Files in pdolder/MixFishSim
Mixed Fishery fleet dynamics simulation tool

.Rbuildignore
.Rinstignore
.gitignore
DESCRIPTION
MixFishSim.pdf
NAMESPACE
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/define_spawn.R R/deg2rad.R R/delay_difference.R R/find_f.R R/find_spat_f.R R/find_spat_f_pops.R R/get_bearing.R R/go_fish.R R/go_fish_fleet.R R/init_closure.R R/init_fleet.R R/init_moveCov.R R/init_pop.R R/init_sim.R R/init_survey.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_pop_summary.R R/plot_realised_stepF.R R/plot_spatiotemp_hab.R R/plot_survey.R R/plot_vessel_move.R R/rad2.deg.R R/run_sim.R R/step_length.R R/sum_fleet_catches.R R/sum_fleets_catches.R R/test_step.R analysis/Closure_Analysis_Cond.R analysis/Closure_Analysis_Runs0.R analysis/Closure_Analysis_Runs1.R analysis/Closure_Analysis_Runs10.R analysis/Closure_Analysis_Runs11.R analysis/Closure_Analysis_Runs12.R analysis/Closure_Analysis_Runs13.R analysis/Closure_Analysis_Runs14.R analysis/Closure_Analysis_Runs2.R analysis/Closure_Analysis_Runs3.R analysis/Closure_Analysis_Runs4.R analysis/Closure_Analysis_Runs5.R analysis/Closure_Analysis_Runs6.R analysis/Closure_Analysis_Runs7.R analysis/Closure_Analysis_Runs8.R analysis/Closure_Analysis_Runs9.R analysis/Condition_Rec.R analysis/Data_Aggregation_space.pdf analysis/Data_Aggregation_time.pdf analysis/KillerFigure.R analysis/Plot_Bio.R analysis/Plot_activity.R analysis/Plots.R analysis/Plots_Combined.R analysis/scenarios.R
analysis/scenarios.csv
man/Recr.Rd man/Recr_mat.Rd man/baranov_f.Rd man/close_areas.Rd man/combine_logs.Rd man/create_fields.Rd man/create_hab.Rd man/create_spawn_hab.Rd man/define_spawn.Rd man/deg2rad.Rd man/delay_diff.Rd man/distance_calc.Rd man/find_f.Rd man/find_spat_f.Rd man/find_spat_f_pops.Rd man/get_bearing.Rd man/go_fish.Rd man/go_fish_fleet.Rd man/init_closure.Rd man/init_fleet.Rd man/init_moveCov.Rd man/init_pop.Rd man/init_sim.Rd man/init_survey.Rd man/make_step.Rd man/move_population.Rd man/move_prob.Rd man/move_prob_Lst.Rd man/norm_fun.Rd man/plot_catch_comp.Rd man/plot_daily_fdyn.Rd man/plot_fleet_trip.Rd man/plot_pop_summary.Rd man/plot_realised_stepF.Rd man/plot_spatiotemp_hab.Rd man/plot_survey.Rd man/plot_vessel_move.Rd man/rad2deg.Rd man/run_sim.Rd man/step_length.Rd man/sum_fleet_catches.Rd man/sum_fleets_catches.Rd man/test_step.Rd
src/Movement.cpp
src/RcppExports.cpp
tests/.Rd2pdf19449/Rd2.tex
tests/CondTest.R tests/FullTest.R tests/Plot_Bio.R tests/build.R tests/closure_test.R
tests/habitat.png
tests/moveCovTest.R
tests/plots/Proportion_in_cell.png
tests/plots/annual_summary.png
tests/plots/catch_comp.png
tests/plots/catch_comp_clusters.png
tests/plots/fDynamics.png
tests/plots/fleet_moves.png
tests/plots/fleets_move.png
tests/plots/habitat.png
tests/plots/spatial_survey.png
tests/plots/step_function.png
tests/plots/survey_index.png
tests/plots/vessel_move.png
tests/plots/vessel_move_value.png
tests/plots/vessel_multi_move.png
tests/testthat.R tests/vonMises.R write_up/EcolMod_guidance.pdf write_up/Plots/Plot_temp_effect.R
write_up/Supplementary.fdb_latexmk
write_up/Supplementary.fls
write_up/Supplementary.pdf
write_up/Supplementary.spl
write_up/Supplementary.tex
write_up/VAST_fit/VAST_mixfishsim.R
write_up/VAST_fit/results/2018-02-05_M0/Aniso.png
write_up/VAST_fit/results/2018-02-05_M0/Diag--Encounter_prob.png
write_up/VAST_fit/results/2018-02-05_M0/Eps_Pos--Factor_1.png
write_up/VAST_fit/results/2018-02-05_M0/Eps_Pos--Factor_2.png
