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All functions

BeeBDCQuery()
Query the bee taxonomy and country checklist
ChaoWrapper()
Parallel estimation of species richness in a community using iChao
ColTypeR()
Sets up column names and types
GBIFissues()
Flags records with GBIF issues
harmoniseR()
Harmonise taxonomy of occurrence data
PaigeIntegrater()
Integrate manually-cleaned data from Paige Chesshire
USGS_formatter()
Find, import, and format USGS data to Darwin Core
atlasDownloader()
Download occurrence data from the Atlas of Living Australia (ALA)
bees3sp
A flagged dataset of 105 random bee occurrence records from the three species
beesChecklist()
Download a country-level checklist of bees from Discover Life
beesCountrySubset
A simple scientificName and country_suggested test dataset
beesFlagged
A flagged dataset of 100 random bee occurrence records
beesRaw
A dataset of 100 random bee occurrence records without flags or filters applied
beesTaxonomy()
Download a nearly complete taxonomy of bees globally
chordDiagramR()
Build a chord diagram of duplicate occurrence links
coordUncerFlagR()
Flag occurrences with an uncertainty threshold
countryHarmoniseR()
Match and harmonise country names
countryNameCleanR()
Fix country name issues using a user-input list
countryOutlieRs()
Flag country-level outliers with a provided checklist.
dataProvTables()
Build a table of data providers for bee occurrence records
dataSaver()
Simple function to save occurrence AND EML data as a list
dateFindR()
Find dates in other columns
diagonAlley()
Find fill-down errors
dirMaker()
Set up global directory paths and create folders
dupePlotR()
Create a compound bar graph of duplicate data sources
dupeSummary()
Identifies duplicate occurrence records
fileFinder()
Finds files within a directory
flagAbsent()
Flags occurrences that are marked as absent
flagLicense()
Flag license protected records
flagRecorder()
Loads, appends, and saves occurrence flag data
flagSummaryTable()
Build a per-species summary for each and all flags
formattedCombiner()
Combine the formatted USGS data with the main dataset
ggRichnessWrapper()
ggplot2 extension for a Chao- and iNEXT-wrapper outputs
iNEXTwrapper()
Parallel estimation of species richness in a community using iNEXT
idMatchR()
Attempt to match database_ids from a prior run
importOccurrences()
Imports the most-recent repoMerge data
interactiveMapR()
Creates interactive html maps for species
jbd_CfC_chunker()
Get country names from coordinates
jbd_Ctrans_chunker()
Wraps jbd_coordinates_transposed to identify and fix transposed occurrences
jbd_coordCountryInconsistent()
Flags coordinates that are inconsistent with the stated country name
jbd_coordinates_precision()
Flags coordinates for imprecision
jbd_coordinates_transposed()
Identify transposed geographic coordinates
jbd_create_figures()
Create figures reporting the results of the bdc/BeeBDC packages
manualOutlierFindeR()
Finds outliers, and their duplicates, as determined by experts
plotFlagSummary()
Generate a plot summarising flagged data
readr_BeeBDC() readr_EPEL() readr_ASP() readr_BMin() readr_BMont() readr_Ecd() readr_Gai() readr_CAES() readr_KP() readr_EcoS() readr_GeoL() readr_EaCO() readr_MABC() readr_Col() readr_FSCA() readr_SMC() readr_Bal() readr_Lic() readr_Arm() readr_Dor() readr_MEPB() readr_BBD() readr_MPUJ() readr_STRI() readr_PALA() readr_JoLa() readr_VicWam()
A wrapper for all of the data readr_functions
repoFinder()
Find GBIF, ALA, iDigBio, and SCAN files in a directory
repoMerge()
Import occurrences from GBIF, ALA, iDigBio, and SCAN downloads
richnessEstimateR()
Estimate country, continental, and global species richnesses
richnessPrepR()
Prepare occurrence, taxonomy, and checklist data for richness estimation
summaryFun()
Create or update the .summary flag column
summaryMaps()
Create country-level summary maps of species and occurrence numbers
taxadbToBeeBDC()
Import and convert taxadb taxonomies to BeeBDC format