traitecoevo: a collection of tools for trait-based ecology & evolution

Here you will find links to various pieces of software and analysis code, supporting projects on trait-based ecology & evolution. Common features across the items listed are that they:
  1) Involve either Daniel Falster, Rich FitzJohn, Will Cornwell, or Matt Pennell, and
  2) Are either tools that you can potentially use in your own work, or analyses that are reproducible.
This is not meant to be a comprehensive overview of ALL relevant tools, or all of our work, just some stuff we made and thought you might find useful. Wherever possible we've provided links to github or other code packages.

R Packages containing traitecevo methods or data

Package name Description Paper Maintainer
plant Dynamics of forest trait ecology & evolution Methods in Ecology & Evolution Daniel Falster
taxonlookup A versioned taxonomic lookup table for land plants Methods in Ecology & Evolution Will Cornwell
phyndr An algorithm to maximize the overlap between traits & phylogenies Methods in Ecology & Evolution Matt Pennell BAAD: a Biomass And Allometry Database for woody plants Ecology Daniel Falster
arbutus Assessing the adequacy for models of trait evolution American Naturalist Matt Pennell
ksi Identifying distinctive clades with respect to traits Journal of Ecology Will Cornwell
traitfill Estimating the state of unsampled species for binary traits Journal of Ecology Will Cornwell

Repositories supporting specific papers

Short title Authors Year Journal Reproducible Complexity of analysis
Plant: package for modelling forest trait ecology and evolution Falster, FitzJohn, et al. 2016 Methods in Ecology & Evolution All analyses & ms Medium
Maximizing the overlap of phylogenetic and comparative data Pennell, FitzJohn, Cornwell 2016 Methods in Ecology & Evolution All analyses & ms Low
Leaf mass per area drives differences biomass distribution Duursma & Falster 2016 New Phytologist All analyses & ms Low
On the link between functional traits and growth rate Gibert, Falster, et al. 2016 Journal of Ecology All analyses & ms Low
Warming strengthens positive feedback between shrubs and fire Camac, et al. 2016 BioRxiv All analyses & ms Medium
Effects of litter traits on surface fires Cornwell, et al. 2015 New Phytologist Figures Low
Competitive coexistence & evolved neutrality Falster et al. 2015 BioRxiv Figures High
Adequacy of trait evolution models Pennell, FitzJohn,Cornwell et al 2015 American Naturalist All analyses & ms Medium
Quantifying reproductive allocation schedules in plants Wenk & Falster 2015 Ecology & Evolution All analyses & ms Low
Optimal sapwood cross section in relation to leaf area Westoby, Cornwell, Falster 2012 Journal of Theoretical Biology All analyses & figures Low
General model for the scaling of offspring and adult size Falster et al 2008 The American Naturalist All analyses & figures Low

Infrastructure packages supporting R-based work flows

Package name Description Maintainer
remake Package for managing (and reproducing) R-based workflows Rich FitzJohn
dockertest Build docker containers for R projects Rich FitzJohn
rrqueue Distributed task queue for R Rich FitzJohn
stateliner Interface to the Bayesian engine stateline Daniel Falster
callr A way to call R from other programs and calling other programs from R Rich FitzJohn