R Observatory: Metrics for CoalescentPhylo version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CoalescentPhylo

0.1.0Package record

Phylogenetics via Root Distances Method Under the Coalescent

0packages depend

1.4Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Arindam RoyChoudhuryCRAN page ↗GitHub ↗Issues ↗

Estimates phylogenetic trees from allele count data using the root distance method under the Coalescent Model. Given a matrix of allele counts across taxa and loci, the package estimates pairwise root distances under the Coalescent Model using maximum likelihood estimation. Then, it estimates a labeled phylogenetic tree from the estimated root distances. See Peng et al. (2021) doi:10.1016/j.ympev.2021.107142.

Changes in 0.1.0

Initial CRAN submission.

From NEWS.md in the release

Install

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

install.packages("CoalescentPhylo", 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("ArindamRoyChoudhury/CoalescentPhylo")

Development version from ArindamRoyChoudhury/CoalescentPhylo. 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-coalescentphylo

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-CoalescentPhylo

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-CoalescentPhylo

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: 1.8 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK7 OK2026-05-28

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.0

READMENoVignettesNoNEWSYes · 67% structured · mentions 0.1.0Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 2
Examples that run: 100%2 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 50%

How these are measured

Downloads

1.4K

CRAN downloads in the past year

Rank #17,168 · ~4/day · ~121/mo

Releases R versions

Daily download trend is not available in this view yet.

23430 days

74690 days

1.4K1 year

Compare downloads with other packages →

Also on28 r2u2 autocran

How downloads are counted

Repository

arindamroychoudhury/coalescentphylo ↗Account: ArindamRoyChoudhury

0Stars

0Forks

0Open issues

0Open PRs

1Releases

8Commits

1Commit identities

8 commits · Last activity 2026-05-19

Responsiveness

not measured

Releases over time

2026-05-11 · 12026-07-07 · 1

How these are measured

PracticesBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/arindamroychoudhury/coalescentphylo on 2026-10-22.

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Installing CoalescentPhylo adds 18 packages (13 with compiled code, 14 MB of source tarballs). Heaviest: igraph 4.8 MB, phangorn 1.9 MB, Rcpp 1.8 MB.

Depends (1)

R >= 3.5.0

Imports (5)

apeparallelpbapply phangorn rootSolve

LinkingTo (0)

none

Suggests (0)

none

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 (2)

Arindam RoyChoudhury

Ying Li

Author

Releases (1)

0.1.0Latest
record
2026-05-27 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-05-27
Total releases: 1 / 1 yrs
License: AGPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 19 KB / 1 file
Download size: 36 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("CoalescentPhylo")

Format

RoyChoudhury, A., & Li, Y. (2026). CoalescentPhylo: Phylogenetics via Root Distances Method Under the Coalescent (Version 0.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.CoalescentPhylo

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 CoalescentPhylo version 0.1.0 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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