/* $Id: imach.c,v 1.65 2002/12/11 16:58:19 lievre Exp $
Interpolated Markov Chain
Short summary of the programme:
This program computes Healthy Life Expectancies from
cross-longitudinal data. Cross-longitudinal data consist in: -1- a
first survey ("cross") where individuals from different ages are
interviewed on their health status or degree of disability (in the
case of a health survey which is our main interest) -2- at least a
second wave of interviews ("longitudinal") which measure each change
(if any) in individual health status. Health expectancies are
computed from the time spent in each health state according to a
model. More health states you consider, more time is necessary to reach the
Maximum Likelihood of the parameters involved in the model. The
simplest model is the multinomial logistic model where pij is the
probability to be observed in state j at the second wave
conditional to be observed in state i at the first wave. Therefore
the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
'age' is age and 'sex' is a covariate. If you want to have a more
complex model than "constant and age", you should modify the program
where the markup *Covariates have to be included here again* invites
you to do it. More covariates you add, slower the
convergence.
The advantage of this computer programme, compared to a simple
multinomial logistic model, is clear when the delay between waves is not
identical for each individual. Also, if a individual missed an
intermediate interview, the information is lost, but taken into
account using an interpolation or extrapolation.
hPijx is the probability to be observed in state i at age x+h
conditional to the observed state i at age x. The delay 'h' can be
split into an exact number (nh*stepm) of unobserved intermediate
states. This elementary transition (by month or quarter trimester,
semester or year) is model as a multinomial logistic. The hPx
matrix is simply the matrix product of nh*stepm elementary matrices
and the contribution of each individual to the likelihood is simply
hPijx.
Also this programme outputs the covariance matrix of the parameters but also
of the life expectancies. It also computes the stable prevalence.
Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
Institut national d'études démographiques, Paris.
This software have been partly granted by Euro-REVES, a concerted action
from the European Union.
It is copyrighted identically to a GNU software product, ie programme and
software can be distributed freely for non commercial use. Latest version
can be accessed at http://euroreves.ined.fr/imach .
**********************************************************************/
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <unistd.h>
#define MAXLINE 256
#define GNUPLOTPROGRAM "gnuplot"
/*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
#define FILENAMELENGTH 80
/*#define DEBUG*/
#define windows
#define GLOCK_ERROR_NOPATH -1 /* empty path */
#define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
#define MAXPARM 30 /* Maximum number of parameters for the optimization */
#define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
#define NINTERVMAX 8
#define NLSTATEMAX 8 /* Maximum number of live states (for func) */
#define NDEATHMAX 8 /* Maximum number of dead states (for func) */
#define NCOVMAX 8 /* Maximum number of covariates */
#define MAXN 20000
#define YEARM 12. /* Number of months per year */
#define AGESUP 130
#define AGEBASE 40
#ifdef windows
#define DIRSEPARATOR '\\'
#define ODIRSEPARATOR '/'
#else
#define DIRSEPARATOR '/'
#define ODIRSEPARATOR '\\'
#endif
char version[80]="Imach version 0.9, November 2002, INED-EUROREVES ";
int erreur; /* Error number */
int nvar;
int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
int npar=NPARMAX;
int nlstate=2; /* Number of live states */
int ndeath=1; /* Number of dead states */
int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
int popbased=0;
int *wav; /* Number of waves for this individuual 0 is possible */
int maxwav; /* Maxim number of waves */
int jmin, jmax; /* min, max spacing between 2 waves */
int mle, weightopt;
int **mw; /* mw[mi][i] is number of the mi wave for this individual */
int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
* wave mi and wave mi+1 is not an exact multiple of stepm. */
double jmean; /* Mean space between 2 waves */
double **oldm, **newm, **savm; /* Working pointers to matrices */
double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
FILE *ficlog;
FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
FILE *ficresprobmorprev;
FILE *fichtm; /* Html File */
FILE *ficreseij;
char filerese[FILENAMELENGTH];
FILE *ficresvij;
char fileresv[FILENAMELENGTH];
FILE *ficresvpl;
char fileresvpl[FILENAMELENGTH];
char title[MAXLINE];
char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
char filelog[FILENAMELENGTH]; /* Log file */
char filerest[FILENAMELENGTH];
char fileregp[FILENAMELENGTH];
char popfile[FILENAMELENGTH];
char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
#define NR_END 1
#define FREE_ARG char*
#define FTOL 1.0e-10
#define NRANSI
#define ITMAX 200
#define TOL 2.0e-4
#define CGOLD 0.3819660
#define ZEPS 1.0e-10
#define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
#define GOLD 1.618034
#define GLIMIT 100.0
#define TINY 1.0e-20
static double maxarg1,maxarg2;
#define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
#define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
#define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
#define rint(a) floor(a+0.5)
static double sqrarg;
#define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
#define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
int imx;
int stepm;
/* Stepm, step in month: minimum step interpolation*/
int estepm;
/* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
int m,nb;
int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
double **pmmij, ***probs;
double dateintmean=0;
double *weight;
int **s; /* Status */
double *agedc, **covar, idx;
int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
double ftol=FTOL; /* Tolerance for computing Max Likelihood */
double ftolhess; /* Tolerance for computing hessian */
/**************** split *************************/
static int split( char *path, char *dirc, char *name, char *ext, char *finame )
{
char *ss; /* pointer */
int l1, l2; /* length counters */
l1 = strlen(path ); /* length of path */
if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
ss= strrchr( path, DIRSEPARATOR ); /* find last / */
if ( ss == NULL ) { /* no directory, so use current */
/*if(strrchr(path, ODIRSEPARATOR )==NULL)
printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
#if defined(__bsd__) /* get current working directory */
extern char *getwd( );
if ( getwd( dirc ) == NULL ) {
#else
extern char *getcwd( );
if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
#endif
return( GLOCK_ERROR_GETCWD );
}
strcpy( name, path ); /* we've got it */
} else { /* strip direcotry from path */
ss++; /* after this, the filename */
l2 = strlen( ss ); /* length of filename */
if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
strcpy( name, ss ); /* save file name */
strncpy( dirc, path, l1 - l2 ); /* now the directory */
dirc[l1-l2] = 0; /* add zero */
}
l1 = strlen( dirc ); /* length of directory */
#ifdef windows
if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
#else
if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
#endif
ss = strrchr( name, '.' ); /* find last / */
ss++;
strcpy(ext,ss); /* save extension */
l1= strlen( name);
l2= strlen(ss)+1;
strncpy( finame, name, l1-l2);
finame[l1-l2]= 0;
return( 0 ); /* we're done */
}
/******************************************/
void replace(char *s, char*t)
{
int i;
int lg=20;
i=0;
lg=strlen(t);
for(i=0; i<= lg; i++) {
(s[i] = t[i]);
if (t[i]== '\\') s[i]='/';
}
}
int nbocc(char *s, char occ)
{
int i,j=0;
int lg=20;
i=0;
lg=strlen(s);
for(i=0; i<= lg; i++) {
if (s[i] == occ ) j++;
}
return j;
}
void cutv(char *u,char *v, char*t, char occ)
{
/* cuts string t into u and v where u is ended by char occ excluding it
and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
gives u="abcedf" and v="ghi2j" */
int i,lg,j,p=0;
i=0;
for(j=0; j<=strlen(t)-1; j++) {
if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
}
lg=strlen(t);
for(j=0; j<p; j++) {
(u[j] = t[j]);
}
u[p]='\0';
for(j=0; j<= lg; j++) {
if (j>=(p+1))(v[j-p-1] = t[j]);
}
}
/********************** nrerror ********************/
void nrerror(char error_text[])
{
fprintf(stderr,"ERREUR ...\n");
fprintf(stderr,"%s\n",error_text);
exit(EXIT_FAILURE);
}
/*********************** vector *******************/
double *vector(int nl, int nh)
{
double *v;
v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
if (!v) nrerror("allocation failure in vector");
return v-nl+NR_END;
}
/************************ free vector ******************/
void free_vector(double*v, int nl, int nh)
{
free((FREE_ARG)(v+nl-NR_END));
}
/************************ivector *******************************/
int *ivector(long nl,long nh)
{
int *v;
v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
if (!v) nrerror("allocation failure in ivector");
return v-nl+NR_END;
}
/******************free ivector **************************/
void free_ivector(int *v, long nl, long nh)
{
free((FREE_ARG)(v+nl-NR_END));
}
/******************* imatrix *******************************/
int **imatrix(long nrl, long nrh, long ncl, long nch)
/* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
{
long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
int **m;
/* allocate pointers to rows */
m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
if (!m) nrerror("allocation failure 1 in matrix()");
m += NR_END;
m -= nrl;
/* allocate rows and set pointers to them */
m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
m[nrl] += NR_END;
m[nrl] -= ncl;
for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
/* return pointer to array of pointers to rows */
return m;
}
/****************** free_imatrix *************************/
void free_imatrix(m,nrl,nrh,ncl,nch)
int **m;
long nch,ncl,nrh,nrl;
/* free an int matrix allocated by imatrix() */
{
free((FREE_ARG) (m[nrl]+ncl-NR_END));
free((FREE_ARG) (m+nrl-NR_END));
}
/******************* matrix *******************************/
double **matrix(long nrl, long nrh, long ncl, long nch)
{
long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
double **m;
m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
if (!m) nrerror("allocation failure 1 in matrix()");
m += NR_END;
m -= nrl;
m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
m[nrl] += NR_END;
m[nrl] -= ncl;
for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
return m;
}
/*************************free matrix ************************/
void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
{
free((FREE_ARG)(m[nrl]+ncl-NR_END));
free((FREE_ARG)(m+nrl-NR_END));
}
/******************* ma3x *******************************/
double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
{
long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
double ***m;
m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
if (!m) nrerror("allocation failure 1 in matrix()");
m += NR_END;
m -= nrl;
m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
m[nrl] += NR_END;
m[nrl] -= ncl;
for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
m[nrl][ncl] += NR_END;
m[nrl][ncl] -= nll;
for (j=ncl+1; j<=nch; j++)
m[nrl][j]=m[nrl][j-1]+nlay;
for (i=nrl+1; i<=nrh; i++) {
m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
for (j=ncl+1; j<=nch; j++)
m[i][j]=m[i][j-1]+nlay;
}
return m;
}
/*************************free ma3x ************************/
void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
{
free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
free((FREE_ARG)(m[nrl]+ncl-NR_END));
free((FREE_ARG)(m+nrl-NR_END));
}
/***************** f1dim *************************/
extern int ncom;
extern double *pcom,*xicom;
extern double (*nrfunc)(double []);
double f1dim(double x)
{
int j;
double f;
double *xt;
xt=vector(1,ncom);
for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
f=(*nrfunc)(xt);
free_vector(xt,1,ncom);
return f;
}
/*****************brent *************************/
double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
{
int iter;
double a,b,d,etemp;
double fu,fv,fw,fx;
double ftemp;
double p,q,r,tol1,tol2,u,v,w,x,xm;
double e=0.0;
a=(ax < cx ? ax : cx);
b=(ax > cx ? ax : cx);
x=w=v=bx;
fw=fv=fx=(*f)(x);
for (iter=1;iter<=ITMAX;iter++) {
xm=0.5*(a+b);
tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
/* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
printf(".");fflush(stdout);
fprintf(ficlog,".");fflush(ficlog);
#ifdef DEBUG
printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
/* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
#endif
if (fabs(x-xm) <= (tol2-0.5*(b-a))){
*xmin=x;
return fx;
}
