Package: MonoPhy 1.3.2

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-4.5)MonoPhy_1.3.2.zip(r-4.4)MonoPhy_1.3.2.zip(r-4.3)
MonoPhy_1.3.2.tgz(r-4.4-any)MonoPhy_1.3.2.tgz(r-4.3-any)
MonoPhy_1.3.2.tar.gz(r-4.5-noble)MonoPhy_1.3.2.tar.gz(r-4.4-noble)
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MonoPhy.pdf |MonoPhy.html✨
MonoPhy/json (API)

# Install 'MonoPhy' in R:

install.packages('MonoPhy', repos = c('https://oschwery.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:

5.16 score 6 stars 24 scripts 330 downloads 1 mentions 10 exports 36 dependencies

Last updated 1 months agofrom:ccd56b2512. Checks:OK: 3 NOTE: 4. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 15 2024
R-4.5-win	OK	Nov 15 2024
R-4.5-linux	OK	Nov 15 2024
R-4.4-win	NOTE	Nov 15 2024
R-4.4-mac	NOTE	Nov 15 2024
R-4.3-win	NOTE	Nov 15 2024
R-4.3-mac	NOTE	Nov 15 2024

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

Dependencies:ape cli clusterGeneration coda codetools combinat cpp11 DEoptim digest doParallel expm fastmatch foreach generics glue igraph iterators lattice lifecycle magrittr maps MASS Matrix mnormt nlme numDeriv optimParallel phangorn phytools pkgconfig quadprog RColorBrewer Rcpp rlang scatterplot3d vctrs

MonoPhy Tutorial

Orlando Schwery

Rendered fromMonoPhyVignette.Rmdusingknitr::rmarkdownon Nov 15 2024.

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