CRAN release v2.3.2 (#240)

* Bump version to 2.3.1.9000 * CRAN comments * Bump version to 2.3.2 * update snapshots * add CITATION * update DESCRIPTION * man/ * replace boston_housing with mtcars * roxygen * update cran comments * roxygen * precommit * use DOI
mlr-org · Dec 9, 2024 · 36fcb4d · 36fcb4d
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -2,7 +2,7 @@
 # R specific hooks: https://github.com/lorenzwalthert/precommit
 repos:
   - repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.3.2.9027
+    rev: v0.4.3.9003
     hooks:
       - id: style-files
         args: [--style_pkg=styler.mlr, --style_fun=mlr_style]
@@ -33,7 +33,7 @@ repos:
       # uncomment after https://github.com/lorenzwalthert/precommit/issues/352
       # - id: deps-in-desc
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v5.0.0
     hooks:
       - id: check-added-large-files
         args: ["--maxkb=1000"]

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: mlr3spatiotempcv
 Title: Spatiotemporal Resampling Methods for 'mlr3'
-Version: 2.3.1
+Version: 2.3.2
 Authors@R: c(
     person("Patrick", "Schratz", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-0748-6624")),
@@ -11,10 +11,11 @@ Authors@R: c(
     person("Michel", "Lang", , "[email protected]", role = "ctb",
            comment = c(ORCID = "0000-0001-9754-0393"))
   )
-Description: Extends the mlr3 ML framework with spatio-temporal resampling
-    methods to account for the presence of spatiotemporal autocorrelation
-    (STAC) in predictor variables. STAC may cause highly biased
-    performance estimates in cross-validation if ignored.
+Description: Extends the mlr3 machine learning framework with
+    spatio-temporal resampling methods to account for the presence of
+    spatiotemporal autocorrelation (STAC) in predictor variables. STAC may
+    cause highly biased performance estimates in cross-validation if
+    ignored. A JSS article is available at <doi:10.18637/jss.v111.i07>.
 License: LGPL-3
 URL: https://mlr3spatiotempcv.mlr-org.com/,
     https://github.com/mlr-org/mlr3spatiotempcv,
@@ -64,7 +65,7 @@ Encoding: UTF-8
 LazyData: true
 NeedsCompilation: no
 Roxygen: list(markdown = TRUE, r6 = TRUE)
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.2
 Collate: 
     'aaa.R'
     'ResamplingRepeatedSpCVBlock.R'

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,10 @@
 <!-- NEWS.md is maintained by https://fledge.cynkra.com, contributors should not edit this file -->
 
+# mlr3spatiotempcv 2.3.2
+
+- Internal changes only.
+
+
 # mlr3spatiotempcv 2.3.1
 
 - Add support for new {paradox} version (#234)

diff --git a/R/ResamplingRepeatedSpCVBlock.R b/R/ResamplingRepeatedSpCVBlock.R
@@ -102,7 +102,7 @@ ResamplingRepeatedSpCVBlock = R6Class("ResamplingRepeatedSpCVBlock",
 
     #' @description
     #'  Materializes fixed training and test splits for a given task.
-    #' @param task [Task]\cr
+    #' @param task [mlr3::Task]\cr
     #'  A task to instantiate.
     instantiate = function(task) {
 

diff --git a/R/ResamplingRepeatedSpCVCoords.R b/R/ResamplingRepeatedSpCVCoords.R
@@ -73,7 +73,7 @@ ResamplingRepeatedSpCVCoords = R6Class("ResamplingRepeatedSpCVCoords",
 
     #' @description
     #'  Materializes fixed training and test splits for a given task.
-    #' @param task [Task]\cr
+    #' @param task [mlr3::Task]\cr
     #'  A task to instantiate.
     instantiate = function(task) {
 

diff --git a/R/ResamplingRepeatedSpCVDisc.R b/R/ResamplingRepeatedSpCVDisc.R
@@ -83,7 +83,7 @@ ResamplingRepeatedSpCVDisc = R6Class("ResamplingRepeatedSpCVDisc",
 
     #' @description
     #'  Materializes fixed training and test splits for a given task.
-    #' @param task [Task]\cr
+    #' @param task [mlr3::Task]\cr
     #'  A task to instantiate.
     instantiate = function(task) {
 

diff --git a/R/ResamplingRepeatedSpCVEnv.R b/R/ResamplingRepeatedSpCVEnv.R
@@ -73,7 +73,7 @@ ResamplingRepeatedSpCVEnv = R6Class("ResamplingRepeatedSpCVEnv",
 
