Occupancy Modelling

Quck links:

What is occupancy modelling?
Software
Courses and Course Slides
Sample data and analyses

A complete zip file of this material is available here.

What is occupancy modelling?

The presence or absence of a species in a set of units (polygons, landscape units, territories, etc.) is a fundamental concept in many ecological studies (e.g., resource selection modelling, biodiversity, range). Visits to sampled units can result in a positive detection of a species or a non-detection of the species in that unit. However, a species may not always be detected if present which results in "false negatives". If the issue of detectablity is not accounted for, estimates that rely on the observed (naive) level of occupancy can be misleading.

Occupancy modelling is about methods for estimating species occurrence while accounting for potential false negatives.

A nice introduction is found at: USGS Occupancy Models to Study Wildlife

Software

There are several software packages that can be used for occupancy modelling.

Package	Url
Presence RPresence	https://www.mbr-pwrc.usgs.gov/software/presence.html Presence is a standalong Windoze program customized for the modelling of occupancy data. RPresence is a R package that has the most common functionality of Presence and runs on Windoze, Mac, and Linus platforms.
GenPresencee	https://www.mbr-pwrc.usgs.gov/software/presence.html Used for planning occupancy studies. When you install Presence, GenPresence is automatically installed in the same directory as Presence.
MARK RMark	http://www.phidot.org/software/mark/downloads/ MARK is a standalong Windoze program for capture-recapture, occupancy, and other studies. RMark is an R packages available from CRAN that calls MARK and collects the output for further processing by R. Because RMark calls MARK directly, it only runs under Windoze. It is possible to install part of MARK on a Macintosh to run RMark natively without a virtualization engine.
unmarked	An R package available from CRAN that has a limited set of occupancy models. Because it is writting using S4, the documentation is extremely hard to follow.
JAGS	A program to run Bayesian models written in BUGS. Commonly called from R to handle input/output. Do a google search to find and download.
R Rstudio	Do a google search to find and download. RPresence, RMark, unmarked, and JAGS use R extensively.

Courses

I offer a three day course on an Introduction of Occupancy Modelling covering the following topics. I can also do this or other courses onsite at your organization. Please contact me (Carl Schwarz) for information.

Slides from the course are available in this directory.

A typical course outline

Introduction
- differences/similarities of occupancy and capture-recapture modelling
- fole of detectability
- basic statistical review
- concepts and notations
- binomial data, odds ratios
- basic likelihood
- model selection and multi-model inference
Single-season occupancy models
- basic sampling protocol
- PRESENCE/MARK/RPresence/RMark software to fitting single-season models
- model assumptions
- dealing with missing data
- dealing with heterogeneity
- more advanced features of PRESENCE/MARK/RPresence/RMark - design matrices/covariates
- planning studies; GENPRES software
Multiple-season occupancy models
- sampling protocol
- dynamics of population across seasons
- using PRESENCE/MARK/RPresence/RMark
- alternative parameterizations
- characterizing occupancy dynamics
- modelling spatial correlations in occupancy dynamics
- dealing with missing data
- dealing with covariates
- study design
Species co-occurrence models
- sharing information among species
- species richness or biodiversity
- single season models/ multi season models
Extensions
- modelling spatial correlations in occupancy dynamics
- incorporation of count data
- incorporation of marked animals
- incorporation of telemetry data

Additonal course covering more advance topics in occupancy modelling (e.g. bayesian methods, spatial methods, multi-method, multi-scale) can also be arranged. Please contact me for details.

Sample data, code, and analyses

An alphabetical list of all the data is available.

