Package 'faunabr' reference manual

Title:	Explore Catálogo Taxônomico da Fauna do Brasil Database
Description:	A collection of functions designed to retrieve, filter and spatialize data from the Catálogo Taxônomico da Fauna do Brasil. For more information about the dataset, please visit <https://fauna.jbrj.gov.br/fauna/listaBrasil/>.
Authors:	Weverton Trindade [aut, cre] (ORCID: <https://orcid.org/0000-0003-2045-4555>)
Maintainer:	Weverton Trindade <[email protected]>
License:	GPL (>= 3)
Version:	1.0.1
Built:	2026-05-31 22:32:30 UTC
Source:	https://github.com/wevertonbio/faunabr

Check species names

Description

check_fauna_names checks if the species names are correct and searches for suggestions if the name is misspelled or not found in the Fauna do Brasil database

Usage

check_fauna_names(data, species, max_distance = 0.1,
                         include_subspecies = TRUE)
check_fauna_names(data, species, max_distance = 0.1,
                         include_subspecies = TRUE)

Arguments

data

(data.frame) the data.frame imported with the load_faunabr function.

species

(character) names of the species to be checked.

max_distance

(numeric) Maximum distance (as a fraction) allowed for searching suggestions when the name is misspelled. It can be any value between 0 and 1. The higher the value, the more suggestions are returned. For more details, see agrep. Default = 0.1.

include_subspecies

whether include subspecies when checking names. Default = TRUE.

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 ("valid" or "synonym").
nomenclaturalStatus: the nomenclatural status of the species name. This information is not available for all species.
validName: If the species name is not valid or incorrect, the valid name of the specie. If the species name is valid and correct, the same as input_name and Suggested_name.
family: the family of the specie.

References

Brazilian Zoology Group. Catálogo Taxonômico da Fauna do Brasil. Available at: https://ipt.jbrj.gov.br/jbrj/resource?r=catalogo_taxonomico_da_fauna_do_brasil

Examples

data("fauna_data")
spp <- c("Pantera onça", "Mazama bororo", "Mazama jucunda",
          "Araucaria angustifolia")
check_fauna_names(data = fauna_data, species = spp)
data("fauna_data")
spp <- c("Pantera onça", "Mazama bororo", "Mazama jucunda",
          "Araucaria angustifolia")
check_fauna_names(data = fauna_data, species = spp)

Country Codes and Names

Description

A dataset containing country codes used in the Catálogo Taxonômico da Fauna do Brasil along with their corresponding country names, as defined in faunabr::world_fauna.

Usage

data(country_codes)
data(country_codes)

Format

A data.frame with 244 rows and 2 variables:

map_name: Country names as defined in faunabr::world_fauna.
country_code: Country codes used in the Catálogo Taxonômico da Fauna do Brasil.

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

Description

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

Usage

extract_binomial(species_names)
extract_binomial(species_names)

Arguments

species_names

(character) Scientific names to be converted to binomial names

Value

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

Examples

spp <- c("Panthera onca (Linnaeus, 1758)",
"Zonotrichia capensis subtorquata Swainson, 1837",
"Paraganaspis egeria Díaz & Gallardo, 1996",
"Arrenurus tumulosus intercursor")
spp_new <- extract_binomial(species_names = spp)
spp_new

spp <- c("Panthera onca (Linnaeus, 1758)",
"Zonotrichia capensis subtorquata Swainson, 1837",
"Paraganaspis egeria Díaz & Gallardo, 1996",
"Arrenurus tumulosus intercursor")
spp_new <- extract_binomial(species_names = spp)
spp_new

Get available attributes to filter species

Description

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

Usage

fauna_attributes(data, attribute)
fauna_attributes(data, attribute)

Arguments

data

(data.frame) a data.frame imported with the load_faunabr function or a data.frame generated with the select_fauna function.

attribute

(character) the type of characteristic. Accept more than one option. See detail to see the options.

Details

The attribute argument accepts the following options: phylum, class, family, genus, lifeForm, habitat, states, country, origin, and taxonomicstatus. 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_fauna function.

