Files in pacific-hake/hake-assessment

Stock Assessment for Pacific Hake

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.here

DESCRIPTION

LICENSE

NAMESPACE

NEWS.md R/create-fontsize-str.R R/create-group-df-biomass.R R/create-group-df-index.R R/create-group-df-recr.R R/create-rds-attach-forecasts.R R/create-rds-attach-retrospectives.R R/create-rds-file.R R/create-rds-files-retro.R R/create-rds-natage.R R/create-sens-dirs.R R/data.R R/hake-beamer.R R/hake-pdf.R R/hake.R R/load-can-age-data.R R/load-ct-levels.R R/load-extra-mcmc-age-comps.R R/load-extra-mcmc-atage.R R/load-extra-mcmc-biomass.R R/load-extra-mcmc-catage-biomass.R R/load-extra-mcmc-get-chunk.R R/load-extra-mcmc-get-parameter-chunk.R R/load-extra-mcmc-init-nage.R R/load-extra-mcmc-m.R R/load-extra-mcmc-naa.R R/load-extra-mcmc-recr-cohorts.R R/load-extra-mcmc-recr-devs.R R/load-extra-mcmc-repfiles.R R/load-extra-mcmc-sel.R R/load-extra-mcmc-selwt.R R/load-extra-mcmc.R R/load-forecasts.R R/load-mcmc-vals.R R/load-parameter-priors.R R/load-ss-files.R R/model-setup.R R/plot-age-comp-bubbles-data.R R/plot-age-comp-bubbles.R R/plot-age-comp-comparison-bubbles.R R/plot-age-comp-fit.R R/plot-assessment-history-biomass.R R/plot-assessment-history-disp.R R/plot-autocor.R R/plot-biomass-fished-unfished.R R/plot-biomass.R R/plot-bubbles.R R/plot-catch-by-month.R R/plot-catchability-density.R R/plot-catches.R R/plot-cohort-catch.R R/plot-color.R R/plot-cumulative-catch-cohorts.R R/plot-data-summary.R R/plot-density.R R/plot-depl-fore-comparison.R R/plot-depth-2-panel.R R/plot-depth-4-panel.R R/plot-depth.R R/plot-during-loading.R R/plot-exploitation-fraction.R R/plot-fecundity.R R/plot-fishing-intensity.R R/plot-fore-age-comps.R R/plot-fore-compare.R R/plot-heatmap-sample-size-weight-at-age.R R/plot-heatmap-weight-at-age.R R/plot-historical-probs-retro.R R/plot-historical-probs.R R/plot-intensity-illustration.R R/plot-management-catch-vs-tac-1-to-1.R R/plot-management-catch-vs-tac.R R/plot-map.R R/plot-maturity-ogives.R R/plot-mcmc-diagnostics-all-params.R R/plot-mcmc-diagnostics.R R/plot-mcmc-histogram.R R/plot-mcmc-running-quants.R R/plot-overview-map.R R/plot-pairs.R R/plot-param-density.R R/plot-pearson-bubbles.R R/plot-phase.R R/plot-priors-vs-posts.R R/plot-recdevs.R R/plot-recruitment.R R/plot-rel-biomass.R R/plot-rel-recruitment.R R/plot-retro-recruits.R R/plot-selex-mountains.R R/plot-selex-posteriors.R R/plot-selex-uncertainty.R R/plot-spatial-cpue.R R/plot-spr-illustration.R R/plot-squid.R R/plot-stock-recruitment.R R/plot-survey-biomass.R R/plot-survey-fit-mcmc.R R/plot-survey-index-fits.R R/plot-trace.R R/plot-weight-at-age.R R/plot-weights-lengths.R R/post-process-add-alt-text.R R/post-process-add-appendix-counter-resets.R R/post-process-add-counters.R R/post-process-add-headers-footers.R R/post-process-add-horiz-lines-decision-table.R R/post-process-add-picture-to-title-page.R R/post-process-add-start-appendices-code.R R/post-process-add-vert-space-after-header.R R/post-process-add-xcolor-package.R R/post-process-beamer-add-extra-headers-etc.R R/post-process-beamer-insert-disclaimer.R R/post-process-beamer-insert-title-page-logos.R R/post-process-beamer-make-title-page-plain.R R/post-process-beamer.R R/post-process-convert-section-headers.R R/post-process-error-check.R R/post-process-extract-chunks.R R/post-process-fix-landscape-issues.R R/post-process-fix-tildes.R R/post-process-interlace-chunks.R R/post-process-landscape-figures.R R/post-process-landscape-tables.R R/post-process-longtables.R R/post-process-modify-font-info.R R/post-process-modify-link-colors.R R/post-process-move-table-captions.R R/post-process-object-placement.R R/post-process-remove-title-page-number.R R/post-process-repair-unnumbered-section-links.R R/post-process-set-latex-placement-options.R R/post-process-table-of-contents.R R/post-process.R R/remove-forecast-outputs.R R/render.R R/run-adnuts-timed.R R/run-adnuts.R R/run-catch-levels-copy-input-files.R R/run-ct-levels-default-hr.R R/run-ct-levels-spr-100.R R/run-ct-levels-stable-catch.R R/run-ct-levels.R R/run-extra-forecasts.R R/run-forecasts.R R/run-retrospectives.R