Create a folder containing retrospective runs for a given base-model folder.
Runs are created using settings specified in model_settings and
is formatted for inclusion in a document.
retro_wrapper(mydir, model_settings)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.
Nothing is explicitly returned from retro_wrapper.
The following objects are saved to the disk.
mohnsrho.csv with the following columns:
type: the type of Mohn's rho
Woods Hole Mohn's rho (Legault 2009) used by the Northeast Fisheries Science Center (NEFSC), and
Hurtado-Ferro et al. (2015) used by the Alaska Fisheries Science Center (AFSC)
Quantity: the stock assessment quantity of interest
values: the Mohn's rho values
A set of figures from r4ss::SSplotComparisons
retrofigures4doc.csv for use with sa4ss::add_figure to add retro peels of
spawning stock biomass (SSB) and fraction unfished,
complete with captions and alternative text.
apply(utils::read.csv(file.path("..", paste0(mod_loc, "_retro"), "retrofigures4doc.csv")), 1, function(x) do.call(sa4ss::add_figure, as.list(x)))
mohnsrho.tex for use with sa4ss::read_child()
inside of an environment with results = "asis"
to include a table of Mohn's rho values in a document.
sa4ss::read_child(file.path(paste0(params$model, "_retro"), "mohnsrho.tex"))
retro_output.Rdata with a list of R objects.
The following functions interact with retro_wrapper:
run_diagnostics: calls retro_wrapper
r4ss::retro: the workhorse of retro_wrapper that does the peels