florabr

florabr: Explore and Spatialize Species Distribution Using Flora e Funga do Brasil

https://github.com/wevertonbio/florabr

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florabr: Explore and Spatialize Species Distribution Using Flora e Funga do Brasil

README.Rmd

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# florabr 


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[Flora e Funga do Brasil](https://floradobrasil.jbrj.gov.br/consulta/) is the most comprehensive work to reliably document Brazilian plant, algae and fungi diversity. It involves the work of hundreds of taxonomists, integrating data from plant (including algae) and fungi collected in Brazil during the last two centuries. The database contains detailed and standardized morphological descriptions, illustrations, nomenclatural data, geographic distribution, and keys for the identification of all native and non-native plants and fungi found in Brazil.

The florabr package includes a collection of functions designed to retrieve, filter and spatialize data from the Flora e Funga do Brasil dataset.

## Package citation
Trindade, W. C. (2024). florabr: An R package to explore and spatialize species distribution using Flora e Funga do Brasil. Applications in Plant Sciences, e11616. [10.1002/aps3.11616](https://doi.org/10.1002/aps3.11616)

## Overview of functions

### Download and import Flora e Funga do Brasil Dataset

-   `check_version()`: Check if you have the latest version of Flora e Funga do Brasil dataset available.
-   `get_florabr()`: Download the latest version of Flora e Funga do Brasil database.
-   `load_florabr()`: Load Flora e Funga do Brasil database.
-   `solve_discrepancies()`: Resolve discrepancies between species and subspecies/varieties information.

### Check names

-   `check_names()`: Check species names.
-   `get_binomial()`: Extract the binomial name (Genus + specific epithet) from a complete Scientific Name.
-   `get_synonym()`: Retrieve synonyms for species.

### Select or subset species

-   `get_attributes()`: Get available attributes to filter species.
-   `select_by_vernacular()`: Search for taxa using vernacular names.
-   `select_species()`: Select species based on its characteristics and distribution.
-   `subset_species()`: Extract a subset of species from Flora e Funga do Brasil database.

### Spatialize distribution and use Flora e Funga do Brasil to flag records

-   `get_pam()`: Get a presence-absence matrix of species.
-   `filter_florabr()`: Identify records outside natural ranges according to Flora e Funga do Brasil.
-   `get_spat_occ()`: Get Spatial polygons (SpatVectors) of species based on its distribution (States and Biomes) according to Flora e Funga do Brasil.

## Installation

### Install stable version from CRAN

To install the stable version of `florabr` use:

``` r
install.packages("florabr")
```




### Install development  version from GitHub

You can install the development version of florabr from [GitHub](https://github.com/wevertonbio/florabr) with:

``` r
if(!require(remotes)){
    install.packages("remotes")
}

if(!require(florabr)){
remotes::install_github("wevertonbio/florabr")}

library(florabr)
```

Before downloading the data available in the Flora e Funga do Brasil, we need to create a folder to save the data:

``` r
#Creating a folder in a temporary directory
#Replace 'file.path(tempdir(), "florabr")' by a path folder to be create in your computer
my_dir <- file.path(file.path(tempdir(), "florabr"))
dir.create(my_dir)
```

You can now utilize the `get_florabr` function to retrieve the most recent version of the data:

``` r
get_florabr(output_dir = my_dir, #directory to save the data
            data_version = "latest", #get the most recent version available
            overwrite = T) #Overwrite data, if it exists
```

You also have the option to download an older, specific version of the Flora e Funga do Brasil dataset. To explore the available versions, please refer to [this link](https://ipt.jbrj.gov.br/jbrj/resource?r=lista_especies_flora_brasil). For downloading a particular version, simply replace 'latest' with the desired version number. For example:

``` r
get_florabr(output_dir = my_dir, #directory to save the data
            data_version = "393.385", #Version 393.385, published on 2023-07-21
            overwrite = T) #Overwrite data, if it exists
```

## Loading data

In order to use the other functions of the package, you need to load the data into your environment. To achieve this, utilize the `load_florabr()` function. By default, the function will automatically search for the latest available version in your directory. However, you have the option to specify a particular version using the *data_version* parameter. Additionally, you can choose between two versions of the data: the 'short' version (containing the 19 columns required for run the other functions of the package) or the 'complete' version (with all original 39 columns). The function imports the 'short' version by default.

``` r
#Load the short version
bf <- load_florabr(data_dir = my_dir,
                   data_version = "Latest_available",
                   type = "short") #short
```

## Package website

See the package website () for further functions explanation and vignettes.

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