Files in LobsterScience/bio.lobster

Lobster Stock Assessment Tools for DFO Maritimes

R/ASFMC_triggers.r R/AlbatrossBigelowConv.r R/BarPlotCLF.r R/BarPlotCLF2.r R/BubblePlotCLF.r R/CAplots.r R/CAplotsMultDataSets.r R/CLF.r R/CPUEModelData.r R/CPUEModelData2.r R/CPUEModelData_vic.r R/CPUEModelPlot.r R/CPUEgam.R R/CPUEmodel.r R/CPUEplot.r R/CarapaceLengthFrequencies.r R/CatchRatePlot.r R/ContLegend.r R/Convert_PBSmapping_into_GIS_shapefiles.R R/ExploitationRatePlots.r R/FSRSCatchRatePlot.r R/FSRSModelData.R R/FSRSclf.r R/FSRSmodel.r R/FSRSmodel3dplot.r R/FadjSeason.r R/Fecundity.r R/FisheryPlot.r R/GroundfishSurveyProcess.r R/ILTS_ITQ_All_Data.r R/ILTS_ITQ_sets.r R/IndicatorplotsMultDataSets.r R/LAFSS.r R/LandAbundPlot.r R/LandPlot.r R/LebrisSoM.r R/Lobster.Bycatch.r R/LobsterLogsProcess.r R/LobsterMap.r R/LobsterOffshoregrid.R R/LobsterSurveyProcess.r R/N2P.r R/NEFSC_sets.r R/Ncolor.r R/PortSamplesProcess.r R/PortSummary.r R/RLibrary.r R/RV_sets.r R/RV_sets41.r R/RV_sets_modelledProps.r R/RV_survey_from_ESEtables.r R/Relief.plots.r R/ReliefPlots.r R/ScallopSurveyProcess.r R/SoMplot.R R/SpatialGamLobsterSurvey.R R/SurveyTowData.r R/TempModel.r R/TempModelData.r R/TempModelPlot.R R/TempModelPredict.R R/abundanceDistributionPlot.r R/addSYEAR.r R/age.back.r R/annualTimeCircle.r R/array_map.R R/assignArea.r R/assignDepth.r R/assignStation.r R/assignSubArea2733.r R/atSeaIndicatorPlots.r R/atSeaLandingsLinker.r R/atSeaWeightings.r R/backFillSeasonDates.r R/biasCorrCPUE.r R/binomialPredict.r R/biomass.logistic.recursion.r R/biomass.plt.R R/biomassPlot.R R/blockedBootstrap.r R/bnamR.r R/buildDatObj.r R/bycatch.db.r R/calcAreaSwept.r R/calcIndexStations.R R/clipboard.r R/clusterStatistics.r R/cohortAnalysis.r R/collapse_list.r R/collectorTemperatureData.r R/compareCLF.r R/compileAbundPresAbs.r R/compileAbundPresAbs_vessel_corr.r R/compileODF.r R/constructCatchComp.r R/contour.gen.r R/convert.dd.dddd.r R/createBathyLines.r R/create_seq_from_column.r R/cv_SpaceTimeFolds.R R/db.setup.r R/decision.r R/delayBUGS.r R/deluryLeslie.r R/deprecated_ScallopSurveyProcess.r R/depricated_calcAreaSwept.r R/derivs.r R/dfo.rv.analysis.r R/dfo.rv.analysis_No_Conversions.r R/dfo.rv.jonah.analysis.r R/dfo.rv.other.analysis.r R/diag.plt.R R/dicusum.r R/esonarconversion.R R/exploit.plt.R R/exploitPlot.R R/figure.bugs.r R/figure.habitat.associations.r R/figure.stratified.analysis.r R/fillNA.r R/fillSubstrate.R R/fillSubstrate_vh.R R/find.bio.gis.r R/findPeaks.r R/findValue.r R/findingCL.r R/fisheryFootprint.r R/fishing.season.r R/fit.plt.R R/fitPlot.R R/fixSensorLatLon.r R/gamDevExp_vars.r R/gamTimeTrends.r R/gam_model_list.r R/genran.r R/getBerried.r R/getDegreeDays.r R/getFccir.r R/getFvec.r R/getG.r R/getGridVar.r R/getGridVar2.r R/getGroMat.r R/getIncr.R R/getM.r R/getSeason.r R/getSimList.r R/getTransMatrix.r R/ggLobsterMap.r R/giniFootprint.r R/glmCIs.r R/gridTrends.r R/groundfish.analysis.r R/groundfish.db.r R/habitat.model.data.r R/hcrPlot.r R/identifyPoints.r R/importShapefile.r R/indicatorAttributesMatrixPlot.r R/interpolation.r R/jackknife.r R/ksmooth.gcv.r R/kurtosis.r R/la.r R/legal.r R/lengthOfSeason.r R/load.environment.r R/lobGridPlot.r R/lobIBM.r R/lobLFAAttr.r R/lobLW.r R/lobSortedOrdination.r R/lobster.db - original.r R/lobster.db.r R/lobsterEquilibriumProduction.r R/loess.gcv.r R/lonlat2planar.r R/lvb.r R/mae.R R/makePBS.r R/mavg.r R/meansize.crude.r R/meansize.direct.r R/merge_lists.R R/mls2fsrs.r R/moltModel.R R/moltModelPlot.R R/movingBootstrap.r R/nefsc.analysis.r R/nefsc.analysis_vh.r R/nefsc.db.r R/ni.r R/offFishingYear.r R/pMat.R R/pPrMolt.R R/parse_smoothers.r R/pbs_2_gis.r R/pcaAnalyseData.r R/pdftopng.r R/peR.r R/plot.dicusum.r R/plot.freq.distribution.prior.posterior.r R/plotSurveyIndex.r R/plot_smooth_sdmtmb.R R/postPlot.R R/post_plt.R R/predGrow.r R/predMolt.r R/project.datadirectory.r R/project.figuredirectory.r R/projections.r R/pseudoR2nls.r R/rDailyTemps.R R/rbindFill.r R/readGearSuccessRaw.r R/recruitment.trap.db.r R/red_green.R R/replacementRatio.relF.r R/rescale0_1.r R/rmed.r R/rmse.R R/robust.regression.r2.r R/scallopSurveyIndex_OriginalUnedited.r R/scallopSurveyIndex_vh.r R/scallop_sets.r R/sdmTMB_cv_nomesh.r R/sdmTMBcv_tntpreds.r R/sdmTMBstripDLLs.r R/setupDepletionData.r R/sf_chull.r R/simBubPlot.r R/simMolt.R R/simSummary.r R/simpleHabitatDescription.r R/skewness.r R/snowcrab_sets.r R/spatial_parameters.r R/stdts.plt.r R/stdtsPlot.r R/stochasticReferencePoints.R R/stripDLLs.r R/suitabilityIndices.r R/surveyBubbles.r R/surveyEfficPlot.r R/surveyHistMap.r R/theme_test_adam.r R/thinMatrix.r R/trace.plt.R R/tracePlot.R R/transitionLobster.r R/uploadClickTouch.r R/uploadOlexData.r R/uploadSensors.r R/uploadTempData.r R/waa.plt.R R/waaPlot.R R/weightedCLF.r R/write.dat.R R/writeDat.R R/zero.na.r README.md inst/Assessments/LFA27-33Assessment/1.IndicatorEstimation.CohortAnalysis.r inst/Assessments/LFA27-33Assessment/1c.IndicatorEstimationandCohortsubsettedByWeeks.r inst/Assessments/LFA27-33Assessment/3.LandingsandAbundance.r