BeeDC: An R package and globally synthesised and flagged bee occurrence dataset

Dorey, J. B.; Fischer, E. E.; Chesshire, P. R.; Nava-Bolanos, A.; OReilly, R. L.; Bossert, S.; Collins, S. M.; Lichtenberg, E. M.; Tucker, E. M.; Smith-Pardo, A.; Falcon-Brindis, A.; Guevara, D. A.; Ribeiro, B.; de Pedro, D.; Pickering, J.; James, K.-L.; Parys, K. A.; McCabe, L. M.; Rogan, M. S.; Minckley, R. L.; Velazco, S. J. E.; Griswold, T.; Zarrillo, T. A.; Jetz, W.; Sica, Y. V.; Orr, M. C.; Guzman, L. M.; Ascher, J. A.; Hughes, A. C.; Cobb, N. S.

doi:10.1101/2023.06.30.547152

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bioRxiv · 10.1101/2023.06.30.547152

BeeDC: An R package and globally synthesised and flagged bee occurrence dataset

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Abstract

Species occurrence data are foundational for research, conservation, and science communication, but the limited availability and accessibility of reliable data represents a major obstacle, particularly for insects, which face mounting pressures. We present BeeBDC, a new R package, and a global bee occurrence dataset to address this issue. We combined >18.3 million bee occurrence records from multiple public repositories (GBIF, SCAN, iDigBio, USGS, ALA) and smaller datasets, then standardised, flagged, deduplicated, and cleaned the data using the reproducible BeeBDC R-workflow. Specifically, we harmonised species names (following established global taxonomy), country names, and collection dates and we added record-level flags for a series of potential quality issues. These data are provided in two formats, "cleaned" and "flagged-but-uncleaned". The BeeBDC package with online documentation provides end users the ability to modify filtering parameters to address their research questions. By publishing reproducible R workflows and globally cleaned datasets, we can increase the accessibility and reliability of downstream analyses. This workflow can be implemented for other taxa to support research and conservation.

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Dorey, J. B., Fischer, E. E., Chesshire, P. R., Nava-Bolanos, A., OReilly, R. L., Bossert, S., Collins, S. M., Lichtenberg, E. M., Tucker, E. M., Smith-Pardo, A., Falcon-Brindis, A., Guevara, D. A., Ribeiro, B., de Pedro, D., Pickering, J., James, K.-L., Parys, K. A., McCabe, L. M., Rogan, M. S., Minckley, R. L., Velazco, S. J. E., Griswold, T., Zarrillo, T. A., Jetz, W., Sica, Y. V., Orr, M. C., Guzman, L. M., Ascher, J. A., Hughes, A. C., Cobb, N. S.. 2023-07-02. BeeDC: An R package and globally synthesised and flagged bee occurrence dataset. https://doi.org/10.1101/2023.06.30.547152

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