NOAA-EDAB/ms-keyrun
All information for keyrun review

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All information for keyrun review

.Rbuildignore
.gitattributes
.github/workflows/pkgdown.yml
.github/workflows/secretScan.yml
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/.DS_Store
R/AllSpeciesProportions.r R/SurveyIndexA4.r R/catchAtLengthProportions.r R/catchIndex.r R/fisheryLenSampN.r R/fleets.r R/focalSpecies.r R/mskeyrun.r R/realBiolPar.R R/realFisheryAgecomp.r R/realFisheryLencomp.r R/realSurveyLennumcomp.r R/simBiolPar.R R/simCatchIndex.r R/simCatchIndexFW.r R/simCatchIndexSubannual.r R/simCatchIndexSubannualFW.r R/simFisheryAgeLencomp.r R/simFisheryAgecomp.R R/simFisheryAgecompSubannual.R R/simFisheryLencomp.r R/simFisheryLencompSubannual.r R/simFisheryWtatAge.R R/simFisheryWtatAgeSubannual.R R/simFocalSpecies.R R/simPerCapCons.R R/simStartPars.R R/simSurveyAgeLencomp.R R/simSurveyAgecomp.r R/simSurveyBottemp.R R/simSurveyDietcomp.r R/simSurveyDietcompFW.r R/simSurveyIndex.r R/simSurveyIndexFW.r R/simSurveyInfo.r R/simSurveyLenDietcomp.r R/simSurveyLencomp.r R/simSurveyWtatAge.R R/surveyDietcomp.R R/surveyIndex.r R/surveyIndexA4All.r R/surveyIndexAll.r R/surveyIndexHB.r R/surveyIndexHBAll.r R/surveyLenDietcomp.R R/surveyLenSampN.R README.md data-raw/GB_SOE_strata_set.R data-raw/R/All_Species_Landings_Proportions.R data-raw/R/calc_all_species_proportions.R data-raw/R/capitalize_first_letter.R data-raw/R/clean_lw_data.R data-raw/R/cluster_analysis_all_gears.R data-raw/R/cluster_analysis_filter_gears.R data-raw/R/cluster_by_focal_species.R data-raw/R/cluster_gears.R data-raw/R/create_GB_fleets.R data-raw/R/create_fishery_index.R data-raw/R/create_focal_species.R data-raw/R/create_hydra_main.R data-raw/R/create_lw_table.R data-raw/R/create_real_dietcomp.R data-raw/R/create_real_fishery_agecomp.R data-raw/R/create_real_fishery_lencomp.R data-raw/R/create_real_fishery_lencomp_raw.R data-raw/R/create_real_lendietcomp.R data-raw/R/create_real_survey_lennumcomp.R data-raw/R/create_sim_biolpar.R data-raw/R/create_sim_fishery_agecomp.R data-raw/R/create_sim_fishery_agecomp_subannual.R data-raw/R/create_sim_fishery_agelen.R data-raw/R/create_sim_fishery_index.R data-raw/R/create_sim_fishery_index_fw.R data-raw/R/create_sim_fishery_lencomp.R data-raw/R/create_sim_fishery_lencomp_subannual.R data-raw/R/create_sim_fishery_wtage.R data-raw/R/create_sim_fishery_wtage_subannual.R data-raw/R/create_sim_focal_species.R data-raw/R/create_sim_percapconsumption.R data-raw/R/create_sim_startpars.R data-raw/R/create_sim_survey_agecomp.R data-raw/R/create_sim_survey_agelen.R data-raw/R/create_sim_survey_bottemp.R data-raw/R/create_sim_survey_dietcomp.R data-raw/R/create_sim_survey_dietcomp_fw.R data-raw/R/create_sim_survey_index.R data-raw/R/create_sim_survey_index_fw.R data-raw/R/create_sim_survey_info.R data-raw/R/create_sim_survey_lencomp.R data-raw/R/create_sim_survey_lendietcomp.R