florabr

Brazilian Flora 2020 is the most comprehensive work to reliably document Brazilian plant diversity. It involves the work of hundreds of taxonomists, integrating data from plant 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 found in Brazil.

The florabR package includes a collection of functions designed to retrieve, filter and spatialize data from the Brazilian Flora 2020 dataset.

Overview of functions

Download and import Brazilian Flora Dataset

  • check_version(): Check if you have the latest version of Brazilian Flora dataset available.
  • get_florabr(): Download the latest version of Brazilian Flora 2020 database.
  • load_florabr(): Load Brazilian Flora database.

Check names

  • check_names(): Check species names.
  • get_binomial(): Extract the binomial name (Genus + specific epithet) from a complete Scientific Name.

Select or subset species

Spatialize distribution and use Brazilian Flora to flag records

  • get_pam(): Get a presence-absence matrix of species.
  • filter_florabr(): Identify records outside natural ranges according to Brazilian Flora 2020.
  • get_spat_occ(): Get Spatial polygons (SpatVectors) of species based on its distribution (States and Biomes) according to Brazilian Flora

Installation

Install stable version from CRAN

To install the stable version of florabr use:

install.packages("florabr")


Install development version from GitHub

You can install the development version of florabr from GitHub with:

if(!require(devtools)){
    install.packages("devtools")
}

if(!require(florabr)){
devtools::install_github('wevertonbio/florabr')}

library(florabr)

Before downloading the data available in the Brazilian Flora 2020, we need to create a folder to save the data:

#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:

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 Brazilian Flora dataset. To explore the available versions, please refer to this link. For downloading a particular version, simply replace ‘latest’ with the desired version number. For example:

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.

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

Package website

See the package website (https://wevertonbio.github.io/florabr/) for further functions explanation and vignettes.