auk (version 0.0.1)

auk_ebd: Reference to EBD file

Description

Create a reference to an eBird Basic Dataset (EBD) file in preparation for filtering using AWK.

Usage

auk_ebd(file, file_sampling, sep = "\t")

Arguments

file

character; input file.

file_sampling

character; optional input sampling event data file, required if you intend to zero-fill the data to produce a presence-absence data set. The sampling file consists of just effort information for every eBird checklist. Any species not appearing in the EBD for a given checklist is implicitly considered to have a count of 0. This file should be downloaded at the same time as the EBD to ensure they are in sync.

sep

character; the input field separator, the EBD is tab separated so this should generally not be modified. Must only be a single character and space delimited is not allowed since spaces appear in many of the fields.

Value

An auk_ebd object storing the file reference and the desired filters once created with other package functions.

Details

The EBD can be downloaded as a tab-separated text file from the eBird website after submitting a request for access. As of February 2017, this file is nearly 150 GB making it challenging to work with. If you're only interested in a single species or a small region it is possible to submit a custom download request. This approach is suggested to speed up processing time.

There are two potential pathways for preparing eBird data. Users wishing to produce presence only data, should download the eBird Basic Dataset and reference this file when calling auk_ebd(). Users wishing to produce zero-filled, presence absence data should additionally download the sampling event data file associated with the EBD. This file contains only checklist information and can be used to infer absences. The sampling event data file should be provided to auk_ebd() via the file_sampling argument. For further details consult the vignettes.

Examples

# set up reference to sample EBD file
f <- system.file("extdata/ebd-sample.txt", package = "auk")
auk_ebd(f)
# to produce zero-filled data, provide a sampling event data file
f_ebd <- system.file("extdata/zerofill-ex_ebd.txt", package = "auk")
f_smpl <- system.file("extdata/zerofill-ex_sampling.txt", package = "auk")
auk_ebd(f_ebd, file_sampling = f_smpl)