NEWS

r4ss 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.

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

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"

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

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'

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()

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

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

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)

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