https://github.com/richelbilderbeek/R
My notes on the R programming language
https://github.com/richelbilderbeek/R
Last synced: 7 months ago
JSON representation
My notes on the R programming language
- Host: GitHub
- URL: https://github.com/richelbilderbeek/R
- Owner: richelbilderbeek
- License: gpl-3.0
- Created: 2014-09-23T07:50:31.000Z (about 11 years ago)
- Default Branch: master
- Last Pushed: 2023-09-27T14:47:02.000Z (about 2 years ago)
- Last Synced: 2025-04-06T07:34:13.077Z (8 months ago)
- Language: HTML
- Size: 3.68 MB
- Stars: 7
- Watchers: 3
- Forks: 3
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# R
My notes about R.
## [Presentations](https://github.com/richelbilderbeek/PresentationsAboutR)
[My presentations about R](https://github.com/richelbilderbeek/PresentationsAboutR)
## Professional publications
* 'Raising Your Code to Professional Standards'
was a free article for a journal called 'SDJournal'.
It is still available at
[https://github.com/richelbilderbeek/sdj_raising_your_code_to_professional_standards](https://github.com/richelbilderbeek/sdj_raising_your_code_to_professional_standards)
* [Methods.blog post: The babette R Package: How to Sooth the Phylogenetic BEAST2](https://methodsblog.wordpress.com/2018/06/25/babette-beast2/)
* [rOpenSci blog post: Call BEAST2 for Bayesian evolutionary analysis from R](https://ropensci.org/blog/2020/01/28/babette/)
* [rOpenSci blog post: Selecting the Best Phylogenetic Evolutionary Model](https://ropensci.org/blog/2020/12/01/mcbette-selecting-the-best-inference-model/)
## Academic publications
* Bilderbeek (2020)
mcbette: model comparison using babette.
Journal of Open Source Software 5.54: 2762.
[https://doi.org/10.21105/joss.02762](https://doi.org/10.21105/joss.02762)
* Bilderbeek, Laudanno and Etienne (2020)
Quantifying the impact of an inference model in Bayesian phylogenetics.
Methods in Ecology and Evolution.
[https://doi.org/10.1111/2041-210X.13514](https://doi.org/10.1111/2041-210X.13514)
* Bilderbeek and Etienne (2018)
babette: BEAUti 2, BEAST2 and Tracer for R.
Methods in Ecology and Evolution 9, no. 9: 2034-2040.
[https://doi.org/10.1111/2041-210X.13032](https://doi.org/10.1111/2041-210X.13032)
## Build statuses
Build statuses for my R packages.
Repository |[](https://github.com/informalr/informalr/actions) |[](https://www.codecov.io)
-------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------
[`babette`](https://github.com/ropensci/babette) | |[](https://codecov.io/github/ropensci/babette/branch/master)
[`beastier`](https://github.com/ropensci/beastier) | |[](https://codecov.io/github/ropensci/beastier/branch/master)
[`beastierinstall`](https://github.com/richelbilderbeek/beastierinstall) | |[](https://codecov.io/github/richelbilderbeek/beastierinstall/branch/master)
[`beautier`](https://github.com/ropensci/beautier) | |[](https://codecov.io/github/ropensci/beautier/branch/master)
[`bbbq`](https://github.com/richelbilderbeek/bbbq) | |[](https://codecov.io/github/richelbilderbeek/bbbq/branch/master) [4]
[`cobaltr`](https://github.com/richelbilderbeek/cobaltr) | |[](https://codecov.io/github/richelbilderbeek/cobaltr/branch/master) [3]
[`k3reviews`](https://github.com/richelbilderbeek/k3reviews) | |[](https://codecov.io/github/richelbilderbeek/k3reviews/branch/master)
[`mauricer`](https://github.com/ropensci/mauricer) | |[](https://codecov.io/github/ropensci/mauricer/branch/master)
[`mauricerinstall`](https://github.com/richelbilderbeek/mauricerinstall) | |[](https://codecov.io/github/richelbilderbeek/mauricerinstall/branch/master)
[`mcbette`](https://github.com/ropensci/mcbette) | |[](https://codecov.io/github/ropensci/mcbette/branch/master)
[`mcbetteinstall`](https://github.com/richelbilderbeek/mcbetteinstall) | |[](https://codecov.io/github/richelbilderbeek/mcbetteinstall/branch/master)
[`mhcnuggetsr`](https://github.com/richelbilderbeek/mhcnuggetsr) | |[](https://codecov.io/github/richelbilderbeek/mhcnuggetsr/branch/master)
[`mhcnuggetsrinstall`](https://github.com/richelbilderbeek/mhcnuggetsrinstall) | |[](https://codecov.io/github/richelbilderbeek/mhcnuggetsrinstall/branch/master)
[`ncbi`](https://github.com/richelbilderbeek/ncbi) | |[](https://codecov.io/github/richelbilderbeek/ncbi/branch/master)
[`ncbi_peregrine`](https://github.com/richelbilderbeek/ncbi_peregrine) | |[](https://codecov.io/github/richelbilderbeek/ncbi_peregrine/branch/master)
[`netmhc2pan`](https://github.com/richelbilderbeek/netmhc2pan) | |[](https://codecov.io/github/richelbilderbeek/netmhc2pan/branch/master) [1]
[`netmhc2paninstall`](https://github.com/richelbilderbeek/netmhc2paninstall) | |[](https://codecov.io/github/richelbilderbeek/netmhc2paninstall/branch/master) [1]
[`peregrine`](https://github.com/richelbilderbeek/peregrine) | |[](https://codecov.io/github/richelbilderbeek/peregrine/branch/master)
[`pirouette`](https://github.com/richelbilderbeek/pirouette) | |[](https://codecov.io/github/richelbilderbeek/pirouette/branch/master) [2]
[`pureseqtmr`](https://github.com/richelbilderbeek/pureseqtmr) | |[](https://codecov.io/github/richelbilderbeek/pureseqtmr/branch/master)
[`pureseqtmrinstall`](https://github.com/richelbilderbeek/pureseqtmrinstall) | |[](https://codecov.io/github/richelbilderbeek/pureseqtmrinstall/branch/master)
[`sprentrez`](https://github.com/richelbilderbeek/sprentrez) | |[](https://codecov.io/github/richelbilderbeek/sprentrez/branch/master)
[`tmhmm`](https://github.com/richelbilderbeek/tmhmm) | |[](https://codecov.io/github/richelbilderbeek/tmhmm/branch/master) [1]
[`tmhmminstall`](https://github.com/richelbilderbeek/tmhmminstall) | |[](https://codecov.io/github/richelbilderbeek/tmhmminstall/branch/master) [1]
[`tracerer`](https://github.com/ropensci/tracerer) | |[](https://codecov.io/github/ropensci/tracerer/branch/master)
* [1] Cannot get 100% code coverage, because one needs to request an (expiring) download URL for this tool
* [2] Cannot get 100% code coverage, because all tests do not fit within one hour yet
* [3] Cannot get 100% code coverage, because installing COBALT is a +750 MB download: I will need to do some trick to test install/uninstall errors :+1:
* [4] Cannot get 100% code coverage, due to using untested code from other dev
## Links
* [My rpkg.net profile](https://scholar.rpkg.net/aut/Richel+Bilderbeek)