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Read Soil Beta Diversity from TERN

Source: R/read_soil_diversity.R
read_soil_diversity.Rd

Wrapper around read_tern() for retrieving the v1.0 datasets for soil bacteria and soil fungi Beta Diversity from the TERN Data Portal. The Beta Diversity datasets were constructed using Digital Soil Mapping techniques together with Biome of Australia Soil Environments (BASE) DNA sequences, and provide Non-metric MultiDimensional Scaling (NMDS) axes for soil bacteria and fungi at 90m X 90m spatial resolution across Australia.

Usage

read_soil_diversity(
  collection = "Bacteria",
  axis = 1L,
  api_key = get_key(),
  max_tries = NULL,
  initial_delay = NULL
)

Arguments

collection

One of "Bacteria" (default) or "Fungi".

axis

NMDS axis number: 1 (default), 2, or 3.

api_key

A character string containing your TERN API key. Defaults to automatic detection from your .Renviron or .Rprofile. See get_key() for setup.

max_tries

Maximum number of download retries before an error is raised. Default=NULL, in which case the maximum retry number is resolved from the option nert.max_tries if that option exists. (Defaults to 3 retries if nert.max_tries has not been set.)

initial_delay

Initial retry delay in seconds (doubles with each attempt). Default=NULL, in which case the initial delay is resolved from the option nert.initial_delay if that option exists. (Defaults to a 1 second initial delay if nert.initial_delay has not been set.)

Value

A terra::SpatRaster object of the requested Beta Diversity NMDS axis.

References

Dobarco, M., Wadoux, A. & Xue, P. (2024). Soil and Landscape Grid National Soil Attribute Maps - Soil Bacteria and Fungi Beta Diversity (3" resolution) - Release 1. Version 1.0. Terrestrial Ecosystem Research Network. (Dataset). doi:10.25919/4x7n-y874 .

TERN Soil Beta Diversity Point-of-truth metadata URL: https://geonetwork.tern.org.au/geonetwork/srv/eng/catalog.search#/metadata/4a428d52-dda6-4097-8dd9-d3ec63973029

See also

read_tern()

Examples

if (FALSE) { # interactive()
# Read bacterial diversity NMDS axis 1
r <- read_soil_diversity()
autoplot(r)

# Read fungal diversity NMDS axis 2
r_f2 <- read_soil_diversity(collection = "Fungi", axis = 2)
autoplot(r_f2)
}