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Docs #132

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4205296
fix: remove mlr3proba
sebffischer Aug 8, 2022
5cb0039
docs: add docu for PipeOpFilter
sebffischer Aug 8, 2022
f26f83c
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 8, 2022
3d018c3
fix: example
sebffischer Aug 8, 2022
c45bfbc
Merge branch 'docs' of github.com:mlr-org/mlr3filters into docs
sebffischer Aug 8, 2022
e01bfbb
fix: example filter importance + document
sebffischer Aug 8, 2022
56faaba
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 8, 2022
f1551be
fix: examples
sebffischer Aug 8, 2022
6e55f7d
Merge branch 'docs' of github.com:mlr-org/mlr3filters into docs
sebffischer Aug 8, 2022
8032f7b
docs: document
sebffischer Aug 8, 2022
5207148
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 8, 2022
681ed5b
docs: improve filter docs
sebffischer Aug 16, 2022
f006715
docs: improve filter docs
sebffischer Aug 16, 2022
70f9573
add survival filter
sebffischer Aug 16, 2022
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5 changes: 2 additions & 3 deletions DESCRIPTION
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Expand Up @@ -37,7 +37,7 @@ Suggests:
lgr,
mlr3learners,
mlr3measures,
mlr3proba,
mlr3pipelines,
praznik,
rpart,
testthat (>= 3.0.0),
Expand All @@ -47,15 +47,14 @@ Config/testthat/parallel: true
Encoding: UTF-8
NeedsCompilation: no
Roxygen: list(markdown = TRUE, r6 = TRUE)
RoxygenNote: 7.2.0
RoxygenNote: 7.2.1
Collate:
'Filter.R'
'mlr_filters.R'
'FilterAUC.R'
'FilterAnova.R'
'FilterCMIM.R'
'FilterCarScore.R'
'FilterCarSurvScore.R'
'FilterCorrelation.R'
'FilterDISR.R'
'FilterFindCorrelation.R'
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1 change: 0 additions & 1 deletion NAMESPACE
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Expand Up @@ -7,7 +7,6 @@ export(FilterAUC)
export(FilterAnova)
export(FilterCMIM)
export(FilterCarScore)
export(FilterCarSurvScore)
export(FilterCorrelation)
export(FilterDISR)
export(FilterFindCorrelation)
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10 changes: 10 additions & 0 deletions R/FilterAUC.R
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Expand Up @@ -22,6 +22,16 @@
#' filter = flt("auc")
#' filter$calculate(task)
#' head(as.data.table(filter), 3)
#'
#' if (requireNamespace("mlr3pipelines")) {
#' library("mlr3pipelines")
#' task = mlr3::tsk("spam")
#'
#' graph = po("filter", filter = flt("auc"), filter.cutoff = 0.1) %>>%
#' po("learner", mlr3::lrn("classif.rpart"))
#'
#' graph$train(task)
#' }
FilterAUC = R6Class("FilterAUC",
inherit = Filter,

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10 changes: 10 additions & 0 deletions R/FilterAnova.R
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Expand Up @@ -26,6 +26,16 @@
#'
#' # transform to p-value
#' 10^(-filter$scores)
#'
#' if (requireNamespace("mlr3pipelines")) {
#' library("mlr3pipelines")
#' task = mlr3::tsk("spam")
#'
#' graph = po("filter", filter = flt("anova"), filter.cutoff = 20) %>>%
#' po("learner", mlr3::lrn("classif.rpart"))
#'
#' graph$train(task)
#' }
FilterAnova = R6Class("FilterAnova",
inherit = Filter,

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20 changes: 16 additions & 4 deletions R/FilterCMIM.R
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Expand Up @@ -19,10 +19,22 @@
#' @template seealso_filter
#' @export
#' @examples
#' task = mlr3::tsk("iris")
#' filter = flt("cmim")
#' filter$calculate(task, nfeat = 2)
#' as.data.table(filter)
#' if (requireNamespace("praznik")) {
#' task = mlr3::tsk("iris")
#' filter = flt("cmim")
#' filter$calculate(task, nfeat = 2)
#' as.data.table(filter)
#' }
#'
#' if (requireNamespace("mlr3pipelines") && requireNamespace("praznik")) {
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I'd favor using mlr3misc::require_namespaces(c("mlr3pipelines", "praznik")) in cases with n > 1.

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Fine for me.

