diff --git a/DESCRIPTION b/DESCRIPTION index d84e705e..6eb82fdf 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -32,6 +32,7 @@ Suggests: care, caret, carSurv, + gausscov, FSelectorRcpp, knitr, lgr, @@ -58,6 +59,7 @@ Collate: 'FilterCorrelation.R' 'FilterDISR.R' 'FilterFindCorrelation.R' + 'FilterGausscovF1st.R' 'FilterImportance.R' 'FilterInformationGain.R' 'FilterJMI.R' diff --git a/NAMESPACE b/NAMESPACE index a2f9dd63..7c868326 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -11,6 +11,7 @@ export(FilterCarSurvScore) export(FilterCorrelation) export(FilterDISR) export(FilterFindCorrelation) +export(FilterGausscovF1st) export(FilterImportance) export(FilterInformationGain) export(FilterJMI) diff --git a/R/FilterGausscovF1st.R b/R/FilterGausscovF1st.R new file mode 100644 index 00000000..fff53920 --- /dev/null +++ b/R/FilterGausscovF1st.R @@ -0,0 +1,72 @@ +#' @title Gaussian Covariate Stepwise Selection +#' +#' @name mlr_filters_gauscovf1st +#' +#' @description Gaussian covariate filter calling +#' [gausscov::f1st()] in package \CRANpkg{gausscov}. Please read +#' original documentation for the function form the \CRANpkg{gausscov} +#' package. +#' +#' Filter supports only regression tasks. +#' +#' @family Filter +#' @template seealso_filter +#' @export +#' @examples +#' if (requireNamespace("FilterGausscovF1st")) { +#' ## Gaussian Covariance (default) +#' task = mlr3::tsk("mtcars") +#' filter = flt("gausscov_f1st") +#' filter$calculate(task) +#' head(filter$scores, 3) +#' as.data.table(filter) +#' } +FilterGausscovF1st = R6Class( + "FilterGausscovF1st", + inherit = Filter, + + public = list( + + #' @description Create a GaussCov object. + initialize = function() { + param_set = ps( + p0 = p_dbl(lower = 0, upper = 1, default = 0.01), + kmn = p_int(lower = 0, default = 0), + kmx = p_int(lower = 0, default = 0), + mx = p_int(lower = 1, default = 21), + kex = p_int(lower = 0, default = 0), + sub = p_lgl(default = TRUE), + inr = p_lgl(default = TRUE), + xinr = p_lgl(default = FALSE), + qq = p_int(lower = 0, default = 0) + ) + + super$initialize( + id = "gausscov_f1st", + task_types = c("regr"), + param_set = param_set, + feature_types = c("integer", "numeric"), + packages = "gausscov", + label = "Gauss Covariance f1st", + man = "mlr3filters::mlr_filters_gausscov_f1st" + ) + } + ), + + private = list( + .calculate = function(task, nfeat) { + pv = self$param_set$values + x = as.matrix(task$data(cols = task$feature_names)) + y = as.matrix(task$truth()) + res = invoke(gausscov::f1st, y = y, x = x, .args = pv) + res_1 = res[[1]] + res_1 = res_1[res_1[, 1] != 0, ] + scores = res_1[, 2] + attrs = task$feature_names[res_1[, 1]] + set_names(scores, attrs) + } + ) +) + +#' @include mlr_filters.R +mlr_filters$add("gausscov_f1st", FilterGausscovF1st) diff --git a/man/Filter.Rd b/man/Filter.Rd index 711c07a3..e8fae340 100644 --- a/man/Filter.Rd +++ b/man/Filter.Rd @@ -26,6 +26,7 @@ Other Filter: \code{\link{mlr_filters_correlation}}, \code{\link{mlr_filters_disr}}, \code{\link{mlr_filters_find_correlation}}, +\code{\link{mlr_filters_gauscovf1st}}, \code{\link{mlr_filters_importance}}, \code{\link{mlr_filters_information_gain}}, \code{\link{mlr_filters_jmim}}, diff --git a/man/mlr_filters.Rd b/man/mlr_filters.Rd index 01ba242f..3bab7848 100644 --- a/man/mlr_filters.Rd +++ b/man/mlr_filters.Rd @@ -41,6 +41,7 @@ Other Filter: \code{\link{mlr_filters_correlation}}, \code{\link{mlr_filters_disr}}, \code{\link{mlr_filters_find_correlation}}, +\code{\link{mlr_filters_gauscovf1st}}, \code{\link{mlr_filters_importance}}, \code{\link{mlr_filters_information_gain}}, \code{\link{mlr_filters_jmim}}, diff --git a/man/mlr_filters_anova.Rd b/man/mlr_filters_anova.Rd index d9057aee..a394525d 100644 --- a/man/mlr_filters_anova.Rd +++ b/man/mlr_filters_anova.Rd @@ -56,6 +56,7 @@ Other Filter: \code{\link{mlr_filters_correlation}}, \code{\link{mlr_filters_disr}}, \code{\link{mlr_filters_find_correlation}}, +\code{\link{mlr_filters_gauscovf1st}}, \code{\link{mlr_filters_importance}}, \code{\link{mlr_filters_information_gain}}, \code{\link{mlr_filters_jmim}}, diff --git a/man/mlr_filters_auc.Rd b/man/mlr_filters_auc.Rd index cc721d1f..85180b76 100644 --- a/man/mlr_filters_auc.Rd +++ b/man/mlr_filters_auc.Rd @@ -52,6 +52,7 @@ Other Filter: \code{\link{mlr_filters_correlation}}, \code{\link{mlr_filters_disr}}, \code{\link{mlr_filters_find_correlation}}, +\code{\link{mlr_filters_gauscovf1st}}, \code{\link{mlr_filters_importance}}, \code{\link{mlr_filters_information_gain}}, \code{\link{mlr_filters_jmim}}, diff --git a/man/mlr_filters_carscore.Rd b/man/mlr_filters_carscore.Rd index cc31336d..94c049c3 100644 --- a/man/mlr_filters_carscore.Rd +++ b/man/mlr_filters_carscore.Rd @@ -54,6 +54,7 @@ Other Filter: \code{\link{mlr_filters_correlation}}, \code{\link{mlr_filters_disr}}, \code{\link{mlr_filters_find_correlation}}, +\code{\link{mlr_filters_gauscovf1st}}, \code{\link{mlr_filters_importance}}, \code{\link{mlr_filters_information_gain}}, \code{\link{mlr_filters_jmim}}, diff --git a/man/mlr_filters_carsurvscore.Rd b/man/mlr_filters_carsurvscore.Rd index 113297fc..de4947be 100644 --- a/man/mlr_filters_carsurvscore.Rd +++ b/man/mlr_filters_carsurvscore.Rd @@ -30,6 +30,7 @@ Other Filter: \code{\link{mlr_filters_correlation}}, \code{\link{mlr_filters_disr}}, \code{\link{mlr_filters_find_correlation}}, +\code{\link{mlr_filters_gauscovf1st}}, \code{\link{mlr_filters_importance}}, \code{\link{mlr_filters_information_gain}}, \code{\link{mlr_filters_jmim}}, diff --git a/man/mlr_filters_cmim.Rd b/man/mlr_filters_cmim.Rd index f837cbcb..428f3dd0 100644 --- a/man/mlr_filters_cmim.Rd +++ b/man/mlr_filters_cmim.Rd @@ -67,6 +67,7 @@ Other Filter: \code{\link{mlr_filters_correlation}}, \code{\link{mlr_filters_disr}}, \code{\link{mlr_filters_find_correlation}}, +\code{\link{mlr_filters_gauscovf1st}}, \code{\link{mlr_filters_importance}}, \code{\link{mlr_filters_information_gain}}, \code{\link{mlr_filters_jmim}}, diff --git a/man/mlr_filters_correlation.Rd b/man/mlr_filters_correlation.Rd index 92ce9a6e..9ee9b1b7 100644 --- a/man/mlr_filters_correlation.Rd +++ b/man/mlr_filters_correlation.Rd @@ -63,6 +63,7 @@ Other Filter: \code{\link{mlr_filters_cmim}}, \code{\link{mlr_filters_disr}}, \code{\link{mlr_filters_find_correlation}}, +\code{\link{mlr_filters_gauscovf1st}}, \code{\link{mlr_filters_importance}}, \code{\link{mlr_filters_information_gain}}, \code{\link{mlr_filters_jmim}}, diff --git a/man/mlr_filters_disr.Rd b/man/mlr_filters_disr.Rd index 62ae92bc..64ccea2d 100644 --- a/man/mlr_filters_disr.Rd +++ b/man/mlr_filters_disr.Rd @@ -67,6 +67,7 @@ Other Filter: \code{\link{mlr_filters_cmim}}, \code{\link{mlr_filters_correlation}}, \code{\link{mlr_filters_find_correlation}}, +\code{\link{mlr_filters_gauscovf1st}}, \code{\link{mlr_filters_importance}}, \code{\link{mlr_filters_information_gain}}, \code{\link{mlr_filters_jmim}}, diff --git a/man/mlr_filters_find_correlation.Rd b/man/mlr_filters_find_correlation.Rd index 00cc2323..6fa9d5de 100644 --- a/man/mlr_filters_find_correlation.Rd +++ b/man/mlr_filters_find_correlation.Rd @@ -56,6 +56,7 @@ Other Filter: \code{\link{mlr_filters_cmim}}, \code{\link{mlr_filters_correlation}}, \code{\link{mlr_filters_disr}}, +\code{\link{mlr_filters_gauscovf1st}}, \code{\link{mlr_filters_importance}}, \code{\link{mlr_filters_information_gain}}, \code{\link{mlr_filters_jmim}}, diff --git a/man/mlr_filters_gauscovf1st.Rd b/man/mlr_filters_gauscovf1st.Rd new file mode 100644 index 00000000..aaec214c --- /dev/null +++ b/man/mlr_filters_gauscovf1st.Rd @@ -0,0 +1,104 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/FilterGausscovF1st.R +\name{mlr_filters_gauscovf1st} +\alias{mlr_filters_gauscovf1st} +\alias{FilterGausscovF1st} +\title{Gaussian Covariate Stepwise Selection} +\description{ +Gaussian covariate filter calling +\code{\link[gausscov:f1st]{gausscov::f1st()}} in package \CRANpkg{gausscov}. Please read +original documentation for the function form the \CRANpkg{gausscov} +package. + +Filter supports only regression tasks. +} +\examples{ +if (requireNamespace("FilterGausscovF1st")) { + ## Gaussian Covariance (default) + task = mlr3::tsk("mtcars") + filter = flt("gausscov_f1st") + filter$calculate(task) + head(filter$scores, 3) + as.data.table(filter) +} +} +\seealso{ +\itemize{ +\item \link[mlr3pipelines:mlr_pipeops_filter]{PipeOpFilter} for filter-based feature selection. +\item \link[mlr3misc:Dictionary]{Dictionary} of \link[=Filter]{Filters}: \link{mlr_filters} +} + +Other Filter: +\code{\link{Filter}}, +\code{\link{mlr_filters_anova}}, +\code{\link{mlr_filters_auc}}, +\code{\link{mlr_filters_carscore}}, +\code{\link{mlr_filters_carsurvscore}}, +\code{\link{mlr_filters_cmim}}, +\code{\link{mlr_filters_correlation}}, +\code{\link{mlr_filters_disr}}, +\code{\link{mlr_filters_find_correlation}}, +\code{\link{mlr_filters_importance}}, +\code{\link{mlr_filters_information_gain}}, +\code{\link{mlr_filters_jmim}}, +\code{\link{mlr_filters_jmi}}, +\code{\link{mlr_filters_kruskal_test}}, +\code{\link{mlr_filters_mim}}, +\code{\link{mlr_filters_mrmr}}, +\code{\link{mlr_filters_njmim}}, +\code{\link{mlr_filters_performance}}, +\code{\link{mlr_filters_permutation}}, +\code{\link{mlr_filters_relief}}, +\code{\link{mlr_filters_selected_features}}, +\code{\link{mlr_filters_variance}}, +\code{\link{mlr_filters}} +} +\concept{Filter} +\section{Super class}{ +\code{\link[mlr3filters:Filter]{mlr3filters::Filter}} -> \code{FilterGausscovF1st} +} +\section{Methods}{ +\subsection{Public methods}{ +\itemize{ +\item \href{#method-FilterGausscovF1st-new}{\code{FilterGausscovF1st$new()}} +\item \href{#method-FilterGausscovF1st-clone}{\code{FilterGausscovF1st$clone()}} +} +} +\if{html}{\out{ +
Inherited methods + +
+}} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-FilterGausscovF1st-new}{}}} +\subsection{Method \code{new()}}{ +Create a GaussCov object. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{FilterGausscovF1st$new()}\if{html}{\out{
