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NEWS.md

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r4ss 1.48.0 (27 March 2023)

  • Bug fixes and cosmetic changes
    • Use {pkgdown} to develop a better website
    • Change logo
    • Update install instructions on README to use {pak}

r4ss 1.47.0 (31 January 2023)

  • Support new SS3 option to estimate separate Dirichlet-multinomial parameters for retained vs discards
    • SS3 version 3.30.21 models will also have all info on D-M parameters read directly from Report.sso instead of the data file
  • Numerous minor bug fixes
  • Adds dependency on 'dplyr' and 'magrittr'

r4ss 1.46.1 (29 July 2022)

  • Major revamp of all functions that run the Stock Synthesis executable #722
    • Functions that run the executable have been renamed: #723:
      • run_SS_models() -> run() (now has defaults which allow you to simply call run() in the current working directory as well as and better support for having the Stock Synthesis executable in your path)
      • SS_profile() -> profile()
      • SS_doRetro() -> retro()
      • SS_RunJitter() -> jitter()
      • SS_tune_comps() -> tune_comps()
    • Functions have more consistent inputs (e.g., always dir instead of mydir, File, or masterdir, and now defaulting to the current working directory)
    • Input show_in_console = FALSE can be used with all these functions and will pipe output to a text file keeping R console cleaner while models run
  • Deprecates functions that relate to 3.24 models, like SS_readdat_3.24() (although SS_output() is still compatible back to version 3.24) #718
  • Introduces new "simple_small" example model but removes older examples, reducing total package size #700
  • Uses new columns names in BIOLOGY output #711
  • Numerous bug fixes
  • Adds dependency on 'tidyr'
  • Removes never-completed function SSbootstrap()

r4ss 1.44.0 (23 May 2022)

  • Minor improvements and bug fixes
  • Compatibility with SS3 version 3.30.19
  • Submitted to CRAN

r4ss 1.43.2 (04 April 2022)

  • Standardize version = "3.30" in read and write functions and deprecate NULL as an option

r4ss 1.43.1 (18 February 2022)

  • Added Common Utility Functions

r4ss 1.39.1 (18 August 2020)

  • Numerous bug fixes and minor improvements
  • Compatibility with SS version 3.30.16

r4ss 1.38.0 (25 March 2020)

  • Numerous bug fixes and minor improvements
  • Compatibility with SS version 3.30.15
  • Expansion of capabilities for functions to read and write SS input files
  • Dependent on fewer packages but now depends on R version 3.5.0 or newer

r4ss 1.36.1 (16 October 2019)

  • Numerous minor bug fixes and minor improvements
  • Compatibility with SS versions 3.24 through 3.30.14
  • Submitted to CRAN

r4ss 1.33.1 (5 November 2018)

  • Numerous minor bug fixes and minor improvements
  • Compatibility with SS versions 3.24 through 3.30.13-beta

r4ss 1.30.1 (February 2, 2018)

  • Fix bugs in new stock-recruit plot, and cohort lines added to bubbles

r4ss 1.30.0 (January 25, 2018)

  • Limited support for models that use Dirichlet-Multinomial likelihood (currently only works for age compositions, not length comps)

r4ss 1.29.1 (January 11, 2018)

  • Support for SS version 3.30.10.00 available on VLab today
  • Some changes in column names and other variables to match cleanup of terminology in latest Stock Synthesis
  • New Vignette (very limited but provides a start to be improved on)

r4ss 1.25.0 - 1.28.0

  • Slacked off on updating this NEWS file

r4ss 1.24.3

  • Implemented automated R package check on Travis-CI

r4ss 1.24.2

  • SS_varadjust now works for use in automating variance adjustments at the bottom of the control file
  • Improvements related to testing SS version 3.30 including converting SS_readdat into a wrapper function that calls separate functions for SS v3.24 and v3.30

r4ss 1.24.1

  • Minor bug fixes and other small edits

r4ss 1.24.0

  • First CRAN update since r4ss 1.22.1 in July 2014.
  • Variety of new defaults in plots
  • Help from various new contributors
  • See https://github.com/r4ss/r4ss for more detail on changes and new features