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FilterKruskalTest.R
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FilterKruskalTest.R
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#' @title Kruskal-Wallis Test Filter
#'
#' @name mlr_filters_kruskal_test
#'
#' @description Kruskal-Wallis rank sum test filter calling
#' [stats::kruskal.test()].
#'
#' The filter value is `-log10(p)` where `p` is the \eqn{p}-value. This
#' transformation is necessary to ensure numerical stability for very small
#' \eqn{p}-values.
#'
#' @family Filter
#' @template seealso_filter
#' @export
#' @examples
#' task = mlr3::tsk("iris")
#' filter = flt("kruskal_test")
#' filter$calculate(task)
#' as.data.table(filter)
#'
#' # transform to p-value
#' 10^(-filter$scores)
FilterKruskalTest = R6Class("FilterKruskalTest", inherit = Filter,
public = list(
#' @description Create a FilterKruskalTest object.
#' @param id (`character(1)`)\cr
#' Identifier for the filter.
#' @param task_type (`character()`)\cr
#' Types of the task the filter can operator on. E.g., `"classif"` or
#' `"regr"`.
#' @param param_set ([paradox::ParamSet])\cr
#' Set of hyperparameters.
#' @param feature_types (`character()`)\cr
#' Feature types the filter operates on.
#' Must be a subset of
#' [`mlr_reflections$task_feature_types`][mlr3::mlr_reflections].
#' @param packages (`character()`)\cr
#' Set of required packages.
#' Note that these packages will be loaded via [requireNamespace()], and
#' are not attached.
initialize = function(id = "kruskal_test",
task_type = "classif",
param_set = ParamSet$new(list(
ParamFct$new("na.action", default = "na.omit",
levels = c("na.omit", "na.fail", "na.exclude", "na.pass"))
)),
packages = "stats",
feature_types = c("integer", "numeric")) {
super$initialize(
id = id,
task_type = task_type,
param_set = param_set,
feature_types = feature_types,
packages = packages,
man = "mlr3filters::mlr_filters_kruskal_test"
)
}
),
private = list(
.calculate = function(task, nfeat) {
na.action = self$param_set$values$na.action %??%
self$param_set$default$na.action
data = task$data(cols = task$feature_names)
g = task$truth()
-log10(map_dbl(data, function(x) {
kruskal.test(x = x, g = g, na.action = na.action)$p.value
}))
}
)
)
#' @include mlr_filters.R
mlr_filters$add("kruskal_test", FilterKruskalTest)