README.md

In richelbilderbeek/wiritttea: WIRITTTE analysis

wiritttea

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

What If Reproductive Isolation Takes Time To Establish Analysis.

Build status of builds that wiritttea relies on

master|develop|project ---|---|--- | | beastscriptr | | nLTT | | PBD | | RBeast | | ribir | | wiritttes

Installing wiritttea

The wiritttea package is absent on CRAN.

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

devtools::install_github("richelbilderbeek/wiritttea")

Using wiritttea as a package dependency

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

Remotes:
  richelbilderbeek/wiritttea

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/wiritttea/scripts/*.* ~/Peregrine

Copy all files from Peregrine to FTP

scp [e-mail]:/home/p230198/GitHubs/wiritttea/scripts/*.RDa ftp.richelbilderbeek.nl

my_pass="secret"

for filename in `ls *.RDa`
do
  curl -T $filename ftp://ftp.richelbilderbeek.nl --user richelbilderbeek.nl:my_pass
done

Workflow

On Peregrine, from the wiritttea root folder:

cd scripts
./run [superfolder] [subfolder]

for example:

cd scripts
./run /home/richel/wirittte_data 20171003

The raw data (the .RDa files) will be looked for in the folder /home/richel/wirittte_data/20171003.

The subfolder name is used to distinguish different datasets. For example, running the example above successfully will create many files of the form [type]_[subfolder].csv, for example parameters_20171003.csv.

This will first create a dataset, then analyse this.

Creating raw data

Data is created by simulation.

The first round of output will be RDa ('R Data') files. Each RDa will contain the paramaters of a run, its incipient species tree, sampled species trees, alignments and its posteriors.

Measurements

The RDa files are processed and multiple csv ('Comma Seperated files') will be created in the folder inst/extdata.

Each csv contains a collected [something] of all the raw data files. These can be parameters, simulation duration and summary statistics.

The benefit of these csv files is that they will speed up local analysis.

Analysing data

scp [e-mail]:/home/p230198/GitHubs/wiritttea/inst/exdata/*.csv ~/GitHubs/wiritttea/inst/extdata

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/wiritttea

This will create a folder called wiritttea.

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:

cd scripts
sudo ./install_r_packages

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

Article

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

About the demo folder

These are scripts that should not be checked by R CMD check. This is because they are used to analyse already-produced data in specific local folders. These scripts demonstrate how to use this package, but are not part of the package's core functionality.

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/wiritttea documentation built on May 27, 2019, 8:02 a.m.