--- imach/src/imach.c 2001/03/13 18:10:26 1.2 +++ imach/src/imach.c 2001/05/09 14:25:42 1.10 @@ -51,6 +51,8 @@ #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 */ @@ -59,15 +61,14 @@ #define NLSTATEMAX 8 /* Maximum number of live states (for func) */ #define NDEATHMAX 8 /* Maximum number of dead states (for func) */ #define NCOVMAX 8 /* Maximum number of covariates */ -#define MAXN 80000 +#define MAXN 20000 #define YEARM 12. /* Number of months per year */ #define AGESUP 130 #define AGEBASE 40 int nvar; -static int cptcov; -int cptcovn; +int cptcovn, cptcovage=0, cptcoveff=0,cptcov; int npar=NPARMAX; int nlstate=2; /* Number of live states */ int ndeath=1; /* Number of dead states */ @@ -75,9 +76,11 @@ int ncovmodel, ncov; /* Total number 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; @@ -89,9 +92,6 @@ FILE *ficreseij; FILE *ficresvpl; char fileresvpl[FILENAMELENGTH]; - - - #define NR_END 1 #define FREE_ARG char* #define FTOL 1.0e-10 @@ -125,18 +125,53 @@ int stepm; /* Stepm, step in month: minimum step interpolation*/ 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 *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 *s; /* pointer */ + int l1, l2; /* length counters */ + + l1 = strlen( path ); /* length of path */ + if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH ); + s = strrchr( path, '\\' ); /* find last / */ + if ( s == NULL ) { /* no directory, so use current */ +#if defined(__bsd__) /* get current working directory */ + extern char *getwd( ); + + if ( getwd( dirc ) == NULL ) { +#else + extern char *getcwd( ); + + if ( getcwd( dirc, FILENAME_MAX ) == NULL ) { +#endif + return( GLOCK_ERROR_GETCWD ); + } + strcpy( name, path ); /* we've got it */ + } else { /* strip direcotry from path */ + s++; /* after this, the filename */ + l2 = strlen( s ); /* length of filename */ + if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH ); + strcpy( name, s ); /* save file name */ + strncpy( dirc, path, l1 - l2 ); /* now the directory */ + dirc[l1-l2] = 0; /* add zero */ + } + l1 = strlen( dirc ); /* length of directory */ + if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; } + return( 0 ); /* we're done */ +} + /******************************************/ @@ -166,25 +201,23 @@ int nbocc(char *s, char occ) void cutv(char *u,char *v, char*t, char occ) { - int i,lg,j,p; + int i,lg,j,p=0; i=0; - if (t[0]== occ) p=0; for(j=0; j<=strlen(t)-1; j++) { - if((t[j]!= occ) && (t[j+1]==occ)) p=j+1; + if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; } lg=strlen(t); for(j=0; j=(p+1))(v[j-p-1] = t[j]); } } - /********************** nrerror ********************/ void nrerror(char error_text[]) @@ -615,15 +648,27 @@ 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 Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/ + } + for (k=1; k<=cptcovage;k++) + cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; + for (k=1; k<=cptcovprod;k++) + cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; + + /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/ + /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/ + out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); savm=oldm; @@ -758,9 +803,13 @@ double ***hpxij(double ***po, int nhstep /* Covariates have to be included here again */ cov[1]=1.; cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM; - if (cptcovn>0){ - 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, @@ -782,7 +831,7 @@ 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 */ @@ -792,30 +841,31 @@ 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[Tvar[k]][i]; - /* printf("k=%d cptcovn=%d %lf\n",k,cptcovn,covar[Tvar[k]][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; @@ -827,7 +877,6 @@ printf(" %d\n",s[4][i]); for(k=1,l=0.; k<=nlstate; k++) l += ll[k]; /* printf("l1=%f l2=%f ",ll[1],ll[2]); */ l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */ - return -l; } @@ -983,7 +1032,8 @@ double hessii( double x[], double delta, } } delti[theta]=delts; - return res; + return res; + } double hessij( double x[], double delti[], int thetai,int thetaj) @@ -1116,13 +1166,14 @@ void freqsummary(char fileres[], int ag freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3); j1=0; - j=cptcovn; + j=cptcoveff; if (cptcovn<1) {j=1;ncodemax[1]=1;} for(k1=1; k1<=j;k1++){ for(i1=1; i1<=ncodemax[k1];i1++){ j1++; - + /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]); + scanf("%d", i);*/ for (i=-1; i<=nlstate+ndeath; i++) for (jk=-1; jk<=nlstate+ndeath; jk++) for(m=agemin; m <= agemax+3; m++) @@ -1131,8 +1182,9 @@ void freqsummary(char fileres[], int ag for (i=1; i<=imx; i++) { bool=1; if (cptcovn>0) { - for (z1=1; z1<=cptcovn; z1++) - if (covar[Tvar[z1]][i]!