Aim

The handout aims at familiarising students with the statistical package RJAGS, and with more ‘sophisticated’ Bayesian hierarchical models than those in the Lecture handouts.

Students will be able to:

• use cvd package in R, by using the reference material, for the statistical analysis of contingency tables.

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Material:

Handouts and Exercises for Contigency tables, and Log linear models

Handouts and Exercises for Likelihood methods

Sheet for Computer practical 1 (questions) ; (solutions)

Sheet for Computer practical 1a (questions) ; (solutions)

Sheet for Computer practical 2 (questions) ; (solutions)

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Reference list

The material below is not examinable material, but it contains references that students can follow if they want to further explore the concepts introduced.

• Reference for R:
  • Cheat sheet with basic commands for R
• Reference of rmarkdown (optional)
  • R Markdown cheatsheet
  • R Markdown Reference Guide
  • knitr options
• Reference for Latex (optional):
  • Latex Cheat Sheet

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Setting up the computing environment

CIS computers

1. Go to Appsanywhere and log in with your CIS account details

   • https://appsanywhere.durham.ac.uk/login

From AppHub, load the modules:

2. Git (wait until it opens)

3. LaTex (Latex - Miktex Texworks 2.9.6753) (wait until it opens)

4. rstudio (RStudio 1.2.5003 with RStan and Rtools) (wait until it opens)

Your personal computers (Do not do it on CIS computers)

There is not need to do this in CIS computers as the required foftware is (supposed to be) properly installed.

The instructions below are at your own risk…

We recommend the use of LINUX operation system.

Briefly, you need to do the following:

1. Install LaTex (optional but recommended)
   • Source: download it from https://www.tug.org/texlive/acquire-netinstall.html
   • Debian: apt-get install texlive-full
   • Fedora: yum install texlive texlive-latex
   • windows: download it from https://miktex.org/howto/install-miktex
   • macos: download it from https://www.tug.org/mactex/
2. Install R computing environment version R 3.6.3 or later.
   • Source: download the installer from: https://cran.r-project.org/, and install it according to the installation instructions
   • Debian: sudo apt install r-base
   • Fedora: yum install -y R
   • windows: download it from https://cran.r-project.org/
     • I recomend tyou to install Rtools as well, for you to be able to instal R packages.
   • macos: download it from https://www.tug.org/mactex/
3. Install the latest Rstudio (recommended)
   • Any OS: Download it from here: https://www.rstudio.com/products/rstudio/download/