R/table-above-avg-cohorts-yrs.R R/table-age-data.R R/table-assessment-changes.R R/table-at-age.R R/table-biomass.R R/table-catch-by-fleet.R R/table-catch.R R/table-ci-posteriors.R R/table-cohort.R R/table-decision-original.R R/table-decision.R R/table-fishing-intensity.R R/table-fore-age-props.R R/table-landings-tac.R R/table-maturity-ogive.R R/table-median-posteriors.R R/table-ovary-sampling.R R/table-param-est-bounds.R R/table-param-est-last-year-hardcoded.R R/table-param-est.R R/table-parameters-long-summary.R R/table-recruitment.R R/table-reference-points.R R/table-risk.R R/table-sampling-by-month.R R/table-sampling-history.R R/table-survey-by-country.R R/table-survey-history.R R/table-yearly-model-compare.R R/tables-input-age-data.R R/utils-add-major-ticks.R R/utils-add-newlines.R R/utils-add-utm-columns.R R/utils-alt-text-inject-tags.R R/utils-as-ts-mcmc.R R/utils-beta.R R/utils-bind-cols-quiet.R R/utils-calc-ageerror.R R/utils-calc-fishery-ages.R R/utils-calc-historical-probs.R R/utils-calc-lw-params.R R/utils-calc-mcmc-param-stats.R R/utils-calc-mcmc.R R/utils-calc-quantiles.R R/utils-calc-refpt-quants.R R/utils-calc-retro-stats.R R/utils-calc-risk.R R/utils-calc-sum-rec-devs.R R/utils-calc-total-catch.R R/utils-calc-yoob.R R/utils-canada-create-age-proportions-csv.R R/utils-canada-create-commercial-waa.R R/utils-canada-create-fleet-month-catch-csv-files.R R/utils-canada-create-fleet-year-catch-csv-files.R R/utils-canada-extract-depth-data-from-db.R R/utils-canada-extract-fleet-catch.R R/utils-canada-extract-samples-from-db.R R/utils-canada-extract-sampling-by-month.R R/utils-canada-get-fleet-samples.R R/utils-canada-load-catch-data.R R/utils-canada-load-sample-data.R R/utils-canada-sql-inject-fishery-filters.R R/utils-check-catch-levels.R R/utils-check-forecasts.R R/utils-clean-all.R R/utils-clean.R R/utils-cohort-catch.R R/utils-combine-historical-probs.R R/utils-compute-hexagon-xy.R R/utils-convert-ctl-file-param-dfs.R R/utils-create-data-hake.R R/utils-create-depth-by-year-csv-files.R R/utils-create-version-dirs.R R/utils-curr-time-date.R R/utils-delete-files.R R/utils-dirclip.R R/utils-draw-arrows-yoob.R R/utils-enact-privacy-rule.R R/utils-extract-alt-text-knitr.R R/utils-extract-inline-rcode.R R/utils-extract-inside-catch.R R/utils-extract-label-from-figure-filename.R R/utils-extract-mcmc-quant.R R/utils-extract-rep-table.R R/utils-extract-sigma-r.R R/utils-extract-survey-index-fits.R R/utils-f.R R/utils-firstup.R R/utils-fit-lw.R R/utils-fix-posteriors.R R/utils-fix-title-case-for-csl.R R/utils-get-age-comp-limits.R R/utils-get-age-prop.R R/utils-get-age-proportions-by-fleet.R R/utils-get-assess-yr.R R/utils-get-col-name-from-key-title.R R/utils-get-crs.R R/utils-get-doc-type.R R/utils-get-key-nuisance-posts.R R/utils-get-obj-sizes.R R/utils-get-os.R R/utils-get-param-est-comparison-df.R R/utils-get-post-cols.R R/utils-get-posterior-data.R R/utils-get-prior-data.R R/utils-get-prior-string.R R/utils-get-rec-ci.R R/utils-get-ss3-name.R R/utils-get-year-range.R R/utils-goback.R R/utils-gotest-beamer-get-src-dest-filenames.R R/utils-gotest-doc-get-src-dest-filenames.R R/utils-gotest.R R/utils-heatmap-add-extrap-yrs-wa.R R/utils-heatmap-calc-function.R R/utils-heatmap-extract-sample-size.R R/utils-heatmap-get-wa-ggplot-vals.R R/utils-heatmap-set-colors.R R/utils-hexcoords.R R/utils-insert-row.R R/utils-latex-functions.R R/utils-linebreaker.R R/utils-make-major-tick-labels.R R/utils-model-comparisons-nuts.R R/utils-modify-starter-mcmc-type.R R/utils-mutsel.R R/utils-number-to-word.R R/utils-obj-sizes.R R/utils-pacea-save.R R/utils-pad-num.R R/utils-pad-weight-at-age.R R/utils-plot-assessment-timeline.R R/utils-read-bookdown-file.R R/utils-replace-dotted-paths.R R/utils-rich-colors-short.R R/utils-save-nuts-fits.R R/utils-set-ct-levels.R R/utils-set-dirs.R R/utils-split-prior-info.R R/utils-stop-quietly.R R/utils-system.R R/utils-theme.R R/utils-top-coh.R R/utils-update-catch-sums.R R/utils-update-ss3-ageing-error.R R/utils-update-ss3-catch.R R/utils-update-ss3-maturity.R R/utils-us-extract-sampling-by-month.r R/utils-vec2df.R R/utils-yaml-check-margin-format.R R/zzz.R README.md

