Files in hmorzaria/pssalmonsurvival
Sensitivity analysis of salmon survival in Puget Sound
.Rbuildignore
.gitattributes
.github/.gitignore
.github/workflows/pkgdown.yaml
.gitignore
DESCRIPTION
LICENSE.md
NAMESPACE
NEWS.md
R/data-dietcheck.R
R/data-dietcheckcum.R
R/data-ensemblebiomass.R
R/data-ensemblebiomasscum.R
R/data-ensemblenumbersage.R
R/data-ensemblenumbersagescenarios.R
R/data-ensemblenumberscum.R
R/data-ensemblewagecum.R
R/data-ensemblewageind.R
R/data-functionalgroups.R
R/data-groupguilds.R
R/data-indsalmoneffect.R
R/data-ppreymatrix.R
R/data-predgroups.R
R/data-salmonbybasin.R
R/data-salmoneffect.R
R/data-salmongroups.R
R/data-scenariocategories.R
R/extract_base_cum_survival.R
R/get_salmonpredators.R
R/get_shapefile.R
R/make_forcing.R
R/make_map.R
R/make_trajectories.R
R/plot_dietcheck.R
R/plot_dietcheckcum.R
R/plot_ensemble_cum_survival_scenarios.R
R/plot_ensemble_survival.R
R/plot_ensemble_survival_scenarios.R
R/plot_ensemble_survival_scenarios_timeseries.R
R/plot_ensemblebiomass.R
R/plot_foodweb.R
R/plot_interaction_effect.R
R/plot_predation.R
R/plot_predators.R
R/plot_predatorscum.R
R/plot_salmon_abundance.R
R/plot_watage.R
R/plot_watage_cum.R
R/round_num.R
R/salmon_colors.R
R/utils-pipe.R
README.md
_pkgdown.yml
data-raw/PugetSoundAtlantisFunctionalGroups.csv
data-raw/ensemble_biomass_survivalscenarios_cum.csv
data-raw/ensemble_biomass_survivalscenarios_ind.csv
data-raw/ensemble_dietcheck_survivalscenarios.csv
data-raw/ensemble_dietcheck_survivalscenarios_cum.csv
data-raw/ensemble_numbers_age.csv
data-raw/ensemble_numbers_survivalscenarios.csv
data-raw/ensemble_numbers_survivalscenarios_cum.csv
data-raw/ensemble_salmon_wage_scenarios_cum.csv
data-raw/ensemble_salmon_wage_scenarios_ind.csv
data-raw/group_guilds.csv
data-raw/indsalmon_effect.csv
data-raw/predator_groups.csv
data-raw/preprocess.R
data-raw/ps_prey_matrix_final.csv
data-raw/salmon_by_basin.csv
data-raw/salmon_effect.csv
data-raw/salmon_groups.csv
data-raw/scenario_categories.csv
data/dietcheck.rda
data/dietcheckcum.rda
data/ensemblebiomass.rda
data/ensemblebiomasscum.rda
data/ensemblenumbersage.rda
data/ensemblenumbersagescenarios.rda
data/ensemblenumberscum.rda
data/ensemblewagecum.rda
data/ensemblewageind.rda
data/functionalgroups.rda
data/groupguilds.rda
data/indsalmoneffect.rda
data/ppreymatrix.rda
data/predgroups.rda
data/salmonbybasin.rda
data/salmoneffect.rda
data/salmongroups.rda
data/scenariocategories.rda
docs/404.html
docs/LICENSE.html
docs/articles/amps_model_map.png
docs/articles/index.html
docs/articles/ps_foodweb.png
docs/articles/salmon_survival_files/figure-html/map model extent-1.png
docs/articles/salmon_survival_files/figure-html/plot biomass base runs-1.png
docs/articles/salmon_survival_files/figure-html/plot biomass base runs-2.png
docs/articles/salmon_survival_files/figure-html/plot biomass base runs-3.png
docs/articles/salmon_survival_files/figure-html/plot biomass base runs-4.png
docs/articles/salmon_survival_files/figure-html/plot biomass base runs-5.png
docs/articles/salmon_survival_files/figure-html/plot cumulative impacts-1.png
docs/articles/salmon_survival_files/figure-html/plot cumulative impacts-2.png
docs/articles/salmon_survival_files/figure-html/plot food web-1.png
docs/articles/salmon_survival_files/figure-html/plot salmon time series-1.png
docs/articles/salmon_survival_files/figure-html/plot survival base runs-1.png
docs/articles/salmon_survival_files/figure-html/plot survival base runs-2.png
docs/articles/salmon_survival_files/figure-html/plot survival base runs-3.png
docs/articles/salmon_survival_files/figure-html/plot survival base runs-4.png
docs/articles/salmon_survival_files/figure-html/plot survival base runs-5.png
docs/articles/salmon_survival_files/figure-html/plot survival base runs-6.png
docs/articles/salmon_survival_files/figure-html/plot survival scenarios-1.png
docs/articles/salmon_survival_files/figure-html/plot survival scenarios-2.png
docs/articles/salmon_survival_files/figure-html/plot survival timeseries scenarios-1.png