     #' @description
     #'  Materializes fixed training and test splits for a given task.
-    #' @param task [Task]\cr
+    #' @param task [mlr3::Task]\cr
     #'  A task to instantiate.
     instantiate = function(task) {
 

diff --git a/R/ResamplingRepeatedSpCVTiles.R b/R/ResamplingRepeatedSpCVTiles.R
@@ -100,7 +100,7 @@ ResamplingRepeatedSpCVTiles = R6Class("ResamplingRepeatedSpCVTiles",
 
     #' @description
     #'  Materializes fixed training and test splits for a given task.
-    #' @param task [Task]\cr
+    #' @param task [mlr3::Task]\cr
     #'  A task to instantiate.
     instantiate = function(task) {
 

diff --git a/R/ResamplingRepeatedSpCVknndm.R b/R/ResamplingRepeatedSpCVknndm.R
@@ -96,7 +96,7 @@ ResamplingRepeatedSpCVKnndm = R6Class("ResamplingRepeatedSpCVKnndm",
 
     #' @description
     #'  Materializes fixed training and test splits for a given task.
-    #' @param task [Task]\cr
+    #' @param task [mlr3::Task]\cr
     #'  A task to instantiate.
     instantiate = function(task) {
 

diff --git a/R/ResamplingRepeatedSptCVCstf.R b/R/ResamplingRepeatedSptCVCstf.R
@@ -74,7 +74,7 @@ ResamplingRepeatedSptCVCstf = R6Class("ResamplingRepeatedSptCVCstf",
 
     #' @description
     #'  Materializes fixed training and test splits for a given task.
-    #' @param task [Task]\cr
+    #' @param task [mlr3::Task]\cr
     #'   A task to instantiate.
     instantiate = function(task) {
       task = assert_task(task)

diff --git a/R/ResamplingSpCVBlock.R b/R/ResamplingSpCVBlock.R
@@ -73,7 +73,7 @@ ResamplingSpCVBlock = R6Class("ResamplingSpCVBlock",
 
     #' @description
     #'  Materializes fixed training and test splits for a given task.
-    #' @param task [Task]\cr
+    #' @param task [mlr3::Task]\cr
     #'  A task to instantiate.
     instantiate = function(task) {
       mlr3misc::require_namespaces(c("blockCV", "sf"))

diff --git a/R/ResamplingSpCVBuffer.R b/R/ResamplingSpCVBuffer.R
@@ -54,7 +54,7 @@ ResamplingSpCVBuffer = R6Class("ResamplingSpCVBuffer",
 
     #' @description
     #'  Materializes fixed training and test splits for a given task.
-    #' @param task [Task]\cr
+    #' @param task [mlr3::Task]\cr
     #'  A task to instantiate.
     instantiate = function(task) {
 

diff --git a/R/ResamplingSpCVCoords.R b/R/ResamplingSpCVCoords.R
@@ -48,7 +48,7 @@ ResamplingSpCVCoords = R6Class("ResamplingSpCVCoords",
 
     #' @description
     #'  Materializes fixed training and test splits for a given task.
-    #' @param task [Task]\cr
+    #' @param task [mlr3::Task]\cr
     #'  A task to instantiate.
     instantiate = function(task) {
 

diff --git a/R/ResamplingSpCVDisc.R b/R/ResamplingSpCVDisc.R
@@ -58,7 +58,7 @@ ResamplingSpCVDisc = R6Class("ResamplingSpCVDisc",
 
     #' @description
     #'  Materializes fixed training and test splits for a given task.
-    #' @param task [Task]\cr
+    #' @param task [mlr3::Task]\cr
     #'  A task to instantiate.
     instantiate = function(task) {
 

diff --git a/R/ResamplingSpCVEnv.R b/R/ResamplingSpCVEnv.R
@@ -53,7 +53,7 @@ ResamplingSpCVEnv = R6Class("ResamplingSpCVEnv",
 