data-raw/R/create_sim_survey_wtage.R data-raw/R/create_species_rules_table.R data-raw/R/create_survey_index.R data-raw/R/explore_landings_by_gear.R data-raw/R/format_herring_data.R data-raw/R/format_skate_data.R data-raw/R/get_fishery_length_sample_n.r data-raw/R/get_herring_data.R data-raw/R/get_landings_by_gear.R data-raw/R/get_length_sample_n.R data-raw/R/get_winterskate_data.R data-raw/R/hydra_format.R data-raw/R/hydra_process_GB_comland.R data-raw/R/hydra_pull_GB_lengths.R data-raw/R/make_species_datasets_for_mskeyrun.R data-raw/R/plot_landings.R data-raw/R/plot_landings_proportions.R data-raw/R/plot_stock_areas.R data-raw/R/pull_comland.R data-raw/R/pull_survdat.R data-raw/R/run_cluster.R data-raw/R/test_mscatch_data_pull.R data-raw/R/test_mscatch_data_pull_hydra_GB.R data-raw/build_dietdata.R data-raw/build_simdata.R data-raw/calc_protected_data.R data-raw/code/Query.Comm.Landings.Data.EDAB.R data-raw/code/RerunAtlantisomSnippets.R data-raw/code/SimPlotFunctions.R data-raw/code/TestSimCatch.R data-raw/create_shapefile_mskeyrun.R
data-raw/data/Landings_VTR_Geret_Data_summarized.rds
data-raw/data/Landings_VTR_proportions_all_species.rds
data-raw/data/focalSpecies.rds
data-raw/data/gearCodeTable.rds
data-raw/data/lengthWeigthAge.rds
data-raw/data/nordic_groups_v04.csv
data-raw/data/survdat.RData
data-raw/data/survdatLW.rds
data-raw/data/survdat_Albatross.RData
data-raw/data/survdat_Bigelow.RData
data-raw/data/survdat_bio.RData
data-raw/diagnostics/DiagnosticPlotExamples.Rmd data-raw/diagnostics/SimPlots.R data-raw/diagnostics/VisDietComps.R data-raw/diet_data_pull.R data-raw/get_landings_vtr_geret.r
data-raw/gis/EPU_extended.cpg
data-raw/gis/EPU_extended.dbf
data-raw/gis/EPU_extended.prj
data-raw/gis/EPU_extended.sbn
data-raw/gis/EPU_extended.sbx
data-raw/gis/EPU_extended.shp
data-raw/gis/EPU_extended.shp.xml
data-raw/gis/EPU_extended.shx
data-raw/gis/EPU_strata.dbf
data-raw/gis/EPU_strata.prj
data-raw/gis/EPU_strata.sbn
data-raw/gis/EPU_strata.sbx
data-raw/gis/EPU_strata.shp
data-raw/gis/EPU_strata.shp.xml
data-raw/gis/EPU_strata.shx
data-raw/gis/GB_SOE_strata.dbf
data-raw/gis/GB_SOE_strata.prj
data-raw/gis/GB_SOE_strata.shp
data-raw/gis/GB_SOE_strata.shx
data-raw/gis/GB_SOE_strata_stat.dbf
data-raw/gis/GB_SOE_strata_stat.prj
data-raw/gis/GB_SOE_strata_stat.shp
data-raw/gis/GB_SOE_strata_stat.shx
data-raw/gis/GB_stat_EPU.dbf
data-raw/gis/GB_stat_EPU.prj
data-raw/gis/GB_stat_EPU.shp
data-raw/gis/GB_stat_EPU.shx
data-raw/gis/NES_LME_coast.dbf
data-raw/gis/NES_LME_coast.prj
data-raw/gis/NES_LME_coast.sbn
data-raw/gis/NES_LME_coast.sbx
data-raw/gis/NES_LME_coast.shp
data-raw/gis/NES_LME_coast.shp.xml
data-raw/gis/NES_LME_coast.shx
data-raw/gis/Statistical_Areas_2010.dbf
data-raw/gis/Statistical_Areas_2010.prj
data-raw/gis/Statistical_Areas_2010.sbn
data-raw/gis/Statistical_Areas_2010.sbx
data-raw/gis/Statistical_Areas_2010.shp
