Data news

Data updates

Here I will try to manage a list of data updates and the over-arching changes in the datasets. These changes are commensurate with those in the “Package news” section where changes of functions within BeeBDC themselves are documented.

Bees taxonomy

The bee taxonomy files have been changed as below. Most changes represent a new pull from Discover Life and most also represent new manual additions due to mistakes, missing names, changes on Discover Life, or recent taxonomic revisions.

• 2026-07-09 current: https://api.figshare.com/v2/file/download/66453893

  • This version fixes an issue where not all names on Discover Life are separated by the usual delimiter and so not all synonyms are recognised. Additionally, recent Australian revisions by Leijs and Walker are included in addition to the new Discover Life pull. This is a major improvement on the prior version.

• 2026-05-04: https://api.figshare.com/v2/file/download/64193731

• 2026-01-12: https://open.flinders.edu.au/ndownloader/files/60945820

• 2024-06-17: https://open.flinders.edu.au/ndownloader/files/47089969

• 2023-11-29: https://open.flinders.edu.au/ndownloader/files/43331472

• 2023-10-10: https://open.flinders.edu.au/ndownloader/files/42613126

• 2023-09-20: https://open.flinders.edu.au/ndownloader/files/42402264

• Original: https://open.flinders.edu.au/ndownloader/files/42320595

Bees checklist

The updated checklist files represent new pulls from Discover Life.

• 2026-01-12 current: https://open.flinders.edu.au/ndownloader/files/60945823

• 2024-06-17: https://open.flinders.edu.au/ndownloader/files/47092720

• Original: https://open.flinders.edu.au/ndownloader/files/42320598

Bee occurrence dataset

The bee occurrence dataset has ended up being updated least frequently. This is in part because it takes this longest and because I prioritise updating the package and allowing researchers to use the datasets and functions as they see fit. This is, however, naive as many researchers will simply take the dateset provided and run with it. There are known issues with the dataset version and, thanks to Zach Portman, it has been pointed out that these should be made more obvious and documented. This may not be perfect documentation but major issues are highlighted below.

Clean and unclean datasets

• Upcoming version…

  • A completely new 2026 pull is in the making…

• Version 1.3.4 runs of early data — 05_cleaned_database_2023v1_3_3.csv.zip and 05_unCleaned_database_2023v1_3_3.csv.zip — This new run of an early dataset from start to finish using BeeBDC version 1.3.4 has the following changes:

  • Now has 19,890,804 rows of data (uncleaned).

  • Has the below taxonomic issues fixed. However, this process has highlighted that some names are not formatting correctly from the Discover Life taxonomy (bee taxonomy version 2026-05-04) and will be updated in BeeBDC 1.4.0 or before.

  • Better matches from BeeBDC::jbd_coordCountryInconsistent() and BeeBDC::dateFindR().

  • BeeBDC::harmoniseR() now matches names in the verbatimScientificName column if there is no match from the scientificName column.

  • Addition of flags from BeeBDC::continentOutlieRs().

  • BeeBDC::flagAbsent() also now checks if individualCount == 0.

• 05_cleaned_database_2024-02-15.csv.zip and 05_unCleaned_database_2024-02-15.csv.zip

  • Both of these datasets have an issue with 27 names where names were “successfully” matched to genus/subgenus-level taxa (this mostly applies to species-level names). This was a problem that was fixed in BeeBDC’s Bee taxonomy list from version 1.0.2. However, it was perpetuated because I re-ran the dataset thinking to fix it, but needed to run it from an earlier step, rather than just over the top of the original data versions. Hence, the problems persisted. The problem names are as below and are over-applied in the dataset are in the table below. Note, that these numbers are generated comparing the v1_3_3 data which has 19,890,804 rows (about a million more). Please consider using those datasets, where these issues are removed.

    scientificName	Additional false records (v1_3_3 data)
    Andrena columbiana Viereck, 1917	21,217
    Andrena Fabricius, 1775	20,050
    Apis mellifera Linnaeus, 1758	5,151
    Bombus hypnorum (Linnaeus, 1758)	87,703
    Coelioxys texanus Cresson, 1872	7,681
    Colletes kincaidii Cockerell, 1898	25,953
    Colletes Latreille, 1802	13,398
    Dasypoda argentata Panzer, 1809	99
    Dufourea longispinis (Wu, 1987)	8
    Euglossa macrorhyncha Dressler, 1982	6,273
    Halictus	16,199
    Halictus Latreille, 1804	4,847
    Halictus simplex Blüthgen, 1923	45,594
    Lasioglossum albipenne (Robertson, 1890)	179,682
    Lasioglossum Curtis, 1833	50,920
    Leioproctus boroniae (Cockerell, 1921)	2
    Leioproctus leai (Cockerell, 1913)	26,794
    Leioproctus michenerianus (E. A. B. Almeida, 2008)	4
    Macropis steironematis Robertson, 1891	41
    Megachile brevis Say, 1837	32,603
    Megachile Latreille, 1802	16,884
    Melecta diligens Lieftinck, 1983	484
    Melissodes microstictus Cockerell, 1905	38,447
    Osmia coloradensis Cresson, 1878	20,262
    Osmia Panzer, 1806	8,201
    Perditomorpha arnaui Moure, 1954	55
    Xylocopa virginica (Linnaeus, 1771)	20,270

  • Download links:

    • 05_cleaned_database_2024-02-15.csv.zip

    • 05_unCleaned_database_2024-02-15.csv.zip