Add help method for filters (#68)

* Filters now have a help method `$help()` which opens the respective help page (#68)
mlr-org · Mar 14, 2020 · 12af76f · 12af76f
1 parent 64e9a51
commit 12af76f
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Showing 40 changed files with 155 additions and 46 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -3,10 +3,15 @@ repos:
     rev: v0.0.0.9027
     hooks:
     -   id: style-files
-        args: [--style_fun=mlr_style]
+        args: [--style_pkg=styler, --style_fun=mlr_style]
     -   id: parsable-R
     -   id: no-browser-statement
     -   id: readme-rmd-rendered
     -   id: roxygenize
     -   id: use-tidy-description
-    -   id: codemeta-description-updated
+    #-   id: codemeta-description-updated
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.5.0
+    hooks:
+    -   id: check-added-large-files
+        args: ['--maxkb=200']
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -35,7 +35,7 @@ Imports:
     backports,
     checkmate,
     data.table,
-    mlr3 (>= 0.1.2),
+    mlr3 (>= 0.1.8),
     mlr3misc,
     paradox,
     R6
@@ -52,7 +52,7 @@ Suggests:
 Encoding: UTF-8
 NeedsCompilation: no
 Roxygen: list(markdown = TRUE, r6 = TRUE)
-RoxygenNote: 7.0.2
+RoxygenNote: 7.1.0
 Collate:
     'Filter.R'
     'mlr_filters.R'

diff --git a/R/Filter.R b/R/Filter.R
@@ -31,6 +31,11 @@ Filter = R6Class("Filter",
     feature_types = NULL,
     packages = NULL,
 
+    #' @field man (`character(1)`)\cr
+    #'   String in the format `[pkg]::[topic]` pointing to a manual page for this object.
+    #'   Defaults to `NA`, but can be set by child classes.
+    man = NULL,
+
     #' @field scores
     #'   Stores the calculated filter score values as named numeric vector.
     #'   The vector is sorted in decreasing order with possible `NA` values
@@ -58,9 +63,13 @@ Filter = R6Class("Filter",
     #'   Set of required packages.
     #'   Note that these packages will be loaded via [requireNamespace()], and
     #'   are not attached.
+    #' @param man (`character(1)`)\cr
+    #'   String in the format `[pkg]::[topic]` pointing to a manual page for
+    #'   this object. The referenced help package can be opened via method
+    #'   `$help()`.
     initialize = function(id, task_type, task_properties = character(),
       param_set = ParamSet$new(), feature_types = character(),
-      packages = character()) {
+      packages = character(), man = NA_character_) {
 
       self$id = assert_string(id)
       self$task_type = assert_subset(task_type, mlr_reflections$task_types$type,
@@ -73,6 +82,7 @@ Filter = R6Class("Filter",
       self$packages = assert_character(packages, any.missing = FALSE,
         unique = TRUE)
       self$scores = set_names(numeric(), character())
+      self$man = assert_string(man, na.ok = TRUE)
     },
 
     #' @description
@@ -95,6 +105,12 @@ Filter = R6Class("Filter",
       }
     },
 
+    #' @description
+    #' Opens the corresponding help page referenced by field `$man`.
+    help = function() {
+      open_help(self$man) # nocov
+    },
+
     #' @description
     #'   Calculates the filter score values for the provided [mlr3::Task] and
     #'   stores them in field `scores`. `nfeat` determines the minimum number of

diff --git a/R/FilterAUC.R b/R/FilterAUC.R
@@ -52,7 +52,8 @@ FilterAUC = R6Class("FilterAUC", inherit = Filter,
         task_type = task_type,
         task_properties = task_properties,
         feature_types = feature_types,
-        packages = packages
+        packages = packages,
+        man = "mlr3filters::mlr_filters_auc"
       )
     }
   ),

diff --git a/R/FilterAnova.R b/R/FilterAnova.R
@@ -54,7 +54,8 @@ FilterAnova = R6Class("FilterAnova", inherit = Filter,
         id = id,
         packages = packages,
         feature_types = feature_types,
-        task_type = task_type
+        task_type = task_type,
+        man = "mlr3filters::mlr_filters_anova"
       )
     }
   ),

