Occupancy Modelling Course

  • Start Date: October 23, 2018
  • End Date: October 25, 2018
  • Time: 8:30 am - 4:30 pm
  • City: Revelstoke BC
  • Venue: Okanagan College - 1401 1 St W, Revelstoke, BC
  • Instructor: Dr. Carl Schwarz

Course Description

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 results 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 level of occupancy can be misleading. This workshop covers methods for modelling species occurrence while accounting for potential false negatives.

Bring: Laptop computer pre-loaded with software (see below)


  • Basic knowledge of statistics
  • Basic R knowledge is helpful but not necessary

Required Software: Please download and install the following files. You may need administrator access

  to install the software.

(a) Several software packages will be used.
The following software is available for Windows operating systems only.

Presence           https://www.mbr-pwrc.usgs.gov/software/presence.html
GenPresence    https://www.mbr-pwrc.usgs.gov/software/presence.html
MARK                http://www.phidot.org/software/mark/downloads/
RMark                R package available from CRAN

The following software is available for Windows and Mac operating systems.
These are R packages and need to be installed.

RPresence      https://www.mbr-pwrc.usgs.gov/software/presence.html
unmarked       CRAN website

(optional) if interested in Bayesian analysis of occupancy data
JAGS              http://www.stat.sfu.ca/~cschwarz/CourseNotes/HowGetSoftware.html

Follow instructions at this website.

(b) R/Rstudio http://www.stat.sfu.ca/~cschwarz/CourseNotes/HowGetSoftware.html
Also install the R packages as listed at this website.
Be sure to create your own personal library as noted at the website.

(c) Adobe Reader: Course reading will be available in PDF format.
You will need to call up some of the material to read from the
screen during the course.
You will be able to annotate the pdf files.

(d) Excel: You will need to unzip files containing example datasets.
Datasets are in an Excel workbook that you will need to open
and “paste” into your program.

(e) Text editor: Notepad, WordPad, or Word, to prepare data files for MARK/PRESENCE/GENPRES.

(f) CourseMaterial:  Will be available in early October.


Course outline


  • differences/similarities of occupancy and capture-recapture modelling
  • role 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/ RPresence/ MARK/ RMark software to fitting single-season models
  • model assumptions
  • dealing with missing data
  • dealing with heterogeneity
  • more advanced features of PRESENCE/ RPresence/ MARK/ RMark – design matrices/covariates
  • planning studies; GENPRES software

Multiple-season occupancy models

  • sampling protocol
  • dynamics of population across seasons
  • using PRESENCE/ RPresence/ MARK/ 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


  • incorporation of count data
  • incorporation of marked animals
  • incorporation of telemetry data


SchwarzDr. Carl Schwarz, Department of Statistics and Actuarial Science, Simon Fraser University. Carl has taught  many courses with CMI, and is back by popular request! Carl has just recently won the SSC Award for Impact of Applied and Collaborative Work 2017.




Preparation for the course

About 2 weeks before the course you will be sent a web link where you can download pre-reading, a course manual, a set of practice exercises to load on your computer before the class.

You will need to bring your own laptop pre-loaded with the required software and downloaded files.

Consider bringing along an external monitor and an external keyboard if you have a small laptop.

** The course starts at 8:30 a.m. sharp, you will need to arrive before that so you can set up your computer.

Thank you to our host Okanagan College


  • Phone 250-837-9311
  • Fax 250-837-9311
  • Email

Mailing Address

  • P.O. Box 2568
  • Revelstoke, British Columbia V0E 2S0
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