News

fungaR 1.0.0

Initial Release

The first official release of the fungaR R package, designed to provide comprehensive access, analysis, and curation tools for fungal data from the Flora e Funga do Brasil (FFB) platform, hosted by the Rio de Janeiro Botanical Garden.

Features

funga_version(): Retrieve metadata and check available dataset versions from the FFB IPT data portal.
funga_download(): Download taxonomic and distributional data in Darwin Core Archive (DwC-A) format for specific or all available versions.
funga_parse(): Parse and organize locally downloaded FFB datasets into a ready-to-use list of tables, subsetting the combined plant/fungi archive down to the Fungi kingdom.
funga_records(): Browse and filter the FFB fungal checklist directly by taxonomic, geographic, and trait-based criteria, without requiring an input name list. Returns each taxon’s distribution and species-profile information (state, phytogeographic domain, endemism, life form, habitat/substrate, vegetation type) concatenated per column.
funga_search(): Resolve your own species name list against the FFB checklist, with exact matching first and fuzzy (Levenshtein-distance) matching as a fallback for typos, including synonym resolution.
funga_match(): Compare two independent species name lists, aligning names that resolve to the same accepted taxon.
funga_get_children_taxa(): Retrieve all child taxa (species, subspecies, varieties, genera, etc.) below a given taxonomic name and rank, following FFB’s real fungi hierarchy (Division > Order > Genus > Species).
mycobank_gap(): Cross-check MycoBank’s global name database against the FFB checklist for a given genus or order, returning by default only species-level names whose own MycoBank locality places them in Brazil but that are still missing from FFB.
mycobank_records(): Retrieve every MycoBank name matching a given species, genus, or order, filtered by default to those with MycoBank Brazil evidence, independent of whether it is already registered in FFB.
spfungorum_gap(): Cross-check Species Fungorum (Index Fungorum, Kew) against the FFB checklist for a given genus, via Index Fungorum’s own public web-service API, returning by default only species-level names whose own reported locality places them in Brazil but that are still missing from FFB.
spfungorum_records(): Retrieve every Index Fungorum name matching a given species or genus, filtered by default to those with a Brazilian reported locality, independent of whether it is already registered in FFB.
funga_distribution_gap(): Cross-check GBIF, speciesLink, and REFLORA for specimen evidence of a taxon in Brazilian states not yet listed in FFB’s official distribution.
Most functions download and parse the FFB dataset automatically and cache it locally, so repeated queries and offline analysis work without re-downloading.
Seamless integration with tidyverse workflows for downstream analyses.
Comprehensive testthat suite, continuous integration via GitHub Actions.

Infrastructure

MIT license.
GitHub Actions: R-CMD-check and test coverage.
Hosted documentation: fungaR-website, with How-To articles for every function and a full Portuguese translation (EN/PT language switcher).

Feedback

Please report bugs or issues at: https://github.com/DBOSlab/fungaR/issues

--- title: "News" format: html: toc: true toc-depth: 3 --- <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> # fungaR 1.0.0 ## Initial Release The first official release of the `fungaR` R package, designed to provide comprehensive access, analysis, and curation tools for fungal data from the [Flora e Funga do Brasil (FFB)](https://floradobrasil.jbrj.gov.br/consulta/) platform, hosted by the [Rio de Janeiro Botanical Garden](https://www.gov.br/jbrj/pt-br). ### Features - `funga_version()`: Retrieve metadata and check available dataset versions from the FFB IPT data portal. - `funga_download()`: Download taxonomic and distributional data in Darwin Core Archive (DwC-A) format for specific or all available versions. - `funga_parse()`: Parse and organize locally downloaded FFB datasets into a ready-to-use list of tables, subsetting the combined plant/fungi archive down to the Fungi kingdom. - `funga_records()`: Browse and filter the FFB fungal checklist directly by taxonomic, geographic, and trait-based criteria, without requiring an input name list. Returns each taxon's distribution and species-profile information (state, phytogeographic domain, endemism, life form, habitat/substrate, vegetation type) concatenated per column. - `funga_search()`: Resolve your own species name list against the FFB checklist, with exact matching first and fuzzy (Levenshtein-distance) matching as a fallback for typos, including synonym resolution. - `funga_match()`: Compare two independent species name lists, aligning names that resolve to the same accepted taxon. - `funga_get_children_taxa()`: Retrieve all child taxa (species, subspecies, varieties, genera, etc.) below a given taxonomic name and rank, following FFB's real fungi hierarchy (Division > Order > Genus > Species). - `mycobank_gap()`: Cross-check MycoBank's global name database against the FFB checklist for a given genus or order, returning by default only species-level names whose own MycoBank locality places them in Brazil but that are still missing from FFB. - `mycobank_records()`: Retrieve every MycoBank name matching a given species, genus, or order, filtered by default to those with MycoBank Brazil evidence, independent of whether it is already registered in FFB. - `spfungorum_gap()`: Cross-check Species Fungorum (Index Fungorum, Kew) against the FFB checklist for a given genus, via Index Fungorum's own public web-service API, returning by default only species-level names whose own reported locality places them in Brazil but that are still missing from FFB. - `spfungorum_records()`: Retrieve every Index Fungorum name matching a given species or genus, filtered by default to those with a Brazilian reported locality, independent of whether it is already registered in FFB. - `funga_distribution_gap()`: Cross-check GBIF, speciesLink, and REFLORA for specimen evidence of a taxon in Brazilian states not yet listed in FFB's official distribution. - Most functions download and parse the FFB dataset automatically and cache it locally, so repeated queries and offline analysis work without re-downloading. - Seamless integration with tidyverse workflows for downstream analyses. - Comprehensive testthat suite, continuous integration via GitHub Actions. ### Infrastructure - MIT license. - GitHub Actions: R-CMD-check and test coverage. - Hosted documentation: [fungaR-website](https://dboslab.github.io/fungaR-website/), with How-To articles for every function and a full Portuguese translation (EN/PT language switcher). ### Feedback Please report bugs or issues at: <https://github.com/DBOSlab/fungaR/issues>