remove vignettes/pdf, apply precommit fixes

Author: pat-s

.pre-commit-config.yaml

@@ -2,18 +2,13 @@
 # R specific hooks: https://github.com/lorenzwalthert/precommit
 repos:
 -   repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.2.2.9004
+    rev: v0.2.2.9006
     hooks:
     -   id: style-files
         args: [--style_pkg=styler.mlr, --style_fun=mlr_style]
         additional_dependencies:
         - mlr-org/styler.mlr
-    -   id: roxygenize
-        additional_dependencies:
-        - git2r
-        - pkgbuild
     -   id: use-tidy-description
-    # -   id: spell-check
         exclude: >
           (?x)^(
           data/.*|
@@ -40,7 +35,6 @@ repos:
     -   id: readme-rmd-rendered
     -   id: parsable-R
     -   id: no-browser-statement
-    -   id: deps-in-desc
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.0.1
     hooks:
@@ -55,4 +49,5 @@ repos:
         entry: Cannot commit .Rhistory, .RData, .Rds or .rds.
         language: fail
         files: '\.Rhistory|\.RData|\.Rds|\.rds$'
+        exclude: "gunpoint.RData|yeast.RData"
         # `exclude: <regex>` to allow committing specific files.

R/BaseWrapper.R

@@ -74,8 +74,7 @@ predictLearner.BaseWrapper = function(.learner, .model, .newdata, ...) {
   args = removeFromDots(names(.learner$par.vals), ...)
   do.call(predictLearner, c(
     list(.learner = .learner$next.learner, .model = .model$learner.model$next.model, .newdata = .newdata),
-    args)
-  )
+    args))
 }
 
 #' @export

R/Filter.R

@@ -163,7 +163,8 @@ makeFilter(
     res = mRMRe::mRMR.classic(data = data, target_indices = target.ind, feature_count = nselect, ...)
     scores = as.numeric(mRMRe::scores(res)[[1L]])
     setNames(scores, res@feature_names[as.integer(mRMRe::solutions(res)[[1L]])])
-  })
+  }
+)
 
 # carscore ----------------
 
@@ -185,7 +186,8 @@ makeFilter(
     data = getTaskData(task, target.extra = TRUE)
     y = care::carscore(Xtrain = data$data, Ytrain = data$target, verbose = FALSE, ...)^2
     setNames(as.double(y), names(y))
-  })
+  }
+)
 
 # randomForestSRC_importance ----------------
 
@@ -221,7 +223,8 @@ rf.importance = makeFilter(
       y = unname(im)
     }
     setNames(y, ns)
-  })
+  }
+)
 .FilterRegister[["rf.importance"]] = rf.importance
 .FilterRegister[["rf.importance"]]$desc = "(DEPRECATED)"
 .FilterRegister[["rf.importance"]]$fun = function(...) {
@@ -247,7 +250,8 @@ randomForestSRC.rfsrc = makeFilter( # nolint
       y = unname(im)
     }
     setNames(y, ns)
-  })
+  }
+)
 .FilterRegister[["randomForestSRC.rfsrc"]] = randomForestSRC.rfsrc
 .FilterRegister[["randomForestSRC.rfsrc"]]$desc = "(DEPRECATED)"
 .FilterRegister[["randomForestSRC.rfsrc"]]$fun = function(...) {
@@ -274,7 +278,8 @@ rf.min.depth = makeFilter(
   supported.features = c("numerics", "factors", "ordered"),
   fun = function(task, nselect, method = "md", ...) {
     # redirected to randomForestSRC.var.select()
-  })
+  }
+)
 .FilterRegister[["rf.min.depth"]] = rf.min.depth
 .FilterRegister[["rf.min.depth"]]$desc = "(DEPRECATED)"
 .FilterRegister[["rf.min.depth"]]$fun = function(...) {
@@ -297,7 +302,8 @@ randomForestSRC.var.select = makeFilter( # nolint
 
     im$varselect[setdiff(rownames(im$varselect), im$topvars), "depth"] = NA
     setNames(im$varselect[, "depth"], rownames(im$varselect))
-  })
+  }
+)
 .FilterRegister[["randomForestSRC.var.select"]] = randomForestSRC.var.select
 .FilterRegister[["randomForestSRC.var.select"]]$desc = "(DEPRECATED)"
 .FilterRegister[["randomForestSRC.var.select"]]$fun = function(...) {
@@ -342,7 +348,8 @@ makeFilter(
       cforest.args))
     im = do.call(party::varimp, c(list(obj = fit), varimp.args))
     im
-  })
+  }
+)
 
 cforest.importance = makeFilter(
   name = "party_cforest.importance",
@@ -370,7 +377,8 @@ cforest.importance = makeFilter(
       cforest.args))
     im = do.call(party::varimp, c(list(obj = fit), varimp.args))
     im
-  })
+  }
+)
 
 .FilterRegister[["cforest.importance"]] = cforest.importance
 .FilterRegister[["cforest.importance"]]$desc = "(DEPRECATED)"
@@ -407,7 +415,8 @@ makeFilter(
       keep.forest = FALSE, importance = (type != 2L))
     im = randomForest::importance(rf, type = type, ...)
     setNames(im, rownames(im))
-  })
+  }
+)
 
 randomForest.importance = makeFilter( # nolint
   name = "randomForest_importance",
@@ -423,7 +432,8 @@ randomForest.importance = makeFilter( # nolint
       keep.forest = FALSE, importance = (type != 2L))
     im = randomForest::importance(rf, type = type, ...)
     setNames(im, rownames(im))
-  })
+  }
+)
 
 .FilterRegister[["randomForest.importance"]] = randomForest.importance
 .FilterRegister[["randomForest.importance"]]$desc = "(DEPRECATED)"
@@ -450,7 +460,8 @@ makeFilter(
   fun = function(task, nselect, ...) {
     data = getTaskData(task, target.extra = TRUE)
     abs(cor(as.matrix(data$data), data$target, use = "pairwise.complete.obs", method = "pearson")[, 1L])
-  })
+  }
+)
 
 # rank.correlation ----------------
 
@@ -470,7 +481,8 @@ makeFilter(
   fun = function(task, nselect, ...) {
     data = getTaskData(task, target.extra = TRUE)
     abs(cor(as.matrix(data$data), data$target, use = "pairwise.complete.obs", method = "spearman")[, 1L])
-  })
+  }
+)
 
 # FSelector_information.gain ----------------
 
@@ -488,7 +500,8 @@ makeFilter(
   fun = function(task, nselect, ...) {
     y = FSelector::information.gain(getTaskFormula(task), data = getTaskData(task))
     setNames(y[["attr_importance"]], getTaskFeatureNames(task))
-  })
+  }
+)
 
 information.gain = makeFilter(
   name = "FSelector_information.gain",
@@ -499,7 +512,8 @@ information.gain = makeFilter(
   fun = function(task, nselect, ...) {
     y = FSelector::information.gain(getTaskFormula(task), data = getTaskData(task))
     setNames(y[["attr_importance"]], getTaskFeatureNames(task))
-  })
+  }
+)
 
 .FilterRegister[["information.gain"]] = information.gain
 .FilterRegister[["information.gain"]]$desc = "(DEPRECATED)"
@@ -525,7 +539,8 @@ makeFilter(
   fun = function(task, nselect, ...) {
     y = FSelector::gain.ratio(getTaskFormula(task), data = getTaskData(task))
     setNames(y[["attr_importance"]], getTaskFeatureNames(task))
-  })
+  }
+)
 
 gain.ratio = makeFilter(
   name = "FSelector_gain.ratio",
@@ -536,7 +551,8 @@ gain.ratio = makeFilter(
   fun = function(task, nselect, ...) {
     y = FSelector::gain.ratio(getTaskFormula(task), data = getTaskData(task))
     setNames(y[["attr_importance"]], getTaskFeatureNames(task))
-  })
+  }
+)
 
 .FilterRegister[["gain.ratio"]] = gain.ratio
 .FilterRegister[["gain.ratio"]]$desc = "(DEPRECATED)"
@@ -561,7 +577,8 @@ makeFilter(
   fun = function(task, nselect, ...) {
     y = FSelector::symmetrical.uncertainty(getTaskFormula(task), data = getTaskData(task))
     setNames(y[["attr_importance"]], getTaskFeatureNames(task))
-  })
+  }
+)
 
 symmetrical.uncertainty = makeFilter(
   name = "FSelector_symmetrical.uncertainty",
@@ -572,7 +589,8 @@ symmetrical.uncertainty = makeFilter(
   fun = function(task, nselect, ...) {
     y = FSelector::symmetrical.uncertainty(getTaskFormula(task), data = getTaskData(task))
     setNames(y[["attr_importance"]], getTaskFeatureNames(task))
-  })
+  }
+)
 
 .FilterRegister[["symmetrical.uncertainty"]] = symmetrical.uncertainty
 .FilterRegister[["symmetrical.uncertainty"]]$desc = "(DEPRECATED)"
@@ -603,7 +621,8 @@ makeFilter(
   fun = function(task, nselect, ...) {
     y = FSelector::chi.squared(getTaskFormula(task), data = getTaskData(task))
     setNames(y[["attr_importance"]], getTaskFeatureNames(task))
-  })
+  }
+)
 
 chi.squared = makeFilter(
   name = "FSelector_chi.squared",
@@ -614,7 +633,8 @@ chi.squared = makeFilter(
   fun = function(task, nselect, ...) {
     y = FSelector::chi.squared(getTaskFormula(task), data = getTaskData(task))
     setNames(y[["attr_importance"]], getTaskFeatureNames(task))
-  })
+  }
+)
 
