auk_zerofill | R Documentation |
Read an eBird Basic Dataset (EBD) file, and associated sampling event data file, to produce a zero-filled, presence-absence dataset. The EBD contains bird sightings and the sampling event data is a set of all checklists, they can be combined to infer absence data by assuming any species not reported on a checklist was had a count of zero.
auk_zerofill(x, ...)
## S3 method for class 'data.frame'
auk_zerofill(
x,
sampling_events,
species,
taxonomy_version,
collapse = FALSE,
unique = TRUE,
rollup = TRUE,
drop_higher = TRUE,
complete = TRUE,
...
)
## S3 method for class 'character'
auk_zerofill(
x,
sampling_events,
species,
taxonomy_version,
collapse = FALSE,
unique = TRUE,
rollup = TRUE,
drop_higher = TRUE,
complete = TRUE,
sep = "\t",
...
)
## S3 method for class 'auk_ebd'
auk_zerofill(
x,
species,
taxonomy_version,
collapse = FALSE,
unique = TRUE,
rollup = TRUE,
drop_higher = TRUE,
complete = TRUE,
sep = "\t",
...
)
collapse_zerofill(x)
x |
filename, |
... |
additional arguments passed to methods. |
sampling_events |
character or |
species |
character; species to include in zero-filled dataset, provided as scientific or English common names, or a mixture of both. These names must match the official eBird Taxomony (ebird_taxonomy). To include all species, leave this argument blank. |
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 |
collapse |
logical; whether to call |
unique |
logical; should |
rollup |
logical; should |
drop_higher |
logical; whether to remove taxa above species during the
rollup process, e.g. "spuhs" like "duck sp.". See |
complete |
logical; if |
sep |
character; single character used to separate fields within a row. |
auk_zerofill()
generates an auk_zerofill
object consisting of a list with
elements observations
and sampling_events
. observations
is a data frame
giving counts and binary presence/absence data for each species.
sampling_events
is a data frame with checklist level information. The two
data frames can be connected via the checklist_id
field. This format is
efficient for storage since the checklist columns are not duplicated for each
species, however, working with the data often requires joining the two data
frames together.
To return a data frame, set collapse = TRUE
. Alternatively,
zerofill_collapse()
generates a data frame from an auk_zerofill
object,
by joining the two data frames together to produce a single data frame in
which each row provides both checklist and species information for a
sighting.
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.
By default, an auk_zerofill
object, or a data frame if collapse = TRUE
.
auk_zerofill(data.frame)
: EBD data frame.
auk_zerofill(character)
: Filename of EBD.
auk_zerofill(auk_ebd)
: auk_ebd
object output from auk_filter()
. Must
have had a sampling event data file set in the original call to
auk_ebd()
.
Other import:
read_ebd()
# read and zero-fill the ebd data
f_ebd <- system.file("extdata/zerofill-ex_ebd.txt", package = "auk")
f_smpl <- system.file("extdata/zerofill-ex_sampling.txt", package = "auk")
auk_zerofill(x = f_ebd, sampling_events = f_smpl)
# use the species argument to only include a subset of species
auk_zerofill(x = f_ebd, sampling_events = f_smpl,
species = "Collared Kingfisher")
# to return a data frame use collapse = TRUE
ebd_df <- auk_zerofill(x = f_ebd, sampling_events = f_smpl, collapse = TRUE)
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