R Observatory: Metrics for Rogue version 2.2.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

Rogue

2.2.1

Identify Rogue Taxa in Sets of Phylogenetic Trees

2packages depend

15.2Kdownloads / year

74.3%test coverage

13/13checks pass

Overview

About

Maintained by Martin R. SmithFirst published 2021-07-0112 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("Rogue", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("ms609/Rogue")

Development version from ms609/Rogue. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-rogue

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-Rogue

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-Rogue

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 3.2 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.33

74.3%

Coverage · measured lines

100%

Documentation · exports

10

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-25
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-25
9 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 3 earlier snapshots

ERROR2026-04-09
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-26
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 86%
Return-value docs: 100%
References docs: 80%

Downloads

15.2K

CRAN downloads in the past year

Rank #3,635 · ~42/day · ~1.3K/mo

Releases R versions

Daily download trend is not available in this view yet.

65630 days

2.6K90 days

15.2K1 year

Compare downloads with other packages →

Also on419 r2u28 autocran60 c2d4u

Repository

GitHub ↗ ms609/rogue

5Stars

0Forks

10Open issues

1Open PRs

12Releases

281Commits

6Contributors

phylogeneticsconsensus-treer-packagephylogenetic-trees

281 commits · Last activity 2026-06-29 · +25% stars, 30d

Stars over time

2024-12-02 · 32026-08-18 · 5

Repository practices

Upstream repositoryBeta

8 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/ms609/rogue on 2026-08-23.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Research and citation (1)

codemeta.json

Lint, format, editor (2)

lintrRStudio project

Show all practices

Coverage (1)

.covrignore

Git structural (2)

.gitattributesSubmodules

How this is detected·Detection ruleset v1 (2026-07-18)

Development tooling

AI-assisted toolingBeta

Uses AI-assisted development tooling (declared in repo)

Earliest detected marker: copilot on 2025-08-28

copilotclaude

Most recent: claude on 2026-03-20

Evidence

copilot: on 2025-08-28 · evidence PR
claude: on 2026-03-20 · evidence B, D
agents-md: on 2026-03-20 · evidence D

How this is detected·Detection ruleset v2 (updated 2026-07-29)

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (10)

ape cli fastmatchgrDevicesmatrixStats RdpackstatsTreeDist TreeTools (>= 1.9.1.9003)utils

LinkingTo (0)

none

Suggests (5)

knitr PlotTools rmarkdown spelling testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

TreeSearch TreeDist

Code & Tests

People & History

People (2)

Maintainer (1)

Martin R. Smith

Author, Maintainer, Copyright holder

Authors (2)

Martin R. Smith

Author, Maintainer, Copyright holder

Andre J. Aberer

Author, Copyright holder

Copyright holders (2)

Martin R. Smith

Author, Maintainer, Copyright holder

Andre J. Aberer

Author, Copyright holder

Package Timeline

12 releases. Pick two to compare their code metrics. R releases are shown for context.

2.2.1Latest
2026-06-24 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
2.2.0
2026-03-25 · diff ↗
2.1.7
2025-07-01 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
2.1.6
2023-11-29 · diff ↗
R
R 4.3.0 released · 2023-04-21
2.1.5
2023-03-20 · diff ↗
2.1.4
2023-01-16 · diff ↗
2.1.3
2022-09-26 · diff ↗
2.1.2
2022-08-16 · diff ↗
2.1.1
2022-07-20 · diff ↗
R
R 4.2.0 released · 2022-04-22
2.1.0
2022-01-13 · diff ↗
2.0.0
2021-09-13 · diff ↗

Show 2 earlier events

1.0.0
2021-07-01
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-07-01
Total releases: 12 / 5 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.5.0
Download size: 504 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Paleontology Phylogenetics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("Rogue")

Format

Smith, M. R., & Aberer, A. J. (2026). Rogue: Identify Rogue Taxa in Sets of Phylogenetic Trees (Version 2.2.1) [Computer software]. https://doi.org/10.32614/CRAN.package.Rogue

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for Rogue version 2.2.1 [Data set]. HJJB, LLC. Data release v2026-08-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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