R Observatory: Metrics for nodeSub version 1.2.9

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

nodeSub

1.2.9Package record

Simulate DNA Alignments Using Node Substitutions

0packages depend

6.2Kdownloads / year

82.3%test coverage

13/13flavors OK

Overview

About

Maintained by Thijs JanzenCRAN page ↗GitHub ↗Issues ↗

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. 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-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). 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: 3.1 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-04-22

Show 4 earlier changesHide 4 earlier changes

ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-04-06
ERROR13 OK, 1 ERROR2026-04-04
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.9

READMEYes · 264 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 20includes a package overview page
Examples that run: no examples
Exported functions with examples: 0%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 10%

Vignettes (1)

substitution_models HTML

How these are measured

Downloads

6.2K

CRAN downloads in the past year

Rank #8,157 · ~17/day · ~519/mo

Releases R versions

Daily download trend is not available in this view yet.

37430 days

1.1K90 days

6.2K1 year

Compare downloads with other packages →

Also on360 r2u4 autocran

How downloads are counted

Repository

thijsjanzen/nodesub ↗Account: thijsjanzen

1Stars

0Forks

3Open issues

0Open PRs

3Releases

431Commits

3Commit identities

431 commits · Last activity 2025-05-06

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 792
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2019-10-31 · 12026-07-07 · 1

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/thijsjanzen/nodesub on 2026-10-22.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Coverage (1)

Coverage reporting

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

27 external dependencies (excludes base and recommended)

Installing nodeSub adds 93 packages (58 with compiled code, 88 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ncbit 9.4 MB.

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.

How these are counted

Code & Tests

People & History

People (1)

Thijs Janzen

Author, Maintainer since 1.2 (2021)

Releases (8)

Pick two releases to compare their code metrics.

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

Show 6 earlier eventsHide 6 earlier events

1.2.3
record
2022-02-01 · diff ↗
unarchivedReturned to CRAN
2022-01-11
1.2.2
record
2022-01-11 · diff ↗
archivedRemoved from CRAN
2022-01-06
check issues were not corrected in time
1.2
record
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

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 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 nodeSub version 1.2.9 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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