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rbaps

R implementation of the BAPS software for Bayesian Analysis of Population Structure

https://github.com/ocbe-uio/rbaps

Science Score: 85.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 10 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: springer.com
  • ✓
    Committers with academic emails
    2 of 3 committers (66.7%) from academic institutions
  • ✓
    Institutional organization owner
    Organization ocbe-uio has institutional domain (www.med.uio.no)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (16.2%) to scientific vocabulary

Keywords

bayesian-analysis population-structure r-package
Last synced: 6 months ago · JSON representation ·

Repository

R implementation of the BAPS software for Bayesian Analysis of Population Structure

Basic Info
Statistics
  • Stars: 10
  • Watchers: 2
  • Forks: 4
  • Open Issues: 8
  • Releases: 0
Topics
bayesian-analysis population-structure r-package
Created about 6 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog License Citation

README.md

Project Status: WIP - Initial development is in progress, but there has not yet been a stable, usable release suitable for the public. last commit code size check status codecov CodeFactor

rBAPS

R implementation of the compiled Matlab BAPS software for Bayesian Analysis of Population Structure.

Installation

rBAPS is currently under development and a stable version is yet to be released. You can install the development version by issuing the command below on an interactive R session.

r remotes::install_github("ocbe-uio/rBAPS", "develop")

At the current stage, we still recommend using the original BAPS software for production.

Contributing

rBAPS is Open Software licenced under the GPL-3, so all contributions are welcome. You can find a list of tasks we're working on for the first release of rBAPS here. and pitfalls on the PITFALLS.md file.

Found something not to be working as you think it should? Please help us by opening an issue.

References

How to cite this project

After installing the package, issue citation("rBAPS") in R. You will get a pure text and a BibTeX entry of rBAPS. Alternatively, you can use the CITATION.cff file, which conforms to the Citation File Format standard.

Scientific papers

These are some of the scientific publications that served as base for the creation of rBAPS:

  • Corander, J. and Marttinen, P. (2006), Bayesian identification of admixture events using multilocus molecular markers. Molecular Ecology, 15: 2833-2843. doi:10.1111/j.1365-294X.2006.02994.x
  • Corander, J., Sirén, J., & Arjas, E. (2008). Bayesian spatial modeling of genetic population structure. Computational Statistics, 23(1), 111-129. doi:10.1007/s00180-007-0072-x
  • Corander, J., Marttinen, P., Sirén, J. et al. Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations. BMC Bioinformatics 9, 539 (2008) doi:10.1186/1471-2105-9-539
  • Tonkin-Hill G, Lees JA, Bentley SD et al. RhierBAPS: An R implementation of the population clustering algorithm hierBAPS [version 1; peer review: 2 approved]. Wellcome Open Res 2018, 3:93 (https://doi.org/10.12688/wellcomeopenres.14694.1)

Software

Below we list some of the software directly related to rBAPS:

Owner

  • Name: Oslo Centre for Biostatistics and Epidemiology
  • Login: ocbe-uio
  • Kind: organization
  • Location: Oslo, Norway

This is where we host some of the scientific software we produce at OCBE, a joint center between the University of Oslo and the Oslo University Hospital.

Citation (CITATION.cff) 

# YAML 1.2
---
message: "If you use this software, please cite it using these metadata or by issuing `citation(rBAPS)` within an R session"
authors:
  -
    family-names: Leoncio
    given-names: Waldir
    name-suffix: Netto
    email: "w.l.netto@medisin.uio.no"
    affiliation: "Oslo Centre for Biostatistics and Epidemiology"
  -
    family-names: Corander
    given-names: Jukka
    email: "jukka.corander@medisin.uio.no"
    affiliation: "Oslo Centre for Biostatistics and Epidemiology"
  -
    family-names: Tonkin-Hill
    given-names: Gerry
    email: gqt20@cam.ac.uk
title: "rBAPS: Bayesian Analysis of Population Structure"
version: 0.0.0.9000
date-released: 2020-01-01
license: GPL-3.0-or-later
cff-version: 1.1.0

GitHub Events

Total
  • Issues event: 1
  • Issue comment event: 6
  • Push event: 2
  • Fork event: 1
Last Year
  • Issues event: 1
  • Issue comment event: 6
  • Push event: 2
  • Fork event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 472
  • Total Committers: 3
  • Avg Commits per committer: 157.333
  • Development Distribution Score (DDS): 0.439
Past Year
  • Commits: 96
  • Committers: 1
  • Avg Commits per committer: 96.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Waldir Leoncio w****o@g****m 265
Waldir Leoncio w****o@m****o 206
Gerry Tonkin-Hill g****4@s****k 1
Committer Domains (Top 20 + Academic)
sanger.ac.uk: 1 medisin.uio.no: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 25
  • Total pull requests: 0
  • Average time to close issues: 6 months
  • Average time to close pull requests: N/A
  • Total issue authors: 2
  • Total pull request authors: 0
  • Average comments per issue: 0.8
  • 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
  • wleoncio (24)
  • fabio-marcelo (1)
Pull Request Authors
Top Labels
Issue Labels
enhancement (20) bug (3) help wanted (2) good first issue (2) documentation (1)
Pull Request Labels

Dependencies

DESCRIPTION cran
  • R6 * imports
  • Rsamtools * imports
  • adegenet * imports
  • ape * imports
  • matlab2r * imports
  • methods * imports
  • vcfR * imports
  • testthat >= 2.1.0 suggests
.github/workflows/build.yml 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/linter.yml actions
  • actions/checkout v3 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