refloraR: An R package for efficiently retrieving and analyzing plant specimen data from the Herbário Virtual Reflora
Abstract 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.
Authors
- Fabiana Ranzato Filardi (ORCID: https://orcid.org/0000-0002-0372-4325)
- Domingos Cardoso (ORCID: https://orcid.org/0000-0001-7072-2656)
- Rafaela Campostrini Forzza (ORCID: https://orcid.org/0000-0002-7035-9313)
- Ana Flávia Alves Versiane (ORCID: https://orcid.org/0000-0001-9634-0365)
- Paula Leitman (ORCID: https://orcid.org/0000-0002-2997-3784)
- Carlos Calderón del Cid (ORCID: https://orcid.org/0000-0002-3897-4615)
Institutions
- Universidade de São Paulo (BR)
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro (BR)
- Instituto Chico Mendes de Conservação da Biodiversidade (BR)
Publication Details
- Journal
- Applications in Plant Sciences
- Published
- 2026-09-16
- DOI
- https://doi.org/10.1002/aps3.70081
- Primary Topic
- Species Distribution and Climate Change
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- Fundação de Amparo à Pesquisa do Estado de São Paulo
- Conselho Nacional de Desenvolvimento Científico e Tecnológico
- Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro