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data.mexdolphin.R
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data.mexdolphin.R
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#' @name mexdolphin
#' @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`. 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`:}{ A `SpatialPointsDataFrame` object containing the
#' locations of detected dolphin groups, with their size as an attribute.}
#' \item{`samplers`:}{ A `SpatialLinesDataFrame` 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 `SpatialPolygonsDataFrame` object defining the
#' boundary of the
#' survey region.}
#' \item{`simulated`:}{ A `SpatialPointsDataFrame` 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, package = "inlabru")
#' ggplot() +
#' gg(mexdolphin$mesh) +
#' gg(mexdolphin$ppoly, color = "blue") +
#' gg(mexdolphin$samplers) +
#' gg(mexdolphin$points, aes(size = size), color = "red") +
#' coord_equal()
#'
#' ggplot() +
#' gg(mexdolphin$mesh, col = mexdolphin$lambda, mask = mexdolphin$ppoly) +
#' coord_equal()
#' }
#' }
"mexdolphin"
#' @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")
#' 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"