AREAData: automatically updating epidemiological data pipeline

Daily climate and human data, automatically updated and released in a format to support epidemiological forecasting.

TP Smith, M Stemkovski, A Koontz, WD Pearse

Data in Brief 43: 108438

Tyrell: COVID-19 toolkit

Internal reproducible data cleaning and analysis pipeline to support our funded COVID-19 work

TP Smith, WD Pearse

SymbiotaR2: Symbiota2 R interface

R Package for searching and downloading data stored in a Symbiota2 portal

Koontz A, Brandt B, Dyreson C, and Pearse WD

Journal of Open Source Software 5(56): 2917

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

Bioinformatics 31(17): 2888-2890

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 NĂ¼st

Journal of Open Source Software 3(25): 721

phest: phenology estimation

R package that calculates phenology estimators

Pearse WD, Stemkovski M

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)

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)

Austin: MCMCMC for the brave

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

Pearse WD