NMFS - UW Salmon Modeling Framework Review Committee

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DATE: March 27, 1997
MEMORANDUM FOR: Salmon Model Review Group and interested parties
SUBJECT: Notes from Feb 21 1997 meeting NMFS Montlake Laboratory
FROM: Robert Kope, Tom Wainwright, Jim Anderson

CONTENTS

1. project goals reviewed
2. status of oversight committee
3. scheduling
4. communication and travel
5. working groups

^ data structure

^ migration

^ maturation

^ calibration and optimization

^ definitions

^ model I/O

^ model certification

^ model comparison

^ data

^ documentation

6. Jim Norris Report
7. Rich Comstock Report
8. People for workgroups
9. Next meeting
10. Distribution List

PROJECT GOALS REVIEWED

Kope - discussed background for the models

ESA requires consultation for any federal activity that may impact a listed species. The intent is to establish consistent jeopardy standards for ESA consultations and recovery planning. Two interests for models

1. risk assessment for developing consistent standards for listing and recovery
2. evaluating impact of harvest on listed stocks

The long-term goals of this project as stated before are:

1. Provide a common framework for both conservation risk assessment and harvest management analysis.
2. Incorporate life cycle (production) models for both species to evaluate harvest and conservation strategies.
3. Incorporate formal risk-assessment methodologies.
4. Allow flexibility to accommodate new methods and model designs.
5. Provide an interface with the largest possible subset of the ocean and freshwater databases maintained by PSMFC.
6. Expand the geographic scope of current harvest models.
7. Link coho and chinook salmon harvest models.

Discussion noted we can divide the effort into a harvest model effort and a habitat model effort. The two efforts would eventually be joined but the oversight committee being formed is to address the issues of harvest modeling. The two models are:

1. RAM (Risk Assessment Model) - A coastwide salmonid conservation and extinction risk assessment model. This model will apply the Bayesian risk assessment paradigm to multi-species and multi-population assessments in support of recovery and restoration planning for protected stocks. The model will eventually incorporate effects of harvest, hatchery, and habitat management as well as ocean variability and metapopulation structure.
2. HAM (Harvest Assessment Model) - An integrated chinook and coho harvest model. This model will be directed toward assessing year-to-year management regulations and longer-term harvest management policies. It will incorporate spatial aspects of migration and harvest and explicitly include bycatch and non-landed mortality components.

STATUS OF THE OVERSIGHT COMMITTEE

As defined previously the Oversight Committee mainly will focus on the Harvest Assessment Model. The Oversight Committee responsibilities include

A. Specification activities:

set delivery dates of a management model

identify functionality for ESA and comanagement

assist in developing conceptual framework

identify input and output requirements

work on a regular, but informal basis, with development team

B. Certification activities

identify and provide data for calibration

data to certify that general model can be configured to FRAM, SFM, SSM and CRiSP2

evaluate sensitivity of model to define critical assumptions and implications

communicate results and characteristics of model to management community

use model in negotiation process

Legal issues of who can participate in the Oversight Committee are framed by the unfunded mandates reform act which exempts committees composed entirely of government representatives from the requirements of the Federal Advisory Committee Reform Act. This provides no basis for formal participation of the Canadian representatives, but they are encouraged to participate in an informal capacity.

Jim Scott suggested we have PSC as the oversight organization since it already has a certification process. He also added he likes the role of the guidance panel as outlined in the notes from the Dec 20 1996 meeting.

It was made clear that to obtain a model for management, the fish managers must be closely involved with all aspects of the model development.

SCHEDULING:

Replacement for FRAM is needed by 1998.

The new model will be modified to split groups in to marked and unmarked, tagged and untagged groups. The model will be able to deal with groups both individually and together.

In developing a general coastwide model we look at the currently available models. We are developing a general structure that should be applicable for a multispecies-multistock analyses.

Our short-term goal is to have a prototype model running by the end of Sep 97. By this we mean a generalized model that can be configured to duplicate the output of one of the existing models, such as the PSC chinook model. For the longer-term our goal is to have a model that can be used to evaluate selective fisheries for the 1998 season. That would require having a model certified sometime in Feb 98.

COMMUNICATION AND TRAVEL:

The issues of communication of the Oversight Committee and the informal subgroups was addressed. It was suggested that PSFMC might assist in this supporting travel for the Oversight Committee and any subgroups.