bash-scripts/copy-base-model-input-files.sh

bash-scripts/copy-ss-files.sh

bash-scripts/create-file-list-for-google-sync.sh

bash-scripts/create-model-docs.sh

bash-scripts/create-rds-attach-forecasts.sh

bash-scripts/create-rds-attach-retrospectives.sh

bash-scripts/create-rds-base.sh

bash-scripts/create-rds-bridge.sh

bash-scripts/create-rds-burnin-models.sh

bash-scripts/create-rds-retrospectives.sh

bash-scripts/create-rds-sensitivities.sh

bash-scripts/create-rds-test-models.sh

bash-scripts/create-rds-test.sh

bash-scripts/create-sensitivity-dirs.sh

bash-scripts/generic-create-rds.sh

bash-scripts/generic-run-models.sh

bash-scripts/get-assess-year.sh

bash-scripts/run-base-model.sh

bash-scripts/run-bridge-models.sh

bash-scripts/run-burnin-test-models.sh

bash-scripts/run-catch-levels.sh

bash-scripts/run-fore-retro.sh

bash-scripts/run-forecasts.sh

bash-scripts/run-retrospectives.sh

bash-scripts/run-sample-size-models.sh

bash-scripts/run-sensitivity-models-1.sh

bash-scripts/run-sensitivity-models-2.sh

bash-scripts/run-test-model.sh

bash-scripts/sync-model-files.sh

bash-scripts/test-get-assess-year.sh

bash-scripts/test-model-loop.sh

bash-scripts/zzz-misc.sh

beamer/.gitignore

beamer/jmc/presentation-canada/000-launcher.rmd beamer/jmc/presentation-canada/010-overview.rmd beamer/jmc/presentation-canada/020-catches.rmd beamer/jmc/presentation-canada/030-model-estimates.rmd beamer/jmc/presentation-canada/040-cohorts.rmd beamer/jmc/presentation-canada/090-summary.rmd

beamer/jmc/presentation-canada/_bookdown.yml

beamer/jmc/presentation-us/000-launcher.rmd beamer/jmc/presentation-us/010-overview.rmd beamer/jmc/presentation-us/020-catches.rmd beamer/jmc/presentation-us/030-model-estimates.rmd beamer/jmc/presentation-us/040-cohorts.rmd beamer/jmc/presentation-us/050-past-management.rmd beamer/jmc/presentation-us/060-projections.rmd beamer/jmc/presentation-us/070-decision-tables.rmd beamer/jmc/presentation-us/080-probability-tables.rmd beamer/jmc/presentation-us/090-summary.rmd

beamer/jmc/presentation-us/_bookdown.yml

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beamer/jmc/presentation/_bookdown.yml

beamer/jtc/000-launcher.rmd beamer/jtc/010-catch.rmd beamer/jtc/020-depths.rmd beamer/jtc/030-catch-rates.rmd beamer/jtc/040-spatial-cpue.rmd beamer/jtc/045-sampling-summary.rmd beamer/jtc/050-raw-lengths.rmd beamer/jtc/060-raw-weights.rmd beamer/jtc/070-ages.rmd beamer/jtc/072-ages-survey.rmd beamer/jtc/079-unused.rmd beamer/jtc/080-thanks.rmd

beamer/jtc/_bookdown.yml

beamer/rm_knitr_caches

beamer/srg/assessment/000-launcher.rmd beamer/srg/assessment/010-outline.rmd beamer/srg/assessment/011-changes.rmd beamer/srg/assessment/012-mcmc-diagnostics.rmd beamer/srg/assessment/013-fits-to-data.rmd beamer/srg/assessment/014-estimated-quantities.rmd beamer/srg/assessment/015-srg-recommends.rmd beamer/srg/assessment/016-summary.rmd

