R Observatory: Metrics for aptg version 0.4.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

aptg

0.4.0

Automatic Phylogenetic Tree Generator

0packages depend

263downloads / year

47.5%test coverage

13/13checks pass

Overview

About

Maintained by Christophe BenjaminFirst published 2026-07-193 releasesCRAN page ↗GitHub ↗

Generates phylogenetic trees and distance matrices from a list of taxon names, or from a higher taxon expanded down to a chosen lower rank. Trees are obtained as induced subtrees of the Open Tree of Life synthetic tree using the 'rotl' package (Michonneau, Brown and Winter, 2016, doi:10.1111/2041-210X.12593). Expansion of a higher taxon to its descendants uses 'taxize' (Chamberlain and Szocs, 2013, doi:10.12688/f1000research.2-191.v2).

Install

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

install.packages("aptg", 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("christophebenjamin/aptg")

Development version from christophebenjamin/aptg. 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-aptg

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-aptg

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-aptg

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

Health

CRAN checks

13OK

Slowest check: 2.4 min · r-release-macos-x86_64

Code health

Yes

Tests · ratio 0.17

47.5%

Coverage · measured lines

100%

Documentation · exports

4

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
OK2026-07-20
7 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 223 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 83%
Return-value docs: 100%
References docs: 0%

Downloads

263

CRAN downloads in the past year

Rank #24,312 · ~1/day · ~22/mo

Releases R versions

Daily download trend is not available in this view yet.

26030 days

26290 days

2631 year

Compare downloads with other packages →

Also on4 r2u26 autocran

Repository

GitHub ↗ christophebenjamin/aptg

Repository practices

Upstream repositoryBeta

Repository github.com/christophebenjamin/aptg is linked, but repository-practices checks have not run for it yet.

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

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (4)

ape rotl taxizestats

LinkingTo (0)

none

Suggests (6)

fishtree rgbif geosphere testthat knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Christophe Benjamin

Author, Maintainer

Authors (1)

Christophe Benjamin

Author, Maintainer

Package Timeline

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

0.4.0Latest
2026-07-19 · current release · diff ↗
unarchivedReturned to CRAN
2026-07-19
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
R
R 4.2.0 released · 2022-04-22
archivedRemoved from CRAN
2021-10-13
policy violation On Internet access
R
R 4.1.0 released · 2021-05-18
0.1.1
2021-01-10 · diff ↗
unarchivedReturned to CRAN
2021-01-10
R
R 4.0.0 released · 2020-04-24
archivedRemoved from CRAN
2020-02-28
check problems were not corrected despite reminders
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21

Show 2 earlier events

0.1.0
2017-03-31
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2026-07-19
Total releases: 3 / 1 yrs
License: MIT + file LICENSE OSI
Download size: 26 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("aptg")

Format

Benjamin, C. (2026). aptg: Automatic Phylogenetic Tree Generator (Version 0.4.0) [Computer software]. https://doi.org/10.32614/CRAN.package.aptg

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 aptg version 0.4.0 [Data set]. HJJB, LLC. Data release v2026-08-16. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-16, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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