diff --git a/R/FilterCMIM.R b/R/FilterCMIM.R
@@ -47,7 +47,8 @@ FilterCMIM = R6Class("FilterCMIM", inherit = Filter,
         task_type = task_type,
         param_set = param_set,
         feature_types = feature_types,
-        packages = packages
+        packages = packages,
+        man = "mlr3filters::mlr_filters_cmim"
       )
     }
   ),

diff --git a/R/FilterCarScore.R b/R/FilterCarScore.R
@@ -57,7 +57,9 @@ FilterCarScore = R6Class("FilterCarScore", inherit = Filter,
         task_type = task_type,
         param_set = param_set,
         feature_types = feature_types,
-        packages = packages
+        packages = packages,
+        man = "mlr3filters::mlr_filters_carscore"
+
       )
       self$param_set$values = list(verbose = FALSE)
     }

diff --git a/R/FilterCorrelation.R b/R/FilterCorrelation.R
@@ -57,7 +57,8 @@ FilterCorrelation = R6Class("FilterCorrelation", inherit = Filter,
         task_type = task_type,
         param_set = param_set,
         feature_types = feature_types,
-        packages = packages
+        packages = packages,
+        man = "mlr3filters::mlr_filters_correlation"
       )
     }
   ),

diff --git a/R/FilterDISR.R b/R/FilterDISR.R
@@ -47,7 +47,8 @@ FilterDISR = R6Class("FilterDISR", inherit = Filter,
         task_type = task_type,
         param_set = param_set,
         feature_types = feature_types,
-        packages = packages
+        packages = packages,
+        man = "mlr3filters::mlr_filters_disr"
       )
     }
   ),

diff --git a/R/FilterFindCorrelation.R b/R/FilterFindCorrelation.R
@@ -65,7 +65,8 @@ FilterFindCorrelation = R6Class("FilterFindCorrelation", inherit = Filter,
         task_type = task_type,
         param_set = param_set,
         feature_types = feature_types,
-        packages = packages
+        packages = packages,
+        man = "mlr3filters::mlr_filters_find_correlation"
       )
     }
   ),

diff --git a/R/FilterImportance.R b/R/FilterImportance.R
@@ -55,7 +55,8 @@ FilterImportance = R6Class("FilterImportance", inherit = Filter,
         task_type = task_type,
         feature_types = feature_types,
         packages = packages,
-        param_set = param_set
+        param_set = param_set,
+        man = "mlr3filters::mlr_filters_importance"
       )
     }
   ),

diff --git a/R/FilterInformationGain.R b/R/FilterInformationGain.R
@@ -64,7 +64,8 @@ FilterInformationGain = R6Class("FilterInformationGain", inherit = Filter,
         task_type = task_type,
         param_set = param_set,
         feature_types = feature_types,
-        packages = packages
+        packages = packages,
+        man = "mlr3filters::mlr_filters_information_gain"
       )
     }
   ),

diff --git a/R/FilterJMI.R b/R/FilterJMI.R
@@ -47,7 +47,8 @@ FilterJMI = R6Class("FilterJMI", inherit = Filter,
         task_type = task_type,
         param_set = param_set,
         feature_types = feature_types,
-        packages = packages
+        packages = packages,
+        man = "mlr3filters::mlr_filters_jmi"
       )
     }
   ),

diff --git a/R/FilterJMIM.R b/R/FilterJMIM.R
@@ -47,7 +47,8 @@ FilterJMIM = R6Class("FilterJMIM", inherit = Filter,
         task_type = task_type,
         param_set = param_set,
         feature_types = feature_types,
-        packages = packages
+        packages = packages,
+        man = "mlr3filters::mlr_filters_jmim"
       )
     }
   ),

diff --git a/R/FilterKruskalTest.R b/R/FilterKruskalTest.R
@@ -53,7 +53,8 @@ FilterKruskalTest = R6Class("FilterKruskalTest", inherit = Filter,
         task_type = task_type,
         param_set = param_set,
         feature_types = feature_types,
-        packages = packages
+        packages = packages,
+        man = "mlr3filters::mlr_filters_kruskal_test"
       )
     }
   ),

diff --git a/R/FilterMIM.R b/R/FilterMIM.R
@@ -47,7 +47,8 @@ FilterMIM = R6Class("FilterMIM", inherit = Filter,
         task_type = task_type,
         param_set = param_set,
         feature_types = feature_types,
-        packages = packages
+        packages = packages,
+        man = "mlr3filters::mlr_filters_mim"
       )
     }
   ),

