# Presentation: 071723

##  Stock Synthesis:an Integrated Analysis Modelto Enable Sustainable Fisheries

**Richard Methot**
**NOAA Fisheries Service**
**Seattle, WA**

**Notes:**
I’m here to describe an integrated analysis model designed for the assessment data typically available for west coast groundfish and broadly applicable to a wide range of assessment situations.

## OUTLINE

**OUTLINE**

**Management Needs**
**Stock Assessment Role**
**Data Requirements**
**Stock Synthesis**
**Some Technical Advancements**
**Getting to Ecosystem**

## Control Rules, Status Determinations and Operational Models

**Control Rules, Status Determinations**** and Operational Models**

**Is stock overfished or is overfishing occurring?**
**What level of future catch will prevent overfishing, rebuild overfished stocks and achieve optimum yield?**

## Stock Assessment Defined

**Stock Assessment Defined**

**Simplest System**
**Link control rule to simple data-based indicator of trend in B or F**
**Easy to communicate; assumptions are buried**
**Hard to tell when you’ve got it wrong**
**Hard to put current level in historical context**

**Full Model**
**Estimate level, trend and forecast for abundance and mortality to implement control rules**
**Cross-calibrates data types**
**Complex to review and communicate**
**Bridges to integrated ecosystem assessment**

**Collecting, analyzing, and reporting demographic information to determine the effects of fishing on fish populations**

## Idealized Assessment System

**Idealized Assessment System**

**Standardized, timely, comprehensive data**
**Standardized models at the sweet spot of complexity**
**Trusted process thru adequate review of data and models**
**Timely updates using trusted process**
**Clear communication of results, with uncertainty, to clients**

## STOCK ASSESSMENT PROCESS

**POPULATION MODEL:**
**(Abundance, mortality)**

**STOCK STATUS**

**OPTIMUM**
** ****YIELD**

_**CATCH**_
**RETAINED AND**
**DISCARDED CATCH;**
**AGE/SIZE DATA**

_**BIOLOGY**_
** ****NATURAL MORTALITY, **
**GROWTH, **
** ****REPRODUCTION**

_**ABUNDANCE TREND**_
** ****RESOURCE SURVEY**
**or FISHERY CPUE,**
**AGE/SIZE DATA**

_**ADVANCED MODELS**_
**  ****HABITAT**
**  ****CLIMATE**
**  ****ECOSYSTEM**
**  ****MANMADE STRESS**

**SOCIOECONOMICS**

**STOCK ASSESSMENT PROCESS**

**FORECAST**

**Conceptually like NOAA Weather’s data assimilation models, but time scale is month/year, not hour/day**

## Fish Biology and Life History

**Fish Biology and Life History**

- Ease:  Length & Weight >> Age > Eggs & Maturity >>> Mortality

## Abundance IndexFishery-Independent Surveys

**Abundance Index****Fishery-Independent Surveys**

## Source of Abundance Indexes

**Source of Abundance Indexes**

**Each survey may support multiple assessments**
**Each assessment may use data from multiple surveys**

## Catch: What’s Been Removed

**Must account for all fishing mortality**
**Commercial and recreational**
**Retained and discarded**
**Discard survival fraction**
**Model finds F that matches observed catch given estimated population abundance**
**Because catch is nearly always the most complete and most precise of any other data in the model**
**But also possible to treat catch as a quantity that is imprecise and then to estimate F as a parameter taking into account the fit to all types of data**

## Catch Components

**Commercial retained catch**
**fish ticket census**
**Commercial discard**
**observer program**
**Recreational kept catch**
**catch/angler trip x N angler trips**
**Recreational releases**
**Interview x N angler trips**

## Catch per Unit Effort

**To estimate total catch:**
**Catch = CPUE x Total Effort**
**So CPUE must be effort weighted**
**As an index of population abundance**
**Relative biomass index = CPUE x stock area**
**So CPUE must be stratified by area so heavily fished sites are not overly weighted**