ftemp=fu;
if (fabs(e) > tol1) {
r=(x-w)*(fx-fv);
q=(x-v)*(fx-fw);
p=(x-v)*q-(x-w)*r;
q=2.0*(q-r);
if (q > 0.0) p = -p;
q=fabs(q);
etemp=e;
e=d;
if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
d=CGOLD*(e=(x >= xm ? a-x : b-x));
else {
d=p/q;
u=x+d;
if (u-a < tol2 || b-u < tol2)
d=SIGN(tol1,xm-x);
}
} else {
d=CGOLD*(e=(x >= xm ? a-x : b-x));
}
u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
fu=(*f)(u);
if (fu <= fx) {
if (u >= x) a=x; else b=x;
SHFT(v,w,x,u)
SHFT(fv,fw,fx,fu)
} else {
if (u < x) a=u; else b=u;
if (fu <= fw || w == x) {
v=w;
w=u;
fv=fw;
fw=fu;
} else if (fu <= fv || v == x || v == w) {
v=u;
fv=fu;
}
}
}
nrerror("Too many iterations in brent");
*xmin=x;
return fx;
}
/****************** mnbrak ***********************/
void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
double (*func)(double))
{
double ulim,u,r,q, dum;
double fu;
*fa=(*func)(*ax);
*fb=(*func)(*bx);
if (*fb > *fa) {
SHFT(dum,*ax,*bx,dum)
SHFT(dum,*fb,*fa,dum)
}
*cx=(*bx)+GOLD*(*bx-*ax);
*fc=(*func)(*cx);
while (*fb > *fc) {
r=(*bx-*ax)*(*fb-*fc);
q=(*bx-*cx)*(*fb-*fa);
u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
(2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
ulim=(*bx)+GLIMIT*(*cx-*bx);
if ((*bx-u)*(u-*cx) > 0.0) {
fu=(*func)(u);
} else if ((*cx-u)*(u-ulim) > 0.0) {
fu=(*func)(u);
if (fu < *fc) {
SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
SHFT(*fb,*fc,fu,(*func)(u))
}
} else if ((u-ulim)*(ulim-*cx) >= 0.0) {
u=ulim;
fu=(*func)(u);
} else {
u=(*cx)+GOLD*(*cx-*bx);
fu=(*func)(u);
}
SHFT(*ax,*bx,*cx,u)
SHFT(*fa,*fb,*fc,fu)
}
}
/*************** linmin ************************/
int ncom;
double *pcom,*xicom;
double (*nrfunc)(double []);
void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
{
double brent(double ax, double bx, double cx,
double (*f)(double), double tol, double *xmin);
double f1dim(double x);
void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
double *fc, double (*func)(double));
int j;
double xx,xmin,bx,ax;
double fx,fb,fa;
ncom=n;
pcom=vector(1,n);
xicom=vector(1,n);
nrfunc=func;
for (j=1;j<=n;j++) {
pcom[j]=p[j];
xicom[j]=xi[j];
}
ax=0.0;
xx=1.0;
mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
*fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
#ifdef DEBUG
printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
#endif
for (j=1;j<=n;j++) {
xi[j] *= xmin;
p[j] += xi[j];
}
free_vector(xicom,1,n);
free_vector(pcom,1,n);
}
/*************** powell ************************/
void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
double (*func)(double []))
{
void linmin(double p[], double xi[], int n, double *fret,
double (*func)(double []));
int i,ibig,j;
double del,t,*pt,*ptt,*xit;
double fp,fptt;
double *xits;
pt=vector(1,n);
ptt=vector(1,n);
xit=vector(1,n);
xits=vector(1,n);
*fret=(*func)(p);
for (j=1;j<=n;j++) pt[j]=p[j];
for (*iter=1;;++(*iter)) {
fp=(*fret);
ibig=0;
del=0.0;
printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
for (i=1;i<=n;i++)
printf(" %d %.12f",i, p[i]);
fprintf(ficlog," %d %.12f",i, p[i]);
printf("\n");
fprintf(ficlog,"\n");
for (i=1;i<=n;i++) {
for (j=1;j<=n;j++) xit[j]=xi[j][i];
fptt=(*fret);
#ifdef DEBUG
printf("fret=%lf \n",*fret);
fprintf(ficlog,"fret=%lf \n",*fret);
#endif
printf("%d",i);fflush(stdout);
fprintf(ficlog,"%d",i);fflush(ficlog);
linmin(p,xit,n,fret,func);
if (fabs(fptt-(*fret)) > del) {
del=fabs(fptt-(*fret));
ibig=i;
}
#ifdef DEBUG
printf("%d %.12e",i,(*fret));
fprintf(ficlog,"%d %.12e",i,(*fret));
for (j=1;j<=n;j++) {
xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
printf(" x(%d)=%.12e",j,xit[j]);
fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
}
for(j=1;j<=n;j++) {
printf(" p=%.12e",p[j]);
fprintf(ficlog," p=%.12e",p[j]);
}
printf("\n");
fprintf(ficlog,"\n");
#endif
}
if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
#ifdef DEBUG
int k[2],l;
k[0]=1;
k[1]=-1;
printf("Max: %.12e",(*func)(p));
fprintf(ficlog,"Max: %.12e",(*func)(p));
for (j=1;j<=n;j++) {
printf(" %.12e",p[j]);
fprintf(ficlog," %.12e",p[j]);
}
printf("\n");
fprintf(ficlog,"\n");
for(l=0;l<=1;l++) {
for (j=1;j<=n;j++) {
ptt[j]=p[j]+(p[j]-pt[j])*k[l];
printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
}
printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
}
#endif
free_vector(xit,1,n);
free_vector(xits,1,n);
free_vector(ptt,1,n);
free_vector(pt,1,n);
return;
}
if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
for (j=1;j<=n;j++) {
ptt[j]=2.0*p[j]-pt[j];
xit[j]=p[j]-pt[j];
pt[j]=p[j];
}
fptt=(*func)(ptt);
if (fptt < fp) {
t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
if (t < 0.0) {
linmin(p,xit,n,fret,func);
for (j=1;j<=n;j++) {
xi[j][ibig]=xi[j][n];
xi[j][n]=xit[j];
}
#ifdef DEBUG
printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
for(j=1;j<=n;j++){
printf(" %.12e",xit[j]);
fprintf(ficlog," %.12e",xit[j]);
}
printf("\n");
fprintf(ficlog,"\n");
#endif
}
}
}
}
/**** Prevalence limit (stable prevalence) ****************/
double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
{
/* Computes the prevalence limit in each live state at age x by left multiplying the unit
matrix by transitions matrix until convergence is reached */
int i, ii,j,k;
double min, max, maxmin, maxmax,sumnew=0.;
double **matprod2();
double **out, cov[NCOVMAX], **pmij();
double **newm;
double agefin, delaymax=50 ; /* Max number of years to converge */
for (ii=1;ii<=nlstate+ndeath;ii++)
for (j=1;j<=nlstate+ndeath;j++){
oldm[ii][j]=(ii==j ? 1.0 : 0.0);
}
cov[1]=1.;
/* Even if hstepm = 1, at least one multiplication by the unit matrix */
for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
newm=savm;
/* Covariates have to be included here again */
cov[2]=agefin;
for (k=1; k<=cptcovn;k++) {
cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
/* printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
}
for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
for (k=1; k<=cptcovprod;k++)
cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
/*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
/*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
/*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
savm=oldm;
oldm=newm;
maxmax=0.;
for(j=1;j<=nlstate;j++){
min=1.;
max=0.;
for(i=1; i<=nlstate; i++) {
sumnew=0;
for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
prlim[i][j]= newm[i][j]/(1-sumnew);
max=FMAX(max,prlim[i][j]);
min=FMIN(min,prlim[i][j]);
}
maxmin=max-min;
maxmax=FMAX(maxmax,maxmin);
}
if(maxmax < ftolpl){
return prlim;
}
}
}
/*************** transition probabilities ***************/
double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
{
double s1, s2;
/*double t34;*/
int i,j,j1, nc, ii, jj;
for(i=1; i<= nlstate; i++){
for(j=1; j<i;j++){
for (nc=1, s2=0.;nc <=ncovmodel; nc++){
/*s2 += param[i][j][nc]*cov[nc];*/
s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
/*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
}
ps[i][j]=s2;
/*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
}
for(j=i+1; j<=nlstate+ndeath;j++){
for (nc=1, s2=0.;nc <=ncovmodel; nc++){
s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
/*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
}
ps[i][j]=s2;
}
}
/*ps[3][2]=1;*/
for(i=1; i<= nlstate; i++){
s1=0;
for(j=1; j<i; j++)
s1+=exp(ps[i][j]);
for(j=i+1; j<=nlstate+ndeath; j++)
s1+=exp(ps[i][j]);
ps[i][i]=1./(s1+1.);
for(j=1; j<i; j++)
ps[i][j]= exp(ps[i][j])*ps[i][i];
for(j=i+1; j<=nlstate+ndeath; j++)
ps[i][j]= exp(ps[i][j])*ps[i][i];
/* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
} /* end i */
for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
for(jj=1; jj<= nlstate+ndeath; jj++){
ps[ii][jj]=0;
ps[ii][ii]=1;
}
}
/* for(ii=1; ii<= nlstate+ndeath; ii++){
for(jj=1; jj<= nlstate+ndeath; jj++){
printf("%lf ",ps[ii][jj]);
}
printf("\n ");
}
printf("\n ");printf("%lf ",cov[2]);*/
/*
for(i=1; i<= npar; i++) printf("%f ",x[i]);
goto end;*/
return ps;
}
/**************** Product of 2 matrices ******************/
double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
{
/* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
/* in, b, out are matrice of pointers which should have been initialized
before: only the contents of out is modified. The function returns
a pointer to pointers identical to out */
long i, j, k;
for(i=nrl; i<= nrh; i++)
for(k=ncolol; k<=ncoloh; k++)
for(j=ncl,out[i][k]=0.; j<=nch; j++)
out[i][k] +=in[i][j]*b[j][k];
return out;
}
/************* Higher Matrix Product ***************/
double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
{
/* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month
duration (i.e. until
age (in years) age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.
Output is stored in matrix po[i][j][h] for h every 'hstepm' step
(typically every 2 years instead of every month which is too big).
Model is determined by parameters x and covariates have to be
included manually here.
*/
int i, j, d, h, k;
double **out, cov[NCOVMAX];
double **newm;
/* Hstepm could be zero and should return the unit matrix */
for (i=1;i<=nlstate+ndeath;i++)
for (j=1;j<=nlstate+ndeath;j++){
oldm[i][j]=(i==j ? 1.0 : 0.0);
po[i][j][0]=(i==j ? 1.0 : 0.0);
}
/* Even if hstepm = 1, at least one multiplication by the unit matrix */
for(h=1; h <=nhstepm; h++){
for(d=1; d <=hstepm; d++){
newm=savm;
/* Covariates have to be included here again */
cov[1]=1.;
cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
for (k=1; k<=cptcovage;k++)
cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
for (k=1; k<=cptcovprod;k++)
cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
/*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
/*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
pmij(pmmij,cov,ncovmodel,x,nlstate));
savm=oldm;
oldm=newm;
}
for(i=1; i<=nlstate+ndeath; i++)
for(j=1;j<=nlstate+ndeath;j++) {
po[i][j][h]=newm[i][j];
/*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
*/
}
} /* end h */
return po;
}
/*************** log-likelihood *************/
double func( double *x)
{
int i, ii, j, k, mi, d, kk;
double l, ll[NLSTATEMAX], cov[NCOVMAX];
double **out;
double sw; /* Sum of weights */
double lli; /* Individual log likelihood */
int s1, s2;
double bbh;
long ipmx;
/*extern weight */
/* We are differentiating ll according to initial status */
/* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
/*for(i=1;i<imx;i++)
printf(" %d\n",s[4][i]);
*/
cov[1]=1.;
for(k=1; k<=nlstate; k++) ll[k]=0.;
if(mle==1){
for (i=1,ipmx=0, sw=0.; i<=imx; i++){
for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
for(mi=1; mi<= wav[i]-1; mi++){
for (ii=1;ii<=nlstate+ndeath;ii++)
for (j=1;j<=nlstate+ndeath;j++){
oldm[ii][j]=(ii==j ? 1.0 : 0.0);
savm[ii][j]=(ii==j ? 1.0 : 0.0);
}
for(d=0; d<dh[mi][i]; d++){
newm=savm;
cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
for (kk=1; kk<=cptcovage;kk++) {
cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
}
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
savm=oldm;
oldm=newm;
} /* end mult */
/*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
/* But now since version 0.9 we anticipate for bias and large stepm.
* If stepm is larger than one month (smallest stepm) and if the exact delay
* (in months) between two waves is not a multiple of stepm, we rounded to
* the nearest (and in case of equal distance, to the lowest) interval but now
* we keep into memory the bias bh[mi][i] and also the previous matrix product
* (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
* probability in order to take into account the bias as a fraction of the way
* from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
* -stepm/2 to stepm/2 .
* For stepm=1 the results are the same as for previous versions of Imach.
* For stepm > 1 the results are less biased than in previous versions.
*/
s1=s[mw[mi][i]][i];
s2=s[mw[mi+1][i]][i];
bbh=(double)bh[mi][i]/(double)stepm;
/* bias is positive if real duration
* is higher than the multiple of stepm and negative otherwise.
*/
/* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
/*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
/*if(lli ==000.0)*/
/*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
ipmx +=1;
sw += weight[i];
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
} /* end of wave */
} /* end of individual */
} else if(mle==2){
for (i=1,ipmx=0, sw=0.; i<=imx; i++){
for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
for(mi=1; mi<= wav[i]-1; mi++){
for (ii=1;ii<=nlstate+ndeath;ii++)
for (j=1;j<=nlstate+ndeath;j++){
oldm[ii][j]=(ii==j ? 1.0 : 0.0);
savm[ii][j]=(ii==j ? 1.0 : 0.0);
}
for(d=0; d<=dh[mi][i]; d++){
newm=savm;
cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
for (kk=1; kk<=cptcovage;kk++) {
cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
}
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
savm=oldm;
oldm=newm;
} /* end mult */
/*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
/* But now since version 0.9 we anticipate for bias and large stepm.
