README.md

wiritttes

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What If Reproductive Isolation Takes Time To Establish Simulations.

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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 [email protected]:/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?

How to install

To install this repository, you will need to:

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



richelbilderbeek/wiritttes documentation built on Feb. 23, 2018, 12:18 p.m.