Nothing
# testthat for gg_vimp function
context("partial.rfsrc tests")
test_that("partial.rfsrc regression", {
## Load the cached forest
data(Boston, package = "MASS")
Boston$chas <- as.logical(Boston$chas)
rfsrc_boston <- rfsrc(medv ~ ., data = Boston, ntree = 100)
# Test the cached forest type
expect_is(rfsrc_boston, "rfsrc")
xvar <- c("lstat", "chas")
## Create the correct object
skip("Skip: Test currently fails (partial.rfsrc problem)")
gg_dta <- partial.rfsrc(rfsrc_boston,
xvar.names = xvar,
npts = 10)
expect_equal(gg_dta$xvar.names, xvar)
expect_equal(names(gg_dta$pData), xvar)
expect_equal(gg_dta$pData[[1]]$xvar.name, xvar[1])
expect_equal(gg_dta$pData[[2]]$xvar.name, xvar[2])
expect_equal(length(gg_dta$pData[[1]]$yhat), 10)
expect_equal(length(gg_dta$pData[[2]]$yhat),
length(unique(rfsrc_boston$xvar$chas)))
## Correct npts spec.
gg_dta <- partial.rfsrc(rfsrc_boston,
xvar.names = c("lstat", "chas"),
npts = -1)
## Number of vars spec.
gg_dta <- partial.rfsrc(rfsrc_boston,
nvar = 2,
npts = 3)
## subset by row numbers
gg_dta <- partial.rfsrc(rfsrc_boston,
xvar.names = c("rm"),
subset = which(rfsrc_boston$xvar$chas == 1),
npts = 3)
## subset by logicals
gg_dta <- partial.rfsrc(rfsrc_boston,
xvar.names = c("rm"),
subset = rfsrc_boston$xvar$chas == 1,
npts = 3)
##incorrect subset
expect_error(partial.rfsrc(rfsrc_boston,
xvar.names = c("rm"),
subset = FALSE,
npts = 10))
})
test_that("partial.rfsrc survival", {
## Load the cached forest
data(pbc, package = "randomForestSRC")
# For whatever reason, the age variable is in days... makes no sense to me
for (ind in seq_len(dim(pbc)[2])) {
if (!is.factor(pbc[, ind])) {
if (length(unique(pbc[which(!is.na(pbc[, ind])), ind])) <= 2) {
if (sum(range(pbc[, ind], na.rm = TRUE) == c(0, 1)) == 2) {
pbc[, ind] <- as.logical(pbc[, ind])
}
}
} else {
if (length(unique(pbc[which(!is.na(pbc[, ind])), ind])) <= 2) {
if (sum(sort(unique(pbc[, ind])) == c(0, 1)) == 2) {
pbc[, ind] <- as.logical(pbc[, ind])
}
if (sum(sort(unique(pbc[, ind])) == c(FALSE, TRUE)) == 2) {
pbc[, ind] <- as.logical(pbc[, ind])
}
}
}
if (!is.logical(pbc[, ind]) &
length(unique(pbc[which(!is.na(pbc[, ind])), ind])) <= 5) {
pbc[, ind] <- factor(pbc[, ind])
}
}
# Convert age to years
pbc$age <- pbc$age / 364.24
pbc$years <- pbc$days / 364.24
pbc <- pbc[, -which(colnames(pbc) == "days")]
pbc$treatment <- as.numeric(pbc$treatment)
pbc$treatment[which(pbc$treatment == 1)] <- "DPCA"
pbc$treatment[which(pbc$treatment == 2)] <- "placebo"
pbc$treatment <- factor(pbc$treatment)
dta_train <- pbc[-which(is.na(pbc$treatment)), ]
# Create a test set from the remaining patients
pbc_test <- pbc[which(is.na(pbc$treatment)), ]
rfsrc_pbc <- rfsrc(Surv(years, status) ~ .,
dta_train, nsplit = 10,
na.action = "na.impute", ntree = 100)
# Test the cached forest type
expect_is(rfsrc_pbc, "rfsrc")
xvar <- c("age", "copper")
## Create the correct object
skip("Skip: Test currently fails (partial.rfsrc problem)")
gg_dta <- partial.rfsrc(rfsrc_pbc,
xvar.names = xvar,
npts = 10, surv.type = "surv")
expect_equal(gg_dta$xvar.names, xvar)
expect_equal(names(gg_dta$pData), xvar)
expect_equal(gg_dta$pData[[1]]$xvar.name, xvar[1])
expect_equal(gg_dta$pData[[2]]$xvar.name, xvar[2])
expect_equal(length(gg_dta$pData[[1]]$yhat), 10)
# pretend we have an unsupervised forest
rfsrc_pbc$family <- "unsupv"
expect_error(partial.rfsrc(rfsrc_pbc,
npts = 10))
})
test_that("partial.rfsrc classification", {
## Load the cached forest
rfsrc_iris <- rfsrc(Species ~ ., data = iris, ntree = 100)
partial_iris <- randomForestSRC::plot.variable(rfsrc_iris,
partial = TRUE,
show.plots = FALSE)
# Test the cached forest type
expect_is(rfsrc_iris, "rfsrc")
skip("Skip: Test currently fails (partial.rfsrc problem)")
## Create the correct object
gg_dta <- partial.rfsrc(rfsrc_iris,
npts = 10)
## Create the correct object
gg_dta <- partial.rfsrc(rfsrc_iris,
npts = 10, which.outcome = "versicolor")
## Create the correct object
gg_dta <- partial.rfsrc(rfsrc_iris,
npts = 10, which.outcome = 2)
# Wrong "rfsrc" type
expect_error(partial.rfsrc(partial_iris,
npts = 10))
# No "forest" stored in rfsrc object
rfsrc_iris$forest <- NULL
expect_error(partial.rfsrc(rfsrc_iris,
npts = 10))
# Incorrect xvar name.
expect_error(partial.rfsrc(rfsrc_iris, xvar.names = "lmstat",
npts = 10))
})
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