easybgm (version 0.2.1)

network: Network plot

Description

The network plot visualizes the strength of interactions between two nodes, the partial associations. Solely edges with a posterior inclusion probability larger than the exc_prob argument (default = 0.5) are shown. Edge thickness and saturation represent the strength of the association; the thicker the edge, the stronger the association. Red edges indicate negative relations and blue edges indicate positive associations.

Usage

plot_network(output, exc_prob = 0.5, evidence_thresh = 10, dashed = FALSE, ...)

Value

Returns a plot

Arguments

output

Output object from the easybgm function. Supports also objects from the bgm function of the bgms package.

exc_prob

The threshold for excluding edges. All edges with a lower inclusion probability will not be shown. The default is set to 0.5 in line with the median probability plot.

evidence_thresh

If dashed = TRUE, users can specify the threshold for sufficient evidence for inclusion. All edges with evidence lower than evidence_tresh are dashed.

dashed

A binary parameter indicating whether edges with inconclusive evidence should be dashed. Default is FALSE

...

Additional arguments passed onto qgraph.

Examples

library(easybgm)
library(bgms)

data <- na.omit(Wenchuan)
fit <- easybgm(data, type = "continuous",
                iter = 1000  # for demonstration only (> 5e4 recommended)
                )

plot_network(fit)

# Shows all edges with an inclusion probability larger than 0.1
plot_network(fit, exc_prob = 0.1)

# Indicate which edges have insufficient evidence for inclusion through a dashed line
plot_network(fit, dashed = TRUE, evidence_thresh = 10)