simOccttd: Simulate time-to-detection occupancy data (single visits)

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

Simulate time-to-detection occupancy data (single visits)

Description

Function simulates time-to-detection occupancy design data under the model of Garrard et al. (2008), also see Bornand et al. (2014)

Usage

simOccttd(M = 250, mean.psi = 0.4, mean.lambda = 0.3,
  beta1 = 1, alpha1 = -1, Tmax = 10, show.plot = TRUE, verbose = TRUE)

Arguments

M	Number of sites
mean.psi	intercept of occupancy probability
mean.lambda	intercept of Poisson rate parameter
beta1	slope of continuous covariate B on logit(psi)
alpha1	slope of continuous covariate A on log(lambda)
Tmax	maximum search time (in arbitrary units, which are same as response), response will be censored at Tmax
show.plot	choose whether to show plots or not. Set to FALSE when running simulations.
verbose	if TRUE, output will be written to the console.

Value

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

covA	Simulated values of covariate A, a vector of length M
covB	Simulated values of covariate B, a vector of length M
psi	Probability of occurrence at each site, a vector of length M
z	Realized occurrence at each site, a 0/1 vector of length M
ttd.temp	Uncensored simulated time-to-detection at each site, a vector of length M
ttd	Censored simulated time-to-detection at each site, a vector of length M
d	Censoring indicator, a 0/1 vector of length M
sum.z	Total number of sites occupied
n.obs	Total number of sites where the species was observed

Author(s)

Marc Kéry & Andy Royle

References

Garrard, G.E., Bekessy, S.A., McCarthy, M.A., & Wintle, B.A. (2008) When have we looked hard enough? A novel method for setting minimum survey effort protocols for flora surveys. Austral Ecology, 33, 986-998.

Bornand, C.N., Kéry, M., Bueche, L., & Fischer, M. (2014) Hide and seek in vegetation: time-to-detection is an efficient design for estimating detectability and occurrence. Methods in Ecology and Evolution, 5, 433-442.

Kéry, M. & Royle, J.A. (2016) Applied Hierarchical Modeling in Ecology AHM1 - 10.12.1.

Examples

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

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