beamer/srg/assessment/_bookdown.yml

beamer/srg/data/000-launcher.rmd beamer/srg/data/010-review.rmd beamer/srg/data/013-ages.rmd beamer/srg/data/014-surveys.rmd beamer/srg/data/015-weight-at-age.rmd beamer/srg/data/016-spatiotemporal-models.rmd

beamer/srg/data/_bookdown.yml

beamer/srg/management/000-launcher.rmd beamer/srg/management/010-past-management.rmd beamer/srg/management/011-projections.rmd beamer/srg/management/012-decision-tables.rmd beamer/srg/management/013-summary.rmd

beamer/srg/management/_bookdown.yml

beamer/srg/requests/template/000-launcher.rmd beamer/srg/requests/template/010-request.rmd beamer/srg/requests/template/020-request.rmd beamer/srg/requests/template/030-request.rmd beamer/srg/requests/template/040-request.rmd beamer/srg/requests/template/050-request.rmd beamer/srg/requests/template/060-request.rmd

beamer/srg/requests/template/_bookdown.yml

beamer/srg/sensitivity/000-launcher.rmd beamer/srg/sensitivity/010-overview.rmd beamer/srg/sensitivity/011-sensitivities-to-h-m-sigmar.rmd beamer/srg/sensitivity/012-removal-of-age1-index.rmd beamer/srg/sensitivity/013-weighting.rmd beamer/srg/sensitivity/014-tv-selectivity-phi.rmd beamer/srg/sensitivity/015-retrospectives.rmd beamer/srg/sensitivity/016-historical.rmd beamer/srg/sensitivity/017-recruitment.rmd beamer/srg/sensitivity/020-summary.rmd

beamer/srg/sensitivity/_bookdown.yml

data-raw/pd-canada-areas-and-vessel-ids.R data-raw/pd-data-table-filenames.R data-raw/pd-data-tables.R data-raw/pd-document-settings.R data-raw/pd-filesystem-settings.R data-raw/pd-key-posteriors.R data-raw/pd-paths-and-filenames.R data-raw/pd-plot-settings.R data-raw/pd-reference-points.R data-raw/pd-regular-expressions.R data-raw/pd-ss-filenames.R data-raw/pd-tac-catch-proportions.R data-raw/ps-messages.R

