#' Filter the eBird data by Bird Conservation Region
#'
#' Define a filter for the eBird Basic Dataset (EBD) to extract data for a set
#' of [Bird Conservation
#' Regions](https://nabci-us.org/resources/bird-conservation-regions/) (BCRs).
#' BCRs are ecologically distinct regions in North America with similar bird
#' communities, habitats, and resource management issues. 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 bcr integer; BCRs to filter by. BCRs are identified by an integer,
#' from 1 to 66, that can be looked up in the [bcr_codes] table.
#' @param replace logical; multiple calls to `auk_bcr()` are additive,
#' unless `replace = FALSE`, in which case the previous list of states 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
#' # bcr codes can be looked up in bcr_codes
#' dplyr::filter(bcr_codes, bcr_name == "Central Hardwoods")
#' system.file("extdata/ebd-sample.txt", package = "auk") %>%
#' auk_ebd() %>%
#' auk_bcr(bcr = 24)
#'
#' # filter to bcr 24
#' ebd <- auk_ebd(system.file("extdata/ebd-sample.txt", package = "auk"))
#' auk_bcr(ebd, bcr = 24)
auk_bcr <- function(x, bcr, replace = FALSE) {
UseMethod("auk_bcr")
}
#' @export
auk_bcr.auk_ebd <- function(x, bcr, replace = FALSE) {
# checks
assertthat::assert_that(
all(is_integer(bcr)),
all(bcr %in% auk::bcr_codes$bcr_code),
assertthat::is.flag(replace)
)
bcr <- as.integer(bcr)
# check for bcr column
if (!"bcr" %in% x$col_idx$id) {
stop("BCR column missing from EBD")
}
if (!is.null(x$col_idx_sampling) && !"bcr" %in% x$col_idx_sampling$id) {
stop("BCR column missing from sampling event data")
}
# set filter list
if (replace) {
x$filters$bcr <- bcr
} else {
x$filters$bcr <- c(x$filters$bcr, bcr)
}
x$filters$bcr <- sort(unique(x$filters$bcr))
return(x)
}
#' @export
auk_bcr.auk_sampling <- function(x, bcr, replace = FALSE) {
auk_bcr.auk_ebd(x, bcr, replace)
}
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