A WEB page will be used to exchange information between the subgroups group the Oversight Committee and the model development team. A Web based list server has been implement and can be used to organize communications on specific topics see the harvest web page:

"Comments can be added to the Web using the hypertext notes at" http://www.cqs.washington.edu/harvest

The web list server could eventually include a salmon management web group that will connect all salmon harvest management activities in the region. Software to develop a community web page has recently become available (www.throw.com). This might have value to our model development and salmon management in general. Anderson will review this and see if its worth implementing

WORKING GROUPS:

We identified the need for informal working groups to address specific issues. Currently identified issues are:

Model structure: To develop the model code structure

Migration algorithms: To identify the types of algorithms for ocean migration

Maturation algorithms: To formulate maturation rates in terms of fish migration to rivers

Calibration and optimization: To define procedures for calibration model with CWT and fishing effort data. Identify algorithms to find optimum harvest strategies within the model

Definitions: to standardize definitions between models

Model I/O: To define input-output requirements for harvest management

Certification: develop a process to certify a model for management

Model Comparison: compare existing models to the new model Data: Obtain data for comparison of existing models to the new model

Documentation: to be developed by UW.

Risk Assessment: to identify risk assessment model function from the recommendations of the risk assessment workshop panel report (anticipated to be available in March 1997).

Notes on the issues facing the working groups are discussed below

MODEL DATA STRUCTURE:

Progress on developing model structure was presented by Jim Norris

The model structure will

1. synthesize all existing models into a general format based on processes rather than data structures;
2. allow for different algorithms for each model process;
3. provide a flexible calibration procedure;
4. track cohorts (eg marking and tagging status) separately.

MIGRATION:

A work group for migration model development:

A first task is to collect literature. This should include a literature survey of the migration models available. This will be collected and distributed to the groups as a series of papers. Jim Anderson will employ a student (David Caccia) to put the literature together on migration.

MATURATION:

The approach would be to express maturation as an age specific migration rate into the river

Kope has algorithm to express maturation function in migration framework

Johnson concerned about maturation to migration basis framework

Scott noted it may be difficult to calibrate a migration-maturation structure with CWT

Noted: age of maturation changes from year to year and may relate to ocean distribution of fish as related to ocean circulation and fish growth

CALIBRATION AND OPTIMIZATION:

Model calibration will be considerably involved and will be considered at a later meeting. We anticipate creating an informal model calibration subgroup that will address the issued in detail.

The discussion of "optimization" occured in several contexts. One was how to calibrate the model. Jim Scott remarked that his staff advised that we should use optimization routines to find the set of free parameters (ie calibrated parameters) that give the best fit of the model outputs to corresponding observed data.

A second context was in the basic model computation enine. Here the problem is that of finding single year harvest levels that satisfy complex policy objectives, such as equalizing Indian and Non-Indian catches, meeting minimum escapement goals, allocating catches within Indian and Non-Indian fisheries. These types of optimization algorithms would run during simulation years as part of the computation engine. Someone observed that there may be multiple solutions and that it will be difficult to identify these and select between them during within year computations.

A third context was that of designing code that "optimizes" overall computation speed.

DEFINITIONS:

Blair Holtby noted model specifications are need to define equivalence of terminology between the new and existing models. This led to a specific task to identify common nomenclature for the models. A table will be developed to identify equivalent model terms and parameters. Lead on this was Jim Packer 902- 2754. Jim Scott and Larry Lavoy will assist. The goal is to have a table ready for the next meeting.

MODEL I/O:

Input Output specification must be identified by managers using the model. To do this we will first spend time with the FRAM model to understanding its output and how this meets the needs of managers.

Blair Holtby suggested a model needs risk assessment output specifications including:

(short term risk = comanagement issue) risk of not achieving an escapement foal with in a seasons

(long term risk = ESA issue) risk of long term extinction

MODEL CERTIFICATION:

The harvest assessment model will need to be certified for use by fisheries managers. A certified model would be used by the formal fisheries technical committees responsible for making recommendations for harvest management. These committees generally will not have time to evaluate a new model. In this case our task is to provide enough information so the technical teams can understand the steps we have made to validate our model for management. The Oversight Committee might take this function of certifying the model. The certification will include model documentation and comparison to existing models with a common data set.

Membership in the certification group.

The certification is likely to be a PFMC and PSC process. Our model Oversight Committee can help idenfity how we can assist these groups in model certification.

It was noted that Canada has similar issues upcoming and they wish to participate in our process to the degree possible.

MODEL COMPARISON:

An important step in certification is to compare the model to the existing models. This will involve a subgroup to run the existing models and compare them to the new model.

