StrathE2E2
End-to-End Marine Food Web Model

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Functions
187
Source code
138
Man pages
32
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StrathE2E2: End-to-End Marine Food Web Model
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API

API for StrathE2E2
End-to-End Marine Food Web Model

Global functions
CredInt_make_aamass_results Source code
CredInt_make_annual_flux_results Source code
CredInt_make_daily_flux_results Source code
CredInt_make_daily_migration_results Source code
CredInt_make_daily_results Source code
CredInt_make_monthly_results Source code
CredInt_make_network_results Source code
CredInt_make_parameter_results Source code
CredInt_make_target_results Source code
GetCredInt Source code
StrathE2E.run Source code
StrathE2E2 Man page
StrathE2E_fit Source code
aggregate_model_output Source code
assemble_flow_matrix_from_model_annual_output Source code
boxplot_annual_compare_observations Source code
boxplot_annual_compare_observations_with_ci Source code
boxplot_annual_compare_runs Source code
boxplot_monthly_compare_observations Source code
boxplot_monthly_compare_observations_with_ci Source code
boxplot_monthly_compare_runs Source code
build_annual_drivers Source code
build_initial_state Source code
build_model Source code
build_model_parameters Source code
build_model_run Source code
calculate_error_function Source code
calculate_uptakes Source code
check.exists Source code
compare_two_runs_aam Source code
compare_two_runs_catch Source code
concatenate_raw_mc_data_files Source code
concatenate_raw_sensitivity_data_files Source code
create.folder Source code
csvname Source code
derive_annual_results_inshore Source code
derive_annual_results_offshore Source code
derive_annual_results_wholedomain Source code
derive_model_target_results Source code
disaggregate_landings_discards_by_gear Source code
e2e_calculate_hrscale Man page Source code
e2e_compare_obs Man page Source code
e2e_compare_runs_bar Man page Source code
e2e_compare_runs_box Man page Source code
e2e_copy Man page Source code
e2e_extract_hr Man page Source code
e2e_extract_start Man page Source code
e2e_get_parmdoc Man page Source code
e2e_get_senscrit Man page Source code
e2e_ls Man page Source code
e2e_merge_sens_mc Man page Source code
e2e_optimize_act Man page Source code
e2e_optimize_eco Man page Source code
e2e_optimize_hr Man page Source code
e2e_plot_biomass Man page Source code
e2e_plot_catch Man page Source code
e2e_plot_eco Man page Source code
e2e_plot_edrivers Man page Source code
e2e_plot_fdrivers Man page Source code
e2e_plot_migration Man page Source code
e2e_plot_opt_diagnostics Man page Source code
e2e_plot_sens_mc Man page Source code
e2e_plot_trophic Man page Source code
e2e_plot_ts Man page Source code
e2e_plot_ycurve Man page Source code
e2e_process_sens_mc Man page Source code
e2e_read Man page Source code
e2e_run Man page Source code
e2e_run_mc Man page Source code
e2e_run_sens Man page Source code
e2e_run_ycurve Man page Source code
elt Source code
extract_ACTmult_to_parmsfolder Source code
extract_HRmult_to_parmsfolder Source code
extract_final_year_of_run_plus_volumetric_data Source code
extract_simulated_catch_land_disc_by_gear_for_given_year Source code
extract_timeseries_annual_landings Source code
fishing_fleet_model Source code
fyplot1 Source code
fyplot2 Source code
fyplot3 Source code
fyplot3_hab Source code
fyplot4 Source code
generate_df_yield_curve_data Source code
generate_pf_yield_curve_data Source code
genshowall Source code
get.example.results Source code
get.model.file Source code
get.model.path Source code
get.variant.path Source code
hasExamples Source code
interpolate_drivers Source code
isdefined Source code
makepath Source code
monthly_averages_of_final_year Source code
optimize_activity_mult_eco Source code
optimize_activity_mult_hr Source code
perturb_parameters Source code
perturb_parameters_all Source code
plot_act_hr_optimization_diagnostics Source code
plot_df_yield_curve Source code
plot_eco_hr_act_eco_optimization_diagnostics Source code
plot_final_year_migration_data Source code
plot_final_year_migration_data_with_ci Source code
plot_final_year_time_series_data Source code
plot_final_year_time_series_data_with_ci Source code
plot_final_year_trophic_data Source code
plot_final_year_trophic_data_with_ci Source code
plot_for_each_gear_catch_by_guild Source code
plot_for_each_guild_catch_by_gear Source code
plot_full_length_timeseries Source code
plot_gear_activity_distribution Source code
plot_gear_guild_discard_rates Source code
plot_gear_guild_harvest_ratios Source code
plot_gear_guild_offal_rates Source code
plot_inshore_vs_offshore_anavmass Source code
plot_inshore_vs_offshore_anavmass_with_ci Source code
plot_mc_parameter_likelihoods Source code
plot_pf_yield_curve Source code
plot_seabed_abrasion_area_ratios Source code
plot_sensitivity_results Source code
plot_time_series_annual_land_disc Source code
postprocess_mc_data Source code
postprocess_sens_data Source code
process_sensitivity_analysis_results Source code
read.model.setup Source code
read_SD_credint Source code
read_SD_ecology Source code
read_SD_fishing Source code
read_SD_sensitivity Source code
read_annual_target_data Source code
read_biological_event_timings Source code
read_chemistry_drivers Source code
read_fishing_fleet_model Source code
read_fitted_parameters Source code
read_fixed_parameters Source code
read_initial_state Source code
read_monthly_target_data Source code
read_physical_parameters Source code
read_physics_drivers Source code
readcsv Source code
remove.dirsep Source code
showall Source code
showallsort Source code
sourcefile Source code
store_fleet_model_output Source code
tsmonthplot1 Source code
tsmonthplot2 Source code
tsmonthplot3 Source code
tsplot1 Source code
tsplot2 Source code
tsplot3 Source code
write_fitted_parameters Source code
writecsv Source code
writecsv.list Source code
writecsv.local Source code
StrathE2E2 documentation built on Jan. 23, 2021, 1:07 a.m.

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