Files in noaa-garfo/discaRd
Cochran bycatch estimation
.Rbuildignore
.gitignore
CAMS/DOC/10-discards_060622.html
CAMS/DOC/Steps to run discard for CAMS.docx
CAMS/DOC/dest_strata_squid_ex.JPG
CAMS/DOC/discaRd.png
CAMS/DOC/discard_documention_beamer.Rmd
CAMS/DOC/discard_documention_beamer.nav
CAMS/DOC/discard_documention_beamer.pdf
CAMS/DOC/discard_documention_beamer.snm
CAMS/DOC/discard_documention_beamer.tex
CAMS/DOC/discard_documention_beamer.toc
CAMS/DOC/discard_documention_beamer.vrb
CAMS/DOC/discard_documention_beamer_files/figure-beamer/table_flow0-1.pdf
CAMS/DOC/discard_steps_documentation.Rmd
CAMS/DOC/discard_steps_documentation.pdf
CAMS/DOC/discard_steps_for_CAMS.Rmd
CAMS/DOC/discard_steps_for_CAMS.html
CAMS/DOC/document_CAMS_DISCARDS_ALL_YEARS.Rmd
CAMS/DOC/document_CAMS_DISCARDS_ALL_YEARS.html
CAMS/DOC/document_CAMS_DISCARD_MORTALITY_STOCK.Rmd
CAMS/DOC/document_CAMS_DISCARD_MORTALITY_STOCK.html
CAMS/DOC/document_CAMS_GEARCODE_STRATA.Rmd
CAMS/DOC/document_CAMS_GEARCODE_STRATA.html
CAMS/DOC/document_CAMS_OBDBS.Rmd
CAMS/DOC/document_CAMS_OBDBS.html
CAMS/DOC/document_CAMS_OBDBS_files/figure-gfm/table_flow0-1.png
CAMS/DOC/document_CAMS_OBS_CATCH.Rmd
CAMS/DOC/document_CAMS_OBS_CATCH.html
CAMS/DOC/document_CAMS_OBS_CATCH_files/figure-gfm/table_flow0-1.png
CAMS/DOC/document_CAMS_STATAREA_STOCK.Rmd
CAMS/DOC/document_CAMS_STATAREA_STOCK.html
CAMS/DOC/document_GF_EM_DELTA_VTR_DISCARD.Rmd
CAMS/DOC/document_GF_EM_DELTA_VTR_DISCARD.html
CAMS/DOC/document_MV_NEMIS_ALL_PTNS_EM_TRIPS_I.Rmd
CAMS/DOC/document_MV_NEMIS_ALL_PTNS_EM_TRIPS_I.html
CAMS/DOC/document_OBS_PRORATE_files/figure-gfm/table_flow0-1.png
CAMS/DOC/dropped_obs_data_metrics.Rmd
CAMS/MODULES/APRIL/april_loop_062122.Rmd
CAMS/MODULES/APRIL/april_loop_module.Rmd
CAMS/MODULES/APRIL/april_module_summary.Rmd
CAMS/MODULES/APRIL/april_module_summary.html
CAMS/MODULES/CALENDAR/January_comparisons.csv
CAMS/MODULES/CALENDAR/January_kall.csv
CAMS/MODULES/CALENDAR/january_loop_062122.R
CAMS/MODULES/CALENDAR/january_loop_062122.Rmd
CAMS/MODULES/CALENDAR/january_loop_module.Rmd
CAMS/MODULES/CALENDAR/january_module_summary.Rmd
CAMS/MODULES/CALENDAR/january_module_summary.html
CAMS/MODULES/GROUNDFISH/OLD_FILES/CAMS_DISCARD_EXAMPLE_GF19_snippet.xlsx
CAMS/MODULES/GROUNDFISH/OLD_FILES/MULTS_module.Rmd
CAMS/MODULES/GROUNDFISH/OLD_FILES/MULTS_module_stock_as_region.Rmd
CAMS/MODULES/GROUNDFISH/OLD_FILES/May_comparisons.csv
CAMS/MODULES/GROUNDFISH/OLD_FILES/check_YTF_discard_source_CAMS_061622.Rmd
CAMS/MODULES/GROUNDFISH/OLD_FILES/check_YTF_discard_source_CAMS_061622.html
