Title:	Explore Flora e Funga do Brasil Database
Version:	1.3.0
Description:	A collection of functions designed to retrieve, filter and spatialize data from the Flora e Funga do Brasil dataset. For more information about the dataset, please visit https://floradobrasil.jbrj.gov.br/consulta/.
Imports:	XML (≥ 3.99.0.14), data.table (≥ 1.14.8), httr (≥ 1.4.6), terra (≥ 1.7.39), stats (≥ 4.2.3), utils(≥ 4.2.3), grDevices (≥ 4.2.3), doSNOW (≥ 1.0.20), parallel (≥ 4.3.1), foreach (≥ 1.5.2)
License:	GPL (≥ 3)
Encoding:	UTF-8
RoxygenNote:	7.2.3
Depends:	R (≥ 2.10)
LazyData:	true
Suggests:	knitr, rmarkdown, testthat (≥ 3.0.0)
VignetteBuilder:	knitr
URL:	https://wevertonbio.github.io/florabr/
BugReports:	https://github.com/wevertonbio/florabr/issues
Config/testthat/edition:	3
NeedsCompilation:	no
Packaged:	2024-09-09 16:47:41 UTC; wever
Author:	Weverton Trindade [aut, cre]
Maintainer:	Weverton Trindade <wevertonf1993@gmail.com>
Repository:	CRAN
Date/Publication:	2024-09-09 17:00:02 UTC

Flora e Funga do Brasil database - Version 393.401

Description

A dataset containing a subset of the Flora e Funga do Brasil database (version 393.401)

Usage

data(bf_data)

Format

A data.frame with 50010 rows and 23 variables:

species

Species names

scientificName

Complete scientific name of the species

acceptedName

Accepted name of the species (NA when the name in species is already an accepted name)

kingdom

Kingdom to which species belongs (Plantae or Fungi)

group

Major group to which species belongs (Angiosperms, Gymnosperms, Ferns and Lycophytes, Bryophytes, and Algae)

subgroup

Subgroup to which species belongs. Only available for Bryophytes (Mosses, Hornworts, and Liverworts)

phylum

Phylum to which species belongs

class

Class to which species belongs

order

Order to which species belongs

family

Family to which species belongs

genus

Genus to which species belongs

lifeForm

Life form of the species (e.g: Tree, Herb, Shrub, etc.)

habitat

Habitat type of the species (e.g., Terrestrial, Rupicolous, Epiphytic, etc.)

biome

Biomes with confirmed occurrences of the species

states

Federal states with confirmed occurrences of the species

vegetation

Vegetation types with confirmed occurrences of the species

origin

Indicates whether the species is Native, Naturalized, or Cultivated in Brazil

endemism

Indicates whether the species is Endemic or Non-endemic to Brazil

taxonomicStatus

Indicates the level of recognition and acceptance of the species (Accepted or Synonym)

nomenclaturalStatus

Indicates the legitimacy and validity of the species name (Correct, Illegitimate, Uncertain_Application, etc.)

vernacularName

Locally or culturally used name for the species

taxonRank

Taxonomic rank (Species, Genus, Family, Order, etc). This data contains only Species

id

Unique id for species

References

Flora e Funga do Brasil. Jardim Botânico do Rio de Janeiro. Available at: http://floradobrasil.jbrj.gov.br/

SpatVector of the biomes of Brazil

Description

A simplified and packed SpatVector of the polygons of the biomes present in Brazilian territory. The spatial data was originally obtained from geobr::read_biomes. Borders have been simplified by removing vertices of borders using terra::simplifyGeom. It's necessary unpack the Spatvectos using terra::unwrap

@usage data(biomes) biomes <- terra::unwrap(biomes)

Usage

biomes

Format

A SpatVector with 6 geometries and 1 attribute:

name_biome

The name of the biome (Amazon, Caatinga, Cerrado, Atlantic_Forest, Pampa, and Pantanal)

SpatVector of the Brazil's national borders

Description

A simplified and packed SpatVector of the Brazil's national borders. The spatial data was originally obtained from geobr::read_country. Borders have been simplified by removing vertices of borders using terra::simplifyGeom. It's necessary unpack the Spatvectos using terra::unwrap

@usage data(brazil) brazil <- terra::unwrap(brazil)

Usage

brazil

Format

A SpatVector with 1 geometry and 0 attribute

Check species names

Description

check_names checks if the species names are correct and searches for suggestions if the name is misspelled or not found in the Flora e Funga do Brasil database

match_names finds approximate matches to the specified pattern (species) within each element of the string x (species_to_match). It is used internally by check_names.

