Age-structured fishery, survey, biological, and covariate data for Northern
cod (Gadus morhua) in Northwest Atlantic Fisheries Organization (NAFO)
Divisions 2J3KL. The data are adapted from Northern cod assessment inputs
and arranged for use with fit_tam(). They provide a reproducible example
for fitting and comparing alternative observation and population-process
models; they are not a reproduction of the full official assessment.
Usage
data(cod_obs)Format
A tam_data object containing five data frames:
catch: Commercial catch numbers at age (year,age,obs), in thousands of fish; observations can be missing.F_y_blockandF_a_blockare candidate fishing-mortality mean groups.index: DFO autumn research-vessel (RV) abundance index at age (year,age,obs), withsurvey, survey timingsamp_time = 0.8, and catchability age groupq_block. Survey observations have been expanded using 12,048,556 trawl units and expressed in thousands of fish.weight: Annual stock weight at age (obs, kg).maturity: Annual proportion mature at age (obs, from 0 to 1).pop_covariates: A complete year-age table withM_a_block(candidate natural-mortality age groups),allometric_M_assumption(a weight-based baseline M, per year).
Catch and RV indices have unit = "thousand fish"; individual weights have
unit = "kg". Multiplying thousands of fish by kg per fish yields tonnes.
The additional columns are candidate explanatory variables, not fitted
effects unless referenced in the corresponding model formulas.
Source
Derived from NCAM::inputs, with covariate preparation in
data-raw/cod_obs.R. See the cited assessment and framework publications
for the underlying surveys, fishery data, model structure, and provenance.
Details
Assessment provenance. The data originate from inputs to the Northern cod assessment model (NCAM), used in the extended framework (xteNCAM). The stock's 2026 assessment, based on observations available through 2025, is documented by Regular et al. (in press) and summarized in DFO (2026). The framework methods and additional data sources are documented by DFO (2024) and Regular et al. (2025a, 2025b). Only a subset of the assessment inputs is included here: for example, tagging observations, juvenile and Sentinel surveys, and the full Smith Sound likelihood are not supplied as separate observations. Differences between results from tinyAM and the official assessment should therefore not be interpreted as discrepancies in the published stock assessment.
Natural mortality assumptions. allometric_M_assumption uses
M = M0 * weight^(-0.305), following the weight-scaling approach of
Lorenzen (1996). The multiplier M0 is calibrated so that the arithmetic
mean of these M values over source weight records for ages 5-14 is 0.30 per
year, before restricting the example to the catch years. The mean over the
packaged subset can therefore differ from 0.30.
This is a constructed example baseline, not an independently estimated
natural-mortality series.
Mortality blocks. M_a_block defines broad age groups that can be used
to allow natural mortality responses to differ among younger and older fish.
The fishing-mortality variables F_y_block and F_a_block provide analogous
options for modelling fishing mortality. F_y_block divides the time series
into periods broadly reflecting changes in the Northern cod fishery, including
the 1992 moratorium, subsequent limited fishing and closures, the
establishment of the stewardship fishery in 2006, and the return to
commercial fishing in 2024. F_a_block distinguishes individual ages,
allowing age-specific fishing mortality or selectivity to be modelled.
These groupings are illustrative model-design variables, not observations
or assumptions imposed by the accepted assessment. They have no effect
unless explicitly included in the corresponding model settings, and
alternative groupings may be defined to explore competing hypotheses.
References
DFO. 2024. Northern (2J3KL) Atlantic Cod Assessment Framework. DFO Can. Sci. Advis. Sec. Sci. Advis. Rep. 2024/046. https://publications.gc.ca/collections/collection_2025/mpo-dfo/fs70-6/Fs70-6-2024-046-eng.pdf
DFO. 2026. NAFO Divisions 2J3KL Northern Cod (Gadus morhua) Stock Assessment to 2026. DFO Can. Sci. Advis. Sec. Sci. Advis. Rep. 2026/030. https://csas-scas.dfo-mpo.gc.ca/publications-publications/f7f156a8-b0ef-4840-b2e0-4573fb325faa
Regular, P.M., Robertson, G.J., Kumar, R., Varkey, D.A., Gregory, R.S., Lewis, R.S., Skanes, K., Gullage, N., Koen-Alonso, M., and Dwyer, K.S. 2025a. Extending the Northern Cod Assessment Model - Part I: Bridging Gaps with Additional Data and Model Variations. DFO Can. Sci. Advis. Sec. Res. Doc. 2025/034. https://publications.gc.ca/collections/collection_2025/mpo-dfo/fs70-5/Fs70-5-2025-034-eng.pdf
Regular, P.M., Kumar, R., Varkey, D.A., Koen-Alonso, M., and Stenson, G.B. 2025b. Extending the Northern Cod Assessment Model - Part II: Quantifying the Impact of Capelin and Seals. DFO Can. Sci. Advis. Sec. Res. Doc. 2025/035. https://publications.gc.ca/collections/collection_2025/mpo-dfo/fs70-5/Fs70-5-2025-035-eng.pdf
Regular, P.M., Skanes, K., Novaczek, E., Robertson, G.J., Rideout, R.M., Trueman, S., Kumar, R., Gregory, R.S., Koen-Alonso, M., and Munro, H. In press. Assessment of the Northern Cod (Gadus morhua) Stock in NAFO Divisions 2J3KL in 2026. DFO Can. Sci. Advis. Sec. Res. Doc.
