R Observatory: Metrics for junctions version 2.1.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

junctions

2.1.4

The Breakdown of Genomic Ancestry Blocks in Hybrid Lineages

1packages depend

4.8Kdownloads / year

98.8%test coverage

13/13checks pass

Overview

About

Maintained by Thijs JanzenFirst published 2018-01-1710 releasesCRAN page ↗GitHub ↗

Individual based simulations of hybridizing populations, where the accumulation of junctions is tracked. Furthermore, mathematical equations are provided to verify simulation outcomes. Both simulations and mathematical equations are based on Janzen (2018, doi:10.1101/058107) and Janzen (2022, doi:10.1111/1755-0998.13519).

Install

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

install.packages("junctions", 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/junctions")

Development version from thijsjanzen/junctions. 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-junctions

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-junctions

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-junctions

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

Health

CRAN checks

13OK

Slowest check: 4.9 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.86

98.8%

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
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-05
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-03-29
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 · 427 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 92%
Documented parameters: 100%
Return-value docs: 94%
References docs: 6%

Downloads

4.8K

CRAN downloads in the past year

Rank #6,475 · ~13/day · ~399/mo

Releases R versions

Daily download trend is not available in this view yet.

22630 days

1.3K90 days

4.8K1 year

Compare downloads with other packages →

Also on411 r2u30 autocran

Repository

GitHub ↗ thijsjanzen/junctions

2Stars

0Forks

0Open issues

0Open PRs

2Releases

415Commits

2Contributors

415 commits · Last activity 2026-03-06

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/thijsjanzen/junctions on 2026-08-23.

Continuous integration (2)

GitHub ActionsTravis CI

Lint, format, editor (2)

lintrRStudio project

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

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Depends (1)

RcppParallel

Imports (3)

nloptr Rcpp tibble

LinkingTo (3)

nloptr Rcpp RcppParallel

Suggests (7)

dplyr ggplot2 knitr magrittr rmarkdown testthat tidyr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

GenomeAdmixR

Code & Tests

People & History

People (1)

Maintainer (1)

Thijs Janzen

Author, Maintainer

Authors (1)

Thijs Janzen

Author, Maintainer

Listed in earlier versions (1)

Agner Fog

no longer listed · 1.0

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
2.1.4Latest
2026-03-07 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
2.1.3
2025-04-09 · diff ↗
2.1.1
2025-03-12 · diff ↗
R
R 4.4.0 released · 2024-04-24
2.1.0
2024-02-13 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
2.0.3
2022-02-24 · diff ↗
2.0.1
2021-05-26 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.1.1
2021-04-16 · diff ↗
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
1.1
2018-08-13 · diff ↗

Show 4 earlier events

R
R 3.5.0 released · 2018-04-23
1.0.1
2018-04-17 · diff ↗
1.0
2018-01-17
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2018-01-17
Total releases: 10 / 8 yrs
License: GPL (>= 2) OSI
Download size: 953 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("junctions")

Format

Janzen, T. (2026). junctions: The Breakdown of Genomic Ancestry Blocks in Hybrid Lineages (Version 2.1.4) [Computer software]. https://doi.org/10.32614/CRAN.package.junctions

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 junctions version 2.1.4 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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