kdetrees: Nonparametric method for identifying discordant phylogenetic trees

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.

AuthorGrady Weyenberg and Ruriko Yoshida
Date of publication2014-05-30 01:09:11
MaintainerGrady Weyenberg <grady.weyenberg@uky.edu>
LicenseGPL-2
Version0.1.5
http://github.com/grady/kdetrees

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Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.