indicators: Top driving species in phyloregions

In phyloregion: Biogeographic Regionalization and Macroecology

Top driving species in phyloregions

Description

This function applies a KL-divergence approach to a list of indicator species in phyloregions.

Usage

indicators(
  theta,
  top_indicators = 5,
  method = c("poisson", "bernoulli"),
  options = c("min", "max"),
  shared = FALSE
)

Arguments

theta	A matrix or data.frame of cluster probability distributions from a topics modeling.
top_indicators	Integer to obtain the top driving species in clusters.
method	The model assumption for KL divergence measurement. Available choices are "poisson" (default) and "bernoulli".
options	Option "min" selects species that maximize the minimum KL divergence of a phyloregion vs all other phyloregions. Option "max" selects species that maximize the maximum KL divergence of a phyloregion against all other phyloregions.
shared	Logical if TRUE, lists top species driving patterns in more than one phyloregion.

Value

A list of top indicator species and their indicator values

Examples

data(africa)
indsp <- indicators(africa$theta, top_indicators = 5,
                    options = "max", method = "poisson")

phyloregion documentation built on Aug. 15, 2023, 9:07 a.m.