Nonparametric method for identifying discordant phylogenetic trees


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Documentation for package ‘kdetrees’ version 0.1.5

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kdetrees-package kdetrees
apicomplexa Apicomplexa gene trees sample data set.
as.data.frame.kdetrees Convert kdetrees object to data.frame
as.matrix.multiPhylo dissimilarity map tree vectorization
bw.nn nearest-neighbor adaptive bandwidth selection
dist.diss Compute pairwise tree distances
estimate estimate densities from kernel matrix
hist.kdetrees Create a histogram of tree density estimates
kdetrees Identify discordant trees in a sample
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.