NEWS.md

In r4ss/r4ss: R Code for Stock Synthesis

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 https://github.com/r4ss/r4ss/pull/722
• Functions that run the executable have been renamed: https://github.com/r4ss/r4ss/issues/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) https://github.com/r4ss/r4ss/pull/718
• Introduces new "simple_small" example model but removes older examples, reducing total package size https://github.com/r4ss/r4ss/pull/700
• Uses new columns names in BIOLOGY output https://github.com/r4ss/r4ss/pull/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

r4ss/r4ss documentation built on April 30, 2024, 4:42 a.m.