This repository contains all the text, source code, and supporting material for the book Phylogenetic Biology, by Casey Dunn.

The formatted book can be viewed at http://dunnlab.org/phylogenetic_biology/index.html .

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

The order of files in the book is specified in _bookdown.yml.

In phylogenetic_biology, execute:

bookdown::render_book("index.Rmd", "bookdown::gitbook")

To run tests of the code, launch an R console from the manuscript/ directory of this repository and run:

library( testthat )
test_dir( "tests/testthat/" )

Make sure you have docker installed.

In docker/, build the container image with:

docker build -t phylogenetic_biology .

The model for executing the manuscript in docker follows that at https://github.com/caseywdunn/comparative_expression_2017/tree/master/docker .

To run an RStudio session:

docker run --rm  -dP -e PASSWORD=secret123 -e USERID=$UID -v /path/to/phylogenetic_biology:/phylogenetic_biology -p 8787:8787 phylogenetic_biology

Then go to http://localhost:8787/ in your browser. Log in with user/password rstudio/secret123 (Password can be anything except "rstudio"). From the console, you can jump to the repo's R directory with the R command:

setwd("/phylogenetic_biology")

And then build the book with:

library(bookdown)
bookdown::render_book("index.rmd", "bookdown::gitbook")