Inside Dogfish Stock Assessment for British Columbia

Install dependencies

GitHub R packages

# install.packages("remotes")
remotes::install_github("pbs-assess/gfdata")
remotes::install_github("pbs-assess/gfplot")
remotes::install_github("luke-a-rogers/ssio")
remotes::install_github("r4ss/r4ss")
remotes::install_github("Cole-Monnahan-NOAA/adnuts")
remotes::install_github("PIFSCstockassessments/ss3diags")

Stock Synthesis 3.30

• Download the latest release of Stock Synthesis 3.30
• Confirm that the ss3 executable is available in the R $PATH, for example using r4ss::check_exe()

Fleets

Fleets are defined by a combination of gear type (e.g. “Hook and line”) and type (e.g. “landings”). Because fleet definitions may differ between models, data files for catch (catch.rds), indexes (index.rds), and lengths (length.rds) are stored (in data/ss3/) with gear and type columns, to allow the analyst to define fleets specific to each model fit (typically in ss3/xxx/00-fleets.R) in combination with the R package ssio (under development).

Project status

• Preliminary data uploaded and formatted
• Simplified model structure adapted from dogfish-assess/ repo
• Trial ss3 model in ss3/T00/ runs on 8 fleets

Next steps

• Iterate trial model fits in ss3/T00/ to explore base model options
• Develop base model in ss3/A00/ using ss3/T00/ workflow
• Develop additional (sensitivity) model fits