Files in natoyaj/TestPackage

IBTSspatial

DESCRIPTION

Hauls_With_Age/Hauls_with_Age_data.csv

Hauls_With_Age/Hauls_with_Age_data.xlsx

IBTSindices.Rproj

Mis-readingOfOtolith/CodYears2012and2016/EFAN-ark_ringlesing nordsjøtorsk 2016_alder og gytesoner.xlsx

Mis-readingOfOtolith/CodYears2012and2016/North Sea cod otolith exchange 2011-2012 (002).xlsx

Mis-readingOfOtolith/CodYears2012and2016/Report North Sea cod otolith exchange 2011-2012 (002).pdf

Mis-readingOfOtolith/CodYears2012and2016/Ringlesing nordsjørtorskotolitter HI 2016 (002).docx

Mis-readingOfOtolith/SaitheYears2008-2009-2010-2013-2015-2016/EFAN-ark_ringlesing sei 2009_alder og gytesoner.xls

Mis-readingOfOtolith/SaitheYears2008-2009-2010-2013-2015-2016/EFAN-ark_ringlesing sei 2009_alder.pdf

Mis-readingOfOtolith/SaitheYears2008-2009-2010-2013-2015-2016/EFAN-ark_ringlesing sei 2010_alder og gytesoner.xls

Mis-readingOfOtolith/SaitheYears2008-2009-2010-2013-2015-2016/EFAN-ark_ringlesing sei 2015_alder og gytesoner.xlsx

Mis-readingOfOtolith/SaitheYears2008-2009-2010-2013-2015-2016/EFAN-ark_ringlesing sei 2016_alder og gytesoner.xlsx

Mis-readingOfOtolith/SaitheYears2008-2009-2010-2013-2015-2016/Ringlesing seiotolittar HI 2015.pdf Mis-readingOfOtolith/SaitheYears2008-2009-2010-2013-2015-2016/Ringlesing seiotolittar HI 2016 JAG.pdf Mis-readingOfOtolith/SaitheYears2008-2009-2010-2013-2015-2016/SaitheOtolithExchange2013.pdf

Mis-readingOfOtolith/SaitheYears2008-2009-2010-2013-2015-2016/Sei 2008 AGE COMPARISONS VIa.xls

Mis-readingOfOtolith/SaitheYears2008-2009-2010-2013-2015-2016/Sei 2008 Final report_saithe oto exchange 0708.doc

NAMESPACE

OtolAndHaul_1_5_per_5cm_haulBased1997_1999.xlsx

OtolithsAndHauls_Results_1997_1999/OtolAndHaul_1_5_per_5cm_areaBased1997_1999.csv

OtolithsAndHauls_Results_1997_1999/OtolAndHaul_1_5_per_5cm_areaBased1997_1999.xlsx

OtolithsAndHauls_Results_1997_1999/OtolAndHaul_1_5_per_5cm_haulBased1997_1999.csv

OtolithsAndHauls_Results_1997_1999/OtolAndHaul_1_5_per_5cm_haulBased1997_1999.xlsx

OtolithsAndHauls_Results_2015_2018/OtolAndHaul_1_5_per_5cm_areaBased2015_2018.csv

OtolithsAndHauls_Results_2015_2018/OtolAndHaul_1_5_per_5cm_areaBased2015_2018.xlsx

OtolithsOnly_1_per_xcm_areaBased.xlsx

OtolithsOnly_1_per_xcm_haulBased.xlsx

OtolithsOnly_Results/OtolithsOnly_1_per_xcm_areaBased.csv

OtolithsOnly_Results/OtolithsOnly_1_per_xcm_areaBased.xlsx

OtolithsOnly_Results/OtolithsOnly_1_per_xcm_haulBased.csv

OtolithsOnly_Results/OtolithsOnly_1_per_xcm_haulBased.xlsx

OtolithsOnly_Results/OtolithsOnly_y_per_5cm_areaBased.csv

OtolithsOnly_Results/OtolithsOnly_y_per_5cm_areaBased.xlsx

OtolithsOnly_Results/OtolithsOnly_y_per_5cm_haulBased.csv

OtolithsOnly_Results/OtolithsOnly_y_per_5cm_haulBased.xlsx

Papers/manuscript/BibliographyIbts.bib

Papers/manuscript/IBTSPlan.tex

Papers/manuscript/IBTSpaper.pdf

Papers/manuscript/IBTSpaper.tex

Papers/manuscript/IBTSpaperModel.tex

Papers/manuscript/IBTSpaperWithoutModel.aux

Papers/manuscript/IBTSpaperWithoutModelFinalUpdate.tex

Papers/manuscript/IBTSpaperWithoutModelWithCommentsALL.tex

Papers/manuscript/IBTSpaperWithoutModelWithCommentsForJon.tex

Papers/manuscript/comments_ibts_ms.txt

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Papers/manuscript/ibtsBib.bib

