kernel.arrangement: Functional arrangement of kernel density hypervolumes.

In BAT: Biodiversity Assessment Tools

Functional arrangement of kernel density hypervolumes.

Description

Functional arrangement of a community, measuring the distribution of species within the total functional space at multiple spatial scales. This is a specific function to be used with an Hypervolume object, preferably, from kernel.build function.

Usage

kernel.arrangement(
  comm,
  stat = "PNCP",
  distances = seq(0, 1, 0.01),
  type = "SES",
  alpha = 0.05,
  runs = 99,
  plot = TRUE
)

Arguments

comm	A 'Hypervolume' object, built using function kernel.build.
stat	statistic to be calculated. One of c("PNCP", "NNCP"), meaning "cumulative proportion of pairwise neighbors" and "cumulative proportion of nearest neighbors", respectively.
distances	vector of distances to be considered in calculations
type	Envelope type for testing significance. One of c("ecdf", "norm", "SES"), meaning "empirical cumulative distribution", "normalized envelope" (between 0-1, 0.5 indicate randomness, more than 0.5 - clustered; less than 0.5 - inhibition), and "standardized effect size" respectively.
alpha	alpha value to consider in significance testing (p-value).
runs	number of simulations for significance testing
plot	whether to plot the results

Details

This function measures the functional arrangement (Carvalho & Cardoso, 2025) of a n-dimensional hypervolume, namely the distribution of species within the total trait space at multiple spatial scales.

Value

A list with observed PNCP or NNCP values, a matrix of simulated values at r distances (r x sim), and standard effect size.

References

Carvalho, J.C. & Cardoso, P. (2025) Quantifying species distribution within the functional space.

Examples

## Not run: 
comm = c(100,3,0,5,3)
names(comm) = c("SpA", "SpB", "SpC", "SpD", "SpE")

trait = data.frame(body = c(1,2,3,4,2), beak = c(1,5,4,1,2))
rownames(trait) = names(comm)

hv = kernel.build(comm, trait, method.hv = "svm", svm.nu = 0.01, svm.gamma = 0.25)
kernel.arrangement(hv)

## End(Not run)

BAT documentation built on Aug. 8, 2025, 6:35 p.m.