The package provides the functionality to conduct model diagnostics for SS models. The standard diagnostic included in this package are standard required analysis for West Coast Groundfish stock assessments. The package was designed to perform model diagnostics and create plots and tables in a standardized format. The standardized approach will facilitate the use of these outputs in the assessment template approach sa4ss.
The diagnostics created by the package are:
- jitter runs to ensure model convergence at the MLE
- retrospective runs to examine model sensitivity to recent data
- likelihood profiles across parameters
nwfscDiag can be installed via github:
install.packages("remotes")
remotes::install_github("nwfsc-assess/nwfscDiag")
The package depends upon a few other packages and they should be installed upon installation of the package. The dependant packages are:
install.packages('plyr')
remotes::install_github('r4ss/r4ss')
Please report any issues with this package by posting a new github issue at https://github.com/nwfsc-assess/nwfscDiag/issues.