Software

pez: phylogenetics for the environmental s(z)ciences

R package to calculate phylogenetic diversity metrics, Phylogenetic Generalized Linear Mixed Models, and more.

Pearse WD, Cadotte MW, Cavender-Bares J, Ives AR, Tucker CM, Walker SC, Helmus MR

phyloGenerator: an automated phylogeny generation tool for ecologists

Python (version 1) and Ruby (version 2) program that automates phylogeny construction. Awarded the Robert May Prize by the British Ecological Society.

Pearse WD, Purvis A

Methods in Ecology and Evolution 4(7), 692-698

Suppdata: downloading supplementary data from published manuscripts

R package to download the supplementary data from papers using only their DOI

Pearse WD, Chamberlain SA, with vital contributions from Daniel Nüst

Journal of Open Source Software 3(25, 721

phest: phenology estimation

R package that calculates phenology estimators

Pearse WD, Stemkovski M

https://github.com/willpearse/phest

MADtraits: Make A Database of traits

R package that automates the download of over 4 million pieces of trait data

The Bio Nerd Herd (run by the Pearse Lab)

https://github.com/willpearse/MADtraits

MADcomm: Make A Database of community data

R package that automates the download of over 16 million pieces of ecological community data

The Bio Nerd Herd (run by the Pearse Lab)

https://github.com/willpearse/MADcomm

Austin: MCMCMC for the brave

C++ Multiple Chain Monte Carlo Markov Chain. Really more of a toy, but useful for classwork

Pearse WD

https://github.com/willpearse/astin

Tyrell: COVID-19 toolkit

Reproducible data cleaning and analysis pipeline to support our lab’s funded COVID-19 work

Pearse WD & Smith T

https://github.com/pearselab/tyrell