plotbf2: Plot the estimated Bayes factors

In geoBayes: Analysis of Geostatistical Data using Bayes and Empirical Bayes Methods

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,
  ...
)

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.

Value

This function returns nothing.

Examples

## Not run: 
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)")

## End(Not run)

geoBayes documentation built on Aug. 21, 2023, 9:08 a.m.