data-tables/assessment-changes.csv

data-tables/assessment-history-dispersion.csv

data-tables/assessment-history-probs.csv

data-tables/assessment-history.csv

data-tables/can-catch-by-year.csv

data-tables/can-ft-age-proportions.csv

data-tables/can-ft-catch-by-month.csv

data-tables/can-jv-age-proportions.csv

data-tables/can-jv-catch-by-month.csv

data-tables/can-raw-ft-age-counts.csv

data-tables/can-raw-jv-age-counts.csv

data-tables/can-raw-ss-age-counts.csv

data-tables/can-ss-age-proportions.csv

data-tables/can-ss-catch-by-month.csv

data-tables/can-weight-at-age.csv

data-tables/catch-targets-biomass.csv

data-tables/depth-can-ft-bottom.csv

data-tables/depth-can-ft-gear.csv

data-tables/depth-can-ss-bottom.csv

data-tables/depth-can-ss-gear.csv

data-tables/depth-us-atsea-bottom.csv

data-tables/depth-us-atsea-fishing.csv

data-tables/fishery-sampling-history.csv

data-tables/further-tac-details.csv

data-tables/kriging-parameters.csv

data-tables/landings-tac-history.csv

data-tables/length-weight-age/LWAdata_1975to2020.csv

data-tables/length-weight-age/LWAdata_1975to2021.csv

data-tables/length-weight-age/LWAdata_2008.csv

data-tables/length-weight-age/LWAdata_2009.csv

data-tables/length-weight-age/LWAdata_2010.csv

data-tables/length-weight-age/LWAdata_2011.csv

data-tables/length-weight-age/LWAdata_2012.csv

data-tables/length-weight-age/LWAdata_2013.csv

data-tables/length-weight-age/LWAdata_2014.csv

data-tables/length-weight-age/LWAdata_2015.csv

data-tables/length-weight-age/LWAdata_2016.csv

data-tables/length-weight-age/LWAdata_2017.csv

data-tables/length-weight-age/LWAdata_2018.csv

data-tables/length-weight-age/LWAdata_2019.csv

data-tables/length-weight-age/LWAdata_2020.csv

data-tables/length-weight-age/LWAdata_2021.csv

data-tables/length-weight-age/LWAdata_2022.csv

data-tables/length-weight-age/wtatage_all_samplesize.csv

data-tables/map-data/port-locations.csv

data-tables/map-data/state-locations.csv

data-tables/maturity-ogives.csv

data-tables/maturity-samples.csv

data-tables/maturity-table.csv

data-tables/ovary-samples.csv

data-tables/recruitment-question-responses.csv

data-tables/survey-by-country.csv

data-tables/survey-history.csv

data-tables/survey-weight-at-age.csv

data-tables/us-catch-by-month.csv

data-tables/us-cp-age-proportions.csv

data-tables/us-cp-age-raw.csv

data-tables/us-cp-catch-by-month.csv

data-tables/us-cp-catch-rate-by-month.csv

data-tables/us-ms-age-proportions.csv

data-tables/us-ms-age-raw.csv

data-tables/us-ms-catch-by-month.csv

data-tables/us-ms-catch-rate-by-month.csv

data-tables/us-research-catch-by-month.csv

data-tables/us-sb-age-proportions.csv

data-tables/us-sb-age-raw.csv

data-tables/us-shore-catch-by-month.csv

data-tables/us-ti-catch-by-month.csv

data-tables/us-weight-at-age.csv

data-tables/wtatage-all-samplesize.csv

data/age_bubble_cohorts.rda

data/age_diag_line_color.rda

data/age_diag_line_type.rda

data/age_diag_line_width.rda

data/age_diag_linecolor.rda

data/age_diag_linetype.rda

data/age_diag_linewidth.rda

data/age_fill_color.rda

data/age_fillcolor.rda

data/assess_changes_df.rda

data/assess_changes_fn.rda

data/assess_history_df.rda

data/assess_history_fn.rda

data/assess_history_probs_df.rda

data/assess_history_probs_fn.rda

data/axis_label_color.rda

data/axis_tick_font_size.rda

data/axis_title_font_size.rda

data/b_0.rda

data/b_0_bold_for_latex_table.rda

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data/b_msy.rda

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data/bspr_40.rda

data/bspr_40_10_noit.rda

data/bspr_40_for_latex_table.rda

