imach/src/imach.c - view

File: [Local Repository] / imach / src / imach.c
Revision 1.34: download - view: text, annotated - select for diffs
Wed Mar 13 17:19:16 2002 UTC (22 years, 1 month ago) by brouard
Branches: MAIN
CVS tags: HEAD

CHANGE ncov to ncovcol
There was a confusion with older ncov parameter. In fact it was the
number of columns, between id and date of birth, which can be used for
covariates. In the program we use ncovmodel for the real number of
covariates. Version 0.8 !

/* $Id: imach.c,v 1.34 2002/03/13 17:19:16 brouard 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 probabibility 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 prevalence limits. 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 "..\\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 int erreur; /* Error number */ int nvar; int cptcovn, 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 */ 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 *ficgp,*ficresprob,*ficpop; FILE *ficreseij; char filerese[FILENAMELENGTH]; FILE *ficresvij; char fileresv[FILENAMELENGTH]; FILE *ficresvpl; char fileresvpl[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 m,nb; int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage; double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint; double **pmmij, ***probs, ***mobaverage; 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 *s; /* pointer */ int l1, l2; /* length counters */ l1 = strlen( path ); /* length of path */ if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH ); #ifdef windows s = strrchr( path, '\\' ); /* find last / */ #else s = strrchr( path, '/' ); /* find last / */ #endif if ( s == NULL ) { /* no directory, so use current */ #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 */ s++; /* after this, the filename */ l2 = strlen( s ); /* length of filename */ if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH ); strcpy( name, s ); /* 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 s = strrchr( name, '.' ); /* find last / */ s++; strcpy(ext,s); /* save extension */ l1= strlen( name); l2= strlen( s)+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) { 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(1); } /*********************** 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); #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); /* 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); #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); for (i=1;i<=n;i++) printf(" %d %.12f",i, p[i]); printf("\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); #endif printf("%d",i);fflush(stdout); linmin(p,xit,n,fret,func); if (fabs(fptt-(*fret)) > del) { del=fabs(fptt-(*fret)); ibig=i; } #ifdef DEBUG printf("%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]); } for(j=1;j<=n;j++) printf(" p=%.12e",p[j]); printf("\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)); for (j=1;j<=n;j++) printf(" %.12e",p[j]); printf("\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]); } printf("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); for(j=1;j<=n;j++) printf(" %.12e",xit[j]); printf("\n"); #endif } } } } /**** Prevalence limit ****************/ 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 Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+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]);*/ 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 */ 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.; 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); 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]]); /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ ipmx +=1; sw += weight[i]; ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; } /* end of wave */ } /* end of individual */ 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"); powell(p,xi,npar,ftol,&iter,&fret,func); printf("\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"); for (i=1;i<=npar;i++){ printf("%d",i);fflush(stdout); 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); hess[i][j]=hessij(p,delti,i,j); hess[j][i]=hess[i][j]; /*printf(" %lf ",hess[i][j]);*/ } } } printf("\n"); printf("\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"); for (i=1;i<=npar;i++) { for (j=1;j<=npar;j++) { printf("%.3e ",hess[i][j]); } printf("\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]); } printf("\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); #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); #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 *Tvar, 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; 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); 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;} 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; 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) printf("Total"); else printf("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) printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); else printf(" %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) printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); else printf(" %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 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]); if(i <= (int) agemax) fprintf(ficresp,"\n"); printf("\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); probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX); 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; freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i]; /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += 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; } } } } } } 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 **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] of 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 j, k=0,jk, ju, jl; double sum=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) printf("Warning, no any valid information for:%d line=%d\n",num[i],i); } 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(jl <= -ju) dh[mi][i]=jk; else dh[mi][i]=jk+1; if(dh[mi][i]==0) dh[mi][i]=1; /* At least one step */ } } } jmean=sum/k; printf("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; int cptcode=0; cptcoveff=0; for (k=0; k<19; 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++) { ij=(int)(covar[Tvar[j]][i]); Ndum[ij]++; /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/ if (ij > cptcode) cptcode=ij; } for (i=0; i<=cptcode; i++) { if(Ndum[i]!=0) ncodemax[j]++; } ij=1; for (i=1; i<=ncodemax[j]; i++) { for (k=0; k<=19; k++) { if (Ndum[k] != 0) { nbcode[Tvar[j]][ij]=k; ij++; } if (ij > ncodemax[j]) break; } } } for (k=0; k<19; k++) Ndum[k]=0; for (i=1; i<=ncovmodel-2; i++) { ij=Tvar[i]; Ndum[ij]++; } ij=1; for (i=1; i<=10; i++) { if((Ndum[i]!=0) && (i<=ncovcol)){ Tvaraff[ij]=i; ij++; } } cptcoveff=ij-1; } /*********** Health Expectancies ****************/ void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij) { /* Health expectancies */ int i, j, nhstepm, hstepm, h, nstepm, k; double age, agelim,hf; double ***p3mat; fprintf(ficreseij,"# Health expectancies\n"); fprintf(ficreseij,"# Age"); for(i=1; i<=nlstate;i++) for(j=1; j<=nlstate;j++) fprintf(ficreseij," %1d-%1d",i,j); fprintf(ficreseij,"\n"); k=1; /* For example stepm=6 months */ hstepm=k*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */ hstepm=stepm; /* or (b) 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 k= 2 years, = 2/6 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); /* 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. */ 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 ); for(i=1; i<=nlstate;i++) for(j=1; j<=nlstate;j++){ fprintf(ficreseij," %9.4f", eij[i][j][(int)age]); } fprintf(ficreseij,"\n"); free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); } } /************ Variance ******************/ void varevsij(char fileres[], 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) { /* 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; int i, j, nhstepm, hstepm, h; int k, cptcode; double *xp; double **gp, **gm; double ***gradg, ***trgradg; double ***p3mat; double age,agelim; int theta; fprintf(ficresvij,"# Covariances of life expectancies\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); 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 */ 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) { for(i=1; i<=nlstate;i++) prlim[i][i]=probs[(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]; } } 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) { for(i=1; i<=nlstate;i++) prlim[i][i]=probs[(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]; } } for(j=1; j<= nlstate; j++) for(h=0; h<=nhstepm; h++){ gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta]; } } /* End theta */ trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); for(h=0; h<=nhstepm; h++) for(j=1; j<=nlstate;j++) for(theta=1; theta <=npar; theta++) trgradg[h][j][theta]=gradg[h][theta][j]; 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]; } } h=1; if (stepm >= YEARM) h=stepm/YEARM; fprintf(ficresvij,"%.0f ",age ); for(i=1; i<=nlstate;i++) for(j=1; j<=nlstate;j++){ fprintf(ficresvij," %.4f", h*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(xp,1,npar); free_matrix(doldm,1,nlstate,1,npar); free_matrix(dnewm,1,nlstate,1,nlstate); } /************ 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 prevalences limit\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 fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij) { int i, j; int k=0, cptcode; double **dnewm,**doldm; double *xp; double *gp, *gm; double **gradg, **trgradg; double age,agelim, cov[NCOVMAX]; int theta; char fileresprob[FILENAMELENGTH]; strcpy(fileresprob,"prob"); strcat(fileresprob,fileres); if((ficresprob=fopen(fileresprob,"w"))==NULL) { printf("Problem with resultfile: %s\n", fileresprob); } printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob); xp=vector(1,npar); dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath)); cov[1]=1; for (age=bage; age<=fage; age ++){ cov[2]=age; gradg=matrix(1,npar,1,9); trgradg=matrix(1,9,1,npar); gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath)); gm=vector(1,(nlstate+ndeath)*(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+ndeath); 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+ndeath); i++){ for(j=1; j<=(nlstate+ndeath);j++){ k=k+1; gm[k]=pmmij[i][j]; } } for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++) gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta]; } for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++) for(theta=1; theta <=npar; theta++) trgradg[j][theta]=gradg[theta][j]; matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov); matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg); pmij(pmmij,cov,ncovmodel,x,nlstate); k=0; for(i=1; i<=(nlstate+ndeath); i++){ for(j=1; j<=(nlstate+ndeath);j++){ k=k+1; gm[k]=pmmij[i][j]; } } /*printf("\n%d ",(int)age); for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){ printf("%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); for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){ if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]); if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]); } 