Files in natoyaj/TestPackage
IBTSspatial

DESCRIPTION
IBTSindices.Rproj
NAMESPACE
Papers/manuscript/IBTSpaper.pdf
Papers/manuscript/IBTSpaper.tex
Papers/manuscript/figures/ALKdatrasQ1year2018RFA1.jpeg
Papers/manuscript/figures/ALKhaulQ1year2018RFA1.jpeg
Papers/manuscript/figures/ALKmodelQ1year2018RFA1HaulWithMostObservations.jpeg
Papers/manuscript/figures/MSEcod2018.jpeg
Papers/manuscript/figures/MSEsaithe2018.jpeg
Papers/manuscript/figures/RSEcod2018.jpeg
Papers/manuscript/figures/RSEsaithe2018.jpeg
Papers/manuscript/figures/cod2018Q1BiasCorr.jpeg
Papers/manuscript/figures/mesh.jpeg
Papers/manuscript/figures/removalCod.jpeg
Papers/manuscript/figures/removalSaithe.jpeg
Papers/manuscript/figures/saithe2017Q3BiasCorr.jpeg
Papers/manuscript/figures/saithe2017Q3DATRASStratifedBiasCorr.jpeg
Papers/manuscript/figures/spatialALKQ1year2018RFA9Age1.jpeg
Papers/manuscript/figures/spatialALKQ1year2018RFA9Age2.jpeg
Papers/manuscript/figures/surveyarea.esp
Papers/manuscript/figures/surveyarea.pdf
Papers/manuscript/figuresNotUsed/cod2017Q3BiasCorr.jpeg
Papers/manuscript/figuresNotUsed/cod2017Q3BiasCorr.pdf
Papers/manuscript/figuresNotUsed/cod2017Q3BootstrapProcedures.jpeg
Papers/manuscript/figuresNotUsed/cod2017Q3Percentile.jpeg
Papers/manuscript/figuresNotUsed/cod2017Q3table.csv
Papers/manuscript/figuresNotUsed/cod2017Q3table.xlsx
Papers/manuscript/figuresNotUsed/cod2018Q1ReducedData.jpeg
Papers/manuscript/figuresNotUsed/codQ12015Hauls.jpeg
Papers/manuscript/figuresNotUsed/codQ12015Hauls10cm.jpeg
Papers/manuscript/figuresNotUsed/codQ12015Hauls20cm.jpeg
Papers/manuscript/figuresNotUsed/codQ12015Hauls5cm.jpeg
Papers/manuscript/figuresNotUsed/icesroundfishmap.JPG
Papers/manuscript/figuresNotUsed/recWeightings.JPG
Papers/manuscript/figuresNotUsed/saithe2017Q3Percentile.jpeg
Papers/manuscript/figuresNotUsed/saithe2017Q3ReducedData.jpeg
Papers/manuscript/figuresNotUsed/saithe2018Q1BiasCorr.jpeg
Papers/manuscript/figuresNotUsed/saitheQ12015Hauls.jpeg
Papers/manuscript/figuresNotUsed/saitheQ12015Hauls10cm.jpeg
Papers/manuscript/figuresNotUsed/saitheQ12015Hauls20cm.jpeg
Papers/manuscript/figuresNotUsed/saitheQ12015Hauls5cm.jpeg
Papers/manuscript/figuresNotUsed/saitheQ32015Hauls.jpeg
Papers/manuscript/figuresNotUsed/saitheQ32015Hauls5cm.jpeg
Papers/manuscript/ibtsBib.bib
Papers/manuscript/results/mean.10cm.rda
Papers/manuscript/results/mean.1cm.rda
Papers/manuscript/results/mean.2cm.rda
Papers/manuscript/results/mean.3cm.rda
Papers/manuscript/results/mean.4cm.rda
Papers/manuscript/results/mean.5cm.rda
Papers/manuscript/results/mean.5cm500.rda
Papers/manuscript/results/mean.7cm.rda
Papers/manuscript/results/mean17.1cm.rda
Papers/manuscript/results/mean17.2cm.rda
Papers/manuscript/results/mean17.3cm.rda
Papers/manuscript/results/mean17.5cm.rda
Papers/manuscript/results/mean17.7cm.rda
Papers/manuscript/results/mean18.4cm.rda
Papers/manuscript/results/runOlav/RemovalCodDl1year2018Q1nSim1000haulBased
Papers/manuscript/results/runOlav/RemovalCodDl2year2018Q1nSim1000haulBased
Papers/manuscript/results/runOlav/RemovalCodDl3year2018Q1nSim1000haulBased
Papers/manuscript/results/runOlav/RemovalCodDl3year2018Q1nSim1000modelBased
Papers/manuscript/results/runOlav/RemovalCodDl4year2018Q1nSim1000haulBased
Papers/manuscript/results/runOlav/RemovalCodDl4year2018Q1nSim1000modelBased
Papers/manuscript/results/runOlav/RemovalCodDl5year2018Q1nSim1000haulBased