data/can_ages_lst.rda

data/can_catch_by_year_fn.rda

data/can_depths_rds_fn.rda

data/can_ft_age_df.rda

data/can_ft_age_props_fn.rda

data/can_ft_bottom_depth_df.rda

data/can_ft_bottom_depth_fn.rda

data/can_ft_catch_by_month_df.rda

data/can_ft_catch_by_month_fn.rda

data/can_ft_gear_depth_df.rda

data/can_ft_gear_depth_fn.rda

data/can_ft_num_fish.rda

data/can_jv_age_df.rda

data/can_jv_age_props_fn.rda

data/can_jv_catch_by_month_df.rda

data/can_jv_catch_by_month_fn.rda

data/can_jv_num_fish.rda

data/can_landings_dr.rda

data/can_landings_tac_fn.rda

data/can_major_hake_areas.rda

data/can_raw_ft_age_counts_fn.rda

data/can_raw_ft_age_props_fn.rda

data/can_raw_jv_age_counts_fn.rda

data/can_raw_jv_age_props_fn.rda

data/can_raw_ss_age_counts_fn.rda

data/can_raw_ss_age_props_fn.rda

data/can_sample_data_rds.rda

data/can_sample_data_rds_fn.rda

data/can_sample_dr.rda

data/can_ss_age_df.rda

data/can_ss_age_props_fn.rda

data/can_ss_bottom_depth_df.rda

data/can_ss_bottom_depth_fn.rda

data/can_ss_catch_by_month_df.rda

data/can_ss_catch_by_month_fn.rda

data/can_ss_gear_depth_df.rda

data/can_ss_gear_depth_fn.rda

data/can_ss_num_fish.rda

data/can_waa_fn.rda

data/canada_depth_sql_fn.rda

data/caption_adjustments_fn.rda

data/catch_targets_biomass_fn.rda

data/catch_targets_df.rda

data/comp_report_fn.rda

data/control_fn.rda

data/covar_fn.rda

data/ct.rda

data/ct_levels_catch_tol.rda

data/ct_levels_max_iter.rda

data/ct_levels_path.rda

data/ct_levels_spr_tol.rda

data/data_fn.rda

data/data_new_ssnew_fn.rda

data/data_ssnew_fn.rda

data/data_tables_path.rda

data/default_hr_path.rda

data/derposts_fn.rda

data/doc_path.rda

data/f_35.rda

data/f_40.rda

data/f_40_40_10.rda

data/f_40_40_10_for_latex_table.rda

data/f_40_for_latex_table.rda

data/f_45.rda

data/f_45_40_10.rda

data/f_msy.rda

data/f_spr.rda

data/fishing_rate.rda

data/forecast_descriptions_fn.rda

data/forecast_fn.rda

data/forecast_probs.rda

data/forecasts_path.rda

data/forecasts_prepend.rda

data/freezer_trawlers.rda

data/fspr_35.rda

data/fspr_40.rda

data/fspr_40_10.rda

data/fspr_40_10_for_latex_table.rda

data/fspr_40_10_noit.rda

data/fspr_40_bold.rda

data/fspr_40_bold_for_latex_table.rda

data/fspr_40_for_latex_table.rda

data/fspr_45.rda

data/fspr_50.rda

data/further_tac_details_fn.rda

data/further_tac_df.rda

data/key_posteriors.rda

data/key_posteriors_file.rda

data/key_posteriors_fn.rda

data/key_posteriors_titles.rda

data/kriging_pars_df.rda

data/kriging_pars_fn.rda

data/landings_tac_fn.rda

data/large_cohorts.rda

data/lbs_to_kilos.rda

data/main_alpha.rda

data/main_fill.rda

data/major_tick_length.rda

data/maturity_estimates_df.rda

data/maturity_estimates_fn.rda

data/maturity_ogives_df.rda

data/maturity_samples_df.rda

data/maturity_samples_fn.rda

data/mcmc_path.rda

data/minor_tick_length.rda

data/model_output_log_fn.rda

data/nuisance_posteriors_file.rda

data/nuisance_posteriors_fn.rda

data/object_placement_fn.rda

data/ordered_decision_table_paths.rda

data/out_csv_dir.rda

data/out_csv_path.rda

data/output_permissions.rda

data/ovary_samples_df.rda

data/ovary_samples_fn.rda

data/par_fn.rda

data/parallelism_warning.rda

data/plot_retro_yrs.rda

data/ports_df.rda

data/ports_fn.rda

data/posts_fn.rda

data/probs.rda

data/probs_forecast.rda

data/psv_fn.rda

data/r_0.rda

data/r_0_for_latex_table.rda

data/recruit_dev_start_yr.rda

data/refpt_bo_linecolor.rda

data/refpt_bo_linetype.rda

data/refpt_bo_linewidth.rda

data/refpt_lrp_linecolor.rda

data/refpt_lrp_linetype.rda

data/refpt_lrp_linewidth.rda

data/refpt_usr_linecolor.rda