* If stepm is larger than one month (smallest stepm) and if the exact delay
* (in months) between two waves is not a multiple of stepm, we rounded to
* the nearest (and in case of equal distance, to the lowest) interval but now
* we keep into memory the bias bh[mi][i] and also the previous matrix product
* (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
* probability in order to take into account the bias as a fraction of the way
* from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
* -stepm/2 to stepm/2 .
* For stepm=1 the results are the same as for previous versions of Imach.
* For stepm > 1 the results are less biased than in previous versions.
*/
s1=s[mw[mi][i]][i];
s2=s[mw[mi+1][i]][i];
bbh=(double)bh[mi][i]/(double)stepm;
/* bias is positive if real duration
* is higher than the multiple of stepm and negative otherwise.
*/
lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
/* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
/*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
/*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
/*if(lli ==000.0)*/
/*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
ipmx +=1;
sw += weight[i];
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
} /* end of wave */
} /* end of individual */
} else if(mle==3){ /* exponential inter-extrapolation */
for (i=1,ipmx=0, sw=0.; i<=imx; i++){
for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
for(mi=1; mi<= wav[i]-1; mi++){
for (ii=1;ii<=nlstate+ndeath;ii++)
for (j=1;j<=nlstate+ndeath;j++){
oldm[ii][j]=(ii==j ? 1.0 : 0.0);
savm[ii][j]=(ii==j ? 1.0 : 0.0);
}
for(d=0; d<dh[mi][i]; d++){
newm=savm;
cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
for (kk=1; kk<=cptcovage;kk++) {
cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
}
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
savm=oldm;
oldm=newm;
} /* end mult */
/*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
/* But now since version 0.9 we anticipate for bias and large stepm.
* If stepm is larger than one month (smallest stepm) and if the exact delay
* (in months) between two waves is not a multiple of stepm, we rounded to
* the nearest (and in case of equal distance, to the lowest) interval but now
* we keep into memory the bias bh[mi][i] and also the previous matrix product
* (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
* probability in order to take into account the bias as a fraction of the way
* from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
* -stepm/2 to stepm/2 .
* For stepm=1 the results are the same as for previous versions of Imach.
* For stepm > 1 the results are less biased than in previous versions.
*/
s1=s[mw[mi][i]][i];
s2=s[mw[mi+1][i]][i];
bbh=(double)bh[mi][i]/(double)stepm;
/* bias is positive if real duration
* is higher than the multiple of stepm and negative otherwise.
*/
/* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
/*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
/*if(lli ==000.0)*/
/*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
ipmx +=1;
sw += weight[i];
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
} /* end of wave */
} /* end of individual */
}else{ /* ml=4 no inter-extrapolation */
for (i=1,ipmx=0, sw=0.; i<=imx; i++){
for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
for(mi=1; mi<= wav[i]-1; mi++){
for (ii=1;ii<=nlstate+ndeath;ii++)
for (j=1;j<=nlstate+ndeath;j++){
oldm[ii][j]=(ii==j ? 1.0 : 0.0);
savm[ii][j]=(ii==j ? 1.0 : 0.0);
}
for(d=0; d<dh[mi][i]; d++){
newm=savm;
cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
for (kk=1; kk<=cptcovage;kk++) {
cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
}
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
savm=oldm;
oldm=newm;
} /* end mult */
lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
ipmx +=1;
sw += weight[i];
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
} /* end of wave */
} /* end of individual */
} /* End of if */
for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
/* printf("l1=%f l2=%f ",ll[1],ll[2]); */
l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
return -l;
}
/*********** Maximum Likelihood Estimation ***************/
void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
{
int i,j, iter;
double **xi,*delti;
double fret;
xi=matrix(1,npar,1,npar);
for (i=1;i<=npar;i++)
for (j=1;j<=npar;j++)
xi[i][j]=(i==j ? 1.0 : 0.0);
printf("Powell\n"); fprintf(ficlog,"Powell\n");
powell(p,xi,npar,ftol,&iter,&fret,func);
printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
}
/**** Computes Hessian and covariance matrix ***/
void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
{
double **a,**y,*x,pd;
double **hess;
int i, j,jk;
int *indx;
double hessii(double p[], double delta, int theta, double delti[]);
double hessij(double p[], double delti[], int i, int j);
void lubksb(double **a, int npar, int *indx, double b[]) ;
void ludcmp(double **a, int npar, int *indx, double *d) ;
hess=matrix(1,npar,1,npar);
printf("\nCalculation of the hessian matrix. Wait...\n");
fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
for (i=1;i<=npar;i++){
printf("%d",i);fflush(stdout);
fprintf(ficlog,"%d",i);fflush(ficlog);
hess[i][i]=hessii(p,ftolhess,i,delti);
/*printf(" %f ",p[i]);*/
/*printf(" %lf ",hess[i][i]);*/
}
for (i=1;i<=npar;i++) {
for (j=1;j<=npar;j++) {
if (j>i) {
printf(".%d%d",i,j);fflush(stdout);
fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
hess[i][j]=hessij(p,delti,i,j);
hess[j][i]=hess[i][j];
/*printf(" %lf ",hess[i][j]);*/
}
}
}
printf("\n");
fprintf(ficlog,"\n");
printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
a=matrix(1,npar,1,npar);
y=matrix(1,npar,1,npar);
x=vector(1,npar);
indx=ivector(1,npar);
for (i=1;i<=npar;i++)
for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
ludcmp(a,npar,indx,&pd);
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++){
matcov[i][j]=x[i];
}
}
printf("\n#Hessian matrix#\n");
fprintf(ficlog,"\n#Hessian matrix#\n");
for (i=1;i<=npar;i++) {
for (j=1;j<=npar;j++) {
printf("%.3e ",hess[i][j]);
fprintf(ficlog,"%.3e ",hess[i][j]);
}
printf("\n");
fprintf(ficlog,"\n");
}
/* Recompute Inverse */
for (i=1;i<=npar;i++)
for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
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");
}
*/
free_matrix(a,1,npar,1,npar);
free_matrix(y,1,npar,1,npar);
free_vector(x,1,npar);
free_ivector(indx,1,npar);
free_matrix(hess,1,npar,1,npar);
}
/*************** hessian matrix ****************/
double hessii( double x[], double delta, int theta, double delti[])
{
int i;
int l=1, lmax=20;
double k1,k2;
double p2[NPARMAX+1];
double res;
double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
double fx;
int k=0,kmax=10;
double l1;
fx=func(x);
for (i=1;i<=npar;i++) p2[i]=x[i];
for(l=0 ; l <=lmax; l++){
l1=pow(10,l);
delts=delt;
for(k=1 ; k <kmax; k=k+1){
delt = delta*(l1*k);
p2[theta]=x[theta] +delt;
k1=func(p2)-fx;
p2[theta]=x[theta]-delt;
k2=func(p2)-fx;
/*res= (k1-2.0*fx+k2)/delt/delt; */
res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
#ifdef DEBUG
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);
#endif
/*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
k=kmax;
}
else if((k1 >khi/nkhif) || (k2 >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;
}
}
}
delti[theta]=delts;
return res;
}
double hessij( double x[], double delti[], int thetai,int thetaj)
{
int i;
int l=1, l1, lmax=20;
double k1,k2,k3,k4,res,fx;
double p2[NPARMAX+1];
int k;
fx=func(x);
for (k=1; k<=2; 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 DEBUG
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
}
return res;
}
/************** Inverse of matrix **************/
void ludcmp(double **a, int n, int *indx, double *d)
{
int i,imax,j,k;
double big,dum,sum,temp;
double *vv;
vv=vector(1,n);
*d=1.0;
for (i=1;i<=n;i++) {
big=0.0;
for (j=1;j<=n;j++)
if ((temp=fabs(a[i][j])) > big) big=temp;
if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
vv[i]=1.0/big;
}
for (j=1;j<=n;j++) {
for (i=1;i<j;i++) {
sum=a[i][j];
for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
a[i][j]=sum;
}
big=0.0;
for (i=j;i<=n;i++) {
sum=a[i][j];
for (k=1;k<j;k++)
sum -= a[i][k]*a[k][j];
a[i][j]=sum;
if ( (dum=vv[i]*fabs(sum)) >= big) {
big=dum;
imax=i;
}
}
if (j != imax) {
for (k=1;k<=n;k++) {
dum=a[imax][k];
a[imax][k]=a[j][k];
a[j][k]=dum;
}
*d = -(*d);
vv[imax]=vv[j];
}
indx[j]=imax;
if (a[j][j] == 0.0) a[j][j]=TINY;
if (j != n) {
dum=1.0/(a[j][j]);
for (i=j+1;i<=n;i++) a[i][j] *= dum;
}
}
free_vector(vv,1,n); /* Doesn't work */
;
}
void lubksb(double **a, int n, int *indx, double b[])
{
int i,ii=0,ip,j;
double sum;
for (i=1;i<=n;i++) {
ip=indx[i];
sum=b[ip];
b[ip]=b[i];
if (ii)
for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
else if (sum) ii=i;
b[i]=sum;
}
for (i=n;i>=1;i--) {
sum=b[i];
for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
b[i]=sum/a[i][i];
}
}
/************ Frequencies ********************/
void freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
{ /* Some frequencies */
int i, m, jk, k1,i1, j1, bool, z1,z2,j;
int first;
double ***freq; /* Frequencies */
double *pp;
double pos, k2, dateintsum=0,k2cpt=0;
FILE *ficresp;
char fileresp[FILENAMELENGTH];
pp=vector(1,nlstate);
probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
strcpy(fileresp,"p");
strcat(fileresp,fileres);
if((ficresp=fopen(fileresp,"w"))==NULL) {
printf("Problem with prevalence resultfile: %s\n", fileresp);
fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
exit(0);
}
freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
j1=0;
j=cptcoveff;
if (cptcovn<1) {j=1;ncodemax[1]=1;}
first=1;
for(k1=1; k1<=j;k1++){
for(i1=1; i1<=ncodemax[k1];i1++){
j1++;
/*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
scanf("%d", i);*/
for (i=-1; i<=nlstate+ndeath; i++)
for (jk=-1; jk<=nlstate+ndeath; jk++)
for(m=agemin; m <= agemax+3; m++)
freq[i][jk][m]=0;
dateintsum=0;
k2cpt=0;
for (i=1; i<=imx; i++) {
bool=1;
if (cptcovn>0) {
for (z1=1; z1<=cptcoveff; z1++)
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
bool=0;
}
if (bool==1){
for(m=firstpass; m<=lastpass; m++){
k2=anint[m][i]+(mint[m][i]/12.);
if ((k2>=dateprev1) && (k2<=dateprev2)) {
if(agev[m][i]==0) agev[m][i]=agemax+1;
if(agev[m][i]==1) agev[m][i]=agemax+2;
if (m<lastpass) {
freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
}
if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
dateintsum=dateintsum+k2;
k2cpt++;
}
}
}
}
}
fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
if (cptcovn>0) {
fprintf(ficresp, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
fprintf(ficresp, "**********\n#");
}
for(i=1; i<=nlstate;i++)
fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
fprintf(ficresp, "\n");
for(i=(int)agemin; i <= (int)agemax+3; i++){
if(i==(int)agemax+3){
fprintf(ficlog,"Total");
}else{
if(first==1){
first=0;
printf("See log file for details...\n");
}
fprintf(ficlog,"Age %d", i);
}
for(jk=1; jk <=nlstate ; jk++){
for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
pp[jk] += freq[jk][m][i];
}
for(jk=1; jk <=nlstate ; jk++){
for(m=-1, pos=0; m <=0 ; m++)
pos += freq[jk][m][i];
if(pp[jk]>=1.e-10){
if(first==1){
printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
}
fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
}else{
if(first==1)
printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
}
}
for(jk=1; jk <=nlstate ; jk++){
for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
pp[jk] += freq[jk][m][i];
}
for(jk=1,pos=0; jk <=nlstate ; jk++)
pos += pp[jk];
for(jk=1; jk <=nlstate ; jk++){
if(pos>=1.e-5){
if(first==1)
printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
}else{
if(first==1)
printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
}
if( i <= (int) agemax){
if(pos>=1.e-5){
fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
probs[i][jk][j1]= pp[jk]/pos;
/*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
}
else
fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
}
}
for(jk=-1; jk <=nlstate+ndeath; jk++)
for(m=-1; m <=nlstate+ndeath; m++)
if(freq[jk][m][i] !=0 ) {
if(first==1)
printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
}
if(i <= (int) agemax)
fprintf(ficresp,"\n");
if(first==1)
printf("Others in log...\n");
fprintf(ficlog,"\n");
}
}
}
dateintmean=dateintsum/k2cpt;
fclose(ficresp);
free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
free_vector(pp,1,nlstate);
/* End of Freq */
}
/************ Prevalence ********************/
void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)
{ /* Some frequencies */
int i, m, jk, k1, i1, j1, bool, z1,z2,j;
double ***freq; /* Frequencies */
double *pp;
double pos, k2;
pp=vector(1,nlstate);
freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
j1=0;
j=cptcoveff;
if (cptcovn<1) {j=1;ncodemax[1]=1;}
for(k1=1; k1<=j;k1++){
for(i1=1; i1<=ncodemax[k1];i1++){
j1++;
for (i=-1; i<=nlstate+ndeath; i++)
for (jk=-1; jk<=nlstate+ndeath; jk++)
for(m=agemin; m <= agemax+3; m++)
freq[i][jk][m]=0;
for (i=1; i<=imx; i++) {
bool=1;
if (cptcovn>0) {
for (z1=1; z1<=cptcoveff; z1++)
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
bool=0;
}
if (bool==1) {
for(m=firstpass; m<=lastpass; m++){
k2=anint[m][i]+(mint[m][i]/12.);
if ((k2>=dateprev1) && (k2<=dateprev2)) {
if(agev[m][i]==0) agev[m][i]=agemax+1;
if(agev[m][i]==1) agev[m][i]=agemax+2;
if (m<lastpass) {
if (calagedate>0)
freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
else
freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];
}
}
}
}
}
for(i=(int)agemin; i <= (int)agemax+3; i++){
for(jk=1; jk <=nlstate ; jk++){
for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
pp[jk] += freq[jk][m][i];
}
for(jk=1; jk <=nlstate ; jk++){
for(m=-1, pos=0; m <=0 ; m++)
pos += freq[jk][m][i];
}
for(jk=1; jk <=nlstate ; jk++){
for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
pp[jk] += freq[jk][m][i];
}
for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
for(jk=1; jk <=nlstate ; jk++){
if( i <= (int) agemax){
if(pos>=1.e-5){
probs[i][jk][j1]= pp[jk]/pos;
}
}
}/* end jk */
}/* end i */
} /* end i1 */
} /* end k1 */
free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
free_vector(pp,1,nlstate);
} /* End of Freq */
/************* Waves Concatenation ***************/
void concatwav(int wav[], int **dh, int **bh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)
{
/* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
Death is a valid wave (if date is known).
mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
and mw[mi+1][i]. dh depends on stepm.
*/
int i, mi, m;
/* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
double sum=0., jmean=0.;*/
int first;
int j, k=0,jk, ju, jl;
double sum=0.;
first=0;
jmin=1e+5;
jmax=-1;
jmean=0.;
for(i=1; i<=imx; i++){
mi=0;
m=firstpass;
while(s[m][i] <= nlstate){
if(s[m][i]>=1)
mw[++mi][i]=m;
if(m >=lastpass)
break;
else
m++;
}/* end while */
if (s[m][i] > nlstate){
mi++; /* Death is another wave */
/* if(mi==0) never been interviewed correctly before death */
/* Only death is a correct wave */
mw[mi][i]=m;
}
wav[i]=mi;
if(mi==0){
if(first==0){
printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
first=1;
}
if(first==1){
fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
}
} /* end mi==0 */
}
for(i=1; i<=imx; i++){
for(mi=1; mi<wav[i];mi++){
if (stepm <=0)
dh[mi][i]=1;
else{
if (s[mw[mi+1][i]][i] > nlstate) {
if (agedc[i] < 2*AGESUP) {
j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
if(j==0) j=1; /* Survives at least one month after exam */
k=k+1;
if (j >= jmax) jmax=j;
if (j <= jmin) jmin=j;
sum=sum+j;
/*if (j<0) printf("j=%d num=%d \n",j,i); */
}
}
else{
j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
k=k+1;
if (j >= jmax) jmax=j;
else if (j <= jmin)jmin=j;
/* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
sum=sum+j;
}
jk= j/stepm;
jl= j -jk*stepm;
ju= j -(jk+1)*stepm;
if(mle <=1){
if(jl==0){
dh[mi][i]=jk;
bh[mi][i]=0;
}else{ /* We want a negative bias in order to only have interpolation ie
* at the price of an extra matrix product in likelihood */
dh[mi][i]=jk+1;
bh[mi][i]=ju;
}
}else{
if(jl <= -ju){
dh[mi][i]=jk;
bh[mi][i]=jl; /* bias is positive if real duration
* is higher than the multiple of stepm and negative otherwise.
*/
}
else{
dh[mi][i]=jk+1;
bh[mi][i]=ju;
}
if(dh[mi][i]==0){
dh[mi][i]=1; /* At least one step */
bh[mi][i]=ju; /* At least one step */
printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);
}
if(i==298 || i==287 || i==763 ||i==1061)printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d",bh[mi][i],ju,jl,dh[mi][i],jk,stepm);
}
} /* end if mle */
} /* end wave */
}
jmean=sum/k;
printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
}
/*********** Tricode ****************************/
void tricode(int *Tvar, int **nbcode, int imx)
{
int Ndum[20],ij=1, k, j, i, maxncov=19;
int cptcode=0;
cptcoveff=0;
for (k=0; k<maxncov; k++) Ndum[k]=0;
for (k=1; k<=7; k++) ncodemax[k]=0;
for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
modality*/
ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
Ndum[ij]++; /*store the modality */
/*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
Tvar[j]. If V=sex and male is 0 and
female is 1, then cptcode=1.*/
}
for (i=0; i<=cptcode; i++) {
if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
}
ij=1;
for (i=1; i<=ncodemax[j]; i++) {
for (k=0; k<= maxncov; k++) {
if (Ndum[k] != 0) {
nbcode[Tvar[j]][ij]=k;
/* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
ij++;
}
if (ij > ncodemax[j]) break;
}
}
}
for (k=0; k< maxncov; k++) Ndum[k]=0;
for (i=1; i<=ncovmodel-2; i++) {
/* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
ij=Tvar[i];
Ndum[ij]++;
}
ij=1;
for (i=1; i<= maxncov; i++) {
if((Ndum[i]!=0) && (i<=ncovcol)){
Tvaraff[ij]=i; /*For printing */
ij++;
}
}
cptcoveff=ij-1; /*Number of simple covariates*/
}
/*********** Health Expectancies ****************/
void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
{
/* Health expectancies */
int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
double age, agelim, hf;
double ***p3mat,***varhe;
double **dnewm,**doldm;
double *xp;
double **gp, **gm;
double ***gradg, ***trgradg;
int theta;
varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
xp=vector(1,npar);
dnewm=matrix(1,nlstate*2,1,npar);
doldm=matrix(1,nlstate*2,1,nlstate*2);
fprintf(ficreseij,"# Health expectancies\n");
fprintf(ficreseij,"# Age");
for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++)
fprintf(ficreseij," %1d-%1d (SE)",i,j);
fprintf(ficreseij,"\n");
if(estepm < stepm){
printf ("Problem %d lower than %d\n",estepm, stepm);
}
else hstepm=estepm;
/* We compute the life expectancy from trapezoids spaced every estepm months
* This is mainly to measure the difference between two models: for example
* if stepm=24 months pijx are given only every 2 years and by summing them
* we are calculating an estimate of the Life Expectancy assuming a linear
* progression inbetween and thus overestimating or underestimating according
* to the curvature of the survival function. If, for the same date, we
* estimate the model with stepm=1 month, we can keep estepm to 24 months
* to compare the new estimate of Life expectancy with the same linear
* hypothesis. A more precise result, taking into account a more precise
* curvature will be obtained if estepm is as small as stepm. */
/* For example we decided to compute the life expectancy with the smallest unit */
/* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
nhstepm is the number of hstepm from age to agelim
nstepm is the number of stepm from age to agelin.
Look at hpijx to understand the reason of that which relies in memory size
and note for a fixed period like estepm months */
/* We decided (b) to get a life expectancy respecting the most precise curvature of the
survival function given by stepm (the optimization length). Unfortunately it
means that if the survival funtion is printed only each two years of age and if
you sum them up and add 1 year (area under the trapezoids) you won't get the same
results. So we changed our mind and took the option of the best precision.
*/
hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
agelim=AGESUP;
for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
/* nhstepm age range expressed in number of stepm */
nstepm=(int) rint((agelim-age)*YEARM/stepm);
/* Typically if 20 years nstepm = 20*12/6=40 stepm */
/* if (stepm >= YEARM) hstepm=1;*/
nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
gp=matrix(0,nhstepm,1,nlstate*2);
gm=matrix(0,nhstepm,1,nlstate*2);
/* Computed by stepm unit matrices, product of hstepm matrices, stored
in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
/* Computing Variances of health expectancies */
for(theta=1; theta <=npar; theta++){
for(i=1; i<=npar; i++){
xp[i] = x[i] + (i==theta ?delti[theta]:0);
}
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
cptj=0;
for(j=1; j<= nlstate; j++){
for(i=1; i<=nlstate; i++){
cptj=cptj+1;
for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
}
}
}
for(i=1; i<=npar; i++)
xp[i] = x[i] - (i==theta ?delti[theta]:0);
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
cptj=0;
for(j=1; j<= nlstate; j++){
for(i=1;i<=nlstate;i++){
cptj=cptj+1;
for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
}
}
}
for(j=1; j<= nlstate*2; j++)
for(h=0; h<=nhstepm-1; h++){
gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
}
}
/* End theta */
trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
for(h=0; h<=nhstepm-1; h++)
for(j=1; j<=nlstate*2;j++)
for(theta=1; theta <=npar; theta++)
trgradg[h][j][theta]=gradg[h][theta][j];
for(i=1;i<=nlstate*2;i++)
for(j=1;j<=nlstate*2;j++)
varhe[i][j][(int)age] =0.;
printf("%d|",(int)age);fflush(stdout);
fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
for(h=0;h<=nhstepm-1;h++){
for(k=0;k<=nhstepm-1;k++){
matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
for(i=1;i<=nlstate*2;i++)
for(j=1;j<=nlstate*2;j++)
varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
}
}
/* Computing expectancies */
for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++)
for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
/* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
}
fprintf(ficreseij,"%3.0f",age );
cptj=0;
for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++){
cptj++;
fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
}
fprintf(ficreseij,"\n");
free_matrix(gm,0,nhstepm,1,nlstate*2);
free_matrix(gp,0,nhstepm,1,nlstate*2);
free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
}
printf("\n");
fprintf(ficlog,"\n");
free_vector(xp,1,npar);
free_matrix(dnewm,1,nlstate*2,1,npar);
free_matrix(doldm,1,nlstate*2,1,nlstate*2);
free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
}
/************ 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)
{
/* Variance of health expectancies */
/* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
/* double **newm;*/
double **dnewm,**doldm;
double **dnewmp,**doldmp;
int i, j, nhstepm, hstepm, h, nstepm ;
int k, cptcode;
double *xp;
double **gp, **gm; /* for var eij */
double ***gradg, ***trgradg; /*for var eij */
double **gradgp, **trgradgp; /* for var p point j */
double *gpp, *gmp; /* for var p point j */
double **varppt; /* for var p point j nlstate to nlstate+ndeath */
double ***p3mat;
double age,agelim, hf;
double ***mobaverage;
int theta;
char digit[4];
char digitp[25];
char fileresprobmorprev[FILENAMELENGTH];
if(popbased==1){
if(mobilav!=0)
strcpy(digitp,"-populbased-mobilav-");
else strcpy(digitp,"-populbased-nomobil-");
}
else
strcpy(digitp,"-stablbased-");
if (mobilav!=0) {
mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
printf(" Error in movingaverage mobilav=%d\n",mobilav);
}
}
strcpy(fileresprobmorprev,"prmorprev");
sprintf(digit,"%-d",ij);
/*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
strcat(fileresprobmorprev,digit); /* Tvar to be done */
strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
strcat(fileresprobmorprev,fileres);
if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
printf("Problem with resultfile: %s\n", fileresprobmorprev);
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
}
printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");
fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
for(j=nlstate+1; j<=(nlstate+ndeath);j++){
fprintf(ficresprobmorprev," p.%-d SE",j);
for(i=1; i<=nlstate;i++)
fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
}
fprintf(ficresprobmorprev,"\n");
if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
exit(0);
}
else{
fprintf(ficgp,"\n# Routine varevsij");
}
if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
printf("Problem with html file: %s\n", optionfilehtm);
fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
exit(0);
}
else{
fprintf(fichtm,"\n<li><h4> Computing probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
fprintf(fichtm,"\n<br>%s (à revoir) <br>\n",digitp);
}
varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are the stable prevalence in health states i\n");
fprintf(ficresvij,"# Age");
for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++)
fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
fprintf(ficresvij,"\n");
xp=vector(1,npar);
dnewm=matrix(1,nlstate,1,npar);
doldm=matrix(1,nlstate,1,nlstate);
dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
gpp=vector(nlstate+1,nlstate+ndeath);
gmp=vector(nlstate+1,nlstate+ndeath);
trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
if(estepm < stepm){
printf ("Problem %d lower than %d\n",estepm, stepm);
}
else hstepm=estepm;
/* For example we decided to compute the life expectancy with the smallest unit */
/* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
nhstepm is the number of hstepm from age to agelim
nstepm is the number of stepm from age to agelin.
