--- imach096d/src/imach.c 2000/12/28 18:49:56 1.1 +++ imach096d/src/imach.c 2003/02/04 20:55:29 1.69 @@ -1,37 +1,45 @@ - -/*********************** Imach ************************************** - This program computes Healthy Life Expectancies from cross-longitudinal - data. Cross-longitudinal consist in a first survey ("cross") where - individuals from different ages are interviewed on their health status - or degree of disability. At least a second wave of interviews - ("longitudinal") should measure each new individual health status. - Health expectancies are computed from the transistions observed between - waves and are computed for each degree of severity of disability (number - of life states). More degrees you consider, more time is necessary to - reach the Maximum Likekilhood of the parameters involved in the model. - The simplest model is the multinomial logistic model where pij is - the probabibility to be observed in state j at the second wave conditional - to be observed in state i at the first wave. Therefore the model is: - log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex' - is a covariate. If you want to have a more complex model than "constant and - age", you should modify the program where the markup - *Covariates have to be included here again* invites you to do it. - More covariates you add, less is the speed of the convergence. - - The advantage that this computer programme claims, comes from that if the - delay between waves is not identical for each individual, or if some - individual missed an interview, the information is not rounded or 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. +/* $Id: imach.c,v 1.69 2003/02/04 20:55:29 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, quarter, + semester or year) is modelled 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. + of the life expectancies. It also computes the stable prevalence. Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr). Institut national d'études démographiques, Paris. @@ -48,12 +56,16 @@ #include #define MAXLINE 256 +#define GNUPLOTPROGRAM "gnuplot" +/*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/ #define FILENAMELENGTH 80 /*#define DEBUG*/ -/*#define win*/ +#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*ncov */ +#define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */ #define NINTERVMAX 8 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */ @@ -63,24 +75,57 @@ #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 0.91, November 2002, INED-EUROREVES "; +int erreur; /* Error number */ int nvar; - +int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov; int npar=NPARMAX; int nlstate=2; /* Number of live states */ int ndeath=1; /* Number of dead states */ -int ncov; /* Total number of covariables including constant a12*1 +b12*x ncov=2 */ +int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */ +int popbased=0; int *wav; /* Number of waves for this individuual 0 is possible */ int maxwav; /* Maxim number of waves */ +int jmin, jmax; /* min, max spacing between 2 waves */ int mle, weightopt; int **mw; /* mw[mi][i] is number of the mi wave for this individual */ int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */ +int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between + * wave mi and wave mi+1 is not an exact multiple of stepm. */ +double jmean; /* Mean space between 2 waves */ double **oldm, **newm, **savm; /* Working pointers to matrices */ double **oldms, **newms, **savms; /* Fixed working pointers to matrices */ -FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest; -FILE *ficgp, *fichtm; +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* @@ -102,7 +147,7 @@ FILE *ficgp, *fichtm; 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) @@ -114,19 +159,71 @@ 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=2,*cod; +int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage; double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint; -double **pmmij; +double **pmmij, ***probs; +double dateintmean=0; double *weight; int **s; /* Status */ double *agedc, **covar, idx; - +int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff; double ftol=FTOL; /* Tolerance for computing Max Likelihood */ double ftolhess; /* Tolerance for computing hessian */ +/**************** split *************************/ +static int split( char *path, char *dirc, char *name, char *ext, char *finame ) +{ + char *ss; /* pointer */ + int l1, l2; /* length counters */ + + l1 = strlen(path ); /* length of path */ + if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH ); + ss= strrchr( path, DIRSEPARATOR ); /* find last / */ + if ( ss == NULL ) { /* no directory, so use current */ + /*if(strrchr(path, ODIRSEPARATOR )==NULL) + printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/ +#if defined(__bsd__) /* get current working directory */ + extern char *getwd( ); + + if ( getwd( dirc ) == NULL ) { +#else + extern char *getcwd( ); + + if ( getcwd( dirc, FILENAME_MAX ) == NULL ) { +#endif + return( GLOCK_ERROR_GETCWD ); + } + strcpy( name, path ); /* we've got it */ + } else { /* strip direcotry from path */ + ss++; /* after this, the filename */ + l2 = strlen( ss ); /* length of filename */ + if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH ); + strcpy( name, ss ); /* save file name */ + strncpy( dirc, path, l1 - l2 ); /* now the directory */ + dirc[l1-l2] = 0; /* add zero */ + } + l1 = strlen( dirc ); /* length of directory */ +#ifdef windows + if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; } +#else + if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; } +#endif + ss = strrchr( name, '.' ); /* find last / */ + ss++; + strcpy(ext,ss); /* save extension */ + l1= strlen( name); + l2= strlen(ss)+1; + strncpy( finame, name, l1-l2); + finame[l1-l2]= 0; + return( 0 ); /* we're done */ +} + /******************************************/ @@ -141,21 +238,37 @@ void replace(char *s, char*t) if (t[i]== '\\') s[i]='/'; } } -void cut(char *u,char *v, char*t) + +int nbocc(char *s, char occ) +{ + int i,j=0; + int lg=20; + i=0; + lg=strlen(s); + for(i=0; i<= lg; i++) { + if (s[i] == occ ) j++; + } + return j; +} + +void cutv(char *u,char *v, char*t, char occ) { - int i,lg,j,p; + /* 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); j++) { - if(t[j]=='\\') p=j; + 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]); } } @@ -166,7 +279,7 @@ void nrerror(char error_text[]) { fprintf(stderr,"ERREUR ...\n"); fprintf(stderr,"%s\n",error_text); - exit(1); + exit(EXIT_FAILURE); } /*********************** vector *******************/ double *vector(int nl, int nh) @@ -339,8 +452,10 @@ double brent(double ax, double bx, doubl 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))){ @@ -465,6 +580,7 @@ void linmin(double p[], double xi[], int *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; @@ -477,10 +593,7 @@ void linmin(double p[], double xi[], int /*************** 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; @@ -498,16 +611,21 @@ void powell(double p[], double **xi, int 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)); @@ -515,13 +633,18 @@ void powell(double p[], double **xi, int } #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++) + 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))) { @@ -530,15 +653,21 @@ void powell(double p[], double **xi, int k[0]=1; k[1]=-1; printf("Max: %.12e",(*func)(p)); - for (j=1;j<=n;j++) + 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 @@ -566,18 +695,22 @@ void powell(double p[], double **xi, int } #ifdef DEBUG printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig); - for(j=1;j<=n;j++) + 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 ****************/ +/**** Prevalence limit (stable prevalence) ****************/ -double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl) +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 */ @@ -593,15 +726,28 @@ double **prevalim(double **prlim, int nl for (j=1;j<=nlstate+ndeath;j++){ oldm[ii][j]=(ii==j ? 