kdetrees: Nonparametric method for identifying discordant phylogenetic trees
Version 0.1.5

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.

Browse man pages Browse package API and functions Browse package files

AuthorGrady Weyenberg and Ruriko Yoshida
Date of publication2014-05-30 01:09:11
MaintainerGrady Weyenberg <grady.weyenberg@uky.edu>
LicenseGPL-2
Version0.1.5
URL http://github.com/grady/kdetrees
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("kdetrees")

Man pages

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
kdetrees-package: kdetrees
normkern: Generalized Gaussian kernel
plot.kdetrees: Plot the unnormalized density estimates for each tree.
print.kdetrees: Summarize a kdetrees object in human-readable form.

Functions

apicomplexa Man page
as.data.frame.kdetrees Man page Source code
as.matrix.multiPhylo Man page Source code
bw.nn Man page Source code
dist.diss Man page Source code
estimate Man page Source code
hist.kdetrees Man page Source code
kdetrees Man page Source code
kdetrees-package Man page
kdetrees.complete Man page Source code
normkern Man page Source code
plot.kdetrees Man page Source code
print.kdetrees Man page Source code

Files

inst
inst/CITATION
inst/doc
inst/doc/simulation.Rnw
inst/doc/simulation.pdf
inst/doc/kdetrees.pdf
inst/doc/simulation.R
inst/doc/kdetrees.R
inst/doc/kdetrees.Rnw
NAMESPACE
data
data/apicomplexa.rda
R
R/kde.R
R/kernels.R
R/util.R
R/bw.R
R/kdetrees-package.R
R/dist.diss.R
vignettes
vignettes/simulation.Rnw
vignettes/img
vignettes/img/roc.pdf
vignettes/img/tpr.pdf
vignettes/img/rocmix.pdf
vignettes/img/tprBW.pdf
vignettes/img/bench.pdf
vignettes/kdetrees.Rnw
vignettes/sim
vignettes/sim/results.Rda
vignettes/sim/bench.Rda
vignettes/sim/sims.rda
vignettes/sim/tprmix1.Rda
vignettes/sim/deftprmix.Rda
vignettes/sim/mix2.Rda
vignettes/sim/result.Rda
vignettes/sim/species.nex
vignettes/sim/species1k.nex
vignettes/sim/coalescent.nex
vignettes/sim/my-pmcoa.R
vignettes/sim/rocresult.Rda
vignettes/sim/treesim.py
vignettes/sim/rocsim.Rda
vignettes/sim/genetrees.tre
vignettes/sim/tprmix.Rda
vignettes/sim/species5.nex
vignettes/sim/rocmix.Rda
vignettes/sim/species2.nex
vignettes/sim/set8-outliers.pdf
vignettes/sim/set8-all.pdf
vignettes/sim/tpr.Rda
vignettes/references.bib
MD5
build
build/vignette.rds
DESCRIPTION
ChangeLog
man
man/apicomplexa.Rd
man/print.kdetrees.Rd
man/hist.kdetrees.Rd
man/kdetrees-package.Rd
man/as.matrix.multiPhylo.Rd
man/bw.nn.Rd
man/plot.kdetrees.Rd
man/normkern.Rd
man/kdetrees.Rd
man/kdetrees.complete.Rd
man/estimate.Rd
man/as.data.frame.kdetrees.Rd
man/dist.diss.Rd
kdetrees documentation built on May 19, 2017, 10:22 a.m.