The R package ss3diags enables users to apply advanced diagnostics to
evaluate a Stock Synthesis model. Diagnostics include residual analyses,
hindcast cross-validation techniques, and retrospective analyses.
Functions also allow users to reproduce the key model diagnostics plots
that are presented in the paper ‘A Cookbook for Using Model Diagnostics
in Integrated Stock Assessments’ (Carvalho et
al. 2021).
The ss3diags Github repository provides step-by-step R recipes on how
to:
- Run jitter analysis
- Conduct retrospective analysis
- Use hindcast cross-validation
- Do log-likelood profiling for R0
- Run the ASPM diagnostic
- Evaluate model fit
with Stock Synthesis by making use of a comprehensive collection of R
functions available in the R packages
r4ss and ss3diags.
ss3diags is not currently supported on CRAN. You can install the
development version of ss3diags from GitHub
with:
# install.packages("remotes")
remotes::install_github("PIFSCstockassessments/ss3diags")Once the package is installed it can be loaded by:
library(ss3diags)For examples of how to run common diagnostic tests for SS models and
visualize the results of those diagnostic tests using the r4ss and
ss3diags packages, please refer to the articles on the package
website.
If you would like to contribute to ss3diags or have suggestions for
diagnostic tests to include in the package, you can submit a new
issue or
email Meg at megumi.oshima@noaa.gov.
To cite ss3diags for a publication you can use
citation("ss3diags")
#> To cite package 'ss3diags' in publications use:
#>
#> Winker H, Carvalho F, Cardinale M, Kell L, Oshima M, Fletcher E
#> (2023). _ss3diags: Stock Synthesis Model Diagnostics for Intergated
#> Stock Assessments_. R package version 2.1.1,
#> <https://github.com/PIFSCstockassessments/ss3diags>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> title = {ss3diags: Stock Synthesis Model Diagnostics for Intergated Stock Assessments},
#> author = {Henning Winker and Felipe Carvalho and Massimiliano Cardinale and Laurence Kell and Megumi Oshima and Eric Fletcher},
#> year = {2023},
#> note = {R package version 2.1.1},
#> url = {https://github.com/PIFSCstockassessments/ss3diags},
#> }The United States Department of Commerce (DOC) GitHub project code is provided on an ‘as is’ basis and the user assumes responsibility for its use. DOC has relinquished control of the information and no longer has responsibility to protect the integrity, confidentiality, or availability of the information. Any claims against the Department of Commerce stemming from the use of its GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.”