Example	Source/Data	Presence/RPresence	MARK/RMark	Unmarked	JAGS
Helper files (additional functionality)		RPresence Adding new derived parameters. Model averaging derived parameters. '	RMark Adding new derived parameters. Model averaging derived parameters. Stacking multi-season data to fit a random occupancy model (gamma = 1- epsilon) using a single-season model.
Single Species - Single Season
Salamander Psi - no covariates p - visit level covariates	salamander.xls Data source	Presence files RPresence files	MARK files RMark files	unmarked files	JAGS files
Salamander - missing values Psi - no covariates p - visit level covariates	salamander.xls Data source	Presence files RPresence files	MARK files RMark files	unmarked files	JAGS files
Salamander - goodness of fit Psi - no covariates p - visit level covariates	salamander.xls Data source		MARK files	unmarked files
Weta Psi - categorical covariates p - visit level and site-visit covariates	weta.xls Data source	Presence files RPresence files	MARK files RMark files	unmarked files	JAGS files
Blue Gross Beaks Psi - categorical and continuous covariates p - site-visit covariates	blgr.csv Data source	Presence files Rpresence files	MARK files RMark files	unmarked files	JAGS files
American Toad Psi - categorical and continuous covariates p - site-visit covariates	AmericanToad.xls Data source	Presence files RPresence files	RMark files
Brook Trout Psi - continuous covariates p - site-visit covariates	BrookTrout.xls Data source	Presence files RPresence files	MARK files RMark files
SSSS-sample Psi - categorical covariates p - no covariates	SSSS-sample.inp Data source		MARK files
Bull Frogs Psi - no covariates p - no covariates Mixture model; Royle-Nichols Poisson Abundance model	bullfrog.inp Data source		MARK files RMark files
Pronghorn Antelope Psi - continuous and categorical covariates p - no covariates	pronghorn.csv Data source	Presence files RPresence files	RMark files
Yellow Bellied Toad Psi - no covariates p - continuous site-visit covariates	YellowBelliedToad.xlsx Data source	RPresence files	RMark files

Single Species - Multi Season
Northern Spotted Owl Psi - no covariates p - no covariates gamma/epsilon - no covariates	NSO.csv Data source	Presence files RPresence files	MARK files RMark files	unmarked files	JAGS files
Grand Skinks Psi - categorical covariates p - no covariates gamma/epsilon - categorical covariate	GrandSkinks.xls Data source	Presence files RPresence files	RMark files
Salamander Multi-Season Psi - categorical and continuous covariates p - no covariates gamma/epsilon - categorical and continuous covariate	SalamanderMultiSeason.xls Data source	Presence files RPresence files	MARK files RMark files
Redbreasted Sunfish Psi - categorical and continuous covariates p - no covariates gamma/epsilon - continuous covariate	Data source	RPresence files	MARK files RMark files
House finches Psi - categorical and continuous covariates p - no covariates gamma/epsilon - continuous covariate	Data source	Presence files
Butterflies	Butterfly.csv Data source	RPresence files	RMark files	unmarked files
Nightingales No covariates.	nightingales.csv Data source	RPresence files	RMark files
Rabbits and cats Cove et al (2018)	Original Data Updated Data You may need both sets of data Data source	RPresence files	MARK files RMark files	unmarked files

Multi Species - Single Season
Co-occurence of two salamanders	Salamander2.xls Data source	Presence files RPresence files	MARK files RMark files
Spotted and Barred Owls	SpottedAndBarredOwls.xls Data source	Presence files RPresence files	RMark files
Co-occurence of two species of Trout	Trout2.xlsx Data source	RPresence files	RMark files
Co-occurence of two species of small carnivores Coyotes, bobcats, etc	Data Files Data source		RMark files
Co-occurence of two species of bears Black bears vs. grizzly bears Ladle et al. (2018)	Data Files Data source	RPresence files	RMark files
Co-occurence of Rabbits and cats Cove et al (2018)	Original Data Updated Data You may need both sets of data Data source		RMark files

Multi Species - Multi Season
Co-occurence of three small mammals Coyotes, raccoons, possums	Data from paper in long format Data source		RMark files
Rabbits and cats Partial analysis. Cove et al (2018)	Original Data Updated Data You may need both sets of data Data source and code book		MARK files RMark files

Multi State - Single Season
California Spotted Owl	CalSpottedOwl.xls Data source	Presence files RPresence files	MARK files RMark files
Coose Bass	CoosaBass.xls Data source	Presence files RPresence files	MARK files RMark files

Multi State - Multi Season
Hawks	Hawk.csv Data source	RPresence files	RMark files		JAGS files

Email comments or suggestions to cschwarz.stat.sfu.ca@gmail.com
Last updated 2025-016