plotProxy {ipsecr}

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, ...)
    

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.

Value

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

See Also

proxy.ms

Examples

# 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)