Articles
Overview
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 directorylibrary(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: Simulations
- Ex 11: Catchability
- Ex 12: Multiple stocks and region and movement
- Ex 13: Using WHAM without ASAP