Top driving species in phyloregions — indicators • phyloregion

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

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.

A list of top indicator species and their indicator values

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