Usage

check_names(data, species, max_distance = 0.1,
                   include_subspecies= FALSE, include_variety = FALSE,
                   kingdom = "Plantae", parallel = FALSE, ncores = 1,
                   progress_bar = FALSE)

match_names(
  species,
  species_to_match,
  max_distance = 0.1,
  parallel = FALSE,
  ncores = 1,
  progress_bar = FALSE
)

Arguments

Value

a data.frame with the following columns:

• input_name: the species names informed in species argument

• Spelling: indicates if the species name is Correct (a perfect match with a species name in the Flora e Funga do Brasil), Probably_incorrect (partial match), or Not_found (no match with any species).

• Suggested name: If Spelling is Correct, it is the same as the input_name. If Spelling is Probably_correct, one or more suggested names are listed, found according to the maximum distance. If Spelling is "Not_found", the value is NA.

• Distance: The integer Levenshtein edit distance. It represents the number of single-character edits (insertions, deletions, or substitutions) required to transform the input_name into the Suggested_name.

• taxonomicStatus: the taxonomic status of the species name ("Accepted" or "Synonym").

• nomenclaturalStatus: the nomenclatural status of the species name. This information is not available for all species.

• acceptedName: If the species name is not accepted or incorrect, the accepted name of the specie. If the species name is accepted and correct, the same as input_name and Suggested_name.

• family: the family of the specie.

References

Flora e Funga do Brasil. Jardim Botânico do Rio de Janeiro. Available at: http://floradobrasil.jbrj.gov.br/

Examples

data("bf_data", package = "florabr")
spp <- c("Butia cattarinensis", "Araucaria angustifolia")
check_names(data = bf_data, species = spp)

Check if you have the latest version of Flora e Funga do Brasil data available

Description

This function checks if you have the latest version of the Flora e Funga do Brasil data available in a specified directory.

Usage

check_version(data_dir)

Arguments

Value

A message informing whether you have the latest version of Flora e Funga do Brasil available in the data_dir

Examples

#Check if there is a version of Flora e Funga do Brasil data available in the
#current directory
check_version(data_dir = getwd())

Identify records outside natural ranges according to Flora e Funga do Brasil

Description

This function removes or flags records outside of the species' natural ranges according to information provided by the Flora e Funga do Brasil database.

Usage

filter_florabr(data, occ, species = "species", long = "x", lat = "y",
                      by_state = TRUE, buffer_state = 20, by_biome = TRUE,
                      buffer_biome = 20, by_endemism = TRUE,
                      buffer_brazil = 20, state_vect = NULL,
                      state_column = NULL, biome_vect = NULL,
                      biome_column = NULL, br_vect = NULL,
                      value = "flag&clean", keep_columns = TRUE,
                      verbose = TRUE)

Arguments

Details

If by_state = TRUE and/or by_biome = TRUE, the function takes polygons representing the states and/or biomes with confirmed occurrences of the specie, draws a buffer around the polygons, and tests if the records of the species fall inside it. If by_endemism = TRUE, the function checks if the species is endemic to brazil. If it is endemic, the function tests if the records of the specie fall inside a polygon representing the boundaries of brazil (with a buffer).

Value

Depending on the 'value' argument. If value = "flag", it returns the same data.frame provided in data with additional columns indicating if the record falls inside the natural range of the specie (TRUE) or outside (FALSE). If value = "clean", it returns a data.frame with only the records that passes all the tests (TRUE for all the filters). If value = "flag&clean" (Default), it returns a list with two data.frames: one with the flagged records and one with the cleaned records.

