Compute phylogenetic clusters by cutting tree at branches with large changes in coalescent odds

Compute phylogenetic clusters by cutting tree at branches with large changes in coalescent odds

Usage

computeclusters(f, clth = NULL, rescale = TRUE, includeinternals = TRUE)

Arguments

f

A model fit from `codls`

clth

Numeric threshold change in coalescent log odds. If NULL, will guess a good threshold based on the CH index

rescale

if TRUE (default), coalescent log odds are rescaled (mean zero, unit variance) prior to applying thresholds

includeinternals

if TRUE (default), internal nodes are also included in cluster output

Value

A data frame with cluster asignment for each tip