workshop_prep

bayou Workshop Preparation

Instructor: Josef C Uyeda (josef.uyeda@gmail.com)

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Before you arrive, please try installing the following software (including verifying they are the appropriate versions!).

Required Software

1. R (Download page)

   • Please update R to the latest version (at least R 3.3.0 or later). Older versions of R may cause issues during the workshop.

2. Rstudio (Download page)

   • I will be using Rstudio to lead this workshop, and I strongly recommend you use it too. In particular, we I will be demonstrating code using R markdown and R notebooks. R Notebooks are only available in version 1.0 or higher of RStudio

Install Rtools if using Windows

1. Rtools (Download page)

   • If you are on Windows, you will need Rtools to properly compile and install bayou. Please make sure that your version of Rtools matches the version of R you are currently running.

Install Xcode if using Mac OSX

1. XCode (Installation instructions)

   • If you are using Mac OSX, you will need to make sure you have Xcode to properly compile and install bayou.

Install R Packages

1. Run the following code in R to install the packages. Do this before coming to the workshop as installation can take a while, and it's possible you may hit some snags.

install.packages("devtools") # Required
install.packages("geiger") # Required
install.packages("phytools") # Required
install.packages("knitr") # Required
install.packages("rprojroot") # Required
install.packages("rmarkdown") # Required
install.packages("foreach") # Optional
install.packages("doParallel") # Optional
install.packages("treeplyr") # Optional
devtools::install_github("uyedaj/bayou", ref="dev") ## Note: Not CRAN version

Make sure that bayou has installed without errors.

Optional Software

1. git (Download page)

   • git will allow you to easily clone the directory with workshop materials.

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