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#' Check for Missing Values
#'
#' `check_missing` creates a *specification* of a recipe
#' operation that will check if variables contain missing values.
#'
#' @param recipe A recipe object. The check will be added to the
#' sequence of operations for this recipe.
#' @param ... One or more selector functions to choose which
#' variables are checked in the check See [selections()]
#' for more details. For the `tidy` method, these are not
#' currently used.
#' @param role Not used by this check since no new variables are
#' created.
#' @param trained A logical for whether the selectors in `...`
#' have been resolved by [prep()].
#' @param columns A character string of variable names that will
#' be populated (eventually) by the terms argument.
#' @param id A character string that is unique to this step to identify it.
#' @param skip A logical. Should the check be skipped when the
#' recipe is baked by [bake.recipe()]? While all operations are baked
#' when [prep.recipe()] is run, some operations may not be able to be
#' conducted on new data (e.g. processing the outcome variable(s)).
#' Care should be taken when using `skip = TRUE` as it may affect
#' the computations for subsequent operations.
#' @return An updated version of `recipe` with the new check
#' added to the sequence of existing operations (if any). For the
#' `tidy` method, a tibble with columns `terms` (the
#' selectors or variables selected).
#' @export
#' @details This check will break the `bake` function if any of the checked
#' columns does contain `NA` values. If the check passes, nothing is changed
#' to the data.
#' @examples
#' library(modeldata)
#' data(credit_data)
#' is.na(credit_data) %>% colSums()
#'
#' # If the test passes, `new_data` is returned unaltered
#' recipe(credit_data) %>%
#' check_missing(Age, Expenses) %>%
#' prep() %>%
#' bake(credit_data)
#'
#' # If your training set doesn't pass, prep() will stop with an error
#'
#' \dontrun{
#' recipe(credit_data) %>%
#' check_missing(Income) %>%
#' prep()
#' }
#'
#' # If `new_data` contain missing values, the check will stop bake()
#'
#' train_data <- credit_data %>% dplyr::filter(Income > 150)
#' test_data <- credit_data %>% dplyr::filter(Income <= 150 | is.na(Income))
#'
#' rp <- recipe(train_data) %>%
#' check_missing(Income) %>%
#' prep()
#'
#' bake(rp, train_data)
#' \dontrun{
#' bake(rp, test_data)
#' }
check_missing <-
function(recipe,
...,
role = NA,
trained = FALSE,
columns = NULL,
skip = FALSE,
id = rand_id("missing")) {
add_check(
recipe,
check_missing_new(
terms = ellipse_check(...),
role = role,
trained = trained,
columns = columns,
skip = skip,
id = id
)
)
}
check_missing_new <-
function(terms, role, trained, columns, skip, id) {
check(subclass = "missing",
prefix = "check_",
terms = terms,
role = role,
trained = trained,
columns = columns,
skip = skip,
id = id)
}
prep.check_missing <- function(x, training, info = NULL, ...) {
col_names <- eval_select_recipes(x$terms, training, info)
check_missing_new(terms = x$terms,
role = x$role,
trained = TRUE,
columns = col_names,
skip = x$skip,
id = x$id)
}
bake.check_missing <- function(object, new_data, ...) {
col_names <- object$columns
subset_to_check <- new_data[col_names]
nr_na <- colSums(is.na(subset_to_check))
if (any(nr_na > 0)) {
with_na <- names(nr_na[nr_na > 0])
with_na_str <- paste(paste0("`", with_na, "`"), collapse = ", ")
rlang::abort(paste0("The following columns contain missing values: ",
with_na_str, "."))
}
new_data
}
print.check_missing <-
function(x, width = max(20, options()$width - 30), ...) {
cat("Check missing values for ", sep = "")
printer(x$columns, x$terms, x$trained, width = width)
invisible(x)
}
#' @rdname check_missing
#' @param x A `check_missing` object.
#' @export
tidy.check_missing <- function(x, ...) {
if (is_trained(x)) {
res <- tibble(terms = x$columns)
} else {
res <- tibble(terms = sel2char(x$terms))
}
res$id <- x$id
res
}
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