# plotbf2: Plot the estimated Bayes factors In geoBayes: Analysis of Geostatistical Data using Bayes and Empirical Bayes Methods

## Description

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

## Usage

 ```1 2``` ```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

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37``` ```## 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 May 2, 2019, 3:14 a.m.