References

Flora e Funga do Brasil. Jardim Botânico do Rio de Janeiro. Available at: http://floradobrasil.jbrj.gov.br/

Examples

data("bf_data") #Load Flora e Funga do Brasil data
data("occurrences") #Load occurrences
pts <- subset(occurrences, species == "Myrcia hatschbachii")
fd <- filter_florabr(data = bf_data, occ = pts,
                    by_state = TRUE, buffer_state = 20,
                    by_biome = TRUE, buffer_biome = 20,
                    by_endemism = TRUE, buffer_brazil = 20,
                    state_vect = NULL,
                    biome_vect = NULL, br_vect = NULL,
                    value = "flag&clean", keep_columns = TRUE,
                    verbose = FALSE)

Get available attributes to filter species

Description

This function displays all the options available to filter species by its characteristics

Usage

get_attributes(data, attribute)

Arguments

Details

The attribute argument accepts the following options: kingdom, group, subgroup, phylum, class, order, family, lifeform, habitat, vegetation, origin, endemism, biome, states, taxonomicstatus or nomenclaturalstatus. These options represent different characteristics of species that can be used for filtering.

Value

a list of data.frames with the available options to use in the select_species function.

References

Flora e Funga do Brasil. Jardim Botânico do Rio de Janeiro. Available at: http://floradobrasil.jbrj.gov.br/

Examples

data("bf_data") #Load Flora e Funga do Brasil data
# Get available biomes, life forms and states to filter species
d <- get_attributes(data = bf_data,
                    attribute = c("biome", "lifeform", "states"))

Extract the binomial name (Genus + specific epithet + infraspecific epithet (optional)) from a full Scientific Name

Description

Extract the binomial name (Genus + specific epithet + infraspecific epithet (optional)) from a full Scientific Name

Usage

get_binomial(species_names,
                   include_subspecies = TRUE,
                   include_variety = TRUE)

Arguments

Value

A vector with the binomial names (Genus + specific epithet).

Examples

spp <- c("Araucaria angustifolia (Bertol.) Kuntze",
         "Araucaria angustifolia var. alba Reitz",
         "Butia catarinensis Noblick & Lorenzi",
         "Butia eriospatha subsp. punctata",
         "Adesmia paranensis Burkart")
spp_new <- get_binomial(species_names = spp,
                       include_subspecies = TRUE,
                       include_variety = TRUE)
spp_new

Download the latest version of Flora e Funga do Brasil database

Description

This function downloads the latest or an older version of Flora e Funga do Brasil database, merges the information into a single data.frame, and saves this data.frame in the specified directory.

Usage

get_florabr(output_dir, data_version = "latest",
                 solve_discrepancy = FALSE, overwrite = TRUE,
                 verbose = TRUE, remove_files = TRUE)

Arguments

Value

The function downloads the latest version of the Flora e Funga do Brasil database from the official source. It then merges the information into a single data.frame, containing details on species, taxonomy, occurrence, and other relevant data. The merged data.frame is then saved as a file in the specified output directory. The data is saved in a format that allows easy loading using the load_florabr function for further analysis in R.

References

Flora e Funga do Brasil. Jardim Botânico do Rio de Janeiro. Available at: http://floradobrasil.jbrj.gov.br/

Examples

## Not run: 
#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)
#Download, merge and save data
get_florabr(output_dir = my_dir, data_version = "latest",
            solve_discrepancy = FALSE, overwrite = TRUE, verbose = TRUE)

## End(Not run)

Get a presence-absence matrix

Description

Get a presence-absence matrix of species based on its distribution (states, biomes and vegetation types) according to Flora e Funga do Brasil.

