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()
SS_output()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.printstats in SS_output() from TRUE to FALSE to reduce console output.table_pars() Information on all model parameterstable_parcounts() Count of different parameter typestable_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 methodSSexecutivesummary() -> 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 lengthBug 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"
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()dir instead of
mydir, File, or masterdir, and now defaulting to the current
working directory)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 runSS_readdat_3.24() (although SS_output() is still compatible back
to version 3.24) https://github.com/r4ss/r4ss/pull/718SSbootstrap()