All functions

BeeBDCQuery()

Query the bee taxonomy and country checklist

ColTypeR()

Sets up column names and types

GBIFissues()

Flags records with GBIF issues

harmoniseR()

Harmonise taxonomy of bee 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

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

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

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

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