## Integrated Analysis Models

**Integrated Analysis Models**

_**Population**_** Model – the core**
**Recruitment, mortality, growth**
_**Observation**_** Model – first layer**
**Derive Expected Values for Data**
**Likelihood-based **_**Statistical**_** Model – second layer**
**Quantify Goodness-of-Fit**
**Algorithm to Search for Parameter Set that **_**Maximizes**_** the **_**Likelihood**_
**Cast results in terms of **_**management quantities**_
**Propagate **_**uncertainty**_** in fit onto confidence for management quantities**

**Notes:**
The general class of models termed Integrated Analysis incorporate a Population Model, an Observation Model, a Statistical Model, and a means to search for the best-fitting set of parameters

Generally, fishing mortality is treated as being separable into a age-specific selectivity and a year-specific level, but there are many permutations on this theme.

## Stock Synthesis History

**Anchovy synthesis (~1985)**
**Generalized model for west coast groundfish (1988)**
**Complete re-code in ADMB as SS2 (2003)**
**Add Graphical Interface (2005)**
**SS_V3 adds tag-recapture and other features (2009)**

## Age-Length Structured Population

**Age-Length Structured Population**

**Notes:**
Let’s explore the concept of length and age based modeling in more detail
The left panel shows the numbers at age in the population distributed across lengths according to the mean growth curve and population variance about this curve.  I’ve put a larger, non-equilibrium number at age 5 to aid in the demonstration.
We’ll sample this population with this size-selectivity curve

## Sampling & Observation Processes

**Sampling & Observation Processes**

**With size-selectivity**

**And ageing imprecision**

**Notes:**
The result on the left is a size-selective sample of the population, the smallest fish are gone
Now we cannot exactly observe the real age of fish, Here on the right we see the catch at observed age is blurred along the age axis.  Some misaged 5 year olds have inflated the apparent occurrence of 4 and 3 year olds.
What I’ve shown is a representation of actual processes at work to generate our data;
in order to assure unbiased results,  we need to engineer these same processes into the  model to generate expected values that are truly comparable to the data.  We build the process into the model rather than attempt to transform the data.

The next step is to accumulate these expected values to either the length or the age’ axis.

## Expected Values for Observations

**Expected Values for Observations**

**Notes:**
Reminder in the upper left is the size selectivity
The lower left shows the size composition in the population and in the sample
The upper right shows the age composition in the population, in the sample, and as observed by our age determination process
Finally, the lower right shows the necessary consequences of these biologically realistic factors on mean size at age in the population, the sample and as observed by our age determination process

## Discard & Retention

**Discard & Retention**

## Integrates Time Series Estimation with Productivity Inference

**Integrates Time Series Estimation with Productivity Inference**

## Integrated Analysis

**Integrated Analysis**

**Produces comprehensive estimates of model uncertainty**
**Smoothly transitions from pre-data era, to data-rich era, to forecast**
**Stabilizing factor:**
**Continuous population dynamics process**

## Stock Synthesis Structure

_**AREA**_
**Age-specific movement between areas**

_**FLEET / SURVEY**_
**Length-, age-, gender selectivity**

_**NUMBERS-AT-AGE**_
**Cohorts: gender, birth season, growth pattern;**
**“****Morphs” can be nested within cohorts to achieve size-survivorship;**
**Distributed among areas**

_**RECRUITMENT**_
**Expected recruitment is a function of total female spawning biomass;**
**Optional environmental input;**
**apportioned among cohorts and morphs;**
**Forecast recruitments are estimated, so get variance**

**Stock Synthesis Structure**

_**CATCH**_
**F to match observed catch;**
**Catch partitioned into retained and discarded, with discard mortality**

_**PARAMETERS**_
**Can have prior/penalty;**
**Time-vary as time blocks, random annual deviations, or a function of input environmental data**