inst/Assessments/LFA27-33Assessment/ContextualIndicators.r inst/Assessments/LFA27-33Assessment/ContextualIndicatorsSetup.r inst/Assessments/LFA27-33Assessment/LFA2732Assessment.r inst/Assessments/LFA27-33Assessment/LFA33Assessment.r inst/Assessments/LFA34Assessment/1.DataImport.r inst/Assessments/LFA34Assessment/10.refpoints.r inst/Assessments/LFA34Assessment/2.stratifiedAnalysis.r inst/Assessments/LFA34Assessment/2a.stratifiedAnalysisCommercial.r inst/Assessments/LFA34Assessment/2b.stratifiedAnalysisBerried.r inst/Assessments/LFA34Assessment/2c.stratifiedAnalysisRecruits.r inst/Assessments/LFA34Assessment/3.ginifisheryFootprint.r inst/Assessments/LFA34Assessment/4.RVPredatorIndex.r inst/Assessments/LFA34Assessment/5.temperatureRVConditions.r inst/Assessments/LFA34Assessment/6.landingsEffortRelF.R inst/Assessments/LFA34Assessment/9.plot.scallop.surveys.r inst/Assessments/LFA34Assessment/LFA34Assessment.r inst/Assessments/LFA34Assessment/SpatialSurveyIndexTweedie.R inst/Assessments/LFA35-38Assessment/1.DataImport.r inst/Assessments/LFA35-38Assessment/10.landingsSurveyRelF.r inst/Assessments/LFA35-38Assessment/11.LFA3538Assessment.R inst/Assessments/LFA35-38Assessment/12.refpoints.r inst/Assessments/LFA35-38Assessment/13.CPUEextended.r inst/Assessments/LFA35-38Assessment/14.lobster.sim.36.r inst/Assessments/LFA35-38Assessment/14.lobster.sim.r inst/Assessments/LFA35-38Assessment/16.refpoints.r inst/Assessments/LFA35-38Assessment/17.CPUEextended.r inst/Assessments/LFA35-38Assessment/18ContextualIndicators.R inst/Assessments/LFA35-38Assessment/2.stratifiedAnalysis.r inst/Assessments/LFA35-38Assessment/3.stratifiedAnalysisCommercial.r inst/Assessments/LFA35-38Assessment/4.scallopSurveyIndicators.R inst/Assessments/LFA35-38Assessment/5.stratifiedAnalysisRecruits.r inst/Assessments/LFA35-38Assessment/6.stratifiedAnalysisBerried.r inst/Assessments/LFA35-38Assessment/7.giniFisheryFootprint.r inst/Assessments/LFA35-38Assessment/8.PredatorIndex.r inst/Assessments/LFA35-38Assessment/9.bottomTemperature.r inst/Assessments/LFA35-38Assessment/99.SoM.r inst/Assessments/LFA35-38Assessment/LFA3538Assessment.r inst/Assessments/LFA35-38Assessment/lobster.sim.r inst/Assessments/LFA41Assessment/1.DataImport.r inst/Assessments/LFA41Assessment/10.PredatorIndex.r inst/Assessments/LFA41Assessment/11.environmentalConditions.r inst/Assessments/LFA41Assessment/13.observerLengthFreqs.r inst/Assessments/LFA41Assessment/13.observerLengthFreqsNoSeason.r inst/Assessments/LFA41Assessment/15.indicators.r inst/Assessments/LFA41Assessment/16.refpoints.r inst/Assessments/LFA41Assessment/17.sampleSizesNsets.r inst/Assessments/LFA41Assessment/1a.mapSurveyBubbles.r inst/Assessments/LFA41Assessment/2.stratifiedAnalysis.r inst/Assessments/LFA41Assessment/20.pezzackIndicators.r inst/Assessments/LFA41Assessment/22.sizeFreqsSurvey.r inst/Assessments/LFA41Assessment/23.Update.r inst/Assessments/LFA41Assessment/25.Landings.r inst/Assessments/LFA41Assessment/2a.stratifiedAnalysisLargeFemales.r inst/Assessments/LFA41Assessment/2b.stratifiedSexRatios.r inst/Assessments/LFA41Assessment/2c.stratifiedSizeFrequencies.r inst/Assessments/LFA41Assessment/2d.stratifiedAnalysisCommercial.r inst/Assessments/LFA41Assessment/2e.femalestratifiedSizeFrequencies.r inst/Assessments/LFA41Assessment/2g.stratifiedAnalysisRecruits.r inst/Assessments/LFA41Assessment/3.reproductivePotential.r inst/Assessments/LFA41Assessment/3a.reproductivePotentialRefPoints.r inst/Assessments/LFA41Assessment/4.figureSexRatios.r inst/Assessments/LFA41Assessment/5a.figureLengthFreqs.r inst/Assessments/LFA41Assessment/7.fisheryFootprint.r inst/Assessments/LFA41Assessment/7a.commercialCatchRates.r inst/Assessments/LFA41Assessment/8.seasonal landings.r inst/Assessments/LFA41Assessment/9.habitat.model.r inst/FSAR/LFA35.r inst/FSAR/LFA35vh.r inst/FisherySummaryPlots/stackedBarLandings.r inst/Frameworks/LFA2733Framework/1.IndicatorEstimation.CohortAnalysis.r inst/Frameworks/LFA2733Framework/1a.IndicatorsSensitivitytoWeekofSeasonFSRSCommercial.r inst/Frameworks/LFA2733Framework/1b.AtSeaIndicatorsWeekOfSeasonSensitivityLFA27.r inst/Frameworks/LFA2733Framework/1c.IndicatorEstimationandCohortsubsettedByWeeks.r inst/Frameworks/LFA2733Framework/2.PlotsofIndicators.r inst/Frameworks/LFA2733Framework/3.LandingsandAbundance.r inst/Frameworks/LFA2733Framework/4.CCIR.r inst/Frameworks/LFA2733Framework/4.ReferencePoints.r inst/Frameworks/LFA2733Framework/5.temperature.r inst/Frameworks/LFA2733Framework/6.Indicators.r inst/Frameworks/LFA2733Framework/7.Phaseplots.r inst/Frameworks/LFA2733Framework/8.spModeling.r inst/Frameworks/LFA2733Framework/9.Effort.r inst/Frameworks/LFA2733Framework/CCIRtest.r inst/Frameworks/LFA2733Framework/LFA2733Framework2017.R inst/Frameworks/LFA2733Framework/LFA2733Framework2017vic.R inst/Frameworks/LFA2733Framework/areaPerLFAless100m.R inst/Frameworks/LFA2733Framework/lobster.sim.r inst/Frameworks/LFA2733Framework/miscPlots.r inst/Frameworks/LFA2733Framework/seasonaleggchange.r