SISG: Module 8

Instructors: Jon Wakefield and Ken Rice

This page, updated throughout the course, will feature slides from our sessions, and examples for you to try.

Prior to the module, please install up-to-date versions of R and RStudio on the laptop you will use during the summer institute. Both are free.

R is available from this list of sites.
RStudio is available here.

Other software that will be useful, but only used in parts of the module:

Stan: Windows users first need the Rtools toolchain, Mac users may need the toolchain and corresponding tools. Then install R's rstan package.
JAGS: Download and install JAGS itself , then install R's rjags package
INLA: To get the INLA package for R, follow the non-standard procedure here
WinBUGS: you will need WinBUGS and the R2WinBUGS R package. If you don't remember where to point and click, watch the (unrated) WinBUGS the Movie (may require the Ruffle Extension to view. Note making WinBUGS work on a Mac requires a Windows emulator such as HomeBrew, and you may prefer just to use JAGS instead.

Script files are posted following each session; these will contain our R code for the exercises. To make them work on your computer, remember to modify file names and locations appropriately. Also note that many different 'correct' solutions are possible. All times/dates are Pacfic, i.e. Seattle time.

The module has 10 sessions, each of 80 minutes. The standard format for a session is approximately:

50 minutes of pre-recorded lecture material
20 minutes of code demonstrations and exercises for you to try, with small-group "breakout" Zoom sessions available, attended by other class participants, and Teaching Assistants. Please help each other out!
10 minute discussion of exercises, where the instructors will present possible solutions and answer questions

Please join the module's Slack channel, where you can ask questions and see real-time updates from the instructors and TAs.

Resources for Session 10: most of the examples run the HWE example - each example is self-contained

Comments forms and attendance certificates are available here - requires SISG account.

The R site, which includes the Comprehensive R Archive Network (CRAN) of downloads and packages
A reference card of common R commands (and a slightly longer reference card)

Some recommended books;

A First Course in Bayesian Statistical Methods (Hoff, 2009) - available free with UW login
Bayesian and Frequentist Regression Methods (Wakefield, 2013) - available from with UW login
Foulkes, Applied Statistical Genetics with R For Population-based Association Studies, 2009; this book covers a lot of the material we'll discuss, although seldom from a Bayesian point of view.