Access and wrangle data from traits.build trait databases • traits.use

traits.use helps you load, explore and wrangle data from trait databases built with traits.build, such as AusTraits, the Australian plant trait database. It works with any traits.build database, whichever group of organisms or region it covers.

With traits.use you can:

load a database from its DOI (load_database()), downloading each release once per computer and keeping it in a cache shared by all your projects;
filter it to particular traits, taxa or datasets (extract_trait(), extract_taxa(), extract_dataset(), extract_data()), keeping every table consistent;
join information from the database’s other tables onto the trait values (join_location_coordinates(), join_taxa(), join_methods(), join_context_properties() and more);
reshape and flatten it (trait_pivot_wider(), as_wide_table(), flatten_database()), or combine several databases (bind_databases());
look up traits, references and properties (lookup_trait(), database$sources$Falster_2005), list the references to cite for the data you use, as text or BibTeX (get_references()), summarise what it contains (summarise_database()), and plot trait distributions and locations.

Installation

traits.use is not yet on CRAN. Install the development version from GitHub:

# install.packages("remotes")
remotes::install_github("traitecoevo/traits.use", dependencies = TRUE, upgrade = "ask")

Leave out dependencies = TRUE for a lighter installation without the packages used for plotting.

Getting started

library(traits.use)

# Load any traits.build database from its DOI. It is downloaded the first
# time and loaded from your cache after that (see ?database_cache_dir); give
# `path` to keep a copy with a project instead
database <- load_database("10.5281/zenodo.11188867")

# Or try the package without downloading anything, on the small subset of
# AusTraits that comes with it
database <- austraits_lite

# Pick out the traits you want, then add site coordinates to each value
wood_density <- database |>
  extract_trait("wood_density") |>
  join_location_coordinates()

summarise_database(wood_density, "family")

The Getting Started tutorial in the austraits package walks through these functions using AusTraits. The traits.build book explains how a traits.build database is structured: its tables, identifiers and how they link.

For AusTraits users

AusTraits is built with traits.build, so everything in traits.use works on it: load a release with load_database() and its DOI. The austraits package adds what is specific to AusTraits: load_austraits() loads a release by version number, plot_locations() draws a map of Australia, and the Getting Started tutorial uses AusTraits throughout. AusTraits releases on Zenodo also include the data as plain-text .csv files for users of Python and other tools. You can look up each trait’s definition in the AusTraits Plant Dictionary.

The current functions support AusTraits 5.0.0 and later. For older releases (4.2 and earlier), install an older version of the austraits package:

remotes::install_github("traitecoevo/austraits@v2.2.2", dependencies = TRUE, upgrade = "ask")

To check which version of AusTraits you have loaded, run database$build_info$version.

History

traits.use began in 2021 as the austraits R package, an interface to the AusTraits plant trait database (Falster et al. 2021). In 2024 (austraits 3.0) its functions were generalised to work with any database compiled with traits.build, not just AusTraits. As other traits.build databases appeared, the general-purpose code was split out in 2026 into this package, traits.use, carrying over the full development history and its contributors. The austraits package continues as a thin AusTraits-specific layer built on traits.use (austraits#188).

Citation

Please consider citing traits.use if you use it in your work:

citation("traits.use")
#> To cite traits.use in publications, please use the first reference
#> below. If you use AusTraits data, please also cite the AusTraits
#> database (second reference).
#> 
#>   Wenk, E., Kar, F., Falster, D. and Indiarto, D. (2026) traits.use:
#>   Access and Wrangle Data from 'traits.build' Trait Databases. R
#>   package version 0.1.1. https://github.com/traitecoevo/traits.use
#> 
#>   Falster, D., Gallagher, R., Wenk, E.H. et al. (2021) AusTraits, a
#>   curated plant trait database for the Australian flora. Scientific
#>   Data 8, 254. https://doi.org/10.1038/s41597-021-01006-6
#> 
#> To see these entries in BibTeX format, use 'print(<citation>,
#> bibtex=TRUE)', 'toBibtex(.)', or set
#> 'options(citation.bibtex.max=999)'.

Find a bug?

Please let us know on the issue tracker.

AusTraits family

traits.use is part of the AusTraits family of packages maintained by the AusTraits team. See austraits.org for the project, the data, and the people behind it. To see how AusTraits itself is compiled, look at austraits.build.

Contributing? Issues across the family are tracked on one board, AusTraits #9, and new issues are auto-added. Please read the issue & labelling guide in austraits-meta, the family’s cross-package knowledge and governance hub, before filing.

Acknowledgements

AusTraits is made possible by contributions from our partner organisations — the University of New South Wales, Western Sydney University, Botanic Gardens of Sydney, the University of Melbourne, the Atlas of Living Australia, and the Australian Government Department of Climate Change, Energy, the Environment and Water — and from our advisory board, data contributors, and past partners.

AusTraits is a co-investment partnership with the Australian Research Data Commons (ARDC) through the Planet Research Data Commons (DOI: 10.3565/nyk4-4r91). The ARDC is enabled by the Australian Government’s National Collaborative Research Infrastructure Strategy (NCRIS).