diff --git a/R/FilterMRMR.R b/R/FilterMRMR.R
@@ -47,7 +47,8 @@ FilterMRMR = R6Class("FilterMRMR", inherit = Filter,
         task_type = task_type,
         param_set = param_set,
         feature_types = feature_types,
-        packages = packages
+        packages = packages,
+        man = "mlr3filters::mlr_filters_mrmr"
       )
     }
   ),

diff --git a/R/FilterNJMIM.R b/R/FilterNJMIM.R
@@ -47,7 +47,8 @@ FilterNJMIM = R6Class("FilterNJMIM", inherit = Filter,
         task_type = task_type,
         param_set = param_set,
         feature_types = feature_types,
-        packages = packages
+        packages = packages,
+        man = "mlr3filters::mlr_filters_njmim"
       )
     }
   ),

diff --git a/R/FilterPerformance.R b/R/FilterPerformance.R
@@ -46,29 +46,27 @@ FilterPerformance = R6Class("FilterPerformance", inherit = Filter,
     #'   [mlr3::Resampling] to be used within resampling.
     #' @param measure ([mlr3::Measure])\cr
     #'   [mlr3::Measure] to be used for evaluating the performance.
-    #' @param packages (`character()`)\cr
-    #'   Set of required packages.
-    #'   Note that these packages will be loaded via [requireNamespace()], and
-    #'   are not attached.
     initialize = function(id = "performance",
       task_type = learner$task_type,
       param_set = learner$param_set,
       feature_types = learner$feature_types,
       learner = mlr3::lrn("classif.rpart"),
       resampling = mlr3::rsmp("holdout"),
-      measure = mlr3::msr("classif.ce"),
-      packages = learner$packages) {
+      measure = mlr3::msr("classif.ce")) {
 
       self$learner = learner = assert_learner(as_learner(learner, clone = TRUE),
         properties = "importance")
       self$resampling = assert_resampling(as_resampling(resampling))
       self$measure = assert_measure(as_measure(measure,
         task_type = learner$task_type, clone = TRUE), learner = learner)
+      packages = unique(c(self$learner$packages, self$measure$packages))
 
       super$initialize(
         id = id,
         task_type = task_type,
-        feature_types = feature_types
+        feature_types = feature_types,
+        packages = packages,
+        man = "mlr3filters::mlr_filters_performance"
       )
     }
   ),

diff --git a/R/FilterVariance.R b/R/FilterVariance.R
@@ -47,7 +47,8 @@ FilterVariance = R6Class("FilterVariance", inherit = Filter,
         task_type = task_type,
         param_set = param_set,
         feature_types = feature_types,
-        packages = packages
+        packages = packages,
+        man = "mlr3filters::mlr_filters_variance"
       )
       self$param_set$values = list(na.rm = TRUE)
     }

diff --git a/codemeta.json b/codemeta.json
@@ -14,14 +14,14 @@
   ],
   "issueTracker": "https://github.com/mlr-org/mlr3filters/issues",
   "license": "https://spdx.org/licenses/LGPL-3.0",
-  "version": "0.1.1.9002",
+  "version": "0.2.0.9000",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
-    "version": "3.6.2",
+    "version": "3.6.3",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 3.6.2 (2019-12-12)",
+  "runtimePlatform": "R version 3.6.3 Patched (2020-02-29 r77919)",
   "provider": {
     "@id": "https://cran.r-project.org",
     "@type": "Organization",
@@ -226,7 +226,7 @@
       "@type": "SoftwareApplication",
       "identifier": "mlr3",
       "name": "mlr3",
-      "version": ">= 0.1.2",
+      "version": ">= 0.1.8",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -274,7 +274,7 @@
   ],
   "releaseNotes": "https://github.com/mlr-org/mlr3filters/blob/master/NEWS.md",
   "readme": "https://github.com/mlr-org/mlr3filters/blob/master/README.md",
-  "fileSize": "22.613KB",
+  "fileSize": "23.59KB",
   "contIntegration": "https://codecov.io/github/mlr-org/mlr3filters?branch=master",
   "keywords": [
     "filter",