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Assign Australian Marine Bioregions to sample locations

Source: R/pr_add_bioregions.R
pr_add_Bioregions.Rd

Add bioregion classification to samples based on their geographic coordinates. Uses Australian marine bioregion boundaries (IMCRA 4.0) from the Integrated Marine and Coastal Regionalisation of Australia.

Usage

pr_add_Bioregions(dat, near_dist_km = 0)

Arguments

dat

A dataframe containing columns Longitude and Latitude with geographic coordinates in decimal degrees (WGS84)

near_dist_km

Buffer distance (in kilometres) to use when assigning bioregions to samples that fall outside boundaries. Default is 0 (no buffer). Typical values:

  • 0 - Exact match only, samples outside boundaries are labelled "None"

  • 50 - Assigns samples within 50 km of a bioregion

  • 250 - More generous buffer, useful for CPR transects near boundaries

Value

A dataframe with two additional columns:

  • BioRegion: Name of the marine bioregion

  • Colour: Hex colour code for that bioregion (for plotting)

Details

Bioregion Classification

The function assigns samples to one of the following Australian marine bioregions:

  • Temperate East: Coastal waters off NSW and southern Queensland

  • South-east: Bass Strait and waters off Tasmania

  • South-west: Southern and western Australian waters

  • North-west: Waters off northwest Western Australia

  • Coral Sea: Offshore waters northeast of Queensland

  • None: Samples that don't fall within any bioregion

Assignment Method

The function uses spatial operations to:

  1. Convert coordinates to spatial features (sf objects)

  2. Match samples to bioregions using polygon intersection

  3. For samples outside boundaries, find the nearest bioregion within near_dist_km

  4. Prioritise Coral Sea assignments to handle boundary overlaps

  5. Add a colour column for plotting consistency

Buffer Distance

The near_dist_km parameter is particularly useful for:

  • CPR samples collected near bioregion boundaries

  • Offshore samples that may fall just outside defined regions

  • Creating continuous coverage for transect data

Use larger buffers (e.g., 250 km) for offshore CPR data, smaller or no buffer for coastal NRS data.

Data Requirements

Input dataframe must include Longitude and Latitude columns. The function handles coordinate transformations automatically.

See also

  • pr_get_CPRData() which calls this function internally

  • mbr for the marine bioregion spatial data

Examples

# Add bioregions with exact matching (no buffer)
dat <- pr_get_Raw("cpr_derived_indices_data") %>%
  pr_add_Bioregions()

# Add bioregions with 250 km buffer for offshore samples
dat <- pr_get_Raw("cpr_derived_indices_data") %>%
  pr_add_Bioregions(near_dist_km = 250)

# Check bioregion assignments
table(dat$BioRegion)
#> 
#>             Coral Sea                  None                 North 
#>                  4105                  1108                   348 
#>            North-west            South-east            South-west 
#>                  1119                 11671                  3620 
#> Southern Ocean Region        Temperate East 
#>                  7783                  7065