Reference to eBird data file

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. If file is not found as specified, it will be looked for in the directory specified by the EBD_PATH environment variable.

file_sampling

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.

sep

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.

Value

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

Details

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.

See also

Other objects: auk_sampling()

Examples

# 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: /usr/local/lib/R/site-library/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: /usr/local/lib/R/site-library/auk/extdata/zerofill-ex_ebd.txt 
#>   Sampling events: /usr/local/lib/R/site-library/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