Look at hpijx to understand the reason of that which relies in memory size
and note for a fixed period like k years */
/* We decided (b) to get a life expectancy respecting the most precise curvature of the
survival function given by stepm (the optimization length). Unfortunately it
means that if the survival funtion is printed only each two years of age and if
you sum them up and add 1 year (area under the trapezoids) you won't get the same
results. So we changed our mind and took the option of the best precision.
*/
hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
agelim = AGESUP;
for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
gp=matrix(0,nhstepm,1,nlstate);
gm=matrix(0,nhstepm,1,nlstate);
for(theta=1; theta <=npar; theta++){
for(i=1; i<=npar; i++){ /* Computes gradient */
xp[i] = x[i] + (i==theta ?delti[theta]:0);
}
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
if (popbased==1) {
if(mobilav ==0){
for(i=1; i<=nlstate;i++)
prlim[i][i]=probs[(int)age][i][ij];
}else{ /* mobilav */
for(i=1; i<=nlstate;i++)
prlim[i][i]=mobaverage[(int)age][i][ij];
}
}
for(j=1; j<= nlstate; j++){
for(h=0; h<=nhstepm; h++){
for(i=1, gp[h][j]=0.;i<=nlstate;i++)
gp[h][j] += prlim[i][i]*p3mat[i][j][h];
}
}
/* This for computing forces of mortality (h=1)as a weighted average */
for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
for(i=1; i<= nlstate; i++)
gpp[j] += prlim[i][i]*p3mat[i][j][1];
}
/* end force of mortality */
for(i=1; i<=npar; i++) /* Computes gradient */
xp[i] = x[i] - (i==theta ?delti[theta]:0);
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
if (popbased==1) {
if(mobilav ==0){
for(i=1; i<=nlstate;i++)
prlim[i][i]=probs[(int)age][i][ij];
}else{ /* mobilav */
for(i=1; i<=nlstate;i++)
prlim[i][i]=mobaverage[(int)age][i][ij];
}
}
for(j=1; j<= nlstate; j++){
for(h=0; h<=nhstepm; h++){
for(i=1, gm[h][j]=0.;i<=nlstate;i++)
gm[h][j] += prlim[i][i]*p3mat[i][j][h];
}
}
/* This for computing force of mortality (h=1)as a weighted average */
for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
for(i=1; i<= nlstate; i++)
gmp[j] += prlim[i][i]*p3mat[i][j][1];
}
/* end force of mortality */
for(j=1; j<= nlstate; j++) /* vareij */
for(h=0; h<=nhstepm; h++){
gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
}
for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
}
} /* End theta */
trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
for(h=0; h<=nhstepm; h++) /* veij */
for(j=1; j<=nlstate;j++)
for(theta=1; theta <=npar; theta++)
trgradg[h][j][theta]=gradg[h][theta][j];
for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
for(theta=1; theta <=npar; theta++)
trgradgp[j][theta]=gradgp[theta][j];
hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
for(i=1;i<=nlstate;i++)
for(j=1;j<=nlstate;j++)
vareij[i][j][(int)age] =0.;
for(h=0;h<=nhstepm;h++){
for(k=0;k<=nhstepm;k++){
matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
for(i=1;i<=nlstate;i++)
for(j=1;j<=nlstate;j++)
vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
}
}
/* pptj */
matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
for(j=nlstate+1;j<=nlstate+ndeath;j++)
for(i=nlstate+1;i<=nlstate+ndeath;i++)
varppt[j][i]=doldmp[j][i];
/* end ppptj */
hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
if (popbased==1) {
if(mobilav ==0){
for(i=1; i<=nlstate;i++)
prlim[i][i]=probs[(int)age][i][ij];
}else{ /* mobilav */
for(i=1; i<=nlstate;i++)
prlim[i][i]=mobaverage[(int)age][i][ij];
}
}
/* This for computing force of mortality (h=1)as a weighted average */
for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
for(i=1; i<= nlstate; i++)
gmp[j] += prlim[i][i]*p3mat[i][j][1];
}
/* end force of mortality */
fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
for(j=nlstate+1; j<=(nlstate+ndeath);j++){
fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
for(i=1; i<=nlstate;i++){
fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
}
}
fprintf(ficresprobmorprev,"\n");
fprintf(ficresvij,"%.0f ",age );
for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++){
fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
}
fprintf(ficresvij,"\n");
free_matrix(gp,0,nhstepm,1,nlstate);
free_matrix(gm,0,nhstepm,1,nlstate);
free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
} /* End age */
free_vector(gpp,nlstate+1,nlstate+ndeath);
free_vector(gmp,nlstate+1,nlstate+ndeath);
free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
/* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);
fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);
fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);
fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);
/* fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
*/
fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
free_vector(xp,1,npar);
free_matrix(doldm,1,nlstate,1,nlstate);
free_matrix(dnewm,1,nlstate,1,npar);
free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
fclose(ficresprobmorprev);
fclose(ficgp);
fclose(fichtm);
}
/************ 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)
{
/* Variance of prevalence limit */
/* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
double **newm;
double **dnewm,**doldm;
int i, j, nhstepm, hstepm;
int k, cptcode;
double *xp;
double *gp, *gm;
double **gradg, **trgradg;
double age,agelim;
int theta;
fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
fprintf(ficresvpl,"# Age");
for(i=1; i<=nlstate;i++)
fprintf(ficresvpl," %1d-%1d",i,i);
fprintf(ficresvpl,"\n");
xp=vector(1,npar);
dnewm=matrix(1,nlstate,1,npar);
doldm=matrix(1,nlstate,1,nlstate);
hstepm=1*YEARM; /* Every year of age */
hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
agelim = AGESUP;
for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
if (stepm >= YEARM) hstepm=1;
nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
gradg=matrix(1,npar,1,nlstate);
gp=vector(1,nlstate);
gm=vector(1,nlstate);
for(theta=1; theta <=npar; theta++){
for(i=1; i<=npar; i++){ /* Computes gradient */
xp[i] = x[i] + (i==theta ?delti[theta]:0);
}
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
for(i=1;i<=nlstate;i++)
gp[i] = prlim[i][i];
for(i=1; i<=npar; i++) /* Computes gradient */
xp[i] = x[i] - (i==theta ?delti[theta]:0);
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
for(i=1;i<=nlstate;i++)
gm[i] = prlim[i][i];
for(i=1;i<=nlstate;i++)
gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
} /* End theta */
trgradg =matrix(1,nlstate,1,npar);
for(j=1; j<=nlstate;j++)
for(theta=1; theta <=npar; theta++)
trgradg[j][theta]=gradg[theta][j];
for(i=1;i<=nlstate;i++)
varpl[i][(int)age] =0.;
matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
for(i=1;i<=nlstate;i++)
varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
fprintf(ficresvpl,"%.0f ",age );
for(i=1; i<=nlstate;i++)
fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
fprintf(ficresvpl,"\n");
free_vector(gp,1,nlstate);
free_vector(gm,1,nlstate);
free_matrix(gradg,1,npar,1,nlstate);
free_matrix(trgradg,1,nlstate,1,npar);
} /* End age */
free_vector(xp,1,npar);
free_matrix(doldm,1,nlstate,1,npar);
free_matrix(dnewm,1,nlstate,1,nlstate);
}
/************ Variance of one-step probabilities ******************/
void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
{
int i, j=0, i1, k1, l1, t, tj;
int k2, l2, j1, z1;
int k=0,l, cptcode;
int first=1, first1;
double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
double **dnewm,**doldm;
double *xp;
double *gp, *gm;
double **gradg, **trgradg;
double **mu;
double age,agelim, cov[NCOVMAX];
double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
int theta;
char fileresprob[FILENAMELENGTH];
char fileresprobcov[FILENAMELENGTH];
char fileresprobcor[FILENAMELENGTH];
double ***varpij;
strcpy(fileresprob,"prob");
strcat(fileresprob,fileres);
if((ficresprob=fopen(fileresprob,"w"))==NULL) {
printf("Problem with resultfile: %s\n", fileresprob);
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
}
strcpy(fileresprobcov,"probcov");
strcat(fileresprobcov,fileres);
if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
printf("Problem with resultfile: %s\n", fileresprobcov);
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
}
strcpy(fileresprobcor,"probcor");
strcat(fileresprobcor,fileres);
if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
printf("Problem with resultfile: %s\n", fileresprobcor);
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
}
printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
fprintf(ficresprob,"# Age");
fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
fprintf(ficresprobcov,"# Age");
fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
fprintf(ficresprobcov,"# Age");
for(i=1; i<=nlstate;i++)
for(j=1; j<=(nlstate+ndeath);j++){
fprintf(ficresprob," p%1d-%1d (SE)",i,j);
fprintf(ficresprobcov," p%1d-%1d ",i,j);
fprintf(ficresprobcor," p%1d-%1d ",i,j);
}
fprintf(ficresprob,"\n");
fprintf(ficresprobcov,"\n");
fprintf(ficresprobcor,"\n");
xp=vector(1,npar);
dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
first=1;
if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
exit(0);
}
else{
fprintf(ficgp,"\n# Routine varprob");
}
if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
printf("Problem with html file: %s\n", optionfilehtm);
fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
exit(0);
}
else{
fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
fprintf(fichtm,"\n");
fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
}
cov[1]=1;
tj=cptcoveff;
if (cptcovn<1) {tj=1;ncodemax[1]=1;}
j1=0;
for(t=1; t<=tj;t++){
for(i1=1; i1<=ncodemax[t];i1++){
j1++;
if (cptcovn>0) {
fprintf(ficresprob, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
fprintf(ficresprob, "**********\n#");
fprintf(ficresprobcov, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
fprintf(ficresprobcov, "**********\n#");
fprintf(ficgp, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
fprintf(ficgp, "**********\n#");
fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
fprintf(ficresprobcor, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
fprintf(ficgp, "**********\n#");
}
for (age=bage; age<=fage; age ++){
cov[2]=age;
for (k=1; k<=cptcovn;k++) {
cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
}
for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
for (k=1; k<=cptcovprod;k++)
cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
gp=vector(1,(nlstate)*(nlstate+ndeath));
gm=vector(1,(nlstate)*(nlstate+ndeath));
for(theta=1; theta <=npar; theta++){
for(i=1; i<=npar; i++)
xp[i] = x[i] + (i==theta ?delti[theta]:0);
pmij(pmmij,cov,ncovmodel,xp,nlstate);
k=0;
for(i=1; i<= (nlstate); i++){
for(j=1; j<=(nlstate+ndeath);j++){
k=k+1;
gp[k]=pmmij[i][j];
}
}
for(i=1; i<=npar; i++)
xp[i] = x[i] - (i==theta ?delti[theta]:0);
pmij(pmmij,cov,ncovmodel,xp,nlstate);
k=0;
for(i=1; i<=(nlstate); i++){
for(j=1; j<=(nlstate+ndeath);j++){
k=k+1;
gm[k]=pmmij[i][j];
}
}
for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];
}
for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
for(theta=1; theta <=npar; theta++)
trgradg[j][theta]=gradg[theta][j];
matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
pmij(pmmij,cov,ncovmodel,x,nlstate);
k=0;
for(i=1; i<=(nlstate); i++){
for(j=1; j<=(nlstate+ndeath);j++){
k=k+1;
mu[k][(int) age]=pmmij[i][j];
}
}
for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
varpij[i][j][(int)age] = doldm[i][j];
/*printf("\n%d ",(int)age);
for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
}*/
fprintf(ficresprob,"\n%d ",(int)age);
fprintf(ficresprobcov,"\n%d ",(int)age);
fprintf(ficresprobcor,"\n%d ",(int)age);
for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
}
i=0;
for (k=1; k<=(nlstate);k++){
for (l=1; l<=(nlstate+ndeath);l++){
i=i++;
fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
for (j=1; j<=i;j++){
fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
}
}
}/* end of loop for state */
} /* end of loop for age */
/* Confidence intervalle of pij */
/*
fprintf(ficgp,"\nset noparametric;unset label");
fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
fprintf(fichtm,"\n<br>Probability with confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
*/
/* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
first1=1;
for (k2=1; k2<=(nlstate);k2++){
for (l2=1; l2<=(nlstate+ndeath);l2++){
if(l2==k2) continue;
j=(k2-1)*(nlstate+ndeath)+l2;
for (k1=1; k1<=(nlstate);k1++){
for (l1=1; l1<=(nlstate+ndeath);l1++){
if(l1==k1) continue;
i=(k1-1)*(nlstate+ndeath)+l1;
if(i<=j) continue;
for (age=bage; age<=fage; age ++){
if ((int)age %5==0){
v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
mu1=mu[i][(int) age]/stepm*YEARM ;
mu2=mu[j][(int) age]/stepm*YEARM;
c12=cv12/sqrt(v1*v2);
/* Computing eigen value of matrix of covariance */
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.;
/* Eigen vectors */
v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
/*v21=sqrt(1.-v11*v11); *//* error */
v21=(lc1-v1)/cv12*v11;
v12=-v21;
v22=v11;
tnalp=v21/v11;
if(first1==1){
first1=0;
printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
}
fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
/*printf(fignu*/
/* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
/* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
if(first==1){
first=0;
fprintf(ficgp,"\nset parametric;unset label");
fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
}else{
first=0;
fprintf(fichtm," %d (%.3f),",(int) age, c12);
fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
