Package: MonoPhy 1.3.1

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_1.3.1.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

Datasets:

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

On CRAN:

10 exports 6 stars 1.51 score 134 dependencies 1 mentions 21 scripts 924 downloads

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:AssessMonophyly CollapseMonophyletics GetAncNodes GetIntruderTaxa GetIntruderTips GetOutlierTaxa GetOutlierTips GetResultMonophyly GetSummaryMonophyly PlotMonophyly

Dependencies:ape askpass assertthat backports base64enc bit bit64 bold bslib cachem checkmate cli clipr cluster clusterGeneration coda codetools colorspace combinat cpp11 crayon crul curl data.table DEoptim digest doParallel dplyr evaluate expm fansi farver fastmap fastmatch fontawesome foreach foreign Formula fs generics ggplot2 ggseqlogo glue gridExtra gtable highr Hmisc hms htmlTable htmltools htmlwidgets httpcode httr igraph isoband iterators jquerylib jsonlite knitr labeling lattice lazyeval lifecycle magrittr maps MASS Matrix memoise mgcv mime mnormt munsell natserv nlme nnet numDeriv openssl optimParallel pbapply phangorn phytools pillar pkgconfig plyr prettyunits progress purrr quadprog R6 rappdirs ratelimitr RColorBrewer Rcpp readr rentrez rex ritis rlang rmarkdown rncl rotl rpart rredlist rstudioapi sass scales scatterplot3d solrium stringi stringr sys taxize tibble tidyselect tinytex triebeard tzdb urltools utf8 vctrs viridis viridisLite vroom WikidataQueryServiceR WikidataR WikipediR wikitaxa withr worrms xfun XML xml2 yaml zoo

MonoPhy Tutorial

Orlando Schwery

Rendered fromMonoPhyVignette.Rmdusingknitr::rmarkdownon Sep 02 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