Changelog

Source: NEWS.md

r4ss 1.55.0 (June 2026)

• Adds support for tables of mean size at age:
  • “$mean_size_by_cohort” is new output starting with SS3 version 3.30.25
  • “$mean_size_Jan_1” was available in Report.sso previously but is now parsed by SS_output()
  • “$mean_size_timeseries" is identical to the table "$growthseries” which has always been available in r4ss, but the new name will make it easier to keep track of along side the other tables

r4ss 1.54.0 (April 2026)

• Replace base R message(), warning(), and stop() calls with cli equivalents (cli::cli_inform(), cli::cli_warn(), and cli::cli_abort()) throughout the package for improved message formatting.
• Change default value of printstats in SS_output() from TRUE to FALSE to reduce console output.

r4ss 1.52.0 (April 2025)

• Add several functions for making tables. The functions all save .rda files containing a list of dataframe and caption.
  • table_pars() Information on all model parameters
  • table_parcounts() Count of different parameter types
  • table_ts() Annual time series of various quantities (biomass, recruitment, etc.)
  • table_config() Description of model configurations (bins, age range, etc.)
  • table_compweights() Composition weights and sample sizes if using the Francis method
• Revised two existing functions and renamed them for consistency:
  • SSexecutivesummary() -> table_exec_summary() makes a set of tables commonly used in the executive summary of Pacific Fishery Management Council (PFMC) stock assessments, but many may be useful for other assessments as well.
  • SStablebiology() -> table_biology() tables of biology at age and selectivity at age and length

r4ss 1.51.0 (18 December 2024)

• Bug fixes
• Compatibility with SS3 version 3.30.23 and 3.30.23.1

r4ss 1.50.0 (29 July 2024)

• Bug fixes

• Clean up columns names in functions for reading input files to match the .ss_new files written by SS3 as shown in the table below.

  old	new
  “Yr”	“year”
  “Seas”	“month”
  “FltSvy”	“fleet”
  “Gender”	“sex”
  “Part”	“part”
  “Ageerr”	“ageerr”

r4ss 1.49.3 (24 July 2024)

• Replaces magrittr pipe %>% with native pipe |>
• Minimum R version is now 4.1.0

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)

CRAN release: 2022-05-26

• 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)

CRAN release: 2019-10-18

• 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

CRAN release: 2015-12-23

• 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