Selection of species based on its characteristics and distribution

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

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".

Value

A new dataframe with the filtered species.

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

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")