simOccttd {AHMbook}R Documentation

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)

[Package AHMbook version 0.2.3 Index]