Files in afsc-gap-products/akfishcondition
Groundfish morphometric condition indicator
.Rbuildignore
.gitattributes
.github/workflows/secretScan.yml
.gitignore
0_update_condition_data.Rmd
0_update_indicator.R
1_make_species_by_stratum_plots.R
AI_GroundfishCondition_2024.Rmd
AI_GroundfishCondition_2024.docx
CopyOfEBS_references.bib
DESCRIPTION
EBS_GroundfishCondition_2024.Rmd
EBS_GroundfishCondition_2024.docx
EBS_references.bib
ESP_Pacific_cod.Rmd
ESP_Pacific_cod_EBS.Rmd
ESP_Pacific_cod_GOA.Rmd
LICENSE.md
NAMESPACE
NEWS
R/calc_lw_residuals.R
R/calc_lw_residuals_multimodel.R
R/data.R
R/get_condition_data.R
R/make_vast_table.R
R/plot_anomaly_timeseries.R
R/plot_species_bar.R
R/plot_stratum_species_bar.R
R/plot_stratum_stacked_bar.R
R/plot_two_timeseries.R
R/plot_xy_corr.R
R/poststratify_goa_hauls.R
R/run_condition_doy.R
R/run_sbw_condition.R
R/run_sbw_condition_multimodel.R
R/sysdata.rda
R/themes.R
R/utils.R
R/vast_functions.R
R/weight_lw_residuals.R
README.md
analysis/AI_age_length_Pacific cod.png
analysis/AI_age_length_Pacific ocean perch.png
analysis/AI_age_length_northern rockfish.png
analysis/AI_age_weight_Pacific ocean perch.png
analysis/ai_hauls_with_catch_and_length.png
analysis/ai_pcod_condition_wide.R
analysis/bt_vs_vast_condition.R
analysis/ebs_hauls_with_catch_and_length.png
analysis/ex_run_vast_with_akfishcondition.R
analysis/gamm_weight_at_age.R
analysis/goa_hauls_with_catch_and_length.png
analysis/run_vast.r
analysis/species_correlation_among_regions.R
analysis/stratum_vs_vast.R
analysis/vast_vs_old.r
analysis/weight_at_age.R
archive/2018_EBS_GroundfishCondition.Rmd
archive/2019_EBS_GroundfishCondition.Rmd
archive/AI_GroundfishCondition_2020.Rmd
archive/AI_GroundfishCondition_2020.docx
archive/AI_GroundfishCondition_SR.Rmd
archive/AI_GroundfishCondition_SR.docx
archive/EBS_GroundfishCondition_2020.Rmd
archive/EBS_GroundfishCondition_2020.docx
archive/EBS_GroundfishCondition_2021.Rmd
archive/EBS_GroundfishCondition_2021.docx
archive/ESP_Pacific cod_2020.Rmd
archive/ESP_Pacific-cod_2020.docx
archive/ESP_Pacific_cod.Rmd
archive/ESP_Pacific_cod.docx
archive/GOA_GroundfishCondition_2020.Rmd
archive/GOA_GroundfishCondition_2020.docx
archive/GOA_GroundfishCondition_2021.Rmd
archive/GOA_GroundfishCondition_2021.docx
data/AI_INDICATOR.rda
data/EBS_INDICATOR.rda
data/ESR_SETTINGS.rda
data/GOA_INDICATOR.rda
data/NBS_INDICATOR.rda
data/PCOD_ESP.rda
doc/ex_vast.R
fish-and-fisheries.csl
inst/extdata/2022_ESR.zip
inst/extdata/raw_lw_bio.rda
inst/scripts/make_ebsshelf_cpue.sql
inst/scripts/make_nbs_cpue.sql
inst/scripts/test_akfishcondition_queries.R
inst/sql/VAST_ai_cpue.sql
inst/sql/VAST_ebs_cpue.sql
inst/sql/VAST_ebs_length_weight.sql
inst/sql/VAST_goa_cpue.sql
inst/sql/VAST_nbs_cpue.sql
inst/sql/VAST_nbs_length_weight.sql
inst/sql/ai_biomass.sql
inst/sql/ai_length_weight.sql
inst/sql/ebs_biomass.sql
inst/sql/ebs_length_weight.sql
inst/sql/goa_biomass.sql
inst/sql/goa_length_weight.sql
inst/sql/nbs_biomass.sql
