auk_species {auk}

Filter the eBird data by species

Description

Define a filter for the eBird Basic Dataset (EBD) based on species. This function only defines the filter and, once all filters have been defined, auk_filter() should be used to call AWK and perform the filtering.

Usage

auk_species(x, species, taxonomy_version, replace = FALSE)

Arguments

x

auk_ebd object; reference to object created by auk_ebd().

species

character; species to filter by, provided as scientific or English common names, or a mixture of both. These names must match the official eBird Taxomony (ebird_taxonomy).

taxonomy_version

integer; the version (i.e. year) of the taxonomy. In most cases, this should be left empty to use the version of the taxonomy included in the package. See get_ebird_taxonomy().

replace

logical; multiple calls to auk_species() are additive, unless replace = FALSE, in which case the previous list of species to filter by will be removed and replaced by that in the current call.

Details

The list of species is checked against the eBird taxonomy for validity. This taxonomy is updated once a year in August. The auk package includes a copy of the eBird taxonomy, current at the time of release; however, if the EBD and auk versions are not aligned, you may need to explicitly specify which version of the taxonomy to use, in which case the eBird API will be queried to get the correct version of the taxonomy.

Value

An auk_ebd object.

See Also

Other filter: auk_bbox(), auk_bcr(), auk_breeding(), auk_complete(), auk_country(), auk_county(), auk_date(), auk_distance(), auk_duration(), auk_exotic(), auk_extent(), auk_filter(), auk_last_edited(), auk_observer(), auk_project(), auk_protocol(), auk_state(), auk_time(), auk_year()

Examples

# common and scientific names can be mixed
species <- c("Canada Jay", "Pluvialis squatarola")
system.file("extdata/ebd-sample.txt", package = "auk") %>%
  auk_ebd() %>%
  auk_species(species)
  
# alternatively, without pipes
ebd <- auk_ebd(system.file("extdata/ebd-sample.txt", package = "auk"))
auk_species(ebd, species)