Published by the Foundation for Open Access Statistics Editors-in-chief: Bettina Grün, Torsten Hothorn, Rebecca Killick, Edzer Pebesma, Achim Zeileis    ISSN 1548-7660; CODEN JSSOBK
Authors: Gabriel Becker, Cory Barr, Robert Gentleman, Michael Lawrence
Title: Enhancing Reproducibility and Collaboration via Management of R Package Cohorts
Abstract: Science depends on collaboration, result reproduction, and the development of supporting software tools. Each of these requires careful management of software versions. We present a unified model for installing, managing, and publishing software contexts in R. It introduces the package manifest as a central data structure for representing versionspecific, decentralized package cohorts. The manifest points to package sources on arbitrary hosts and in various forms, including tarballs and directories under version control. We provide a high-level interface for creating and switching between side-by-side package libraries derived from manifests. Finally, we extend package installation to support the retrieval of exact package versions as indicated by manifests, and to maintain provenance for installed packages. The provenance information enables the user to publish libraries or sessions as manifests, hence completing the loop between publication and deployment. We have implemented this model across three software packages, switchr, switchrGist and GRANBase, and have released the source code under the Artistic 2.0 license.

Page views:: 5457. Submitted: 2015-01-12. Published: 2017-11-29.
Paper: Enhancing Reproducibility and Collaboration via Management of R Package Cohorts     Download PDF (Downloads: 1603)
switchr_0.12.6.tar.gz: R source package Download (Downloads: 110; 489KB)
switchrGist_0.2.2.tar.gz: R source package Download (Downloads: 103; 2KB)
GRANBase_1.6.5.tar.gz: R source package Download (Downloads: 88; 988KB) Replication materials Download (Downloads: 86; 95KB)

DOI: 10.18637/jss.v082.i01

This work is licensed under the licenses
Paper: Creative Commons Attribution 3.0 Unported License
Code: GNU General Public License (at least one of version 2 or version 3) or a GPL-compatible license.