Visually Exploring Random Forests • ggRandomForests

ggRandomForests overview: predicted survival, variable importance, OOB error, and partial dependence

ggRandomForests provides ggplot2-based diagnostic and exploration plots for random forests fit with randomForestSRC (>= 3.4.0) or randomForest. It keeps the data step apart from the figure step, so you can inspect, save, or reuse the tidy object on its own. Listed in the ggplot2 extensions gallery.

Installation

# CRAN (stable)
install.packages("ggRandomForests")

# Development version from GitHub
# install.packages("remotes")
remotes::install_github("ehrlinger/ggRandomForests")

Quick start

library(randomForestSRC)
library(ggRandomForests)

# 1. Fit a forest (regression)
rf <- rfsrc(medv ~ ., data = MASS::Boston, importance = TRUE)

# 2. Check convergence: did the forest grow enough trees?
plot(gg_error(rf))

# 3. Rank predictors by importance
plot(gg_vimp(rf))

# 4. Marginal dependence for top variables
gg_v <- gg_variable(rf)
plot(gg_v, xvar = "lstat")
plot(gg_v, xvar = rf$xvar.names, panel = TRUE, se = FALSE)

# 5. Partial dependence for a single predictor
pv <- plot.variable(rf, xvar.names = "lstat", partial = TRUE, show.plots = FALSE)
pd <- gg_partial(pv)
plot(pd)

For survival forests, see the package vignette:

vignette("ggRandomForests")

For variable importance with varPro — partial dependence, importance z-scores, beta importance, individual/local importance, and isolation forests — see the dedicated vignette:

vignette("varpro", package = "ggRandomForests")

The unsupervised varPro tools — gg_udependent(), gg_beta_uvarpro(), and gg_sdependent(), which read structure off a uvarpro() fit with no outcome — have their own short vignette:

vignette("uvarpro", package = "ggRandomForests")

Function reference

Grouped by what you are trying to look at. The first column is the function you call, the second is what you hand it.

The forest itself

Function	Input	What you get
`gg_error()`	`rfsrc` / `randomForest`	OOB error vs. number of trees
`gg_vimp()`	`rfsrc` / `randomForest`	Variable importance ranking
`gg_rfsrc()`	`rfsrc` / `randomForest`	Predicted vs. observed values
`gg_variable()`	`rfsrc` / `randomForest`	Marginal dependence data frame

Partial dependence

Function	Input	What you get
`gg_partial()`	`plot.variable` output	Partial dependence (continuous + categorical)
`gg_partial_rfsrc()`	`rfsrc` model	Partial dependence via `partial.rfsrc`
`surv_partial.rfsrc()`	`rfsrc` survival forest	Survival partial dependence, one or more predictors
`quantile_pts()`	numeric vector	Quantile cut points for coplot panels

Survival

Function	Input	What you get
`gg_survival()`	`rfsrc` survival forest, or a data frame	Kaplan–Meier / Nelson–Aalen estimates
`gg_brier()`	`rfsrc` (survival)	Time-resolved Brier score and CRPS
`kaplan()`	data frame + interval/censor columns	Nonparametric Kaplan–Meier estimate
`nelson()`	data frame + interval/censor columns	Nonparametric Nelson–Aalen estimate

Classification and ROC

Function	Input	What you get
`gg_roc()`	`rfsrc` / `randomForest` (class)	ROC curve data
`calc_roc()`	`rfsrc` / `randomForest` (class)	The sensitivity/specificity sweep behind `gg_roc()`
`calc_auc()`	`gg_roc` object	Area under the curve

varPro — variable priority

These read a varPro fit rather than a forest. varpro() is the supervised fit; uvarpro() is the unsupervised one, which needs no outcome.

Function	Input	What you get
`gg_varpro()`	`varpro` fit	Release-rule variable importance
`gg_beta_varpro()`	`varpro` fit	Per-variable lasso-beta importance
`gg_ivarpro()`	`varpro` fit	Individual (local) variable importance
`gg_partial_varpro()`	`varpro` fit	Partial dependence (alias: `gg_partialpro()`)
`gg_isopro()`	`isopro` fit	Isolation-forest anomaly scores
`gg_udependent()`	`uvarpro` fit	Variable dependency graph
`gg_beta_uvarpro()`	`uvarpro` fit	Per-variable lasso-beta importance
`gg_sdependent()`	`uvarpro` fit	Signal-variable detection
`varpro_feature_names()`	character vector	Original names behind one-hot encoded features

SHAP

Function	Input	What you get
`gg_shap()`	`rfsrc` / `randomForest`	Shapley additive explanation values
`shap_importance()`	`gg_shap` object	Global importance bar chart
`shap_beeswarm()`	`gg_shap` object	Beeswarm summary plot
`shap_dependence()`	`gg_shap` object	Dependence plot for one predictor

Each gg_* function has a matching plot() S3 method that hands back a single plottable object: a ggplot you extend with +, or a patchwork composite for the multi-panel methods. Every gg_* object also has print() and summary() methods: print() shows a short header at the REPL rather than dumping every row (use head() when you want the rows), and summary() gives you a diagnostics object you can print or keep.

Why ggRandomForests?

The package is built on one decision: keep the data step and the figure step apart. The gg_* functions pull a tidy data object out of the forest; the plot() methods turn that object into a ggplot2 figure. Two things follow from that split.

First, the data object stands on its own. It carries everything its plot needs, so you can save it, inspect it, or come back to it later without keeping the original forest — which can be large — in memory.

Second, you are never locked into the default figure. Because a plot() method returns a single plottable object (a ggplot, or a patchwork composite for the multi-panel methods), you can add layers, swap scales, or apply a theme; and if the default is not what you want, you can ignore it entirely and build the figure from the tidy data yourself.

Recent changes

See NEWS.md for the full changelog. Recent highlights:

v3.5.1 gg_roc() on an rfsrc forest now honors the documented which_outcome = 0, which had been returning an unusable two-row object; gg_partial_rfsrc() rejects a non-forest with a real error instead of “argument is of length zero”. Also a test-only fix for the gcc-UBSAN report filed against 3.5.0.
v3.5.0 varPro fixes: plot.gg_varpro() no longer draws a phantom “NA” category, gg_partial_varpro() warns when you name a variable the fit cannot reach, and scale = "chf" now honors xvar.names instead of computing every variable. Vignette figures render with ragg, which cut the source tarball from 4.7 MB to 2.3 MB.
v3.4.0 Unsupervised varPro wrappers (gg_beta_uvarpro(), gg_sdependent()) with their own vignette; gg_partial_rfsrc() now handles factor predictors correctly.
v3.3.0 varPro partial plots default to interpretable scales — probability for classification, survival S(τ) for survival.
v3.1.0 varPro integration: release-rule importance, partial dependence, local importance, anomaly scores, and the dependency graph.

References

Breiman, L. (2001). Random forests, Machine Learning, 45:5–32.

Ishwaran H. and Kogalur U.B. randomForestSRC: Random Forests for Survival, Regression and Classification. R package version >= 3.4.0. https://cran.r-project.org/package=randomForestSRC

Ishwaran H. and Kogalur U.B. (2007). Random survival forests for R. R News 7(2), 25–31.

Ishwaran H., Kogalur U.B., Blackstone E.H. and Lauer M.S. (2008). Random survival forests. Ann. Appl. Statist. 2(3), 841–860.

Liaw A. and Wiener M. (2002). Classification and Regression by randomForest. R News 2(3), 18–22.

Wickham H. (2009). ggplot2: Elegant Graphics for Data Analysis. Springer New York.

ggRandomForests: Visually Exploring Random Forests