Learning how to use occupancy modeling (and other hierarchical models) can be challenging, especially for those of us who aren't natural "quants"...
But don't worry! Below are some of the resources I've found helpful over the years. I know there are more out there (I just haven't included them for one reason or another), but feel free to contact me and let me know if there's something you think I should add. Plus, here's a link to some slides I put together to help explain occupancy and occupancy modeling: LINK Note, there aren't a lot of words, as my power point style is to talk and use the slides as an aid. But, I still think you might find them helpful. Please let me know if you find any errors or think something is misleading! |
The best introductions to occupancy modeling, in my humble opinion:
Occupancy Models to Study Wildlife. USGS Fact Sheet 2005-3096
https://pubs.er.usgs.gov/publication/fs20053096
Chapter 15: Occupancy Modeling in Estimation of Parameters for Animal Populations*
https://larkinpowell.wixsite.com/larkinpowell/estimation-of-parameters-for-animal-pop
Chapter 13: Analyzing Camera Trap Data with PRESENCE in Problem-solving in Conservation Biology
https://onlinelibrary.wiley.com/doi/book/10.1002/9781444319576
* but read the whole book! The intro chapters on linear modeling and AIC are so incredibly helpful, I think they should be required reading for all advanced undergrads and grad students in applied ecology/wildlife/conservation!
And a more technical introduction, but a really phenomenal resource to get past the black boxes:
Exercises in Occupancy Modeling and Estimation
http://www.uvm.edu/rsenr/vtcfwru/spreadsheets/?Page=occupancy/occupancy.htm
Ways to actually run occupancy models
1. PRESENCE
A standalone program created by Darryl Mackenzie and Jim Hines, currently maintained by Jim Hines, Computer Specialist at the USGS Patuxent Wildlife Research Center.
2. MARK
A program created and maintained by Gary White, Professor Emeritus in the Department of Fish, Wildlife and Conservation Biology at Colorado State University.
3. RPresence
An R package for running some of the occupancy models available in Program PRESENCE, plus some additional helpful routines.
4. rmark
An R package that mimics program MARK, includes occupancy models.
5. unmarked (this is what I use for occupancy modeling)
An R package created by Ian Fiske and currently maintained by Andy Royle, Research Statistician at the USGS Patuxent Wildlife Research Center. Here are some tip and tricks that I've picked up for dealing unmarked.
5b. AICcmodavg
An R package that contains a lot of useful functions when using unmarked. Created by Marc J. Mazerolle with portions of code contributed by Dan Linden.
6. You can also do occupancy modeling in a Bayesian framework, but that's out of my area of expertise.
Past Workshop Materials
Using R to Build and Compare Statistical Models
This Google Site hosts a workshop presented by Michael Conroy, a Senior Research Scientist at the University of Georgia and retired member of the USGS Cooperative Fish and Wildlife Unit. Offers lectures and exercises on ecological statistics, occupancy modelling, and capture-recapture analysis.
Occupancy, Abundance, and Species Richness
This Google Site hosts a workshop presented by Marc Kéry, Richard Chandler, and Andy Royle of the USGS Patuxent Wildlife Research Center and Swiss Ornithological Institute. Workshop goals are to provide overview of hierarchical models for abundance, occurrence, and communities, while synthesizing developments in the field.
Books/Book Chapters
Occupancy Modeling and Estimation (the classic text, now in its second edition)
https://www.sciencedirect.com/book/9780124071971/occupancy-estimation-and-modeling
Hierarchical Modeling and Inference in Ecology
https://pubs.er.usgs.gov/publication/5200344
Applied Hierarchical Modeling in Ecology
https://www.sciencedirect.com/book/9780128013786/applied-hierarchical-modeling-in-ecology
Program MARK – a ‘gentle introduction’. Chapter 21.
