Analysis and Reporting in Reproducible Research

Return to Reproducible Research Methodology

Document Processing

https://en.wikipedia.org/wiki/LaTeX LaTeX

https://en.wikipedia.org/wiki/Literate_Programming Literate Programming

Approaches Aimed at Reproducible Reports

R-Based Methods

knitr: the latest R reproducible reporting method; works with LaTeX, html, and other formats
https://www.stat.uni-muenchen.de/~leisch/Sweave Sweave embeds R (or S) code into a LaTeX file. A simple SweaveExample.
The https://cran.r-project.org/package=odfWeave odfWeave R package supports embedding R code into OpenOffice ODF files
The https://cran.r-project.org/package=R2wd R2wd R package supports the creation of a Microsoft Word document using R code. A simple R2wdExample.
Using R for Reproducible Research - Terri Scott

SAS-Based Methods

https://stat.uiowa.edu/~rlenth/SASweave SASweave embeds SAS code into a LaTeX file. It also supports having both R and SAS code in the same file. A simple SASweaveExample.

Software-independent Methods

https://www.cs.uiowa.edu/~rlenth/StatWeave StatWeave is designed to be usable with any statistical software, currently R, SAS, Stata, and Maple are supported. It is still in development, but the beta version is usable.

Approaches Involving More Than Code and Background/Interpretation Text

Emacs `org` mode

Emacs https://orgmode.org/worg/org-contrib/babel/intro.php org mode provides a way to build a self-contained workflow file with not only code and interpretations but also embedded work and planning items, according to Tony Rossini (Novartis Pharma AG, Basel)

Reproducible Interactive Approaches

https://galaxy.psu.edu galaxy for genomic processing and basic analysis

Genomic data management and processing is done via a web graphical user interface, but the history of the steps selected is saved in a re-executable, modifiable fashion. This history can be shared with other galaxy users. galaxy is free.