**Notes:**
So, let me recap SS2 structural features

## Stock Synthesis Data

**Stock Synthesis Data**

**Retained catch**
**CPUE and survey abundance**

**Age composition**
**Within length range**
**Size composition**
**By biomass or numbers**
**Within gender and discard/retained**
**Weight bins or length bins**
**Mean length-at-age**

**% Discard**
**Mean body weight**
**Tag-recapture**
**Stock composition**

## Variance Estimation

**Variance Estimation**

**Inverse Hessian (parametric quadratic approximation)**
**Likelihood profiles**
**MCMC (brute force, non-parametric)**
**Parametric bootstrap**

## Risk Assessment

**Risk Assessment**

**Calculate future benefits and probability of overfishing and stock depletion as a function of harvest policy for each future year**
**Accounting for:**
**Uncertainty in current stock abundance**
**Variability in future recruitment**
**Uncertain estimate of benchmarks**
**Incomplete control of fishery catch**
**Time lag between data acquisition and mgmt revision**
**Model scenarios**
**retrospective biases**
**Pr(ecosystem or climate shift)**
**Impacts on other ecosystem components**

## ADMB

**Auto-Differentiation Model Builder**
**C++ overlay developed by Dave Fournier in 1980s**
**Co-evolved with advancement of fishery models**
**Recently purchased by Univ Cal (NCEAS) using a private grant**
**Now available publically and will become open source software**

## Graphical Interface:  Toolbox

## Stock Synthesis Overview

**Stock Synthesis Overview**

**Age-structured simulation model of population**
**Recruitment, natural and fishing mortality, growth**
**Observation sub-model derives expected values for observed data of various kinds and is robust to missing observations**
**Survey abundance, catch, proportions-at-age or length**
**Can work with limited data when flexible options set to mimic simplifying assumptions of simple models**
**Can include environmental covariates affecting population and observation processes**

**Notes:**
Today’s state-of-the-science advanced fishery assessment models work as dynamic simulations of the population process
An observation model derives expected values for the various kinds of available data.
Here I show the observed and predicted values for a triennial survey of relative population biomass (abundance).  We get data like these from our fishery-independent surveys conducted on NOAA Fishery Survey Vessels and some chartered vessels.
I also show an example of the observed and predicted proportions-at-age for one year’s fishery catch.  We get such data by sampling the fishery landings and determining ages of a subset of the fish.

Additional point:
An example of such a model is the Stock Synthesis program developed by NOAA fishery scientist Richard Methot and used for over 20 assessments in the Pacific region in 2005.

## An Example

**Simple vs. complex model structure**
**Time-varying model parameter**
**First, motivation for an advanced approach to catchability**

## Calibrating Abundance Index

**Calibrating Abundance Index**

**The observed annual abundance index, ****O****t****, is basically density (CPUE) averaged over the spatial extent of the stock**
**Call model’s estimate of abundance, ****A****t**
**In model:  E(****O****t****) = *****q***** x ****A****t**** ****+ e**
**Where *****q***** is an estimated model parameter**
**Concept of *****q***** remains the same across a range of data scenarios:**

## Calibrating Abundance Index

**Calibrating Abundance Index**

**If ****O**** time series comes from a single Fisheries Survey Vessel**
**If survey vessel A replaces survey B and a calibration experiment is done**
**If ****O**** come from four chartered fishing vessels each covering the entire area**
**If ****O**** come from hundreds of fishing vessels using statistical model to adjust for spatial and seasonal effort concentration**

## Abundance Index Time Series

**Abundance Index Time Series**

**Each set-up is correct, but what’s wrong with the big picture?**
***q *****is not perfectly constant for any method!**
**Some methods standardize *****q***** better than others**
**Building models that admit the inherent variability in *****q******t***** and constrain *****q***** variability through information about standardization and calibration can:**
**achieve a scalable approach across methods;**
**incorporate *****q***** uncertainty in overall C.I.;**
**Show value of calibration and standardization**

## Example

**Fishery catch**
**CPUE, CV=0.1, density-dependent q**
**Triennial fishery-independent survey, CV=0.3**
**Age and size composition, sample size = 125 fish**

## Results:all data, all parms, random walk q

**Blue line = true values; red dot = estimate with 95% CI**

## Fishery q

## CPUE only, Simple Model, constant q

## Bias and Precision in Forecast Catch

**Error bar is +/- 1 std error**

## NEXT STEPS

**Tier III Assessments**
**Spatially explicit**
**Linked to ecosystem processes**

## Space:  The Final Frontier

**Space:  The Final Frontier**

**“****Unit Stock” paradigm:**
**Sufficient mixing so that localized recruitment and mortality is diffused throughout range of stock**
**Spatially explicit data is processed to stock-wide averages**
**Marine Protected Area paradigm:**
**Little mixing so that protected fish stay protected**
**Challenge: Implement spatially explicit assessment structure with movement and without bloating data requirements**

## Stock Assessment – Ecosystem Connection

**OPTIMUM**
** ****YIELD**

_**SINGLE SPECIES**_
_**ASSESSMENT**_
_**MODEL**_
**Tactical**

_**TIME SERIES**_
_**OF RESULTS**_
** ****BIOMASS,**
**RECRUITMENT,**
**GROWTH,**
**MORTALITY**

**Stock Assessment – Ecosystem Connection**

_**INTEGRATED**_
_**ECOSYSTEM ASSESSMENT**_
** ****CUMULATIVE EFFECTS OF FISHERIES AND OTHER FACTORS**
**Strategic**

_**INDICATORS**_
** ****ENVIRONMENTAL,**
**ECOSYSTEM,**
**OCEANOGRAPHIC**

**SHORT-TERM**

**LONG-TERM**

**TWO-WAY**

_**RESEARCH ON**_
_**INDICATOR**_
_**EFFECTS**_** **

**Notes:**
SA model (whether Tier II or Tier III) produces time series of results
This time series is enough to forecast Optimum Yield, at least in the short-term (few years)
This time series also feeds into Holistic ecosystem model by providing information on changes in important ecosystem components
Results of the holistic ecosystem model can provide information on cumulative effects and interactions, thus ability to adjust long-term OY.  But we are just beginning to attain this capability.

We also can make direct measurements of environmental factors and obtain some factors as results of ecosystem models.
These measurements alone are not enough to improve single-species asmt models.
There also needs to be applied research to determine plausible linkages between environmental factors (like ocean temperature) and assessment factors (like growth) that normally are assumed to be constant.

## Getting to Tier III

**Getting to Tier III**

| Process | Tier II | Tier III |
| --- | --- | --- |
| Average Productivity
(Spawner-Recruitment) | Empirical over decades of fishing | Predict from Ecosystem Food Web and Climate Regimes |
| Annual Recruitment | Annual random process with measurable outcome | Predictable from ecosystem and environmental factors |
| Growth & Reproduction | Measurable, but often held constant | Predictable from ecosystem and environmental factors |
| Survey Catchability | Usually Constant or random walk | Linked to environmental factors |
| Natural Mortality | Mean level based on crude relationships and wishful thinking | Feasible?, or just wishful thinking on larger scale? |

## How Are We Doing?

**How Are We Doing?**

**Assessments of 230 FSSI stocks following SAIP and increased EASA funds**

## Summary

**Summary**

**Stock Synthesis Integrated Analysis Model**
**Flexible to accommodate multiple fisheries and surveys**
**Explicitly models pop-dyn and observation processes (movement, ageing imprecision, size and age selectivity, discard, etc.)**
**Parameters can be a function of environmental and ecosystem time series**
**Estimates precision of results**
**Estimates stock productivity, MSY and other management quantities and forecasts**