Frequently Asked Questions

What is Flora e Funga do Brasil?

Flora e Funga do Brasil (FFB) is the taxonomic checklist that documents Brazil’s plant, algal, and fungal diversity — the richest in the world. Maintained by the Rio de Janeiro Botanical Garden and curated collaboratively by hundreds of taxonomists and mycologists, it records accepted names, synonyms, taxonomic classification, geographic distribution, endemism, nutritional/ecological mode, and substrate/host information for every documented fungal species.

What can I use fungaR for?

The fungaR package lets researchers and taxonomists download, parse, filter, and explore the fungal portion of the Flora e Funga do Brasil checklist directly from R. You can browse the checklist by taxonomic, geographic, or trait-based criteria, resolve your own species name lists against it (with fuzzy matching for typos), explore the taxonomic hierarchy, and cross-check MycoBank and Brazilian occurrence repositories to curate new species and state records for contribution back to FFB.

Do I need a list of species names to use fungaR?

No. funga_records() lets you browse and filter the FFB fungal checklist directly (e.g. all accepted species in a family, or all endemics in a given state) without providing any input names. If you already have your own species list — from a fungarium, field survey, or collaborator — funga_search() and funga_match() resolve those names against the checklist instead, with exact matching first and fuzzy (Levenshtein-distance) matching as a fallback for typos.

Does fungaR require an internet connection?

Only the first time you query a given dataset version, or MycoBank’s bulk name list. funga_download()/funga_parse() and mycobank_gap()/mycobank_records() fetch and cache their respective datasets locally, and every other function reuses that cache automatically, so repeated queries and offline analysis work without a new download. spfungorum_gap()/spfungorum_records() query Index Fungorum’s web service directly each time, since there is no bulk export to cache.

How do I install fungaR?

Visit the Get Started guide for installation instructions from GitHub.

Is fungaR free to use?

Yes. fungaR is open source, licensed under the MIT License.

Is this website available in Portuguese?

Yes. Every page has an EN/PT toggle in the navigation bar. Once you switch languages, the choice is remembered for the rest of your visit — you won’t need to switch again as you navigate between pages.

What output can fungaR generate?

fungaR returns tidy data frames (and, for funga_parse(), a structured list of DwC-A tables) ready for downstream analysis. funga_records() can save results directly to CSV, while mycobank_gap(), mycobank_records(), spfungorum_gap(), spfungorum_records(), and funga_distribution_gap() produce structured .xlsx spreadsheets — including each name’s original URL — designed for a taxonomist’s manual review.

Why does FFB use “Division” instead of “Class” for fungi, and no family-rank record?

FFB classifies fungi by Division (phylum-equivalent, e.g. Ascomycota, Basidiomycota) rather than Class, and does not register a standalone taxon record at family rank for Fungi — family is stored only as a classification column on genus/species records. funga_get_children_taxa() handles this automatically: rank = "family" still works, matched directly on that column instead of walking a family-rank row that does not exist.

What does the `habitat` field mean for fungi in `funga_records()`?

For fungi, FFB’s habitat field records the substrate/host the specimen was collected on (e.g. "Planta viva - raiz", "Tronco em decomposição", "Solo", "Outro fungo") rather than a plant growth habitat, since FFB does not publish a separate named host-taxon field. Use it to browse the checklist by substrate/host type.

Who is the developer of fungaR?

Development is led by JBRJ, with financial support from CNPq and FINEP. Main developer:

Domingos Cardoso (@DBOSlab)

View the code and contribute on GitHub: https://github.com/DBOSlab/fungaR

Why the name fungaR?

The name pairs “Funga” — for Flora e Funga do Brasil’s fungal component, the checklist it interfaces with — with the R programming language, reflecting the package’s goal of making the national fungal checklist directly and reproducibly accessible from R.

Where can I report bugs or request features?

Submit issues on GitHub: fungaR Issues.

Where can I ask questions and discuss fungaR?

Join our community via GitHub Discussions to ask questions, suggest ideas, or help others.

How does fungaR relate to Flora e Funga do Brasil?

The fungaR package is a programmatic interface to the fungal side of the Flora e Funga do Brasil IPT data portal: it downloads, parses, and queries the same checklist data published on the platform, and also helps taxonomic experts prepare new fungal names and records for contribution back to it.

Can I contribute new fungal names or records to Flora e Funga do Brasil?

Yes. fungaR includes mycobank_gap(), spfungorum_gap(), and funga_distribution_gap() specifically to help taxonomic experts find candidates worth submitting — cross-checking MycoBank’s and Index Fungorum’s global name databases, and Brazilian occurrence repositories (GBIF, speciesLink, REFLORA), against the current FFB checklist to flag species and state records that are plausibly Brazilian but still missing. If you already have a taxon in mind rather than needing an FFB comparison, mycobank_records()/spfungorum_records() retrieve everything those repositories have on record for it directly. To submit new names or corrections to the platform itself, see the contribution guidelines at floradobrasil.jbrj.gov.br/consulta or contact the FFB coordination team at floraefungadobrasil@jbrj.gov.br.

