Multivoxel Pattern Analysis in R

This package is under development.

Introduction

rMVPA is an R library for multivariate pattern analysis of neuroimaging data. The goal of this library is to make MVPA analyses easy. It can be used both programmatically from within R or using a command line interface. ‘rMVPA’ provides a lightweight model registry and efficient resampling methods for machine learning. What rMVPA provides is the infrastructure for conducting machine learning analyses on neuroimaging data.

Documentation and vignettes: https://bbuchsbaum.github.io/rMVPA/

Installation

Using devtools

To install rMVPA from within R, use the devtools function install_github. You will need the development version of neuroim2 as well.

From within R:

#library(devtools)
install_github("bbuchsbaum/neuroim2")
install_github("bbuchsbaum/rMVPA")

Using git from the command line

git clone git@github.com:bbuchsbaum/rMVPA.git
R CMD install rMVPA

Optionally install command line scripts for “coding-free” MVPA analysis:

wget https://raw.githubusercontent.com/bbuchsbaum/rMVPA/master/scripts/MVPA_Searchlight.R

wget https://raw.githubusercontent.com/bbuchsbaum/rMVPA/master/scripts/MVPA_Regional.R

Then, move these files to a folder on your PATH and make them executable:

chmod +x MVPA_Searchlight.R

chmod +x MVPA_Regional.R

The MS-ReVE functionality is implemented in R/contrast_rsa_model.R. There is no file named contrast_rsa.R; all references should use the contrast_rsa_model.R filename.