Examples

data("fauna_data") #Load data example
# Get available states, countries and lifeForms to filter species
d <- fauna_attributes(data = fauna_data,
                    attribute = c("country", "lifeform", "states"))
data("fauna_data") #Load data example
# Get available states, countries and lifeForms to filter species
d <- fauna_attributes(data = fauna_data,
                    attribute = c("country", "lifeform", "states"))

Search for taxa using vernacular names

Description

Search for taxa using vernacular names

Usage

fauna_by_vernacular(data, names, exact = FALSE)
fauna_by_vernacular(data, names, exact = FALSE)

Arguments

data

(data.frame) the data.frame imported with the load_faunabr function or generated with the function select_fauna.

names

(character) vernacular name ("Nome comum") of the species to be searched

exact

(logic) if TRUE, the function will search only for exact matches. For example, if names = "veado-mateiro" and exact = TRUE, the function will return only the species popularly known as "veado-mateiro". On the other hand, if names = "veado-mateiro" and exact = FALSE, the function will return other results as "Veado-mateiro-pequeno". Default = FALSE

Value

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

Examples

data("fauna_data") #Load Fauna do Brasil data
#Search for species whose vernacular name is 'veado-mateiro'
veado_exact <- fauna_by_vernacular(data = fauna_data,
                                   names = "veado-mateiro",
                                   exact = TRUE)
veado_exact
#Search for species whose vernacular name is 'veado_mateiro', allowing non-exact
#matches
veado_not_exact <- fauna_by_vernacular(data = fauna_data,
                                       names = "veado-mateiro",
                                      exact = FALSE)

data("fauna_data") #Load Fauna do Brasil data
#Search for species whose vernacular name is 'veado-mateiro'
veado_exact <- fauna_by_vernacular(data = fauna_data,
                                   names = "veado-mateiro",
                                   exact = TRUE)
veado_exact
#Search for species whose vernacular name is 'veado_mateiro', allowing non-exact
#matches
veado_not_exact <- fauna_by_vernacular(data = fauna_data,
                                       names = "veado-mateiro",
                                      exact = FALSE)

Catálogo Taxonômico da Fauna do Brasil database - Version 1.17

Description

A dataset containing a subset of the Catálogo Taxonômico da Fauna do Brasil database (version 1.17)

Usage

data(fauna_data)
data(fauna_data)

Format

A data.frame with 9558 rows and 19 variables:

species: Species names
subspecies: Subspecies names
scientificName: Complete scientific name of the species
validName: Valid name of the species (NA when the name in species is already a valid name)
kingdom: Kingdom to which species belongs (Animalia)
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: free_living_individual, colonial, sessile, etc.)
habitat: Habitat type of the species (e.g., terrestrial, arboreal, freshwater, etc.)
states: Federal states with confirmed occurrences of the species
countryCode: Countries with confirmed occurrences of the species
origin: Indicates whether the species is native, introduced, domesticated, cryptogenic or invasive
taxonomicStatus: Indicates the level of recognition and acceptance of the species (valid or synonym)
nomenclaturalStatus: Indicates the legitimacy and validity of the species name (original_combination, changed_combination, etc.)
vernacularName: Locally or culturally used name for the species
taxonRank: Taxonomic rank (Species, Genus, Family, Order, etc). This data contains only Species

References

Brazilian Zoology Group. Catálogo Taxonômico da Fauna do Brasil. Available at: https://ipt.jbrj.gov.br/jbrj/resource?r=catalogo_taxonomico_da_fauna_do_brasil

Resolve discrepancies between species and subspecies information

Description

Resolve discrepancies between species and subspecies information

Usage

fauna_discrepancies(data)
fauna_discrepancies(data)

Arguments

data

(data.frame) the data.frame imported with the load_faunabr function.

Details

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

Value

a data.frame with the discrepancies solved

Examples

data("fauna_data") #Load fauna e Funga do Brasil data
#Check if discrepancies were solved in the dataset
attr(fauna_data, "solved_discrepancies")
#Solve discrepancies
fauna_solved <- fauna_discrepancies(fauna_data)
#Check if discrepancies were solved in the dataset
attr(fauna_solved, "solved_discrepancies")
data("fauna_data") #Load fauna e Funga do Brasil data
#Check if discrepancies were solved in the dataset
attr(fauna_data, "solved_discrepancies")
#Solve discrepancies
fauna_solved <- fauna_discrepancies(fauna_data)
#Check if discrepancies were solved in the dataset
attr(fauna_solved, "solved_discrepancies")

Get a presence-absence matrix

Description

Get a presence-absence matrix of species based on its distribution (brazilian states and/or countries) according to Fauna do Brasil.