Papers/manuscript/results/runOlav/RemovalSaitheDl1year2017Q3nSim1000haulBased
Papers/manuscript/results/runOlav/RemovalSaitheDl2year2017Q3nSim1000haulBased
Papers/manuscript/results/runOlav/RemovalSaitheDl3year2017Q3nSim1000haulBased
Papers/manuscript/results/runOlav/RemovalSaitheDl4year2017Q3nSim1000haulBased
Papers/manuscript/results/runOlav/RemovalSaitheDl5year2017Q3nSim1000haulBased
Papers/manuscript/results/runOlav/Saithe2017Q3n1000datras
Papers/manuscript/results/runOlav/Saithe2017Q3n1000haulBased
Papers/manuscript/results/runOlav/Saithe2017Q3n1000modelBased
Papers/manuscript/results/runOlav/cod2018Q1n1000datras
Papers/manuscript/results/runOlav/cod2018Q1n1000haulBased
Papers/manuscript/results/runOlav/cod2018Q1n1000modelBased
Papers/papers/A proposal for a consistent use of the NS-IBTS data.pdf Papers/papers/ASC2018abstractComments.pdf Papers/papers/Advanced statistics - Bootstrapping Haukoos 2005.pdf
Papers/papers/An analysis of the North Sea International Bottom Trawl Survey-JourdainIMR.docx
Papers/papers/Baudron-2014-Adverse consequences.pdf Papers/papers/Bias in using an ALK to estimate Age frequency.pdf Papers/papers/Casper W Berg- Estimaitng abundance and biomass.pdf Papers/papers/Casper W Berg- Evaluation of alternative age-based methods.pdf Papers/papers/Casper W Berg- Spatial age-length key modelling using continuation ratio logits.pdf
Papers/papers/Categorical Analysis AGRESTI 2005.PDF
Papers/papers/Combined-ratio product estimator of finite population mean.pdf Papers/papers/Effects of measurement errors Walters and Ludwig 1981.pdf Papers/papers/Efficient statistical estimators (Aanes and Vølstad).pdf Papers/papers/Efficient statistical estimators.pdf Papers/papers/Estimation of Effective sample size.pdf Papers/papers/Evaluation of ALK sample sizes.pdf Papers/papers/Flexible mixture modeling via the multivariate t distribution with the Box-Cox transformation- an alternative to the skew-t distribution.pdf Papers/papers/ICES Advice on fishing opportunities, catch, and effort Greater North Sea and Celtic Seas ecoregions.pdf Papers/papers/Indices_Calculation_Steps_IBTS.pdf Papers/papers/Length-based methods in Fisheries D Pauly.pdf Papers/papers/Mackerel paper (vølstad et al).pdf Papers/papers/Mackerel paper.pdf Papers/papers/Measurement Errors and Uncertainty in Parameter Estimates Ludwig and Walter 1981.pdf Papers/papers/Multivariate Normal Distribution Important Chapter 4.pdf Papers/papers/Multivariate-Non-normal distribtuions.pdf Papers/papers/NygardskoleUke7-14,2018.pdf Papers/papers/Optimum allocation for estimating age composition Lai.pdf Papers/papers/Pennington and Volstad 1994 Intra-haul correlation.pdf Papers/papers/Predicting an ordinal outcome -Mark Lunt.pdf Papers/papers/Ratio Estimation with a Stratified SRS.pdf Papers/papers/Ratio Estimators in Stratified Random Sampling C.Kafilar et al 2003.pdf Papers/papers/Ratio estimation with Stratified Random Sampling.pdf Papers/papers/Report of the Benchmark Workshop on North Sea Stocks (WKNSEA) wknsea_2016- 14-16 March 2016.pdf Papers/papers/Resampling variance estimation for complex survey data -Kolenikov 2010.pdf Papers/papers/Resampling variance estimation for complex survey data-Stanislav 2010.pdf Papers/papers/SISP 10 - Manual for the International Bottom Trawl Surveys - Revision IX.pdf Papers/papers/Species Composition, Biomass