobcor); |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor); |
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor); |
Line 4571 fprintf(fichtm," \n<ul><li><b>Graphs</b>
|
Line 4773 fprintf(fichtm," \n<ul><li><b>Graphs</b>
|
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, 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\">",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- Pij or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2.svg\">%s_%d-2.svg</a><br> \ |
<img src=\"%s_%d-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- Iij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\ |
Line 4596 divided by h: hPij/h : <a href=\"%s_%d-3
|
Line 4798 divided by h: hPij/h : <a href=\"%s_%d-3
|
<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); |
} |
} |
for(cpt=1; cpt<=nlstate;cpt++) { |
for(cpt=1; cpt<=nlstate;cpt++) { |
fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s%d%d.svg\">%s%d%d.svg</a> <br> \ |
fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d%d.svg\">%s_%d%d.svg</a> <br> \ |
<img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1); |
<img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1); |
} |
} |
/* } /\* end i1 *\/ */ |
/* } /\* end i1 *\/ */ |
Line 4606 divided by h: hPij/h : <a href=\"%s_%d-3
|
Line 4808 divided by h: hPij/h : <a href=\"%s_%d-3
|
fprintf(fichtm,"\ |
fprintf(fichtm,"\ |
\n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\ |
\n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\ |
- Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \ |
- Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \ |
- 95%% confidence intervals and Wald tests of the estimated parameters are in the log file.<br> \ |
- 95%% confidence intervals and Wald tests of the estimated parameters are in the log file if optimization has been done (mle != 0).<br> \ |
But because parameters are usually highly correlated (a higher incidence of disability \ |
But because parameters are usually highly correlated (a higher incidence of disability \ |
and a higher incidence of recovery can give very close observed transition) it might \ |
and a higher incidence of recovery can give very close observed transition) it might \ |
be very useful to look not only at linear confidence intervals estimated from the \ |
be very useful to look not only at linear confidence intervals estimated from the \ |
Line 4666 See page 'Matrix of variance-covariance
|
Line 4868 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 4698 void printinggnuplot(char fileresu[], ch
|
Line 4900 void printinggnuplot(char fileresu[], ch
|
/*#endif */ |
/*#endif */ |
m=pow(2,cptcoveff); |
m=pow(2,cptcoveff); |
|
|
|
/* Contribution to likelihood */ |
|
/* Plot the probability implied in the likelihood */ |
|
fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n"); |
|
fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";"); |
|
/* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */ |
|
fprintf(ficgp,"\nset ter pngcairo size 640, 480"); |
|
/* nice for mle=4 plot by number of matrix products. |
|
replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */ |
|
/* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */ |
|
/* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */ |
|
fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_")); |
|
fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$12):5 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk)); |
|
fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_")); |
|
fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$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_")); */ |
|
|
strcpy(dirfileres,optionfilefiname); |
strcpy(dirfileres,optionfilefiname); |
strcpy(optfileres,"vpl"); |
strcpy(optfileres,"vpl"); |
/* 1eme*/ |
/* 1eme*/ |
Line 4816 plot [%.f:%.f] ", ageminpar, agemaxpar)
|
Line 5047 plot [%.f:%.f] ", ageminpar, agemaxpar)
|
} /* end covariate */ |
} /* end covariate */ |
|
|
/* Survival functions (period) from state i in state j by final state j */ |
/* Survival functions (period) from state i in state j by final state j */ |
for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */ |
for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */ |
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */ |
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */ |
k=3; |
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); |
Line 4849 plot [%.f:%.f] ", ageminpar, agemaxpar)
|
Line 5080 plot [%.f:%.f] ", ageminpar, agemaxpar)
|
} /* end cpt state*/ |
} /* end cpt state*/ |
} /* end covariate */ |
} /* end covariate */ |
|
|
