Files in NOAA-EDAB/ECSA
Ecosystem Context for Stock Advice
.Rbuildignore
.gitignore
DESCRIPTION
ECSA.Rproj
LICENSE.md
NAMESPACE
R/STARS_v18.R
R/create_buttons.R
R/create_template.R
R/crop_to_strata.R
R/fit_regime_and_trend.R
R/get_diet.R
R/get_strata.R
R/gls_summary.R
R/map_strata.R
R/merge_to_bookdown.R
R/plot_sae.R
R/render_ecsa.R
R/resample_strat.R
R/stars_to_series.R
R/stock_env.R
R/tab_plotly.R
README.Rmd
README.md
analysis/mk_evaluation.Rmd
analysis/mk_evaluation.pdf
analysis/template_instructions.R
data-raw/biomass_fall.rdata
data-raw/biomass_spring.rdata
data-raw/chlorophyll_conc_fall.rdata
data-raw/chlorophyll_conc_spring.rdata
data-raw/collapse_into_stack.R
data-raw/fall_acared_occ_prob.rdata
data-raw/fall_alewif_occ_prob.rdata
data-raw/fall_allfsh_occ_prob.rdata
data-raw/fall_amepla_occ_prob.rdata
data-raw/fall_amesha_occ_prob.rdata
data-raw/fall_amlobs_occ_prob.rdata
data-raw/fall_angshr_occ_prob.rdata
data-raw/fall_armsea_occ_prob.rdata
data-raw/fall_atlarg_occ_prob.rdata
data-raw/fall_atlcod_occ_prob.rdata
data-raw/fall_atlcro_occ_prob.rdata
data-raw/fall_atlhal_occ_prob.rdata
data-raw/fall_atlher_occ_prob.rdata
data-raw/fall_atlmac_occ_prob.rdata
data-raw/fall_atlmen_occ_prob.rdata
data-raw/fall_atlpou_occ_prob.rdata
data-raw/fall_atlwol_occ_prob.rdata
data-raw/fall_blabas_occ_prob.rdata
data-raw/fall_bluefi_occ_prob.rdata
data-raw/fall_butter_occ_prob.rdata
data-raw/fall_haddoc_occ_prob.rdata
data-raw/fall_lonsqd_occ_prob.rdata
data-raw/fall_monkfi_occ_prob.rdata
data-raw/fall_ocpout_occ_prob.rdata
data-raw/fall_offhak_occ_prob.rdata
data-raw/fall_redhak_occ_prob.rdata
data-raw/fall_sae_tb_sum.csv
data-raw/fall_scupzz_occ_prob.rdata
data-raw/fall_seasca_occ_prob.rdata
data-raw/fall_silhak_occ_prob.rdata
data-raw/fall_strbas_occ_prob.rdata
data-raw/fall_sumflo_occ_prob.rdata
data-raw/fall_window_occ_prob.rdata
data-raw/fall_winflo_occ_prob.rdata
data-raw/fall_yelflo_occ_prob.rdata
data-raw/menhaden_strata_raw.csv
data-raw/occurrence_prob_fall.rdata
data-raw/occurrence_prob_spring.rdata
data-raw/salinity_fall_bottom.rdata
data-raw/salinity_fall_surface.rdata
data-raw/salinity_spring_bottom.rdata
data-raw/salinity_spring_surface.rdata
data-raw/spri_acared_occ_prob.rdata
data-raw/spri_alewif_occ_prob.rdata
data-raw/spri_allfsh_occ_prob.rdata
data-raw/spri_amepla_occ_prob.rdata
data-raw/spri_amesha_occ_prob.rdata
data-raw/spri_amlobs_occ_prob.rdata
data-raw/spri_angshr_occ_prob.rdata
data-raw/spri_armsea_occ_prob.rdata
data-raw/spri_atlarg_occ_prob.rdata
data-raw/spri_atlcod_occ_prob.rdata
data-raw/spri_atlcro_occ_prob.rdata
data-raw/spri_atlhal_occ_prob.rdata
data-raw/spri_atlher_occ_prob.rdata
data-raw/spri_atlmac_occ_prob.rdata
data-raw/spri_atlmen_occ_prob.rdata
data-raw/spri_atlpou_occ_prob.rdata
data-raw/spri_atlwol_occ_prob.rdata
data-raw/spri_butter_occ_prob.rdata
data-raw/spri_haddoc_occ_prob.rdata
data-raw/spri_lonsqd_occ_prob.rdata
data-raw/spri_ocpout_occ_prob.rdata
data-raw/spri_offhak_occ_prob.rdata
data-raw/spri_redhak_occ_prob.rdata
data-raw/spri_seasca_occ_prob.rdata
data-raw/spri_silhak_occ_prob.rdata
data-raw/spri_strbas_occ_prob.rdata
data-raw/spri_sumflo_occ_prob.rdata
data-raw/spri_window_occ_prob.rdata
data-raw/spri_winflo_occ_prob.rdata
data-raw/spri_yelflo_occ_prob.rdata
data-raw/spring_atlher_occ_prob.rdata
data-raw/spring_atlmac_occ_prob.rdata
data-raw/spring_blabas_occ_prob.rdata
data-raw/spring_bluefi_occ_prob.rdata
data-raw/spring_butter_occ_prob.rdata
