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

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

Context {#sec:context}

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 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. The usefulness of the report depends on its data remaining up-to-date. Since the initial 2019 report, three new years of survey and commercial data have become available, as well as updated stock assessment Research Documents, Science Advisory Reports, and Science Responses.

DFO Science Branch has requested an update to the groundfish data synopsis report including all commercial and survey data available up to the end of 2021. The advice arising from this CSAS Science Response will provide an overview of available groundfish data and fishing and population trends to inform DFO Science and Fisheries Management staff in stock monitoring and prioritization. This update applies the previously peer-reviewed approach to generate up-to-date figures representing data such as biomass indices, commercial catch, species distribution, and age and length composition data for the r no_species species.

This Science Response results from the Science Response Process of March 29, 2022 on A data synopsis for British Columbia groundfish: 2021 update.

Background {#sec:background}

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 have been 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 across all survey and commercial samples.

For surveys, the report focuses on the Synoptic Bottom Trawl surveys (Figure \@ref(fig:intro-maps)), the Outside Hard Bottom Long Line (HBLL) surveys (Figure \@ref(fig:intro-maps)), and the International Pacific Halibut Commission (IPHC) Fishery Independent Setline surveys. These surveys provide the greatest spatial and taxonomic coverage of the species in this report. Survey biomass index trends are also shown for the Hecate Strait Multispecies Assemblage (MSA HS) survey and the Inside HBLL survey. The report includes counts of available fish specimens from biological samples on all surveys. A brief description of the included surveys is included 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 Long Line (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 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/report-rmd/intro-maps.R"))

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

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