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.

R largely facilitates reproducible research using literate programming; 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 algorithms.

Basic packages can be structured into the following groups:

• LaTeX Markup : The Hmisc, xtable and tables packages contain functions to write R objects into LaTeX representations. Hmisc also includes methods for translating strings to proper LaTeX markup (e.g., ">=" to "$\geq$"). Animations can be inserted into LaTeX documents being converted to PDF via the animation package. The pictex function in the base grDevices package is a PicTeX graphics driver and the tikzDevice can convert R graphics to TikZ markup. The tth package can convert TeX to HTML.
• HTML Markup : The R2HTML package has drivers that allow Sweave to process HTML documents via Sweave. Both R2HTML and hwriter can be used to build HTML pages sequentially. R2HTML, xtable and hwriter can also convert some R objects into HTML representations. knitr also has facilities to weave R code with HTML as well as convert markdown to HTML.
• ODF Markup : The odfWeave package extends Sweave to the Open Document Format . Word processing tools, such as OpenOffice.org, can then be used to blend content and programs. Many word processors can be used to translate the ODF document to other formats (e.g., Word, PDF, HTML, etc.)
• Microsoft Formats : The R2wd and R2PPT packages for Windows can be used to communicate between R and Word or PowerPoint via the COM interface. Document elements (e.g. sections, text, images, etc) that are created in R can be inserted into the document from R. The rtf can also be used to create RTF format documents directly from R. Commercial R products that work with RTF and/or Word are RTFGen , Inference for R and SWord .The output from other packages (odfWeave and R2HTML) can also be opened by Word. RExcel can integrate code with Microsoft Excel. Additionally, the table1xls can convert summary tables to Excel files.
• Plain Text Formats : R code and output in Sweave files can be converted into AsciiDoc and other structured text formats using the ascii package. The markdown and knitr packages have tools for markdown format.
• Syntax Highlighting : The SweaveListingUtils package can also provide enhanced control over how R code chunks and their output are rendered in LaTeX.
• Caching of R Objects : The cacheSweave and weaver packages allow caching of specific code chunks. The cacher and R.cache packages can also be used but are not integrated with Sweave. The SRPM package (for shared reproducibility package management) creates an R package that organize the results of an Sweave document into different directories (e.g., article, figures, etc). knitr also has the ability to cache the results of code chunks.
• Others : The brew and R.rsp packages contain alternative approaches to embedding R code into various markups. knitr is a comprehensive package derived from Sweave that includes code formatting, highlighting, caching, fine control of graphics, conditional evaluation, multiple markup formats and other features. The pander package can write R objects into Pandoc's markdown and also to convert those or complex reports to PDF/HTML/docx/ODT. The rapport package builds on pander and provides a way to create reproducible statistical report templates with graphs, tables and annotations to be applied to any R data frame and export the results in different formats. The installr package for Windows can download and install MikTeX, pandoc (and other software), as well as quickly update R itself.

An incomplete list of packages which facilitate literate programming for specific types of analysis or objects:

• The base R utils package has generic functions to convert objects to LaTeX (via toLatex) and BibTeX (via toBibtex). The bibtex can also be used to parse BibTeX files.
• Functions for creating LaTeX representations of summary statistics and visualizations can be found in the Hmisc, reporttools, and r2lh packages. Hmisc also has functions for marking up data frames and the quantreg and memisc packages can mark up matrices.
• Cross-tabulations can be converted to LaTeX code using the Hmisc and memisc packages.
• The xtable and rms packages provide LaTeX representations of some common models (e.g., Cox proportional hazards model, etc.). For example, processing an aov object with the xtable function will generate LaTeX markup of the ANOVA table. Similarly, methods exist for glm, prcomp, ts and other types of objects.
• The quantreg contains LaTeX markup functions for quantile regression fit summaries.
• Standardized exams can be created using the exams package
• The odfWeave.survey and TeachingSampling packages provide ODF and LaTeX functions, respectively, for survey sampling objects. The suRtex package can create LaTeX markup of descriptive statistical summaries of survey data.
• The texreg has functions to create nice LaTeX and HTML representations of one or more objects (e.g. lm, lme4, etc.). The stargazer has similar functionality for showing models and summary tables in LaTeX and ASCII.
• The sparktex package can create LaTeX representations of sparklines .
• LaTeX markup for several object types can be created using the papeR package.