Occurrence Data Cleaning


[Up] [Top]

Documentation for package ‘BeeBDC’ version 1.0.4

Help Pages

atlasDownloader Download occurrence data from the Atlas of Living Australia (ALA)
BeeBDCQuery Query the bee taxonomy and country checklist
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
ColTypeR Sets up column names and types
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
GBIFissues Flags records with GBIF issues
harmoniseR Harmonise taxonomy of bee occurrence data
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_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
jbd_Ctrans_chunker Wraps jbd_coordinates_transposed to identify and fix transposed occurrences
manualOutlierFindeR Finds outliers, and their duplicates, as determined by experts
PaigeIntegrater Integrate manually-cleaned data from Paige Chesshire
plotFlagSummary Generate a plot summarising flagged data
readr_Arm A wrapper for all of the data readr_functions
readr_ASP A wrapper for all of the data readr_functions
readr_Bal A wrapper for all of the data readr_functions
readr_BBD A wrapper for all of the data readr_functions
readr_BeeBDC A wrapper for all of the data readr_functions
readr_BMin A wrapper for all of the data readr_functions
readr_BMont A wrapper for all of the data readr_functions
readr_CAES A wrapper for all of the data readr_functions
readr_Col A wrapper for all of the data readr_functions
readr_Dor A wrapper for all of the data readr_functions
readr_EaCO A wrapper for all of the data readr_functions
readr_Ecd A wrapper for all of the data readr_functions
readr_EcoS A wrapper for all of the data readr_functions
readr_EPEL A wrapper for all of the data readr_functions
readr_FSCA A wrapper for all of the data readr_functions
readr_Gai A wrapper for all of the data readr_functions
readr_GeoL A wrapper for all of the data readr_functions
readr_JoLa A wrapper for all of the data readr_functions
readr_KP A wrapper for all of the data readr_functions
readr_Lic A wrapper for all of the data readr_functions
readr_MABC A wrapper for all of the data readr_functions
readr_MEPB A wrapper for all of the data readr_functions
readr_MPUJ A wrapper for all of the data readr_functions
readr_PALA A wrapper for all of the data readr_functions
readr_SMC A wrapper for all of the data readr_functions
readr_STRI A wrapper for all of the data readr_functions
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
USGS_formatter Find, import, and format USGS data to Darwin Core