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This package has been moved to https://github.com/forestry-labs/Rforestry













Travis-CI Build Status

DOI

forestry: Provides Functions for Fast Random Forests

Sören Künzel, Edward Liu, Theo Saarinen, Allen Tang, Jasjeet Sekhon

Introduction

forestry is a fast implementation of Honest Random Forests.

How to install

  1. The GFortran compiler has to be up to date. GFortran Binaries can be found here.
  2. The devtools package has to be installed. You can install it using, install.packages("devtools").
  3. The package contains compiled code, and you must have a development environment to install the development version. You can use devtools::has_devel() to check whether you do. If no development environment exists, Windows users download and install Rtools and macOS users download and install Xcode.
  4. The latest development version can then be installed using devtools::install_github("soerenkuenzel/forestry") .

Usage

set.seed(292315)
library(forestry)
test_idx <- sample(nrow(iris), 3)
x_train <- iris[-test_idx, -1]
y_train <- iris[-test_idx, 1]
x_test <- iris[test_idx, -1]

rf <- forestry(x = x_train, y = y_train)
weights = predict(rf, x_test, aggregation = "weightMatrix")$weightMatrix

weights %*% y_train
predict(rf, x_test)

Ridge Random Forest

A fast implementation of random forests using ridge penalized splitting and ridge regression for predictions.

Example:

set.seed(49)
library(forestry)

n <- c(100)
a <- rnorm(n)
b <- rnorm(n)
c <- rnorm(n)
y <- 4*a + 5.5*b - .78*c
x <- data.frame(a,b,c)
forest <- forestry(x, y, ridgeRF = TRUE)
predict(forest, x)

Monotonic Constraints

A parameter controlling monotonic constraints for features in forestry.

x <- rnorm(150)+5
y <- .15*x + .5*sin(3*x)
data_train <- data.frame(x1 = x, x2 = rnorm(150)+5, y = y + rnorm(150, sd = .4))

monotone_rf <- forestry(x = data_train %>% select(-y),
                        y = data_train$y,
                        monotonicConstraints = c(-1,-1),
                        nodesizeStrictSpl = 5,
                        nthread = 1,
                        ntree = 25)
predict(monotone_rf, feature.new = data_train %>% select(-y))

OOB Predictions

We can return the predictions for the training dataset using only the trees in which each observation was out of bag. Note that when there are few trees, or a high proportion of the observations sampled, there may be some observations which are not out of bag for any trees. The predictions for these are returned NaN.

library(forestry)

# Train a forest
rf <- forestry(x = iris[,-1], 
               y = iris[,1],
               ntree = 500)
               
# Get the OOB predictions for the training set
oob_preds <- getOOBpreds(rf)

# This should be equal to the OOB error
sum((oob_preds -  iris[,1])^2)
getOOB(rf)