Alpha Diversity (Per-Site)

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.

Value

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

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

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)