raket
raket is not intended to be fully tested!
The experiment itself is the test| Branch |  |
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| develop |  |
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- raket provides the R code used by [1]
- raket_werper provides the scripts used by [1]
raket is an R package that uses
- PBD: to generate incipient species trees and sample a species tree
- pirouette: to convert a species phylogeny to a posterior
- nLTT: to compare a species tree to all species trees in the posterior
Download raket locally
git clone https://github.com/richelbilderbeek/raketPipeline
See the README in the scripts folder
Installation
If you use the devtools R package, this is easy:
devtools::install_github("richelbilderbeek/raket")raket assumes that BEAST2 is installed. To install BEAST2, from R do:
beastier::install_beast2()This will download and extract BEAST2 to:
| OS | Full path |
|---|---|
| Linux | ~/.local/share/beast/bin/beast.jar |
| Windows | C:/Users/<username>/Local/beast/bin/beast.jar |
FAQ
See FAQ.
There is a feature I miss
See CONTRIBUTING, at Submitting use cases
I want to collaborate
See CONTRIBUTING, at 'Submitting code'
I think I have found a bug
See CONTRIBUTING, at 'Submitting bugs'
There's something else I want to say
Sure, just add an Issue. Or send an email.
Package dependencies
| Package | |
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| babette |  |
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| beautier |  |
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| beastier |  |
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| phangorn |  |
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| pirouette |  |
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| tracerer |  |
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External links
References
- [1] Bilderbeek, Richel JC, and Rampal S. Etienne. "The error when inferring phylogenies with incipient species by a birth-death model.". First registration at the Open Source Framework on 2018-06-14. Second registration at the Open Source Framework on 2018-09-03.
