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Improved documentation

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Waldir Leoncio 2020-01-14 11:29:42 +01:00
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DESCRIPTION
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Package: rBAPS Package: rBAPS
Title: Bayesian Analysis of Population Structure Title: Bayesian Analysis of Population Structure
Version: 0.0.0.9000 Version: 0.0.0.9000
Date: 2020-01-14
Authors@R: Authors@R:
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README.md
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## References ## 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.
### Scientific papers ### 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](https://doi.org/10.1111/j.1365-294X.2006.02994.x) - 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](https://doi.org/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](https://link.springer.com/content/pdf/10.1007/s00180-007-0072-x.pdf) - 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](https://link.springer.com/content/pdf/10.1007/s00180-007-0072-x.pdf)
- 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](https://doi.org/10.1186/1471-2105-9-539) - 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](https://doi.org/10.1186/1471-2105-9-539)
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### Software ### Software
Below we list some of the software directly related to rBAPS:
- [Original BAPS software](http://www.helsinki.fi/bsg/software/BAPS/) - [Original BAPS software](http://www.helsinki.fi/bsg/software/BAPS/)
- [RhierBAPS: An R implementation of the population clustering algorithm hierBAPS](https://github.com/gtonkinhill/rhierbaps) - [RhierBAPS: An R implementation of the population clustering algorithm hierBAPS](https://github.com/gtonkinhill/rhierbaps)
- [fastbaps: A fast genetic clustering algorithm that approximates a Dirichlet Process Mixture model](https://github.com/gtonkinhill/fastbaps) - [fastbaps: A fast genetic clustering algorithm that approximates a Dirichlet Process Mixture model](https://github.com/gtonkinhill/fastbaps)

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TODO.md
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@ -33,4 +33,5 @@ Function | Argument | Value | Matlab output | R output
As general remarks, one should keep in mind that: As general remarks, one should keep in mind that:
- For compliance with IEC 60559, the `round` in base R rounds .5 to the nearest even integer, whereas the homonym function in Matlab rounds up (or down, if negative). - For compliance with IEC 60559, the `round` in base R rounds .5 to the nearest even integer, whereas the homonym function in Matlab rounds up (or down, if negative).
- Some clobal variables have been added as a new (last) argument to the function they appear in.