runEllipseSim: Run SECR simulations with Elliptical or Circular Home Ranges

In MurrayEfford/secrBVN: Bivariate Normal Home Range SECR

Run SECR simulations with Elliptical or Circular Home Ranges

Description

A wrapper for other bvn functions.

Usage

runEllipseSim(nrepl = 100, sigmaX = 25, sigmaY = 25, theta = NULL,
    type = c("uniform","BVN"), g0 = 0.2, lambda0 = 0.4, p = 0.95, 
    traps = NULL, trapargs = NULL, noccasions = 5, buffer = 100, 
    D = 10, extractfn = derived, seed = NULL, 
    ncores = NULL, Ndist = "fixed",
    secrfn = c("secr.fit", "anisotropic.fit"), ...) 

Arguments

nrepl	integer number of replicates
sigmaX	numeric or function
sigmaY	numeric
theta	real orientation of ellipses (radians)
type	uniform ellipse vs bivariate normal
g0	numeric intercept of detection function (type = "uniform")
lambda0	numeric intercept of hazard function (type = "BVN")
p	numeric truncation probability for uniform elliptical home ranges
traps	secr traps object, or function to generate one
trapargs	list of arguments for trap building function, if is.function(traps)
noccasions	integer number of sampling occasions
buffer	real width of simulation and estimation buffer metres
D	real population density animals/ha
extractfn	function used to summarise each simulated model fit
seed	integer random number seed
ncores	integer number of cores to use (used in 1.3.0 to setNumThreads)
secrfn	character; name of function to call or NULL
Ndist	character string for distribution of number of individuals (see sim.popn)
...	other arguments passed to secrfn

Details

If traps is not specified, a default 6 x 6 grid of binary proximity detectors is constructed with make.grid.

If sigmaX is a function it is used as in simpopn.bvn to generate individual home ranges (population attribute ‘s2xy’).

If sigmaY = NULL simulates detections of animals with circular halfnormal and uniform home ranges using sim.capthist, rather than the ad hoc code in simcapt.bvn. This is technically redundant as the same result may be achieved with sigmaX = sigmaY, but is a useful check.

Value

A list with one component for each replicate, comprising a list with components

npop	number of individuals in simulated population
nCH	number of individuals detected
ncapt	number of detections

And, if secrfn not NULL,

fit	result of extractfn applied to fitted secr model (default, a 2 x 4 matrix from derived
pred	result of predict applied to fitted secr model (default, a 2 x 5 data.frame)

See Also

simpopn.bvn, simcapt.bvn, secr.fit, anisotropic.fit

Examples

## Not run: 
nrepl <- 20
tr <- make.grid(6,6, spacing = 50, detector = "proximity")
sigmaX <- 25/2; sigmaY <- 25*2
details <- list(distribution = "binomial")
sims <- runEllipseSim (nrepl, sigmaX, sigmaY, buffer = 200, ncores = 2, 
                       traps = tr, g0 = 0.2, D = 4, CL = TRUE, 
                       details = details) 

## End(Not run)

MurrayEfford/secrBVN documentation built on Oct. 14, 2022, 5:20 a.m.