docs/articles/salmon_survival_files/figure-html/plot survival timeseries scenarios-2.png
docs/articles/salmon_survival_files/figure-html/plot survival timeseries scenarios-3.png
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man/dietcheck.Rd
man/dietcheckcum.Rd
man/ensemblebiomass.Rd
man/ensemblebiomasscum.Rd
man/ensemblenumbersage.Rd
man/ensemblenumbersagescenarios.Rd
man/ensemblenumberscum.Rd
man/ensemblewagecum.Rd
man/ensemblewageind.Rd
man/extract_base_cum_survival.Rd
man/functionalgroups.Rd
man/get_salmonpredators.Rd
man/get_shapefile.Rd
man/groupguilds.Rd
man/indsalmoneffect.Rd
man/make_forcing.Rd
man/make_map.Rd
man/make_trajectories.Rd
man/pipe.Rd
man/plot_dietcheck.Rd
man/plot_dietcheckcum.Rd
man/plot_ensemble_cum_survival_scenarios.Rd
man/plot_ensemble_survival.Rd
man/plot_ensemble_survival_scenarios.Rd
man/plot_ensemble_survival_scenarios_timeseries.Rd
man/plot_ensemblebiomass.Rd
man/plot_foodweb.Rd
man/plot_interaction_effect.Rd
man/plot_predation.Rd
man/plot_predators.Rd
man/plot_predatorscum.Rd
man/plot_salmon_abundance.Rd
man/plot_watage.Rd
man/plot_watage_cum.Rd
man/ppreymatrix.Rd
man/predgroups.Rd
man/round_num.Rd
man/salmon_colors.Rd
man/salmonbybasin.Rd
man/salmoneffect.Rd
man/scenariocategories.Rd
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modelfiles/PugetSound_force_Porpoise_1/PugetSound_force_Porpoise_1.prm
modelfiles/PugetSound_force_Porpoise_1/amps_cal.sh
modelfiles/PugetSound_force_Porpoise_1_2/Porpoise10_Nums_ncforcing_1_2.cdf
modelfiles/PugetSound_force_Porpoise_1_2/Porpoise10_Nums_ncforcing_1_2.nc
modelfiles/PugetSound_force_Porpoise_1_2/Porpoise1_Nums_ncforcing_1_2.cdf
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modelfiles/PugetSound_force_Porpoise_1_2/Porpoise2_Nums_ncforcing_1_2.cdf
modelfiles/PugetSound_force_Porpoise_1_2/Porpoise2_Nums_ncforcing_1_2.nc
modelfiles/PugetSound_force_Porpoise_1_2/Porpoise3_Nums_ncforcing_1_2.cdf
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modelfiles/PugetSound_force_Porpoise_1_2/Porpoise4_Nums_ncforcing_1_2.cdf
modelfiles/PugetSound_force_Porpoise_1_2/Porpoise4_Nums_ncforcing_1_2.nc
modelfiles/PugetSound_force_Porpoise_1_2/Porpoise5_Nums_ncforcing_1_2.cdf
modelfiles/PugetSound_force_Porpoise_1_2/Porpoise5_Nums_ncforcing_1_2.nc
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modelfiles/PugetSound_force_hatchery_competition_1/CohoHY_Fish3_Nums_ncforcing_1.cdf
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modelfiles/PugetSound_force_hatchery_competition_1/amps_cal.sh
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modelfiles/PugetSound_force_hatchery_competition_1_2/CohoHY_Fish2_Nums_ncforcing_1_2.nc
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modelfiles/PugetSound_force_herring_trend_1_2/Herring_PS3_Nums_ncforcing_1_2.cdf
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modelfiles/PugetSound_force_herring_trend_1_2/Herring_PS5_Nums_ncforcing_1_2.cdf
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modelfiles/PugetSound_force_herring_trend_1_2/Herring_PS6_Nums_ncforcing_1_2.cdf
modelfiles/PugetSound_force_herring_trend_1_2/Herring_PS6_Nums_ncforcing_1_2.nc
modelfiles/PugetSound_force_herring_trend_1_2/Herring_PS7_Nums_ncforcing_1_2.cdf
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modelfiles/PugetSound_force_herring_trend_1_2/PugetSound_force_herring_trend_1_2.prm
modelfiles/PugetSound_force_herring_trend_1_2/amps_cal.sh
modelfiles/PugetSound_force_mammal_predation_0_8/California_sea_lion10_Nums_ncforcing_0_8.cdf
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modelfiles/PugetSound_force_mammal_predation_0_8/California_sea_lion1_Nums_ncforcing_0_8.cdf
modelfiles/PugetSound_force_mammal_predation_0_8/California_sea_lion1_Nums_ncforcing_0_8.nc
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modelfiles/PugetSound_force_mammal_predation_0_8/California_sea_lion2_Nums_ncforcing_0_8.nc
modelfiles/PugetSound_force_mammal_predation_0_8/California_sea_lion3_Nums_ncforcing_0_8.cdf
modelfiles/PugetSound_force_mammal_predation_0_8/California_sea_lion3_Nums_ncforcing_0_8.nc
