Changes in version 1.56.0 - 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() Changes in version 1.55.0 - 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 Changes in version 1.54.0 - 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. Changes in version 1.52.0 - 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 Changes in version 1.51.0 - Bug fixes - Compatibility with SS3 version 3.30.23 and 3.30.23.1 Changes in version 1.50.0 - 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" Changes in version 1.49.3 - Replaces magrittr pipe %>% with native pipe |> - Minimum R version is now 4.1.0 Changes in version 1.48.0 - Bug fixes and cosmetic changes - Use {pkgdown} to develop a better website - Change logo - Update install instructions on README to use {pak} Changes in version 1.47.0 - 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' Changes in version 1.46.1 - 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() Changes in version 1.44.0 (2022-05-26) - Minor improvements and bug fixes - Compatibility with SS3 version 3.30.19 - Submitted to CRAN Changes in version 1.43.2 - Standardize version = "3.30" in read and write functions and deprecate NULL as an option Changes in version 1.43.1 - Added Common Utility Functions Changes in version 1.39.1 - Numerous bug fixes and minor improvements - Compatibility with SS version 3.30.16 Changes in version 1.38.0 - 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 Changes in version 1.36.1 (2019-10-18) - Numerous minor bug fixes and minor improvements - Compatibility with SS versions 3.24 through 3.30.14 - Submitted to CRAN Changes in version 1.33.1 - Numerous minor bug fixes and minor improvements - Compatibility with SS versions 3.24 through 3.30.13-beta Changes in version 1.30.1 - Fix bugs in new stock-recruit plot, and cohort lines added to bubbles Changes in version 1.30.0 - Limited support for models that use Dirichlet-Multinomial likelihood (currently only works for age compositions, not length comps) Changes in version 1.29.1 - 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) Changes in version 1.28.0 - Slacked off on updating this NEWS file Changes in version 1.24.3 - Implemented automated R package check on Travis-CI Changes in version 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 Changes in version 1.24.1 - Minor bug fixes and other small edits Changes in version 1.24.0 (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