--- imach/src/imach.c 2002/07/19 18:49:30 1.52 +++ imach/src/imach.c 2002/07/23 23:59:37 1.53 @@ -1,4101 +1,4127 @@ -/* $Id: imach.c,v 1.52 2002/07/19 18:49:30 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 - probability to be observed in state j at the second wave - conditional to be observed in state i at the first wave. Therefore - the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where - 'age' is age and 'sex' is a covariate. If you want to have a more - complex model than "constant and age", you should modify the program - where the markup *Covariates have to be included here again* invites - you to do it. More covariates you add, slower the - convergence. - - The advantage of this computer programme, compared to a simple - multinomial logistic model, is clear when the delay between waves is not - identical for each individual. Also, if a individual missed an - intermediate interview, the information is lost, but taken into - account using an interpolation or extrapolation. - - hPijx is the probability to be observed in state i at age x+h - conditional to the observed state i at age x. The delay 'h' can be - split into an exact number (nh*stepm) of unobserved intermediate - states. This elementary transition (by month or quarter trimester, - semester or year) is model as a multinomial logistic. The hPx - matrix is simply the matrix product of nh*stepm elementary matrices - and the contribution of each individual to the likelihood is simply - hPijx. - - Also this programme outputs the covariance matrix of the parameters but also - of the life expectancies. It also computes the 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 -#include -#include -#include - -#define MAXLINE 256 -#define GNUPLOTPROGRAM "gnuplot" -/*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/ -#define FILENAMELENGTH 80 -/*#define DEBUG*/ -#define windows -#define GLOCK_ERROR_NOPATH -1 /* empty path */ -#define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */ - -#define MAXPARM 30 /* Maximum number of parameters for the optimization */ -#define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */ - -#define NINTERVMAX 8 -#define NLSTATEMAX 8 /* Maximum number of live states (for func) */ -#define NDEATHMAX 8 /* Maximum number of dead states (for func) */ -#define NCOVMAX 8 /* Maximum number of covariates */ -#define MAXN 20000 -#define YEARM 12. /* Number of months per year */ -#define AGESUP 130 -#define AGEBASE 40 -#ifdef windows -#define DIRSEPARATOR '\\' -#define ODIRSEPARATOR '/' -#else -#define DIRSEPARATOR '/' -#define ODIRSEPARATOR '\\' -#endif - -char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES "; -int erreur; /* Error number */ -int nvar; -int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov; -int npar=NPARMAX; -int nlstate=2; /* Number of live states */ -int ndeath=1; /* Number of dead states */ -int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */ -int popbased=0; - -int *wav; /* Number of waves for this individuual 0 is possible */ -int maxwav; /* Maxim number of waves */ -int jmin, jmax; /* min, max spacing between 2 waves */ -int mle, weightopt; -int **mw; /* mw[mi][i] is number of the mi wave for this individual */ -int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */ -double jmean; /* Mean space between 2 waves */ -double **oldm, **newm, **savm; /* Working pointers to matrices */ -double **oldms, **newms, **savms; /* Fixed working pointers to matrices */ -FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop; -FILE *ficlog; -FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor; -FILE *ficresprobmorprev; -FILE *fichtm; /* Html File */ -FILE *ficreseij; -char filerese[FILENAMELENGTH]; -FILE *ficresvij; -char fileresv[FILENAMELENGTH]; -FILE *ficresvpl; -char fileresvpl[FILENAMELENGTH]; -char title[MAXLINE]; -char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH]; -char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH]; - -char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH]; -char filelog[FILENAMELENGTH]; /* Log file */ -char filerest[FILENAMELENGTH]; -char fileregp[FILENAMELENGTH]; -char popfile[FILENAMELENGTH]; - -char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH]; - -#define NR_END 1 -#define FREE_ARG char* -#define FTOL 1.0e-10 - -#define NRANSI -#define ITMAX 200 - -#define TOL 2.0e-4 - -#define CGOLD 0.3819660 -#define ZEPS 1.0e-10 -#define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); - -#define GOLD 1.618034 -#define GLIMIT 100.0 -#define TINY 1.0e-20 - -static double maxarg1,maxarg2; -#define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2)) -#define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2)) - -#define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a)) -#define rint(a) floor(a+0.5) - -static double sqrarg; -#define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg) -#define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} - -int imx; -int stepm; -/* Stepm, step in month: minimum step interpolation*/ - -int estepm; -/* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/ - -int m,nb; -int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage; -double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint; -double **pmmij, ***probs, ***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 ); - s= strrchr( path, DIRSEPARATOR ); /* find last / */ - if ( s == NULL ) { /* no directory, so use current */ - /*if(strrchr(path, ODIRSEPARATOR )==NULL) - printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/ -#if defined(__bsd__) /* get current working directory */ - extern char *getwd( ); - - if ( getwd( dirc ) == NULL ) { -#else - extern char *getcwd( ); - - if ( getcwd( dirc, FILENAME_MAX ) == NULL ) { -#endif - return( GLOCK_ERROR_GETCWD ); - } - strcpy( name, path ); /* we've got it */ - } else { /* strip direcotry from path */ - 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) -{ - /* cuts string t into u and v where u is ended by char occ excluding it - and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2) - gives u="abcedf" and v="ghi2j" */ - int i,lg,j,p=0; - i=0; - for(j=0; j<=strlen(t)-1; j++) { - if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; - } - - lg=strlen(t); - for(j=0; j=(p+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); - fprintf(ficlog,".");fflush(ficlog); -#ifdef DEBUG - printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol); - fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol); - /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */ -#endif - if (fabs(x-xm) <= (tol2-0.5*(b-a))){ - *xmin=x; - return fx; - } - ftemp=fu; - if (fabs(e) > tol1) { - r=(x-w)*(fx-fv); - q=(x-v)*(fx-fw); - p=(x-v)*q-(x-w)*r; - q=2.0*(q-r); - if (q > 0.0) p = -p; - q=fabs(q); - etemp=e; - e=d; - if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) - d=CGOLD*(e=(x >= xm ? a-x : b-x)); - else { - d=p/q; - u=x+d; - if (u-a < tol2 || b-u < tol2) - d=SIGN(tol1,xm-x); - } - } else { - d=CGOLD*(e=(x >= xm ? a-x : b-x)); - } - u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); - fu=(*f)(u); - if (fu <= fx) { - if (u >= x) a=x; else b=x; - SHFT(v,w,x,u) - SHFT(fv,fw,fx,fu) - } else { - if (u < x) a=u; else b=u; - if (fu <= fw || w == x) { - v=w; - w=u; - fv=fw; - fw=fu; - } else if (fu <= fv || v == x || v == w) { - v=u; - fv=fu; - } - } - } - nrerror("Too many iterations in brent"); - *xmin=x; - return fx; -} - -/****************** mnbrak ***********************/ - -void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, - double (*func)(double)) -{ - double ulim,u,r,q, dum; - double fu; - - *fa=(*func)(*ax); - *fb=(*func)(*bx); - if (*fb > *fa) { - SHFT(dum,*ax,*bx,dum) - SHFT(dum,*fb,*fa,dum) - } - *cx=(*bx)+GOLD*(*bx-*ax); - *fc=(*func)(*cx); - while (*fb > *fc) { - r=(*bx-*ax)*(*fb-*fc); - q=(*bx-*cx)*(*fb-*fa); - u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ - (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); - ulim=(*bx)+GLIMIT*(*cx-*bx); - if ((*bx-u)*(u-*cx) > 0.0) { - fu=(*func)(u); - } else if ((*cx-u)*(u-ulim) > 0.0) { - fu=(*func)(u); - if (fu < *fc) { - SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) - SHFT(*fb,*fc,fu,(*func)(u)) - } - } else if ((u-ulim)*(ulim-*cx) >= 0.0) { - u=ulim; - fu=(*func)(u); - } else { - u=(*cx)+GOLD*(*cx-*bx); - fu=(*func)(u); - } - SHFT(*ax,*bx,*cx,u) - SHFT(*fa,*fb,*fc,fu) - } -} - -/*************** linmin ************************/ - -int ncom; -double *pcom,*xicom; -double (*nrfunc)(double []); - -void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) -{ - double brent(double ax, double bx, double cx, - double (*f)(double), double tol, double *xmin); - double f1dim(double x); - void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, - double *fc, double (*func)(double)); - int j; - double xx,xmin,bx,ax; - double fx,fb,fa; - - ncom=n; - pcom=vector(1,n); - xicom=vector(1,n); - nrfunc=func; - for (j=1;j<=n;j++) { - pcom[j]=p[j]; - xicom[j]=xi[j]; - } - ax=0.0; - xx=1.0; - mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); - *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); -#ifdef DEBUG - printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin); - fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin); -#endif - for (j=1;j<=n;j++) { - xi[j] *= xmin; - p[j] += xi[j]; - } - free_vector(xicom,1,n); - free_vector(pcom,1,n); -} - -/*************** powell ************************/ -void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, - double (*func)(double [])) -{ - void linmin(double p[], double xi[], int n, double *fret, - double (*func)(double [])); - int i,ibig,j; - double del,t,*pt,*ptt,*xit; - double fp,fptt; - double *xits; - pt=vector(1,n); - ptt=vector(1,n); - xit=vector(1,n); - xits=vector(1,n); - *fret=(*func)(p); - for (j=1;j<=n;j++) pt[j]=p[j]; - for (*iter=1;;++(*iter)) { - fp=(*fret); - ibig=0; - del=0.0; - printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret); - fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret); - for (i=1;i<=n;i++) - printf(" %d %.12f",i, p[i]); - fprintf(ficlog," %d %.12f",i, p[i]); - printf("\n"); - fprintf(ficlog,"\n"); - for (i=1;i<=n;i++) { - for (j=1;j<=n;j++) xit[j]=xi[j][i]; - fptt=(*fret); -#ifdef DEBUG - printf("fret=%lf \n",*fret); - fprintf(ficlog,"fret=%lf \n",*fret); -#endif - printf("%d",i);fflush(stdout); - fprintf(ficlog,"%d",i);fflush(ficlog); - linmin(p,xit,n,fret,func); - if (fabs(fptt-(*fret)) > del) { - del=fabs(fptt-(*fret)); - ibig=i; - } -#ifdef DEBUG - printf("%d %.12e",i,(*fret)); - fprintf(ficlog,"%d %.12e",i,(*fret)); - for (j=1;j<=n;j++) { - xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5); - printf(" x(%d)=%.12e",j,xit[j]); - fprintf(ficlog," x(%d)=%.12e",j,xit[j]); - } - for(j=1;j<=n;j++) { - printf(" p=%.12e",p[j]); - fprintf(ficlog," p=%.12e",p[j]); - } - printf("\n"); - fprintf(ficlog,"\n"); -#endif - } - if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { -#ifdef DEBUG - int k[2],l; - k[0]=1; - k[1]=-1; - printf("Max: %.12e",(*func)(p)); - fprintf(ficlog,"Max: %.12e",(*func)(p)); - for (j=1;j<=n;j++) { - printf(" %.12e",p[j]); - fprintf(ficlog," %.12e",p[j]); - } - printf("\n"); - fprintf(ficlog,"\n"); - for(l=0;l<=1;l++) { - for (j=1;j<=n;j++) { - ptt[j]=p[j]+(p[j]-pt[j])*k[l]; - printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]); - fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]); - } - printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p))); - fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p))); - } -#endif - - - free_vector(xit,1,n); - free_vector(xits,1,n); - free_vector(ptt,1,n); - free_vector(pt,1,n); - return; - } - if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); - for (j=1;j<=n;j++) { - ptt[j]=2.0*p[j]-pt[j]; - xit[j]=p[j]-pt[j]; - pt[j]=p[j]; - } - fptt=(*func)(ptt); - if (fptt < fp) { - t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); - if (t < 0.0) { - linmin(p,xit,n,fret,func); - for (j=1;j<=n;j++) { - xi[j][ibig]=xi[j][n]; - xi[j][n]=xit[j]; - } -#ifdef DEBUG - printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig); - fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig); - for(j=1;j<=n;j++){ - printf(" %.12e",xit[j]); - fprintf(ficlog," %.12e",xit[j]); - } - printf("\n"); - fprintf(ficlog,"\n"); -#endif - } - } - } -} - -/**** Prevalence limit ****************/ - -double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij) -{ - /* Computes the prevalence limit in each live state at age x by left multiplying the unit - matrix by transitions matrix until convergence is reached */ - - int i, ii,j,k; - double min, max, maxmin, maxmax,sumnew=0.; - double **matprod2(); - double **out, cov[NCOVMAX], **pmij(); - double **newm; - double agefin, delaymax=50 ; /* Max number of years to converge */ - - for (ii=1;ii<=nlstate+ndeath;ii++) - for (j=1;j<=nlstate+ndeath;j++){ - oldm[ii][j]=(ii==j ? 1.0 : 0.0); - } - - cov[1]=1.; - - /* Even if hstepm = 1, at least one multiplication by the unit matrix */ - for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){ - newm=savm; - /* Covariates have to be included here again */ - cov[2]=agefin; - - for (k=1; k<=cptcovn;k++) { - cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; - /* printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/ - } - for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; - for (k=1; k<=cptcovprod;k++) - cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; - - /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/ - /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/ - /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/ - out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); - - savm=oldm; - oldm=newm; - maxmax=0.; - for(j=1;j<=nlstate;j++){ - min=1.; - max=0.; - for(i=1; i<=nlstate; i++) { - sumnew=0; - for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k]; - prlim[i][j]= newm[i][j]/(1-sumnew); - max=FMAX(max,prlim[i][j]); - min=FMIN(min,prlim[i][j]); - } - maxmin=max-min; - maxmax=FMAX(maxmax,maxmin); - } - if(maxmax < ftolpl){ - return prlim; - } - } -} - -/*************** transition probabilities ***************/ - -double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate ) -{ - double s1, s2; - /*double t34;*/ - int i,j,j1, nc, ii, jj; - - for(i=1; i<= nlstate; i++){ - for(j=1; ji 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; ji) { - printf(".%d%d",i,j);fflush(stdout); - fprintf(ficlog,".%d%d",i,j);fflush(ficlog); - hess[i][j]=hessij(p,delti,i,j); - hess[j][i]=hess[i][j]; - /*printf(" %lf ",hess[i][j]);*/ - } - } - } - printf("\n"); - fprintf(ficlog,"\n"); - - printf("\nInverting the hessian to get the covariance matrix. Wait...\n"); - fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n"); - - a=matrix(1,npar,1,npar); - y=matrix(1,npar,1,npar); - x=vector(1,npar); - indx=ivector(1,npar); - for (i=1;i<=npar;i++) - for (j=1;j<=npar;j++) a[i][j]=hess[i][j]; - ludcmp(a,npar,indx,&pd); - - for (j=1;j<=npar;j++) { - for (i=1;i<=npar;i++) x[i]=0; - x[j]=1; - lubksb(a,npar,indx,x); - for (i=1;i<=npar;i++){ - matcov[i][j]=x[i]; - } - } - - printf("\n#Hessian matrix#\n"); - fprintf(ficlog,"\n#Hessian matrix#\n"); - for (i=1;i<=npar;i++) { - for (j=1;j<=npar;j++) { - printf("%.3e ",hess[i][j]); - fprintf(ficlog,"%.3e ",hess[i][j]); - } - printf("\n"); - fprintf(ficlog,"\n"); - } - - /* Recompute Inverse */ - for (i=1;i<=npar;i++) - for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; - ludcmp(a,npar,indx,&pd); - - /* printf("\n#Hessian matrix recomputed#\n"); - - for (j=1;j<=npar;j++) { - for (i=1;i<=npar;i++) x[i]=0; - x[j]=1; - lubksb(a,npar,indx,x); - for (i=1;i<=npar;i++){ - y[i][j]=x[i]; - printf("%.3e ",y[i][j]); - fprintf(ficlog,"%.3e ",y[i][j]); - } - printf("\n"); - fprintf(ficlog,"\n"); - } - */ - - free_matrix(a,1,npar,1,npar); - free_matrix(y,1,npar,1,npar); - free_vector(x,1,npar); - free_ivector(indx,1,npar); - free_matrix(hess,1,npar,1,npar); - - -} - -/*************** hessian matrix ****************/ -double hessii( double x[], double delta, int theta, double delti[]) -{ - int i; - int l=1, lmax=20; - double k1,k2; - double p2[NPARMAX+1]; - double res; - double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4; - double fx; - int k=0,kmax=10; - double l1; - - fx=func(x); - for (i=1;i<=npar;i++) p2[i]=x[i]; - for(l=0 ; l <=lmax; l++){ - l1=pow(10,l); - delts=delt; - for(k=1 ; k khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */ - k=kmax; l=lmax*10.; - } - else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ - delts=delt; - } - } - } - delti[theta]=delts; - return res; - -} - -double hessij( double x[], double delti[], int thetai,int thetaj) -{ - int i; - int l=1, l1, lmax=20; - double k1,k2,k3,k4,res,fx; - double p2[NPARMAX+1]; - int k; - - fx=func(x); - for (k=1; k<=2; k++) { - for (i=1;i<=npar;i++) p2[i]=x[i]; - p2[thetai]=x[thetai]+delti[thetai]/k; - p2[thetaj]=x[thetaj]+delti[thetaj]/k; - k1=func(p2)-fx; - - p2[thetai]=x[thetai]+delti[thetai]/k; - p2[thetaj]=x[thetaj]-delti[thetaj]/k; - k2=func(p2)-fx; - - p2[thetai]=x[thetai]-delti[thetai]/k; - p2[thetaj]=x[thetaj]+delti[thetaj]/k; - k3=func(p2)-fx; - - p2[thetai]=x[thetai]-delti[thetai]/k; - p2[thetaj]=x[thetaj]-delti[thetaj]/k; - k4=func(p2)-fx; - res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */ -#ifdef DEBUG - printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); - fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); -#endif - } - return res; -} - -/************** Inverse of matrix **************/ -void ludcmp(double **a, int n, int *indx, double *d) -{ - int i,imax,j,k; - double big,dum,sum,temp; - double *vv; - - vv=vector(1,n); - *d=1.0; - for (i=1;i<=n;i++) { - big=0.0; - for (j=1;j<=n;j++) - if ((temp=fabs(a[i][j])) > big) big=temp; - if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); - vv[i]=1.0/big; - } - for (j=1;j<=n;j++) { - for (i=1;i= 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; - int first; - double ***freq; /* Frequencies */ - double *pp; - double pos, k2, dateintsum=0,k2cpt=0; - FILE *ficresp; - char fileresp[FILENAMELENGTH]; - - pp=vector(1,nlstate); - probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX); - strcpy(fileresp,"p"); - strcat(fileresp,fileres); - if((ficresp=fopen(fileresp,"w"))==NULL) { - printf("Problem with prevalence resultfile: %s\n", fileresp); - fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp); - exit(0); - } - freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3); - j1=0; - - j=cptcoveff; - if (cptcovn<1) {j=1;ncodemax[1]=1;} - - first=1; - - for(k1=1; k1<=j;k1++){ - for(i1=1; i1<=ncodemax[k1];i1++){ - j1++; - /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]); - scanf("%d", i);*/ - for (i=-1; i<=nlstate+ndeath; i++) - for (jk=-1; jk<=nlstate+ndeath; jk++) - for(m=agemin; m <= agemax+3; m++) - freq[i][jk][m]=0; - - dateintsum=0; - k2cpt=0; - for (i=1; i<=imx; i++) { - bool=1; - if (cptcovn>0) { - for (z1=1; z1<=cptcoveff; z1++) - if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) - bool=0; - } - if (bool==1) { - for(m=firstpass; m<=lastpass; m++){ - k2=anint[m][i]+(mint[m][i]/12.); - if ((k2>=dateprev1) && (k2<=dateprev2)) { - if(agev[m][i]==0) agev[m][i]=agemax+1; - if(agev[m][i]==1) agev[m][i]=agemax+2; - if (m1) && (agev[m][i]< (agemax+3))) { - dateintsum=dateintsum+k2; - k2cpt++; - } - } - } - } - } - - fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); - - if (cptcovn>0) { - fprintf(ficresp, "\n#********** Variable "); - for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); - fprintf(ficresp, "**********\n#"); - } - for(i=1; i<=nlstate;i++) - fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i); - fprintf(ficresp, "\n"); - - for(i=(int)agemin; i <= (int)agemax+3; i++){ - if(i==(int)agemax+3){ - fprintf(ficlog,"Total"); - }else{ - if(first==1){ - first=0; - printf("See log file for details...\n"); - } - fprintf(ficlog,"Age %d", i); - } - for(jk=1; jk <=nlstate ; jk++){ - for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++) - pp[jk] += freq[jk][m][i]; - } - for(jk=1; jk <=nlstate ; jk++){ - for(m=-1, pos=0; m <=0 ; m++) - pos += freq[jk][m][i]; - if(pp[jk]>=1.e-10){ - if(first==1){ - printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); - } - fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); - }else{ - if(first==1) - printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk); - fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk); - } - } - - for(jk=1; jk <=nlstate ; jk++){ - for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++) - pp[jk] += freq[jk][m][i]; - } - - for(jk=1,pos=0; jk <=nlstate ; jk++) - pos += pp[jk]; - for(jk=1; jk <=nlstate ; jk++){ - if(pos>=1.e-5){ - if(first==1) - printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); - fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); - }else{ - if(first==1) - printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); - fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); - } - if( i <= (int) agemax){ - if(pos>=1.e-5){ - fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos); - probs[i][jk][j1]= pp[jk]/pos; - /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/ - } - else - fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos); - } - } - - for(jk=-1; jk <=nlstate+ndeath; jk++) - for(m=-1; m <=nlstate+ndeath; m++) - if(freq[jk][m][i] !=0 ) { - if(first==1) - printf(" %d%d=%.0f",jk,m,freq[jk][m][i]); - fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]); - } - if(i <= (int) agemax) - fprintf(ficresp,"\n"); - if(first==1) - printf("Others in log...\n"); - fprintf(ficlog,"\n"); - } - } - } - dateintmean=dateintsum/k2cpt; - - fclose(ficresp); - free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3); - free_vector(pp,1,nlstate); - - /* End of Freq */ -} - -/************ Prevalence ********************/ -void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate) -{ /* Some frequencies */ - - int i, m, jk, k1, i1, j1, bool, z1,z2,j; - double ***freq; /* Frequencies */ - double *pp; - double pos, k2; - - pp=vector(1,nlstate); - 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; - if (m0) - freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i]; - else - freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; - freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i]; - } - } - } - } - } - for(i=(int)agemin; i <= (int)agemax+3; i++){ - for(jk=1; jk <=nlstate ; jk++){ - for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++) - pp[jk] += freq[jk][m][i]; - } - for(jk=1; jk <=nlstate ; jk++){ - for(m=-1, pos=0; m <=0 ; m++) - pos += freq[jk][m][i]; - } - - for(jk=1; jk <=nlstate ; jk++){ - for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++) - pp[jk] += freq[jk][m][i]; - } - - for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk]; - - for(jk=1; jk <=nlstate ; jk++){ - if( i <= (int) agemax){ - if(pos>=1.e-5){ - probs[i][jk][j1]= pp[jk]/pos; - } - } - }/* end jk */ - }/* end i */ - } /* end i1 */ - } /* end k1 */ - - - free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3); - free_vector(pp,1,nlstate); - -} /* End of Freq */ - -/************* Waves Concatenation ***************/ - -void concatwav(int wav[], int **dh, int **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 first; - int j, k=0,jk, ju, jl; - double sum=0.; - first=0; - jmin=1e+5; - jmax=-1; - jmean=0.; - for(i=1; i<=imx; i++){ - mi=0; - m=firstpass; - while(s[m][i] <= nlstate){ - if(s[m][i]>=1) - mw[++mi][i]=m; - if(m >=lastpass) - break; - else - m++; - }/* end while */ - if (s[m][i] > nlstate){ - mi++; /* Death is another wave */ - /* if(mi==0) never been interviewed correctly before death */ - /* Only death is a correct wave */ - mw[mi][i]=m; - } - - wav[i]=mi; - if(mi==0){ - if(first==0){ - printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i); - first=1; - } - if(first==1){ - fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i); - } - } /* end mi==0 */ - } - - for(i=1; i<=imx; i++){ - for(mi=1; mi 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); - fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean); - } - -/*********** Tricode ****************************/ -void tricode(int *Tvar, int **nbcode, int imx) -{ - int Ndum[20],ij=1, k, j, i; - 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, int estepm,double delti[],double **matcov ) - -{ - /* Health expectancies */ - int i, j, nhstepm, hstepm, h, nstepm, k, cptj; - double age, agelim, hf; - double ***p3mat,***varhe; - double **dnewm,**doldm; - double *xp; - double **gp, **gm; - double ***gradg, ***trgradg; - int theta; - - varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage); - xp=vector(1,npar); - dnewm=matrix(1,nlstate*2,1,npar); - doldm=matrix(1,nlstate*2,1,nlstate*2); - - fprintf(ficreseij,"# Health expectancies\n"); - fprintf(ficreseij,"# Age"); - for(i=1; i<=nlstate;i++) - for(j=1; j<=nlstate;j++) - fprintf(ficreseij," %1d-%1d (SE)",i,j); - fprintf(ficreseij,"\n"); - - if(estepm < stepm){ - printf ("Problem %d lower than %d\n",estepm, stepm); - } - else hstepm=estepm; - /* We compute the life expectancy from trapezoids spaced every estepm months - * This is mainly to measure the difference between two models: for example - * if stepm=24 months pijx are given only every 2 years and by summing them - * we are calculating an estimate of the Life Expectancy assuming a linear - * progression inbetween and thus overestimating or underestimating according - * to the curvature of the survival function. If, for the same date, we - * estimate the model with stepm=1 month, we can keep estepm to 24 months - * to compare the new estimate of Life expectancy with the same linear - * hypothesis. A more precise result, taking into account a more precise - * curvature will be obtained if estepm is as small as stepm. */ - - /* For example we decided to compute the life expectancy with the smallest unit */ - /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. - nhstepm is the number of hstepm from age to agelim - nstepm is the number of stepm from age to agelin. - Look at hpijx to understand the reason of that which relies in memory size - and note for a fixed period like estepm months */ - /* We decided (b) to get a life expectancy respecting the most precise curvature of the - survival function given by stepm (the optimization length). Unfortunately it - means that if the survival funtion is printed only each two years of age and if - you sum them up and add 1 year (area under the trapezoids) you won't get the same - results. So we changed our mind and took the option of the best precision. - */ - hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ - - agelim=AGESUP; - for (age=bage; age<=fage; age ++){ /* If stepm=6 months */ - /* nhstepm age range expressed in number of stepm */ - nstepm=(int) rint((agelim-age)*YEARM/stepm); - /* Typically if 20 years nstepm = 20*12/6=40 stepm */ - /* if (stepm >= YEARM) hstepm=1;*/ - nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ - p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); - gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2); - gp=matrix(0,nhstepm,1,nlstate*2); - gm=matrix(0,nhstepm,1,nlstate*2); - - /* Computed by stepm unit matrices, product of hstepm matrices, stored - in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */ - hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij); - - - hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ - - /* Computing Variances of health expectancies */ - - for(theta=1; theta <=npar; theta++){ - for(i=1; i<=npar; i++){ - xp[i] = x[i] + (i==theta ?delti[theta]:0); - } - hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); - - cptj=0; - for(j=1; j<= nlstate; j++){ - for(i=1; i<=nlstate; i++){ - cptj=cptj+1; - for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){ - gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.; - } - } - } - - - for(i=1; i<=npar; i++) - xp[i] = x[i] - (i==theta ?delti[theta]:0); - hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); - - cptj=0; - for(j=1; j<= nlstate; j++){ - for(i=1;i<=nlstate;i++){ - cptj=cptj+1; - for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){ - gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.; - } - } - } - for(j=1; j<= nlstate*2; j++) - for(h=0; h<=nhstepm-1; h++){ - gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta]; - } - } - -/* End theta */ - - trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar); - - for(h=0; h<=nhstepm-1; h++) - for(j=1; j<=nlstate*2;j++) - for(theta=1; theta <=npar; theta++) - trgradg[h][j][theta]=gradg[h][theta][j]; - - - for(i=1;i<=nlstate*2;i++) - for(j=1;j<=nlstate*2;j++) - varhe[i][j][(int)age] =0.; - - printf("%d|",(int)age);fflush(stdout); - fprintf(ficlog,"%d|",(int)age);fflush(ficlog); - for(h=0;h<=nhstepm-1;h++){ - for(k=0;k<=nhstepm-1;k++){ - matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov); - matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]); - for(i=1;i<=nlstate*2;i++) - for(j=1;j<=nlstate*2;j++) - varhe[i][j][(int)age] += doldm[i][j]*hf*hf; - } - } - /* Computing expectancies */ - for(i=1; i<=nlstate;i++) - for(j=1; j<=nlstate;j++) - for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){ - eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf; - -/* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/ - - } - - fprintf(ficreseij,"%3.0f",age ); - cptj=0; - for(i=1; i<=nlstate;i++) - for(j=1; j<=nlstate;j++){ - cptj++; - fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) ); - } - fprintf(ficreseij,"\n"); - - free_matrix(gm,0,nhstepm,1,nlstate*2); - free_matrix(gp,0,nhstepm,1,nlstate*2); - free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2); - free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar); - free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); - } - printf("\n"); - fprintf(ficlog,"\n"); - - free_vector(xp,1,npar); - free_matrix(dnewm,1,nlstate*2,1,npar); - free_matrix(doldm,1,nlstate*2,1,nlstate*2); - free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage); -} - -/************ Variance ******************/ -void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased) -{ - /* Variance of health expectancies */ - /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/ - /* double **newm;*/ - double **dnewm,**doldm; - double **dnewmp,**doldmp; - int i, j, nhstepm, hstepm, h, nstepm ; - int k, cptcode; - double *xp; - double **gp, **gm; /* for var eij */ - double ***gradg, ***trgradg; /*for var eij */ - double **gradgp, **trgradgp; /* for var p point j */ - double *gpp, *gmp; /* for var p point j */ - double **varppt; /* for var p point j nlstate to nlstate+ndeath */ - double ***p3mat; - double age,agelim, hf; - int theta; - char digit[4]; - char digitp[16]; - - char fileresprobmorprev[FILENAMELENGTH]; - - if(popbased==1) - strcpy(digitp,"-populbased-"); - else - strcpy(digitp,"-stablbased-"); - - strcpy(fileresprobmorprev,"prmorprev"); - sprintf(digit,"%-d",ij); - /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/ - strcat(fileresprobmorprev,digit); /* Tvar to be done */ - strcat(fileresprobmorprev,digitp); /* Popbased or not */ - strcat(fileresprobmorprev,fileres); - if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) { - printf("Problem with resultfile: %s\n", fileresprobmorprev); - fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev); - } - printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); - fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); - fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n"); - fprintf(ficresprobmorprev,"# Age cov=%-d",ij); - for(j=nlstate+1; j<=(nlstate+ndeath);j++){ - fprintf(ficresprobmorprev," p.%-d SE",j); - for(i=1; i<=nlstate;i++) - fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j); - } - fprintf(ficresprobmorprev,"\n"); - if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { - printf("Problem with gnuplot file: %s\n", optionfilegnuplot); - fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot); - exit(0); - } - else{ - fprintf(ficgp,"\n# Routine varevsij"); - } - if((fichtm=fopen(optionfilehtm,"a"))==NULL) { - printf("Problem with html file: %s\n", optionfilehtm); - fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm); - exit(0); - } - else{ - fprintf(fichtm,"\n

