Occupancy
Modelling
          Presented by
StatMathComp
Consulting
by Schwarz, Inc
          Carl James Schwarz  
       
Fellow of the American Statistical Association
        Accredited Professional Statistician
           P.Stat. (Statistical Society of Canada),
           PStat® (American Statistical Association)

Occupancy Modelling

Quck links: 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.
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 Follow istructions at http://www.stat.sfu.ca/~cschwarz/CourseNotes/HowGetSoftware.html
A program to run Bayesian models written in BUGS. Commonly called from R to handle input/output.
R
Rstudio
Follow istructions at http://www.stat.sfu.ca/~cschwarz/CourseNotes/HowGetSoftware.html
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. It is often offered through the Columbia Mountain Institute of Applied Ecology (http://www.cmiae.org). A sample offering is found at http://cmiae.org/event/occupancy-modelling-course/.

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

  1. Introduction
  2. Single-season occupancy models
  3. Multiple-season occupancy models
  4. Species co-occurrence models
  5. Extensions
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 Notes 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
 
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
 
Multi Species - Multi Season
Co-occurence of three small mammals
Coyotes, raccoons, possums
Data from paper in long format
Data source
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


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Email comments or suggestions to cschwarz@stat.sfu.ca
Last updated 2018-12-26