austraits

austraits allow users to access, explore and wrangle data from traits.build relational databases. It is also an R interface to AusTraits, the Australian plant trait database. This package contains functions for joining data from various tables, filtering to specific records, combining multiple databases and visualising the distribution of the data. We expect this package will assist users in working with traits.build databases.

Installation

This package is not on CRAN yet and is still under active development. For the current stable release of austraits, which has full capabilities of the functions used in vignettes (e.g. plotting functions), use:

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

library(austraits) 

For a lightweight installation where dependencies for plotting and producing the vignettes will not be installed, use:

remotes::install_github("traitecoevo/austraits", upgrade = "ask")

Details for AusTraits users

Retrieve AusTraits data

• For R users, the AusTraits database can be accessed through the austraits package using load_austraits()

• For Python or other users, the Zenodo download includes a .zip file containing all the data in plain text (.csv files) and associated meta-data

Backwards compatibility with past AusTraits versions

From September 2024, austraits functions were revamped to support all traits.build compiled databases, rather than being linked to austraits.build.

Versions of austraits.build (the AusTraits plant trait database) < 5.0 are no longer supported by the latest version of the package. If you are working with an older version of AusTraits, please install an older version of austraits:

For austraits.build versions 4.2 and older:

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

library(austraits)

Note, if you are unsure what version of AusTraits you are working with, run:

austraits$build_info$version

Getting started 👀

We highly recommend taking a look at our Getting Started tutorial on our website before jumping into the austraits R package!

If you prefer to view this vignette in R, we recommend installing the package with build_vignettes = TRUE.

remotes::install_github("traitecoevo/austraits", 
                        dependencies = TRUE, upgrade = "ask", 
                        build_vignettes = TRUE)

vignette("austraits")

Cheat sheet

Learn more about AusTraits

AusTraits is a relational database, you can learn more about it’s structure from the traits.build book.

You can also learn about the definitions of each plant trait with the AusTraits Plant Dictionary!

Show us some support 💚

Please consider citing austraits, we would super appreciate it!

citation("austraits")
#> To cite austraits in publications use:
#> 
#>   Falster, D., Gallagher, R., Wenk, E.H. et al. AusTraits, a curated
#>   plant trait database for the Australian flora. Sci Data 8, 254
#>   (2021). https://doi.org/10.1038/s41597-021-01006-6
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Article{,
#>     title = {AusTraits, a curated plant trait database for the Australian flora},
#>     author = {Daniel Falster and Rachael Gallagher and Elizabeth Wenk et al.},
#>     journal = {Scientific Data},
#>     year = {2021},
#>     volume = {8},
#>     number = {1},
#>     pages = {254 - 274},
#>     url = {https://doi.org/10.1038/s41597-021-01006-6},
#>   }

Behind the scenes 🛠

Check out austraits.build, if you are interested in how AusTraits the database is managed and created

Find a bug? 🐛

Thank you for finding it! Head over to the GitHub Issues tab and let us know about it! We will try to get to it as soon as we can!

AusTraits family

austraits 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.

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).