#' Filter the eBird data by country
#'
#' Define a filter for the eBird Basic Dataset (EBD) based on a set of
#' countries. This function only defines the filter and, once all filters have
#' been defined, [auk_filter()] should be used to call AWK and perform the
#' filtering.
#'
#' @param x `auk_ebd` or `auk_sampling` object; reference to file created by
#' [auk_ebd()] or [auk_sampling()].
#' @param country character; countries to filter by. Countries can either be
#' expressed as English names or
#' [ISO 2-letter country codes](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2).
#' English names are matched via regular expressions using
#' [countrycode][countrycode()], so there is some flexibility in names.
#' @param replace logical; multiple calls to `auk_country()` are additive,
#' unless `replace = FALSE`, in which case the previous list of countries to
#' filter by will be removed and replaced by that in the current call.
#'
#' @details This function can also work with on an `auk_sampling` object if the
#' user only wishes to filter the sampling event data.
#'
#' @return An `auk_ebd` object.
#' @export
#' @family filter
#' @examples
#' # country names and ISO2 codes can be mixed
#' # not case sensitive
#' country <- c("CA", "United States", "mexico")
#' system.file("extdata/ebd-sample.txt", package = "auk") %>%
#' auk_ebd() %>%
#' auk_country(country)
#'
#' # alternatively, without pipes
#' ebd <- auk_ebd(system.file("extdata/ebd-sample.txt", package = "auk"))
#' auk_country(ebd, country)
auk_country <- function(x, country, replace = FALSE) {
UseMethod("auk_country")
}
#' @export
auk_country.auk_ebd <- function(x, country, replace = FALSE) {
# checks
assertthat::assert_that(
is.character(country),
assertthat::is.flag(replace)
)
# convert country names to codes
name_codes <- countrycode::countrycode(country,
origin = "country.name",
destination = "iso2c",
warn = FALSE)
# lookup codes
code_codes <- countrycode::countrycode(country,
origin = "iso2c",
destination = "iso2c",
warn = FALSE)
# combine, preference to codes
country_codes <- dplyr::coalesce(code_codes, name_codes)
# some codes don't match to countrycodes package, treat seperately
no_code <- is.na(country_codes)
country_codes[no_code] <- missing_countries(country[no_code])
# check codes are valid
valid_codes <- !is.na(country_codes)
if (!all(valid_codes)) {
m <- paste0("The following countries are not valid: \n\t",
paste(country[!valid_codes], collapse =", "))
stop(m)
}
# add countries to filter list
if (replace) {
x$filters$country <- country_codes
} else {
x$filters$country <- c(x$filters$country, country_codes)
}
x$filters$country <- sort(unique(x$filters$country))
x$filters$state <- character()
x$filters$county <- character()
return(x)
}
#' @export
auk_country.auk_sampling <- function(x, country, replace = FALSE) {
auk_country.auk_ebd(x, country, replace)
}
missing_countries <- function(x) {
cc <- structure(c("AC", "CP", "CS", "XX", "XK", "FM"),
.Names = c("ashmore and cartier islands",
"clipperton island",
"coral sea islands", "high seas",
"kosovo", "micronesia"))
# convert country names to codes
name_codes <- cc[match(toupper(x), cc)]
# lookup codes
code_codes <- cc[tolower(x)]
# combine, preference to codes
out <- dplyr::coalesce(code_codes, name_codes)
names(out) <- NULL
out
}
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