spaccEndemism: Spatial Endemism Accumulation

In spacc: Fast Spatial Species Accumulation Curves

Spatial Endemism Accumulation

Description

Compute the number of endemic species (species found only within the accumulated area) as sites are added spatially. Complements the standard SAC by tracking species unique to each spatial extent.

Usage

spaccEndemism(
  x,
  coords,
  n_seeds = 50L,
  method = "knn",
  distance = c("euclidean", "haversine"),
  map = FALSE,
  parallel = TRUE,
  n_cores = NULL,
  progress = TRUE,
  seed = NULL
)

Arguments

x	A site-by-species matrix (presence/absence or abundance).
coords	A data.frame with columns x and y, or a spacc_dist object.
n_seeds	Integer. Number of random starting points. Default 50.
method	Character. Accumulation method. Default "knn".
distance	Character. Distance method: "euclidean" or "haversine".
map	Logical. If TRUE, compute per-site endemism by running accumulation from each site as seed. Stores a site_values data.frame enabling plot(type = "map") and as_sf(). Default FALSE.
parallel	Logical. Use parallel processing? Default TRUE.
n_cores	Integer. Number of cores.
progress	Logical. Show progress? Default TRUE.
seed	Integer. Random seed.

Details

At each accumulation step k, an endemic species is one that is present in the accumulated sites (1..k) but absent from all remaining unvisited sites (k+1..n). This tracks how many species are unique to the area sampled so far.

The endemism curve typically starts low (few endemics at small areas), increases as the region grows, and eventually equals total richness when all sites are included.

Value

An object of class spacc_endemism containing:

richness	Matrix of cumulative richness (n_seeds x n_sites)
endemism	Matrix of endemic species count (n_seeds x n_sites)
site_values	Per-site endemism data.frame (if map = TRUE)
coords, n_seeds, n_sites, method	Parameters used

References

Kier, G., Kreft, H., Lee, T.M., et al. (2009). A global assessment of endemism and species richness across island and mainland regions. Proceedings of the National Academy of Sciences, 106, 9322-9327.

May, F., Gerstner, K., McGlinn, D.J., et al. (2018). mobsim: an R package for the simulation and measurement of biodiversity across spatial scales. Methods in Ecology and Evolution, 9, 1401-1408.

See Also

spacc(), spaccHill()

Examples

coords <- data.frame(x = runif(50), y = runif(50))
species <- matrix(rbinom(50 * 30, 1, 0.3), nrow = 50)

end <- spaccEndemism(species, coords, n_seeds = 30)
plot(end)

spacc documentation built on June 20, 2026, 5:07 p.m.