--- imach/src/imach.c 2001/05/02 17:34:41 1.4 +++ imach/src/imach.c 2002/06/26 23:25:02 1.50 @@ -1,34 +1,42 @@ - -/*********************** 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 Likelihood of the parameters involved in the model. - The simplest model is the multinomial logistic model where pij is - the probabibility to be observed in state j at the second wave conditional - to be observed in state i at the first wave. Therefore the model is: - log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex' - is a covariate. If you want to have a more complex model than "constant and - age", you should modify the program where the markup - *Covariates have to be included here again* invites you to do it. - More covariates you add, 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 1.50 2002/06/26 23:25:02 brouard Exp $ + Interpolated Markov Chain + + Short summary of the programme: + + This program computes Healthy Life Expectancies from + cross-longitudinal data. Cross-longitudinal data consist in: -1- a + first survey ("cross") where individuals from different ages are + interviewed on their health status or degree of disability (in the + case of a health survey which is our main interest) -2- at least a + second wave of interviews ("longitudinal") which measure each change + (if any) in individual health status. Health expectancies are + computed from the time spent in each health state according to a + model. More health states you consider, more time is necessary to reach the + Maximum Likelihood of the parameters involved in the model. The + simplest model is the multinomial logistic model where pij is the + probability to be observed in state j at the second wave + conditional to be observed in state i at the first wave. Therefore + the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where + 'age' is age and 'sex' is a covariate. If you want to have a more + complex model than "constant and age", you should modify the program + where the markup *Covariates have to be included here again* invites + you to do it. More covariates you add, slower the + convergence. + + The advantage of this computer programme, compared to a simple + multinomial logistic model, is clear when the delay between waves is not + identical for each individual. Also, if a individual missed an + intermediate interview, the information is lost, but taken into + account using an interpolation or extrapolation. + + hPijx is the probability to be observed in state i at age x+h + conditional to the observed state i at age x. The delay 'h' can be + split into an exact number (nh*stepm) of unobserved intermediate + states. This elementary transition (by month or quarter trimester, + semester or year) is model as a multinomial logistic. The hPx + matrix is simply the matrix product of nh*stepm elementary matrices + and the contribution of each individual to the likelihood is simply + hPijx. Also this programme outputs the covariance matrix of the parameters but also of the life expectancies. It also computes the prevalence limits. @@ -48,9 +56,13 @@ #include #define MAXLINE 256 +#define GNUPLOTPROGRAM "gnuplot" +/*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/ #define FILENAMELENGTH 80 /*#define DEBUG*/ #define windows +#define GLOCK_ERROR_NOPATH -1 /* empty path */ +#define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */ #define MAXPARM 30 /* Maximum number of parameters for the optimization */ #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */ @@ -63,34 +75,55 @@ #define YEARM 12. /* Number of months per year */ #define AGESUP 130 #define AGEBASE 40 +#ifdef windows +#define DIRSEPARATOR '\\' +#define ODIRSEPARATOR '/' +#else +#define DIRSEPARATOR '/' +#define ODIRSEPARATOR '\\' +#endif - +char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES "; +int erreur; /* Error number */ int nvar; -static int cptcov; -int cptcovn; +int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov; int npar=NPARMAX; int nlstate=2; /* Number of live states */ int ndeath=1; /* Number of dead states */ -int ncovmodel, ncov; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=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 */ +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 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* @@ -112,7 +145,7 @@ FILE *ficreseij; 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) @@ -124,19 +157,71 @@ 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=4,*cod, *ncodemax; +int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage; double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint; -double **pmmij; +double **pmmij, ***probs, ***mobaverage; +double dateintmean=0; double *weight; int **s; /* Status */ double *agedc, **covar, idx; -int **nbcode, *Tcode, *Tvar, **codtab; +int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff; double ftol=FTOL; /* Tolerance for computing Max Likelihood */ double ftolhess; /* Tolerance for computing hessian */ +/**************** split *************************/ +static int split( char *path, char *dirc, char *name, char *ext, char *finame ) +{ + char *s; /* pointer */ + int l1, l2; /* length counters */ + + l1 = strlen( path ); /* length of path */ + if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH ); + s= strrchr( path, DIRSEPARATOR ); /* find last / */ + if ( s == NULL ) { /* no directory, so use current */ + /*if(strrchr(path, ODIRSEPARATOR )==NULL) + printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/ +#if defined(__bsd__) /* get current working directory */ + extern char *getwd( ); + + if ( getwd( dirc ) == NULL ) { +#else + extern char *getcwd( ); + + if ( getcwd( dirc, FILENAME_MAX ) == NULL ) { +#endif + return( GLOCK_ERROR_GETCWD ); + } + strcpy( name, path ); /* we've got it */ + } else { /* strip direcotry from path */ + s++; /* after this, the filename */ + l2 = strlen( s ); /* length of filename */ + if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH ); + strcpy( name, s ); /* save file name */ + strncpy( dirc, path, l1 - l2 ); /* now the directory */ + dirc[l1-l2] = 0; /* add zero */ + } + l1 = strlen( dirc ); /* length of directory */ +#ifdef windows + if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; } +#else + if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; } +#endif + s = strrchr( name, '.' ); /* find last / */ + s++; + strcpy(ext,s); /* save extension */ + l1= strlen( name); + l2= strlen( s)+1; + strncpy( finame, name, l1-l2); + finame[l1-l2]= 0; + return( 0 ); /* we're done */ +} + /******************************************/ @@ -166,7 +251,10 @@ int nbocc(char *s, char occ) 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)-1; j++) { if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; @@ -175,8 +263,8 @@ void cutv(char *u,char *v, char*t, char lg=strlen(t); for(j=0; j=(p+1))(v[j-p-1] = t[j]); @@ -362,8 +450,10 @@ 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))){ @@ -488,6 +578,7 @@ 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; @@ -518,16 +609,21 @@ 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)); @@ -535,13 +631,18 @@ 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))) { @@ -550,15 +651,21 @@ 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 @@ -586,9 +693,13 @@ 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 } } @@ -613,15 +724,26 @@ 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; - if (cptcovn>0){ - for (k=1; k<=cptcovn;k++) {cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];/*printf("Tcode[ij]=%d nbcode=%d\n",Tcode[ij],nbcode[k][Tcode[ij]]);*/} - } + 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; @@ -646,7 +768,7 @@ double **prevalim(double **prlim, int nl } } -/*************** transition probabilities **********/ +/*************** transition probabilities ***************/ double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate ) { @@ -672,6 +794,8 @@ double **pmij(double **ps, double *cov, ps[i][j]=s2; } } + /*ps[3][2]=1;*/ + for(i=1; i<= nlstate; i++){ s1=0; for(j=1; j0){ - for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]]; - } + for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; + for (k=1; k<=cptcovage;k++) + cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; + for (k=1; k<=cptcovprod;k++) + cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; + + /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/ /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/ out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, @@ -780,7 +909,7 @@ double ***hpxij(double ***po, int nhstep /*************** log-likelihood *************/ double func( double *x) { - int i, ii, j, k, mi, d; + int i, ii, j, k, mi, d, kk; double l, ll[NLSTATEMAX], cov[NCOVMAX]; double **out; double sw; /* Sum of weights */ @@ -790,29 +919,31 @@ double func( double *x) /* We are differentiating ll according to initial status */ /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/ /*for(i=1;i0){ - for (k=1; k<=cptcovn;k++) cov[2+k]=covar[1+k-1][i]; - } - out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, - 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); - savm=oldm; - oldm=newm; - - + cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM; + for (kk=1; kk<=cptcovage;kk++) { + cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; + } + + out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, + 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); + savm=oldm; + oldm=newm; + + } /* end mult */ - + lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ ipmx +=1; @@ -839,11 +970,12 @@ void mlikeli(FILE *ficres,double p[], in for (i=1;i<=npar;i++) for (j=1;j<=npar;j++) xi[i][j]=(i==j ? 1.0 : 0.0); - printf("Powell\n"); + printf("Powell\n"); fprintf(ficlog,"Powell\n"); powell(p,xi,npar,ftol,&iter,&fret,func); printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p)); - fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p)); + fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p)); + fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p)); } @@ -860,28 +992,34 @@ void hesscov(double **matcov, double p[] void lubksb(double **a, int npar, int *indx, double b[]) ; void ludcmp(double **a, int npar, int *indx, double *d) ; - hess=matrix(1,npar,1,npar); printf("\nCalculation of the hessian matrix. Wait...\n"); + fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n"); for (i=1;i<=npar;i++){ printf("%d",i);fflush(stdout); + fprintf(ficlog,"%d",i);fflush(ficlog); hess[i][i]=hessii(p,ftolhess,i,delti); /*printf(" %f ",p[i]);*/ + /*printf(" %lf ",hess[i][i]);*/ } - + for (i=1;i<=npar;i++) { for (j=1;j<=npar;j++) { if (j>i) { printf(".%d%d",i,j);fflush(stdout); + fprintf(ficlog,".%d%d",i,j);fflush(ficlog); hess[i][j]=hessij(p,delti,i,j); - hess[j][i]=hess[i][j]; + 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); @@ -901,11 +1039,14 @@ 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 */ @@ -922,8 +1063,10 @@ 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"); } */ @@ -965,6 +1108,7 @@ 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 0) { - for (z1=1; z1<=cptcovn; z1++) - if (covar[Tvar[z1]][i]!= nbcode[Tvar[z1]][codtab[j1][z1]]) bool=0; - } - if (bool==1) { - for(m=firstpass; m<=lastpass-1; m++){ - if(agev[m][i]==0) agev[m][i]=agemax+1; - if(agev[m][i]==1) agev[m][i]=agemax+2; - freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; - freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i]; - } - } - } - if (cptcovn>0) { - fprintf(ficresp, "\n#Variable"); - for (z1=1; z1<=cptcovn; z1++) fprintf(ficresp, " V%d=%d",Tvar[z1],nbcode[Tvar[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(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++; + } + } + } + } + } - for(i=(int)agemin; i <= (int)agemax+3; i++){ - if(i==(int)agemax+3) - printf("Total"); - else - printf("Age %d", i); - for(jk=1; jk <=nlstate ; jk++){ - for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++) - pp[jk] += freq[jk][m][i]; - } - for(jk=1; jk <=nlstate ; jk++){ - for(m=-1, pos=0; m <=0 ; m++) - pos += freq[jk][m][i]; - if(pp[jk]>=1.e-10) - printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); - else - printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk); - } - for(jk=1; jk <=nlstate ; jk++){ - for(m=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); + 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 calagedate) +{ /* Some frequencies */ + + int i, m, jk, k1, i1, j1, bool, z1,z2,j; + double ***freq; /* Frequencies */ + double *pp; + double pos, k2; + + pp=vector(1,nlstate); + probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX); + + freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3); + j1=0; + + j=cptcoveff; + if (cptcovn<1) {j=1;ncodemax[1]=1;} + + for(k1=1; k1<=j;k1++){ + for(i1=1; i1<=ncodemax[k1];i1++){ + j1++; + + for (i=-1; i<=nlstate+ndeath; i++) + for (jk=-1; jk<=nlstate+ndeath; jk++) + for(m=agemin; m <= agemax+3; m++) + freq[i][jk][m]=0; + + for (i=1; i<=imx; i++) { + bool=1; + if (cptcovn>0) { + for (z1=1; z1<=cptcoveff; z1++) + if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) + bool=0; + } + if (bool==1) { + for(m=firstpass; m<=lastpass; m++){ + k2=anint[m][i]+(mint[m][i]/12.); + if ((k2>=dateprev1) && (k2<=dateprev2)) { + if(agev[m][i]==0) agev[m][i]=agemax+1; + if(agev[m][i]==1) agev[m][i]=agemax+2; + if (m0) + freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i]; + else + freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; + freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i]; + } + } + } + } + } + for(i=(int)agemin; i <= (int)agemax+3; i++){ + for(jk=1; jk <=nlstate ; jk++){ + for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++) + pp[jk] += freq[jk][m][i]; + } + for(jk=1; jk <=nlstate ; jk++){ + for(m=-1, pos=0; m <=0 ; m++) + pos += freq[jk][m][i]; + } + + for(jk=1; jk <=nlstate ; jk++){ + for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++) + pp[jk] += freq[jk][m][i]; + } + + for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk]; + + for(jk=1; jk <=nlstate ; jk++){ + if( i <= (int) agemax){ + if(pos>=1.e-5){ + probs[i][jk][j1]= pp[jk]/pos; + } + } + }/* end jk */ + }/* end i */ + } /* end i1 */ + } /* end k1 */ + + free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3); + free_vector(pp,1,nlstate); + } /* End of Freq */ /************* Waves Concatenation ***************/ @@ -1212,9 +1493,15 @@ void concatwav(int wav[], int **dh, int */ 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; @@ -1234,8 +1521,15 @@ 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++){ @@ -1244,14 +1538,22 @@ 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); */ + } } else{ j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12)); k=k+1; if (j >= jmax) jmax=j; else if (j <= jmin)jmin=j; + /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */ sum=sum+j; } jk= j/stepm; @@ -1266,108 +1568,305 @@ float sum=0.; } } } - 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[80],ij, k, j, i; + int Ndum[20],ij=1, k, j, i; int cptcode=0; - for (k=0; k<79; k++) Ndum[k]=0; + cptcoveff=0; + + for (k=0; k<19; k++) Ndum[k]=0; for (k=1; k<=7; k++) ncodemax[k]=0; - - for (j=1; j<=cptcovn; j++) { + + for (j=1; j<=(cptcovn+2*cptcovprod); j++) { for (i=1; i<=imx; i++) { ij=(int)(covar[Tvar[j]][i]); Ndum[ij]++; + /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/ if (ij > cptcode) cptcode=ij; } - /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/ + for (i=0; i<=cptcode; i++) { if(Ndum[i]!=0) ncodemax[j]++; } - ij=1; + + for (i=1; i<=ncodemax[j]; i++) { - for (k=0; k<=79; k++) { + for (k=0; k<=19; k++) { if (Ndum[k] != 0) { nbcode[Tvar[j]][ij]=k; + ij++; } if (ij > ncodemax[j]) break; } } - } + } - } + for (k=0; k<19; k++) Ndum[k]=0; + + for (i=1; i<=ncovmodel-2; i++) { + ij=Tvar[i]; + Ndum[ij]++; + } + + ij=1; + for (i=1; i<=10; i++) { + if((Ndum[i]!=0) && (i<=ncovcol)){ + Tvaraff[ij]=i; + ij++; + } + } + + cptcoveff=ij-1; +} /*********** Health Expectancies ****************/ -void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij) +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; + 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 inbetween and thus overestimating or underestimating according + * to the curvature of the survival function. If, for the same date, we + * estimate the model with stepm=1 month, we can keep estepm to 24 months + * to compare the new estimate of Life expectancy with the same linear + * hypothesis. A more precise result, taking into account a more precise + * curvature will be obtained if estepm is as small as stepm. */ + + /* For example we decided to compute the life expectancy with the smallest unit */ + /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. + nhstepm is the number of hstepm from age to agelim + nstepm is the number of stepm from age to agelin. + Look at hpijx to understand the reason of that which relies in memory size + and note for a fixed period like estepm months */ + /* We decided (b) to get a life expectancy respecting the most precise curvature of the + survival function given by stepm (the optimization length). Unfortunately it + means that if the survival funtion is printed only each two years of age and if + you sum them up and add 1 year (area under the trapezoids) you won't get the same + results. So we changed our mind and took the option of the best precision. + */ + hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ agelim=AGESUP; for (age=bage; age<=fage; age ++){ /* If stepm=6 months */ /* nhstepm age range expressed in number of stepm */ - 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, 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); } + 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, int ij) +void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased) { /* Variance of health expectancies */ /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/ - double **newm; + /* double **newm;*/ double **dnewm,**doldm; - int i, j, nhstepm, hstepm, h; + double **dnewmp,**doldmp; + int i, j, nhstepm, hstepm, h, nstepm ; int k, cptcode; - double *xp; - double **gp, **gm; - double ***gradg, ***trgradg; + double *xp; + double **gp, **gm; /* for var eij */ + double ***gradg, ***trgradg; /*for var eij */ + double **gradgp, **trgradgp; /* for var p point j */ + double *gpp, *gmp; /* for var p point j */ + double **varppt; /* for var p point j nlstate to nlstate+ndeath */ double ***p3mat; - double age,agelim; + double age,agelim, hf; int theta; + char digit[4]; + char digitp[16]; + + char fileresprobmorprev[FILENAMELENGTH]; + + if(popbased==1) + strcpy(digitp,"-populbased-"); + else + strcpy(digitp,"-stablbased-"); + + strcpy(fileresprobmorprev,"prmorprev"); + sprintf(digit,"%-d",ij); + /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/ + strcat(fileresprobmorprev,digit); /* Tvar to be done */ + strcat(fileresprobmorprev,digitp); /* Popbased or not */ + strcat(fileresprobmorprev,fileres); + if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) { + printf("Problem with resultfile: %s\n", fileresprobmorprev); + fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev); + } + printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); + fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); + fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n"); + fprintf(ficresprobmorprev,"# Age cov=%-d",ij); + for(j=nlstate+1; j<=(nlstate+ndeath);j++){ + fprintf(ficresprobmorprev," p.%-d SE",j); + for(i=1; i<=nlstate;i++) + fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j); + } + fprintf(ficresprobmorprev,"\n"); + if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { + printf("Problem with gnuplot file: %s\n", optionfilegnuplot); + fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot); + exit(0); + } + else{ + fprintf(ficgp,"\n# Routine varevsij"); + } + if((fichtm=fopen(optionfilehtm,"a"))==NULL) { + printf("Problem with html file: %s\n", optionfilehtm); + fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm); + exit(0); + } + else{ + fprintf(fichtm,"\n