data-raw/gis/Statistical_Areas_2010.shp.xml
data-raw/gis/Statistical_Areas_2010.shx
data-raw/gis/strata.dbf
data-raw/gis/strata.prj
data-raw/gis/strata.sbn
data-raw/gis/strata.sbx
data-raw/gis/strata.shp
data-raw/gis/strata.shp.xml
data-raw/gis/strata.shx
data-raw/model-input-files/.gitignore
data-raw/model-input-files/MSCAA/9Species.dat
data-raw/model-input-files/MSCAA/9Species.pin
data-raw/model-input-files/MSCAA/9Species.tpl
data-raw/model-input-files/MSCAA/AllTogether.dat
data-raw/model-input-files/MSCAA/AllTogether.pin
data-raw/model-input-files/MSCAA/AllTogether.tpl
data-raw/model-input-files/MSCAA/klclib.cxx
data-raw/model-input-files/MSCAA/stats.cxx
data-raw/model-input-files/MSSPM/Biomass.csv
data-raw/model-input-files/MSSPM/Catch.csv
data-raw/model-input-files/Rpath/REco_params.RData
data-raw/model-input-files/hydra-est/Observed_data_new.dat
data-raw/model-input-files/hydra-est/create_DataFile.R
data-raw/model-input-files/hydra-est/hydra_est_3_4_10species.dat
data-raw/model-input-files/hydra-est/hydra_est_3_4_10species.pin
data-raw/model-input-files/hydra-est/hydra_est_3_5.dat
data-raw/model-input-files/hydra-est/hydra_est_3_5.pin
data-raw/model-input-files/hydra-est/ofv_weights.dat
data-raw/model-input-files/hydra-est/ofv_weights_10species.dat
data-raw/plot_shapefiles.R data-raw/simulated-data/config/NOBA2Config.R data-raw/simulated-data/config/NOBA_sacc38Config.R data-raw/simulated-data/config/msfishery.R data-raw/simulated-data/config/msfishery_01.R data-raw/simulated-data/config/msfishery_fw.R data-raw/simulated-data/config/mssurvey_fall.R data-raw/simulated-data/config/mssurvey_fall_01.R data-raw/simulated-data/config/mssurvey_fall_fw.R data-raw/simulated-data/config/mssurvey_spring.R data-raw/simulated-data/config/mssurvey_spring_01.R data-raw/simulated-data/config/mssurvey_spring_fw.R data-raw/simulated-data/config/omdimensions.R
data-raw/simulated-data/msinput/hydra/README.txt
data-raw/simulated-data/msinput/hydra/foodweb_NOBA.csv
data-raw/simulated-data/msinput/hydra/growth_covariates_NOBA.csv
data-raw/simulated-data/msinput/hydra/growth_species_NOBA_era1_BTS_fall_allbox_effic1.csv
data-raw/simulated-data/msinput/hydra/growth_species_NOBA_era1_BTS_fall_nearbox_qmix_selmix.csv
data-raw/simulated-data/msinput/hydra/growth_species_NOBA_era1_BTS_spring_allbox_effic1.csv
data-raw/simulated-data/msinput/hydra/growth_species_NOBA_era1_BTS_spring_nearbox_qmix_selmix.csv
data-raw/simulated-data/msinput/hydra/growth_species_NOBA_era2_BTS_fall_allbox_effic1.csv
data-raw/simulated-data/msinput/hydra/growth_species_NOBA_era2_BTS_fall_nearbox_qmix_selmix.csv
data-raw/simulated-data/msinput/hydra/growth_species_NOBA_era2_BTS_spring_allbox_effic1.csv
data-raw/simulated-data/msinput/hydra/growth_species_NOBA_era2_BTS_spring_nearbox_qmix_selmix.csv
data-raw/simulated-data/msinput/hydra/growth_species_NOBA_era3_BTS_fall_allbox_effic1.csv
