Last updated on 2019-01-26 by Max Kuhn

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, package reproducibility, code/data formatting tools, format convertors, and object caching.

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:

• summary tables/statistics: Hmisc, NMOF, papeR, quantreg, rapport, reporttools, sparktex, tables,xtable, ztable
• tables/cross-tabulations: Hmisc, lazyWeave, knitLatex, knitr, reporttools, ztable
• graphics: animation, Hmisc, grDevices:::pictex, sparktex, tikzDevice
• statistical models/methods: apsrtable, memisc, quantreg, rms, stargazer, suRtex, texreg, xtable, ztable
• bibtex: bibtex and RefManageR
• others: latex2exp converts LaTeX equations to plotmath expressions.

Miscellaneous Tools

• Hmisc contains a function to correctly escape special characters. resumer creates resumes. Standardized exams can be created using the exams package.

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:

• summary tables/statistics: stargazer
• tables/cross-tabulations: DT, formattable, htmlTable, HTMLUtils, hwriter, knitr, lazyWeave, SortableHTMLTables, texreg, ztable
• statistical models/methods: rapport, stargazer, xtable
• others: knitcitations, RefManageR

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:

• summary tables/statistics: papeR
• tables/cross-tabulations: DT, formattable, htmlTable, knitr, lazyWeave, papeR
• statistical models/methods: pander, papeR, rapport, texreg
• others: RefManageR

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

OpenDocument Format (ODF)

Object Conversion Functions:

• statistical models/methods: rapport

Microsoft Formats

R2wd (windows only) can 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.

Miscellaneous Tools

Package Reproducibility

R also has tools for ensuring that specific packages versions can be required for analyses. checkpoint, rbundler and packrat 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.

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. tth facilitates TeX to HTML/MathML conversions.

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 and archivist.

Links

• The Sweave Homepage
• knitr: Elegant, flexible and fast dynamic report generation with R
• Bioconductor package: weaver
• Wikipedia: Literate Programming
• Harrell: Site for Reproducible Research
• Koenker, Zeileis: On Reproducible Econometric Research
• Peng: Reproducible Research and Biostatistics
• Rossini, Leisch: Literate Statistical Practice
• Baggerly, Coombes: Deriving Chemosensitivity from Cell Lines: Forensic Bioinformatics and Reproducible Research in High-Throughput Biology
• Leisch: Sweave, Part I: Mixing R and LaTeX
• Leisch: Sweave, Part II: Package Vignettes
• Betebenner: Using Control Structures with Sweave
• Garbade, Burgard: Using R/Sweave in Everyday Clinical Practice
• Kuhn: Sweave and the Open Document Format - The odfWeave Package
• Gorjanc: Using Sweave with LyX
• Lecoutre: The R2HTML Package