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

    • \n"); + } + varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); - fprintf(ficresvij,"# Covariances of life expectancies\n"); + 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++) @@ -1377,73 +1876,160 @@ void varevsij(char fileres[], double *** 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 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=(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 */ xp[i] = x[i] + (i==theta ?delti[theta]:0); } hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); + + if (popbased==1) { + for(i=1; i<=nlstate;i++) + prlim[i][i]=probs[(int)age][i][ij]; + } + for(j=1; j<= nlstate; j++){ for(h=0; h<=nhstepm; h++){ for(i=1, gp[h][j]=0.;i<=nlstate;i++) gp[h][j] += prlim[i][i]*p3mat[i][j][h]; } } - + /* This for computing forces of mortality (h=1)as a weighted average */ + for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){ + for(i=1; i<= nlstate; i++) + gpp[j] += prlim[i][i]*p3mat[i][j][1]; + } + /* end force of mortality */ + for(i=1; i<=npar; i++) /* Computes gradient */ xp[i] = x[i] - (i==theta ?delti[theta]:0); hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); + + if (popbased==1) { + for(i=1; i<=nlstate;i++) + prlim[i][i]=probs[(int)age][i][ij]; + } + for(j=1; j<= nlstate; j++){ for(h=0; h<=nhstepm; h++){ for(i=1, gm[h][j]=0.;i<=nlstate;i++) gm[h][j] += prlim[i][i]*p3mat[i][j][h]; } } - for(j=1; j<= nlstate; j++) + /* This for computing force of mortality (h=1)as a weighted average */ + for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){ + for(i=1; i<= nlstate; i++) + gmp[j] += prlim[i][i]*p3mat[i][j][1]; + } + /* end force of mortality */ + + for(j=1; j<= nlstate; j++) /* vareij */ for(h=0; h<=nhstepm; h++){ gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta]; } + for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */ + gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta]; + } + } /* End theta */ - trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); + 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; } } - h=1; - if (stepm >= YEARM) h=stepm/YEARM; + + /* pptj */ + matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov); + matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp); + for(j=nlstate+1;j<=nlstate+ndeath;j++) + for(i=nlstate+1;i<=nlstate+ndeath;i++) + varppt[j][i]=doldmp[j][i]; + /* end ppptj */ + hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij); + prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij); + + if (popbased==1) { + for(i=1; i<=nlstate;i++) + prlim[i][i]=probs[(int)age][i][ij]; + } + + /* This for computing force of mortality (h=1)as a weighted average */ + for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){ + for(i=1; i<= nlstate; i++) + gmp[j] += prlim[i][i]*p3mat[i][j][1]; + } + /* end force of mortality */ + + fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij); + for(j=nlstate+1; j<=(nlstate+ndeath);j++){ + fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j])); + for(i=1; i<=nlstate;i++){ + fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]); + } + } + fprintf(ficresprobmorprev,"\n"); + fprintf(ficresvij,"%.0f ",age ); for(i=1; i<=nlstate;i++) for(j=1; j<=nlstate;j++){ - fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]); + fprintf(ficresvij," %.4f", vareij[i][j][(int)age]); } fprintf(ficresvij,"\n"); free_matrix(gp,0,nhstepm,1,nlstate); @@ -1452,10 +2038,29 @@ 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 */ - + free_vector(gpp,nlstate+1,nlstate+ndeath); + free_vector(gmp,nlstate+1,nlstate+ndeath); + free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath); + free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/ + fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65"); + /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */ + fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";"); + fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); + fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); + fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); + fprintf(fichtm,"\n
    File (multiple files are possible if covariates are present): %s\n",fileresprobmorprev,fileresprobmorprev); + fprintf(fichtm,"\n
    Probability is computed over estepm=%d months 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,npar); - free_matrix(dnewm,1,nlstate,1,nlstate); + free_matrix(doldm,1,nlstate,1,nlstate); + free_matrix(dnewm,1,nlstate,1,npar); + free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); + free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar); + free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); + fclose(ficresprobmorprev); + fclose(ficgp); + fclose(fichtm); } @@ -1474,7 +2079,7 @@ void varprevlim(char fileres[], double * double age,agelim; int theta; - fprintf(ficresvpl,"# Standard deviation of prevalences limit\n"); + fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n"); fprintf(ficresvpl,"# Age"); for(i=1; i<=nlstate;i++) fprintf(ficresvpl," %1d-%1d",i,i); @@ -1542,19 +2147,906 @@ void varprevlim(char fileres[], double * } +/************ 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; + double **dnewm,**doldm; + double *xp; + double *gp, *gm; + double **gradg, **trgradg; + double **mu; + double age,agelim, cov[NCOVMAX]; + double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */ + int theta; + char fileresprob[FILENAMELENGTH]; + char fileresprobcov[FILENAMELENGTH]; + char fileresprobcor[FILENAMELENGTH]; + + double ***varpij; + + strcpy(fileresprob,"prob"); + strcat(fileresprob,fileres); + if((ficresprob=fopen(fileresprob,"w"))==NULL) { + printf("Problem with resultfile: %s\n", fileresprob); + fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob); + } + strcpy(fileresprobcov,"probcov"); + strcat(fileresprobcov,fileres); + if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) { + printf("Problem with resultfile: %s\n", fileresprobcov); + fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov); + } + strcpy(fileresprobcor,"probcor"); + strcat(fileresprobcor,fileres); + if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) { + printf("Problem with resultfile: %s\n", fileresprobcor); + fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor); + } + printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob); + fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob); + printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov); + fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov); + printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); + fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); + + fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n"); + fprintf(ficresprob,"# Age"); + fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n"); + fprintf(ficresprobcov,"# Age"); + fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n"); + fprintf(ficresprobcov,"# Age"); + for(i=1; i<=nlstate;i++) + for(j=1; j<=(nlstate+ndeath);j++){ + fprintf(ficresprob," p%1d-%1d (SE)",i,j); + fprintf(ficresprobcov," p%1d-%1d ",i,j); + fprintf(ficresprobcor," p%1d-%1d ",i,j); + } + fprintf(ficresprob,"\n"); + fprintf(ficresprobcov,"\n"); + fprintf(ficresprobcor,"\n"); + xp=vector(1,npar); + dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); + doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath)); + mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage); + varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage); + first=1; + if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { + printf("Problem with gnuplot file: %s\n", optionfilegnuplot); + fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot); + exit(0); + } + else{ + fprintf(ficgp,"\n# Routine varprob"); + } + if((fichtm=fopen(optionfilehtm,"a"))==NULL) { + printf("Problem with html file: %s\n", optionfilehtm); + fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm); + exit(0); + } + else{ + fprintf(fichtm,"\n