http://www.phidot.org/software/mark/docs/book/pdf/chap21.pdf
Estimation of Parameters for Animal Populations
https://larkinpowell.wixsite.com/larkinpowell/estimation-of-parameters-for-animal-pop
Camera Trapping for Wildlife Research, Chapter 6
https://pelagicpublishing.com/products/camera-trapping-for-wildlife-research
University Course Files
WILD 8390: Estimation of Parameters of Fish and Wildlife Populations
University of Georgia, https://sites.google.com/site/wild8390
FW 544: Quantitative Decision Analysis for Fish and Wildlife Management
Oregon State University, https://sites.google.com/site/fw544quantdecisanalfwm
WFCON 697: Hierarchical Models of Animal Occurence, Abundance, and Survival
University of Massachusetts at Amherst, https://sites.google.com/site/hierarchicalmodelingcourse
WFSC 578: Wildlife Population Dynamics
The University of Arizona, https://cals.arizona.edu/classes/wfsc578/
AEC 501: Ornithology
North Carolina State University:
-> Lecture: Introduction to Occupancy Models: https://projects.ncsu.edu/cals/course/zo501/2016%20Sampling%20Lab/IntroR.and.Occupancy.pdf
-> Lecture Key and Notes (Powerpoint Direct Download): https://projects.ncsu.edu/cals/course/zo501/.../IntroR.and.Occupancy.Key.pptx
Discussion Forums
-> unmarked Google Group
-> Phidot forum
Important Papers
Occupancy Models to Study Wildlife. USGS Fact Sheet 2005-3096
https://pubs.er.usgs.gov/publication/fs20053096
Chapter 15: Occupancy Modeling in Estimation of Parameters for Animal Populations*
https://larkinpowell.wixsite.com/larkinpowell/estimation-of-parameters-for-animal-pop
Chapter 13: Analyzing Camera Trap Data with PRESENCE in Problem-solving in Conservation Biology
https://onlinelibrary.wiley.com/doi/book/10.1002/9781444319576
* but read the whole book! The intro chapters on linear modeling and AIC are so incredibly helpful, I think they should be required reading for all advanced undergrads and grad students in applied ecology/wildlife/conservation!
And a more technical introduction, but a really phenomenal resource to get past the black boxes:
Exercises in Occupancy Modeling and Estimation
http://www.uvm.edu/rsenr/vtcfwru/spreadsheets/?Page=occupancy/occupancy.htm
Ways to actually run occupancy models
1. PRESENCE
A standalone program created by Darryl Mackenzie and Jim Hines, currently maintained by Jim Hines, Computer Specialist at the USGS Patuxent Wildlife Research Center.
2. MARK
A program created and maintained by Gary White, Professor Emeritus in the Department of Fish, Wildlife and Conservation Biology at Colorado State University.
3. RPresence
An R package for running some of the occupancy models available in Program PRESENCE, plus some additional helpful routines.
4. rmark
An R package that mimics program MARK, includes occupancy models.
5. unmarked (this is what I use for occupancy modeling)
An R package created by Ian Fiske and currently maintained by Andy Royle, Research Statistician at the USGS Patuxent Wildlife Research Center. Here are some tip and tricks that I've picked up for dealing unmarked.
5b. AICcmodavg
An R package that contains a lot of useful functions when using unmarked. Created by Marc J. Mazerolle with portions of code contributed by Dan Linden.
6. You can also do occupancy modeling in a Bayesian framework, but that's out of my area of expertise.
Past Workshop Materials
Using R to Build and Compare Statistical Models
This Google Site hosts a workshop presented by Michael Conroy, a Senior Research Scientist at the University of Georgia and retired member of the USGS Cooperative Fish and Wildlife Unit. Offers lectures and exercises on ecological statistics, occupancy modelling, and capture-recapture analysis.
Occupancy, Abundance, and Species Richness
This Google Site hosts a workshop presented by Marc Kéry, Richard Chandler, and Andy Royle of the USGS Patuxent Wildlife Research Center and Swiss Ornithological Institute. Workshop goals are to provide overview of hierarchical models for abundance, occurrence, and communities, while synthesizing developments in the field.