1.0 : 0.0); } - /* Even if hstepm = 1, at least one multiplication by the unit matrix */ + + 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[1]=1.; - cov[2]=agefin; - out=matprod2(newm, pmij(pmmij,cov,ncov,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); -/* printf("age=%f agefin=%f po=%f pn=%f\n",age,agefin,oldm[1][1],newm[1][1]);*/ - + 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.; @@ -624,9 +770,9 @@ double **prevalim(double **prlim, int nl } } -/*************** transition probabilities **********/ +/*************** transition probabilities ***************/ -double **pmij(double **ps, double *cov, int ncov, double *x, int nlstate ) +double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate ) { double s1, s2; /*double t34;*/ @@ -634,22 +780,24 @@ double **pmij(double **ps, double *cov, 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; j 1 the results are less biased than in previous versions. + */ + s1=s[mw[mi][i]][i]; + s2=s[mw[mi+1][i]][i]; + bbh=(double)bh[mi][i]/(double)stepm; + /* bias is positive if real duration + * is higher than the multiple of stepm and negative otherwise. + */ + /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/ + lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */ + /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/ + /*if(lli ==000.0)*/ + /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */ + ipmx +=1; + sw += weight[i]; + ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; + } /* end of wave */ + } /* end of individual */ + } else if(mle==2){ + for (i=1,ipmx=0, sw=0.; i<=imx; i++){ + for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; + for(mi=1; mi<= wav[i]-1; mi++){ + for (ii=1;ii<=nlstate+ndeath;ii++) + for (j=1;j<=nlstate+ndeath;j++){ + oldm[ii][j]=(ii==j ? 1.0 : 0.0); + savm[ii][j]=(ii==j ? 1.0 : 0.0); + } + for(d=0; d<=dh[mi][i]; d++){ + newm=savm; + cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM; + for (kk=1; kk<=cptcovage;kk++) { + cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; + } + out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, + 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); + savm=oldm; + oldm=newm; + } /* end mult */ + + /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */ + /* But now since version 0.9 we anticipate for bias and large stepm. + * If stepm is larger than one month (smallest stepm) and if the exact delay + * (in months) between two waves is not a multiple of stepm, we rounded to + * the nearest (and in case of equal distance, to the lowest) interval but now + * we keep into memory the bias bh[mi][i] and also the previous matrix product + * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the + * probability in order to take into account the bias as a fraction of the way + * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies + * -stepm/2 to stepm/2 . + * For stepm=1 the results are the same as for previous versions of Imach. + * For stepm > 1 the results are less biased than in previous versions. + */ + s1=s[mw[mi][i]][i]; + s2=s[mw[mi+1][i]][i]; + bbh=(double)bh[mi][i]/(double)stepm; + /* bias is positive if real duration + * is higher than the multiple of stepm and negative otherwise. + */ + lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */ + /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/ + /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */ + /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/ + /*if(lli ==000.0)*/ + /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */ + ipmx +=1; + sw += weight[i]; + ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; + } /* end of wave */ + } /* end of individual */ + } else if(mle==3){ /* exponential inter-extrapolation */ + for (i=1,ipmx=0, sw=0.; i<=imx; i++){ + for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; + for(mi=1; mi<= wav[i]-1; mi++){ + for (ii=1;ii<=nlstate+ndeath;ii++) + for (j=1;j<=nlstate+ndeath;j++){ + oldm[ii][j]=(ii==j ? 1.0 : 0.0); + savm[ii][j]=(ii==j ? 1.0 : 0.0); + } + for(d=0; d 1 the results are less biased than in previous versions. + */ + s1=s[mw[mi][i]][i]; + s2=s[mw[mi+1][i]][i]; + bbh=(double)bh[mi][i]/(double)stepm; + /* bias is positive if real duration + * is higher than the multiple of stepm and negative otherwise. + */ + /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */ + lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */ + /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/ + /*if(lli ==000.0)*/ + /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */ + ipmx +=1; + sw += weight[i]; + ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; + } /* end of wave */ + } /* end of individual */ + }else{ /* ml=4 no inter-extrapolation */ + for (i=1,ipmx=0, sw=0.; i<=imx; i++){ + for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; + for(mi=1; mi<= wav[i]-1; mi++){ + for (ii=1;ii<=nlstate+ndeath;ii++) + for (j=1;j<=nlstate+ndeath;j++){ + oldm[ii][j]=(ii==j ? 1.0 : 0.0); + savm[ii][j]=(ii==j ? 1.0 : 0.0); + } + for(d=0; di) { 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]; + 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); @@ -872,11 +1198,14 @@ void hesscov(double **matcov, double p[] } 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 */ @@ -893,8 +1222,10 @@ void hesscov(double **matcov, double p[] 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"); } */ @@ -936,6 +1267,7 @@ double hessii( double x[], double delta, #ifdef DEBUG printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx); + fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx); #endif /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */ if((k1 =1.e-10) - printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); - else - printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk); - } - for(jk=1; jk <=nlstate ; jk++){ - for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++) - pp[jk] += freq[jk][m][i]; - } - for(jk=1,pos=0; jk <=nlstate ; jk++) - pos += pp[jk]; - for(jk=1; jk <=nlstate ; jk++){ - if(pos>=1.e-5) - printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); - else - printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); - if( i <= (int) agemax){ - if(pos>=1.e-5) - fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos); - else - fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos); + 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"); } } - for(jk=-1; jk <=nlstate+ndeath; jk++) - for(m=-1; m <=nlstate+ndeath; m++) - if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]); - if(i <= (int) agemax) - fprintf(ficresp,"\n"); - printf("\n"); } - + dateintmean=dateintsum/k2cpt; + fclose(ficresp); free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3); free_vector(pp,1,nlstate); + + /* End of Freq */ +} + +/************ Prevalence ********************/ +void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedatem) +{ + /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people + in each health status at the date of interview (if between dateprev1 and dateprev2). + We still use firstpass and lastpass as another selection. + */ + + int i, m, jk, k1, i1, j1, bool, z1,z2,j; + double ***freq; /* Frequencies */ + double *pp; + double pos; + double y2; /* in fractional years */ + + 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++) { /* Each individual */ + 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++){/* Other selection (we can limit to certain interviews*/ + y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */ + if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */ + if(agev[m][i]==0) agev[m][i]=agemax+1; + if(agev[m][i]==1) agev[m][i]=agemax+2; + if (m0) /* We compute prevalence at exact age, agev in fractional years */ + freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedatem %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]; + } + } + } /* end selection of waves */ + } + } + 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) +void concatwav(int wav[], int **dh, int **bh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm) { /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i. Death is a valid wave (if date is known). mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i - dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i] + dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i] and mw[mi+1][i]. dh depends on stepm. */ int i, mi, m; - int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1; -float sum=0.; - + /* 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; @@ -1185,8 +1684,15 @@ float sum=0.; } wav[i]=mi; - if(mi==0) - printf("Warning, no any valid information for:%d line=%d\n",num[i],i); + 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++){ @@ -1195,195 +1701,566 @@ float sum=0.; dh[mi][i]=1; else{ if (s[mw[mi+1][i]][i] > nlstate) { + if (agedc[i] < 2*AGESUP) { j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); - if(j=0) j=1; /* Survives at least one month after exam */ + 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); */ + /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/ + } } else{ j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12)); + /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/ 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 */ - } - } + if(mle <=1){ + if(jl==0){ + dh[mi][i]=jk; + bh[mi][i]=0; + }else{ /* We want a negative bias in order to only have interpolation ie + * at the price of an extra matrix product in likelihood */ + dh[mi][i]=jk+1; + bh[mi][i]=ju; + } + }else{ + if(jl <= -ju){ + dh[mi][i]=jk; + bh[mi][i]=jl; /* bias is positive if real duration + * is higher than the multiple of stepm and negative otherwise. + */ + } + else{ + dh[mi][i]=jk+1; + bh[mi][i]=ju; + } + if(dh[mi][i]==0){ + dh[mi][i]=1; /* At least one step */ + bh[mi][i]=ju; /* At least one step */ + printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i); + } + } + } /* end if mle */ + } /* end wave */ } - printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k); + jmean=sum/k; + printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean); + fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean); + } + +/*********** Tricode ****************************/ +void tricode(int *Tvar, int **nbcode, int imx) +{ + + int Ndum[20],ij=1, k, j, i, maxncov=19; + int cptcode=0; + cptcoveff=0; + + for (k=0; k cptcode) cptcode=ij; /* getting the maximum of covariable + Tvar[j]. If V=sex and male is 0 and + female is 1, then cptcode=1.*/ + } + + for (i=0; i<=cptcode; i++) { + if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */ + } + + ij=1; + for (i=1; i<=ncodemax[j]; i++) { + for (k=0; k<= maxncov; k++) { + if (Ndum[k] != 0) { + nbcode[Tvar[j]][ij]=k; + /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */ + + ij++; + } + if (ij > ncodemax[j]) break; + } + } + } + + for (k=0; k< maxncov; k++) Ndum[k]=0; + + for (i=1; i<=ncovmodel-2; i++) { + /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ + ij=Tvar[i]; + Ndum[ij]++; + } + + ij=1; + for (i=1; i<= maxncov; i++) { + if((Ndum[i]!=0) && (i<=ncovcol)){ + Tvaraff[ij]=i; /*For printing */ + ij++; + } + } + + cptcoveff=ij-1; /*Number of simple covariates*/ } /*********** Health Expectancies ****************/ -void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm) +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; - double age, agelim,hf; - double ***p3mat; - - FILE *ficreseij; - char filerese[FILENAMELENGTH]; - - strcpy(filerese,"e"); - strcat(filerese,fileres); - if((ficreseij=fopen(filerese,"w"))==NULL) { - printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0); - } - printf("Computing Health Expectancies: result on file '%s' \n", filerese); + 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",i,j); + fprintf(ficreseij," %1d-%1d (SE)",i,j); fprintf(ficreseij,"\n"); - hstepm=1*YEARM; /* Every j years of age (in month) */ - hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ + 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 in between 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 */ - nhstepm=(int) rint((agelim-age)*YEARM/stepm); - /* Typically if 20 years = 20*12/6=40 stepm */ - if (stepm >= YEARM) hstepm=1; - nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */ + 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); + 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; h++){ - eij[i][j][(int)age] +=p3mat[i][j][h]; + 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]);*/ + } - - hf=1; - if (stepm >= YEARM) hf=stepm/YEARM; - fprintf(ficreseij,"%.0f",age ); + + fprintf(ficreseij,"%3.0f",age ); + cptj=0; for(i=1; i<=nlstate;i++) for(j=1; j<=nlstate;j++){ - fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]); + 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); } - fclose(ficreseij); + 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 fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl) +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 **newm;*/ double **dnewm,**doldm; - int i, j, nhstepm, hstepm, h; - int k; - FILE *ficresvij; - char fileresv[FILENAMELENGTH]; + double **dnewmp,**doldmp; + int i, j, nhstepm, hstepm, h, nstepm ; + int k, cptcode; double *xp; - double **gp, **gm; - double ***gradg, ***trgradg; + 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; + double age,agelim, hf; + double ***mobaverage; int theta; + char digit[4]; + char digitp[25]; - strcpy(fileresv,"v"); - strcat(fileresv,fileres); - if((ficresvij=fopen(fileresv,"w"))==NULL) { - printf("Problem with variance resultfile: %s\n", fileresv);exit(0); - } - printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); + char fileresprobmorprev[FILENAMELENGTH]; + if(popbased==1){ + if(mobilav!=0) + strcpy(digitp,"-populbased-mobilav-"); + else strcpy(digitp,"-populbased-nomobil-"); + } + else + strcpy(digitp,"-stablbased-"); + + if (mobilav!=0) { + mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); + if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ + fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); + printf(" Error in movingaverage mobilav=%d\n",mobilav); + } + } - fprintf(ficresvij,"# Covariances of life expectancies\n"); - fprintf(ficresvij,"# Age"); - for(i=1; i<=nlstate;i++) - for(j=1; j<=nlstate;j++) - fprintf(ficresvij," Cov(e%1d, e%1d)",i,j); - fprintf(ficresvij,"\n"); + 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 before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm); + 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 over estepm months as a weighted average (i.e global mortality independent of initial healh state)

    • \n"); + fprintf(fichtm,"\n
    %s
    \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); - - hstepm=1*YEARM; /* Every year of age */ - hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ + 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 every two years of age and if + you sum them up and add 1 year (area under the trapezoids) you won't get the same + 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=(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 */ + 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 */ + for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/ xp[i] = x[i] + (i==theta ?delti[theta]:0); } - hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm); - prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl); + hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); + prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); + + if (popbased==1) { + if(mobilav ==0){ + for(i=1; i<=nlstate;i++) + prlim[i][i]=probs[(int)age][i][ij]; + }else{ /* mobilav */ + for(i=1; i<=nlstate;i++) + prlim[i][i]=mobaverage[(int)age][i][ij]; + } + } + for(j=1; j<= nlstate; j++){ for(h=0; h<=nhstepm; h++){ for(i=1, gp[h][j]=0.;i<=nlstate;i++) gp[h][j] += prlim[i][i]*p3mat[i][j][h]; } } - - for(i=1; i<=npar; i++) /* Computes gradient */ + /* This for computing probability of death (h=1 means + computed over hstepm matrices product = hstepm*stepm months) + as a weighted average of prlim. + */ + for(j=nlstate+1;j<=nlstate+ndeath;j++){ + for(i=1,gpp[j]=0.; i<= nlstate; i++) + gpp[j] += prlim[i][i]*p3mat[i][j][1]; + } + /* end probability of death */ + + for(i=1; i<=npar; i++) /* Computes gradient x - delta */ xp[i] = x[i] - (i==theta ?delti[theta]:0); - hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm); - prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl); + hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); + prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); + + if (popbased==1) { + if(mobilav ==0){ + for(i=1; i<=nlstate;i++) + prlim[i][i]=probs[(int)age][i][ij]; + }else{ /* mobilav */ + for(i=1; i<=nlstate;i++) + prlim[i][i]=mobaverage[(int)age][i][ij]; + } + } + for(j=1; j<= nlstate; j++){ for(h=0; h<=nhstepm; h++){ for(i=1, gm[h][j]=0.;i<=nlstate;i++) gm[h][j] += prlim[i][i]*p3mat[i][j][h]; } } - for(j=1; j<= nlstate; j++) + /* This for computing probability of death (h=1 means + computed over hstepm matrices product = hstepm*stepm months) + as a weighted average of prlim. + */ + for(j=nlstate+1;j<=nlstate+ndeath;j++){ + for(i=1,gmp[j]=0.; i<= nlstate; i++) + gmp[j] += prlim[i][i]*p3mat[i][j][1]; + } + /* end probability of death */ + + 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); + trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */ - for(h=0; h<=nhstepm; h++) + 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]; + 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 */ + /* x centered again */ + hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij); + prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij); + + if (popbased==1) { + if(mobilav ==0){ + for(i=1; i<=nlstate;i++) + prlim[i][i]=probs[(int)age][i][ij]; + }else{ /* mobilav */ + for(i=1; i<=nlstate;i++) + prlim[i][i]=mobaverage[(int)age][i][ij]; } } - h=1; - if (stepm >= YEARM) h=stepm/YEARM; + + /* This for computing probability of death (h=1 means + computed over hstepm (estepm) matrices product = hstepm*stepm months) + as a weighted average of prlim. + */ + for(j=nlstate+1;j<=nlstate+ndeath;j++){ + for(i=1,gmp[j]=0.;i<= nlstate; i++) + gmp[j] += prlim[i][i]*p3mat[i][j][1]; + } + /* end probability of death */ + + 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", h*vareij[i][j][(int)age]); + fprintf(ficresvij," %.4f", vareij[i][j][(int)age]); } fprintf(ficresvij,"\n"); free_matrix(gp,0,nhstepm,1,nlstate); @@ -1392,40 +2269,53 @@ void varevsij(char fileres[], double *** free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar); free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); } /* End age */ - fclose(ficresvij); - free_vector(xp,1,npar); - free_matrix(doldm,1,nlstate,1,npar); - free_matrix(dnewm,1,nlstate,1,nlstate); + 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(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",fileresprobmorprev); + fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev); + fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev); + 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", estepm,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); + if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); + fclose(ficresprobmorprev); + fclose(ficgp); + fclose(fichtm); } /************ Variance of prevlim ******************/ -void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl) +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 health expectancies */ - /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/ + /* 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; - FILE *ficresvpl; - char fileresvpl[FILENAMELENGTH]; + int k, cptcode; double *xp; double *gp, *gm; double **gradg, **trgradg; double age,agelim; int theta; - - 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); - - - fprintf(ficresvpl,"# Standard deviation of prevalences limit\n"); + + fprintf(ficresvpl,"# Standard deviation of stable prevalences \n"); fprintf(ficresvpl,"# Age"); for(i=1; i<=nlstate;i++) fprintf(ficresvpl," %1d-%1d",i,i); @@ -1450,13 +2340,13 @@ void varprevlim(char fileres[], double * 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); + 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); + prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); for(i=1;i<=nlstate;i++) gm[i] = prlim[i][i]; @@ -1486,48 +2376,956 @@ void varprevlim(char fileres[], double * free_matrix(gradg,1,npar,1,nlstate); free_matrix(trgradg,1,nlstate,1,npar); } /* End age */ - fclose(ficresvpl); + 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#\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#\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#\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(ficresprobcor, "**********\n#"); + } + + for (age=bage; age<=fage; age ++){ + cov[2]=age; + for (k=1; k<=cptcovn;k++) { + cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]]; + } + for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; + for (k=1; k<=cptcovprod;k++) + cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; + + gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath)); + trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); + gp=vector(1,(nlstate)*(nlstate+ndeath)); + gm=vector(1,(nlstate)*(nlstate+ndeath)); + + for(theta=1; theta <=npar; theta++){ + for(i=1; i<=npar; i++) + xp[i] = x[i] + (i==theta ?delti[theta]:0); + + pmij(pmmij,cov,ncovmodel,xp,nlstate); + + k=0; + for(i=1; i<= (nlstate); i++){ + for(j=1; j<=(nlstate+ndeath);j++){ + k=k+1; + gp[k]=pmmij[i][j]; + } + } + + for(i=1; i<=npar; i++) + xp[i] = x[i] - (i==theta ?delti[theta]:0); + + pmij(pmmij,cov,ncovmodel,xp,nlstate); + k=0; + for(i=1; i<=(nlstate); i++){ + for(j=1; j<=(nlstate+ndeath);j++){ + k=k+1; + gm[k]=pmmij[i][j]; + } + } + + for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) + gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta]; + } + + for(j=1; j<=(nlstate)*(nlstate+ndeath);j++) + for(theta=1; theta <=npar; theta++) + trgradg[j][theta]=gradg[theta][j]; + + matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); + matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg); + free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath)); + free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath)); + free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); + free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); + + pmij(pmmij,cov,ncovmodel,x,nlstate); + + k=0; + for(i=1; i<=(nlstate); i++){ + for(j=1; j<=(nlstate+ndeath);j++){ + k=k+1; + mu[k][(int) age]=pmmij[i][j]; + } + } + for(i=1;i<=(nlstate)*(nlstate+ndeath);i++) + for(j=1;j<=(nlstate)*(nlstate+ndeath);j++) + varpij[i][j][(int)age] = doldm[i][j]; + + /*printf("\n%d ",(int)age); + for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){ + printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i])); + fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i])); + }*/ + + fprintf(ficresprob,"\n%d ",(int)age); + fprintf(ficresprobcov,"\n%d ",(int)age); + fprintf(ficresprobcor,"\n%d ",(int)age); + + for (i=1; i<=(nlstate)*(nlstate+ndeath);i++) + fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age])); + for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){ + fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]); + fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]); + } + i=0; + for (k=1; k<=(nlstate);k++){ + for (l=1; l<=(nlstate+ndeath);l++){ + i=i++; + fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l); + fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l); + for (j=1; j<=i;j++){ + fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]); + fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age])); + } + } + }/* end of loop for state */ + } /* end of loop for age */ + + /* Confidence intervalle of pij */ + /* + fprintf(ficgp,"\nset noparametric;unset label"); + fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\""); + fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65"); + fprintf(fichtm,"\n
    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_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage); + free_vector(xp,1,npar); + fclose(ficresprob); + fclose(ficresprobcov); + fclose(ficresprobcor); + fclose(ficgp); + fclose(fichtm); +} + + +/******************* Printing html file ***********/ +void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \ + int lastpass, int stepm, int weightopt, char model[],\ + int imx,int jmin, int jmax, double jmeanint,char rfileres[],\ + int popforecast, int estepm ,\ + double jprev1, double mprev1,double anprev1, \ + double jprev2, double mprev2,double anprev2){ + int jj1, k1, i1, cpt; + /*char optionfilehtm[FILENAMELENGTH];*/ + if((fichtm=fopen(optionfilehtm,"a"))==NULL) { + printf("Problem with %s \n",optionfilehtm), exit(0); + fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); + } + + fprintf(fichtm,"