CAMS/MODULES/GROUNDFISH/OLD_FILES/check_catch_table_sectors.sql
CAMS/MODULES/GROUNDFISH/OLD_FILES/check_pounds_by_source_table.sql
CAMS/MODULES/GROUNDFISH/OLD_FILES/compare_gear_strata_gftrips19.Rdata
CAMS/MODULES/GROUNDFISH/OLD_FILES/compare_kall_dmis_cams.Rmd
CAMS/MODULES/GROUNDFISH/OLD_FILES/compare_kall_dmis_cams.html
CAMS/MODULES/GROUNDFISH/OLD_FILES/control_script.Rmd
CAMS/MODULES/GROUNDFISH/OLD_FILES/dmis2019_groundfish_discard.csv
CAMS/MODULES/GROUNDFISH/OLD_FILES/dmis2019_groundfish_discard_CAMS_comparison_012122.xlsx
CAMS/MODULES/GROUNDFISH/OLD_FILES/drate_nan_example.JPG
CAMS/MODULES/GROUNDFISH/OLD_FILES/examine_groundfish_loop_results.R
CAMS/MODULES/GROUNDFISH/OLD_FILES/examine_groundfish_loop_results.Rmd
CAMS/MODULES/GROUNDFISH/OLD_FILES/generic_loop_groundfish.Rmd
CAMS/MODULES/GROUNDFISH/OLD_FILES/generic_loop_groundfish_split.Rmd
CAMS/MODULES/GROUNDFISH/OLD_FILES/grant_tables_cams_garfo.sql
CAMS/MODULES/GROUNDFISH/OLD_FILES/groundfish_CY_example_pull.sql
CAMS/MODULES/GROUNDFISH/OLD_FILES/groundfish_comparison_notes.Rmd
CAMS/MODULES/GROUNDFISH/OLD_FILES/groundfish_comparison_notes.md
CAMS/MODULES/GROUNDFISH/OLD_FILES/groundfish_loop_050422.R
CAMS/MODULES/GROUNDFISH/OLD_FILES/groundfish_loop_results_gftrips_only_012122.csv
CAMS/MODULES/GROUNDFISH/OLD_FILES/groundfish_loop_results_gftrips_only_012622.csv
CAMS/MODULES/GROUNDFISH/OLD_FILES/groundfish_loop_results_gftrips_only_020922.csv
CAMS/MODULES/GROUNDFISH/OLD_FILES/groundfish_loop_results_gftrips_only_021822.csv
CAMS/MODULES/GROUNDFISH/OLD_FILES/groundfish_module_summary.html
CAMS/MODULES/GROUNDFISH/OLD_FILES/groundfish_module_summary.md
CAMS/MODULES/GROUNDFISH/OLD_FILES/groundfish_module_summary_files/figure-markdown_github/make diagnostic plot-1.png
CAMS/MODULES/GROUNDFISH/OLD_FILES/groundfish_module_summary_files/figure-markdown_github/plot 2-1.png
CAMS/MODULES/GROUNDFISH/OLD_FILES/oblen_camsobs_examples.Rmd
CAMS/MODULES/GROUNDFISH/OLD_FILES/recombine_groundfish_loop.R
CAMS/MODULES/GROUNDFISH/OLD_FILES/recombine_groundfish_loop.Rmd
CAMS/MODULES/GROUNDFISH/OLD_FILES/scallop_flatfish_module.Rmd
CAMS/MODULES/GROUNDFISH/OLD_FILES/test_YTF_discard_output_061622.R
CAMS/MODULES/GROUNDFISH/OLD_FILES/test_sql_import_run.r
CAMS/MODULES/GROUNDFISH/OLD_FILES/test_sql_preview.sql
CAMS/MODULES/GROUNDFISH/OLD_FILES/use_fst_vs_RDS.R
CAMS/MODULES/GROUNDFISH/OLD_FILES/zero_obs_kall.JPG
CAMS/MODULES/GROUNDFISH/groundfish_loop_050422.Rmd
CAMS/MODULES/GROUNDFISH/groundfish_module_summary.Rmd
CAMS/MODULES/HERRING/Atlantic_herring_loop_module.Rmd