Books/Book Chapters
Occupancy Modeling and Estimation (the classic text, now in its second edition)
https://www.sciencedirect.com/book/9780124071971/occupancy-estimation-and-modeling
Hierarchical Modeling and Inference in Ecology
https://pubs.er.usgs.gov/publication/5200344
Applied Hierarchical Modeling in Ecology
https://www.sciencedirect.com/book/9780128013786/applied-hierarchical-modeling-in-ecology
Program MARK – a ‘gentle introduction’. Chapter 21.
http://www.phidot.org/software/mark/docs/book/pdf/chap21.pdf
Estimation of Parameters for Animal Populations
https://larkinpowell.wixsite.com/larkinpowell/estimation-of-parameters-for-animal-pop
Camera Trapping for Wildlife Research, Chapter 6
https://pelagicpublishing.com/products/camera-trapping-for-wildlife-research
University Course Files
WILD 8390: Estimation of Parameters of Fish and Wildlife Populations
University of Georgia, https://sites.google.com/site/wild8390
FW 544: Quantitative Decision Analysis for Fish and Wildlife Management
Oregon State University, https://sites.google.com/site/fw544quantdecisanalfwm
WFCON 697: Hierarchical Models of Animal Occurence, Abundance, and Survival
University of Massachusetts at Amherst, https://sites.google.com/site/hierarchicalmodelingcourse
WFSC 578: Wildlife Population Dynamics
The University of Arizona, https://cals.arizona.edu/classes/wfsc578/
AEC 501: Ornithology
North Carolina State University:
-> Lecture: Introduction to Occupancy Models: https://projects.ncsu.edu/cals/course/zo501/2016%20Sampling%20Lab/IntroR.and.Occupancy.pdf
-> Lecture Key and Notes (Powerpoint Direct Download): https://projects.ncsu.edu/cals/course/zo501/.../IntroR.and.Occupancy.Key.pptx
Discussion Forums
-> unmarked Google Group
-> Phidot forum
Important Papers
- Single Season Models (MacKenzie et al. 2002): Researchgate link
- Multi-season Models (MacKenzie et al. 2003): https://doi.org/10.1890/02-3090
- Single Season Goodness of Fit (MacKenzie and Bailey 2004): http://www.jstor.org/stable/1400484
- Basic Co-occurrence (MacKenzie et al. 2004): https://doi.org/10.1111/j.0021-8790.2004.00828.x
- Survey Design (MacKenzie and Royle 2005): https://doi.org/10.1111/j.1365-2664.2005.01098.x
- Rare Species (MacKenzie et al. 2005): https://doi.org/10.1890/04-1060
- Species Richness (Dorazio et al. 2006): http://www.jstor.org/stable/20069014
- Resource Selection (MacKenzie 2006): https://wildlife.onlinelibrary.wiley.com/doi/abs/10.2193/0022-541X(2006)70%5B367:MTPORU%5D2.0.CO;2
- Multi-scale/method (Nichols et al. 2008): https://doi.org/10.1111/j.1365-2664.2008.01509.x
- Multi-state (MacKenzie et al. 2009): https://doi.org/10.1890/08-0141.1
- Survey Design (Guillera‐Arroita et al. 2010): https://doi.org/10.1111/j.2041-210X.2010.00017.x
- Co-occurrence with covariates (Richmond et al. 2010): http://www.jstor.org/stable/25741366
- Cluster Sampling (Hines et al. 2010): https://doi.org/10.1890/09-0321.1
- Integrated Habitat-Occupancy (MacKenzie et al. 2011): https://doi.org/0.1111/j.2041-210X.2011.00110.x
- Advances and applications (Bailey et al. 2014): https://doi.org/10.1111/2041-210X.12100
- Advances and applications (Guillera‐Arroita 2016): https://doi.org/10.1111/ecog.02445