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test_that("learners work: surv ", {
requirePackagesOrSkip("prodlim")
requirePackagesOrSkip("proMatrixdlim")
requirePackagesOrSkip("Hmisc", default.method = "load")
# settings to make learners faster and deal with small sample size
hyperpars = list(
surv.cforest = list(mtry = 1L)
)
# normal survival analysis
sub.task = subsetTask(surv.task, subset = c(1:70),
features = getTaskFeatureNames(surv.task)[c(1, 2)])
lrns = listLearnersCustom("surv", create = TRUE)
lapply(lrns, testThatLearnerParamDefaultsAreInParamSet)
lapply(lrns, testBasicLearnerProperties, task = sub.task,
hyperpars = hyperpars)
# survival analysis with factors
lrns = listLearnersCustom("surv", properties = "factors", create = TRUE)
lapply(lrns, testThatLearnerHandlesFactors, task = sub.task,
hyperpars = hyperpars)
# survival analysis with ordered factors
lrns = listLearnersCustom("surv", properties = "ordered", create = TRUE)
lapply(lrns, testThatLearnerHandlesFactors, task = sub.task,
hyperpars = hyperpars)
# surv with weights
# normal size of surv.task necessary otherwise cvglmnet does not converge
lrns = listLearnersCustom("surv", properties = "weights", create = TRUE)
suppressWarnings(
lapply(lrns, testThatLearnerRespectsWeights, hyperpars = hyperpars,
task = surv.task, train.inds = surv.train.inds,
test.inds = surv.test.inds,
weights = rep(c(1L, 5L), length.out = length(surv.train.inds)),
pred.type = "response", get.pred.fun = getPredictionResponse)
)
# survival with missings
lrns = listLearnersCustom("surv", properties = "missings", create = TRUE)
lapply(lrns, testThatLearnerHandlesMissings, task = sub.task,
hyperpars = hyperpars)
# surv with oobpreds
lrns = listLearnersCustom("surv", properties = "oobpreds", create = TRUE)
lapply(lrns, testThatGetOOBPredsWorks, task = sub.task)
# survival variable importance
lrns = listLearnersCustom("surv", properties = "featimp", create = TRUE)
lapply(lrns, testThatLearnerHandlesMissings, task = surv.task,
hyperpars = hyperpars)
foo = capture.output(lapply(lrns, testThatLearnerCanCalculateImportance, task = surv.task,
hyperpars = hyperpars))
})
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