Fast OpenMP parallel processing unified treatment of Breiman's random
forests (Breiman 2001) for a variety of data settings. Regression and
classification forests are grown when the response is numeric or
categorical (factor), while survival and competing risk forests
(Ishwaran et al. 2008, 2012) are grown for right-censored survival
data. Multivariate regression and classification responses as well as
mixed outcomes (regression/classification responses) are also handled.
Also includes unsupervised forests and quantile regression forests,
quantileReg. Different splitting rules invoked under
deterministic or random splitting are available for all families.
Variable predictiveness can be assessed using variable importance
(VIMP) measures for single, as well as grouped variables. Missing
data (for x-variables and y-outcomes) can be imputed on both training
and test data. The underlying code is based on Ishwaran and Kogalur's
now retired randomSurvivalForest package (Ishwaran and Kogalur
2007), and has been significantly refactored for improved
computational speed.
This package contains many useful functions and users should read the help file in its entirety for details. However, we briefly mention several key functions that may make it easier to navigate and understand the layout of the package.
This is the main entry point to the package. It grows a random forest
using user supplied training data. We refer to the resulting object
as a RF-SRC grow object. Formally, the resulting object has class
(rfsrc, grow).
A fast implementation of rfsrc using subsampling.
predict.rfsrc, predict
Used for prediction. Predicted values are obtained by dropping the
user supplied test data down the grow forest. The resulting object
has class (rfsrc, predict).
Used for variable selection. The function max.subtree
extracts maximal subtree information from a RF-SRC object which is
used for selecting variables by making use of minimal depth variable
selection. The function var.select provides
an extensive set of variable selection options and is a wrapper to
max.subtree.
Fast imputation mode for RF-SRC. Both rfsrc and
predict.rfsrc are capable of imputing missing data.
However, for users whose only interest is imputing data, this function
provides an efficient and fast interface for doing so.
Used to extract the partial effects of a variable or variables on the ensembles.
Regular stable releases of this package are available on CRAN at cran.r-project.org/package=randomForestSRC
Interim unstable development builds with bug fixes and sometimes additional functionality are available at github.com/kogalur/randomForestSRC
Bugs may be reported via github.com/kogalur/randomForestSRC/issues/new. Please provide the accompanying information with any reports:
sessionInfo()
A minimal reproducible example consisting of the following items:
a minimal dataset, necessary to reproduce the error
the minimal runnable code necessary to reproduce the error, which can be run on the given dataset
the necessary information on the used packages, R version and system it is run on
in the case of random processes, a seed (set by set.seed()) for reproducibility
This package implements OpenMP shared-memory parallel programming if the target architecture and operating system support it. This is the default mode of execution.
Additional instructions for configuring OpenMP parallel processing are available at kogalur.github.io/randomForestSRC/building.html.
An understanding of resource utilization (CPU and RAM) is necessary when running the package using OpenMP and Open MPI parallel execution. Memory usage is greater when running with OpenMP enabled. Diligence should be used not to overtax the hardware available.
Breiman L. (2001). Random forests, Machine Learning, 45:5-32.
Ishwaran H. and Kogalur U.B. (2007). Random survival forests for R, Rnews, 7(2):25-31.
Ishwaran H. (2007). Variable importance in binary regression trees and forests, Electronic J. Statist., 1:519-537.
Ishwaran H., Kogalur U.B., Blackstone E.H. and Lauer M.S. (2008). Random survival forests, Ann. App. Statist., 2:841-860.
Ishwaran H., Kogalur U.B., Gorodeski E.Z, Minn A.J. and Lauer M.S. (2010). High-dimensional variable selection for survival data. J. Amer. Statist. Assoc., 105:205-217.
Ishwaran H., Kogalur U.B., Chen X. and Minn A.J. (2011). Random survival forests for high-dimensional data. Stat. Anal. Data Mining, 4:115-132
Ishwaran H., Gerds T.A., Kogalur U.B., Moore R.D., Gange S.J. and Lau B.M. (2014). Random survival forests for competing risks. Biostatistics, 15(4):757-773.
Ishwaran H. and Malley J.D. (2014). Synthetic learning machines. BioData Mining, 7:28.
Ishwaran H. (2015). The effect of splitting on random forests. Machine Learning, 99:75-118.
Ishwaran H. and Lu M. (2018). Standard errors and confidence intervals for variable importance in random forest regression, classification, and survival. Statistics in Medicine (in press).
Mantero A. and Ishwaran H. (2017). Unsupervised random forests.
O'Brien R. and Ishwaran H. (2017). A random forests quantile classifier for class imbalanced data.
Tang F. and Ishwaran H. (2017). Random forest missing data algorithms. Statistical Analysis and Data Mining, 10, 363-377.
plot.competing.risk,
plot.rfsrc,
plot.survival,
plot.variable,
predict.rfsrc,
print.rfsrc,
quantileReg,
rfsrcFast,
rfsrcSyn,