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Trait Ecology & Evolution · UNSW Sydney

Open tools for understanding plants through their traits.

We are the Cornsters: the joint labs of Profs Daniel Falster and Will Cornwell at UNSW Sydney. Our mission is to understand how plant traits shape ecology and evolution, from single leaves to whole floras. We build the open data, models and software that work needs, and share them so that others can use them too.

Explore the tools Install from R-universe

AusTraits family
plant family
HAVPlot family
ecoacoustics family
Species lists & change
Apps & packages
Papers & code

01Plant trait data

AusTraits family

AusTraits is an open, curated database of traits for the Australian flora, harmonised from hundreds of sources. Around it sit the tools that build it, define its traits, resolve its plant names and serve its data.

austraits.org → Paper →

AusTraits

Databasestable

The database itself, with source data and the build for every release. Explore it through the data portal or the HTTP API.

Website Data portal API GitHub

austraits

R packagestable

Access the AusTraits database from R and wrangle data from any traits.build database.

Docs GitHub R-universe

traits.build

R packagestable

A workflow for harmonising trait data from diverse sources into a documented, standard structure. AusTraits is built with it.

Docs Manual Template GitHub R-universe

APD

Trait dictionarystable

The AusTraits Plant Dictionary, with reviewed definitions for nearly 500 plant traits and machine-readable endpoints.

APCalign

R package · Web appstable

Resolve and update the names of Australian plants against the Australian Plant Census.

Docs Web app GitHub CRAN R-universe

taxonAlign

R packagedeveloping

Align taxon names to any taxonomic reference, and generate a reference list for any taxon group in any region.

austraits-means

Data productdeveloping

Species- and community-level trait means for the Australian flora, built from AusTraits with climate and occurrence data.

responses.build

R packageexperimental

An offshoot of traits.build for physiological response-curve data, such as leaf gas exchange, hydraulic vulnerability and fluorescence curves.

02Vegetation models

plant family

The plant model simulates how traits shape the growth, competition and evolution of plants in forests. The family around it adds documentation, community assembly, site and species set-up, leaf physiology, fire and visualisation.

Overstorey guide → Paper →

plant

R package · C++stable

Trait-driven models of size-, patch- and trait-structured forest demography, ecology and evolution.

Docs GitHub R-universe

Overstorey

Guidedeveloping

A field guide to the plant model, with user guides, theory and worked notebooks.

regnans

R packagedeveloping

Extends plant to community assembly and trait evolution, with solvers for resident equilibria and invasion fitness.

fieldtrial

R packageexperimental

Sets up plant runs by bundling a site’s environmental drivers with species’ trait trade-offs and sourced parameter sets.

odelia

C++ library · Rdeveloping

A fast, header-only C++ ODE solver with reverse-mode automatic differentiation and an R interface.

phylloptim

C++ · Rexperimental

A leaf gas-exchange model in which stomatal behaviour emerges from plant hydraulics through gain–risk optimisation.

framecpp

C++ · Rexperimental

Forest flammability using FRaME fire mechanics in C++, generalised from discrete strata to continuous size distributions.

standViz

R packageexperimental

Interactive 3D views of forest stands simulated with plant, drawn as individual trees growing through time.

03Vegetation plot data

HAVPlot family

HAVPlot, the Harmonised Australian Vegetation Plot dataset, brings vegetation plot surveys from across Australia into one compilation of more than 200,000 plots. We are rebuilding it as an open, documented workflow that does for plot data what AusTraits does for trait data. The repositories will open as the work matures.

HAVPlot

Databasedeveloping

A harmonised compilation of Australian vegetation plot data, built from many sources into a single documented database.

PaperNot yet public

plots.build

R packageexperimental

A workflow for harmonising vegetation plot data from diverse sources. It is the plot-data counterpart to traits.build.

Not yet public

04Nature sounds

ecoacoustics family

Tools for finding species in sound recordings: gathering recordings from citizen-science archives, running and combining automated detectors such as BirdNET and Google Perch, and turning their detections into data for analysis.

birdnetprocess

R packagedeveloping

Process and visualise the large volumes of detections produced by BirdNET.

ecoacoustic_utilities

R packagedeveloping

Download and analyse ecoacoustic recordings from iNaturalist and the Atlas of Living Australia.

perch-head

Pythonexperimental

Train and run custom classifier heads on Google Perch embeddings, for recognising species beyond Perch’s own vocabulary.

score-ensemble

Pythonexperimental

Parameter-free, score-level ensembling of two acoustic detectors.

05Who lives where, and what has changed

Species lists & change detection

Tools for building species lists for any place from herbarium collections and citizen-science records, and for tracking how those lists change: new discoveries, species long gone unobserved, and the curation of “all time” floras for national parks.

infinitylists

R package · Web appstable

Generate place-based species lists for anywhere in the world, from collection data and iNaturalist records in the ALA and GBIF.

Web app GitHub R-universe

royalNP_alltime_flora

Versioned data · Rstable

The “all time” plant species list for Royal National Park, NSW, with a script that checks the ALA for candidate new discoveries since the list was made.

yosemiteNP_alltime_flora

Versioned data · Rstable

The “all time” plant species list for Yosemite National Park, California, with a script that checks GBIF for candidate new discoveries since the list was made.

