R/location_slice.R

In pastclim: Manipulate Time Series of Climate Reconstructions

#' Extract local climate for one or more locations for a given time slice.
#'
#' This function extract local climate for a set of locations at the appropriate
#' times (selecting the closest time slice available for the specific date
#' associated with each location).
#'
#' @param x a data.frame with columns x and y coordinates(see `coords` for
#'   standard coordinate names, or how to use custom ones), plus optional
#'   columns `time_bp` or `time_ce` (depending on the units used) and `name`.
#'   Alternatively, a vector of cell numbers.
#' @param time_bp used if no `time_bp` column is present in `x`: the dates in
#'   years before present (negative values represent time before present, i.e.
#'   1950, positive values time in the future) for each location.
#' @param time_ce time in years CE as an alternative to `time_bp`.Only one of
#'   `time_bp` or `time_ce` should be used.
#' @param coords a vector of length two giving the names of the "x" and "y"
#'   coordinates, as found in `data`. If left to NULL, the function will try to
#'   guess the columns based on standard names `c("x", "y")`, `c("X","Y")`,
#'   `c("longitude", "latitude")`, or `c("lon", "lat")`
#' @param bio_variables vector of names of variables to be extracted.
#' @param dataset string defining the dataset to use. If set to "custom", then a
#'   single nc file is used from "path_to_nc"
#' @param path_to_nc the path to the custom nc file containing the palaeoclimate
#'   reconstructions. All the variables of interest need to be included in this
#'   file.
#' @param nn_interpol boolean determining whether nearest neighbour
#'   interpolation is used to estimate climate for cells that lack such
#'   information (i.e. they are under water or ice). By default, interpolation
#'   is only performed from the first ring of nearest neighbours; if climate is
#'   not available, NA will be returned for that location. The number of
#'   neighbours can be changed with the argument `directions`. `nn_interpol`
#'   defaults to TRUE.
#' @param buffer boolean determining whether the variable will be returned as
#'   the mean of a buffer around the focal cell. If set to TRUE, it overrides
#'   `nn_interpol` (which provides the same estimates as `buffer` but only for
#'   locations that are in cells with an NA). The buffer size is determined by
#'   the argument `directions`. `buffer` defaults to FALSE.
#' @param directions character or matrix to indicate the directions in which
#'   cells are considered connected when using `nn_interpol` or `buffer`. The
#'   following character values are allowed: "rook" or "4" for the horizontal
#'   and vertical neighbours; "bishop" to get the diagonal neighbours; "queen"
#'   or "8" to get the vertical, horizontal and diagonal neighbours; or "16" for
#'   knight and one-cell queen move neighbours. If directions is a matrix it
#'   should have odd dimensions and have logical (or 0, 1) values.
#' @returns a data.frame with the climatic variables of interest.
#' @export

location_slice <-
  function(x,
           time_bp = NULL,
           time_ce = NULL,
           coords = NULL,
           bio_variables,
           dataset,
           path_to_nc = NULL,
           nn_interpol = TRUE,
           buffer = FALSE,
           directions = 8) {
    # get the region series for this dataset
    climate_brick <- region_series(
      bio_variables = bio_variables,
      dataset = dataset,
      path_to_nc = path_to_nc
    )
    # now simply wrap around location_slice_from_region_series
    location_slice_from_region_series(
      x = x,
      time_bp = time_bp,
      time_ce = time_ce,
      coords = coords,
      region_series = climate_brick,
      nn_interpol = nn_interpol,
      buffer = buffer,
      directions = directions
    )
  }


#' Extract local climate for one or more locations for a given time slice.
#'
#' Deprecated version of [location_slice()]
#'
#' @param ... arguments to be passed to [location_slice()]
#' @returns a data.frame with the climatic variables of interest
#' @keywords deprecated
#' @export

climate_for_locations <- function(...) {
  warning("DEPRECATED: use 'location_slice' instead")
  # if (!is.null(path_to_nc)) {
  #   stop(
  #     "the use of pastclimData is now deprecated",
  #     "use 'set_path_data' instead"
  #   )
  # }
  location_slice(...)
}