  • Computing probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)

    • \n"); - } - varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); - - fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are the stable prevalence in health states i\n"); - fprintf(ficresvij,"# Age"); - for(i=1; i<=nlstate;i++) - for(j=1; j<=nlstate;j++) - fprintf(ficresvij," Cov(e%1d, e%1d)",i,j); - fprintf(ficresvij,"\n"); - - xp=vector(1,npar); - dnewm=matrix(1,nlstate,1,npar); - doldm=matrix(1,nlstate,1,nlstate); - dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar); - doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); - - gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath); - gpp=vector(nlstate+1,nlstate+ndeath); - gmp=vector(nlstate+1,nlstate+ndeath); - trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/ - - if(estepm < stepm){ - printf ("Problem %d lower than %d\n",estepm, stepm); - } - else hstepm=estepm; - /* For example we decided to compute the life expectancy with the smallest unit */ - /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. - nhstepm is the number of hstepm from age to agelim - nstepm is the number of stepm from age to agelin. - Look at hpijx to understand the reason of that which relies in memory size - and note for a fixed period like k years */ - /* We decided (b) to get a life expectancy respecting the most precise curvature of the - survival function given by stepm (the optimization length). Unfortunately it - means that if the survival funtion is printed only each two years of age and if - you sum them up and add 1 year (area under the trapezoids) you won't get the same - results. So we changed our mind and took the option of the best precision. - */ - hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ - agelim = AGESUP; - for (age=bage; age<=fage; age ++){ /* If stepm=6 months */ - nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ - nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ - p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); - gradg=ma3x(0,nhstepm,1,npar,1,nlstate); - gp=matrix(0,nhstepm,1,nlstate); - gm=matrix(0,nhstepm,1,nlstate); - - - for(theta=1; theta <=npar; theta++){ - for(i=1; i<=npar; i++){ /* Computes gradient */ - xp[i] = x[i] + (i==theta ?delti[theta]:0); - } - hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); - prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); - - if (popbased==1) { - 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]; - } - } - /* This for computing forces of mortality (h=1)as a weighted average */ - for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){ - for(i=1; i<= nlstate; i++) - gpp[j] += prlim[i][i]*p3mat[i][j][1]; - } - /* end force of mortality */ - - for(i=1; i<=npar; i++) /* Computes gradient */ - xp[i] = x[i] - (i==theta ?delti[theta]:0); - hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); - prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); - - if (popbased==1) { - 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]; - } - } - /* This for computing force of mortality (h=1)as a weighted average */ - for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){ - for(i=1; i<= nlstate; i++) - gmp[j] += prlim[i][i]*p3mat[i][j][1]; - } - /* end force of mortality */ - - for(j=1; j<= nlstate; j++) /* vareij */ - for(h=0; h<=nhstepm; h++){ - gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta]; - } - for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */ - gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta]; - } - - } /* End theta */ - - trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */ - - for(h=0; h<=nhstepm; h++) /* veij */ - for(j=1; j<=nlstate;j++) - for(theta=1; theta <=npar; theta++) - trgradg[h][j][theta]=gradg[h][theta][j]; - - for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */ - for(theta=1; theta <=npar; theta++) - trgradgp[j][theta]=gradgp[theta][j]; - - hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ - for(i=1;i<=nlstate;i++) - for(j=1;j<=nlstate;j++) - vareij[i][j][(int)age] =0.; - - for(h=0;h<=nhstepm;h++){ - for(k=0;k<=nhstepm;k++){ - matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov); - matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]); - for(i=1;i<=nlstate;i++) - for(j=1;j<=nlstate;j++) - vareij[i][j][(int)age] += doldm[i][j]*hf*hf; - } - } - - /* pptj */ - matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov); - matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp); - for(j=nlstate+1;j<=nlstate+ndeath;j++) - for(i=nlstate+1;i<=nlstate+ndeath;i++) - varppt[j][i]=doldmp[j][i]; - /* end ppptj */ - hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij); - prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij); - - if (popbased==1) { - for(i=1; i<=nlstate;i++) - prlim[i][i]=probs[(int)age][i][ij]; - } - - /* This for computing force of mortality (h=1)as a weighted average */ - for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){ - for(i=1; i<= nlstate; i++) - gmp[j] += prlim[i][i]*p3mat[i][j][1]; - } - /* end force of mortality */ - - fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij); - for(j=nlstate+1; j<=(nlstate+ndeath);j++){ - fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j])); - for(i=1; i<=nlstate;i++){ - fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]); - } - } - fprintf(ficresprobmorprev,"\n"); - - fprintf(ficresvij,"%.0f ",age ); - for(i=1; i<=nlstate;i++) - for(j=1; j<=nlstate;j++){ - fprintf(ficresvij," %.4f", vareij[i][j][(int)age]); - } - fprintf(ficresvij,"\n"); - free_matrix(gp,0,nhstepm,1,nlstate); - free_matrix(gm,0,nhstepm,1,nlstate); - free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate); - free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar); - free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); - } /* End age */ - free_vector(gpp,nlstate+1,nlstate+ndeath); - free_vector(gmp,nlstate+1,nlstate+ndeath); - free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath); - free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/ - fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65"); - /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */ - fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";"); - fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); - fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); - fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); - fprintf(fichtm,"\n
    File (multiple files are possible if covariates are present): %s\n",fileresprobmorprev,fileresprobmorprev); - fprintf(fichtm,"\n
    Probability is computed over estepm=%d months.

