In pbs-assess/gfsynopsis: Data Synopsis Reports for PBS Groundfish

.spp <- gfsynopsis::get_spp_names()
no_species <- nrow(.spp)

Introduction {#sec:introduction}

The combination of fishery-dependent data, such as catch and effort, and fishery-independent survey data, such as biomass indices and age compositions, form the backbone of most fisheries stock assessments. Fisheries and Oceans Canada (DFO) manages vast quantities of such data on groundfish species in British Columbia (BC). However, formal stock assessments are not conducted on an annual basis for most stocks, and so much of these data are not summarized to represent the nature of the data holdings.

The original groundfish data synopsis report was developed to provide a snapshot of long-term and recent population and fishing trends, as well as data availability, for all major BC groundfish species of commercial and conservation interest [@anderson2019synopsis; @anderson2020fisheries]. The report was published as a Canadian Science Advisory Secretariat (CSAS) Research Document [@anderson2019synopsis] to facilitate review of the methods, with the intent to update the report on a regular schedule. In 2022, the first update was published as a Science Response including data up to 2021 [@synopsis2022]. In this version, we update the report to include 2022 data as well as adding several additional species, surveys, and spatiotemporal modeling of survey data. We also update referenced stock assessment Research Documents, Science Advisory Reports, and Science Responses. We intend to publish updates of this report on an annual or biennial schedule.

The groundfish data synopsis report generation is automated---pulling data from databases, fitting models, generating visualizations, and stitching the document together to facilitate rapid publication, reproducibility, and transparency. The goals of the report are to (1) facilitate regular review by groundfish scientists and managers of trends in survey indices and stock composition across all species to provide information for discussion on assessment priorities; (2) generate standardized datasets, biological model fits, and visualizations that will help assessment scientists develop operating models and select candidate management procedures for groundfish stocks; and (3) increase data transparency between DFO, the fishing industry, First Nations, non-governmental organizations, and the general public.

The main figures of the synopsis report are presented in two-page species-by-species subsections that visually synthesize most available data for each species. The report covers r no_species groundfish species that are either of commercial, recreational, conservation, or First Nations interest, or are regularly caught in our research surveys. The report focuses on the surveys and data types applicable to the widest array of these species.

Each set of pages for a single species is laid out in the same format. The page layout begins with the species common name, the species scientific name, and the DFO species code, which usually corresponds to the page number referencing the species in @hart1988. The figures are laid out such that the first page has survey (Figure \@ref(fig:intro-maps)) time series trends and spatial patterns on the left and commercial time series by Pacific Marine Fisheries Commission areas (Figure \@ref(fig:management-map)) and spatial patterns on the right. The second page focuses on biological samples from both fishery dependent and independent sources. This page presents length and age data, maturity data, and an overview of available numbers of sampled fish per year across all survey and commercial samples.

For surveys, the report has focused on the Synoptic Bottom Trawl surveys (Figure \@ref(fig:intro-maps)), the Outside Hard Bottom Longline (HBLL OUT) surveys, the Inside Hard Bottom Longline surveys (HBLL INS) (Figure \@ref(fig:intro-maps)), and the International Pacific Halibut Commission (IPHC) Fishery Independent Setline surveys. In this version, we have added data from the Multispecies Small-mesh Bottom Trawl Survey on West Coast Vancouver Island (MSSM WCVI) (formerly known as the "Shrimp Survey") as well as including length and age composition data for the Inside HBLL survey. We show survey biomass index trends for the Hecate Strait Multispecies Assemblage (MSA HS) survey. The report includes counts of available fish specimens from biological samples on all surveys. A brief description of the included surveys is provided in Appendix F of @anderson2019synopsis along with associated references for details on design and implementation.