Usage

fauna_pam(data, by_state = TRUE, by_country= FALSE,
               remove_empty_sites = TRUE,
               return_richness_summary = TRUE,
               return_spatial_richness = TRUE,
               return_plot = TRUE)
fauna_pam(data, by_state = TRUE, by_country= FALSE,
               remove_empty_sites = TRUE,
               return_richness_summary = TRUE,
               return_spatial_richness = TRUE,
               return_plot = TRUE)

Arguments

data

(data.frame) a data.frame imported with the load_faunabr function or generated by either select_fauna or subset_fauna functions

by_state

(logical) get occurrences by State. Default = TRUE

by_country

(logical) get occurrences by countries. Default = FALSE

remove_empty_sites

(logical) remove empty sites (sites without any species) from final presence-absence matrix. Default = TRUE

return_richness_summary

(logical) return a data.frame with the number of species in each site. Default = TRUE

return_spatial_richness

(logical) return a SpatVector with the number of species in each site. Default = TRUE

return_plot

(logical) plot map with the number of species in each site. Only works if return_spatial_richness = TRUE. Default = TRUE

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 (by State and/or country)

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

Examples

#Test function
data("fauna_data") #Load fauna e Funga do Brasil data
#Select native species of mammals with occurrence only in Brazil
br_mammals <- select_fauna(data = fauna_data,
                           include_subspecies = FALSE, phylum = "all",
                           class = "Mammalia",
                           order = "all", family = "all",
                           genus = "all",
                           lifeForm = "all", filter_lifeForm = "in",
                           habitat = "all", filter_habitat = "in",
                           states = "all", filter_states = "in",
                           country = "BR", filter_country = "only",
                           origin = "all", taxonomicStatus = "valid")
#Get presence-absence matrix in states
pam_mammals <- fauna_pam(data = br_mammals, by_state = TRUE,
                         by_country = FALSE,
                         remove_empty_sites = TRUE,
                         return_richness_summary = TRUE,
                         return_spatial_richness = TRUE,
                         return_plot = TRUE)
#Test function
data("fauna_data") #Load fauna e Funga do Brasil data
#Select native species of mammals with occurrence only in Brazil
br_mammals <- select_fauna(data = fauna_data,
                           include_subspecies = FALSE, phylum = "all",
                           class = "Mammalia",
                           order = "all", family = "all",
                           genus = "all",
                           lifeForm = "all", filter_lifeForm = "in",
                           habitat = "all", filter_habitat = "in",
                           states = "all", filter_states = "in",
                           country = "BR", filter_country = "only",
                           origin = "all", taxonomicStatus = "valid")
#Get presence-absence matrix in states
pam_mammals <- fauna_pam(data = br_mammals, by_state = TRUE,
                         by_country = 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 countrys) according to Fauna do Brasil

Description

Get Spatial polygons (SpatVectors) of species based on its distribution (states and countrys) according to Fauna do Brasil

Usage

fauna_spat_occ(data, species, state = TRUE, country = TRUE,
                      spat_state = NULL, spat_country = NULL, verbose = TRUE)
fauna_spat_occ(data, species, state = TRUE, country = TRUE,
                      spat_state = NULL, spat_country = NULL, verbose = TRUE)

Arguments

data

(data.frame) the data.frame imported with the load_faunabr function.

species

(character) one or more species names (only genus and specific epithet, eg. "Panthera onca")

state

(logical) get SpatVector of states with occurrence of the species? Default = TRUE

country

(logical) get SpatVector of countrys with occurrence of the species? Default = TRUE

spat_state

(SpatVector) a SpatVector of the Brazilian states. By default, it uses the SpatVector provided by geobr::read_state(). It can be another Spatvector, but the structure must be identical to 'faunabr::states', with a column called "abbrev_state" identifying the states codes.

spat_country

(SpatVector) a SpatVector of the world countries. By default, it uses the SpatVector provided by rnaturalearth::ne_countries. It can be another Spatvector, but the structure must be identical to 'faunabr::world_fauna', with a column called "country_code" identifying the country codes.

verbose

(logical) Whether to display species being filtered during function execution. Set to TRUE to enable display, or FALSE to run silently. Default = TRUE.

