Classification Random Forest SRC Learner
Source:R/learner_randomForestSRC_classif_rfsrc.R
mlr_learners_classif.rfsrc.Rd
Random forest for classification.
Calls randomForestSRC::rfsrc()
from randomForestSRC.
Meta Information
Task type: “classif”
Predict Types: “response”, “prob”
Feature Types: “logical”, “integer”, “numeric”, “factor”
Required Packages: mlr3, mlr3extralearners, randomForestSRC
Parameters
Id | Type | Default | Levels | Range |
ntree | integer | 500 | \([1, \infty)\) | |
mtry | integer | - | \([1, \infty)\) | |
mtry.ratio | numeric | - | \([0, 1]\) | |
nodesize | integer | 15 | \([1, \infty)\) | |
nodedepth | integer | - | \([1, \infty)\) | |
splitrule | character | gini | gini, auc, entropy | - |
nsplit | integer | 10 | \([0, \infty)\) | |
importance | character | FALSE | FALSE, TRUE, none, permute, random, anti | - |
block.size | integer | 10 | \([1, \infty)\) | |
bootstrap | character | by.root | by.root, by.node, none, by.user | - |
samptype | character | swor | swor, swr | - |
samp | untyped | - | - | |
membership | logical | FALSE | TRUE, FALSE | - |
sampsize | untyped | - | - | |
sampsize.ratio | numeric | - | \([0, 1]\) | |
na.action | character | na.omit | na.omit, na.impute | - |
nimpute | integer | 1 | \([1, \infty)\) | |
proximity | character | FALSE | FALSE, TRUE, inbag, oob, all | - |
distance | character | FALSE | FALSE, TRUE, inbag, oob, all | - |
forest.wt | character | FALSE | FALSE, TRUE, inbag, oob, all | - |
xvar.wt | untyped | - | - | |
split.wt | untyped | - | - | |
forest | logical | TRUE | TRUE, FALSE | - |
var.used | character | FALSE | FALSE, all.trees | - |
split.depth | character | FALSE | FALSE, all.trees, by.tree | - |
seed | integer | - | \((-\infty, -1]\) | |
do.trace | logical | FALSE | TRUE, FALSE | - |
statistics | logical | FALSE | TRUE, FALSE | - |
get.tree | untyped | - | - | |
outcome | character | train | train, test | - |
ptn.count | integer | 0 | \([0, \infty)\) | |
cores | integer | 1 | \([1, \infty)\) | |
save.memory | logical | FALSE | TRUE, FALSE | - |
perf.type | character | - | gmean, misclass, brier, none | - |
case.depth | logical | FALSE | TRUE, FALSE | - |
marginal.xvar | untyped | NULL | - |
Custom mlr3 parameters
mtry
: This hyperparameter can alternatively be set via the added hyperparametermtry.ratio
asmtry = max(ceiling(mtry.ratio * n_features), 1)
. Note thatmtry
andmtry.ratio
are mutually exclusive.sampsize
: This hyperparameter can alternatively be set via the added hyperparametersampsize.ratio
assampsize = max(ceiling(sampsize.ratio * n_obs), 1)
. Note thatsampsize
andsampsize.ratio
are mutually exclusive.cores
: This value is set as the optionrf.cores
during training and is set to 1 by default.
References
Breiman, Leo (2001). “Random Forests.” Machine Learning, 45(1), 5–32. ISSN 1573-0565, doi:10.1023/A:1010933404324 .
See also
as.data.table(mlr_learners)
for a table of available Learners in the running session (depending on the loaded packages).Chapter in the mlr3book: https://mlr3book.mlr-org.com/basics.html#learners
mlr3learners for a selection of recommended learners.
mlr3cluster for unsupervised clustering learners.
mlr3pipelines to combine learners with pre- and postprocessing steps.
mlr3tuning for tuning of hyperparameters, mlr3tuningspaces for established default tuning spaces.
Super classes
mlr3::Learner
-> mlr3::LearnerClassif
-> LearnerClassifRandomForestSRC
Methods
Inherited methods
Method importance()
The importance scores are extracted from the model slot importance
, returned for
'all'.
