/harvest/discussion/

As of April 18, the page includes minutes for the Dec 20, 1996 and Feb 21, 1997 meetings and discussion sections for:

-- Model Vision
-- Main Engine Overview
-- Code Object Evaluation
-- Time Objects
-- Geographic Objects.

Each code object section includes a general description of the object, what services the object provides, the data needs for the object, and the methods the object will have. Some objects also include a discussion about how existing models treat the object.

Jim presented a summary overhead of the Model Vision (see web page for full text of the Model Vision). There was a general discussion about model parameterization and calibration.

Doug Eggers noted that these types of large models tend to require more information than is currently available and this creates calibration problems. Jim commented that we will undoubtedly have to decide which parameters to fix and which to allow to float free during any calibraton process. His goal is to develop a flexible calibration framework such that the fixed parameters, control variables, and objective function can be defined relatively easily. He mentioned the "Solver" tool in Excel as an example. Pete Lawson commented that we will have to consider the trade-offs (e.g., predictive power) between a model with lots of parameters vs one with fewer parameters.

Jim Norris presented the draft Main Engine Overview for discussion. He stated that his objective was to create a model framework organized around biological processes rather than currently available data. Here's the draft main computing engine:

void RunTheModel()
{
for (int year = 0; year < Chronographer->nyears(); ++years) {
YearInit(year);

for (int TimeStep = 0; TimeStep < Chronographer->nsteps(); ++TimeStep){

PhysEnvManager.update_physical_environment(); BiolEnvManager.update_biological_environment(); AgeManager.age_cohorts();
NatMortManager.take_natural_mortality(); GrowthManager.grow_cohorts();
FisheryManager.take_fishing_mortality(); SpawningManager.spawn_cohorts();
MigrationManager.migrate_cohorts();
DataManager.timestep_wrapup();
}

DataManager.year_wrapup();
}
}


Jim explained in general terms what each component will do and referred committee members to the web page for full written descriptions. He noted that the FisheryManager object was still a little fuzzy due to the potential need to adjust catches over several time steps to meet some management objectives (e.g., allocation between Tribal and Non-Tribal fisheries, allocation between gear types, meeting escapement goals).

Gary Morishima asked how meta-populations (e.g., the Columbia River stocks) would be treated during the spawning process. Jim replied that spawning will occur by geographic areas rather than individual stocks, so hopefully any meta-population processes could be incorporated within the spawning area object. Gary also suggested that we need to include a method for simulating catch sampling (i.e., data gathering). Jim felt that the FisheryManager object would handle this function.

There was a discussion about the TimeStep definition. The currently proposed definition is:

"A TimeStep is a period of time during which all fisheries within a given region are assumed to be working on the same abundance of fish."

This definition assumes that fisheries within a given region and time step do not interact with one another. Jim noted that for gauntlet type of fisheries the user will have to select time steps appropriately to model the impacts one fishery may have on another. He also noted that Tom Wainwright had suggested on the web page that the definition should be relaxed or generalized so a TimeStep wasn't defined only in terms of the fishing process. Jim noted that the central issue regarding the TimeStep definition is what assumptions we want to make regarding the types of processes and algorithms we will allow during a TimeStep. He also noted that further comments about the TimeStep definition are on the web page.

Jim Scott suggested that the growth process should occur prior to the natural mortality process. Jim Norris concurred and will make the change.

Gary Morishima asked who would be building the models within the flexible framework--users, UW, PSC, States, Tribes, others? Jim answered that the initial version will be developed by UW and this committee, but later versions may be developed by anyone. Troy noted that we are attempting to build good abstract processes to cover any forseen (and unforeseen) implementations, assuming that somebody will eventually want to add new modules.

There was further discussion of model calibration and the problem of multiple solutions to objective functions that span multiple time steps (e.g., allocation and escapement goals). No specific recommendations emerged.

Jim Scott asked if fish growth would be independent of fishery. Jim responded that modeling growth and the potential effects of size selective fisheries would be a difficult problem. He described a method he used for sablefish analysis that involved dividing a cohort into 10 growth groups--five for each sex--each with a separate L infinity term in the von Bertalanfy growth function. This technique might create too many cohorts to keep track of in the model. Jim mentioned that it might be helpful for analyzing the effects of size selective fisheries on a small synthetic group of stocks.

Jim stated that the goal for October was to create a prototype model that (1) had a migration component based on Ken Newman's migration model and (2) would mimic the PSC Chinook Model when configured for a coho stock. The next step would be to mimic another existing model (e.g., FRAM, PM, PSC Selective Fishery Model). There was further discussion about how to compare the existing models and which ones should be selected for mimicing by the new model. Jim noted that the goal was to be able to put all of the models into a migration matrix format, and that the parameters for each migration matrix would be generated outside the main computing engine. No specific conclusions were reached during this discussion, but later in the meeting a work group was formed to address these issues.