CAMS/MODULES/MARCH/march_loop_062122.Rmd
CAMS/MODULES/MARCH/march_loop_module.Rmd
CAMS/MODULES/MARCH/march_module_summary.Rmd
CAMS/MODULES/MARCH/march_module_summary.html
CAMS/MODULES/MAY/OLD_FILES/Hake_comparisons.csv
CAMS/MODULES/MAY/OLD_FILES/May_comparisons.csv
CAMS/MODULES/MAY/OLD_FILES/May_kall.csv
CAMS/MODULES/MAY/OLD_FILES/Skate_comparisons.csv
CAMS/MODULES/MAY/OLD_FILES/may_loop_062122.R
CAMS/MODULES/MAY/OLD_FILES/may_loop_module.Rmd
CAMS/MODULES/MAY/OLD_FILES/may_loop_module_SBRM.Rmd
CAMS/MODULES/MAY/OLD_FILES/may_loop_module_stock_gear.Rmd
CAMS/MODULES/MAY/OLD_FILES/may_module_summary.Rmd
CAMS/MODULES/MAY/OLD_FILES/rethink_broad_stock.R
CAMS/MODULES/MAY/hake_module_summary.Rmd
CAMS/MODULES/MAY/may_loop_062122.Rmd
CAMS/MODULES/MAY/may_module_summary.html
CAMS/MODULES/MAY/skate_module_summary.Rmd
CAMS/MODULES/MAY/skate_module_summary.html
CAMS/MODULES/MSB_module.Rmd
CAMS/MODULES/MSB_module_V2.Rmd
CAMS/MODULES/NOVEMBER/OLD_FILES/November_comparisons.csv
CAMS/MODULES/NOVEMBER/OLD_FILES/November_kall.csv
CAMS/MODULES/NOVEMBER/OLD_FILES/november_loop_062122.R
CAMS/MODULES/NOVEMBER/OLD_FILES/november_loop_module.Rmd
CAMS/MODULES/NOVEMBER/november_loop_062122.Rmd
CAMS/MODULES/NOVEMBER/november_module_summary.Rmd
CAMS/MODULES/NOVEMBER/november_module_summary.html
CAMS/MODULES/SBRM/sbrm_loop_062122.Rmd
CAMS/MODULES/SBRM/sbrm_species_022222.csv
CAMS/MODULES/control_script_Winiarski.Rmd
CAMS/MODULES/dogfish_module.Rmd
CAMS/MODULES/generic_loop_module.Rmd
CAMS/MODULES/monkfish_module.Rmd
CAMS/OLD_FILES/CAMS_discaRd_ACL_comparison.JPG
CAMS/OLD_FILES/COD_STOCK_example.JPG
CAMS/OLD_FILES/GAR master gear codes.xlsx
CAMS/OLD_FILES/SMB_FY2019_discRd_BG_example.xlsx
CAMS/OLD_FILES/TEST/brant_obs_mesh.sql
CAMS/OLD_FILES/TEST/check_catch_obs_table.sql
CAMS/OLD_FILES/TEST/convert_names_to_MAPS_part1.sql
CAMS/OLD_FILES/TEST/dan_c_discard_base_tables.sql
CAMS/OLD_FILES/TEST/explore_link1_match.sql
CAMS/OLD_FILES/TEST/explore_obs_match.sql
CAMS/OLD_FILES/TEST/explore_trips_obs_mtach_discrepancies.sql
CAMS/OLD_FILES/TEST/get_GF_discards_dmis.sql
CAMS/OLD_FILES/TEST/get_obs_mockup.sql
CAMS/OLD_FILES/TEST/make_bdat_focal.R
CAMS/OLD_FILES/TEST/make_catch_obs_brants_version.sql
CAMS/OLD_FILES/TEST/make_catch_obs_tables.sql
CAMS/OLD_FILES/TEST/play_with_mortality.R
CAMS/OLD_FILES/TEST/scallop_trip_CHECK.sql
CAMS/OLD_FILES/TEST/scratch_gear_mapping_for_merge.sql
CAMS/OLD_FILES/TEST/scratch_paper.sql
CAMS/OLD_FILES/TEST/scratch_work2.sql
CAMS/OLD_FILES/TEST/scratch_work3.sql
CAMS/OLD_FILES/TEST/test_new_cams_catch.sql
