Bayesian Inference using Stan: CSTAT workshop

How to install stan

Install rstudio, R and Rtools

https://rstudio.com/products/rstudio/download/

https://cran.r-project.org/

https://cran.r-project.org/bin/windows/Rtools/

Note for those working with MacOS: please see suggestions below.

Install rstan

https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started

Useful links

Stan is the programming language that we will use to implement MCMC Bayesian inference

https://mc-stan.org/

Rstan is the r-interfase to the stan programming language

http://mc-stan.org/rstan/

Several packages in R are part of the stan ecosystem

bayesplot

https://mc-stan.org/bayesplot/

rtanarm

https://mc-stan.org/rstanarm/

shinystan

https://mc-stan.org/shinystan/

Installing compile tools in MacOS

Connie Rojas, a workshop participant, sent the following instructions for installing the compile tools (and stan) in macOS. Thanks for your contribution!!!

1. Download Xcode from Mac App store Xcode (Developer Tools) Open it and make note of the version (mines was v 12.4)

2. Download Xcode Command Line tools

https://developer.apple.com/download/more/?=command%20line%20tools

I downloaded “Command Line Tools for Xcode 12.4” to match my Xcode version

Download and run Installer.

3. Download the gfortran version for your specific operating system https://github.com/fxcoudert/gfortran-for-macOS/releases I have macOS BigSur v 11.1, so I downloaded the .dmg file under the "gfortran 10.2 for Big Sur (macOS 11), for Intel processors" section

Run the Installer

4. Now, follow the instructions for the Installation of R Stan https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started