Fishing sensitivity final

[jcaracappa1]

Fishing Sensitivity Analyses into Dev

Parameter Changes

• at_run.prm : Changed default time from 730 to 20805 (1964-2020)
• added neus_init.nc, neus_init_nofill.nc, and neus_tmerc_RM2.bgm back into repo
• sbatch_scenario_array_base.sh : Reference slurm array job on cloud

Fishing Sensitivity Analysis Scripts (R/fishing_sensitivity/)

• call_catch_file_projected_mean.R : Creates a new catch file with a projection period with some mean contemporary catch level
• call_fish_sens_proj_catch_scalar.R : Generates catch scalar projection scenarios
• call_fish_sens_proj_catch_spike.R : Creates catch spike disturbance scenarios
• call_missing_runs.R - Reruns existing scenario and to fill in scenario runs that were skipped
• call_random_catch_scenarios.R : generates randomized catch scenarios
• check_scenario_completion.R : Verifies that scenarios completed correctly
• combine_scenario_output.R : Combines statistical outputs from multiple run sets
• convert_filename.R : Renames scenario output
• export_scenario_output.R : Concatenates scenario timeseries output to single data files
• export_scenario_stats.R : Calculates metrics for each scenario to single data file
• make_baseline_run_data.R : calculates stats for baseline run
• make_catch_spike_recovery_stats.R : Calculates recovery stats for each scenario
• make_fish_sens_proj_catch_scalar_species.R : Creates catch.ts, force.prm, and run.sh files for each catch scalar scenario
• make_fish_sens_proj_catch_spike_species.R : Creates catch.ts, force.prm, and run.sh files for each spike disturbance scenario
• make_foodweb_stats.R : Analyzes diet output for each run scenario for common food web stats
• make_random_catch_scenarios.R : Creates catch.ts, force.prm, and run.sh files for each randomized catch scenario
• make_random_catch_stats.R : Creates statistics for random catch scenarios
• plot_catch_scalar_raw.R : Plots raw scenario output by species by scalar for catch scalar runs
• plot_catch_scalar_summary.R : Plots catch scalar summary plots
• plot_catch_spike_raw.R : Plots raw scenario output by species by scalar for spike disturbances
• plot_catch_spike_summary.R : Plots summary plots for spike disturbance runs
• plot_model_timeline.R : Creates diagnostic for scenario temporal components
• plot_random_catch_permutations.R : Creates example of catch timeseries randomization
• plot_random_catch_summary.R : Creates summary plots of randomized catch runs
• profile_test.R : Test efficiency of various scripts
• rename_outputs.R: renames scenario outputs

R Scripts

• Geometry/NEUS 1-5 Map.R : Added an unlabeled map of polygons with coastline for presentations (Goemetry/NEUS_1_5_with_Coastline_noLabels.png)
• R/edit_param_FSPB.R : Commented out example
• R/get_atl_paramfiles.R : fixed reference shell script name
• R/get_age_mat.R : now writes to diagnostics folder
• R/load_nc_tmep.R : changed error to warning
• R/test_postprocessing.R : changed directories

Other

• .gitignore : fixed wrong bgm name, added init_nofill.nc, reorganized all ignored files and excluded scenario files
• Geometry/box_layer_index.csv : Improved box-layer index to handle the Atlantis layer reversal
• removed outdated catch files in currentVersion/CatchFiles
• diagnostics/group_mature_age.csv : reference age for each species
• diagnostics/scenario_db/ : keeps track of different scenario names and critical info

[jcaracappa1]

@RGamble1 @andybeet merging fishing sensitivity to dev. Did a lot of cleanup of dev too

[RGamble1]

@andybeet @jcaracappa1 Looks good to me