}/* if first */
} /* age mod 5 */
} /* end loop age */
fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
first=1;
} /*l12 */
} /* k12 */
} /*l1 */
}/* k1 */
} /* loop covariates */
}
free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
free_vector(xp,1,npar);
fclose(ficresprob);
fclose(ficresprobcov);
fclose(ficresprobcor);
fclose(ficgp);
fclose(fichtm);
}
/******************* Printing html file ***********/
void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
int lastpass, int stepm, int weightopt, char model[],\
int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
int popforecast, int estepm ,\
double jprev1, double mprev1,double anprev1, \
double jprev2, double mprev2,double anprev2){
int jj1, k1, i1, cpt;
/*char optionfilehtm[FILENAMELENGTH];*/
if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
printf("Problem with %s \n",optionfilehtm), exit(0);
fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
}
fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
- Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
- Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
- Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
- Life expectancies by age and initial health status (estepm=%2d months):
<a href=\"e%s\">e%s</a> <br>\n</li>", \
jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
m=cptcoveff;
if (cptcovn < 1) {m=1;ncodemax[1]=1;}
jj1=0;
for(k1=1; k1<=m;k1++){
for(i1=1; i1<=ncodemax[k1];i1++){
jj1++;
if (cptcovn > 0) {
fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
for (cpt=1; cpt<=cptcoveff;cpt++)
fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
}
/* Pij */
fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>
<img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
/* Quasi-incidences */
fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
<img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
/* Stable prevalence in each health state */
for(cpt=1; cpt<nlstate;cpt++){
fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
<img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
}
for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
<img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
}
fprintf(fichtm,"\n<br>- Total life expectancy by age and
health expectancies in states (1) and (2): e%s%d.png<br>
<img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
} /* end i1 */
}/* End k1 */
fprintf(fichtm,"</ul>");
fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
- Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
- Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
- Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
- Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
- Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
- Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
- Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
if(popforecast==1) fprintf(fichtm,"\n
- Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
- Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
<br>",fileres,fileres,fileres,fileres);
else
fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);
fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
m=cptcoveff;
if (cptcovn < 1) {m=1;ncodemax[1]=1;}
jj1=0;
for(k1=1; k1<=m;k1++){
for(i1=1; i1<=ncodemax[k1];i1++){
jj1++;
if (cptcovn > 0) {
fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
for (cpt=1; cpt<=cptcoveff;cpt++)
fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
}
for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
interval) in state (%d): v%s%d%d.png <br>
<img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
}
} /* end i1 */
}/* End k1 */
fprintf(fichtm,"</ul>");
fclose(fichtm);
}
/******************* Gnuplot file **************/
void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
int ng;
if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
printf("Problem with file %s",optionfilegnuplot);
fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
}
/*#ifdef windows */
fprintf(ficgp,"cd \"%s\" \n",pathc);
/*#endif */
m=pow(2,cptcoveff);
/* 1eme*/
for (cpt=1; cpt<= nlstate ; cpt ++) {
for (k1=1; k1<= m ; k1 ++) {
fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
else fprintf(ficgp," \%%*lf (\%%*lf)");
}
fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
else fprintf(ficgp," \%%*lf (\%%*lf)");
}
fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);
for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
else fprintf(ficgp," \%%*lf (\%%*lf)");
}
fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
}
}
/*2 eme*/
for (k1=1; k1<= m ; k1 ++) {
fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
for (i=1; i<= nlstate+1 ; i ++) {
k=2*i;
fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
for (j=1; j<= nlstate+1 ; j ++) {
if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
else fprintf(ficgp," \%%*lf (\%%*lf)");
}
if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
for (j=1; j<= nlstate+1 ; j ++) {
if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
else fprintf(ficgp," \%%*lf (\%%*lf)");
}
fprintf(ficgp,"\" t\"\" w l 0,");
fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
for (j=1; j<= nlstate+1 ; j ++) {
if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
else fprintf(ficgp," \%%*lf (\%%*lf)");
}
if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
else fprintf(ficgp,"\" t\"\" w l 0,");
}
}
/*3eme*/
for (k1=1; k1<= m ; k1 ++) {
for (cpt=1; cpt<= nlstate ; cpt ++) {
k=2+nlstate*(2*cpt-2);
fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
/*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
*/
for (i=1; i< nlstate ; i ++) {
fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
}
}
}
/* CV preval stat */
for (k1=1; k1<= m ; k1 ++) {
for (cpt=1; cpt<nlstate ; cpt ++) {
k=3;
fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
for (i=1; i< nlstate ; i ++)
fprintf(ficgp,"+$%d",k+i+1);
fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
l=3+(nlstate+ndeath)*cpt;
fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
for (i=1; i< nlstate ; i ++) {
l=3+(nlstate+ndeath)*cpt;
fprintf(ficgp,"+$%d",l+i+1);
}
fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
}
}
/* proba elementaires */
for(i=1,jk=1; i <=nlstate; i++){
for(k=1; k <=(nlstate+ndeath); k++){
if (k != i) {
for(j=1; j <=ncovmodel; j++){
fprintf(ficgp,"p%d=%f ",jk,p[jk]);
jk++;
fprintf(ficgp,"\n");
}
}
}
}
for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
for(jk=1; jk <=m; jk++) {
fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
if (ng==2)
fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
else
fprintf(ficgp,"\nset title \"Probability\"\n");
fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
i=1;
for(k2=1; k2<=nlstate; k2++) {
k3=i;
for(k=1; k<=(nlstate+ndeath); k++) {
if (k != k2){
if(ng==2)
fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
else
fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
ij=1;
for(j=3; j <=ncovmodel; j++) {
if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
ij++;
}
else
fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
}
fprintf(ficgp,")/(1");
for(k1=1; k1 <=nlstate; k1++){
fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
ij=1;
for(j=3; j <=ncovmodel; j++){
if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
ij++;
}
else
fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
}
fprintf(ficgp,")");
}
fprintf(ficgp,") t \"p%d%d\" ", k2,k);
if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
i=i+ncovmodel;
}
} /* end k */
} /* end k2 */
} /* end jk */
} /* end ng */
fclose(ficgp);
} /* end gnuplot */
/*************** Moving average **************/
int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
int i, cpt, cptcod;
int modcovmax =1;
int mobilavrange, mob;
double age;
modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
a covariate has 2 modalities */
if (cptcovn<1) modcovmax=1; /* At least 1 pass */
if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
if(mobilav==1) mobilavrange=5; /* default */
else mobilavrange=mobilav;
for (age=bage; age<=fage; age++)
for (i=1; i<=nlstate;i++)
for (cptcod=1;cptcod<=modcovmax;cptcod++)
mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
/* We keep the original values on the extreme ages bage, fage and for
fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
we use a 5 terms etc. until the borders are no more concerned.
*/
for (mob=3;mob <=mobilavrange;mob=mob+2){
for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
for (i=1; i<=nlstate;i++){
for (cptcod=1;cptcod<=modcovmax;cptcod++){
mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
for (cpt=1;cpt<=(mob-1)/2;cpt++){
mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
}
mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
}
}
}/* end age */
}/* end mob */
}else return -1;
return 0;
}/* End movingaverage */
/************** Forecasting ******************/
prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){
int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
int *popage;
double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
double *popeffectif,*popcount;
double ***p3mat;
double ***mobaverage;
char fileresf[FILENAMELENGTH];
agelim=AGESUP;
calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
strcpy(fileresf,"f");
strcat(fileresf,fileres);
if((ficresf=fopen(fileresf,"w"))==NULL) {
printf("Problem with forecast resultfile: %s\n", fileresf);
fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
}
printf("Computing forecasting: result on file '%s' \n", fileresf);
fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
if (cptcoveff==0) ncodemax[cptcoveff]=1;
if (mobilav!=0) {
mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
printf(" Error in movingaverage mobilav=%d\n",mobilav);
}
}
stepsize=(int) (stepm+YEARM-1)/YEARM;
if (stepm<=12) stepsize=1;
agelim=AGESUP;
hstepm=1;
hstepm=hstepm/stepm;
yp1=modf(dateintmean,&yp);
anprojmean=yp;
yp2=modf((yp1*12),&yp);
mprojmean=yp;
yp1=modf((yp2*30.5),&yp);
jprojmean=yp;
if(jprojmean==0) jprojmean=1;
if(mprojmean==0) jprojmean=1;
fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);
for(cptcov=1;cptcov<=i2;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
k=k+1;
fprintf(ficresf,"\n#******");
for(j=1;j<=cptcoveff;j++) {
fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
}
fprintf(ficresf,"******\n");
fprintf(ficresf,"# StartingAge FinalAge");
for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {
fprintf(ficresf,"\n");
fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);
for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
nhstepm = nhstepm/hstepm;
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
oldm=oldms;savm=savms;
hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
for (h=0; h<=nhstepm; h++){
if (h==(int) (calagedate+YEARM*cpt)) {
fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
}
for(j=1; j<=nlstate+ndeath;j++) {
kk1=0.;kk2=0;
for(i=1; i<=nlstate;i++) {
if (mobilav==1)
kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
else {
kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
}
}
if (h==(int)(calagedate+12*cpt)){
fprintf(ficresf," %.3f", kk1);
}
}
}
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
}
}
}
}
if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
fclose(ficresf);
}
/************** Forecasting ******************/
populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
int *popage;
double calagedate, agelim, kk1, kk2;
double *popeffectif,*popcount;
double ***p3mat,***tabpop,***tabpopprev;
double ***mobaverage;
char filerespop[FILENAMELENGTH];
tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
agelim=AGESUP;
calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
strcpy(filerespop,"pop");
strcat(filerespop,fileres);
if((ficrespop=fopen(filerespop,"w"))==NULL) {
printf("Problem with forecast resultfile: %s\n", filerespop);
fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
}
printf("Computing forecasting: result on file '%s' \n", filerespop);
fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
if (cptcoveff==0) ncodemax[cptcoveff]=1;
if (mobilav!=0) {
mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
printf(" Error in movingaverage mobilav=%d\n",mobilav);
}
}
stepsize=(int) (stepm+YEARM-1)/YEARM;
if (stepm<=12) stepsize=1;
agelim=AGESUP;
hstepm=1;
hstepm=hstepm/stepm;
if (popforecast==1) {
if((ficpop=fopen(popfile,"r"))==NULL) {
printf("Problem with population file : %s\n",popfile);exit(0);
fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
}
popage=ivector(0,AGESUP);
popeffectif=vector(0,AGESUP);
popcount=vector(0,AGESUP);
i=1;
while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
imx=i;
for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
}
for(cptcov=1;cptcov<=i2;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
k=k+1;
fprintf(ficrespop,"\n#******");
for(j=1;j<=cptcoveff;j++) {
fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
}
fprintf(ficrespop,"******\n");
fprintf(ficrespop,"# Age");
for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
if (popforecast==1) fprintf(ficrespop," [Population]");
for (cpt=0; cpt<=0;cpt++) {
fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
nhstepm = nhstepm/hstepm;
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
oldm=oldms;savm=savms;
hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
for (h=0; h<=nhstepm; h++){
if (h==(int) (calagedate+YEARM*cpt)) {
fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
}
for(j=1; j<=nlstate+ndeath;j++) {
kk1=0.;kk2=0;
