Models for Marine Ecosystem-Based Management
2022-12-06
Welcome
Models for Marine Ecosystem-Based Management: Hello! This is a course taught by Dr. Gavin Fay at UMass Dartmouth in fall 2022. The course is supported through Dr. Fay’s CINAR fellowship in Quantitative Fisheries and Ecosystem Science. Course can be attended by students and staff at CINAR institutions and all UMass campuses (if you are not at one of these institutions but are interested in the class please email Gavin).
Description: This course provides instruction, demonstration, and exercises in quantitative modeling tools used for Ecosystem Based Management (EBM) of living marine resources. There is an increasing need for fisheries and wildlife professionals to provide scientific advice for management in an ecosystem context. Part 1 of the course will provide students with hands on experience applying fisheries stock assessment and population models that include ecosystem effects, and consider the policy implications of including this information. Part 2 of the course will focus on broader multiple-use and human dimensions and include economic and behavioral models and models for marine spatial planning. The final section of the course will introduce whole-of-ecosystem models and demonstrate how these can be used to provide strategic advice for marine management and consider a broad suite of objectives. Although the examples used will be in a marine context, the types of models and methods discussed in the course have application in other systems.
Course Objectives: 1. Familiarity with a range of models used for ecosystem-based management and experience using some of them. 2. Understanding of the benefits, challenges, and limitations of using these models to provide scientific advice for management.
Credits: 3
Class modality: In person at UMassD-SMAST in New Bedford, with all course sessions also available for remote attendance via Zoom. Some guest lectures remote learning only. There are two sub-module ‘workshops’ during the course - a TMB training in September, and a sequence of class sessions on the R implementation of Ecopath with Ecosim (EwE) foodweb modeling software, Rpath. Students who are interested in attending just one or both of these sub-modules should email Dr. Fay ASAP.
Class location: SMAST-E 247, synchronous via Zoom (registered students will receive the link)
Class time: T/Th 1:00pm - 2:30pm (see exceptions in schedule below)
Code of Conduct; This course follows the Fay Lab code of conduct, which applies to all class spaces, including classroom, myCourses, Zoom calls, class GoogleDocs, and student hours. You can also read my lab's lab culture and philosophy, which underpins my approach to teaching and collaboration. During our initial session we will co-create our community guidelines for the semester.
COVID-19: We are in the middle of a global pandemic and things are not normal. I want you to succeed in this course and will do what I can to help support your being able to meet our learning objectives. Please communicate with me if there are additional things I can do to help support you. I will not ask you to disclose information related to your reasons for such requests outside of what is needed to provide possible solutions.
Agenda
(subject to change)
| Date | Week | Day | Topic |
|---|---|---|---|
| 1-Sep | 1 | Th | Software installation troubleshooting (9am) |
| 1-Sep | 1 | Th | Introduction to EBM |
| 6-Sep | 2 | T | TMB Workshop I (9am) |
| 6-Sep | 2 | T | TMB Workshop II |
| 8-Sep | 2 | Th | TMB Workshop III (9am) |
| 8-Sep | 2 | Th | TMB Workshop IV |
| 13-Sep | 3 | T | Course topics & fisheries assessment methods review |
| 15-Sep | 3 | Th | Extended Stock assessment models |
| 20-Sep | 4 | T | Qualitative modeling I Project descriptions due |
| 22-Sep | 4 | Th | Qualitative modeling II Homework 1 due (dynamic reference points) |
| 27-Sep | 5 | T | Multispecies models - estimating species interactions |
