R Observatory: Metrics for aphylo version 0.3-6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

aphylo

0.3-6

Statistical Inference and Prediction of Annotations in Phylogenetic Trees

0packages depend

6.3Kdownloads / year

80.1%test coverage

13/13checks pass

Overview

About

Maintained by George Vega YonFirst published 2022-01-217 releasesCRAN page ↗GitHub ↗

Implements a parsimonious evolutionary model to analyze and predict gene-functional annotations in phylogenetic trees as described in Vega Yon et al. (2021) doi:10.1371/journal.pcbi.1007948. Focusing on computational efficiency, 'aphylo' makes it possible to estimate pooled phylogenetic models, including thousands (hundreds) of annotations (trees) in the same run. The package also provides the tools for visualization of annotated phylogenies, calculation of posterior probabilities (prediction) and goodness-of-fit assessment featured in Vega Yon et al. (2021).

Install

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

install.packages("aphylo", 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("USCbiostats/aphylo")

Development version from USCbiostats/aphylo. 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-aphylo

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-aphylo

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-aphylo

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

Health

CRAN checks

13OK

Slowest check: 7.4 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.01

80.1%

Coverage · measured lines

100%

Documentation · exports

9

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
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 79%
Return-value docs: 100%
References docs: 3%

Downloads

6.3K

CRAN downloads in the past year

Rank #5,947 · ~17/day · ~521/mo

Releases R versions

Daily download trend is not available in this view yet.

29930 days

1.4K90 days

6.3K1 year

Compare downloads with other packages →

Also on482 r2u52 autocran48 c2d4u

Repository

GitHub ↗ uscbiostats/aphylo

6Stars

2Forks

8Open issues

0Open PRs

4Releases

356Commits

3Contributors

rphylogeneticsannotationsr-packagercpparmadilloinference

356 commits · Last activity 2026-08-16

Stars over time

2022-04-29 · 62026-07-07 · 6

Repository practices

Upstream repositoryBeta

8 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/uscbiostats/aphylo on 2026-08-16.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (3)

data-raw/MakefileDev Container

Docs source (1)

README.qmd

Lint, format, editor (1)

RStudio project

Show all practices

Coverage (1)

Codecov

Git structural (1)

.gitattributes

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

Development tooling

AI-assisted toolingBeta

Uses AI-assisted development tooling (declared in repo)

Earliest detected marker: copilot on 2025-09-02

copilot

Most recent: copilot on 2025-09-02

Evidence

copilot: on 2025-09-02 · evidence A, PR · sole bot-author seen

How this is detected·Detection ruleset v2 (updated 2026-07-29)

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.5.0ape

Imports (8)

RcppMatrixmethodscoda fmcmcutilsMASSxml2

LinkingTo (1)

Rcpp

Suggests (5)

covr knitr tinytest AUC rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

George Vega Yon

Author, Maintainer

Authors (1)

George Vega Yon

Author, Maintainer

Copyright holders (1)

USC Biostatistics

Copyright holder

Funders (1)

National Cancer Institute (NCI)

Funder

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.3-6Latest
2026-01-09 · current release · diff ↗
0.3-5
2025-11-20 · diff ↗
unarchivedReturned to CRAN
2025-11-20
archivedRemoved from CRAN
2025-06-12
issues were not corrected despite reminders
R
R 4.5.0 released · 2025-04-11
0.3-4
2024-12-04 · diff ↗
unarchivedReturned to CRAN
2024-12-03
archivedRemoved from CRAN
2024-12-03
issues were not corrected despite reminders
R
R 4.4.0 released · 2024-04-24
0.3-3
2023-09-07 · diff ↗
unarchivedReturned to CRAN
2023-09-07
archivedRemoved from CRAN
2023-08-14
issues were not corrected in time
R
R 4.3.0 released · 2023-04-21
0.3-2
2022-12-21 · diff ↗
0.3-1
2022-12-20 · diff ↗

Show 5 earlier events

unarchivedReturned to CRAN
2022-12-20
archivedRemoved from CRAN
2022-12-05
issues were not corrected despite reminders
R
R 4.2.0 released · 2022-04-22
0.2-1
2022-01-21
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2022-01-21
Total releases: 7 / 4 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5.0
Bundled data: 0.3 KB / 2 files
Download size: 912 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("aphylo")

Format

Vega Yon, G., National Cancer Institute (NCI), & USC Biostatistics. (2026). aphylo: Statistical Inference and Prediction of Annotations in Phylogenetic Trees (Version 0.3-6) [Computer software]. https://doi.org/10.32614/CRAN.package.aphylo

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 aphylo version 0.3-6 [Data set]. HJJB, LLC. Data release v2026-08-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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