--- imach/src/imach.c 2003/06/12 10:43:20 1.41.2.1 +++ imach/src/imach.c 2002/07/19 18:49:30 1.52 @@ -1,4 +1,4 @@ -/* $Id: imach.c,v 1.41.2.1 2003/06/12 10:43:20 brouard Exp $ +/* $Id: imach.c,v 1.52 2002/07/19 18:49:30 brouard Exp $ Interpolated Markov Chain Short summary of the programme: @@ -56,12 +56,11 @@ #include #define MAXLINE 256 -#define GNUPLOTPROGRAM "wgnuplot" +#define GNUPLOTPROGRAM "gnuplot" /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/ #define FILENAMELENGTH 80 /*#define DEBUG*/ - -/*#define windows*/ +#define windows #define GLOCK_ERROR_NOPATH -1 /* empty path */ #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */ @@ -76,11 +75,18 @@ #define YEARM 12. /* Number of months per year */ #define AGESUP 130 #define AGEBASE 40 +#ifdef windows +#define DIRSEPARATOR '\\' +#define ODIRSEPARATOR '/' +#else +#define DIRSEPARATOR '/' +#define ODIRSEPARATOR '\\' +#endif - +char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES "; int erreur; /* Error number */ int nvar; -int cptcovn, cptcovage=0, cptcoveff=0,cptcov; +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 */ @@ -97,13 +103,27 @@ double jmean; /* Mean space between 2 wa double **oldm, **newm, **savm; /* Working pointers to matrices */ double **oldms, **newms, **savms; /* Fixed working pointers to matrices */ FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop; -FILE *ficgp,*ficresprob,*ficpop; +FILE *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* @@ -162,12 +182,10 @@ static int split( char *path, char *dirc l1 = strlen( path ); /* length of path */ if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH ); -#ifdef windows - s = strrchr( path, '\\' ); /* find last / */ -#else - s = strrchr( path, '/' ); /* find last / */ -#endif + 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( ); @@ -233,6 +251,9 @@ int nbocc(char *s, char occ) void cutv(char *u,char *v, char*t, char occ) { + /* cuts string t into u and v where u is ended by char occ excluding it + and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2) + gives u="abcedf" and v="ghi2j" */ int i,lg,j,p=0; i=0; for(j=0; j<=strlen(t)-1; j++) { @@ -429,8 +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))){ @@ -555,6 +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; @@ -585,16 +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)); @@ -602,13 +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))) { @@ -617,15 +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 @@ -653,9 +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 } } @@ -926,10 +970,11 @@ 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(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)); } @@ -950,8 +995,10 @@ void hesscov(double **matcov, double p[] 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]);*/ @@ -961,6 +1008,7 @@ void hesscov(double **matcov, double p[] for (j=1;j<=npar;j++) { if (j>i) { printf(".%d%d",i,j);fflush(stdout); + fprintf(ficlog,".%d%d",i,j);fflush(ficlog); hess[i][j]=hessij(p,delti,i,j); hess[j][i]=hess[i][j]; /*printf(" %lf ",hess[i][j]);*/ @@ -968,8 +1016,10 @@ void hesscov(double **matcov, double p[] } } 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); @@ -989,11 +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 */ @@ -1010,8 +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"); } */ @@ -1053,6 +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 =1.e-10) + if(pp[jk]>=1.e-10){ + if(first==1){ 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); + } + 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++){ @@ -1280,10 +1352,15 @@ void freqsummary(char fileres[], int ag 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(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); @@ -1297,10 +1374,16 @@ void freqsummary(char fileres[], int ag 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(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"); - printf("\n"); + if(first==1) + printf("Others in log...\n"); + fprintf(ficlog,"\n"); } } } @@ -1331,10 +1414,10 @@ void prevalence(int agemin, float agemax j=cptcoveff; if (cptcovn<1) {j=1;ncodemax[1]=1;} - for(k1=1; k1<=j;k1++){ + 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++) @@ -1353,43 +1436,44 @@ void prevalence(int agemin, float agemax 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]; + 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++) + 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; - } - } - } - + 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); @@ -1411,9 +1495,10 @@ void concatwav(int wav[], int **dh, int int i, mi, m; /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1; double sum=0., jmean=0.;*/ - + int first; int j, k=0,jk, ju, jl; double sum=0.; + first=0; jmin=1e+5; jmax=-1; jmean=0.; @@ -1436,8 +1521,15 @@ void concatwav(int wav[], int **dh, int } 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++){ @@ -1478,7 +1570,9 @@ void concatwav(int wav[], int **dh, int } 