Lorenzen, K. 1996. The relationship between body weight and natural mortality in juvenile and adult fish: a comparison of natural ecosystems and aquaculture. J. Fish Biol. 49: 627-642. doi:10.1111/j.1095-8649.1996.tb00060.x
Examples
data(cod_obs)
names(cod_obs)
#> [1] "catch" "index" "weight" "maturity"
#> [5] "pop_covariates"
print(cod_obs)
#>
#> ── tinyAM data ─────────────────────────────────────────────────────────────────
#>
#> ── catch: 1512 rows, 6 columns ──
#>
#> Years 1954–2025; ages 0–20
#> year age obs unit F_y_block F_a_block
#> 1 1954 0 NA thousand fish 1954-1991 0-1
#> 2 1955 0 NA thousand fish 1954-1991 0-1
#> 3 1956 0 NA thousand fish 1954-1991 0-1
#> 4 1957 0 NA thousand fish 1954-1991 0-1
#> 5 1958 0 NA thousand fish 1954-1991 0-1
#> ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮
#> 1508 2021 20 0 thousand fish 2006-2022 18-20
#> 1509 2022 20 0 thousand fish 2006-2022 18-20
#> 1510 2023 20 0 thousand fish 2023-2025 18-20
#> 1511 2024 20 0 thousand fish 2023-2025 18-20
#> 1512 2025 20 0 thousand fish 2023-2025 18-20
#>
#> ── index: 1512 rows, 7 columns ──
#>
#> Years 1954–2025; ages 0–20
#> year age obs survey samp_time q_block unit
#> 1 1954 0 NA Fall 2J3KL 0.8 0 thousand fish
#> 2 1954 1 NA Fall 2J3KL 0.8 1 thousand fish
#> 3 1954 2 NA Fall 2J3KL 0.8 2 thousand fish
#> 4 1954 3 NA Fall 2J3KL 0.8 3 thousand fish
#> 5 1954 4 NA Fall 2J3KL 0.8 4 thousand fish
#> ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮
#> 1508 2025 16 74.00868 Fall 2J3KL 0.8 6-20 thousand fish
#> 1509 2025 17 120.43751 Fall 2J3KL 0.8 6-20 thousand fish
#> 1510 2025 18 0.00000 Fall 2J3KL 0.8 6-20 thousand fish
#> 1511 2025 19 0.00000 Fall 2J3KL 0.8 6-20 thousand fish
#> 1512 2025 20 0.00000 Fall 2J3KL 0.8 6-20 thousand fish
#>
#> ── weight: 1512 rows, 4 columns ──
#>
#> Years 1954–2025; ages 0–20
#> year age obs unit
#> 1 1954 0 2.965967e-04 kg
#> 24 1955 0 2.965967e-04 kg
#> 47 1956 0 2.965967e-04 kg
#> 70 1957 0 2.965967e-04 kg
#> 93 1958 0 2.965967e-04 kg
#> ⋮ ⋮ ⋮ ⋮ ⋮
#> 1562 2021 20 1.406005e+01 kg
#> 1585 2022 20 1.453274e+01 kg
#> 1608 2023 20 1.426399e+01 kg
#> 1631 2024 20 1.409146e+01 kg
#> 1654 2025 20 1.369174e+01 kg
#>
#> ── maturity: 1512 rows, 3 columns ──
#>
#> Years 1954–2025; ages 0–20
#> year age obs
#> 1 1954 0 0
#> 2 1955 0 0
#> 3 1956 0 0
#> 4 1957 0 0
#> 5 1958 0 0
#> ⋮ ⋮ ⋮ ⋮
#> 1708 2021 20 1
#> 1709 2022 20 1
#> 1710 2023 20 1
#> 1711 2024 20 1
#> 1712 2025 20 1
#>
#> ── pop_covariates: 1512 rows, 4 columns ──
#>
#> Years 1954–2025; ages 0–20
#> year age allometric_M_assumption M_a_block
#> 1 1954 0 4.9990199 0-1
#> 2 1955 0 4.9990199 0-1
#> 3 1956 0 4.9990199 0-1
#> 4 1957 0 4.9990199 0-1
#> 5 1958 0 4.9990199 0-1
#> ⋮ ⋮ ⋮ ⋮ ⋮
#> 1508 2021 20 0.1873957 8-20
#> 1509 2022 20 0.1855152 8-20
#> 1510 2023 20 0.1865744 8-20
#> 1511 2024 20 0.1872682 8-20
#> 1512 2025 20 0.1889190 8-20