    \n", stepm,digitp,digit); - /* fprintf(fichtm,"\n
    Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year

    \n", stepm,YEARM,digitp,digit); -*/ - fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit); - - free_vector(xp,1,npar); - free_matrix(doldm,1,nlstate,1,nlstate); - free_matrix(dnewm,1,nlstate,1,npar); - free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); - free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar); - free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); - fclose(ficresprobmorprev); - fclose(ficgp); - fclose(fichtm); - -} - -/************ Variance of prevlim ******************/ -void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij) -{ - /* Variance of prevalence limit */ - /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/ - double **newm; - double **dnewm,**doldm; - int i, j, nhstepm, hstepm; - int k, cptcode; - double *xp; - double *gp, *gm; - double **gradg, **trgradg; - double age,agelim; - int theta; - - fprintf(ficresvpl,"# Standard deviation of prevalence's 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 optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax) -{ - int i, j=0, i1, k1, l1, t, tj; - int k2, l2, j1, z1; - int k=0,l, cptcode; - int first=1, first1; - double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp; - double **dnewm,**doldm; - double *xp; - double *gp, *gm; - double **gradg, **trgradg; - double **mu; - double age,agelim, cov[NCOVMAX]; - double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */ - int theta; - char fileresprob[FILENAMELENGTH]; - char fileresprobcov[FILENAMELENGTH]; - char fileresprobcor[FILENAMELENGTH]; - - double ***varpij; - - strcpy(fileresprob,"prob"); - strcat(fileresprob,fileres); - if((ficresprob=fopen(fileresprob,"w"))==NULL) { - printf("Problem with resultfile: %s\n", fileresprob); - fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob); - } - strcpy(fileresprobcov,"probcov"); - strcat(fileresprobcov,fileres); - if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) { - printf("Problem with resultfile: %s\n", fileresprobcov); - fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov); - } - strcpy(fileresprobcor,"probcor"); - strcat(fileresprobcor,fileres); - if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) { - printf("Problem with resultfile: %s\n", fileresprobcor); - fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor); - } - printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob); - fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob); - printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov); - fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov); - printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); - fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); - - fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n"); - fprintf(ficresprob,"# Age"); - fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n"); - fprintf(ficresprobcov,"# Age"); - fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n"); - fprintf(ficresprobcov,"# Age"); - - - for(i=1; i<=nlstate;i++) - for(j=1; j<=(nlstate+ndeath);j++){ - fprintf(ficresprob," p%1d-%1d (SE)",i,j); - fprintf(ficresprobcov," p%1d-%1d ",i,j); - fprintf(ficresprobcor," p%1d-%1d ",i,j); - } - fprintf(ficresprob,"\n"); - fprintf(ficresprobcov,"\n"); - fprintf(ficresprobcor,"\n"); - xp=vector(1,npar); - dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); - doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath)); - mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage); - varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage); - first=1; - if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { - printf("Problem with gnuplot file: %s\n", optionfilegnuplot); - fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot); - exit(0); - } - else{ - fprintf(ficgp,"\n# Routine varprob"); - } - if((fichtm=fopen(optionfilehtm,"a"))==NULL) { - printf("Problem with html file: %s\n", optionfilehtm); - fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm); - exit(0); - } - else{ - fprintf(fichtm,"\n

  • Computing and drawing one step probabilities with their confidence intervals

    • \n"); - fprintf(fichtm,"\n"); - - fprintf(fichtm,"\n

  • Computing matrix of variance-covariance of step probabilities

    • \n"); - fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the pij, pkl to understand the covariance between two incidences. They are expressed in year-1 in order to be less dependent of stepm.
    \n"); - fprintf(fichtm,"\n
    We have drawn x'cov-1x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis.
    When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.
    \n"); - - } - - - cov[1]=1; - tj=cptcoveff; - if (cptcovn<1) {tj=1;ncodemax[1]=1;} - j1=0; - for(t=1; t<=tj;t++){ - for(i1=1; i1<=ncodemax[t];i1++){ - j1++; - - if (cptcovn>0) { - fprintf(ficresprob, "\n#********** Variable "); - for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); - fprintf(ficresprob, "**********\n#"); - fprintf(ficresprobcov, "\n#********** Variable "); - for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); - fprintf(ficresprobcov, "**********\n#"); - - fprintf(ficgp, "\n#********** Variable "); - for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); - fprintf(ficgp, "**********\n#"); - - - fprintf(fichtm, "\n
    ********** Variable "); - for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); - fprintf(fichtm, "**********\n
    "); - - fprintf(ficresprobcor, "\n#********** Variable "); - for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); - fprintf(ficgp, "**********\n#"); - } - - for (age=bage; age<=fage; age ++){ - cov[2]=age; - for (k=1; k<=cptcovn;k++) { - cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]]; - } - for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; - for (k=1; k<=cptcovprod;k++) - cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; - - gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath)); - trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); - gp=vector(1,(nlstate)*(nlstate+ndeath)); - gm=vector(1,(nlstate)*(nlstate+ndeath)); - - for(theta=1; theta <=npar; theta++){ - for(i=1; i<=npar; i++) - xp[i] = x[i] + (i==theta ?delti[theta]:0); - - pmij(pmmij,cov,ncovmodel,xp,nlstate); - - k=0; - for(i=1; i<= (nlstate); i++){ - for(j=1; j<=(nlstate+ndeath);j++){ - k=k+1; - gp[k]=pmmij[i][j]; - } - } - - for(i=1; i<=npar; i++) - xp[i] = x[i] - (i==theta ?delti[theta]:0); - - pmij(pmmij,cov,ncovmodel,xp,nlstate); - k=0; - for(i=1; i<=(nlstate); i++){ - for(j=1; j<=(nlstate+ndeath);j++){ - k=k+1; - gm[k]=pmmij[i][j]; - } - } - - for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) - gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta]; - } - - for(j=1; j<=(nlstate)*(nlstate+ndeath);j++) - for(theta=1; theta <=npar; theta++) - trgradg[j][theta]=gradg[theta][j]; - - matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); - matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg); - - pmij(pmmij,cov,ncovmodel,x,nlstate); - - k=0; - for(i=1; i<=(nlstate); i++){ - for(j=1; j<=(nlstate+ndeath);j++){ - k=k+1; - mu[k][(int) age]=pmmij[i][j]; - } - } - for(i=1;i<=(nlstate)*(nlstate+ndeath);i++) - for(j=1;j<=(nlstate)*(nlstate+ndeath);j++) - varpij[i][j][(int)age] = doldm[i][j]; - - /*printf("\n%d ",(int)age); - for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){ - printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i])); - fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i])); - }*/ - - fprintf(ficresprob,"\n%d ",(int)age); - fprintf(ficresprobcov,"\n%d ",(int)age); - fprintf(ficresprobcor,"\n%d ",(int)age); - - for (i=1; i<=(nlstate)*(nlstate+ndeath);i++) - fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age])); - for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){ - fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]); - fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]); - } - i=0; - for (k=1; k<=(nlstate);k++){ - for (l=1; l<=(nlstate+ndeath);l++){ - i=i++; - fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l); - fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l); - for (j=1; j<=i;j++){ - fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]); - fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age])); - } - } - }/* end of loop for state */ - } /* end of loop for age */ - - /* Confidence intervalle of pij */ - /* - fprintf(ficgp,"\nset noparametric;unset label"); - fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\""); - fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65"); - fprintf(fichtm,"\n
    Probability with confidence intervals expressed in year-1 :pijgr%s.png, ",optionfilefiname,optionfilefiname); - fprintf(fichtm,"\n
    ",optionfilefiname); - fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname); - fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob); - */ - - /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/ - first1=1; - for (k2=1; k2<=(nlstate);k2++){ - for (l2=1; l2<=(nlstate+ndeath);l2++){ - if(l2==k2) continue; - j=(k2-1)*(nlstate+ndeath)+l2; - for (k1=1; k1<=(nlstate);k1++){ - for (l1=1; l1<=(nlstate+ndeath);l1++){ - if(l1==k1) continue; - i=(k1-1)*(nlstate+ndeath)+l1; - if(i<=j) continue; - for (age=bage; age<=fage; age ++){ - if ((int)age %5==0){ - v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM; - v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM; - cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM; - mu1=mu[i][(int) age]/stepm*YEARM ; - mu2=mu[j][(int) age]/stepm*YEARM; - c12=cv12/sqrt(v1*v2); - /* Computing eigen value of matrix of covariance */ - lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; - lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; - /* Eigen vectors */ - v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12)); - /*v21=sqrt(1.-v11*v11); *//* error */ - v21=(lc1-v1)/cv12*v11; - v12=-v21; - v22=v11; - tnalp=v21/v11; - if(first1==1){ - first1=0; - printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp); - } - fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp); - /*printf(fignu*/ - /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */ - /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */ - if(first==1){ - first=0; - fprintf(ficgp,"\nset parametric;unset label"); - fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2); - fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65"); - fprintf(fichtm,"\n
    Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year-1 :varpijgr%s%d%1d%1d-%1d%1d.png, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2); - fprintf(fichtm,"\n
    ",optionfilefiname, j1,k1,l1,k2,l2); - fprintf(fichtm,"\n
    Correlation at age %d (%.3f),",(int) age, c12); - fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2); - fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2); - fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2); - fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\ - mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\ - mu2,std,v21,sqrt(lc1),v22,sqrt(lc2)); - }else{ - first=0; - fprintf(fichtm," %d (%.3f),",(int) age, c12); - fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2); - fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2); - fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\ - mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\ - mu2,std,v21,sqrt(lc1),v22,sqrt(lc2)); - }/* if first */ - } /* age mod 5 */ - } /* end loop age */ - fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2); - first=1; - } /*l12 */ - } /* k12 */ - } /*l1 */ - }/* k1 */ - } /* loop covariates */ - free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage); - free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath)); - free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath)); - free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage); - 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); - fclose(ficresprobcov); - fclose(ficresprobcor); - fclose(ficgp); - fclose(fichtm); -} - - -/******************* Printing html file ***********/ -void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \ - int lastpass, int stepm, int weightopt, char model[],\ - int imx,int jmin, int jmax, double jmeanint,char rfileres[],\ - int popforecast, int estepm ,\ - double jprev1, double mprev1,double anprev1, \ - double jprev2, double mprev2,double anprev2){ - int jj1, k1, i1, cpt; - /*char optionfilehtm[FILENAMELENGTH];*/ - if((fichtm=fopen(optionfilehtm,"a"))==NULL) { - printf("Problem with %s \n",optionfilehtm), exit(0); - fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); - } - - fprintf(fichtm,"

    • Result files (first order: no variance)

      \n - - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): p%s
      \n - - Estimated transition probabilities over %d (stepm) months: pij%s
      \n - - Stable prevalence in each health state: pl%s
      \n - - Life expectancies by age and initial health status (estepm=%2d months): - e%s
      \n
      • ", \ - jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres); - -fprintf(fichtm," \n
      • Graphs

        • "); - - 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,"

        ************ 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
        "); - } - /* Pij */ - fprintf(fichtm,"
        - Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png
        -",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); - /* Quasi-incidences */ - fprintf(fichtm,"
        - Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png
        -",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); - /* Stable prevalence in each health state */ - for(cpt=1; cpt- Stable prevalence in each health state : p%s%d%d.png
        -",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.png
        -",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.png
        -",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); - } /* end i1 */ - }/* End k1 */ - fprintf(fichtm,"
      "); - - - fprintf(fichtm,"\n

    • Result files (second order: variances)

      \n - - Parameter file with estimated parameters and covariance matrix: %s
      \n - - Variance of one-step probabilities: prob%s
      \n - - Variance-covariance of one-step probabilities: probcov%s
      \n - - Correlation matrix of one-step probabilities: probcor%s
      \n - - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): v%s
      \n - - Health expectancies with their variances (no covariance): t%s
      \n - - Standard deviation of stable prevalences: vpl%s
      \n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres); - - if(popforecast==1) fprintf(fichtm,"\n - - Prevalences forecasting: f%s
      \n - - Population forecasting (if popforecast=1): pop%s
      \n -
      ",fileres,fileres,fileres,fileres); - else - fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)

      • \n",popforecast, stepm, model); -fprintf(fichtm,"
      • Graphs

        • "); - - 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,"

