Changelog • ss3diags

ss3diags 2.2.2

This version is compatible with the changes introduced with r4ss 1.50.0 and above.

Updated r4ss dependency to version 1.50.0 and above. (#113, #114, #115)
- Removed local get_ss3_exe function, which r4ss::get_r4ss_exe() supersedes it
- Updated references to match updated r4ss new naming conventions (#113)
Change to native R’s pipes; replacing magrittr pipes
SSrmse: Parameter quants, the “quantity” for calcuating RMSE, is now checked for these valid options: cpue, len, age, size, and con
SSPlotHCxval: Remove redundant parameter uncertainty (#95)
Added renv to help with github actions
Omitted LazyData in DESCRIPTION due to removal of Rdata files.

Change r4ss dependency to ONLY version 1.49.3 for compatibility.
- r4ss 1.50.0 introduces a major changes to its read/write functions that breaks compatibility with existing ss3diags functions, but will be resolved in a future update. (#109)
Set NA_character_ as gh::gh() token to resolve SAML authentication errors downloading ss3 binaries from nfms-ost/ss3-source-code used in test scripts. (#110)
- Added local get_ss3_exe function, based on r4ss::get_ss3_exe(), with gh::gh() token fixes
- Once r4ss dependency is updated to 1.50.0+, local function will be superceded by r4ss::get_ss3_exe()
Update RoxygenNote to 7.3.2

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).

Added new logo. Thanks @pdimens (#76, #77)
Added options to SSdeltaMVLN for Variance-Coveriance approximation and bias correction. Thanks @N-DucharmeBarth-NOAA (#64)
Updated r4ss dependency (#84)
- 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.

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.

Changed r4ss dependency to 1.44.0 (CRAN version) and above.
Replaced default R CMD CHECK workflow with NOAA-fish-tools/ghactions4r’s version.
Fixed Ensemble Quantile Shading Issues (#4)
Replaced the example datasets in the ss3diags cookbook, and the handbook with the current “simple” ensemble model.
Fixup minor code documentation formatting issues.
Implemented NOAA-fish-tools/ghactions4r integrated code styler and documentation for pull requests.
- SSmase and SSplotHcxval: Fixed up code styler’s dollar subset conversion issues. example:`message(‘x$name is 1,2,3,4’)`

Changed r4ss CRAN version (1.36.1) dependency to development version
Refactored common ssplot subfunctions, renamed, and used equilvants in r4ss util
- legendfun -> r4ss::add_legend
- pngfun -> r4ss::save_png
- rc -> r4ss::rich_colors_short
- sspar -> r4ss::sspar
Fix SSplotRetro.R indention causing issues with code styler

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.

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.