inst/sql/nbs_length_weight.sql
man/AI_INDICATOR.Rd
man/EBS_INDICATOR.Rd
man/ESR_SETTINGS.Rd
man/GOA_INDICATOR.Rd
man/NBS_INDICATOR.Rd
man/PCOD_ESP.Rd
man/bundle_vast_condition.Rd
man/calc_lw_residuals.Rd
man/calc_lw_residuals_multimodel.Rd
man/get_condition_data.Rd
man/make_vast_table.Rd
man/plot_anomaly_timeseries.Rd
man/plot_species_bar.Rd
man/plot_species_stratum_bar.Rd
man/plot_stratum_stacked_bar.Rd
man/plot_two_timeseries.Rd
man/plot_xy_corr.Rd
man/poststratify_goa_hauls.Rd
man/run_condition_doy.Rd
man/run_vast_condition.Rd
man/set_plot_order.Rd
man/set_stratum_order.Rd
man/st_line_midpoints.Rd
man/theme_blue_strip.Rd
man/theme_condition_index.Rd
man/theme_pngs.Rd
man/weight_lw_residuals.Rd
past_years/2019/2019_EBS_GroundfishCondition.Rmd
past_years/2020/2020_ESR.zip
past_years/2020/AI_GroundfishCondition_2020.Rmd
past_years/2020/EBS_GroundfishCondition_2020.Rmd
past_years/2020/EBS_GroundfishCondition_2020.docx
past_years/2020/ESP_Pacific cod_2020.Rmd
past_years/2020/ESP_Pacific-cod_2020.docx
past_years/2020/GOA_GroundfishCondition_2020.Rmd
past_years/2020/GOA_GroundfishCondition_2020.docx
past_years/2021/2021_ESR.zip
past_years/2021/EBS_GroundfishCondition_2021.Rmd
past_years/2021/EBS_GroundfishCondition_2021.docx
past_years/2021/ESP_Pacific_cod.Rmd
past_years/2021/ESP_Pacific_cod.docx
past_years/2021/GOA_GroundfishCondition_2021.Rmd
past_years/2021/GOA_GroundfishCondition_2021.docx
past_years/2022/AI_GroundfishCondition_2022.Rmd
past_years/2022/AI_GroundfishCondition_2022.docx
past_years/2022/EBS_GroundfishCondition_2022.Rmd
past_years/2022/EBS_GroundfishCondition_2022.docx
past_years/2022/plots.7z
past_years/2023/EBS_GroundfishCondition_2023.Rmd
past_years/2023/EBS_GroundfishCondition_2023.docx
past_years/2023/EBS_references.bib
past_years/2023/ESP_Pacific_cod.Rmd
past_years/2023/ESP_Pacific_cod.docx
past_years/2023/ESP_Pacific_cod_EBS.Rmd
past_years/2023/ESP_Pacific_cod_GOA.Rmd
past_years/2023/ESP_Pacific_cod_GOA.docx
past_years/2023/GOA_GroundfishCondition_2023.Rmd
past_years/2023/GOA_GroundfishCondition_2023.docx
past_years/2023/MapAI.png
past_years/2023/MapGOA.png
past_years/2023/ebs_nbs_survey_area.png
past_years/2023/fish-and-fisheries.csl
plots/AI/AI_condition.png
plots/AI/AI_condition_by_stratum.png
plots/AI/Atka mackerel/AI_CONDITION_Atka mackerel.png
plots/AI/Atka mackerel/AI_STRATUM_CONDITION_Atka mackerel.png
plots/AI/Pacific cod/AI_CONDITION_Pacific cod.png
plots/AI/Pacific cod/AI_STRATUM_CONDITION_Pacific cod.png
plots/AI/Pacific ocean perch/AI_CONDITION_Pacific ocean perch.png
plots/AI/Pacific ocean perch/AI_STRATUM_CONDITION_Pacific ocean perch.png
plots/AI/arrowtooth flounder/AI_CONDITION_arrowtooth flounder.png
plots/AI/arrowtooth flounder/AI_STRATUM_CONDITION_arrowtooth flounder.png
plots/AI/northern rockfish/AI_CONDITION_northern rockfish.png
plots/AI/northern rockfish/AI_STRATUM_CONDITION_northern rockfish.png
plots/AI/southern rock sole/AI_CONDITION_southern rock sole.png
