R implementation of the compiled Matlab BAPS software for Bayesian Analysis of Population Structure.
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", "develop")At the current stage, we still recommend using the original BAPS software for production.
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.
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.
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)
Below we list some of the software directly related to rBAPS: