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

Institutions

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

Controls
|||
ALL TIME
JAN
FEB
MAR
APR
MAY
JUN
JUL
AUG
SEP
article

refloraR: An R package for efficiently retrieving and analyzing plant specimen data from the Herbário Virtual Reflora

Fabiana Ranzato Filardi, Domingos Cardoso, Rafaela Campostrini Forzza, Ana Flávia Alves Versiane et al.
Applications in Plant Sciences
Species Distribution and Climate Change
article

refloraR: An R package for efficiently retrieving and analyzing plant specimen data from the Herbário Virtual Reflora

Fabiana Ranzato Filardi, Domingos Cardoso, Rafaela Campostrini Forzza, Ana Flávia Alves Versiane, Paula Leitman, Carlos Calderón del Cid
article en

Abstract

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.

Applications in Plant Sciences
Universidade de São Paulo (BR), Instituto de Pesquisas Jardim Botânico do Rio de Janeiro (BR), Instituto Chico Mendes de Conservação da Biodiversidade (BR)
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
Life in Land
Openalex Percentile: Top 13%
Species Distribution and Climate Change
AI Navigator

Ask Laika to Summarize, Analyze, and Connect papers live on the map.

Summarize Papers & Methodologies

Extract key findings, datasets, and comparative methods across publications.

Benchmark Rankings & Visual Analytics

Rank top research institutions, authors, funders, topics, and journals by Field-Weighted Citation Impact (FWCI) and paper volume with instant charts.

Connect Distant Disciplines

Bridge topological clusters on the map to find hidden collaborative intersections.