Create a reference to an eBird Basic Dataset (EBD) file in preparation for filtering using AWK.
auk_ebd(file, file_sampling, sep = "\t")character; input file. If file is not found as specified, it will
be looked for in the directory specified by the EBD_PATH environment
variable.
character; optional input sampling event data (i.e.
checklists) file, required if you intend to zero-fill the data to produce a
presence-absence data set. This 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 basic dataset to ensure they are in
sync. If file is not found as specified, it will be looked for in the
directory specified by the EBD_PATH environment variable.
character; the input field separator, the eBird data are 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.
An auk_ebd object storing the file reference and the desired
filters once created with other package functions.
eBird data 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 basic dataset 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.
Other objects:
auk_sampling()
# get the path to the example data included in the package
# in practice, provide path to ebd, e.g. f <- "data/ebd_relFeb-2018.txt
f <- system.file("extdata/ebd-sample.txt", package = "auk")
auk_ebd(f)
#> Input
#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt
#>
#> Output
#> Filters not executed
#>
#> Filters
#> Species: all
#> 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
# to produce zero-filled data, provide a checklist file
f_ebd <- system.file("extdata/zerofill-ex_ebd.txt", package = "auk")
f_cl <- system.file("extdata/zerofill-ex_sampling.txt", package = "auk")
auk_ebd(f_ebd, file_sampling = f_cl)
#> Input
#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/zerofill-ex_ebd.txt
#> Sampling events: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/zerofill-ex_sampling.txt
#>
#> Output
#> Filters not executed
#>
#> Filters
#> Species: all
#> 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