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Rogue  

Identify Rogue Taxa in Sets of Phylogenetic Trees
View on CRAN: Click here


Download and install Rogue package within the R console
Install from CRAN:
install.packages("Rogue")

Install from Github:
library("remotes")
install_github("cran/Rogue")

Install by package version:
library("remotes")
install_version("Rogue", "2.1.6")



Attach the package and use:
library("Rogue")
Maintained by
Martin R. Smith
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2021-07-01
Latest Update: 2023-03-20
Description:
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>.
How to cite:
Martin R. Smith (2021). Rogue: Identify Rogue Taxa in Sets of Phylogenetic Trees. R package version 2.1.6, https://cran.r-project.org/web/packages/Rogue
Previous versions and publish date:
1.0.0 (2021-07-01 09:30), 2.0.0 (2021-09-13 17:30), 2.1.0 (2022-01-13 13:02), 2.1.1 (2022-07-20 15:30), 2.1.2 (2022-08-16 16:10), 2.1.3 (2022-09-26 13:00), 2.1.4 (2023-01-16 15:30), 2.1.5 (2023-03-20 14:20)
Other packages that cited Rogue R package
View Rogue citation profile
Other R packages that Rogue depends, imports, suggests or enhances
Functions, R codes and Examples using the Rogue R package
Some associated functions: GraphGeodesic . Rogue-package . RogueTaxa . TipInstability . TipVolatility . 
Some associated R codes: Rogue-package.R . RogueTaxa.R . SPIC.R . stability.R . utilities.R . zz_RogueNaRok.R . zzz.R .  Full Rogue package functions and examples
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