CRAN/E | Rogue

Rogue

Identify Rogue Taxa in Sets of Phylogenetic Trees

Installation

About

Rogue ("wildcard") taxa are leaves with uncertain phylogenetic position. Their position may vary from tree to tree under inference methods that yield a tree set (e.g. bootstrapping, Bayesian tree searches, maximum parsimony). The presence of rogue taxa in a tree set can potentially remove all information from a consensus tree. The information content of a consensus tree - a function of its resolution and branch support values - can often be increased by removing rogue taxa. 'Rogue' provides an explicitly information-theoretic approach to rogue detection (Smith 2022) doi:10.1093/sysbio/syab099, and an interface to 'RogueNaRok' (Aberer et al. 2013) doi:10.1093/sysbio/sys078.

Citation Rogue citation info
github.com/ms609/Rogue/
github.com/aberer/RogueNaRok/
github.com/ms609/RogueNaRok/
System requirements C99
Bug report File report

Key Metrics

Version 2.1.6
R ≥ 3.5.0
Published 2023-11-29 201 days ago
Needs compilation? yes
License GPL (≥ 3)
CRAN checks Rogue results
Language en-GB

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Maintainer

Maintainer

Martin R. Smith

Authors

Martin R. Smith

aut / cre / cph

Andre J. Aberer

aut / cph

Material

NEWS
Reference manual
Package source

In Views

Phylogenetics

Vignettes

Detecting rogue taxa in Bayesian posterior tree sets

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

Rogue archive

Depends

R ≥ 3.5.0

Imports

ape ≥ 5.0
cli ≥ 3.0
fastmatch
grDevices
matrixStats
Rdpack ≥ 0.7
Rfast
stats
TreeDist
> 2.2.0
TreeTools ≥ 1.9.1.9003
utils

Suggests

knitr
PlotTools
rmarkdown
spelling
testthat

Reverse Imports

TreeSearch

Reverse Suggests

TreeDist