R Observatory: Metrics for phyclust version 0.1-34

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

phyclust

0.1-34Package record

Phylogenetic Clustering (Phyloclustering)

3packages dependsuggested by 1

32.8Kdownloads / year

–test coverage

0/13flavors OK

Overview

About

Maintained by Wei-Chen ChenCRAN page ↗GitHub ↗Website ↗Issues ↗

Phylogenetic clustering (phyloclustering) is an evolutionary Continuous Time Markov Chain model-based approach to identify population structure from molecular data without assuming linkage equilibrium. The package phyclust (Chen 2011) provides a convenient implementation of phyloclustering for DNA and SNP data, capable of clustering individuals into subpopulations and identifying molecular sequences representative of those subpopulations. It is designed in C for performance, interfaced with R for visualization, and incorporates other popular open source programs including ms (Hudson 2002) doi:10.1093/bioinformatics/18.2.337, seq-gen (Rambaut and Grassly 1997) doi:10.1093/bioinformatics/13.3.235, Hap-Clustering (Tzeng 2005) doi:10.1002/gepi.20063 and PAML baseml (Yang 1997, 2007) doi:10.1093/bioinformatics/13.5.555, doi:10.1093/molbev/msm088, for simulating data, additional analyses, and searching the best tree. See the phyclust website for more information, documentations and examples.

Install

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

install.packages("phyclust", 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("snoweye/phyclust")

Development version from snoweye/phyclust. 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-phyclust

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-phyclust

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-phyclust

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

13NOTE

Check messages

NOTERd filesr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64

checkRd: (-1) 11_d.init.method.Rd:22-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.procedure.Rd:21-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.procedure.Rd:24-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.procedure.Rd:27-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.procedure.Rd:31-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) as.star.tree.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) as.star.tree.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) as.star.tree.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) as.star.tree.Rd:29: Lost braces in \itemize; meant \describe ?

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Wei-Chen Chen <wccsnow@gmail.com>’

Found the following (possibly) invalid file URIs:
  URI: phyclust/doc/Documents/tzeng-Readme.txt
    From: inst/doc/phyclust-guide.pdf
  URI: phyclust/inst/doc/Documents/tzeng-Readme.txt
    From: inst/doc/phyclust-guide.pdf

CRAN check page ↗

Slowest check: 4.2 min · r-devel-windows-x86_64

Status changes

NOTE13 NOTENow
NOTE14 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1-34

READMEYes · 168 wordsVignettesYes · 1 · staticNEWSNoCitation fileYes · software entry onlyWebsiteYes

Help pages: 65 (2 internal)includes a package overview page
Examples that run: 5%3 run in a plain check · 60 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 50%
Help pages citing references: 100%

Also includes 11 demo scripts (run with demo())

Vignettes (1)

phyclust-guide PDF

How these are measured

Downloads

32.8K

CRAN downloads in the past year

Rank #1,940 · ~90/day · ~2.7K/mo

Releases R versions

Daily download trend is not available in this view yet.

3.2K30 days

9.8K90 days

32.8K1 year

Compare downloads with other packages →

Also on1K r2u6 autocran5.4K conda_forge153 c2d4u

How downloads are counted

Repository

snoweye/phyclust ↗Account: snoweye

10Stars

3Forks

0Open issues

1Open PRs

0Releases

76Commits

3Commit identities

License file reads as GPL-2.0 · 76 commits · Last activity 2023-09-06

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 2
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-07-21 · 102026-07-07 · 10

How these are measured

PracticesBeta

Checks run against github.com/snoweye/phyclust on 2026-10-18.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

1 external dependency (excludes base and recommended)

Installing phyclust adds 3 packages (3 with compiled code, 3.4 MB of source tarballs). Heaviest: Rcpp 1.8 MB, ape 1.4 MB, digest 231 KB.

Depends (2)

R >= 3.0.0ape

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

3direct

2indirect

Imports 3

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

iNEXT.3D dispRity iNEXT.beta3D

Suggests, most downloaded first

coala

How these are counted

Code & Tests

Datasets

People & History

People (3)

Wei-Chen Chen

Author, Maintainer since 0.1-1 (2010)

Karin Dorman

Author · added in 0.1-13

Yan-Han Chen

Contributor · added in 0.1-26

Listed in earlier versions (2)

Karin S. Dorman

no longer listed · 0.1-1 to 0.1-12

Ranjan Maitra

no longer listed · 0.1-1

Releases (33)

Pick two releases to compare their code metrics.

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R 4.6.0 released · 2026-04-24
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R 4.5.0 released · 2025-04-11
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R 4.4.0 released · 2024-04-24
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R 4.3.0 released · 2023-04-21
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R 4.2.0 released · 2022-04-22
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R 4.1.0 released · 2021-05-18
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R 4.0.0 released · 2020-04-24
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R 3.6.0 released · 2019-04-26
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R 3.5.0 released · 2018-04-23
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R 3.4.0 released · 2017-04-21
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R 3.3.0 released · 2016-05-03
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R 3.2.0 released · 2015-04-16
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R 3.0.0 released · 2013-04-03
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R 2.15.0 released · 2012-03-30
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R 2.14.0 released · 2011-10-31
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R 2.13.0 released · 2011-04-13
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R 2.12.0 released · 2010-10-15
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R 2.11.0 released · 2010-04-22
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2010-01-29
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R 2.10.0 released · 2009-10-26

Package metadata

First published: 2010-01-29
Total releases: 33 / 16 yrs
License: GPL (>= 2) OSI
Copyright: See phyclust/inst/Documents/ for files in src/msdir/, src/seq-gen/, src/paml_baseml, and R/ttzeng-*.r.
Minimum R: ≥ 3.0.0
Bundled data: 145 KB / 9 files
Download size: 645 KB

Appears in task views

Phylogenetics

Cite

Cite this package

Run in R for the authors' entry:

citation("phyclust")

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

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 phyclust version 0.1-34 [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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