inst/Frameworks/LFA3438Framework/FisheriesFootprint3438.R inst/Frameworks/LFA3438Framework/LFA34-38Framework/1.DataImport.r inst/Frameworks/LFA3438Framework/LFA34-38Framework/10.PredatorIndex.r inst/Frameworks/LFA3438Framework/LFA34-38Framework/11.environmentalConditions.r inst/Frameworks/LFA3438Framework/LFA34-38Framework/12.landingsEffortRelF.R inst/Frameworks/LFA3438Framework/LFA34-38Framework/16.refpoints.r inst/Frameworks/LFA3438Framework/LFA34-38Framework/17.CPUEextended.r inst/Frameworks/LFA3438Framework/LFA34-38Framework/1a.mapSurveyBubbles.r inst/Frameworks/LFA3438Framework/LFA34-38Framework/1b.surveyEfficiencies.r inst/Frameworks/LFA3438Framework/LFA34-38Framework/2.create_grids.r inst/Frameworks/LFA3438Framework/LFA34-38Framework/2.stratifiedAnalysis.r inst/Frameworks/LFA3438Framework/LFA34-38Framework/2a.stratifiedAnalysisLargeFemales.r inst/Frameworks/LFA3438Framework/LFA34-38Framework/2b.stratifiedSexRatios.r inst/Frameworks/LFA3438Framework/LFA34-38Framework/2c.stratifiedSizeFrequencies.r inst/Frameworks/LFA3438Framework/LFA34-38Framework/2d.stratifiedAnalysisCommercial.r inst/Frameworks/LFA3438Framework/LFA34-38Framework/2e.femalestratifiedSizeFrequencies.r inst/Frameworks/LFA3438Framework/LFA34-38Framework/2g.stratifiedAnalysisBerried.r inst/Frameworks/LFA3438Framework/LFA34-38Framework/2g.stratifiedAnalysisRecruits.r inst/Frameworks/LFA3438Framework/LFA34-38Framework/2h.LFA40StratifiedAnalysis.r inst/Frameworks/LFA3438Framework/LFA34-38Framework/3.CombineSurveyData.r inst/Frameworks/LFA3438Framework/LFA34-38Framework/3.CombineSurveyData_test.r inst/Frameworks/LFA3438Framework/LFA34-38Framework/3.reproductivePotential.r inst/Frameworks/LFA3438Framework/LFA34-38Framework/3a.reproductivePotentialRefPoints.r inst/Frameworks/LFA3438Framework/LFA34-38Framework/4.figureSexRatios.r inst/Frameworks/LFA3438Framework/LFA34-38Framework/5a.figureLengthFreqs.r inst/Frameworks/LFA3438Framework/LFA34-38Framework/6.habitatAssociations.R inst/Frameworks/LFA3438Framework/LFA34-38Framework/7.fisheryFootprint.r inst/Frameworks/LFA3438Framework/LFA34-38Framework/8.DFALFA34.r inst/Frameworks/LFA3438Framework/LFA34-38Framework/9.plot.scallop.surveys.r inst/Frameworks/LFA3438Framework/LFA34-38Framework/ILTSmodelComps.r inst/Frameworks/LFA3438Framework/LFA34-38Framework/LFA3438Framework2018.R inst/Frameworks/LFA3438Framework/LFA34-38Framework/PopulationModel.R inst/Frameworks/LFA3438Framework/LFA34-38Framework/SpatialSurveyIndexModel.R inst/Frameworks/LFA3438Framework/LFA34-38Framework/SpatialSurveyIndexTweedie.R inst/Frameworks/LFA3438Framework/LFA34-38Framework/SurveyIndicators.R inst/Frameworks/LFA3438Framework/LFA34-38Framework/Survey_Collector_Figures.R inst/Frameworks/LFA3438Framework/LFA34-38Framework/lobster.sim.r inst/Frameworks/LFA3438Framework/LFA34-38Framework/maps.r inst/Frameworks/LFA3438Framework/LFA34-38Framework/samplesizes.r inst/Frameworks/LFA3438Framework/LFA34Assessment/1.DataImport.r inst/Frameworks/LFA3438Framework/LFA34Assessment/10.refpoints.r inst/Frameworks/LFA3438Framework/LFA34Assessment/2.stratifiedAnalysis.r inst/Frameworks/LFA3438Framework/LFA34Assessment/2a.stratifiedAnalysisCommercial.r inst/Frameworks/LFA3438Framework/LFA34Assessment/2b.stratifiedAnalysisBerried.r inst/Frameworks/LFA3438Framework/LFA34Assessment/2c.stratifiedAnalysisRecruits.r inst/Frameworks/LFA3438Framework/LFA34Assessment/3.ginifisheryFootprint.r inst/Frameworks/LFA3438Framework/LFA34Assessment/4.RVPredatorIndex.r inst/Frameworks/LFA3438Framework/LFA34Assessment/5.temperatureRVConditions.r inst/Frameworks/LFA3438Framework/LFA34Assessment/6.landingsEffortRelF.R inst/Frameworks/LFA3438Framework/LFA34Assessment/9.plot.scallop.surveys.r inst/Frameworks/LFA3438Framework/LFA34Assessment/LFA34Assessment.r inst/Frameworks/LFA3438Framework/LFA34Assessment/SpatialSurveyIndexTweedie.R inst/Frameworks/LFA3438Framework/LFA35-38Assessment/1.DataImport.r inst/Frameworks/LFA3438Framework/LFA35-38Assessment/10.landingsSurveyRelF.r inst/Frameworks/LFA3438Framework/LFA35-38Assessment/11.LFA3538Assessment.R inst/Frameworks/LFA3438Framework/LFA35-38Assessment/12.refpoints.r inst/Frameworks/LFA3438Framework/LFA35-38Assessment/13.CPUEextended.r inst/Frameworks/LFA3438Framework/LFA35-38Assessment/14.lobster.sim.r inst/Frameworks/LFA3438Framework/LFA35-38Assessment/16.refpoints.r inst/Frameworks/LFA3438Framework/LFA35-38Assessment/17.CPUEextended.r inst/Frameworks/LFA3438Framework/LFA35-38Assessment/2.stratifiedAnalysis.r inst/Frameworks/LFA3438Framework/LFA35-38Assessment/3.stratifiedAnalysisCommercial.r inst/Frameworks/LFA3438Framework/LFA35-38Assessment/4.scallopSurveyIndicators.R inst/Frameworks/LFA3438Framework/LFA35-38Assessment/5.stratifiedAnalysisRecruits.r inst/Frameworks/LFA3438Framework/LFA35-38Assessment/6.stratifiedAnalysisBerried.r inst/Frameworks/LFA3438Framework/LFA35-38Assessment/7.giniFisheryFootprint.r inst/Frameworks/LFA3438Framework/LFA35-38Assessment/8.PredatorIndex.r inst/Frameworks/LFA3438Framework/LFA35-38Assessment/9.bottomTemperature.r