     #' @description
     #'  Materializes fixed training and test splits for a given task.
-    #' @param task [Task]\cr
+    #' @param task [mlr3::Task]\cr
     #'  A task to instantiate.
     instantiate = function(task) {
 

diff --git a/R/ResamplingSpCVKnndm.R b/R/ResamplingSpCVKnndm.R
@@ -74,7 +74,7 @@ ResamplingSpCVKnndm = R6Class("ResamplingSpCVKnndm",
 
     #' @description
     #'  Materializes fixed training and test splits for a given task.
-    #' @param task [Task]\cr
+    #' @param task [mlr3::Task]\cr
     #'   A task to instantiate.
     instantiate = function(task) {
       task = assert_task(task)

diff --git a/R/ResamplingSpCVTiles.R b/R/ResamplingSpCVTiles.R
@@ -57,7 +57,7 @@ ResamplingSpCVTiles = R6Class("ResamplingSpCVTiles",
 
     #' @description
     #'  Materializes fixed training and test splits for a given task.
-    #' @param task [Task]\cr
+    #' @param task [mlr3::Task]\cr
     #'  A task to instantiate.
     instantiate = function(task) {
 

diff --git a/R/ResamplingSptCVCstf.R b/R/ResamplingSptCVCstf.R
@@ -52,7 +52,7 @@ ResamplingSptCVCstf = R6Class("ResamplingSptCVCstf",
 
     #' @description
     #'  Materializes fixed training and test splits for a given task.
-    #' @param task [Task]\cr
+    #' @param task [mlr3::Task]\cr
     #'   A task to instantiate.
     instantiate = function(task) {
       task = assert_task(task)

diff --git a/R/TaskClassifST.R b/R/TaskClassifST.R
@@ -1,6 +1,6 @@
 #' @title Create a Spatiotemporal Classification Task
 #'
-#' @description This task specializes [Task] and [TaskSupervised] for
+#' @description This task specializes [mlr3::Task] and [mlr3::TaskSupervised] for
 #' spatiotemporal classification problems. The target column is assumed to be a
 #' factor. The `task_type` is set to `"classif"` and `"spatiotemporal"`.
 #'

diff --git a/R/TaskRegrST.R b/R/TaskRegrST.R
@@ -1,7 +1,7 @@
 #' @title Create a Spatiotemporal Regression Task
 #'
 #' @description
-#' This task specializes [Task] and [TaskSupervised] for spatiotemporal
+#' This task specializes [mlr3::Task] and [mlr3::TaskSupervised] for spatiotemporal
 #' classification problems.
 #'
 #' A spatial example task is available via `tsk("ecuador")`, a spatiotemporal

diff --git a/R/Task_classif_diplodia.R b/R/Task_classif_diplodia.R
@@ -3,7 +3,7 @@
 #' @docType data
 #' @usage data(diplodia)
 #' @name mlr_tasks_diplodia
-#' @format [R6::R6Class] inheriting from [TaskClassif].
+#' @format [R6::R6Class] inheriting from [mlr3::TaskClassif].
 #'
 #' @section Usage:
 #' ```

diff --git a/R/Task_classif_ecuador.R b/R/Task_classif_ecuador.R
@@ -3,7 +3,7 @@
 #' @docType data
 #' @usage data(ecuador)
 #' @name mlr_tasks_ecuador
-#' @format [R6::R6Class] inheriting from [TaskClassif].
+#' @format [R6::R6Class] inheriting from [mlr3::TaskClassif].
 #'
 #' @section Usage:
 #' ```

diff --git a/R/Task_regr_cookfarm_profiles.R b/R/Task_regr_cookfarm_profiles.R
@@ -3,7 +3,7 @@
 #' @docType data
 #' @usage data(cookfarm_mlr3)
 #' @name mlr_tasks_cookfarm_mlr3
-#' @format [R6::R6Class] inheriting from [TaskRegr].
+#' @format [R6::R6Class] inheriting from [mlr3::TaskRegr].
 #'
 #' @section Usage:
 #' ```

diff --git a/R/as_task_classif_st.R b/R/as_task_classif_st.R
@@ -5,10 +5,10 @@
 #' This is a S3 generic for the following objects:
 #'
 #' 1. [TaskClassifST]: Ensure the identity.
-#' 1. [data.frame()] and [DataBackend]: Provides an alternative to the
+#' 1. [data.frame()] and [mlr3::DataBackend]: Provides an alternative to the
 #'    constructor of [TaskClassifST].
 #' 1. [sf::sf]: Extracts spatial meta data before construction.
-#' 1. [TaskRegr]: Calls [convert_task()].
+#' 1. [mlr3::TaskRegr]: Calls [mlr3::convert_task()].
 #'
 #' @param x (any)\cr
 #'   Object to convert.

