sumplot: Summarise and Plot Ellipse Simulations

In MurrayEfford/secrBVN: Bivariate Normal Home Range SECR

Summarise and Plot Ellipse Simulations

Description

A list of outputs from runEllipseSim is summarised and optionally plotted.

Usage

simsum(simlist, component = c("fit","pred"), parm = "D", trueval = 4, 
    compact = c("av.nCH", "nvalid", "RB", "RSE", "rRMSE", "COV"), dec = 3,
    maxfactor = 10)
    
simplot(simlist, component = c("fit","pred"), parm = "D", trueval = 4, 
    xval = 1:4, xlim = c(0.7, 4.3), ylim = c(-0.2, 0.2),
    legend = TRUE, pchi = c(21, 16, 22, 24), cexi = rep(1.2,4), ...) 

Arguments

simlist	list, each component an output from runEllipseSim
component	character; from which set of output should parm be summarised?
parm	character name of parameter to summarise, default density
trueval	numeric true value of parm, default 4 animals / ha
compact	character vector for summary statistics to include in output (NULL for all)
dec	integer number of decimal places in output
maxfactor	numeric; extreme estimate filter (see Details)
xval	numeric vector of values
xlim	numeric limits of x-axis
ylim	numeric limits of y-axis
legend	logical; if TRUE a legend is displayed
pchi	numeric vector for symbol to use for each component of simlist
cexi	numeric vector for symbol size to use for each component of simlist
...	other arguments passed to points

Details

For each replicate the input simlist has components “fit“ generated by extractfn and “pred“ generated by predict.secr. Argument ‘component’ chooses between these.

These functions meet the needs of Efford in prep. as shown in the package vignette, and may not be useful for novel applications.

Each component of simlist should have the same number of components (ellipse scenarios).

Estimates with absolute value greater than maxfactor * trueval are set to NA (maxfactor is ignored if NULL).

The ... argument allows a few options such as "type = 'o'", but colour (bg) is set internally to white.

Value

List of output matrices (tables) (returned invisibly by simplot).

See Also

runEllipseSim

Examples

## Not run: 

nrepl <- 20
tr <- make.grid(6,6, spacing = 50, detector = 'proximity')
simrandom <- vector('list')
simrandomBVN <- vector('list')
for (i in 1:4) {
    sigmaX <- 25/i^0.5; sigmaY <- 25*i^0.5
    details <- list(distribution = 'binomial')
    ## uniform
    simrandom[[i]] <- runEllipseSim (nrepl, sigmaX, sigmaY, buffer = 200, ncores = 2,
                                          traps = tr, g0 = 0.2, D = 4, type = 'uniform', 
                                          CL = TRUE, detectfn = 'HHN', details = details)
    ## bvn
    simrandomBVN[[i]] <- runEllipseSim (nrepl, sigmaX, sigmaY, buffer = 200, ncores = 2,
                                             traps = tr, lambda0 = 0.4, D = 4, type = 'BVN', 
                                             CL = TRUE, detectfn = 'HHN', details = details)
    message ('Completed aspect ratio ', i)
}

simplot(list(Uniform = simrandom, BVN = simrandomBVN), legend = TRUE)

simsum(list(Uniform = simrandom36.2, BVN = simrandomBVN36.2))


## End(Not run)

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