CRAN Task View: Reproducible Research

Maintainer:John Blischak, Alison Hill
Contact:jdblischak at gmail.com
Version:2020-03-04
URL:https://CRAN.R-project.org/view=ReproducibleResearch

The goal of reproducible research is to tie specific instructions to data analysis and experimental data so that scholarship can be recreated, better understood and verified. Packages in R for this purpose can be split into groups for: literate programming, pipeline toolkits, package reproducibility, project workflows, code/data formatting tools, format convertors, and object caching.

The maintainers gratefully acknowledge Anna Krystalli , Max Kuhn , Will Landau , Ben Marwick , and Daniel NĂ¼st for their useful feedback and contributions.

Literate Programming

The primary way that R facilitates reproducible research is using a document that is a combination of content and data analysis code. The Sweave function (in the base R utils package) and the knitr package can be used to blend the subject matter and R code so that a single document defines the content and the analysis. The brew and R.rsp packages contain alternative approaches to embedding R code into various markups.

The resources for literate programming are best organized by the document type/markup language:

LaTeX

Both Sweave and knitr can process LaTeX files. lazyWeave can create LaTeX documents from scratch.

Object Conversion Functions:

Miscellaneous Tools

HTML

The knitr package can process HTML files directly. Sweave can also work with HTML by way of the R2HTML package. lazyWeave can create HTML format documents from scratch.

Object Conversion Functions:

Miscellaneous Tools: htmltools has various tools for working with HTML. tufterhandout for creating Tufte-style handouts

Markdown

The knitr package can process markdown files without assistance. The packages markdown and rmarkdown have general tools for working with documents in this format. lazyWeave can create markdown format documents from scratch.

Object Conversion Functions:

Miscellaneous Tools: tufterhandout for creating Tufte-style handouts. kfigr allows for figure indexing in markdown documents.

OpenDocument Format (ODF)

Object Conversion Functions:

Microsoft Formats

R2wd (windows only) can also create Word documents from scratch and R2PPT (also windows only) can create PowerPoint slides. The rtf package does the same for Rich Text Format documents.

Pipeline Toolkits

Pipeline toolkits help maintain and verify reproducibility. They synchronize computational output with the underlying code and data, and they tell the user when everything is up to date. In other words, they provide concrete evidence that results are re-creatable from the starting materials, and the data analysis project does not need to rerun from scratch. The drake package is such a pipeline toolkit. It is similar to GNU Make , but it is R-focused.

Package Reproducibility

R also has tools for ensuring that specific packages versions can be required for analyses. checkpoint, rbundler, packrat and renv install packages required for a project to a local archive as they existed at a specified point in time. This allows specific package versions to be maintained over time and different users. The miniCRAN package facilitates the creation of local CRAN-like repositories.

Project Workflows

Successfully completing a data analysis project often requires much more than statistics and visualizations. Efficiently managing the code, data, and results as the project matures helps reduce stress and errors. The following "workflow" packages assist the R programmer by managing project infrastructure and/or facilitating a reproducible workflow.

Workflow utility packages provide single-use functions to implement project infrastructure or solve a specific problem. As a typical example, usethis::use_git() initializes a Git repository, ignores common R files, and commits all project files.

Workflow framework packages provide an organized directory structure and helper functions to assist during the development of the project. As a typical example, ProjectTemplate::create.project() creates an organized setup with many subdirectories, and ProjectTemplate::run.project() executes each R script that is saved in the src/ subdirectory.

Formatting Tools

formatR, highlight, and highr can be used to color and/or format R code.

Packages humanFormat, lubridate, prettyunits, and rprintf have functions to better format data.

Format Convertors

pander can be used for rendering R objects into Pandoc's markdown. knitr has the function pandoc that can call an installed version of Pandoc to convert documents between formats such as Markdown, HTML, LaTeX, PDF and Word.

Object Caching Packages

When using Sweave and knitr it can be advantageous to cache the results of time consuming code chunks if the document will be re-processed (i.e. during debugging). knitr facilitates object caching and the Bioconductor package weaver can be used with Sweave.

Non-literate programming packages to facilitating caching/archiving are R.cache, archivist, and storr.

CRAN packages:

Related links: