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.
marineBackground(occs, clipToOcean = TRUE, verbose = TRUE, ...)A data.frame with at least two columns
named "longitude" and "latitude" or that
can be coerced into this format.
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.
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.
A SpatVector
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.
# \donttest{
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)
#> Using longitude and latitude
#> as x and y coordinates, respectively.
#> Loading required package: sp
# }