README.md

In brfitzpatrick/forestviews: Visualise the paths through random forests

forestviews

network flow visualisation of the paths through a random forest

Sankey diagrams and parallel coordinates plots of all paths from root to leaf nodes through the binary trees that constitute a random forest.

Installation:

Install the devtools package and use it to install forestviews:

install.packages('devtools')
library('devtools')
install_github(repo = 'brfitzpatrick/forestviews')

Example Usage:

Load the data and packages we will use:

library(mlbench)
data(Satellite)
library(randomForest)
library(networkD3)
library(forestviews)

Fit a random forest:

rf.1 <- randomForest(classes ~ ., data = Satellite, mtry = 8, keep.forest = TRUE, ntree = 25, importance = TRUE)

Calculate all paths through the random forest:

rf.1.all.paths <- rf_pathfinder(rf = rf.1)

Sankey Diagram:

Convert these paths to a d3network:

nd3 <- rf_sankey(all.paths.out = rf.1.all.paths, all.nodes = FALSE, plot.node.lim = 6)

Plot the network as an interactive Sankey Diagram (this plot will open in your web browser):

sankeyNetwork(Links = nd3$links, Nodes = nd3$nodes , Source = 'source', Target = 'target', Value = 'value', NodeID = 'name', units = 'Count', fontSize = 12, nodeWidth = 30, NodeGroup = NULL)

Parallel Coordinates Plots:

Simple usage:

rf.pc <- rf_parcoor(all.paths.out = rf.1.all.paths, plot = TRUE, all.nodes = TRUE, plot.title = '', grey.scale = FALSE)
rf.pc

Grey scale version:

rf.pc.grey <- rf_parcoor(all.paths.out = rf.1.all.paths, plot = TRUE, all.nodes = TRUE, plot.title = '', grey.scale = TRUE)
rf.pc.grey

Project Website

See the project website for an example of an interactive Sankey diagram.

Reference

The visualisation techniques implemented in forestviews are introduced in our manuscript on this topic. A pre-print of this manuscript is available from arXiv.

brfitzpatrick/forestviews documentation built on May 14, 2019, 8:17 a.m.