 .FilterRegister[["chi.squared"]] = chi.squared
 .FilterRegister[["chi.squared"]]$desc = "(DEPRECATED)"
@@ -652,7 +672,8 @@ makeFilter(
   fun = function(task, nselect, ...) {
     y = FSelector::relief(getTaskFormula(task), data = getTaskData(task), ...)
     setNames(y[["attr_importance"]], getTaskFeatureNames(task))
-  })
+  }
+)
 
 relief = makeFilter(
   name = "FSelector_relief",
@@ -663,7 +684,8 @@ relief = makeFilter(
   fun = function(task, nselect, ...) {
     y = FSelector::relief(getTaskFormula(task), data = getTaskData(task), ...)
     setNames(y[["attr_importance"]], getTaskFeatureNames(task))
-  })
+  }
+)
 
 .FilterRegister[["relief"]] = relief
 .FilterRegister[["relief"]]$desc = "(DEPRECATED)"
@@ -693,7 +715,8 @@ makeFilter(
   fun = function(task, nselect, ...) {
     y = FSelector::oneR(getTaskFormula(task), data = getTaskData(task))
     setNames(y[["attr_importance"]], getTaskFeatureNames(task))
-  })
+  }
+)
 
 oneR = makeFilter( # nolint
   name = "FSelector_oneR",
@@ -704,7 +727,8 @@ oneR = makeFilter( # nolint
   fun = function(task, nselect, ...) {
     y = FSelector::oneR(getTaskFormula(task), data = getTaskData(task))
     setNames(y[["attr_importance"]], getTaskFeatureNames(task))
-  })
+  }
+)
 
 .FilterRegister[["oneR"]] = oneR
 .FilterRegister[["oneR"]]$desc = "(DEPRECATED)"
@@ -768,7 +792,8 @@ univariate = makeFilter(
       res = -1.0 * res
     }
     setNames(res, fns)
-  })
+  }
+)
 .FilterRegister[["univariate"]] = univariate
 .FilterRegister[["univariate"]]$desc = "(DEPRECATED)"
 .FilterRegister[["univariate"]]$fun = function(...) {
@@ -799,7 +824,8 @@ makeFilter(
       aov.t = aov(f, data = data)
       summary(aov.t)[[1L]][1L, "F value"]
     })
-  })
+  }
+)
 
 # kruskal.test ----------------
 
@@ -827,7 +853,8 @@ makeFilter(
       t = kruskal.test(f, data = data)
       unname(t$statistic)
     })
-  })
+  }
+)
 
 # variance ----------------
 
@@ -850,7 +877,8 @@ makeFilter(
     sapply(getTaskFeatureNames(task), function(feat.name) {
       var(data[[feat.name]], na.rm = na.rm)
     })
-  })
+  }
+)
 
 # permutation.importance ----------------
 
@@ -882,7 +910,8 @@ makeFilter(
     imp = as.numeric(imp$res)
     names(imp) = getTaskFeatureNames(task)
     return(imp)
-  })
+  }
+)
 
 # auc ----------------
 
@@ -908,7 +937,8 @@ makeFilter(
       measureAUC(x, y, task$task.desc$negative, task$task.desc$positive)
     }, y = data$target)
     abs(0.5 - score)
-  })
+  }
+)
 
 #' Filters from the package \pkg{praznik} use the mutual information criteria in a greedy forward fashion:
 #' \dQuote{praznik_CMIM}, \dQuote{praznik_DISR}, \dQuote{praznik_JMIM}, \dQuote{praznik_JMI},
@@ -1071,7 +1101,7 @@ makeFilter(
     res = setNames(res$importance, res$attributes)
     replace(res, is.nan(res), 0) # FIXME: this is a technical fix, need to report upstream
   }
-  )
+)
 
 # FSelectorRcpp_info.gain ----------------
 
@@ -1127,7 +1157,8 @@ makeFilter(
     lrn = makeLearner(lrn.type, importance = "permutation", ...)
     mod = train(lrn, task)
     ranger::importance(mod$learner.model)
-  })
+  }
+)
 
 ranger.permutation = makeFilter(
   name = "ranger_permutation",
@@ -1140,7 +1171,8 @@ ranger.permutation = makeFilter(
     lrn = makeLearner(lrn.type, importance = "permutation", ...)
     mod = train(lrn, task)
     ranger::importance(mod$learner.model)
-  })
+  }
+)
 
 .FilterRegister[["ranger.permutation"]] = ranger.permutation
 .FilterRegister[["ranger.permutation"]]$desc = "(DEPRECATED)"
@@ -1170,7 +1202,8 @@ makeFilter(
     lrn = makeLearner(lrn.type, importance = "impurity", ...)
     mod = train(lrn, task)
     ranger::importance(mod$learner.model)
-  })
+  }
+)
 
 ranger.impurity = makeFilter(
   name = "ranger_impurity",
@@ -1183,7 +1216,8 @@ ranger.impurity = makeFilter(
     lrn = makeLearner(lrn.type, importance = "impurity", ...)
     mod = train(lrn, task)
     ranger::importance(mod$learner.model)
-  })
+  }
+)
 
 
 .FilterRegister[["ranger.impurity"]] = ranger.impurity