From 1ebcbba2a9015e2fcb583b2bf086607690911890 Mon Sep 17 00:00:00 2001 From: Waldir Leoncio Date: Tue, 14 Jan 2020 11:29:42 +0100 Subject: [PATCH] Improved documentation --- DESCRIPTION | 1 + README.md | 8 ++++++++ TODO.md | 3 ++- 3 files changed, 11 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 381c665..1fffe4a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,7 @@ Package: rBAPS Title: Bayesian Analysis of Population Structure Version: 0.0.0.9000 +Date: 2020-01-14 Authors@R: c( person( diff --git a/README.md b/README.md index eadc557..3a5a7ba 100644 --- a/README.md +++ b/README.md @@ -15,8 +15,14 @@ rBAPS is Open Software licenced under the [GPL-3](https://tldrlegal.com/license/ ## 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 +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., 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) @@ -24,6 +30,8 @@ rBAPS is Open Software licenced under the [GPL-3](https://tldrlegal.com/license/ ### Software +Below we list some of the software directly related to rBAPS: + - [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) - [fastbaps: A fast genetic clustering algorithm that approximates a Dirichlet Process Mixture model](https://github.com/gtonkinhill/fastbaps) \ No newline at end of file diff --git a/TODO.md b/TODO.md index 5fee7dd..af48ff9 100644 --- a/TODO.md +++ b/TODO.md @@ -33,4 +33,5 @@ Function | Argument | Value | Matlab output | R output 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). \ No newline at end of file +- 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. \ No newline at end of file