traits.build-template

An example repository showing the standard layout of a traits.build trait database. Clone it to get started quickly: it contains two small example datasets already wired into a working build pipeline, so you can see how raw data, configuration, and metadata come together into a harmonised database and then adapt the structure for your own data.

What this is

traits.build is a data model, workflow, and R package for compiling harmonised ecological trait databases (it is the engine behind AusTraits). A traits.build database is just a repository that follows a fixed folder layout; this template is a minimal, runnable instance of that layout.

For a full, worked walk-through that uses this very template, see the compilation tutorial in the traits.build book.

Repository structure

Path	Purpose
config/	Database-wide configuration: metadata.yml (database title, version, sources), traits.yml (trait definitions and allowed values), unit_conversions.csv (recognised units and conversions), and taxon_list.csv (the reference taxonomy).
data/	One sub-folder per source dataset (example_dataset_1/, example_dataset_2/), each with a data.csv (the raw study data) and a metadata.yml (how that study maps onto the database's traits, contexts, and metadata).
R/	Project-specific helper code (custom_R_code.R) that individual datasets can call during processing.
remake.yml	The build pipeline: it wires the config and per-dataset files together into the final austraits object and exports it to export/data/curr/austraits.rds. This file is auto-generated by traits.build from remake.yml.whisker — edit the whisker source, not remake.yml directly.

Clone and build

# 1. Clone the template
# git clone https://github.com/traitecoevo/traits.build-template.git

# 2. Install the build engine
# install.packages("remotes")
remotes::install_github("traitecoevo/traits.build")

# 3. Build the database from the repository root
library(traits.build)
remake::make("all")

# The compiled database is the `austraits` object,
# also written to export/data/curr/austraits.rds
austraits <- readRDS("export/data/curr/austraits.rds")

Note on build tooling. The pipeline currently uses remake, which is no longer actively maintained. The traits.build build tooling is expected to move to targets in a future release. The layout above describes current usage; expect the remake.yml mechanism to change.

How to cite

If you use traits.build (or this template), please cite:

Wenk E, Bal P, Coleman D, Gallagher R, Yang S, Falster DS (2024) traits.build: A data model, workflow and R package for building harmonised ecological trait databases. Ecological Informatics 83:102773. https://doi.org/10.1016/j.ecoinf.2024.102773

AusTraits family

traits.build-template 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).