Package: BeeBDC 1.2.1

James B. Dorey

BeeBDC: Occurrence Data Cleaning

Flags and checks occurrence data that are in Darwin Core format. The package includes generic functions and data as well as some that are specific to bees. This package is meant to build upon and be complimentary to other excellent occurrence cleaning packages, including 'bdc' and 'CoordinateCleaner'. This package uses datasets from several sources and particularly from the Discover Life Website, created by Ascher and Pickering (2020). For further information, please see the original publication and package website. Publication - Dorey et al. (2023) <doi:10.1101/2023.06.30.547152> and package website - Dorey et al. (2023) <https://github.com/jbdorey/BeeBDC>.

Authors:James B. Dorey [aut, cre, cph], Robert L. O'Reilly [aut], Silas Bossert [aut], Erica E. Fischer [aut]

BeeBDC_1.2.1.tar.gz
BeeBDC_1.2.1.tar.gz(r-4.5-noble)BeeBDC_1.2.1.tar.gz(r-4.4-noble)
BeeBDC_1.2.1.tgz(r-4.4-emscripten)BeeBDC_1.2.1.tgz(r-4.3-emscripten)
BeeBDC.pdf |BeeBDC.html✨
BeeBDC/json (API)
NEWS

# Install 'BeeBDC' in R:
install.packages('BeeBDC', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/jbdorey/beebdc/issues

Datasets:
  • bees3sp - A flagged dataset of 105 random bee occurrence records from the three species
  • beesFlagged - A flagged dataset of 100 random bee occurrence records
  • beesRaw - A dataset of 100 random bee occurrence records without flags or filters applied
  • testChecklist - An example of the beesChecklist file
  • testTaxonomy - An example of the beesTaxonomy file

3.85 score 6 scripts 307 downloads 44 exports 102 dependencies

Last updated 18 days agofrom:8e309296de. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 05 2024
R-4.5-linuxOKNov 05 2024

Exports:atlasDownloaderBeeBDCQuerybeesChecklistbeesTaxonomychordDiagramRColTypeRcontinentOutlieRscoordUncerFlagRcountryNameCleanRcountryOutlieRsdataProvTablesdataSaverdateFindRdiagonAlleydirMakerdupePlotRdupeSummaryfileFinderflagAbsentflagLicenseflagRecorderflagSummaryTableformattedCombinerGBIFissuesharmoniseRidMatchRimportOccurrencesinteractiveMapRjbd_CfC_chunkerjbd_coordCountryInconsistentjbd_coordinates_precisionjbd_coordinates_transposedjbd_create_figuresjbd_Ctrans_chunkermanualOutlierFindeRPaigeIntegraterplotFlagSummaryreadr_BeeBDCrepoFinderrepoMergesummaryFunsummaryMapstaxadbToBeeBDCUSGS_formatter

Dependencies:abindaskpassbitbit64circlizeclassclassIntclicliprcolorspaceCoordinateCleanercowplotcpp11crayoncrulcurldata.tableDBIdplyre1071fansifarverforcatsgenericsgeosphereggplot2ggspatialGlobalOptionsgluegtableherehmshttpcodehttrigraphisobandjpegjsonliteKernSmoothlabelinglatticelazyevallifecyclelubridatemagrittrMASSMatrixmgcvmgsubmimemunsellnlmeoaiopensslopenxlsxpaletteerpillarpkgconfigplyrpngprettyunitsprismaticprogressproxypurrrR6RColorBrewerRcppreadrrematch2rgbifrlangrnaturalearthrosmrprojrootrstudioapis2scalessfshapespstringistringrsysterratibbletidyrtidyselecttimechangetriebeardtzdbunitsurltoolsutf8vctrsviridisLitevroomwhiskerwithrwkxml2zip

Basic workflow

Rendered frombasic_workflow.Rmdusingknitr::rmarkdownon Nov 05 2024.

Last update: 2023-10-09
Started: 2023-09-15

BeeBDC vignette

Rendered fromBeeBDC_main.Rmdusingknitr::rmarkdownon Nov 05 2024.

Last update: 2024-11-04
Started: 2023-09-15

Readme and manuals

Help Manual

Help pageTopics
Download occurrence data from the Atlas of Living Australia (ALA)atlasDownloader
Query the bee taxonomy and country checklistBeeBDCQuery
A flagged dataset of 105 random bee occurrence records from the three speciesbees3sp
Download a country-level checklist of bees from Discover LifebeesChecklist
A flagged dataset of 100 random bee occurrence recordsbeesFlagged
A dataset of 100 random bee occurrence records without flags or filters appliedbeesRaw
Download a nearly complete taxonomy of bees globallybeesTaxonomy
Build a chord diagram of duplicate occurrence linkschordDiagramR
Sets up column names and typesColTypeR
Flag continent-level outliers with a provided checklist.continentOutlieRs
Flag occurrences with an uncertainty thresholdcoordUncerFlagR
Fix country name issues using a user-input listcountryNameCleanR
Flag country-level outliers with a provided checklist.countryOutlieRs
Build a table of data providers for bee occurrence recordsdataProvTables
Simple function to save occurrence AND EML data as a listdataSaver
Find dates in other columnsdateFindR
Find fill-down errorsdiagonAlley
Set up global directory paths and create foldersdirMaker
Create a compound bar graph of duplicate data sourcesdupePlotR
Identifies duplicate occurrence recordsdupeSummary
Finds files within a directoryfileFinder
Flags occurrences that are marked as absentflagAbsent
Flag license protected recordsflagLicense
Loads, appends, and saves occurrence flag dataflagRecorder
Build a per-species summary for each and all flagsflagSummaryTable
Combine the formatted USGS data with the main datasetformattedCombiner
Flags records with GBIF issuesGBIFissues
Harmonise taxonomy of bee occurrence dataharmoniseR
Attempt to match database_ids from a prior runidMatchR
Imports the most-recent repoMerge dataimportOccurrences
Creates interactive html maps for speciesinteractiveMapR
Get country names from coordinatesjbd_CfC_chunker
Flags coordinates that are inconsistent with the stated country namejbd_coordCountryInconsistent
Flags coordinates for imprecisionjbd_coordinates_precision
Identify transposed geographic coordinatesjbd_coordinates_transposed
Create figures reporting the results of the bdc/BeeBDC packagesjbd_create_figures
Wraps jbd_coordinates_transposed to identify and fix transposed occurrencesjbd_Ctrans_chunker
Finds outliers, and their duplicates, as determined by expertsmanualOutlierFindeR
Integrate manually-cleaned data from Paige ChesshirePaigeIntegrater
Generate a plot summarising flagged dataplotFlagSummary
A wrapper for all of the data readr_functionsreadr_Arm readr_ASP readr_Bal readr_BBD readr_BeeBDC readr_BMin readr_BMont readr_CAES readr_Col readr_Dor readr_EaCO readr_Ecd readr_EcoS readr_EPEL readr_FSCA readr_Gai readr_GeoL readr_JoLa readr_KP readr_Lic readr_MABC readr_MEPB readr_MPUJ readr_PALA readr_SMC readr_STRI readr_VicWam
Find GBIF, ALA, iDigBio, and SCAN files in a directoryrepoFinder
Import occurrences from GBIF, ALA, iDigBio, and SCAN downloadsrepoMerge
Create or update the .summary flag columnsummaryFun
Create country-level summary maps of species and occurrence numberssummaryMaps
Import and convert taxadb taxonomies to BeeBDC formattaxadbToBeeBDC
An example of the beesChecklist filetestChecklist
An example of the beesTaxonomy filetestTaxonomy
Find, import, and format USGS data to Darwin CoreUSGS_formatter