https://github.com/biometris/statgenibd

See https://biometris.github.io/statgenIBD for a full description
https://github.com/biometris/statgenibd

cran genetics hmm ibd r-package

Last synced: 4 months ago
JSON representation

See https://biometris.github.io/statgenIBD for a full description

• Host: GitHub
• URL: https://github.com/biometris/statgenibd
• Owner: Biometris
• Created: 2021-08-06T09:23:15.000Z (almost 5 years ago)
• Default Branch: main
• Last Pushed: 2025-07-08T12:22:13.000Z (11 months ago)
• Last Synced: 2026-01-26T14:56:13.155Z (5 months ago)
• Topics: cran, genetics, hmm, ibd, r-package
• Language: R
• Homepage: https://biometris.github.io/statgenIBD
• Size: 12.3 MB
• Stars: 0
• Watchers: 3
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.Rmd
  • Changelog: NEWS.md

Awesome Lists containing this project

README

          
---

output: github_document

---

```{r, include = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>",

  fig.path = "man/figures/README-",

  out.width = "100%"

)

```

# statgenIBD 

[![](https://www.r-pkg.org/badges/version/statgenIBD)](https://www.r-pkg.org/pkg/statgenIBD)

[![CRAN RStudio mirror downloads](https://cranlogs.r-pkg.org/badges/statgenIBD)](https://www.r-pkg.org/pkg/statgenIBD)

[![R-CMD-check](https://github.com/Biometris/statgenIBD/workflows/R-CMD-check/badge.svg)](https://github.com/Biometris/statgenIBD/actions?workflow=R-CMD-check)

[![codecov](https://codecov.io/gh/Biometris/statgenIBD/branch/main/graph/badge.svg)](https://app.codecov.io/gh/Biometris/statgenIBD)

[![DOI](https://zenodo.org/badge/393325500.svg)](https://doi.org/10.5281/zenodo.14810487)

**statgenIBD** is an R package for calculating Identity By Descent (IBD) probabilities for biparental, three and four-way crosses. Calculations are based on Hidden Markov Models (HMM) and inheritance vectors. The HMM calculations are implemented in `Rcpp/C++`.

For more complicated pedigrees [RABBIT](https://github.com/Biometris/RABBIT) can be used to calculate the IBDs. 

## Installation

* Install from CRAN:

```{r, eval = FALSE}

install.packages("statgenIBD")

```

* Install latest development version from GitHub (requires [remotes](https://github.com/r-lib/remotes) package):

```{r, eval = FALSE}

remotes::install_github("Biometris/statgenIBD", ref = "develop", dependencies = TRUE)