CAMS/OLD_FILES/TEST/test_using_merged_table.R
CAMS/OLD_FILES/center_gear_info_DL.xlsx
CAMS/OLD_FILES/check_catch_obs_table.Rmd
CAMS/OLD_FILES/check_catch_obs_table.html
CAMS/OLD_FILES/explore_multiple_trips_haul.xlsx
CAMS/OLD_FILES/mesh_cat_sources.png
CAMS/OLD_FILES/munge_MAPS_support_tables.Rmd
CAMS/OLD_FILES/squid_ex_table.JPG
CAMS/OLD_FILES/stat_areas_defined.Rdata
CAMS/OLD_FILES/subrip_match_explorations.xlsx
CAMS/TESTS_AND_EXAMPLES/EM_CAMS_OBS_CATCH_MATCH_EXAMPLE.sql
CAMS/TESTS_AND_EXAMPLES/MERGE_CAMS_CATCH_OBS.sql
CAMS/TESTS_AND_EXAMPLES/MERGE_CAMS_CATCH_OBS_MINLNK1.sql
CAMS/TESTS_AND_EXAMPLES/MERGE_CAMS_CATCH_OBS_TEST.sql
CAMS/TESTS_AND_EXAMPLES/R/NEGEAR_GEARCODE_MAPPING.xlsx
CAMS/TESTS_AND_EXAMPLES/R/cams_discard_functions.R
CAMS/TESTS_AND_EXAMPLES/R/create_discard_view.R
CAMS/TESTS_AND_EXAMPLES/R/keyring_roracle_helper.R
CAMS/TESTS_AND_EXAMPLES/R/make_cams_obdbs.R
CAMS/TESTS_AND_EXAMPLES/R/make_stg_obs_vtr_mapped.R
CAMS/TESTS_AND_EXAMPLES/R/run_make_cams_obdbs.R
CAMS/TESTS_AND_EXAMPLES/R/test_make_bdat_focal_fix.R
CAMS/TESTS_AND_EXAMPLES/check_GF_DCaless.sql
CAMS/TESTS_AND_EXAMPLES/check_ashleys_link3.sql
CAMS/TESTS_AND_EXAMPLES/check_wigley_caless_051823.Rmd
CAMS/TESTS_AND_EXAMPLES/disc_var_example_062722.sql
CAMS/TESTS_AND_EXAMPLES/discard_parallel.R
CAMS/TESTS_AND_EXAMPLES/explore_dropped_hauls.sql
CAMS/TESTS_AND_EXAMPLES/explore_hauls_multi_subtrip.sql
CAMS/TESTS_AND_EXAMPLES/herring_latlon_test.sql
CAMS/TESTS_AND_EXAMPLES/make_cams_obs_catch_owh.sql
CAMS/TESTS_AND_EXAMPLES/make_obdbs_prorate.sql
CAMS/TESTS_AND_EXAMPLES/make_obdbs_table_cams.sql
CAMS/TESTS_AND_EXAMPLES/make_obdbs_table_cams_v2.sql
CAMS/TESTS_AND_EXAMPLES/match_discard_oblen_example.sql
CAMS/TESTS_AND_EXAMPLES/sql_loop_examples.sql
CAMS/TESTS_AND_EXAMPLES/summarize_area0_obs.sql
CAMS/TESTS_AND_EXAMPLES/summarize_dropped_hauls.sql
CAMS/TESTS_AND_EXAMPLES/test_make_obdbs_top.sql
CAMS/TESTS_AND_EXAMPLES/test_run_obdbs.sh
CAMS/bens_discarRd_prj/.Rbuildignore
CAMS/bens_discarRd_prj/.gitignore
CAMS/bens_discarRd_prj/_pkgdown.yml
CAMS/control_script.R
CAMS/control_script_generic.R
DESCRIPTION
DEV/cochran.trans.calc_alt.r
DEV/get.cochran.ss.by.strat_alt.r
DEV/get.cochran.ss.by.strat_orig.r
NAMESPACE
R/add_nobs.R
R/assign_discard_source.R
R/assign_strata.R
R/bootr.strat.r
R/cochran.calc.ss.r
R/cochran.trans.calc.r
R/discard_generic.R
R/discard_generic_diagnostic.R
R/discard_groundfish.R
R/discard_groundfish_diagnostic.R
R/discard_herring.R
R/discard_herring_diagnostic.R
R/eflalo.r
R/get.bydat.r
R/get.cochran.ss.by.strat.r
R/get.trans.rate.r
