simWigglyOcc: Simulate static occupancy data

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

Simulate static occupancy data

Description

Function to generate a static occupancy data set with really wiggly covariate relationships in occupancy and detection probability.

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

wigglyOcc(seed = 1, show.plot = TRUE, verbose = TRUE)

Arguments

seed	Seed for random number generator
show.plot	choose whether to show plots or not. Set to FALSE when using function in simulations.
verbose	if TRUE, output will be written to the console.

Value

A list with the following elements:

M	Number of sites
J	Number of replicate surveys
Xsite	Simulated site covariate, a vector of length M
Xsurvey	Simulated survey covariate, a M x J matrix
psi	Occupancy probability, a vector of length M
z	Realized occupancy, a 0/1 vector of length M
p	Detection probability, a M x J matrix
y	detection history, a M x J matrix of 0/1

Author(s)

Marc Kéry & Andy Royle

References

Kéry, M. & Royle, J.A. (2016) Applied Hierarchical Modeling in Ecology AHM1 - 10.14.

Examples

# Generate data with the default arguments and look at the structure:
tmp <- wigglyOcc()
str(tmp)

mikemeredith/AHMbook documentation built on Dec. 5, 2022, 12:58 p.m.