In iantaylor-NOAA/Lingcod_2021: Estimate the Status of Lingcod off the US West Coast in 2021

Model changes from the last assessment

The following is a brief list of changes that were made to the model configuration compared to the previous assessment [@haltuch2019lingcod].

Data

• Change the boundary between north and south from \CAOR to \CapeM
• Add new data from 2017-2020
• Add new ages from earlier years in the \gls{s-wcgbt}
• Re-analyze all data inputs from the raw data with the exception of the trawl logbook index which was re-stratified to account for the change in boundary

Fleet structure

• Early and late periods of the \gls{s-tri} were combined into a continuous time-series ```{asis, opts.label = "south", echo = TRUE}
• The recreational CPFV DebWV index and associated length compositions were separated from the California recreational fleet into into a new fleet to allow different assumptions about selectivity

```{asis, opts.label = "north", echo = TRUE}
- A California recreational fishery for the catches
and length compositions between \CapeM and \CAOR was added

Biology

• Use new area-specific age-based maturity estimates
• Update weight-length relationship to include additional samples
• Separate $M$ priors for males and females based on a lower maximum age (18 for females, 13 for males, compared to 21 for both sexes)
• Estimate female $M$ instead of fixing it at the mean of the prior
• Estimate all 5 growth parameters within each model rather than fixing the parameter controlling the length at age 14

Recruitment

• Fix $\sigma_R$ = 0.6 for both models (in the 2017 assessment, $\sigma_R$ had been iteratively tuned to 0.55 for the north model and 0.75 for the south)
• Estimate the stock-recruit steepness parameter with a prior instead of fixing it at 0.7
• Extend the end of the "main" period of recruitment deviations and the recruitment bias adjustment settings by three years to account for the additional survey data from 2017-2019 (no surveys were conducted in 2020 do the pandemic)

Selectivity and retention

• Estimate three double-normal selectivity parameters within each time block for each fleet (whereas the previous model had fewer or more parameters estimated depending on the fleet or time block)
• Fix the retention parameters for the early period of the commercial TW and FG fisheries to retain all selected fish prior to 1998
• Revise the blocking on numerous selectivity parameters
• Turn off male selectivity offsets to simplify the model

Software and workflow

• Use a newer version of Stock Synthesis, version 3.30.17.01
• Use previously unavailable or updated versions of numerous R packages related to processing input and output files for the assessment, including nwfscDiag, sa4ss, r4ss, and PacFIN.Utilities.
• Created a lingcod R package in a publicly accessible repository on github to provide a transparent and reproducible system for processing the data, modifying the model files, and writing these reports.

iantaylor-NOAA/Lingcod_2021 documentation built on Oct. 30, 2024, 6:42 p.m.