Files in jae0/snowcrab

Snow crab assessment suite for aegis* and associated projects.

.gitignore

DESCRIPTION

LICENSE

NAMESPACE

R/CW.interval.male.r R/LDx.core.r R/LDx.r R/ZIMgamma.R R/adjust.depth.for.drift.r R/aggregate_by.R R/aggregate_simulations.R R/aggregated.fish.stats.r R/allometry.snowcrab.r R/biomass.summary.table.r R/bodysize.r R/ca_database_functions.r R/carstm_estimation_runtypes.R R/choose.transition.matrix.r R/clean.surface.area.r R/colour.palettes.r R/compute.proportions.r R/convert.graphics.format.r R/convert.to.vector.r R/convert2factor.r R/cpue.aggregate.r R/create.histograms.yearly.r R/create.projection.summary.r R/cummulative.landings.r R/cw_to_instar.R R/data.quality.check.r R/decibar2depth.r R/decompose.into.sets.r R/delury.leslie.r R/determine.origin.r R/effects.data.export.r R/eggdata.r R/ellipse.2d.r R/empirical.ranges.r R/error.propagate.r R/errorbars.r R/esonarconversion.R R/est.size.at.maturity.r R/estimate.biomass.r R/estimate.number.r R/expand.weights.r R/exploitationrates.r R/export.to.clipboard.r R/export.to.shapefile.r R/extract.solution.r R/extract.summary.data.for.one.variable.r R/fb.r R/fecundity.allometric.r R/fecundity.indirect.r R/feeding_networks_functions.R R/figure.cpue.timeseries.r R/figure.crab.groundfish.survey.r R/figure.effort.timeseries.r R/figure.exploitation.rate.r R/figure.growth.instar.r R/figure.immature.male.r R/figure.immature.skipmoulter.male.r R/figure.interpolated.results.r R/figure.landings.timeseries.r R/figure.mature.CC12.male.r R/figure.mature.CC34.male.r R/figure.mature.CC5.male.r R/figure.observed.size.freq.r R/figure.sizefreq.carapacecondition.R R/figure.timeseries.bycatch.r R/figure.timeseries.errorbars.r R/figure.timeseries.interpolated.r R/figure.timeseries.larvae.r R/figure.timeseries.snowcrab.habitat.r R/figure.timeseries.snowcrab.habitat.temperatures.r R/figure.timeseries.survey.direct.R R/figure.timeseries.survey.r R/figure.timeseries.survey_oneoff.r R/figure.timeseries.surveyindex.fishablebiomass.R R/figure_area_based_extraction_from_carstm.R R/filter.class.r R/filter.durometer.r R/filter.eggPr.r R/filter.independent.variables.r R/filter.mat.r R/filter.prediction.locations.r R/filter.region.r R/filter.season.r R/filter.set.r R/filter.sex.r R/filter.shell.r R/filter.size.r R/filter.stage.fmat.r R/filter.stage.r R/filter.towquality.r R/fishery.model.jags.r R/fishery.stats.by.region.r R/fishery_data.R R/fishery_model.r R/fishery_model_data_inputs.R R/fishing.area.designations.r R/format.crude.odds.r R/get.annual.timeseries.r R/get.cohort.data.r R/get.effects.from.model.r R/get.fishery.stats.by.region.r R/get.hist.data.r R/get.main.effects.r R/get.marked.r R/get.move.r R/get.population.projection.parameters.r R/get.rawdata.historical.r R/get.recaps.r R/get.stepwise.model.results.r R/get.structured.data.r R/graphics.convert.r R/grid.logbook.r R/gridSets.r R/habitat.template.lookup.r R/habitat.usage.r R/hist.legal.r