R Observatory: Metrics for Rclade version 1.1.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

Rclade

1.1.5Package record

Automated Deep-Time Phylogenetic Tree Collapsing and Visualization

0packages depend

466downloads / year

–test coverage

12/13flavors OK

Overview

About

Maintained by Zeng ZichaoCRAN page ↗GitHub ↗Website ↗Issues ↗

Provides a single-function pipeline for automated collapsing and visualization of large phylogenetic trees with geological timescales. Automatically parses taxonomic labels from multiple formats (GTDB, Silva, NCBI, embedded, custom), identifies Most Recent Common Ancestors (MRCAs), assigns color-blind-safe palettes, executes batch collapsing with automatic nesting-aware ordering, integrates 'deeptime' geologic time scales with adaptive time breaks and unit switching, and manages smart legend layout. Supports special ancestral node identifiers (LUCA, LACA, LBCA) for highlighting key nodes in the tree of life. Provides external taxonomy file support for trees with incomplete or missing taxonomic labels. Features real-time logging with timestamps, step tracking, and multiple log levels. Includes comprehensive input validation for tree and sequence file formats. Reduces a 60-line manual workflow to a single function call while preserving full compatibility with the 'ggtree'/'deeptime' ecosystem. The visualization pipeline builds on 'ggtree' Yu et al. (2017) doi:10.1111/2041-210X.12628, 'deeptime' Gearty (2025) doi:10.1080/20964471.2025.2537516, and 'ape' Paradis and Schliep (2019) doi:10.1093/bioinformatics/bty633.

Changes in 1.1.5

CRAN resubmission. Addresses the three issues raised by the CRAN

reviewer for 1.1.4:

**Single quotes in Description**: Single quotes are now reserved for R package names only ('ggtree', 'deeptime', 'ape'). Quotes were removed around acronyms and database names (GTDB, Silva, NCBI, MRCAs, LUCA, LACA, LBCA), and "geoscales" is now described in words as geologic time scales because it is not a package name.
**Reference format in Description**: The bibliographic references now use the authors (year) <doi:...> form with the year in parentheses: Yu et al. (2017) <doi:10.1111/2041-210X.12628>, Gearty (2025) <doi:10.1080/20964471.2025.2537516>, and Paradis and Schliep (2019) <doi:10.1093/bioinformatics/bty633>.

Show all changes in 1.1.5Hide the rest of the changes in 1.1.5

**Console output in R/selftest.R**: run_rclade_selftest() and its internal helpers now report progress with message() (stderr) instead of cat(), so all self-test output can be suppressed with suppressMessages(). A new verbose argument (default TRUE) allows fully silent runs. The returned exit code (0/1) and the outcome of every individual check are unchanged.

No changes to package behaviour, exports, or test outcomes relative

to 1.1.4.

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("Rclade", 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("zengzichao/Rclade")

Development version from zengzichao/Rclade. 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-rclade

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

Health

CRAN checks

1ERROR12OK

Check messages

ERRORpackage dependenciesr-oldrel-macos-x86_64

Package required and available but unsuitable version: ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

CRAN check page ↗

Slowest check: 4.8 min · r-oldrel-windows-x86_64

Status changes

ERROR12 OK, 1 ERRORNow
ERROR5 OK, 1 ERROR2026-09-27

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.5

READMEYes · 103 wordsVignettesYes · 3 · dynamicNEWSYes · 100% structured · mentions 1.1.5Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 150 (122 internal)
Examples that run: 100%5 run in a plain check
Exported functions with examples: 19%
Documented parameters: 98%
Return-value docs: 100%
Help pages citing references: 1%

Vignettes (3)

How these are measured

Downloads

466

CRAN downloads in the past year

Rank #24,654 · ~1/day · ~39/mo

Releases R versions

Daily download trend is not available in this view yet.

46630 days

46690 days

4661 year

Compare downloads with other packages →

Also on5 r2u

How downloads are counted

Repository

zengzichao/rclade ↗Account: ZengZichao

2Stars

0Forks

0Open issues

1Open PRs

9Releases

47Commits

1Commit identities

bioinformaticsdata-visualizationdeeptimeggtreephylogenetic-treephylogeneticsr-packagetaxonomy

47 commits · Last activity 2026-10-01

Responsiveness

How these are sampled

PRs merged (all time): 38%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 0

PRs over time

2026-09-27 · 02026-10-01 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/zengzichao/rclade on 2026-10-18.

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 (5)

Contributing guideIssue templatesPR templateSecurity policyCODEOWNERS

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-10-01 · The repository has a site deploy workflow

pkgdown site last built 2026-10-01

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 4 practices

Reproducibility and dev environment (2)

data-raw/Dockerfile

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Research and citation (1)

Zenodo

Automation and maintenance (1)

Dependabot

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

23 external dependencies (excludes base and recommended)

Installing Rclade adds 60 packages (35 with compiled code, 52 MB of source tarballs). Heaviest: stringi 11 MB, deeptime 7.4 MB, ggplot2 6.0 MB. 1 more not on CRAN is not measured.

Depends (1)

R >= 4.1.0

Imports (8)

ape ggtree deeptime ggplot2 rlang stringr tidytree viridisLite

LinkingTo (0)

none

Suggests (15)

treeio phangorn RColorBrewer cowplot (>= 1.1)patchwork shiny optparse yaml vdiffr testthat knitr rmarkdown covr filelock withr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Zeng Zichao

Author, Maintainer since 1.1.5 (2026)

Releases (1)

1.1.5Latest
record
2026-09-26 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-09-26
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 3.1 KB / 2 files
Download size: 352 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("Rclade")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1111/2041-210x.12628, 10.1080/20964471.2025.2537516.

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 Rclade version 1.1.5 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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