  • Computing and drawing one step probabilities with their confidence intervals

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

  • Computing matrix of variance-covariance of step probabilities

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

    • Result files (first order: no variance)

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

        • "); + + m=cptcoveff; + if (cptcovn < 1) {m=1;ncodemax[1]=1;} + + jj1=0; + for(k1=1; k1<=m;k1++){ + for(i1=1; i1<=ncodemax[k1];i1++){ + jj1++; + if (cptcovn > 0) { + fprintf(fichtm,"

        ************ Results for covariates"); + for (cpt=1; cpt<=cptcoveff;cpt++) + fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]); + fprintf(fichtm," ************\n
        "); + } + /* Pij */ + fprintf(fichtm,"
        - Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png
        +",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); + /* Quasi-incidences */ + fprintf(fichtm,"
        - Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png
        +",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); + /* Stable prevalence in each health state */ + for(cpt=1; cpt- Stable prevalence in each health state : p%s%d%d.png
        +",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1); + } + for(cpt=1; cpt<=nlstate;cpt++) { + fprintf(fichtm,"\n
        - Health life expectancies by age and initial health state (%d): exp%s%d%d.png
        +",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1); + } + fprintf(fichtm,"\n
        - Total life expectancy by age and +health expectancies in states (1) and (2): e%s%d.png
        +",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); + } /* end i1 */ + }/* End k1 */ + fprintf(fichtm,"
      "); + + + fprintf(fichtm,"\n

    • Result files (second order: variances)

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

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

        • "); + + m=cptcoveff; + if (cptcovn < 1) {m=1;ncodemax[1]=1;} + + jj1=0; + for(k1=1; k1<=m;k1++){ + for(i1=1; i1<=ncodemax[k1];i1++){ + jj1++; + if (cptcovn > 0) { + fprintf(fichtm,"

