BayesNetBP (version 1.6.1)

PlotCGBN: Plot the Bayesian network

Description

Plot and compare two Bayesian networks with different evidence(s) absorbed and propagated.

Usage

PlotCGBN(
  tree.1,
  tree.2,
  fontsize = NULL,
  pbar = FALSE,
  plotting = TRUE,
  epsilon = 10^-6
)

Arguments

tree.1

a '>ClusterTree

tree.2

a '>ClusterTree

fontsize

font size for the node labels

pbar

logical(1) whether to show progress bar

plotting

logical(1) whether to output plot

epsilon

numeric(1) the KL divergence is undefined if certain states of a discrete variable have probabilities of 0. In this case, a small positive number epsilon is assigned as their probabilities for calculating the divergence. The probabilities of other states are shrunked proportionally to ensure they sum up to 1.

Value

a plot of Bayesian network

a vector of signed symmetric Kullback-Leibler divergence

Details

Network visualization of the node-specific differences between Bayesian Networks with the same topology, but evidence that has been absorbed and propagated. The change of marginal distribution of each node is measured by signed and symmetric Kullback-Leibler divergence. The sign indicates the direction of change, with tree.1 considered as the baseline. The magnitude of the change is reflected by the value. Nodes that are white are d-separated from the evidence. This function requires Rgraphviz package.

References

Cowell, R. G. (2005). Local propagation in conditional Gaussian Bayesian networks. Journal of Machine Learning Research, 6(Sep), 1517-1550.

Yu H, Moharil J, Blair RH (2020). BayesNetBP: An R Package for Probabilistic Reasoning in Bayesian Networks. Journal of Statistical Software, 94(3), 1-31. <doi:10.18637/jss.v094.i03>.

Examples

# NOT RUN {
library("Rgraphviz")
data(toytree)
tree.post <- AbsorbEvidence(toytree, c("Nr1i3"), list(1))
PlotCGBN(tree.1=toytree, tree.2=tree.post)
# }