= nbcode[Tvar[z1]][codtab[j1][z1]]) bool=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-1; m++){ @@ -1144,10 +1196,10 @@ void freqsummary(char fileres[], int ag } } 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#"); + 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"); @@ -1215,9 +1267,14 @@ 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 j, k=0,jk, ju, jl; + double sum=0.; +jmin=1e+5; + jmax=-1; +jmean=0.; for(i=1; i<=imx; i++){ mi=0; m=firstpass; @@ -1247,13 +1304,18 @@ 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; + else if (j <= jmin)jmin=j; + sum=sum+j; + if (j<0) printf("j=%d num=%d ",j,i); + } } else{ j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12)); - /*printf("i=%d agevi+1=%lf agevi=%lf j=%d\n", i,agev[mw[mi+1][i]][i],agev[mw[mi][i]][i],j);*/ - k=k+1; if (j >= jmax) jmax=j; else if (j <= jmin)jmin=j; @@ -1271,30 +1333,35 @@ 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); } /*********** 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++; @@ -1302,9 +1369,25 @@ void tricode(int *Tvar, int **nbcode, in if (ij > ncodemax[j]) break; } } - } + } - } + for (k=0; k<19; k++) Ndum[k]=0; + + for (i=1; i<=ncovmodel; i++) { + ij=Tvar[i]; + Ndum[ij]++; + } + + ij=1; + for (i=1; i<=10; i++) { + if((Ndum[i]!=0) && (i<=ncov)){ + Tvaraff[ij]=i; + ij++; + } + } + + cptcoveff=ij-1; +} /*********** Health Expectancies ****************/ @@ -1557,7 +1640,7 @@ void varprevlim(char fileres[], double * int main() { - 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; @@ -1569,7 +1652,7 @@ int main() int *indx; char line[MAXLINE], linepar[MAXLINE]; char title[MAXLINE]; - char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH]; + char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH]; char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH]; char filerest[FILENAMELENGTH]; char fileregp[FILENAMELENGTH]; @@ -1578,7 +1661,7 @@ int main() 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 i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij; int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab; int hstepm, nhstepm; @@ -1594,8 +1677,9 @@ int main() double ***eij, ***vareij; double **varpl; /* Variances of prevalence limits by age */ double *epj, vepp; - char version[80]="Imach version 62c, May 1999, INED-EUROREVES "; + char version[80]="Imach version 64b, May 2001, INED-EUROREVES "; char *alph[]={"a","a","b","c","d","e"}, str[4]; + char z[1]="c", occ; #include #include @@ -1606,13 +1690,17 @@ int main() gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */ - printf("\nIMACH, Version 0.63"); + printf("\nIMACH, Version 0.64b"); printf("\nEnter the parameter file name: "); #ifdef windows scanf("%s",pathtot); getcwd(pathcd, size); - cutv(path,optionfile,pathtot,'\\'); + /*cygwin_split_path(pathtot,path,optionfile); + printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/ + /* cutv(path,optionfile,pathtot,'\\');*/ + +split(pathtot, path,optionfile); chdir(path); replace(pathc,path); #endif @@ -1651,13 +1739,9 @@ int main() 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; - } + 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 */ @@ -1749,7 +1833,6 @@ int main() printf("\n"); - if(mle==1){ /*-------- data file ----------*/ if((ficres =fopen(fileres,"w"))==NULL) { printf("Problem with resultfile: %s\n", fileres);goto end; @@ -1777,7 +1860,7 @@ int main() s=imatrix(1,maxwav+1,1,n); adl=imatrix(1,maxwav+1,1,n); tab=ivector(1,NCOVMAX); - ncodemax=ivector(1,NCOVMAX); + ncodemax=ivector(1,8); i=1; while (fgets(line, MAXLINE, fic) != NULL) { @@ -1802,53 +1885,91 @@ int main() } 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\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]));*/ - - /*printf("%d %.lf %.lf %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),(covar[3][i]), (covar[4][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]));*/ + /*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]));*/ i=i+1; } } - /*scanf("%d",i);*/ + /*scanf("%d",i);*/ imx=i-1; /* Number of individuals */ - + /* Calculation of the number of parameter from char model*/ - Tvar=ivector(1,8); + Tvar=ivector(1,15); + Tprod=ivector(1,15); + Tvaraff=ivector(1,15); + Tvard=imatrix(1,15,1,2); + Tage=ivector(1,15); if (strlen(model) >1){ - j=0; + 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); + 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,'+'); + if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); + /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/ + /*scanf("%d",i);*/ + if (strchr(strb,'*')) { + cutv(strd,strc,strb,'*'); + if (strcmp(strc,"age")==0) { + cptcovprod--; + cutv(strb,stre,strd,'V'); + Tvar[i]=atoi(stre); + cptcovage++; + Tage[cptcovage]=i; + /*printf("stre=%s ", stre);*/ + } + else if (strcmp(strd,"age")==0) { + cptcovprod--; + cutv(strb,stre,strc,'V'); + Tvar[i]=atoi(stre); + cptcovage++; + Tage[cptcovage]=i; } else { - cutv(strd,strc,strb,'V'); - Tvar[i+1]=atoi(strc); + cutv(strb,stre,strc,'V'); + Tvar[i]=ncov+k1; + cutv(strb,strc,strd,'V'); + Tprod[k1]=i; + Tvard[k1][1]=atoi(strc); + Tvard[k1][2]=atoi(stre); + Tvar[cptcovn+k2]=Tvard[k1][1]; + Tvar[cptcovn+k2+1]=Tvard[k1][2]; + for (k=1; k<=lastobs;k++) + covar[ncov+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); + else { + /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/ + /* scanf("%d",i);*/ + cutv(strd,strc,strb,'V'); + Tvar[i]=atoi(strc); + } + strcpy(modelsav,stra); + /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav); + scanf("%d",i);*/ } - } - /*printf("tvar=%d ",Tvar[1]);*/ - /*scanf("%d ",i);*/ +} + + /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]); + printf("cptcovprod=%d ", cptcovprod); + scanf("%d ",i);*/ fclose(fic); + /* if(mle==1){*/ if (weightopt != 1) { /* Maximisation without weights*/ for(i=1;i<=n;i++) weight[i]=1.0; } @@ -1858,23 +1979,22 @@ int main() 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 (mint[m][i]==99 || anint[m][i]==9999) s[m][i]=-1; if(s[m][i] >0){ if (s[m][i] == nlstate+1) { if(agedc[i]>0) if(moisdc[i]!=99 && andc[i]!=9999) agev[m][i]=agedc[i]; - else{ + else { + if (andc[i]!=9999){ printf("Warning negative age at death: %d line:%d\n",num[i],i); agev[m][i]=-1; + } } } else if(s[m][i] !=9){ /* Should no more exist */ agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]); - if(mint[m][i]==99 || anint[m][i]==9999){ + if(mint[m][i]==99 || anint[m][i]==9999) agev[m][i]=1; - /* printf("i=%d m=%d agev=%lf \n",i,m, agev[m][i]); */ - } else if(agev[m][i] 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; } @@ -1945,13 +2065,14 @@ Tcode=ivector(1,100); } } + /*for(i=1; i <=m ;i++){ for(k=1; k <=cptcovn; k++){ - printf("i=%d k=%d %d ",i,k,codtab[i][k]); + printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff); } printf("\n"); } - scanf("%d",i);*/ + scanf("%d",i);*/ /* Calculates basic frequencies. Computes observed prevalence at single age and prints on file fileres'p'. */ @@ -1966,9 +2087,10 @@ Tcode=ivector(1,100); /* 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) */ - /*scanf("%d",i);*/ - 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); @@ -1992,10 +2114,11 @@ Tcode=ivector(1,100); } } } - + if(mle==1){ /* 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++){ @@ -2050,6 +2173,8 @@ Tcode=ivector(1,100); 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) { @@ -2058,7 +2183,7 @@ chdir(pathcd); #ifdef windows fprintf(ficgp,"cd \"%s\" \n",pathc); #endif -m=pow(2,cptcovn); +m=pow(2,cptcoveff); /* 1eme*/ for (cpt=1; cpt<= nlstate ; cpt ++) { @@ -2157,41 +2282,61 @@ fprintf(ficgp,"\nset out \"v%s%d%d.gif\" } /* proba elementaires */ - for(i=1,jk=1; i <=nlstate; i++){ + for(i=1,jk=1; i <=nlstate; i++){ for(k=1; k <=(nlstate+ndeath); k++){ if (k != i) { - /* fprintf(ficgp,"%1d%1d ",i,k);*/ for(j=1; j <=ncovmodel; j++){ - fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]); + /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/ + /*fprintf(ficgp,"%s",alph[1]);*/ + fprintf(ficgp,"p%d=%f ",jk,p[jk]); jk++; fprintf(ficgp,"\n"); } } } - } + } + for(jk=1; jk <=m; jk++) { fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot [%.f:%.f] ",agemin,agemax); - for(i=1; i <=nlstate; i++) { - for(k=1; k <=(nlstate+ndeath); k++){ - if (k != i) { - fprintf(ficgp," exp(a%d%d+b%d%d*x",i,k,i,k); - for(j=3; j <=ncovmodel; j++) - fprintf(ficgp,"+%s%d%d*%d",alph[j],i,k,nbcode[Tvar[j-2]][codtab[jk][j-2]]); - fprintf(ficgp,")/(1"); - for(k1=1; k1 <=(nlstate+ndeath); k1++) - if (k1 != i) { - fprintf(ficgp,"+exp(a%d%d+b%d%d*x",i,k1,i,k1); - for(j=3; j <=ncovmodel; j++) - fprintf(ficgp,"+%s%d%d*%d",alph[j],i,k,nbcode[Tvar[j-2]][codtab[jk][j-2]]); - fprintf(ficgp,")"); + i=1; + for(k2=1; k2<=nlstate; k2++) { + k3=i; + for(k=1; k<=(nlstate+ndeath); k++) { + if (k != k2){ + fprintf(ficgp," exp(p%d+p%d*x",i,i+1); +ij=1; + for(j=3; j <=ncovmodel; j++) { + if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { + fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); + ij++; } - fprintf(ficgp,") t \"p%d%d\" ", i,k); - if ((i+k)!