Value

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

Examples

library(terra)
data("fauna_data")
spp <- c("Panthera onca", "Mazama jucunda")
#Get states, countrys and intersection states-countrys of species
spp_spt <- fauna_spat_occ(data = fauna_data, species = spp, state = TRUE,
                          country = TRUE, verbose = TRUE)
#Plot states with confirmed occurrence of Panthera onca and Mazama jucunda
plot(spp_spt$`Panthera onca`$states)
plot(spp_spt$`Mazama jucunda`$states)
#Plot countries with confirmed occurrence of Panthera onca and Mazama jucunda
plot(spp_spt$`Panthera onca`$countries)
plot(spp_spt$`Mazama jucunda`$countries)

library(terra)
data("fauna_data")
spp <- c("Panthera onca", "Mazama jucunda")
#Get states, countrys and intersection states-countrys of species
spp_spt <- fauna_spat_occ(data = fauna_data, species = spp, state = TRUE,
                          country = TRUE, verbose = TRUE)
#Plot states with confirmed occurrence of Panthera onca and Mazama jucunda
plot(spp_spt$`Panthera onca`$states)
plot(spp_spt$`Mazama jucunda`$states)
#Plot countries with confirmed occurrence of Panthera onca and Mazama jucunda
plot(spp_spt$`Panthera onca`$countries)
plot(spp_spt$`Mazama jucunda`$countries)

Retrieve synonyms for species

Description

Retrieve synonyms for species

Usage

fauna_synonym(data, species,
                   include_subspecies = TRUE)
fauna_synonym(data, species,
                   include_subspecies = TRUE)

Arguments

data

(data.frame) the data.frame imported with the load_faunabr function

species

(character) names of the species

include_subspecies

(logical) include subspecies that are synonyms of the species? Default = TRUE

Value

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

Examples

data("fauna_data") #Load Flora e Funga do Brasil data
#Species to extract synonyms
spp <- c("Panthera onca", "Mazama jucunda", "Subulo gouzoubira")
spp_synonyms <- fauna_synonym(data = fauna_data, species = spp,
                              include_subspecies = FALSE)
spp_synonyms

data("fauna_data") #Load Flora e Funga do Brasil data
#Species to extract synonyms
spp <- c("Panthera onca", "Mazama jucunda", "Subulo gouzoubira")
spp_synonyms <- fauna_synonym(data = fauna_data, species = spp,
                              include_subspecies = FALSE)
spp_synonyms

Check if you have the latest version of Fauna do Brasil data available

Description

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

Usage

fauna_version(data_dir)
fauna_version(data_dir)

Arguments

data_dir

the directory where the data should be located.

Value

A message informing whether you have the latest version of Fauna do Brasil available in the data_dir

Examples

#Check if there is a version of Fauna do Brasil data available in the
#current directory
fauna_version(data_dir = getwd())
#Check if there is a version of Fauna do Brasil data available in the
#current directory
fauna_version(data_dir = getwd())

Identify records outside natural ranges according to Fauna do Brasil

Description

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

Usage

filter_faunabr(data, occ, species = "species", long = "x", lat = "y",
                      by_state = TRUE, buffer_state = 20, by_country = TRUE,
                      buffer_country = 20, value = "flag&clean",
                      keep_columns = TRUE, spat_state = NULL,
                      spat_country = NULL, verbose = TRUE)
filter_faunabr(data, occ, species = "species", long = "x", lat = "y",
                      by_state = TRUE, buffer_state = 20, by_country = TRUE,
                      buffer_country = 20, value = "flag&clean",
                      keep_columns = TRUE, spat_state = NULL,
                      spat_country = NULL, verbose = TRUE)

Arguments

data

(data.frame) the data.frame imported with the load_faunabr function.

occ

(data.frame) a data.frame with the records of the species.

species

(character) column name in occ with species names. Default = "species"

long

(character) column name in occ with longitude data. Default = "x"

lat

(character) column name in occ with latitude data. Default = "y"

by_state

(logical) filter records by state? Default = TRUE

buffer_state

(numeric) buffer (in km) around the polygons of the states of occurrence of the specie. Default = 20.

by_country

(logical) filter records by country? Default = TRUE

buffer_country

(numeric) buffer (in km) around the polygons of the countries of occurrence of the specie. Default = 20.

value

(character) Defines output values. See Value section. Default = "flag&clean".

keep_columns

(logical) if TRUE, keep all the original columns of the input occ. If False, keep only the columns species, long and lat. Default = TRUE

spat_state

spat_country

verbose

(logical) Whether to display species being filtered during function execution. Set to TRUE to enable display, or FALSE to run silently. Default = TRUE.

