Course description
We will present an accessible overview of single-species, multi-species, and integrated spatially-explicit occupancy modeling with a focus on implementing these models using the spOccupancy R package. Emphasis will be placed on practical software tools rather than statistical details. Basic proficiency in R and generalized linear models is a prerequesite.
Prior to the workshop getting started
This workshop offers lecture, discussion, and hands-on exercises. We strongly encourage you to work along with us on the exercises. To participate fully in the exercises, you’ll need a fairly recent version of R (\(\geqslant\) 3.5).
Installing spOccupancy
The course will focus on using the spOccupancy package to fit spatial occupancy models. spOccupancy can be installed from CRAN using install.packages('spOccupancy'). Note we will be using some recent functionality incorporated into spOccupancy v0.7.2, so please re-install spOccupancy if you have installed it prior to November 1, 2023.
Installing additional R packages
In the exercises, we will use additional R packages for exploratory data analysis and visualizations. To fully participate in the exercises, you will need to install the packages below if you do not have them. The code below can be run in R to only install those packages that don’t currently exist on your system.
required.packages <- c('MCMCvis', 'ggplot2', 'pals', 'sf', 'maps')
new.packages <- required.packages[!(required.packages %in% installed.packages()[, 'Package'])]
if (length(new.packages) > 0) {
install.packages(new.packages)
}Course schedule (download full zip on the course Github page)
- 8:00 - 9:45AM Introduction to occupancy modeling
- Single-species occupancy models
- Single-species spatial occupancy models
- Brief primer on Bayesian analysis using MCMC
- Exercise 1: Amphibian occupancy in the fragmented Brazilian Atlantic Forest
- 9:45AM - 10:00AM Break/Q&A
- 10:00AM - 11:00AM Multi-species occupancy modeling
- Multi-species occupancy models
- Spatial multi-species occupancy models
- Exercise 2: Breeding bird distributions across Switzerland
- 11:00AM - 11:10AM: Break/Q&A
- 11:10AM - 11:50AM: Multiseason spatial occupancy modeling
- Multi-season spatial occupancy models
- Exercise 3: Trends in Wood Thrush occupancy across the eastern US
- 11:50AM - 12:00PM: Wrap up and Q&A