/* CV preval stable (period) */ |
/* CV preval stable (period) for each covariate */ |
for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */ |
for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */ |
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */ |
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */ |
k=3; |
k=3; |
fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt); |
fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt); |
Line 6276 void syscompilerinfo(int logged)
|
Line 6507 void syscompilerinfo(int logged)
|
|
|
} |
} |
|
|
int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){ |
int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyear){ |
/*--------------- Prevalence limit (period or stable prevalence) --------------*/ |
/*--------------- Prevalence limit (period or stable prevalence) --------------*/ |
int i, j, k, i1 ; |
int i, j, k, i1 ; |
double ftolpl = 1.e-10; |
/* double ftolpl = 1.e-10; */ |
double age, agebase, agelim; |
double age, agebase, agelim; |
|
double tot; |
|
|
strcpy(filerespl,"PL_"); |
strcpy(filerespl,"PL_"); |
strcat(filerespl,fileresu); |
strcat(filerespl,fileresu); |
if((ficrespl=fopen(filerespl,"w"))==NULL) { |
if((ficrespl=fopen(filerespl,"w"))==NULL) { |
printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1; |
printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1; |
fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1; |
fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1; |
} |
} |
printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl); |
printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl); |
fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl); |
fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl); |
pstamp(ficrespl); |
pstamp(ficrespl); |
fprintf(ficrespl,"# Period (stable) prevalence \n"); |
fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl); |
fprintf(ficrespl,"#Age "); |
fprintf(ficrespl,"#Age "); |
for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i); |
for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i); |
fprintf(ficrespl,"\n"); |
fprintf(ficrespl,"\n"); |
|
|
/* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */ |
/* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */ |
|
|
Line 6326 int prevalence_limit(double *p, double *
|
Line 6558 int prevalence_limit(double *p, double *
|
for(j=1;j<=cptcoveff;j++) { |
for(j=1;j<=cptcoveff;j++) { |
fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); |
fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); |
} |
} |
for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i); |
for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i); |
fprintf(ficrespl,"\n"); |
fprintf(ficrespl,"Total Years_to_converge\n"); |
|
|
for (age=agebase; age<=agelim; age++){ |
for (age=agebase; age<=agelim; age++){ |
/* for (age=agebase; age<=agebase; age++){ */ |
/* for (age=agebase; age<=agebase; age++){ */ |
prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); |
prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyear, 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, *ncvyear); |
} /* Age */ |
} /* Age */ |
/* was end of cptcod */ |
/* was end of cptcod */ |
} /* cptcov */ |
} /* cptcov */ |
Line 6430 int main(int argc, char *argv[])
|
Line 6665 int main(int argc, char *argv[])
|
#endif |
#endif |
int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav); |
int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav); |
int i,j, k, n=MAXN,iter=0,m,size=100, cptcod; |
int i,j, k, n=MAXN,iter=0,m,size=100, cptcod; |
|
int ncvyearnp=0; |
|
int *ncvyear=&ncvyearnp; /* Number of years needed for the period prevalence to converge */ |
int jj, ll, li, lj, lk; |
int jj, ll, li, lj, lk; |
int numlinepar=0; /* Current linenumber of parameter file */ |
int numlinepar=0; /* Current linenumber of parameter file */ |
int num_filled; |
int num_filled; |
Line 6478 int main(int argc, char *argv[])
|
Line 6714 int main(int argc, char *argv[])
|
double ***param; /* Matrix of parameters */ |
double ***param; /* Matrix of parameters */ |
double *p; |
double *p; |
double **matcov; /* Matrix of covariance */ |
double **matcov; /* Matrix of covariance */ |
|
double **hess; /* Hessian matrix */ |
double ***delti3; /* Scale */ |
double ***delti3; /* Scale */ |
double *delti; /* Scale */ |
double *delti; /* Scale */ |
double ***eij, ***vareij; |
double ***eij, ***vareij; |
Line 6537 int main(int argc, char *argv[])
|
Line 6774 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 6684 int main(int argc, char *argv[])
|
Line 6930 int main(int argc, char *argv[])
|
} |
} |
printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt); |
printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt); |
} |
} |
|
/* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */ |
|
ftolpl=6.e-3; /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */ |
/* Third parameter line */ |
/* Third parameter line */ |
while(fgets(line, MAXLINE, ficpar)) { |
while(fgets(line, MAXLINE, ficpar)) { |
/* If line starts with a # it is a comment */ |
/* If line starts with a # it is a comment */ |
Line 6714 int main(int argc, char *argv[])
|
Line 6961 int main(int argc, char *argv[])
|
} |
} |
} |
} |
/* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */ |
/* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */ |
|
printf("model=1+age+%s\n",model);fflush(stdout); |
} |
} |
/* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */ |
/* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */ |
/* numlinepar=numlinepar+3; /\* In general *\/ */ |
/* numlinepar=numlinepar+3; /\* In general *\/ */ |
/* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */ |
/* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */ |
if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */ |
fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); |
model[strlen(model)-1]='\0'; |
fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); |
fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); |
|
fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); |
|
fflush(ficlog); |
fflush(ficlog); |
/* if(model[0]=='#'|| model[0]== '\0'){ */ |
/* if(model[0]=='#'|| model[0]== '\0'){ */ |
if(model[0]=='#'){ |
if(model[0]=='#'){ |
Line 6786 int main(int argc, char *argv[])
|
Line 7032 int main(int argc, char *argv[])
|
fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso); |
fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso); |
param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); |
param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); |
matcov=matrix(1,npar,1,npar); |
matcov=matrix(1,npar,1,npar); |
|
hess=matrix(1,npar,1,npar); |
} |
} |
else{ |
else{ |
/* Read guessed parameters */ |
/* Read guessed parameters */ |
Line 6894 run imach with mle=-1 to get a correct t
|
Line 7141 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 7089 Please run with mle=-1 to get a correct
|
Line 7337 Please run with mle=-1 to get a correct
|
* 15 i=8 1 2 2 2 |
* 15 i=8 1 2 2 2 |
* 16 2 2 2 2 |
* 16 2 2 2 2 |
*/ |
*/ |
for(h=1; h <=100 ;h++){ |
/* /\* 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++){ *\/ */ |
/* printf("k=%d %d ",k,codtabm(h,k)); */ |
/* /\* printf("k=%d %d ",k,codtabm(h,k)); *\/ */ |
/* codtab[h][k]=codtabm(h,k); */ |
/* /\* codtab[h][k]=codtabm(h,k); *\/ */ |
/* } */ |
/* /\* } *\/ */ |
/* printf("\n"); */ |
/* /\* printf("\n"); *\/ */ |
} |
/* } */ |
/* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */ |
/* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */ |
/* for(i=1; i <=pow(2,cptcoveff-k);i++){ /\* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 *\/ */ |
/* for(i=1; i <=pow(2,cptcoveff-k);i++){ /\* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 *\/ */ |
/* for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */ |
/* for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */ |
Line 7136 Please run with mle=-1 to get a correct
|
Line 7384 Please run with mle=-1 to get a correct
|
printf("Problem with file %s",optionfilegnuplot); |
printf("Problem with file %s",optionfilegnuplot); |
} |
} |
else{ |
else{ |
fprintf(ficgp,"\n# %s\n", version); |
fprintf(ficgp,"\n# IMaCh-%s\n", version); |
fprintf(ficgp,"# %s\n", optionfilegnuplot); |
fprintf(ficgp,"# %s\n", optionfilegnuplot); |
//fprintf(ficgp,"set missing 'NaNq'\n"); |
//fprintf(ficgp,"set missing 'NaNq'\n"); |
fprintf(ficgp,"set datafile missing 'NaNq'\n"); |
fprintf(ficgp,"set datafile missing 'NaNq'\n"); |
Line 7163 Please run with mle=-1 to get a correct
|
Line 7411 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-Japan Society for the Promotion of Sciences 日本学術振興会 (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - <a href=https://software.intel.com/en-us>Intel Software 2015</a></font><br> \ |
|
<hr size=\"2\" color=\"#EC5E5E\"> \n\ |
|
<font size=\"2\">IMaCh-%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\ |
\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 7361 Interval (in months) between two waves:
|
Line 7611 Interval (in months) between two waves:
|
#endif |
#endif |
fclose(ficrespow); |
fclose(ficrespow); |
|
|
hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); |
hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz); |