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) { @@ -1518,9 +1612,9 @@ void tricode(int *Tvar, int **nbcode, in for (k=0; k<19; k++) Ndum[k]=0; for (i=1; i<=ncovmodel-2; i++) { - ij=Tvar[i]; - Ndum[ij]++; - } + ij=Tvar[i]; + Ndum[ij]++; + } ij=1; for (i=1; i<=10; i++) { @@ -1530,7 +1624,7 @@ void tricode(int *Tvar, int **nbcode, in } } - cptcoveff=ij-1; + cptcoveff=ij-1; } /*********** Health Expectancies ****************/ @@ -1640,14 +1734,10 @@ void evsij(char fileres[], double ***eij } } } - - - 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 */ @@ -1657,14 +1747,16 @@ void evsij(char fileres[], double ***eij 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]; - + 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.; - for(h=0;h<=nhstepm-1;h++){ + 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]); @@ -1673,8 +1765,6 @@ void evsij(char fileres[], double ***eij varhe[i][j][(int)age] += doldm[i][j]*hf*hf; } } - - /* Computing expectancies */ for(i=1; i<=nlstate;i++) for(j=1; j<=nlstate;j++) @@ -1700,6 +1790,9 @@ void evsij(char fileres[], double ***eij 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); @@ -1707,22 +1800,73 @@ void evsij(char fileres[], double ***eij } /************ 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, int estepm) +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; + double **dnewmp,**doldmp; int i, j, nhstepm, hstepm, h, nstepm ; int k, cptcode; double *xp; - double **gp, **gm; - double ***gradg, ***trgradg; + double **gp, **gm; /* for var eij */ + double ***gradg, ***trgradg; /*for var eij */ + double **gradgp, **trgradgp; /* for var p point j */ + double *gpp, *gmp; /* for var p point j */ + double **varppt; /* for var p point j nlstate to nlstate+ndeath */ double ***p3mat; double age,agelim, hf; int theta; + char digit[4]; + char digitp[16]; + + char fileresprobmorprev[FILENAMELENGTH]; + + if(popbased==1) + strcpy(digitp,"-populbased-"); + else + strcpy(digitp,"-stablbased-"); + + strcpy(fileresprobmorprev,"prmorprev"); + sprintf(digit,"%-d",ij); + /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/ + strcat(fileresprobmorprev,digit); /* Tvar to be done */ + strcat(fileresprobmorprev,digitp); /* Popbased or not */ + strcat(fileresprobmorprev,fileres); + if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) { + printf("Problem with resultfile: %s\n", fileresprobmorprev); + fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev); + } + printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); + fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); + fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n"); + fprintf(ficresprobmorprev,"# Age cov=%-d",ij); + for(j=nlstate+1; j<=(nlstate+ndeath);j++){ + fprintf(ficresprobmorprev," p.%-d SE",j); + for(i=1; i<=nlstate;i++) + fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j); + } + fprintf(ficresprobmorprev,"\n"); + if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { + printf("Problem with gnuplot file: %s\n", optionfilegnuplot); + fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot); + exit(0); + } + else{ + fprintf(ficgp,"\n# Routine varevsij"); + } + if((fichtm=fopen(optionfilehtm,"a"))==NULL) { + printf("Problem with html file: %s\n", optionfilehtm); + fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm); + exit(0); + } + else{ + fprintf(fichtm,"\n

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

    • \n"); + } + varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); - fprintf(ficresvij,"# 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++) @@ -1732,6 +1876,13 @@ void varevsij(char fileres[], double *** xp=vector(1,npar); dnewm=matrix(1,nlstate,1,npar); doldm=matrix(1,nlstate,1,nlstate); + dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar); + doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); + + gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath); + gpp=vector(nlstate+1,nlstate+ndeath); + gmp=vector(nlstate+1,nlstate+ndeath); + trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/ if(estepm < stepm){ printf ("Problem %d lower than %d\n",estepm, stepm); @@ -1759,6 +1910,7 @@ void varevsij(char fileres[], double *** 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); @@ -1777,7 +1929,13 @@ void varevsij(char fileres[], double *** 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); @@ -1794,20 +1952,34 @@ void varevsij(char fileres[], double *** gm[h][j] += prlim[i][i]*p3mat[i][j][h]; } } + /* This for computing force of mortality (h=1)as a weighted average */ + for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){ + for(i=1; i<= nlstate; i++) + gmp[j] += prlim[i][i]*p3mat[i][j][1]; + } + /* end force of mortality */ - for(j=1; j<= nlstate; j++) + 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++) @@ -1823,6 +1995,37 @@ void varevsij(char fileres[], double *** } } + /* 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++){ @@ -1835,10 +2038,31 @@ 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.

