| BICompare {RPANDA} | R Documentation |
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)