---
format:
  html:
    toc: true
    page-layout: custom
execute:
  echo: false
  eval: true
  freeze: auto
  cache: false
  warning: false
  message: false
  include: true
  # ENABLE inline R code evaluation
  inline: true
resources:
  - figures/
---

```{r setup, include=FALSE}
library(fungaR)

ffb_versions <- tryCatch(
  funga_version(),
  error = function(e) NULL
)

if (!is.null(ffb_versions) && nrow(ffb_versions) > 0) {
  latest_row <- ffb_versions[ffb_versions$Latest %in% TRUE, ]
  if (nrow(latest_row) == 0) latest_row <- ffb_versions[1, ]
  n_versions <- nrow(ffb_versions)
  latest_version <- latest_row$Version[1]
  latest_records <- format(as.numeric(gsub(",", "", latest_row$Records[1])), big.mark = ",")
  latest_date <- latest_row$Published_on[1]
} else {
  n_versions <- NA
  latest_version <- NA
  latest_records <- NA
  latest_date <- NA
}
```

<style>
  .floating-logos {
    position: fixed;
    top: 60px;
    right: 450px;
    width: 150px;
    opacity: 0.85;
    z-index: 1;
  }

  .floating-logos img {
    display: block;
    width: 100%;
    margin-bottom: 12px;
    border-radius: 4px;
  }
</style>

<div class="floating-logos">

  <a href="https://github.com/DBOSlab/fungaR"
     target="_blank"
     title="fungaR on GitHub">
    <img src="/figures/fungaR_hex_sticker.png"
         alt="fungaR logo">
  </a>

  <a href="https://redefunga.com.br/site/"
     target="_blank"
     title="The Rede Funga">
    <img src="/figures/rede_taxon_br_funga.png"
         alt="rede funga logo">
  </a>
  
  <a href="https://www.gov.br/jbrj/pt-br"
     target="_blank"
     title="Jardim Botânico do Rio de Janeiro">
    <img src="/figures/jbrj_marca.png"
         alt="Jardim Botânico do Rio de Janeiro">
  </a>

</div>

::: whitebox
::: {style="padding-left: 100px; padding-right: 50px; display: inline-block;"}

::: {layout-ncol="2"}

::: {style="text-align: left;"}

\
`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 provides a comprehensive interface to download, parse, filter, and explore checklist data from the FFB IPT data portal — from browsing by taxonomic, geographic, or trait criteria to resolving your own species name lists against it, and cross-checking MycoBank and Brazilian occurrence repositories to help curate species and records still missing from the platform.\
\

```{=html}
<div class="stat-strip">
  <div class="stat-card">
    <span class="stat-number">`r ifelse(is.na(n_versions), "—", n_versions)`</span>
    <span class="stat-label">FFB dataset versions published</span>
  </div>
  <div class="stat-card">
    <span class="stat-number">`r ifelse(is.na(latest_version), "—", latest_version)`</span>
    <span class="stat-label">Latest version</span>
  </div>
  <div class="stat-card">
    <span class="stat-number">`r ifelse(is.na(latest_records), "—", latest_records)`</span>
    <span class="stat-label">Records in latest release</span>
  </div>
  <div class="stat-card">
    <span class="stat-number">`r ifelse(is.na(latest_date), "—", latest_date)`</span>
    <span class="stat-label">Published on</span>
  </div>
</div>
```

These figures are retrieved live from the FFB IPT metadata via `funga_version()` every time this page is built — the same call you would run yourself before deciding which dataset version to work with. Note that FFB publishes plants and fungi together in one combined release; `funga_parse()` is what subsets this down to the Fungi kingdom.\
\

## Flora e Funga do Brasil

Brazil harbors one of the richest fungal diversities in the world, spanning lichenized and non-lichenized fungi across every biome in the country. Assembling a complete, continuously updated checklist of this diversity has been a decades-long collaborative effort involving hundreds of taxonomists and mycologists across the country.

The project began in 2008 as the *Lista de Espécies da Flora do Brasil*, a first attempt to compile a national species checklist validated by specialists. It evolved into [Flora do Brasil 2020](http://doi.org/10.47871/jbrj2021004), launched to meet Brazil's commitments under the Global Strategy for Plant Conservation of the Convention on Biological Diversity, and — following the incorporation of fungi — into its current form, [Flora e Funga do Brasil](https://floradobrasil.jbrj.gov.br/consulta/).

For each accepted fungal name, the checklist records nomenclatural status (accepted, synonym, or doubtful), taxonomic classification (Division, Order, Family, Genus), geographic distribution across Brazilian states and phytogeographic domains, endemism status, nutritional/ecological mode (e.g. saprobic, parasitic, lichenized, mycorrhizal), and substrate/host information. This structured, validated backbone underpins mycological research, conservation assessments, and biodiversity informatics across the country.

Data are published as versioned Darwin Core Archives through the [FFB IPT Data Portal](https://ipt.jbrj.gov.br/jbrj/resource?r=lista_especies_flora_brasil), hosted by the [Rio de Janeiro Botanical Garden (JBRJ)](https://www.gov.br/jbrj/pt-br). `fungaR` reads directly from this portal, so every result reflects the checklist as curated by the taxonomist community at the time of the query.

If you are a taxonomist and wish to contribute new fungal names, updates, or corrections to Flora e Funga do Brasil, see the [contribution guidelines](https://floradobrasil.jbrj.gov.br/consulta/) on the platform itself, or contact the FFB coordination team at **floraefungadobrasil\@jbrj.gov.br**. `fungaR`'s `mycobank_gap()`, `spfungorum_gap()`, and `funga_distribution_gap()` functions can help you find candidates worth submitting.\
\

## Rede de Taxonomistas da Funga do Brasil

The [Rede de Taxonomistas da Funga do Brasil (RTFB)](https://redefunga.com.br/site/) brings together the specialists dedicated to documenting and validating data on fungi, lichens, and myxomycetes in FFB — the official reference base for government and society. The network grew naturally out of the long-standing effort of hundreds of people in Brazilian mycology to document fungal diversity, through initiatives such as the Flora e Funga do Brasil, the Herbário Virtual Reflora, the INCT Herbário Virtual da Flora e dos Fungos, the Catálogo da Vida do Brasil, the INCT Fungos do Brasil, and, more recently, the CNPq-funded Funga do Brasil Universal Project — all sharing the goal of strengthening collaboration between taxonomists and institutions.

RTFB's purpose is to connect people, share knowledge, and promote the continuous updating of information on Brazil's fungal diversity within FFB, the authoritative base for cataloguing fungal names. This work contributes directly to fungi being recognized in public policy, red lists, conservation plans, environmental regulations, and bioeconomy initiatives, driving the development of mycology in the country. The network's own site serves as the main digital platform gathering information about its members, publications, news, and events, and connecting with other national and international initiatives.

Its main goals include:

- Giving visibility to the network and bringing together taxonomist specialists on a platform with approved, verified profiles.
- Facilitating access to publications and content related to fungal taxonomy.
- Sharing news, events, and research results.
- Providing data tools, including specimen counters in collections, identification status, and species assessed by CNCFlora/IUCN.
- Integrating information with external databases, such as Flora e Funga do Brasil and IUCN, among others.

`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.\
\
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### [Get Started](/get-started/index.qmd)

Welcome new users! Start learning how to install `fungaR`
:::

::: {style="text-align: center;"}
### [Articles](/articles/index.qmd)

"How-to" articles to help you learn how to use `fungaR`
:::
:::
:::
:::

:::