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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)
  • 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 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).

ss3diags 2.1.1

  • 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.

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.
  • 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, renamed, and used equilvants in r4ss util
  • 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.

ss3diags 1.0.8

  • Fixed MASE

ss3diags 1.0.7

  • Bug fixes

ss3diags 1.0.6

  • Improved SSdiagsMCMC

ss3diags 1.0.5

  • Updated SSdeltaMVLN

ss3diags 1.0.4

  • Reference: authors changes

ss3diags 1.0.3

  • Added annF_ quantaties

ss3diags 1.0.2

  • Added aut

ss3diags 1.0.1

  • Added SSplotH