Software

NOTE: this page became out of date as soon as I started working full time as a research software engineer; I need to curate my list again, but now that I'm developing software fulltime there's a lot more things that aren't in here - see my github profile for more information (though even then, there's quite a bit in various organisational accounts...) Almost all of the software below are R packages. 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.
• phyndr: Match phylogenetic and trait data (paper forthcoming).
• plant: Simulation model of a forests for exploring trait-driven ecological and evolutionary dynamics.
• traitfill: Impute categorical missing data based on taxonomic structure.

Research infrastructure and tools

• remake: reproducible build system for R. This package takes the good ideas from "make" and reimagines them with data analysis in R in mind.
• rrqueue: Scalable distributed job queues with R and Redis. Based on ideas from rq but with an R-ish flavour.
• storr: Key-value databases, with different backends (memory, disk, Redis). Includes support for memory caching, content-addressable lookup, indexable serialisation, and fetching externally stored data on demand.
• RedisAPI: Automatically generated consistent wrapper around all Redis commands.
• RedisHeartbeat: Heartbeat pattern, using Redis: signal that an R process is alive by using an expiring key as a dead man switch. RedisHeartbeat runs on a separate thread so does not block any R calculations.
• rrlite: Interface to rlite: a self-contained, serverless, zero-configuration, transactional redis-compatible database engine (rlite is to Redis what SQLite is to mysql).
• RcppR6: Generate interfaces to C++ classes using R6. Allows compiled objects to be interacted with dynamically in R as reference (R6) classes. Includes support for mapping C++ templated types onto R's generic (S3) type system.
• dockertest: Generate dockerfiles and containers from R package metadata, remake files or from minimal yaml configuration. Allows offline rapid testing of packages in a clean environment.
• callr: Simple R -> shell and shell -> R calling. Run R by writing small json files. Automatically install missing packages, even from github. Run shell with output only on error.
• experimentr: Control large computational experiments on multiprocessor machines or on HPC infrastructure.
• drat.builder: Tools to help keep a drat repository up to date.
• jqr: R interface to jq, for manipulating JSON data. Includes a pipe-based DSL.
• 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.

Documenting research

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

Distributing and versioning of data

• taxonlookup: curated higher-level taxonomy for land plants.
• baad.data: Biomass And Allometry Database (the actual database is baad).

Fun things

• stegasaur: Steganography for R (encode arbitrary R objects invisibly in images).
• rainbowrite: Port of lolcat for R.
• rfiglet: Port of figlet for R.
• remoji: Emoji support for R

Other contributions

• geiger: a suite of methods and models for studying evolutionary radiations.
• cowsay: cowsay with more animals in R.
• docdbi: generic interface for nosql database in R.