--- title: "Frequently Asked Questions" 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> ### What is Flora e Funga do Brasil? Flora e Funga do Brasil (FFB) is the taxonomic checklist that documents Brazil's plant, algal, and fungal diversity — the richest in the world. Maintained by the Rio de Janeiro Botanical Garden and curated collaboratively by hundreds of taxonomists and mycologists, it records accepted names, synonyms, taxonomic classification, geographic distribution, endemism, nutritional/ecological mode, and substrate/host information for every documented fungal species. ### What can I use fungaR for? The `fungaR` package lets researchers and taxonomists download, parse, filter, and explore the fungal portion of the [Flora e Funga do Brasil](https://floradobrasil.jbrj.gov.br/consulta/) checklist directly from R. You can browse the checklist by taxonomic, geographic, or trait-based criteria, resolve your own species name lists against it (with fuzzy matching for typos), explore the taxonomic hierarchy, and cross-check MycoBank and Brazilian occurrence repositories to curate new species and state records for contribution back to FFB. ### Do I need a list of species names to use fungaR? No. `funga_records()` lets you browse and filter the FFB fungal checklist directly (e.g. all accepted species in a family, or all endemics in a given state) without providing any input names. If you already have your own species list — from a fungarium, field survey, or collaborator — `funga_search()` and `funga_match()` resolve those names against the checklist instead, with exact matching first and fuzzy (Levenshtein-distance) matching as a fallback for typos. ### Does fungaR require an internet connection? Only the first time you query a given dataset version, or MycoBank's bulk name list. `funga_download()`/`funga_parse()` and `mycobank_gap()`/`mycobank_records()` fetch and cache their respective datasets locally, and every other function reuses that cache automatically, so repeated queries and offline analysis work without a new download. `spfungorum_gap()`/`spfungorum_records()` query Index Fungorum's web service directly each time, since there is no bulk export to cache. ### How do I install fungaR? Visit the [Get Started guide](/get-started/index.qmd) for installation instructions from GitHub. ### Is fungaR free to use? Yes. `fungaR` is open source, licensed under the [MIT License](https://opensource.org/license/mit/). ### Is this website available in Portuguese? Yes. Every page has an EN/PT toggle in the navigation bar. Once you switch languages, the choice is remembered for the rest of your visit — you won't need to switch again as you navigate between pages. ### What output can fungaR generate? `fungaR` returns tidy data frames (and, for `funga_parse()`, a structured list of DwC-A tables) ready for downstream analysis. `funga_records()` can save results directly to CSV, while `mycobank_gap()`, `mycobank_records()`, `spfungorum_gap()`, `spfungorum_records()`, and `funga_distribution_gap()` produce structured `.xlsx` spreadsheets — including each name's original URL — designed for a taxonomist's manual review. ### Why does FFB use "Division" instead of "Class" for fungi, and no family-rank record? FFB classifies fungi by Division (phylum-equivalent, e.g. Ascomycota, Basidiomycota) rather than Class, and does not register a standalone taxon record at family rank for Fungi — family is stored only as a classification column on genus/species records. `funga_get_children_taxa()` handles this automatically: `rank = "family"` still works, matched directly on that column instead of walking a family-rank row that does not exist. ### What does the `habitat` field mean for fungi in `funga_records()`? For fungi, FFB's `habitat` field records the substrate/host the specimen was collected on (e.g. `"Planta viva - raiz"`, `"Tronco em decomposição"`, `"Solo"`, `"Outro fungo"`) rather than a plant growth habitat, since FFB does not publish a separate named host-taxon field. Use it to browse the checklist by substrate/host type. ### Who is the developer of fungaR? Development is led by [JBRJ](https://www.gov.br/jbrj/pt-br), with financial support from [CNPq](https://www.gov.br/cnpq/pt-br) and [FINEP](http://www.finep.gov.br). Main developer: - Domingos Cardoso ([\@DBOSlab](https://github.com/DBOSlab)) View the code and contribute on GitHub: [https://github.com/DBOSlab/fungaR](https://github.com/DBOSlab/fungaR) ### Why the name fungaR? The name pairs "Funga" — for Flora e Funga do Brasil's fungal component, the checklist it interfaces with — with the R programming language, reflecting the package's goal of making the national fungal checklist directly and reproducibly accessible from R. ### Where can I report bugs or request features? Submit issues on GitHub: [fungaR Issues](https://github.com/DBOSlab/fungaR/issues). ### Where can I ask questions and discuss fungaR? Join our community via [GitHub Discussions](https://github.com/DBOSlab/fungaR/discussions) to ask questions, suggest ideas, or help others. ### How does fungaR relate to Flora e Funga do Brasil? The `fungaR` package is a programmatic interface to the fungal side of the Flora e Funga do Brasil IPT data portal: it downloads, parses, and queries the same checklist data published on the platform, and also helps taxonomic experts prepare new fungal names and records for contribution back to it. ### Can I contribute new fungal names or records to Flora e Funga do Brasil? Yes. `fungaR` includes `mycobank_gap()`, `spfungorum_gap()`, and `funga_distribution_gap()` specifically to help taxonomic experts find candidates worth submitting — cross-checking MycoBank's and Index Fungorum's global name databases, and Brazilian occurrence repositories (GBIF, speciesLink, REFLORA), against the current FFB checklist to flag species and state records that are plausibly Brazilian but still missing. If you already have a taxon in mind rather than needing an FFB comparison, `mycobank_records()`/`spfungorum_records()` retrieve everything those repositories have on record for it directly. To submit new names or corrections to the platform itself, see the contribution guidelines at [floradobrasil.jbrj.gov.br/consulta](https://floradobrasil.jbrj.gov.br/consulta/) or contact the FFB coordination team at **floraefungadobrasil\@jbrj.gov.br**.