--- imach/src/imach.c 2001/05/02 17:34:41 1.4 +++ imach/src/imach.c 2001/05/17 16:07:14 1.11 @@ -8,7 +8,7 @@ Health expectancies are computed from the transistions observed between waves and are computed for each degree of severity of disability (number of life states). More degrees you consider, more time is necessary to - reach the Maximum Likelihood of the parameters involved in the model. + reach the Maximum Likelihood of the parameters involved in the model. The simplest model is the multinomial logistic model where pij is the probabibility to be observed in state j at the second wave conditional to be observed in state i at the first wave. Therefore the model is: @@ -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 */ @@ -66,8 +68,7 @@ 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 */ +} + /******************************************/ @@ -166,7 +201,7 @@ 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; for(j=0; j<=strlen(t)-1; j++) { if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; @@ -175,8 +210,8 @@ void cutv(char *u,char *v, char*t, char lg=strlen(t); for(j=0; j=(p+1))(v[j-p-1] = t[j]); @@ -613,15 +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; @@ -756,9 +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, @@ -780,7 +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 */ @@ -790,29 +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[1+k-1][i]; - } - out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, - 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); - savm=oldm; - oldm=newm; - - + cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM; + for (kk=1; kk<=cptcovage;kk++) { + cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; + } + + out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, + 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); + savm=oldm; + oldm=newm; + + } /* end mult */ - + lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ ipmx +=1; @@ -1113,13 +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++) @@ -1128,8 +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++){ @@ -1141,10 +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"); @@ -1212,9 +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; @@ -1244,8 +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; + 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)); @@ -1266,30 +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++; @@ -1297,9 +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 ****************/ @@ -1552,7 +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; @@ -1564,7 +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]; @@ -1573,7 +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; @@ -1589,8 +1677,9 @@ int main() double ***eij, ***vareij; double **varpl; /* Variances of prevalence limits by age */ double *epj, vepp; - char version[80]="Imach version 0.64, May 2000, INED-EUROREVES "; + 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 @@ -1601,23 +1690,19 @@ 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 scanf("%s",pathtot); - cygwin_split_path(pathtot,path,optionfile); - printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile); - chdir(path); - - /*size=30; - getcwd(pathcd, size); - printf("pathcd=%s, path=%s, optionfile=%s\n",pathcd,path,optionfile); - cutv(path,optionfile,pathtot,'\\'); + getcwd(pathcd, size); + /*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); - printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile); - */ #endif #ifdef unix scanf("%s",optionfile); @@ -1654,13 +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 */ @@ -1752,7 +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; @@ -1805,7 +1885,7 @@ 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 %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i]), (mint[5][i]), (anint[5][i]), (s[5][i]), (mint[6][i]), (anint[6][i]), (s[6][i]));*/ + /*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; } @@ -1815,40 +1895,81 @@ int main() 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; + + 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(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+1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k]; + covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k]; + k1++; + k2=k2+2; } - else {cutv(strd,strc,strb,'V'); - Tvar[i+1]=atoi(strc); - } - 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; } @@ -1863,9 +1984,11 @@ int main() 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 */ @@ -1922,19 +2045,19 @@ printf("Total number of individuals= %d, concatwav(wav, dh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm); -Tcode=ivector(1,100); - nbcode=imatrix(1,nvar,1,8); - ncodemax[1]=1; - if (cptcovn > 0) tricode(Tvar,nbcode,imx); - + Tcode=ivector(1,100); + nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); + ncodemax[1]=1; + if (cptcovn > 0) tricode(Tvar,nbcode,imx); + codtab=imatrix(1,100,1,10); h=0; - m=pow(2,cptcovn); + m=pow(2,cptcoveff); - for(k=1;k<=cptcovn; k++){ + for(k=1;k<=cptcoveff; k++){ for(i=1; i <=(m/pow(2,k));i++){ for(j=1; j <= ncodemax[k]; j++){ - for(cpt=1; cpt <=(m/pow(2,cptcovn+1-k)); cpt++){ + for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){ h++; if (h>m) h=1;codtab[h][k]=j; } @@ -1942,22 +2065,19 @@ 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'. */ freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax); - - /*scanf("%d ",i);*/ - - pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ @@ -1967,9 +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) */ - - 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); @@ -1993,10 +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++){ @@ -2051,15 +2173,17 @@ 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) { - printf("Problem with file graph.plt");goto end; + printf("Problem with file graph.gp");goto end; } #ifdef windows fprintf(ficgp,"cd \"%s\" \n",pathc); #endif -m=pow(2,cptcovn); +m=pow(2,cptcoveff); /* 1eme*/ for (cpt=1; cpt<= nlstate ; cpt ++) { @@ -2126,7 +2250,7 @@ fprintf(ficgp,"\nset out \"v%s%d%d.gif\" /*3eme*/ - for (k1=1; k1<= m ; k1 ++) { + for (k1=1; k1<= m ; k1 ++) { for (cpt=1; cpt<= nlstate ; cpt ++) { k=2+nlstate*(cpt-1); fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt); @@ -2135,10 +2259,10 @@ fprintf(ficgp,"\nset out \"v%s%d%d.gif\" } 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 (k1=1; k1<= m ; k1 ++) { for (cpt=1; cpt
    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
      @@ -2246,11 +2395,11 @@ fprintf(ficgp,"\nset out \"pe%s%d.gif\" - 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; @@ -2258,10 +2407,10 @@ fprintf(ficgp,"\nset out \"pe%s%d.gif\" 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); @@ -2276,7 +2425,7 @@ interval) in state (%d): v%s%d%d.gif
      - Health life expectancies by age and initial health state (%d): exp%s%d%d.gif
      -",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1); +",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1); } fprintf(fichtm,"\n
      - Total life expectancy by age and health expectancies in states (1) and (2): e%s%d.gif
      @@ -2309,16 +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++){ @@ -2351,8 +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 */ @@ -2410,17 +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"); @@ -2464,7 +2613,7 @@ fclose(fichtm); fclose(ficrest); fclose(ficpar); free_vector(epj,1,nlstate+1); - /*scanf("%d ",i); */ + /* scanf("%d ",i); */ /*------- Variance limit prevalence------*/ @@ -2481,8 +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); @@ -2521,7 +2670,10 @@ strcpy(fileresvpl,"vpl"); #ifdef windows chdir(pathcd); #endif - system("wgnuplot graph.plt"); + /*system("wgnuplot graph.plt");*/ + /*system("../gp37mgw/wgnuplot graph.plt");*/ + /*system("cd ../gp37mgw");*/ + system("..\\gp37mgw\\wgnuplot graph.plt"); #ifdef windows while (z[0] != 'q') { @@ -2531,7 +2683,7 @@ 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); }