ss3diags 2.2.1

• 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  • Once r4ss dependency is updated to 1.50.0+, local function will be superceded by r4ss::get_ss3_exe()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

ss3diags 2.2.0

• Add vignettes tutorials for implementing and interpreting diagnostic analyses (#78, #75, #73, and #68). The vignettes replaces 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).

ss3diags 2.1.1

• Added new logo. Thanks @pdimens (#76)
• 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.

ss3diags 2.1.0

• Modularized RMSE calculations as a standalone function so that it can be called independently from SSplotJABBAres() as SSrmse(). (#50)
• Bugfixes to 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 season validation: Fixed an issue with invalid season message with subset operators ($,[[) breaking the code styler; Clarified invalid season message to more readable. (#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

This coincides with r4ss 1.44.0 and its matching version found on CRAN.

• 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")

ss3diags 2.0.2

• Changed r4ss CRAN version (1.36.1) dependency to development version.
• Refactored common ssplot subfunctions to use equivalent r4ss ssplot utility functions.
  • 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