R Observatory: Metrics for nodeSub version 1.2.9

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

nodeSub

1.2.9

Simulate DNA Alignments Using Node Substitutions

0packages depend

6.5Kdownloads / year

82.3%test coverage

13/13checks pass

Overview

About

Maintained by Thijs JanzenFirst published 2021-09-308 releasesCRAN page ↗GitHub ↗

Simulate DNA sequences for the node substitution model. In the node substitution model, substitutions accumulate additionally during a speciation event, providing a potential mechanistic explanation for substitution rate variation. This package provides tools to simulate such a process, simulate a reference process with only substitutions along the branches, and provides tools to infer phylogenies from alignments. More information can be found in Janzen (2021) doi:10.1093/sysbio/syab085.

Install

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

install.packages("nodeSub", 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("thijsjanzen/nodeSub")

Development version from thijsjanzen/nodeSub. 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-nodesub

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-nodeSub

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-nodeSub

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

Health

CRAN checks

13OK

Slowest check: 3.5 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.40

82.3%

Coverage · measured lines

100%

Documentation · exports

16

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
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 4 earlier snapshots

ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-06
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-04
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 264 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: not tracked
Documented parameters: 100%
Return-value docs: 100%
References docs: 10%

Downloads

6.5K

CRAN downloads in the past year

Rank #7,306 · ~18/day · ~542/mo

Releases R versions

Daily download trend is not available in this view yet.

18230 days

1.2K90 days

6.5K1 year

Compare downloads with other packages →

Also on419 r2u

Repository

GitHub ↗ thijsjanzen/nodesub

1Stars

0Forks

3Open issues

0Open PRs

3Releases

431Commits

3Contributors

431 commits · Last activity 2025-05-06

Stars over time

2019-10-31 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/thijsjanzen/nodesub on 2026-08-09.

Continuous integration (1)

GitHub Actions

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

27 external dependencies (excludes base and recommended)

Depends (2)

ape Rcpp

Imports (14)

beastier beautier DDD geiger lifecycle pbapply phangorn phylobase rappdirs Rmpfr stringr testit tibble tracerer

LinkingTo (1)

Rcpp

Suggests (10)

dplyr ggplot2 knitr magrittr nLTT rmarkdown RPANDA testthat tidyr TreeSim

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Thijs Janzen

Author, Maintainer

Authors (1)

Thijs Janzen

Author, Maintainer

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.2.9Latest
2025-05-06 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.2.8
2023-11-14 · diff ↗
unarchivedReturned to CRAN
2023-11-14
archivedRemoved from CRAN
2023-10-24
requires archived package 'beautier'
1.2.7
2023-09-15 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.2.5
2022-08-19 · diff ↗
unarchivedReturned to CRAN
2022-08-19
archivedRemoved from CRAN
2022-08-08
requires archived package 'beautier'
1.2.4
2022-05-24 · diff ↗
unarchivedReturned to CRAN
2022-05-24
archivedRemoved from CRAN
2022-05-23
requires archived package 'nLTT'
R
R 4.2.0 released · 2022-04-22

Show 6 earlier events

1.2.3
2022-02-01 · diff ↗
1.2.2
2022-01-11 · diff ↗
unarchivedReturned to CRAN
2022-01-11
archivedRemoved from CRAN
2022-01-06
check issues were not corrected in time
1.2
2021-09-30
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-09-30
Total releases: 8 / 5 yrs
License: GPL-3 OSI
Download size: 79 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("nodeSub")

Format

Janzen, T. (2025). nodeSub: Simulate DNA Alignments Using Node Substitutions (Version 1.2.9) [Computer software]. https://doi.org/10.32614/CRAN.package.nodeSub

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 nodeSub version 1.2.9 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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