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

    \n", stepm,YEARM,digitp,digit); +*/ + fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit); + free_vector(xp,1,npar); - free_matrix(doldm,1,nlstate,1,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); } @@ -1857,7 +2081,7 @@ 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); @@ -1926,67 +2150,142 @@ void varprevlim(char fileres[], double * } /************ Variance of one-step probabilities ******************/ -void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax) +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, i1, k1, j1, z1; - int k=0, cptcode; + int i, j=0, i1, k1, l1, t, tj; + int k2, l2, j1, z1; + int k=0,l, cptcode; + int first=1, first1; + double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp; double **dnewm,**doldm; double *xp; double *gp, *gm; double **gradg, **trgradg; + double **mu; double age,agelim, cov[NCOVMAX]; + double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */ int theta; char fileresprob[FILENAMELENGTH]; + char fileresprobcov[FILENAMELENGTH]; + char fileresprobcor[FILENAMELENGTH]; + + double ***varpij; strcpy(fileresprob,"prob"); strcat(fileresprob,fileres); if((ficresprob=fopen(fileresprob,"w"))==NULL) { printf("Problem with resultfile: %s\n", fileresprob); + fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob); + } + strcpy(fileresprobcov,"probcov"); + strcat(fileresprobcov,fileres); + if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) { + printf("Problem with resultfile: %s\n", fileresprobcov); + fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov); + } + strcpy(fileresprobcor,"probcor"); + strcat(fileresprobcor,fileres); + if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) { + printf("Problem with resultfile: %s\n", fileresprobcor); + fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor); } printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob); + fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob); + printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov); + fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov); + printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); + fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); -fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n"); + fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n"); fprintf(ficresprob,"# Age"); - for(i=1; i<=nlstate;i++) - for(j=1; j<=(nlstate+ndeath);j++) - fprintf(ficresprob," p%1d-%1d (SE)",i,j); + 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"); - xp=vector(1,npar); - dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); - doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath)); - + } + + cov[1]=1; - j=cptcoveff; - if (cptcovn<1) {j=1;ncodemax[1]=1;} + tj=cptcoveff; + if (cptcovn<1) {tj=1;ncodemax[1]=1;} j1=0; - for(k1=1; k1<=1;k1++){ - for(i1=1; i1<=ncodemax[k1];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#"); - } - + 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,1,9); - trgradg=matrix(1,9,1,npar); - gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath)); - gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath)); + 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++) @@ -1995,7 +2294,7 @@ fprintf(ficresprob,"#One-step probabilit pmij(pmmij,cov,ncovmodel,xp,nlstate); k=0; - for(i=1; i<= (nlstate+ndeath); i++){ + for(i=1; i<= (nlstate); i++){ for(j=1; j<=(nlstate+ndeath);j++){ k=k+1; gp[k]=pmmij[i][j]; @@ -2007,92 +2306,231 @@ fprintf(ficresprob,"#One-step probabilit pmij(pmmij,cov,ncovmodel,xp,nlstate); k=0; - for(i=1; i<=(nlstate+ndeath); i++){ + 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+ndeath)*(nlstate+ndeath); i++) + for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta]; } - for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++) + for(j=1; j<=(nlstate)*(nlstate+ndeath);j++) for(theta=1; theta <=npar; theta++) trgradg[j][theta]=gradg[theta][j]; - matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov); - matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg); + 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+ndeath); i++){ + for(i=1; i<=(nlstate); i++){ for(j=1; j<=(nlstate+ndeath);j++){ k=k+1; - gm[k]=pmmij[i][j]; + mu[k][(int) age]=pmmij[i][j]; } } - - /*printf("\n%d ",(int)age); - for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){ + 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+ndeath)*(nlstate+ndeath-1);i++) - fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i])); - - } - } + for (i=1; i<=(nlstate)*(nlstate+ndeath);i++) + fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age])); + for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){ + fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]); + fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]); + } + i=0; + for (k=1; k<=(nlstate);k++){ + for (l=1; l<=(nlstate+ndeath);l++){ + i=i++; + fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l); + fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l); + for (j=1; j<=i;j++){ + fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]); + fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age])); + } + } + }/* end of loop for state */ + } /* end of loop for age */ + + /* Confidence intervalle of pij */ + /* + fprintf(ficgp,"\nset noparametric;unset label"); + fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\""); + fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65"); + fprintf(fichtm,"\n
