Branch|| ---|---|--- master|| develop||
What If Reproductive Isolation Takes Time To Establish Analysis.
wiritttea
relies onmaster|develop|project ---|---|--- | | beastscriptr | | nLTT | | PBD | | RBeast | | ribir | | wiritttes
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")
wiritttea
as a package dependencyIf your package uses wiritttea
, add the following to the DESCRIPTION
its Remotes
section:
Remotes:
richelbilderbeek/wiritttea
module load git; git pull
scp p230198@peregrine.hpc.rug.nl:/home/p230198/GitHubs/wiritttea/scripts/*.* ~/Peregrine
scp p230198@peregrine.hpc.rug.nl:/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
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.
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.
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.
scp p230198@peregrine.hpc.rug.nl:/home/p230198/GitHubs/wiritttea/inst/exdata/*.csv ~/GitHubs/wiritttea/inst/extdata
do_test_simulations
To install this repository, you will need to:
Steps are shown below.
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
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
You will need to install BEAST2.
You can do this from the BEAST2 GitHub.
In Linux, you can install it with:
./install_beast2
The article-in-preparation can be found at the closed wirittte_article GitHub
demo
folderThese 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.
Phylogeny
and Peregrine
folders may be of helpAdd the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.