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#' check a baseline and mixture file together to ensure the known_collections are valid if they exist
#'
#' Simple function that checks for known_collections columns in a reference and mixture and
#' makes sure that they are compliant.
#' If there is a non-NA entry in the Mixture frame's known_collection column this
#' function returns TRUE. Otherwise it returns FALSE.
#' @param R reference data frame
#' @param M mixture data frame
#' @export
#' @keywords internal
check_known_collections <- function(R, M) {
ret <- FALSE
if(!is.null(R[["known_collection"]]) && is.null(M[["known_collection"]])) {
stop("Reference data frame has known_collection column, but not the mixture data frame.")
}
if(!is.null(M[["known_collection"]]) && is.null(R[["known_collection"]])) {
stop("Mixture data frame has known_collection column, but not the reference data frame.")
}
if(!is.null(R[["known_collection"]])) {
if(!is.character(R[["known_collection"]])) {
stop("Column known_collection in reference data frame must be a character vector.")
}
}
if(!is.null(M[["known_collection"]])) {
if(!is.character(M[["known_collection"]])) {
stop("Column known_collection in mixture data frame must be a character vector.")
}
KC <- M[["known_collection"]]
uKC <- unique(KC[!is.na(KC)])
mKC <- setdiff(uKC, unique(R[["collection"]]))
if(length(mKC) > 0) {
stop("These known_collection entries in mixture data frame not found amongst reference collections: ",
paste(mKC, collapse = ", "), ". Please fix that and try again.")
}
ret <- any(!is.na(KC))
}
ret
}
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