Usage

get_pam(data, by_biome = TRUE, by_state = TRUE,
               by_vegetation = FALSE, remove_empty_sites = TRUE,
               return_richness_summary = TRUE,
               return_spatial_richness = TRUE,
               return_plot = TRUE)

Arguments

Value

If return_richness_summary and/or return_spatial_richness is set to TRUE, return a list with:

• PAM: the presence-absence matrix (PAM)

• Richness_summary: a data.frame with the number of species in each site

• Spatial_richness: a SpatVector with the number of species in each site (only by State and biome)

If return_richness_summary and return_spatial_richness is set to FALSE, return a presence-absence matrix

References

Flora e Funga do Brasil. Jardim Botânico do Rio de Janeiro. Available at: http://floradobrasil.jbrj.gov.br/

Examples

data("bf_data") #Load Flora e Funga do Brasil data
#Select endemic and native species of trees with occurrence only in Amazon
am_trees <- select_species(data = bf_data,
                          include_subspecies = FALSE,
                          include_variety = FALSE,
                          kingdom = "Plantae",
                          group = "All", subgroup = "All",
                          family = "All", genus = "All",
                          lifeForm = "Tree", filter_lifeForm = "only",
                          habitat = "All", filter_habitat = "in",
                          biome = "Amazon",
                          filter_biome = "only",
                          state = "All", filter_state = "and",
                          vegetation = "All",
                          filter_vegetation = "in",
                          endemism = "Endemic", origin = "Native",
                          taxonomicStatus = "Accepted",
                          nomenclaturalStatus = "All")
#Get presence-absence matrix
pam_am <- get_pam(data = am_trees, by_biome = TRUE, by_state = TRUE,
                 by_vegetation = FALSE, remove_empty_sites = TRUE,
                 return_richness_summary = TRUE,
                 return_spatial_richness = TRUE,
                 return_plot = TRUE)

Get Spatial polygons (SpatVectors) of species based on its distribution (states and biomes) according to Flora e Funga do Brasil

Description

Get Spatial polygons (SpatVectors) of species based on its distribution (states and biomes) according to Flora e Funga do Brasil

Usage

get_spat_occ(
  data,
  species,
  state = TRUE,
  biome = TRUE,
  intersection = TRUE,
  state_vect = NULL,
  state_column = NULL,
  biome_vect = NULL,
  biome_column = NULL,
  verbose = TRUE
)

Arguments

Value

A list with SpatVectors of states and/or biomes and/or Intersections for each specie.

References

Flora e Funga do Brasil. Jardim Botânico do Rio de Janeiro. Available at: http://floradobrasil.jbrj.gov.br/

Examples

library(terra)
data("bf_data") #Load Flora e Funga do Brasil data
spp <- c("Araucaria angustifolia", "Adesmia paranensis") #Example species
#Get states, biomes and intersection states-biomes of species
spp_spt <- get_spat_occ(data = bf_data, species = spp, state = TRUE,
                       biome = TRUE, intersection = TRUE, state_vect = NULL,
                       biome_vect = NULL, verbose = TRUE)


#Plot states of occurrence of Araucaria angustifolia
plot(spp_spt[[1]]$states, main = names(spp_spt)[[1]])
#Plot biomes of occurrence of Araucaria angustifolia
plot(spp_spt[[2]]$biomes, main = names(spp_spt)[[2]])
#Plot intersection between states and biomes of occurrence of
#Araucaria angustifolia
plot(spp_spt[[1]]$states_biomes)

Retrieve synonyms for species

Description

Retrieve synonyms for species

Usage

get_synonym(data, species,
                   include_subspecies = TRUE, include_variety = TRUE)

Arguments

Value

A data.frame containing unique synonyms of the specified species along with relevant information on taxonomic and nomenclatural statuses.

References

Flora e Funga do Brasil. Jardim Botânico do Rio de Janeiro. Available at: http://floradobrasil.jbrj.gov.br/

Examples

data("bf_data") #Load Flora e Funga do Brasil data
#Species to extract synonyms
spp <- c("Araucaria angustifolia", "Adesmia paranensis")
spp_synonyms <- get_synonym(data = bf_data, species = spp,
                            include_subspecies = TRUE,
                            include_variety = TRUE)
spp_synonyms

Load Flora e Funga do Brasil database

Description

Load Flora e Funga do Brasil database

Usage

load_florabr(data_dir, data_version = "Latest_available",
                    type = "short", verbose = TRUE)

Arguments

Details

The parameter type accepts two arguments. If type = short, it will load a data.frame with the 20 columns needed to run the other functions of the package: species, scientificName, acceptedName, kingdom, Group, Subgroup, family, genus, lifeForm, habitat, Biome, States, vegetationType, Origin, Endemism, taxonomicStatus, nomenclaturalStatus, vernacularName, taxonRank, and id If type = complete, it will load a data.frame with all 39 variables available in Flora e Funga do Brasil database.