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but it needs argument quietly = TRUE then 😞

#' library("mlr3pipelines")
#' task = mlr3::tsk("spam")
#'
#' graph = po("filter", filter = flt("cmim"), filter.cutoff = 0.5) %>>%
#' po("learner", mlr3::lrn("classif.rpart"))
#'
#' graph$train(task)
#' }
FilterCMIM = R6Class("FilterCMIM",
inherit = Filter,

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20 changes: 16 additions & 4 deletions R/FilterCarScore.R
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Expand Up @@ -14,16 +14,28 @@
#' @template seealso_filter
#' @export
#' @examples
#' task = mlr3::tsk("mtcars")
#' filter = flt("carscore")
#' filter$calculate(task)
#' head(as.data.table(filter), 3)
#' if (requireNamespace("care")) {
#' task = mlr3::tsk("mtcars")
#' filter = flt("carscore")
#' filter$calculate(task)
#' head(as.data.table(filter), 3)
#' }
#'
#' ## changing filter settings
#' filter = flt("carscore")
#' filter$param_set$values = list("diagonal" = TRUE)
#' filter$calculate(task)
#' head(as.data.table(filter), 3)
#'
#' if (requireNamespace("mlr3pipelines") && requireNamespace("care")) {
#' library("mlr3pipelines")
#' task = mlr3::tsk("mtcars")
#'
#' graph = po("filter", filter = flt("carscore"), filter.cutoff = 0.2) %>>%
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I'd avoid setting filter.cutoff as users might takes this as a "good default" then as its listed in an example.

I see you're setting a different value in each example. Should we calculate a random dynamic value and add a comment that this value should be tuned in practice?

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Adding a comment that this value should be tuned: 👍

I don't think a random value is helping, this is just confusing.

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I don't think a random value is helping, this is just confusing.

Agree, this might not be obvious. Maybe the combination of a hardcoded value across all examples and a comment about the tuning need might be the best middle way.

#' po("learner", mlr3::lrn("regr.rpart"))
#'
#' graph$train(task)
#' }
FilterCarScore = R6Class("FilterCarScore",
inherit = Filter,

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63 changes: 0 additions & 63 deletions R/FilterCarSurvScore.R
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9 changes: 9 additions & 0 deletions R/FilterCorrelation.R
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Expand Up @@ -26,6 +26,15 @@
#' filter$param_set$values = list("method" = "spearman")
#' filter$calculate(task)
#' as.data.table(filter)
#' if (requireNamespace("mlr3pipelines")) {
#' library("mlr3pipelines")
#' task = mlr3::tsk("boston_housing")
#'
#' graph = po("filter", filter = flt("correlation"), filter.cutoff = 0.2) %>>%
#' po("learner", mlr3::lrn("regr.rpart"))
#'
#' graph$train(task)
#' }
FilterCorrelation = R6Class("FilterCorrelation",
inherit = Filter,

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20 changes: 16 additions & 4 deletions R/FilterDISR.R
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Expand Up @@ -19,10 +19,22 @@
#' @template seealso_filter
#' @export
#' @examples
#' task = mlr3::tsk("iris")
#' filter = flt("disr")
#' filter$calculate(task)
#' as.data.table(filter)
#' if (requireNamespace("praznik")) {
#' task = mlr3::tsk("iris")
#' filter = flt("disr")
#' filter$calculate(task)
#' as.data.table(filter)
#' }
#'
#' if (requireNamespace("mlr3pipelines") && requireNamespace("praznik")) {
#' library("mlr3pipelines")
#' task = mlr3::tsk("spam")
#'
#' graph = po("filter", filter = flt("disr"), filter.cutoff = 0.2) %>>%
#' po("learner", mlr3::lrn("classif.rpart"))
#'
#' graph$train(task)
#' }
FilterDISR = R6Class("FilterDISR",
inherit = Filter,

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12 changes: 11 additions & 1 deletion R/FilterFindCorrelation.R
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Expand Up @@ -19,7 +19,7 @@
#' @template seealso_filter
#' @export
#' @examples
#' ## Pearson (default)
#' # Pearson (default)
#' task = mlr3::tsk("mtcars")
#' filter = flt("find_correlation")
#' filter$calculate(task)
Expand All @@ -29,6 +29,16 @@
#' filter = flt("find_correlation", method = "spearman")
#' filter$calculate(task)
#' as.data.table(filter)
#'
#' if (requireNamespace("mlr3pipelines")) {
#' library("mlr3pipelines")
#' task = mlr3::tsk("spam")
#'
#' graph = po("filter", filter = flt("find_correlation"), filter.cutoff = 0.4) %>>%
#' po("learner", mlr3::lrn("classif.rpart"))
#'
#' graph$train(task)
#' }
FilterFindCorrelation = R6Class("FilterFindCorrelation",
inherit = Filter,