Papers/manuscript/results/olav/resamplingNandotoliths/resampleCodDl5N100year1997Q1n2datras1

Papers/manuscript/results/olav/resamplingNandotoliths/resampleCodDl5N100year1997Q1n2datras5

Papers/manuscript/results/olav/resamplingNandotoliths/resampleCodDl5N100year1997Q1n500datras1

Papers/manuscript/results/olav/resamplingNandotoliths/resampleCodDl5N100year1997Q1n500datras5

Papers/manuscript/results/olav/resamplingNandotoliths/resampleCodDl5N100year1997Q1n500haulBased1

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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/configurations.R R/getEstimatesCPUEWithUncertainty.R R/plots.R R/readIBTSdata.R R/removeData.R R/simDatrasData.R R/utils.R

data/ALKs_results.csv

data/NS_CodCat_TS_IndexArea.csv

data/NS_Cod_EXT_TS_IndexArea.csv

data/NS_Cod_TS_IndexArea.csv

data/OtolithsOnly_1_per_xcm_areaBased.csv

data/OtolithsOnly_1_per_xcm_haulBased.csv

data/areaRFA.RData

inst/bathymetry/wgs84_raster_north_sea_crop/README.txt

inst/bathymetry/wgs84_raster_north_sea_crop/ns_halfres.rds

inst/extdata/ALKs_results.xlsx

inst/extdata/CPUEallRec.csv

inst/extdata/Catch-rates-countries.csv

inst/extdata/Exchange Data_2019-01-14 10_38_42.zip

inst/extdata/NS_Cod_TS_IndexArea.csv

inst/extdata/OtolithsOnly_1_per_xcm_areaBased.csv

inst/extdata/OtolithsOnly_1_per_xcm_haulBased.csv

inst/extdata/OtolithsOnly_y_per_5cm_areaBased.csv

inst/extdata/OtolithsOnly_y_per_5cm_haulBased.csv

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/CPUEnorthSea.Rd man/CPUErfa.Rd man/calcmCPUEnorthSea.Rd man/calcmCPUErfa.Rd man/calcmCPUErfaWithALKDatras.Rd man/calcmCPUErfaWithALKHaulbased.Rd man/calcmCPUEstatRec.Rd man/calcmCPUEstatRecWithALK.Rd man/calcmCPUEstatRecWithALKNew.Rd man/calculateALKDatras.Rd man/calculateALKHaulbased.Rd man/calculateALKModel.Rd man/confALK.Rd man/findLoc.Rd man/investigateRemoval.Rd man/readIBTSData.Rd man/removeDataDetailedCA.Rd man/removeObsFromHaul.Rd man/selectHaulIdsHiearchical.Rd man/simCaHlSimultaniousyStratified.Rd man/simModelFisher.Rd man/simTrawlHaulsBySelection.Rd man/simTrawlHaulsCAdatras.Rd man/simTrawlHaulsHLdatras.Rd man/simTrawlHaulsHiearchical.Rd man/simulateAgeHaulBased.Rd script/TablePlots.R script/TablePlotsBars.R script/TablePlotsOverlay.R script/assessment.R script/constructPlotModel.R script/constructTableWeights.R script/fullHaulBasedALKforPlot.R script/plotALKestimates.R script/plotRemove.R script/produceResults.R script/quotaSamplingCheck.R script/reproduceIndices.R script/resampleHauls.R script/resultsSeveralYears.R script/scriptPlotRemove.R script/survey_area_maps.R

tests/areaBasedALK/runExpected.Rdata

tests/areaBasedALK/script.R

tests/bootstrapDatras/runExpected.RData

tests/bootstrapDatras/script.R tests/compareRuns.R

tests/haulBasedALK/runExpected.Rdata

tests/haulBasedALK/script.R

tests/removeNandO/runExpected.RData

tests/removeNandO/script.R

tests/resampleO/runExpected.RData

tests/resampleO/script.R tests/runCompare.R

tests/stratifiedHLpseudoBootstrap/runExpected.RData

tests/stratifiedHLpseudoBootstrap/script.R tests/testthat/tests.R

natoyaj/TestPackage documentation built on March 11, 2020, 7:46 a.m.