inst/Frameworks/LFA3438Framework/LFA35-38Assessment/99.SoM.r inst/Frameworks/LFA3438Framework/LFA35-38Assessment/LFA3538Assessment.r inst/Frameworks/LFA3438Framework/LFA35-38Assessment/lobster.sim.r inst/Frameworks/LFA3438Framework/Landings34-38_2018.R inst/Frameworks/LFA3438Framework/extra/1.CohortAnalysis.r inst/Frameworks/LFA35-38Framework_2024/Dive Survey/Current_diveformatting.R inst/Frameworks/LFA35-38Framework_2024/Dive Survey/OpenData_diveformatting.R inst/Frameworks/LFA35-38Framework_2024/Dive Survey/alldiveSummary.R inst/Frameworks/LFA35-38Framework_2024/Dive Survey/combinedDiveAnalysis.R inst/Frameworks/LFA35-38Framework_2024/Dive Survey/currentdiveAnalysis.R inst/Frameworks/LFA35-38Framework_2024/Dive Survey/historicdiveAnalysis.R inst/Frameworks/LFA35-38Framework_2024/FW summarys and maps/HistoricLandings.R inst/Frameworks/LFA35-38Framework_2024/FW summarys and maps/ILTSAlternateSummary.R inst/Frameworks/LFA35-38Framework_2024/FW summarys and maps/LocationsMaps.R inst/Frameworks/LFA35-38Framework_2024/FW summarys and maps/catchData.R inst/Frameworks/LFA35-38Framework_2024/FW summarys and maps/iltsSummaryTables.R inst/Frameworks/LFA35-38Framework_2024/FW summarys and maps/importData.r inst/Frameworks/LFA35-38Framework_2024/FW summarys and maps/rvSummaryTables.R inst/Frameworks/LFA35-38Framework_2024/FW summarys and maps/seasonstimeline.R inst/Frameworks/LFA35-38Framework_2024/FW summarys and maps/surveyMapBubbles.R inst/Frameworks/LFA35-38Framework_2024/Scallop Survey/PreviousscallopRecruitAbund.R inst/Frameworks/LFA35-38Framework_2024/Scallop Survey/PullUpdatedInshoreScallopSurveyStrataDomain.R inst/Frameworks/LFA35-38Framework_2024/Scallop Survey/firstattempt_scallopSummaryTables.R inst/Frameworks/LFA35-38Framework_2024/Scallop Survey/scallopSurvey_alltowsbycatch.R inst/Frameworks/LFA35-38Framework_2024/Scallop Survey/scalsurSummaryTab.R inst/Frameworks/LFA41Framework/1.DataImport.r inst/Frameworks/LFA41Framework/10.PredatorIndex.r inst/Frameworks/LFA41Framework/11.environmentalConditions.r inst/Frameworks/LFA41Framework/12.NOTUSED.relativeF.r inst/Frameworks/LFA41Framework/13.observerLengthFreqs.r inst/Frameworks/LFA41Framework/14.cusumAnalysis.r inst/Frameworks/LFA41Framework/15.indicators.r inst/Frameworks/LFA41Framework/16.refpoints.r inst/Frameworks/LFA41Framework/17.sampleSizesNsets.r inst/Frameworks/LFA41Framework/1a.mapSurveyBubbles.r inst/Frameworks/LFA41Framework/1b.surveyEfficiencies.r inst/Frameworks/LFA41Framework/2.stratifiedAnalysis.r inst/Frameworks/LFA41Framework/20.pezzackIndicators.r inst/Frameworks/LFA41Framework/21.surplusProductionModelling.r inst/Frameworks/LFA41Framework/21.two.phase.surplusProductionModelling.r inst/Frameworks/LFA41Framework/22.sizeFreqsSurvey.r inst/Frameworks/LFA41Framework/23.SPmodellingKsensitivity.r inst/Frameworks/LFA41Framework/24.RemovalReferenceExploring.r inst/Frameworks/LFA41Framework/25.Landings.r inst/Frameworks/LFA41Framework/2a.stratifiedAnalysisLargeFemales.r inst/Frameworks/LFA41Framework/2b.stratifiedSexRatios.r inst/Frameworks/LFA41Framework/2c.stratifiedSizeFrequencies.r inst/Frameworks/LFA41Framework/2d.stratifiedAnalysisCommercial.r inst/Frameworks/LFA41Framework/2e.femalestratifiedSizeFrequencies.r inst/Frameworks/LFA41Framework/2f.stratifiedAnalysisforCusum.r inst/Frameworks/LFA41Framework/2g.stratifiedAnalysisRecruits.r inst/Frameworks/LFA41Framework/3.reproductivePotential.r inst/Frameworks/LFA41Framework/3a.reproductivePotentialRefPoints.r inst/Frameworks/LFA41Framework/4.figureSexRatios.r inst/Frameworks/LFA41Framework/5a.figureLengthFreqs.r inst/Frameworks/LFA41Framework/6.habitatAssociations.R inst/Frameworks/LFA41Framework/7.fisheryFootprint.r inst/Frameworks/LFA41Framework/7a.commercialCatchRates.r inst/Frameworks/LFA41Framework/8.seasonal landings.r inst/Frameworks/LFA41Framework/9.habitat.model.r inst/Frameworks/LFA41Framework/FinalIndicators/1.DataImport.r inst/Frameworks/LFA41Framework/FinalIndicators/10.PredatorIndex.r inst/Frameworks/LFA41Framework/FinalIndicators/11.environmentalConditions.r inst/Frameworks/LFA41Framework/FinalIndicators/13.observerLengthFreqs.r inst/Frameworks/LFA41Framework/FinalIndicators/13.observerLengthFreqsNoSeason.r inst/Frameworks/LFA41Framework/FinalIndicators/15.indicators.r inst/Frameworks/LFA41Framework/FinalIndicators/16.refpoints.r inst/Frameworks/LFA41Framework/FinalIndicators/17.sampleSizesNsets.r inst/Frameworks/LFA41Framework/FinalIndicators/1a.mapSurveyBubbles.r inst/Frameworks/LFA41Framework/FinalIndicators/1b.surveyEfficiencies.r inst/Frameworks/LFA41Framework/FinalIndicators/2.stratifiedAnalysis.r inst/Frameworks/LFA41Framework/FinalIndicators/20.pezzackIndicators.r inst/Frameworks/LFA41Framework/FinalIndicators/21.surplusProductionModelling.r inst/Frameworks/LFA41Framework/FinalIndicators/21.two.phase.surplusProductionModelling.r inst/Frameworks/LFA41Framework/FinalIndicators/22.sizeFreqsSurvey.r inst/Frameworks/LFA41Framework/FinalIndicators/23.SPmodellingKsensitivity.r