Software

I write software for several reasons:

Research outputs designed for resuse

• diversitree: Comparative phylogenetic analyses of diversification in R. A very broad collection of tools for fitting evolutionary models to phylogenetic trees
• arbutus: Assessing the adequacy of phylogenetic models of quantitative trait evolution (with Matt Pennell).
• TRAMPR: TRFLP Analysis and Matching Package for R. Matches profiles from a (now-dated) sequencing technology against a known set of species.

Documenting research

• ksi: Komogorov-Smirnov Importance Statistic
• mosaic: Fit non-monotonic curves to hybrid zone data.

Non-research software

• sowsear: Frictionless literate programming: generate knitr files from R scripts. Using this means you are always writing literate programs.
• rodeint: An R interface to Boost.odeint. This interface wraps almost all of the functionality of odeint into a consistent and simple interface (8 functions!), and allows integration of ODE systems in R or compiled code.

Things in progress

• forest: New phylogenetics tree structures in R for faster, easier and more efficient analyses, and for better algorithms by getting the book-keeping out of the way.
• ghwiki: Scripts to turn GitHub wikis into an automatic lab notebook.

Other contributions

I have contributed code to geiger (a suite of methods and models for studying evolutionary radiations), ape (analyses of phylogenetics and evolution) and cowsay (cowsay with more animals in R).