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kdetrees (version 0.1.3)

Nonparametric method for identifying discordant trees

Description

Given a set of phylogenetic trees on a group of taxa (for example trees based on individual gene sequences), we present a method for identifying a subset of trees which are discordant with the other trees in the set. These discordant trees may arise from either biologically interesting phenomena (horizontal gene transfers, for example) or more mundane sequencing or annotation errors.

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Version

Install

install.packages('kdetrees')

Monthly Downloads

9

Version

0.1.3

License

GPL-2

Maintainer

Ruriko Yoshida

Last Published

August 21st, 2013

Functions in kdetrees (0.1.3)

as.data.frame.kdetrees

Convert kdetrees object to data.frame
estimate

estimate densities from kernel matrix
kdetrees

Identify discordant trees in a sample
as.matrix.multiPhylo

dissimilarity map tree vectorization
dist.diss

Compute pairwise tree distances
hist.kdetrees

Create a histogram of tree density estimates
kdetrees-package

kdetrees
apicomplexa

Apicomplexa gene trees sample data set.
bw.nn

nearest-neighbor adaptive bandwidth selection
kdetrees.complete

Complete kdetrees analysis convenience function
normkern

Generalized Gaussian kernel
plot.kdetrees

Plot the unnormalized density estimates for each tree.
print.kdetrees

Summarize a kdetrees object in human-readable form.