README.md

In richelbilderbeek/raket: What If Speciation Takes Time?

raket

raket is not intended to be fully tested!
The experiment itself is the test

Branch||| ---|---|---|--- master||| develop|||

• 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/raket

Pipeline

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|| ---|---|--- babette|| beautier|| beastier|| phangorn|| pirouette|| tracerer||

External links

• BEAST2 GitHub

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.

richelbilderbeek/raket documentation built on Dec. 31, 2019, 7:41 p.m.