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mscatch:
An R package for
calculating landings-at-length and age

24 March 2022

Andy Beet
Northeast Fisheries Science Center

Contributors:
Sarah Gaichas, Sean Lucey, Kiersten Curti
EDAB, numerous Population Dynamics Scientists

1 / 23

Background: catch at length/age

  • Determine how landings data are aggregated based on available length samples

  • How are missing length samples handled

  • Need to recognize species specific rules for calculating catch at length & age

    • life history traits
    • where in time to borrow length samples
    • length-weight relationships
    • Is species aged?
  • Need to know data sources

  • Initial meeting with Kiersten, Gary, Paul to formulate a set of rules/decision tree

2 / 23

Stock Efficiency

  • StockEff already does some of this, why reinvent the wheel?
    • Excel template for species to be added to commercial module
    • Creates a record of how data was made

Why not just use these templates?

  • Interest centers on the decision making process prior to entering information into this template

  • Multispecies models require data for many species on a different spatial footprint from assessments

Template found on StockEff Confluence

3 / 23

mscatch as an R package

  • Address the decision making process

  • Define species specific rules.

  • Reproducible with documentation of decisions (Transparency)

  • Multispecies length and age based models require data on a different spatial footprint from assessments

    • Many challenges
    • Alternate spatial footprints could result in the absence of species data (eg. Mackerel, herring on Georges Bank)
    • Encompass multiple species stocks (eg. Winter flounder on Georges Bank)
  • Evaluate the performance of multispecies assessment models

4 / 23

Sample output:

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Sample output:

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Sample output:

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Sample output:

8 / 23

Walkthrough

  • Currently borrows length samples:
    • from previous QTR/SEMESTER
    • use nearest neighbor in time
    • use nearest neighbor from another gear type
  • uses survey length-weight data to fit relationship

  • Process for handling missing length samples will be expanded to incorporate today's discussion.

9 / 23

Species specific considerations: Rules

  • How are gear types aggregated?

  • How are market codes aggregated?

  • How are landing aggregated temporally? QTR, SEMESTER, ANNUAL?

  • What are the rules implemented when length samples are missing?

    • What are the minimum number of samples required?
    • 200 mt landings for every 100 fish lengths measured?
    • borrow samples from nearest neighbor? previous year? within last 5 years?
    • combine temporally?
    • combine gears?
10 / 23

Species specific considerations: Data

  • Sources for length-weight data/parameters?

    • From survey and/or commercial?
    • Fit own relationship or use parameters pulled from svdbs database (Wigley et al)
    • How many length-weight relationships are used? QTR, SEMESTER, sex, gear type?
  • Sources for discard data?

    • Are length samples available?
    • Add to totals prior to length expansion?
  • Sources for age data?

    • From survey and/or commercial?
    • Age-length same level of aggregation or futher aggregate?
  • Sources for foreign data?

  • What is the first year of data used in assessment?

  • Stock area definition? Statistical areas?

11 / 23

A case study: Mackerel

  • All gears combined into a single gear type

  • Temporal aggregation: semesters (Jan-Jun, Jul-Dec)

  • Market codes:

    • SQ, ES, SV combined to SMALL
    • MD
    • XG, JB, LG combined into LARGE
  • Missing samples: Borrow sample from previous semester within the same market category

    • 5 year average over both semesters
    • market category time series average
  • Length-weight relationships: 6 (3 time intervals per semester)

    • Fitted to bottom trawl data (after QA/QC for anomalous values)
  • Age-length data: from Bottom trawl survey and Commercial data. Combine

  • Age-length key: By Year

  • Start date: 1992

12 / 23

A case study: Yellowtail

  • All gears combined into a single gear type

  • Temporal aggregation: semesters (Jan-Jun, Jul-Dec)

  • Market codes: SQ, MD, PW combined to SMALL, LG

  • Missing samples: No Borrowing of samples.

    • Combine Semesters
    • Bump catch at age totals
  • Length-weight relationships: 3 semester (annual if collapsed)

    • Fitted to bottom trawl data
  • Age-length data: (pooled sexes)

    • US landings from Commercial data.
    • Canadian landings from survey and commercial
  • Age-length key: semester

  • Start date: 1973

13 / 23

A case study: Herring

  • Landings: from state of Maine

  • Gears: Mobile (Trawl, purse Seines: 050,170,120,121,122,124,370), Fixed (all other gear types)

  • Temporal aggregation: quarter year

  • Market codes: All unclassified

  • Missing samples: No Borrowing of samples.

