Stan and rethinking

Installing Stan and rethinking

You’ll need to download a few packages in order to code starting in Week 2, and they’re not as simple as going to CRAN. According to McElreath, there are 3 steps. (See here for his explaination, but I’ll try to help here too):

Install C++ toolchain

You might have one of these already. On a Mac, check by opening the Terminal app and running this code:

clang++ --version

If you get anything other than command not found, you’re gold.

  • On a Mac, download and install the app Xcode.
  • On a Windows, install C++ in Visual Studio.

Install CmdStanR

In R, run this code:

install.packages("cmdstanr", 
                 repos = c('https://stan-dev.r-universe.dev', getOption("repos")))

Install rethinking

In R, run this code:

install.packages("shape")
install.packages("rethinking", 
                 repos=c(cran="https://cloud.r-project.org",
                         rethinking="http://xcelab.net/R"))

If you’re asked whether you want to install from these sources (compilation of C/C++/Fortran), say yes.

Install brms and tidybayes

While you’re here, install these packages for later.

install.packages(c("brms", "tidybayes"))