Yosemite_Royal_longunobserved_newdiscovery

Analysisdeveloping

Compares Yosemite and Royal National Parks to track which species have gone long unobserved and which are new discoveries, through time.

lost_flowers

Thesis code · Data

An honours thesis on plant species in Royal National Park that have long gone unrecorded, with the data, code and figures behind it.

06Everything else

Apps & packages

Standalone apps, R packages and data packages for statistics, remote sensing, animal movement and more.

smatr

R packagestable

Estimation and inference for allometric lines by (standardised) major axis regression.

Docs GitHub CRAN R-universe

hmde

R packagestable

Hierarchical Bayesian models that estimate differential-equation parameters, such as growth rates, from repeated measurements.

Docs GitHub CRAN R-universe

litterfitter

R packagestable

Fit and compare alternative models for single-cohort litter decomposition data.

Docs GitHub CRAN R-universe

saltbush

R packagestable

Process drone imagery to calculate spectral diversity, linking diversity seen from the sky with diversity on the ground.

earthtones

R packagestable

Derive a colour palette from satellite imagery of any location on Earth.

Docs GitHub CRAN R-universe

baad.data

Data packagestable

The Biomass And Allometry Database (BAAD) for woody plants, delivered as a versioned R package.

Paper GitHub R-universe

leaf13C

Data packagestable

A global dataset of bulk leaf δ¹³C values.

GitHub R-universe

bmsma

R packageexperimental

Bayesian multilevel fits of standardised major axis lines to bivariate data.

GitHub R-universe

rabbit

R packagedeveloping

Standardise raw tri-axial accelerometer data and extract metrics of movement dynamics.

Retired packages

Still public and citable, but no longer actively developed.

fungaltraitsA dynamic database of fungal trait measurements.
taxonlookupA versioned, dynamically updating taxonomic lookup table for land plants.Paper
growthformVersioned growth-form data for the world’s vascular plants.
phyndrMaximise the overlap between trait data and phylogenies.Paper
datastorrSimple data versioning and distribution through GitHub releases.
versioned_data_templateThe minimum set of tools to set up and distribute a versioned dataset.
ksiFind distinctive clades with the Kolmogorov–Smirnov importance statistic.Paper
traitfillEstimate the state of unsampled species for binary traits.Paper
RevolveAn adaptive dynamics toolkit for R.
katana_launch_RLaunch series of R jobs on UNSW’s Katana HPC cluster.
stan_crossval_demoAn example workflow for efficient k-fold cross-validation with Stan.
dockertestRun R package tests in Docker containers.
rrqueueA distributed task queue for R, using Redis.
statelinerConnect R to the stateline distributed MCMC engine.

07Reproducible research

Papers & code

Papers whose analyses you can reproduce from the code and data in a public repository. For full publication lists, see our Google Scholar profiles.

Daniel Falster on Google Scholar → Will Cornwell on Google Scholar →

austraits_msFalster et al. (2021) AusTraits, a curated plant trait database for the Australian flora. Scientific Data.Paper
multi_trait_successionFalster et al. (2017) Multitrait successional forest dynamics enable diverse competitive coexistence. PNAS.Paper
growth_trajectoriesFalster et al. How functional traits influence plant growth and shade tolerance across the life cycle.Paper
plant_paperFalster et al. (2016) plant: a package for modelling forest trait ecology and evolution. Methods in Ecology and Evolution.Paper
phyndr-msPennell, FitzJohn & Cornwell (2016) A simple approach for maximizing the overlap of phylogenetic and comparative data. Methods in Ecology and Evolution.Paper
baadanalysisDuursma & Falster (2016) Leaf mass per area, not total leaf area, drives differences in above-ground biomass distribution among woody plant functional types. New Phytologist.Paper
Growth_trait_metaanalysisGibert et al. (2016) On the link between functional traits and growth rate: meta-analysis shows effects change with plant size, as predicted. Journal of Ecology.Paper
modeladequacyPennell et al. (2015) Model adequacy and the macroevolution of angiosperm functional traits. American Naturalist.Paper
competition_kernelsEmergent shapes of trait-based competition functions from resource-based models.
mortality_bciA tropical tree mortality model, using Barro Colorado Island as a case study.
reproductive_allocation_kuringgaiCode reproducing papers by Lizzy Wenk on reproductive allocation in plant species of Ku-ring-gai Chase National Park.
colors_in_citizen_scienceThe reliability of colour data extracted from citizen-science images.

About

traitecoevo is the shared GitHub home of the Cornsters (Cornwell + Falster): the labs of Daniel Falster and Will Cornwell at UNSW Sydney, with our students, postdocs and collaborators. The tools here grew out of our research, and many are now used well beyond it.

Current and past lab members are listed on our lab websites:

Falster lab → Cornwell lab →

Install our R packages

Most of our R packages are built on R-universe, so you can install them without extra tools:

install.packages(
  "austraits",
  repos = c("https://traitecoevo.r-universe.dev",
            "https://cloud.r-project.org")
)