Merge pull request #833 from mlr-org/examplesif

replaced dontshow with examplesif
mlr-org · Oct 8, 2024 · c823f18 · c823f18
2 parents e52460b + df6fff8
commit c823f18
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Showing 75 changed files with 118 additions and 228 deletions.
diff --git a/R/GraphLearner.R b/R/GraphLearner.R
@@ -138,8 +138,7 @@
 #'
 #' @family Learners
 #' @export
-#' @examples
-#' \dontshow{ if (requireNamespace("rpart")) \{ }
+#' @examplesIf requireNamespace("rpart")
 #' library("mlr3")
 #'
 #' graph = po("pca") %>>% lrn("classif.rpart")
@@ -158,7 +157,6 @@
 #'
 #' # Feature importance (of principal components):
 #' lr$graph_model$pipeops$classif.rpart$learner_model$importance()
-#' \dontshow{ \} }
 GraphLearner = R6Class("GraphLearner", inherit = Learner,
   public = list(
     impute_selected_features = FALSE,

diff --git a/R/PipeOpADAS.R b/R/PipeOpADAS.R
@@ -50,8 +50,7 @@
 #' @template seealso_pipeopslist
 #' @include PipeOpTaskPreproc.R
 #' @export
-#' @examples
-#' \dontshow{ if (requireNamespace("smotefamily")) \{ }
+#' @examplesIf requireNamespace("smotefamily")
 #' library("mlr3")
 #'
 #' # Create example task
@@ -69,7 +68,6 @@
 #' adas_result = pop$train(list(task))[[1]]$data()
 #' nrow(adas_result)
 #' table(adas_result$target)
-#' \dontshow{ \} }
 PipeOpADAS = R6Class("PipeOpADAS",
   inherit = PipeOpTaskPreproc,
   public = list(

diff --git a/R/PipeOpBLSmote.R b/R/PipeOpBLSmote.R
@@ -58,8 +58,7 @@
 #' @template seealso_pipeopslist
 #' @include PipeOpTaskPreproc.R
 #' @export
-#' @examples
-#' \dontshow{ if (requireNamespace("smotefamily")) \{ }
+#' @examplesIf requireNamespace("smotefamily")
 #' library("mlr3")
 #'
 #' # Create example task
@@ -74,7 +73,6 @@
 #' bls_result = pop$train(list(task))[[1]]$data()
 #' nrow(bls_result)
 #' table(bls_result$result)
-#' \dontshow{ \} }
 PipeOpBLSmote = R6Class("PipeOpBLSmote",
   inherit = PipeOpTaskPreproc,
   public = list(

diff --git a/R/PipeOpBoxCox.R b/R/PipeOpBoxCox.R
@@ -47,8 +47,7 @@
 #' @section Methods:
 #' Only methods inherited from [`PipeOpTaskPreproc`]/[`PipeOp`].
 #'
-#' @examples
-#' \dontshow{ if (requireNamespace("bestNormalize")) \{ }
+#' @examplesIf requireNamespace("bestNormalize")
 #' library("mlr3")
 #'
 #' task = tsk("iris")
@@ -58,7 +57,7 @@
 #' pop$train(list(task))[[1]]$data()
 #'
 #' pop$state
-#' \dontshow{ \} }
+#'
 #' @family PipeOps
 #' @include PipeOpTaskPreproc.R
 #' @template seealso_pipeopslist

diff --git a/R/PipeOpClassifAvg.R b/R/PipeOpClassifAvg.R
@@ -63,8 +63,7 @@
 #' @include PipeOpEnsemble.R
 #' @export
 #'
-#' @examples
-#' \dontshow{ if (requireNamespace("rpart")) \{ }
+#' @examplesIf requireNamespace("rpart")
 #' \donttest{
 #' library("mlr3")
 #'
@@ -78,7 +77,6 @@
 #'
 #' resample(tsk("iris"), GraphLearner$new(gr), rsmp("holdout"))
 #' }
-#' \dontshow{ \} }
 PipeOpClassifAvg = R6Class("PipeOpClassifAvg",
   inherit = PipeOpEnsemble,
   public = list(