= (nlstate*2+ndeath)) fprintf(ficgp,","); - } - } - } -fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk); + else + fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]); + } + fprintf(ficgp,")/(1"); + + for(k1=1; k1 <=nlstate; k1++){ + fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1); +ij=1; + for(j=3; j <=ncovmodel; j++){ + if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { + fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); + ij++; + } + else + fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]); + } + fprintf(ficgp,")"); + } + fprintf(ficgp,") t \"p%d%d\" ", k2,k); + if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,","); + i=i+ncovmodel; + } + } + } + fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk); } + fclose(ficgp); chdir(path); @@ -2209,7 +2354,7 @@ chdir(path); /*free_matrix(covar,1,NCOVMAX,1,n);*/ fclose(ficparo); fclose(ficres); - } + /* }*/ /*________fin mle=1_________*/ @@ -2230,11 +2375,18 @@ chdir(path); fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage); /*--------- index.htm --------*/ - if((fichtm=fopen("index.htm","w"))==NULL) { - printf("Problem with index.htm \n");goto end; + strcpy(optionfilehtm,optionfile); + strcat(optionfilehtm,".htm"); + if((fichtm=fopen(optionfilehtm,"w"))==NULL) { + printf("Problem with %s \n",optionfilehtm);goto end; } - fprintf(fichtm,"
    Imach, Version 0.63
  • Outputs files

    \n + fprintf(fichtm,"
      Imach, Version 0.64b
      +Titre=%s
      Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s
      +Total number of observations=%d
      +Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf
      +
      +
    • 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
      @@ -2243,11 +2395,11 @@ chdir(path); - 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); + - Standard deviation of stationary prevalences: vpl%s

      ",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres); - fprintf(fichtm,"
    • Graphs
      • \n

      "); + fprintf(fichtm,"

    • Graphs

      • "); - m=cptcovn; + m=cptcoveff; if (cptcovn < 1) {m=1;ncodemax[1]=1;} j1=0; @@ -2255,10 +2407,10 @@ chdir(path); 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,"
      ************ Results for covariates"); + for (cpt=1; cpt<=cptcoveff;cpt++) + fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]); + fprintf(fichtm," ************\n
      "); } fprintf(fichtm,"
      - Probabilities: pe%s%d.gif
      ",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1); @@ -2306,16 +2458,16 @@ fclose(fichtm); agebase=agemin; agelim=agemax; 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#******"); + for(j=1;j<=cptcoveff;j++) + fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); fprintf(ficrespl,"******\n"); for (age=agebase; age<=agelim; age++){ @@ -2348,8 +2500,8 @@ fclose(fichtm); 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 */ @@ -2407,17 +2559,17 @@ fclose(fichtm); for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ 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++) + for(j=1;j<=cptcoveff;j++) fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]); fprintf(ficreseij,"******\n"); fprintf(ficresvij,"\n#****** "); - for(j=1;j<=cptcovn;j++) + for(j=1;j<=cptcoveff;j++) fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]); fprintf(ficresvij,"******\n"); @@ -2478,8 +2630,8 @@ strcpy(fileresvpl,"vpl"); 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]]); + 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); @@ -2518,7 +2670,8 @@ strcpy(fileresvpl,"vpl"); #ifdef windows chdir(pathcd); #endif - system("wgnuplot ../gp37mgw/graph.plt"); + /*system("wgnuplot graph.plt");*/ + system("../gp37mgw/wgnuplot graph.plt"); #ifdef windows while (z[0] != 'q') { @@ -2528,7 +2681,7 @@ strcpy(fileresvpl,"vpl"); if (z[0] == 'c') system("./imach"); else if (z[0] == 'e') { chdir(path); - system("index.htm"); + system(optionfilehtm); } else if (z[0] == 'q') exit(0); }