BICompare: Identify modalities in a phylogeny

In hmorlon/PANDA: Phylogenetic ANalyses of DiversificAtion

Identify modalities in a phylogeny

Description

Computes the BIC values for a specified number of modalities in the distance matrix of a phylogenetic tree and that of randomly bifurcating trees; identifies these modalities using k-means clustering.

Usage

BICompare(phylo,t,meth=c("ultrametric"))

Arguments

phylo	an object of type 'phylo' (see ape documentation)
t	the number of modalities to be tested
meth	whether the randomly bifurcating "control" tree should be ultrametric or non-ultrametric

Value

a list with the following components:

BIC_test	BIC values for finding t modalities in the distance matrix of a tree and the lowest five percent of 1000 random ("control") trees
clusters	a vector specifying which nodes in the tree belong to each of t modalities
BSS/TSS	the ratio of between-cluster sum of squares over total sum of squares

Author(s)

E Lewitus

References

Lewitus, E., Morlon, H., Characterizing and comparing phylogenies from their Laplacian spectrum, bioRxiv doi: http://dx.doi.org/10.1101/026476

See Also

plot_BICompare, spectR, JSDtree

Examples

data(Cetacea)

BICompare(Cetacea,5)

hmorlon/PANDA documentation built on Jan. 13, 2025, 5:35 a.m.