for(i=1; i<=nlstate;i++) {
if (mobilav==1)
kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
else {
kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
}
}
if (h==(int)(calagedate+12*cpt)){
tabpop[(int)(agedeb)][j][cptcod]=kk1;
/*fprintf(ficrespop," %.3f", kk1);
if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
}
}
for(i=1; i<=nlstate;i++){
kk1=0.;
for(j=1; j<=nlstate;j++){
kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
}
tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
}
if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)
fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
}
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
}
}
/******/
for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
nhstepm = nhstepm/hstepm;
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
oldm=oldms;savm=savms;
hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
for (h=0; h<=nhstepm; h++){
if (h==(int) (calagedate+YEARM*cpt)) {
fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
}
for(j=1; j<=nlstate+ndeath;j++) {
kk1=0.;kk2=0;
for(i=1; i<=nlstate;i++) {
kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
}
if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);
}
}
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
}
}
}
}
if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
if (popforecast==1) {
free_ivector(popage,0,AGESUP);
free_vector(popeffectif,0,AGESUP);
free_vector(popcount,0,AGESUP);
}
free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
fclose(ficrespop);
}
/***********************************************/
/**************** Main Program *****************/
/***********************************************/
int main(int argc, char *argv[])
{
int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
double agedeb, agefin,hf;
double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
double fret;
double **xi,tmp,delta;
double dum; /* Dummy variable */
double ***p3mat;
double ***mobaverage;
int *indx;
char line[MAXLINE], linepar[MAXLINE];
char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
int firstobs=1, lastobs=10;
int sdeb, sfin; /* Status at beginning and end */
int c, h , cpt,l;
int ju,jl, mi;
int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
int mobilav=0,popforecast=0;
int hstepm, nhstepm;
double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
double bage, fage, age, agelim, agebase;
double ftolpl=FTOL;
double **prlim;
double *severity;
double ***param; /* Matrix of parameters */
double *p;
double **matcov; /* Matrix of covariance */
double ***delti3; /* Scale */
double *delti; /* Scale */
double ***eij, ***vareij;
double **varpl; /* Variances of prevalence limits by age */
double *epj, vepp;
double kk1, kk2;
double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
char *alph[]={"a","a","b","c","d","e"}, str[4];
char z[1]="c", occ;
#include <sys/time.h>
#include <time.h>
char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
/* long total_usecs;
struct timeval start_time, end_time;
gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
getcwd(pathcd, size);
printf("\n%s",version);
if(argc <=1){
printf("\nEnter the parameter file name: ");
scanf("%s",pathtot);
}
else{
strcpy(pathtot,argv[1]);
}
/*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
/*cygwin_split_path(pathtot,path,optionfile);
printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
/* cutv(path,optionfile,pathtot,'\\');*/
split(pathtot,path,optionfile,optionfilext,optionfilefiname);
printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
chdir(path);
replace(pathc,path);
/*-------- arguments in the command line --------*/
/* Log file */
strcat(filelog, optionfilefiname);
strcat(filelog,".log"); /* */
if((ficlog=fopen(filelog,"w"))==NULL) {
printf("Problem with logfile %s\n",filelog);
goto end;
}
fprintf(ficlog,"Log filename:%s\n",filelog);
fprintf(ficlog,"\n%s",version);
fprintf(ficlog,"\nEnter the parameter file name: ");
fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
fflush(ficlog);
/* */
strcpy(fileres,"r");
strcat(fileres, optionfilefiname);
strcat(fileres,".txt"); /* Other files have txt extension */
/*---------arguments file --------*/
if((ficpar=fopen(optionfile,"r"))==NULL) {
printf("Problem with optionfile %s\n",optionfile);
fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
goto end;
}
strcpy(filereso,"o");
strcat(filereso,fileres);
if((ficparo=fopen(filereso,"w"))==NULL) {
printf("Problem with Output resultfile: %s\n", filereso);
fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
goto end;
}
/* Reads comments: lines beginning with '#' */
while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);
puts(line);
fputs(line,ficparo);
}
ungetc(c,ficpar);
fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);
puts(line);
fputs(line,ficparo);
}
ungetc(c,ficpar);
covar=matrix(0,NCOVMAX,1,n);
cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
/* Read guess parameters */
/* Reads comments: lines beginning with '#' */
while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);
puts(line);
fputs(line,ficparo);
}
ungetc(c,ficpar);
param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
for(i=1; i <=nlstate; i++)
for(j=1; j <=nlstate+ndeath-1; j++){
fscanf(ficpar,"%1d%1d",&i1,&j1);
fprintf(ficparo,"%1d%1d",i1,j1);
if(mle==1)
printf("%1d%1d",i,j);
fprintf(ficlog,"%1d%1d",i,j);
for(k=1; k<=ncovmodel;k++){
fscanf(ficpar," %lf",¶m[i][j][k]);
if(mle==1){
printf(" %lf",param[i][j][k]);
fprintf(ficlog," %lf",param[i][j][k]);
}
else
fprintf(ficlog," %lf",param[i][j][k]);
fprintf(ficparo," %lf",param[i][j][k]);
}
fscanf(ficpar,"\n");
if(mle==1)
printf("\n");
fprintf(ficlog,"\n");
fprintf(ficparo,"\n");
}
npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
p=param[1][1];
/* Reads comments: lines beginning with '#' */
while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);
puts(line);
fputs(line,ficparo);
}
ungetc(c,ficpar);
delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
for(i=1; i <=nlstate; i++){
for(j=1; j <=nlstate+ndeath-1; j++){
fscanf(ficpar,"%1d%1d",&i1,&j1);
printf("%1d%1d",i,j);
fprintf(ficparo,"%1d%1d",i1,j1);
for(k=1; k<=ncovmodel;k++){
fscanf(ficpar,"%le",&delti3[i][j][k]);
printf(" %le",delti3[i][j][k]);
fprintf(ficparo," %le",delti3[i][j][k]);
}
fscanf(ficpar,"\n");
printf("\n");
fprintf(ficparo,"\n");
}
}
delti=delti3[1][1];
/* Reads comments: lines beginning with '#' */
while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);
puts(line);
fputs(line,ficparo);
}
ungetc(c,ficpar);
matcov=matrix(1,npar,1,npar);
for(i=1; i <=npar; i++){
fscanf(ficpar,"%s",&str);
if(mle==1)
printf("%s",str);
fprintf(ficlog,"%s",str);
fprintf(ficparo,"%s",str);
for(j=1; j <=i; j++){
fscanf(ficpar," %le",&matcov[i][j]);
if(mle==1){
printf(" %.5le",matcov[i][j]);
fprintf(ficlog," %.5le",matcov[i][j]);
}
else
fprintf(ficlog," %.5le",matcov[i][j]);
fprintf(ficparo," %.5le",matcov[i][j]);
}
fscanf(ficpar,"\n");
if(mle==1)
printf("\n");
fprintf(ficlog,"\n");
fprintf(ficparo,"\n");
}
for(i=1; i <=npar; i++)
for(j=i+1;j<=npar;j++)
matcov[i][j]=matcov[j][i];
if(mle==1)
printf("\n");
fprintf(ficlog,"\n");
/*-------- Rewriting paramater file ----------*/
strcpy(rfileres,"r"); /* "Rparameterfile */
strcat(rfileres,optionfilefiname); /* Parameter file first name*/
strcat(rfileres,"."); /* */
strcat(rfileres,optionfilext); /* Other files have txt extension */
if((ficres =fopen(rfileres,"w"))==NULL) {
printf("Problem writing new parameter file: %s\n", fileres);goto end;
fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
}
fprintf(ficres,"#%s\n",version);
/*-------- data file ----------*/
if((fic=fopen(datafile,"r"))==NULL) {
printf("Problem with datafile: %s\n", datafile);goto end;
fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
}
n= lastobs;
severity = vector(1,maxwav);
outcome=imatrix(1,maxwav+1,1,n);
num=ivector(1,n);
moisnais=vector(1,n);
annais=vector(1,n);
moisdc=vector(1,n);
andc=vector(1,n);
agedc=vector(1,n);
cod=ivector(1,n);
weight=vector(1,n);
for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
mint=matrix(1,maxwav,1,n);
anint=matrix(1,maxwav,1,n);
s=imatrix(1,maxwav+1,1,n);
tab=ivector(1,NCOVMAX);
ncodemax=ivector(1,8);
i=1;
while (fgets(line, MAXLINE, fic) != NULL) {
if ((i >= firstobs) && (i <=lastobs)) {
for (j=maxwav;j>=1;j--){
cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
strcpy(line,stra);
cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
}
cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
for (j=ncovcol;j>=1;j--){
cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
}
num[i]=atol(stra);
/*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
i=i+1;
}
}
/* printf("ii=%d", ij);
scanf("%d",i);*/
imx=i-1; /* Number of individuals */
/* for (i=1; i<=imx; i++){
if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
}*/
/* for (i=1; i<=imx; i++){
if (s[4][i]==9) s[4][i]=-1;
printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
/* Calculation of the number of parameter from char model*/
Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
Tprod=ivector(1,15);
Tvaraff=ivector(1,15);
Tvard=imatrix(1,15,1,2);
Tage=ivector(1,15);
if (strlen(model) >1){ /* If there is at least 1 covariate */
j=0, j1=0, k1=1, k2=1;
j=nbocc(model,'+'); /* j=Number of '+' */
j1=nbocc(model,'*'); /* j1=Number of '*' */
cptcovn=j+1;
cptcovprod=j1; /*Number of products */
strcpy(modelsav,model);
if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
printf("Error. Non available option model=%s ",model);
fprintf(ficlog,"Error. Non available option model=%s ",model);
goto end;
}
/* This loop fills the array Tvar from the string 'model'.*/
for(i=(j+1); i>=1;i--){
cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
/* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
/*scanf("%d",i);*/
if (strchr(strb,'*')) { /* Model includes a product */
cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
if (strcmp(strc,"age")==0) { /* Vn*age */
cptcovprod--;
cutv(strb,stre,strd,'V');
Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
cptcovage++;
Tage[cptcovage]=i;
/*printf("stre=%s ", stre);*/
}
else if (strcmp(strd,"age")==0) { /* or age*Vn */
cptcovprod--;
cutv(strb,stre,strc,'V');
Tvar[i]=atoi(stre);
cptcovage++;
Tage[cptcovage]=i;
}
else { /* Age is not in the model */
cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
Tvar[i]=ncovcol+k1;
cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
Tprod[k1]=i;
Tvard[k1][1]=atoi(strc); /* m*/
Tvard[k1][2]=atoi(stre); /* n */
Tvar[cptcovn+k2]=Tvard[k1][1];
Tvar[cptcovn+k2+1]=Tvard[k1][2];
for (k=1; k<=lastobs;k++)
covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
k1++;
k2=k2+2;
}
}
else { /* no more sum */
/*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
/* scanf("%d",i);*/
cutv(strd,strc,strb,'V');
Tvar[i]=atoi(strc);
}
strcpy(modelsav,stra);
/*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
scanf("%d",i);*/
} /* end of loop + */
} /* end model */
/*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
/* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
printf("cptcovprod=%d ", cptcovprod);
fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
scanf("%d ",i);
fclose(fic);*/
/* if(mle==1){*/
if (weightopt != 1) { /* Maximisation without weights*/
for(i=1;i<=n;i++) weight[i]=1.0;
}
/*-calculation of age at interview from date of interview and age at death -*/
agev=matrix(1,maxwav,1,imx);
for (i=1; i<=imx; i++) {
for(m=2; (m<= maxwav); m++) {
if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
anint[m][i]=9999;
s[m][i]=-1;
}
if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
}
}
for (i=1; i<=imx; i++) {
agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
for(m=1; (m<= maxwav); m++){
if(s[m][i] >0){
if (s[m][i] >= nlstate+1) {
if(agedc[i]>0)
if(moisdc[i]!=99 && andc[i]!=9999)
agev[m][i]=agedc[i];
/*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
else {
if (andc[i]!=9999){
printf("Warning negative age at death: %d line:%d\n",num[i],i);
fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
agev[m][i]=-1;
}
}
}
else if(s[m][i] !=9){ /* Should no more exist */
agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
if(mint[m][i]==99 || anint[m][i]==9999)
agev[m][i]=1;
else if(agev[m][i] <agemin){
agemin=agev[m][i];
/*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
}
else if(agev[m][i] >agemax){
agemax=agev[m][i];
/* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
}
/*agev[m][i]=anint[m][i]-annais[i];*/
/* agev[m][i] = age[i]+2*m;*/
}
else { /* =9 */
agev[m][i]=1;
s[m][i]=-1;
}
}
else /*= 0 Unknown */
agev[m][i]=1;
}
}
for (i=1; i<=imx; i++) {
for(m=1; (m<= maxwav); m++){
if (s[m][i] > (nlstate+ndeath)) {
printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
goto end;
}
}
}
printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
free_vector(severity,1,maxwav);
free_imatrix(outcome,1,maxwav+1,1,n);
free_vector(moisnais,1,n);
free_vector(annais,1,n);
/* free_matrix(mint,1,maxwav,1,n);
free_matrix(anint,1,maxwav,1,n);*/
free_vector(moisdc,1,n);
free_vector(andc,1,n);
wav=ivector(1,imx);
dh=imatrix(1,lastpass-firstpass+1,1,imx);
bh=imatrix(1,lastpass-firstpass+1,1,imx);
mw=imatrix(1,lastpass-firstpass+1,1,imx);
/* Concatenates waves */
concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
/* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
Tcode=ivector(1,100);
nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
ncodemax[1]=1;
if (cptcovn > 0) tricode(Tvar,nbcode,imx);
codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
