Description Usage Arguments Value Author(s) References See Also Examples
Survival data contained in (t,δ, x) must be translated to data
suitable for the BART survival analysis model; see surv.bart
for more details.
1 | surv.pre.bart( times, delta, x.train=NULL, x.test=NULL )
|
times |
The time of event or right-censoring. |
delta |
The event indicator: 1 is an event while 0 is censored. |
x.train |
Explanatory variables for training (in sample) data. |
x.test |
Explanatory variables for test (out of sample) data. |
surv.pre.bart
returns a list.
Besides the items listed below, the list has
a times
component giving the unique times and K
which is the number of
unique times.
y.train |
A vector of binary responses. |
X.train |
A matrix with the rows of the training data. |
X.test |
A matrix with the rows of the test data, if any. |
Rodney Sparapani: rsparapa@mcw.edu
Sparapani, R., Logan, B., McCulloch, R., and Laud, P. (2016) Nonparametric survival analysis using Bayesian Additive Regression Trees (BART). Statistics in Medicine, 16:2741-53.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 | ## Not run:
require(survbart)
## load survival package for the advanced lung cancer example
require(survival)
group <- -which(is.na(lung[ , 7])) ## remove missing row for ph.karno
times <- lung[group, 2] ##lung$time
delta <- lung[group, 3]-1 ##lung$status: 1=censored, 2=dead
##delta: 0=censored, 1=dead
summary(times)
table(delta)
x.train <- as.matrix(lung[group, c(4, 5, 7)]) ## matrix of observed covariates
## lung$age: Age in years
## lung$sex: Male=1 Female=2
## lung$ph.karno: Karnofsky performance score (dead=0:normal=100:by=10)
## rated by physician
dimnames(x.train)[[2]] <- c('age(yr)', 'M(1):F(2)', 'ph.karno(0:100:10)')
summary(x.train[ , 1])
table(x.train[ , 2])
table(x.train[ , 3])
x.test <- matrix(nrow=84, ncol=3) ## matrix of covariate scenarios
dimnames(x.test)[[2]] <- dimnames(x.train)[[2]]
i <- 1
for(age in 5*(9:15)) for(sex in 1:2) for(ph.karno in 10*(5:10)) {
x.test[i, ] <- c(age, sex, ph.karno)
i <- i+1
}
data.constructed <- surv.pre.bart(times=times, delta=delta, x.train=x.train, x.test=x.test)
## End(Not run)
|
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