spaccHillBeta: Spatial Hill Number Beta Diversity

In spacc: Fast Spatial Species Accumulation Curves

Spatial Hill Number Beta Diversity

Description

Compute multisite beta diversity as gamma/alpha decomposition of Hill numbers along the spatial accumulation curve (Jost 2007 framework).

Usage

spaccHillBeta(
  x,
  coords,
  q = c(0, 1, 2),
  n_seeds = 50L,
  distance = c("euclidean", "haversine"),
  parallel = TRUE,
  n_cores = NULL,
  progress = TRUE,
  seed = NULL
)

Arguments

x	A site-by-species matrix (rows = sites, cols = species).
coords	A data.frame with columns x and y, or a spacc_dist object.
q	Numeric vector. Orders of diversity. Default c(0, 1, 2).
n_seeds	Integer. Number of random starting points. Default 50.
distance	Character. "euclidean" or "haversine".
parallel	Logical. Use parallel processing? Default TRUE.
n_cores	Integer. Number of cores. Default NULL.
progress	Logical. Show progress? Default TRUE.
seed	Integer. Random seed.

Details

At each accumulation step k, the function computes:

• Gamma: Hill number of the pooled community (all k sites combined)

• Alpha: Generalized mean of per-site Hill numbers (Jost's power mean)

• Beta: gamma / alpha (effective number of distinct communities)

Beta = 1 means all sites are identical; beta = k means all sites are completely different. This provides the Hill-number analogue of the Baselga-based spaccBeta().

Value

An object of class spacc_hill_beta containing:

gamma	Named list of n_seeds x n_sites matrices (one per q)
alpha	Named list of n_seeds x n_sites matrices (one per q)
beta	Named list of n_seeds x n_sites matrices (one per q)
q	Vector of q values
coords	Original coordinates
n_seeds, n_sites, n_species	Dimensions

References

Jost, L. (2007). Partitioning diversity into independent alpha and beta components. Ecology, 88, 2427-2439.

See Also

spaccBeta() for P/A-based Baselga partitioning, spaccHill() for Hill accumulation without beta decomposition

Examples

coords <- data.frame(x = runif(40), y = runif(40))
species <- matrix(rpois(40 * 20, 2), nrow = 40)

hb <- spaccHillBeta(species, coords, n_seeds = 10, progress = FALSE)
plot(hb)

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