R/data.mexdolphin.R

In fbachl/inlabru: Bayesian Latent Gaussian Modelling using INLA and Extensions

#' @name mexdolphin_sf
#' @title Pan-tropical spotted dolphins in the Gulf of Mexico
#' @docType data
#' @description This a version of the `mexdolphins` dataset from the package
#'   `dsm`, reformatted as point process data for use with `inlabru`, with the
#'   parts stored in `sf` format. The data are from a combination of several
#'   NOAA shipboard surveys conducted on pan-tropical spotted dolphins in the
#'   Gulf of Mexico. 47 observations of groups of dolphins were detected. The
#'   group size was recorded, as well as the Beaufort sea state at the time of
#'   the observation. Transect width is 16 km, i.e. maximal detection distance 8
#'   km (transect half-width 8 km).
#'
#' @format A list of objects:
#'  \describe{
#'    \item{`points`:}{ An `sf` object containing the locations of
#'    detected dolphin groups, with their size as an attribute.}
#'    \item{`samplers`:}{ An `sf` object containing the transect lines
#'    that were surveyed.}
#'    \item{`mesh`:}{ An `fm_mesh_2d` object containing a Delaunay triangulation
#'    mesh (a type of discretization of continuous space) covering the survey
#'    region.}
#'    \item{`ppoly`:}{ An `sf` object defining the boundary of the
#'    survey region.}
#'    \item{`simulated`:}{ A `sf` object containing the locations of a
#'    *simulated* population of dolphin groups. The population was simulated
#'    from a `inlabru`
#'    model fitted to the actual survey data. Note that the simulated data
#'    do not have any associated
#'    size information.}
#'  }
#' @source
#' Library `dsm`.
#'
#' @references
#' Halpin, P.N., A.J. Read, E. Fujioka, B.D. Best, B. Donnelly, L.J. Hazen, C.
#' Kot, K. Urian, E. LaBrecque, A. Dimatteo, J. Cleary, C. Good, L.B. Crowder,
#' and K.D. Hyrenbach. 2009. OBIS-SEAMAP: The world data center for marine
#' mammal, sea bird, and sea turtle distributions. Oceanography 22(2):104-115
#'
#' NOAA Southeast Fisheries Science Center. 1996. Report of a Cetacean Survey of
#' Oceanic and Selected Continental Shelf Waters of the Northern Gulf of Mexico
#' aboard NOAA Ship Oregon II (Cruise 220)
#'
#' @examples
#' \donttest{
#' if (require("ggplot2", quietly = TRUE)) {
#'   data(mexdolphin_sf, package = "inlabru", envir = environment())
#'   ggplot() +
#'     gg(mexdolphin_sf$mesh) +
#'     gg(mexdolphin_sf$ppoly, color = "blue", alpha = 0, linewidth = 1) +
#'     gg(mexdolphin_sf$samplers) +
#'     gg(mexdolphin_sf$points, aes(size = size), color = "red") +
#'     scale_size_area()
#'
#'   ggplot() +
#'     gg(mexdolphin_sf$mesh,
#'       color = mexdolphin_sf$lambda,
#'       mask = mexdolphin_sf$ppoly
#'     )
#' }
#' }
"mexdolphin_sf"

#' @describeIn mexdolphin_sf Convert `mexdolphin_sf` to `sp` format. Replaces
#'   the old `mexdolphin` dataset.
#' @export
#'
#' @examples
#' \donttest{
#' if (require("ggplot2", quietly = TRUE) &&
#'   require("sp", quietly = TRUE)) {
#'   mexdolphin <- mexdolphin_sp()
#'   ggplot() +
#'     gg(mexdolphin$mesh) +
#'     gg(mexdolphin$ppoly, color = "blue") +
#'     gg(mexdolphin$samplers) +
#'     gg(mexdolphin$points, aes(size = size), color = "red") +
#'     scale_size_area() +
#'     coord_equal()
#'
#'   ggplot() +
#'     gg(mexdolphin$mesh,
#'       col = mexdolphin$lambda,
#'       mask = mexdolphin$ppoly
#'     ) +
#'     coord_equal()
#' }
#' }
mexdolphin_sp <- function() {
  dat <- inlabru::mexdolphin_sf
  out <- list(
    points = sf::as_Spatial(dat$points),
    samplers = sf::as_Spatial(dat$samplers),
    mesh = dat$mesh,
    ppoly = sf::as_Spatial(dat$ppoly),
    lambda = dat$lambda,
    simulated = sf::as_Spatial(dat$simulated),
    depth = sf::as_Spatial(dat$depth)
  )
  sp::coordnames(out$points) <- c("x", "y")
  sp::coordnames(out$samplers) <- c("x", "y")
  sp::coordnames(out$ppoly) <- c("x", "y")
  sp::coordnames(out$simulated) <- c("x", "y")
  sp::coordnames(out$depth) <- c("x", "y")
  out
}

#' @title Deprecated alias for sp version of the mexdolphin dataset
#' @name mexdolphin
#' @rdname mexdolphin
#' @description
#' Deprecated dataset name for the `sp` version
#' of [mexdolphin_sf]. Use [mexdolphin_sp()] instead.
#' @seealso [mexdolphin_sf]
#' @keywords internal
NULL