        ************ 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
        "); - } - for(cpt=1; cpt<=nlstate;cpt++) { - fprintf(fichtm,"
        - Observed and stationary prevalence (with confident -interval) in state (%d): v%s%d%d.png
        -",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1); - } - } /* end i1 */ - }/* End k1 */ - fprintf(fichtm,"
      "); -fclose(fichtm); -} - -/******************* Gnuplot file **************/ -void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){ - - int m,cpt,k1,i,k,j,jk,k2,k3,ij,l; - int ng; - if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { - printf("Problem with file %s",optionfilegnuplot); - fprintf(ficlog,"Problem with file %s",optionfilegnuplot); - } - -#ifdef windows - fprintf(ficgp,"cd \"%s\" \n",pathc); -#endif -m=pow(2,cptcoveff); - - /* 1eme*/ - for (cpt=1; cpt<= nlstate ; cpt ++) { - for (k1=1; k1<= m ; k1 ++) { - -#ifdef windows - fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1); - fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1); -#endif -#ifdef unix -fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1); -fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,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 png small\nset size 0.65,0.65\n"); -#endif - } - } - /*2 eme*/ - - for (k1=1; k1<= m ; k1 ++) { - fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1); - fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage); - - for (i=1; i<= nlstate+1 ; i ++) { - k=2*i; - fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1); - for (j=1; j<= nlstate+1 ; j ++) { - if (j==i) fprintf(ficgp," \%%lf (\%%lf)"); - else fprintf(ficgp," \%%*lf (\%%*lf)"); -} - if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,"); - else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1); - fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1); - for (j=1; j<= nlstate+1 ; j ++) { - if (j==i) fprintf(ficgp," \%%lf (\%%lf)"); - else fprintf(ficgp," \%%*lf (\%%*lf)"); -} - fprintf(ficgp,"\" t\"\" w l 0,"); - fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1); - for (j=1; j<= nlstate+1 ; j ++) { - if (j==i) fprintf(ficgp," \%%lf (\%%lf)"); - else fprintf(ficgp," \%%*lf (\%%*lf)"); -} - if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0"); - else fprintf(ficgp,"\" t\"\" w l 0,"); - } - } - - /*3eme*/ - - for (k1=1; k1<= m ; k1 ++) { - for (cpt=1; cpt<= nlstate ; cpt ++) { - k=2+nlstate*(2*cpt-2); - fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1); - fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt); - /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); - for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); -fprintf(ficgp,"\" t \"e%d1\" w l",cpt); -fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); - for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); -fprintf(ficgp,"\" t \"e%d1\" w l",cpt); - -*/ - for (i=1; i< nlstate ; i ++) { - fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1); - - } - } - } - - /* CV preval stat */ - for (k1=1; k1<= m ; k1 ++) { - for (cpt=1; cpt=(ageminpar-((int)calagedate %12)/12.); agedeb--){ - nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); - nhstepm = nhstepm/hstepm; - - p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); - oldm=oldms;savm=savms; - hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); - - for (h=0; h<=nhstepm; h++){ - if (h==(int) (calagedate+YEARM*cpt)) { - fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm); - } - for(j=1; j<=nlstate+ndeath;j++) { - kk1=0.;kk2=0; - for(i=1; i<=nlstate;i++) { - if (mobilav==1) - kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; - else { - kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; - } - - } - if (h==(int)(calagedate+12*cpt)){ - fprintf(ficresf," %.3f", kk1); - - } - } - } - free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); - } - } - } - } - - if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); - - fclose(ficresf); -} -/************** Forecasting ******************/ -populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ - - int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; - int *popage; - double calagedate, agelim, kk1, kk2, 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(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate); - - - strcpy(filerespop,"pop"); - strcat(filerespop,fileres); - if((ficrespop=fopen(filerespop,"w"))==NULL) { - printf("Problem with forecast resultfile: %s\n", filerespop); - fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); - } - printf("Computing forecasting: result on file '%s' \n", filerespop); - fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); - - if (cptcoveff==0) ncodemax[cptcoveff]=1; - - if (mobilav==1) { - mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); - movingaverage(agedeb, fage, ageminpar, 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); - fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); - } - popage=ivector(0,AGESUP); - popeffectif=vector(0,AGESUP); - popcount=vector(0,AGESUP); - - i=1; - while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; - - imx=i; - for (i=1; i=(ageminpar-((int)calagedate %12)/12.); agedeb--){ - nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); - nhstepm = nhstepm/hstepm; - - p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); - oldm=oldms;savm=savms; - hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); - - for (h=0; h<=nhstepm; h++){ - if (h==(int) (calagedate+YEARM*cpt)) { - fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); - } - for(j=1; j<=nlstate+ndeath;j++) { - kk1=0.;kk2=0; - for(i=1; i<=nlstate;i++) { - if (mobilav==1) - kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; - else { - kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; - } - } - if (h==(int)(calagedate+12*cpt)){ - tabpop[(int)(agedeb)][j][cptcod]=kk1; - /*fprintf(ficrespop," %.3f", kk1); - if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/ - } - } - for(i=1; i<=nlstate;i++){ - kk1=0.; - for(j=1; j<=nlstate;j++){ - kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; - } - tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)]; - } - - if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++) - fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); - } - free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); - } - } - - /******/ - - for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { - fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); - for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ - nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); - nhstepm = nhstepm/hstepm; - - p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); - oldm=oldms;savm=savms; - hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); - for (h=0; h<=nhstepm; h++){ - if (h==(int) (calagedate+YEARM*cpt)) { - fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); - } - for(j=1; j<=nlstate+ndeath;j++) { - kk1=0.;kk2=0; - for(i=1; i<=nlstate;i++) { - kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; - } - if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1); - } - } - free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); - } - } - } - } - - if (mobilav==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 ageminpar=1.e20,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 path[80],pathc[80],pathcd[80],pathtot[80],model[80]; - int firstobs=1, lastobs=10; - int sdeb, sfin; /* Status at beginning and end */ - int c, h , cpt,l; - int ju,jl, mi; - int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij; - int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab; - int mobilav=0,popforecast=0; - int hstepm, nhstepm; - double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate; - - double bage, fage, age, agelim, agebase; - double ftolpl=FTOL; - double **prlim; - double *severity; - double ***param; /* Matrix of parameters */ - double *p; - double **matcov; /* Matrix of covariance */ - double ***delti3; /* Scale */ - double *delti; /* Scale */ - double ***eij, ***vareij; - double **varpl; /* Variances of prevalence limits by age */ - double *epj, vepp; - double kk1, kk2; - double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2; - - - char *alph[]={"a","a","b","c","d","e"}, str[4]; - - - char z[1]="c", occ; -#include -#include - char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80]; - - /* long total_usecs; - struct timeval start_time, end_time; - - gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */ - getcwd(pathcd, size); - - printf("\n%s",version); - if(argc <=1){ - printf("\nEnter the parameter file name: "); - scanf("%s",pathtot); - } - else{ - strcpy(pathtot,argv[1]); - } - /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/ - /*cygwin_split_path(pathtot,path,optionfile); - printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/ - /* cutv(path,optionfile,pathtot,'\\');*/ - - split(pathtot,path,optionfile,optionfilext,optionfilefiname); - printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname); - chdir(path); - replace(pathc,path); - -/*-------- arguments in the command line --------*/ - - /* Log file */ - strcat(filelog, optionfilefiname); - strcat(filelog,".log"); /* */ - if((ficlog=fopen(filelog,"w"))==NULL) { - printf("Problem with logfile %s\n",filelog); - goto end; - } - fprintf(ficlog,"Log filename:%s\n",filelog); - fprintf(ficlog,"\n%s",version); - fprintf(ficlog,"\nEnter the parameter file name: "); - fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname); - fflush(ficlog); - - /* */ - strcpy(fileres,"r"); - strcat(fileres, optionfilefiname); - strcat(fileres,".txt"); /* Other files have txt extension */ - - /*---------arguments file --------*/ - - if((ficpar=fopen(optionfile,"r"))==NULL) { - printf("Problem with optionfile %s\n",optionfile); - fprintf(ficlog,"Problem with optionfile %s\n",optionfile); - goto end; - } - - strcpy(filereso,"o"); - strcat(filereso,fileres); - if((ficparo=fopen(filereso,"w"))==NULL) { - printf("Problem with Output resultfile: %s\n", filereso); - fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso); - goto end; - } - - /* Reads comments: lines beginning with '#' */ - while((c=getc(ficpar))=='#' && c!= EOF){ - ungetc(c,ficpar); - fgets(line, MAXLINE, ficpar); - puts(line); - fputs(line,ficparo); - } - ungetc(c,ficpar); - - fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); - printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); - fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); -while((c=getc(ficpar))=='#' && c!= EOF){ - ungetc(c,ficpar); - fgets(line, MAXLINE, ficpar); - puts(line); - fputs(line,ficparo); - } - ungetc(c,ficpar); - - - covar=matrix(0,NCOVMAX,1,n); - cptcovn=0; - 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); - if(mle==1) - printf("%1d%1d",i,j); - fprintf(ficlog,"%1d%1d",i,j); - for(k=1; k<=ncovmodel;k++){ - fscanf(ficpar," %lf",¶m[i][j][k]); - if(mle==1){ - printf(" %lf",param[i][j][k]); - fprintf(ficlog," %lf",param[i][j][k]); - } - else - fprintf(ficlog," %lf",param[i][j][k]); - fprintf(ficparo," %lf",param[i][j][k]); - } - fscanf(ficpar,"\n"); - if(mle==1) - printf("\n"); - fprintf(ficlog,"\n"); - fprintf(ficparo,"\n"); - } - - npar= (nlstate+ndeath-1)*nlstate*ncovmodel; - - p=param[1][1]; - - /* Reads comments: lines beginning with '#' */ - while((c=getc(ficpar))=='#' && c!= EOF){ - ungetc(c,ficpar); - fgets(line, MAXLINE, ficpar); - puts(line); - fputs(line,ficparo); - } - ungetc(c,ficpar); - - delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); - delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */ - for(i=1; i <=nlstate; i++){ - for(j=1; j <=nlstate+ndeath-1; j++){ - fscanf(ficpar,"%1d%1d",&i1,&j1); - printf("%1d%1d",i,j); - fprintf(ficparo,"%1d%1d",i1,j1); - for(k=1; k<=ncovmodel;k++){ - fscanf(ficpar,"%le",&delti3[i][j][k]); - printf(" %le",delti3[i][j][k]); - fprintf(ficparo," %le",delti3[i][j][k]); - } - fscanf(ficpar,"\n"); - printf("\n"); - fprintf(ficparo,"\n"); - } - } - delti=delti3[1][1]; - - /* Reads comments: lines beginning with '#' */ - while((c=getc(ficpar))=='#' && c!= EOF){ - ungetc(c,ficpar); - fgets(line, MAXLINE, ficpar); - puts(line); - fputs(line,ficparo); - } - ungetc(c,ficpar); - - matcov=matrix(1,npar,1,npar); - for(i=1; i <=npar; i++){ - fscanf(ficpar,"%s",&str); - if(mle==1) - printf("%s",str); - fprintf(ficlog,"%s",str); - fprintf(ficparo,"%s",str); - for(j=1; j <=i; j++){ - fscanf(ficpar," %le",&matcov[i][j]); - if(mle==1){ - printf(" %.5le",matcov[i][j]); - fprintf(ficlog," %.5le",matcov[i][j]); - } - else - fprintf(ficlog," %.5le",matcov[i][j]); - fprintf(ficparo," %.5le",matcov[i][j]); - } - fscanf(ficpar,"\n"); - if(mle==1) - printf("\n"); - fprintf(ficlog,"\n"); - fprintf(ficparo,"\n"); - } - for(i=1; i <=npar; i++) - for(j=i+1;j<=npar;j++) - matcov[i][j]=matcov[j][i]; - - if(mle==1) - printf("\n"); - fprintf(ficlog,"\n"); - - - /*-------- Rewriting paramater file ----------*/ - strcpy(rfileres,"r"); /* "Rparameterfile */ - strcat(rfileres,optionfilefiname); /* Parameter file first name*/ - strcat(rfileres,"."); /* */ - strcat(rfileres,optionfilext); /* Other files have txt extension */ - if((ficres =fopen(rfileres,"w"))==NULL) { - printf("Problem writing new parameter file: %s\n", fileres);goto end; - fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end; - } - fprintf(ficres,"#%s\n",version); - - /*-------- data file ----------*/ - if((fic=fopen(datafile,"r"))==NULL) { - printf("Problem with datafile: %s\n", datafile);goto end; - fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end; - } - - n= lastobs; - severity = vector(1,maxwav); - outcome=imatrix(1,maxwav+1,1,n); - num=ivector(1,n); - moisnais=vector(1,n); - annais=vector(1,n); - moisdc=vector(1,n); - andc=vector(1,n); - agedc=vector(1,n); - cod=ivector(1,n); - weight=vector(1,n); - for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */ - mint=matrix(1,maxwav,1,n); - anint=matrix(1,maxwav,1,n); - s=imatrix(1,maxwav+1,1,n); - 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 (s[4][i]==9) s[4][i]=-1; - printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i]));}*/ - - - /* Calculation of the number of parameter from char model*/ - Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */ - Tprod=ivector(1,15); - Tvaraff=ivector(1,15); - Tvard=imatrix(1,15,1,2); - Tage=ivector(1,15); - - if (strlen(model) >1){ - 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); - fprintf(ficlog,"Error. Non available option model=%s ",model); - goto end; - } - - for(i=(j+1); i>=1;i--){ - cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ - if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */ - /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/ - /*scanf("%d",i);*/ - if (strchr(strb,'*')) { /* Model includes a product */ - cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/ - if (strcmp(strc,"age")==0) { /* Vn*age */ - cptcovprod--; - cutv(strb,stre,strd,'V'); - Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/ - cptcovage++; - Tage[cptcovage]=i; - /*printf("stre=%s ", stre);*/ - } - else if (strcmp(strd,"age")==0) { /* or age*Vn */ - cptcovprod--; - cutv(strb,stre,strc,'V'); - Tvar[i]=atoi(stre); - cptcovage++; - Tage[cptcovage]=i; - } - else { /* Age is not in the model */ - cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/ - Tvar[i]=ncovcol+k1; - cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */ - Tprod[k1]=i; - Tvard[k1][1]=atoi(strc); /* m*/ - Tvard[k1][2]=atoi(stre); /* n */ - Tvar[cptcovn+k2]=Tvard[k1][1]; - Tvar[cptcovn+k2+1]=Tvard[k1][2]; - for (k=1; k<=lastobs;k++) - covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k]; - k1++; - k2=k2+2; - } - } - else { /* no more sum */ - /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/ - /* scanf("%d",i);*/ - cutv(strd,strc,strb,'V'); - Tvar[i]=atoi(strc); - } - strcpy(modelsav,stra); - /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav); - scanf("%d",i);*/ - } /* end of loop + */ - } /* end model */ - - /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]); - printf("cptcovprod=%d ", cptcovprod); - fprintf(ficlog,"cptcovprod=%d ", cptcovprod); - scanf("%d ",i);*/ - fclose(fic); - - /* if(mle==1){*/ - if (weightopt != 1) { /* Maximisation without weights*/ - for(i=1;i<=n;i++) weight[i]=1.0; - } - /*-calculation of age at interview from date of interview and age at death -*/ - agev=matrix(1,maxwav,1,imx); - - for (i=1; i<=imx; i++) { - for(m=2; (m<= maxwav); m++) { - if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){ - anint[m][i]=9999; - s[m][i]=-1; - } - if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1; - } - } - - for (i=1; i<=imx; i++) { - agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]); - for(m=1; (m<= maxwav); m++){ - if(s[m][i] >0){ - if (s[m][i] >= nlstate+1) { - if(agedc[i]>0) - if(moisdc[i]!=99 && andc[i]!=9999) - agev[m][i]=agedc[i]; - /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/ - else { - if (andc[i]!=9999){ - printf("Warning negative age at death: %d line:%d\n",num[i],i); - fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i); - agev[m][i]=-1; - } - } - } - else if(s[m][i] !=9){ /* Should no more exist */ - agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]); - if(mint[m][i]==99 || anint[m][i]==9999) - agev[m][i]=1; - else if(agev[m][i] agemax){ - agemax=agev[m][i]; - /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/ - } - /*agev[m][i]=anint[m][i]-annais[i];*/ - /* agev[m][i] = age[i]+2*m;*/ - } - else { /* =9 */ - agev[m][i]=1; - s[m][i]=-1; - } - } - else /*= 0 Unknown */ - agev[m][i]=1; - } - - } - for (i=1; i<=imx; i++) { - for(m=1; (m<= maxwav); m++){ - if (s[m][i] > (nlstate+ndeath)) { - printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath); - fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath); - goto end; - } - } - } - -printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); - fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); - - free_vector(severity,1,maxwav); - free_imatrix(outcome,1,maxwav+1,1,n); - free_vector(moisnais,1,n); - free_vector(annais,1,n); - /* free_matrix(mint,1,maxwav,1,n); - free_matrix(anint,1,maxwav,1,n);*/ - free_vector(moisdc,1,n); - free_vector(andc,1,n); - - - wav=ivector(1,imx); - dh=imatrix(1,lastpass-firstpass+1,1,imx); - 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;codtab[h][Tvar[k]]=j; - /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/ - } - } - } - } - /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); - codtab[1][2]=1;codtab[2][2]=2; */ - /* for(i=1; i <=m ;i++){ - for(k=1; k <=cptcovn; k++){ - printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); - } - printf("\n"); - } - scanf("%d",i);*/ - - /* Calculates basic frequencies. Computes observed prevalence at single age - and prints on file fileres'p'. */ - - - - pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ - oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ - newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ - savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ - oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */ - - /* For Powell, parameters are in a vector p[] starting at p[1] - so we point p on param[1][1] so that p[1] maps on param[1][1][1] */ - p=param[1][1]; /* *(*(*(param +1)+1)+0) */ - - if(mle==1){ - mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func); - } - - /*--------- results files --------------*/ - fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model); - - - jk=1; - fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); - printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); - fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); - for(i=1,jk=1; i <=nlstate; i++){ - for(k=1; k <=(nlstate+ndeath); k++){ - if (k != i) - { - printf("%d%d ",i,k); - fprintf(ficlog,"%d%d ",i,k); - fprintf(ficres,"%1d%1d ",i,k); - for(j=1; j <=ncovmodel; j++){ - printf("%f ",p[jk]); - fprintf(ficlog,"%f ",p[jk]); - fprintf(ficres,"%f ",p[jk]); - jk++; - } - printf("\n"); - fprintf(ficlog,"\n"); - fprintf(ficres,"\n"); - } - } - } - if(mle==1){ - /* Computing hessian and covariance matrix */ - ftolhess=ftol; /* Usually correct */ - hesscov(matcov, p, npar, delti, ftolhess, func); - } - fprintf(ficres,"# Scales (for hessian or gradient estimation)\n"); - printf("# Scales (for hessian or gradient estimation)\n"); - fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n"); - for(i=1,jk=1; i <=nlstate; i++){ - for(j=1; j <=nlstate+ndeath; j++){ - if (j!=i) { - fprintf(ficres,"%1d%1d",i,j); - printf("%1d%1d",i,j); - fprintf(ficlog,"%1d%1d",i,j); - for(k=1; k<=ncovmodel;k++){ - printf(" %.5e",delti[jk]); - fprintf(ficlog," %.5e",delti[jk]); - fprintf(ficres," %.5e",delti[jk]); - jk++; - } - printf("\n"); - fprintf(ficlog,"\n"); - fprintf(ficres,"\n"); - } - } - } - - 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"); - if(mle==1) - printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); - fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); - for(i=1;i<=npar;i++){ - /* if (k>nlstate) k=1; - i1=(i-1)/(ncovmodel*nlstate)+1; - fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]); - printf("%s%d%d",alph[k],i1,tab[i]);*/ - fprintf(ficres,"%3d",i); - if(mle==1) - printf("%3d",i); - fprintf(ficlog,"%3d",i); - for(j=1; j<=i;j++){ - fprintf(ficres," %.5e",matcov[i][j]); - if(mle==1) - printf(" %.5e",matcov[i][j]); - fprintf(ficlog," %.5e",matcov[i][j]); - } - fprintf(ficres,"\n"); - if(mle==1) - printf("\n"); - fprintf(ficlog,"\n"); - k++; - } - - while((c=getc(ficpar))=='#' && c!= EOF){ - ungetc(c,ficpar); - fgets(line, MAXLINE, ficpar); - puts(line); - fputs(line,ficparo); - } - ungetc(c,ficpar); - estepm=0; - fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); - if (estepm==0 || estepm < stepm) estepm=stepm; - if (fage <= 2) { - bage = ageminpar; - fage = agemaxpar; - } - - fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n"); - fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); - fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); - - while((c=getc(ficpar))=='#' && c!= EOF){ - ungetc(c,ficpar); - fgets(line, MAXLINE, ficpar); - puts(line); - fputs(line,ficparo); - } - ungetc(c,ficpar); - - fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\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 -------------*/ - strcpy(optionfilegnuplot,optionfilefiname); - strcat(optionfilegnuplot,".gp"); - if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) { - printf("Problem with file %s",optionfilegnuplot); - } - fclose(ficgp); - printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p); -/*--------- index.htm --------*/ - - strcpy(optionfilehtm,optionfile); - strcat(optionfilehtm,".htm"); - if((fichtm=fopen(optionfilehtm,"w"))==NULL) { - printf("Problem with %s \n",optionfilehtm), exit(0); - } - - fprintf(fichtm," %s
      \n -Title=%s
      Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s
      \n -\n -Total number of observations=%d
      \n -Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf
      \n -
      -

      • Parameter files

        \n - - Copy of the parameter file: o%s
        \n - - Log file of the run: %s
        \n - - Gnuplot file name: %s
      \n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot); - fclose(fichtm); - - printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2); - -/*------------ free_vector -------------*/ - chdir(path); - - free_ivector(wav,1,imx); - free_imatrix(dh,1,lastpass-firstpass+1,1,imx); - free_imatrix(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); - - - /*--------------- 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; - fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end; - } - printf("Computing prevalence limit: result on file '%s' \n", filerespl); - fprintf(ficlog,"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=ageminpar; - 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#******"); - printf("\n#******"); - fprintf(ficlog,"\n#******"); - for(j=1;j<=cptcoveff;j++) { - fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); - printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); - fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); - } - fprintf(ficrespl,"******\n"); - printf("******\n"); - fprintf(ficlog,"******\n"); - - for (age=agebase; age<=agelim; age++){ - prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); - fprintf(ficrespl,"%.0f",age ); - for(i=1; i<=nlstate;i++) - fprintf(ficrespl," %.5f", prlim[i][i]); - fprintf(ficrespl,"\n"); - } - } - } - fclose(ficrespl); - - /*------------- h Pij x at various ages ------------*/ - - strcpy(filerespij,"pij"); strcat(filerespij,fileres); - if((ficrespij=fopen(filerespij,"w"))==NULL) { - printf("Problem with Pij resultfile: %s\n", filerespij);goto end; - fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end; - } - printf("Computing pij: result on file '%s' \n", filerespij); - fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij); - - stepsize=(int) (stepm+YEARM-1)/YEARM; - /*if (stepm<=24) stepsize=2;*/ - - agelim=AGESUP; - hstepm=stepsize*YEARM; /* Every year of age */ - hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ - - /* hstepm=1; aff par mois*/ - - 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 */ - - /* nhstepm=nhstepm*YEARM; aff par mois*/ - - p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); - oldm=oldms;savm=savms; - hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); - fprintf(ficrespij,"# Age"); - for(i=1; i<=nlstate;i++) - for(j=1; j<=nlstate+ndeath;j++) - fprintf(ficrespij," %1d-%1d",i,j); - fprintf(ficrespij,"\n"); - for (h=0; h<=nhstepm; h++){ - fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm ); - for(i=1; i<=nlstate;i++) - for(j=1; j<=nlstate+ndeath;j++) - fprintf(ficrespij," %.5f", p3mat[i][j][h]); - fprintf(ficrespij,"\n"); - } - free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); - fprintf(ficrespij,"\n"); - } - } - } - - varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax); - - fclose(ficrespij); - - - /*---------- Forecasting ------------------*/ - if((stepm == 1) && (strcmp(model,".")==0)){ - prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1); - if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1); - } - else{ - erreur=108; - printf("Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); - fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); - } - - - /*---------- Health expectancies and variances ------------*/ - - strcpy(filerest,"t"); - strcat(filerest,fileres); - if((ficrest=fopen(filerest,"w"))==NULL) { - printf("Problem with total LE resultfile: %s\n", filerest);goto end; - fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end; - } - printf("Computing Total LEs with variances: file '%s' \n", filerest); - fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); - - - strcpy(filerese,"e"); - strcat(filerese,fileres); - if((ficreseij=fopen(filerese,"w"))==NULL) { - printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0); - fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0); - } - printf("Computing Health Expectancies: result on file '%s' \n", filerese); - fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese); - - strcpy(fileresv,"v"); - strcat(fileresv,fileres); - if((ficresvij=fopen(fileresv,"w"))==NULL) { - printf("Problem with variance resultfile: %s\n", fileresv);exit(0); - fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0); - } - printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); - fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); - calagedate=-1; - prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate); - - 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 ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); - fprintf(ficreseij,"******\n"); - - fprintf(ficresvij,"\n#****** "); - for(j=1;j<=cptcoveff;j++) - fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); - fprintf(ficresvij,"******\n"); - - eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); - oldm=oldms;savm=savms; - evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov); - - vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); - oldm=oldms;savm=savms; - varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0); - if(popbased==1){ - varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased); - } - - - 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]; - /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/ - } - epj[nlstate+1] +=epj[j]; - } - - for(i=1, vepp=0.;i <=nlstate;i++) - for(j=1;j <=nlstate;j++) - vepp += vareij[i][j][(int)age]; - fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp)); - for(j=1;j <=nlstate;j++){ - fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age])); - } - fprintf(ficrest,"\n"); - } - } - } -free_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); - 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); - - fprintf(fichtm,"\n"); - fclose(fichtm); - fclose(ficgp); - - - if(erreur >0){ - printf("End of Imach with error or warning %d\n",erreur); - fprintf(ficlog,"End of Imach with error or warning %d\n",erreur); - }else{ - printf("End of Imach\n"); - fprintf(ficlog,"End of Imach\n"); - } - printf("See log file on %s\n",filelog); - fclose(ficlog); - /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */ - - /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/ - /*printf("Total time was %d uSec.\n", total_usecs);*/ - /*------ End -----------*/ - - - end: -#ifdef windows - /* chdir(pathcd);*/ -#endif - /*system("wgnuplot graph.plt");*/ - /*system("../gp37mgw/wgnuplot graph.plt");*/ - /*system("cd ../gp37mgw");*/ - /* system("..\\gp37mgw\\wgnuplot graph.plt");*/ - strcpy(plotcmd,GNUPLOTPROGRAM); - strcat(plotcmd," "); - strcat(plotcmd,optionfilegnuplot); - system(plotcmd); - -#ifdef windows - while (z[0] != 'q') { - /* chdir(path); */ - printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: "); - scanf("%s",z); - if (z[0] == 'c') system("./imach"); - else if (z[0] == 'e') system(optionfilehtm); - else if (z[0] == 'g') system(plotcmd); - else if (z[0] == 'q') exit(0); - } -#endif -} - - +/* $Id: imach.c,v 1.53 2002/07/23 23:59:37 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 + probability to be observed in state j at the second wave + conditional to be observed in state i at the first wave. Therefore + the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where + 'age' is age and 'sex' is a covariate. If you want to have a more + complex model than "constant and age", you should modify the program + where the markup *Covariates have to be included here again* invites + you to do it. More covariates you add, slower the + convergence. + + The advantage of this computer programme, compared to a simple + multinomial logistic model, is clear when the delay between waves is not + identical for each individual. Also, if a individual missed an + intermediate interview, the information is lost, but taken into + account using an interpolation or extrapolation. + + hPijx is the probability to be observed in state i at age x+h + conditional to the observed state i at age x. The delay 'h' can be + split into an exact number (nh*stepm) of unobserved intermediate + states. This elementary transition (by month or quarter trimester, + semester or year) is model as a multinomial logistic. The hPx + matrix is simply the matrix product of nh*stepm elementary matrices + and the contribution of each individual to the likelihood is simply + hPijx. + + Also this programme outputs the covariance matrix of the parameters but also + of the life expectancies. It also computes the 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 +#include +#include +#include + +#define MAXLINE 256 +#define GNUPLOTPROGRAM "gnuplot" +/*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/ +#define FILENAMELENGTH 80 +/*#define DEBUG*/ +#define unix +#define GLOCK_ERROR_NOPATH -1 /* empty path */ +#define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */ + +#define MAXPARM 30 /* Maximum number of parameters for the optimization */ +#define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */ + +#define NINTERVMAX 8 +#define NLSTATEMAX 8 /* Maximum number of live states (for func) */ +#define NDEATHMAX 8 /* Maximum number of dead states (for func) */ +#define NCOVMAX 8 /* Maximum number of covariates */ +#define MAXN 20000 +#define YEARM 12. /* Number of months per year */ +#define AGESUP 130 +#define AGEBASE 40 +#ifdef windows +#define DIRSEPARATOR '\\' +#define ODIRSEPARATOR '/' +#else +#define DIRSEPARATOR '/' +#define ODIRSEPARATOR '\\' +#endif + +char version[80]="Imach version 0.8j, July 2002, INED-EUROREVES "; +int erreur; /* Error number */ +int nvar; +int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov; +int npar=NPARMAX; +int nlstate=2; /* Number of live states */ +int ndeath=1; /* Number of dead states */ +int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */ +int popbased=0; + +int *wav; /* Number of waves for this individuual 0 is possible */ +int maxwav; /* Maxim number of waves */ +int jmin, jmax; /* min, max spacing between 2 waves */ +int mle, weightopt; +int **mw; /* mw[mi][i] is number of the mi wave for this individual */ +int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */ +double jmean; /* Mean space between 2 waves */ +double **oldm, **newm, **savm; /* Working pointers to matrices */ +double **oldms, **newms, **savms; /* Fixed working pointers to matrices */ +FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop; +FILE *ficlog; +FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor; +FILE *ficresprobmorprev; +FILE *fichtm; /* Html File */ +FILE *ficreseij; +char filerese[FILENAMELENGTH]; +FILE *ficresvij; +char fileresv[FILENAMELENGTH]; +FILE *ficresvpl; +char fileresvpl[FILENAMELENGTH]; +char title[MAXLINE]; +char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH]; +char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH]; + +char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH]; +char filelog[FILENAMELENGTH]; /* Log file */ +char filerest[FILENAMELENGTH]; +char fileregp[FILENAMELENGTH]; +char popfile[FILENAMELENGTH]; + +char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH]; + +#define NR_END 1 +#define FREE_ARG char* +#define FTOL 1.0e-10 + +#define NRANSI +#define ITMAX 200 + +#define TOL 2.0e-4 + +#define CGOLD 0.3819660 +#define ZEPS 1.0e-10 +#define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); + +#define GOLD 1.618034 +#define GLIMIT 100.0 +#define TINY 1.0e-20 + +static double maxarg1,maxarg2; +#define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2)) +#define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2)) + +#define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a)) +#define rint(a) floor(a+0.5) + +static double sqrarg; +#define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg) +#define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} + +int imx; +int stepm; +/* Stepm, step in month: minimum step interpolation*/ + +int estepm; +/* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/ + +int m,nb; +int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage; +double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint; +double **pmmij, ***probs, ***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 ); + s= strrchr( path, DIRSEPARATOR ); /* find last / */ + if ( s == NULL ) { /* no directory, so use current */ + /*if(strrchr(path, ODIRSEPARATOR )==NULL) + printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/ +#if defined(__bsd__) /* get current working directory */ + extern char *getwd( ); + + if ( getwd( dirc ) == NULL ) { +#else + extern char *getcwd( ); + + if ( getcwd( dirc, FILENAME_MAX ) == NULL ) { +#endif + return( GLOCK_ERROR_GETCWD ); + } + strcpy( name, path ); /* we've got it */ + } else { /* strip direcotry from path */ + 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) +{ + /* cuts string t into u and v where u is ended by char occ excluding it + and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2) + gives u="abcedf" and v="ghi2j" */ + int i,lg,j,p=0; + i=0; + for(j=0; j<=strlen(t)-1; j++) { + if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; + } + + lg=strlen(t); + for(j=0; j=(p+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); + fprintf(ficlog,".");fflush(ficlog); +#ifdef DEBUG + printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol); + fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol); + /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */ +#endif + if (fabs(x-xm) <= (tol2-0.5*(b-a))){ + *xmin=x; + return fx; + } + ftemp=fu; + if (fabs(e) > tol1) { + r=(x-w)*(fx-fv); + q=(x-v)*(fx-fw); + p=(x-v)*q-(x-w)*r; + q=2.0*(q-r); + if (q > 0.0) p = -p; + q=fabs(q); + etemp=e; + e=d; + if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) + d=CGOLD*(e=(x >= xm ? a-x : b-x)); + else { + d=p/q; + u=x+d; + if (u-a < tol2 || b-u < tol2) + d=SIGN(tol1,xm-x); + } + } else { + d=CGOLD*(e=(x >= xm ? a-x : b-x)); + } + u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); + fu=(*f)(u); + if (fu <= fx) { + if (u >= x) a=x; else b=x; + SHFT(v,w,x,u) + SHFT(fv,fw,fx,fu) + } else { + if (u < x) a=u; else b=u; + if (fu <= fw || w == x) { + v=w; + w=u; + fv=fw; + fw=fu; + } else if (fu <= fv || v == x || v == w) { + v=u; + fv=fu; + } + } + } + nrerror("Too many iterations in brent"); + *xmin=x; + return fx; +} + +/****************** mnbrak ***********************/ + +void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, + double (*func)(double)) +{ + double ulim,u,r,q, dum; + double fu; + + *fa=(*func)(*ax); + *fb=(*func)(*bx); + if (*fb > *fa) { + SHFT(dum,*ax,*bx,dum) + SHFT(dum,*fb,*fa,dum) + } + *cx=(*bx)+GOLD*(*bx-*ax); + *fc=(*func)(*cx); + while (*fb > *fc) { + r=(*bx-*ax)*(*fb-*fc); + q=(*bx-*cx)*(*fb-*fa); + u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ + (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); + ulim=(*bx)+GLIMIT*(*cx-*bx); + if ((*bx-u)*(u-*cx) > 0.0) { + fu=(*func)(u); + } else if ((*cx-u)*(u-ulim) > 0.0) { + fu=(*func)(u); + if (fu < *fc) { + SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) + SHFT(*fb,*fc,fu,(*func)(u)) + } + } else if ((u-ulim)*(ulim-*cx) >= 0.0) { + u=ulim; + fu=(*func)(u); + } else { + u=(*cx)+GOLD*(*cx-*bx); + fu=(*func)(u); + } + SHFT(*ax,*bx,*cx,u) + SHFT(*fa,*fb,*fc,fu) + } +} + +/*************** linmin ************************/ + +int ncom; +double *pcom,*xicom; +double (*nrfunc)(double []); + +void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) +{ + double brent(double ax, double bx, double cx, + double (*f)(double), double tol, double *xmin); + double f1dim(double x); + void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, + double *fc, double (*func)(double)); + int j; + double xx,xmin,bx,ax; + double fx,fb,fa; + + ncom=n; + pcom=vector(1,n); + xicom=vector(1,n); + nrfunc=func; + for (j=1;j<=n;j++) { + pcom[j]=p[j]; + xicom[j]=xi[j]; + } + ax=0.0; + xx=1.0; + mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); + *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); +#ifdef DEBUG + printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin); + fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin); +#endif + for (j=1;j<=n;j++) { + xi[j] *= xmin; + p[j] += xi[j]; + } + free_vector(xicom,1,n); + free_vector(pcom,1,n); +} + +/*************** powell ************************/ +void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, + double (*func)(double [])) +{ + void linmin(double p[], double xi[], int n, double *fret, + double (*func)(double [])); + int i,ibig,j; + double del,t,*pt,*ptt,*xit; + double fp,fptt; + double *xits; + pt=vector(1,n); + ptt=vector(1,n); + xit=vector(1,n); + xits=vector(1,n); + *fret=(*func)(p); + for (j=1;j<=n;j++) pt[j]=p[j]; + for (*iter=1;;++(*iter)) { + fp=(*fret); + ibig=0; + del=0.0; + printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret); + fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret); + for (i=1;i<=n;i++) + printf(" %d %.12f",i, p[i]); + fprintf(ficlog," %d %.12f",i, p[i]); + printf("\n"); + fprintf(ficlog,"\n"); + for (i=1;i<=n;i++) { + for (j=1;j<=n;j++) xit[j]=xi[j][i]; + fptt=(*fret); +#ifdef DEBUG + printf("fret=%lf \n",*fret); + fprintf(ficlog,"fret=%lf \n",*fret); +#endif + printf("%d",i);fflush(stdout); + fprintf(ficlog,"%d",i);fflush(ficlog); + linmin(p,xit,n,fret,func); + if (fabs(fptt-(*fret)) > del) { + del=fabs(fptt-(*fret)); + ibig=i; + } +#ifdef DEBUG + printf("%d %.12e",i,(*fret)); + fprintf(ficlog,"%d %.12e",i,(*fret)); + for (j=1;j<=n;j++) { + xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5); + printf(" x(%d)=%.12e",j,xit[j]); + fprintf(ficlog," x(%d)=%.12e",j,xit[j]); + } + for(j=1;j<=n;j++) { + printf(" p=%.12e",p[j]); + fprintf(ficlog," p=%.12e",p[j]); + } + printf("\n"); + fprintf(ficlog,"\n"); +#endif + } + if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { +#ifdef DEBUG + int k[2],l; + k[0]=1; + k[1]=-1; + printf("Max: %.12e",(*func)(p)); + fprintf(ficlog,"Max: %.12e",(*func)(p)); + for (j=1;j<=n;j++) { + printf(" %.12e",p[j]); + fprintf(ficlog," %.12e",p[j]); + } + printf("\n"); + fprintf(ficlog,"\n"); + for(l=0;l<=1;l++) { + for (j=1;j<=n;j++) { + ptt[j]=p[j]+(p[j]-pt[j])*k[l]; + printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]); + fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]); + } + printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p))); + fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p))); + } +#endif + + + free_vector(xit,1,n); + free_vector(xits,1,n); + free_vector(ptt,1,n); + free_vector(pt,1,n); + return; + } + if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); + for (j=1;j<=n;j++) { + ptt[j]=2.0*p[j]-pt[j]; + xit[j]=p[j]-pt[j]; + pt[j]=p[j]; + } + fptt=(*func)(ptt); + if (fptt < fp) { + t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); + if (t < 0.0) { + linmin(p,xit,n,fret,func); + for (j=1;j<=n;j++) { + xi[j][ibig]=xi[j][n]; + xi[j][n]=xit[j]; + } +#ifdef DEBUG + printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig); + fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig); + for(j=1;j<=n;j++){ + printf(" %.12e",xit[j]); + fprintf(ficlog," %.12e",xit[j]); + } + printf("\n"); + fprintf(ficlog,"\n"); +#endif + } + } + } +} + +/**** Prevalence limit ****************/ + +double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij) +{ + /* Computes the prevalence limit in each live state at age x by left multiplying the unit + matrix by transitions matrix until convergence is reached */ + + int i, ii,j,k; + double min, max, maxmin, maxmax,sumnew=0.; + double **matprod2(); + double **out, cov[NCOVMAX], **pmij(); + double **newm; + double agefin, delaymax=50 ; /* Max number of years to converge */ + + for (ii=1;ii<=nlstate+ndeath;ii++) + for (j=1;j<=nlstate+ndeath;j++){ + oldm[ii][j]=(ii==j ? 1.0 : 0.0); + } + + cov[1]=1.; + + /* Even if hstepm = 1, at least one multiplication by the unit matrix */ + for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){ + newm=savm; + /* Covariates have to be included here again */ + cov[2]=agefin; + + for (k=1; k<=cptcovn;k++) { + cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; + /* printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/ + } + for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; + for (k=1; k<=cptcovprod;k++) + cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; + + /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/ + /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/ + /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/ + out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); + + savm=oldm; + oldm=newm; + maxmax=0.; + for(j=1;j<=nlstate;j++){ + min=1.; + max=0.; + for(i=1; i<=nlstate; i++) { + sumnew=0; + for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k]; + prlim[i][j]= newm[i][j]/(1-sumnew); + max=FMAX(max,prlim[i][j]); + min=FMIN(min,prlim[i][j]); + } + maxmin=max-min; + maxmax=FMAX(maxmax,maxmin); + } + if(maxmax < ftolpl){ + return prlim; + } + } +} + +/*************** transition probabilities ***************/ + +double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate ) +{ + double s1, s2; + /*double t34;*/ + int i,j,j1, nc, ii, jj; + + for(i=1; i<= nlstate; i++){ + for(j=1; ji 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; ji) { + printf(".%d%d",i,j);fflush(stdout); + fprintf(ficlog,".%d%d",i,j);fflush(ficlog); + hess[i][j]=hessij(p,delti,i,j); + hess[j][i]=hess[i][j]; + /*printf(" %lf ",hess[i][j]);*/ + } + } + } + printf("\n"); + fprintf(ficlog,"\n"); + + printf("\nInverting the hessian to get the covariance matrix. Wait...\n"); + fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n"); + + a=matrix(1,npar,1,npar); + y=matrix(1,npar,1,npar); + x=vector(1,npar); + indx=ivector(1,npar); + for (i=1;i<=npar;i++) + for (j=1;j<=npar;j++) a[i][j]=hess[i][j]; + ludcmp(a,npar,indx,&pd); + + for (j=1;j<=npar;j++) { + for (i=1;i<=npar;i++) x[i]=0; + x[j]=1; + lubksb(a,npar,indx,x); + for (i=1;i<=npar;i++){ + matcov[i][j]=x[i]; + } + } + + printf("\n#Hessian matrix#\n"); + fprintf(ficlog,"\n#Hessian matrix#\n"); + for (i=1;i<=npar;i++) { + for (j=1;j<=npar;j++) { + printf("%.3e ",hess[i][j]); + fprintf(ficlog,"%.3e ",hess[i][j]); + } + printf("\n"); + fprintf(ficlog,"\n"); + } + + /* Recompute Inverse */ + for (i=1;i<=npar;i++) + for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; + ludcmp(a,npar,indx,&pd); + + /* printf("\n#Hessian matrix recomputed#\n"); + + for (j=1;j<=npar;j++) { + for (i=1;i<=npar;i++) x[i]=0; + x[j]=1; + lubksb(a,npar,indx,x); + for (i=1;i<=npar;i++){ + y[i][j]=x[i]; + printf("%.3e ",y[i][j]); + fprintf(ficlog,"%.3e ",y[i][j]); + } + printf("\n"); + fprintf(ficlog,"\n"); + } + */ + + free_matrix(a,1,npar,1,npar); + free_matrix(y,1,npar,1,npar); + free_vector(x,1,npar); + free_ivector(indx,1,npar); + free_matrix(hess,1,npar,1,npar); + + +} + +/*************** hessian matrix ****************/ +double hessii( double x[], double delta, int theta, double delti[]) +{ + int i; + int l=1, lmax=20; + double k1,k2; + double p2[NPARMAX+1]; + double res; + double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4; + double fx; + int k=0,kmax=10; + double l1; + + fx=func(x); + for (i=1;i<=npar;i++) p2[i]=x[i]; + for(l=0 ; l <=lmax; l++){ + l1=pow(10,l); + delts=delt; + for(k=1 ; k khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */ + k=kmax; l=lmax*10.; + } + else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ + delts=delt; + } + } + } + delti[theta]=delts; + return res; + +} + +double hessij( double x[], double delti[], int thetai,int thetaj) +{ + int i; + int l=1, l1, lmax=20; + double k1,k2,k3,k4,res,fx; + double p2[NPARMAX+1]; + int k; + + fx=func(x); + for (k=1; k<=2; k++) { + for (i=1;i<=npar;i++) p2[i]=x[i]; + p2[thetai]=x[thetai]+delti[thetai]/k; + p2[thetaj]=x[thetaj]+delti[thetaj]/k; + k1=func(p2)-fx; + + p2[thetai]=x[thetai]+delti[thetai]/k; + p2[thetaj]=x[thetaj]-delti[thetaj]/k; + k2=func(p2)-fx; + + p2[thetai]=x[thetai]-delti[thetai]/k; + p2[thetaj]=x[thetaj]+delti[thetaj]/k; + k3=func(p2)-fx; + + p2[thetai]=x[thetai]-delti[thetai]/k; + p2[thetaj]=x[thetaj]-delti[thetaj]/k; + k4=func(p2)-fx; + res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */ +#ifdef DEBUG + printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); + fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); +#endif + } + return res; +} + +/************** Inverse of matrix **************/ +void ludcmp(double **a, int n, int *indx, double *d) +{ + int i,imax,j,k; + double big,dum,sum,temp; + double *vv; + + vv=vector(1,n); + *d=1.0; + for (i=1;i<=n;i++) { + big=0.0; + for (j=1;j<=n;j++) + if ((temp=fabs(a[i][j])) > big) big=temp; + if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); + vv[i]=1.0/big; + } + for (j=1;j<=n;j++) { + for (i=1;i= 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; + int first; + double ***freq; /* Frequencies */ + double *pp; + double pos, k2, dateintsum=0,k2cpt=0; + FILE *ficresp; + char fileresp[FILENAMELENGTH]; + + pp=vector(1,nlstate); + probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX); + strcpy(fileresp,"p"); + strcat(fileresp,fileres); + if((ficresp=fopen(fileresp,"w"))==NULL) { + printf("Problem with prevalence resultfile: %s\n", fileresp); + fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp); + exit(0); + } + freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3); + j1=0; + + j=cptcoveff; + if (cptcovn<1) {j=1;ncodemax[1]=1;} + + first=1; + + for(k1=1; k1<=j;k1++){ + for(i1=1; i1<=ncodemax[k1];i1++){ + j1++; + /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]); + scanf("%d", i);*/ + for (i=-1; i<=nlstate+ndeath; i++) + for (jk=-1; jk<=nlstate+ndeath; jk++) + for(m=agemin; m <= agemax+3; m++) + freq[i][jk][m]=0; + + dateintsum=0; + k2cpt=0; + for (i=1; i<=imx; i++) { + bool=1; + if (cptcovn>0) { + for (z1=1; z1<=cptcoveff; z1++) + if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) + bool=0; + } + if (bool==1) { + for(m=firstpass; m<=lastpass; m++){ + k2=anint[m][i]+(mint[m][i]/12.); + if ((k2>=dateprev1) && (k2<=dateprev2)) { + if(agev[m][i]==0) agev[m][i]=agemax+1; + if(agev[m][i]==1) agev[m][i]=agemax+2; + if (m1) && (agev[m][i]< (agemax+3))) { + dateintsum=dateintsum+k2; + k2cpt++; + } + } + } + } + } + + fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); + + if (cptcovn>0) { + fprintf(ficresp, "\n#********** Variable "); + for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); + fprintf(ficresp, "**********\n#"); + } + for(i=1; i<=nlstate;i++) + fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i); + fprintf(ficresp, "\n"); + + for(i=(int)agemin; i <= (int)agemax+3; i++){ + if(i==(int)agemax+3){ + fprintf(ficlog,"Total"); + }else{ + if(first==1){ + first=0; + printf("See log file for details...\n"); + } + fprintf(ficlog,"Age %d", i); + } + for(jk=1; jk <=nlstate ; jk++){ + for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++) + pp[jk] += freq[jk][m][i]; + } + for(jk=1; jk <=nlstate ; jk++){ + for(m=-1, pos=0; m <=0 ; m++) + pos += freq[jk][m][i]; + if(pp[jk]>=1.e-10){ + if(first==1){ + printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); + } + fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); + }else{ + if(first==1) + printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk); + fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk); + } + } + + for(jk=1; jk <=nlstate ; jk++){ + for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++) + pp[jk] += freq[jk][m][i]; + } + + for(jk=1,pos=0; jk <=nlstate ; jk++) + pos += pp[jk]; + for(jk=1; jk <=nlstate ; jk++){ + if(pos>=1.e-5){ + if(first==1) + printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); + fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); + }else{ + if(first==1) + printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); + fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); + } + if( i <= (int) agemax){ + if(pos>=1.e-5){ + fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos); + probs[i][jk][j1]= pp[jk]/pos; + /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/ + } + else + fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos); + } + } + + for(jk=-1; jk <=nlstate+ndeath; jk++) + for(m=-1; m <=nlstate+ndeath; m++) + if(freq[jk][m][i] !=0 ) { + if(first==1) + printf(" %d%d=%.0f",jk,m,freq[jk][m][i]); + fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]); + } + if(i <= (int) agemax) + fprintf(ficresp,"\n"); + if(first==1) + printf("Others in log...\n"); + fprintf(ficlog,"\n"); + } + } + } + dateintmean=dateintsum/k2cpt; + + fclose(ficresp); + free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3); + free_vector(pp,1,nlstate); + + /* End of Freq */ +} + +/************ Prevalence ********************/ +void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate) +{ /* Some frequencies */ + + int i, m, jk, k1, i1, j1, bool, z1,z2,j; + double ***freq; /* Frequencies */ + double *pp; + double pos, k2; + + pp=vector(1,nlstate); + + freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3); + j1=0; + + j=cptcoveff; + if (cptcovn<1) {j=1;ncodemax[1]=1;} + + for(k1=1; k1<=j;k1++){ + for(i1=1; i1<=ncodemax[k1];i1++){ + j1++; + + for (i=-1; i<=nlstate+ndeath; i++) + for (jk=-1; jk<=nlstate+ndeath; jk++) + for(m=agemin; m <= agemax+3; m++) + freq[i][jk][m]=0; + + for (i=1; i<=imx; i++) { + bool=1; + if (cptcovn>0) { + for (z1=1; z1<=cptcoveff; z1++) + if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) + bool=0; + } + if (bool==1) { + for(m=firstpass; m<=lastpass; m++){ + k2=anint[m][i]+(mint[m][i]/12.); + if ((k2>=dateprev1) && (k2<=dateprev2)) { + if(agev[m][i]==0) agev[m][i]=agemax+1; + if(agev[m][i]==1) agev[m][i]=agemax+2; + if (m0) + freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i]; + else + freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; + freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i]; + } + } + } + } + } + for(i=(int)agemin; i <= (int)agemax+3; i++){ + for(jk=1; jk <=nlstate ; jk++){ + for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++) + pp[jk] += freq[jk][m][i]; + } + for(jk=1; jk <=nlstate ; jk++){ + for(m=-1, pos=0; m <=0 ; m++) + pos += freq[jk][m][i]; + } + + for(jk=1; jk <=nlstate ; jk++){ + for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++) + pp[jk] += freq[jk][m][i]; + } + + for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk]; + + for(jk=1; jk <=nlstate ; jk++){ + if( i <= (int) agemax){ + if(pos>=1.e-5){ + probs[i][jk][j1]= pp[jk]/pos; + } + } + }/* end jk */ + }/* end i */ + } /* end i1 */ + } /* end k1 */ + + + free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3); + free_vector(pp,1,nlstate); + +} /* End of Freq */ + +/************* Waves Concatenation ***************/ + +void concatwav(int wav[], int **dh, int **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 first; + int j, k=0,jk, ju, jl; + double sum=0.; + first=0; + jmin=1e+5; + jmax=-1; + jmean=0.; + for(i=1; i<=imx; i++){ + mi=0; + m=firstpass; + while(s[m][i] <= nlstate){ + if(s[m][i]>=1) + mw[++mi][i]=m; + if(m >=lastpass) + break; + else + m++; + }/* end while */ + if (s[m][i] > nlstate){ + mi++; /* Death is another wave */ + /* if(mi==0) never been interviewed correctly before death */ + /* Only death is a correct wave */ + mw[mi][i]=m; + } + + wav[i]=mi; + if(mi==0){ + if(first==0){ + printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i); + first=1; + } + if(first==1){ + fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i); + } + } /* end mi==0 */ + } + + for(i=1; i<=imx; i++){ + for(mi=1; mi 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); + fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean); + } + +/*********** Tricode ****************************/ +void tricode(int *Tvar, int **nbcode, int imx) +{ + int Ndum[20],ij=1, k, j, i; + 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, int estepm,double delti[],double **matcov ) + +{ + /* Health expectancies */ + int i, j, nhstepm, hstepm, h, nstepm, k, cptj; + double age, agelim, hf; + double ***p3mat,***varhe; + double **dnewm,**doldm; + double *xp; + double **gp, **gm; + double ***gradg, ***trgradg; + int theta; + + varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage); + xp=vector(1,npar); + dnewm=matrix(1,nlstate*2,1,npar); + doldm=matrix(1,nlstate*2,1,nlstate*2); + + fprintf(ficreseij,"# Health expectancies\n"); + fprintf(ficreseij,"# Age"); + for(i=1; i<=nlstate;i++) + for(j=1; j<=nlstate;j++) + fprintf(ficreseij," %1d-%1d (SE)",i,j); + fprintf(ficreseij,"\n"); + + if(estepm < stepm){ + printf ("Problem %d lower than %d\n",estepm, stepm); + } + else hstepm=estepm; + /* We compute the life expectancy from trapezoids spaced every estepm months + * This is mainly to measure the difference between two models: for example + * if stepm=24 months pijx are given only every 2 years and by summing them + * we are calculating an estimate of the Life Expectancy assuming a linear + * progression inbetween and thus overestimating or underestimating according + * to the curvature of the survival function. If, for the same date, we + * estimate the model with stepm=1 month, we can keep estepm to 24 months + * to compare the new estimate of Life expectancy with the same linear + * hypothesis. A more precise result, taking into account a more precise + * curvature will be obtained if estepm is as small as stepm. */ + + /* For example we decided to compute the life expectancy with the smallest unit */ + /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. + nhstepm is the number of hstepm from age to agelim + nstepm is the number of stepm from age to agelin. + Look at hpijx to understand the reason of that which relies in memory size + and note for a fixed period like estepm months */ + /* We decided (b) to get a life expectancy respecting the most precise curvature of the + survival function given by stepm (the optimization length). Unfortunately it + means that if the survival funtion is printed only each two years of age and if + you sum them up and add 1 year (area under the trapezoids) you won't get the same + results. So we changed our mind and took the option of the best precision. + */ + hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ + + agelim=AGESUP; + for (age=bage; age<=fage; age ++){ /* If stepm=6 months */ + /* nhstepm age range expressed in number of stepm */ + nstepm=(int) rint((agelim-age)*YEARM/stepm); + /* Typically if 20 years nstepm = 20*12/6=40 stepm */ + /* if (stepm >= YEARM) hstepm=1;*/ + nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ + p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2); + gp=matrix(0,nhstepm,1,nlstate*2); + gm=matrix(0,nhstepm,1,nlstate*2); + + /* Computed by stepm unit matrices, product of hstepm matrices, stored + in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */ + hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij); + + + hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ + + /* Computing Variances of health expectancies */ + + for(theta=1; theta <=npar; theta++){ + for(i=1; i<=npar; i++){ + xp[i] = x[i] + (i==theta ?delti[theta]:0); + } + hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); + + cptj=0; + for(j=1; j<= nlstate; j++){ + for(i=1; i<=nlstate; i++){ + cptj=cptj+1; + for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){ + gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.; + } + } + } + + + for(i=1; i<=npar; i++) + xp[i] = x[i] - (i==theta ?delti[theta]:0); + hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); + + cptj=0; + for(j=1; j<= nlstate; j++){ + for(i=1;i<=nlstate;i++){ + cptj=cptj+1; + for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){ + gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.; + } + } + } + for(j=1; j<= nlstate*2; j++) + for(h=0; h<=nhstepm-1; h++){ + gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta]; + } + } + +/* End theta */ + + trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar); + + for(h=0; h<=nhstepm-1; h++) + for(j=1; j<=nlstate*2;j++) + for(theta=1; theta <=npar; theta++) + trgradg[h][j][theta]=gradg[h][theta][j]; + + + for(i=1;i<=nlstate*2;i++) + for(j=1;j<=nlstate*2;j++) + varhe[i][j][(int)age] =0.; + + printf("%d|",(int)age);fflush(stdout); + fprintf(ficlog,"%d|",(int)age);fflush(ficlog); + for(h=0;h<=nhstepm-1;h++){ + for(k=0;k<=nhstepm-1;k++){ + matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov); + matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]); + for(i=1;i<=nlstate*2;i++) + for(j=1;j<=nlstate*2;j++) + varhe[i][j][(int)age] += doldm[i][j]*hf*hf; + } + } + /* Computing expectancies */ + for(i=1; i<=nlstate;i++) + for(j=1; j<=nlstate;j++) + for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){ + eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf; + +/* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/ + + } + + fprintf(ficreseij,"%3.0f",age ); + cptj=0; + for(i=1; i<=nlstate;i++) + for(j=1; j<=nlstate;j++){ + cptj++; + fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) ); + } + fprintf(ficreseij,"\n"); + + free_matrix(gm,0,nhstepm,1,nlstate*2); + free_matrix(gp,0,nhstepm,1,nlstate*2); + free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2); + free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar); + free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + } + printf("\n"); + fprintf(ficlog,"\n"); + + free_vector(xp,1,npar); + free_matrix(dnewm,1,nlstate*2,1,npar); + free_matrix(doldm,1,nlstate*2,1,nlstate*2); + free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage); +} + +/************ Variance ******************/ +void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav) +{ + /* Variance of health expectancies */ + /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/ + /* double **newm;*/ + double **dnewm,**doldm; + double **dnewmp,**doldmp; + int i, j, nhstepm, hstepm, h, nstepm ; + int k, cptcode; + double *xp; + double **gp, **gm; /* for var eij */ + double ***gradg, ***trgradg; /*for var eij */ + double **gradgp, **trgradgp; /* for var p point j */ + double *gpp, *gmp; /* for var p point j */ + double **varppt; /* for var p point j nlstate to nlstate+ndeath */ + double ***p3mat; + double age,agelim, hf; + double ***mobaverage; + int theta; + char digit[4]; + char digitp[16]; + + char fileresprobmorprev[FILENAMELENGTH]; + + if(popbased==1) + strcpy(digitp,"-populbased-"); + else + strcpy(digitp,"-stablbased-"); + if(mobilav==1) + strcat(digitp,"mobilav-"); + else + strcat(digitp,"nomobil-"); + if (mobilav==1) { + mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); + movingaverage(probs, bage, fage, mobaverage); + } + + strcpy(fileresprobmorprev,"prmorprev"); + sprintf(digit,"%-d",ij); + /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/ + strcat(fileresprobmorprev,digit); /* Tvar to be done */ + strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */ + strcat(fileresprobmorprev,fileres); + if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) { + printf("Problem with resultfile: %s\n", fileresprobmorprev); + fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev); + } + printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); + fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); + fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n"); + fprintf(ficresprobmorprev,"# Age cov=%-d",ij); + for(j=nlstate+1; j<=(nlstate+ndeath);j++){ + fprintf(ficresprobmorprev," p.%-d SE",j); + for(i=1; i<=nlstate;i++) + fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j); + } + fprintf(ficresprobmorprev,"\n"); + if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { + printf("Problem with gnuplot file: %s\n", optionfilegnuplot); + fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot); + exit(0); + } + else{ + fprintf(ficgp,"\n# Routine varevsij"); + } + if((fichtm=fopen(optionfilehtm,"a"))==NULL) { + printf("Problem with html file: %s\n", optionfilehtm); + fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm); + exit(0); + } + else{ + fprintf(fichtm,"\n