data-raw/spring_lonsqd_occ_prob.rdata
data-raw/spring_monkfi_occ_prob.rdata
data-raw/spring_sae_tb_sum.csv
data-raw/spring_scupzz_occ_prob.rdata
data-raw/spring_strbas_occ_prob.rdata
data-raw/stock_list.R
data-raw/stocks-strata_10042018.csv
data-raw/sum_ocl_byunit_sprfall.csv
data-raw/sum_ocl_spr and fall.csv
data-raw/temperature_fall_bottom.rdata
data-raw/temperature_fall_surface.rdata
data-raw/temperature_spring_bottom.rdata
data-raw/temperature_spring_surface.rdata
data-raw/treatment-selection.csv
data-raw/zoo_fall_rasters_1yr.rdata
data-raw/zoo_fall_rasters_5yr.rdata
data-raw/zoo_fall_rasters_5yr_clim.rdata
data-raw/zoo_spring_rasters_1yr.rdata
data-raw/zoo_spring_rasters_5yr.rdata
data-raw/zoo_spring_rasters_5yr_clim.rdata
data-raw/zooplankton_lookup.csv
data/Survdat.RData
data/all_strata.csv
data/allfhsg.RData
data/df_diet.RData
data/df_survdat.rda
data/gridded/centropages_fall_zoo_1977-2016.rdata
data/gridded/centropages_spring_zoo_1977-2016.rdata
data/gridded/chl_fall_1997-2018.rdata
data/gridded/chl_monthly_1997-2018.rdata
data/gridded/chl_spring_1997-2018.rdata
data/gridded/fall_sae_tb_sum.csv
data/gridded/menhaden_strata_raw.csv
data/gridded/pseudocalanus_fall_zoo_1977-2016.rdata
data/gridded/pseudocalanus_spring_zoo_1977-2016.rdata
data/gridded/sal_bottom_fall_spdf.rdata
data/gridded/sal_bottom_spring_spdf.rdata
data/gridded/sal_surface_fall_spdf.rdata
data/gridded/sal_surface_spring_spdf.rdata
data/gridded/spring_sae_tb_sum.csv
data/gridded/stock_list.R
data/gridded/stocks-strata_10042018.csv
data/gridded/sumflo_occupancy_PA_fall.rdata
data/gridded/sumflo_occupancy_PA_spring.rdata
data/gridded/temora_fall_zoo_1977-2016.rdata
data/gridded/temora_spring_zoo_1977-2016.rdata
data/gridded/temp_bottom_fall_spdf.rdata
data/gridded/temp_bottom_spring_spdf.rdata
data/gridded/temp_surface_fall_spdf.rdata
data/gridded/temp_surface_spring_spdf.rdata
data/gridded/zooplankton_lookup.csv
data/seasonal_stock_strata.csv
data/species_list.csv
data/stock_data/stock_list.csv
data/stock_list.csv
data/strata_shapefiles/BTS_Strata.dbf
data/strata_shapefiles/BTS_Strata.prj
data/strata_shapefiles/BTS_Strata.sbn
data/strata_shapefiles/BTS_Strata.sbx
data/strata_shapefiles/BTS_Strata.shp
data/strata_shapefiles/BTS_Strata.shp.xml
data/strata_shapefiles/BTS_Strata.shx
data/strata_shapefiles/shellfish_strata.cpg
data/strata_shapefiles/shellfish_strata.dbf
data/strata_shapefiles/shellfish_strata.prj
data/strata_shapefiles/shellfish_strata.sbn
data/strata_shapefiles/shellfish_strata.sbx
data/strata_shapefiles/shellfish_strata.shp
data/strata_shapefiles/shellfish_strata.shp.xml
data/strata_shapefiles/shellfish_strata.shx
data/sumflo_hab_area.csv
data/sumflodietraw.RData
docs/ECSA_bibliography.bib
docs/_output.yml
docs/acadian-redfish.html
docs/acadian-redfish.rmd
docs/acadian-redfish_files/fall_bottom_sal.csv
docs/acadian-redfish_files/fall_bottom_temp.csv
docs/acadian-redfish_files/fall_chl.csv
docs/acadian-redfish_files/fall_cope.csv
docs/acadian-redfish_files/fall_noncope.csv
docs/acadian-redfish_files/fall_occ_prob.csv
docs/acadian-redfish_files/fall_surface_temp.csv
docs/acadian-redfish_files/figure-html/strata-map-1.png
docs/acadian-redfish_files/spring_bottom_sal.csv
docs/acadian-redfish_files/spring_bottom_temp
docs/acadian-redfish_files/spring_bottom_temp.csv
docs/acadian-redfish_files/spring_chl.csv
docs/acadian-redfish_files/spring_cope.csv
docs/acadian-redfish_files/spring_noncope.csv
