--- imach/src/imach.c 2001/05/02 17:34:41 1.4
+++ imach/src/imach.c 2001/05/02 18:44:18 1.9
@@ -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;
@@ -1245,10 +1305,16 @@ float sum=0.;
else{
if (s[mw[mi+1][i]][i] > nlstate) {
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>28)) printf("j=%d num=%d ",j,i);*/
+ 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;
}
else{
j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
+ /*if ((j<0) || (j>28)) printf("j=%d num=%d ",j,i);*/
k=k+1;
if (j >= jmax) jmax=j;
else if (j <= jmin)jmin=j;
@@ -1266,30 +1332,35 @@ 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 +1368,25 @@ 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 +1639,7 @@ 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 +1651,7 @@ 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 +1660,7 @@ 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 +1676,9 @@ 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 62c, May 1999, INED-EUROREVES ";
char *alph[]={"a","a","b","c","d","e"}, str[4];
+
char z[1]="c", occ;
#include
#include
@@ -1601,23 +1689,19 @@ 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 +1738,9 @@ 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 +1832,6 @@ 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 +1884,7 @@ 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 +1894,81 @@ 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 +1983,11 @@ 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 +2044,19 @@ 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 +2064,19 @@ 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 +2086,10 @@ 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 +2113,11 @@ 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 +2172,17 @@ 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 +2249,7 @@ 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 +2258,10 @@ 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 +2394,11 @@ 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 +2406,10 @@ 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 +2424,7 @@ 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 +2457,16 @@ 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 +2499,8 @@ 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 +2558,17 @@ 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 +2612,7 @@ fclose(fichtm);
fclose(ficrest);
fclose(ficpar);
free_vector(epj,1,nlstate+1);
- /*scanf("%d ",i); */
+ /* scanf("%d ",i); */
/*------- Variance limit prevalence------*/
@@ -2481,8 +2629,8 @@ 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 +2669,8 @@ strcpy(fileresvpl,"vpl");
#ifdef windows
chdir(pathcd);
#endif
- system("wgnuplot graph.plt");
+ /*system("wgnuplot graph.plt");*/
+ system("../gp37mgw/wgnuplot graph.plt");
#ifdef windows
while (z[0] != 'q') {