data-raw/simulated-data/msinput/hydra/growth_species_NOBA_era3_BTS_fall_nearbox_qmix_selmix.csv
data-raw/simulated-data/msinput/hydra/growth_species_NOBA_era3_BTS_spring_allbox_effic1.csv
data-raw/simulated-data/msinput/hydra/growth_species_NOBA_era3_BTS_spring_nearbox_qmix_selmix.csv
data-raw/simulated-data/msinput/hydra/growth_species_NOBA_test_era1_BTS_fall_allbox_effic1.csv
data-raw/simulated-data/msinput/hydra/intake_species_NOBA.csv
data-raw/simulated-data/msinput/hydra/length_sizebins_NOBA.csv
data-raw/simulated-data/msinput/hydra/lengthweight_species_NOBA.csv
data-raw/simulated-data/msinput/hydra/maturity_covariates_NOBA.csv
data-raw/simulated-data/msinput/hydra/mortality_M1_NOBA.csv
data-raw/simulated-data/msinput/hydra/mortality_M2sizePreference_NOBA.csv
data-raw/simulated-data/msinput/hydra/observation_biomass_NOBA_BTS_fall_allbox_effic1.csv
data-raw/simulated-data/msinput/hydra/observation_biomass_NOBA_BTS_fall_nearbox_qmix_selmix.csv
data-raw/simulated-data/msinput/hydra/observation_biomass_NOBA_BTS_spring_allbox_effic1.csv
data-raw/simulated-data/msinput/hydra/observation_biomass_NOBA_BTS_spring_nearbox_qmix_selmix.csv
data-raw/simulated-data/msinput/hydra/observation_biomass_NOBA_allsurvs.csv
data-raw/simulated-data/msinput/hydra/observation_catch_NOBA_allfisheries.csv
data-raw/simulated-data/msinput/hydra/observation_catch_NOBA_census.csv
data-raw/simulated-data/msinput/hydra/observation_catch_NOBA_nearbox.csv
data-raw/simulated-data/msinput/hydra/observation_diets_NOBA_allsurvs.csv
data-raw/simulated-data/msinput/hydra/observation_effort_NOBA.csv
data-raw/simulated-data/msinput/hydra/observation_lengths_NOBA_BTS_fall_allbox_effic1.csv
data-raw/simulated-data/msinput/hydra/observation_lengths_NOBA_BTS_fall_nearbox_qmix_selmix.csv
data-raw/simulated-data/msinput/hydra/observation_lengths_NOBA_BTS_spring_allbox_effic1.csv
data-raw/simulated-data/msinput/hydra/observation_lengths_NOBA_BTS_spring_nearbox_qmix_selmix.csv
data-raw/simulated-data/msinput/hydra/observation_lengths_NOBA_allfisheries.csv
data-raw/simulated-data/msinput/hydra/observation_lengths_NOBA_allsurvs.csv
data-raw/simulated-data/msinput/hydra/observation_temperature_NOBA_BTS_fall_allbox_effic1.csv
data-raw/simulated-data/msinput/hydra/observation_temperature_NOBA_BTS_fall_nearbox_qmix_selmix.csv
data-raw/simulated-data/msinput/hydra/observation_temperature_NOBA_BTS_spring_allbox_effic1.csv
data-raw/simulated-data/msinput/hydra/observation_temperature_NOBA_BTS_spring_nearbox_qmix_selmix.csv
data-raw/simulated-data/msinput/hydra/recruitment_covariates_NOBA.csv
data-raw/simulated-data/msinput/hydra/sexratio_NOBA.csv
data-raw/simulated-data/msinput/hydra/singletons_NOBA.csv
data-raw/simulated-data/msinput/hydra/speciesList_NOBA.csv
data-raw/simulated-data/msinput/msspm/BTS_fall_allbox_effic1.csv
data-raw/simulated-data/msinput/msspm/BTS_fall_nearbox_qmix_selmix.csv
data-raw/simulated-data/msinput/msspm/BTS_spring_allbox_effic1.csv
