--- imach/src/imach.c 2001/05/02 17:47:10 1.6 +++ imach/src/imach.c 2001/05/09 14:25:42 1.10 @@ -68,8 +68,7 @@ int nvar; -static int cptcov; -int cptcovn, cptcovage=0; +int cptcovn, cptcovage=0, cptcoveff=0,cptcov; int npar=NPARMAX; int nlstate=2; /* Number of live states */ int ndeath=1; /* Number of dead states */ @@ -77,9 +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; @@ -131,12 +132,12 @@ 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 */ @@ -657,13 +658,17 @@ double **prevalim(double **prlim, int nl cov[2]=agefin; 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+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; @@ -798,9 +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, @@ -832,34 +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 (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++){ @@ -1188,10 +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"); @@ -1259,9 +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; @@ -1291,8 +1304,15 @@ 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)); @@ -1313,30 +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=1, k, j, i, Ntvar[20]; + 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++; @@ -1344,8 +1369,24 @@ 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 ****************/ @@ -1599,7 +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; @@ -1611,7 +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]; @@ -1620,7 +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,k2,k3,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; @@ -1636,7 +1677,7 @@ 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; @@ -1649,7 +1690,7 @@ int main() gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */ - printf("\nIMACH, Version 0.64a"); + printf("\nIMACH, Version 0.64b"); printf("\nEnter the parameter file name: "); #ifdef windows @@ -1698,13 +1739,9 @@ split(pathtot, path,optionfile); 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(0,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 */ @@ -1858,81 +1895,81 @@ split(pathtot, path,optionfile); imx=i-1; /* Number of individuals */ /* Calculation of the number of parameter from char model*/ - Tvar=ivector(1,15); + 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, j1=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) { - if (j1==0){ - cutv(stra,strb,modelsav,'V'); - Tvar[1]=atoi(strb); - } - else if (j1==1) { - cutv(stra,strb,modelsav,'*'); - /* printf("stra=%s strb=%s modelsav=%s ",stra,strb,modelsav);*/ - Tage[1]=1; cptcovage++; - if (strcmp(stra,"age")==0) { - cutv(strd,strc,strb,'V'); - Tvar[1]=atoi(strc); - } - else if (strcmp(strb,"age")==0) { - cutv(strd,strc,stra,'V'); - Tvar[1]=atoi(strc); - } - else {printf("Error"); exit(0);} - } + 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,'+'); - /*printf("%s %s %s\n", stra,strb,modelsav);*/ - if (strchr(strb,'*')) { - cutv(strd,strc,strb,'*'); - if (strcmp(strc,"age")==0) { - cutv(strb,stre,strd,'V'); - Tvar[i+1]=atoi(stre); - cptcovage++; - Tage[cptcovage]=i+1; - printf("stre=%s ", stre); - } - else if (strcmp(strd,"age")==0) { - cutv(strb,stre,strc,'V'); - Tvar[i+1]=atoi(stre); - cptcovage++; - Tage[cptcovage]=i+1; - } - else { - 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'); - /* printf("%s %s %s", strd,strc,strb);*/ - - Tvar[i+1]=atoi(strc); - } - strcpy(modelsav,stra); - } - cutv(strd,strc,stra,'V'); - Tvar[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; + } + } + 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 %d cptcovage=%d %d",Tvar[1],Tvar[2],cptcovage,Tage[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(mle==1){*/ if (weightopt != 1) { /* Maximisation without weights*/ for(i=1;i<=n;i++) weight[i]=1.0; } @@ -1947,9 +1984,11 @@ split(pathtot, path,optionfile); 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 */ @@ -2007,18 +2046,18 @@ printf("Total number of individuals= %d, Tcode=ivector(1,100); - nbcode=imatrix(1,nvar,1,8); - ncodemax[1]=1; - if (cptcovn > 0) tricode(Tvar,nbcode,imx); - + 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; } @@ -2026,9 +2065,10 @@ printf("Total number of individuals= %d, } } - /* for(i=1; i <=m ;i++){ + + /*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"); } @@ -2036,7 +2076,7 @@ printf("Total number of individuals= %d, /* Calculates basic frequencies. Computes observed prevalence at single age and prints on file fileres'p'. */ - freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax); + freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax); pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ @@ -2047,9 +2087,10 @@ printf("Total number of individuals= %d, /* For Powell, parameters are in a vector p[] starting at p[1] so we point p on param[1][1] so that p[1] maps on param[1][1][1] */ p=param[1][1]; /* *(*(*(param +1)+1)+0) */ - - mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func); + if(mle==1){ + mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func); + } /*--------- results files --------------*/ fprintf(ficres,"\ntitle=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model); @@ -2073,10 +2114,11 @@ printf("Total number of individuals= %d, } } } - + 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++){ @@ -2131,6 +2173,8 @@ printf("Total number of individuals= %d, 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) { @@ -2139,7 +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 ++) { @@ -2260,15 +2304,28 @@ fprintf(ficgp,"\nset out \"v%s%d%d.gif\" for(k=1; k<=(nlstate+ndeath); k++) { if (k != k2){ fprintf(ficgp," exp(p%d+p%d*x",i,i+1); - - for(j=3; j <=ncovmodel; j++) +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++; + } + else fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]); - fprintf(ficgp,")/(1"); + } + 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); - for(j=3; j <=ncovmodel; j++) +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); @@ -2297,7 +2354,7 @@ chdir(path); /*free_matrix(covar,1,NCOVMAX,1,n);*/ fclose(ficparo); fclose(ficres); - } + /* }*/ /*________fin mle=1_________*/ @@ -2318,11 +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,"