Add vignettes tutorials for implementing and interpreting diagnostic analyses (#78, #75, #73, and #68). The vignettes replaced the “Cookbook recipe” R scripts with updated code.
Removed Rdata files (ss3diags::simple, ss3diags::retroSimple, and ss3diags::mcmcSimple). These objects are now automatically produced in the vignettes.
Removed deprecated data objects from function arguments (#100).
Created generic functions to re-use common parameter documentation via roxygen tag @inheritParams (#66 and #2).
Update r4ss dependency.
Replacing installation of SS3 in container during R-CMD-Check GitHub Action workflow to use r4ss::get_ss_exe() (#97).
Dependency resolves r4ss function name conflicts w/ dplyr and kableExtra libraries (#83). Side effect of nmfs-fish-tools/ghactions4r#69
Removed dplyr from NAMESPACE. Removed roxygen import calls from SSplotJABBAres() and SSrmse(), and appended dplyr function calls with the double colon operator (dplyr::) (#82)
Updated default summaryoutput used in SSplotModelComp() for ss3diags::retroSimple and default ss3rep used in SSplotRunsTest() for ss3diags::simple
Updated ss3diags citation.
Minor documentation link fixes.
ss3diags 2.1.0
RMSE calculations are modularized as a standalone function that can be called independently from SSplotJABBAres() as SSrmse(). (#50)
Bugfixes with adjusting y-axis limits with SSplotRunstest and SSplotJABBAres: Use the ylim parameter to adjust y-axis limits. (#46)
Added option to remove median trajectory for SSplotKobe() (#3)
Added rlang, dplyr, and magrittr dependencies.
SSmase and SSplotHcxval: Corrected validation messsage to clarify validation issue and to fix an issue with the code styler. (#33, #35)
Added Date field to DESCRIPTION. DESCRIPTION metadata are now used to generate package citations. (#25)
Package vingettes formatted to html_vignette to reduce file size. Removed redundant PDF and word document versions of ss3diags_Handbook vignette.
Updated documentation and fixes.
Enabled markdown support for roxygen.
Enabled Cross-reference links.
ss3diags 2.0.3
Changed r4ss dependency to 1.44.0 (CRAN version) and above.
Replaced default R CMD CHECK workflow with NOAA-fish-tools/ghactions4r’s version.
Fix SSplotRetro.R indention causing issues with code styler
ss3diags 2.0.1
Minor README Updates and corrections
Change in SSplotJABBAres to show the combined seasonal data as boxplots
Fixup links to Cookbook sripts.
Formatted DESCRIPTION URL and BugReports links to the PIFSCstockassessments repo too add to its R package site.
ss3diags 2.0.0
ss3iags is now installed as an R-package. Package documentation is upatded to reflect these chenges.
A simple, cod-like, Stock Synthesis model, simulated via ss3sim, replaces Pacific North Hake (pac.hke) and North Atlantic Shortfin Mako Shark (natl.sma) example datasets.
SSplotRetro: fixed bug so that the shading in uncertainty area shows up when xlims are specified.
SSplotJABBAres: added ‘con’ option to subplots argument so conditional age-at-length data can be plotted. Also added a seas argument so user can specify if data should be combined across seasons within a year or kept separate.
SScompsTA1.8: added a seas argument so users can specify if data should be combined across seasons within a year or kept separate.
SSplot functions (SSplotModelComp, SSplotEnsemble, SSplotHCxval, SSplotJABBAres, SSplotRetro): Marked plot, png, pdf, print, and new as deprecated. They will be defunct in a future version.
Added a NEWS.md file to track changes to the package.
