indicators {phyloregion}

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")