Package: MonoPhy 1.3.1
![](https://github.com/oschwery/MonoPhy/raw/HEAD/man/figures/logo.png)
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:
MonoPhy_1.3.1.tar.gz
MonoPhy_1.3.1.zip(r-4.5)MonoPhy_1.3.1.zip(r-4.4)MonoPhy_1.3.1.zip(r-4.3)
MonoPhy_1.3.1.tgz(r-4.4-any)MonoPhy_1.3.1.tgz(r-4.3-any)
MonoPhy_1.3.1.tar.gz(r-4.5-noble)MonoPhy_1.3.1.tar.gz(r-4.4-noble)
MonoPhy_1.3.1.tgz(r-4.4-emscripten)MonoPhy_1.3.1.tgz(r-4.3-emscripten)
MonoPhy.pdf |MonoPhy.html✨
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
- Ericacsubfams - Example dataset for the package MonoPhy.
- Ericactree - Example dataset for the package MonoPhy.
- Ericactribes - Example dataset for the package MonoPhy.
Last updated 4 months agofrom:993154f3dd. Checks:OK: 7. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Sep 02 2024 |
R-4.5-win | OK | Aug 03 2024 |
R-4.5-linux | OK | Sep 02 2024 |
R-4.4-win | OK | Aug 03 2024 |
R-4.4-mac | OK | Aug 03 2024 |
R-4.3-win | OK | Aug 03 2024 |
R-4.3-mac | OK | Aug 03 2024 |
Exports:AssessMonophylyCollapseMonophyleticsGetAncNodesGetIntruderTaxaGetIntruderTipsGetOutlierTaxaGetOutlierTipsGetResultMonophylyGetSummaryMonophylyPlotMonophyly
Dependencies:apeaskpassassertthatbackportsbase64encbitbit64boldbslibcachemcheckmateclicliprclusterclusterGenerationcodacodetoolscolorspacecombinatcpp11crayoncrulcurldata.tableDEoptimdigestdoParalleldplyrevaluateexpmfansifarverfastmapfastmatchfontawesomeforeachforeignFormulafsgenericsggplot2ggseqlogogluegridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttpcodehttrigraphisobanditeratorsjquerylibjsonliteknitrlabelinglatticelazyevallifecyclemagrittrmapsMASSMatrixmemoisemgcvmimemnormtmunsellnatservnlmennetnumDerivopenssloptimParallelpbapplyphangornphytoolspillarpkgconfigplyrprettyunitsprogresspurrrquadprogR6rappdirsratelimitrRColorBrewerRcppreadrrentrezrexritisrlangrmarkdownrnclrotlrpartrredlistrstudioapisassscalesscatterplot3dsolriumstringistringrsystaxizetibbletidyselecttinytextriebeardtzdburltoolsutf8vctrsviridisviridisLitevroomWikidataQueryServiceRWikidataRWikipediRwikitaxawithrworrmsxfunXMLxml2yamlzoo
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 |