R Observatory: Metrics for apex version 1.0.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

apex

1.0.7

Phylogenetic Methods for Multiple Gene Data

1packages depend

54.8Kdownloads / year

25.7%test coverage

13/13checks pass

Overview

About

Maintained by Klaus SchliepFirst published 2015-04-157 releasesCRAN page ↗GitHub ↗

Toolkit for the analysis of multiple gene data (Jombart et al. 2017) doi:10.1111/1755-0998.12567. 'apex' implements the new S4 classes 'multidna', 'multiphyDat' and associated methods to handle aligned DNA sequences from multiple genes.

Install

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

install.packages("apex", 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("thibautjombart/apex")

Development version from thibautjombart/apex. 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-apex

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-apex

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-apex

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

Health

CRAN checks

13OK

Slowest check: 3.8 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.02

25.7%

Coverage · measured lines

100%

Documentation · exports

7

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

READMEYes · 918 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 60%
References docs: 0%

Downloads

54.8K

CRAN downloads in the past year

Rank #2,213 · ~150/day · ~4.6K/mo

Releases R versions

Daily download trend is not available in this view yet.

2.5K30 days

9.1K90 days

54.8K1 year

Compare downloads with other packages →

Also on132 r2u41 autocran64 c2d4u

Repository

GitHub ↗ thibautjombart/apex

5Stars

3Forks

4Open issues

0Open PRs

2Releases

236Commits

6Contributors

236 commits · Last activity 2025-07-24

Stars over time

2022-03-13 · 52026-07-07 · 5

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/thibautjombart/apex on 2026-08-16.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

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

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (4)

R >= 3.1.3methodsape phangorn

Imports (4)

utilsgraphicsstatsadegenet

LinkingTo (0)

none

Suggests (3)

testthat knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

phangorn

Code & Tests

People & History

People (5)

Maintainer (1)

Klaus Schliep

Author, Maintainer

Authors (5)

Klaus Schliep

Author, Maintainer

Eric Archer

Author · added in 1.0.1

Rebecca Harris

Author

Thibaut Jombart

Author

Zhian Namir Kamvar

Author

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
1.0.7Latest
2025-07-24 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.0.6
2024-01-31 · diff ↗
unarchivedReturned to CRAN
2024-01-31
archivedRemoved from CRAN
2023-08-19
email to the maintainer is undeliverable
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
1.0.4
2020-04-11 · diff ↗
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
1.0.3
2017-09-23 · diff ↗
R
R 3.4.0 released · 2017-04-21

Show 6 earlier events

1.0.2
2016-12-05 · diff ↗
R
R 3.3.0 released · 2016-05-03
1.0.1
2015-09-07 · diff ↗
R
R 3.2.0 released · 2015-04-16
1.0.0
2015-04-15
R
R 3.1.0 released · 2014-04-10

Package metadata

First published: 2015-04-15
Total releases: 7 / 11 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.1.3
Download size: 811 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Phylogenetics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("apex")

Format

Schliep, K., Archer, E., Harris, R., Jombart, T., & Kamvar, Z. N. (2025). apex: Phylogenetic Methods for Multiple Gene Data (Version 1.0.7) [Computer software]. https://doi.org/10.32614/CRAN.package.apex

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 apex version 1.0.7 [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.

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