Nothing
suppressWarnings(RNGversion("3.5.2"))
library("trtf")
library("survival")
library("partykit")
data("GBSG2", package = "TH.data")
set.seed(290875)
### Make UL and Windooze happy
options(digits = 5)
yvar <- numeric_var("y", support = c(100, 2000), bounds = c(0, Inf))
By <- Bernstein_basis(yvar, order = 5, ui = "incre")
m <- ctm(response = By, todistr = "MinExt")
GBSG2$y <- with(GBSG2, Surv(time, cens))
tf <- traforest(m, formula = y ~ horTh + age + menostat + tsize + tgrade +
pnodes + progrec + estrec, data = GBSG2,
control = ctree_control(splitstat = "quad", teststat = "quad",
testtype = "Teststatistic", mincriterion = 1, minbucket = 50),
ntree = 12, trace = FALSE, cores = 1)
predict(tf, newdata = GBSG2[1:3,], type = "weights")
predict(tf, newdata = GBSG2[1:3,], type = "node")
(cf <- predict(tf, newdata = GBSG2[1:3,], type = "coef"))
logLik(tf, newdata = GBSG2[1:3,])
sapply(1:length(tf$nodes), function(i) logLik(gettree(tf, i)))
varimp(tf)
mod <- mlt(m, data = GBSG2)
logLik(mod)
logLik(mod, newdata = GBSG2[1:3,])
layout(matrix(1:2, nr = 1))
coef(mod) <- cf[[1]]
plot(mod, newdata = data.frame(1), type = "survivor")
coef(mod) <- cf[[2]]
plot(mod, newdata = data.frame(1), type = "survivor", add = TRUE)
coef(mod) <- cf[[3]]
plot(mod, newdata = data.frame(1), type = "survivor", add = TRUE)
simulate(tf, newdata = GBSG2[1:3,], nsim = 3)
cmod <- coxph(Surv(time, cens) ~ horTh + age + menostat + tsize + tgrade +
pnodes + progrec + estrec, data = GBSG2)
plot(survfit(cmod, newdata = GBSG2[1:3,]))
### sanity checks; no mclapply on Windows
if (.Platform$OS.type != "windows") {
p11 <- predict(tf, newdata = GBSG2[1:11,], type = "weights")
p12 <- predict(tf, newdata = GBSG2[1:11,], type = "weights", cores = 2)
stopifnot(all.equal(p11, p12))
p21 <- predict(tf, newdata = GBSG2[1:11,], type = "node")
p22 <- predict(tf, newdata = GBSG2[1:11,], type = "node", cores = 2)
stopifnot(all.equal(p21, p22))
p31 <- predict(tf, newdata = GBSG2[1:11,])
p32 <- predict(tf, newdata = GBSG2[1:11,], cores = 2)
stopifnot(all.equal(p31, p32))
p41 <- predict(tf, newdata = GBSG2[1:11,], type = "coef")
p42 <- predict(tf, newdata = GBSG2[1:11,], cores = 2, type = "coef")
stopifnot(all.equal(p41, p42))
}
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