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26 changes: 21 additions & 5 deletions R/FilterImportance.R
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Expand Up @@ -11,11 +11,27 @@
#' @template seealso_filter
#' @export
#' @examples
#' task = mlr3::tsk("iris")
#' learner = mlr3::lrn("classif.rpart")
#' filter = flt("importance", learner = learner)
#' filter$calculate(task)
#' as.data.table(filter)
#' if (requireNamespace("MASS")) {
#' task = mlr3::tsk("iris")
#' learner = mlr3::lrn("classif.rpart")
#' filter = flt("importance", learner = learner)
#' filter$calculate(task)
#' as.data.table(filter)
#' }
#'
#' if (requireNamespace("mlr3pipelines") && requireNamespace("mlr3learners") &&
#' requireNamespace("MASS")) {
#' library("mlr3learners")
#' library("mlr3pipelines")
#' task = mlr3::tsk("spam")
#'
#' learner = mlr3::lrn("classif.rpart")
#'
#' graph = po("filter", filter = flt("importance", learner = learner), filter.cutoff = 100) %>>%
#' po("learner", mlr3::lrn("classif.lda"))
#'
#' graph$train(task)
#' }
FilterImportance = R6Class("FilterImportance",
inherit = Filter,

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36 changes: 25 additions & 11 deletions R/FilterInformationGain.R
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Expand Up @@ -15,19 +15,33 @@
#' @template seealso_filter
#' @export
#' @examples
#' ## InfoGain (default)
#' task = mlr3::tsk("pima")
#' filter = flt("information_gain")
#' filter$calculate(task)
#' head(filter$scores, 3)
#' as.data.table(filter)
#' if (requireNamespace("FSelectorRcpp")) {
#' ## InfoGain (default)
#' task = mlr3::tsk("pima")
#' filter = flt("information_gain")
#' filter$calculate(task)
#' head(filter$scores, 3)
#' as.data.table(filter)
#'
#' ## GainRatio
#' ## GainRatio
#'
#' filterGR = flt("information_gain")
#' filterGR$param_set$values = list("type" = "gainratio")
#' filterGR$calculate(task)
#' head(as.data.table(filterGR), 3)
#' filterGR = flt("information_gain")
#' filterGR$param_set$values = list("type" = "gainratio")
#' filterGR$calculate(task)
#' head(as.data.table(filterGR), 3)
#'
#' }
#'
#' if (requireNamespace("mlr3pipelines") && requireNamespace("FSelectorRcpp")) {
#' library("mlr3pipelines")
#' task = mlr3::tsk("spam")
#'
#' graph = po("filter", filter = flt("information_gain"), filter.cutoff = 0.1) %>>%
#' po("learner", mlr3::lrn("classif.rpart"))
#'
#' graph$train(task)
#'
#' }
FilterInformationGain = R6Class("FilterInformationGain",
inherit = Filter,

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20 changes: 16 additions & 4 deletions R/FilterJMI.R
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Expand Up @@ -20,10 +20,22 @@
#' @template seealso_filter
#' @export
#' @examples
#' task = mlr3::tsk("iris")
#' filter = flt("jmi")
#' filter$calculate(task, nfeat = 2)
#' as.data.table(filter)
#' if (requireNamespace("praznik")) {
#' task = mlr3::tsk("iris")
#' filter = flt("jmi")
#' filter$calculate(task, nfeat = 2)
#' as.data.table(filter)
#' }
#'
#' if (requireNamespace("mlr3pipelines") && requireNamespace("praznik")) {
#' library("mlr3pipelines")
#' task = mlr3::tsk("spam")
#'
#' graph = po("filter", filter = flt("jmi"), filter.cutoff = 0.2) %>>%
#' po("learner", mlr3::lrn("classif.rpart"))
#'
#' graph$train(task)
#' }
FilterJMI = R6Class("FilterJMI",
inherit = Filter,

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21 changes: 17 additions & 4 deletions R/FilterJMIM.R
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Expand Up @@ -19,10 +19,23 @@
#' @template seealso_filter
#' @export
#' @examples
#' task = mlr3::tsk("iris")
#' filter = flt("jmim")
#' filter$calculate(task, nfeat = 2)
#' as.data.table(filter)
#' if (requireNamespace("praznik")) {
#' task = mlr3::tsk("iris")
#' filter = flt("jmim")
#' filter$calculate(task, nfeat = 2)
#' as.data.table(filter)
#' }
#'
#'
#' if (requireNamespace("mlr3pipelines") && requireNamespace("praznik")) {
#' library("mlr3pipelines")
#' task = mlr3::tsk("spam")
#'
#' graph = po("filter", filter = flt("jmim"), filter.cutoff = 0.5) %>>%
#' po("learner", mlr3::lrn("classif.rpart"))
#'
#' graph$train(task)
#' }
FilterJMIM = R6Class("FilterJMIM",
inherit = Filter,

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