Man pages for grady/kdetrees
Nonparametric method for identifying discordant phylogenetic trees

adjustClassifierParameterAdjust Classification Tuning Parameter for fitted kdetrees...
apicomplexaApicomplexa gene trees sample data set.
as.data.frame.kdetreesConvert kdetrees object to data.frame
as.matrix.multiPhylodissimilarity map tree vectorization
bhv.constsFind BHV constant lower bound
bhv.orthant.lbLower orthant bound for tree t with bw h.
bw.nnnearest-neighbor adaptive bandwidth selection
cutoffFind cutoff value based on IQR
dG.expPolyPfaffian matrix for Exponential-polynomial distribution
dist.dissCompute pairwise tree distances
estimateestimate densities from kernel matrix
GpartialEvaluate
hgm.expPolyNormalizing constant for Exponential-Polynomial distribution
hist.kdetreesCreate a histogram of tree density estimates
internal.blensExtract vector of internal branch lengths
kdetreesIdentify discordant trees in a sample
kdetrees.completeComplete kdetrees analysis convenience function
kdetrees-packagekdetrees
load.treesRead Newick trees from a set of files.
make.thetaCreate a theta vector from a phylo object
normkernGeneralized Gaussian kernel
NorthantCount semi-labeled rooted trees on n taxa
plot.kdetreesPlot the unnormalized density estimates for each tree.
print.kdetreesSummarize a kdetrees object in human-readable form.
sort.kdetreesReorder objects in a kdetrees object based on current density...
which.outliersFind outlier indices based on Tukey's IQR method.
grady/kdetrees documentation built on Jan. 28, 2018, 10:33 a.m.