Man pages for BeeBDC
Occurrence Data Cleaning

atlasDownloaderDownload occurrence data from the Atlas of Living Australia...
BeeBDCQueryQuery the bee taxonomy and country checklist
bees3spA flagged dataset of 105 random bee occurrence records from...
beesChecklistDownload a country-level checklist of bees from Discover Life
beesCountrySubsetA simple scientificName and country_suggested test dataset
beesFlaggedA flagged dataset of 100 random bee occurrence records
beesRawA dataset of 100 random bee occurrence records without flags...
beesTaxonomyDownload a nearly complete taxonomy of bees globally
ChaoWrapperParallel estimation of species richness in a community using...
chordDiagramRBuild a chord diagram of duplicate occurrence links
ColTypeRSets up column names and types
continentOutlieRsFlag continent-level outliers with a provided checklist.
coordUncerFlagRFlag occurrences with an uncertainty threshold
countryHarmoniseRMatch and harmonise country names
countryNameCleanRFix country name issues using a user-input list
countryOutlieRsFlag country-level outliers with a provided checklist.
dataProvTablesBuild a table of data providers for bee occurrence records
dataSaverSimple function to save occurrence AND EML data as a list
dateFindRFind dates in other columns
diagonAlleyFind fill-down errors
dirMakerSet up global directory paths and create folders
dupePlotRCreate a compound bar graph of duplicate data sources
dupeSummaryIdentifies duplicate occurrence records
fileFinderFinds files within a directory
flagAbsentFlags occurrences that are marked as absent
flagLicenseFlag license protected records
flagRecorderLoads, appends, and saves occurrence flag data
flagSummaryTableBuild a per-species summary for each and all flags
formattedCombinerCombine the formatted USGS data with the main dataset
GBIFissuesFlags records with GBIF issues
ggRichnessWrapperggplot2 extension for a Chao- and iNEXT-wrapper outputs
harmoniseRHarmonise taxonomy of occurrence data
idMatchRAttempt to match database_ids from a prior run
importOccurrencesImports the most-recent repoMerge data
iNEXTwrapperParallel estimation of species richness in a community using...
interactiveMapRCreates interactive html maps for species
jbd_CfC_chunkerGet country names from coordinates
jbd_coordCountryInconsistentFlags coordinates that are inconsistent with the stated...
jbd_coordinates_precisionFlags coordinates for imprecision
jbd_coordinates_transposedIdentify transposed geographic coordinates
jbd_create_figuresCreate figures reporting the results of the bdc/BeeBDC...
jbd_Ctrans_chunkerWraps jbd_coordinates_transposed to identify and fix...
manualOutlierFindeRFinds outliers, and their duplicates, as determined by...
PaigeIntegraterIntegrate manually-cleaned data from Paige Chesshire
plotFlagSummaryGenerate a plot summarising flagged data
readr_BeeBDCA wrapper for all of the data readr_functions
repoFinderFind GBIF, ALA, iDigBio, and SCAN files in a directory
repoMergeImport occurrences from GBIF, ALA, iDigBio, and SCAN...
richnessEstimateREstimate country, continental, and global species richnesses
richnessPrepRPrepare occurrence, taxonomy, and checklist data for richness...
summaryFunCreate or update the .summary flag column
summaryMapsCreate country-level summary maps of species and occurrence...
taxadbToBeeBDCImport and convert taxadb taxonomies to BeeBDC format
testChecklistAn example of the beesChecklist file
testTaxonomyAn example of the beesTaxonomy file
USGS_formatterFind, import, and format USGS data to Darwin Core
BeeBDC documentation built on Nov. 5, 2025, 5:25 p.m.