The new model will be compared to FRAM

Pete Lawson suggested we need exact equivalence of the new model to the existing models. This may or may not be entirely possible. If a one-to-one equivalence is not possible the Oversight Committee will need to resolve the issue if differences in the model are significant and if changes need to be made to resolve differences.

Need to work with and through the technical advisory committees for the various fishery management group

FRAM is the only existing model for coastwide coho

PSC or CRiSP2 model is the only existing coastwide chinook model

DATA:

Comstock distributed three data maps to be used for comparison of models:

fish (catch sampling effort stock), age, time period. Note we may have catch and fish sampling different. Need to have one set of definitions for the data reconstruction and comparison.

Rich Comstock and Rick Moore: can reconstruct data for comparison of the models in three time steps.

Rich Comstock will work with Norma Sands, Rick Moore and Peter Lawson the week after the meeting. Was this done? what was accomplished?

DOCUMENTATION:

A manual theory, calibration and validation: UW will take the lead in model documentation with assistance of NMFS and the Oversight Committee.

Develop an executive summary showing main issues of the documentation. This would give fisheries managers a quick overview of the model.

The CRiSP 2 manual is currently being updated. This can be used as a framework for the new manual.

JIM NORRIS REPORT ON MODEL DEVELOPMENT

On the issue of fish migration in the model

A migration matrix will be computed outside the model

The matrix will be stock and year specific. The Newman one dimensional migration model is one way to define migration but we can define other methods that allow branching of the linear model. A third way is to represent migration by spatial boxes. A fourth way is to have a 2-dimension diffusion model.

All migration models are likely to use CWT and effort data. A question was asked, is there another or better way to estimate migration. It is also possible to incorporate a numerical simulation model such as NERKAsim

Organization of the data structure follows the convention

REGION Number -> Fishery unit -> Harvest Object

Time Step: A period of time during which it is assumed that all fisheries within a given geographic region are operating on the same abundance of fish from each cohort.

The mathematical implication is that the independent variables used within the harvest functions are the same for all fisheries within the time step and region.

TASKS PRIOR TO NEXT MEETING

Objects definition meeting

Comparison of terminology in the different models

Tasks by the model development group

Norris: develop object structure for model

Norris: identify nomenclature of model terms

Scott: consider issues of optimization routines

RICH COMSTOCK PRESENTATION ON DATA

Rich Comstock described his data for model comparison including

CWT recovery

catch and effort data

identifying statistical catch areas

Rich is working with Ken Newman on a frequent basis

Question- What will be done with the PM model. It has a heuristic migration model. The PM model has been converted to the PYTHON objected oriented code, which is similar to C++.

PEOPLE MENTIONED FOR WORK GROUPS

1. model nomenclature table - 3 Jims and Packard
2. conceptual framework objects - Jim Norris, Troy Frever and Rich Comstock
3. model functionality for fisheries management this included needed I/O: Scott, Dan Bottom (?), Doug Gill
4. calibration issues: Ken Newman. Rich. Comstock.
5. literature on migration and climate ecology: Jim Anderson will find a student
6. list server and web page issues: Anderson and staff

NEXT MEETING APRIL 18 at NMFS Montlake Lab

DISTRIBUTION LIST

Jim Anderson	UW
Robert Bayley	NMFS
Jim Berkson	CRITFC
Rich Comstock	USFWS
Carrie Cook-Tabor	USFWS/NMFS
Judy Cress	UW
Rich Dixon	CDFG
Peter Dygert	NMFS
John Geibel	CDFG
Brent Hargreaves	DFO
Ken Henry	NMFS, REFM
Blair Holtby	DFO
Ron Kadowaki	DFO
Jeff Koenigs	ADFG
Robert Kope	NMFS
Pete Lawson	ODFW/NMFS
Steve Lindley	NMFS
Richard Methot	NMFS
Marianne McClure	CRITFC
Rod McInnis	NMFS
Rick Moore	WDFW
Gary Morishima	QIN
Ken Newman	U of Idaho
Jim Norris	UW
Mike Prager	NMFS
Bill Robinson	NMFS
Norma Jean Sands	ADFG
Jim Scott	NWIFC
Steve Smith	NMFS
Dan Viele	NMFS
Tom Wainwright	NMFS
Brian Riddel	Department of Fisheries and Oceans, Nanaimo BC V9R 5K6

Those who don't have email address on this list will each receive a hard copy in the mail.