    • Computing probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)

      • \n"); + fprintf(fichtm,"\n
      %s (à revoir)
      \n",digitp); + } + varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); + + fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are the stable prevalence in health states i\n"); + fprintf(ficresvij,"# Age"); + for(i=1; i<=nlstate;i++) + for(j=1; j<=nlstate;j++) + fprintf(ficresvij," Cov(e%1d, e%1d)",i,j); + fprintf(ficresvij,"\n"); + + xp=vector(1,npar); + dnewm=matrix(1,nlstate,1,npar); + doldm=matrix(1,nlstate,1,nlstate); + dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar); + doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); + + gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath); + gpp=vector(nlstate+1,nlstate+ndeath); + gmp=vector(nlstate+1,nlstate+ndeath); + trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/ + + if(estepm < stepm){ + printf ("Problem %d lower than %d\n",estepm, stepm); + } + else hstepm=estepm; + /* For example we decided to compute the life expectancy with the smallest unit */ + /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. + nhstepm is the number of hstepm from age to agelim + nstepm is the number of stepm from age to agelin. + Look at hpijx to understand the reason of that which relies in memory size + and note for a fixed period like k years */ + /* We decided (b) to get a life expectancy respecting the most precise curvature of the + survival function given by stepm (the optimization length). Unfortunately it + means that if the survival funtion is printed only each two years of age and if + you sum them up and add 1 year (area under the trapezoids) you won't get the same + results. So we changed our mind and took the option of the best precision. + */ + hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ + agelim = AGESUP; + for (age=bage; age<=fage; age ++){ /* If stepm=6 months */ + nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ + nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ + p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + gradg=ma3x(0,nhstepm,1,npar,1,nlstate); + gp=matrix(0,nhstepm,1,nlstate); + gm=matrix(0,nhstepm,1,nlstate); + + + for(theta=1; theta <=npar; theta++){ + for(i=1; i<=npar; i++){ /* Computes gradient */ + xp[i] = x[i] + (i==theta ?delti[theta]:0); + } + hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); + prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); + + if (popbased==1) { + if(mobilav !=1){ + for(i=1; i<=nlstate;i++) + prlim[i][i]=probs[(int)age][i][ij]; + }else{ /* mobilav=1 */ + for(i=1; i<=nlstate;i++) + prlim[i][i]=mobaverage[(int)age][i][ij]; + } + } + + for(j=1; j<= nlstate; j++){ + for(h=0; h<=nhstepm; h++){ + for(i=1, gp[h][j]=0.;i<=nlstate;i++) + gp[h][j] += prlim[i][i]*p3mat[i][j][h]; + } + } + /* This for computing forces of mortality (h=1)as a weighted average */ + for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){ + for(i=1; i<= nlstate; i++) + gpp[j] += prlim[i][i]*p3mat[i][j][1]; + } + /* end force of mortality */ + + for(i=1; i<=npar; i++) /* Computes gradient */ + xp[i] = x[i] - (i==theta ?delti[theta]:0); + hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); + prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); + + if (popbased==1) { + if(mobilav !=1){ + for(i=1; i<=nlstate;i++) + prlim[i][i]=probs[(int)age][i][ij]; + }else{ /* mobilav=1 */ + for(i=1; i<=nlstate;i++) + prlim[i][i]=mobaverage[(int)age][i][ij]; + } + } + + for(j=1; j<= nlstate; j++){ + for(h=0; h<=nhstepm; h++){ + for(i=1, gm[h][j]=0.;i<=nlstate;i++) + gm[h][j] += prlim[i][i]*p3mat[i][j][h]; + } + } + /* This for computing force of mortality (h=1)as a weighted average */ + for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){ + for(i=1; i<= nlstate; i++) + gmp[j] += prlim[i][i]*p3mat[i][j][1]; + } + /* end force of mortality */ + + for(j=1; j<= nlstate; j++) /* vareij */ + for(h=0; h<=nhstepm; h++){ + gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta]; + } + for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */ + gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta]; + } + + } /* End theta */ + + trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */ + + for(h=0; h<=nhstepm; h++) /* veij */ + for(j=1; j<=nlstate;j++) + for(theta=1; theta <=npar; theta++) + trgradg[h][j][theta]=gradg[h][theta][j]; + + for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */ + for(theta=1; theta <=npar; theta++) + trgradgp[j][theta]=gradgp[theta][j]; + + hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ + for(i=1;i<=nlstate;i++) + for(j=1;j<=nlstate;j++) + vareij[i][j][(int)age] =0.; + + for(h=0;h<=nhstepm;h++){ + for(k=0;k<=nhstepm;k++){ + matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov); + matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]); + for(i=1;i<=nlstate;i++) + for(j=1;j<=nlstate;j++) + vareij[i][j][(int)age] += doldm[i][j]*hf*hf; + } + } + + /* pptj */ + matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov); + matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp); + for(j=nlstate+1;j<=nlstate+ndeath;j++) + for(i=nlstate+1;i<=nlstate+ndeath;i++) + varppt[j][i]=doldmp[j][i]; + /* end ppptj */ + hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij); + prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij); + + if (popbased==1) { + if(mobilav !=1){ + for(i=1; i<=nlstate;i++) + prlim[i][i]=probs[(int)age][i][ij]; + }else{ /* mobilav=1 */ + for(i=1; i<=nlstate;i++) + prlim[i][i]=mobaverage[(int)age][i][ij]; + } + } + + /* This for computing force of mortality (h=1)as a weighted average */ + for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){ + for(i=1; i<= nlstate; i++) + gmp[j] += prlim[i][i]*p3mat[i][j][1]; + } + /* end force of mortality */ + + fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij); + for(j=nlstate+1; j<=(nlstate+ndeath);j++){ + fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j])); + for(i=1; i<=nlstate;i++){ + fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]); + } + } + fprintf(ficresprobmorprev,"\n"); + + fprintf(ficresvij,"%.0f ",age ); + for(i=1; i<=nlstate;i++) + for(j=1; j<=nlstate;j++){ + fprintf(ficresvij," %.4f", vareij[i][j][(int)age]); + } + fprintf(ficresvij,"\n"); + free_matrix(gp,0,nhstepm,1,nlstate); + free_matrix(gm,0,nhstepm,1,nlstate); + free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate); + free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar); + free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + } /* End age */ + free_vector(gpp,nlstate+1,nlstate+ndeath); + free_vector(gmp,nlstate+1,nlstate+ndeath); + free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath); + free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/ + fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65"); + /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */ + fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";"); + fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); + fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); + fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); + fprintf(fichtm,"\n
      File (multiple files are possible if covariates are present): %s\n",fileresprobmorprev,fileresprobmorprev); + fprintf(fichtm,"\n
      Probability is computed over estepm=%d months.

