## ----opts, echo = FALSE, message = FALSE, warning = FALSE---------------------
knitr::opts_chunk$set(collapse = TRUE, comment = " ", fig.width = 7, fig.height = 7, fig.align = "center")

## ----eval = FALSE-------------------------------------------------------------
# install.packages("BDgraph")

## ----loadpkg, message = FALSE, warning = FALSE--------------------------------
library(BDgraph)

## ----fig.align = 'center'-----------------------------------------------------
set.seed(20)

data.sim = bdgraph.sim(n = 200, p = 15, graph = "scale-free", vis = TRUE)

## -----------------------------------------------------------------------------
bdgraph.obj = bdgraph(data = data.sim, method = "ggm", iter = 5000, verbose = FALSE)

## ----fig.align = 'center', fig.width = 3, fig.height = 3----------------------
conf.mat(actual = data.sim, pred = bdgraph.obj, cutoff = 0.5)

conf.mat.plot(actual = data.sim, pred = bdgraph.obj, cutoff = 0.5)

## ----fig.align = 'center'-----------------------------------------------------
compare(data.sim, bdgraph.obj, main = c("Target", "BDgraph"), vis = TRUE)

## ----fig.align = 'center', fig.width = 3, fig.height = 3----------------------
bdgraph.mpl.obj = bdgraph.mpl(data = data.sim, method = "ggm", iter = 5000, verbose = FALSE)

conf.mat(actual = data.sim, pred = bdgraph.mpl.obj)
conf.mat.plot(actual = data.sim, pred = bdgraph.mpl.obj)

## ----fig.align = 'center'-----------------------------------------------------
compare(list(bdgraph.obj, bdgraph.mpl.obj), data.sim, 
        main = c("Target", "BDgraph", "BDgraph.mpl"), vis = TRUE)

## ----fig.align = 'center'-----------------------------------------------------
plotroc(list(bdgraph.obj, bdgraph.mpl.obj), data.sim, cut = 200,
        labels = c("BDgraph", "BDgraph.mpl"), color = c("blue", "red"))

## ----fig.align = 'center'-----------------------------------------------------
set.seed(2)

data.sim = bdgraph.sim(n = 300, p = 10, type = "mixed", graph = "random", vis = TRUE)

## -----------------------------------------------------------------------------
bdgraph.obj = bdgraph(data = data.sim, method = "gcgm", iter = 5000, verbose = FALSE)

## ----fig.align = 'center'-----------------------------------------------------
compare(bdgraph.obj, data.sim, main = c("Target", "BDgraph"), vis = TRUE)

## ----fig.align = 'center'-----------------------------------------------------
plotroc(bdgraph.obj, data.sim, labels = "BDgraph", color = "blue")