}} +} + +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-FilterGausscovF1st-clone}{}}} +\subsection{Method \code{clone()}}{ +The objects of this class are cloneable with this method. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{FilterGausscovF1st$clone(deep = FALSE)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{deep}}{Whether to make a deep clone.} +} +\if{html}{\out{
}} +} +} +} diff --git a/man/mlr_filters_importance.Rd b/man/mlr_filters_importance.Rd index 618ec2d6..9caf8298 100644 --- a/man/mlr_filters_importance.Rd +++ b/man/mlr_filters_importance.Rd @@ -50,6 +50,7 @@ Other Filter: \code{\link{mlr_filters_correlation}}, \code{\link{mlr_filters_disr}}, \code{\link{mlr_filters_find_correlation}}, +\code{\link{mlr_filters_gauscovf1st}}, \code{\link{mlr_filters_information_gain}}, \code{\link{mlr_filters_jmim}}, \code{\link{mlr_filters_jmi}}, diff --git a/man/mlr_filters_information_gain.Rd b/man/mlr_filters_information_gain.Rd index 67795ddf..f656239b 100644 --- a/man/mlr_filters_information_gain.Rd +++ b/man/mlr_filters_information_gain.Rd @@ -61,6 +61,7 @@ Other Filter: \code{\link{mlr_filters_correlation}}, \code{\link{mlr_filters_disr}}, \code{\link{mlr_filters_find_correlation}}, +\code{\link{mlr_filters_gauscovf1st}}, \code{\link{mlr_filters_importance}}, \code{\link{mlr_filters_jmim}}, \code{\link{mlr_filters_jmi}}, diff --git a/man/mlr_filters_jmi.Rd b/man/mlr_filters_jmi.Rd index cb67300e..167d6dff 100644 --- a/man/mlr_filters_jmi.Rd +++ b/man/mlr_filters_jmi.Rd @@ -68,6 +68,7 @@ Other Filter: \code{\link{mlr_filters_correlation}}, \code{\link{mlr_filters_disr}}, \code{\link{mlr_filters_find_correlation}}, +\code{\link{mlr_filters_gauscovf1st}}, \code{\link{mlr_filters_importance}}, \code{\link{mlr_filters_information_gain}}, \code{\link{mlr_filters_jmim}}, diff --git a/man/mlr_filters_jmim.Rd b/man/mlr_filters_jmim.Rd index f00531bf..0843340f 100644 --- a/man/mlr_filters_jmim.Rd +++ b/man/mlr_filters_jmim.Rd @@ -68,6 +68,7 @@ Other Filter: \code{\link{mlr_filters_correlation}}, \code{\link{mlr_filters_disr}}, \code{\link{mlr_filters_find_correlation}}, +\code{\link{mlr_filters_gauscovf1st}}, \code{\link{mlr_filters_importance}}, \code{\link{mlr_filters_information_gain}}, \code{\link{mlr_filters_jmi}}, diff --git a/man/mlr_filters_kruskal_test.Rd b/man/mlr_filters_kruskal_test.Rd index de903a36..120266db 100644 --- a/man/mlr_filters_kruskal_test.Rd +++ b/man/mlr_filters_kruskal_test.Rd @@ -64,6 +64,7 @@ Other Filter: \code{\link{mlr_filters_correlation}}, \code{\link{mlr_filters_disr}}, \code{\link{mlr_filters_find_correlation}}, +\code{\link{mlr_filters_gauscovf1st}}, \code{\link{mlr_filters_importance}}, \code{\link{mlr_filters_information_gain}}, \code{\link{mlr_filters_jmim}}, diff --git a/man/mlr_filters_mim.Rd b/man/mlr_filters_mim.Rd index 9404074b..529e3c79 100644 --- a/man/mlr_filters_mim.Rd +++ b/man/mlr_filters_mim.Rd @@ -68,6 +68,7 @@ Other Filter: \code{\link{mlr_filters_correlation}}, \code{\link{mlr_filters_disr}}, \code{\link{mlr_filters_find_correlation}}, +\code{\link{mlr_filters_gauscovf1st}}, \code{\link{mlr_filters_importance}}, \code{\link{mlr_filters_information_gain}}, \code{\link{mlr_filters_jmim}}, diff --git a/man/mlr_filters_mrmr.Rd b/man/mlr_filters_mrmr.Rd index d29ac31d..dc8abdfa 100644 --- a/man/mlr_filters_mrmr.Rd +++ b/man/mlr_filters_mrmr.Rd @@ -68,6 +68,7 @@ Other Filter: \code{\link{mlr_filters_correlation}}, \code{\link{mlr_filters_disr}}, \code{\link{mlr_filters_find_correlation}}, +\code{\link{mlr_filters_gauscovf1st}}, \code{\link{mlr_filters_importance}}, \code{\link{mlr_filters_information_gain}}, \code{\link{mlr_filters_jmim}}, diff --git a/man/mlr_filters_njmim.Rd b/man/mlr_filters_njmim.Rd index da4d0fc4..474f0328 100644 --- a/man/mlr_filters_njmim.Rd +++ b/man/mlr_filters_njmim.Rd @@ -68,6 +68,7 @@ Other Filter: \code{\link{mlr_filters_correlation}}, \code{\link{mlr_filters_disr}}, \code{\link{mlr_filters_find_correlation}}, +\code{\link{mlr_filters_gauscovf1st}}, \code{\link{mlr_filters_importance}}, \code{\link{mlr_filters_information_gain}}, \code{\link{mlr_filters_jmim}}, diff --git a/man/mlr_filters_performance.Rd b/man/mlr_filters_performance.Rd index 17cfa071..1d080c27 100644 --- a/man/mlr_filters_performance.Rd +++ b/man/mlr_filters_performance.Rd @@ -49,6 +49,7 @@ Other Filter: \code{\link{mlr_filters_correlation}}, \code{\link{mlr_filters_disr}}, \code{\link{mlr_filters_find_correlation}}, +\code{\link{mlr_filters_gauscovf1st}}, \code{\link{mlr_filters_importance}}, \code{\link{mlr_filters_information_gain}}, \code{\link{mlr_filters_jmim}}, diff --git a/man/mlr_filters_permutation.Rd b/man/mlr_filters_permutation.Rd index a14dbaf3..9548bdf4 100644 --- a/man/mlr_filters_permutation.Rd +++ b/man/mlr_filters_permutation.Rd @@ -62,6 +62,7 @@ Other Filter: \code{\link{mlr_filters_correlation}}, \code{\link{mlr_filters_disr}}, \code{\link{mlr_filters_find_correlation}}, +\code{\link{mlr_filters_gauscovf1st}}, \code{\link{mlr_filters_importance}}, \code{\link{mlr_filters_information_gain}}, \code{\link{mlr_filters_jmim}}, diff --git a/man/mlr_filters_relief.Rd b/man/mlr_filters_relief.Rd index ccc8f956..01cce628 100644 --- a/man/mlr_filters_relief.Rd +++ b/man/mlr_filters_relief.Rd @@ -53,6 +53,7 @@ Other Filter: \code{\link{mlr_filters_correlation}}, \code{\link{mlr_filters_disr}}, \code{\link{mlr_filters_find_correlation}}, +\code{\link{mlr_filters_gauscovf1st}}, \code{\link{mlr_filters_importance}}, \code{\link{mlr_filters_information_gain}}, \code{\link{mlr_filters_jmim}}, diff --git a/man/mlr_filters_selected_features.Rd b/man/mlr_filters_selected_features.Rd index 4f6519b3..4506381e 100644 --- a/man/mlr_filters_selected_features.Rd +++ b/man/mlr_filters_selected_features.Rd @@ -57,6 +57,7 @@ Other Filter: \code{\link{mlr_filters_correlation}}, \code{\link{mlr_filters_disr}}, \code{\link{mlr_filters_find_correlation}}, +\code{\link{mlr_filters_gauscovf1st}}, \code{\link{mlr_filters_importance}}, \code{\link{mlr_filters_information_gain}}, \code{\link{mlr_filters_jmim}}, diff --git a/man/mlr_filters_variance.Rd b/man/mlr_filters_variance.Rd index f6c149c5..be06063d 100644 --- a/man/mlr_filters_variance.Rd +++ b/man/mlr_filters_variance.Rd @@ -52,6 +52,7 @@ Other Filter: \code{\link{mlr_filters_correlation}}, \code{\link{mlr_filters_disr}}, \code{\link{mlr_filters_find_correlation}}, +\code{\link{mlr_filters_gauscovf1st}}, \code{\link{mlr_filters_importance}}, \code{\link{mlr_filters_information_gain}}, \code{\link{mlr_filters_jmim}}, diff --git a/tests/testthat/test-FilterGausscovF1st.R b/tests/testthat/test-FilterGausscovF1st.R new file mode 100644 index 00000000..472361f2 --- /dev/null +++ b/tests/testthat/test-FilterGausscovF1st.R @@ -0,0 +1,8 @@ +test_that("FilterGaussCovF1st works as expected", { + data = as.data.table(mtcars) + task = as_task_regr(data, target = "mpg") + + scores = flt("gausscov_f1st")$calculate(task)$scores + + expect_numeric(scores) +})