The R package ss3diags enables Stock Synthesis users to reproduce the key model diagnostics plots that presented in the paper 'A Cookbook for Using Model Diagnostics in Integrated Stock Assessments' with the R script ss3diags_CookbookPlots.R.
A handbook with detailed User guidelines for Advanced Model Diagnostics with ss3diags is currently being finalized.
In addition, the ss3diags Github respository provides fully commented step-by-step R recipes on how to:
- Do log-likelood profiling for R0
- Run the ASPM diagnostic
- Conduct iterative hindcasts for restrospective analysis with forecasts
- Do Jitter tests
...with Stock Synthesis by making use of a comprehensive collection of R functions available in the R package r4ss
Installing ss3diags requires the librabry(devtools), which can be install by 'install.packages('devtools')' and a R version >= 3.5. Then simply install ss3diags from github with the command:
install_github("jabbamodel/ss3diags")
library(ss3diags)
Documented Core functions in ss3diags include:
SSrunstest()
SSplotRunstest()
SSplotJABBAres()
SSplotModelcomp()
SSplotRetro()
SShcbias()
SSplotHCxval()
SSmase()
SSdeltaMVLN()
SSplotEnsemble()
Reference
Carvalho, F., Winker, H., Courtney, D., Kapur, M., Kell, L., Cardinale, M., Schirripag, M., Kitakado, T., Yemane, D., Piner, K.R., Maunder, M.N., Taylor, I., Wetzel, C.R., Doering, K., Johnsonm, K.F., Methot, R.D., in press. A Cookbook for Using Model Diagnostics in Integrated Stock Assessments. Fisheries Research.