spaccFunc: Spatial Functional Diversity Accumulation
In spacc: Fast Spatial Species Accumulation Curves

spaccFunc

R Documentation

Spatial Functional Diversity Accumulation

Description

Compute spatial accumulation of functional diversity metrics based on traits.

Usage

spaccFunc(
  x,
  coords,
  traits,
  metric = c("fdis", "fric"),
  n_seeds = 50L,
  method = "knn",
  distance = c("euclidean", "haversine"),
  parallel = TRUE,
  n_cores = NULL,
  progress = TRUE,
  seed = NULL,
  map = FALSE
)

Arguments

`x`	A site-by-species matrix (abundance data recommended).
`coords`	A data.frame with columns `x` and `y`, or a `spacc_dist` object.
`traits`	A species-by-traits matrix. Row names should match species (columns of x).
`metric`	Character vector. Metrics to compute: `"fdis"`: Functional Dispersion (mean distance to centroid) `"fric"`: Functional Richness (convex hull volume approximation) `"rao"`: Rao's quadratic entropy (abundance-weighted mean pairwise Euclidean trait distance)
`n_seeds`	Integer. Number of random starting points. Default 50.
`method`	Character. Accumulation method. Default `"knn"`.
`distance`	Character. Site distance method: `"euclidean"` or `"haversine"`.
`parallel`	Logical. Use parallel processing? Default `TRUE`.
`n_cores`	Integer. Number of cores.
`progress`	Logical. Show progress? Default `TRUE`.
`seed`	Integer. Random seed.
`map`	Logical. If `TRUE`, run accumulation from every site as seed and store per-site final values for spatial mapping. Enables `as_sf()` and `plot(type = "map")`. Default `FALSE`.

Details

Functional diversity metrics quantify trait space occupation:

FDis (Functional Dispersion): Abundance-weighted mean distance from the community centroid in trait space. Captures functional divergence.
FRic (Functional Richness): Volume of trait space occupied (convex hull). Requires more species than traits to compute.

Value

An object of class spacc_func containing:

`curves`	Named list of matrices, one per metric (n_seeds x n_sites)
`metric`	Metrics computed
`coords`, `n_seeds`, `n_sites`, `method`	Parameters used

References

Laliberté, E. & Legendre, P. (2010). A distance-based framework for measuring functional diversity from multiple traits. Ecology, 91, 299-305.

Examples


coords <- data.frame(x = runif(50), y = runif(50))
species <- matrix(rpois(50 * 20, 2), nrow = 50)

# Trait matrix (species x traits)
traits <- matrix(rnorm(20 * 3), nrow = 20)
rownames(traits) <- paste0("sp", 1:20)
colnames(species) <- rownames(traits)

func <- spaccFunc(species, coords, traits, metric = c("fdis", "fric"))
plot(func)

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