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.
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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
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Upcoming version…
- A completely new 2026 pull is in the making…
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Version 1.3.4 runs of early data — 05_cleaned_database_2023v1_3_4.csv.zip and 05_unCleaned_database_2023v1_3_4.csv.zip — This new run of an early dataset from start to finish using BeeBDC version 1.3.4 has the following changes:
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()andBeeBDC::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.
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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 17 scientificNames where names were “successfully” matched to genus/subgenus-level taxa. 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. Not as well that five species (across 38 records) match a species name where they are missing an entry in the genus column. These appear in the names_clean column, however, they are correctly flagged under the .invalidName column.
A .csv file with the database_id for the problematic genera records is available at LINK.
scientificName verbatimScientificName_old n_old verbatimScientificName_v1.3.4 n_v1.3.4 Lasioglossum rohweri Lasioglossum 23 Lasioglossum 23 Lasioglossum albuquerquense Lasioglossum 5 Lasioglossum 5 Megachile texana Megachile 3 Megachile 3 Augochloropsis metallica Bombus 2 Bombus 2 Megachile apicalis Megachile 1 Megachile 1 Megachile inermis Bombus 1 Bombus 1 Andrena columbiana Viereck, 1917 Andrena 21534 NA NA Apis mellifera Linnaeus, 1758 Apis 3226 NA NA Apis mellifera Linnaeus, 1758 Apis (Apis) 45 NA NA Bombus hypnorum (Linnaeus, 1758) Bombus 42394 NA NA Bombus hypnorum (Linnaeus, 1758) Bombus (Psithyrus) 989 NA NA Bombus hypnorum (Linnaeus, 1758) Bombus (Melanopygus) 1 NA NA Bombus hypnorum (Linnaeus, 1758) Bombus (Pyrobombus) 4 NA NA Bombus hypnorum (Linnaeus, 1758) Bombus (Mendacibombus) 2 NA NA Coelioxys texanus Cresson, 1872 Coelioxys 3233 NA NA Coelioxys texanus Cresson, 1872 Coelioxys (Cyrtocoelioxys) 228 NA NA Coelioxys texanus Cresson, 1872 Coelioxys (Glyptocoelioxys) 112 NA NA Coelioxys texanus Cresson, 1872 Coelioxys (Acrocoelioxys) 56 NA NA Coelioxys texanus Cresson, 1872 Coelioxys (Neocoelioxys) 13 NA NA Coelioxys texanus Cresson, 1872 Coelioxys (Melanocoelioxys) 2 NA NA Coelioxys texanus Cresson, 1872 Coelioxys (Haplocoelioxys) 2 NA NA Colletes kincaidii Cockerell, 1898 Colletes 13969 NA NA Dasypoda argentata Panzer, 1809 Dasypoda 15 NA NA Dufourea longispinis (Wu, 1987) Halictoides 4 NA NA Euglossa macrorhyncha Dressler, 1982 Euglossa 2389 NA NA Euglossa macrorhyncha Dressler, 1982 Euglossa (Glossura) 90 NA NA Halictus simplex Blüthgen, 1923 Halictus 25346 NA NA Lasioglossum albipenne (Robertson, 1890) Lasioglossum 102320 NA NA Leioproctus leai (Cockerell, 1913) Leioproctus 18544 NA NA Leioproctus leai (Cockerell, 1913) Leioproctus (Andrenopsis) 9 NA NA Leioproctus leai (Cockerell, 1913) Leioproctus (Baeocolletes) 6 NA NA Leioproctus leai (Cockerell, 1913) Leioproctus (Cladocerapis) 176 NA NA Leioproctus leai (Cockerell, 1913) Leioproctus (Euryglossidia) 82 NA NA Leioproctus leai (Cockerell, 1913) Leioproctus (Exleycolletes) 22 NA NA Leioproctus leai (Cockerell, 1913) Leioproctus (Filiglossa) 86 NA NA Leioproctus leai (Cockerell, 1913) Leioproctus (Lamprocolletes) 12 NA NA Leioproctus leai (Cockerell, 1913) Leioproctus (Leioproctus) 1230 NA NA Leioproctus leai (Cockerell, 1913) Leioproctus (Protomorpha) 58 NA NA Leioproctus leai (Cockerell, 1913) Leioproctus (Protodiscelis) 150 NA NA Leioproctus leai (Cockerell, 1913) Leioproctus (Perditomorpha) 118 NA NA Leioproctus leai (Cockerell, 1913) Leioproctus (Tetraglossula) 90 NA NA Leioproctus leai (Cockerell, 1913) Leioproctus (Pygopasiphae) 6 NA NA Leioproctus leai (Cockerell, 1913) Leioproctus (Nomiocolletes) 4 NA NA Leioproctus leai (Cockerell, 1913) Leioproctus (Goniocolletes) 82 NA NA Macropis steironematis Robertson, 1891 Macropis 11 NA NA Megachile brevis Say, 1837 Megachile 19739 NA NA Melecta diligens Lieftinck, 1983 Melecta (Melecta) 6 NA NA Melecta diligens Lieftinck, 1983 Melecta 287 NA NA Melissodes microstictus Cockerell, 1905 Melissodes 26646 NA NA Osmia coloradensis Cresson, 1878 Osmia 10852 NA NA Xylocopa virginica (Linnaeus, 1771) Xylocopa 9448 NA NA Xylocopa virginica (Linnaeus, 1771) Xylocopa (Koptortosoma) 1216 NA NA Xylocopa virginica (Linnaeus, 1771) Xylocopa (Lestis) 155 NA NA Xylocopa virginica (Linnaeus, 1771) Xylocopa (Schonnherria) 75 NA NA Xylocopa virginica (Linnaeus, 1771) Xylocopa (Mesotrichia) 18 NA NA