Sablefish Research
1
Overview
Gitbook outline
Future things to consider
2
A list of objectives/milestones that we have set along the project life
3
Current Alaskan sablefish stock assessment model
Process equations
Initialisation (
\(g\left(.\right)\)
)
Population dynamics (
\(f\left(.\right)\)
)
Observation equations (
\(ll\left( . \right)\)
)
Catch at age
Relative abundance indices
Catch at length
Symbol Notation
Inference
TODO
4
Spatial stock assessment model for Alaskan sablefish
Process equations
Population dynamics
Initialisation
Growth
Recruitment
Fishing mortality
Tag release events
Observation equations
Catch at age
Catch at length
Proportions at age
Relative abundance indices
Tag recovery observations
5
Survey data
Survey design
Abundance (catch rate) data
Age data
Length frequencies
Age frequencies
5.0.1
Direct ageing estimators
5.0.2
Age length key estimators
Continuation ratio logits (CRL)
Estimating initial input sample sizes for multinomial composition data
Age-length data
Appendix
6
Fishery dependent data
Catch data
Length data
Catch at length estimator
Age data
Age-length data
7
Tagging data exploration
Data grooming
Exploratory analysis of the tag data
Single area recovery model
Lincoln-Peterson estimator
Integrating tagging observations in spatial age-structured models
Tagging things to consider with relevant references
Releasing tags
Things to consider for tag release
8
Initial model setup
Model start time
Model spatial resolution of the model
Fishery structure
Repeat regression analysis on survey LF data
9
Model iterations
Single Area model
Include tagging data
Three area model
Five area model
Issues
Comparison
10
Five area model permutations
Notes about this model
11
Next steps
Simulation Scenarios
12
Estimating age-based movement
First attempt
Second attempt
Simulation summary
Setup simulations
Simulation with fixed age-based ogive
Simulation estimate a50 parameter of age-based ogive
Simulation estimate a50 and a to95 parameter of age-based ogive
13
Tag likelihoods
Likelihoods
Poisson
Negative Binomial
Multinomial:release conditioned
Recapture conditioned
Simple simulation
14
Growth
Growth estimation using the Laslett–Eveson–Polacheck (LEP) method
Age-at-length growth model
Tag recapture growth data
Simulation test the “LEP” method
Next steps
15
Review/summarise reference points
Spatial reference points
summarise
Kritzer and Sale (2004)
summarise
D. R. Goethel and Berger (2017)
summarise
MS Kapur et al. (2021)
summarise
Fenske (2022)
summarise
Reuchlin-Hugenholtz et al. (2016)
16
Sex ratios in age and length composition data
A simple simulation
Results
Future research that was not considered in this simple simulation
Scenario 1
Scenario 2
17
Fishing mortality approaches
Set up a simulation
Appendix - Hybrid approach
18
Initialising the plus group in spatial models
19
Beverton-Holt stock recruitment relationship
19.1
Formulation 1
19.2
Formulation 2
19.3
Formulation 3
19.4
Formulation 4
19.4.1
Reparameterisation to formulation 1
19.4.2
Reparameterisation to formulation 2
References
20
Glossary of terms
NOAA Website
Alaskan sablefish research
References