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Published on: March 8, 2018
refloraR: An R package for efficiently retrieving and analyzing plant specimen data from the Herbário Virtual Reflora
Carlos Calderón Del Cid1, Ana Flávia Alves Versiane2, Paula Leitman2
1Universidade de São Paulo São Paulo São Paulo Brazil.
Premise:
Advances in the digitization of herbarium collections are enabling open access to specimen data for research and conservation. In Brazil, the Herbário Virtual Reflora (HVR) hosts over 4.8 million high-resolution images of botanical specimens and their associated data from 86 national and international herbaria.
Methods And Results:
To facilitate access and use of HVR data in biodiversity research, we developed the R package refloraR. This tool interacts with the HVR Integrated Publishing Toolkit (IPT) to download, parse, summarize, and filter herbarium records in Darwin Core Archive (DwC-A) and dataframes. It also retrieves occurrence records and indeterminate specimens for any hierarchical level. We provide a working example that combines the refloraR functions for quantifying indeterminate specimens as an indicator of taxonomic gaps within and among collections.
Conclusions:
The refloraR package supports reproducible workflows in systematics, conservation, and ecology. By enabling the efficient retrieval of specimen data, it integrates the HVR into modern biodiversity informatics and democratizes access to natural history collections.
