Data and code for BC Pacific Spiny Dogfish operating models

• Raw datasets from PBS databases are in data/raw.
• Derived datasets are in data/generated.
• Analysis scripts are in analysis.
• Geostatistical indexes are pushed in data/generated so the corresponding scripts in analysis can be skipped.
• SS3 model configurations are in ss3.
• R code to run SS3 models and generate figures from model output are in ss3.
• The MCMC sampling sampling and forecasting files will take a long time to run.

Required CRAN packages

install.packages("remotes")
install.packages("tidyverse")
install.packages("cowplot")
install.packages("RColorBrewer")
install.packages("here")
install.packages("future")
install.packages("rnaturalearth")
install.packages("snowfall")
install.packages("viridis")
install.packages("reshape2")
install.packages("raster")
install.packages("terra")
install.packages("concaveman")
install.packages("ggforce")

install.packages("MSEtool")
install.packages("DLMtool")
install.packages("SAMtool")
install.packages("sdmTMB")
install.packages("r4ss")

Required non-CRAN packages

remotes::install_github("pbs-assess/gfdata")
remotes::install_github("pbs-assess/gfiphc")
remotes::install_github("pbs-assess/gfplot")
remotes::install_github("pbs-assess/csasdown")
remotes::install_github("pbs-assess/rosettafish")

Stock Synthesis executable

Available at https://github.com/nmfs-stock-synthesis/stock-synthesis/releases/tag/v3.30.20