## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 6,
  fig.height = 4
)

## -----------------------------------------------------------------------------
library(bgms)

# Analyse a subset of the Wenchuan dataset
?Wenchuan
data = Wenchuan[, 1:5]
head(data)

## ----eval=FALSE---------------------------------------------------------------
# fit = bgm(data, seed = 1234)

## ----include=FALSE------------------------------------------------------------
fit = bgm(data, seed = 1234, chains = 2, display_progress = "none", verbose = FALSE)

## -----------------------------------------------------------------------------
summary(fit)

## -----------------------------------------------------------------------------
coef(fit)

## ----fig.width= 7, fig.height= 7----------------------------------------------
library(qgraph)

median_probability_network = coef(fit)$pairwise
median_probability_network[coef(fit)$indicator < 0.5] = 0.0

qgraph(median_probability_network,
  theme = "TeamFortress",
  maximum = 1,
  fade = FALSE,
  color = c("#f0ae0e"), vsize = 10, repulsion = .9,
  label.cex = 1, label.scale = "FALSE",
  labels = colnames(data)
)