diversityPartition: Alpha-Beta-Gamma Diversity Partitioning

In spacc: Fast Spatial Species Accumulation Curves

Alpha-Beta-Gamma Diversity Partitioning

Description

Decompose regional (gamma) diversity into local (alpha) and turnover (beta) components using multiplicative partitioning of Hill numbers.

Usage

diversityPartition(x, q = c(0, 1, 2), weights = "equal", coords = NULL)

Arguments

x	A site-by-species matrix (abundance data).
q	Numeric vector. Orders of diversity. Default c(0, 1, 2).
weights	Character or numeric. Site weights for alpha calculation: "equal": Equal weights (default) "proportional": Weights proportional to site abundance Numeric vector of custom weights
coords	Optional data.frame with columns x and y for spatial mapping. When provided, enables as_sf() and plot(type = "map").

Details

This function implements Jost (2007) multiplicative partitioning:

\gamma = \alpha \times \beta

Where:

• Alpha: Mean effective number of species per site

• Beta: Effective number of distinct communities (1 = all identical, n_sites = all completely different)

• Gamma: Total effective number of species in the region

Beta diversity is interpreted as the effective number of communities:

• Beta = 1: All sites have identical composition

• Beta = n_sites: Sites share no species

Value

An object of class spacc_partition containing:

alpha	Mean alpha diversity (effective number of species per site)
beta	Beta diversity (effective number of communities)
gamma	Gamma diversity (regional species pool)
q	Orders of diversity
n_sites	Number of sites
n_species	Total species count

References

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

Chao, A., Chiu, C.H. & Jost, L. (2014). Unifying species diversity, phylogenetic diversity, functional diversity, and related similarity and differentiation measures through Hill numbers. Annual Review of Ecology, Evolution, and Systematics, 45, 297-324.

See Also

alphaDiversity(), gammaDiversity(), spaccBeta() for spatial beta diversity accumulation

Examples

# Simulated community data
species <- matrix(rpois(50 * 30, 2), nrow = 50)

# Partition diversity
part <- diversityPartition(species, q = c(0, 1, 2))
print(part)

# Beta near 1 = homogeneous region
# Beta near n_sites = heterogeneous region

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