R/extract.R

In mverse: Tidy Multiverse Analysis Made Simple

#' @rdname extract
#' @export
extract <- function(...) {
  UseMethod("extract")
}

#' Extract branched values.
#'
#' \code{extract} returns a tibble of selected values
#' across the multiverse in a long format.
#'
#' @examples
#' # Define mutate branches.
#' hurricane_strength <- mutate_branch(
#'   # damage vs. wind speed vs.pressure
#'   NDAM,
#'   HighestWindSpeed,
#'   Minpressure_Updated_2014,
#'   # Standardized versions
#'   scale(NDAM),
#'   scale(HighestWindSpeed),
#'   -scale(Minpressure_Updated_2014),
#' )
#' y <- mutate_branch(
#'   alldeaths, log(alldeaths + 1)
#' )
#' # Create a mverse and add the branches.
#' mv <- create_multiverse(hurricane) %>%
#'   add_mutate_branch(hurricane_strength, y)
#' execute_multiverse(mv)
#' # Extract all branched columns from all universes
#' extract(mv)
#' # Specify the columns to extract from each universe using columns
#' # You can select both branched and non-branched columns
#' extract(mv, columns = c("hurricane_strength", "NDAM"))
#' # Specify the universe to extract from using universe
#' extract(mv, universe = 1)
#' # Specify the number of universes to extract from using nuni
#' # The universes are randomly selected
#' extract(mv, nuni = 3)
#' # Specify the proportion of data to extract from each universe using
#' # frow. The rows are randomly selected
#' extract(mv, frow = 0.7)
#' @param .mverse a \code{mverse} object.
#' @param columns a character vector of column names to extract.
#' @param nuni a positive integer for the number of universes to extract.
#' @param frow proportion of rows to extract from each universe.
#' @param include_branch_options when \code{TRUE} (default), include the mutate
#'   statements used to specified the options for each branched columns
#' @param ... Ignored.
#' @details This method extracts data values across
#' the multiverse. You can specify a subset of data
#' to extract using \code{columns}, \code{universe},
#'  \code{nuni}, and \code{frow}.
#'
#' You can specify the columns to extract from each
#' universe by passing the column names as a character
#' vector to \code{columns}. The default values is
#' \code{NULL} extracting all columns with branches.
#'
#' Use \code{universe} to specify a set of universes
#' by their integer ids. Use \code{nuni} to specify
#' the number of universes to extract data from. The
#' method then selects the subset randomly. Specifying
#' \code{universe} manually will override \code{nuni} value.
#' By default, they are both set to \code{NULL} and
#' the method returns data from all universes.
#'
#' Use \code{frow} to randomly extract a fraction of
#' data from each universe. The default value is \code{NULL}
#' and all rows are returned as they are. Note if you select
#' 1 the method will return shuffle rows in each universe
#' before returning them. If \code{frow} is greater than 1,
#' the method randomly samples rows with replacement.
#' @return a tibble containing the selected columns
#'   across the multiverse.
#' @name extract
#' @export
extract.mverse <- function(.mverse, columns = NULL,
                           nuni = NULL, frow = NULL,
                           include_branch_options = TRUE, ...) {
  stopifnot(inherits(.mverse, "mverse"))
  mtable <- summary.mverse(.mverse)
  branched_columns <- unlist(
    sapply(
      c(
        attr(.mverse, "branches_list"),
        attr(.mverse, "branches_conditioned_list")
      ),
      function(x) if (inherits(x, "mutate_branch")) x$name
    )
  )
  if (is.null(columns)) {
    columns <- branched_columns
  } else {
    branched_columns <- branched_columns[branched_columns %in% columns]
  }
  columns <- c("universe", columns)
  universe <- mtable$universe
  if (!is.null(nuni)) {
    if (length(nuni) > 1) {
      warning("Only the first value of nuni is used.")
      nuni <- nuni[1]
    }
    stopifnot(
      "nuni must be less than or equal to the number of universes." =
        length(universe) >= nuni
    )
    universe <- sample(universe, nuni)
  }
  stopifnot(length(universe) > 0)
  extracted <- lapply(
    universe, function(x) {
      ex <- multiverse::extract_variable_from_universe(.mverse, x, .data_mverse)
      if (!is.null(frow)) {
        stopifnot("frow must be a positive value." = frow > 0)
        ex <- dplyr::sample_frac(ex,
          size = frow,
          replace = (frow > 1)
        )
      }
      ex$universe <- x
      ex
    }
  )
  extracted <- dplyr::bind_rows(extracted)
  if (include_branch_options) {
    extracted %>%
      dplyr::left_join(mtable, by = "universe") %>%
      dplyr::select(
        dplyr::all_of(c(columns, paste0(branched_columns, "_branch")))
      )
  } else {
    dplyr::select(dplyr::all_of(c(extracted, columns)))
  }
}