About refloraR

Open source tools to explore plant specimen collections from REFLORA Virtual Herbarium

Overview

refloraR is an R package for exploring plant specimen collections from the REFLORA Virtual Herbarium, hosted by the Rio de Janeiro Botanical Garden. The package interacts with the REFLORA Integrated Publishing Toolkit (IPT) by readily downloading full specimen records in Darwin Core Format. It also provides functions to summarize and filter data by taxonomic or geographical criteria.

The REFLORA Programme

Brazil holds the richest plant diversity in the world (BFG 2022). Historically, many plant specimens were sent to European herbaria during the 18th–19th centuries. These collections formed the basis for many species descriptions and the monumental Flora brasiliensis (Martius, Eichler & Urban, 1840–1906).

Launched in 2010, the REFLORA/CNPq Programme aimed to digitize and repatriate information on Brazilian plant specimens stored abroad. In 2014, the programme expanded in partnership with SiBBr and IFN. The data are published via the REFLORA Virtual Herbarium.

Developed by the JBRJ and COPPE/UFRJ, the platform supports taxonomic validation and collaboration via the Flora e Funga do Brasil initiative.

The REFLORA Virtual Herbarium

The Reflora Virtual Herbarium was commissioned by CNPq to JBRJ in 2010 to provide centralized, high-resolution, publicly accessible data on Brazilian specimens. It replicates key functions of physical herbarium curation. Curators can re-determine and typify specimens, while taxonomists contribute to species validation. Over 900 taxonomists have contributed to the platform.

Early partners included herbaria K, P, and RB, with later support from SiBBr and IFN. The initiative continues to digitize Brazilian and international collections.

Package Description

Package: refloraR
Type: R Package
Version: 1.0.0

Authors: Domingos Cardoso (@DBOSlab ORCID) and Carlos Calderón (@caldecid ORCID)

Maintainer: Domingos Cardoso (domingoscardoso@jbrj.gov.br)

Features

Retrieve specimen records by taxonomic/geographic filters
Summarize collections and data availability
Supports Darwin Core Archive (DwC-A) standards
Fully integrates with tidyverse workflows
Includes data visualization and mapping support

Contribute

You can contribute to refloraR by:

Opening issues for feedback or bug reports
Submitting pull requests for fixes or enhancements
Suggesting or developing new features (please open an issue for discussion first)

License

refloraR is open source software. Open tools empower science through reproducibility, accessibility, and equitable knowledge sharing.

Acknowledgements

Development of refloraR is led by the Rio de Janeiro Botanical Garden (JBRJ), in collaboration with the biodiversity and informatics communities. We also gratefully acknowledge the financial support provided by CNPq - Conselho Nacional de Desenvolvimento Científico e Tecnológico, Brazil’s National Council for Scientific and Technological Development, and FINEP - Financiadora de Estudos e Projetos, Brazil’s Funding Authority for Studies and Projects.

--- title: "About refloraR" subtitle: "Open source tools to explore plant specimen collections from REFLORA Virtual Herbarium" format: html: toc: true --- <style> body { background-image: url('/figures/reflora_bg.png'); background-repeat: repeat-y; background-size: cover; background-attachment: fixed; background-position: top center; position: relative; z-index: 0; } .background-overlay { position: fixed; top: 0; left: 0; width: 100%; height: 100%; background-color: rgba(255, 255, 255, 0.8); /* white with 80% opacity */ z-index: -1; } </style> ## Overview `refloraR` is an R package for exploring plant specimen collections from the [REFLORA Virtual Herbarium](https://ipt.jbrj.gov.br/reflora), hosted by the [Rio de Janeiro Botanical Garden](https://www.gov.br/jbrj). The package interacts with the REFLORA Integrated Publishing Toolkit (IPT) by readily downloading full specimen records in Darwin Core Format. It also provides functions to summarize and filter data by taxonomic or geographical criteria. ## The REFLORA Programme Brazil holds the richest plant diversity in the world ([BFG 2022](https://doi.org/10.1002/tax.12640)). Historically, many plant specimens were sent to European herbaria during the 18th–19th centuries. These collections formed the basis for many species descriptions and the monumental *Flora brasiliensis* ([Martius, Eichler & Urban, 1840–1906](https://www.biodiversitylibrary.org/bibliography/454)). Launched in 2010, the REFLORA/CNPq Programme aimed to digitize and repatriate information on Brazilian plant specimens stored abroad. In 2014, the programme expanded in partnership with SiBBr and IFN. The data are published via the [REFLORA Virtual Herbarium](https://floradobrasil.jbrj.gov.br/reflora/herbarioVirtual/ConsultaPublicoHVUC/ConsultaPublicoHVUC.do). Developed by the [JBRJ](https://www.gov.br/jbrj) and [COPPE/UFRJ](https://coppe.ufrj.br/en/home-en/), the platform supports taxonomic validation and collaboration via the [Flora e Funga do Brasil](https://floradobrasil.jbrj.gov.br/consulta/) initiative. ## The REFLORA Virtual Herbarium The Reflora Virtual Herbarium was commissioned by CNPq to JBRJ in 2010 to provide centralized, high-resolution, publicly accessible data on Brazilian specimens. It replicates key functions of physical herbarium curation. Curators can re-determine and typify specimens, while taxonomists contribute to species validation. Over 900 taxonomists have contributed to the platform. Early partners included herbaria [**K**](https://www.kew.org), [**P**](https://www.mnhn.fr/fr/collection-des-plantes-vasculaires), and [**RB**](https://www.gov.br/jbrj), with later support from [**SiBBr**](https://www.sibbr.gov.br) and [**IFN**](https://www.gov.br/florestal/pt-br/assuntos/ifn). The initiative continues to digitize Brazilian and international collections. ## Package Description Package: `refloraR` Type: R Package Version: 1.0.0 Authors: Domingos Cardoso ([\@DBOSlab](https://github.com/DBOSlab) [ORCID](https://orcid.org/0000-0001-7072-2656)) and Carlos Calderón ([\@caldecid](https://github.com/caldecid) [ORCID](https://orcid.org/0000-0002-3897-4615)) Maintainer: Domingos Cardoso (<domingoscardoso@jbrj.gov.br>) ### Features - Retrieve specimen records by taxonomic/geographic filters - Summarize collections and data availability - Supports Darwin Core Archive (DwC-A) standards - Fully integrates with tidyverse workflows - Includes data visualization and mapping support ## Contribute You can contribute to `refloraR` by: - Opening issues for feedback or bug reports - Submitting pull requests for fixes or enhancements - Suggesting or developing new features (please open an issue for discussion first) ## License `refloraR` is [open source software](/LICENSE.md). Open tools empower science through reproducibility, accessibility, and equitable knowledge sharing. ## Acknowledgements Development of `refloraR` is led by the [Rio de Janeiro Botanical Garden (JBRJ)](https://www.gov.br/jbrj), in collaboration with the biodiversity and informatics communities. We also gratefully acknowledge the financial support provided by [CNPq - Conselho Nacional de Desenvolvimento Científico e Tecnológico](https://www.gov.br/cnpq/pt-br), Brazil's National Council for Scientific and Technological Development, and [FINEP - Financiadora de Estudos e Projetos](https://www.gov.br/finep/pt-br), Brazil's Funding Authority for Studies and Projects.