The beginnings…
TreeTracer is an R package for creating trace plots of trees from random forests fit using the randomForest R package. Trace plots are useful tools for visually comparing trees from a random forest. See Urbanek (2008) for additional information about trace plots.
# Load packages
library(dplyr)
library(ggpcp)
library(ggplot2)
library(TreeTracer)# Load the Palmer penguins data
penguins <- na.omit(palmerpenguins::penguins)# Select the features for training the model
penguin_features <-
penguins %>%
select(bill_length_mm, bill_depth_mm, flipper_length_mm, body_mass_g)# Create a parallel coordinate plot of features that will
# be used to fit a random forest colored by the variable
# of interest to predict (species)
penguins %>%
ggplot(aes(color = species)) +
geom_pcp(aes(
vars = vars(
bill_length_mm,
bill_depth_mm,
flipper_length_mm,
body_mass_g
)
), alpha = 0.5) +
scale_color_brewer(palette = "Paired")
# Fit a random forest
set.seed(71)
penguin_rf <-
randomForest::randomForest(
species ~ bill_length_mm + bill_depth_mm + flipper_length_mm + body_mass_g,
data = penguins,
ntree = 50
)# Print feature importance
penguin_rf$importance %>%
data.frame() %>%
arrange(desc(MeanDecreaseGini))## MeanDecreaseGini
## bill_length_mm 86.66136
## flipper_length_mm 79.23500
## bill_depth_mm 29.98416
## body_mass_g 14.95287
# Trace plots of trees in the forest
trace_plot(
rf = penguin_rf,
train = penguin_features,
tree_ids = 1:penguin_rf$ntree,
alpha = 0.4
) +
theme(aspect.ratio = 1)
Urbanek, Simon. 2008. “Visualizing Trees and Forests.” In Handbook of Data Visualization, edited by Chun-houh Chen, Wolfgang Härdle, and Antony Unwin, 3:243–66. Berlin, Germany: Springer-Verlag. https://doi.org/10.1007/978-3-540-33037-0.