Fisheries Ecology and Management Fall 2008

FAS 6932 Sections 1616 and Sections 8902 (see registration info below)

Location: Fisheries Program Millhopper Location

Possibly available as a web-based distance learning course. For more information on distance options contact Bill Pine (billpine@ufl.edu)

Time: Lecture Friday 9:00-11:30 (mostly discussion) Lab Friday 1:00-3:00.

Instructors: Dr. Carl Walters and Dr. Steve Martell

Prerequisites: There are no prerequisites for this class. Students should be familiar with basic spreadsheet operations. Students are also encouraged to read the Walters and Martell text "Fisheries Ecology and Management" prior to class.

Registration information: Note for Fall 2008 there are two sections because the course will basically be split into two parts (see below)

Students who have taken Carl's class from Fall 2006 should register for FAS 6932 Section 8902, 3 credits by contacting Sherry Giardina

Students who did not take the class in Fall 2006 should register for FAS 6932 Section 1616, 4 credits via online registration system

Description and background information

This is a special course offered by the Program in Fisheries and Aquatic Science. This course is a graduate course on fisheries stock assessment and management. This course will focus on modern stock assessment models and why these methods work, why they sometimes fail, and how they can be improved and used in evaluating management decisions. This course will be based on the book "Fisheries Ecology and Management" authored by Carl Walters and Steve Martell.

Students are expected to have some experience with basic fisheries management concepts and an interest in building computer models to evaluate trade-offs in management decisions.

SPECIAL NOTE ON THE FALL 2008 VERSION OF THIS COURSE:

Due to unavoidable travel and research conflicts, Carl Walters will not be joining us this year until October - December 2008 and then March - April 2009. To maximize learning opportunities for students there will be two sections of this course that cover different material. Dr. Steve Martell (UBC) will be joining us for a seven week short course (August 29 - October 10) that will be similar to a variety of assessment courses and workshops Dr. Martell has taught in recent years. This portion of the course will assume that students have a basic understanding of fish population dynamics and some experience with stock assessment methods and terminology. Preliminary lecture topics for Dr. Martell are below. Dr. Walters will then be teaching his regular fisheries stock assessment course from October 17 - December 7 including a three-day Ecopath workshop December 5-7. Preliminary lecture topics for Dr. Walters are below Dr. Walters will resume his regularly scheduled teaching at UF in Fall 2009. All students interested in quantitative fisheries are welcome and encouraged to participate in both sections. The two sections allow students who have received previous credit for this course to receive credit for Dr. Martell's portion this term.

Dr. Martell's lectures for Fall 2008

Friday August 29

1. Basic R workshop, graphing, data reading, leading into an overview of non-linear parameter estimation: top-ten tips and tricks to ensure global convergence, using the information matrix to compute covariance and correlation matrix. Things to do: familiarize students with grouper data, fit growth curves, plot landings data

Friday September 5

2. Continue R orientation, move into simulation-estimation experiments: Monte Carlo methods for evaluating estimator performance, ensuring the estimator is unbiased, evaluating alternative data for field experiments and population monitoring.

Friday September 12

3. Bayesian methods for fitting models to data: Importance Sampling, Markov Chain Monte Carlo methods (MCMC), Gibbs Samplers, the Metropolis-Hastings algorithm.Convergence diagnostics (CODA package in R) and conveying uncertainty in management decision variables.

Friday September 19

4. Parameter transformations: how to transform model parameterizations to reduce the amount of variable confounding and improve the statistical properties and mixing rates in MCMC methods.

Friday September 26

5. Introduction to Automatic Differentiation Model Builder (ADMB): using ADMB as an analyst tool, simulation-estimation experiments, Likelihood profiling, MCMC methods, calling ADMB from R. Begin stock assessment case history.

Friday October 3

6. Continue stock assessment case history

Friday October 10

7. Finalize stock assessment case history

Dr. Walters lectures for Fall 2008

Friday October 17

8. Basic population dynamics and responses to harvesting: the central roles of recruitment relationships and yield per recruit patterns. Basic population modeling; age structured population models; compensatory recruitment responses; growth-mortality interactions.

Friday October 24 NO CLASS, HOLIDAY

Friday October 31

9. Design of feedback harvest policies for coping with unpredictable variation in natural populations. How feedback policies work; effect of management objective on form of best feedback relationship; feedback created by effort response dynamics; open loop optimization for population rebuilding and feedback policy design; coping with regime shifts.

Friday November 7

10. Harvest management tactics for limiting exploitation rates. Input vs output controls; control of fishing effort; direct control of fishing mortality; preventing pathological growth in fishing mortality in range-contracting stocks; options for regulation of open access recreational fisheries.

Friday November 14

11. Basic stock assessment models and techniques. State and observation models and model fitting; importance of relative abundance data; using stock reduction analysis to obtain long-term perspectives; use and misuse of age-size composition data.

Friday November 21

12. Assessment of recruitment relationships. Patterns of recruitment variation; causes of severe bias in estimating recruitment parameters; experimental management policies for determining limits to compensation; estimating recruitment relationships in integrated stock assessment models.

Friday November 28 NO CLASS, HOLIDAY

13. Spatial and temporal dynamics of fishing effort. How effort varies with fish abundance; long term capital investment and fleet capacity dynamics; interaction of effort with fishing regulations; design of MPA policies; effect of enhancement programs on effort dynamics and impact on wild stocks.

Friday-Sunday December 5, 6, 7

14. Workshop (3 days) on use of Ecopath/Ecosim software for analysis of impacts of trophic interactions on fisheries dynamics and policies.

Construction of Ecopath mass balance models; representing age structure and trophic ontogeny effects using multistanza population models; policy gaming with Ecosim; fitting Ecosim models to historical data; Ecospace models for evaluating ecosystem scale impacts of marine protected areas.

Assignments

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Links to Lectures (from Fall 2006)

Lecture 5 Tuesday Q and A session (note use your slider bar to fast forward through the first 5 mins when nothing is being discussed)