    Probability with confidence intervals expressed in year-1 :pijgr%s.png, ",optionfilefiname,optionfilefiname); + fprintf(fichtm,"\n
    ",optionfilefiname); + fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname); + fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob); + */ + + /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/ + first1=1; + for (k2=1; k2<=(nlstate);k2++){ + for (l2=1; l2<=(nlstate+ndeath);l2++){ + if(l2==k2) continue; + j=(k2-1)*(nlstate+ndeath)+l2; + for (k1=1; k1<=(nlstate);k1++){ + for (l1=1; l1<=(nlstate+ndeath);l1++){ + if(l1==k1) continue; + i=(k1-1)*(nlstate+ndeath)+l1; + if(i<=j) continue; + for (age=bage; age<=fage; age ++){ + if ((int)age %5==0){ + v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM; + v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM; + cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM; + mu1=mu[i][(int) age]/stepm*YEARM ; + mu2=mu[j][(int) age]/stepm*YEARM; + c12=cv12/sqrt(v1*v2); + /* Computing eigen value of matrix of covariance */ + lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; + lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; + /* Eigen vectors */ + v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12)); + /*v21=sqrt(1.-v11*v11); *//* error */ + v21=(lc1-v1)/cv12*v11; + v12=-v21; + v22=v11; + tnalp=v21/v11; + if(first1==1){ + first1=0; + printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp); + } + fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp); + /*printf(fignu*/ + /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */ + /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */ + if(first==1){ + first=0; + fprintf(ficgp,"\nset parametric;unset label"); + fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2); + fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65"); + fprintf(fichtm,"\n
    Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year-1 :varpijgr%s%d%1d%1d-%1d%1d.png, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2); + fprintf(fichtm,"\n
    ",optionfilefiname, j1,k1,l1,k2,l2); + fprintf(fichtm,"\n
    Correlation at age %d (%.3f),",(int) age, c12); + fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2); + fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2); + fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2); + fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\ + mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\ + mu2,std,v21,sqrt(lc1),v22,sqrt(lc2)); + }else{ + first=0; + fprintf(fichtm," %d (%.3f),",(int) age, c12); + fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2); + fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2); + fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\ + mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\ + mu2,std,v21,sqrt(lc1),v22,sqrt(lc2)); + }/* if first */ + } /* age mod 5 */ + } /* end loop age */ + fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2); + first=1; + } /*l12 */ + } /* k12 */ + } /*l1 */ + }/* k1 */ + } /* loop covariates */ + free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage); free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath)); free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath)); + free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage); free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); } free_vector(xp,1,npar); fclose(ficresprob); - + fclose(ficresprobcov); + fclose(ficresprobcor); + fclose(ficgp); + fclose(fichtm); } + /******************* Printing html file ***********/ void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \ - int lastpass, int stepm, int weightopt, char model[],\ - int imx,int jmin, int jmax, double jmeanint,char optionfile[], \ - char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\ - char version[], int popforecast, int estepm ){ + 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; - FILE *fichtm; /*char optionfilehtm[FILENAMELENGTH];*/ - - strcpy(optionfilehtm,optionfile); - strcat(optionfilehtm,".htm"); - if((fichtm=fopen(optionfilehtm,"w"))==NULL) { + 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," %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 -
