About fungaR

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

Overview

fungaR is an R package for accessing, analyzing, and curating fungal taxonomic and distributional data 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 (including fungi-specific traits such as nutritional mode and substrate/host) to resolving your own species name lists against it.

Beyond data retrieval, fungaR also assists taxonomic experts contributing to FFB by cross-checking MycoBank, Species Fungorum (Index Fungorum), and Brazilian occurrence repositories — GBIF, speciesLink, and the Reflora Virtual Herbarium — to flag fungal species and state records that are plausibly Brazilian but still missing from the platform.

Flora e Funga do Brasil

Brazil harbors one of the richest fungal diversities in the world. 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 fungal name, FFB records nomenclatural status, taxonomic classification (Division, Order, Family, Genus), geographic distribution, endemism, nutritional/ecological mode, and substrate/host information — a validated taxonomic backbone assembled collaboratively by hundreds of taxonomists and mycologists, and published as versioned Darwin Core Archives.

Rede de Taxonomistas da Funga do Brasil

The Rede de Taxonomistas da Funga do Brasil (RTFB) is a network connecting the specialists who document and validate Brazil’s fungal, lichen, and myxomycete diversity in FFB. It grew out of decades of collaborative work across initiatives such as the Catálogo de Plantas e Fungos do Brasil and the INCT Herbário Virtual da Flora e dos Fungos, and now serves as a shared platform for its members, their publications, and community news. fungaR’s curation tools (mycobank_gap(), mycobank_records(), spfungorum_gap(), spfungorum_records(), and funga_distribution_gap()) are designed to support exactly this kind of collaborative curation work.

Package Description

Package: fungaR 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 (including substrate/host) criteria
Exact and fuzzy (Levenshtein-distance) name resolution against the checklist
Taxonomic hierarchy traversal at any rank, from division down to species, on FFB’s real fungi hierarchy
Cross-checking MycoBank, Index Fungorum, GBIF, speciesLink, and REFLORA to flag species and state records missing from FFB, or retrieving MycoBank/Index Fungorum records for a Brazilian taxon directly
Tidyverse-integrated workflows throughout

Contribute

You can contribute to fungaR 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

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

Acknowledgements

Development of fungaR is led by the Rio de Janeiro Botanical Garden (JBRJ), in collaboration with the mycological, biodiversity, and informatics communities — including the taxonomic expertise of colleagues such as Elisandro Ricardo Drechsler-Santos. 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 fungaR" subtitle: "Open source tools for accessing, analyzing, and curating fungal data from the Flora e Funga do Brasil platform" format: html: toc: true --- <style> body { 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 `fungaR` is an R package for accessing, analyzing, and curating fungal taxonomic and distributional data 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 (including fungi-specific traits such as nutritional mode and substrate/host) to resolving your own species name lists against it. Beyond data retrieval, `fungaR` also assists taxonomic experts contributing to FFB by cross-checking [MycoBank](https://www.mycobank.org), [Species Fungorum](https://www.speciesfungorum.org) (Index Fungorum), and Brazilian occurrence repositories — [GBIF](https://www.gbif.org), [speciesLink](https://specieslink.net), and the [Reflora Virtual Herbarium](https://ipt.jbrj.gov.br/reflora/) — to flag fungal species and state records that are plausibly Brazilian but still missing from the platform. ## Flora e Funga do Brasil Brazil harbors one of the richest fungal diversities in the world. 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 fungal name, FFB records nomenclatural status, taxonomic classification (Division, Order, Family, Genus), geographic distribution, endemism, nutritional/ecological mode, and substrate/host information — a validated taxonomic backbone assembled collaboratively by hundreds of taxonomists and mycologists, and published as versioned Darwin Core Archives. ## Rede de Taxonomistas da Funga do Brasil The [Rede de Taxonomistas da Funga do Brasil (RTFB)](https://redefunga.com.br/site/) is a network connecting the specialists who document and validate Brazil's fungal, lichen, and myxomycete diversity in FFB. It grew out of decades of collaborative work across initiatives such as the Catálogo de Plantas e Fungos do Brasil and the INCT Herbário Virtual da Flora e dos Fungos, and now serves as a shared platform for its members, their publications, and community news. `fungaR`'s curation tools (`mycobank_gap()`, `mycobank_records()`, `spfungorum_gap()`, `spfungorum_records()`, and `funga_distribution_gap()`) are designed to support exactly this kind of collaborative curation work. ## Package Description Package: `fungaR` 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 (including substrate/host) criteria - Exact and fuzzy (Levenshtein-distance) name resolution against the checklist - Taxonomic hierarchy traversal at any rank, from division down to species, on FFB's real fungi hierarchy - Cross-checking MycoBank, Index Fungorum, GBIF, speciesLink, and REFLORA to flag species and state records missing from FFB, or retrieving MycoBank/Index Fungorum records for a Brazilian taxon directly - Tidyverse-integrated workflows throughout ## Contribute You can contribute to `fungaR` 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 `fungaR` is [open source software](/LICENSE.md). Open tools empower science through reproducibility, accessibility, and equitable knowledge sharing. ## Acknowledgements Development of `fungaR` is led by the [Rio de Janeiro Botanical Garden (JBRJ)](https://www.gov.br/jbrj), in collaboration with the mycological, biodiversity, and informatics communities — including the taxonomic expertise of colleagues such as Elisandro Ricardo Drechsler-Santos. 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.