Files in natoyaj/TestPackage
IBTSspatial

.Rbuildignore
.gitignore
DESCRIPTION
IBTSpaper1/.gitignore
IBTSpaper1/Allcode40cm2015.png
IBTSpaper1/IBTSpaper.out
IBTSpaper1/IBTSpaper.pdf
IBTSpaper1/IBTSpaper.tex
IBTSpaper1/IBTSpaperBackup.out
IBTSpaper1/IBTSpaperBackup.tex
IBTSpaper1/IBTSpaperBackup1.tex
IBTSpaper1/cod2015Q1.jpeg
IBTSpaper1/cod2015Q1Map.jpeg
IBTSpaper1/cod2017Q3BiasCorr.jpeg
IBTSpaper1/cod2017Q3BiasCorr.pdf
IBTSpaper1/cod2017Q3BootstrapProcedures.jpeg
IBTSpaper1/cod2017Q3Percentile.jpeg
IBTSpaper1/cod2017Q3table.csv
IBTSpaper1/cod2017Q3table.xlsx
IBTSpaper1/codQ12015Hauls.jpeg
IBTSpaper1/codQ12015Hauls10cm.jpeg
IBTSpaper1/codQ12015Hauls20cm.jpeg
IBTSpaper1/codQ12015Hauls5cm.jpeg
IBTSpaper1/ibtsBib.bib
IBTSpaper1/icesroundfishmap.JPG
IBTSpaper1/latLon059 .png
IBTSpaper1/latLon1058Skagen .png
IBTSpaper1/map40cmCod .png
IBTSpaper1/recWeightings.JPG
IBTSpaper1/saithe2015Q1.jpeg
IBTSpaper1/saithe2015Q1Map.jpeg
IBTSpaper1/saithe2015Q3.jpeg
IBTSpaper1/saithe2015Q3Map.jpeg
IBTSpaper1/saithe2017Q3BiasCorr.jpeg
IBTSpaper1/saithe2017Q3Percentile.jpeg
IBTSpaper1/saitheQ12015Hauls.jpeg
IBTSpaper1/saitheQ12015Hauls10cm.jpeg
IBTSpaper1/saitheQ12015Hauls20cm.jpeg
IBTSpaper1/saitheQ12015Hauls5cm.jpeg
IBTSpaper1/saitheQ32015Hauls.jpeg
IBTSpaper1/saitheQ32015Hauls5cm.jpeg
IBTSpaper1/surveyarea.pdf
IBTSpaper1New/.gitignore
IBTSpaper1New/Allcode40cm2015.png
IBTSpaper1New/IBTSpaper.out
IBTSpaper1New/IBTSpaper.pdf
IBTSpaper1New/IBTSpaper.tex
IBTSpaper1New/IBTSpaperBackup.out
IBTSpaper1New/IBTSpaperBackup.tex
IBTSpaper1New/IBTSpaperBackup1.tex
IBTSpaper1New/cod2015Q1.jpeg
IBTSpaper1New/cod2015Q1Map.jpeg
IBTSpaper1New/cod2017Q3BiasCorr.jpeg
IBTSpaper1New/cod2017Q3BiasCorr.pdf
IBTSpaper1New/cod2017Q3BootstrapProcedures.jpeg
IBTSpaper1New/cod2017Q3Percentile.jpeg
IBTSpaper1New/cod2017Q3table.csv
IBTSpaper1New/cod2017Q3table.xlsx
IBTSpaper1New/cod2018Q1BiasCorr.jpeg
IBTSpaper1New/cod2018Q1Map.jpeg
IBTSpaper1New/cod2018Q1ReducedData.jpeg
IBTSpaper1New/codQ12015Hauls.jpeg
IBTSpaper1New/codQ12015Hauls10cm.jpeg
IBTSpaper1New/codQ12015Hauls20cm.jpeg
IBTSpaper1New/codQ12015Hauls5cm.jpeg
IBTSpaper1New/ibtsBib.bib
IBTSpaper1New/icesroundfishmap.JPG
IBTSpaper1New/latLon059 .png
IBTSpaper1New/latLon1058Skagen .png
IBTSpaper1New/map40cmCod .png
IBTSpaper1New/recWeightings.JPG
IBTSpaper1New/saithe2015Q1.jpeg
IBTSpaper1New/saithe2015Q1Map.jpeg
IBTSpaper1New/saithe2015Q3.jpeg
IBTSpaper1New/saithe2015Q3Map.jpeg
IBTSpaper1New/saithe2017Q3BiasCorr.jpeg
IBTSpaper1New/saithe2017Q3Percentile.jpeg
IBTSpaper1New/saithe2017Q3ReducedData.jpeg
IBTSpaper1New/saithe2018Q1BiasCorr.jpeg
IBTSpaper1New/saithe2018Q1Map.jpeg
IBTSpaper1New/saitheQ12015Hauls.jpeg
IBTSpaper1New/saitheQ12015Hauls10cm.jpeg
IBTSpaper1New/saitheQ12015Hauls20cm.jpeg
IBTSpaper1New/saitheQ12015Hauls5cm.jpeg
IBTSpaper1New/saitheQ32015Hauls.jpeg
IBTSpaper1New/saitheQ32015Hauls5cm.jpeg
IBTSpaper1New/surveyarea.esp
IBTSpaper1New/surveyarea.pdf
NAMESPACE
Paper/.gitignore
Paper/30cm2014.png
Paper/40cm2015.png
Paper/A proposal for a consistent use of the NS-IBTS data.pdf
Paper/ASC - ICES CM 2018.docx
Paper/ASC2018 abstract.aux
Paper/ASC2018 abstract.bbl
Paper/ASC2018 abstract.blg
Paper/ASC2018 abstract.log
Paper/ASC2018 abstract.pdf
Paper/ASC2018 abstract.tex
Paper/ASC2018abstractComments.pdf Paper/Abstract template.pdf Paper/Advanced statistics - Bootstrapping Haukoos 2005.pdf
Paper/Allcode40cm2015.png
Paper/An analysis of the North Sea International Bottom Trawl Survey-JourdainIMR.docx
Paper/Baudron-2014-Adverse consequences.pdf Paper/Bias in using an ALK to estimate Age frequency.pdf Paper/Casper W Berg- Estimaitng abundance and biomass.pdf Paper/Casper W Berg- Evaluation of alternative age-based methods.pdf Paper/Casper W Berg- Spatial age-length key modelling using continuation ratio logits.pdf
Paper/Categorical Analysis AGRESTI 2005.PDF
Paper/Combined-ratio product estimator of finite population mean.pdf Paper/DATRAS_FAQs.pdf
Paper/Distance sampling Estimating abundance of biological parameters (Buckland et al 2001).JPG
Paper/Effects of measurement errors Walters and Ludwig 1981.pdf Paper/Efficient statistical estimators (Aanes and Vølstad).pdf Paper/Efficient statistical estimators.pdf Paper/Estimation of Effective sample size.pdf Paper/Evaluation of ALK sample sizes.pdf
Paper/Finse Presentation-FINAL.pptx
Paper/Finse Presentation-Uncertainty Estimation of the North Sea International Bottom.pptx
Paper/Finse Presentation-Uncertainty Estimation of the North Sea International BottomFINAL.pptx
Paper/Flexible mixture modeling via the multivariate t distribution with the Box-Cox transformation- an alternative to the skew-t distribution.pdf Paper/Gadus morhua1.pdf
Paper/HERRING_picture.jpg
Paper/IBTS Report 2006.doc
Paper/IBTSQ1.JPG
Paper/IBTSWG Presentation 2018.pptx
Paper/IBTSWG multiannual ToRs 2015.pdf
Paper/IBTSWG-2018-Query.pptx
Paper/IBTSWG-Questions.pptx
Paper/IBTSWG-QuestionsUpdate.pptx
Paper/IBTSnewPaper.aux
Paper/IBTSnewPaper.bbl
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Paper/IBTSnewPaperAPRILUPDATED.pdf
Paper/IBTSnewPaperAPRILUPDATED.tex
Paper/IBTSnewPaperBeforeOlav-NatoyaEditedFebruar2018.aux
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Paper/IBTSnewPaperBeforeOlav-NatoyaEditedFebruar2018.tex
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Paper/IBTSnewPaperBeforeOlavEditedFebruar2018.tex
Paper/ICES Advice on fishing opportunities, catch, and effort Greater North Sea and Celtic Seas ecoregions.pdf
Paper/ICES-FishMap.zip
Paper/ICES-FishMap/Saithe.pdf Paper/ICES-FishMap/cod.pdf Paper/ICES-FishMap/greygurnard.pdf Paper/ICES-FishMap/haddock.pdf Paper/ICES-FishMap/herring.pdf Paper/ICES-FishMap/horsemackerel.pdf Paper/ICES-FishMap/mackerel.pdf Paper/ICES-FishMap/norwaypout.pdf Paper/ICES-FishMap/plaice.pdf Paper/ICES-FishMap/redmullet.pdf Paper/ICES-FishMap/sole.pdf Paper/ICES-FishMap/sprat.pdf Paper/ICES-FishMap/spurdog.pdf Paper/ICES-FishMap/thornback.pdf Paper/ICES-FishMap/whiting.pdf Paper/ICESreportAugust2017.pdf