        ************ Results for covariates"); + for (cpt=1; cpt<=cptcoveff;cpt++) + fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]); + fprintf(fichtm," ************\n
        "); + } + for(cpt=1; cpt<=nlstate;cpt++) { + fprintf(fichtm,"
        - Observed and stationary prevalence (with confident +interval) in state (%d): v%s%d%d.png
        +",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1); + } + } /* end i1 */ + }/* End k1 */ + fprintf(fichtm,"
      "); +fclose(fichtm); +} + +/******************* Gnuplot file **************/ +void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){ + + int m,cpt,k1,i,k,j,jk,k2,k3,ij,l; + int ng; + if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { + printf("Problem with file %s",optionfilegnuplot); + fprintf(ficlog,"Problem with file %s",optionfilegnuplot); + } + +#ifdef windows + fprintf(ficgp,"cd \"%s\" \n",pathc); +#endif +m=pow(2,cptcoveff); + + /* 1eme*/ + for (cpt=1; cpt<= nlstate ; cpt ++) { + for (k1=1; k1<= m ; k1 ++) { + +#ifdef windows + fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1); + fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1); +#endif +#ifdef unix +fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1); +fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres); +#endif + +for (i=1; i<= nlstate ; i ++) { + if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)"); + else fprintf(ficgp," \%%*lf (\%%*lf)"); +} + fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1); + for (i=1; i<= nlstate ; i ++) { + if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)"); + else fprintf(ficgp," \%%*lf (\%%*lf)"); +} + fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1); + for (i=1; i<= nlstate ; i ++) { + if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)"); + else fprintf(ficgp," \%%*lf (\%%*lf)"); +} + fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1)); +#ifdef unix +fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n"); +#endif + } + } + /*2 eme*/ + + for (k1=1; k1<= m ; k1 ++) { + fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1); + fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage); + + for (i=1; i<= nlstate+1 ; i ++) { + k=2*i; + fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1); + for (j=1; j<= nlstate+1 ; j ++) { + if (j==i) fprintf(ficgp," \%%lf (\%%lf)"); + else fprintf(ficgp," \%%*lf (\%%*lf)"); +} + if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,"); + else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1); + fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1); + for (j=1; j<= nlstate+1 ; j ++) { + if (j==i) fprintf(ficgp," \%%lf (\%%lf)"); + else fprintf(ficgp," \%%*lf (\%%*lf)"); +} + fprintf(ficgp,"\" t\"\" w l 0,"); + fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1); + for (j=1; j<= nlstate+1 ; j ++) { + if (j==i) fprintf(ficgp," \%%lf (\%%lf)"); + else fprintf(ficgp," \%%*lf (\%%*lf)"); +} + if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0"); + else fprintf(ficgp,"\" t\"\" w l 0,"); + } + } + + /*3eme*/ + + for (k1=1; k1<= m ; k1 ++) { + for (cpt=1; cpt<= nlstate ; cpt ++) { + k=2+nlstate*(2*cpt-2); + fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1); + fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt); + /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); + for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); +fprintf(ficgp,"\" t \"e%d1\" w l",cpt); +fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); + for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); +fprintf(ficgp,"\" t \"e%d1\" w l",cpt); + +*/ + for (i=1; i< nlstate ; i ++) { + fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1); + + } + } + } + + /* CV preval stat */ + for (k1=1; k1<= m ; k1 ++) { + for (cpt=1; cpt=(ageminpar-((int)calagedate %12)/12.); agedeb--){ + nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); + nhstepm = nhstepm/hstepm; + + p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + oldm=oldms;savm=savms; + hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); + + for (h=0; h<=nhstepm; h++){ + if (h==(int) (calagedate+YEARM*cpt)) { + fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm); + } + for(j=1; j<=nlstate+ndeath;j++) { + kk1=0.;kk2=0; + for(i=1; i<=nlstate;i++) { + if (mobilav==1) + kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; + else { + kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; + } + + } + if (h==(int)(calagedate+12*cpt)){ + fprintf(ficresf," %.3f", kk1); + + } + } + } + free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + } + } + } + } + + if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); + + fclose(ficresf); +} +/************** Forecasting ******************/ +populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ + + int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; + int *popage; + double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; + double *popeffectif,*popcount; + double ***p3mat,***tabpop,***tabpopprev; + char filerespop[FILENAMELENGTH]; + + tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); + tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); + agelim=AGESUP; + calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; + + prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate); + + + strcpy(filerespop,"pop"); + strcat(filerespop,fileres); + if((ficrespop=fopen(filerespop,"w"))==NULL) { + printf("Problem with forecast resultfile: %s\n", filerespop); + fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); + } + printf("Computing forecasting: result on file '%s' \n", filerespop); + fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); + + if (cptcoveff==0) ncodemax[cptcoveff]=1; + + if (mobilav==1) { + mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); + movingaverage(agedeb, fage, ageminpar, mobaverage); + } + + stepsize=(int) (stepm+YEARM-1)/YEARM; + if (stepm<=12) stepsize=1; + + agelim=AGESUP; + + hstepm=1; + hstepm=hstepm/stepm; + + if (popforecast==1) { + if((ficpop=fopen(popfile,"r"))==NULL) { + printf("Problem with population file : %s\n",popfile);exit(0); + fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); + } + popage=ivector(0,AGESUP); + popeffectif=vector(0,AGESUP); + popcount=vector(0,AGESUP); + + i=1; + while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; + + imx=i; + for (i=1; i=(ageminpar-((int)calagedate %12)/12.); agedeb--){ + nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); + nhstepm = nhstepm/hstepm; + + p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + oldm=oldms;savm=savms; + hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); + + for (h=0; h<=nhstepm; h++){ + if (h==(int) (calagedate+YEARM*cpt)) { + fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); + } + for(j=1; j<=nlstate+ndeath;j++) { + kk1=0.;kk2=0; + for(i=1; i<=nlstate;i++) { + if (mobilav==1) + kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; + else { + kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; + } + } + if (h==(int)(calagedate+12*cpt)){ + tabpop[(int)(agedeb)][j][cptcod]=kk1; + /*fprintf(ficrespop," %.3f", kk1); + if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/ + } + } + for(i=1; i<=nlstate;i++){ + kk1=0.; + for(j=1; j<=nlstate;j++){ + kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; + } + tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)]; + } + + if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++) + fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); + } + free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + } + } + + /******/ + + for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { + fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); + for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ + nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); + nhstepm = nhstepm/hstepm; + + p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + oldm=oldms;savm=savms; + hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); + for (h=0; h<=nhstepm; h++){ + if (h==(int) (calagedate+YEARM*cpt)) { + fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); + } + for(j=1; j<=nlstate+ndeath;j++) { + kk1=0.;kk2=0; + for(i=1; i<=nlstate;i++) { + kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; + } + if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1); + } + } + free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + } + } + } + } + + if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); + + if (popforecast==1) { + free_ivector(popage,0,AGESUP); + free_vector(popeffectif,0,AGESUP); + free_vector(popcount,0,AGESUP); + } + free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); + free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); + fclose(ficrespop); +} + /***********************************************/ /**************** Main Program *****************/ /***********************************************/ -/*int main(int argc, char *argv[])*/ -int main() +int main(int argc, char *argv[]) { - int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod; + 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; @@ -1563,20 +3055,17 @@ int main() double ***p3mat; 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],model[20]; + 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,**adl,*tab; + int mobilav=0,popforecast=0; int hstepm, nhstepm; + double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate; + double bage, fage, age, agelim, agebase; double ftolpl=FTOL; double **prlim; @@ -1589,56 +3078,76 @@ 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", occ; #include #include char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80]; + /* long total_usecs; struct timeval start_time, end_time; gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */ + getcwd(pathcd, size); + printf("\n%s",version); + if(argc <=1){ + printf("\nEnter the parameter file name: "); + scanf("%s",pathtot); + } + else{ + strcpy(pathtot,argv[1]); + } + /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/ + /*cygwin_split_path(pathtot,path,optionfile); + printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/ + /* cutv(path,optionfile,pathtot,'\\');*/ - printf("\nIMACH, Version 0.64a"); - printf("\nEnter the parameter file name: "); - -#ifdef windows - scanf("%s",pathtot); - cygwin_split_path(pathtot,path,optionfile); - printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile); - chdir(path); - - /*size=30; - getcwd(pathcd, size); - printf("pathcd=%s, path=%s, optionfile=%s\n",pathcd,path,optionfile); - cutv(path,optionfile,pathtot,'\\'); + split(pathtot,path,optionfile,optionfilext,optionfilefiname); + printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname); chdir(path); replace(pathc,path); - printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile); - */ -#endif -#ifdef unix - scanf("%s",optionfile); -#endif /*-------- 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; + printf("Problem with Output resultfile: %s\n", filereso); + fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso); + goto end; } /* Reads comments: lines beginning with '#' */ @@ -1650,17 +3159,21 @@ int main() } 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\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); - 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\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model); - 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\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model); - - covar=matrix(1,NCOVMAX,1,n); - if (strlen(model)<=1) cptcovn=0; - else { - j=0; - j=nbocc(model,'+'); - cptcovn=j+1; + fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); + printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); + fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); +while((c=getc(ficpar))=='#' && c!= EOF){ + ungetc(c,ficpar); + fgets(line, MAXLINE, ficpar); + puts(line); + fputs(line,ficparo); } + ungetc(c,ficpar); + + + covar=matrix(0,NCOVMAX,1,n); + cptcovn=0; + if (strlen(model)>1) cptcovn=nbocc(model,'+')+1; ncovmodel=2+cptcovn; nvar=ncovmodel-1; /* Suppressing age as a basic covariate */ @@ -1680,18 +3193,28 @@ int main() 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); + 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*ncovmodel; + npar= (nlstate+ndeath-1)*nlstate*ncovmodel; + p=param[1][1]; /* Reads comments: lines beginning with '#' */ @@ -1734,33 +3257,50 @@ int main() 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) + printf("\n"); + fprintf(ficlog,"\n"); - if(mle==1){ - /*-------- data file ----------*/ - if((ficres =fopen(fileres,"w"))==NULL) { - printf("Problem with resultfile: %s\n", fileres);goto end; + /*-------- 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; @@ -1782,7 +3322,7 @@ int main() tab=ivector(1,NCOVMAX); ncodemax=ivector(1,8); - i=1; + i=1; while (fgets(line, MAXLINE, fic) != NULL) { if ((i >= firstobs) && (i <=lastobs)) { @@ -1800,72 +3340,139 @@ int main() 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=ncov;j>=1;j--){ + for (j=ncovcol;j>=1;j--){ cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra); } num[i]=atol(stra); - - /*printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.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]), (mint[5][i]), (anint[5][i]), (s[5][i]), (mint[6][i]), (anint[6][i]), (s[6][i]));*/ + + /*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; } } - - /*scanf("%d",i);*/ + /* 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(1,8); + Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */ + Tprod=ivector(1,15); + Tvaraff=ivector(1,15); + Tvard=imatrix(1,15,1,2); + Tage=ivector(1,15); if (strlen(model) >1){ - j=0; + j=0, j1=0, k1=1, k2=1; j=nbocc(model,'+'); + j1=nbocc(model,'*'); cptcovn=j+1; + cptcovprod=j1; strcpy(modelsav,model); - if (j==0) { - cutv(stra,strb,modelsav,'V'); Tvar[1]=atoi(strb); + 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; } - else { - for(i=j; i>=1;i--){ - cutv(stra,strb,modelsav,'+'); - if (strchr(strb,'*')) { - cutv(strd,strc,strb,'*'); - cutv(strb,stre,strc,'V');Tvar[i+1]=ncov+1; - cutv(strb,strc,strd,'V'); - for (k=1; k<=lastobs;k++) - covar[ncov+1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k]; + + for(i=(j+1); i>=1;i--){ + cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ + if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */ + /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/ + /*scanf("%d",i);*/ + if (strchr(strb,'*')) { /* Model includes a product */ + cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/ + if (strcmp(strc,"age")==0) { /* Vn*age */ + cptcovprod--; + cutv(strb,stre,strd,'V'); + Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/ + cptcovage++; + Tage[cptcovage]=i; + /*printf("stre=%s ", stre);*/ } - else {cutv(strd,strc,strb,'V'); - Tvar[i+1]=atoi(strc); + 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; } - strcpy(modelsav,stra); } - cutv(strd,strc,stra,'V'); - Tvar[1]=atoi(strc); - } - } - /*printf("tvar=%d ",Tvar[1]); - scanf("%d ",i);*/ + else { /* no more sum */ + /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/ + /* scanf("%d",i);*/ + cutv(strd,strc,strb,'V'); + Tvar[i]=atoi(strc); + } + strcpy(modelsav,stra); + /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav); + scanf("%d",i);*/ + } /* end of loop + */ + } /* end model */ + + /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]); + printf("cptcovprod=%d ", cptcovprod); + fprintf(ficlog,"cptcovprod=%d ", cptcovprod); + scanf("%d ",i);*/ fclose(fic); + /* if(mle==1){*/ if (weightopt != 1) { /* Maximisation without weights*/ for(i=1;i<=n;i++) weight[i]=1.0; } /*-calculation of age at interview from date of interview and age at death -*/ agev=matrix(1,maxwav,1,imx); - + + for (i=1; i<=imx; i++) { + for(m=2; (m<= maxwav); m++) { + if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){ + anint[m][i]=9999; + s[m][i]=-1; + } + if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1; + } + } + for (i=1; i<=imx; i++) { agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]); for(m=1; (m<= maxwav); m++){ if(s[m][i] >0){ - if (s[m][i] == nlstate+1) { + if (s[m][i] >= nlstate+1) { if(agedc[i]>0) if(moisdc[i]!=99 && andc[i]!=9999) - agev[m][i]=agedc[i]; - else{ + agev[m][i]=agedc[i]; + /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/ + else { + if (andc[i]!=9999){ printf("Warning negative age at death: %d line:%d\n",num[i],i); + fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i); agev[m][i]=-1; + } } } else if(s[m][i] !