    • 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\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$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:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); + for (i=1; i<= nlstate ; i ++) { + if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)"); + else fprintf(ficgp," \%%*lf (\%%*lf)"); + } + fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%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)calagedatem %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) (calagedatem+YEARM*yearp)) { + fprintf(ficresf,"\n"); + for(j=1;j<=cptcoveff;j++) + fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); + fprintf(ficresf,"%.f %.f ",anproj1+yearp,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)(calagedatem+12*yearp)){ + fprintf(ficresf," %.3f", kk1); + + } + } + } + free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + } + } + } + } + + if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); + + fclose(ficresf); +} +/************** Forecasting ******************/ +populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ + + int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; + int *popage; + double calagedatem, agelim, kk1, kk2; + double *popeffectif,*popcount; + double ***p3mat,***tabpop,***tabpopprev; + double ***mobaverage; + char filerespop[FILENAMELENGTH]; + + tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); + tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); + agelim=AGESUP; + calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; + + prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedatem); + + + strcpy(filerespop,"pop"); + strcat(filerespop,fileres); + if((ficrespop=fopen(filerespop,"w"))==NULL) { + printf("Problem with forecast resultfile: %s\n", filerespop); + fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); + } + printf("Computing forecasting: result on file '%s' \n", filerespop); + fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); + + if (cptcoveff==0) ncodemax[cptcoveff]=1; + + if (mobilav!=0) { + mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); + if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ + fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); + printf(" Error in movingaverage mobilav=%d\n",mobilav); + } + } + + stepsize=(int) (stepm+YEARM-1)/YEARM; + if (stepm<=12) stepsize=1; + + agelim=AGESUP; + + hstepm=1; + hstepm=hstepm/stepm; + + if (popforecast==1) { + if((ficpop=fopen(popfile,"r"))==NULL) { + printf("Problem with population file : %s\n",popfile);exit(0); + fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); + } + popage=ivector(0,AGESUP); + popeffectif=vector(0,AGESUP); + popcount=vector(0,AGESUP); + + i=1; + while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; + + imx=i; + for (i=1; i=(ageminpar-((int)calagedatem %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) (calagedatem+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)(calagedatem+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+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; + } + + if (h==(int)(calagedatem+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)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %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) (calagedatem+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)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1); + } + } + free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + } + } + } + } + + if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); + + if (popforecast==1) { + free_ivector(popage,0,AGESUP); + free_vector(popeffectif,0,AGESUP); + free_vector(popcount,0,AGESUP); + } + free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); + free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); + fclose(ficrespop); +} /***********************************************/ /**************** Main Program *****************/ /***********************************************/ -/*int main(int argc, char *argv[])*/ -int main() +int main(int argc, char *argv[]) { - - int i,j, k, n=MAXN,iter,m,size; + int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav); + int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod; double agedeb, agefin,hf; - double agemin=1.e20, agemax=-1.e20; + 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 title[MAXLINE]; - char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH]; - char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH]; - char filerest[FILENAMELENGTH]; - char fileregp[FILENAMELENGTH]; - char path[80],pathc[80],pathcd[80],pathtot[80]; + 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,jk,aa,bb, stepsize; - int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab; - + int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij; + int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; + int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */ + int mobilav=0,popforecast=0; int hstepm, nhstepm; + double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedatem; + double bage, fage, age, agelim, agebase; double ftolpl=FTOL; double **prlim; @@ -1540,88 +3338,77 @@ int main() double ***eij, ***vareij; double **varpl; /* Variances of prevalence limits by age */ double *epj, vepp; - char version[80]="Imach version 0.64, May 2000, INED-EUROREVES "; + 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"; + + + 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; + struct timeval start_time, end_time; - gettimeofday(&start_time, (struct timezone*)0); */ /* at first 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,'\\');*/ - printf("\nIMACH, Version 0.64"); - printf("\nEnter the parameter file name: "); -#define windows 1 -#ifdef windows - scanf("%s",pathtot); - getcwd(pathcd, size); - cut(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); -#endif -#ifdef unix - scanf("%s",optionfile); -#endif -/*-------- arguments in the command line --------*/ + /*-------- 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, optionfile); + 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);goto end; - } - -/*--------- index.htm --------*/ - - if((fichtm=fopen("index.htm","w"))==NULL) { - printf("Problem with index.htm \n");goto end; + printf("Problem with Output resultfile: %s\n", filereso); + fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso); + goto end; } - fprintf(fichtm,"
      • Outputs files

        \n - - Observed prevalence in each state: p%s
        \n -- Estimated parameters and the covariance matrix: %s
        - - Stationary prevalence in each state: pl%s
        - - Transition probabilities: pij%s
        - - Copy of the parameter file: o%s
        - - Life expectancies by age and initial health status: e%s
        - - Variances of life expectancies by age and initial health status: v%s
        - - Health expectancies with their variances: t%s
        - - Standard deviation of stationary prevalences: vpl%s

        ",fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres); - - fprintf(fichtm,"
      • Graphs

        "); - -for(cpt=1; cpt -
        ",strtok(optionfile, "."),strtok(optionfile, "."),cpt); - for(cpt=1; cpt<=nlstate;cpt++) - fprintf(fichtm,"- Observed and stationary prevalence (with confident -interval) in state (%d): v%s%d.gif
        -
        ",cpt,strtok(optionfile, "."),cpt,strtok(optionfile, "."),cpt); - - for(cpt=1; cpt<=nlstate;cpt++) - fprintf(fichtm,"- Health life expectancies by age and initial health state (%d): exp%s%d.gif
        -
        ",cpt,strtok(optionfile, "."),cpt,strtok(optionfile, "."),cpt); - - fprintf(fichtm,"- Total life expectancy by age and - health expectancies in states (1) and (2): e%s.gif
        -
      ",strtok(optionfile, "."),strtok(optionfile, ".")); - - -fclose(fichtm); - /* Reads comments: lines beginning with '#' */ while((c=getc(ficpar))=='#' && c!= EOF){ ungetc(c,ficpar); @@ -1631,11 +3418,24 @@ fclose(fichtm); } ungetc(c,ficpar); - fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt); - printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt); - fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt); + 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); - nvar=ncov-1; /* Suppressing age as a basic covariate */ + + covar=matrix(0,NCOVMAX,1,n); + cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/ + if (strlen(model)>1) cptcovn=nbocc(model,'+')+1; + + ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */ + nvar=ncovmodel-1; /* Suppressing age as a basic covariate */ /* Read guess parameters */ /* Reads comments: lines beginning with '#' */ @@ -1647,23 +3447,33 @@ fclose(fichtm); } ungetc(c,ficpar); - param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncov); - for(i=1; i <=nlstate; i++) + param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); + for(i=1; i <=nlstate; i++) for(j=1; j <=nlstate+ndeath-1; j++){ fscanf(ficpar,"%1d%1d",&i1,&j1); fprintf(ficparo,"%1d%1d",i1,j1); - printf("%1d%1d",i,j); - for(k=1; k<=ncov;k++){ + 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]); - printf(" %lf",param[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"); - printf("\n"); + if(mle==1) + printf("\n"); + fprintf(ficlog,"\n"); fprintf(ficparo,"\n"); } - npar= (nlstate+ndeath-1)*nlstate*ncov; + npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ + p=param[1][1]; /* Reads comments: lines beginning with '#' */ @@ -1675,14 +3485,14 @@ fclose(fichtm); } ungetc(c,ficpar); - delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncov); + 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<=ncov;k++){ + 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]); @@ -1706,138 +3516,322 @@ fclose(fichtm); matcov=matrix(1,npar,1,npar); for(i=1; i <=npar; i++){ fscanf(ficpar,"%s",&str); - printf("%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]); - printf(" %.5le",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"); - printf("\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]; - printf("\n"); - - - if(mle==1){ - /*-------- data file ----------*/ - if((ficres =fopen(fileres,"w"))==NULL) { - printf("Problem with resultfile: %s\n", fileres);goto end; + if(mle==1) + printf("\n"); + fprintf(ficlog,"\n"); + + + /*-------- Rewriting paramater file ----------*/ + strcpy(rfileres,"r"); /* "Rparameterfile */ + strcat(rfileres,optionfilefiname); /* Parameter file first name*/ + strcat(rfileres,"."); /* */ + strcat(rfileres,optionfilext); /* Other files have txt extension */ + if((ficres =fopen(rfileres,"w"))==NULL) { + printf("Problem writing new parameter file: %s\n", fileres);goto end; + fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end; + } + fprintf(ficres,"#%s\n",version); + + /*-------- data file ----------*/ + if((fic=fopen(datafile,"r"))==NULL) { + printf("Problem with datafile: %s\n", datafile);goto end; + fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end; + } + + n= lastobs; + severity = vector(1,maxwav); + outcome=imatrix(1,maxwav+1,1,n); + num=ivector(1,n); + moisnais=vector(1,n); + annais=vector(1,n); + moisdc=vector(1,n); + andc=vector(1,n); + agedc=vector(1,n); + cod=ivector(1,n); + weight=vector(1,n); + for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */ + mint=matrix(1,maxwav,1,n); + anint=matrix(1,maxwav,1,n); + s=imatrix(1,maxwav+1,1,n); + tab=ivector(1,NCOVMAX); + ncodemax=ivector(1,8); + + i=1; + while (fgets(line, MAXLINE, fic) != NULL) { + if ((i >= firstobs) && (i <=lastobs)) { + + for (j=maxwav;j>=1;j--){ + cutv(stra, strb,line,' '); s[j][i]=atoi(strb); + strcpy(line,stra); + cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra); + cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra); + } + + cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra); + cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra); + + cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra); + cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra); + + cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra); + for (j=ncovcol;j>=1;j--){ + cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra); + } + num[i]=atol(stra); + + /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){ + printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/ + + i=i+1; } - fprintf(ficres,"#%s\n",version); + } + /* printf("ii=%d", ij); + scanf("%d",i);*/ + imx=i-1; /* Number of individuals */ + + /* for (i=1; i<=imx; i++){ + if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3; + if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3; + if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3; + }*/ + /* for (i=1; i<=imx; i++){ + if (s[4][i]==9) s[4][i]=-1; + printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i]));}*/ + + + /* Calculation of the number of parameter from char model*/ + Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */ + Tprod=ivector(1,15); + Tvaraff=ivector(1,15); + Tvard=imatrix(1,15,1,2); + Tage=ivector(1,15); + + if (strlen(model) >1){ /* If there is at least 1 covariate */ + j=0, j1=0, k1=1, k2=1; + j=nbocc(model,'+'); /* j=Number of '+' */ + j1=nbocc(model,'*'); /* j1=Number of '*' */ + cptcovn=j+1; + cptcovprod=j1; /*Number of products */ - if((fic=fopen(datafile,"r"))==NULL) { - printf("Problem with datafile: %s\n", datafile);goto end; + 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; } - 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); - covar=matrix(1,NCOVMAX,1,n); - s=imatrix(1,maxwav+1,1,n); - adl=imatrix(1,maxwav+1,1,n); - tab=ivector(1,NCOVMAX); - i=1; - while (fgets(line, MAXLINE, fic) != NULL) { - if ((i >= firstobs) && (i =1;i--){ + cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ + if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */ + /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/ + /*scanf("%d",i);*/ + if (strchr(strb,'*')) { /* Model includes a product */ + cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/ + if (strcmp(strc,"age")==0) { /* Vn*age */ + cptcovprod--; + cutv(strb,stre,strd,'V'); + Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/ + cptcovage++; + Tage[cptcovage]=i; + /*printf("stre=%s ", stre);*/ + } + else if (strcmp(strd,"age")==0) { /* or age*Vn */ + cptcovprod--; + cutv(strb,stre,strc,'V'); + Tvar[i]=atoi(stre); + cptcovage++; + Tage[cptcovage]=i; + } + else { /* Age is not in the model */ + cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/ + Tvar[i]=ncovcol+k1; + cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */ + Tprod[k1]=i; + Tvard[k1][1]=atoi(strc); /* m*/ + Tvard[k1][2]=atoi(stre); /* n */ + Tvar[cptcovn+k2]=Tvard[k1][1]; + Tvar[cptcovn+k2+1]=Tvard[k1][2]; + for (k=1; k<=lastobs;k++) + covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k]; + k1++; + k2=k2+2; + } + } + else { /* no more sum */ + /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/ + /* scanf("%d",i);*/ + cutv(strd,strc,strb,'V'); + Tvar[i]=atoi(strc); + } + strcpy(modelsav,stra); + /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav); + scanf("%d",i);*/ + } /* end of loop + */ + } /* end model */ + + /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products. + If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/ + + /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]); + printf("cptcovprod=%d ", cptcovprod); + fprintf(ficlog,"cptcovprod=%d ", cptcovprod); + + scanf("%d ",i); + fclose(fic);*/ + + /* if(mle==1){*/ + if (weightopt != 1) { /* Maximisation without weights*/ + for(i=1;i<=n;i++) weight[i]=1.0; + } + /*-calculation of age at interview from date of interview and age at death -*/ + agev=matrix(1,maxwav,1,imx); - if (weightopt != 1) { /* Maximisation without weights*/ - for(i=1;i<=n;i++) weight[i]=1.0; + 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; } - /*-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++) { - 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) + } + + for (i=1; i<=imx; i++) { + agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]); + for(m=1; (m<= maxwav); m++){ + if(s[m][i] >0){ + if (s[m][i] >= nlstate+1) { + if(agedc[i]>0) + if(moisdc[i]!=99 && andc[i]!=9999) agev[m][i]=agedc[i]; - else{ - printf("Warning negative age at death: %d line:%d\n",num[i],i); - agev[m][i]=-1; - } - } - else if(s[m][i] !=9){ /* Should no more exist */ - agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]); - if(mint[m][i]==99 || anint[m][i]==9999) - agev[m][i]=1; - else if(agev[m][i] 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);*/ + /*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; + } } - /*agev[m][i]=anint[m][i]-annais[i];*/ - /* agev[m][i] = age[i]+2*m;*/ - } - else { /* =9 */ + }< + else if(s[m][i] !=9){ /* Standard case, age in fractional + years but with the precision of a + month */ + 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; - s[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 /*= 0 Unknown */ + else { /* =9 */ agev[m][i]=1; + s[m][i]=-1; + } } - + else /*= 0 Unknown */ + agev[m][i]=1; } - for (i=1; i<=imx; i++) { - for(m=1; (m<= maxwav); m++){ - if (s[m][i] > (nlstate+ndeath)) { - printf("Error: Wrong value in nlstate or ndeath\n"); - goto end; - } + + } + 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); + 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); + 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); + wav=ivector(1,imx); + dh=imatrix(1,lastpass-firstpass+1,1,imx); + bh=imatrix(1,lastpass-firstpass+1,1,imx); + mw=imatrix(1,lastpass-firstpass+1,1,imx); - /* Concatenates waves */ - concatwav(wav, dh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm); + /* Concatenates waves */ + concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm); + + /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */ + + Tcode=ivector(1,100); + nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); + ncodemax[1]=1; + if (cptcovn > 0) tricode(Tvar,nbcode,imx); + + codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of + the estimations*/ + h=0; + m=pow(2,cptcoveff); + + for(k=1;k<=cptcoveff; k++){ + for(i=1; i <=(m/pow(2,k));i++){ + for(j=1; j <= ncodemax[k]; j++){ + for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){ + h++; + if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j; + /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/ + } + } + } + } + /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); + codtab[1][2]=1;codtab[2][2]=2; */ + /* for(i=1; i <=m ;i++){ + for(k=1; k <=cptcovn; k++){ + printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); + } + printf("\n"); + } + scanf("%d",i);*/ - /* Calculates basic frequencies. Computes observed prevalence at single age - and prints on file fileres'p'. */ - freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx); + /* 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 */ @@ -1845,198 +3839,161 @@ printf("Total number of individuals= %d, 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) */ - - mlikeli(ficres,p, npar, ncov, nlstate, ftol, func); + + /* For Powell, parameters are in a vector p[] starting at p[1] + so we point p on param[1][1] so that p[1] maps on param[1][1][1] */ + p=param[1][1]; /* *(*(*(param +1)+1)+0) */ + if(mle>=1){ /* Could be 1 or 2 */ + mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func); + } - /*--------- results files --------------*/ - fprintf(ficres,"\ntitle=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt); - - jk=1; - fprintf(ficres,"# Parameters\n"); - printf("# Parameters\n"); - for(i=1,jk=1; i <=nlstate; i++){ - for(k=1; k <=(nlstate+ndeath); k++){ - if (k != i) - { - printf("%d%d ",i,k); - fprintf(ficres,"%1d%1d ",i,k); - for(j=1; j <=ncov; j++){ - printf("%f ",p[jk]); - fprintf(ficres,"%f ",p[jk]); - jk++; - } - printf("\n"); - fprintf(ficres,"\n"); - } - } - } + /*--------- 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); + - /* Computing hessian and covariance matrix */ - ftolhess=ftol; /* Usually correct */ - hesscov(matcov, p, npar, delti, ftolhess, func); - fprintf(ficres,"# Scales\n"); - printf("# Scales\n"); - for(i=1,jk=1; i <=nlstate; i++){ - for(j=1; j <=nlstate+ndeath; j++){ - if (j!=i) { - fprintf(ficres,"%1d%1d",i,j); - printf("%1d%1d",i,j); - for(k=1; k<=ncov;k++){ - printf(" %.5e",delti[jk]); - fprintf(ficres," %.5e",delti[jk]); - jk++; + 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\n"); - printf("# Covariance\n"); - for(i=1;i<=npar;i++){ - /* if (k>nlstate) k=1; - i1=(i-1)/(ncov*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); + } + } + + fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); + if(mle==1) + printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); + fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); + for(i=1,k=1;i<=npar;i++){ + /* if (k>nlstate) k=1; + i1=(i-1)/(ncovmodel*nlstate)+1; + fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]); + printf("%s%d%d",alph[k],i1,tab[i]); + */ + fprintf(ficres,"%3d",i); + if(mle==1) printf("%3d",i); - for(j=1; j<=i;j++){ - fprintf(ficres," %.5e",matcov[i][j]); + 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(ficres,"\n"); - printf("\n"); - k++; - } - - while((c=getc(ficpar))=='#' && c!= EOF){ - ungetc(c,ficpar); - fgets(line, MAXLINE, ficpar); - puts(line); - fputs(line,ficparo); + 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); - - fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage); - - if (fage <= 2) { - bage = agemin; - fage = agemax; - } - - fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n"); - fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage); -/*------------ gnuplot -------------*/ -chdir(pathcd); - if((ficgp=fopen("graph.gp","w"))==NULL) { - printf("Problem with file graph.gp");goto end; + fgets(line, MAXLINE, ficpar); + puts(line); + fputs(line,ficparo); } -#ifdef windows - fprintf(ficgp,"cd \"%s\" \n",pathc); -#endif - /* 1eme*/ + ungetc(c,ficpar); - for (cpt=1; cpt<= nlstate ; cpt ++) { -#ifdef windows - fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" u 1:%d \"\%%lf",agemin,fage,fileres,cpt*2); -#endif -#ifdef unix -fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:%d \"\%%lf",agemin,fage,fileres,cpt*2); -#endif - for (i=1; i<= nlstate ; i ++) fprintf(ficgp," \%%lf (\%%lf)"); - fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" u 1:($%d+2*$%d) \"\%%lf",fileres,2*cpt,cpt*2+1); - for (i=1; i<= nlstate ; i ++) fprintf(ficgp," \%%lf (\%%lf)"); - fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" u 1:($%d-2*$%d) \"\%%lf",fileres,2*cpt,2*cpt+1); - for (i=1; i<= nlstate ; i ++) fprintf(ficgp," \%%lf (\%%lf)"); - fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" u 1:($%d) t\"Observed prevalence \" w l 2",fileres,2+4*(cpt-1)); -#ifdef unix -fprintf(ficgp,"\nset ter gif small size 400,300"); -#endif -fprintf(ficgp,"\nset out \"v%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt); - + estepm=0; + fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); + if (estepm==0 || estepm < stepm) estepm=stepm; + if (fage <= 2) { + bage = ageminpar; + fage = agemaxpar; } - /*2 eme*/ - - fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage); - for (i=1; i<= nlstate+1 ; i ++) { -k=2*i; - fprintf(ficgp,"\"t%s\" u 1:%d \"\%%lf \%%lf (\%%lf) \%%lf (\%%lf)",fileres,k); - for (j=1; j< nlstate ; j ++) fprintf(ficgp," \%%lf (\%%lf)"); - if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,"); - else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1); - fprintf(ficgp,"\"t%s\" u 1:($%d-2*$%d) \"\%%lf \%%lf (\%%lf) \%%lf (\%%lf)",fileres,k,k+1); - for (j=1; j< nlstate ; j ++) fprintf(ficgp," \%%lf (\%%lf)"); - fprintf(ficgp,"\" t\"\" w l 0,"); -fprintf(ficgp,"\"t%s\" u 1:($%d+2*$%d) \"\%%lf \%%lf (\%%lf) \%%lf (\%%lf)",fileres,k,k+1); - for (j=1; j< nlstate ; j ++) fprintf(ficgp," \%%lf (\%%lf)"); - if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0"); -else fprintf(ficgp,"\" t\"\" w l 0,"); - } - fprintf(ficgp,"\nset out \"e%s.gif\" \nreplot\n\n",strtok(optionfile, ".")); - - /*3eme*/ -for (cpt=1; cpt<= nlstate ; cpt ++) { - k=2+nlstate*(cpt-1); - fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k,cpt); -for (i=1; i< nlstate ; i ++) { -fprintf(ficgp,",\"e%s\" u 1:%d t \"e%d%d\" w l",fileres,k+1,cpt,i+1); -} -fprintf(ficgp,"\nset out \"ex%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt); -} - -/* CV preval stat */ -for (cpt=1; cpt %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(bh,1,lastpass-firstpass+1,1,imx); + free_imatrix(mw,1,lastpass-firstpass+1,1,imx); + free_ivector(num,1,n); + free_vector(agedc,1,n); + /*free_matrix(covar,0,NCOVMAX,1,n);*/ + /*free_matrix(covar,1,NCOVMAX,1,n);*/ + fclose(ficparo); + fclose(ficres); + + + /*--------------- Prevalence limit (stable prevalence) --------------*/ strcpy(filerespl,"pl"); strcat(filerespl,fileres); if((ficrespl=fopen(filerespl,"w"))==NULL) { - printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end; + printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end; + fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end; } - printf("Computing prevalence limit: result on file '%s' \n", filerespl); - fprintf(ficrespl,"#Prevalence limit\n"); + printf("Computing stable prevalence: result on file '%s' \n", filerespl); + fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl); + fprintf(ficrespl,"#Stable prevalence \n"); fprintf(ficrespl,"#Age "); for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i); fprintf(ficrespl,"\n"); prlim=matrix(1,nlstate,1,nlstate); - 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 */ - - agebase=agemin; - agelim=agemax; + + agebase=ageminpar; + agelim=agemaxpar; ftolpl=1.e-10; - for (age=agebase; age<=agelim; age++){ - prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl); - fprintf(ficrespl,"%.0f",age ); - for(i=1; i<=nlstate;i++) - fprintf(ficrespl," %.5f", prlim[i][i]); - fprintf(ficrespl,"\n"); + i1=cptcoveff; + if (cptcovn < 1){i1=1;} + + for(cptcov=1,k=0;cptcov<=i1;cptcov++){ + for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ + k=k+1; + /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/ + fprintf(ficrespl,"\n#******"); + printf("\n#******"); + fprintf(ficlog,"\n#******"); + for(j=1;j<=cptcoveff;j++) { + fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); + printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); + fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); + } + fprintf(ficrespl,"******\n"); + printf("******\n"); + fprintf(ficlog,"******\n"); + + for (age=agebase; age<=agelim; age++){ + prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); + fprintf(ficrespl,"%.0f ",age ); + for(j=1;j<=cptcoveff;j++) + fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); + 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; + /*if (stepm<=24) stepsize=2;*/ agelim=AGESUP; hstepm=stepsize*YEARM; /* Every year of age */ hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ - for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */ - nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ - nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */ - p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); - oldm=oldms;savm=savms; - hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm); - 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,"%.0f %.0f",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"); + + /* hstepm=1; aff par mois*/ + + for(cptcov=1,k=0;cptcov<=i1;cptcov++){ + for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ + k=k+1; + fprintf(ficrespij,"\n#****** "); + for(j=1;j<=cptcoveff;j++) + fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); + fprintf(ficrespij,"******\n"); + + for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */ + nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ + nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */ + + /* nhstepm=nhstepm*YEARM; aff par mois*/ + + p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + oldm=oldms;savm=savms; + hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); + fprintf(ficrespij,"# Age"); + for(i=1; i<=nlstate;i++) + for(j=1; j<=nlstate+ndeath;j++) + fprintf(ficrespij," %1d-%1d",i,j); + fprintf(ficrespij,"\n"); + for (h=0; h<=nhstepm; h++){ + fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm ); + for(i=1; i<=nlstate;i++) + for(j=1; j<=nlstate+ndeath;j++) + fprintf(ficrespij," %.5f", p3mat[i][j][h]); + fprintf(ficrespij,"\n"); + } + free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + fprintf(ficrespij,"\n"); + } } - 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); - /*---------- Health expectancies and variances ------------*/ + + /*---------- Forecasting ------------------*/ + /*if((stepm == 1) && (strcmp(model,".")==0)){*/ + if(prevfcast==1){ + if(stepm ==1){ + prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilavproj, 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); + } + } - 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); - - vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); - oldm=oldms;savm=savms; - varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl); + + /*---------- 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 Total LEs with variances: file '%s' \n", filerest); - fprintf(ficrest,"#Total LEs with variances: e.. (std) "); - for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i); - fprintf(ficrest,"\n"); - - hf=1; - if (stepm >= YEARM) hf=stepm/YEARM; - epj=vector(1,nlstate+1); - for(age=bage; age <=fage ;age++){ - prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl); - fprintf(ficrest," %.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]*hf*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," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp)); - for(j=1;j <=nlstate;j++){ - fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age])); + 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); + + calagedatem=-1; + + prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedatem); + + if (mobilav!=0) { + mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); + if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ + fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); + printf(" Error in movingaverage mobilav=%d\n",mobilav); + } + } + + for(cptcov=1,k=0;cptcov<=i1;cptcov++){ + for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ + k=k+1; + fprintf(ficrest,"\n#****** "); + for(j=1;j<=cptcoveff;j++) + fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); + fprintf(ficrest,"******\n"); + + fprintf(ficreseij,"\n#****** "); + for(j=1;j<=cptcoveff;j++) + fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); + fprintf(ficreseij,"******\n"); + + fprintf(ficresvij,"\n#****** "); + for(j=1;j<=cptcoveff;j++) + fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); + fprintf(ficresvij,"******\n"); + + eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); + oldm=oldms;savm=savms; + evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov); + + vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); + oldm=oldms;savm=savms; + varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav); + if(popbased==1){ + varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav); + } + + + fprintf(ficrest,"#Total LEs with variances: e.. (std) "); + for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i); + fprintf(ficrest,"\n"); + + epj=vector(1,nlstate+1); + for(age=bage; age <=fage ;age++){ + prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); + if (popbased==1) { + if(mobilav ==0){ + for(i=1; i<=nlstate;i++) + prlim[i][i]=probs[(int)age][i][k]; + }else{ /* mobilav */ + for(i=1; i<=nlstate;i++) + prlim[i][i]=mobaverage[(int)age][i][k]; + } + } + + fprintf(ficrest," %4.0f",age); + for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){ + for(i=1, epj[j]=0.;i <=nlstate;i++) { + epj[j] += prlim[i][i]*eij[i][j][(int)age]; + /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/ + } + epj[nlstate+1] +=epj[j]; + } + + for(i=1, vepp=0.;i <=nlstate;i++) + for(j=1;j <=nlstate;j++) + vepp += vareij[i][j][(int)age]; + fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp)); + for(j=1;j <=nlstate;j++){ + fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age])); + } + fprintf(ficrest,"\n"); + } + free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage); + free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage); + free_vector(epj,1,nlstate+1); } - fprintf(ficrest,"\n"); } + free_vector(weight,1,n); + free_imatrix(Tvard,1,15,1,2); + free_imatrix(s,1,maxwav+1,1,n); + free_matrix(anint,1,maxwav,1,n); + free_matrix(mint,1,maxwav,1,n); + free_ivector(cod,1,n); + free_ivector(tab,1,NCOVMAX); + fclose(ficreseij); + fclose(ficresvij); fclose(ficrest); fclose(ficpar); - free_vector(epj,1,nlstate+1); + + /*------- Variance of stable prevalence------*/ - /*------- Variance limit prevalence------*/ + strcpy(fileresvpl,"vpl"); + strcat(fileresvpl,fileres); + if((ficresvpl=fopen(fileresvpl,"w"))==NULL) { + printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl); + exit(0); + } + printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl); - 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); - - - 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); - - + for(cptcov=1,k=0;cptcov<=i1;cptcov++){ + for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ + k=k+1; + fprintf(ficresvpl,"\n#****** "); + for(j=1;j<=cptcoveff;j++) + fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); + fprintf(ficresvpl,"******\n"); + + varpl=matrix(1,nlstate,(int) bage, (int) fage); + oldm=oldms;savm=savms; + varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k); + free_matrix(varpl,1,nlstate,(int) bage, (int)fage); + } + } + + fclose(ficresvpl); + + /*---------- End : free ----------------*/ free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath); free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath); free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath); free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath); + free_matrix(covar,0,NCOVMAX,1,n); free_matrix(matcov,1,npar,1,npar); free_vector(delti,1,npar); + free_matrix(agev,1,maxwav,1,imx); + free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); + if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); + free_ivector(ncodemax,1,8); + free_ivector(Tvar,1,15); + free_ivector(Tprod,1,15); + free_ivector(Tvaraff,1,15); + free_ivector(Tage,1,15); + free_ivector(Tcode,1,100); + + fprintf(fichtm,"\n"); + fclose(fichtm); + fclose(ficgp); - free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncov); - printf("End of Imach\n"); + 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: + end: #ifdef windows - chdir(pathcd); + /* chdir(pathcd);*/ #endif - system("gnuplot graph.gp"); + /*system("wgnuplot graph.plt");*/ + /*system("../gp37mgw/wgnuplot graph.plt");*/ + /*system("cd ../gp37mgw");*/ + /* system("..\\gp37mgw\\wgnuplot graph.plt");*/ + strcpy(plotcmd,GNUPLOTPROGRAM); + strcat(plotcmd," "); + strcat(plotcmd,optionfilegnuplot); + printf("Starting: %s\n",plotcmd);fflush(stdout); + system(plotcmd); -#ifdef windows + /*#ifdef windows*/ while (z[0] != 'q') { - chdir(pathcd); - printf("\nType e to edit output files, c to start again, and q for exiting: "); + /* 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') { - chdir(path); - system("index.htm"); - } + else if (z[0] == 'e') system(optionfilehtm); + else if (z[0] == 'g') system(plotcmd); else if (z[0] == 'q') exit(0); } -#endif + /*#endif */ } +