Software
Our lab is committed to free and open provision of scientific source code and data, both to make our research transparent and reproducible, and because we believe that scientific code and data are essentially public goods to which all researchers should contribute.
The packages below are the ones we develop or contribute to directly. For the fuller picture, including code and data accompanying individual papers, see the group software page, the Theoretical Ecology GitHub organisation, and my own GitHub account — as well as the sites and GitHub accounts of individual group members.
Main packages
DHARMa
An R package for residual diagnostics for hierarchical (multi-level / mixed) regression models.
BayesianTools
An R package for the Bayesian calibration of process-based models.
Further packages from the group
sjSDM
Scalable joint species distribution modelling, estimating the full species covariance matrix rather than approximating it.
cito
Deep neural networks in R with ordinary formula syntax, plus the explainable-AI tools needed to interpret them.
Contributions to other projects
rLPJGUESS
An R wrapper around the LPJ-GUESS dynamic global vegetation model, with support for parallel runs.
ProfoundData
The PROFOUND database of European forest data, for calibrating, validating and benchmarking vegetation models.
threePGN
A Fortran implementation of the 3PGN forest growth model, callable from R.
NUCOMBog
A model of vegetation, carbon, nitrogen and water dynamics in undisturbed open bog ecosystems.