Returns
Named numeric()
.
Method selected_features()
Selected features are extracted from the model slot var.used
.
Note: Due to a known issue in randomForestSRC
, enabling var.used = "all.trees"
causes prediction to fail. Therefore, this setting should be used exclusively
for feature selection purposes and not when prediction is required.
Examples
# Define the Learner
learner = lrn("classif.rfsrc", importance = "TRUE")
print(learner)
#>
#> ── <LearnerClassifRandomForestSRC> (classif.rfsrc): Random Forest ──────────────
#> • Model: -
#> • Parameters: importance=TRUE
#> • Packages: mlr3, mlr3extralearners, and randomForestSRC
#> • Predict Types: [response] and prob
#> • Feature Types: logical, integer, numeric, and factor
#> • Encapsulation: none (fallback: -)
#> • Properties: importance, missings, multiclass, oob_error, selected_features,
#> twoclass, and weights
#> • Other settings: use_weights = 'use'
# Define a Task
task = tsk("sonar")
# Create train and test set
ids = partition(task)
# Train the learner on the training ids
learner$train(task, row_ids = ids$train)
print(learner$model)
#> Sample size: 139
#> Frequency of class labels: 73, 66
#> Number of trees: 500
#> Forest terminal node size: 1
#> Average no. of terminal nodes: 17.01
#> No. of variables tried at each split: 8
#> Total no. of variables: 60
#> Resampling used to grow trees: swor
#> Resample size used to grow trees: 88
#> Analysis: RF-C
#> Family: class
#> Splitting rule: gini *random*
#> Number of random split points: 10
#> Imbalanced ratio: 1.1061
#> (OOB) Brier score: 0.14223359
#> (OOB) Normalized Brier score: 0.56893435
#> (OOB) AUC: 0.90618514
#> (OOB) Log-loss: 0.44457203
#> (OOB) PR-AUC: 0.89992792
#> (OOB) G-mean: 0.76992018
#> (OOB) Requested performance error: 0.20863309, 0.06849315, 0.36363636
#>
#> Confusion matrix:
#>
#> predicted
#> observed M R class.error
#> M 68 5 0.0685
#> R 24 42 0.3636
#>
#> (OOB) Misclassification rate: 0.2086331
print(learner$importance())
#> V11 V12 V9 V13 V52
#> 0.0616111248 0.0425140870 0.0371713933 0.0277114994 0.0244339596
#> V45 V36 V47 V43 V37
#> 0.0218271680 0.0210763866 0.0207814483 0.0193441684 0.0176258970
#> V10 V1 V17 V35 V49
#> 0.0171415537 0.0165069105 0.0133915902 0.0127562179 0.0123498420
#> V51 V44 V16 V46 V5
#> 0.0114701041 0.0114549337 0.0112089420 0.0112022737 0.0110320338
#> V34 V21 V28 V26 V23
#> 0.0107409362 0.0106046110 0.0094003812 0.0091679092 0.0085776983
#> V27 V30 V18 V48 V32
#> 0.0084367072 0.0083043422 0.0078632806 0.0075805556 0.0074330103
#> V39 V20 V4 V38 V8
#> 0.0074161511 0.0072644397 0.0072554117 0.0064233952 0.0064121250
#> V40 V22 V14 V42 V15
#> 0.0064048479 0.0063736979 0.0062630286 0.0062393120 0.0059909120
#> V19 V59 V7 V6 V41
#> 0.0057035921 0.0056534127 0.0053815890 0.0051118997 0.0051046392
#> V33 V54 V60 V2 V29
#> 0.0049574700 0.0042201156 0.0042085316 0.0040901288 0.0033696461
#> V57 V50 V3 V25 V58
#> 0.0031885466 0.0027484560 0.0026214246 0.0025002846 0.0022049244
#> V24 V53 V31 V55 V56
#> 0.0022041176 0.0008756977 0.0008728488 0.0007364633 -0.0003072044
# Make predictions for the test rows
predictions = learner$predict(task, row_ids = ids$test)
# Score the predictions
predictions$score()
#> classif.ce
#> 0.1884058