Nothing
## run BART and generate survival
## 08/26/15
surv.bart <- function(
x.train, y.train=NULL, times=NULL, delta=NULL,
x.test = matrix(0.0, 0L, 0L),
k = 2.0, ## BEWARE: do NOT use k for other purposes below
power = 2.0, base = 0.95,
binaryOffset = NULL,
ntree = 50L,
ndpost = 10000L, nskip = 250L,
printevery = 100L,
keepevery = 10L, keeptrainfits = TRUE,
usequants = FALSE, numcut = 100L, printcutoffs = 0L,
verbose = TRUE,
seed = 99L, ## not used here: only used by mc.surv.bart
mc.cores = 2L ## not used here: only used by mc.surv.bart
)
{
if(length(y.train)==0) {
surv <- surv.pre.bart(times, delta, x.train, x.test)
y.train <- surv$y.train
x.train <- surv$X.train
x.test <- surv$X.test
times <- surv$times
K <- surv$K
if(length(binaryOffset)==0) {
lambda <- sum(delta)/sum(times)
delta <- mean(times[2:K]-times[1:(K-1)])
binaryOffset <- qnorm(1-exp(-lambda*delta))
}
}
else {
if(length(binaryOffset)==0) binaryOffset <- 0
times <- unique(sort(x.train[ , 1]))
K <- length(times)
}
post <- bart(x.train=x.train, y.train=y.train, x.test=x.test,
k=k,
power=power, base=base,
binaryOffset=binaryOffset,
ntree=ntree,
ndpost=ndpost, nskip=nskip,
printevery=printevery, keepevery=keepevery, keeptrainfits=keeptrainfits,
usequants=usequants, numcut=numcut, printcutoffs=printcutoffs,
verbose=verbose)
post$times <- times
post$K <- K
if(length(x.test)>0) {
H <- nrow(x.test)/K ## the number of different settings
post$surv.test <- 1-pnorm(post$yhat.test)
for(h in 1:H) for(j in 2:K)
post$surv.test[ , K*(h-1)+j] <-
post$surv.test[ , K*(h-1)+j-1]*post$surv.test[ , K*(h-1)+j]
post$surv.test.mean <- apply(post$surv.test, 2, mean)
}
return(post)
}
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