alphaDiversity: Alpha Diversity (Per-Site)

In spacc: Fast Spatial Species Accumulation Curves

Alpha Diversity (Per-Site)

Description

Compute Hill numbers for each site individually.

Usage

alphaDiversity(x, q = c(0, 1, 2), coords = NULL)

Arguments

x	A site-by-species matrix (abundance data).
q	Numeric vector. Orders of diversity. Default c(0, 1, 2).
coords	Optional data.frame with columns x and y for spatial mapping. When provided, returns a spacc_alpha object with as_sf() and plot(type = "map") support.

Details

Alpha diversity represents local (within-site) diversity. For Hill numbers:

• q=0: Species richness

• q=1: Exponential of Shannon entropy

• q=2: Inverse Simpson concentration

Value

If coords is NULL, a data.frame with columns for each q value. If coords is provided, a spacc_alpha object.

References

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

See Also

gammaDiversity() for regional diversity, diversityPartition() for full alpha-beta-gamma decomposition

Examples

species <- matrix(rpois(50 * 30, 2), nrow = 50)
alpha <- alphaDiversity(species, q = c(0, 1, 2))
head(alpha)

# Mean alpha diversity
colMeans(alpha)

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