    -
    • Outputs files
      \n - - Copy of the parameter file: o%s
      \n - - Gnuplot file name: %s
      \n - - Observed prevalence in each state: p%s
      \n - - Stationary prevalence in each state: pl%s
      \n - - Transition probabilities: pij%s
      \n - - Life expectancies by age and initial health status (estepm=%2d months): e%s
      \n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,estepm,fileres,fileres); - - fprintf(fichtm,"\n - - Parameter file with estimated parameters and the covariance matrix: %s
      \n - - Variance of one-step probabilities: prob%s
      \n - - Variances of life expectancies by age and initial health status (estepm=%d months): v%s
      \n - - Health expectancies with their variances: t%s
      \n - - Standard deviation of stationary prevalences: vpl%s
      \n",rfileres,rfileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres); + 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 @@ -2100,7 +2538,7 @@ Interval (in months) between two waves:
        ",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

        • "); +fprintf(fichtm,"

        • Graphs

          • "); m=cptcoveff; if (cptcovn < 1) {m=1;ncodemax[1]=1;} @@ -2108,46 +2546,32 @@ fprintf(fichtm,"

        • Graphs

          • "); 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
          "); - } - fprintf(fichtm,"
          - Probabilities: pe%s%d.gif
          -",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); - for(cpt=1; cpt- Prevalence of disability : p%s%d%d.gif
          -",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1); - } - for(cpt=1; cpt<=nlstate;cpt++) { - fprintf(fichtm,"
          - Observed and stationary prevalence (with confident -interval) in state (%d): v%s%d%d.gif
          -",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1); + 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,"\n
          - Health life expectancies by age and initial health state (%d): exp%s%d%d.gif
          -",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1); + 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); } - fprintf(fichtm,"\n
          - Total life expectancy by age and -health expectancies in states (1) and (2): e%s%d.gif
          -",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); -fprintf(fichtm,"\n"); - } - } + } /* end i1 */ + }/* End k1 */ + fprintf(fichtm,"
        "); fclose(fichtm); } /******************* Gnuplot file **************/ -void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){ +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; - - strcpy(optionfilegnuplot,optionfilefiname); - strcat(optionfilegnuplot,".gp.txt"); - if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) { + int ng; + if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { printf("Problem with file %s",optionfilegnuplot); + fprintf(ficlog,"Problem with file %s",optionfilegnuplot); } #ifdef windows @@ -2159,7 +2583,14 @@ m=pow(2,cptcoveff); for (cpt=1; cpt<= nlstate ; cpt ++) { for (k1=1; k1<= m ; k1 ++) { - 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",ageminpar,fage,fileres,k1-1,k1-1); +#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)"); @@ -2176,14 +2607,16 @@ for (i=1; i<= nlstate ; i ++) { else fprintf(ficgp," \%%*lf (\%%*lf)"); } fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1)); - -fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1); +#ifdef unix +fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n"); +#endif } } /*2 eme*/ for (k1=1; k1<= m ; k1 ++) { - fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage); + fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1); + fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage); for (i=1; i<= nlstate+1 ; i ++) { k=2*i; @@ -2208,7 +2641,6 @@ fprintf(ficgp,"\nset out \"v%s%d%d.gif\" if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0"); else fprintf(ficgp,"\" t\"\" w l 0,"); } - fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1); } /*3eme*/ @@ -2216,7 +2648,8 @@ fprintf(ficgp,"\nset out \"v%s%d%d.gif\" for (k1=1; k1<= m ; k1 ++) { for (cpt=1; cpt<= nlstate ; cpt ++) { k=2+nlstate*(2*cpt-2); - fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt); + fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1); + fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt); /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%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); @@ -2229,15 +2662,15 @@ fprintf(ficgp,"\" t \"e%d1\" w l",cpt); 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); } - fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1); - } } + } /* CV preval stat */ for (k1=1; k1<= m ; k1 ++) { for (cpt=1; cpt=1;i--){ - cutv(stra,strb,modelsav,'+'); - if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); + 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,'*')) { - cutv(strd,strc,strb,'*'); - if (strcmp(strc,"age")==0) { + 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); + Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/ cptcovage++; Tage[cptcovage]=i; /*printf("stre=%s ", stre);*/ } - else if (strcmp(strd,"age")==0) { + else if (strcmp(strd,"age")==0) { /* or age*Vn */ cptcovprod--; cutv(strb,stre,strc,'V'); Tvar[i]=atoi(stre); cptcovage++; Tage[cptcovage]=i; } - else { - cutv(strb,stre,strc,'V'); + 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'); + cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */ Tprod[k1]=i; - Tvard[k1][1]=atoi(strc); - Tvard[k1][2]=atoi(stre); + 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++) @@ -2947,7 +3421,7 @@ while((c=getc(ficpar))=='#' && c!= EOF){ k2=k2+2; } } - else { + else { /* no more sum */ /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/ /* scanf("%d",i);*/ cutv(strd,strc,strb,'V'); @@ -2956,11 +3430,12 @@ while((c=getc(ficpar))=='#' && c!= EOF){ 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); @@ -2993,6 +3468,7 @@ while((c=getc(ficpar))=='#' && c!= EOF){ 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; } } @@ -3025,13 +3501,15 @@ while((c=getc(ficpar))=='#' && c!= EOF){ 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); @@ -3107,102 +3585,118 @@ printf("Total number of individuals= %d, jk=1; fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); + fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); for(i=1,jk=1; i <=nlstate; i++){ for(k=1; k <=(nlstate+ndeath); k++){ if (k != i) { printf("%d%d ",i,k); + fprintf(ficlog,"%d%d ",i,k); fprintf(ficres,"%1d%1d ",i,k); for(j=1; j <=ncovmodel; j++){ printf("%f ",p[jk]); + fprintf(ficlog,"%f ",p[jk]); fprintf(ficres,"%f ",p[jk]); jk++; } printf("\n"); + fprintf(ficlog,"\n"); fprintf(ficres,"\n"); } } } - if(mle==1){ - /* Computing hessian and covariance matrix */ - ftolhess=ftol; /* Usually correct */ - hesscov(matcov, p, npar, delti, ftolhess, func); - } - fprintf(ficres,"# Scales (for hessian or gradient estimation)\n"); - printf("# Scales (for hessian or gradient estimation)\n"); - 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"); - } - } + if(mle==1){ + /* Computing hessian and covariance matrix */ + ftolhess=ftol; /* Usually correct */ + hesscov(matcov, p, npar, delti, ftolhess, func); + } + fprintf(ficres,"# Scales (for hessian or gradient estimation)\n"); + printf("# Scales (for hessian or gradient estimation)\n"); + fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n"); + for(i=1,jk=1; i <=nlstate; i++){ + for(j=1; j <=nlstate+ndeath; j++){ + if (j!=i) { + fprintf(ficres,"%1d%1d",i,j); + printf("%1d%1d",i,j); + fprintf(ficlog,"%1d%1d",i,j); + for(k=1; k<=ncovmodel;k++){ + printf(" %.5e",delti[jk]); + fprintf(ficlog," %.5e",delti[jk]); + fprintf(ficres," %.5e",delti[jk]); + jk++; + } + printf("\n"); + fprintf(ficlog,"\n"); + fprintf(ficres,"\n"); + } } - - k=1; - fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); - printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); - for(i=1;i<=npar;i++){ - /* if (k>nlstate) k=1; - i1=(i-1)/(ncovmodel*nlstate)+1; - fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]); - printf("%s%d%d",alph[k],i1,tab[i]);*/ - fprintf(ficres,"%3d",i); - printf("%3d",i); - for(j=1; j<=i;j++){ - fprintf(ficres," %.5e",matcov[i][j]); - printf(" %.5e",matcov[i][j]); - } - fprintf(ficres,"\n"); - printf("\n"); - k++; - } - - while((c=getc(ficpar))=='#' && c!= EOF){ - ungetc(c,ficpar); - fgets(line, MAXLINE, ficpar); - puts(line); - fputs(line,ficparo); - } - ungetc(c,ficpar); - estepm=0; - fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); - if (estepm==0 || estepm < stepm) estepm=stepm; - if (fage <= 2) { - bage = ageminpar; - fage = agemaxpar; - } - - fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n"); - fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); - fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); - - while((c=getc(ficpar))=='#' && c!= EOF){ - ungetc(c,ficpar); - fgets(line, MAXLINE, ficpar); - puts(line); - fputs(line,ficparo); - } - ungetc(c,ficpar); + } + + k=1; + fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); + if(mle==1) + printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); + fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); + for(i=1;i<=npar;i++){ + /* if (k>nlstate) k=1; + i1=(i-1)/(ncovmodel*nlstate)+1; + fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]); + printf("%s%d%d",alph[k],i1,tab[i]);*/ + fprintf(ficres,"%3d",i); + if(mle==1) + printf("%3d",i); + fprintf(ficlog,"%3d",i); + for(j=1; j<=i;j++){ + fprintf(ficres," %.5e",matcov[i][j]); + if(mle==1) + printf(" %.5e",matcov[i][j]); + fprintf(ficlog," %.5e",matcov[i][j]); + } + fprintf(ficres,"\n"); + if(mle==1) + printf("\n"); + fprintf(ficlog,"\n"); + k++; + } + + while((c=getc(ficpar))=='#' && c!