Package index • atlantisdiagnostics

Processing model output

Processing output from an atlantis run

process_atl_output(): Creates post-processing output for Atlantis

process_catch_fleet(): Creates post-processing Catch output for Atlantis

get_atl_paramfiles(): Creates a dataframe of atlantis parameter files based on standard output

get_forcing_temperature(): Read in temperature forcing by box or from output.nc

get_param_FXXX_SY(): Get adult distribution (FXXX_SY) values from a biology prm file

get_param_move_temp(): Get min_move_temp & max_move_temp values from a biology prm file

get_param_recruit_hdistrib(): Get horizontal distribution recruitment values from a biology prm file

get_param_recruit_vdistrib(): Get vertical distribution recruitment values from a biology prm file

get_param_vert(): Get adult distribution (vertDAY_XXX, vertNIGHT_XXX) values from a biology prm file

get_run_prm(): Get parameters from the run prm file

Plotting model output

Plotting the output from an atlantis run

make_atlantis_diagnostic_figures(): Creates standard diagnostic figures for Atlantis output

Diagnostic checks

Determining if the model is behaving as expected

diag_cohortBiomass(): Test for distribution of biomass over age class

diag_combine(): Combine all diagnostic output

diag_fleet_catch(): Test fleet catch

diag_footprints(): Compares the redistribution footprints for groups in the model

diag_maxsize(): Test for max fish size

diag_persistence(): Test for functional group persistence

diag_reasonability(): Test for functional group reasonability

diag_stability(): Test for functional group stability

diag_temp_thresholds(): Compares the temperature forcing data to the Group temperature thresholds

Miscellaneous

Miscellaneous functions

compare_spatial_vars(): Creates post-processing output for Atlantis

atlantisdiagnostics atlantisdiagnostics-package: atlantisdiagnostics: Tools for calibrating Atlantis ecosystem models