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blockForest  

Block Forests: Random Forests for Blocks of Clinical and Omics Covariate Data
View on CRAN: Click here


Download and install blockForest package within the R console
Install from CRAN:
install.packages("blockForest")

Install from Github:
library("remotes")
install_github("cran/blockForest")

Install by package version:
library("remotes")
install_version("blockForest", "0.2.6")



Attach the package and use:
library("blockForest")
Maintained by
Marvin N. Wright
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2018-12-30
Latest Update: 2023-03-31
Description:
A random forest variant 'block forest' ('BlockForest') tailored to the prediction of binary, survival and continuous outcomes using block-structured covariate data, for example, clinical covariates plus measurements of a certain omics data type or multi-omics data, that is, data for which measurements of different types of omics data and/or clinical data for each patient exist. Examples of different omics data types include gene expression measurements, mutation data and copy number variation measurements. Block forest are presented in Hornung & Wright (2019). The package includes four other random forest variants for multi-omics data: 'RandomBlock', 'BlockVarSel', 'VarProb', and 'SplitWeights'. These were also considered in Hornung & Wright (2019), but performed worse than block forest in their comparison study based on 20 real multi-omics data sets. Therefore, we recommend to use block forest ('BlockForest') in applications. The other random forest variants can, however, be consulted for academic purposes, for example, in the context of further methodological developments. Reference: Hornung, R. & Wright, M. N. (2019) Block Forests: random forests for blocks of clinical and omics covariate data. BMC Bioinformatics 20:358. .
How to cite:
Marvin N. Wright (2018). blockForest: Block Forests: Random Forests for Blocks of Clinical and Omics Covariate Data. R package version 0.2.6, https://cran.r-project.org/web/packages/blockForest
Previous versions and publish date:
0.1.7 (2018-12-30 18:20), 0.2.0 (2019-04-10 13:45), 0.2.3 (2019-07-03 18:10), 0.2.4 (2019-12-06 10:50), 0.2.5 (2022-10-20 16:05)
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