View source: R/predict.xgb.Booster.surv.R
predict.xgb.Booster.surv | R Documentation |
predict.xgb.Booster.surv
is a method for xgb.Booster.surv
objects that enables preidcting either risk (implemented also in the xgboost package)
or the full survival curve.
## S3 method for class 'xgb.Booster.surv'
predict(object, newdata, type = "risk", times = NULL)
object |
an xgb.Booster.surv object obtained by |
newdata |
a data.frame/matrix to make predictions for |
type |
either "risk" or "surv" |
times |
times at which to estimate the survival curve at. Default is original dataset unique death times. |
for type = "risk"
a vector of risk scores, for type = "surv"
a matrix with
columns corresponding to times and rows corresponding to input newdata rows.
xgb.train.surv
library(survival)
data("lung")
library(survXgboost)
library(xgboost)
lung <- lung[complete.cases(lung), ] # doesn't handle missing values at the moment
lung$status <- lung$status - 1 # format status variable correctly such that 1 is event/death and 0 is censored/alive
label <- ifelse(lung$status == 1, lung$time, -lung$time)
val_ind <- sample.int(nrow(lung), 0.1 * nrow(lung))
x_train <- as.matrix(lung[-val_ind, !names(lung) %in% c("time", "status")])
x_label <- label[-val_ind]
x_val <- xgb.DMatrix(as.matrix(lung[val_ind, !names(lung) %in% c("time", "status")]),
label = label[val_ind])
# train surv_xgboost
surv_xgboost_model <- xgb.train.surv(
params = list(
objective = "survival:cox",
eval_metric = "cox-nloglik",
eta = 0.05 # larger eta leads to algorithm not converging, resulting in NaN predictions
), data = x_train, label = x_label,
watchlist = list(val2 = x_val),
nrounds = 1000, early_stopping_rounds = 30
)
# predict survival curves
times <- seq(10, 1000, 50)
survival_curves <- predict(object = surv_xgboost_model, newdata = x_train, type = "surv", times = times)
matplot(times, t(survival_curves[1:5, ]), type = "l")
# predict risk score
risk_scores <- predict(object = surv_xgboost_model, newdata = x_train, type = "risk")
hist(risk_scores)
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