Harmonised Australian Vegetation Plot dataset (HAVPlot)

Brief description

These data are a harmonized collation of vegetation survey plot datasets from across Australia, representing 205,084 plots. Source data were obtained from the main custodians of vegetation plot information in Australia, being primarily state/territory and federal government agencies. The collated source data were harmonised to a common structured data format through customised scripts written in R. The data provided here are those for which the source data licenses enable adaptation and sharing, though data were also collated and harmonised from a number of sources that could not be included in this data release due to license restrictions. Important methodological attributes have been incorporated where possible, including the taxonomic scope of each survey and the size/shape of the survey plots used. This harmonised dataset may enable a wide variety of analyses that improve our understanding of Australian plant diversity and vegetation patterns.

Lineage

Given the absence of an existing large-scale harmonised plant community survey plot dataset for Australia, we obtained and collated data primarily from state/territory and federal agencies, that are custodians of the largest survey datasets. In some cases we downloaded data directly from publicly accessible websites, while for others we required assistance and permission to obtain relevant data.

Given the different formats of the source data, we developed a simple, customised and structured data format to harmonise across sources, based broadly on the Veg-X schema (Wiser, et al. 2011), with existing standards for data fields used wherever possible (Veg-X, Darwin Core). Source data were harmonised to the common format using a customised script in R. Taxonomic nomenclature was standardised to the Australian Plant Census (CHAH 2022), using code adapted from Falster et al. (2021), with only vascular plant species retained.

Key methodological aspects of the component datasets were also incorporated, including the taxonomic scope of the vegetation survey (e.g. all vascular plants , dominant species only) and the size / configuration of the plot that was surveyed. Obtaining such information often involved identifying publications related to the data and cataloguing the methods described.

Data products
The data were formatted and prepared into the following files, linked by common identifiers:
• project.csv – this file describes attributes of the projects undertaken to sample survey plots. Most projects are associated with surveying multiple plots over space and time, using a common methodology.
• plot.csv – this file describes attributes of the plots that have been surveyed. A plot is a fixed area/location in space, that may be surveyed at one or more times, for one or more attributes (e.g. plant species, soil attributes).
• plotObservation.csv – this file describes the attributes associated with the observations taken at a plot at a particular time (date). There may be multiple plot observations for a single plot.
• aggregateOrganismObservation.csv – this file describes the attributes of plant species observed in a specific plot observation, such as the species observed and any measure of abundance that was made.
• aggregateSoilObservation.csv – this file describes the attributes of the soil that were made in a specific plot observation.
• speciesAttributes.csv – this file describes the attributes associated with species names included in the dataset, where the scientific name for each plant species is that accepted by the Australian Plant Census (CHAH 2022).

The contents (data fields) of each file listed above are described in the file: HAVPlot_Data_Format.csv

The sources of the plot data provided here are shown in the file: HAVPlot_source_citations.docx . Use of the data provided here should comply with the data license conditions of the source data.

A coded example (using R) for combining and manipulating the component HAVPlot data files is provided in the file: HAVPlot_data_query_example_R_code.R

Summary
The HAVPlot data comprise 213,101 observations across 205,084 plots. A summary of the full HAVPlot data are also available in Mokany et al. (2022).

References
CHAH (2022). Australian Plant Census, Centre of Australian National Biodiversity Research. Council of Heads of Australasian Herbaria (CHAH). https://id.biodiversity.org.au/tree/51354547.
Falster, D., et al. 2021. AusTraits, a curated plant trait database for the Australian flora. - Scientific Data 8: 254.
Mokany, K., et al. 2022. Patterns and drivers of plant diversity across Australia. – Ecography (in review).
Wiser, S. K., et al. 2011. Veg-X - an exchange standard for plot-based vegetation data. - Journal of Vegetation Science 22: 598-609.