      \n", stepm,digitp,digit); + /* fprintf(fichtm,"\n
      Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year

      \n", stepm,YEARM,digitp,digit); +*/ + fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit); + + free_vector(xp,1,npar); + free_matrix(doldm,1,nlstate,1,nlstate); + free_matrix(dnewm,1,nlstate,1,npar); + free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); + free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar); + free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); + free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); + fclose(ficresprobmorprev); + fclose(ficgp); + fclose(fichtm); + +} + +/************ Variance of prevlim ******************/ +void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij) +{ + /* Variance of prevalence limit */ + /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/ + double **newm; + double **dnewm,**doldm; + int i, j, nhstepm, hstepm; + int k, cptcode; + double *xp; + double *gp, *gm; + double **gradg, **trgradg; + double age,agelim; + int theta; + + fprintf(ficresvpl,"# Standard deviation of prevalence's 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 optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax) +{ + int i, j=0, i1, k1, l1, t, tj; + int k2, l2, j1, z1; + int k=0,l, cptcode; + int first=1, first1; + double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp; + double **dnewm,**doldm; + double *xp; + double *gp, *gm; + double **gradg, **trgradg; + double **mu; + double age,agelim, cov[NCOVMAX]; + double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */ + int theta; + char fileresprob[FILENAMELENGTH]; + char fileresprobcov[FILENAMELENGTH]; + char fileresprobcor[FILENAMELENGTH]; + + double ***varpij; + + strcpy(fileresprob,"prob"); + strcat(fileresprob,fileres); + if((ficresprob=fopen(fileresprob,"w"))==NULL) { + printf("Problem with resultfile: %s\n", fileresprob); + fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob); + } + strcpy(fileresprobcov,"probcov"); + strcat(fileresprobcov,fileres); + if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) { + printf("Problem with resultfile: %s\n", fileresprobcov); + fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov); + } + strcpy(fileresprobcor,"probcor"); + strcat(fileresprobcor,fileres); + if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) { + printf("Problem with resultfile: %s\n", fileresprobcor); + fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor); + } + printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob); + fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob); + printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov); + fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov); + printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); + fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); + + fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n"); + fprintf(ficresprob,"# Age"); + fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n"); + fprintf(ficresprobcov,"# Age"); + fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n"); + fprintf(ficresprobcov,"# Age"); + + + for(i=1; i<=nlstate;i++) + for(j=1; j<=(nlstate+ndeath);j++){ + fprintf(ficresprob," p%1d-%1d (SE)",i,j); + fprintf(ficresprobcov," p%1d-%1d ",i,j); + fprintf(ficresprobcor," p%1d-%1d ",i,j); + } + fprintf(ficresprob,"\n"); + fprintf(ficresprobcov,"\n"); + fprintf(ficresprobcor,"\n"); + xp=vector(1,npar); + dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); + doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath)); + mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage); + varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage); + first=1; + if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { + printf("Problem with gnuplot file: %s\n", optionfilegnuplot); + fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot); + exit(0); + } + else{ + fprintf(ficgp,"\n# Routine varprob"); + } + if((fichtm=fopen(optionfilehtm,"a"))==NULL) { + printf("Problem with html file: %s\n", optionfilehtm); + fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm); + exit(0); + } + else{ + fprintf(fichtm,"\n

    • Computing and drawing one step probabilities with their confidence intervals

      • \n"); + fprintf(fichtm,"\n"); + + fprintf(fichtm,"\n

    • Computing matrix of variance-covariance of step probabilities

      • \n"); + fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the pij, pkl to understand the covariance between two incidences. They are expressed in year-1 in order to be less dependent of stepm.
      \n"); + fprintf(fichtm,"\n
      We have drawn x'cov-1x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis.
      When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.
      \n"); + + } + + + cov[1]=1; + tj=cptcoveff; + if (cptcovn<1) {tj=1;ncodemax[1]=1;} + j1=0; + for(t=1; t<=tj;t++){ + for(i1=1; i1<=ncodemax[t];i1++){ + j1++; + + if (cptcovn>0) { + fprintf(ficresprob, "\n#********** Variable "); + for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); + fprintf(ficresprob, "**********\n#"); + fprintf(ficresprobcov, "\n#********** Variable "); + for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); + fprintf(ficresprobcov, "**********\n#"); + + fprintf(ficgp, "\n#********** Variable "); + for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); + fprintf(ficgp, "**********\n#"); + + + fprintf(fichtm, "\n
      ********** Variable "); + for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); + fprintf(fichtm, "**********\n
      "); + + fprintf(ficresprobcor, "\n#********** Variable "); + for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); + fprintf(ficgp, "**********\n#"); + } + + for (age=bage; age<=fage; age ++){ + cov[2]=age; + for (k=1; k<=cptcovn;k++) { + cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]]; + } + for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; + for (k=1; k<=cptcovprod;k++) + cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; + + gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath)); + trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); + gp=vector(1,(nlstate)*(nlstate+ndeath)); + gm=vector(1,(nlstate)*(nlstate+ndeath)); + + for(theta=1; theta <=npar; theta++){ + for(i=1; i<=npar; i++) + xp[i] = x[i] + (i==theta ?delti[theta]:0); + + pmij(pmmij,cov,ncovmodel,xp,nlstate); + + k=0; + for(i=1; i<= (nlstate); i++){ + for(j=1; j<=(nlstate+ndeath);j++){ + k=k+1; + gp[k]=pmmij[i][j]; + } + } + + for(i=1; i<=npar; i++) + xp[i] = x[i] - (i==theta ?delti[theta]:0); + + pmij(pmmij,cov,ncovmodel,xp,nlstate); + k=0; + for(i=1; i<=(nlstate); i++){ + for(j=1; j<=(nlstate+ndeath);j++){ + k=k+1; + gm[k]=pmmij[i][j]; + } + } + + for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) + gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta]; + } + + for(j=1; j<=(nlstate)*(nlstate+ndeath);j++) + for(theta=1; theta <=npar; theta++) + trgradg[j][theta]=gradg[theta][j]; + + matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); + matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg); + + pmij(pmmij,cov,ncovmodel,x,nlstate); + + k=0; + for(i=1; i<=(nlstate); i++){ + for(j=1; j<=(nlstate+ndeath);j++){ + k=k+1; + mu[k][(int) age]=pmmij[i][j]; + } + } + for(i=1;i<=(nlstate)*(nlstate+ndeath);i++) + for(j=1;j<=(nlstate)*(nlstate+ndeath);j++) + varpij[i][j][(int)age] = doldm[i][j]; + + /*printf("\n%d ",(int)age); + for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){ + printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i])); + fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i])); + }*/ + + fprintf(ficresprob,"\n%d ",(int)age); + fprintf(ficresprobcov,"\n%d ",(int)age); + fprintf(ficresprobcor,"\n%d ",(int)age); + + for (i=1; i<=(nlstate)*(nlstate+ndeath);i++) + fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age])); + for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){ + fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]); + fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]); + } + i=0; + for (k=1; k<=(nlstate);k++){ + for (l=1; l<=(nlstate+ndeath);l++){ + i=i++; + fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l); + fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l); + for (j=1; j<=i;j++){ + fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]); + fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age])); + } + } + }/* end of loop for state */ + } /* end of loop for age */ + + /* Confidence intervalle of pij */ + /* + fprintf(ficgp,"\nset noparametric;unset label"); + fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\""); + fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65"); + fprintf(fichtm,"\n
      Probability with confidence intervals expressed in year-1 :pijgr%s.png, ",optionfilefiname,optionfilefiname); + fprintf(fichtm,"\n
      ",optionfilefiname); + fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname); + fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob); + */ + + /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/ + first1=1; + for (k2=1; k2<=(nlstate);k2++){ + for (l2=1; l2<=(nlstate+ndeath);l2++){ + if(l2==k2) continue; + j=(k2-1)*(nlstate+ndeath)+l2; + for (k1=1; k1<=(nlstate);k1++){ + for (l1=1; l1<=(nlstate+ndeath);l1++){ + if(l1==k1) continue; + i=(k1-1)*(nlstate+ndeath)+l1; + if(i<=j) continue; + for (age=bage; age<=fage; age ++){ + if ((int)age %5==0){ + v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM; + v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM; + cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM; + mu1=mu[i][(int) age]/stepm*YEARM ; + mu2=mu[j][(int) age]/stepm*YEARM; + c12=cv12/sqrt(v1*v2); + /* Computing eigen value of matrix of covariance */ + lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; + lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; + /* Eigen vectors */ + v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12)); + /*v21=sqrt(1.-v11*v11); *//* error */ + v21=(lc1-v1)/cv12*v11; + v12=-v21; + v22=v11; + tnalp=v21/v11; + if(first1==1){ + first1=0; + printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp); + } + fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp); + /*printf(fignu*/ + /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */ + /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */ + if(first==1){ + first=0; + fprintf(ficgp,"\nset parametric;unset label"); + fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2); + fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65"); + fprintf(fichtm,"\n
      Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year-1 :varpijgr%s%d%1d%1d-%1d%1d.png, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2); + fprintf(fichtm,"\n
      ",optionfilefiname, j1,k1,l1,k2,l2); + fprintf(fichtm,"\n
      Correlation at age %d (%.3f),",(int) age, c12); + fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2); + fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2); + fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2); + fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\ + mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\ + mu2,std,v21,sqrt(lc1),v22,sqrt(lc2)); + }else{ + first=0; + fprintf(fichtm," %d (%.3f),",(int) age, c12); + fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2); + fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2); + fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\ + mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\ + mu2,std,v21,sqrt(lc1),v22,sqrt(lc2)); + }/* if first */ + } /* age mod 5 */ + } /* end loop age */ + fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2); + first=1; + } /*l12 */ + } /* k12 */ + } /*l1 */ + }/* k1 */ + } /* loop covariates */ + free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage); + free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath)); + free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath)); + free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage); + 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); + fclose(ficresprobcov); + fclose(ficresprobcor); + fclose(ficgp); + fclose(fichtm); +} + + +/******************* Printing html file ***********/ +void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \ + int lastpass, int stepm, int weightopt, char model[],\ + int imx,int jmin, int jmax, double jmeanint,char rfileres[],\ + int popforecast, int estepm ,\ + double jprev1, double mprev1,double anprev1, \ + double jprev2, double mprev2,double anprev2){ + int jj1, k1, i1, cpt; + /*char optionfilehtm[FILENAMELENGTH];*/ + if((fichtm=fopen(optionfilehtm,"a"))==NULL) { + printf("Problem with %s \n",optionfilehtm), exit(0); + fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); + } + + fprintf(fichtm,"

      • Result files (first order: no variance)

        \n + - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): p%s
        \n + - Estimated transition probabilities over %d (stepm) months: pij%s
        \n + - Stable prevalence in each health state: pl%s
        \n + - Life expectancies by age and initial health status (estepm=%2d months): + e%s
        \n
        • ", \ + jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres); + +fprintf(fichtm," \n
        • Graphs

          • "); + + 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,"

          ************ 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
          "); + } + /* Pij */ + fprintf(fichtm,"
          - Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png
          +",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); + /* Quasi-incidences */ + fprintf(fichtm,"
          - Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png
          +",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); + /* Stable prevalence in each health state */ + for(cpt=1; cpt- Stable prevalence in each health state : p%s%d%d.png
          +",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.png
          +",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.png
          +",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); + } /* end i1 */ + }/* End k1 */ + fprintf(fichtm,"
        "); + + + fprintf(fichtm,"\n

      • Result files (second order: variances)

        \n + - Parameter file with estimated parameters and covariance matrix: %s
        \n + - Variance of one-step probabilities: prob%s
        \n + - Variance-covariance of one-step probabilities: probcov%s
        \n + - Correlation matrix of one-step probabilities: probcor%s
        \n + - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): v%s
        \n + - Health expectancies with their variances (no covariance): t%s
        \n + - Standard deviation of stable prevalences: vpl%s
        \n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres); + + if(popforecast==1) fprintf(fichtm,"\n + - Prevalences forecasting: f%s
        \n + - Population forecasting (if popforecast=1): pop%s
        \n +
        ",fileres,fileres,fileres,fileres); + else + fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)

        • \n",popforecast, stepm, model); +fprintf(fichtm,"
        • Graphs

          • "); + + 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,"

