Package: RDBEScore 0.3.5

Colin Millar

RDBEScore: Functions for the ICES Regional Database and Estimation System (RDBES)

The RDBEScore package provides functions to import and work with fisheries data downloaded from the ICES RDBES database. It also contains functions to perform estimation analysis using the resulting objects.

Authors:c, person, person, person, person, person, person, person, person, person, person, person, person, person, person, person, person, person, person, person, person, person, person, person )

RDBEScore_0.3.5.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
RDBEScore/json (API)
NEWS

# Install 'RDBEScore' in R:
install.packages('RDBEScore', repos = c('https://ices-tools-prod.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ices-tools-dev/rdbescore/issues

Pkgdown/docs site:https://ices-tools-dev.github.io

Datasets:
  • DefaultFileNames - The default files names when you download data from the RDBES.
  • designVariables - A dataset containing the RDBES "design variable" names
  • H1Example - A dataset containing test RDBES data for H1 in the RDBESDataObject structure
  • H5Example - A dataset containing test RDBES data for H5 in the RDBESDataObject structure
  • H7Example - A dataset containing test RDBES data for H7 in the RDBESDataObject structure
  • H8ExampleEE1 - A dataset containing test RDBES data for H8 in the RDBESDataObject structure
  • icesSpecWoRMS - ICES Species (WoRMS) code list snapshot
  • mapColNamesFieldR - A dataset containing the mapping from database column names to R field names
  • Pckg_SDAResources_agstrat_H1 - A RDBESDataObject converted from package SDAResources dataset agstrat
  • Pckg_survey_apiclus2_H1 - A Multi-Stage RDBESDataObject converted from package survey dataset apiclus2
  • Pckg_survey_apistrat_H1 - A RDBESDataObject converted from package survey dataset apistrat
  • shrimps - One quarter of sample data from swedish shrimp landings of the SWE_OTB_CRU_32-69_0_0 fishery
  • shrimpsStrat - One quarter of sample data from swedish shrimp catches of the SWE_OTB_CRU_32-69_0_0 fishery
  • tablesInRDBESHierarchies - The tables required for each RDBES hierarchy.
  • wormsAphiaRecord - A dataset containing aphia records for species found in icesSpecWoRMS

On CRAN:

Conda:

5.39 score 1 stars 42 scripts 30 exports 16 dependencies

Last updated from:9077812f23. Checks:9 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK331
source / vignettesOK219
linux-release-x86_64OK325
macos-release-arm64OK448
macos-oldrel-arm64OK260
windows-develOK410
windows-releaseOK394
windows-oldrelOK383
wasm-releaseOK97

Exports:addCLtoLowerCSapplyGenerateProbscheckRDBESDataObjectcombineRDBESDataObjectscreateRDBESDataObjectcreateRDBESEstObjectdoBVestimCANUMdoEstimationForAllStrataestimestimMCexportEstimationResultsToInterCatchFormatfilterAndTidyRDBESDataObjectfilterRDBESDataObjectfilterRDBESEstObjectfindAndKillOrphansfixSLidsgenerateMissingSSRowsgenerateNAsUsingSLgenerateProbsgenerateZerosUsingSLgetLinkedDataFromLevelgetTablesInRDBESHierarchylistPackageFunctionsnewRDBESDataObjectremoveBrokenSpeciesListLinksremoveBrokenVesselLinksrunChecksOnSelectionAndProbsupdateSAwithTaxonFromSLvalidateRDBESDataObjectvalidateRDBESEstObject

Dependencies:clidata.tabledplyrgenericsgluelifecyclemagrittrpillarpkgconfigR6rlangtibbletidyselectutf8vctrswithr

01a Data import

Rendered fromv01a-data-import.Rmdusingknitr::rmarkdownon May 06 2026.

Last update: 2025-10-15
Started: 2025-10-15

01b Manipulating RDBESDataObjects

Rendered fromv01b-manipulating-rdbesdataobjects.Rmdusingknitr::rmarkdownon May 06 2026.

