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.

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

Contributing

rBAPS is Open Software licenced under the GPL-3, so all contributions are welcome. You can find a list of todos and pitfalls on the TODO.md file.

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:

• Original BAPS software
• RhierBAPS: An R implementation of the population clustering algorithm hierBAPS
• fastbaps: A fast genetic clustering algorithm that approximates a Dirichlet Process Mixture model