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

# Install 'MonoPhy' in R:
install.packages('MonoPhy', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.62 score 21 scripts 343 downloads 1 mentions 10 exports 36 dependencies

Last updated 6 days agofrom:fef2986358. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKOct 18 2024
R-4.5-linuxOKOct 18 2024

Exports:AssessMonophylyCollapseMonophyleticsGetAncNodesGetIntruderTaxaGetIntruderTipsGetOutlierTaxaGetOutlierTipsGetResultMonophylyGetSummaryMonophylyPlotMonophyly

Dependencies:apecliclusterGenerationcodacodetoolscombinatcpp11DEoptimdigestdoParallelexpmfastmatchforeachgenericsglueigraphiteratorslatticelifecyclemagrittrmapsMASSMatrixmnormtnlmenumDerivoptimParallelphangornphytoolspkgconfigquadprogRColorBrewerRcpprlangscatterplot3dvctrs

MonoPhy Tutorial

Orlando Schwery

Rendered fromMonoPhyVignette.Rmdusingknitr::rmarkdownon Oct 18 2024.

Last update: 2024-05-06
Started: 2015-10-19