MonoPhy: Allows to Explore Monophyly (or Lack of it) of Taxonomic Groups in a Phylogeny
Version 1.2

Requires rooted resolved phylogeny as input and creates a table of genera, their monophyly-status, which taxa cause problems in monophyly etc. Different information can be extracted from the output and a plot function allows visualization of the results in a number of ways.

Browse man pages Browse package API and functions Browse package files

AuthorOrlando Schwery
Date of publication2016-07-26 17:48:01
MaintainerOrlando Schwery <oschwery@vols.utk.edu>
LicenseGPL-3
Version1.2
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("MonoPhy")

Man pages

AssessMonophyly: Assesses monophyly (or lack of it) of taxonomic groups in a...
GetAncNodes: Get MRCA nodes of taxonomic groups from 'AssessMonophyly'...
GetIntruderTaxa: Get taxa or tips which are intruders or outliers to a taxon...
GetResultMonophyly: Get main result table from 'AssessMonophyly' output
MonophylyData: Example dataset for the package MonoPhy.
MonoPhy-package: Allows to explore monophyly (or lack of it) of taxonomic...
PlotMonophyly: Plot output of AssessMonophyly

Functions

AssessMonophyly Man page Source code
Ericacsubfams Man page
Ericactree Man page
Ericactribes Man page
GetAncNodes Man page Source code
GetIntruderTaxa Man page Source code
GetIntruderTips Man page Source code
GetOutlierTaxa Man page Source code
GetOutlierTips Man page Source code
GetResultMonophyly Man page Source code
GetSummaryMonophyly Man page Source code
MonoPhy Man page
MonoPhy-package Man page
MonophylyData Man page
PlotMonophyly Man page Source code

Files

inst
inst/CITATION
inst/doc
inst/doc/MonoPhyVignette.Rmd
inst/doc/MonoPhyVignette.html
inst/doc/MonoPhyVignette.R
tests
tests/testthat.R
tests/testthat
tests/testthat/test_solutions.R
NAMESPACE
data
data/Ericactree.rda
data/Ericacsubfams.rda
data/Ericactribes.rda
R
R/GetSummaryMonophyly.R
R/PlotMonophyly.R
R/GetIntruderTaxa.R
R/GetOutlierTips.R
R/GetAncNodes.R
R/AssessMonophyly.R
R/GetOutlierTaxa.R
R/GetIntruderTips.R
R/GetResultMonophyly.R
vignettes
vignettes/MonoPhyVignette.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/PlotMonophyly.Rd
man/MonoPhy-package.Rd
man/AssessMonophyly.Rd
man/GetResultMonophyly.Rd
man/MonophylyData.Rd
man/GetIntruderTaxa.Rd
man/GetAncNodes.Rd
MonoPhy documentation built on May 20, 2017, 4:21 a.m.