ausplotsR: A new R package to download and analyse vegetation and soil data collected by Australia’s most comprehensive ecosystem monitoring program

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This post was provided by Samantha Munroe

TERN monitoring plot locations as generated within the ausplotsR package coded by percent fractional green cover. Image credit: Munroe et al. (2021).

This Behind the paper post refers to the article “ausplotsR: An R package for rapid extraction and analysis of vegetation and soil data collected by Australia’s Terrestrial Ecosystem Research Network” by Samantha Munroe et al. published in the Journal of Vegetation Science (https://doi.org/10.1111/jvs.13046).

To tackle some of the world’s most serious environmental problems, scientists need ‘big data’. Critical issues such as the damaging impacts of invasive species on native wildlife, the preservation of essential ecosystem services, or the ongoing threats posed by global warming, can only be addressed with detailed and large-scale environmental data sets. The new R package ausplotsR gives scientists free and instant access to a decade of soil and vegetation data, collected at over 780 environmental monitoring sites across Australia. These data enable researchers worldwide to detect better and understand changes in terrestrial ecosystems and meet today’s greatest environmental challenges.

ausplotsR was developed by scientists and technicians with the Terrestrial Ecosystem Research Network (TERN), Australia’s ecosystem observatory. TERN collects vital environmental data and samples from around Australia by conducting field surveys, using remote-sensing technology such as drones and satellites, and by monitoring specific sites across the country in great detail. TERN shares these data to enable world-leading research on climate change, biodiversity, water and soil. So far, TERN has established plots across every major terrestrial environment in Australia, recording >5,000 unique plant species and collecting >65,000 plant and soil samples for analysis. The ausplotsR package was designed to provide unrestricted and simple access to the TERN plot survey database. 

TERN’s plot database includes a wide range of data types, such as measurements of vascular plant species presence, growth form, height, and cover, which are useful for predictive modelling and validation of remote sensing applications. Species identification data are also globally compatible and simple to sort. Soil characteristics such as texture, pH, electrical conductivity, and bulk density are also available. ausplotsR provides information on TERN’s substantial soil and plant sample collection, which can be requested by scientists anywhere in the world for things like genetic or stable isotope analysis. These data are particularly valuable because many TERN field sites are found in some of the most remote areas of the country. As a result, ausplotsR gives scientists digital access to data that might otherwise be financially or physically impossible to collect.

TERN field teams of between 2 and 6 people survey each plot to record a wide range of data, including plant species presence, cover, and soil characteristics. a) Coffin Bay National Park, South Australia, Australia; shrubland; b) Giles Point, Pilbara Western Australia, Australia; low open woodland. Photo Credit: Tamara Potter.

ausplotsR, like so many other packages for the R environment, did not start out as a package designed for widespread use. Lead developer Dr Greg Guerin initially wrote much of the underlying code to create a more convenient way for TERN staff to review and analyse TERN data. Before ausplotsR, staff had to import and compile 1000s of rows of data for every plot, each saved as its own spreadsheet. However, it quickly became clear that this in-house tool would also be invaluable to researchers working in a variety of scientific fields. Since early versions of the package were released in 2018, ausplotsR has served over ten thousand requests for data to over 350 users. These users have downloaded 5,000,000 sites of data and 1.2 billion total records.

Its popularity is undoubtedly due to just how easy ausplotsR makes it to access and integrate TERN data into a wide range of scientific analyses. Data is imported directly into R, avoiding the need to gain permission to access data or store data in large, memory-chewing files. Convenient data formatting, as well as functions that calculate a variety of popular vegetation metrics, support seamless integration with a range of ecological, statistical, and graphical R packages. ausplotsR also allows users to easily map plots and graph variables such as the relative cover of plant growth forms. Most importantly, even the most novice of R users can quickly implement the easy-to-understand functions.

The ausplotsR package allows users to easily and quickly graph things like fractional vegetation cover or relative cover of plant growth forms for multiple plots, as shown in the example above comparing two visits to the same plot. Image credit: Greg Guerin.

The ausplotsR package will continue to evolve to enrich and simplify TERN data interpretation. Some of the next big steps will be designing tools that allow researchers to search across the vast TERN field sample library more easily and generate lists of samples to request for laboratory analysis. To date, TERN data has been used in over 1600 peer-reviewed publications, and we are confident that with the release of ausplotsR this number will significantly grow, enabling important and impactful ecological research on Australian ecosystems.

Brief personal summary: Dr Samantha Munroe is a postdoctoral fellow at the University of Adelaide (Australia) and a Data Scientist with TERN. At TERN she designs innovative strategies, tools, and software to help produce world-class ecosystem data. She has over 10 years of experience studying the distribution of plants and animals on land and at sea, and is a tireless campaigner for Women in STEM and public science communication.