Details

If by_state = TRUE and/or by_country = TRUE, the function takes polygons representing the states and/or countrys with confirmed occurrences of the specie, draws a buffer around the polygons, and tests if the records of the species fall inside it.

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.

Examples

data("fauna_data") #Load fauna e Funga do Brasil data
data("occurrences") #Load occurrences
pts <- subset(occurrences, species == "Panthera onca")
fd <- filter_faunabr(data = fauna_data,
                     occ = pts, long = "x", lat = "y", species = "species",
                     by_state = TRUE, buffer_state = 20,
                     by_country = TRUE, buffer_country = 20,
                     value = "flag&clean", keep_columns = TRUE,
                     verbose = FALSE)
data("fauna_data") #Load fauna e Funga do Brasil data
data("occurrences") #Load occurrences
pts <- subset(occurrences, species == "Panthera onca")
fd <- filter_faunabr(data = fauna_data,
                     occ = pts, long = "x", lat = "y", species = "species",
                     by_state = TRUE, buffer_state = 20,
                     by_country = TRUE, buffer_country = 20,
                     value = "flag&clean", keep_columns = TRUE,
                     verbose = FALSE)

Download the latest version of Catálogo Taxonômico da Fauna do Brasil

Description

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

Usage

get_faunabr(output_dir, data_version = "latest",
                 solve_discrepancies = TRUE, translate = TRUE,
                 overwrite = TRUE, verbose = TRUE)
get_faunabr(output_dir, data_version = "latest",
                 solve_discrepancies = TRUE, translate = TRUE,
                 overwrite = TRUE, verbose = TRUE)

Arguments

output_dir

(character) a directory to save the data downloaded from Fauna do Brasil

data_version

(character) Version of the Fauna do Brasil database to download. Use "latest" to get the most recent version, which is updated frequently. Alternatively, specify an older version (e.g., data_version = "1.2").Default value is "latest".

solve_discrepancies

Resolve inconsistencies between species and subspecies information. When set to TRUE (default), species information is updated based on unique data from subspecies. For example, if a subspecies occurs in a certain state, it implies that the species also occurs in that state.

translate

(logical) whether to translate the original dataset ("lifeForm", "origin", "habitat", and "taxonRank") from Portuguese to English. Default is TRUE.

overwrite

(logical) If TRUE, data is overwritten. Default = TRUE.

verbose

(logical) Whether to display messages during function execution. Set to TRUE to enable display, or FALSE to run silently. Default = TRUE.

Value

The function downloads the latest version of the Catálogo Taxonômico da Fauna 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_faunabr function for further analysis in R.

References

Brazilian Zoology Group. Catálogo Taxonômico da Fauna do Brasil. Available at: https://ipt.jbrj.gov.br/jbrj/resource?r=catalogo_taxonomico_da_fauna_do_brasil

Examples

## Not run: 
#Creating a folder in a temporary directory
#Replace 'file.path(tempdir(), "faunaabr")' by a path folder to be create in
#your computer
my_dir <- file.path(file.path(tempdir(), "faunabr"))
dir.create(my_dir)
#Download, merge and save data
get_faunabr(output_dir = my_dir)

## End(Not run)
## Not run: 
#Creating a folder in a temporary directory
#Replace 'file.path(tempdir(), "faunaabr")' by a path folder to be create in
#your computer
my_dir <- file.path(file.path(tempdir(), "faunabr"))
dir.create(my_dir)
#Download, merge and save data
get_faunabr(output_dir = my_dir)