modelfiles/PugetSound_force_mammal_predation_0_8/California_sea_lion4_Nums_ncforcing_0_8.cdf
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modelfiles/PugetSound_force_mammal_predation_0_8/California_sea_lion7_Nums_ncforcing_0_8.cdf
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modelfiles/PugetSound_force_mammal_predation_0_8/California_sea_lion9_Nums_ncforcing_0_8.cdf
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modelfiles/PugetSound_force_mammal_predation_0_8/Harbor_seal3_Nums_ncforcing_0_8.cdf
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modelfiles/PugetSound_force_mammal_predation_0_8/Harbor_seal9_Nums_ncforcing_0_8.cdf
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modelfiles/PugetSound_force_mammal_predation_0_8/Pinniped10_Nums_ncforcing_0_8.cdf
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modelfiles/PugetSound_force_mammal_predation_0_8/Pinniped2_Nums_ncforcing_0_8.cdf
modelfiles/PugetSound_force_mammal_predation_0_8/Pinniped2_Nums_ncforcing_0_8.nc
modelfiles/PugetSound_force_mammal_predation_0_8/Pinniped3_Nums_ncforcing_0_8.cdf
modelfiles/PugetSound_force_mammal_predation_0_8/Pinniped3_Nums_ncforcing_0_8.nc
modelfiles/PugetSound_force_mammal_predation_0_8/Pinniped4_Nums_ncforcing_0_8.cdf
modelfiles/PugetSound_force_mammal_predation_0_8/Pinniped4_Nums_ncforcing_0_8.nc
modelfiles/PugetSound_force_mammal_predation_0_8/Pinniped5_Nums_ncforcing_0_8.cdf
modelfiles/PugetSound_force_mammal_predation_0_8/Pinniped5_Nums_ncforcing_0_8.nc
modelfiles/PugetSound_force_mammal_predation_0_8/Pinniped6_Nums_ncforcing_0_8.cdf
modelfiles/PugetSound_force_mammal_predation_0_8/Pinniped6_Nums_ncforcing_0_8.nc
modelfiles/PugetSound_force_mammal_predation_0_8/Pinniped7_Nums_ncforcing_0_8.cdf
modelfiles/PugetSound_force_mammal_predation_0_8/Pinniped7_Nums_ncforcing_0_8.nc
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modelfiles/PugetSound_force_mammal_predation_0_8/Pinniped8_Nums_ncforcing_0_8.nc
modelfiles/PugetSound_force_mammal_predation_0_8/Pinniped9_Nums_ncforcing_0_8.cdf
modelfiles/PugetSound_force_mammal_predation_0_8/Pinniped9_Nums_ncforcing_0_8.nc
modelfiles/PugetSound_force_mammal_predation_0_8/PugetSound_force_mammal_predation_0_8.prm
modelfiles/PugetSound_force_mammal_predation_0_8/amps_cal.sh
modelfiles/PugetSound_force_mammal_predation_1/California_sea_lion10_Nums_ncforcing_1.cdf
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modelfiles/PugetSound_force_mammal_predation_1/California_sea_lion2_Nums_ncforcing_1.nc
modelfiles/PugetSound_force_mammal_predation_1/California_sea_lion3_Nums_ncforcing_1.cdf
modelfiles/PugetSound_force_mammal_predation_1/California_sea_lion3_Nums_ncforcing_1.nc
modelfiles/PugetSound_force_mammal_predation_1/California_sea_lion4_Nums_ncforcing_1.cdf
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modelfiles/PugetSound_force_mammal_predation_1/California_sea_lion5_Nums_ncforcing_1.cdf
modelfiles/PugetSound_force_mammal_predation_1/California_sea_lion5_Nums_ncforcing_1.nc
modelfiles/PugetSound_force_mammal_predation_1/California_sea_lion6_Nums_ncforcing_1.cdf
modelfiles/PugetSound_force_mammal_predation_1/California_sea_lion6_Nums_ncforcing_1.nc
modelfiles/PugetSound_force_mammal_predation_1/California_sea_lion7_Nums_ncforcing_1.cdf
modelfiles/PugetSound_force_mammal_predation_1/California_sea_lion7_Nums_ncforcing_1.nc
modelfiles/PugetSound_force_mammal_predation_1/California_sea_lion8_Nums_ncforcing_1.cdf
modelfiles/PugetSound_force_mammal_predation_1/California_sea_lion8_Nums_ncforcing_1.nc
modelfiles/PugetSound_force_mammal_predation_1/California_sea_lion9_Nums_ncforcing_1.cdf
modelfiles/PugetSound_force_mammal_predation_1/California_sea_lion9_Nums_ncforcing_1.nc
modelfiles/PugetSound_force_mammal_predation_1/Harbor_seal10_Nums_ncforcing_1.cdf
modelfiles/PugetSound_force_mammal_predation_1/Harbor_seal10_Nums_ncforcing_1.nc
modelfiles/PugetSound_force_mammal_predation_1/Harbor_seal1_Nums_ncforcing_1.cdf
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