From b9345b4ed45e8cc3ae7e5f40406a7ebe9832753b Mon Sep 17 00:00:00 2001 From: Sebastian Fischer Date: Tue, 3 Dec 2024 09:23:36 +0100 Subject: [PATCH 1/2] ... --- DESCRIPTION | 2 +- LICENSE | 165 ++++++++++++++++++ NEWS.md | 2 + R/learner_ranger_surv_ranger.R | 5 +- tests/testthat/test_C50_classif_C50.R | 2 +- .../test_paramtest_ranger_surv_ranger.R | 3 +- 6 files changed, 174 insertions(+), 5 deletions(-) create mode 100644 LICENSE diff --git a/DESCRIPTION b/DESCRIPTION index 18661ef99..c10ded999 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -88,7 +88,7 @@ Suggests: randomForest, randomPlantedForest, randomForestSRC (>= 3.3.0), - ranger (>= 0.16.0), + rangera(>= 0.17.0), remotes, reticulate (>= 1.16), rpart, diff --git a/LICENSE b/LICENSE new file mode 100644 index 000000000..0a041280b --- /dev/null +++ b/LICENSE @@ -0,0 +1,165 @@ + GNU LESSER GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + + This version of the GNU Lesser General Public License incorporates +the terms and conditions of version 3 of the GNU General Public +License, supplemented by the additional permissions listed below. + + 0. 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Combined Libraries. + + You may place library facilities that are a work based on the +Library side by side in a single library together with other library +facilities that are not Applications and are not covered by this +License, and convey such a combined library under terms of your +choice, if you do both of the following: + + a) Accompany the combined library with a copy of the same work based + on the Library, uncombined with any other library facilities, + conveyed under the terms of this License. + + b) Give prominent notice with the combined library that part of it + is a work based on the Library, and explaining where to find the + accompanying uncombined form of the same work. + + 6. Revised Versions of the GNU Lesser General Public License. + + The Free Software Foundation may publish revised and/or new versions +of the GNU Lesser General Public License from time to time. Such new +versions will be similar in spirit to the present version, but may +differ in detail to address new problems or concerns. + + Each version is given a distinguishing version number. If the +Library as you received it specifies that a certain numbered version +of the GNU Lesser General Public License "or any later version" +applies to it, you have the option of following the terms and +conditions either of that published version or of any later version +published by the Free Software Foundation. If the Library as you +received it does not specify a version number of the GNU Lesser +General Public License, you may choose any version of the GNU Lesser +General Public License ever published by the Free Software Foundation. + + If the Library as you received it specifies that a proxy can decide +whether future versions of the GNU Lesser General Public License shall +apply, that proxy's public statement of acceptance of any version is +permanent authorization for you to choose that version for the +Library. diff --git a/NEWS.md b/NEWS.md index 7f6d1a1a1..40d5ece44 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # dev +* Add missing `na.action` parameter to `lrn("surv.ranger")` + # mlr3extralearners 1.0.0 * Add "Prediction types" doc section for all 30 survival learners + make sure it is consistent #347 diff --git a/R/learner_ranger_surv_ranger.R b/R/learner_ranger_surv_ranger.R index 3e0a2afbe..c53ae1b1a 100644 --- a/R/learner_ranger_surv_ranger.R +++ b/R/learner_ranger_surv_ranger.R @@ -86,7 +86,8 @@ LearnerSurvRanger = R6Class("LearnerSurvRanger", write.forest = p_lgl(default = TRUE, tags = "train"), min.bucket = p_int(default = 3, tags = "train"), time.interest = p_int(default = NULL, lower = 1L, special_vals = list(NULL), tags = "train"), - node.stats = p_lgl(default = FALSE, tags = "train") + node.stats = p_lgl(default = FALSE, tags = "train"), + na.action = p_fct(default = "na.learn", c("na.learn", "na.omit", "na.fail")) ) ps$values = list(num.threads = 1L) @@ -96,7 +97,7 @@ LearnerSurvRanger = R6Class("LearnerSurvRanger", param_set = ps, predict_types = c("crank", "distr"), feature_types = c("logical", "integer", "numeric", "character", "factor", "ordered"), - properties = c("weights", "importance", "oob_error"), + properties = c("weights", "importance", "oob_error", "missings"), packages = c("mlr3extralearners", "ranger"), man = "mlr3extralearners::mlr_learners_surv.ranger", label = "Random Forest" diff --git a/tests/testthat/test_C50_classif_C50.R b/tests/testthat/test_C50_classif_C50.R index ec78501d8..e1f3dac17 100644 --- a/tests/testthat/test_C50_classif_C50.R +++ b/tests/testthat/test_C50_classif_C50.R @@ -1,6 +1,6 @@ test_that("autotest", { learner = LearnerClassifC50$new() - learner$param_set$values = list(trials = 30L) + learner$param_set$values = list(trials = 1L) expect_learner(learner) result = run_autotest(learner) expect_true(result, info = result$error) diff --git a/tests/testthat/test_paramtest_ranger_surv_ranger.R b/tests/testthat/test_paramtest_ranger_surv_ranger.R index 0b1cfb779..e5b6102ab 100644 --- a/tests/testthat/test_paramtest_ranger_surv_ranger.R +++ b/tests/testthat/test_paramtest_ranger_surv_ranger.R @@ -15,7 +15,8 @@ test_that("surv.ranger", { "status.variable.name", # handled via mlr3 "classification", # handled via mlr3 "quantreg", # regression only - "mtry.ratio" # custom hyperpar + "mtry.ratio", # custom hyperpar + "poisson.tau" # for poisson splitrule ) paramtest = run_paramtest(learner, fun, exclude, tag = "train") From f2fb05effeaf241db913936c8faa5f20d469ea5a Mon Sep 17 00:00:00 2001 From: Sebastian Fischer Date: Tue, 3 Dec 2024 09:50:14 +0100 Subject: [PATCH 2/2] ... --- DESCRIPTION | 2 +- NEWS.md | 2 -- R/learner_ranger_surv_ranger.R | 5 ++--- tests/testthat/test_paramtest_ranger_surv_ranger.R | 3 ++- 4 files changed, 5 insertions(+), 7 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index c10ded999..aeb57e9d3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -88,7 +88,7 @@ Suggests: randomForest, randomPlantedForest, randomForestSRC (>= 3.3.0), - rangera(>= 0.17.0), + ranger (>= 0.17.0), remotes, reticulate (>= 1.16), rpart, diff --git a/NEWS.md b/NEWS.md index 40d5ece44..7f6d1a1a1 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,7 +1,5 @@ # dev -* Add missing `na.action` parameter to `lrn("surv.ranger")` - # mlr3extralearners 1.0.0 * Add "Prediction types" doc section for all 30 survival learners + make sure it is consistent #347 diff --git a/R/learner_ranger_surv_ranger.R b/R/learner_ranger_surv_ranger.R index c53ae1b1a..3e0a2afbe 100644 --- a/R/learner_ranger_surv_ranger.R +++ b/R/learner_ranger_surv_ranger.R @@ -86,8 +86,7 @@ LearnerSurvRanger = R6Class("LearnerSurvRanger", write.forest = p_lgl(default = TRUE, tags = "train"), min.bucket = p_int(default = 3, tags = "train"), time.interest = p_int(default = NULL, lower = 1L, special_vals = list(NULL), tags = "train"), - node.stats = p_lgl(default = FALSE, tags = "train"), - na.action = p_fct(default = "na.learn", c("na.learn", "na.omit", "na.fail")) + node.stats = p_lgl(default = FALSE, tags = "train") ) ps$values = list(num.threads = 1L) @@ -97,7 +96,7 @@ LearnerSurvRanger = R6Class("LearnerSurvRanger", param_set = ps, predict_types = c("crank", "distr"), feature_types = c("logical", "integer", "numeric", "character", "factor", "ordered"), - properties = c("weights", "importance", "oob_error", "missings"), + properties = c("weights", "importance", "oob_error"), packages = c("mlr3extralearners", "ranger"), man = "mlr3extralearners::mlr_learners_surv.ranger", label = "Random Forest" diff --git a/tests/testthat/test_paramtest_ranger_surv_ranger.R b/tests/testthat/test_paramtest_ranger_surv_ranger.R index e5b6102ab..923bd95f8 100644 --- a/tests/testthat/test_paramtest_ranger_surv_ranger.R +++ b/tests/testthat/test_paramtest_ranger_surv_ranger.R @@ -16,7 +16,8 @@ test_that("surv.ranger", { "classification", # handled via mlr3 "quantreg", # regression only "mtry.ratio", # custom hyperpar - "poisson.tau" # for poisson splitrule + "poisson.tau", # for poisson splitrule + "na.action" # not yet implemented for survival forest ) paramtest = run_paramtest(learner, fun, exclude, tag = "train")