R/histogram_with_kernel.r R/histograms.size.maturity.r R/histograms.size.maturity.single.area.r R/histograms.size.maturity.update.r R/histograms.size.maturity_oneoff.r R/identify_modes.R R/identify_neigbours.R R/inflection.pt.r R/interpolate.missing.xyz.r R/interpolation.db.r R/inverse.logit.r R/isEsonar.r R/jackknifeCPUE.r R/jags.extract.r R/landings.decomposed.r R/load.environment.r R/load.minilog.rawdata.one.file.per.day.r R/load.minilog.rawdata.r R/load.netmind.rawdata.r R/load.seabird.rawdata.r R/logbook.db.r R/logbook.determine.region.r R/logbook.fisheries.stats.merge.r R/logbook.prorate.r R/logistic.display.local.r R/lookup.biomass.vars.r R/lookup.numbers.vars.r R/make.classes.r R/make.evenness.spatial.r R/make.fisheries.ts.r R/make.hist.r R/make.histograms.r R/make.maturity.spatial.r R/make.mortality.r R/makeMap.r R/makePBS.r R/map.basemap.with.cfa.lines.r R/map.cfas.r R/map.fisheries.data.r R/map.larval.distributions.r R/map.logbook.locations.r R/map.maturity.r R/map.movement.r R/map.observer.locations.r R/map.set.information.r R/map.survey.locations.r R/map.temperatures.r R/matrix.form.r R/maturity_region_year.r R/mb.r R/mean.weights.by.category.r R/meanweights_by_arealunit_modelled.R R/minilog.db.r R/minilogDate.r R/net.configuration.r R/netmind.db.r R/netmindDate.r R/no.grid.logbook.r R/nodes2matrix.r R/observer.compute.fisheries.exploitation.r R/observer.data.formats.r R/observer.db.r R/observer.get.counts.by.class.r R/observer.historical.data.concatenate.r R/observer.historical.data.r R/observer.load.rawdata.r R/offset.ageclass.r R/offset.time.r R/ordinate.r R/plot.freq.distribution.prior.posterior.r R/plot.projections.r R/plot_histogram_carapace_width.R R/plot_x__y_density.R R/predict.mass.g.from.CW.mm.r R/predict.maturity.males.r R/predictmaturity.r R/predictweights.r R/prep.maturity.data.r R/projected.exploitation.rate.r R/proportion.cc.r R/proportion.legal.r R/proportion.soft.r R/range.cap.r R/recode.time.maturity.r R/recode.time.r R/region.decompose.r R/regrid.lonlat.r R/remove.na.r R/removeDuplicateswithNA.r R/rename.bio.snowcrab.variables.r R/rename.df.r R/rescale.min.max.r R/seabird.db.r R/seabirdDate.r R/setmerge.r R/setup.lattice.options.r R/sex.ratios.r R/sim.markov.r R/size.at.maturity.r R/size_at_maturity.R R/size_distributions.R R/smooth_data.R R/snowcrab.db.r R/snowcrab.lookup.mapparams.R R/snowcrab.lookupnames.r R/snowcrab.timeseries.db.r R/snowcrab.variablelist.R R/snowcrab_historical_data.R R/snowcrab_landings_db.r R/snowcrab_load_key_results_to_memory.R R/snowcrab_mapping_features.R R/snowcrab_parameters.R R/snowcrab_tacs.R R/subset.biomass.r R/sum.data.r R/tab.4.tex.r R/table.view.r R/table_counts.r R/tagging.example.usage.r R/tapply2.r R/transition.matrices.r R/trimWhiteSpace.r R/tripcode.to.timestamp.r R/ts.collapse.r R/ts.data.r R/ts.landings.and.tacs.r R/ts.plotandsave.r R/unadjusted.odds.r R/variable.recode.r R/zeroInflate.r README.md