## End(Not run)

Load Brazilian Fauna database

Description

Load Brazilian Fauna database

Usage

load_faunabr(data_dir, data_version = "latest",
                    type = "short", verbose = TRUE, encoding = "UTF-8")
load_faunabr(data_dir, data_version = "latest",
                    type = "short", verbose = TRUE, encoding = "UTF-8")

Arguments

data_dir

(character) the same directory used to save the data downloaded from Brazilian Fauna using the get_faunabr function.

data_version

(character) the version of Brazilian Fauna database to be loaded. It can be "latest", which will load the latest version available; or another specified version, for example "1.2". Default = "latest".

type

(character) it determines the number of columns that will be loaded. It can be "short" or "complete". Default = "short". See details.

verbose

(logical) Whether to display messages during function execution. Set to TRUE to enable display, or FALSE to run silently. Default = TRUE.

encoding

(character) the declared encodings for special characters. Character strings in R can be declared to be encoded in "latin1" or "UTF-8". Default: "UTF-8".

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, subspecies, scientificName, validName, kingdom, phylum, class, order, family, genus, lifeForm, habitat, states, countryCode, origin, taxonomicStatus, nomenclaturalStatus, vernacularName, and taxonRank. If type = complete, it will load a data.frame with all 31 variables available in Brazilian Fauna database.

Value

A data.frame with the specified version (Default is the latest available) of the Brazilian Fauna database. This data.frame is necessary to run most of the functions of the package.

References

Brazilian Zoology Group. Catálogo Taxonômico da Fauna do Brasil. Available at: https://ipt.jbrj.gov.br/jbrj/resource?r=catalogo_taxonomico_da_fauna_do_brasil

Examples

## Not run: 
#Creating a folder in a temporary directory
#Replace 'file.path(tempdir(), "faunabr")' by a path folder to be create in
#your computer
my_dir <- file.path(file.path(tempdir(), "faunabr"))
dir.create(my_dir)
#Download, merge and save data
get_fauna(output_dir = my_dir, data_version = "latest", overwrite = TRUE,
            verbose = TRUE)
#Load data
df <- load_faunabr(data_dir = my_dir, data_version = "latest",
                   type = "short")

## End(Not run)
## Not run: 
#Creating a folder in a temporary directory
#Replace 'file.path(tempdir(), "faunabr")' by a path folder to be create in
#your computer
my_dir <- file.path(file.path(tempdir(), "faunabr"))
dir.create(my_dir)
#Download, merge and save data
get_fauna(output_dir = my_dir, data_version = "latest", overwrite = TRUE,
            verbose = TRUE)
#Load data
df <- load_faunabr(data_dir = my_dir, data_version = "latest",
                   type = "short")

## End(Not run)

Helpers for translating data

Description

A list of data.frames used by faunabr::translate_faunabr() function. faunabr::map_translation.

Usage

data(map_translation)
data(map_translation)

Format

A list with 5 data.frames ("lifeForm", "origin", "habitat", "taxonRank", and "taxonomicStatus"). Each data.frame has 2 columns:

pt_br: The attribute in Brazilian Portuguese.
en: The attribute in English.

Records of animal species

Description

A dataset containing records of 2 species downloaded from GBIF, with additional fake data. The records were obtained with plantR::rgbif2

Usage

data(occurrences)
data(occurrences)

Format

A data.frame with 2798 rows and 3 variables:

species: Species names (Panthera onca and Chaetomys subspinosus)
x: Longitude
y: Latitude
source: record downloaded from GBIF or fake data

References

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

Selection of species based on its characteristics and distribution

Description

select_fauna allows filter species based on its characteristics and distribution available in Brazilian Fauna

Usage

select_fauna(data, include_subspecies = FALSE, phylum = "all",
                      class = "all", order = "all", family = "all",
                      genus = "all",
                      lifeForm = "all", filter_lifeForm = "in",
                      habitat = "all", filter_habitat = "in",
                      states = "all", filter_states = "in",
                      country = "all", filter_country = "in",
                      origin = "all", taxonomicStatus = "valid")
select_fauna(data, include_subspecies = FALSE, phylum = "all",
                      class = "all", order = "all", family = "all",
                      genus = "all",
                      lifeForm = "all", filter_lifeForm = "in",
                      habitat = "all", filter_habitat = "in",
                      states = "all", filter_states = "in",
                      country = "all", filter_country = "in",
                      origin = "all", taxonomicStatus = "valid")