inst/Frameworks/LFA41Framework/FinalIndicators/24.RemovalReferenceExploring.r inst/Frameworks/LFA41Framework/FinalIndicators/2a.stratifiedAnalysisLargeFemales.r inst/Frameworks/LFA41Framework/FinalIndicators/2b.stratifiedSexRatios.r inst/Frameworks/LFA41Framework/FinalIndicators/2c.stratifiedSizeFrequencies.r inst/Frameworks/LFA41Framework/FinalIndicators/2d.stratifiedAnalysisCommercial.r inst/Frameworks/LFA41Framework/FinalIndicators/2e.femalestratifiedSizeFrequencies.r inst/Frameworks/LFA41Framework/FinalIndicators/2g.stratifiedAnalysisRecruits.r inst/Frameworks/LFA41Framework/FinalIndicators/2h.LFA40StratifiedAnalysis.r inst/Frameworks/LFA41Framework/FinalIndicators/3.reproductivePotential.r inst/Frameworks/LFA41Framework/FinalIndicators/3a.reproductivePotentialRefPoints.r inst/Frameworks/LFA41Framework/FinalIndicators/4.figureSexRatios.r inst/Frameworks/LFA41Framework/FinalIndicators/5a.figureLengthFreqs.r inst/Frameworks/LFA41Framework/FinalIndicators/6.habitatAssociations.R inst/Frameworks/LFA41Framework/FinalIndicators/7.fisheryFootprint.r inst/Frameworks/LFA41Framework/FinalIndicators/7a.commercialCatchRates.r inst/Frameworks/LFA41Framework/FinalIndicators/8.seasonal landings.r inst/Frameworks/LFA41Framework/FinalIndicators/9.habitat.model.r inst/Frameworks/LFA41Framework/maps.r inst/Frameworks/LFA41Framework/temperaturebathymerge.r inst/IP/#median lengths of bycatch.r inst/IP/ASMFCTriggers3334.r inst/IP/AnalysisOfSlipData.r inst/IP/BNAMlongTS.r inst/IP/BYCATCH_YIHAO/GetData.r inst/IP/CPUEEstimatesUsingMissingLogbooks.r inst/IP/CPUEInfo/CPUE_all_lfas_with_RefLines.r inst/IP/CPUEInfo/CollabYouyuLu/cpue_temp.r inst/IP/CPUEInfo/EstimatingTrapHaulsFromSlipsByWeek.r inst/IP/CPUEInfo/ZonalCPUE.r inst/IP/CPUEInfo/hyperstability_hyperdepletionPlots.r inst/IP/CPUEInfo/unbiasedCPUE.r inst/IP/CPUEInfo/unbiasedCPUE41.r inst/IP/CPUEInfo/unbiasedCPUEJMartin.r inst/IP/CPUEInfo/unbiasedCPUEMFolkins.r inst/IP/CPUEInfo/unbiasedCPUETStevens.r inst/IP/CatchabilityTemp.r inst/IP/CenterOfGravity34.r inst/IP/ClimateChangeModelling/#berried female predict to hadMPI dailies.r inst/IP/ClimateChangeModelling/#comparing nwarc to glorys and observations_bilinearInterp.r inst/IP/ClimateChangeModelling/1.CreateMeshforModelling.r inst/IP/ClimateChangeModelling/ExploringTempModelSurfaces.r inst/IP/ClimateChangeModelling/HSITanaka.r inst/IP/ClimateChangeModelling/ModelBerriedSpatTemp.r inst/IP/ClimateChangeModelling/ModelBerriedSpatTempSpatial+.r inst/IP/ClimateChangeModelling/ModelKgkm2SpatRAWTemp.r inst/IP/ClimateChangeModelling/ModelKgkm2SpatTemp.r inst/IP/ClimateChangeModelling/ModelKgkm2SpatTempFeb102022tw.r inst/IP/ClimateChangeModelling/ModelKgkm2SpatTempJuly102023bino.r inst/IP/ClimateChangeModelling/ModelKgkm2SpatTempMay12023bino.r inst/IP/ClimateChangeModelling/ModellindDataFrame.R inst/IP/ClimateChangeModelling/ModellindDataFrameGlorysOnly.R inst/IP/ClimateChangeModelling/ModellindDataFrameSizeData.R inst/IP/ClimateChangeModelling/ReadandFormatClimateData.r inst/IP/ClimateChangeModelling/SMBClimateData.r inst/IP/ClimateChangeModelling/SurveyDataOnly.r inst/IP/ClimateChangeModelling/TemperaturePredictionSurfaces.r inst/IP/ClimateChangeModelling/Workflow.Rmd inst/IP/ClimateChangeModelling/berried female predict to HAD dailies.r inst/IP/ClimateChangeModelling/berried female predict to MPI dailies.r inst/IP/ClimateChangeModelling/berriedFemalePredictNov2023.r inst/IP/ClimateChangeModelling/berried_female_predict_canMPI_dailies.r inst/IP/ClimateChangeModelling/berried_female_predict_hadMPI_dailies.r inst/IP/ClimateChangeModelling/biasCorrection Glorys Forecasts.r inst/IP/ClimateChangeModelling/climatologyGlorys.r inst/IP/ClimateChangeModelling/comparing_nwarc_glorys_observations.r inst/IP/ClimateChangeModelling/dailyTempsHadCanMPI.r inst/IP/ClimateChangeModelling/glorysClimatologyTemperaturePredictionSurfaces.r inst/IP/ClimateChangeModelling/glorysbyLFASummary.r inst/IP/ClimateChangeModelling/nwarc_decadal_climatologies.r inst/IP/ClimateChangeModelling/validatingClimateModels.r inst/IP/ClimateChangeModelling/workingNWARC.r inst/IP/Climate_change_canada_envt_data.r inst/IP/DEM.r inst/IP/DigitizingOldFigs.r inst/IP/FSRS.load.from.text.r inst/IP/FootprintMapping/1.EstimatingTrapHaulsFromSlipsandSplit2Grids.r inst/IP/FootprintMapping/1.EstimatingTrapHaulsFromSlipsandSplit2GridsWEEKOFSEASON.r inst/IP/FootprintMapping/1a.EstimatingTrapHaulsFromSlipsandSplit2Grids.r inst/IP/FootprintMapping/1b.EstimatingLandingsFromSlipsSplit2Grids.r inst/IP/FootprintMapping/2.VesselCharacteristics.r inst/IP/FootprintMapping/DepletionWithinGrid.r inst/IP/FootprintMapping/DepthofFishingbyLFA.r inst/IP/FootprintMapping/FSRS_temperature_anomaly_footprints.r inst/IP/FootprintMapping/FootPrintsDepthPruned.r inst/IP/FootprintMapping/LFA33-38and41FootPrints.r inst/IP/FootprintMapping/MoreFootprints.r inst/IP/FootprintMapping/OffshorefisheryFootprint.r inst/IP/GLORYS_ESS_Shrimp.r inst/IP/GLORYStemperatureData.R inst/IP/LFA34/SurveyRefPoints2LandingsCPUE.r inst/IP/LFA34/TemperatureTrendsandLandings.r