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); } free_vector(xp,1,npar); fclose(ficresprob); } /******************* 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 optionfile[],char optionfilehtm[],char rfileres[] ){ int jj1, k1, i1, cpt; FILE *fichtm; /*char optionfilehtm[FILENAMELENGTH];*/ strcpy(optionfilehtm,optionfile); strcat(optionfilehtm,".htm"); if((fichtm=fopen(optionfilehtm,"w"))==NULL) { printf("Problem with %s \n",optionfilehtm), exit(0); } fprintf(fichtm,"<body><ul> Imach, Version 0.8 <hr size=\"2\" color=\"#EC5E5E\"> Title=%s Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s Total number of observations=%d Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf <hr size=\"2\" color=\"#EC5E5E\"> <li>Outputs files \n - Observed prevalence in each state: <a href=\"p%s\">p%s</a> \n - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> - Transition probabilities: <a href=\"pij%s\">pij%s</a> - Copy of the parameter file: <a href=\"o%s\">o%s</a> - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a> - Health expectancies with their variances: <a href=\"t%s\">t%s</a> - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> - Prevalences forecasting: <a href=\"f%s\">f%s</a> - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> ",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres); fprintf(fichtm," <li>Graphs</li>"); 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\">"); } fprintf(fichtm," - Probabilities: pe%s%d.gif <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); for(cpt=1; cpt<nlstate;cpt++){ fprintf(fichtm," - Prevalence of disability : p%s%d%d.gif <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1); } for(cpt=1; cpt<=nlstate;cpt++) { fprintf(fichtm," - Observed and stationary prevalence (with confident interval) in state (%d): v%s%d%d.gif <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1); } for(cpt=1; cpt<=nlstate;cpt++) { fprintf(fichtm,"\n - Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1); } fprintf(fichtm,"\n - Total life expectancy by age and health expectancies in states (1) and (2): e%s%d.gif <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); fprintf(fichtm,"\n</body>"); } } fclose(fichtm); } /******************* Gnuplot file **************/ void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){ int m,cpt,k1,i,k,j,jk,k2,k3,ij,l; strcpy(optionfilegnuplot,optionfilefiname); strcat(optionfilegnuplot,".plt"); if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) { printf("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 ++) { #ifdef windows fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1); #endif #ifdef unix fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres); #endif for (i=1; i<= nlstate ; i ++) { if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)"); else fprintf(ficgp," \%%*lf (\%%*lf)"); } fprintf(ficgp,"\" t\"Stationary 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)); #ifdef unix fprintf(ficgp,"\nset ter gif small size 400,300"); #endif fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1); } } /*2 eme*/ for (k1=1; k1<= m ; k1 ++) { fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,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,"); } fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1); } /*3eme*/ for (k1=1; k1<= m ; k1 ++) { for (cpt=1; cpt<= nlstate ; cpt ++) { k=2+nlstate*(cpt-1); fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,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+i,cpt,i+1); } fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1); } } /* CV preval stat */ for (k1=1; k1<= m ; k1 ++) { for (cpt=1; cpt<nlstate ; cpt ++) { k=3; fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemaxpar,fileres,k1,k+cpt+1,k+1); for (i=1; i< nlstate ; i ++) fprintf(ficgp,"+$%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); fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1); } } /* 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(jk=1; jk <=m; jk++) { fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot [%.f:%.f] ",agemin,agemaxpar); i=1; for(k2=1; k2<=nlstate; k2++) { k3=i; for(k=1; k<=(nlstate+ndeath); k++) { if (k != k2){ 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; } } } fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk); } fclose(ficgp); } /* end gnuplot */ /*************** Moving average **************/ void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){ int i, cpt, cptcod; for (agedeb=agemin; agedeb<=fage; agedeb++) for (i=1; i<=nlstate;i++) for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++) mobaverage[(int)agedeb][i][cptcod]=0.; for (agedeb=agemin+4; agedeb<=fage; agedeb++){ for (i=1; i<=nlstate;i++){ for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ for (cpt=0;cpt<=4;cpt++){ mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod]; } mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5; } } } } /************** Forecasting ******************/ prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double agemin, 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; char fileresf[FILENAMELENGTH]; agelim=AGESUP; calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM; prevalence(agemin, 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); } printf("Computing forecasting: result on file '%s' \n", fileresf); if (cptcoveff==0) ncodemax[cptcoveff]=1; if (mobilav==1) { mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); movingaverage(agedeb, fage, agemin, mobaverage); } 