    • Combine quarters to semesters for gear type
    • Combine quarters to Year for gear type
  • Length-weight relationships: (same as aggregation)

    • Fitted to commercial length samples
  • Age-length data:

    • Separate database.
  • Age-length key: Year, Semester, gear type

  • Start date: 1965

14 / 23

Questions

  • What are we missing?

  • What diagnostics are useful?

  • Helpful to post species specific diagnostics and length and age compositions for feedback

  • Can you help supply information for other species?

    • Cod
    • Haddock
    • Spiny Dog
    • Winter skate
    • silver hake
15 / 23

A case study: Haddock

  • Landings:

  • Gears: combine all gears: otter (050,010,057)

  • Temporal aggregation: semester

  • Market codes:

    • LG, XG combined to LG?
    • SR (snapper)
    • SK (scrod)
  • Missing samples:

  • Length-weight relationships: 2 (spring and fall)

    • survey (2005 data)
  • Age-length data:

  • Age-length key:

  • Start date: 1964

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A case study: Cod (GB)

  • Landings: East 561-562, West 521-522,525,526,537-539

  • Gears: 050, 010 (longline bottom), 100 (Gill net)

  • Temporal aggregation: quartely

  • Market codes:

  • Missing samples:

    • pool semester
    • pool annual
    • borrow from adjacent area
  • Length-weight relationships: 4 (by semester and region)

    • survey data (1992-2007)
    • Canadian lw based on Canadian observer (by semester)
  • Age-length data:

  • Age-length key:

  • minimum number of samples: 2

  • Start date: 1981

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A case study: Winter Flounder (GB)

  • Landings:

    • 522-525, 542,543, 551-552,561-562
  • Gears: 050 (otter)

  • Temporal aggregation: quarterly

  • Market codes:

    • LS (1201), XG (1204) combined to LS (Lemon sole)
    • LG (1205), LM (1202) combined to LG
    • SQ (1203), MD (1206), PW (1207) combined SMALL
  • Missing samples:

  • Length-weight relationships:

  • Age-length data:

  • Age-length key:

  • Start date: 1964

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A case study: Winter Flounder (SNEMA)

  • Landings:

    • 521,526,533-539,611-613
  • Gears: 050 (otter)

  • Temporal aggregation: semester

  • Market codes:

    • LS (1201), XG (1204), LG (1205), LM (1202) combined to LG
    • SQ (1203), PW (1207) combined SMALL
    • MD (1206), UN (1200) combined MEDIUM
  • Missing samples: No borrowing

    • combine quarter to semester
    • combine to year
  • Length-weight relationships: single relationship

    • from survey through 2010
  • Age-length data:

    • commercial data. for discards survey data
  • Age-length key: year, semester

  • Start date: 1982

19 / 23

A case study: Spiny dogfish

  • Landings:

  • Gears: 050 (otter), fixed (010,020,100,101)?

  • Temporal aggregation: Annual

  • Market codes: All unclassified

  • Missing samples:

  • Length-weight relationships: 2 (males and females)

  • Age-length data: None

  • Age-length key: None

  • Start date:

20 / 23

A case study: Winter Skate

  • Landings: survey proportions applied to skate population

  • Gears:

  • Temporal aggregation:

  • Market codes:

  • Missing samples:

  • Length-weight relationships:

  • Age-length data: None

  • Age-length key: None

  • Start date:

21 / 23

A case study: Silver hake

  • Landings:

  • Gears: 050, + ?

  • Temporal aggregation: semester

  • Market codes:

    • SQ
  • Missing samples:

    • combine to year(s)
  • Length-weight relationships:

  • Age-length data: survey (1973-2009)

  • Age-length key: Borrow ages from adjacent years

  • Start date: 1955

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A case study: Monkfish

  • Landings: No age structured assessment

  • Gears: 050, 100, 132

  • Temporal aggregation:

  • Market codes: SQ, LG

  • Missing samples:

  • Length-weight relationships:

  • Age-length data: None

  • Age-length key: None

  • Start date:

23 / 23

Background: catch at length/age

  • Determine how landings data are aggregated based on available length samples

  • How are missing length samples handled

  • Need to recognize species specific rules for calculating catch at length & age

    • life history traits
    • where in time to borrow length samples
    • length-weight relationships
    • Is species aged?
  • Need to know data sources

  • Initial meeting with Kiersten, Gary, Paul to formulate a set of rules/decision tree

2 / 23
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