--- imach096d/src/imach.c 2001/03/13 18:10:26 1.2 +++ imach096d/src/imach.c 2001/05/02 17:47:10 1.6 @@ -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 */ @@ -59,7 +61,7 @@ #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 @@ -67,7 +69,7 @@ int nvar; static int cptcov; -int cptcovn; +int cptcovn, cptcovage=0; int npar=NPARMAX; int nlstate=2; /* Number of live states */ int ndeath=1; /* Number of dead states */ @@ -89,9 +91,6 @@ FILE *ficreseij; FILE *ficresvpl; char fileresvpl[FILENAMELENGTH]; - - - #define NR_END 1 #define FREE_ARG char* #define FTOL 1.0e-10 @@ -125,7 +124,7 @@ 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; @@ -138,6 +137,41 @@ double ftol=FTOL; /* Tolerance for compu double ftolhess; /* Tolerance for computing hessian */ +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 */ +} + + /******************************************/ void replace(char *s, char*t) @@ -166,25 +200,23 @@ 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 +647,23 @@ 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][k]]; + +/*printf("Tcode[ij]=%d nbcode=%d\n",Tcode[ij],nbcode[k][Tcode[ij]]);*/ + } + for (k=1; k<=cptcovage;k++) + cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; + out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); savm=oldm; @@ -782,7 +822,7 @@ 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 */ @@ -794,26 +834,30 @@ double func( double *x) /*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]);*/ - } - } + newm=savm; + cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM; + for (kk=1; kk<=cptcovage;kk++) { + cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; + /*printf("%d %d",kk,Tage[kk]);*/ + } + /*cov[4]=covar[1][i]*cov[2];scanf("%d", i);*/ + /*cov[3]=pow(cov[2],2)/1000.;*/ + 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]]); @@ -827,7 +871,6 @@ 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 +1026,8 @@ double hessii( double x[], double delta, } } delti[theta]=delts; - return res; + return res; + } double hessij( double x[], double delti[], int thetai,int thetaj) @@ -1252,8 +1296,6 @@ float sum=0.; } 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; @@ -1276,11 +1318,11 @@ float sum=0.; /*********** Tricode ****************************/ void tricode(int *Tvar, int **nbcode, int imx) { - int Ndum[80],ij, k, j, i; + int Ndum[80],ij=1, k, j, i, Ntvar[20]; int cptcode=0; for (k=0; k<79; k++) Ndum[k]=0; for (k=1; k<=7; k++) ncodemax[k]=0; - + for (j=1; j<=cptcovn; j++) { for (i=1; i<=imx; i++) { ij=(int)(covar[Tvar[j]][i]); @@ -1303,8 +1345,8 @@ void tricode(int *Tvar, int **nbcode, in } } } - - } + +} /*********** Health Expectancies ****************/ @@ -1578,7 +1620,7 @@ 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; int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab; int hstepm, nhstepm; @@ -1596,6 +1638,7 @@ int main() double *epj, vepp; char version[80]="Imach version 62c, May 1999, INED-EUROREVES "; char *alph[]={"a","a","b","c","d","e"}, str[4]; + char z[1]="c", occ; #include #include @@ -1606,13 +1649,17 @@ int main() gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */ - printf("\nIMACH, Version 0.63"); + printf("\nIMACH, Version 0.64a"); 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 @@ -1651,7 +1698,7 @@ 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); + covar=matrix(0,NCOVMAX,1,n); if (strlen(model)<=1) cptcovn=0; else { j=0; @@ -1749,7 +1796,6 @@ 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 +1823,7 @@ 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 +1848,91 @@ 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); + Tage=ivector(1,15); if (strlen(model) >1){ - j=0; + j=0, j1=0; j=nbocc(model,'+'); + j1=nbocc(model,'*'); cptcovn=j+1; - + strcpy(modelsav,model); if (j==0) { - cutv(stra,strb,modelsav,'V'); Tvar[1]=atoi(strb); + 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);} + } } 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,'*'); - 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]; + 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]; + } } else { cutv(strd,strc,strb,'V'); - Tvar[i+1]=atoi(strc); + /* printf("%s %s %s", strd,strc,strb);*/ + + Tvar[i+1]=atoi(strc); } - strcpy(modelsav,stra); + strcpy(modelsav,stra); } - /*cutv(strd,strc,stra,'V');*/ + cutv(strd,strc,stra,'V'); Tvar[1]=atoi(strc); } } - /*printf("tvar=%d ",Tvar[1]);*/ - /*scanf("%d ",i);*/ + + /* printf("tvar=%d %d cptcovage=%d %d",Tvar[1],Tvar[2],cptcovage,Tage[1]); + scanf("%d ",i);*/ fclose(fic); + if(mle==1){ if (weightopt != 1) { /* Maximisation without weights*/ for(i=1;i<=n;i++) weight[i]=1.0; } @@ -1858,7 +1942,6 @@ 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) @@ -1871,10 +1954,8 @@ int main() } 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); @@ -1945,17 +2026,17 @@ Tcode=ivector(1,100); } } - /*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("\n"); } - scanf("%d",i);*/ + scanf("%d",i);*/ /* Calculates basic frequencies. Computes observed prevalence at single age and prints on file fileres'p'. */ - freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax); + 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 */ @@ -1966,7 +2047,7 @@ 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); @@ -2157,41 +2238,48 @@ 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); + 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); + 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,"+p%d*%d",i+j-1,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,")"); - } - 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); + + 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++) + 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); @@ -2234,7 +2322,7 @@ chdir(path); printf("Problem with index.htm \n");goto end; } - fprintf(fichtm,"
    Imach, Version 0.63
  • Outputs files

    \n + fprintf(fichtm,"
      Imach, Version 0.64a
    • 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
      @@ -2313,9 +2401,9 @@ fclose(fichtm); 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#****** "); + fprintf(ficrespl,"\n#******"); for(j=1;j<=cptcovn;j++) - fprintf(ficrespl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]); + fprintf(ficrespl," V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]); fprintf(ficrespl,"******\n"); for (age=agebase; age<=agelim; age++){ @@ -2518,7 +2606,7 @@ strcpy(fileresvpl,"vpl"); #ifdef windows chdir(pathcd); #endif - system("wgnuplot ../gp37mgw/graph.plt"); + system("wgnuplot graph.plt"); #ifdef windows while (z[0] != 'q') {