kdetrees: Nonparametric method for identifying discordant phylogenetic trees

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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.

Author
Grady Weyenberg and Ruriko Yoshida
Date of publication
2014-05-30 01:09:11
Maintainer
Grady Weyenberg <grady.weyenberg@uky.edu>
License
GPL-2
Version
0.1.5
URLs

View on CRAN

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.

Files in this package

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