Value

A data.frame with the specified version (Default is the latest available) of the Flora e Funga do Brasil database. This data.frame is necessary to run most of the functions of the package.

References

Flora e Funga do Brasil. Jardim Botânico do Rio de Janeiro. Available at: http://floradobrasil.jbrj.gov.br/

Examples

## Not run: 
#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)
#Download, merge and save data
get_florabr(output_dir = my_dir, data_version = "latest", overwrite = TRUE,
            verbose = TRUE)
#Load data
df <- load_florabr(data_dir = my_dir, data_version = "Latest_available",
type = "short")

## End(Not run)

Records of plant species

Description

A dataset containing records of 7 plant species downloaded from GBIF. The records were obtained with plantR::rgbif2

Usage

data(occurrences)

Format

A data.frame with 1521 rows and 3 variables:

species

Species names (Araucaria angustifolia, Abatia americana, Passiflora edmundoi, Myrcia hatschbachii, Serjania pernambucensis, Inga virescens, and Solanum restingae)

x

Longitude

y

Latitude

References

GBIF, 2024. florabr R package: Records of plant species. https://doi.org/10.15468/DD.QPGEB7

Search for taxa using vernacular names

Description

Search for taxa using vernacular names

Usage

select_by_vernacular(data, names, exact = FALSE)

Arguments

Value

a data.frame with the species with vernacular names that match the input names

References

Flora e Funga do Brasil. Jardim Botânico do Rio de Janeiro. Available at: http://floradobrasil.jbrj.gov.br/

Flora e Funga do Brasil. Jardim Botânico do Rio de Janeiro. Available at: http://floradobrasil.jbrj.gov.br/

Examples

data("bf_data") #Load Flora e Funga do Brasil data
#Search for species whose vernacular name is 'pinheiro'
pinheiro_exact <- select_by_vernacular(data = bf_data,
                                       names = "pinheiro",
                                       exact = TRUE)
pinheiro_exact
#Search for species whose vernacular name is 'pinheiro', allowing non-exact
#matches
pinheiro_not_exact <- select_by_vernacular(data = bf_data,
                                          names = "pinheiro",
                                          exact = FALSE)
head(pinheiro_not_exact)

Selection of species based on its characteristics and distribution

Description

select_species allows filter species based on its characteristics and distribution available in Flora e Funga do Brasil

Usage

select_species(data,
                      include_subspecies = FALSE, include_variety = FALSE,
                      kingdom = "Plantae", group = "All", subgroup = "All",
                      phylum = "All", class ="All", order = "All",
                      family = "All", genus = "All",
                      lifeForm = "All", filter_lifeForm = "in",
                      habitat = "All", filter_habitat = "in",
                      biome = "All", filter_biome = "in",
                      state = "All", filter_state = "in",
                      vegetation = "All", filter_vegetation = "in",
                      endemism = "All", origin = "All",
                      taxonomicStatus = "Accepted",
                      nomenclaturalStatus = "All")

Arguments

Details

It's possible to choose 4 ways to filter by lifeForm, by habitat, by biome, by state and by vegetation type: "in": selects species that have any occurrence of the determined values. It allows multiple matches. For example, if biome = c("Amazon", Cerrado" and filter_biome = "in", it will select all species that occur in the Amazon and Cerrado, some of which may also occur in other biomes.

"only": selects species that have only occurrence of the determined values. It allows only single matches. For example, if biome = c("Amazon", "Cerrado") and filter_biome = "only", it will select all species that occur exclusively in both the Amazon and Cerrado biomes, without any occurrences in other biomes.

