Resources

There are multiple resources, including online material and books, to help you become acquainted with R, RStudio, and phylogenetics in R.

R programming:

• The R Book by Mick Crawley

Literate programming and graphics:

• Dynamic Documents with R and knitr by Yihui Xie
• ggplot2: Elegant Graphics for Data Analysis by Hadley Wickham

RStudio:

• Learning RStudio for R Statistical Computing by Mark van der Loo and Edwin de Jonge

Phylogenetics:

• Analysis of Phylogenetics and Evolution with R by Emmanuel Paradis
• The Phylogenetic Handbook, Second Edition edited by Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme