Phylogenetics: R Primer

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Adiantum.png EEB 349: Phylogenetics
This lab represents an introduction to the R computing language, which will be useful for upcoming homework assignments as well as for software written as R extensions (i.e. APE)

What is R?

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R is one of two programming languages that we will use this semester (the other being Python). One might make the case that programs like PAUP that are associated with a unique command language also represent programming languages; however, R and Python are different in being general purpose (i.e. not written specifically for phylogenetics).

While R and Python share many similarities, R excels in tasks that involve statistics and creating plots. While a spreadsheet program like Excel can create charts, it is often easier to create the plot you need in R. The purpose of this lab is to introduce you to R by showing you how to make various plots related to probability distributions. This will also enable you to learn about several important probability distributions that serve as prior distributions in Bayesian phylogenetics.

Installing R

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If you have a Mac, ...
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If you have Windows, ...
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