diff --git a/R/as_task_regr_st.R b/R/as_task_regr_st.R
@@ -6,10 +6,10 @@
 #' This is a S3 generic, specialized for at least the following objects:
 #'
 #' 1. [TaskRegrST]: Ensure the identity.
-#' 1. [data.frame()] and [DataBackend]: Provides an alternative to the
+#' 1. [data.frame()] and [mlr3::DataBackend]: Provides an alternative to the
 #'    constructor of [TaskRegrST].
 #' 1. [sf::sf]: Extracts spatial meta data before construction.
-#' 1. [TaskClassif]: Calls [convert_task()].
+#' 1. [mlr3::TaskClassif]: Calls [mlr3::convert_task()].
 #'
 #' @param x (any)\cr
 #'   Object to convert.

diff --git a/R/autoplot.R b/R/autoplot.R
@@ -48,7 +48,7 @@
 #' When no single fold is selected, the [ggsci::scale_color_ucscgb()] palette
 #' is used to display all partitions.
 #' If you want to change the colors, call `<plot> + <color-palette>()`.
-#' @return [ggplot()] or list of ggplot2 objects.
+#' @return [ggplot2::ggplot()] or list of ggplot2 objects.
 #' @name autoplot.ResamplingSpCVBlock
 #' @seealso
 #'   - mlr3book chapter on ["Spatial Analysis"](https://mlr3book.mlr-org.com/chapters/chapter13/beyond_regression_and_classification.html#sec-spatiotemporal)
@@ -874,11 +874,11 @@ plot.ResamplingRepeatedSpCVKnndm = function(x, ...) {
 #'
 #' @name autoplot.ResamplingCV
 #' @param object `[Resampling]`\cr
-#'   mlr3 spatial resampling object of class [ResamplingCV] or
-#'   [ResamplingRepeatedCV].
+#'   mlr3 spatial resampling object of class [mlr3::ResamplingCV] or
+#'   [mlr3::ResamplingRepeatedCV].
 #' @param x `[Resampling]`\cr
-#'   mlr3 spatial resampling object of class [ResamplingCV] or
-#'   [ResamplingRepeatedCV].
+#'   mlr3 spatial resampling object of class [mlr3::ResamplingCV] or
+#'   [mlr3::ResamplingRepeatedCV].
 #' @inheritParams autoplot.ResamplingSpCVBlock
 #' @export
 #' @seealso
@@ -960,9 +960,9 @@ autoplot.ResamplingRepeatedCV = function( # nolint
 #'
 #' @name autoplot.ResamplingCustomCV
 #' @param object `[Resampling]`\cr
-#'   mlr3 spatial resampling object of class [ResamplingCustomCV].
+#'   mlr3 spatial resampling object of class [mlr3::ResamplingCustomCV].
 #' @param x `[Resampling]`\cr
-#'   mlr3 spatial resampling object of class [ResamplingCustomCV].
+#'   mlr3 spatial resampling object of class [mlr3::ResamplingCustomCV].
 #' @inheritParams autoplot.ResamplingSpCVBlock
 #' @export
 #' @seealso

diff --git a/README.md b/README.md
@@ -57,7 +57,7 @@ This list does not claim to be comprehensive.
 | Name          | Language | Resources                                                                                                                     |
 | ------------- | -------- | ----------------------------------------------------------------------------------------------------------------------------- |
 | blockCV       | R        | [CRAN](https://cran.r-project.org/package=blockCV)                                                                            |
-| CAST          | R        | [Paper](https://www.sciencedirect.com/science/article/pii/S1364815217310976), [CRAN](https://cran.r-project.org/package=CAST) |
+| CAST          | R        | [Paper](https://doi.org/10.1016/j.envsoft.2017.12.001), [CRAN](https://cran.r-project.org/package=CAST) |
 | ENMeval       | R        | [CRAN](https://cran.r-project.org/package=ENMeval)                                                                            |
 | spatialsample | R        | [CRAN](https://cran.r-project.org/package=spatialsample)                                                                      |
 | sperrorest    | R        | [CRAN](https://cran.r-project.org/package=sperrorest)                                                                         |