"not_in": selects species that don't have occurrence of the determined values. It allows single and multiple matches. For example, if biome = c("Amazon", "Cerrado") and filter_biome = "not_in", it will select all species without occurrences in the Amazon and Cerrado biomes.

"and": selects species that have occurrence in all determined values. It allows single and multiple matches. For example, if biome = c("Amazon", "Cerrado") and filter_biome = "and", it will select all species that occurs only in both the Amazon and Cerrado biomes, including species that occurs in other biomes too.

To get the complete list of arguments available for family, genus, lifeForm, habitat, biome, state, and nomenclaturalStatus, use the function get_attributes

Value

A new dataframe with the filtered species.

References

Flora e Funga do Brasil. Jardim Botânico do Rio de Janeiro. Available at: http://floradobrasil.jbrj.gov.br/

Examples

data("bf_data") #Load Flora e Funga do Brasil data
#'Select endemic and native species of trees with disjunct occurrence in
# Atlantic Forest and Amazon
am_af_only <- select_species(data = bf_data,
                             include_subspecies = FALSE,
                             include_variety = FALSE,
                             kingdom = "Plantae",
                             group = "All", subgroup = "All",
                             phylum = "All", class ="All", order = "All",
                             family = "All", genus = "All",
                             lifeForm = "Tree", filter_lifeForm = "only",
                             habitat = "All", filter_habitat = "in",
                             biome = c("Atlantic_Forest","Amazon"),
                             filter_biome = "only",
                             state = "All", filter_state = "and",
                             vegetation = "All",
                             filter_vegetation = "in",
                             endemism = "Endemic", origin = "Native",
                             taxonomicStatus = "All",
                             nomenclaturalStatus = "All")

Resolve discrepancies between species and subspecies/varieties information

Description

Resolve discrepancies between species and subspecies/varieties information

Usage

solve_discrepancies(data)

Arguments

Details

In the original dataset, discrepancies may exist between species and subspecies/varieties information. An example of a discrepancy is when a species occurs only in one biome (e.g., Amazon), but a subspecies or variety of the same species occurs in another biome (e.g., Cerrado). This function rectifies such discrepancies by considering distribution (states, biomes, and vegetation), life form, and habitat. For instance, if a subspecies is recorded in a specific biome, it implies that the species also occurs in that biome.

Value

a data.frame with the discrepancies solved

Examples

data("bf_data") #Load Flora e Funga do Brasil data
#Check if discrepancies were solved in the dataset
attr(bf_data, "solve_discrepancies")
#Solve discrepancies
bf_solved <- solve_discrepancies(bf_data)
#Check if discrepancies were solved in the dataset
attr(bf_solved, "solve_discrepancies")

SpatVector of the federal states of Brazil

Description

A simplified and packed SpatVector of the polygons of the federal states of Brazil. The spatial data was originally obtained from geobr::read_state. Borders have been simplified by removing vertices of borders using terra::simplifyGeom. It's necessary unpack the Spatvectos using terra::unwrap

@usage data(states) states <- terra::unwrap(states)

Usage

states

Format

A SpatVector with 27 geometries and 3 attributes:

abbrev_state

State acronym

name_state

State's full name

name_region

The region to which the state belongs

Extract a subset of species from Flora e Funga do Brasil database

Description

Returns a data.frame with a subset of species from Flora e Funga do Brasil database

Usage

subset_species(data, species,
                      include_subspecies = FALSE,
                      include_variety = FALSE,
                      kingdom = "Plantae")

Arguments

Value

A data.frame with the selected species.

References

Flora e Funga do Brasil. Jardim Botânico do Rio de Janeiro. Available at: http://floradobrasil.jbrj.gov.br/

Examples

data("bf_data") #Load Flora e Funga do Brasil data
#Species to extract from database
spp <- c("Araucaria angustifolia", "Adesmia paranensis")
spp_bf <- subset_species(data = bf_data, species = spp,
                      include_subspecies = FALSE,
                      include_variety = FALSE)
spp_bf