docs/acadian-redfish_files/spring_occ_prob.csv
docs/acadian-redfish_files/spring_surface_sal.csv
docs/acadian-redfish_files/spring_surface_temp.csv
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docs/american-lobster_gom-gb_files/fall_cope.csv
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docs/american-lobster_gom-gb_files/spring_occ_prob.csv
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docs/american-lobster_gom-gb_files/spring_surface_temp.csv
docs/american-lobster_sne.html
docs/american-lobster_sne.rmd
docs/american-lobster_sne_files/fall_bottom_sal.csv
docs/american-lobster_sne_files/fall_bottom_temp.csv
docs/american-lobster_sne_files/fall_chl.csv
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docs/american-lobster_sne_files/fall_occ_prob.csv
docs/american-lobster_sne_files/fall_surface_temp.csv
docs/american-lobster_sne_files/figure-html/strata-map-1.png
docs/american-lobster_sne_files/spring_bottom_sal.csv
docs/american-lobster_sne_files/spring_bottom_temp.csv
docs/american-lobster_sne_files/spring_chl.csv
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docs/american-lobster_sne_files/spring_noncope.csv
docs/american-lobster_sne_files/spring_occ_prob.csv
docs/american-lobster_sne_files/spring_surface_sal.csv
docs/american-lobster_sne_files/spring_surface_temp.csv
docs/atlantic-halibut.html
docs/atlantic-halibut.rmd
docs/atlantic-halibut_files/fall_bottom_sal.csv
docs/atlantic-halibut_files/fall_bottom_temp.csv
docs/atlantic-halibut_files/fall_chl.csv
docs/atlantic-halibut_files/fall_cope.csv
docs/atlantic-halibut_files/fall_noncope.csv
docs/atlantic-halibut_files/fall_occ_prob.csv
docs/atlantic-halibut_files/fall_surface_temp.csv
docs/atlantic-halibut_files/figure-html/strata-map-1.png
docs/atlantic-halibut_files/spring_bottom_sal.csv
docs/atlantic-halibut_files/spring_bottom_temp.csv
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docs/atlantic-halibut_files/spring_cope.csv
docs/atlantic-halibut_files/spring_noncope.csv
docs/atlantic-halibut_files/spring_occ_prob.csv
docs/atlantic-halibut_files/spring_surface_sal.csv
docs/atlantic-halibut_files/spring_surface_temp.csv
docs/atlantic-herring.html
docs/atlantic-herring_draft.html
docs/atlantic-herring_draft.rmd
docs/atlantic-herring_draft_files/figure-html/strata-map-1.png
docs/atlantic-herring_files/figure-html/doc-correction-1.png
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docs/atlantic-mackerel.html
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docs/atlantic-menhaden.html
docs/atlantic-menhaden.rmd
docs/atlantic-wolffish.html
docs/atlantic-wolffish.rmd
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docs/atlantic-wolffish_files/fall_bottom_temp.csv
docs/atlantic-wolffish_files/fall_chl.csv
docs/atlantic-wolffish_files/fall_cope.csv
docs/atlantic-wolffish_files/fall_noncope.csv
docs/atlantic-wolffish_files/fall_occ_prob.csv
docs/atlantic-wolffish_files/fall_surface_temp.csv
docs/atlantic-wolffish_files/figure-html/strata-map-1.png
docs/atlantic-wolffish_files/spring_bottom_sal.csv
docs/atlantic-wolffish_files/spring_bottom_temp.csv
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docs/black-sea-bass_north.html
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docs/black-sea-bass_south.html
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docs/bluefish.html
docs/bluefish.pdf
docs/bluefish.rmd
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