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#' Down-Sample a Data Set Based on a Factor Variable
#'
#' @description
#' \if{html}{\figure{lifecycle-soft-deprecated.svg}{alt="lifecycle-soft-deprecated"}}
#'
#' `step_downsample` is now available as `themis::step_downsample()`. This
#' function creates a *specification* of a recipe step that will remove
#' rows of a data set to make the occurrence of levels in a specific factor
#' level equal.
#'
#' @inheritParams step_center
#' @param ... One or more selector functions to choose which
#' variable is used to sample the data. See [selections()]
#' for more details. The selection should result in _single
#' factor variable_. For the `tidy` method, these are not
#' currently used.
#' @param role Not used by this step since no new variables are
#' created.
#' @param column A character string of the variable name that will
#' be populated (eventually) by the `...` selectors.
#' @param under_ratio A numeric value for the ratio of the
#' minority-to-majority frequencies. The default value (1) means
#' that all other levels are sampled down to have the same
#' frequency as the least occurring level. A value of 2 would mean
#' that the majority levels will have (at most) (approximately)
#' twice as many rows than the minority level.
#' @param ratio Deprecated argument; same as `under_ratio`
#' @param target An integer that will be used to subsample. This
#' should not be set by the user and will be populated by `prep`.
#' @param seed An integer that will be used as the seed when downsampling.
#' @return An updated version of `recipe` with the new step
#' added to the sequence of existing steps (if any). For the
#' `tidy` method, a tibble with columns `terms` which is
#' the variable used to sample.
#' @details
#' Down-sampling is intended to be performed on the _training_ set alone. For
#' this reason, the default is `skip = TRUE`. It is advisable to use
#' `prep(recipe, retain = TRUE)` when preparing the recipe; in this way
#' `bake(object, new_data = NULL)` can be used to obtain the down-sampled
#' version of the data.
#'
#' If there are missing values in the factor variable that is used
#' to define the sampling, missing data are selected at random in
#' the same way that the other factor levels are sampled. Missing
#' values are not used to determine the amount of data in the
#' minority level
#'
#' For any data with factor levels occurring with the same
#' frequency as the minority level, all data will be retained.
#'
#' All columns in the data are sampled and returned by [bake()].
#'
#' Keep in mind that the location of down-sampling in the step
#' may have effects. For example, if centering and scaling,
#' it is not clear whether those operations should be conducted
#' _before_ or _after_ rows are removed.
#'
#' When used in modeling, users should strongly consider using the
#' option `skip = TRUE` so that the extra sampling is _not_
#' conducted outside of the training set.
#'
#' @keywords datagen
#' @concept preprocessing
#' @concept subsampling
#' @export
#' @examples
#' library(modeldata)
#' data(okc)
#'
#' sort(table(okc$diet, useNA = "always"))
#'
#' ds_rec <- recipe( ~ ., data = okc) %>%
#' step_downsample(diet) %>%
#' prep(training = okc)
#'
#' table(bake(ds_rec, new_data = NULL)$diet, useNA = "always")
#'
#' # since `skip` defaults to TRUE, baking the step has no effect
#' baked_okc <- bake(ds_rec, new_data = okc)
#' table(baked_okc$diet, useNA = "always")
step_downsample <-
function(recipe, ..., under_ratio = 1, ratio = NA, role = NA, trained = FALSE,
column = NULL, target = NA, skip = TRUE,
seed = sample.int(10^5, 1), id = rand_id("downsample")) {
lifecycle::deprecate_soft("0.1.13",
"recipes::step_downsample()",
"themis::step_downsample()")
if (!is.na(ratio) & all(under_ratio != ratio)) {
message(
paste(
"The `ratio` argument is now deprecated in favor of `under_ratio`.",
"`ratio` will be removed in a subsequent version."
)
)
if (!is.na(ratio)) {
under_ratio <- ratio
}
}
add_step(recipe,
step_downsample_new(
terms = ellipse_check(...),
under_ratio = under_ratio,
ratio = ratio,
role = role,
trained = trained,
column = column,
target = target,
skip = skip,
seed = seed,
id = id
))
}
step_downsample_new <-
function(terms, under_ratio, ratio, role, trained, column, target, skip, seed, id) {
step(
subclass = "downsample",
terms = terms,
under_ratio = under_ratio,
ratio = ratio,
role = role,
trained = trained,
column = column,
target = target,
skip = skip,
id = id,
seed = seed,
id = id
)
}
#' @export
prep.step_downsample <- function(x, training, info = NULL, ...) {
col_name <- eval_select_recipes(x$terms, training, info)
if (length(col_name) != 1)
rlang::abort("Please select a single factor variable.")
if (!is.factor(training[[col_name]]))
rlang::abort(paste0(col_name, " should be a factor variable."))
obs_freq <- table(training[[col_name]])
minority <- min(obs_freq)
step_downsample_new(
terms = x$terms,
under_ratio = x$under_ratio,
ratio = x$ratio,
role = x$role,
trained = TRUE,
column = col_name,
target = floor(minority * x$under_ratio),
skip = x$skip,
seed = x$seed,
id = x$id
)
}
subsamp <- function(x, num) {
n <- nrow(x)
if (nrow(x) == num)
out <- x
else
# downsampling is done without replacement
out <- x[sample(1:n, min(num, n)), ]
out
}
#' @export
bake.step_downsample <- function(object, new_data, ...) {
if (any(is.na(new_data[[object$column]])))
missing <- new_data[is.na(new_data[[object$column]]),]
else
missing <- NULL
split_up <- split(new_data, new_data[[object$column]])
# Downsample with seed for reproducibility
with_seed(
seed = object$seed,
code = {
new_data <- map_dfr(split_up, subsamp, num = object$target)
if (!is.null(missing)) {
new_data <- bind_rows(new_data, subsamp(missing, object$target))
}
}
)
as_tibble(new_data)
}
print.step_downsample <-
function(x, width = max(20, options()$width - 26), ...) {
cat("Down-sampling based on ", sep = "")
printer(x$column, x$terms, x$trained, width = width)
invisible(x)
}
#' @rdname step_downsample
#' @param x A `step_downsample` object.
#' @export
tidy.step_downsample <- function(x, ...) {
if (is_trained(x)) {
res <- tibble(terms = x$column)
}
else {
term_names <- sel2char(x$terms)
res <- tibble(terms = unname(term_names))
}
res$id <- x$id
res
}
# ------------------------------------------------------------------------------
#' @rdname tunable.step
#' @export
tunable.step_downsample <- function(x, ...) {
tibble::tibble(
name = "under_ratio",
call_info = list(
list(pkg = "dials", fun = "under_ratio")
),
source = "recipe",
component = "step_downsample",
component_id = x$id
)
}
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