marineBackground: Marine background shapefile generation

View source: R/marineBackground.R

marineBackgroundR Documentation

Marine background shapefile generation

Description

Automatically generates background shapefiles for sampling pseudoabsences and/or background points for niche modeling or species distribution modeling. Delineating background sampling regions can be one of the trickiest parts of generating a good model. Automatically generated background shapefiles should be inspected carefully prior to model use.

Useful references, among others:

  • Barve N, Barve V, Jiménez-Valverde A, Lira-Noriega A, Maher SP, Peterson AT, Soberón J, Villalobos F. 2011. The crucial role of the accessible area in ecological niche modeling and species distribution modeling. Ecological modelling 222:1810-9.

  • Merow, C, Smith MJ, Silander JA. 2013. A practical guide to MaxEnt for modeling species’ distributions: what it does, and why inputs and settings matter." Ecography 36: 1058-69.

  • Murphy SJ. 2021. Sampling units derived from geopolitical boundaries bias biodiversity analyses. Global Ecology and Biogeography 30: 1876-88.

Usage

marineBackground(occs, clipToOcean = TRUE, verbose = TRUE, ...)

Arguments

occs

A data.frame with at least two columns named "longitude" and "latitude" or that can be coerced into this format.

clipToOcean

logical. Clips shapefile to oceans where species occurs. Useful in cases where buffers jump over narrow peninsulas (e.g. Isthmus of Panama). Can be quite artificial at ocean boundaries.

verbose

logical. Switching to FALSE mutes message describing which columns in occs are interpreted as x and y coordinates.

...

Additional optional arguments to pass to getDynamicAlphaHull.

Details

The meat of this function is a special-case wrapper around getDynamicAlphaHull() from the rangeBuilder package. The function documented here is especially useful in cases where one wants to automatically generate training regions that overlap the international date line. Regions that exceed the line are cut and pasted into the appropriate hemisphere instead of being deleted.

If the argument buff is not supplied, a buffer is calculated by taking the mean between the 10th and 90th percentile of horizontal distances between occurrence points.

If getDynamicAlphaHull() cannot satisfy the provided conditions, the occurrences are buffered and then a minimum convex hull is drawn around the buffer polygons.

Value

A SpatVector

See Also

getDynamicAlphaHull

Examples


library(terra)
# Create sample raster
r <- rast(ncol=10, nrow=10)
values(r) <- 1:100

# Create test occurrences
set.seed(0)
longitude <- sample(-50:50,
                    size = 20, replace = FALSE)
set.seed(0)
latitude <- sample(-30:30,
                   size = 20, replace = FALSE)
occurrences <- as.data.frame(cbind(longitude,latitude))

# Here's the function
result <- marineBackground(occs = occurrences, buff = 100000,
                           fraction = .9, partCount = 2, clipToOcean = FALSE)



voluModel documentation built on May 29, 2024, 2:03 a.m.