R Observatory: Metrics for rapidphylo version 0.1.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

rapidphylo

0.1.2

Rapidly Estimates Phylogeny from Large Allele Frequency Data Using Root Distances Method

0packages depend

2Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Arindam RoyChoudhuryFirst published 2022-12-013 releasesCRAN page ↗GitHub ↗

Rapidly estimates tree-topology from large allele frequency data using Root Distances Method, under a Brownian Motion Model. See Peng et al. (2021) doi:10.1016/j.ympev.2021.107142.

Install

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

install.packages("rapidphylo", 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/rapidphylo")

Development version from ArindamRoyChoudhury/rapidphylo. 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-rapidphylo

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-rapidphylo

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-rapidphylo

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

Health

CRAN checks

13OK

Slowest check: 1.8 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

3

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
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 67%
Return-value docs: 100%
References docs: 50%

Downloads

2K

CRAN downloads in the past year

Rank #20,986 · ~5/day · ~164/mo

Releases R versions

Daily download trend is not available in this view yet.

14530 days

52490 days

2K1 year

Compare downloads with other packages →

Also on97 r2u16 autocran

Repository

GitHub ↗ arindamroychoudhury/rapidphylo

0Stars

0Forks

0Open issues

0Open PRs

0Releases

Last activity 2023-02-02

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/arindamroychoudhury/rapidphylo on 2026-08-16.

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (3)

ape phangornstats

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (4)

Maintainer (1)

Arindam RoyChoudhury

Author, Maintainer, Copyright holder

Authors (4)

Arindam RoyChoudhury

Author, Maintainer, Copyright holder

Laura Kubatko

Author, Thesis advisor

Ying Li

Author

Jing Peng

Author

Copyright holders (1)

Arindam RoyChoudhury

Author, Maintainer, Copyright holder

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.1.2Latest
2023-02-01 · current release · diff ↗
0.1.1
2022-12-19 · diff ↗
0.1.0
2022-12-01
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-12-01
Total releases: 3 / 4 yrs
License: AGPL-3 OSI
Minimum R: ≥ 4.1.0
Bundled data: 112 KB / 1 file
Download size: 121 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("rapidphylo")

Format

RoyChoudhury, A., Kubatko, L., Li, Y., & Peng, J. (2023). rapidphylo: Rapidly Estimates Phylogeny from Large Allele Frequency Data Using Root Distances Method (Version 0.1.2) [Computer software]. https://doi.org/10.32614/CRAN.package.rapidphylo

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 rapidphylo version 0.1.2 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →