geoBayes (version 0.7.4)

plotbf2: Plot the estimated Bayes factors

Description

This function plots the estimated logarithm Bayes factors from the function bf2new.

Usage

plotbf2(
  bf2obj,
  pars = c("linkp", "phi", "omg", "kappa"),
  profile = length(pars) > 2,
  ...
)

Value

This function returns nothing.

Arguments

bf2obj

Output from the function bf2new.

pars

A vector with the names of the parameters to plot.

profile

Whether it should produce a profile plot or a contour plot if the length of pars is 2.

...

Other input to be passed to either plot or contour.

Details

Depending on whether pars has length 1 or 2, this function creates a line or a contour plot of the estimated Bayes factors. If its length is 3 or 4, then it produces multiple profile plots. In this case the variable is fixed at different values and the maximum Bayes factor corresponding to the fixed value is plotted against that value.

Examples

if (FALSE) {
data(rhizoctonia)
### Define the model
corrf <- "spherical"
kappa <- 0
ssqdf <- 1
ssqsc <- 1
betm0 <- 0
betQ0 <- .01
family <- "binomial.probit"
### Skeleton points
philist <- c(100, 140, 180)
omglist <- c(.5, 1)
parlist <- expand.grid(linkp=0, phi=philist, omg=omglist, kappa = kappa)
### MCMC sizes
Nout <- 100
Nthin <- 1
Nbi <- 0
### Take MCMC samples
runs <- list()
for (i in 1:NROW(parlist)) {
  runs[[i]] <- mcsglmm(Infected ~ 1, family, rhizoctonia, weights = Total,
                       atsample = ~ Xcoord + Ycoord,
                       Nout = Nout, Nthin = Nthin, Nbi = Nbi,
                       betm0 = betm0, betQ0 = betQ0,
                       ssqdf = ssqdf, ssqsc = ssqsc,
                       phi = parlist$phi[i], omg = parlist$omg[i],
                       linkp = parlist$linkp[i], kappa = parlist$kappa[i],
                       corrfcn = corrf,
                       corrtuning=list(phi = 0, omg = 0, kappa = 0))
}
bf <- bf1skel(runs)
bfall <- bf2new(bf, phi = seq(100, 200, 10), omg = seq(0, 2, .2))
plotbf2(bfall, c("phi", "omg"))
plotbf2(bfall, c("phi", "omg"), profile = TRUE, type = "b", ylab="log(BF)")
}