inst/julia/Manifest.toml

inst/julia/Project.toml

inst/julia/README.md

inst/julia/logistic_discrete.jl

inst/julia/logistic_discrete_functions.jl

inst/julia/snowcrab_startup.jl

inst/markdown/02.tables.qmd

inst/markdown/03.biomass_index_carstm.md inst/markdown/04.snowcrab_fishery_model_turing.md

inst/markdown/51_bycatch.qmd

inst/markdown/Makefile

inst/markdown/README.md

inst/markdown/feeding_networks_report.qmd

inst/markdown/media/SRR-RS2021-eng.docx

inst/markdown/media/area_map.png

inst/markdown/media/australian_leptomithrax_gaimardii.png

inst/markdown/media/beamer_additional.sty

inst/markdown/media/carstm_prediction_domain.png

inst/markdown/media/columns.tex

inst/markdown/media/csas.csl

inst/markdown/media/custom.css

inst/markdown/media/ecology-letters.csl

inst/markdown/media/harvest_control_rules.png

inst/markdown/media/kingcrab_aggregation.png

inst/markdown/media/maritimes_currents.png

inst/markdown/media/movement.png

inst/markdown/media/movement0.png

inst/markdown/media/nw_atlantic_ocean_currents.jpg

inst/markdown/media/preamble.tex

inst/markdown/media/recycle.png

inst/markdown/media/sar-as2023-eng.docx

inst/markdown/media/snowcrab.bib

inst/markdown/media/snowcrab_cfas.png

inst/markdown/media/snowcrab_image.png

inst/markdown/media/snowcrab_male.png

inst/markdown/media/snowcrab_male_and_female.png

inst/markdown/media/snowcrab_movement_distances.png

inst/markdown/media/snowcrab_movement_rates.png

inst/markdown/media/snowcrab_zoea.png

inst/markdown/media/stmv_concept.png

inst/markdown/media/template.tex

inst/markdown/media/vh_fb.png

inst/markdown/media/vh_i.png

inst/markdown/media/vh_mf.png

inst/markdown/media/vh_mm.png

inst/markdown/media/viable_habitat.png

inst/markdown/media/viable_habitat_depth_temp.png

inst/markdown/media/viable_habitat_posteriors_time.png

inst/markdown/quick_test.rmd inst/markdown/snowcrab_presentation_assessment.rmd inst/markdown/snowcrab_presentation_general_summary.rmd inst/markdown/snowcrab_presentation_methods.rmd inst/markdown/snowcrab_sar.rmd inst/markdown/snowcrab_working_paper.rmd inst/papers/egg.maturation.r inst/papers/paper.alaska.habitat.r inst/requests/4x.interim.figs.2015.r inst/requests/4xpaper.catch.rates.survey.catches.r inst/requests/ben_maturity_extraction.r inst/requests/catchratesbyMLstationsNENS.r inst/requests/cfa4x.early.season.catch.rates.r inst/requests/cfanorth.counts.r inst/requests/extract.temperature.r inst/requests/landings.by.polygon.r inst/requests/nens.landings.premay15.r inst/requests/requests.r inst/requests/save.set.complete.shapefile.r inst/requests/shrimp.R inst/requests/stannsbank.survey.stations.r inst/requests/surveryInterpolation.r inst/requests/vps.tagging.movement.classification.r inst/scripts/01.snowcrab.r inst/scripts/02.figures.r inst/scripts/02.tables.r inst/scripts/03.biomass_index_carstm.r inst/scripts/04.snowcrab_fishery_model_turing.r inst/scripts/11.4X.Advisory.Presentation.r inst/scripts/13.Emera.Tagging.r inst/scripts/13.otn.tagging.r inst/scripts/50_size_distributions.md inst/scripts/93.biomass_index_carstm.r inst/scripts/93.biomass_index_carstm_2022_comparisons.r inst/scripts/93.biomass_index_carstm_2022_variation1.r inst/scripts/93.biomass_index_carstm_2022_variation2.r inst/scripts/93.biomass_index_carstm_2022_variation3.r inst/scripts/93.biomass_index_sizestructured_carstm.r inst/scripts/99.abundance_estimation_stmv.r inst/scripts/99.biomass_index_carstm_paper.r inst/scripts/99.generic_carstm.R inst/scripts/99.machine.learing.R inst/scripts/99.misc_figures_to_be_assessed.r inst/scripts/99.snowcrab.framework.2020.R inst/scripts/99.snowcrab_size_structured.r inst/scripts/99.tables.r inst/scripts/99_data_extraction_jae.R inst/scripts/99_retired_snowcrab_fishery_model_stan.R inst/scripts/README.md

inst/sql/db.marfis/crab2_pro_rated.sql

inst/sql/db.observer/crt_view_crabdetails.sql

inst/sql/db.observer/crt_view_sncrabsets.sql

inst/sql/db.observer/crt_view_sntrawlbycatch.sql

inst/sql/db.observer/observer.bycatches.sql

inst/sql/db.observer/smple_sql.sql

inst/sql/db.snowcrab/cleanup.bash

inst/sql/db.snowcrab/createTables.sql

inst/sql/db.snowcrab/extract.from.oracle.sql

inst/sql/db.snowcrab/test.sql

inst/tex/4x_advisory.tex

inst/tex/NENS PreRap.tex

inst/tex/Older/2015_4x_advisory.tex

inst/tex/Older/2016_4x_advisory.tex

inst/tex/RAP.2018.Assessment.tex

inst/tex/RAP.2018.Fishery Presentation.tex

inst/tex/RAP.Presentation.Assessment.tex

inst/tex/RAP.tex

inst/tex/RapFigures.tex

inst/tex/ReportInterim4X.tex

inst/tex/ResDoc.tex

inst/tex/variablenames.tex

jae0/snowcrab documentation built on Feb. 27, 2024, 2:42 p.m.