data-raw/simulated-data/msinput/msspm/BTS_spring_nearbox_qmix_selmix.csv
data-raw/simulated-data/msinput/msspm/README.txt
data-raw/simulated-data/msinput/msspm/diet_BTS_fall_allbox_effic1.csv
data-raw/simulated-data/msinput/msspm/diet_BTS_fall_nearbox_qmix_selmix.csv
data-raw/simulated-data/msinput/msspm/diet_BTS_spring_allbox_effic1.csv
data-raw/simulated-data/msinput/msspm/diet_BTS_spring_nearbox_qmix_selmix.csv
data-raw/simulated-data/msinput/msspm/fishery_census.csv
data-raw/simulated-data/msinput/msspm/fishery_nearbox.csv
data/AllSpeciesProportions.rda
data/SurveyIndexA4.rda
data/SurveyIndexA4All.rda
data/SurveyIndexHB.rda
data/SurveyIndexHBAll.rda
data/catchAtLengthProportions.rda
data/catchIndex.rda
data/fisheryLenSampN.rda
data/fleets.rda
data/focalSpecies.rda
data/realBiolPar.rda
data/realFisheryAgecomp.rda
data/realFisheryLencomp.rda
data/realFisheryLencompRaw.rda
data/realSurveyLennumcomp.rda
data/simBiolPar.rda
data/simCatchIndex.rda
data/simCatchIndexFW.rda
data/simCatchIndexSubannual.rda
data/simCatchIndexSubannualFW.rda
data/simFisheryAgeLencomp.rda
data/simFisheryAgecomp.rda
data/simFisheryAgecompSubannual.rda
data/simFisheryLencomp.rda
data/simFisheryLencompSubannual.rda
data/simFisheryWtatAge.rda
data/simFisheryWtatAgeSubannual.rda
data/simFocalSpecies.rda
data/simPerCapCons.rda
data/simStartPars.rda
data/simSurveyAgeLencomp.rda
data/simSurveyAgecomp.rda
data/simSurveyBottemp.rda
data/simSurveyDietcomp.rda
data/simSurveyDietcompFW.rda
data/simSurveyIndex.rda
data/simSurveyIndexFW.rda
data/simSurveyInfo.rda
data/simSurveyLenDietcomp.rda
data/simSurveyLencomp.rda
data/simSurveyWtatAge.rda
data/surveyDietcomp.rda
data/surveyIndex.rda
data/surveyIndexAll.rda
data/surveyLenDietcomp.rda
data/surveyLenSampN.rda
man/AllSpeciesProportions.Rd man/catchAtLengthProportions.Rd man/catchIndex.Rd man/fisheryLenSampN.Rd man/fleets.Rd man/focalSpecies.Rd man/mskeyrun.Rd man/realBiolPar.Rd man/realFisheryAgecomp.Rd man/realFisheryLencomp.Rd man/realSurveyLennumcomp.Rd man/simBiolPar.Rd man/simCatchIndex.Rd man/simCatchIndexFW.Rd man/simCatchIndexSubannual.Rd man/simCatchIndexSubannualFW.Rd man/simFisheryAgeLencomp.Rd man/simFisheryAgecomp.Rd man/simFisheryAgecompSubannual.Rd man/simFisheryLencomp.Rd man/simFisheryLencompSubannual.Rd man/simFisheryWtatAge.Rd man/simFisheryWtatAgeSubannual.Rd man/simFocalSpecies.Rd man/simPerCapCons.Rd man/simStartPars.Rd man/simSurveyAgeLencomp.Rd man/simSurveyAgecomp.Rd man/simSurveyBottemp.Rd man/simSurveyDietcomp.Rd man/simSurveyDietcompFW.Rd man/simSurveyIndex.Rd man/simSurveyIndexFW.Rd man/simSurveyInfo.Rd man/simSurveyLenDietcomp.Rd man/simSurveyLencomp.Rd man/simSurveyWtatAge.Rd man/surveyDietcomp.Rd man/surveyIndex.Rd man/surveyIndexA4.Rd man/surveyIndexA4All.Rd man/surveyIndexAll.Rd man/surveyIndexHB.Rd man/surveyIndexHBAll.Rd man/surveyLenDietcomp.Rd man/surveyLenSampN.Rd
pkgdown/_pkgdown.yml
vignettes/.gitignore