Last update: 2025-10-17
Started: 2025-10-15

02a Generating probabilities

Rendered fromv02a-generating-probabilities.Rmdusingknitr::rmarkdownon May 06 2026.

Last update: 2025-10-15
Started: 2025-10-15

02b Generating zeros for species not observed

Rendered fromv02b-Generating-zeros-for-species-not-observed.Rmdusingknitr::rmarkdownon May 06 2026.

Last update: 2025-10-15
Started: 2025-10-15

02c Generating NAs for species not targeted by sampling

Rendered fromv02c-Generating-NAs-for-species-not-targeted-by-sampling.Rmdusingknitr::rmarkdownon May 06 2026.

Last update: 2025-10-15
Started: 2025-10-15

02d Update SA with taxon from SL

Rendered fromv02d-update-SA-with-taxon-from-SL.Rmdusingknitr::rmarkdownon May 06 2026.

Last update: 2025-10-15
Started: 2025-10-15

03a Estimating population parameters: unbiased estimator

Rendered fromv03a-Estimating-population-parameters-unbiased-estimator.Rmdusingknitr::rmarkdownon May 06 2026.

Last update: 2025-10-15
Started: 2025-10-15

03b Estimating population parameters: ratio estimator

Rendered fromv03b-Estimating-population-parameters-ratio-estimator.Rmdusingknitr::rmarkdownon May 06 2026.

Last update: 2025-10-15
Started: 2025-10-15

04 Create IC format from estimation results

Rendered fromv04-Create-IC-format-from-estimation-results.Rmdusingknitr::rmarkdownon May 06 2026.