| 29-Sep | 5 | Th | Species Distribution Modeling with sdmTMB (Dr. Eric Ward, NOAA NWFSC)Homework 2 due (SES modeling) |
| 4-Oct | 6 | T | More species distribution modeling |
| 6-Oct | 6 | Th | More Models of Intermediate Complexity for Ecosystems (MICE) |
| 11-Oct | 7 | T | NO CLASS - MONDAY SCHEDULE |
| 13-Oct | 7 | Th | ICES WGSAM (Working Group for Multispecies Stock Assessment Methods) 10/10-10/14 in Woods Hole, MA and online Homework 3 due (multispecies modeling) |
| 18-Oct | 8 | T | Ecosystem Indicator Analyses (Dr. Scott Large, NOAA NEFSC) |
| 20-Oct | 8 | Th | Food web models I (Rpath module, Dr. Sean Lucey, NOAA NEFSC) |
| 25-Oct | 9 | T | Food web models II (Rpath module, Dr. Sean Lucey, NOAA NEFSC) |
| 27-Oct | 9 | Th | Ecosystem MSEs (Rpath module, Dr. Sean Lucey, NOAA NEFSC) Project plans due |
| 1-Nov | 10 | T | State-space modeling for EBFM (Dr. Greg Britten, MIT) |
| 3-Nov | 10 | Th | Woods Hole Assessment Model (WHAM) (Dr. Tim Miller, NOAA NEFSC) Homework 4 due (Rpath tradeoff analysis) |
| 8-Nov | 11 | T | Climate-linked fisheries stock assessment (Amanda Hart, GMRI) |
| 10-Nov | 11 | Th | Multispecies policy analysis - fishery ecosystem plans |
| 15-Nov | 12 | T | Multispecies MSE & fleet dynamics |
| 17-Nov | 12 | Th | Marine spatial planning |
| 22-Nov | 13 | T | Whole of system models I |
| 24-Nov | 13 | Th | NO CLASS - THANKSGIVING |
| 29-Nov | 14 | T | Whole of system models II |
| 01-Dec | 14 | Th | Whole of system models III Project drafts accepted |
| 02-Dec | |
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| 06-Dec | 15 | T | Multicriteria Decision Analysis |
| 08-Dec | 15 | Th | NO CLASS |
| 13-Dec | 16 | T |
Project presentations Project reports due |
Prerequisites: Students should have taken coursework in applied statistics (e.g. MAR 535, Biological Statistics), or equivalent. Experience with the programming language R at the advanced beginner level is required (contact Dr. Fay if you would like recommendations for brief training materials that cover the necessary background). Students should also be familiar with modeling and estimation approaches for fisheries assessment and conservation management (e.g. MAR544), or seek permission from the instructor. While MAR530 (ecosystem-based fisheries management) provides useful background material for this class, it is not required.
Evaluation procedures: 1. Five homework assignments (12% each). 2. Final project (40%). The aim of the project will be to apply some of the modeling methods covered during the course to a research-related task, and can be carried out individually or in small groups (2-3). For group projects, all group members must have readily-identifiable tasks and the same grade for the project will be assigned to all members of a group. Students are encouraged to select topics which are relevant to their thesis research and/or could form the basis for a short publication. Deliverables on project progression through the semester are a short (~1 paragraph) project description, a brief meeting with Dr. Fay to discuss the proposed project, a project plan (detailed outline including key literature, and clear description of methods/experimental design), a verbal (8 minute) presentation of the methods and results at the end of the semester, and a written description of the methods and results of the project in the form of a draft scientific manuscript (Introduction, Methods, Results, Discussion).
Failure to complete any of these requirements for evaluation will result in a score of zero for missing components. A final grade of 'incomplete' may be recorded at the request of the student and the discretion of the professor.
No academic dishonesty, including plagiarism, will be tolerated and the University Academic Integrity policy applies.
Course materials: This website (built in R!) provides access to the workshop materials and will be updated during the course as we progress (and adapt).
