Files in Blevy2/READ-PDB-blevy2-MFS2

Mixed Fishery fleet dynamics simulation tool

GB_3species.Rmd Generic Species.Rmd Manuscript/Draft1.Rmd Manuscript/Draft1.pdf Manuscript/Draft1_withcomments.pdf Manuscript/Draft1cml.pdf Manuscript/Draft2.Rmd Manuscript/Example_from_Chris.Rmd Manuscript/IBMWG_Manuscript.pdf MixFishSim.pdf R/BENS(old)_init_survey.R R/BENS_create_hab.R R/BENS_init_survey.R R/BENS_plot_habitat.R R/BENS_plot_spatiotemp_hab_justtemp.R R/Bens_plot_pop_spatiotemp.R R/Bens_plot_spatiotemp_hab.R R/RcppExports.R R/Recr.R R/Recr_mat.R R/baranov_f.R R/close_areas.R R/combine_logs.R R/create_fields.R R/create_hab.R R/create_spawn_hab.R R/create_spawn_hab_Bens.R R/define_spawn.R R/define_spawn_Bens.R R/deg2rad.R R/delay_difference.R R/distance_CalcR.R R/find_f.R R/find_spat_f.R R/find_spat_f_naive.R R/find_spat_f_pops.R R/get_bearing.R R/go_fish.R R/go_fish_Bens.R R/go_fish_fleet.R R/go_fish_orig.R R/init_closure.R R/init_fleet.R R/init_moveCov.R R/init_moveCov_Bens.R R/init_moveCov_Bens2.R R/init_moveCov_Bens3.R R/init_moveCov_Bens4.R R/init_pop.R R/init_pop_Bens.R R/init_pop_Bens_param_estimate.R R/init_sim.R R/init_sim_Bens.R R/init_sim_Bens_nofish.R R/init_survey.R R/logistic.R R/make_step.R R/norm_dist.R R/package_init.R R/plot_catch_comp.R R/plot_daily_fdyn.R R/plot_fleet_trip.R R/plot_habitat.R R/plot_pop_summary.R R/plot_realised_stepF.R R/plot_spatiotemp_hab.R R/plot_survey.R R/plot_vessel_move.R R/rad2deg.R R/run_sim.R R/run_sim_param_estimate.R R/step_length.R R/sum_fleet_catches.R R/sum_fleets_catches.R R/test_step.R R/use_past_knowledge.R README.md TestScripts/Analyze_Survey.R TestScripts/Calc_strat_mean/calc_srs_index_survey_BENS.R TestScripts/Calc_strat_mean/fn_srs_survey_BENS.R TestScripts/Environmental_Interp_Kern_Dens.R TestScripts/Environmental_Interp_Kern_Dens_Cod_GB.R TestScripts/Environmental_Interp_Kern_Dens_Haddock_GB.R TestScripts/Environmental_Interp_Kern_Dens_YellowtailFlounder.R TestScripts/Estimate_Ratio_summary.R TestScripts/FVCOM_extract.R TestScripts/FVCOM_extract_Bens.R TestScripts/FVCOM_extract_Bens_JustSurveyDates.R TestScripts/FVCOM_extract_Bens_TempTimeseries.R TestScripts/Fish_life.R TestScripts/GB_habitat_create.R TestScripts/Generic_Species_Profile.R TestScripts/Plots_for_paper_presentation.R TestScripts/Plotting.R TestScripts/Strat_Rand_Samp.R TestScripts/TempTolerance.R TestScripts/Test_from_andy_beet.R TestScripts/VAST_ModelSelection_Error_All.R TestScripts/VAST_ModelSelection_Error_YT.R TestScripts/VAST_StratMean_Error_Comparison_All.R TestScripts/VAST_StratMean_Error_Comparison_All_withCovs.R TestScripts/VAST_StratMean_Error_Comparison_All_withCovs_ForPaper.R TestScripts/Visualize_covariate_response.R TestScripts/add_2_movecov_yrs.R TestScripts/anisotropy.R TestScripts/compile_results.R TestScripts/lrren_Bens.R TestScripts/model-based/model_based_estimation.R TestScripts/moveCov_FVCOM_Data.R TestScripts/moveCov_longer_time.R TestScripts/moveCov_longer_time_BensMethod.R TestScripts/movement_check.R TestScripts/param_calc.R TestScripts/param_estimate.R TestScripts/percent_area_occupied.R TestScripts/plot_estimates_by_strat.R TestScripts/plot_predict_BENS.R TestScripts/pos2coord.R TestScripts/rand_samp.R TestScripts/reprex_generic_species.R TestScripts/run_on_ada.R TestScripts/run_survey_BENS.R TestScripts/run_survey_BENS_NEW.R TestScripts/stock_recruit.R TestScripts/strata_area_cell_size.R TestScripts/stratified_mean_limited.R TestScripts/stratified_mean_limited_VAST.R TestScripts/stratified_mean_limited_VAST_Multiple_Surveys.R TestScripts/testpush.R TestScripts/vast_by_strat.R TestScripts/x_y_to_lat_lon.R VAST/Example_EndofCenturyProjections.R VAST/From Chris/GBYT_VAST.R VAST/From Chris/test_haddock.R VAST/From Chris/test_simulate.R VAST/Test_3Species_GeorgesBank.R VAST/Test_3Species_GeorgesBank_Cod_Only.R VAST/Test_3Species_GeorgesBank_Had_Only.R VAST/Test_3Species_GeorgesBank_YT_Only.R