Arguments

data

(data.frame) the data.frame imported with the load_faunabr function.

include_subspecies

(logical) include subspecies? Default = FALSE

phylum

(character) The phyla for filtering the dataset. It can be included more than one phylum. Default = "all".

class

(character) The classes for filtering the dataset. It can be included more than one class. Default = "all".

order

(character) The orders for filtering the dataset. It can be included more than one order. Default = "all".

family

(character) The families for filtering the dataset. It can be included more than one family. Default = "all".

genus

(character) The genus for filtering the dataset. It can be included more than one genus. Default = "all".

lifeForm

(character) The life forms for filtering the dataset. It can be included more than one lifeForm. Default = "all"

filter_lifeForm

(character) The type of filtering for life forms. It can be "in", "only", "not_in" and "and". See details for more about this argument.

habitat

(character) The life habitat for filtering the dataset. It can be included more than one habitat. Default = "all"

filter_habitat

(character) The type of filtering for habitat. It can be "in", "only", "not_in" and "and". See details for more about this argument.

states

(character) The states for filtering the dataset. It can be included more than one state. Default = "all".

filter_states

(character) The type of filtering for states. It can be "in", "only", "not_in" and "and". See Details for more about this argument.

country

(character) The country or countries with confirmed occurrences for filtering the dataset. It can be included more than one country. Default = "all".

filter_country

(character) The type of filtering for country. It can be "in", "only", "not_in" and "and". See details for more about this argument.

origin

(character) The origin for filtering the dataset. It can be "native", "introduced", "cryptogenic", "domesticaded" and "invasora". Default = "all".

taxonomicStatus

(character) The taxonomic status for filtering the dataset. It can be "valid", "synonym" or "all". Default = "valid".

Details

It's possible to choose 4 ways to filter by lifeform, by habitat, by states and by country: "in": selects species that have any occurrence of the determined values. It allows multiple matches. For example, if country = c("brazil", argentina") and filter_country = "in", it will select all species that occur in Brazil and/or Argentina, some of which may also occur in other countries.

"only": selects species that have only occurrence of the determined values. It allows only single matches. For example, if country = c("brazil", argentina") and filter_country = "in", it will select all species that occur exclusively in both countries, without any occurrences in other countries.

"not_in": selects species that don't have occurrence of the determined values. It allows single and multiple matches. For example, if country = c("brazil", argentina") and filter_country = "not_in", it will select all species without occurrences in Brazil and Argentina.

"and": selects species that have occurrence in all determined values. It allows single and multiple matches. For example, if country = c("brazil", argentina") and filter_country = "and", it will select all species that occurs only in both countries,including species that occurs in other countries too.

To get the complete list of arguments available for phylum, class, order, family, genus, lifeForm, habitat, states, country and origins, use the function fauna_attributes

Value

A new dataframe with the filtered species.

References

Brazilian Zoology Group. Catálogo Taxonômico da Fauna do Brasil. Available at: https://ipt.jbrj.gov.br/jbrj/resource?r=catalogo_taxonomico_da_fauna_do_brasil

Examples

data("fauna_data") #Load data example
#Select endemic and native species of birds (Aves) with confirmed occurrence
#in Brazil or Argentina
aves_br_ar <- select_fauna(data = fauna_data, include_subspecies = FALSE,
                           phylum = "all", class = "Aves",
                           order = "all",
                           family = "all",
                           genus = "all",
                           lifeForm = "all", filter_lifeForm = "in",
                           habitat = "all", filter_habitat = "in",
                           states = "all", filter_states = "in",
                           country = c("BR", "AR"),
                           filter_country = "in",
                           origin = "native",
                           taxonomicStatus = "valid")
data("fauna_data") #Load data example
#Select endemic and native species of birds (Aves) with confirmed occurrence
#in Brazil or Argentina
aves_br_ar <- select_fauna(data = fauna_data, include_subspecies = FALSE,
                           phylum = "all", class = "Aves",
                           order = "all",
                           family = "all",
                           genus = "all",
                           lifeForm = "all", filter_lifeForm = "in",
                           habitat = "all", filter_habitat = "in",
                           states = "all", filter_states = "in",
                           country = c("BR", "AR"),
                           filter_country = "in",
                           origin = "native",
                           taxonomicStatus = "valid")

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
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 Fauna do Brasil database

Description

Returns a data.frame with a subset of species from Fauna do Brasil database

Usage

subset_fauna(data, species, include_subspecies = FALSE)
subset_fauna(data, species, include_subspecies = FALSE)

Arguments

data

(data.frame) the data.frame imported with the load_faunabr function.

species

(character) names of the species to be extracted from Fauna do Brasil database.

include_subspecies

(logical) include subspecies? Default = FALSE

Value

A data.frame with the selected species.

