Population Modeling in Ecology

Welcome to statistical modeling in population ecology! This online 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 such as occupancy and abundance as well as population vital rates such as survival, recruitment, and dispersal. The course is comprised of instructional videos with associated datasets and R code. To jump right into the video series, click 'Start Course' below to begin the course from the beginning, or search 'By topic' to skip to specific lessons. Further, please read the 'Additional Instructions' below on downloading/installing the software and packages required to execute the R scripts that accompany each lesson.

Instructor

Gabriel Barrile

Please email gbarrile15@gmail.com with any questions, comments, or requests.

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Video Lessons

Full playlist

Start Course

By topic

Course Overview

Introduction to Population Analysis

Abundance: Closed Binomial N-mixture Model in unmarked

Abundance: Closed Binomial N-mixture Model in rjags

Abundance: Closed Population Estimation in RMark

Abundance: Open Binomial N-mixture Model in unmarked

Occupancy: Single-Season Occupancy Model in unmarked

Occupancy: Single-Season Occupancy Model in rjags

Occupancy: Multi-Season Occupancy Model in RMark

Survival: Cormack-Jolly-Seber Model in RMark

Recruitment: Robust Design Pradel Model in RMark

Dispersal: Robust Design Multi-state Model in RMark

Highlighting Underrepresented Works in Population Ecology and Analysis

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Additional Instructions

Download and install the following programs for your platform:

R and RStudio Desktop

Program MARK and JAGS

Installing packages

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("rjags")
install.packages("RMark")
install.packages("reshape")
install.packages("ggplot2")

Downloading code/data from this repository

Simply 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.

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Acknowledgments

This online course in population analysis was made possible through the funding of Wyoming NSF EPSCoR via the Microbial Ecology Collaborative. A huge thank you also to Western EcoSystems Technology, Inc. (WEST) and the University of Wyoming for hosting and supporting this project. Special thanks to Andrew Tredennick of WEST for supervision and feedback on each lesson and analysis.

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License

<a rel="license" href="http://creativecommons.org/licenses/by/2.0/">Creative Commons Attribution 2.0 Generic License</a>.