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>=(agemin-((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 ",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==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); fclose(ficresf); } /************** Forecasting ******************/ populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double agemin, 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, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; double *popeffectif,*popcount; double ***p3mat,***tabpop,***tabpopprev; 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(agemin, 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); } printf("Computing forecasting: result on file '%s' \n", filerespop); if (cptcoveff==0) ncodemax[cptcoveff]=1; if (mobilav==1) { mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); movingaverage(agedeb, fage, agemin, mobaverage); } 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); } 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>=(agemin-((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>=(agemin-((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==1) 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 i,j, k, n=MAXN,iter,m,size,cptcode, cptcod; double agedeb, agefin,hf; double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20; double fret; double **xi,tmp,delta; double dum; /* Dummy variable */ double ***p3mat; int *indx; char line[MAXLINE], linepar[MAXLINE]; char title[MAXLINE]; char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH]; char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH]; char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH]; char filerest[FILENAMELENGTH]; char fileregp[FILENAMELENGTH]; char popfile[FILENAMELENGTH]; char path[80],pathc[80],pathcd[80],pathtot[80],model[20]; 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,**adl,*tab; int mobilav=0,popforecast=0; int hstepm, nhstepm; double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1; 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 version[80]="Imach version 0.8, March 2002, INED-EUROREVES "; 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 */ 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 --------*/ 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); goto end; } strcpy(filereso,"o"); strcat(filereso,fileres); if((ficparo=fopen(filereso,"w"))==NULL) { printf("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\nmodel=%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; if (strlen(model)>1) cptcovn=nbocc(model,'+')+1; ncovmodel=2+cptcovn; 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); printf("%1d%1d",i,j); for(k=1; k<=ncovmodel;k++){ fscanf(ficpar," %lf",&param[i][j][k]); printf(" %lf",param[i][j][k]); fprintf(ficparo," %lf",param[i][j][k]); } fscanf(ficpar,"\n"); printf("\n"); fprintf(ficparo,"\n"); } npar= (nlstate+ndeath-1)*nlstate*ncovmodel; 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); printf("%s",str); fprintf(ficparo,"%s",str); for(j=1; j <=i; j++){ fscanf(ficpar," %le",&matcov[i][j]); printf(" %.5le",matcov[i][j]); fprintf(ficparo," %.5le",matcov[i][j]); } fscanf(ficpar,"\n"); printf("\n"); fprintf(ficparo,"\n"); } for(i=1; i <=npar; i++) for(j=i+1;j<=npar;j++) matcov[i][j]=matcov[j][i]; printf("\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(ficres,"#%s\n",version); /*-------- data file ----------*/ if((fic=fopen(datafile,"r"))==NULL) { printf("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); adl=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 (covar[1][i]==0) 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); Tprod=ivector(1,15); Tvaraff=ivector(1,15); Tvard=imatrix(1,15,1,2); Tage=ivector(1,15); if (strlen(model) >1){ j=0, j1=0, k1=1, k2=1; j=nbocc(model,'+'); j1=nbocc(model,'*'); cptcovn=j+1; cptcovprod=j1; strcpy(modelsav,model); if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){ printf("Error. Non available option model=%s ",model); goto end; } for(i=(j+1); i>=1;i--){ cutv(stra,strb,modelsav,'+'); if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/ /*scanf("%d",i);*/ if (strchr(strb,'*')) { cutv(strd,strc,strb,'*'); if (strcmp(strc,"age")==0) { cptcovprod--; cutv(strb,stre,strd,'V'); Tvar[i]=atoi(stre); cptcovage++; Tage[cptcovage]=i; /*printf("stre=%s ", stre);*/ } else if (strcmp(strd,"age")==0) { cptcovprod--; cutv(strb,stre,strc,'V'); Tvar[i]=atoi(stre); cptcovage++; Tage[cptcovage]=i; } else { cutv(strb,stre,strc,'V'); Tvar[i]=ncovcol+k1; cutv(strb,strc,strd,'V'); Tprod[k1]=i; Tvard[k1][1]=atoi(strc); Tvard[k1][2]=atoi(stre); 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 { /*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);*/ } } /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]); printf("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; } 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]; else { if (andc[i]!=9999){ printf("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: Wrong value in nlstate or ndeath\n"); goto end; } } } printf("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); mw=imatrix(1,lastpass-firstpass+1,1,imx); /* Concatenates waves */ concatwav(wav, dh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm); 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); 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; } } } } /*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){ 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"); for(i=1,jk=1; i <=nlstate; i++){ for(k=1; k <=(nlstate+ndeath); k++){ if (k != i) { printf("%d%d ",i,k); fprintf(ficres,"%1d%1d ",i,k); for(j=1; j <=ncovmodel; j++){ printf("%f ",p[jk]); fprintf(ficres,"%f ",p[jk]); jk++; } printf("\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"); 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); for(k=1; k<=ncovmodel;k++){ printf(" %.5e",delti[jk]); fprintf(ficres," %.5e",delti[jk]); jk++; } printf("\n"); fprintf(ficres,"\n"); } } } k=1; 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"); 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"); for(i=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); printf("%3d",i); for(j=1; j<=i;j++){ fprintf(ficres," %.5e",matcov[i][j]); printf(" %.5e",matcov[i][j]); } fprintf(ficres,"\n"); printf("\n"); k++; } while((c=getc(ficpar))=='#' && c!