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.

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("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