Explore Flora e Funga do Brasil Database.
florabr
Flora e Funga do Brasil 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.
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:
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 Flora e Funga do Brasil, 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 Flora e Funga do Brasil 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.