R Observatory: Metrics for ibdsim2 version 2.3.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ibdsim2

2.3.3Package record

Simulation of Chromosomal Regions Shared by Family Members

2packages dependsuggested by 1

5.2Kdownloads / year

45.5%test coverage

13/13flavors OK

Overview

About

Maintained by Magnus Dehli VigelandCRAN page ↗GitHub ↗Website ↗

Simulation of chromosomal segments shared identical-by-descent (IBD) among pedigree members. Using sex-specific recombination rates along the human genome (Halldorsson et al. (2019) doi:10.1126/science.aau1043), phased chromosomes are simulated for all pedigree members. Applications include calculation of realised relatedness coefficients and IBD segment distributions. 'ibdsim2' is part of the 'pedsuite' collection of packages for pedigree analysis. A detailed presentation of the 'pedsuite', including a separate chapter on 'ibdsim2', is available in the book 'Pedigree analysis in R' (Vigeland, 2021, ISBN:9780128244302). A 'Shiny' app for visualising and comparing IBD distributions is available at https://magnusdv.shinyapps.io/ibdsim2-shiny/.

Changes in 2.3.3

Package changes

Fixed and substantially sped up profileSimIBD(), particularly for dense marker panels. Seeded results may differ from earlier versions.
ibdsim() is more efficient in some cases, by skipping recombination in pedigree branches that cannot affect the output. (In such cases, seeded results may differ from earlier versions.)
launchApp() now checks all optional app dependencies.
Better input checks in uniformMap() and convertPos().
zeroIBD() now merges adjacent IBD segments before applying length thresholds.
Fixed rare bug in findPattern().

App changes

Improved checks of user input.
Fixed plotting bug when simulated values have no variation.

From NEWS.md in the release

Install

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

install.packages("ibdsim2", 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("magnusdv/ibdsim2")

Development version from magnusdv/ibdsim2. 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-ibdsim2

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-ibdsim2

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-ibdsim2

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: 3.8 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-04-22
ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.3.3

READMEYes · 611 wordsVignettesNoNEWSYes · 100% structured · mentions 2.3.3Citation fileYes · cites a publicationWebsiteYes

Help pages: 21 (1 internal)includes a package overview page
Examples that run: 80%16 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran) · 3 never run
Exported functions with examples: 100%
Documented parameters: 95%
Return-value docs: 100%
Help pages citing references: 10%

How these are measured

Downloads

5.2K

CRAN downloads in the past year

Rank #5,716 · ~14/day · ~437/mo

Releases R versions

Daily download trend is not available in this view yet.

62130 days

1.4K90 days

5.2K1 year

Compare downloads with other packages →

Also on417 r2u7 autocran

How downloads are counted

Repository

magnusdv/ibdsim2 ↗Account: magnusdv

7Stars

1Forks

2Open issues

0Open PRs

11Releases

380Commits

1Commit identities

simulationidentity-by-descentrelatedness

380 commits · Last activity 2026-08-04 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 2
Median days to close, 50 most recently updated closed PRs: 52

Stars over time

2024-05-17 · 52026-09-22 · 7

How these are measured

PracticesBeta

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

Checks run against github.com/magnusdv/ibdsim2 on 2026-10-21.

Continuous integration (1)

GitHub Actions

Docs source (1)

README.Rmd

Reproducibility and dev environment (1)

data-raw/

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing ibdsim2 adds 30 packages (13 with compiled code, 18 MB of source tarballs). Heaviest: ggplot2 6.0 MB, Rcpp 1.8 MB, isoband 1.5 MB.

Depends (2)

R >= 4.2.0pedtools

Imports (4)

Rcpp ggplot2 glue ribd

LinkingTo (1)

Rcpp

Suggests (7)

MASSpatchwork shiny shinyWidgets shinyjs testthat zip

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

Imports 2

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

ibdfindr pedsuite

Suggests, most downloaded first

forrel

How these are counted

Code & Tests

Datasets

People & History

People (1)

Magnus Dehli Vigeland

Author, Maintainer since 1.1 (2020)

Releases (13)

Pick two releases to compare their code metrics.

2.3.3Latest
record
2026-08-04 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
2.3.2
record
2025-11-23 · diff ↗
2.3.1
record
2025-08-22 · diff ↗
2.3.0
record
2025-07-22 · diff ↗
R
R 4.5.0 released · 2025-04-11
2.2.0
record
2025-03-03 · diff ↗
2.1.1
record
2024-09-08 · diff ↗
2.1.0
record
2024-08-17 · diff ↗ ·
added 1 export
launchApp
R
R 4.4.0 released · 2024-04-24
2.0.0
record
2023-08-17 · diff ↗ ·
added 1 export
karyoHaploid
R
R 4.3.0 released · 2023-04-21
1.5.0
record
2022-06-07 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.4.0
record
2021-07-24 · diff ↗ ·
added 2 exports
extractIds, segmentStats
R
R 4.1.0 released · 2021-05-18

Show 4 earlier eventsHide 4 earlier events

1.3.0
record
2020-11-13 · diff ↗ ·
added 4 exports
convertPos, findPattern, mapLen, physRange
1.2
record
2020-07-12 · diff ↗ ·
added 6 exports
customMap, estimateKinship, estimateTwoLocusKinship, haploDraw, loadMap, realisedIdentity
1.1
record
2020-06-28
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-06-28
Total releases: 13 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.2.0
Bundled data: 869 KB / 1 file
Download size: 1.4 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("ibdsim2")

The package provides a citation file, so citation() returns the authors' own entry.

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 ibdsim2 version 2.3.3 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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