Paper/ICESreportAugust2017.tex
Paper/Indices_Calculation_Steps_IBTS.pdf Paper/Length-based methods in Fisheries D Pauly.pdf Paper/Mackerel paper (vølstad et al).pdf Paper/Mackerel paper.pdf
Paper/Map-karte-1-1023-en.gif
Paper/Map-of-the-North-Sea-showing-the-coverage-of-3D-blue-shading-and-2D-black-lines.jpg
Paper/Measurement Errors and Uncertainty in Parameter Estimates Ludwig and Walter 1981.pdf
Paper/Missing data imputation using Amelia package in R _ Ramprakash Veluchamy _ Pulse _ LinkedIn.html
Paper/Missing data imputation using Amelia package in R _ Ramprakash Veluchamy _ Pulse _ LinkedIn_files/8vicjbeqcrhndoa1p07f7p9cc,bwokfxsuvccwdakriomunvhul,f0fs9o94ff50obn12e0n6o581,ccbpl2fqyjima7qsjzs5w6e9a,
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Paper/Missing data imputation using Amelia package in R _ Ramprakash Veluchamy _ Pulse _ LinkedIn_files/px.js(1).download
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Paper/Missing data imputation using Amelia package in R _ Ramprakash Veluchamy _ Pulse _ LinkedIn_files/radar.html
Paper/Multivariate Normal Distribution Important Chapter 4.pdf Paper/Multivariate-Non-normal distribtuions.pdf
Paper/NSIBTS-Q1-2018-Program.doc
Paper/North_Sea_map-en.png
Paper/NygardskoleUke7-14,2018.pdf Paper/Optimum allocation for estimating age composition Lai.pdf Paper/Pennington and Volstad 1994 Intra-haul correlation.pdf
Paper/Picture of cod.htm
Paper/Pollachius virens1.pdf Paper/Predicting an ordinal outcome -Mark Lunt.pdf Paper/Ratio Estimation with a Stratified SRS.pdf Paper/Ratio Estimators in Stratified Random Sampling C.Kafilar et al 2003.pdf Paper/Ratio estimation with Stratified Random Sampling.pdf Paper/Report of the Benchmark Workshop on North Sea Stocks (WKNSEA) wknsea_2016- 14-16 March 2016.pdf Paper/Resampling variance estimation for complex survey data -Kolenikov 2010.pdf Paper/Resampling variance estimation for complex survey data-Stanislav 2010.pdf Paper/SISP 10 - Manual for the International Bottom Trawl Surveys - Revision IX.pdf
Paper/SISP_x_ IBTS Survey Manual_X_22Mar18_clean.docx
Paper/Saithe- general information and fact sheet.pdf Paper/Species Composition, Biomass of DF of the North sea.pdf Paper/Statistical Assessment of ALK Kimura 1977.pdf Paper/Statistics in Practice, Practical Methods for Design and Analysis of Complex Survey.pdf
Paper/Testdoc.tex
Paper/Testdoc1olav.aux
Paper/Testdoc1olav.log
Paper/Testdoc1olav.pdf
Paper/Testdoc1olav.tex
Paper/The Nonexistence of Certain Statistical Procedures in Nonparametric Problems Bahadur 1956.pdf Paper/Three bootstrap methods.pdf Paper/Tranformation types -How to obtain nasty standard errors.pdf
Paper/Tutorial on 5 Powerful R Packages used for imputing missing values.html
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Paper/WGIBTS_Variance_Estimation_2018.pptx
Paper/WGNSSK report 2016-Report of the Working Group on the Assessment of Demersal Stocks in the North Sea and Skagerrak (WGNSSK) .pdf
Paper/WGNSSK_Uncertainty_Estimation_2018.pptx