diff --git a/R/PipeOpEncodeLmer.R b/R/PipeOpEncodeLmer.R
@@ -71,9 +71,7 @@
 #' @template seealso_pipeopslist
 #' @include PipeOpTaskPreproc.R
 #' @export
-#' @examples
-#' \dontshow{ if (requireNamespace("nloptr")) \{ }
-#' \dontshow{ if (requireNamespace("lme4")) \{ }
+#' @examplesIf mlr3misc::require_namespaces(c("nloptr", "lme4"), quietly = TRUE)
 #' library("mlr3")
 #' poe = po("encodelmer")
 #'
@@ -86,8 +84,6 @@
 #' poe$train(list(task))[[1]]$data()
 #'
 #' poe$state
-#' \dontshow{ \} }
-#' \dontshow{ \} }
 PipeOpEncodeLmer = R6Class("PipeOpEncodeLmer",
   inherit = PipeOpTaskPreprocSimple,
   public = list(

diff --git a/R/PipeOpFilter.R b/R/PipeOpFilter.R
@@ -79,9 +79,7 @@
 #' @template seealso_pipeopslist
 #' @include PipeOpTaskPreproc.R
 #' @export
-#' @examples
-#' \dontshow{ if (requireNamespace("mlr3filters")) \{ }
-#' \dontshow{ if (requireNamespace("rpart")) \{ }
+#' @examplesIf mlr3misc::require_namespaces(c("mlr3filters", "rpart"), quietly = TRUE)
 #' library("mlr3")
 #' library("mlr3filters")
 #' \dontshow{data.table::setDTthreads(1)}
@@ -109,8 +107,6 @@
 #' learner = GraphLearner$new(gr)
 #' rr = resample(task, learner, rsmp("holdout"), store_models = TRUE)
 #' rr$learners[[1]]$model$auc$scores
-#' \dontshow{ \} }
-#' \dontshow{ \} }
 PipeOpFilter = R6Class("PipeOpFilter",
   inherit = PipeOpTaskPreprocSimple,
   public = list(

diff --git a/R/PipeOpICA.R b/R/PipeOpICA.R
@@ -72,8 +72,7 @@
 #' @section Methods:
 #' Only methods inherited from [`PipeOpTaskPreproc`]/[`PipeOp`].
 #'
-#' @examples
-#' \dontshow{ if (requireNamespace("fastICA")) \{ }
+#' @examplesIf requireNamespace("fastICA")
 #' library("mlr3")
 #'
 #' task = tsk("iris")
@@ -83,7 +82,6 @@
 #' pop$train(list(task))[[1]]$data()
 #'
 #' pop$state
-#' \dontshow{ \} }
 #' @family PipeOps
 #' @template seealso_pipeopslist
 #' @include PipeOpTaskPreproc.R

diff --git a/R/PipeOpImputeLearner.R b/R/PipeOpImputeLearner.R
@@ -69,8 +69,7 @@
 #' @section Methods:
 #' Only methods inherited from [`PipeOpImpute`]/[`PipeOp`].
 #'
-#' @examples
-#' \dontshow{ if (requireNamespace("rpart")) \{ }
+#' @examplesIf requireNamespace("rpart")
 #' library("mlr3")
 #'
 #' task = tsk("pima")
@@ -94,7 +93,6 @@
 #' new_task = po$train(list(task = task))[[1]]
 #' new_task$missings()
 #'
-#' \dontshow{ \} }
 #' @family PipeOps
 #' @family Imputation PipeOps
 #' @template seealso_pipeopslist

diff --git a/R/PipeOpKernelPCA.R b/R/PipeOpKernelPCA.R
@@ -51,16 +51,14 @@
 #' @section Methods:
 #' Only methods inherited from [`PipeOpTaskPreproc`]/[`PipeOp`].
 #'
-#' @examples
-#' \dontshow{ if (requireNamespace("kernlab")) \{ }
+#' @examplesIf requireNamespace("kernlab")
 #' library("mlr3")
 #'
 #' task = tsk("iris")
 #' pop = po("kernelpca", features = 3)  # only keep top 3 components
 #'
 #' task$data()
 #' pop$train(list(task))[[1]]$data()
-#' \dontshow{ \} }
 #' @family PipeOps
 #' @template seealso_pipeopslist
 #' @include PipeOpTaskPreproc.R