= EOF){ ungetc(c,ficpar); fgets(line, MAXLINE, ficpar); puts(line); fputs(line,ficparo); } ungetc(c,ficpar); fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage); if (fage <= 2) { bage = agemin; 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\n",agemin,agemaxpar,bage,fage); fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage); 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\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2); fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); 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 mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav); fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav); fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav); 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,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); /*------------ gnuplot -------------*/ printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p); /*------------ free_vector -------------*/ chdir(path); free_ivector(wav,1,imx); free_imatrix(dh,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,1,NCOVMAX,1,n);*/ fclose(ficparo); fclose(ficres); /*--------- index.htm --------*/ printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres); /*--------------- Prevalence limit --------------*/ strcpy(filerespl,"pl"); strcat(filerespl,fileres); if((ficrespl=fopen(filerespl,"w"))==NULL) { printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end; } printf("Computing prevalence limit: result on file '%s' \n", filerespl); fprintf(ficrespl,"#Prevalence limit\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); 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 */ k=0; agebase=agemin; agelim=agemaxpar; ftolpl=1.e-10; i1=cptcoveff; if (cptcovn < 1){i1=1;} for(cptcov=1;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#******"); for(j=1;j<=cptcoveff;j++) fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); fprintf(ficrespl,"******\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; } printf("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 */ k=0; for(cptcov=1;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 */ 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 %.0f %.0f",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(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/ 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); free_matrix(mint,1,maxwav,1,n); free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n); free_vector(weight,1,n);} 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); } /*---------- 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; } printf("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); } printf("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); } printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); k=0; for(cptcov=1;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 ",j,nbcode[j][codtab[k][j]]); fprintf(ficreseij,"******\n"); fprintf(ficresvij,"\n#****** "); for(j=1;j<=cptcoveff;j++) fprintf(ficresvij,"V%d=%d ",j,nbcode[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); vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); oldm=oldms;savm=savms; varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k); 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) { for(i=1; i<=nlstate;i++) prlim[i][i]=probs[(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]; } 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," %7.2f (%7.2f)", epj[nlstate+1],sqrt(vepp)); for(j=1;j <=nlstate;j++){ fprintf(ficrest," %7.2f (%7.2f)", epj[j],sqrt(vareij[j][j][(int)age])); } fprintf(ficrest,"\n"); } } } fclose(ficreseij); fclose(ficresvij); fclose(ficrest); fclose(ficpar); free_vector(epj,1,nlstate+1); /*------- Variance limit prevalence------*/ strcpy(fileresvpl,"vpl"); strcat(fileresvpl,fileres); if((ficresvpl=fopen(fileresvpl,"w"))==NULL) { printf("Problem with variance prev lim resultfile: %s\n", fileresvpl); exit(0); } printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl); k=0; for(cptcov=1;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); } } fclose(ficresvpl); /*---------- End : free ----------------*/ free_matrix(varpl,1,nlstate,(int) bage, (int)fage); free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage); free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage); 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(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(erreur >0) printf("End of Imach with error or warning %d\n",erreur); else printf("End of Imach\n"); /* 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); system(plotcmd); #ifdef windows while (z[0] != 'q') { chdir(path); printf("\nType e to edit output files, c to start again, and q for exiting: "); scanf("%s",z); if (z[0] == 'c') system("./imach"); else if (z[0] == 'e') { chdir(path); system(optionfilehtm); } else if (z[0] == 'q') exit(0); } #endif }