inst/IP/LFA36PilotMessAMC.r inst/IP/LFA36SeasonExtensionRecTraps.r inst/IP/LFA38Historic2Contemporary.r inst/IP/LFA41BycatchOct2022.r inst/IP/LandingsComparisons/LFASpecificAnalyses.r inst/IP/LandingsComparisons/Landcycles.R inst/IP/LandingsComparisons/landingsDFA.r inst/IP/LandingsComparisons/lobsterLandingsTrajectoryDetrendedEAFM.r inst/IP/LandingsComparisons/reshapingBNAMsLobLandings.r inst/IP/LobsterFisheryAttributes/EarningAndEffort.r inst/IP/LobsterFisheryAttributes/Fishing Behaviours.r inst/IP/LobsterFisheryAttributes/LFAAttributes.r inst/IP/LobsterFisheryAttributes/LicenceCharacteristics.r inst/IP/LobsterFisheryAttributes/LicencesByPort.r inst/IP/LobsterFisheryAttributes/benfordsLawLogsSlips.r inst/IP/LobsterFisheryAttributes/changesInVessels.r inst/IP/LobsterFisheryAttributes/distanceToFishingHSuit.r inst/IP/LobsterFisheryAttributes/fuel.r inst/IP/LobsterFisheryAttributes/giniIndex.r inst/IP/LobsterFisheryAttributes/prices_inshore_41.r inst/IP/Lobster_BoF_ILTS_extension.r inst/IP/MultiSpeciesDinning.r inst/IP/NOAAPresentation.r inst/IP/NetConversion.r inst/IP/NetConversionNotDensity.r inst/IP/SProd.r inst/IP/ST.r inst/IP/SWNBOFTechReport/1.EstimatingTrapHaulsFromSlipsandSplit2Grids.r inst/IP/ShellHardness.r inst/IP/SnowCrabTempDBPull.r inst/IP/StandardizedCPUE/0.BuildingDataFrame_SableWindGlorysTemp.r inst/IP/StandardizedCPUE/SableWindGlorysTempGAMLFA27.r inst/IP/StandardizedCPUE/SableWindGlorysTempGAMLFA29.r inst/IP/StandardizedCPUE/SableWindGlorysTempGAMLFA30.r inst/IP/StandardizedCPUE/SableWindGlorysTempGAMLFA31A.r inst/IP/StandardizedCPUE/SableWindGlorysTempGAMLFA33.r inst/IP/StandardizedCPUE/SableWindGlorysTempGAMs.r inst/IP/SurveyAnalysis/DFORV_small_dfo_rv_analysis.r inst/IP/TidesCpue.r inst/IP/atSeaDataexplo.r inst/IP/beaverHarbout.r inst/IP/berriedFemalesLocations.r inst/IP/byCatchLobster.r inst/IP/byCatchLobster33-35.r inst/IP/bycatchCSAS/0.RunMeFirst.r inst/IP/bycatchCSAS/1.DailyunbiasedCPUE.r inst/IP/bycatchCSAS/1a.EstimatingTrapHaulsFromSlipsandSplit2Grids.r inst/IP/bycatchCSAS/1b.EstimatingLandingsFromSlipsSplit2Grids.r inst/IP/bycatchCSAS/3.DescriptiveBycatch.r inst/IP/bycatchCSAS/3a.ComparisonOfCPUESamplesToLogs.r inst/IP/bycatchCSAS/3b.SampleCPUE2FisheryCPUE.r inst/IP/bycatchCSAS/4.CreatingDataFrameForModelling.r inst/IP/bycatchCSAS/5.CreateMesh_DataforModellingLFA27.r inst/IP/bycatchCSAS/5.CreateMesh_DataforModellingLFA31A31B.r inst/IP/bycatchCSAS/5.CreateMesh_DataforModellingLFA33-35.r inst/IP/bycatchCSAS/9.EffortFootPrintMaps.r inst/IP/bycatchCSAS/9.LandingPredFootPrintMaps.r inst/IP/bycatchCSAS/Cod/4b.DesignbasedestimatesofCodCatch.R inst/IP/bycatchCSAS/Cod/MapsOfResidualsCodwithinGrid31ab.r inst/IP/bycatchCSAS/Cod/MapsOfResidualsCunnerwithinGrid31ab.r inst/IP/bycatchCSAS/Cod/MapsOfResidualswithinCodGrid27.r inst/IP/bycatchCSAS/Cod/MapsOfResidualswithinGridCod.r inst/IP/bycatchCSAS/Cod/sdmTMBCod27.r inst/IP/bycatchCSAS/Cod/sdmTMBCod31A31B.r inst/IP/bycatchCSAS/Cod/sdmTMBCod33-35.r inst/IP/bycatchCSAS/Cod/sdmTMBCodMM33-35.r inst/IP/bycatchCSAS/Cod/sdmTMBcodMM27.r inst/IP/bycatchCSAS/Cod/sdmTMBcodMM31ab.r inst/IP/bycatchCSAS/Cunner/4c.DesignbasedestimatesofCunnerCatch.R inst/IP/bycatchCSAS/Cunner/MapsOfResidualswithinCunnerGrid27.r inst/IP/bycatchCSAS/Cunner/MapsOfResidualswithinCunnerGrid31ab.r inst/IP/bycatchCSAS/Cunner/sdmTMBCunner27.r inst/IP/bycatchCSAS/Cunner/sdmTMBCunner31A31B.r inst/IP/bycatchCSAS/Cunner/sdmTMBcunnerMM27.r inst/IP/bycatchCSAS/Cunner/sdmTMBcunnerMM31ab.r inst/IP/bycatchCSAS/Cusk/4d.DesignbasedestimatesofCuskCatch.R inst/IP/bycatchCSAS/Cusk/sdmTMBCusk.r inst/IP/bycatchCSAS/Cusk/sdmTMBCuskHurdle.r inst/IP/bycatchCSAS/Cusk/sdmTMBCuskMM.r inst/IP/bycatchCSAS/Extras.DepthDistributionWithinGrids.r inst/IP/bycatchCSAS/JonahCrab/4e.DesignbasedestimatesofJonahCatch.R inst/IP/bycatchCSAS/JonahCrab/MapsOfResidualsJonahwithinGrid31ab.r inst/IP/bycatchCSAS/JonahCrab/MapsOfResidualswithinGridJonah.r inst/IP/bycatchCSAS/JonahCrab/sdmTMBJonahHurdle33-35.r inst/IP/bycatchCSAS/JonahCrab/sdmTMBJonahHurdleMM33-35.r inst/IP/bycatchCSAS/JonahCrab/sdmTMBJonahHurdleRetained.r inst/IP/bycatchCSAS/JonahCrab/sdmTMBJonahHurdleRetainedMM33-35.r inst/IP/bycatchCSAS/JonahCrab/sdmTMBjonah31A31B.r inst/IP/bycatchCSAS/JonahCrab/sdmTMBjonahMM27.r inst/IP/bycatchCSAS/JonahCrab/sdmTMBjonahMM31ab.r inst/IP/bycatchCSAS/Lobster/4a.DesignbasedestimatesLobsterCatch.r inst/IP/bycatchCSAS/Lobster/MapsOfResidualswithinGrid.r inst/IP/bycatchCSAS/Lobster/MapsOfResidualswithinGrid27.r inst/IP/bycatchCSAS/Lobster/MapsOfResidualswithinGrid31ab.r inst/IP/bycatchCSAS/Lobster/sdmTMBLobster27.r inst/IP/bycatchCSAS/Lobster/sdmTMBLobster31A31B.r inst/IP/bycatchCSAS/Lobster/sdmTMBLobster33-35.r inst/IP/bycatchCSAS/Lobster/sdmTMBLobsterMM27.r inst/IP/bycatchCSAS/Lobster/sdmTMBLobsterMM31ab.r inst/IP/bycatchCSAS/Lobster/sdmTMBLobsterMM33-35.r inst/IP/bycatchCSAS/notUsed/2.DFAFishingEffort.r inst/IP/bycatchCSAS/notUsed/4.ModellingLobster.r inst/IP/bycatchCSAS/notUsed/5.ModellingCodBycatch.r inst/IP/bycatchCSAS/notUsed/6.ConnectingPolygons.r