Installing rstan, cmdstan, and rethinking packages on a relatively fresh OS install.

setup.md

Goal: Install rstan, cmdstan, and rethinking in order to work through Rethinking Statistics.

Computing Environment

• MacOS Monterrey running on M1 chip
• MacOS Big Sur running on an Intel chip
• Existing dependencies:
  • Installed XCode command line tools with xcode-select --install.
  • I installed R, RStudio, and could install and run other R packages.

Problem:

• I felt a little lost in the order and detail of the directions from https://github.com/rmcelreath/rethinking/ and https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started and experienced a few false starts.

Solution:

1. Install rstan

I ran install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))

After that finished, running library("rstan") showed no errors.

So I ran example(stan_model, package = "rstan", run.dontrun = TRUE) and this looked good.

No errors, so I restarted r (might not be necessary)

2. Install cmdstanr

As per https://mc-stan.org/cmdstanr/ and https://github.com/rmcelreath/rethinking/

• I ran install.packages("cmdstanr", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
• Then I ran cmdstanr::install_cmdstan()

3. Install rethinking

install.packages(c("coda","mvtnorm","devtools","loo","dagitty","shape")) devtools::install_github("rmcelreath/rethinking")

4. Testing

Finally, I ran the following code from Chapter 2 and it produced the appropriate output.

library(rethinking)
globe.qa <- quap(
    alist(
        W ~ dbinom( W+L ,p) ,  # binomial likelihood
        p ~ dunif(0,1)     # uniform prior
), data=list(W=6,L=3) )

# display summary of quadratic approximation
precis( globe.qa )

produced the following output.

  mean   sd 5.5% 94.5%
p 0.67 0.16 0.42  0.92

May your installs be smooth and troublefree!