Given an eBird Basic Dataset (EBD) and a list of species, split the file into
multiple text files, one for each species. This function is typically used
after auk_filter() has been applied if the resulting file is too large to
be read in all at once.
auk_split(
file,
species,
prefix,
taxonomy_version,
sep = "\t",
overwrite = FALSE
)character; input file.
character; species to filter and split by, provided as scientific or English common names, or a mixture of both. These names must match the official eBird Taxomony (ebird_taxonomy).
character; a file and directory prefix. For example, if
splitting by species "A" and "B" and prefix = "data/ebd_", the resulting
files will be "data/ebd_A.txt" and "data/ebd_B.txt".
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().
character; the input field separator, the eBird file is tab separated by default. Must only be a single character and space delimited is not allowed since spaces appear in many of the fields.
logical; overwrite output files if they already exists.
A vector of output filenames, one for each species.
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 text:
auk_clean(),
auk_select()
if (FALSE) {
species <- c("Canada Jay", "Cyanocitta stelleri")
# get the path to the example data included in the package
# in practice, provide path to a filtered ebd file
# e.g. f <- "data/ebd_filtered.txt
f <- system.file("extdata/ebd-sample.txt", package = "auk")
# output to a temporary directory for example
# in practice, provide the path to the output location
# e.g. prefix <- "output/ebd_"
prefix <- file.path(tempdir(), "ebd_")
species_files <- auk_split(f, species = species, prefix = prefix)
}