simOccttd {AHMbook} | R Documentation |
Function simulates time-to-detection occupancy design data under the model of Garrard et al. (2008), also see Bornand et al. (2014)
simOccttd(M = 250, mean.psi = 0.4, mean.lambda = 0.3, beta1 = 1, alpha1 = -1, Tmax = 10, show.plot = TRUE, verbose = TRUE)
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 |
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. |
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 |
Marc Kéry & Andy Royle
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.
# Generate data with the default arguments and look at the structure tmp <- simOccttd() str(tmp)