write_up/VAST_fit/results/2018-02-05_M0/Eps_Pos--Factor_3.png
write_up/VAST_fit/results/2018-02-05_M0/Eps_Pos--Factor_4.png
write_up/VAST_fit/results/2018-02-05_M0/Eps_Pres--Factor_1.png
write_up/VAST_fit/results/2018-02-05_M0/Eps_Pres--Factor_2.png
write_up/VAST_fit/results/2018-02-05_M0/Eps_Pres--Factor_3.png
write_up/VAST_fit/results/2018-02-05_M0/Eps_Pres--Factor_4.png
write_up/VAST_fit/results/2018-02-05_M0/Factor_loadings--Epsilon1.png
write_up/VAST_fit/results/2018-02-05_M0/Factor_loadings--Epsilon2.png
write_up/VAST_fit/results/2018-02-05_M0/Factor_loadings--Omega1.png
write_up/VAST_fit/results/2018-02-05_M0/Factor_loadings--Omega2.png
write_up/VAST_fit/results/2018-02-05_M0/Factor_maps--Epsilon1.png
write_up/VAST_fit/results/2018-02-05_M0/Factor_maps--Epsilon2.png
write_up/VAST_fit/results/2018-02-05_M0/Factor_maps--Omega1.png
write_up/VAST_fit/results/2018-02-05_M0/Factor_maps--Omega2.png
write_up/VAST_fit/results/2018-02-05_M0/Field_Dens--spp1.png
write_up/VAST_fit/results/2018-02-05_M0/Field_Dens--spp1_Legend.png
write_up/VAST_fit/results/2018-02-05_M0/Field_Dens--spp2.png
write_up/VAST_fit/results/2018-02-05_M0/Field_Dens--spp2_Legend.png
write_up/VAST_fit/results/2018-02-05_M0/Field_Dens--spp3.png
write_up/VAST_fit/results/2018-02-05_M0/Field_Dens--spp3_Legend.png
write_up/VAST_fit/results/2018-02-05_M0/Field_Dens--spp4.png
write_up/VAST_fit/results/2018-02-05_M0/Field_Dens--spp4_Legend.png
write_up/VAST_fit/results/2018-02-05_M0/Field_Pos--spp1.png
write_up/VAST_fit/results/2018-02-05_M0/Field_Pos--spp1_Legend.png
write_up/VAST_fit/results/2018-02-05_M0/Field_Pos--spp2.png
write_up/VAST_fit/results/2018-02-05_M0/Field_Pos--spp2_Legend.png
write_up/VAST_fit/results/2018-02-05_M0/Field_Pos--spp3.png
write_up/VAST_fit/results/2018-02-05_M0/Field_Pos--spp3_Legend.png
write_up/VAST_fit/results/2018-02-05_M0/Field_Pos--spp4.png
write_up/VAST_fit/results/2018-02-05_M0/Field_Pos--spp4_Legend.png
write_up/VAST_fit/results/2018-02-05_M0/Field_Pres--spp1.png
write_up/VAST_fit/results/2018-02-05_M0/Field_Pres--spp1_Legend.png
write_up/VAST_fit/results/2018-02-05_M0/Field_Pres--spp2.png
write_up/VAST_fit/results/2018-02-05_M0/Field_Pres--spp2_Legend.png
write_up/VAST_fit/results/2018-02-05_M0/Field_Pres--spp3.png
write_up/VAST_fit/results/2018-02-05_M0/Field_Pres--spp3_Legend.png
write_up/VAST_fit/results/2018-02-05_M0/Field_Pres--spp4.png
write_up/VAST_fit/results/2018-02-05_M0/Field_Pres--spp4_Legend.png
write_up/VAST_fit/results/2018-02-05_M0/Index.png
write_up/VAST_fit/results/2018-02-05_M0/Record.txt
write_up/VAST_fit/results/2018-02-05_M0/Spatio-temporal_covariances--Analytic.png
write_up/VAST_fit/results/2018-02-05_M0/Spatio-temporal_covariances--Sample.png
write_up/VAST_fit/results/2018-02-05_M0/Table_for_SS3.csv
write_up/VAST_fit/results/2018-02-05_M0/VAST_v4_0_0.cpp
write_up/VAST_fit/results/2018-02-05_M0/parameter_estimates.txt
write_up/comments/mixfishsim_ecolmod_JMG_JJP.pdf
write_up/mixfishsim_ecolmod.aux
write_up/mixfishsim_ecolmod.bbl
write_up/mixfishsim_ecolmod.blg
write_up/mixfishsim_ecolmod.fdb_latexmk
write_up/mixfishsim_ecolmod.fls
write_up/mixfishsim_ecolmod.log
write_up/mixfishsim_ecolmod.out
write_up/mixfishsim_ecolmod.pdf
write_up/mixfishsim_ecolmod.soc
write_up/mixfishsim_ecolmod.spl
write_up/mixfishsim_ecolmod.tex
write_up/mixfishsim_ecolmod.tex.backup
write_up/model2-names.bst
write_up/simulation_framework.bib
pdolder/MixFishSim documentation built on April 20, 2018, 7:01 a.m.