mexdolphin_sf: Pan-tropical spotted dolphins in the Gulf of Mexico

In inlabru: Bayesian Latent Gaussian Modelling using INLA and Extensions

Pan-tropical spotted dolphins in the Gulf of Mexico

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).

Usage

mexdolphin_sf

mexdolphin_sp()

Format

A list of objects:

points:

An sf object containing the locations of detected dolphin groups, with their size as an attribute.

samplers:

An sf object containing the transect lines that were surveyed.

mesh:

An fm_mesh_2d object containing a Delaunay triangulation mesh (a type of discretization of continuous space) covering the survey region.

ppoly:

An sf object defining the boundary of the survey region.

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.

Functions

• mexdolphin_sp(): Convert mexdolphin_sf to sp format. Replaces the old mexdolphin dataset.

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

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
    )
}


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()
}

inlabru documentation built on April 3, 2025, 10:54 p.m.