data/refpt_usr_linetype.rda

data/refpt_usr_linewidth.rda

data/regex-recdev-all.rda

data/regex-recdev-early.rda

data/regex_eml_recdevs.rda

data/regex_extra_mcmc_compreport.rda

data/regex_extra_mcmc_report.rda

data/regex_main_recdevs.rda

data/regex_recdev_all.rda

data/regex_recdev_all_noyrs.rda

data/regex_recdev_early.rda

data/rel_fishing_intensity_for_latex_table.rda

data/report_fn.rda

data/retropectives_path.rda

data/retrospective_yrs.rda

data/retrospectives_path.rda

data/retrospectives_prepend.rda

data/sampling_history_df.rda

data/show_ss_output.rda

data/spr_100_path.rda

data/spr_40.rda

data/sql_path.rda

data/ss_executable.rda

data/ss_input_files.rda

data/sso_path.rda

data/stable_catch_path.rda

data/start_yr.rda

data/start_yr_age_comps.rda

data/starter_fn.rda

data/states_df.rda

data/states_fn.rda

data/surv_yrs.rda

data/survey_by_country_df.rda

data/survey_by_country_fn.rda

data/survey_end_yr.rda

data/survey_history_df.rda

data/survey_history_fn.rda

data/survey_start_yr.rda

data/survey_waa_fn.rda

data/ts_linegap.rda

data/ts_linewidth.rda

data/ts_pointshape.rda

data/ts_pointsize.rda

data/ts_pointstroke.rda

data/ts_refpt_bo_linecolor.rda

data/ts_refpt_bo_linetype.rda

data/ts_refpt_bo_linewidth.rda

data/ts_refpt_lrp_linecolor.rda

data/ts_refpt_lrp_linetype.rda

data/ts_refpt_lrp_linewidth.rda

data/ts_refpt_usr_linecolor.rda

data/ts_refpt_usr_linetype.rda

data/ts_refpt_usr_linewidth.rda

data/ts_ribbon_alpha.rda

data/ts_ribbon_fill.rda

data/ts_ribbon_linetype.rda

data/ts_single_line_color.rda

data/ts_single_model_linecolor.rda

data/ts_single_model_linetype.rda

data/ts_single_model_linewidth.rda

data/ts_single_model_pointcolor.rda

data/ts_single_model_pointshape.rda

data/ts_single_model_pointsize.rda

data/ts_single_model_pointstroke.rda

data/ts_single_model_ribbon_fill.rda

data/ts_single_model_ribbon_linetype.rda

data/unfished_eq_yr.rda

data/us_atsea_bottom_depth_df.rda

data/us_atsea_bottom_depth_fn.rda

data/us_atsea_fishing_depth_df.rda

data/us_atsea_fishing_depth_fn.rda

data/us_cp_age_df.rda

data/us_cp_age_props_fn.rda

data/us_cp_catch_by_month_df.rda

data/us_cp_catch_by_month_fn.rda

data/us_cp_prop_tac.rda

data/us_ms_age_df.rda

data/us_ms_age_props_fn.rda

data/us_ms_catch_by_month_df.rda

data/us_ms_catch_by_month_fn.rda

data/us_ms_prop_tac.rda

data/us_research_catch_by_month_df.rda

data/us_research_catch_by_month_fn.rda

data/us_sb_age_df.rda

data/us_sb_age_props_fn.rda

data/us_ss_age_df.rda

data/us_ss_catch_by_month_df.rda

data/us_ss_catch_by_month_fn.rda

data/us_ss_prop_tac.rda

data/us_ti_ct_by_month_df.rda

data/us_ti_ct_by_month_fn.rda

data/us_waa_fn.rda

data/weight_age_sample_sizes_df.rda

data/weight_age_sample_sizes_fn.rda

data/weight_at_age_df.rda

data/weight_at_age_fn.rda

doc/000-launcher.rmd doc/001-load-packages.rmd doc/002-load-globals.rmd doc/003-load-models.R doc/003-load-models.rmd doc/004-load-project-variables.rmd doc/005-one-page-summary.rmd doc/006-executive-summary.rmd doc/007-introduction.rmd doc/008-data.rmd doc/009-assessment.rmd doc/010-research-needs-loader.rmd doc/010-research-needs/research-needs-extra.rmd doc/010-research-needs/research-needs.rmd doc/011-acknowledgements.rmd doc/012-references.rmd doc/013-tables.rmd doc/014-figures.rmd doc/100-start-appendices.rmd doc/101-appendix-base-mcmc-diagnostics.rmd doc/111-appendix-srg-requests.rmd doc/121-appendix-glossary.rmd doc/131-appendix-fishery-report-canada.rmd doc/132-appendix-fishery-report-us.rmd doc/141-appendix-estimated-parameters.rmd doc/151-appendix-maturity-analysis.rmd doc/999-blank.rmd

