This package is considered a duplicate. The official version of this package is found at:https://oschwery.r-universe.dev/MonoPhy

Package: MonoPhy 1.3.2

Orlando Schwery

MonoPhy: Explore Monophyly of Taxonomic Groups in a Phylogeny

Requires rooted 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. "MonoPhy: a simple R package to find and visualize monophyly issues." Schwery, O. & O'Meara, B.C. (2016) <doi:10.7717/peerj-cs.56>.

Authors:Orlando Schwery [aut, cre], Brian C. O'Meara [aut, ctb], Peter Cowman [ctb]

MonoPhy_1.3.2.tar.gz
MonoPhy_1.3.2.zip(r-4.7)MonoPhy_1.3.2.zip(r-4.6)MonoPhy_1.3.2.zip(r-4.5)
MonoPhy_1.3.2.tgz(r-4.6-any)MonoPhy_1.3.2.tgz(r-4.5-any)
MonoPhy_1.3.2.tar.gz(r-4.7-any)MonoPhy_1.3.2.tar.gz(r-4.6-any)
MonoPhy_1.3.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
MonoPhy/json (API)

# Install 'MonoPhy' in R:

install.packages('MonoPhy', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/oschwery/monophy/issues

Datasets:

Ericacsubfams - Example dataset for the package MonoPhy.
Ericactree - Example dataset for the package MonoPhy.
Ericactribes - Example dataset for the package MonoPhy.

On CRAN:

4.99 score 7 stars 28 scripts 138 downloads 1 mentions 10 exports 45 dependencies

Last updated from:ccd56b2512. Checks:9 OK. Indexed: no.

Target	Result	Time
linux-devel-x86_64	OK	164
source / vignettes	OK	257
linux-release-x86_64	OK	187
macos-release-arm64	OK	100
macos-oldrel-arm64	OK	126
windows-devel	OK	191
windows-release	OK	118
windows-oldrel	OK	106
wasm-release	OK	138

Exports:AssessMonophyly CollapseMonophyletics GetAncNodes GetIntruderTaxa GetIntruderTips GetOutlierTaxa GetOutlierTips GetResultMonophyly GetSummaryMonophyly PlotMonophyly

Dependencies:ape backports checkmate cli clusterGeneration coda codetools combinat cpp11 DEoptim digest doParallel expm foreach future future.apply generics globals glue igraph iterators lattice lifecycle listenv magrittr maps MASS Matrix mnormt nlme numDeriv optimParallel osqp parallelly phangorn phytools pkgconfig progressr RColorBrewer Rcpp RcppArmadillo rlang S7 scatterplot3d vctrs

MonoPhy Tutorial

Orlando Schwery

Rendered fromMonoPhyVignette.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2024-05-05
Started: 2015-09-05

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Explore Monophyly of Taxonomic Groups in a Phylogeny.	MonoPhy-package MonoPhy
Assesses monophyly (or lack of it) of taxonomic groups in a phylogeny.	AssessMonophyly
Get tree with collapsed monophyletic groups	CollapseMonophyletics
Get MRCA nodes of taxonomic groups from 'AssessMonophyly' output	GetAncNodes
Get taxa or tips which are intruders or outliers to a taxon from AssessMonophyly	GetIntruderTaxa GetIntruderTips GetOutlierTaxa GetOutlierTips
Get main result table from 'AssessMonophyly' output	GetResultMonophyly GetSummaryMonophyly
Example dataset for the package MonoPhy.	Ericacsubfams Ericactree Ericactribes MonophylyData
Plot output of AssessMonophyly	PlotMonophyly