tests/testthat/test_paramtest_xgboost_surv_xgboost.R

In mlr-org/mlr3extralearners: Extra Learners For mlr3

x = rvest::read_html("https://xgboost.readthedocs.io/en/latest/parameter.html")
xli = rvest::html_elements(x, "li")
xp = rvest::html_elements(x, "p")
x = c(rvest::html_text2(xli), rvest::html_text2(xp))
x = grep("default=", x, value = TRUE)
x = strsplit(x, split = " ")
x = mlr3misc::map_chr(x, function(x) x[1])
x = gsub(",", replacement = "", x)
# these are defined on the same line as colsample_bytree and cannot be scraped therefore
x = append(x, values = c("colsample_bylevel", "colsample_bynode", "base_score"))
# values which do not match regex
x = append(x, values = c("interaction_constraints", "monotone_constraints", "base_score"))
# only defined in help page but not in signature or website
x = append(x, values = "lambda_bias")
add_params_xgboost = x

test_that("surv.xgboost", {
  learner = suppressWarnings(lrn("surv.xgboost"))
  learner_cox = lrn("surv.xgboost.cox")
  learner_aft = lrn("surv.xgboost.aft")
  fun = list(xgboost::xgb.train, xgboost::xgboost, add_params_xgboost)
  exclude = c(
    "x", # handled by mlr3
    "params", # handled by mlr3
    "data", # handled by mlr3
    "obj", # handled via type parameter
    "verbosity", # handled by mlr3
    "seed", # not available in R package
    "train", # handled by mlr3
    "task", # handled by mlr3
    "model_in", # handled by mlr3
    "model_out", # handled by mlr3
    "model_dir", # handled by mlr3
    "dump_format", # CLI parameter, not for R package
    "name_dump", # CLI parameter, not for R package
    "name_pred", # CLI parameter, not for R package
    "pred_margin", # CLI parameter, not for R package
    "eval_metric", # handled by mlr3
    "objective", # handled by mlr3
    "label", # handled by mlr3
    "weight", # handled by mlr3
    "nthread", # handled by mlr3
    "early_stopping_set", # handled by mlr3
    "aft_loss_distribution", # survival specific
    "aft_loss_distribution_scale" # survival specific
  )

  paramtest = run_paramtest(learner, fun, exclude, tag = "train")
  expect_paramtest(paramtest)
  paramtest_cox = run_paramtest(learner_cox, fun, exclude, tag = "train")
  expect_paramtest(paramtest_cox)
  paramtest_aft = run_paramtest(learner_aft, fun, exclude, tag = "train")
  expect_paramtest(paramtest_aft)
})

test_that("predict surv.xgboost", {
  learner = suppressWarnings(lrn("surv.xgboost"))
  learner_cox = lrn("surv.xgboost.cox")
  learner_aft = lrn("surv.xgboost.aft")

  fun = xgboost:::predict.xgb.Booster # nolint
  exclude = c(
    "object", # handled by mlr3
    "newdata", # handled by mlr3
    "outputmargin", # always FALSE
    "predleaf", # always FALSE
    "predcontrib", # always FALSE
    "approxcontrib", # unused
    "predinteraction", # always FALSE
    "reshape", # handled internally
    "training", # always FALSE
    "objective", # handled by mlr3
    "ntreelimit" # doc says "deprecated, use 'iterationrange' instead"
  )

  paramtest = run_paramtest(learner, fun, exclude, tag = "predict")
  expect_paramtest(paramtest)
  paramtest_cox = run_paramtest(learner_cox, fun, exclude, tag = "predict")
  expect_paramtest(paramtest_cox)
  paramtest_aft = run_paramtest(learner_aft, fun, exclude, tag = "predict")
  expect_paramtest(paramtest_aft)
})