2. DATA SETS FOR MODEL COMPARISONS.

Rich Comstock gave a progress report on data availability, organization, and extraction methods for migration modeling. These data also will be used to compare different migration models.

Two types of data are available:

1. CWT data (including release, recovery, catch/sampling effort data). These will be essential for fitting Ken's State Space Model.

2. Inter-agency run reconstruction data.

There was a brief discussion of the CWT data with three main points:

1. Rich plans to have the CWT Mark Committee examine the map of the PSC location codes to statistical areas.

2. Gary Morishima recommended that Rich check on a persistent problem in the CWT database, namely that the expansion factors sometimes do not match with the Catch/Sample File. Rich said he would check on this.

3. Rich reported that there were large numbers of recoveries in Alaska attributed to mixed gear and unknown gear categories. There is a problem allocating these recoveries to individual fisheries when the gear type is unknown.

Rich and Carrie gave a brief report on the Proportional Migration (PM) Model, including some handouts of class structure from the Python code. Jim Norris asked for a clarification about how geographic areas and fisheries were characterized in the PM Model. For example, the PM Model allocates fish to two troll fisheries and one sport fishery off the West Coast of Vancouver Island (NWVI Troll, SWVI Troll, WCVI Sport). Rich (and Peter Lawson) confirmed that the PM Model treats these as three distinct and non-overlapping areas with separate abundances of fish in each area.

3. JIM SCOTT REPORT ON MODEL FUNCTIONALITY.

Jim Scott distributed an outline for model functionality (listed below) along with several samples of output from current models (e.g., FRAM).

1. Models currently provide point estimates for a wide range of statistics including:

a) catch (shakers, non-retention, total mortality) by stock, age, time period, and fishery;
b) exploitation rates by stock and fishery;
c) exploitation rate scale factors by fishery and time period;
d) stock exploitation rate indices (ratio of predicted exploitation rate to base period);
e) cohort size by stock, age, and time period;
f) mature run size by stock, age, and time period;
h) escapement by stock, age, and time period;
i) treaty/nontreaty allocation accounting.

2. The next generation of models must provide a useful measure of the uncertaintly of the model predictions. Measures could include prediction intervals for key statistics, risk to stock perpetuation, future production versus current catch, etc.

3. The level of stock resolution is currently roughly by region within Puget Sound (e.g., Hood Canal, South Sound), by groups of rivers on the Washington Coast (e.g., Queets and Quinalt, Hoh and Quillayute), and at a greater level of aggregation in other areas (e.g., Oregon Coast).

4. Stock resolution will need to increase in the new model to meet management needs. In order of increasing complexity, these may include:

a) marked and unmarked;
b) hatchery and wild;
c) management units within regions;
d) stocks within management units.

5. The coho version of FRAM has 66 fisheries (each occurring in up to 13 months) from Southeast Alaska to California. Careful consideration will need to be given to the advantages of reducing the resolution to increase the number of CWT recoveries vis a vis increasing the resolution to meet management needs and accurately modeling stock distributions.

6. The model must be easy to use by biologists working under stressful conditions outside of the office. The majority of the model analyses are now done as part of the annual PFMC preseason planning process, an approximately one month period from March to April in each year. Management proposals are typically developed in consultation with user groups and evaluation of the proposals is expected to occur with 12 hours.

There was a discussion about data exchange protocols between the new model and existing models. Troy gave a brief overview of token based input, which will likely be the input format used by the new model. It was decided that until formatted output can be generated from the new model, the new model will simply write data output in ascii format that can be read by existing models. Peter Lawson mentioned that Phil Flanders from ODFW (Newport) was using Visual Basic to create tools for data exchange between models that may be useful for the current project. Jim Norris agreed to contact Phil to learn more about the tools.


4. LITERATURE REVIEW.

Jim Anderson reported that graduate student Dave Caccia was working on a literature review of salmon migration, but does not have a formal product ready at this time.


5. WORKGROUPS.

A Model Comparison Work Group was formed. Rich Comstock will lead with Jim Scott, Peter Lawson, Robert Kope, and Jim Norris participating. A meeting of the work group was scheduled for April 25, 1997 in Olympia to develop specific tasks for the group.


6. NEXT MEETING.

The next meeting will be 9:00 am Thursday June 19 (following the Resource Modeling Association meeting at UW) at the NMFS Montlake Lab.