Last update: 2025-10-15
Started: 2025-10-15

Readme and manuals

Help Manual

Help pageTopics
Add CL data to a lower-level CS table in an RDBESDataObjectaddCLtoLowerCS
Generate probabilities missing from RDBES DataapplyGenerateProbs
Check if a column exists in a data table and has unique valuescheck_key_column
Combine Two RDBES Raw Objects combines 2 RDBESDataObjects into a single RDBESDataObject by merging individual tables one by onecombineRDBESDataObjects
Load raw object and create prepared object Function relies on the data being correctly named following established hierarchycreateDBEPrepObj
Create an RDBES Data ObjectcreateRDBESDataObject
Creates an RDBESEstObject from RDBES datacreateRDBESEstObject
Create a table of RDBES IdscreateTableOfRDBESIds
The default files names when you download data from the RDBES.DefaultFileNames
A dataset containing the RDBES "design variable" namesdesignVariables
Estimate Catch at Number (CANUM) for Biological VariablesdoBVestimCANUM
Generates the DBE estimation object for the upper hierarchy tablesdoDBEestimantionObjUpp
Create design-based point and variance estimates from RDBES estimation object (rdbesEstimObj)doDBestimation
Estimate totals and means, and try to generate samples variances for all strata in an RDBESEstObjectdoEstimationForAllStrata
Estimate Numbers and Mean Values by Length or Age ClassdoEstimationRatio
Generic function for estimation of population total and varianceestim
Multiple Count Estimator for Population Total and VarianceestimMC
Export Estimation Results to InterCatch Exchange FormatexportEstimationResultsToInterCatchFormat
Filter and remove orphan records in an RDBESDataObjectfilterAndTidyRDBESDataObject
Filter an RDBESDataObjectfilterRDBESDataObject
Filter an RDBESEstObjectfilterRDBESEstObject
This function finds and removed any orphan records in an RDBESDataObject. Normally data that has been downloaded from the RDBES will not contain orphan records - however if the data is subsequently filtered it is possible to introduce orphan records.findAndKillOrphans
Internal function to identify orphan records in a given RDBESDataObject tablefindOrphansByTable
Fixes SLid in SL table (facilitating SS-SL joins).fixSLids
Generate any missing SS rows. When FOcatchReg=="All" it is expected that SScatchFraction is either "Catch" OR "Lan"+"Dis". In the latter case, if one is missing the other is to be assumed 0. This function generates SS rows for any missing catch fractions.generateMissingSSRows
Generate NAs in samples using Species List informationgenerateNAsUsingSL
Generate vector of selection or inclusion probabilitiesgenerateProbs
Private function to generate SS rowsgenerateSSRows
Generate a List of Related Data TablesgenerateTestTbls
Generate zeros in samples using Species List informationgenerateZerosUsingSL
Private function used by doEstimationForAllStrata to get the estimatesgetEstimForStratum
Retrieve Linked Data Between RDBES Tables at a Specified LevelgetLinkedDataFromLevel
Get Lower Table from Several Upper Table FieldsgetLowerTableSubsets
Private function to find which FO rows are not matching SSgetMissingSSCatchFraction
Returns the tables for a given hierarchygetTablesInRDBESHierarchy
A dataset containing test RDBES data for H1 in the RDBESDataObject structureH1Example
A dataset containing test RDBES data for H5 in the RDBESDataObject structureH5Example
A dataset containing test RDBES data for H7 in the RDBESDataObject structureH7Example
A dataset containing test RDBES data for H8 in the RDBESDataObject structureH8ExampleEE1
ICES Species (WoRMS) code list snapshoticesSpecWoRMS
Internal function to remove orphan records from an RDBESDataObjectkillOrphans
Extract Functions and Descriptions from an R PackagelistPackageFunctions
Generate a Data TablemakeTbl
A dataset containing the mapping from database column names to R field namesmapColNamesFieldR
Constructor for RDBESDataObject classnewRDBESDataObject
A RDBESDataObject converted from package SDAResources dataset agstratPckg_SDAResources_agstrat_H1
A Multi-Stage RDBESDataObject converted from package survey dataset apiclus2Pckg_survey_apiclus2_H1
A RDBESDataObject converted from package survey dataset apistratPckg_survey_apistrat_H1
Private function to get sub-sample level and top-level SAid for SA dataprepareSubSampleLevelLookup
Print method for RDBESDataObjectprint.RDBESDataObject sort.RDBESDataObject summary.RDBESDataObject
Private function to process the lower hierarchies when creating the RDBESEstObjectprocRDBESEstObjLowHier
Private function to process the upper hierarchies when creating the RDBESEstObjectprocRDBESEstObjUppHier
Remove rows which are not pointing to a valid SpecliestListDetails (SL) records i.e.those rows which have a value of SpeciesListName that does not exist in the SL table.removeBrokenSpeciesListLinks
Remove rows which are not pointing to a valid VesselDetails (VD) records i.e. those rows which have a value of VDid that does not exist in the VD table.removeBrokenVesselLinks
Run basic checks on selection methods and probabilitiesrunChecksOnSelectionAndProbs
For a given RDBESDataObject convert the required columns to the correct data types. (This function can cause an error if we have data in the columns that can't be cast to the desired data type.)setRDBESDataObjectDataTypes
One quarter of sample data from swedish shrimp landings of the SWE_OTB_CRU_32-69_0_0 fisheryshrimps
One quarter of sample data from swedish shrimp catches of the SWE_OTB_CRU_32-69_0_0 fisheryshrimpsStrat
The tables required for each RDBES hierarchy.tablesInRDBESHierarchies
Function which changes the value of SAspeCode in SA.updateSAwithTaxonFromSL
Check Whether an 'RDBESDataObject' is in a Valid FormatcheckRDBESDataObject validateRDBESDataObject
Checks the data types of the columns in an RDBESDataObject against an expected list of data types. Any differences are returnedvalidateRDBESDataObjectDataTypes
check RDBES Raw Object Content Private function to do some basic checks on the content of the RDBESDataObject (e.g. all required field names are present). Function is only used by checkRDBESDataObject and should only be passed a list of non-null objectsvalidateRDBESDataObjectDuplicates
check RDBES Data Object field names Private function to do some checks on the columns of an RDBESDataObject - 1. are all required fields present? 2) are there any extra fields present? It is used by validateRDBESDataObject() and should only be passed a list of non-null objectsvalidateRDBESDataObjectFieldNames
Check whether an object is a valid RDBESEstObjectvalidateRDBESEstObject
A dataset containing aphia records for species found in icesSpecWoRMSwormsAphiaRecord