This website: https://gavinfay.github.io/mebm-models/
GitHub repo: https://github.com/gavinfay/mebm-models
About the instructor
Gavin Fay (he/him) is an Associate Professor of Fisheries Oceanography at the University of Massachusetts Dartmouth’s School for Marine Science and Technology, based in New Bedford, MA. He is a 2020-2022 CINAR Fellow in Quantitative Fisheries & Ecosystem Science, funded through the NOAA Northeast Fisheries Science Center and NOAA Fisheries’ Quantitative Ecology & Socioeconomics Training program (QUEST). This course is part of Dr. Fay’s CINAR Fellowship activities. Email Twitter
Pre-course preparations
Required hardware: Students should have use of a laptop computer for class sessions and assignments. Our class meetings will be a mix of lectures, discussions, and modeling, so it is necessary to have your computer at each meeting.
Software: Our course exercises and modeling will primarily be done in R. You should install R and a suitable IDE (RStudio is one of the most common and will be how I work during the course).
If you already have R and RStudio installed on your machine, please take time before the course to install the latest versions, to help mitigate errors with installs and dependencies during the course. Using the most recent versions of these free software also gives you access to the most current functionality of the tools.
All of the course scripts, models, etc. will be tested using R 4.2.1. and RStudio 2022.07.1 (Build 554).
In addition to having R & RStudio downloaded on your machine, there will also be a RStudio Cloud project for the course, which will contain all necessary dependencies and packages used during the course.
Necessary libraries, and other pieces of software used in the course will be detailed in the relevant materials.
Software installation session & TMB: Gavin will run an optional software installation troubleshooting session at the beginning of the course on Thursday September 01, from 9:00-10:00 in SMAST-E 247. This would be a GREAT time to make sure TMB is working on your machine.
Reading
A recommended reading list covering the individual topics will be posted on this website, as well as a Zotero database for the course. There is no required text for this class, though students will find sections of the following books useful.
- Link, J. 2010. Ecosystem-based fisheries management: confronting tradeoffs. Cambridge Univ. Press, Cambridge.
- McLeod, K., & Leslie, H. (Eds.). 2009. Ecosystem-based management for the oceans. Washington, DC, USA: Island Press.
- Walters, C. J., & S.J. Martell. 2004. Fisheries ecology and management. Princeton University Press.
Title IX statement
The purpose of a university is to disseminate information, as well as to explore a universe of ideas, to encourage diverse perspectives and robust expression, and to foster the development of critical and analytical thinking skills. In many classes, including this one, students and faculty examine and analyze challenging and controversial topics.
If a topic covered in this class triggers post-traumatic stress or other emotional distress, please discuss the matter with the professor or seek out confidential resources available from the Counseling Center, http://www.umassd.edu/counselling/, 508-999-8648 or -8650, or the Victim Advocate in the Center for Women, Gender and Sexuality, http://www.umassd.edu/sexualviolence/, 508-910-4584. In an emergency contact the Department of Public Safety at 508-999-9191 24 hrs./day.
UMass Dartmouth, following national guidance from the Office of Civil Rights, requires that faculty follow UMass Dartmouth policy as a "mandated reporter" of any disclosure of sexual harassment, abuse, and/or violence shared with the faculty member in person and/or via email. These disclosures include but are not limited to reports of sexual assault, relational abuse, relational/domestic violence, and stalking. While faculty are often able to help students locate appropriate channels of assistance on campus, disclosure by the student to the faculty member requires that the faculty member inform the University's Title IX Coordinator in the Office of Diversity, Equity and Inclusion at 508-999-8008 to help ensure that the student's safety and welfare is being addressed, even if the student requests that the disclosure not be shared.
For confidential counseling support and assistance, please go to http://www.umassd.edu/sexualviolence/
Licensing
All materials are released with Creative Commons Attribution Share Alike 4.0 International license.
Acknowledgements
This website is built with bookdown., and the lovely icons by icons8. The course website design was based on both the R for Excel Users course by Julie Lowndes & Allison Horst, and the Data Science in a Box course by Mine Çetinkaya-Rundel, and previous course materials developed by Gavin Fay. All errors are purely by Gavin.