aprof

This page provides tutorials on how to use "aprof" to effectively optimize R code.

© 2018. All rights reserved.

aprof minor release 0.2.5

17 Apr 2015

Changes in the minor release

  1. Added warning for use in Rmd and Rnw files. As of yet no easy workaround exists for use of line-profiling with in knitr. Using the chunkoption engine=”Rscript” fails as line-profiling itself seemed disabled outside of an interactive R session.

minor changes

  1. Using ESS code indentation rules

Installation

Release on GITHUB.

Speeding Up R; Essentials of High Performance Computing for Biologists

29 Mar 2015

Excited to see our paper on code efficiency in the biological sciences released. The paper contains:

  1. A gentle overview of high perforance computing aimed at biologists using R. Download the open access paper

  2. Parallel computing, calling C in R, and Rcpp examples (with the latter two recommended for advanced R users only). Download the appendices

Yale short workshop on code efficiency

18 Nov 2014

Happy to give a short workshop on code efficiency in R.

Participants may choose between the following short tutorials:

  1. Profiling in R, with a bootstrap example (recommended focus). Download

  2. Parallel computing, extending the bootstrap example (for those interested). Download

  3. Getting ready to call C in R (recommended for advanced R users only). Download

Please note that the full tutorial should be available at PLOS Computational Biology very soon. Keep an eye out at PLOS, or check here for the link to the paper and tutorial which will appear once it is online!

The latest version of aprof (0.2.4) can be downloaded here (recommended, see installation instructions) or download a previous version from CRAN (version 0.2.1) in R.

aprof minor release 0.2.4

17 Nov 2014

Changes in the minor release

  1. bugfix: aprof allows for more variable user input in file locations, and hence comes closer to full usage within markdown and (knitr) pdfs.

Installation

See the release on CRAN!

aprof minor release 0.2.3

20 Aug 2014

Changes in the minor release

  1. feature: aprof now expects and handles multiple files in the call stack correctly. This happens when you e.g. source files or use the clipboard - in these cases your source file is not the only file in the call stack. This adaptation is the first step forward toward aprof integration with .Rnw and Rmd files.

Installation

See the release on CRAN!