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 [@synopsis2021data]. A version with data up to 2022 is currently in press as a Technical Report. In this version, we update the report to include 2023 data. We also update referenced stock assessment Research Documents, Science Advisory Reports, and Science Responses.

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)

Updates {#sec:update}

In this report, all figure pages were rebuilt with updated data using the methods described in @anderson2019synopsis, @anderson2020fisheries, @synopsis2021data, and @synopsis2022data.

Additionally:

We updated the recent references at the top of each species page.
The data for the IPHC spatiotemporal model index is now derived directly from the IPHC website. We provide details on this new data processing in Appendix \@ref(app:iphc).
We removed recreational and unknown sectors from the commercial biological samples.
We updated the species name "North Pacific Spiny Dogfish" to "Pacific Spiny Dogfish" in accordance with the latest American Fisheries Society recommendation.