R: Occurrence Data Cleaning

# Occurrence Data Cleaning

## Documentation for package ‘BeeBDC’ version 1.3.4

- DESCRIPTION file
- Package NEWS
- Package README

## 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
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
ChaoWrapper | Parallel estimation of species richness in a community using iChao
chordDiagramR | Build a chord diagram of duplicate occurrence links
ColTypeR | Sets up column names and types
continentOutlieRs | Flag continent-level outliers with a provided checklist.
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
GBIFissues | Flags records with GBIF issues
ggRichnessWrapper | ggplot2 extension for a Chao- and iNEXT-wrapper outputs
harmoniseR | Harmonise taxonomy of occurrence data
idMatchR | Attempt to match database_ids from a prior run
importOccurrences | Imports the most-recent repoMerge data
iNEXTwrapper | Parallel estimation of species richness in a community using iNEXT
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
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
testChecklist | An example of the beesChecklist file
testTaxonomy | An example of the beesTaxonomy file
USGS_formatter | Find, import, and format USGS data to Darwin Core