R Observatory: Metrics for Rogue version 2.2.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

Rogue

2.2.1Package record

Identify Rogue Taxa in Sets of Phylogenetic Trees

1packages dependsuggested by 1

14.3Kdownloads / year

74.3%test coverage

13/13flavors OK

Overview

About

Maintained by Martin R. SmithCRAN page ↗GitHub ↗Issues ↗

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.

Changes in 2.2.1

Improve performance of TipInstability() (and thence ColByStability(), QuickRogue()) through full C++ processing, removing Rfast dependency.

From NEWS.md in the release

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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 3.1 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-25
ERROR9 OK, 2 NOTE, 1 ERROR2026-04-25
NOTE12 OK, 2 NOTE2026-04-10

Show 3 earlier changesHide 3 earlier changes

ERROR11 OK, 2 NOTE, 1 ERROR2026-04-09
NOTE12 OK, 2 NOTE2026-03-26
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.2.1

README· In the repository, left out of the releaseVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 2.2.1Citation fileYes · cites a publication

Help pages: 5 (2 internal)includes a package overview page
Examples that run: 100%4 run in a plain check
Exported functions with examples: 100%
Documented parameters: 86%
Return-value docs: 100%
Help pages citing references: 80% with a bibliography file

Vignettes (1)

Detecting rogue taxa in Bayesian posterior tree sets HTML

How these are measured

Downloads

14.3K

CRAN downloads in the past year

Rank #3,696 · ~39/day · ~1.2K/mo

Releases R versions

Daily download trend is not available in this view yet.

93630 days

2.7K90 days

14.3K1 year

Compare downloads with other packages →

Also on439 r2u3 autocran120 c2d4u

How downloads are counted

Repository

ms609/rogue ↗Account: ms609

5Stars

0Forks

10Open issues

1Open PRs

12Releases

289Commits

7Commit identities

phylogeneticsconsensus-treer-packagephylogenetic-trees

289 commits · Last activity 2026-10-05 · 0% stars, 30d · Default branch at 2.2.1.9000, ahead of CRAN 2.2.1 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): 90%
Median days to close, 50 most recently updated closed issues: 1
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2024-12-02 · 32026-08-18 · 5

How these are measured

PracticesBeta

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

Checks run against github.com/ms609/rogue on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (2)

Code of conductContributing guide

Docs source (2)

pkgdown

GitHub Pages site last deployed 2026-09-25

Coverage (2)

Coverage reporting.covrignore

Show all practicesHide 4 practices

CRAN release process (1)

cran-comments.md

Research and citation (1)

codemeta.json

Lint, format, editor (2)

lintrRStudio project

Git structural (2)

.gitattributesSubmodules

How this is detected·Detection ruleset v4 (2026-10-20)

AI coding toolsBeta

This repository shows signs of AI coding tools.

GitHub Copilotfirst seen 2025-08-28
Pull request: opened by its own account
Claude Codefirst seen 2026-03-20
Seen in the repository: .claude
Named in .Rbuildignore: .claude
Pull request it wrote: opened by a project member
Commits: at least 6 crediting it in the message

Shared conventions any agent may read, so they name no particular tool.

Seen in the repository: AGENTS.md

Models named in its commits

Claude Opus 5.55 commits · Sep 2026
Claude Opus 4.81 commit · Jun 2026

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing Rogue adds 41 packages (27 with compiled code, 34 MB of source tarballs). Heaviest: bslib 5.6 MB, promises 3.1 MB, sass 2.9 MB.

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

1direct

0indirect

Imports 1

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

TreeSearch

Suggests, most downloaded first

TreeDist

How these are counted

Code & Tests

People & History

People (2)

Martin R. Smith

Andre J. Aberer

Author, Copyright holder

RogueNaRok

Releases (12)

Pick two releases to compare their code metrics.

2.2.1Latest
record
2026-06-24 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
2.2.0
record
2026-03-25 · diff ↗
2.1.7
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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
record
2023-11-29 · diff ↗
R
R 4.3.0 released · 2023-04-21
2.1.5
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2023-03-20 · diff ↗
2.1.4
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2023-01-16 · diff ↗
2.1.3
record
2022-09-26 · diff ↗
2.1.2
record
2022-08-16 · diff ↗
2.1.1
record
2022-07-20 · diff ↗
R
R 4.2.0 released · 2022-04-22
2.1.0
record
2022-01-13 · diff ↗ ·
added 1 export
GraphGeodesic
2.0.0
record
2021-09-13 · diff ↗ ·
added 5 exports
ColByStability, Cophenetic, QuickRogue, TipInstability, TipVolatility

Show 2 earlier eventsHide 2 earlier events

1.0.0
record
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

Appears in task views

Paleontology Phylogenetics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("Rogue")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

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 v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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