Bayesian Population Modelling Course

This folder contains scripts and data for my part of the Advanced Population and Community Ecology masters course at the University og Groningen.

Recommended reading: Kéry, Marc, and Michael Schaub. Bayesian population analysis using WinBUGS: a hierarchical perspective. Academic Press, 2011. eBook available to RuG students

The course is based on Just another Gibbs Sampler (or shortly JAGS) software. JAGS code for all exercises in the book is available here https://www.vogelwarte.ch/de/projekte/publikationen/bpa/code-for-running-bpa-using-jags

Before start of the course, please install all the required software:

1. install R (you may also want to RStudio, notepad++ or other GUI of your choise);
2. install JAGS http://mcmc-jags.sourceforge.net;
3. install additional R packages that we will use during the course:

install.packages ('lme4')
install.packages ('lattice')
install.packages ('coda')
install.packages ('R2WinBUGS')
install.packages('rjags')
install.packages ('R2jags')

You can also source some useful functions we will be useing throughout the course

source('https://git.io/fpufJ')

1. GLM in R and JAGS link to the script
2. Mixed effects models in JAGS link to the script
3. State-space models link to the script
4. Capture-recapture models 1 link to the script
5. Real data analyses link to the script

Note that current course havily relies on the Bayesian population analysis book but does not cover it completely, so please read the book if you want to go further.

Capture-recapture modelling can also be done in the frequentist framwork. The main software for this analysis is program Mark by Gary White. RMark R package is an interface to Mark from R written by Jeff Laake. The great explanation of all conemporary CR methods by Evan Cooch is available here.

If you run in to problems with capture-recapture methods ask you question here.