(ref:intro-maps-cap) Synoptic bottom trawl survey boundaries (left) and Hard Bottom Longline (HBLL) survey boundaries (right). Inside HBLL north and south are not differentiated because the delineation is not consistent from year to year. The International Pacific Halibut Commission (IPHC) Fishery Independent Setline survey (FISS) locations are not shown here because they are coast-wide and are illustrated in the right panel of Figure \@ref(fig:survey-maps). Colours match the colour coding throughout the report.

source(here::here("report/tech-report/intro-maps.R"))

knitr::include_graphics(here::here("report/tech-report/figure/3CD5ABCDE.png"), dpi = NA)

\clearpage

Updates {#sec:update}

Summary of updates

In this report, all figure pages were rebuilt with updated data using the methods described in @anderson2019synopsis, @anderson2020fisheries, and @synopsis2022.

We first summarize all major changes. We include methodological details on coastwide spatiotemporal survey modelling in Appendix \@ref(app:stitching).

Updates:

• We added 2022 survey and commercial data.

• We added three species: Eulachon (Thaleichthys pacificus), Popeye (Coryphaenoides cinereus), and Shortbelly Rockfish (Sebastes jordani).

• We added length and age composition data for the Inside HBLL survey.

• We added spatiotemporal model-based biomass indices for (1) coastwide Synoptic surveys, (2) coastwide Outside HBLL surveys, (3) the combined Inside HBLL surveys, (4) the IPHC FISS, and (5) the MSSM WCVI survey. This approach was originally described in @anderson2019synopsis (their Appendix E and F). We expand on details of the approach in this report's Appendix \@ref(app:stitching).

• We made minor changes to the presentation of the IPHC indices to avoid showing index values for species in earlier years when some species were only recorded at aggregated taxonomic levels. Big Skate and Longnose Skate were both explicitly identified starting in 1998, while the more rarely caught Aleutian Skate and Sandpaper Skate only appear in the data from 2006 onwards. For example, the average catch rate of 'Unidentified Skates' was almost 1 fish per effective skate from 1995--1999. See HG predator analysis vignette. Similarly Shortspine Thornyhead only appears in the data in 1998 and was likely classified under 'Unidentified Thornyhead (idiot)' previously.

• We added data from the Multispecies Small-mesh Bottom Trawl Survey (MSSM, formerly referred to as the "shrimp" survey) off West Coast Vancouver Island. We visualize biomass indices and length composition data but omit age composition data because of the rarity with which these data appear. Below, we provide a brief background on the MSSM survey with respect to groundfish.

• We fixed an important erratum: the 2022 report Synoptic survey and HBLL OUT survey maps erroneously displayed data for 2018 and 2019 rather than 2020 and 2021. In this report, we confirm that the maps are displaying the intended 2021 and 2022 survey data.

Multispecies Small Mesh Groundfish Bottom Trawl (MSSM)

Since 1973, DFO has conducted annual surveys at fixed stations in shrimping grounds off West Coast Vancouver Island. This survey was originally designed to collect data to assess stock status of Pink shrimp (Pandalus jordani) populations, but is now a multi-species survey, and is one of the longest continuous bottom trawl time-series that catches groundfish off the coast of WCVI. The survey typically occurs in late April to May with exceptions in 1985 (May 24--June 7) and in 1987 (August 4--14).

Since 1973, changes to the fishing gear used and changes to catch sorting may affect interpretation of the data. Trawl nets were changed in 1976 and 2006. Notably, catch sorting has changed as follows:

• From 1973--1976, weights for large fish were estimated using random sampling.

• Since 1978, large fish were sorted and weighed.

• In 2001, all catch was sorted along a conveyor belt.

• Since 2003 all species have been sorted, identified to species or lowest taxonomic level possible, and weighed.

The MSSM data used in this report are found in GFBio, but a publicly available dataset is available on the Ocean Biodiversity Information System (OBIS) for data up to and including 2021 [@mssm2022obis]. Additional survey details can be found in @rutherfordinprep.

Importantly, prior to 2003 groundfish sorting and species-level identification was not systematic and should be treated with a level of skepticism. We therefore shade this portion of the MSSM biomass indices grey in the figure pages. Additional details on caveats to interpreting the MSSM survey for groundfish as well as comparisons between the MSSM biomass indices and other indices in the same region will be published in a forthcoming Technical Report (Personal communication: J.C. Dunic and S.C Anderson).

pbs-assess/gfsynopsis documentation built on March 26, 2024, 7:30 p.m.