Changes in version 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. Changes in version 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on r4ss::get_ss3_exe(), with gh::gh() token fixes - Once r4ss dependency is updated to 1.50.0+, local function will be superceded by r4ss::get_ss3_exe() - Update RoxygenNote to 7.3.2 Changes in version 2.2.0 - Add vignettes tutorials for implementing and interpreting diagnostic analyses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). Changes in version 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. Changes in version 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. Changes in version 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') Changes in version 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 - 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 Changes in version 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. Changes in version 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. Changes in version 1.0.8 - Fixed MASE Changes in version 1.0.7 - Bug fixes Changes in version 1.0.6 - Improved SSdiagsMCMC Changes in version 1.0.5 - Updated SSdeltaMVLN Changes in version 1.0.4 - Reference: authors changes Changes in version 1.0.3 - Added annF_ quantaties Changes in version 1.0.2 - Added aut Changes in version 1.0.1 - Added SSplotH