Commit d3460236 authored by Iago Mosqueira's avatar Iago Mosqueira
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parent dc06439b
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title: "Stock assessment of North Sea sole (sol.27.4)"
title: "Stock assessment of North Sea sole (sol.27.4) using the Aarts & Poos (AAP) model."
subtitle: "Working Document to WKFlatNSCS, Copenhagen, 17-21 February 2020"
author:
- Iago MOSQUEIRA (WMR) <iago.mosqueira@wur.nl>
......@@ -15,7 +15,8 @@ output:
toc: yes
bibliography: references.bib
tags: [SOL sole North_Sea stock assessment]
abstract:
abstract: |
The stock of North sea sole (sol.27.4) has been assessed using the AAP model, reformulated to improve the fit to the landings data. A new standardized BTS index of abundance has been applied, combined with SNS survey. Trends in biomass and fishing mortality differ from those estimated using the previous model formulation for the last few years.
license: Creative Commons Attribution-ShareAlike 4.0 International Public License
---
......@@ -38,6 +39,12 @@ source("../utilities.R")
# Introduction
This document presents an stock assessment of North Sea sole (sol.27.4) using the statistical catch-at-age model formulated by Aarts & Poos [-@Aarts_2009], commonly called AAP. The model has been extended to better explain patterns in selectivity-at-age by separating the specified number of knots applied to the age dimension of the fishing mortality tensor spline, and those used in the selectivity-at-age spline.
Furthermore, a delta-lognormal GAM standardized index of abundance based on the Beam Trawl Survey (BTS) dataset has been developed and is applied here. Comparisons are made on the results of alternative model runs using the different indices, but a more detailed explanation on those can be found in the the corresponding Working Document.
No update of the catch data has been yet carried out as the same procedure followed in the previous benchmark, and subsequent working groups, will be applied omn the 2019 before the 2020 session of WGNSSK.
## Issue list
**Tuning series**
......@@ -58,7 +65,7 @@ covered by other surveys currently in assessment (SNS, BTS-ISIS).
- Determine MSY (proxy) reference points. Depending on the assessment method and available data.
The work carried out for this benchmark has concentrated on addressing the first items in the list. An standardized BTS index of abundances, using all samples available in DATRAS, has been developed and is presented in a working document to this meeting. Patterns in residuals to the catch-at-age fit for ages 2 and 3 have been improved by separating the parameters controlling the flexibility of the selectivity-at-age and fishing mortality splines. Regarding the settings used for the RCT3 recruitment forecast and its application in the autumn reopening of advice, an ICES workshop will soon meet to discuss the issue in detail, so further work has been carried out. Finally, the determination of candidate reference points is presented below based on the results of the base case stock assessment run.
The work carried out for this benchmark has concentrated on addressing the first items in the list. An standardized BTS index of abundances, using all samples available in DATRAS, has been developed and is presented in a working document to this meeting. Patterns in residuals to the catch-at-age fit for ages 2 and 3 have been improved by separating the parameters controlling the flexibility of the selectivity-at-age and fishing mortality splines. Regarding the settings used for the RCT3 recruitment forecast and its application in the autumn reopening of advice, an ICES workshop will soon meet to discuss the issue in detail, so no further work has been carried out. Finally, the determination of candidate reference points is presented below based on the results of the base case stock assessment run.
# Data
......@@ -142,9 +149,7 @@ No commercial LPUE series has been included in this analysis, following the cons
\clearpage
# Assessment models
## AAP
# Assessment model
The base case stock assessment has been carried out using the currently-employed model, AAP [@Aarts_2009]. This is a traditional discrete-time age-structured population model that estimates separately both landings and discards-at-age. The extensions to the original formulation used in the sol.27.4 assessment since the last benchmark [@ICES_WKNSEA_2015] have been retained, namely:
......@@ -176,10 +181,6 @@ The base case run of AAP employs the following data sources and model settings.
| Tensor spline for F-at-age: k value years | 28 |
## SAM
## a4a
# Stock assessment runs
## Base case (GAM-combined BTS)
......@@ -288,7 +289,7 @@ ggplot(msb %/% quantSums(msb), aes(x=year, y=data, fill=as.factor(age))) +
### Retrospective
The retrospective pattern of the AAP base case model fits can be seen here, for the whole time series, and for the last 11 years only.
The retrospective patterns of the AAP base case model fits can be seen here, for the whole time series, and for the last 11 years only.
```{r mohnsrho}
monhsrho <- data.frame(qname=c("F", "SSB", "REC"),
......
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