inst/IP/bycatchCSAS/notUsed/OLDCod_Bycatch_GAM_GMRF2008on.R inst/IP/bycatchCSAS/notUsed/TestingDiffCoastlines.R inst/IP/bycatchCSAS/notUsed/setUpsdmTMB.r inst/IP/bycatchCSAS/testingCVsdmTMB.r inst/IP/bycatchISDB.r inst/IP/catchability/TCAI.r inst/IP/catchability/TempCatch.r inst/IP/catchability/publishedCatchabilityWithTempData.r inst/IP/ccLFA36.r inst/IP/comparativefishingGroundfishSimpleComps.R inst/IP/comparingLogbooks_Slips.r inst/IP/comparisonOfDaysFishedAcrossYears.r inst/IP/depletionEstimates.r inst/IP/distributionOfLobsterCatch_scallopSurvey.r inst/IP/ganttChart.r inst/IP/grandmanantrapstudy.r inst/IP/landingsDFA.r inst/IP/larval_tows.r inst/IP/loadTIFsAndDecreaseResolution.r inst/IP/lobsterLandingsTrajectoryDetrendedEAFM.r inst/IP/logs_by_port.r inst/IP/maturityXTemp.r inst/IP/maturitymodelling.r inst/IP/mergingLFAPolys.r inst/IP/offshoreLandings2Obs.r inst/IP/ratesOfChangeCPUE.r inst/IP/reshapingBNAMs.r inst/IP/reshapingBNAMsLobLandings.r inst/IP/reshapingBNAMsShrimp.r inst/IP/reshapingBNAMsStAMPA.r inst/IP/scallopAndLobsterTows.r inst/IP/seasonalCatchRatesCRIS.r inst/IP/sexRatioSurveyFishery.r inst/IP/shrimpDFA.r inst/IP/soaktimeFromLogs.r inst/IP/tradeOffLandingsSeasonLength.r inst/IP/tradeOffLandingsSeasonLengthLFA38.r inst/IP/unbiasedCPUE.r inst/IP/windData.r inst/OldPotentiallyDepricatedCode/1.ImportData.R inst/OldPotentiallyDepricatedCode/2.SummarizeData.R inst/OldPotentiallyDepricatedCode/3.SurveyDesignScript.r inst/OldPotentiallyDepricatedCode/4.DelayDifferenceModel.r inst/OldPotentiallyDepricatedCode/5.ILTSMarportSummary.r inst/OldPotentiallyDepricatedCode/6.stratified.analysis.r inst/OldPotentiallyDepricatedCode/7.Change.point.analysis.r inst/OldPotentiallyDepricatedCode/8.jonahcrab.stratified.analysis.r inst/OldPotentiallyDepricatedCode/9.CCIR.r inst/OldPotentiallyDepricatedCode/CPUESpatialTemporalBOF.R inst/OldPotentiallyDepricatedCode/CanUSlandingsComps.r inst/OldPotentiallyDepricatedCode/DataSummary.r inst/OldPotentiallyDepricatedCode/MiscPlotting.r inst/OldPotentiallyDepricatedCode/RVsurvey.stratified.analysis.r inst/OldPotentiallyDepricatedCode/RebuildandDocument.r inst/OldPotentiallyDepricatedCode/VMSplots.r inst/OldPotentiallyDepricatedCode/collectorData.r inst/OldPotentiallyDepricatedCode/initialise.local.environment.r inst/OldPotentiallyDepricatedCode/larval.r inst/OldPotentiallyDepricatedCode/tagging.R inst/OldPotentiallyDepricatedCode/temperature.R inst/Projects/At Sea Catch Composition/At Sea Catch Composition.r inst/Projects/Bait/baitDataForWyeth.r inst/Projects/Collectors/collectorData.r inst/Projects/Dive Survey/Current_diveformatting.R inst/Projects/Dive Survey/OpenData_diveformatting.R inst/Projects/Dive Survey/alldiveSummary.R inst/Projects/Dive Survey/combinedDiveAnalysis.R inst/Projects/Dive Survey/currentdiveAnalysis.R inst/Projects/Dive Survey/historicdiveAnalysis.R inst/Projects/FSRS/DataChecks.R inst/Projects/FSRS/FSRS.DatacheckVH.r inst/Projects/FSRS/FSRS.DatacheckVH2016.r inst/Projects/FSRS/FSRSParticipants.R inst/Projects/FSRS/FSRScpue.r inst/Projects/FlaggCove/flaggCove.R inst/Projects/ILTSSurvey/BoFSurveyDesign.r inst/Projects/ILTSSurvey/BoFSurveyDesign38.r inst/Projects/ILTSSurvey/Calculating Distnaces from Senors.r inst/Projects/ILTSSurvey/CombiningSurveys/CombiningRV_ILTS.r inst/Projects/ILTSSurvey/CombiningSurveys/ILTS_only_new.r inst/Projects/ILTSSurvey/CombiningSurveys/ModelKgkm2SpatTempMay12023bino.r inst/Projects/ILTSSurvey/CombiningSurveys/ModelKgkm2SpatTempOct2023FineMesh.r inst/Projects/ILTSSurvey/CombiningSurveys/SpatialSurveyIndexTweedie.R inst/Projects/ILTSSurvey/ComparativeFishingAnalysis/BBModel/test_Adam_lobster.R inst/Projects/ILTSSurvey/ComparativeFishingAnalysis/CalculatingMensurationComparative.r inst/Projects/ILTSSurvey/ComparativeFishingAnalysis/Fall2019BoFComp.r inst/Projects/ILTSSurvey/ComparativeFishingAnalysis/NetConversion.r inst/Projects/ILTSSurvey/ComparativeFishingAnalysis/NetConversionNotDensity.r inst/Projects/ILTSSurvey/ComparativeFishingAnalysis/NetConversionUpdate2023-removingMensuration.r inst/Projects/ILTSSurvey/ComparativeFishingAnalysis/NetConversionUpdate2023.r inst/Projects/ILTSSurvey/ComparativeFishingAnalysis/NetConversionUpdate2024Cod.r inst/Projects/ILTSSurvey/ComparativeFishingAnalysis/NetConversionUpdate2024JonahCrab.r inst/Projects/ILTSSurvey/ComparativeFishingAnalysis/SurveyTechReport.r inst/Projects/ILTSSurvey/ComparativeFishingAnalysis/winterFlounder.r inst/Projects/ILTSSurvey/GroundFishPlots.r inst/Projects/ILTSSurvey/ILTSMarportSummary.r inst/Projects/ILTSSurvey/ISDBUpload/Build_Loader_File.r inst/Projects/ILTSSurvey/LFA38SurveyDesign.r inst/Projects/ILTSSurvey/MoltStages.r inst/Projects/ILTSSurvey/SurveyDesign.R inst/Projects/ILTSSurvey/SurveyTechReport.r inst/Projects/ILTSSurvey/comparingTouchdownAndWInch.r inst/Projects/ILTSSurvey/esonarconversion.R inst/Projects/ILTSSurvey/esonarconversionScript.R inst/Projects/ILTSSurvey/surveyDataPlots.r inst/Projects/Maturity/Mapping_byproject.R inst/Projects/Maturity/Maps_Locations.r