doc/_bookdown.yml

doc/bib/refs.bib

doc/caption-adjustments.csv

doc/csl/csas.csl

doc/forecast-descriptions.csv

doc/image-files/2024-srg-response-1-2-a.png

doc/image-files/2024-srg-response-1-2-b.png

doc/image-files/DFO.eps

doc/image-files/Fig_S10_temp_model_sensitivities.png

doc/image-files/Fig_S11_model_comparison.png

doc/image-files/Fig_S12_temp_marginal.png

doc/image-files/Fig_S13_age_marginal.png

doc/image-files/Fig_S3_samplingplatform_age_years.png

doc/image-files/Fig_S4_temp_by_depth.png

doc/image-files/Fig_S5_raw_feb_temp.png

doc/image-files/Fig_S6_temp_weight_effect.png

doc/image-files/Fig_S7_cog_latitude.png

doc/image-files/Fig_S8_year_effects_nocovar.png

doc/image-files/Fig_S9_predicted_maps_byage.png

doc/image-files/NOAA.eps

doc/image-files/age1-survey-map.png

doc/image-files/age2-plus-survey-map.png

doc/image-files/blank.png

doc/image-files/hake-bookdown.xcf

doc/image-files/hake-line-drawing.png

doc/image-files/hake-logos.png

doc/image-files/hake-on-board.eps

doc/image-files/hake-picture.eps

doc/image-files/hake-picture.png

doc/image-files/logo_bookdown.png

doc/image-files/logo_knitr.png

doc/image-files/logo_lualatex.png

doc/image-files/logo_pandoc.png

doc/image-files/logo_rmarkdown.png

doc/image-files/logo_yaml.png

doc/image-files/maturity_spline_doy.png

doc/object-placement.csv

doc/preamble.tex

docker/Dockerfile

docker/Rhistory

docker/Rprofile

docker/build-hake-docker-cached.sh

docker/build-hake-docker-scratch.sh

docker/get-set-owner-group.sh

docker/install_r_packages.R

docker/rstudio-prefs.json

docker/run-hake-docker.sh

docker/ss-texlive/Dockerfile

docker/ss-texlive/clean_admb

docker/ss-texlive/clean_ss3

docker/ss-texlive/install_admb.sh

docker/ss-texlive/install_ss3.sh

docker/ss-texlive/install_texlive.sh

docker/ubuntu-essentials/Dockerfile

gear-arrow-down.png

hake.Rproj

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man/regex_extra_mcmc_report.Rd man/regex_main_recdevs.Rd man/regex_recdev_all.Rd man/regex_recdev_early.Rd man/remove_forecast_outputs.Rd man/render.Rd man/replace_dotted_paths.Rd man/report_fn.Rd man/retropectives_path.Rd man/retrospective_yrs.Rd man/retrospectives_prepend.Rd man/rich_colors_short.Rd man/run_adnuts.Rd man/run_adnuts_timed.Rd man/run_catch_levels_copy_input_files.Rd man/run_ct_levels.Rd man/run_ct_levels_default_hr.Rd man/run_ct_levels_spr_100.Rd man/run_ct_levels_stable_catch.Rd man/run_extra_forecasts.Rd man/run_forecasts.Rd man/run_retrospectives.Rd man/sampling_history_df.Rd man/save_nuts_fits.Rd man/set_ct_levels.Rd man/set_dirs.Rd man/show_ss_output.Rd man/split_prior_info.Rd man/spr_100_path.Rd man/sql_path.Rd man/ss_executable.Rd man/ss_input_files.Rd man/sso_path.Rd man/stable_catch_path.Rd man/start_yr.Rd man/start_yr_age_comps.Rd man/starter_fn.Rd man/states_df.Rd man/stop_quietly.Rd man/surv_yrs.Rd man/survey_end_yr.Rd man/survey_history_df.Rd 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man/ts_ribbon_alpha.Rd man/ts_ribbon_linetype.Rd man/ts_single_model_linecolor.Rd man/ts_single_model_linetype.Rd man/ts_single_model_linewidth.Rd man/ts_single_model_pointcolor.Rd man/ts_single_model_pointshape.Rd man/ts_single_model_pointsize.Rd man/ts_single_model_pointstroke.Rd man/ts_single_model_ribbon_fill.Rd man/ts_single_model_ribbon_linetype.Rd man/unfished_eq_yr.Rd man/update_ss3_ageing_error.Rd man/update_ss3_catch.Rd man/update_ss3_maturity.Rd man/us_atsea_bottom_depth_df.Rd man/us_atsea_fishing_depth_df.Rd man/us_cp_age_df.Rd man/us_cp_age_props_fn.Rd man/us_cp_catch_by_month_df.Rd man/us_cp_prop_tac.Rd man/us_extract_sampling_by_month.Rd man/us_ms_age_df.Rd man/us_ms_age_props_fn.Rd man/us_ms_catch_by_month_df.Rd man/us_ms_prop_tac.Rd man/us_research_catch_by_month_df.Rd man/us_sb_age_props_fn.Rd man/us_ss_age_df.Rd man/us_ss_catch_by_month_df.Rd man/us_ss_prop_tac.Rd man/us_ti_ct_by_month_df.Rd man/utils_update_catch_sums.Rd man/vec2df.Rd man/weight_age_sample_sizes_df.Rd man/weight_at_age_fn.Rd man/yaml_check_margin_format.Rd models/2022/01-version/01-base-models/details.Rmd

models/2022/01-version/01-base-models/details.html

models/2022/01-version/02-bridging-models/details.Rmd

models/2022/01-version/02-bridging-models/details.html

models/2022/01-version/03-sensitivity-models/details.Rmd

models/2022/01-version/03-sensitivity-models/details.html

models/2022/01-version/04-request-models/details.Rmd

models/2022/01-version/04-request-models/details.html

models/2022/01-version/this-version.Rmd

models/2022/01-version/this-version.html

models/2022/this-year.Rmd

models/2022/this-year.html

models/2023/01-version/01-base-models/details.Rmd

models/2023/01-version/01-base-models/details.html

models/2023/01-version/02-bridging-models/details.Rmd

models/2023/01-version/02-bridging-models/details.html

models/2023/01-version/03-sensitivity-models/details.Rmd

models/2023/01-version/03-sensitivity-models/details.html

models/2023/01-version/04-request-models/details.Rmd

models/2023/01-version/04-request-models/details.html

models/2023/01-version/05-test-models/details.Rmd

models/2023/01-version/05-test-models/details.html

models/2023/01-version/this-version.Rmd

models/2023/01-version/this-version.html

models/2023/this-year.Rmd

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models/models.Rmd

models/models.html

models/style.css

sandbox/README.md sandbox/andy/HCR-histogram.R sandbox/andy/hdi-calcs.R

sandbox/andy/hdi-notes.Rnw

sandbox/andy/issue-check-text.txt

sandbox/andy/pacea-save/make-mcmc-recruitment-plot.R sandbox/andy/pacea-save/pacea-save.R

sandbox/chris/hake-ages.sql

sandbox/kelli/speed-test.R

sql/canada-depths.sql

vignettes/.gitignore

vignettes/clean-vignettes.sh

vignettes/path-structure.png

vignettes/process-canadian-catch-for-assessment.Rmd vignettes/process-canadian-samples-for-assessment.Rmd vignettes/process-us-catch-for-assessment.Rmd vignettes/run-docker-container.Rmd vignettes/run-models.Rmd vignettes/set-github-gpg-keys.Rmd vignettes/setup-bridge-models.Rmd vignettes/test-burnin-models.Rmd vignettes/test-num-samples.Rmd vignettes/test.Rmd

pacific-hake/hake-assessment documentation built on July 21, 2024, 8:19 a.m.