spaccBeta: Spatial Beta Diversity Accumulation
In spacc: Fast Spatial Species Accumulation Curves

spaccBeta

R Documentation

Spatial Beta Diversity Accumulation

Description

Analyze how beta diversity changes as sites are accumulated spatially. Partitions beta diversity into turnover (species replacement) and nestedness (species loss) components following Baselga (2010).

Usage

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

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"`.
`index`	Character. Dissimilarity index: `"sorensen"` (default) or `"jaccard"`.
`distance`	Character. Distance method: `"euclidean"` or `"haversine"`.
`parallel`	Logical. Use parallel processing? Default `TRUE`.
`n_cores`	Integer. Number of cores.
`progress`	Logical. Show progress? Default `TRUE`.
`seed`	Integer. Random seed.
`map`	Logical. If `TRUE`, run accumulation from every site as seed and store per-site final beta values for spatial mapping. Enables `as_sf()` and `plot(type = "map")`. Default `FALSE`.

Details

At each step of spatial accumulation, beta diversity is calculated between the accumulated species pool and the newly added site. This reveals how species composition changes as you expand spatially.

Interpretation:

High turnover: New sites contribute different species (replacement)
High nestedness: New sites contribute subsets of existing species (loss)

The sum of turnover and nestedness equals total beta diversity.

Value

An object of class spacc_beta containing:

`beta_total`	Matrix of total beta diversity (n_seeds x n_sites-1)
`beta_turnover`	Matrix of turnover component
`beta_nestedness`	Matrix of nestedness component
`distance`	Matrix of cumulative distances
`n_seeds`, `n_sites`, `method`, `index`	Parameters used

References

Baselga, A. (2010). Partitioning the turnover and nestedness components of beta diversity. Global Ecology and Biogeography, 19, 134-143.

Examples


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

beta <- spaccBeta(species, coords, n_seeds = 30)
plot(beta)

# Compare Sorensen vs Jaccard
beta_jac <- spaccBeta(species, coords, index = "jaccard")

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