simDSM: Simulate line transect data for density surface modeling

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

Simulate line transect data for density surface modeling

Description

The function generates a population represented as a binomial point pattern in a heterogeneous landscape with density a function of the covariate Habitat. Data for multiple line transect surveys using a wiggly transect are then simulated, and the pixel IDs for the activity centers of detected individuals returned.

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

simDSM(X, Ntotal = 400, sigma = 0.65, beta1 = 1.0,
    nsurveys = 2, xlim = c(-0.5, 3.5), ylim = c(-0.5, 4.5), show.plots = TRUE)

Arguments

X	a 2-column matrix with coordinates of regularly spaced points along the transect line; see Examples.
Ntotal	the true total number of individuals in the study area.
sigma	scale parameter for the half-normal detection function.
beta1	coefficient for the relationship between the Habitat covariate and population density.
nsurveys	the number of replicate surveys along the transect.
xlim, ylim	the extent of the (rectangular) study area
show.plots	if TRUE, summary plots are displayed.

Value

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

Habitat	a vector for the habitat covariate for each pixel
Habgrid	a 2-column matrix with the coordinates of center of each pixel
nPix	the number of pixels in the study area
N	true number of activity centers in each pixel
U	a 2-column matrix with the locations of ACs for all individuals in the population
Ucap	a 2-column matrix with the locations of ACs for individuals detected at least once
nind	the number of individuals detected at least once
pixel	a nind x nsurvey matrix with the pixel ID for the activity center or NA if the individual was not detected on the survey

Author(s)

Marc Kéry, Andy Royle & Mike Meredith

References

Kéry, M. & Royle, J.A. (2021) Applied Hierarchical Modeling in Ecology AHM2 - 11.10.

Examples

# Run the function with default values and look at the output
library(AHMbook)
data(wigglyLine)
points <- sp::SpatialPoints( wigglyLine )
sLine <- sp::Line(points)
regpoints <- sp::spsample(sLine, 100, type = "regular")
str(simDSM(X = regpoints@coords))

# Generate the data set used in AHM2 11.10
RNGversion("3.5.3")
set.seed(2027, kind = "Mersenne-Twister")
tmp <- simDSM(X = regpoints@coords) # Produces Fig 11.15 in the book

AHMbook documentation built on Aug. 24, 2023, 1:07 a.m.