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/* Automatically generated from all.nw using noweb */
#include "survS.h"
SEXP concordance1(SEXP y, SEXP wt2, SEXP indx2, SEXP ntree2) {
int i, j, k, index;
int child, parent;
int n, ntree;
double *time, *status;
double *twt, *nwt, *count;
double vss, myrank, wsum1, wsum2, wsum3; /*sum of wts below, tied, above*/
double lmean, umean, oldmean, newmean;
double ndeath; /* weighted number of deaths at this point */
SEXP count2;
double *wt;
int *indx;
n = nrows(y);
ntree = asInteger(ntree2);
wt = REAL(wt2);
indx = INTEGER(indx2);
time = REAL(y);
status = time + n;
PROTECT(count2 = allocVector(REALSXP, 5));
count = REAL(count2); /* count5 contains the information matrix */
twt = (double *) R_alloc(2*ntree, sizeof(double));
nwt = twt + ntree;
for (i=0; i< 2*ntree; i++) twt[i] =0.0;
for (i=0; i<5; i++) count[i]=0.0;
vss=0;
for (i=n-1; i>=0; ) {
ndeath =0;
if (status[i]==1) { /* process all tied deaths at this point */
for (j=i; j>=0 && status[j]==1 && time[j]==time[i]; j--) {
ndeath += wt[j];
index = indx[j];
for (k=i; k>j; k--) count[3] += wt[j]*wt[k]; /* tied on time */
count[2] += wt[j] * nwt[index]; /* tied on x */
child = (2*index) +1; /* left child */
if (child < ntree)
count[0] += wt[j] * twt[child]; /*left children */
child++;
if (child < ntree)
count[1] += wt[j] * twt[child]; /*right children */
while (index >0) { /* walk up the tree */
parent = (index-1)/2;
if (index & 1) /* I am the left child */
count[1] += wt[j] * (twt[parent] - twt[index]);
else count[0] += wt[j] * (twt[parent] - twt[index]);
index = parent;
}
}
}
else j = i-1;
/* Add the weights for these obs into the tree and update variance*/
for (; i>j; i--) {
wsum1=0;
oldmean = twt[0]/2;
index = indx[i];
nwt[index] += wt[i];
twt[index] += wt[i];
wsum2 = nwt[index];
child = 2*index +1; /* left child */
if (child < ntree) wsum1 += twt[child];
while (index >0) {
parent = (index-1)/2;
twt[parent] += wt[i];
if (!(index&1)) /* I am a right child */
wsum1 += (twt[parent] - twt[index]);
index=parent;
}
wsum3 = twt[0] - (wsum1 + wsum2); /* sum of weights above */
lmean = wsum1/2;
umean = wsum1 + wsum2 + wsum3/2; /* new upper mean */
newmean = twt[0]/2;
myrank = wsum1 + wsum2/2;
vss += wsum1*(newmean+ oldmean - 2*lmean) * (newmean - oldmean);
vss += wsum3*(newmean+ oldmean+ wt[i]- 2*umean) *(oldmean-newmean);
vss += wt[i]* (myrank -newmean)*(myrank -newmean);
}
count[4] += ndeath * vss/twt[0];
}
UNPROTECT(1);
return(count2);
}
SEXP concordance2(SEXP y, SEXP wt2, SEXP indx2, SEXP ntree2,
SEXP sortstop, SEXP sortstart) {
int i, j, k, index;
int child, parent;
int n, ntree;
int istart, iptr, jptr;
double *time1, *time2, *status, dtime;
double *twt, *nwt, *count;
int *sort1, *sort2;
double vss, myrank;
double wsum1, wsum2, wsum3; /*sum of wts below, tied, above*/
double lmean, umean, oldmean, newmean;
double ndeath;
SEXP count2;
double *wt;
int *indx;
n = nrows(y);
ntree = asInteger(ntree2);
wt = REAL(wt2);
indx = INTEGER(indx2);