inst/Projects/Maturity/Maps_Locations_VH.r inst/Projects/Maturity/Other Mat scripts/BoFMaturityRecap.r inst/Projects/Maturity/Other Mat scripts/maturityCurvesIncMLS.r inst/Projects/Maturity/Other Mat scripts/maturitymodelling.r inst/Projects/Maturity/Other Mat scripts/ogiveFromBerried.r inst/Projects/Maturity/SOM TechReport/LengthFreq_Silva.R inst/Projects/Maturity/SOM TechReport/Maturity_GCIFA.R inst/Projects/Maturity/SOM TechReport/Maturity_RangesLFA.R inst/Projects/Maturity/SOM TechReport/New_ogives.R inst/Projects/Maturity/SOM TechReport/Past_ogives.R inst/Projects/Maturity/SOM TechReport/maturity08_11.R inst/Projects/Maturity/SOM TechReport/maturity22_23.r inst/Projects/Maturity/SOM TechReport/maturity_GCIFA22-24.r inst/Projects/Maturity/SOM TechReport/maturitymodelling_draft.r inst/Projects/Maturity/SOM TechReport/percentchange_mat.R inst/Projects/Maturity/SOM TechReport/qualityCheck.R inst/Projects/NonLobsterRelated/comparativefishingGroundfishSimpleComps.R inst/Projects/ObserverCoverage41/mapObs41.R inst/Projects/ObserverCoverage41/observerCoverageMonitoring.R inst/Projects/OtherSurveys/DMNR/SurveyScripts.r inst/Projects/OtherSurveys/ScallopSurveyConversion.r inst/Projects/PopModel/1.StartUp.r inst/Projects/PopModel/2.StratifiedSurveys.r inst/Projects/PopModel/2a.StratifiedSurveysBySex.r inst/Projects/PopModel/3.ModelledSurvey.r inst/Projects/PopModel/3.ModelledSurveyBySex.r inst/Projects/PopModel/4.Landings.r inst/Projects/PopModel/5.FSRS.r inst/Projects/PopModel/6.EnvironmentalIndices.r inst/Projects/PopModel/7.FemaleProps.r inst/Projects/PopModel/extraStuff.r inst/Projects/RVCalibration/script.r inst/Projects/Scallop Survey/PreviousscallopRecruitAbund.R inst/Projects/Scallop Survey/PullUpdatedInshoreScallopSurveyStrataDomain.R inst/Projects/Scallop Survey/firstattempt_scallopSummaryTables.R inst/Projects/Scallop Survey/scallopSurvey_alltowsbycatch.R inst/Projects/Scallop Survey/scalsurSummaryTab.R inst/Projects/StPetersBay/SPB vs 29.r inst/Projects/Tagging/Lob.Tag.Master.R inst/Projects/TechReport2023/1a.mapSurveyBubbles.r inst/Projects/Transects/transects2018.R inst/Projects/VMS/ggVMSplots.r inst/Projects/Vent/Vent.Report.Rmd inst/Projects/Vent/markdown_examples_amc/1.RunScript.r inst/Projects/Vent/markdown_examples_amc/BycatchTripValidation.Rmd inst/Projects/Vent/vent.study.analysis.r inst/Projects/Vic Map and Figs/1.EstimatingTrapHaulsFromSlipsandSplit2Grids_vh.r inst/Projects/Vic Map and Figs/ConvertkmzR.R inst/Projects/Vic Map and Figs/FootPrintsDepthPruned_vh.r inst/Projects/Vic Map and Figs/LFA33-38FootPrints_VH.r inst/Projects/Vic Map and Figs/LFA33-38and41FootPrints_vh.r inst/Projects/byCatchAnalyses/#jake bycatch code.r inst/Projects/byCatchAnalyses/#median lengths of bycatch.r inst/Projects/byCatchAnalyses/Cod_Bycatch_GAM_GMRF.R inst/Projects/byCatchAnalyses/Cod_Bycatch_GAM_GMRF2008on.R inst/Projects/byCatchAnalyses/Cod_Bycatch_GAM_Script.R inst/Projects/byCatchAnalyses/Cod_Bycatch_GAM_Scriptamc.R inst/Projects/byCatchAnalyses/LFA41.Bycatch.observer.data.V5.2016.r inst/Projects/byCatchAnalyses/SoakTime/ST.r inst/Projects/byCatchAnalyses/SoakTime/SoakTimeCompilation.r inst/Projects/byCatchAnalyses/Vic Bycatch/CheckLoadedTrips.R inst/Projects/byCatchAnalyses/bycatchDataForJake.r inst/Projects/byCatchAnalyses/bycatchISDB.r inst/Projects/byCatchAnalyses/bycatchPresentationFeb2018.r inst/Requests/AquacultureSiting/SMB2023.r inst/Requests/Asselin_locationData.r inst/Requests/BZ.LengthWeight.R inst/Requests/CPUEbyWOSPanelPlot.r inst/Requests/CPUEforRyan.r inst/Requests/ComparisonOfWeightSampling.r inst/Requests/EasternShoreIslands.r inst/Requests/FSRS.LengthWeight.R inst/Requests/FarmersLedge.r inst/Requests/Gord.lfa29.FirstWeek.r inst/Requests/LFA 27 Season Shift/LFA27.Season.Shift.2022.r inst/Requests/LFA 41 Monitoring/FishingActivity.R inst/Requests/LFA27.4percentcutoff.r inst/Requests/LFA36SeasonExtension/LFA36SeasonExtensionRecTraps.r inst/Requests/LFA37.r inst/Requests/LFA37CumEffortbyGrid.r inst/Requests/LFA40/13.observer.r inst/Requests/LFA40/2.stratifiedAnalysis.r inst/Requests/LFA40/2b.stratifiedSexRatios.r inst/Requests/LFA40/2c.stratifiedSizeFrequencies.r inst/Requests/LFA41spatial.r inst/Requests/Liverpool Bay Aquaculture.r inst/Requests/N_Lobster_per_trap_LFA34_Feb_2024.r inst/Requests/ProportionLandings82_to86.r inst/Requests/Roseway.NARW.Closure.r inst/Requests/SMB2020.r inst/Requests/SMB2022.r inst/Requests/SMB2024ILTS.r inst/Requests/ShellDisease.r inst/Requests/SurveyDataLydiaUNB.r inst/Requests/TaggingRecaptureSurvivalExample.r inst/Requests/Wycogomagh Bay Aquaculture.r inst/Requests/all.lfas.cpue.mrlac.r inst/Requests/bays.r inst/Requests/dataForNick.r inst/Requests/fsrs.wind.extraction.r inst/Requests/lengthWeight.R inst/Requests/logSoakTimes.r inst/Requests/offshoreLandings2Obs.r inst/Requests/portmouton.r inst/Requests/scofo.r inst/Requests/slot vs vnotch.2021.r inst/Requests/snow.r inst/Requests/surveyStations.r 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