=9){ /* Should no more exist */ @@ -1896,20 +3503,22 @@ int main() 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"); + printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath); + fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath); goto end; } } } printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); + fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); free_vector(severity,1,maxwav); free_imatrix(outcome,1,maxwav+1,1,n); free_vector(moisnais,1,n); free_vector(annais,1,n); - free_matrix(mint,1,maxwav,1,n); - free_matrix(anint,1,maxwav,1,n); + /* free_matrix(mint,1,maxwav,1,n); + free_matrix(anint,1,maxwav,1,n);*/ free_vector(moisdc,1,n); free_vector(andc,1,n); @@ -1922,303 +3531,183 @@ printf("Total number of individuals= %d, concatwav(wav, dh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm); -Tcode=ivector(1,100); - nbcode=imatrix(1,nvar,1,8); - ncodemax[1]=1; - if (cptcovn > 0) tricode(Tvar,nbcode,imx); - + Tcode=ivector(1,100); + nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); + ncodemax[1]=1; + if (cptcovn > 0) tricode(Tvar,nbcode,imx); + codtab=imatrix(1,100,1,10); h=0; - m=pow(2,cptcovn); + m=pow(2,cptcoveff); - for(k=1;k<=cptcovn; k++){ + 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,cptcovn+1-k)); cpt++){ + for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){ h++; - if (h>m) h=1;codtab[h][k]=j; + 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]);*/ } } } } - - /*for(i=1; i <=m ;i++){ - for(k=1; k <=cptcovn; k++){ - printf("i=%d k=%d %d ",i,k,codtab[i][k]); - } - printf("\n"); - }*/ - /*scanf("%d",i);*/ + /* 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,Tvar,nbcode, ncodemax); - - - /*scanf("%d ",i);*/ - + + pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */ - + /* For Powell, parameters are in a vector p[] starting at p[1] so we point p on param[1][1] so that p[1] maps on param[1][1][1] */ p=param[1][1]; /* *(*(*(param +1)+1)+0) */ - - mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func); + if(mle==1){ + 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\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model); - + fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model); + + jk=1; - fprintf(ficres,"# Parameters\n"); - printf("# Parameters\n"); + 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"); } } } - - /* 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<=ncovmodel;k++){ - printf(" %.5e",delti[jk]); - fprintf(ficres," %.5e",delti[jk]); - jk++; - } - printf("\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)/(ncovmodel*nlstate)+1; - fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]); - printf("%s%d%d",alph[k],i1,tab[i]);*/ - fprintf(ficres,"%3d",i); - printf("%3d",i); - for(j=1; j<=i;j++){ - fprintf(ficres," %.5e",matcov[i][j]); - printf(" %.5e",matcov[i][j]); - } - fprintf(ficres,"\n"); - printf("\n"); - k++; - } - - while((c=getc(ficpar))=='#' && c!= EOF){ - ungetc(c,ficpar); - fgets(line, MAXLINE, ficpar); - puts(line); - fputs(line,ficparo); - } - ungetc(c,ficpar); - - fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&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.plt","w"))==NULL) { - printf("Problem with file graph.plt");goto end; - } -#ifdef windows - fprintf(ficgp,"cd \"%s\" \n",pathc); -#endif -m=pow(2,cptcovn); - - /* 1eme*/ - for (cpt=1; cpt<= nlstate ; cpt ++) { - for (k1=1; k1<= m ; k1 ++) { - -#ifdef windows - fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1); -#endif -#ifdef unix -fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres); -#endif - -for (i=1; i<= nlstate ; i ++) { - if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)"); - else fprintf(ficgp," \%%*lf (\%%*lf)"); -} - fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1); - for (i=1; i<= nlstate ; i ++) { - if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)"); - else fprintf(ficgp," \%%*lf (\%%*lf)"); -} - fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1); - for (i=1; i<= nlstate ; i ++) { - if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)"); - else fprintf(ficgp," \%%*lf (\%%*lf)"); -} - fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1)); -#ifdef unix -fprintf(ficgp,"\nset ter gif small size 400,300"); -#endif -fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1); + if(mle==1){ + /* Computing hessian and covariance matrix */ + ftolhess=ftol; /* Usually correct */ + hesscov(matcov, p, npar, delti, ftolhess, func); } - } - /*2 eme*/ - - for (k1=1; k1<= m ; k1 ++) { - fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage); - - for (i=1; i<= nlstate+1 ; i ++) { - k=2*i; - fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1); - for (j=1; j<= nlstate+1 ; j ++) { - if (j==i) fprintf(ficgp," \%%lf (\%%lf)"); - else fprintf(ficgp," \%%*lf (\%%*lf)"); -} - if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,"); - else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1); - fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1); - for (j=1; j<= nlstate+1 ; j ++) { - if (j==i) fprintf(ficgp," \%%lf (\%%lf)"); - else fprintf(ficgp," \%%*lf (\%%*lf)"); -} - fprintf(ficgp,"\" t\"\" w l 0,"); - fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1); - for (j=1; j<= nlstate+1 ; j ++) { - if (j==i) fprintf(ficgp," \%%lf (\%%lf)"); - else fprintf(ficgp," \%%*lf (\%%*lf)"); -} - if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0"); - else fprintf(ficgp,"\" t\"\" w l 0,"); - } - fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1); - } - - /*3eme*/ - - for (k1=1; k1<= m ; k1 ++) { - for (cpt=1; cpt<= nlstate ; cpt ++) { - k=2+nlstate*(cpt-1); - fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt); - for (i=1; i< nlstate ; i ++) { - fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1); - } - fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1); - } + 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"); + } + } } - - /* CV preval stat */ - for (k1=1; k1<= m ; k1 ++) { - for (cpt=1; cptnlstate) k=1; + i1=(i-1)/(ncovmodel*nlstate)+1; + fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]); + printf("%s%d%d",alph[k],i1,tab[i]);*/ + fprintf(ficres,"%3d",i); + if(mle==1) + printf("%3d",i); + fprintf(ficlog,"%3d",i); + for(j=1; j<=i;j++){ + fprintf(ficres," %.5e",matcov[i][j]); + if(mle==1) + printf(" %.5e",matcov[i][j]); + fprintf(ficlog," %.5e",matcov[i][j]); + } + fprintf(ficres,"\n"); + if(mle==1) + printf("\n"); + fprintf(ficlog,"\n"); + k++; + } + + while((c=getc(ficpar))=='#' && c!= EOF){ + ungetc(c,ficpar); + fgets(line, MAXLINE, ficpar); + puts(line); + fputs(line,ficparo); + } + ungetc(c,ficpar); + estepm=0; + fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); + if (estepm==0 || estepm < stepm) estepm=stepm; + if (fage <= 2) { + bage = ageminpar; + fage = agemaxpar; } - /*________fin mle=1_________*/ + fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n"); + fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); + fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); + while((c=getc(ficpar))=='#' && c!= EOF){ + ungetc(c,ficpar); + fgets(line, MAXLINE, ficpar); + puts(line); + fputs(line,ficparo); + } + ungetc(c,ficpar); + + fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2); + fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); + fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); + + while((c=getc(ficpar))=='#' && c!= EOF){ + ungetc(c,ficpar); + fgets(line, MAXLINE, ficpar); + puts(line); + fputs(line,ficparo); + } + ungetc(c,ficpar); + + + dateprev1=anprev1+mprev1/12.+jprev1/365.; + dateprev2=anprev2+mprev2/12.+jprev2/365.; + fscanf(ficpar,"pop_based=%d\n",&popbased); + fprintf(ficparo,"pop_based=%d\n",popbased); + fprintf(ficres,"pop_based=%d\n",popbased); - /* No more information from the sample is required now */ - /* Reads comments: lines beginning with '#' */ while((c=getc(ficpar))=='#' && c!= EOF){ ungetc(c,ficpar); fgets(line, MAXLINE, ficpar); @@ -2226,65 +3715,68 @@ fprintf(ficgp,"\nset out \"pe%s%d.gif\" fputs(line,ficparo); } ungetc(c,ficpar); - - fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage); - printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage); - fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage); -/*--------- index.htm --------*/ + fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav); +fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav); +fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav); + - if((fichtm=fopen("index.htm","w"))==NULL) { - printf("Problem with index.htm \n");goto end; +while((c=getc(ficpar))=='#' && c!= EOF){ + ungetc(c,ficpar); + fgets(line, MAXLINE, ficpar); + puts(line); + fputs(line,ficparo); } + ungetc(c,ficpar); - fprintf(fichtm,"
        Imach, Version 0.63
      • 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); + fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1); + fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1); + fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1); - fprintf(fichtm,"
      • Graphs
        • \n

