Package: rfPermute 2.5.4

Eric Archer

rfPermute: Estimate Permutation p-Values for Random Forest Importance Metrics

Estimate significance of importance metrics for a Random Forest model by permuting the response variable. Produces null distribution of importance metrics for each predictor variable and p-value of observed. Provides summary and visualization functions for 'randomForest' results.

Authors:Eric Archer [aut, cre]

rfPermute_2.5.4.tar.gz
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rfPermute.pdf |rfPermute.html✨
rfPermute/json (API)

# Install 'rfPermute' in R:

install.packages('rfPermute', repos = c('https://swfsc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ericarcher/rfpermute/issues

Uses libs:

jags– Just Another Gibbs Sampler for Bayesian MCMC
c++– GNU Standard C++ Library v3

Datasets:

symb.metab - Symbiodinium type metabolite profiles

On CRAN:

jags cpp

5.44 score 27 stars 2.0k downloads 42 mentions 20 exports 76 dependencies

Last updated 18 hours agofrom:6fac6a6500. Checks:9 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 26 2025
R-4.5-win	OK	Mar 26 2025
R-4.5-mac	OK	Mar 26 2025
R-4.5-linux	OK	Mar 26 2025
R-4.4-win	OK	Mar 26 2025
R-4.4-mac	OK	Mar 26 2025
R-4.4-linux	OK	Mar 26 2025
R-4.3-win	OK	Mar 26 2025
R-4.3-mac	OK	Mar 26 2025

Exports:as.randomForest balancedSampsize casePredictions classPriors cleanRFdata combineRP confusionMatrix importance pctCorrect plotConfMat plotImportance plotImpPreds plotInbag plotNull plotPredictedProbs plotProximity plotTrace plotVotes rfPermute rfPermuteTutorial

Dependencies:abind class classInt cli clue cluster coda colorspace cpp11 DBI deldir dplyr e1071 fansi farver fBasics generics ggplot2 ggrepel glue gridExtra gss gtable HDInterval igraph isoband KernSmooth kknn labeling lattice lifecycle magrittr MASS Matrix mgcv modeest munsell nlme pillar pkgconfig polyclip proxy purrr R6 randomForest RColorBrewer Rcpp rlang rmutil rpart runjags s2 scales sf spatial spatstat.data spatstat.geom spatstat.univar spatstat.utils stable stabledist statip stringi stringr swfscMisc tibble tidyr tidyselect timeDate timeSeries units utf8 vctrs viridisLite withr wk

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Balanced Sample Size	balancedSampsize
Case Predictions	casePredictions
Class Priors	classPriors
Clean Random Forest Input Data	cleanRFdata
Combine rfPermute objects	combineRP
Confusion Matrix	confusionMatrix plotConfMat
Extract rfPermute Importance Scores and p-values.	importance importance.rfPermute plotImportance
Percent Correctly Classified	pctCorrect
Plot Important Predictor Distribution	plotImpPreds
Plot Inbag distribution	plotInbag
Plot Random Forest Importance Null Distributions	plotNull
Plot Predicted Probabilities	plotPredictedProbs
Plot Random Forest Proximity Scores	plotProximity
Plot Trace	plotTrace
Plot Vote Distribution	plotVotes
Estimate Permutation p-values for Random Forest Importance Metrics	as.randomForest predict.rfPermute print.rfPermute rfPermute rfPermute.default rfPermute.formula rfPermuteTutorial
Diagnostics of 'rfPermute' or 'randomForest' models.	summary summary.randomForest summary.rfPermute
Symbiodinium type metabolite profiles	symb.metab