AHMbook (version 0.2.10)

simDSM: 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)

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

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.

Author

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