Learn R Programming

kdetrees (version 0.1.5)

Nonparametric method for identifying discordant phylogenetic trees

Description

A non-parametric method for identifying potential outlying observations in a collection of phylogenetic trees based on the methods of Owen and Provan (2011). Such discordant trees may indicate problems with sequence annotation or tree reconstruction, or they may represent interesting biological phenomena, such as horizontal gene transfers.

Copy Link

Version

Install

install.packages('kdetrees')

Monthly Downloads

9

Version

0.1.5

License

GPL-2

Issues

Pull Requests

Stars

Forks

Maintainer

Grady Weyenberg

Last Published

May 29th, 2014

Functions in kdetrees (0.1.5)

apicomplexa

Apicomplexa gene trees sample data set.
plot.kdetrees

Plot the unnormalized density estimates for each tree.
bw.nn

nearest-neighbor adaptive bandwidth selection
estimate

estimate densities from kernel matrix
hist.kdetrees

Create a histogram of tree density estimates
kdetrees

Identify discordant trees in a sample
as.data.frame.kdetrees

Convert kdetrees object to data.frame
dist.diss

Compute pairwise tree distances
print.kdetrees

Summarize a kdetrees object in human-readable form.
as.matrix.multiPhylo

dissimilarity map tree vectorization
kdetrees-package

kdetrees
normkern

Generalized Gaussian kernel
kdetrees.complete

Complete kdetrees analysis convenience function