        "); + freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); - m=cptcovn; - if (cptcovn < 1) {m=1;ncodemax[1]=1;} +/*------------ gnuplot -------------*/ + strcpy(optionfilegnuplot,optionfilefiname); + strcat(optionfilegnuplot,".gp"); + if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) { + printf("Problem with file %s",optionfilegnuplot); + } + fclose(ficgp); + printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p); +/*--------- index.htm --------*/ + + strcpy(optionfilehtm,optionfile); + strcat(optionfilehtm,".htm"); + if((fichtm=fopen(optionfilehtm,"w"))==NULL) { + printf("Problem with %s \n",optionfilehtm), exit(0); + } + + fprintf(fichtm," %s

        \n +Title=%s
        Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s
        \n +\n +Total number of observations=%d
        \n +Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf
        \n +
        +

        • Parameter files

          \n + - Copy of the parameter file: o%s
          \n + - Log file of the run: %s
          \n + - Gnuplot file name: %s
        \n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot); + fclose(fichtm); + + printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2); + +/*------------ free_vector -------------*/ + chdir(path); + + free_ivector(wav,1,imx); + free_imatrix(dh,1,lastpass-firstpass+1,1,imx); + free_imatrix(mw,1,lastpass-firstpass+1,1,imx); + free_ivector(num,1,n); + free_vector(agedc,1,n); + /*free_matrix(covar,1,NCOVMAX,1,n);*/ + fclose(ficparo); + fclose(ficres); - j1=0; - for(k1=1; k1<=m;k1++){ - for(i1=1; i1<=ncodemax[k1];i1++){ - j1++; - if (cptcovn > 0) { - fprintf(fichtm,"
        ************ Results for covariates"); - for (cpt=1; cpt<=cptcovn;cpt++) - fprintf(fichtm," V%d=%d ",Tvar[cpt],nbcode[Tvar[cpt]][codtab[j1][cpt]]); - fprintf(fichtm," ************\n
        "); - } - fprintf(fichtm,"
        - Probabilities: pe%s%d.gif
        -",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1); - for(cpt=1; cpt- Prevalence of disability : p%s%d%d.gif
        -",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1); - } - for(cpt=1; cpt<=nlstate;cpt++) { - fprintf(fichtm,"
        - Observed and stationary prevalence (with confident -interval) in state (%d): v%s%d%d.gif
        -",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1); - } - for(cpt=1; cpt<=nlstate;cpt++) { - fprintf(fichtm,"\n
        - Health life expectancies by age and initial health state (%d): exp%s%d%d.gif
        -",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1); - } - fprintf(fichtm,"\n
        - Total life expectancy by age and -health expectancies in states (1) and (2): e%s%d.gif
        -",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1); -fprintf(fichtm,"\n"); - } - } -fclose(fichtm); /*--------------- Prevalence limit --------------*/ @@ -2292,8 +3784,10 @@ fclose(fichtm); strcat(filerespl,fileres); if((ficrespl=fopen(filerespl,"w"))==NULL) { printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end; + fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end; } printf("Computing prevalence limit: result on file '%s' \n", filerespl); + fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl); fprintf(ficrespl,"#Prevalence limit\n"); fprintf(ficrespl,"#Age "); for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i); @@ -2306,20 +3800,27 @@ fclose(fichtm); savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */ k=0; - agebase=agemin; - agelim=agemax; + agebase=ageminpar; + agelim=agemaxpar; ftolpl=1.e-10; - i1=cptcovn; + i1=cptcoveff; if (cptcovn < 1){i1=1;} for(cptcov=1;cptcov<=i1;cptcov++){ for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ k=k+1; /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/ - fprintf(ficrespl,"\n#****** "); - for(j=1;j<=cptcovn;j++) - fprintf(ficrespl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]); + 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); @@ -2331,33 +3832,41 @@ fclose(fichtm); } } 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 */ - + + /* hstepm=1; aff par mois*/ + k=0; for(cptcov=1;cptcov<=i1;cptcov++){ for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ k=k+1; fprintf(ficrespij,"\n#****** "); - for(j=1;j<=cptcovn;j++) - fprintf(ficrespij,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]); + 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); @@ -2366,109 +3875,143 @@ fclose(fichtm); for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespij," %1d-%1d",i,j); fprintf(ficrespij,"\n"); - for (h=0; h<=nhstepm; h++){ - fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm ); + for (h=0; h<=nhstepm; h++){ + fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm ); for(i=1; i<=nlstate;i++) for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespij," %.5f", p3mat[i][j][h]); fprintf(ficrespij,"\n"); - } + } free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); fprintf(ficrespij,"\n"); } } } + varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax); + fclose(ficrespij); + + /*---------- Forecasting ------------------*/ + if((stepm == 1) && (strcmp(model,".")==0)){ + prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1); + if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1); + } + else{ + erreur=108; + printf("Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); + fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); + } + + /*---------- Health expectancies and variances ------------*/ strcpy(filerest,"t"); strcat(filerest,fileres); if((ficrest=fopen(filerest,"w"))==NULL) { printf("Problem with total LE resultfile: %s\n", filerest);goto end; + fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end; } printf("Computing Total LEs with variances: file '%s' \n", filerest); + fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); strcpy(filerese,"e"); strcat(filerese,fileres); if((ficreseij=fopen(filerese,"w"))==NULL) { printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0); + fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0); } printf("Computing Health Expectancies: result on file '%s' \n", filerese); + fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese); - strcpy(fileresv,"v"); + strcpy(fileresv,"v"); strcat(fileresv,fileres); if((ficresvij=fopen(fileresv,"w"))==NULL) { printf("Problem with variance resultfile: %s\n", fileresv);exit(0); + fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0); } printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); + fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); + calagedate=-1; + prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate); k=0; for(cptcov=1;cptcov<=i1;cptcov++){ for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ - k=k+1; + k=k+1; fprintf(ficrest,"\n#****** "); - for(j=1;j<=cptcovn;j++) - fprintf(ficrest,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]); + 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<=cptcovn;j++) - fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]); + 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<=cptcovn;j++) - fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]); + 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); + 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(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k); - + varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0); + if(popbased==1){ + varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased); + } + + fprintf(ficrest,"#Total LEs with variances: e.. (std) "); for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i); fprintf(ficrest,"\n"); - - 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,k); - fprintf(ficrest," %.0f",age); + if (popbased==1) { + for(i=1; i<=nlstate;i++) + prlim[i][i]=probs[(int)age][i][k]; + } + + fprintf(ficrest," %4.0f",age); for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){ for(i=1, epj[j]=0.;i <=nlstate;i++) { - epj[j] += prlim[i][i]*hf*eij[i][j][(int)age]; + 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," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp)); + fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp)); for(j=1;j <=nlstate;j++){ - fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age])); + fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age])); } fprintf(ficrest,"\n"); } } } - - fclose(ficreseij); - fclose(ficresvij); +free_matrix(mint,1,maxwav,1,n); + free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n); + free_vector(weight,1,n); + fclose(ficreseij); + fclose(ficresvij); fclose(ficrest); fclose(ficpar); free_vector(epj,1,nlstate+1); - /*scanf("%d ",i); */ - + /*------- Variance limit prevalence------*/ -strcpy(fileresvpl,"vpl"); + strcpy(fileresvpl,"vpl"); strcat(fileresvpl,fileres); if((ficresvpl=fopen(fileresvpl,"w"))==NULL) { printf("Problem with variance prev lim resultfile: %s\n", fileresvpl); @@ -2476,19 +4019,19 @@ strcpy(fileresvpl,"vpl"); } printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl); - k=0; - for(cptcov=1;cptcov<=i1;cptcov++){ - for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ - k=k+1; - fprintf(ficresvpl,"\n#****** "); - for(j=1;j<=cptcovn;j++) - fprintf(ficresvpl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]); - fprintf(ficresvpl,"******\n"); - - varpl=matrix(1,nlstate,(int) bage, (int) fage); - oldm=oldms;savm=savms; + k=0; + for(cptcov=1;cptcov<=i1;cptcov++){ + for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ + k=k+1; + fprintf(ficresvpl,"\n#****** "); + for(j=1;j<=cptcoveff;j++) + fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); + fprintf(ficresvpl,"******\n"); + + varpl=matrix(1,nlstate,(int) bage, (int) fage); + oldm=oldms;savm=savms; varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k); - } + } } fclose(ficresvpl); @@ -2504,35 +4047,54 @@ strcpy(fileresvpl,"vpl"); free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath); free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath); free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath); - + free_matrix(matcov,1,npar,1,npar); free_vector(delti,1,npar); - + free_matrix(agev,1,maxwav,1,imx); free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); - printf("End of Imach\n"); + fprintf(fichtm,"\n"); + fclose(fichtm); + fclose(ficgp); + + + if(erreur >0){ + printf("End of Imach with error or warning %d\n",erreur); + fprintf(ficlog,"End of Imach with error or warning %d\n",erreur); + }else{ + printf("End of Imach\n"); + fprintf(ficlog,"End of Imach\n"); + } + printf("See log file on %s\n",filelog); + fclose(ficlog); /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */ /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/ /*printf("Total time was %d uSec.\n", total_usecs);*/ /*------ End -----------*/ + end: #ifdef windows - chdir(pathcd); + /* chdir(pathcd);*/ #endif - system("wgnuplot graph.plt"); + /*system("wgnuplot graph.plt");*/ + /*system("../gp37mgw/wgnuplot graph.plt");*/ + /*system("cd ../gp37mgw");*/ + /* system("..\\gp37mgw\\wgnuplot graph.plt");*/ + strcpy(plotcmd,GNUPLOTPROGRAM); + strcat(plotcmd," "); + strcat(plotcmd,optionfilegnuplot); + system(plotcmd); #ifdef windows while (z[0] != 'q') { - chdir(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