plotProxy: Simulate and plot the relationship between a parameter and its designated proxy

Description

As described in the vignette, each parameter is matched to a proxy value computed cheaply from the rawdata by the proxy function. This function provides a visual check on that relationship.

Usage

plotProxy(parameter = "sigma", proxyfn = proxy.ms, traps, mask, detectfn = "HHN", 
    noccasions = 5, basepar = list(), xvals = NULL, nrepl = 100, add = FALSE, 
    trend = TRUE, points = FALSE, boxplot = TRUE, boxplotargs = list(), 
    link = "log", details = NULL, ...)

Value

The simulated proxy values are returned invisibly as a matrix (nrepl x nlevels).

Arguments

parameter: character parameter of interest
proxyfn: function to compute vector of proxy values from a capthist object
traps: traps object
mask: habitat mask object
detectfn: numeric or character code for detection function (see detectfn)
noccasions: integer number of sampling occasions
basepar: named list with central values of parameters
xvals: specified values of focal paramater to simulate (optional)
nrepl: integer number of simulations
add: logical; if TRUE any plot is added to an existing plot
trend: logical; if TRUE a least-squares trend line is plotted
points: logical; if TRUE each simulated value is plotted
boxplot: logical; if TRUE a boxplots is plotted for each level of the focal parameter
boxplotargs: list of arguments for boxplot (optional)
link: character link function for transforming parameter x-axis
details: not used
...: other arguments passed to plot()

Details

Simulation uses the internal functions simpop and simCH.

boxplotargs may be used to override or add to the arguments of boxplot.

This version of plotProxy() does not allow for interference (NT) and assumes a simple SECR model with only 3 or 4 coefficients corresponding to density D and the parameters of the detection model (lambda0 or g0, sigma and possibly z).

Matching of proxies at the level of `beta' parameters may be enabled in a future version.

Examples

Run this code


# try with small number of replicates
trps <- traps(captdata)
msk <- make.mask(trps, buffer = 100)
base <- list(D = 5, lambda0 = 0.2, sigma = 25)
out <- plotProxy (parameter = 'D', traps = trps, mask = msk,
     basepar = base, boxplotargs = list(col='orange'), nrepl = 20)