First class meeting: Room 345 Smith Natural Resources Building


Course preparation


MCMCVis R package

We will use the MCMCvis package to manipulate and visualize JAGS output. The package vignette nicely outlines its capabilities.


JAGS and rjags

We will use JAGS (Just Another Gibbs Sampler) and the rjags package for most of our MCMC computations. Detailed instructions for installing them are found in the JAGS Primer. See the link on Day 4 of the course. It is not necessary that you download them before the course, but it will save you a bit of time for the Day 4 session if you do. Don’t worry if you have any problems, just give us a heads up and we will be ready to trouble shoot at the start of the Day 4 lab.


Statistical notation

Here are some conventions for statistical notation that you might find helpful.


Install course R package BayesNSF

We have prepared an R package that contains all the data you will need to complete our lab exercises. The package is part of the course materials that you now have on your local machine. You will need to do an initial install of this package and do periodic updates throughout the course. For both the install and update the commands are the same.

  1. Download the course R package BayeNSF ver. 1.1 to your computer.

  2. Open R or RStudio run the following line of code to install the BayesNSF package from source. Remember to change the path to wherever files you download from the web are saved locally on your computer.

install.packages("<YOU_SPECIFY_THE_PATH_HERE>/BayesNSF_1.1.tar.gz", repos = NULL, type = "source")
  1. When working in RStudio you load the library like any other R library:
library(BayesNSF)
  1. It is easy to see the help files for BayesNSF type in R, bu the usual (?BayesNSF) doesn’t work. Instead, go to R studio Help, click on packages, and click on BayesNSF

Licensing

All material on this website is licensed under GPLv3.