File: downsample.R

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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
  )
}