diff --git a/R/PipeOpLearner.R b/R/PipeOpLearner.R
@@ -81,8 +81,7 @@
 #' @template seealso_pipeopslist
 #' @include PipeOp.R
 #' @export
-#' @examples
-#' \dontshow{ if (requireNamespace("rpart")) \{ }
+#' @examplesIf requireNamespace("rpart")
 #' library("mlr3")
 #'
 #' task = tsk("iris")
@@ -91,7 +90,6 @@
 #'
 #' lrn_po$train(list(task))
 #' lrn_po$predict(list(task))
-#' \dontshow{ \} }
 PipeOpLearner = R6Class("PipeOpLearner", inherit = PipeOp,
   public = list(
     initialize = function(learner, id = NULL, param_vals = list()) {

diff --git a/R/PipeOpLearnerCV.R b/R/PipeOpLearnerCV.R
@@ -92,8 +92,7 @@
 #' @template seealso_pipeopslist
 #' @include PipeOpTaskPreproc.R
 #' @export
-#' @examples
-#' \dontshow{ if (requireNamespace("rpart")) \{ }
+#' @examplesIf requireNamespace("rpart")
 #' library("mlr3")
 #'
 #' task = tsk("iris")
@@ -114,7 +113,6 @@
 #' graph$pipeops$classif.rpart$learner$predict_type = "prob"
 #'
 #' graph$train(task)
-#' \dontshow{ \} }
 PipeOpLearnerCV = R6Class("PipeOpLearnerCV",
   inherit = PipeOpTaskPreproc,
   public = list(

diff --git a/R/PipeOpNMF.R b/R/PipeOpNMF.R
@@ -87,10 +87,7 @@
 #' @section Methods:
 #' Only methods inherited from [`PipeOpTaskPreproc`]/[`PipeOp`].
 #'
-#' @examples
-#' \dontshow{ if (requireNamespace("NMF")) \{ }
-#' \dontshow{ if (requireNamespace("MASS")) \{ }
-#' if (requireNamespace("NMF")) {
+#' @examplesIf mlr3misc::require_namespaces(c("NMF", "MASS"), quietly = TRUE)
 #' library("mlr3")
 #'
 #' task = tsk("iris")
@@ -100,10 +97,7 @@
 #' pop$train(list(task))[[1]]$data()
 #'
 #' pop$state
-#' }
 #' \dontshow{ try(rm("format.list", envir = .BaseNamespaceEnv$.__S3MethodsTable__.), silent = TRUE)  # BiocGenerics overwrites printer for our tables mlr-org/mlr3#1112 }
-#' \dontshow{ \} }
-#' \dontshow{ \} }
 #' @family PipeOps
 #' @template seealso_pipeopslist
 #' @include PipeOpTaskPreproc.R

diff --git a/R/PipeOpNearmiss.R b/R/PipeOpNearmiss.R
@@ -56,8 +56,7 @@
 #' @template seealso_pipeopslist
 #' @include PipeOpTaskPreproc.R
 #' @export
-#' @examples
-#' \dontshow{ if (requireNamespace("themis")) \{ }
+#' @examplesIf requireNamespace("themis")
 #' library("mlr3")
 #'
 #' # Create example task
@@ -70,7 +69,6 @@
 #' nearmiss_result = pop$train(list(task))[[1]]$data()
 #' nrow(nearmiss_result)
 #' table(nearmiss_result$type)
-#' \dontshow{ \} }
 PipeOpNearmiss = R6Class("PipeOpNearmiss",
   inherit = PipeOpTaskPreproc,
   public = list(

diff --git a/R/PipeOpOVR.R b/R/PipeOpOVR.R
@@ -67,14 +67,12 @@
 #' @template seealso_pipeopslist
 #' @include PipeOp.R
 #' @export
-#' @examples
-#' \dontshow{ if (requireNamespace("rpart")) \{ }
+#' @examplesIf requireNamespace("rpart")
 #' library(mlr3)
 #' task = tsk("iris")
 #' po = po("ovrsplit")
 #' po$train(list(task))
 #' po$predict(list(task))
-#' \dontshow{ \} }
 PipeOpOVRSplit = R6Class("PipeOpOVRSplit",
   inherit = PipeOp,
   public = list(
@@ -175,16 +173,14 @@ mlr_pipeops$add("ovrsplit", PipeOpOVRSplit)
 #' @template seealso_pipeopslist
 #' @include PipeOpEnsemble.R
 #' @export
-#' @examples
-#' \dontshow{ if (requireNamespace("rpart")) \{ }
+#' @examplesIf requireNamespace("rpart")
 #' library(mlr3)
 #' task = tsk("iris")
 #' gr = po("ovrsplit") %>>% lrn("classif.rpart") %>>% po("ovrunite")
 #' gr$train(task)
 #' gr$predict(task)
 #' gr$pipeops$classif.rpart$learner$predict_type = "prob"
 #' gr$predict(task)
-#' \dontshow{ \} }
 PipeOpOVRUnite = R6Class("PipeOpOVRUnite",
   inherit = PipeOpEnsemble,
   public = list(