Paper/WeightsStatRec.docx
Paper/What is intracluster correlation.pdf
Paper/Working document Otolith collection of target species in the IBTS.docx
Paper/alk paper David hirst.doc
Paper/alk paper plots.doc
Paper/categorical analysis-away from anovaT Jaeger.pdf Paper/chapter5-sampling-ratio-method-estimation.pdf
Paper/cod2015Q1.jpeg
Paper/cod2015Q1Map.jpeg
Paper/codQ12015Hauls.jpeg
Paper/codQ12015Hauls.pdf
Paper/codQ12015Hauls10cm.jpeg
Paper/codQ12015Hauls20cm.jpeg
Paper/codQ12015Hauls5cm.jpeg
Paper/code40cm2015.png
Paper/codetest.JPG
Paper/datatable.JPG
Paper/documentation.pdf
Paper/doorspead.JPG
Paper/estimates for IBTS paper.txt
Paper/fishing_areas_ICES.pdf
Paper/headlineHeight.JPG
Paper/ibtsBib.bib
Paper/icesroundfishmap.JPG
Paper/icessurveymap.JPG
Paper/map-showing-the-naval-bases-of-the-north-sea-during-world-war-one-EHTF1A.jpg
Paper/multivariate distributions.pdf Paper/nonpsrsmetric bootstrapping for hierarchical data.pdf
Paper/picture of cod .jpg
Paper/recWeightings.JPG
Paper/saithe2015Q1.jpeg
Paper/saithe2015Q1Map.jpeg
Paper/saithe2015Q3.jpeg
Paper/saithe2015Q3Map.jpeg
Paper/saitheQ12015Hauls.jpeg
Paper/saitheQ12015Hauls10cm.jpeg
Paper/saitheQ12015Hauls10cm.pdf
Paper/saitheQ12015Hauls20cm.jpeg
Paper/saitheQ12015Hauls5cm.jpeg
Paper/saitheQ12015Hauls5cm.pdf
Paper/saitheQ32015Hauls.jpeg
Paper/saitheQ32015Hauls5cm.jpeg
Paper/spatialHyse2011.png
Paper/vaida 2005 AIC methods.pdf
Paper/~$C - ICES CM 2018.docx
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
Roundfish_shapefiles/Shapefile.dbf
Roundfish_shapefiles/Shapefile.prj
Roundfish_shapefiles/Shapefile.shp
Roundfish_shapefiles/Shapefile.shx
Rprof.out
TestPackage.Rproj
cod2017Q3.rda
cod2017Q3table.csv
cod2018Q1.rda
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
div/age15cm.jpeg
div/age25cm.jpeg
div/age35cm.jpeg
div/age45cm.jpeg
div/age55cm.jpeg
div/age65cm.jpeg
div/age75cm.jpeg
div/age85cm.jpeg
div/age95cm.jpeg
div/ageGivenLength.jpeg
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
lonLat-1.225-60.733.txt
lonLat-1.50-59.270.txt
lonLat4.50-58.20.txt
lonLat4.50-58.20PLOT.pdf
lonLat4.90-58.030.txt
lonLat4.90-58.03PLOT.pdf 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
mean.10cm.rda
mean.1cm.rda
mean.2cm.rda
mean.3cm.rda
mean.4cm.rda
mean.5cm.rda
mean.5cm500.rda
mean.7cm.rda
mean17.1cm.rda
mean17.2cm.rda
mean17.3cm.rda
mean17.5cm.rda
mean17.7cm.rda
mean18.4cm.rda
saithe2017Q3.rda
saithe2018Q1.rda
script/CPUEandPlotsIBTS.R script/Plots.R script/PlotsMovedThisFromOuterFolder.R script/TestGitHub.R
script/WeightsStatRecHerringSpratSaithe.Rda
script/calcALK.R script/calcAlkVariance.R script/calcAreaRFA.R
script/cod2018Q1Model.Rdat
script/constructPlotModel.R script/constructTableWeights.R script/dataDescriotion.R script/detetedCode.R script/quotaSamplingCheck.R
script/removeDatrasParallel.Rdata
script/reproduceIndices.R script/survey_area_maps.R tests/testthat.R tests/testthat/test_hierarchical_resampling.R
natoyaj/TestPackage documentation built on Sept. 10, 2018, 11:41 p.m.