vignettes/CompsDat.Rmd vignettes/DataNeeds.Rmd vignettes/DatasetDimensions.Rmd vignettes/GBFleetDecisions.Rmd vignettes/GBFleetDefinitions.Rmd vignettes/GBLandingLengthDataSources.Rmd vignettes/GBLandingsByAge.Rmd vignettes/GBLandingsByLength.Rmd vignettes/GBLengthWeight.Rmd vignettes/GBSurveySet.Rmd vignettes/GBbiomassNumbyLength.rmd vignettes/GBdietcomp.Rmd vignettes/GBsurveycatchviz.Rmd
vignettes/NMFS_JIRA_2020-06-15T_0_11_28-0400.html
vignettes/SimData.Rmd vignettes/SimData_archive.Rmd vignettes/SpeciesEnvDat.Rmd vignettes/allocateLandingsEPU.Rmd
vignettes/apa-annotated-bibliography.csl
vignettes/figures/11_demersal_length_frequency_table2_ATLANTIC_COD.png
vignettes/figures/11_demersal_length_frequency_table2_ATLANTIC_MACKEREL.png
vignettes/figures/11_demersal_length_frequency_table2_GOOSEFISH.png
vignettes/figures/11_demersal_length_frequency_table2_HADDOCK.png
vignettes/figures/11_demersal_length_frequency_table2_SILVER_HAKE.png
vignettes/figures/11_demersal_length_frequency_table2_SPINY_DOGFISH.png
vignettes/figures/11_demersal_length_frequency_table2_WINTER_FLOUNDER.png
vignettes/figures/11_demersal_length_frequency_table2_WINTER_SKATE.png
vignettes/figures/11_demersal_length_frequency_table2_YELLOWTAIL_FLOUNDER.png
vignettes/figures/11_fixedGear_length_frequency_table2_ATLANTIC_COD.png
vignettes/figures/11_fixedGear_length_frequency_table2_ATLANTIC_MACKEREL.png
vignettes/figures/11_fixedGear_length_frequency_table2_GOOSEFISH.png
vignettes/figures/11_fixedGear_length_frequency_table2_HADDOCK.png
vignettes/figures/11_fixedGear_length_frequency_table2_SPINY_DOGFISH.png
vignettes/figures/11_pelagic_length_frequency_table2_ATLANTIC_HERRING.png
vignettes/figures/11_pelagic_length_frequency_table2_ATLANTIC_MACKEREL.png
vignettes/figures/demersalfixed.png
vignettes/figures/demersalfree_y.png
vignettes/figures/dendrogram1.png
vignettes/figures/dendrogram2.png
vignettes/figures/dendrogram3.png
vignettes/figures/dendrogram4.png
vignettes/figures/gear01.png
vignettes/figures/gear02.png
vignettes/figures/gear05.png
vignettes/figures/gear10.png
vignettes/figures/gear12.png
vignettes/figures/gear13.png
vignettes/figures/gear14.png
vignettes/figures/gear17.png
vignettes/figures/gear18.png
vignettes/figures/gear20.png
vignettes/figures/gear21.png
vignettes/figures/gear30.png
vignettes/figures/gear37.png
vignettes/figures/gear38.png
vignettes/figures/gear40.png
vignettes/mskeyrun.Rmd
vignettes/references.bib
vignettes/stockAreas.Rmd
vignettes/supportingFiles/MS-Keyrun Compositional Data Needs (Responses) - Form Responses 1.csv
vignettes/supportingFiles/MS-Keyrun Dataset Dimensions (Responses) - Form Responses 1.csv
vignettes/supportingFiles/MS-Keyrun Species, Environment, Data Format (Responses) - Form Responses 1.csv
vignettes/supportingFiles/readMe.txt
NOAA-EDAB/ms-keyrun documentation built on April 20, 2024, 10:07 a.m.

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