= EOF){ + ungetc(c,ficpar); + fgets(line, MAXLINE, ficpar); + puts(line); + fputs(line,ficparo); + } + ungetc(c,ficpar); + estepm=0; + fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); + if (estepm==0 || estepm < stepm) estepm=stepm; + if (fage <= 2) { + bage = ageminpar; + fage = agemaxpar; + } + + fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n"); + fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); + fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); + + while((c=getc(ficpar))=='#' && c!= EOF){ + ungetc(c,ficpar); + fgets(line, MAXLINE, ficpar); + puts(line); + fputs(line,ficparo); + } + ungetc(c,ficpar); - fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2); - fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); - fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); - - while((c=getc(ficpar))=='#' && c!= EOF){ - ungetc(c,ficpar); - fgets(line, MAXLINE, ficpar); - puts(line); - fputs(line,ficparo); - } - ungetc(c,ficpar); + 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.; @@ -3240,7 +3734,34 @@ while((c=getc(ficpar))=='#' && c!= EOF){ freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); /*------------ gnuplot -------------*/ - printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p); + 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); @@ -3254,19 +3775,17 @@ while((c=getc(ficpar))=='#' && c!= EOF){ fclose(ficparo); fclose(ficres); -/*--------- index.htm --------*/ - - printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm); - /*--------------- Prevalence limit --------------*/ strcpy(filerespl,"pl"); strcat(filerespl,fileres); if((ficrespl=fopen(filerespl,"w"))==NULL) { printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end; + fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end; } printf("Computing prevalence limit: result on file '%s' \n", filerespl); + fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl); fprintf(ficrespl,"#Prevalence limit\n"); fprintf(ficrespl,"#Age "); for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i); @@ -3290,9 +3809,16 @@ while((c=getc(ficpar))=='#' && c!= EOF){ k=k+1; /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/ fprintf(ficrespl,"\n#******"); - for(j=1;j<=cptcoveff;j++) + 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); @@ -3310,8 +3836,10 @@ while((c=getc(ficpar))=='#' && c!= EOF){ 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;*/ @@ -3319,7 +3847,9 @@ while((c=getc(ficpar))=='#' && c!= EOF){ 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++){ @@ -3332,6 +3862,9 @@ while((c=getc(ficpar))=='#' && c!= EOF){ 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); @@ -3341,7 +3874,7 @@ while((c=getc(ficpar))=='#' && c!= EOF){ 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 ); + 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]); @@ -3353,7 +3886,7 @@ while((c=getc(ficpar))=='#' && c!= EOF){ } } - varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax); + varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax); fclose(ficrespij); @@ -3366,6 +3899,7 @@ while((c=getc(ficpar))=='#' && c!= EOF){ 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); } @@ -3375,30 +3909,36 @@ while((c=getc(ficpar))=='#' && c!= EOF){ 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); + 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<=cptcoveff;j++) fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); @@ -3420,8 +3960,10 @@ prevalence(ageminpar, agemax, s, agev, n 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, estepm); - + 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) "); @@ -3509,9 +4051,20 @@ free_matrix(mint,1,maxwav,1,n); free_matrix(agev,1,maxwav,1,imx); free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); - if(erreur >0) + fprintf(fichtm,"\n"); + fclose(fichtm); + fclose(ficgp); + + + if(erreur >0){ printf("End of Imach with error or warning %d\n",erreur); - else printf("End of Imach\n"); + 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);*/ @@ -3520,7 +4073,9 @@ free_matrix(mint,1,maxwav,1,n); end: +#ifdef windows /* chdir(pathcd);*/ +#endif /*system("wgnuplot graph.plt");*/ /*system("../gp37mgw/wgnuplot graph.plt");*/ /*system("cd ../gp37mgw");*/ @@ -3530,7 +4085,7 @@ free_matrix(mint,1,maxwav,1,n); strcat(plotcmd,optionfilegnuplot); system(plotcmd); - /*#ifdef windows*/ +#ifdef windows while (z[0] != 'q') { /* chdir(path); */ printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: "); @@ -3540,7 +4095,7 @@ free_matrix(mint,1,maxwav,1,n); else if (z[0] == 'g') system(plotcmd); else if (z[0] == 'q') exit(0); } - /*#endif */ +#endif }