sim3Occ: Simulate detection/nondetection data for static 3-level...

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

Simulate detection/nondetection data for static 3-level occupancy models

Description

Function generates 3-level occupancy data with possibility of site-specific random variation at every level, "time effects" at the middle and the lower levels and effects of one distinct covariate at each level.

Usage

sim3Occ(nunits = 100, nsubunits = 5, nreps = 3,
  mean.psi = 0.8, beta.Xpsi = 1, sd.logit.psi = 0,
  mean.theta = 0.6, theta.time.range = c(-1, 1), beta.Xtheta = 1, sd.logit.theta = 0,
  mean.p = 0.4, p.time.range = c(-2, 2), beta.Xp = -1, sd.logit.p = 0,
  show.plot = TRUE, verbose = TRUE)

Arguments

nunits	Number of main units (large quadrats)
nsubunits	Number of subunits (nested subsamples within each main unit)
nreps	Number of replicate surveys in every subunit
mean.psi	Mean large-scale, unit-level occupancy probability (psi)
beta.Xpsi	effect on psi of covariate A (at main unit level)
sd.logit.psi	SD of logit(psi), unstructured site variation in psi
mean.theta	Mean small-scale (subunit) occupancy probability (theta)
theta.time.range	range of theta 'intercepts' for subunits
beta.Xtheta	effect on theta of covariate B (at subunit level)
sd.logit.theta	SD of logit(theta), unstructured site variation in theta
mean.p	Mean per-survey detection probability
p.time.range	range of p 'intercepts' for replicates
beta.Xp	effect on p of covariate C (unit by subunit by replicate)
sd.logit.p	SD of logit(p)
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 values of the input arguments and the following additional elements:

theta.time.effect	Simulated time effect on theta, a vector of length nsubunits
p.time.effect	Simulated time effect on p, a vector of length nreps
p	Detection probabiliy, a nunits x nsubunits x nreps array
z	Occupancy indicator for main units, a nunits x 1 array of 0/1
a	Occupancy indicator for subunits, a nunits x nsubunits array of 0/1
y	Detection array, a nunits x nsubunits x nreps array of 0/1
sum.z	True number of occupied main units
obs.sum.z	Observed number of occupied main units
sum.z.a	Number of units with >=1 occupied, surveyed subunit
covA	Simulated covariate A, a vector of length nunits
covB	Simulated covariate B, a nunits x nsubunits matrix
covC	Simulated covariate C, a nunits x nsubunits x nreps array

Author(s)

Marc Kéry & Andy Royle

References

Kéry, M. & Royle, J.A. (2016) Applied Hierarchical Modeling in Ecology AHM1 - 10.10.

Examples

# Generate data with the default arguments and look at the structure:
tmp <- sim3Occ()
str(tmp)

# 'Null' model (model 1)
str(data <- sim3Occ(nunits = 100, nsubunits = 5, nreps = 3, mean.psi = 0.8,
  beta.Xpsi = 0, sd.logit.psi = 0, mean.theta = 0.6, theta.time.range = c(0, 0),
  beta.Xtheta = 0, sd.logit.theta = 0, mean.p = 0.4, p.time.range = c(0,0),
  beta.Xp = 0, sd.logit.p = 0))

# No covariate effects, no random variability (model 2)
str(data <- sim3Occ(nunits = 100, nsubunits = 5, nreps = 3, mean.psi = 0.8,
  beta.Xpsi = 0, sd.logit.psi = 0, mean.theta = 0.6, theta.time.range = c(-1, 1),
  beta.Xtheta = 0, sd.logit.theta = 0, mean.p = 0.4, p.time.range = c(-2,2),
  beta.Xp = 0, sd.logit.p = 0))

# All covariate effects, but no random variability (model 3)
str(data <- sim3Occ(nunits = 100, nsubunits = 5, nreps = 3, mean.psi = 0.8,
  beta.Xpsi = 1, sd.logit.psi = 0, mean.theta = 0.6, theta.time.range = c(-1, 1),
  beta.Xtheta = 1, sd.logit.theta = 0, mean.p = 0.4, p.time.range = c(-2,2),
  beta.Xp = -1, sd.logit.p = 0))

# Most complex model with all effects allowed for by sim function (model 4)
str(data <- sim3Occ(nunits = 100, nsubunits = 5, nreps = 3, mean.psi = 0.8,
  beta.Xpsi = 1, sd.logit.psi = 1, mean.theta = 0.6, theta.time.range = c(-1, 1),
  beta.Xtheta = 1, sd.logit.theta = 1, mean.p = 0.4, p.time.range = c(-2,2),
  beta.Xp = -1, sd.logit.p = 1))

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