Northeast Arctic cod data for the SAM case study

Inputs for the Northeast Arctic cod assessment fit with the State-space Assessment Model (SAM), 1946 to 2024 at ages 3 to 15 with a plus group: catch at age from one fishery and survey indices at age from five surveys, with the estimates SAM returns for the same data, used to check the bridge.

Usage

sgl_rg_neacod_data

Format

A list with components inputs (dimensions, weight, maturity and natural mortality at age, the catch and survey observations at age with their use flags, survey timing, and SAM's observation error, catchability and F key matrices shifted to start at one), sam (SAM's estimates of log numbers and log F at age, log catchability, the observation and process standard deviations, the F correlation across ages, spawning biomass and the negative log likelihood, under compound symmetry in F) and fit_summary (SAM's negative log likelihood under independent, compound symmetric and AR1 F increments).

Source

ICES Arctic Fisheries Working Group input files for Northeast Arctic cod, catches 1946 to 2023 and surveys to 2024, fit with samjr, the R implementation of SAM (Nielsen, A., Berg, C. W. 2014. Estimation of time-varying selectivity in stock assessments using state-space models. Fisheries Research 158: 96-101).