simSpatialDSline: Simulate data for a standardized line transect

In AHMbook: Functions and Data for the Book 'Applied Hierarchical Modeling in Ecology' Vols 1 and 2

Simulate data for a standardized line transect

Description

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. 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.

Usage

simSpatialDSline(N=1000, beta = 1, sigma=0.25, alpha0 = -2, W=1/2, L = 4,
    perp=FALSE, show.plots=TRUE)

Arguments

N	total population size in the rectangle
beta	coefficient of spatial covariate x for the density model.
sigma	scale of half-normal detection function
alpha0	intercept of the hazard function.
W	half-width of the rectangle, which extends W each side of the transect line.
L	length of the transect.
perp	if TRUE, data are simulated for a traditional distance sampling model with perpendicular distances; if FALSE (the default) a model with 'forward distance' data, ie, the distance from the observer to the animal on first detection.
show.plots	if TRUE, summary plots are displayed.

Value

A list with the values of the input arguments and the following additional elements:

delta	the distance between pixel centers (spatial resolution of the raster
grid	2-column matrix with x/y coordinates of all pixels
Habitat	value of habitat covariate for each pixel
Habraster	a Raster object with the habitat covariate
u1, u2	x and y coordinates for all the animals in the population
traps	2-column matrix of trap locations

If perp = TRUE we have

data	a 2-column matrix with x and y coordinates of each animal captured.
pixel	pixel ID for each animal captured.

and if perp = FALSE we have

data	a matrix with rows for each animal captured and columns for trap of first capture, distance from trap to animal, and x and y coordinates of the animal.
pbar	probability that each animal is the population is captured at least once
pixel	pixel ID for each animal captured.

Author(s)

Marc Kéry & Andy Royle

References

Kéry, M. & Royle, J.A. (2021) Applied Hierarchical Modeling in Ecology AHM2 - 11.

Examples

# Run the function with default values and look at the output
str(tmp <- simSpatialDSline(), 1)  # use str(., max.level=1) to limit the amount of output.

AHMbook documentation built on Sept. 12, 2024, 6:37 a.m.