About floraR

Open source tools for accessing, analyzing, and curating plant and algae data from the Flora e Funga do Brasil platform

Overview

floraR is an R package for accessing, analyzing, and curating taxonomic and distributional data on plants and algae from the Flora e Funga do Brasil (FFB) platform, maintained by the Rio de Janeiro Botanical Garden. It offers a comprehensive interface to the FFB IPT data portal: downloading, parsing, filtering, and exploring versioned Darwin Core Archive (DwC-A) checklist data — from browsing by taxonomic, geographic, or trait criteria to resolving your own species name lists against it.

But floraR is designed to do more than retrieve data from FFB: it is meant to help taxonomists expand the current FFB monographs. By cross-checking FFB against global resources - the species distributions of Plants of the World Online and the type specimens collected in Brazil that herbaria publish through GBIF - it points to species that are recorded in Brazil but not yet treated in FFB, giving specialists a concrete starting point for bringing each monograph closer to a complete account of the Brazilian flora.

floraR also assists taxonomic experts contributing to FFB by simplifying the integration of new species names and records from global biodiversity repositories such as IPNI, POWO, REFLORA, and GBIF.

Flora e Funga do Brasil

Brazil harbors the richest plant, algal, and fungal diversity in the world (BFG 2022). The checklist that documents it began in 2008 as the Lista de Espécies da Flora do Brasil, evolved into Flora do Brasil 2020 to meet Brazil’s Global Strategy for Plant Conservation commitments, and — after incorporating fungi — became Flora e Funga do Brasil.

For each accepted name, FFB records nomenclatural status, taxonomic classification, geographic distribution, endemism, life form, habitat, and vegetation type — a validated taxonomic backbone assembled collaboratively by hundreds of taxonomists and published as versioned Darwin Core Archives.

Package Description

Package: floraR Type: R Package Version: 1.0.0

Author: Domingos Cardoso (@DBOSlab ORCID)

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

Features

Comprehensive interface to the Flora e Funga do Brasil IPT data portal
Version tracking and offline-capable parsing of downloaded DwC-A datasets
Checklist filtering by taxonomic, geographic, and trait-based criteria
Exact and fuzzy (Levenshtein-distance) name resolution against the checklist
Taxonomic hierarchy traversal at any rank, from class down to species
Gap analysis: species recorded in Brazil by Plants of the World Online, or with type specimens collected in Brazil (GBIF), but still missing from FFB - to help expand FFB monographs
Candidate new state records: Brazilian states with specimen evidence (GBIF, REFLORA, speciesLink) absent from a taxon’s FFB distribution
Tools for data curation and integration with global biodiversity repositories
Tidyverse-integrated workflows throughout

Contribute

You can contribute to floraR 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

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

Acknowledgements

Development of floraR 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 floraR" subtitle: "Open source tools for accessing, analyzing, and curating plant and algae data from the Flora e Funga do Brasil platform" format: html: toc: true --- <style> body { background-image: url('/figures/ffb-background.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, 0.85); z-index: -1; } </style> ## Overview `floraR` is an R package for accessing, analyzing, and curating taxonomic and distributional data on plants and algae from the [Flora e Funga do Brasil (FFB)](https://floradobrasil.jbrj.gov.br/consulta/) platform, maintained by the [Rio de Janeiro Botanical Garden](https://www.gov.br/jbrj/pt-br). It offers a comprehensive interface to the FFB [IPT data portal](https://ipt.jbrj.gov.br/jbrj/resource?r=lista_especies_flora_brasil): downloading, parsing, filtering, and exploring versioned Darwin Core Archive (DwC-A) checklist data — from browsing by taxonomic, geographic, or trait criteria to resolving your own species name lists against it. But `floraR` is designed to do more than retrieve data from FFB: it is meant to help taxonomists expand the current FFB monographs. By cross-checking FFB against global resources - the species distributions of [Plants of the World Online](https://powo.science.kew.org) and the type specimens collected in Brazil that herbaria publish through [GBIF](https://www.gbif.org) - it points to species that are recorded in Brazil but not yet treated in FFB, giving specialists a concrete starting point for bringing each monograph closer to a complete account of the Brazilian flora. `floraR` also assists taxonomic experts contributing to FFB by simplifying the integration of new species names and records from global biodiversity repositories such as IPNI, POWO, REFLORA, and GBIF. ## Flora e Funga do Brasil Brazil harbors the richest plant, algal, and fungal diversity in the world ([BFG 2022](https://doi.org/10.1002/tax.12640)). The checklist that documents it began in 2008 as the *Lista de Espécies da Flora do Brasil*, evolved into [Flora do Brasil 2020](http://doi.org/10.47871/jbrj2021004) to meet Brazil's Global Strategy for Plant Conservation commitments, and — after incorporating fungi — became [Flora e Funga do Brasil](https://floradobrasil.jbrj.gov.br/consulta/). For each accepted name, FFB records nomenclatural status, taxonomic classification, geographic distribution, endemism, life form, habitat, and vegetation type — a validated taxonomic backbone assembled collaboratively by hundreds of taxonomists and published as versioned Darwin Core Archives. ## Package Description Package: `floraR` Type: R Package Version: 1.0.0 Author: Domingos Cardoso ([\@DBOSlab](https://github.com/DBOSlab) [ORCID](https://orcid.org/0000-0001-7072-2656)) Maintainer: Domingos Cardoso (<domingoscardoso@jbrj.gov.br>) ### Features - Comprehensive interface to the Flora e Funga do Brasil IPT data portal - Version tracking and offline-capable parsing of downloaded DwC-A datasets - Checklist filtering by taxonomic, geographic, and trait-based criteria - Exact and fuzzy (Levenshtein-distance) name resolution against the checklist - Taxonomic hierarchy traversal at any rank, from class down to species - Gap analysis: species recorded in Brazil by Plants of the World Online, or with type specimens collected in Brazil (GBIF), but still missing from FFB - to help expand FFB monographs - Candidate new state records: Brazilian states with specimen evidence (GBIF, REFLORA, speciesLink) absent from a taxon's FFB distribution - Tools for data curation and integration with global biodiversity repositories - Tidyverse-integrated workflows throughout ## Contribute You can contribute to `floraR` 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 `floraR` is [open source software](/LICENSE.md). Open tools empower science through reproducibility, accessibility, and equitable knowledge sharing. ## Acknowledgements Development of `floraR` 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.