Reference

All functions

check_profile_range()

Check the profile range specified

get_jitter_quants()

Create output files with jitter quantities

get_param_values()

Generate likelihood profiles To be called from the run_diagnostics function after creating the model settings using the get_settings function.

get_retro_quants()

Get model values across retrospective runs

get_settings()

Check that all of the settings are in the list

get_settings_profile()

Get default settings for profiles

get_summary()

Generate results from likelihood profiles

jitter_wrapper()

Run r4ss::jitter based on model_settings

plot_jitter()

Generated plots to visualize results

plot_profile()

Generate likelihood profile plots

plot_retro()

Create plots for retrospective runs

pngfun()

Create a .png figure

pretty_decimal()

Format a vector of real numbers with a pretty number of decimal places

profile_wrapper()

Run r4ss::profile() based on model_settings

rerun_profile_vals()

Rerun some of the models in a likelihood profile

retro_wrapper()

Run r4ss::retro based on model_settings

round_any()

Round values

run_diagnostics()

Wrapper to run each of the 3 standard diagnostic items:

  1. Jitter

  2. Profiles across requested SS3 parameters

  3. Retrospectives

run_jitter()

Run r4ss::jitter based on model_settings

run_profile()

Run r4ss::profile() based on model_settings

run_retro()

Run r4ss::retro based on model_settings