RPANDA (version 1.9)

JSDt_cluster: Clustering on the Jensen-Shannon distance between phylogenetic trait data

Description

Computes the Jensen-Shannon distance metric between spectral density profiles of phylogenetic trait data and clusters on those distances.

Usage

JSDt_cluster(phylo,mat,plot=F)

Arguments

phylo

an object of type 'phylo' (see ape documentation)

mat

a matrix of trait data with one trait per column and rows aligned to phylo tips

plot

plot hierarchical cluster in a new window

Value

plots a heatmap and hierarchical cluster with bootstrap support (>0.9) and outputs results of the k-medoids clustering on the optimal number of clusters in the form of a list with the following components

clusters

a list with the following components: size, max_diss, av_diss, diameter, and separation

J-S matrix

a matrix providing the Jensen-Shannon distance values between pairs of phylogenetic trait data

cluster assignment

a table that lists for each trait its cluster assignment and silhouete width

References

Lewitus, E., Morlon, H. (2019) Characterizing and comparing phylogenetic trait data from their normalized Laplacian spectrum, bioRxiv doi: https://doi.org/10.1101/654087

See Also

spectR_t

Examples

# NOT RUN {
data(Cetacea)
n<-length(Cetacea$tip.label)
mat<-replicate(20, rnorm(n)) 
colnames(mat)<-1:dim(mat)[2]
JSDt_cluster(Cetacea,mat)
# }