sort2 = INTEGER(sortstop);
sort1 = INTEGER(sortstart);
time1 = REAL(y);
time2 = time1 + n;
status= time2 + n;
PROTECT(count2 = allocVector(REALSXP, 5));
count = REAL(count2);
twt = (double *) R_alloc(2*ntree, sizeof(double));
nwt = twt + ntree;
for (i=0; i< 2*ntree; i++) twt[i] =0.0;
for (i=0; i<5; i++) count[i]=0.0;
vss =0;
istart = 0; /* where we are with start times */
for (i=0; i<n; ) {
iptr = sort2[i]; /* In reverse death time order */
ndeath =0;
if (status[iptr]==1) {
/* Toss people out of the tree and update variance */
dtime = time2[iptr];
for (; istart < n && time1[sort1[istart]] >= dtime; istart++) {
wsum1 =0;
oldmean = twt[0]/2;
jptr = sort1[istart];
index = indx[jptr];
nwt[index] -= wt[jptr];
twt[index] -= wt[jptr];
wsum2 = nwt[index];
child = 2*index +1; /* left child */
if (child < ntree) wsum1 += twt[child];
while (index >0) {
parent = (index-1)/2;
twt[parent] -= wt[jptr];
if (!(index&1)) /* I am a right child */
wsum1 += (twt[parent] - twt[index]);
index=parent;
}
wsum3 = twt[0] - (wsum1 + wsum2);
lmean = wsum1/2;
umean = wsum1 + wsum2 + wsum3/2; /* new upper mean */
newmean = twt[0]/2;
myrank = wsum1 + wsum2/2;
vss += wsum1*(newmean+ oldmean - 2*lmean) * (newmean-oldmean);
oldmean -= wt[jptr]; /* the z in equations above */
vss += wsum3*(newmean+ oldmean -2*umean) * (newmean-oldmean);
vss -= wt[jptr]* (myrank -newmean)*(myrank -newmean);
}
/* Process deaths */
for (j=i; j <n && status[sort2[j]]==1 && time2[sort2[j]]==dtime; j++) {
jptr = sort2[j];
ndeath += wt[jptr];
index = indx[jptr];
for (k=i; k<j; k++) count[3] += wt[jptr]*wt[sort2[k]];
count[2] += wt[jptr] * nwt[index]; /* tied on x */
child = (2*index) +1; /* left child */
if (child < ntree) count[0] += wt[jptr] * twt[child];
child++;
if (child < ntree) count[1] += wt[jptr] * twt[child];
while (index >0) { /* walk up the tree */
parent = (index-1)/2;
if (index &1) /* I am the left child */
count[1] += wt[jptr] * (twt[parent] - twt[index]);
else count[0] += wt[jptr] * (twt[parent] - twt[index]);
index = parent;
}
}
}
else j = i+1;
/* Add the weights for these obs into the tree and compute variance */
for (; i<j; i++) {
wsum1 =0;
oldmean = twt[0]/2;
iptr = sort2[i];
index = indx[iptr];
nwt[index] += wt[iptr];
twt[index] += wt[iptr];
wsum2 = nwt[index];
child = 2*index +1; /* left child */
if (child < ntree) wsum1 += twt[child];
while (index >0) {
parent = (index-1)/2;
twt[parent] += wt[iptr];
if (!(index&1)) /* I am a right child */
wsum1 += (twt[parent] - twt[index]);
index=parent;
}
wsum3 = twt[0] - (wsum1 + wsum2);
lmean = wsum1/2;
umean = wsum1 + wsum2 + wsum3/2; /* new upper mean */
newmean = twt[0]/2;
myrank = wsum1 + wsum2/2;
vss += wsum1*(newmean+ oldmean - 2*lmean) * (newmean-oldmean);
vss += wsum3*(newmean+ oldmean +wt[iptr] - 2*umean) * (oldmean-newmean);
vss += wt[iptr]* (myrank -newmean)*(myrank -newmean);
}
count[4] += ndeath * vss/twt[0];
}
UNPROTECT(1);
return(count2);
}
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