|
|
for(i=1; i <=NDIM; i++) |
for(i=1; i <=NDIM; i++) |
for(j=i+1;j<=NDIM;j++) |
for(j=i+1;j<=NDIM;j++) |
matcov[i][j]=matcov[j][i]; |
matcov[i][j]=matcov[j][i]; |
|
|
printf("\nCovariance matrix\n "); |
printf("\nCovariance matrix\n "); |
|
fprintf(ficlog,"\nCovariance matrix\n "); |
for(i=1; i <=NDIM; i++) { |
for(i=1; i <=NDIM; i++) { |
for(j=1;j<=NDIM;j++){ |
for(j=1;j<=NDIM;j++){ |
printf("%f ",matcov[i][j]); |
printf("%f ",matcov[i][j]); |
|
fprintf(ficlog,"%f ",matcov[i][j]); |
} |
} |
printf("\n "); |
printf("\n "); fprintf(ficlog,"\n "); |
} |
} |
|
|
printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp); |
printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp); |
Line 7434 Please run with mle=-1 to get a correct
|
Line 7686 Please run with mle=-1 to get a correct
|
free_matrix(ximort,1,NDIM,1,NDIM); |
free_matrix(ximort,1,NDIM,1,NDIM); |
#endif |
#endif |
} /* Endof if mle==-3 mortality only */ |
} /* Endof if mle==-3 mortality only */ |
/* Standard maximisation */ |
/* Standard */ |
else{ /* For mle >=1 */ |
else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */ |
globpr=0;/* debug */ |
globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */ |
/* Computes likelihood for initial parameters */ |
/* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */ |
likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */ |
likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */ |
printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw); |
printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw); |
for (k=1; k<=npar;k++) |
for (k=1; k<=npar;k++) |
printf(" %d %8.5f",k,p[k]); |
printf(" %d %8.5f",k,p[k]); |
printf("\n"); |
printf("\n"); |
globpr=1; /* again, to print the contributions */ |
if(mle>=1){ /* Could be 1 or 2, Real Maximization */ |
|
/* mlikeli uses func not funcone */ |
|
mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func); |
|
} |
|
if(mle==0) {/* No optimization, will print the likelihoods for the datafile */ |
|
globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */ |
|
/* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */ |
|
likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */ |
|
} |
|
globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */ |
likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */ |
likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */ |
printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw); |
printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw); |
for (k=1; k<=npar;k++) |
for (k=1; k<=npar;k++) |
printf(" %d %8.5f",k,p[k]); |
printf(" %d %8.5f",k,p[k]); |
printf("\n"); |
printf("\n"); |
if(mle>=1){ /* Could be 1 or 2, Real Maximisation */ |
|
mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func); |
|
} |
|
|
|
/*--------- results files --------------*/ |
/*--------- results files --------------*/ |
fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model); |
fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model); |
Line 7478 Please run with mle=-1 to get a correct
|
Line 7736 Please run with mle=-1 to get a correct
|
} |
} |
} |
} |
} |
} |
if(mle!=0){ |
if(mle != 0){ |
/* Computing hessian and covariance matrix */ |
/* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */ |
ftolhess=ftol; /* Usually correct */ |
ftolhess=ftol; /* Usually correct */ |
hesscov(matcov, p, npar, delti, ftolhess, func); |
hesscov(matcov, hess, p, npar, delti, ftolhess, func); |
} |
printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n"); |
printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n"); |
fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n"); |
fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n"); |
for(i=1,jk=1; i <=nlstate; i++){ |
for(i=1,jk=1; i <=nlstate; i++){ |
for(k=1; k <=(nlstate+ndeath); k++){ |
for(k=1; k <=(nlstate+ndeath); k++){ |
if (k != i) { |
if (k != i) { |
printf("%d%d ",i,k); |
printf("%d%d ",i,k); |
fprintf(ficlog,"%d%d ",i,k); |
fprintf(ficlog,"%d%d ",i,k); |
for(j=1; j <=ncovmodel; j++){ |
for(j=1; j <=ncovmodel; j++){ |
printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk])); |
printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk])); |
fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk])); |
fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk])); |
jk++; |
jk++; |
} |
|
printf("\n"); |
|
fprintf(ficlog,"\n"); |
} |
} |
printf("\n"); |
|
fprintf(ficlog,"\n"); |
|
} |
} |
} |
} |
} |
} /* end of hesscov and Wald tests */ |
|
|
|
/* */ |
fprintf(ficres,"# Scales (for hessian or gradient estimation)\n"); |