of DF of the North sea.pdf Papers/papers/Statistical Assessment of ALK Kimura 1977.pdf Papers/papers/Statistics in Practice, Practical Methods for Design and Analysis of Complex Survey.pdf Papers/papers/The Nonexistence of Certain Statistical Procedures in Nonparametric Problems Bahadur 1956.pdf Papers/papers/Three bootstrap methods.pdf Papers/papers/Tranformation types -How to obtain nasty standard errors.pdf Papers/papers/WGNSSK report 2016-Report of the Working Group on the Assessment of Demersal Stocks in the North Sea and Skagerrak (WGNSSK) .pdf Papers/papers/What is intracluster correlation.pdf
Papers/papers/alk paper David hirst.doc
Papers/papers/categorical analysis-away from anovaT Jaeger.pdf
Papers/papers/div/ASC - ICES CM 2018.docx
Papers/papers/div/ASC2018 abstract.pdf
Papers/papers/div/ASC2018 abstract.tex
Papers/papers/div/DATRAS_FAQs.pdf
Papers/papers/div/Distance sampling Estimating abundance of biological parameters (Buckland et al 2001).JPG
Papers/papers/div/Finse Presentation-FINAL.pptx
Papers/papers/div/Finse Presentation-Uncertainty Estimation of the North Sea International Bottom.pptx
Papers/papers/div/Finse Presentation-Uncertainty Estimation of the North Sea International BottomFINAL.pptx
Papers/papers/div/IBTS Report 2006.doc
Papers/papers/div/IBTSWG Presentation 2018.pptx
Papers/papers/div/IBTSWG multiannual ToRs 2015.pdf
Papers/papers/div/IBTSWG-2018-Query.pptx
Papers/papers/div/IBTSWG-Questions.pptx
Papers/papers/div/IBTSWG-QuestionsUpdate.pptx
Papers/papers/div/ICES-FishMap/Saithe.pdf Papers/papers/div/ICES-FishMap/cod.pdf Papers/papers/div/ICES-FishMap/greygurnard.pdf Papers/papers/div/ICES-FishMap/haddock.pdf Papers/papers/div/ICES-FishMap/herring.pdf Papers/papers/div/ICES-FishMap/horsemackerel.pdf Papers/papers/div/ICES-FishMap/mackerel.pdf Papers/papers/div/ICES-FishMap/norwaypout.pdf Papers/papers/div/ICES-FishMap/plaice.pdf Papers/papers/div/ICES-FishMap/redmullet.pdf Papers/papers/div/ICES-FishMap/sole.pdf Papers/papers/div/ICES-FishMap/sprat.pdf Papers/papers/div/ICES-FishMap/spurdog.pdf Papers/papers/div/ICES-FishMap/thornback.pdf Papers/papers/div/ICES-FishMap/whiting.pdf Papers/papers/div/ICESreportAugust2017.pdf
Papers/papers/div/ICESreportAugust2017.tex
Papers/papers/div/SISP_x_ IBTS Survey Manual_X_22Mar18_clean.docx
Papers/papers/div/WGIBTS_Variance_Estimation_2018.pptx
Papers/papers/div/WGNSSK_Uncertainty_Estimation_2018.pptx
Papers/papers/div/WeightsStatRec.docx
Papers/papers/div/Working document Otolith collection of target species in the IBTS.docx
Papers/papers/div/chapter5-sampling-ratio-method-estimation.pdf
Papers/papers/div/ibtsBib.bib
Papers/papers/fishing_areas_ICES.pdf Papers/papers/multivariate distributions.pdf Papers/papers/nonpsrsmetric bootstrapping for hierarchical data.pdf Papers/papers/vaida 2005 AIC methods.pdf
R/.gitignore
R/caculateCPUEs.R R/calcALK.R
R/cod2018Q1Model.Rdat
R/configurations.R R/getEstimatesCPUEWithUncertainty.R R/readIBTSdata.R R/removeData.R R/simDatrasData.R R/utils.R
data/areaRFA.RData
data/cod2018Q1.RData
data/designMatrixForReportCod2018Q1.RData
data/designMatrixForReportSaithe2017Q3.RData
data/designMatrixForReportSaithe2018Q1.RData
data/keyIdMeshHaulCod2018Q1.RData
data/keyIdMeshHaulSaithe2017Q3.RData
data/keyIdMeshHaulSaithe2018Q1.RData
data/saithe2017Q3.RData
data/saithe2018Q1.RData
inst/bathymetry/wgs84_raster_north_sea_crop/README.txt
inst/bathymetry/wgs84_raster_north_sea_crop/ns_halfres.rds
inst/extdata/Exchange Data_2018-06-07 15_26_57.zip
inst/modelFit/cod2015.rda
inst/modelFit/keyIdMeshHaulCod2015.rda
inst/modelFit/keyIdMeshHaulSaithe2015.rda
inst/modelFit/saithe2015.rda
inst/shapefiles/ICES_AREA_shapefiles/ICES.mxd
inst/shapefiles/ICES_AREA_shapefiles/ICESdata/ices_areas/ices_areas.cst
inst/shapefiles/ICES_AREA_shapefiles/ICESdata/ices_areas/ices_areas.dbf
inst/shapefiles/ICES_AREA_shapefiles/ICESdata/ices_areas/ices_areas.prj
inst/shapefiles/ICES_AREA_shapefiles/ICESdata/ices_areas/ices_areas.sbn
inst/shapefiles/ICES_AREA_shapefiles/ICESdata/ices_areas/ices_areas.sbx
inst/shapefiles/ICES_AREA_shapefiles/ICESdata/ices_areas/ices_areas.shp
inst/shapefiles/ICES_AREA_shapefiles/ICESdata/ices_areas/ices_areas.shx
inst/shapefiles/ICES_AREA_shapefiles/ICESdata/ices_areas/wfsrequest.txt
inst/shapefiles/ICES_AREA_shapefiles/ices_areas_simplifiedt.dbf
inst/shapefiles/ICES_AREA_shapefiles/ices_areas_simplifiedt.prj
inst/shapefiles/ICES_AREA_shapefiles/ices_areas_simplifiedt.sbn
inst/shapefiles/ICES_AREA_shapefiles/ices_areas_simplifiedt.sbx
inst/shapefiles/ICES_AREA_shapefiles/ices_areas_simplifiedt.shp
inst/shapefiles/ICES_AREA_shapefiles/ices_areas_simplifiedt.shx
inst/shapefiles/ICES_StatRec_mapto_ICES_Areas/StatRec_map_Areas_Full_20170124.cpg
inst/shapefiles/ICES_StatRec_mapto_ICES_Areas/StatRec_map_Areas_Full_20170124.dbf
inst/shapefiles/ICES_StatRec_mapto_ICES_Areas/StatRec_map_Areas_Full_20170124.prj
inst/shapefiles/ICES_StatRec_mapto_ICES_Areas/StatRec_map_Areas_Full_20170124.sbn
inst/shapefiles/ICES_StatRec_mapto_ICES_Areas/StatRec_map_Areas_Full_20170124.sbx
inst/shapefiles/ICES_StatRec_mapto_ICES_Areas/StatRec_map_Areas_Full_20170124.shp
inst/shapefiles/ICES_StatRec_mapto_ICES_Areas/StatRec_map_Areas_Full_20170124.shp.xml
inst/shapefiles/ICES_StatRec_mapto_ICES_Areas/StatRec_map_Areas_Full_20170124.shx
inst/shapefiles/Roundfish_shapefiles/Shapefile.dbf
inst/shapefiles/Roundfish_shapefiles/Shapefile.prj
inst/shapefiles/Roundfish_shapefiles/Shapefile.shp
inst/shapefiles/Roundfish_shapefiles/Shapefile.shx
inst/weightsSaithe/WeightsStatRecHerringSpratSaithe.Rda
man/CPUEage.Rd man/CPUElength.Rd man/CPUEnorthSea.Rd man/calcmCPUEnorthSea.Rd man/calcmCPUErfa.Rd man/calcmCPUErfaWithALK.Rd man/calcmCPUErfaWithALKNew.Rd man/calcmCPUEstatRec.Rd man/calcmCPUEstatRecWithALK.Rd man/calcmCPUEstatRecWithALKNew.Rd man/calculateALK.Rd man/calculateALKModel.Rd man/calculateALKNew.Rd man/confALK.Rd man/findLoc.Rd man/investigateRemoval.Rd man/investigateRemovalParallel.Rd man/readIBTSData.Rd man/removeData.Rd man/removeDataDetailedCA.Rd man/removeDataDetailedHH.Rd man/removeDataDetailedHL.Rd man/removeObsFromHaul.Rd man/selectHaulIdsHiearchical.Rd man/simCaHlSimultaniousyStratified.Rd man/simModelFisher.Rd man/simTrawlHaulsBySelection.Rd man/simTrawlHaulsCASimple.Rd man/simTrawlHaulsCAStratified.Rd man/simTrawlHaulsHLSimple.Rd man/simTrawlHaulsHLStratified.Rd man/simTrawlHaulsHLdatras.Rd man/simTrawlHaulsHiearchical.Rd man/simulateALK.Rd script/constructPlotModel.R script/constructTableWeights.R script/plotRemove.R script/quotaSamplingCheck.R script/reproduceIndices.R script/survey_area_maps.R tests/testthat.R tests/testthat/test_hierarchical_resampling.R
natoyaj/TestPackage documentation built on Nov. 13, 2018, 2:18 p.m.