README.md

In richelbilderbeek/wiritttes: WIRITTE simulation

wiritttes

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

What If Reproductive Isolation Takes Time To Establish Simulations.

Build status of builds that wiritttes relies on

master|develop|project ---|---|--- | | beastier | | beautier | | tracerer | | nLTT | | PBD | | ribir

Installing wiritttes

The wiritttes package is absent on CRAN.

An easy way is to install it from GitHub. Within R, do:

devtools::install_github("richelbilderbeek/wiritttes")

Using wiritttes as a package dependency

If your package uses wiritttes, add the following to the DESCRIPTION its Remotes section:

Remotes:
  richelbilderbeek/wiritttes

Update the package source on Peregrine

module load git; git pull

Copy all files from Peregrine to local computer

scp [e-mail]:/home/p230198/GitHubs/wiritttes/scripts/*.* ~/Peregrine

Workflow

On Peregrine, from the wiritttes root folder:

cd scripts
./run.sh

This will create a dataset consisting of .RDa files. Each RDa will contain the paramaters of a run, its incipient species tree, sampled species trees, alignments and its posteriors.

These files can be analysed by the wiritttea package.

How to create the test examples?

• Run the function do_test_simulations

How to install

To install this repository, you will need to:

• Clone this repository
• Install packages
• Install BEAST2

Steps are shown below.

Clone this repository

From the GNU/Linux terminal, or using Windows Git Bash:

git clone https://github.com/richelbilderbeek/wiritttes

This will create a folder called wiritttes.

You may also need to do this, for GNU/Linux:

sudo apt-get install libcurl4-openssl-dev

Install packages

You will need some packages, which are listed in install_r_packages.R.

In Linux, you can install all of these with:

sudo install_r_packages.sh

Install BEAST2

You will need to install BEAST2.

You can do this from the BEAST2 GitHub.

In Linux, you can install it with:

./install_beast2.sh

Article

The article-in-preparation can be found at the closed wirittte_article GitHub

Resources

• My 2015-11-23 TRES presentation
• My 2016-02-03 TECE presentation
• My 2016 TRES presentation about BEAST2
• My R repository, especially the Phylogeny and Peregrine folders may be of help
• Prolonging the Past Counteracts the Pull of the Present: Protracted Speciation Can Explain Observed Slowdowns in Diversification. Rampal S. Etienne, James Rosindell. 2012
• Nee, Sean, Robert M. May, and Paul H. Harvey. "The reconstructed evolutionary process." Philosophical Transactions of the Royal Society of London B: Biological Sciences 344.1309 (1994): 305-311.
• R coding standard
• Pro Git
• Tidy Data, Hadley Wickham
• R packages, Hadley Wickham
• Advanced R, Hadley Wickham

richelbilderbeek/wiritttes documentation built on May 27, 2019, 8:14 a.m.