Examples

data("fauna_data") #Load data example
#Species to extract from database
spp <- c("Panthera onca", "Mazama jucunda", "Subulo gouzoubira")
spp_subset <- subset_fauna(data = fauna_data, species = spp,
                      include_subspecies = FALSE)
spp_subset
data("fauna_data") #Load data example
#Species to extract from database
spp <- c("Panthera onca", "Mazama jucunda", "Subulo gouzoubira")
spp_subset <- subset_fauna(data = fauna_data, species = spp,
                      include_subspecies = FALSE)
spp_subset

Translate information in Brazilian Fauna database

Description

This function translates information in the "lifeForm", "origin", "habitat", "taxonRank", and "taxonomicStatus" columns between Portuguese and English.

Usage

translate_faunabr(data, map_list = NULL, to = "en")
translate_faunabr(data, map_list = NULL, to = "en")

Arguments

data

(data.frame) the data.frame imported with the load_faunabr function.

map_list

(list) A list of data.frames used for translation. The default is NULL, which means it uses faunabr::map_translation. If not NULL, its structure (list names and data.frame column names) must be identical to faunabr::map_translation.

to

(character) The target language for translation. Available options are "en" to translate from Portuguese to English, and "pt_br" to translate from English to Portuguese. The default is "en".

Value

A data.frame with the values in the "lifeForm", "origin", "habitat", "taxonRank", and "taxonomicStatus" columns translated.

Examples

data("fauna_data") #Load data example (in English)
#Translate to Portuguese
fauna_portugues <- translate_faunabr(data = fauna_data, to = "pt_br")
# See attributes of lifeForm in Portuguese
fauna_attributes(fauna_portugues, attribute = "lifeForm")

data("fauna_data") #Load data example (in English)
#Translate to Portuguese
fauna_portugues <- translate_faunabr(data = fauna_data, to = "pt_br")
# See attributes of lifeForm in Portuguese
fauna_attributes(fauna_portugues, attribute = "lifeForm")

SpatVector of the world countries

Description

A simplified and packed SpatVector of the world country polygons. The spatial data was originally obtained from rnaturalearth::ne_countries. Borders have been simplified by removing vertices of borders using terra::simplifyGeom.It's necessary unpack the Spatvectos using terra::unwrap

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

Usage

world_fauna
world_fauna

Format

A SpatVector with 258 geometries and 1 attribute:

name: The name of the country (argentina, brazil, colombia, etc.)

Package 'faunabr'

Help Index

Check species names

Description

Usage

Arguments

Value

References

Examples

Country Codes and Names

Description

Usage

Format

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

Description

Usage

Arguments

Value

Examples

Get available attributes to filter species

Description

Usage

Arguments

Details

Value

Examples

Search for taxa using vernacular names

Description

Usage

Arguments

Value

Examples

Catálogo Taxonômico da Fauna do Brasil database - Version 1.17

Description

Usage

Format

References

Resolve discrepancies between species and subspecies information

Description

Usage

Arguments

Details

Value

Examples

Get a presence-absence matrix

Description

Usage

Arguments

Value

Examples

Get Spatial polygons (SpatVectors) of species based on its distribution (states and countrys) according to Fauna do Brasil

Description

Usage

Arguments

Value

Examples

Retrieve synonyms for species

Description

Usage

Arguments

Value

Examples

Check if you have the latest version of Fauna do Brasil data available

Description

Usage

Arguments

Value

Examples

Identify records outside natural ranges according to Fauna do Brasil

Description

Usage

Arguments

Details

Value

Examples

Download the latest version of Catálogo Taxonômico da Fauna do Brasil

Description

Usage

Arguments

Value