diff --git a/R/PipeOpProxy.R b/R/PipeOpProxy.R
@@ -54,8 +54,7 @@
 #' @section Methods:
 #' Only methods inherited from [`PipeOp`].
 #'
-#' @examples
-#' \dontshow{ if (requireNamespace("rpart")) \{ }
+#' @examplesIf requireNamespace("rpart")
 #' library("mlr3")
 #' library("mlr3learners")
 #'
@@ -74,7 +73,6 @@
 #' g$param_set$values$learner.content = lrn("classif.rpart")
 #' rr_pca_rpart = resample(task, learner = GraphLearner$new(g), resampling = rsmp("cv", folds = 3))
 #' rr_pca_rpart$aggregate(msr("classif.ce"))
-#' \dontshow{ \} }
 #' @family PipeOps
 #' @template seealso_pipeopslist
 #' @include PipeOp.R

diff --git a/R/PipeOpRandomResponse.R b/R/PipeOpRandomResponse.R
@@ -62,8 +62,7 @@
 #' @template seealso_pipeopslist
 #' @include PipeOp.R
 #' @export
-#' @examples
-#' \dontshow{ if (requireNamespace("rpart")) \{ }
+#' @examplesIf requireNamespace("rpart")
 #' library(mlr3)
 #' library(mlr3learners)
 #'
@@ -80,7 +79,6 @@
 #' g2$pipeops$regr.lm$learner$predict_type = "se"
 #' set.seed(2906)
 #' g2$predict(task2)
-#' \dontshow{ \} }
 PipeOpRandomResponse = R6Class("PipeOpRandomResponse",
   inherit = PipeOp,
   public = list(

diff --git a/R/PipeOpRegrAvg.R b/R/PipeOpRegrAvg.R
@@ -56,8 +56,7 @@
 #' @template seealso_pipeopslist
 #' @include PipeOpEnsemble.R
 #' @export
-#' @examples
-#' \dontshow{ if (requireNamespace("rpart")) \{ }
+#' @examplesIf requireNamespace("rpart")
 #' library("mlr3")
 #'
 #' # Simple Bagging
@@ -69,7 +68,6 @@
 #'   po("classifavg")
 #'
 #' resample(tsk("iris"), GraphLearner$new(gr), rsmp("holdout"))
-#' \dontshow{ \} }
 PipeOpRegrAvg = R6Class("PipeOpRegrAvg",
   inherit = PipeOpEnsemble,
 

diff --git a/R/PipeOpSmote.R b/R/PipeOpSmote.R
@@ -53,8 +53,7 @@
 #' @template seealso_pipeopslist
 #' @include PipeOpTaskPreproc.R
 #' @export
-#' @examples
-#' \dontshow{ if (requireNamespace("smotefamily")) \{ }
+#' @examplesIf requireNamespace("smotefamily")
 #' library("mlr3")
 #'
 #' # Create example task
@@ -68,7 +67,6 @@
 #' pop = po("smote")
 #' smotedata = pop$train(list(task))[[1]]$data()
 #' table(smotedata$result)
-#' \dontshow{ \} }
 PipeOpSmote = R6Class("PipeOpSmote",
   inherit = PipeOpTaskPreproc,
   public = list(

diff --git a/R/PipeOpSmoteNC.R b/R/PipeOpSmoteNC.R
@@ -59,8 +59,7 @@
 #' @template seealso_pipeopslist
 #' @include PipeOpTaskPreproc.R
 #' @export
-#' @examples
-#' \dontshow{ if (requireNamespace("themis")) \{ }
+#' @examplesIf requireNamespace("themis")
 #' library("mlr3")
 #'
 #' # Create example task
@@ -77,7 +76,6 @@
 #' smotenc_result = pop$train(list(task))[[1]]$data()
 #' nrow(smotenc_result)
 #' table(smotenc_result$target)
-#' \dontshow{ \} }
 PipeOpSmoteNC = R6Class("PipeOpSmoteNC",
   inherit = PipeOpTaskPreproc,
   public = list(