This simulates line transect distance sampling data with a spatial distribution of objects in a heterogeneous landscape where the parameter beta controls the effect of habitat. Multiple sample occasions are simulated and temporary emigration is allowed (parameter phi). Habitat is simulated according to a Gaussian random field model defined within the function. Uses a half normal detection model (if perp = TRUE) or a Gaussian hazard model (perp = FALSE).
To recreate the data sets used in the book with R 3.6.0 or later, include sample.kind="Rounding" in the call to set.seed. This should only be used for reproduction of old results.
simSpatialDSte(nsites=28, dim=10, beta=1, lam0=2.5, nsurveys=4, sigma=3,
phi=0.6, theta=2, show.plots=3)A list with the values of the input arguments and the following additional elements:
the number of pixels in each site (= dim^2)
distance from line to edge of square (= dim/2)
true number of individuals at each site
perpendicular distance of each pixel from the line
pixels x sites matrix, value of habitat covariate for each pixel
sites x pixels x surveys array, number of animals detected
sites x surveys matrix, number of animals detected (summed over pixels)
number of sites
number of pixels along each side of the square site
the effect of habitat on the number of individuals in a pixel.
expected population size at each site
the number of replicate surveys
scale of half-normal detection function
probability an individual is available for detection, ie, not temporarily emigrated.
exponential correlation in the spatial covariate.
the number of sites for which plots should be displayed; set to 0 to suppress plotting.
Mizel et al (2018) Appendix S1, based in turn on Kéry & Royle (2016).
Kéry, M. & Royle, J.A. (2016) Applied Hierarchical Modeling in Ecology.
Mizel, J.D., Schmidt, J.H., & Lindberg, M.S. (2018) Accommodating temporary emigration in spatial distance sampling models. Journal of Applied Ecology, 55, 1456-1464.
Kéry, M. & Royle, J.A. (2021) Applied Hierarchical Modeling in Ecology AHM2 - 11.
# Run the function with default values and look at the output
str(tmp <- simSpatialDSte())
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