the estimations*/
h=0;
m=pow(2,cptcoveff);
for(k=1;k<=cptcoveff; k++){
for(i=1; i <=(m/pow(2,k));i++){
for(j=1; j <= ncodemax[k]; j++){
for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
h++;
if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
/* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
}
}
}
}
/* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
codtab[1][2]=1;codtab[2][2]=2; */
/* for(i=1; i <=m ;i++){
for(k=1; k <=cptcovn; k++){
printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
}
printf("\n");
}
scanf("%d",i);*/
/* Calculates basic frequencies. Computes observed prevalence at single age
and prints on file fileres'p'. */
pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
/* For Powell, parameters are in a vector p[] starting at p[1]
so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
p=param[1][1]; /* *(*(*(param +1)+1)+0) */
if(mle>=1){ /* Could be 1 or 2 */
mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
}
/*--------- results files --------------*/
fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
jk=1;
fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
for(i=1,jk=1; i <=nlstate; i++){
for(k=1; k <=(nlstate+ndeath); k++){
if (k != i)
{
printf("%d%d ",i,k);
fprintf(ficlog,"%d%d ",i,k);
fprintf(ficres,"%1d%1d ",i,k);
for(j=1; j <=ncovmodel; j++){
printf("%f ",p[jk]);
fprintf(ficlog,"%f ",p[jk]);
fprintf(ficres,"%f ",p[jk]);
jk++;
}
printf("\n");
fprintf(ficlog,"\n");
fprintf(ficres,"\n");
}
}
}
if(mle==1){
/* Computing hessian and covariance matrix */
ftolhess=ftol; /* Usually correct */
hesscov(matcov, p, npar, delti, ftolhess, func);
}
fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
printf("# Scales (for hessian or gradient estimation)\n");
fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
for(i=1,jk=1; i <=nlstate; i++){
for(j=1; j <=nlstate+ndeath; j++){
if (j!=i) {
fprintf(ficres,"%1d%1d",i,j);
printf("%1d%1d",i,j);
fprintf(ficlog,"%1d%1d",i,j);
for(k=1; k<=ncovmodel;k++){
printf(" %.5e",delti[jk]);
fprintf(ficlog," %.5e",delti[jk]);
fprintf(ficres," %.5e",delti[jk]);
jk++;
}
printf("\n");
fprintf(ficlog,"\n");
fprintf(ficres,"\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)
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");
for(i=1,k=1;i<=npar;i++){
/* if (k>nlstate) k=1;
i1=(i-1)/(ncovmodel*nlstate)+1;
fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
printf("%s%d%d",alph[k],i1,tab[i]);
*/
fprintf(ficres,"%3d",i);
if(mle==1)
printf("%3d",i);
fprintf(ficlog,"%3d",i);
for(j=1; j<=i;j++){
fprintf(ficres," %.5e",matcov[i][j]);
if(mle==1)
printf(" %.5e",matcov[i][j]);
fprintf(ficlog," %.5e",matcov[i][j]);
}
fprintf(ficres,"\n");
if(mle==1)
printf("\n");
fprintf(ficlog,"\n");
k++;
}
while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);
puts(line);
fputs(line,ficparo);
}
ungetc(c,ficpar);
estepm=0;
fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
if (estepm==0 || estepm < stepm) estepm=stepm;
if (fage <= 2) {
bage = ageminpar;
fage = agemaxpar;
}
fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);
puts(line);
fputs(line,ficparo);
}
ungetc(c,ficpar);
fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);
puts(line);
fputs(line,ficparo);
}
ungetc(c,ficpar);
dateprev1=anprev1+mprev1/12.+jprev1/365.;
dateprev2=anprev2+mprev2/12.+jprev2/365.;
fscanf(ficpar,"pop_based=%d\n",&popbased);
fprintf(ficparo,"pop_based=%d\n",popbased);
fprintf(ficres,"pop_based=%d\n",popbased);
while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);
puts(line);
fputs(line,ficparo);
}
ungetc(c,ficpar);
fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);
fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);
puts(line);
fputs(line,ficparo);
}
ungetc(c,ficpar);
fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
/*------------ gnuplot -------------*/
strcpy(optionfilegnuplot,optionfilefiname);
strcat(optionfilegnuplot,".gp");
if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
printf("Problem with file %s",optionfilegnuplot);
}
else{
fprintf(ficgp,"\n# %s\n", version);
fprintf(ficgp,"# %s\n", optionfilegnuplot);
fprintf(ficgp,"set missing 'NaNq'\n");
}
fclose(ficgp);
printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
/*--------- index.htm --------*/
strcpy(optionfilehtm,optionfile);
strcat(optionfilehtm,".htm");
if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
printf("Problem with %s \n",optionfilehtm), exit(0);
}
fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
\n
Total number of observations=%d <br>\n
Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
<hr size=\"2\" color=\"#EC5E5E\">
<ul><li><h4>Parameter files</h4>\n
- Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
- Log file of the run: <a href=\"%s\">%s</a><br>\n
- Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
fclose(fichtm);
printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
/*------------ free_vector -------------*/
chdir(path);
free_ivector(wav,1,imx);
free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
free_ivector(num,1,n);
free_vector(agedc,1,n);
/*free_matrix(covar,0,NCOVMAX,1,n);*/
/*free_matrix(covar,1,NCOVMAX,1,n);*/
fclose(ficparo);
fclose(ficres);
/*--------------- Prevalence limit (stable prevalence) --------------*/
strcpy(filerespl,"pl");
strcat(filerespl,fileres);
if((ficrespl=fopen(filerespl,"w"))==NULL) {
printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
}
printf("Computing stable prevalence: result on file '%s' \n", filerespl);
fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
fprintf(ficrespl,"#Stable prevalence \n");
fprintf(ficrespl,"#Age ");
for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
fprintf(ficrespl,"\n");
prlim=matrix(1,nlstate,1,nlstate);
agebase=ageminpar;
agelim=agemaxpar;
ftolpl=1.e-10;
i1=cptcoveff;
if (cptcovn < 1){i1=1;}
for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
k=k+1;
/*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
fprintf(ficrespl,"\n#******");
printf("\n#******");
fprintf(ficlog,"\n#******");
for(j=1;j<=cptcoveff;j++) {
fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
}
fprintf(ficrespl,"******\n");
printf("******\n");
fprintf(ficlog,"******\n");
for (age=agebase; age<=agelim; age++){
prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
fprintf(ficrespl,"%.0f",age );
for(i=1; i<=nlstate;i++)
fprintf(ficrespl," %.5f", prlim[i][i]);
fprintf(ficrespl,"\n");
}
}
}
fclose(ficrespl);
/*------------- h Pij x at various ages ------------*/
strcpy(filerespij,"pij"); strcat(filerespij,fileres);
if((ficrespij=fopen(filerespij,"w"))==NULL) {
printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
}
printf("Computing pij: result on file '%s' \n", filerespij);
fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
stepsize=(int) (stepm+YEARM-1)/YEARM;
/*if (stepm<=24) stepsize=2;*/
agelim=AGESUP;
hstepm=stepsize*YEARM; /* Every year of age */
hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
/* hstepm=1; aff par mois*/
for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
k=k+1;
fprintf(ficrespij,"\n#****** ");
for(j=1;j<=cptcoveff;j++)
fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
fprintf(ficrespij,"******\n");
for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
/* nhstepm=nhstepm*YEARM; aff par mois*/
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
oldm=oldms;savm=savms;
hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
fprintf(ficrespij,"# Age");
for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate+ndeath;j++)
fprintf(ficrespij," %1d-%1d",i,j);
fprintf(ficrespij,"\n");
for (h=0; h<=nhstepm; h++){
fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate+ndeath;j++)
fprintf(ficrespij," %.5f", p3mat[i][j][h]);
fprintf(ficrespij,"\n");
}
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
fprintf(ficrespij,"\n");
}
}
}
varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
fclose(ficrespij);
/*---------- Forecasting ------------------*/
if((stepm == 1) && (strcmp(model,".")==0)){
prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
}
else{
erreur=108;
printf("Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
}
/*---------- Health expectancies and variances ------------*/
strcpy(filerest,"t");
strcat(filerest,fileres);
if((ficrest=fopen(filerest,"w"))==NULL) {
printf("Problem with total LE resultfile: %s\n", filerest);goto end;
fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
}
printf("Computing Total LEs with variances: file '%s' \n", filerest);
fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
strcpy(filerese,"e");
strcat(filerese,fileres);
if((ficreseij=fopen(filerese,"w"))==NULL) {
printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
}
printf("Computing Health Expectancies: result on file '%s' \n", filerese);
fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
strcpy(fileresv,"v");
strcat(fileresv,fileres);
if((ficresvij=fopen(fileresv,"w"))==NULL) {
printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
}
printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
calagedate=-1;
prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
if (mobilav!=0) {
mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
printf(" Error in movingaverage mobilav=%d\n",mobilav);
}
}
for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
k=k+1;
fprintf(ficrest,"\n#****** ");
for(j=1;j<=cptcoveff;j++)
fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
fprintf(ficrest,"******\n");
fprintf(ficreseij,"\n#****** ");
for(j=1;j<=cptcoveff;j++)
fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
fprintf(ficreseij,"******\n");
fprintf(ficresvij,"\n#****** ");
for(j=1;j<=cptcoveff;j++)
fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
fprintf(ficresvij,"******\n");
eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
oldm=oldms;savm=savms;
evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
oldm=oldms;savm=savms;
varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
if(popbased==1){
varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
}
fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
fprintf(ficrest,"\n");
epj=vector(1,nlstate+1);
for(age=bage; age <=fage ;age++){
prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
if (popbased==1) {
if(mobilav ==0){
for(i=1; i<=nlstate;i++)
prlim[i][i]=probs[(int)age][i][k];
}else{ /* mobilav */
for(i=1; i<=nlstate;i++)
prlim[i][i]=mobaverage[(int)age][i][k];
}
}
fprintf(ficrest," %4.0f",age);
for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
for(i=1, epj[j]=0.;i <=nlstate;i++) {
epj[j] += prlim[i][i]*eij[i][j][(int)age];
/* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
}
epj[nlstate+1] +=epj[j];
}
for(i=1, vepp=0.;i <=nlstate;i++)
for(j=1;j <=nlstate;j++)
vepp += vareij[i][j][(int)age];
fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
for(j=1;j <=nlstate;j++){
fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
}
fprintf(ficrest,"\n");
}
free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
free_vector(epj,1,nlstate+1);
}
}
free_vector(weight,1,n);
free_imatrix(Tvard,1,15,1,2);
free_imatrix(s,1,maxwav+1,1,n);
free_matrix(anint,1,maxwav,1,n);
free_matrix(mint,1,maxwav,1,n);
free_ivector(cod,1,n);
free_ivector(tab,1,NCOVMAX);
fclose(ficreseij);
fclose(ficresvij);
fclose(ficrest);
fclose(ficpar);
/*------- Variance of stable prevalence------*/
strcpy(fileresvpl,"vpl");
strcat(fileresvpl,fileres);
if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
exit(0);
}
printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
k=k+1;
fprintf(ficresvpl,"\n#****** ");
for(j=1;j<=cptcoveff;j++)
fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
fprintf(ficresvpl,"******\n");
varpl=matrix(1,nlstate,(int) bage, (int) fage);
oldm=oldms;savm=savms;
varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
}
}
fclose(ficresvpl);
/*---------- End : free ----------------*/
free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
free_matrix(covar,0,NCOVMAX,1,n);
free_matrix(matcov,1,npar,1,npar);
free_vector(delti,1,npar);
free_matrix(agev,1,maxwav,1,imx);
free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
free_ivector(ncodemax,1,8);
free_ivector(Tvar,1,15);
free_ivector(Tprod,1,15);
free_ivector(Tvaraff,1,15);
free_ivector(Tage,1,15);
free_ivector(Tcode,1,100);
fprintf(fichtm,"\n</body>");
fclose(fichtm);
fclose(ficgp);
if(erreur >0){
printf("End of Imach with error or warning %d\n",erreur);
fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
}else{
printf("End of Imach\n");
fprintf(ficlog,"End of Imach\n");
}
printf("See log file on %s\n",filelog);
fclose(ficlog);
/* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
/* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
/*printf("Total time was %d uSec.\n", total_usecs);*/
/*------ End -----------*/
end:
#ifdef windows
/* chdir(pathcd);*/
#endif
/*system("wgnuplot graph.plt");*/
/*system("../gp37mgw/wgnuplot graph.plt");*/
/*system("cd ../gp37mgw");*/
/* system("..\\gp37mgw\\wgnuplot graph.plt");*/
strcpy(plotcmd,GNUPLOTPROGRAM);
strcat(plotcmd," ");
strcat(plotcmd,optionfilegnuplot);
printf("Starting: %s\n",plotcmd);fflush(stdout);
system(plotcmd);
/*#ifdef windows*/
while (z[0] != 'q') {
/* chdir(path); */
printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
scanf("%s",z);
if (z[0] == 'c') system("./imach");
else if (z[0] == 'e') system(optionfilehtm);
else if (z[0] == 'g') system(plotcmd);
else if (z[0] == 'q') exit(0);
}
/*#endif */
}
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