bayesnetworks

The goal of bayesnetworks is to do MCMC fitting of Bayesian networks, including source & sink constraints and external network info.

Installation

And the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("USCbiostats/bayesnetworks")

Examples

The network is fitted by passing in data and network structure

library(bayesnetworks)
set.seed(1234)

x <- bn_mcmc(X = network$data, graph = network$dag_info, N = 50000)

Some diagnostic plots:

library(ggplot2)

ggplot(x, aes(iter, globalLL)) +
  geom_line()

ggplot(x, aes(iter, FN)) +
  geom_line(aes(color = "FN")) +
  geom_line(aes(y = FP, color = "FP")) +
  labs(y = "value")

ggplot(x, aes(iter, deletions)) +
  geom_line(aes(color = "deletions")) +
  geom_line(aes(y = additions, color = "additions")) +
  labs(y = "count")

Code of Conduct

Please note that the ‘bayesnetworks’ project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.