R/get.weighted.cv.r
R/get_broad_stock_rate.R
R/get_catch_obs.R
R/get_catch_obs_diag.R
R/get_covrow.R
R/get_covrow_bg.R
R/get_date_range.R
R/get_obs_disc_values.R
R/make.obs.flag.dat.r
R/make_assumed_rate.R
R/make_bdat_focal.R
R/make_strata_desc.R
R/not_in.R
R/parse_discard_diag.R
R/run_discard.R
R/scallop_subroutine.R
R/scallop_subroutine_diag.R
R/setup.parallel.r
R/summarise_single_discard_row.R
R/unite_by_source.R
R/vary.bigN.r
R/vary.n.r
README.md
_pkgdown.yml
data/eflalo.rda
discaRd.Rproj
docs/404.html
docs/_pkgdown.yml
docs/apple-touch-icon-120x120.png
docs/apple-touch-icon-152x152.png
docs/apple-touch-icon-180x180.png
docs/apple-touch-icon-60x60.png
docs/apple-touch-icon-76x76.png
docs/apple-touch-icon.png
docs/articles/eflalo_demo.html
docs/articles/eflalo_demo_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/eflalo_demo_files/figure-html/plot_discard-1.png
docs/articles/index.html
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/favicon-16x16.png
docs/favicon-32x32.png
docs/favicon.ico
docs/index.html
docs/link.svg
docs/logo.png
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/Rplot001.png
docs/reference/bootr.strat.html
docs/reference/cochran.calc.ss.html
docs/reference/cochran.trans.calc.html
docs/reference/eflalo.html
docs/reference/figures/logo.png
docs/reference/get.bydat.html
docs/reference/get.cochran.ss.by.strat.html
docs/reference/get.trans.rate-1.png
docs/reference/get.trans.rate.html
docs/reference/get.weighted.cv.html
docs/reference/index.html
docs/reference/make.obs.flag.dat.html
docs/reference/setup.parallel.html
docs/reference/vary.bigN.html
docs/reference/vary.n-1.png
docs/reference/vary.n.html
man/add_nobs.Rd
man/assign_discard_source.Rd
man/assign_strata.Rd
man/bootr.strat.Rd
man/cochran.calc.ss.Rd
man/cochran.trans.calc.Rd
man/discard_generic.Rd
man/discard_generic_diagnostic.Rd
man/discard_groundfish.Rd
man/discard_groundfish_diagnostic.Rd
man/discard_herring.Rd
man/discard_herring_diagnostic.Rd
man/eflalo.Rd
man/figures/logo.png
man/get.bydat.Rd
man/get.cochran.ss.by.strat.Rd
man/get.trans.rate.Rd
man/get.weighted.cv.Rd
man/get_broad_stock_rate.Rd
man/get_catch_obs.Rd
man/get_catch_obs_diag.Rd
man/get_covrow.Rd
man/get_covrow_bg.Rd
man/get_date_range.Rd
man/get_obs_disc_vals.Rd
man/grapes-not-in-grapes.Rd
man/make.obs.flag.dat.Rd
man/make_assumed_rate.Rd
man/make_bdat_focal.Rd
man/make_strata_desc.Rd
man/parse_discard_diag.Rd
man/run_discard.Rd
man/scallop_subroutine.Rd
man/scallop_subroutine_diag.Rd
man/setup.parallel.Rd
man/summarise_single_discard_row.Rd
man/unite_by_source.Rd
