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Technical Documentation, State of the Ecosystem Report

56 Single Species Status Indicator

Description: Summary of the most recent stock assessment results for each assessed species.

Found in: State of the Ecosystem - Gulf of Maine & Georges Bank (2017+), State of the Ecosystem - Mid-Atlantic (2017+)

Indicator category: Synthesis of published information (StockSMART)

Contributor(s): Sarah Gaichas, Andy Beet, Jeff Vieser, Chris Legault

Data steward: Sarah Gaichas

Point of contact: Sarah Gaichas

Public availability statement: All stock assessment results are publicly available at https://apps-st.fisheries.noaa.gov/stocksmart?app=homepage. .

56.1 Methods

56.1.1 Data sources

“Data” used for this indicator are the outputs of stock assessment models and review processes, including reference points (proxies for fishing mortality limits and stock biomass targets and limits), and the current fishing mortality rate and biomass of each stock. These metrics are reported to the a national repository, Stock SMART.

56.1.2 Data extraction

Beginning in 2020 for the 2021 SOE, we used Andy Beet’s stocksmart package to extract assessment results from Stock SMART.

Two data frames are in the stocksmart package, stockAssessmentData and stockAssessmentSummary.

In stockAssessmentData we have time series. Columns are StockName, Stockid, Assessmentid, Year, Value, Metric, Description, Units, AssessmentYear, Jurisdiction, FMP, CommonName, ScientificName, ITIS, AssessmentType, StockArea, RegionalEcosystem and the reported metrics are Catch, Fmort, Recruitment, Abundance, Index.

In stockAssessmentSummary we have assessment metadata. Columns are Stock ID, Stock Name, Jurisdiction, FMP, Science Center, Regional Ecosystem, FSSI Stock?, ITIS Taxon Serial Number, Scientific Name, Common Name, Stock Area, Assessment ID, Assessment Year, Assessment Month, Last Data Year, Review Result, Assessment Model, Model Version, Lead Lab, Citation, Final Assessment Report 1, Final Assessment Report 2, Point of Contact, Life History Data, Abundance Data, Catch Data, Assessment Level, Assessment Frequency, Model Category, Catch Input Data, Abundance Input Data, Biological Input Data, Ecosystem Linkage, Composition Input Data, F Year, Estimated F, F Unit, F Basis, Flimit, Flimit Basis, Fmsy, Fmsy Basis, F/Flimit, F/Fmsy, Ftarget, Ftarget Basis, F/Ftarget, B Year, Estimated B, B Unit, B Basis, Blimit, Blimit Basis, Bmsy, Bmsy Basis, B/Blimit, B/Bmsy, MSY, MSY Unit, Assessment Type.

For 2021-2023, stocksmart was updated with all current assessments, so data extraction was simply:

Year-specific naming conventions for assess and decoder files were dropped in 2021 to facilitate future data updates.

In 2020, assessment summary data were extracted from stockAssessmentSummary for 2019 and prior records, and the 2020 assessments results were added from the preliminary results provided by Jeff Vieser.

  • The assess.csv fields used in previous years were recreated from stockSMART to include necessary metadata:

new2019assess <- stockAssessmentSummary %>%
  filter(`Science Center` == "NEFSC") %>%
  rename(Entity.Name = `Stock Name`) %>%
  rename_all(list(~make.names(.)))
  • Add 2020 assessments and write 2020assess.csv data contribution:

prelim2020 <- read.csv(here("NE Stock Assessment Results.csv")) %>%
  filter(Assessment.Year == 2020) %>%
  rename(Entity.Name = Stock,
         FSSI.Stock. = FSSI,
         Estimated.F = Best.F,
         Estimated.B = Best.B,
         Review.Result = Review.Type) %>%
  select(-c(Year, Status.Stock., Record.Status, TimeSeries.Data.,
            Survey.Links., Adequate, Minimum.F, Maximum.F,
            Minimum.B, Maximum.B, 
            Stock.Level.Relative.to.Bmsy:Decision.memo.related.to.inadequate.rebuilding.progress))


update2020assess <- bind_rows(new2019assess, prelim2020)

write.csv(update2020assess, here("2020assess.csv"))

The decoder.csv data contribution was updated in December 2020 to retain only Entity.Name, Council, and Code fields (used by get_stocks):


newdecoder <- read.csv(here("2019decoder.csv")) %>%
  select(Entity.Name, Code, Council)

write.csv(newdecoder, here("2020decoder.csv"))

For the 2017-2020 SOEs, each assessment document was searched to find the following information (often but not always summarized under a term of reference to determine stock status in the executive summary), and the spreadsheets were updated by hand:

  • Bcur: current year biomass, (most often spawning stock biomass (SSB) or whatever units the reference points are in)

  • Fcur: current year fishing mortality, F

  • Bref: biomass reference point, a proxy of Bmsy (the target)

  • Fref: fishing mortality reference point, a proxy of Fmsy

56.1.3 Data processing

R code used to process the stock status data set for inclusion in the ecodata R package can be found here.

56.1.4 Data analysis

For the 2021 SOE to present, stockSMART variables F/Fmsy and B/Bmsy are renamed F.Fmsy and B.Bmsy, then plotted for each species on an x-y plot, where B.Bmsy is on the x axis and F.Fmsy is on the y axis. The code used to work up this data for the 2024 report can be found at https://sgaichas.github.io/stockstatusindicator/StockStatus2023.html.

2017-2020 SOEs: For each assessed species, Bcur is divided by Bref and Fcur is divided by Fref. They are then plotted for each species on an x-y plot, with Bcur/Bref on the x axis, and Fcur/Fref on the y axis.

catalog link https://noaa-edab.github.io/catalog/stock_status.html