diversityProfile: Diversity Profile

In spacc: Fast Spatial Species Accumulation Curves

Diversity Profile

Description

Compute Hill numbers across a continuous range of diversity orders (q), producing a diversity profile for each site and the regional pool.

Usage

diversityProfile(
  x,
  q = seq(0, 3, by = 0.1),
  type = c("both", "per_site", "regional"),
  coords = NULL
)

Arguments

x	A site-by-species matrix (abundance data).
q	Numeric vector. Orders of diversity to evaluate. Default seq(0, 3, by = 0.1).
type	Character. What to compute: "per_site" (per-site profiles), "regional" (pooled gamma), or "both" (default).
coords	Optional data.frame with columns x and y for spatial mapping. When provided, enables plot(type = "map").

Details

A diversity profile plots effective number of species as a function of the order q. The key property is that Hill numbers are non-increasing in q: D_q \ge D_{q'} for q \le q'.

• q = 0: Species richness (insensitive to abundance)

• q = 1: Exponential of Shannon entropy (all species weighted equally by their proportional abundance)

• q = 2: Inverse Simpson concentration (emphasizes dominant species)

• q > 2: Increasingly dominated by common species

Value

An object of class spacc_profile containing:

per_site	Matrix of per-site diversity (sites x q values), or NULL
regional	Named numeric vector of gamma diversity per q, or NULL
q	Vector of diversity orders used
coords	Coordinates if provided
n_sites	Number of sites
n_species	Number of species

References

Leinster, T. & Cobbold, C.A. (2012). Measuring diversity: the importance of species similarity. Ecology, 93, 477-489.

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() for per-site values at specific q, gammaDiversity() for regional diversity, evenness() for evenness profiles

Examples

species <- matrix(rpois(50 * 30, 2), nrow = 50)
prof <- diversityProfile(species)
print(prof)


plot(prof)

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