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https://github.com/ms609/rogue

Identify rogue taxa in phylogenetic trees within R
https://github.com/ms609/rogue

consensus-tree phylogenetic-trees phylogenetics r-package

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Identify rogue taxa in phylogenetic trees within R

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README 

        
# Rogue



[![Codecov test coverage](https://codecov.io/gh/ms609/Rogue/branch/main/graph/badge.svg)](https://codecov.io/gh/ms609/Rogue?branch=main)

[![CRAN Status Badge](http://www.r-pkg.org/badges/version/Rogue)](https://cran.r-project.org/package=Rogue)

[![CRAN Downloads](http://cranlogs.r-pkg.org/badges/Rogue)](https://cran.r-project.org/package=Rogue)

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[![Project Status: Inactive – The project has reached a stable, usable state but is no longer being actively developed; support/maintenance will be provided as time allows.](http://www.repostatus.org/badges/latest/inactive.svg)](http://www.repostatus.org/#inactive)



"Rogue" implements approaches to identify rogue taxa in phylogenetic analysis.

Rogues are wildcard leaves whose uncertain position reduces the resolution of

consensus trees. Consensus trees that omit rogue taxa can be more informative.



"Rogue" allows the user to select a concept of "information" by which the

quality of consensus trees should be evaluated, and a heuristic approach

by which rogue taxa should be identified.



Rogue detection using the phylogenetic and clustering information content

measures (Smith, 2022) is implemented using a quick heuristic that drops

the least "stable" leaves one at a time,

using an _ad hoc_ definition of stability (Smith, 2022);

and by a more exhaustive (and time-consuming) approach that considers dropping

all possible sets of up to _n_ leaves (Aberer _et al._ 2013).



The latter heuristic is implemented for the relative bipartition 

"information" content and Pattengale's criterion

_via_ [RogueNaRok](https://rnr.h-its.org/about) (Aberer _et al._ 2013).



[![Detecting rogue taxa with information theory](man/figures/Rogue_talk.png)](https://durham.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=86c175f1-6e20-499c-bcf2-adeb0137a4a7)



# Installation



Install and load the stable version from CRAN as normal:

```r

install.packages("Rogue")

library("Rogue")

```



Alternatively, install the development version from GitHub with 

```r

devtools::install_github("ms609/Rogue", args = "--recursive")

```

(Requires [git](https://git-scm.com/) to be installed and added to

your PATH system environment variable; you may also require the "curl" R package.)



# Citing 'Rogue'



If you find this package useful in your work, please consider citing

Smith (2021).



To cite the underlying methods, please cite Aberer _et al._ (2013) ('RogueNaRok')

or Smith (2022), as appropriate.



# References



A.J. Aberer, D. Krompass, A. Stamatakis (2013): Pruning rogue taxa improves

  phylogenetic accuracy: an efficient algorithm and webservice. _Systematic Biology_ 62(1):

  162-166, [doi:10.1093/sysbio/sys078](https://dx.doi.org/10.1093/sysbio/sys078).



M.R. Smith (2021): Rogue: Identify rogue taxa in sets of phylogenetic trees.

  _Zenodo_,

  [doi:10.5281/zenodo.5037327](https://dx.doi.org/10.5281/zenodo.5037327).



M.R. Smith (2022): Using information theory to detect rogue taxa and improve

  consensus trees. _Systematic Biology_ 71(5): 986–1008,

  [doi:10.1093/sysbio/syab099](https://dx.doi.org/10.1093/sysbio/syab099)