fprintf(ficres,"# Scales (for hessian or gradient estimation)\n"); |
printf("# Scales (for hessian or gradient estimation)\n"); |
printf("# Scales (for hessian or gradient estimation)\n"); |
fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n"); |
fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n"); |
Line 7524 Please run with mle=-1 to get a correct
|
Line 7783 Please run with mle=-1 to get a correct
|
} |
} |
|
|
fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); |
fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); |
if(mle>=1) |
if(mle >= 1) /* To big for the screen */ |
printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); |
printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); |
fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); |
fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); |
/* # 121 Var(a12)\n\ */ |
/* # 121 Var(a12)\n\ */ |
Line 7587 Please run with mle=-1 to get a correct
|
Line 7846 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 7717 Please run with mle=-1 to get a correct
|
Line 7976 Please run with mle=-1 to get a correct
|
/*--------------- Prevalence limit (period or stable prevalence) --------------*/ |
/*--------------- Prevalence limit (period or stable prevalence) --------------*/ |
/*#include "prevlim.h"*/ /* Use ficrespl, ficlog */ |
/*#include "prevlim.h"*/ /* Use ficrespl, ficlog */ |
prlim=matrix(1,nlstate,1,nlstate); |
prlim=matrix(1,nlstate,1,nlstate); |
prevalence_limit(p, prlim, ageminpar, agemaxpar); |
prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, ncvyear); |
fclose(ficrespl); |
fclose(ficrespl); |
|
|
#ifdef FREEEXIT2 |
#ifdef FREEEXIT2 |
Line 7879 Please run with mle=-1 to get a correct
|
Line 8138 Please run with mle=-1 to get a correct
|
for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/ |
for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/ |
oldm=oldms;savm=savms; /* ZZ Segmentation fault */ |
oldm=oldms;savm=savms; /* ZZ Segmentation fault */ |
cptcod= 0; /* To be deleted */ |
cptcod= 0; /* To be deleted */ |
varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */ |
varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */ |
fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are "); |
fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are "); |
if(vpopbased==1) |
if(vpopbased==1) |
fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav); |
fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav); |
Line 7891 Please run with mle=-1 to get a correct
|
Line 8150 Please run with mle=-1 to get a correct
|
/* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */ |
/* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */ |
epj=vector(1,nlstate+1); |
epj=vector(1,nlstate+1); |
for(age=bage; age <=fage ;age++){ |
for(age=bage; age <=fage ;age++){ |
prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); /*ZZ Is it the correct prevalim */ |
prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyear, k); /*ZZ Is it the correct prevalim */ |
if (vpopbased==1) { |
if (vpopbased==1) { |
if(mobilav ==0){ |
if(mobilav ==0){ |
for(i=1; i<=nlstate;i++) |
for(i=1; i<=nlstate;i++) |
Line 7903 Please run with mle=-1 to get a correct
|
Line 8162 Please run with mle=-1 to get a correct
|
} |
} |
|
|
fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav); |
fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav); |
|
/* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */ |
/* printf(" age %4.0f ",age); */ |
/* printf(" age %4.0f ",age); */ |
for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){ |
for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){ |
for(i=1, epj[j]=0.;i <=nlstate;i++) { |
for(i=1, epj[j]=0.;i <=nlstate;i++) { |
Line 7963 Please run with mle=-1 to get a correct
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Line 8223 Please run with mle=-1 to get a correct
|
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varpl=matrix(1,nlstate,(int) bage, (int) fage); |
varpl=matrix(1,nlstate,(int) bage, (int) fage); |
oldm=oldms;savm=savms; |
oldm=oldms;savm=savms; |
varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart); |
varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyear, k, strstart); |
free_matrix(varpl,1,nlstate,(int) bage, (int)fage); |
free_matrix(varpl,1,nlstate,(int) bage, (int)fage); |
/*}*/ |
/*}*/ |
} |
} |
Line 7982 Please run with mle=-1 to get a correct
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Line 8242 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); |
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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); |