man/vary.bigN.Rd
man/vary.n.Rd
not_used/bootr.par.r
not_used/bootr.r
not_used/cochran_rse.r
not_used/get.bdat.r
not_used/get.cochran.ss.by.strat.par.r
not_used/get.gf.data.r
not_used/get.scalb.data.r
not_used/get.trips.att.r
not_used/samp.by.strat.r
not_used/sampr.r
not_used/summarise_singe_discard_row.R
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
pkgdown/favicon/apple-touch-icon-76x76.png
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
vignettes/discard_diagnostic.Rmd
vignettes/discard_diagnostic_example_ytf.html
vignettes/discard_diagnostic_example_ytf.qmd
vignettes/discard_diagnostic_example_ytf_files/libs/bootstrap/bootstrap-icons.css
vignettes/discard_diagnostic_example_ytf_files/libs/bootstrap/bootstrap-icons.woff
vignettes/discard_diagnostic_example_ytf_files/libs/bootstrap/bootstrap.min.css
vignettes/discard_diagnostic_example_ytf_files/libs/bootstrap/bootstrap.min.js
vignettes/discard_diagnostic_example_ytf_files/libs/clipboard/clipboard.min.js
vignettes/discard_diagnostic_example_ytf_files/libs/quarto-html/anchor.min.js
vignettes/discard_diagnostic_example_ytf_files/libs/quarto-html/popper.min.js
vignettes/discard_diagnostic_example_ytf_files/libs/quarto-html/quarto-syntax-highlighting.css
vignettes/discard_diagnostic_example_ytf_files/libs/quarto-html/quarto.js
vignettes/discard_diagnostic_example_ytf_files/libs/quarto-html/tippy.css
vignettes/discard_diagnostic_example_ytf_files/libs/quarto-html/tippy.umd.min.js
vignettes/eflalo_demo.R
vignettes/eflalo_demo.html
vignettes/eflalo_demo.rmd
vignettes/images/scallop_trips_ytf_example.PNG
vignettes/images/scallop_trips_ytf_example_2.PNG
vignettes/scallop_trip_treatment.html
vignettes/scallop_trip_treatment.qmd
vignettes/scallop_trip_treatment_files/libs/bootstrap/bootstrap-icons.css
vignettes/scallop_trip_treatment_files/libs/bootstrap/bootstrap-icons.woff
vignettes/scallop_trip_treatment_files/libs/bootstrap/bootstrap.min.css
vignettes/scallop_trip_treatment_files/libs/bootstrap/bootstrap.min.js
vignettes/scallop_trip_treatment_files/libs/clipboard/clipboard.min.js
vignettes/scallop_trip_treatment_files/libs/quarto-html/anchor.min.js
vignettes/scallop_trip_treatment_files/libs/quarto-html/popper.min.js
vignettes/scallop_trip_treatment_files/libs/quarto-html/quarto-syntax-highlighting.css
vignettes/scallop_trip_treatment_files/libs/quarto-html/quarto.js
vignettes/scallop_trip_treatment_files/libs/quarto-html/tippy.css
vignettes/scallop_trip_treatment_files/libs/quarto-html/tippy.umd.min.js
vignettes/wolffish_example.Rmd
