R Observatory: Metrics for apex version 1.0.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

apex

1.0.7Package record

Phylogenetic Methods for Multiple Gene Data

0packages dependsuggested by 1

40.1Kdownloads / year

25.7%test coverage

13/13flavors OK

Overview

About

Maintained by Klaus SchliepCRAN page ↗GitHub ↗Issues ↗

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. 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-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). 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: 3.6 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.7

READMEYes · 918 wordsVignettesYes · 1 · dynamicNEWSYes · 33% structuredCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 19 (1 internal)includes a package overview page
Examples that run: 100%13 run in a plain check
Exported functions with examples: 70%
Documented parameters: 100%
Return-value docs: 60%
Help pages citing references: 0%

Vignettes (1)

apex: Phylogenetic Methods for Multiple Gene Data. HTML

How these are measured

Downloads

40.1K

CRAN downloads in the past year

Rank #2,419 · ~110/day · ~3.3K/mo

Releases R versions

Daily download trend is not available in this view yet.

2.2K30 days

6.7K90 days

40.1K1 year

Compare downloads with other packages →

Also on131 r2u27 autocran146 c2d4u

How downloads are counted

Repository

thibautjombart/apex ↗Account: thibautjombart

5Stars

3Forks

4Open issues

0Open PRs

2Releases

236Commits

6Commit identities

236 commits · Last activity 2025-07-24

Responsiveness

How these are sampled

PRs merged (all time): 82%
Median days to close, 50 most recently updated closed issues: 2
Median days to close, 50 most recently updated closed PRs: 3

Stars over time

2022-03-13 · 52026-07-07 · 5

How these are measured

PracticesBeta

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

Checks run against github.com/thibautjombart/apex on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (1)

README.Rmd

CRAN release process (1)

cran-comments.md

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

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing apex adds 66 packages (41 with compiled code, 75 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, bslib 5.6 MB.

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

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

phangorn

How these are counted

Code & Tests

People & History

People (5)

Klaus Schliep

Author, Maintainer since 1.0.4 (2020)

Eric Archer

Author · added in 1.0.1

Rebecca Harris

Author

Thibaut Jombart

Author

Zhian Namir Kamvar

Author

Previously maintained by Thibaut Jombart (1.0.0 to 1.0.3).

Releases (7)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.0.7Latest
record
2025-07-24 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
unarchivedReturned to CRAN
2024-01-31
1.0.6
record
2024-01-31 · diff ↗
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
record
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
record
2017-09-23 · diff ↗
R
R 3.4.0 released · 2017-04-21

Show 6 earlier eventsHide 6 earlier events

1.0.2
record
2016-12-05 · diff ↗ ·
removed 2 exports
locusNames<-, locusNames

added 3 exports
setLocusNames<-, getLocusNames, getNumInd
R
R 3.3.0 released · 2016-05-03
1.0.1
record
2015-09-07 · diff ↗ ·
added 10 exports
locusNames<-, add.gaps, getNumLoci, getNumSequences, getSequenceNames, getSequences, locusNames, multidna2alignment, multiphyDat2alignment, rm.gaps
R
R 3.2.0 released · 2015-04-16
1.0.0
record
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

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 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 apex version 1.0.7 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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