WHAM tutorial

These vignettes provide an introduction to fitting state-space assessment models using the WHAM package. They get progressively more complex, so we advise working through them in order unless you are only interested in a specific topic.

To run ALL examples (takes ~1 hour):
# setwd("choose/where/to/save/output") # otherwise in working directory
library(wham)
wham.dir <- find.package("wham")
source(file.path(wham.dir, "example_scripts", "run_all_examples.R"))

Ex 1: The basics
Ex 2: Recruitment linked to an environmental covariate (Cold Pool Index)
Ex 3: Projecting / forecasting random effects
Ex 4: Selectivity with time- and age-varying random effects
Ex 5: Time-varying natural mortality linked to the Gulf Stream Index
Ex 6: Numbers-at-age / survival deviations as random effects
Ex 7: Debugging WHAM models
Ex 8: Compare ASAP and WHAM model results
Ex 9: Retrospective predictions
Ex 10: Simulation and MSE
Ex 11: Catchability configurations