Welcome to Population Modeling in Ecology! This course introduces key software packages and fundamental models used in fish and wildlife population analysis. Course content includes the parameterization of models used to estimate ecological state variables (occupancy, abundance) and population vital rates (survival, recruitment, dispersal) of both marked and unmarked populations, accounting for imperfect capture/detection probability. The course will cover closed population models, Cormack-Jolly-Seber models, multistate models, reverse-time Pradel models, and Robust Design models with capture-mark-recapture data, closed and open N-mixture models with repeated count data, and site-occupancy models with detection/nondetection data. Models will be fit using the ‘RMark’ and ‘unmarked’ packages in Program R. Each class will begin with an introduction to the subject material through a brief lecture followed by the application of the concepts through exercises in R (e.g., formatting data, fitting and selecting models, visualizing predicted relationships) using simulated or real datasets. Students will be encouraged to use their own data when possible.
I will post a video lesson each week to introduce the topic that we will cover in the following week. Please watch each weekly video prior to the start of class in the following week. Search for videos under 'Video Lessons' below. Videos will appear under the date on which they were posted. Finally, please read the 'Additional Instructions' below on downloading/installing the software and packages required to execute the R scripts that accompany each lesson.
Gabriel Barrile (Please email gbarrile@uwyo.edu with any questions, comments, or requests.)
Molly Caldwell (Guest Lecturer)
Downloading Individual Folders from GitHub
Abundance: Closed Binomial N-mixture Model in unmarked
Coding Session: Closed Binomial N-mixture Model
Abundance: Open Binomial N-mixture Model in unmarked
Coding Session: Open Binomial N-mixture Model
Abundance: Closed Population Estimation in RMark
Coding Session: Closed Population Estimation in RMark
Occupancy: Closed Occupancy Model in unmarked
Coding Session: Closed Occupancy Model in unmarked
Occupancy: Open Occupancy Model in unmarked
Coding Session: Open Occupancy Model in unmarked
Occupancy: Open Occupancy Model in RMark
Coding Session: Open Occupancy Model in RMark
Survival: Cormack-Jolly-Seber Model in RMark
Coding Session: Cormack-Jolly-Seber Model in RMark
Molly Caldwell Guest Lecture: Wildlife Camera Analysis
Survival: Robust Design with Temporary Emigration in RMark
Coding Session: Robust Design with Temporary Emigration in RMark
Multi-State Capture-Mark-Recapture Model in RMark
Coding Session: Multi-State Capture-Recapture Model in RMark
Download and install the following programs for your platform:
R and RStudio Desktop
Once you have R and RStudio set up on your device, install the following packages via pasting these commands into your prompt (i.e., copy and paste the code into the "Console" of RStudio and hit enter):
install.packages("unmarked")
install.packages("tidyverse")
install.packages("ggplot2")
install.packages("RMark") # you need Program MARK installed on your computer firstSimply click the Code dropdown button at the top-right of this page (scroll up to see it). Then hit Download ZIP in the dropdown menu. If you're not sure where to save it, just download and unzip to your Desktop.
This graduate course is offered through the University of Wyoming. A huge thank you to Jerod Merkle in the Zoology and Physiology Department for supporting this effort.