          ************ 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
          "); + } + for(cpt=1; cpt<=nlstate;cpt++) { + fprintf(fichtm,"
          - Observed and stationary prevalence (with confident +interval) in state (%d): v%s%d%d.png
          +",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1); + } + } /* end i1 */ + }/* End k1 */ + fprintf(fichtm,"
        "); +fclose(fichtm); +} + +/******************* Gnuplot file **************/ +void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){ + + int m,cpt,k1,i,k,j,jk,k2,k3,ij,l; + int ng; + if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { + printf("Problem with file %s",optionfilegnuplot); + fprintf(ficlog,"Problem with file %s",optionfilegnuplot); + } + +#ifdef windows + fprintf(ficgp,"cd \"%s\" \n",pathc); +#endif +m=pow(2,cptcoveff); + + /* 1eme*/ + for (cpt=1; cpt<= nlstate ; cpt ++) { + for (k1=1; k1<= m ; k1 ++) { + fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1); + fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1); + + for (i=1; i<= nlstate ; i ++) { + if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)"); + else fprintf(ficgp," \%%*lf (\%%*lf)"); + } + fprintf(ficgp,"\" t\"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)); + } + } + /*2 eme*/ + + for (k1=1; k1<= m ; k1 ++) { + fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1); + fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage); + + for (i=1; i<= nlstate+1 ; i ++) { + k=2*i; + fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1); + for (j=1; j<= nlstate+1 ; j ++) { + if (j==i) fprintf(ficgp," \%%lf (\%%lf)"); + else fprintf(ficgp," \%%*lf (\%%*lf)"); + } + if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,"); + else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1); + fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1); + for (j=1; j<= nlstate+1 ; j ++) { + if (j==i) fprintf(ficgp," \%%lf (\%%lf)"); + else fprintf(ficgp," \%%*lf (\%%*lf)"); + } + fprintf(ficgp,"\" t\"\" w l 0,"); + fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1); + for (j=1; j<= nlstate+1 ; j ++) { + if (j==i) fprintf(ficgp," \%%lf (\%%lf)"); + else fprintf(ficgp," \%%*lf (\%%*lf)"); + } + if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0"); + else fprintf(ficgp,"\" t\"\" w l 0,"); + } + } + + /*3eme*/ + + for (k1=1; k1<= m ; k1 ++) { + for (cpt=1; cpt<= nlstate ; cpt ++) { + k=2+nlstate*(2*cpt-2); + fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1); + fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt); + /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); + for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); + fprintf(ficgp,"\" t \"e%d1\" w l",cpt); + fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); + for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); + fprintf(ficgp,"\" t \"e%d1\" w l",cpt); + + */ + for (i=1; i< nlstate ; i ++) { + fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1); + + } + } + } + + /* CV preval stat */ + for (k1=1; k1<= m ; k1 ++) { + for (cpt=1; cpt=(ageminpar-((int)calagedate %12)/12.); agedeb--){ + nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); + nhstepm = nhstepm/hstepm; + + p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + oldm=oldms;savm=savms; + hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); + + for (h=0; h<=nhstepm; h++){ + if (h==(int) (calagedate+YEARM*cpt)) { + fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm); + } + for(j=1; j<=nlstate+ndeath;j++) { + kk1=0.;kk2=0; + for(i=1; i<=nlstate;i++) { + if (mobilav==1) + kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; + else { + kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; + } + + } + if (h==(int)(calagedate+12*cpt)){ + fprintf(ficresf," %.3f", kk1); + + } + } + } + free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + } + } + } + } + + if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); + + fclose(ficresf); +} +/************** Forecasting ******************/ +populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ + + int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; + int *popage; + double calagedate, agelim, kk1, kk2, 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(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate); + + + strcpy(filerespop,"pop"); + strcat(filerespop,fileres); + if((ficrespop=fopen(filerespop,"w"))==NULL) { + printf("Problem with forecast resultfile: %s\n", filerespop); + fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); + } + printf("Computing forecasting: result on file '%s' \n", filerespop); + fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); + + if (cptcoveff==0) ncodemax[cptcoveff]=1; + + if (mobilav==1) { + mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); + movingaverage(probs, ageminpar, fage, 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); + fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); + } + popage=ivector(0,AGESUP); + popeffectif=vector(0,AGESUP); + popcount=vector(0,AGESUP); + + i=1; + while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; + + imx=i; + for (i=1; i=(ageminpar-((int)calagedate %12)/12.); agedeb--){ + nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); + nhstepm = nhstepm/hstepm; + + p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + oldm=oldms;savm=savms; + hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); + + for (h=0; h<=nhstepm; h++){ + if (h==(int) (calagedate+YEARM*cpt)) { + fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); + } + for(j=1; j<=nlstate+ndeath;j++) { + kk1=0.;kk2=0; + for(i=1; i<=nlstate;i++) { + if (mobilav==1) + kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; + else { + kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; + } + } + if (h==(int)(calagedate+12*cpt)){ + tabpop[(int)(agedeb)][j][cptcod]=kk1; + /*fprintf(ficrespop," %.3f", kk1); + if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/ + } + } + for(i=1; i<=nlstate;i++){ + kk1=0.; + for(j=1; j<=nlstate;j++){ + kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; + } + tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)]; + } + + if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++) + fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); + } + free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + } + } + + /******/ + + for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { + fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); + for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ + nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); + nhstepm = nhstepm/hstepm; + + p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + oldm=oldms;savm=savms; + hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); + for (h=0; h<=nhstepm; h++){ + if (h==(int) (calagedate+YEARM*cpt)) { + fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); + } + for(j=1; j<=nlstate+ndeath;j++) { + kk1=0.;kk2=0; + for(i=1; i<=nlstate;i++) { + kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; + } + if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1); + } + } + free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + } + } + } + } + + if (mobilav==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 ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20; + + double fret; + double **xi,tmp,delta; + + double dum; /* Dummy variable */ + double ***p3mat; + double ***mobaverage; + int *indx; + char line[MAXLINE], linepar[MAXLINE]; + char path[80],pathc[80],pathcd[80],pathtot[80],model[80]; + int firstobs=1, lastobs=10; + int sdeb, sfin; /* Status at beginning and end */ + int c, h , cpt,l; + int ju,jl, mi; + int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij; + int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab; + int mobilav=0,popforecast=0; + int hstepm, nhstepm; + double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate; + + double bage, fage, age, agelim, agebase; + double ftolpl=FTOL; + double **prlim; + double *severity; + double ***param; /* Matrix of parameters */ + double *p; + double **matcov; /* Matrix of covariance */ + double ***delti3; /* Scale */ + double *delti; /* Scale */ + double ***eij, ***vareij; + double **varpl; /* Variances of prevalence limits by age */ + double *epj, vepp; + double kk1, kk2; + double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2; + + + char *alph[]={"a","a","b","c","d","e"}, str[4]; + + + char z[1]="c", occ; +#include +#include + char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80]; + + /* long total_usecs; + struct timeval start_time, end_time; + + gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */ + getcwd(pathcd, size); + + printf("\n%s",version); + if(argc <=1){ + printf("\nEnter the parameter file name: "); + scanf("%s",pathtot); + } + else{ + strcpy(pathtot,argv[1]); + } + /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/ + /*cygwin_split_path(pathtot,path,optionfile); + printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/ + /* cutv(path,optionfile,pathtot,'\\');*/ + + split(pathtot,path,optionfile,optionfilext,optionfilefiname); + printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname); + chdir(path); + replace(pathc,path); + +/*-------- arguments in the command line --------*/ + + /* Log file */ + strcat(filelog, optionfilefiname); + strcat(filelog,".log"); /* */ + if((ficlog=fopen(filelog,"w"))==NULL) { + printf("Problem with logfile %s\n",filelog); + goto end; + } + fprintf(ficlog,"Log filename:%s\n",filelog); + fprintf(ficlog,"\n%s",version); + fprintf(ficlog,"\nEnter the parameter file name: "); + fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname); + fflush(ficlog); + + /* */ + strcpy(fileres,"r"); + strcat(fileres, optionfilefiname); + strcat(fileres,".txt"); /* Other files have txt extension */ + + /*---------arguments file --------*/ + + if((ficpar=fopen(optionfile,"r"))==NULL) { + printf("Problem with optionfile %s\n",optionfile); + fprintf(ficlog,"Problem with optionfile %s\n",optionfile); + goto end; + } + + strcpy(filereso,"o"); + strcat(filereso,fileres); + if((ficparo=fopen(filereso,"w"))==NULL) { + printf("Problem with Output resultfile: %s\n", filereso); + fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso); + goto end; + } + + /* Reads comments: lines beginning with '#' */ + while((c=getc(ficpar))=='#' && c!= EOF){ + ungetc(c,ficpar); + fgets(line, MAXLINE, ficpar); + puts(line); + fputs(line,ficparo); + } + ungetc(c,ficpar); + + fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); + printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); + fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); +while((c=getc(ficpar))=='#' && c!= EOF){ + ungetc(c,ficpar); + fgets(line, MAXLINE, ficpar); + puts(line); + fputs(line,ficparo); + } + ungetc(c,ficpar); + + + covar=matrix(0,NCOVMAX,1,n); + cptcovn=0; + 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); + if(mle==1) + printf("%1d%1d",i,j); + fprintf(ficlog,"%1d%1d",i,j); + for(k=1; k<=ncovmodel;k++){ + fscanf(ficpar," %lf",¶m[i][j][k]); + if(mle==1){ + printf(" %lf",param[i][j][k]); + fprintf(ficlog," %lf",param[i][j][k]); + } + else + fprintf(ficlog," %lf",param[i][j][k]); + fprintf(ficparo," %lf",param[i][j][k]); + } + fscanf(ficpar,"\n"); + if(mle==1) + printf("\n"); + fprintf(ficlog,"\n"); + fprintf(ficparo,"\n"); + } + + npar= (nlstate+ndeath-1)*nlstate*ncovmodel; + + p=param[1][1]; + + /* Reads comments: lines beginning with '#' */ + while((c=getc(ficpar))=='#' && c!= EOF){ + ungetc(c,ficpar); + fgets(line, MAXLINE, ficpar); + puts(line); + fputs(line,ficparo); + } + ungetc(c,ficpar); + + delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); + delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */ + for(i=1; i <=nlstate; i++){ + for(j=1; j <=nlstate+ndeath-1; j++){ + fscanf(ficpar,"%1d%1d",&i1,&j1); + printf("%1d%1d",i,j); + fprintf(ficparo,"%1d%1d",i1,j1); + for(k=1; k<=ncovmodel;k++){ + fscanf(ficpar,"%le",&delti3[i][j][k]); + printf(" %le",delti3[i][j][k]); + fprintf(ficparo," %le",delti3[i][j][k]); + } + fscanf(ficpar,"\n"); + printf("\n"); + fprintf(ficparo,"\n"); + } + } + delti=delti3[1][1]; + + /* Reads comments: lines beginning with '#' */ + while((c=getc(ficpar))=='#' && c!= EOF){ + ungetc(c,ficpar); + fgets(line, MAXLINE, ficpar); + puts(line); + fputs(line,ficparo); + } + ungetc(c,ficpar); + + matcov=matrix(1,npar,1,npar); + for(i=1; i <=npar; i++){ + fscanf(ficpar,"%s",&str); + if(mle==1) + printf("%s",str); + fprintf(ficlog,"%s",str); + fprintf(ficparo,"%s",str); + for(j=1; j <=i; j++){ + fscanf(ficpar," %le",&matcov[i][j]); + if(mle==1){ + printf(" %.5le",matcov[i][j]); + fprintf(ficlog," %.5le",matcov[i][j]); + } + else + fprintf(ficlog," %.5le",matcov[i][j]); + fprintf(ficparo," %.5le",matcov[i][j]); + } + fscanf(ficpar,"\n"); + if(mle==1) + printf("\n"); + fprintf(ficlog,"\n"); + fprintf(ficparo,"\n"); + } + for(i=1; i <=npar; i++) + for(j=i+1;j<=npar;j++) + matcov[i][j]=matcov[j][i]; + + if(mle==1) + printf("\n"); + fprintf(ficlog,"\n"); + + + /*-------- Rewriting paramater file ----------*/ + strcpy(rfileres,"r"); /* "Rparameterfile */ + strcat(rfileres,optionfilefiname); /* Parameter file first name*/ + strcat(rfileres,"."); /* */ + strcat(rfileres,optionfilext); /* Other files have txt extension */ + if((ficres =fopen(rfileres,"w"))==NULL) { + printf("Problem writing new parameter file: %s\n", fileres);goto end; + fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end; + } + fprintf(ficres,"#%s\n",version); + + /*-------- data file ----------*/ + if((fic=fopen(datafile,"r"))==NULL) { + printf("Problem with datafile: %s\n", datafile);goto end; + fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end; + } + + n= lastobs; + severity = vector(1,maxwav); + outcome=imatrix(1,maxwav+1,1,n); + num=ivector(1,n); + moisnais=vector(1,n); + annais=vector(1,n); + moisdc=vector(1,n); + andc=vector(1,n); + agedc=vector(1,n); + cod=ivector(1,n); + weight=vector(1,n); + for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */ + mint=matrix(1,maxwav,1,n); + anint=matrix(1,maxwav,1,n); + s=imatrix(1,maxwav+1,1,n); + 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 (s[4][i]==9) s[4][i]=-1; + printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i]));}*/ + + + /* Calculation of the number of parameter from char model*/ + Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */ + Tprod=ivector(1,15); + Tvaraff=ivector(1,15); + Tvard=imatrix(1,15,1,2); + Tage=ivector(1,15); + + if (strlen(model) >1){ + 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); + fprintf(ficlog,"Error. Non available option model=%s ",model); + goto end; + } + + for(i=(j+1); i>=1;i--){ + cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ + if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */ + /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/ + /*scanf("%d",i);*/ + if (strchr(strb,'*')) { /* Model includes a product */ + cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/ + if (strcmp(strc,"age")==0) { /* Vn*age */ + cptcovprod--; + cutv(strb,stre,strd,'V'); + Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/ + cptcovage++; + Tage[cptcovage]=i; + /*printf("stre=%s ", stre);*/ + } + else if (strcmp(strd,"age")==0) { /* or age*Vn */ + cptcovprod--; + cutv(strb,stre,strc,'V'); + Tvar[i]=atoi(stre); + cptcovage++; + Tage[cptcovage]=i; + } + else { /* Age is not in the model */ + cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/ + Tvar[i]=ncovcol+k1; + cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */ + Tprod[k1]=i; + Tvard[k1][1]=atoi(strc); /* m*/ + Tvard[k1][2]=atoi(stre); /* n */ + Tvar[cptcovn+k2]=Tvard[k1][1]; + Tvar[cptcovn+k2+1]=Tvard[k1][2]; + for (k=1; k<=lastobs;k++) + covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k]; + k1++; + k2=k2+2; + } + } + else { /* no more sum */ + /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/ + /* scanf("%d",i);*/ + cutv(strd,strc,strb,'V'); + Tvar[i]=atoi(strc); + } + strcpy(modelsav,stra); + /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav); + scanf("%d",i);*/ + } /* end of loop + */ + } /* end model */ + + /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]); + printf("cptcovprod=%d ", cptcovprod); + fprintf(ficlog,"cptcovprod=%d ", cptcovprod); + scanf("%d ",i);*/ + fclose(fic); + + /* if(mle==1){*/ + if (weightopt != 1) { /* Maximisation without weights*/ + for(i=1;i<=n;i++) weight[i]=1.0; + } + /*-calculation of age at interview from date of interview and age at death -*/ + agev=matrix(1,maxwav,1,imx); + + for (i=1; i<=imx; i++) { + for(m=2; (m<= maxwav); m++) { + if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){ + anint[m][i]=9999; + s[m][i]=-1; + } + if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1; + } + } + + for (i=1; i<=imx; i++) { + agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]); + for(m=1; (m<= maxwav); m++){ + if(s[m][i] >0){ + if (s[m][i] >= nlstate+1) { + if(agedc[i]>0) + if(moisdc[i]!=99 && andc[i]!=9999) + agev[m][i]=agedc[i]; + /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/ + else { + if (andc[i]!=9999){ + printf("Warning negative age at death: %d line:%d\n",num[i],i); + fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i); + agev[m][i]=-1; + } + } + } + else if(s[m][i] !=9){ /* Should no more exist */ + agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]); + if(mint[m][i]==99 || anint[m][i]==9999) + agev[m][i]=1; + else if(agev[m][i] agemax){ + agemax=agev[m][i]; + /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/ + } + /*agev[m][i]=anint[m][i]-annais[i];*/ + /* agev[m][i] = age[i]+2*m;*/ + } + else { /* =9 */ + agev[m][i]=1; + s[m][i]=-1; + } + } + else /*= 0 Unknown */ + agev[m][i]=1; + } + + } + for (i=1; i<=imx; i++) { + for(m=1; (m<= maxwav); m++){ + if (s[m][i] > (nlstate+ndeath)) { + printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath); + fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath); + goto end; + } + } + } + +printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); + fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); + + free_vector(severity,1,maxwav); + free_imatrix(outcome,1,maxwav+1,1,n); + free_vector(moisnais,1,n); + free_vector(annais,1,n); + /* free_matrix(mint,1,maxwav,1,n); + free_matrix(anint,1,maxwav,1,n);*/ + free_vector(moisdc,1,n); + free_vector(andc,1,n); + + + wav=ivector(1,imx); + dh=imatrix(1,lastpass-firstpass+1,1,imx); + 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;codtab[h][Tvar[k]]=j; + /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/ + } + } + } + } + /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); + codtab[1][2]=1;codtab[2][2]=2; */ + /* for(i=1; i <=m ;i++){ + for(k=1; k <=cptcovn; k++){ + printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); + } + printf("\n"); + } + scanf("%d",i);*/ + + /* Calculates basic frequencies. Computes observed prevalence at single age + and prints on file fileres'p'. */ + + + + pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ + oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ + newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ + savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ + oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */ + + /* For Powell, parameters are in a vector p[] starting at p[1] + so we point p on param[1][1] so that p[1] maps on param[1][1][1] */ + p=param[1][1]; /* *(*(*(param +1)+1)+0) */ + + if(mle==1){ + mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func); + } + + /*--------- results files --------------*/ + fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model); + + + jk=1; + fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); + printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); + fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); + for(i=1,jk=1; i <=nlstate; i++){ + for(k=1; k <=(nlstate+ndeath); k++){ + if (k != i) + { + printf("%d%d ",i,k); + fprintf(ficlog,"%d%d ",i,k); + fprintf(ficres,"%1d%1d ",i,k); + for(j=1; j <=ncovmodel; j++){ + printf("%f ",p[jk]); + fprintf(ficlog,"%f ",p[jk]); + fprintf(ficres,"%f ",p[jk]); + jk++; + } + printf("\n"); + fprintf(ficlog,"\n"); + fprintf(ficres,"\n"); + } + } + } + if(mle==1){ + /* Computing hessian and covariance matrix */ + ftolhess=ftol; /* Usually correct */ + hesscov(matcov, p, npar, delti, ftolhess, func); + } + fprintf(ficres,"# Scales (for hessian or gradient estimation)\n"); + printf("# Scales (for hessian or gradient estimation)\n"); + fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n"); + for(i=1,jk=1; i <=nlstate; i++){ + for(j=1; j <=nlstate+ndeath; j++){ + if (j!=i) { + fprintf(ficres,"%1d%1d",i,j); + printf("%1d%1d",i,j); + fprintf(ficlog,"%1d%1d",i,j); + for(k=1; k<=ncovmodel;k++){ + printf(" %.5e",delti[jk]); + fprintf(ficlog," %.5e",delti[jk]); + fprintf(ficres," %.5e",delti[jk]); + jk++; + } + printf("\n"); + fprintf(ficlog,"\n"); + fprintf(ficres,"\n"); + } + } + } + + 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"); + if(mle==1) + printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); + fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); + for(i=1;i<=npar;i++){ + /* if (k>nlstate) k=1; + i1=(i-1)/(ncovmodel*nlstate)+1; + fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]); + printf("%s%d%d",alph[k],i1,tab[i]);*/ + fprintf(ficres,"%3d",i); + if(mle==1) + printf("%3d",i); + fprintf(ficlog,"%3d",i); + for(j=1; j<=i;j++){ + fprintf(ficres," %.5e",matcov[i][j]); + if(mle==1) + printf(" %.5e",matcov[i][j]); + fprintf(ficlog," %.5e",matcov[i][j]); + } + fprintf(ficres,"\n"); + if(mle==1) + printf("\n"); + fprintf(ficlog,"\n"); + k++; + } + + while((c=getc(ficpar))=='#' && c!= EOF){ + ungetc(c,ficpar); + fgets(line, MAXLINE, ficpar); + puts(line); + fputs(line,ficparo); + } + ungetc(c,ficpar); + estepm=0; + fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); + if (estepm==0 || estepm < stepm) estepm=stepm; + if (fage <= 2) { + bage = ageminpar; + fage = agemaxpar; + } + + fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n"); + fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); + fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); + + while((c=getc(ficpar))=='#' && c!= EOF){ + ungetc(c,ficpar); + fgets(line, MAXLINE, ficpar); + puts(line); + fputs(line,ficparo); + } + ungetc(c,ficpar); + + fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav); + fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,&mobilav); + fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,&mobilav); + + while((c=getc(ficpar))=='#' && c!= EOF){ + ungetc(c,ficpar); + fgets(line, MAXLINE, ficpar); + puts(line); + fputs(line,ficparo); + } + ungetc(c,ficpar); + + + dateprev1=anprev1+mprev1/12.+jprev1/365.; + dateprev2=anprev2+mprev2/12.+jprev2/365.; + + fscanf(ficpar,"pop_based=%d\n",&popbased); + fprintf(ficparo,"pop_based=%d\n",popbased); + fprintf(ficres,"pop_based=%d\n",popbased); + + while((c=getc(ficpar))=='#' && c!= EOF){ + ungetc(c,ficpar); + fgets(line, MAXLINE, ficpar); + puts(line); + fputs(line,ficparo); + } + ungetc(c,ficpar); + + fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2); +fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2); +fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2); + + +while((c=getc(ficpar))=='#' && c!= EOF){ + ungetc(c,ficpar); + fgets(line, MAXLINE, ficpar); + puts(line); + fputs(line,ficparo); + } + ungetc(c,ficpar); + + fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1); + fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1); + fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1); + + freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); +/*------------ gnuplot -------------*/ + strcpy(optionfilegnuplot,optionfilefiname); + strcat(optionfilegnuplot,".gp"); + if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) { + printf("Problem with file %s",optionfilegnuplot); + } + fclose(ficgp); + printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p); +/*--------- index.htm --------*/ + + strcpy(optionfilehtm,optionfile); + strcat(optionfilehtm,".htm"); + if((fichtm=fopen(optionfilehtm,"w"))==NULL) { + printf("Problem with %s \n",optionfilehtm), exit(0); + } + + fprintf(fichtm," %s
        \n +Title=%s
        Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s
        \n +\n +Total number of observations=%d
        \n +Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf
        \n +
        +

        • Parameter files

          \n + - Copy of the parameter file: o%s
          \n + - Log file of the run: %s
          \n + - Gnuplot file name: %s
        \n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot); + fclose(fichtm); + + printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2); + +/*------------ free_vector -------------*/ + chdir(path); + + free_ivector(wav,1,imx); + free_imatrix(dh,1,lastpass-firstpass+1,1,imx); + free_imatrix(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); + + + /*--------------- 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; + fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end; + } + printf("Computing prevalence limit: result on file '%s' \n", filerespl); + fprintf(ficlog,"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=ageminpar; + 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#******"); + printf("\n#******"); + fprintf(ficlog,"\n#******"); + for(j=1;j<=cptcoveff;j++) { + fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); + printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); + fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); + } + fprintf(ficrespl,"******\n"); + printf("******\n"); + fprintf(ficlog,"******\n"); + + for (age=agebase; age<=agelim; age++){ + prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); + fprintf(ficrespl,"%.0f",age ); + for(i=1; i<=nlstate;i++) + fprintf(ficrespl," %.5f", prlim[i][i]); + fprintf(ficrespl,"\n"); + } + } + } + fclose(ficrespl); + + /*------------- h Pij x at various ages ------------*/ + + strcpy(filerespij,"pij"); strcat(filerespij,fileres); + if((ficrespij=fopen(filerespij,"w"))==NULL) { + printf("Problem with Pij resultfile: %s\n", filerespij);goto end; + fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end; + } + printf("Computing pij: result on file '%s' \n", filerespij); + fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij); + + stepsize=(int) (stepm+YEARM-1)/YEARM; + /*if (stepm<=24) stepsize=2;*/ + + agelim=AGESUP; + hstepm=stepsize*YEARM; /* Every year of age */ + hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ + + /* hstepm=1; aff par mois*/ + + 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 */ + + /* nhstepm=nhstepm*YEARM; aff par mois*/ + + p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + oldm=oldms;savm=savms; + hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); + fprintf(ficrespij,"# Age"); + for(i=1; i<=nlstate;i++) + for(j=1; j<=nlstate+ndeath;j++) + fprintf(ficrespij," %1d-%1d",i,j); + fprintf(ficrespij,"\n"); + for (h=0; h<=nhstepm; h++){ + fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm ); + for(i=1; i<=nlstate;i++) + for(j=1; j<=nlstate+ndeath;j++) + fprintf(ficrespij," %.5f", p3mat[i][j][h]); + fprintf(ficrespij,"\n"); + } + free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + fprintf(ficrespij,"\n"); + } + } + } + + varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax); + + fclose(ficrespij); + + + /*---------- Forecasting ------------------*/ + if((stepm == 1) && (strcmp(model,".")==0)){ + prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1); + if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1); + } + else{ + erreur=108; + printf("Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); + fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); + } + + + /*---------- Health expectancies and variances ------------*/ + + strcpy(filerest,"t"); + strcat(filerest,fileres); + if((ficrest=fopen(filerest,"w"))==NULL) { + printf("Problem with total LE resultfile: %s\n", filerest);goto end; + fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end; + } + printf("Computing Total LEs with variances: file '%s' \n", filerest); + fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); + + + strcpy(filerese,"e"); + strcat(filerese,fileres); + if((ficreseij=fopen(filerese,"w"))==NULL) { + printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0); + fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0); + } + printf("Computing Health Expectancies: result on file '%s' \n", filerese); + fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese); + + strcpy(fileresv,"v"); + strcat(fileresv,fileres); + if((ficresvij=fopen(fileresv,"w"))==NULL) { + printf("Problem with variance resultfile: %s\n", fileresv);exit(0); + fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0); + } + printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); + fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); + calagedate=-1; + prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate); + if (mobilav==1) { + mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); + movingaverage(probs, ageminpar, fage, mobaverage); + } + + 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 ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); + fprintf(ficreseij,"******\n"); + + fprintf(ficresvij,"\n#****** "); + for(j=1;j<=cptcoveff;j++) + fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); + fprintf(ficresvij,"******\n"); + + eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); + oldm=oldms;savm=savms; + evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov); + + vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); + oldm=oldms;savm=savms; + varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav); + if(popbased==1){ + varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav); + } + + + fprintf(ficrest,"#Total LEs with variances: e.. (std) "); + for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i); + fprintf(ficrest,"\n"); + + epj=vector(1,nlstate+1); + for(age=bage; age <=fage ;age++){ + prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); + if (popbased==1) { + if(mobilav !=1){ + for(i=1; i<=nlstate;i++) + prlim[i][i]=probs[(int)age][i][k]; + }else{ /* mobilav=1 */ + for(i=1; i<=nlstate;i++) + prlim[i][i]=mobaverage[(int)age][i][k]; + } + } + + fprintf(ficrest," %4.0f",age); + for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){ + for(i=1, epj[j]=0.;i <=nlstate;i++) { + epj[j] += prlim[i][i]*eij[i][j][(int)age]; + /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/ + } + epj[nlstate+1] +=epj[j]; + } + + for(i=1, vepp=0.;i <=nlstate;i++) + for(j=1;j <=nlstate;j++) + vepp += vareij[i][j][(int)age]; + fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp)); + for(j=1;j <=nlstate;j++){ + fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age])); + } + fprintf(ficrest,"\n"); + } + } + } +free_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); + 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 (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); + + fprintf(fichtm,"\n"); + fclose(fichtm); + fclose(ficgp); + + + if(erreur >0){ + printf("End of Imach with error or warning %d\n",erreur); + fprintf(ficlog,"End of Imach with error or warning %d\n",erreur); + }else{ + printf("End of Imach\n"); + fprintf(ficlog,"End of Imach\n"); + } + printf("See log file on %s\n",filelog); + fclose(ficlog); + /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */ + + /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/ + /*printf("Total time was %d uSec.\n", total_usecs);*/ + /*------ End -----------*/ + + + end: +#ifdef windows + /* chdir(pathcd);*/ +#endif + /*system("wgnuplot graph.plt");*/ + /*system("../gp37mgw/wgnuplot graph.plt");*/ + /*system("cd ../gp37mgw");*/ + /* system("..\\gp37mgw\\wgnuplot graph.plt");*/ + strcpy(plotcmd,GNUPLOTPROGRAM); + strcat(plotcmd," "); + strcat(plotcmd,optionfilegnuplot); + system(plotcmd); + +#ifdef windows + while (z[0] != 'q') { + /* chdir(path); */ + printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: "); + scanf("%s",z); + if (z[0] == 'c') system("./imach"); + else if (z[0] == 'e') system(optionfilehtm); + else if (z[0] == 'g') system(plotcmd); + else if (z[0] == 'q') exit(0); + } +#endif +} + +