aptg

0.4.0

Automatic Phylogenetic Tree Generator

0packages depend

160downloads / year

47.5%test coverage

12/13checks 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)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

# 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

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

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

Dependencies · direct

Check history

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

160

CRAN downloads in the past year

Rank #24,423 · ~0/day · ~13/mo

Releases R versions

Daily download trend is not available in this view yet.

15730 days

15990 days

1601 year

Compare downloads with other packages →

Also on4 r2u8 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: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

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