Package index • BeeBDC

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

diversityPrepR(): Prepare occurrence, taxonomy, and checklist data for diversity estimation

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

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