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Open Source Science

https://github.com/biometris/statgenibd

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

https://github.com/biometris/statgenibd

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.6%) to scientific vocabulary

Keywords

cran genetics hmm ibd r-package
Last synced: 5 months ago · JSON representation

Repository

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

Basic Info
Statistics
  • Stars: 0
  • Watchers: 3
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Topics
cran genetics hmm ibd r-package
Created over 4 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog

README.Rmd 

---
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)

Owner

  • Name: Wageningen Universtiy & Research, Biometris
  • Login: Biometris
  • Kind: organization
  • Email: biometris@wur.nl
  • Location: Wageningen, The Netherlands

Biometris develops statistical and mathematical methods for the quantification of biological processes and processes in our living environment.

GitHub Events

Total
  • Issue comment event: 3
  • Push event: 14
  • Fork event: 1
  • Create event: 1
Last Year
  • Issue comment event: 3
  • Push event: 14
  • Fork event: 1
  • Create event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 219
  • Total Committers: 3
  • Avg Commits per committer: 73.0
  • Development Distribution Score (DDS): 0.046
Past Year
  • Commits: 10
  • Committers: 1
  • Avg Commits per committer: 10.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Rossum, Bart-Jan van b****m@w****l 209
Martin Boer m****r@w****l 8
Johannes Kruisselbrink j****s@k****u 2
Committer Domains (Top 20 + Academic)
wur.nl: 2 kruisselbrink.eu: 1

Issues and Pull Requests

Last synced: over 1 year ago

All Time
  • Total issues: 1
  • Total pull requests: 0
  • Average time to close issues: about 1 month
  • Average time to close pull requests: N/A
  • Total issue authors: 1
  • Total pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • andy3404 (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 459 last-month
  • Total docker downloads: 21,613
  • Total dependent packages: 1
  • Total dependent repositories: 1
  • Total versions: 10
  • Total maintainers: 1
cran.r-project.org: statgenIBD

Calculation of IBD Probabilities

  • Versions: 10
  • Dependent Packages: 1
  • Dependent Repositories: 1
  • Downloads: 459 Last month
  • Docker Downloads: 21,613
Rankings
Docker downloads count: 0.6%
Dependent packages count: 18.1%
Average: 22.0%
Dependent repos count: 23.9%
Downloads: 27.1%
Forks count: 27.8%
Stargazers count: 34.6%
Maintainers (1)
bart-jan.vanrossum@wur.nl
Last synced: 7 months ago

Dependencies

.github/workflows/check.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.4.1 composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/test-coverage.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION cran
  • R >= 3.6 depends
  • Matrix * imports
  • Rcpp * imports
  • data.table * imports
  • ggplot2 * imports
  • rlang * imports
  • stringi * imports
  • knitr * suggests
  • rmarkdown * suggests
  • tinytest * suggests