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Changelog

Source: NEWS.md

r4ss 1.56.0 (August 2026)

  • Improve retro(): several quantities now automatically adjusted, including the end year of main recruitment deviations, the bias adjustment settings, removing blocks which occur after the retro year, and year ranges in forecast file for forecast and benchmark calculations. See #1087 for details.

  • Improve formatting of console comments (via use of cli::cli_alert_* functions instead of cli::cli_inform() as implemented in 1.54.0) #1088

  • Replace default function inputs like "default" with more informative values like replist[["FleetNames"]] #1093

  • Add a new SS_add_parameter_line() function to help with R-based workflows which will copy a parameter line, edit user-selected columns, and then put it in a location selected by the user #1081

  • Make axis labels smarter in comparison plots of biomass ratio #1092

  • Fix a bug causing sex ratio plots to be absent when there’s a mix of sexed and unsexed composition data

  • Avoid creating distracting empty plot window when running SS_plots()

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)

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)

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