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Introduction to Occupancy Modeling, April 27 - May 1, 2026, at the San Diego Zoo.
Species presence/absence is a fundamental concept used in many areas of ecology (e.g., species distributions, habitat modeling, monitoring, and metapopulation studies), but imperfect detection can lead to false absences. Not accounting for false absences can lead to misleading inferences about patterns and dynamics of species occurrence and the factors that influence them. We will learn methods for accounting for imperfect detection with species detection/non-detection data and also discuss important study design considerations. All exercises will be conducted in R, covering data analysis and presentation of results (plotting results, creating maps, etc.).
Class will meet each day 8:30 AM-5PM, with an 1.5-hr break at noon. Dr. MacKenzie will meet with individuals or groups to discuss course materials or projects from school or work.
Participants will have access to all course materials in Canvas, CWS’s learning management system. All materials, including live lectures, will be available to all participants for a 3-month period (ending July 19th).
Webinar: Design advice for species occurrence studies - Darryl’s 5 top tips.
PREREQUISITES
This course is for those with no, or little, experience with occupancy modeling, but more experienced users may also benefit from attending.
Basic data tidying and manipulation tasks in R (e.g., R Boot Camp).
Familiarity with regression, logistic regression, or generalized linear modeling in R is advantageous (e.g., Ecological Statistics and Modeling & Generalized Models).
LEARNING OUTCOMES
Explain the conceptual and statistical foundations of occupancy modeling and its role in estimating ecological patterns under imperfect detection.
Apply single-season occupancy models to analyze ecological data, including incorporation of detection processes, covariates, and unequal sampling effort.
Evaluate model assumptions, compare competing models, and interpret results using probability-based inference and multi-model approaches.
Design effective occupancy-based monitoring studies by selecting sampling units, structuring repeat surveys, and allocating sampling effort appropriately.
Describe and apply multiple-season occupancy models to investigate temporal dynamics such as colonization, extinction, and long-term change.
Analyze and interpret occupancy data using R-based analytical tools.
RECOMMENDED TEXTBOOK
MacKenzie, D. I., Nichols, J. D., Royle, J. A., Pollock, K. H., Bailey, L., & Hines, J. E. 2017. Occupancy estimation and modeling: inferring patterns and dynamics of species occurrence. Elsevier.
INSTRUCTOR
COURSE INFORMATION
In-person Course April 27-May 1 at the San Diego Zoo
In-person April 27-May 1, 2026 at the San Diego Zoo.
8:30 am to 5:00 pm on days 1-4; 8:30 am to 12:00 pm on day 5
Online access to materials (April 27-July 19, 2026) is included with in-person tuition
Tuition: $950 currently employed, $800 student or unemployed
Participants are responsible for their own travel and accommodation.
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Days are broken into two sessions:
Morning: 8:30 a.m. – 12 p.m.
Afternoon: 1:30 p.m. – 5 p.m.
There will be 1 or 2 short breaks during each session; times are subject to change depending on course progression.
Below is a list of topics, in their intended order, although progress and approximate timings are subject to change, as rate of progress through the course will be at whatever speed is appropriate for the class.
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Background: The why, what, and how of estimating population attributes
Occupancy applications
Statistical methods
Maximum-likelihood exercise in R
Single-season model (part I)
Introduction to RPresence package
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Single-season model (parts II & III)
Weta example
Species habitat preference example
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Single-season study design
Sample size exercises
Evaluating designs via simulation
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Multiple-season model
Grand-skink example
Northern spotted owl example
Multiple-season study design
Overview of multi-species modelling for community-level studies
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Summary and discussion
Consulting session
Work on own data
Course ends at noon
“The Occupancy Modeling course offered by CWS is great for beginners or experts working with presence/absence data. Each module is designed to reinforce different occupancy modeling concepts and provides you with tools to best analyze your presence/absence data. I really appreciated the group discussion page that showed different points of view on topics from other students taking the course. Definitely a course worth taking!”
Max Larreur
PhD student, Southern Illinois University
“Darryl MacKenzie is an awesome instructor. He was able to make Occupancy Modeling both interesting and understandable. The real-world examples and discussions helped me apply the methods to my project design. Thanks for the great experience.”
Vickie DeNicola
Vice President of White Buffalo Inc.
CONTINUING EDUCATION CREDIT
This course has been pre-approved for continuing education by (1) the Ecological Society of America for 4 CEUs in Category I(a): Scientific Education and Training (for Occupancy Modeling I only), and (2) The Wildlife Society for 16 CEUs in Category I of the Certified Wildlife Biologist® Renewal/Professional Development Certificate Program. Participants must complete all exercises to earn CEUs and receive a Certificate of Course Completion. See our continuing education credit page for details.
MINIMUM EDUCATION REQUIREMENTS FOR ESA CERTIFICATION
This course is approved by the Ecological Society of America for 1 semester hour of qualified coursework that can be used to meet the minimum education requirements in Physical and Mathematical Science. ESA requires a grade of B- or higher for this course to count towards the academic credit requirements associated with Certification.
CANCELLATION POLICY
Cancellations >60 days before the start date are not subject to cancellation fees. Cancellations 60 days or less before the start date are subject to a 50% cancellation fee. No refunds once the course begins.