ibdfindr

0.3.1

HMM Toolkit for Inferring IBD Segments from SNP Genotypes

1packages depend

5.7Kdownloads / year

55.6%test coverage

13/13checks pass

Overview

About

Maintained by Magnus Dehli VigelandFirst published 2025-08-181 releasesCRAN page ↗GitHub ↗

Implements continuous-time hidden Markov models (HMMs) to infer identity-by-descent (IBD) segments shared by two individuals from their single-nucleotide polymorphism (SNP) genotypes. Provides posterior probabilities at each marker (forward-backward algorithm), prediction of IBD segments (Viterbi algorithm), and functions for visualising results. Supports both autosomal data and X-chromosomal data.

Install

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

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

Development version from magnusdv/ibdfindr. 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-ibdfindr

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-ibdfindr

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

Health

CRAN checks

13OK

Slowest check: 3.2 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.15

55.6%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-05-12
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-05-11
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 341 wordsVignettesNopkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 71%
Return-value docs: 100%
References docs: 20%

Downloads

5.7K

CRAN downloads in the past year

Rank #6,336 · ~16/day · ~475/mo

Releases R versions

Daily download trend is not available in this view yet.

52130 days

1.5K90 days

5.7K1 year

Compare downloads with other packages →

Also on77 r2u34 autocran

Repository

GitHub ↗ magnusdv/ibdfindr

4Stars

0Forks

0Open issues

0Open PRs

1Releases

47Commits

1Contributors

License GPL-3.0 · 47 commits · Last activity 2025-08-18 · 0% stars, 30d

Stars over time

2025-06-26 · 22026-07-07 · 4

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/magnusdv/ibdfindr on 2026-07-26.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.2

Imports (5)

forrel ggplot2 ibdsim2 pedtools ribd

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

pedsuite

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Magnus Dehli Vigeland

Author, Maintainer

Authors (1)

Magnus Dehli Vigeland

Author, Maintainer

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.3.1Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-08-18
Total releases: 1 / 1 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.2
Bundled data: 98 KB / 2 files
Download size: 283 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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