plots/AI/southern rock sole/AI_STRATUM_CONDITION_southern rock sole.png
plots/AI/walleye pollock (100-250 mm)/AI_STRATUM_CONDITION_walleye pollock (100-250 mm).png
plots/AI/walleye pollock (gt250 mm)/AI_CONDITION_walleye pollock (gt250 mm).png
plots/AI/walleye pollock (gt250 mm)/AI_STRATUM_CONDITION_walleye pollock (gt250 mm).png
plots/AI/walleye pollock/AI_CONDITION_walleye pollock.png
plots/AI/walleye pollock/AI_STRATUM_CONDITION_walleye pollock.png
plots/BS/Alaska plaice/EBS_STRATUM_CONDITION_Alaska plaice.png
plots/BS/Alaska plaice/NBS_STRATUM_CONDITION_Alaska plaice.png
plots/BS/EBS_NBS_survey_area.png
plots/BS/EBS_SBW_stratum_stacked_bar.png
plots/BS/EBS_SBW_timeseries.png
plots/BS/EBS_condition.png
plots/BS/ESP_EBS_PCOD_condition.png
plots/BS/NBS_SBW_stratum_stacked_bar.png
plots/BS/NBS_SBW_timeseries.png
plots/BS/NBS_condition.png
plots/BS/Pacific cod/EBS_STRATUM_CONDITION_Pacific cod.png
plots/BS/Pacific cod/NBS_STRATUM_CONDITION_Pacific cod.png
plots/BS/arrowtooth flounder/EBS_STRATUM_CONDITION_arrowtooth flounder.png
plots/BS/flathead sole/EBS_STRATUM_CONDITION_flathead sole.png
plots/BS/northern rock sole/EBS_STRATUM_CONDITION_northern rock sole.png
plots/BS/walleye pollock (100-250 mm)/EBS_STRATUM_CONDITION_walleye pollock (100-250 mm).png
plots/BS/walleye pollock (100-250 mm)/NBS_STRATUM_CONDITION_walleye pollock (100-250 mm).png
plots/BS/walleye pollock (gt250 mm)/EBS_STRATUM_CONDITION_walleye pollock (gt250 mm).png
plots/BS/walleye pollock (gt250 mm)/NBS_STRATUM_CONDITION_walleye pollock (gt250 mm).png
plots/BS/yellowfin sole/EBS_STRATUM_CONDITION_yellowfin sole.png
plots/BS/yellowfin sole/NBS_STRATUM_CONDITION_yellowfin sole.png
plots/GOA/Dover sole/GOA_STRATUM_CONDITION_Dover sole.png
plots/GOA/ESP_GOA_PCOD_condition.png
plots/GOA/GOA_condition_by_stratum_1.png
plots/GOA/GOA_condition_by_stratum_2.png
plots/GOA/GOAbyyear_1.png
plots/GOA/GOAbyyear_2.png
plots/GOA/Pacific cod/GOA_STRATUM_CONDITION_Pacific cod.png
plots/GOA/Pacific ocean perch/GOA_STRATUM_CONDITION_Pacific ocean perch.png
plots/GOA/arrowtooth flounder/GOA_STRATUM_CONDITION_arrowtooth flounder.png
plots/GOA/blackspotted rockfish/GOA_STRATUM_CONDITION_blackspotted rockfish.png
plots/GOA/dusky rockfish/GOA_STRATUM_CONDITION_dusky rockfish.png
plots/GOA/flathead sole/GOA_STRATUM_CONDITION_flathead sole.png
plots/GOA/northern rock sole/GOA_STRATUM_CONDITION_northern rock sole.png
plots/GOA/northern rockfish/GOA_STRATUM_CONDITION_northern rockfish.png
plots/GOA/rex sole/GOA_STRATUM_CONDITION_rex sole.png
plots/GOA/rougheye rockfish/GOA_STRATUM_CONDITION_rougheye rockfish.png
plots/GOA/sharpchin rockfish/GOA_STRATUM_CONDITION_sharpchin rockfish.png
plots/GOA/shortraker rockfish/GOA_STRATUM_CONDITION_shortraker rockfish.png
plots/GOA/southern rock sole/GOA_STRATUM_CONDITION_southern rock sole.png
plots/GOA/walleye pollock (100-250 mm)/GOA_STRATUM_CONDITION_walleye pollock (100-250 mm).png
plots/GOA/walleye pollock (gt250 mm)/GOA_STRATUM_CONDITION_walleye pollock (gt250 mm).png
