Setting up the specifications, running the profile using r4ss::profile(),
and generating figures and tables can be tedious, error prone, and time
consuming. Thus, profile_wrapper() aims to further decrease the work
needed to generate a profile that is easily included in a assessment report
for the Pacific Fisheries Management Council. See the See Also section for
information on a workflow to use this function.
run_profile(mydir, model_settings, para)Directory where model files are located.
There is no default entry for mydir.
An example of user input could be
mydir = file.path("C:/my_models", "base_model").
A list of all model settings. Typically, created using get_settings but users can create their own list, as long as it has all of the necessary components for the function at hand.
A character string specifying the SS3 parameter name that the profile pertains to. The parameter name should match the name in the control.ss_new file from SS3.
Nothing is explicitly returned from profile_wrapper().
The following objects are saved to the disk:
*_profile_output.Rdata
*_trajectories_* from r4ss::SSplotComparisons()
piner_panel_*.png
parameter_panel_*.png
run_diag_warning.txt
a copy of the control file saved to model_settings$newctlfile
backup_oldctlfile.ss
backup_ss.par
The following functions interact with profile_wrapper():
get_settings(): populates a list of settings for model_settings
run_diagnostics(): calls profile_wrapper() which calls this function.
r4ss::profile(): the workhorse of profile_wrapper() that does the
parameter profiles