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.
auk_species(x, species, taxonomy_version, replace = FALSE)auk_ebd object; reference to object created by auk_ebd().
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).
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().
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.
An auk_ebd object.
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.
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()
# 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)
#> Input
#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt
#>
#> Output
#> Filters not executed
#>
#> Filters
#> Species: Perisoreus canadensis, Pluvialis squatarola
#> Countries: all
#> States: all
#> Counties: all
#> BCRs: all
#> Bounding box: full extent
#> Years: all
#> Date: all
#> Start time: all
#> Last edited date: all
#> Protocol: all
#> Project code: all
#> Duration: all
#> Distance travelled: all
#> Records with breeding codes only: no
#> Exotic Codes: all
#> Complete checklists only: no
# alternatively, without pipes
ebd <- auk_ebd(system.file("extdata/ebd-sample.txt", package = "auk"))
auk_species(ebd, species)
#> Input
#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt
#>
#> Output
#> Filters not executed
#>
#> Filters
#> Species: Perisoreus canadensis, Pluvialis squatarola
#> Countries: all
#> States: all
#> Counties: all
#> BCRs: all
#> Bounding box: full extent
#> Years: all
#> Date: all
#> Start time: all
#> Last edited date: all
#> Protocol: all
#> Project code: all
#> Duration: all
#> Distance travelled: all
#> Records with breeding codes only: no
#> Exotic Codes: all
#> Complete checklists only: no