Plotting Function for All Basic Quantities

Convenience wrapper that calls all core SPoRC plotting functions and writes their output to a single PDF file. Equivalent to calling get_biological_plot, get_data_fitted_plot, get_ts_plot, get_selex_plot, and get_nLL_plot in sequence and printing each to the same device.

Usage

plot_all_basic(data, rep, sd_rep, model_names, out_path)

Arguments

data

List of length n_models, where each element is a SPoRC data list. Passed to get_biological_plot, get_data_fitted_plot, and get_nLL_plot.

rep

List of length n_models, where each element is a SPoRC report list (i.e. the output of obj$report() after optimisation). Passed to get_biological_plot, get_ts_plot, get_selex_plot, and get_nLL_plot.

sd_rep

List of length n_models, where each element is a SPoRC sdreport list (i.e. the output of sdreport(obj)). Passed to get_ts_plot for delta-method confidence intervals.

model_names

Character vector of length n_models giving display names for each model run. Passed to all sub-functions as legend and facet labels.

out_path

Path to the output directory. The PDF is written to here::here(out_path, "plot_results.pdf") at 25 × 13 inches per page.

Value

Called for its side effect. Writes plot_results.pdf to out_path and returns NULL invisibly.

See also

Other Plotting: get_biological_plot(), get_data_fitted_plot(), get_selex_plot(), get_ts_plot(), theme_sablefish()

Examples

if (FALSE) { # \dontrun{
  plot_all_basic(
    data        = list(data1, data2),
    rep         = list(rep1, rep2),
    sd_rep      = list(sd_rep1, sd_rep2),
    model_names = c("Base", "Sensitivity"),
    out_path    = here::here()
  )
} # }