threshold_edges: Threshold Edges by Weight, Count, Proportion or Density

In cograph: Analysis and Visualization of Complex Networks

Threshold Edges by Weight, Count, Proportion or Density

Description

Keeps the edges that satisfy every criterion supplied. This is the network equivalent of qgraph's minimum/cut arguments and of tna::prune(), except that it returns a network rather than a plot setting, so the thresholded network can be analysed, not only drawn.

Usage

threshold_edges(
  x,
  minimum = NULL,
  maximum = NULL,
  proportion = NULL,
  density = NULL,
  top = NULL,
  absolute = TRUE,
  keep_isolates = TRUE,
  keep_format = FALSE,
  directed = NULL
)

Arguments

x	Network input: cograph_network, matrix, igraph, network, tna, or an edge-list data frame.
minimum	Numeric. Keep edges whose weight is at least this value.
maximum	Numeric. Keep edges whose weight is at most this value.
proportion	Numeric in (0, 1]. Keep this fraction of the edges, the strongest first.
density	Numeric in (0, 1]. Keep as many of the strongest edges as gives this density (edges as a fraction of the possible edges).
top	Integer. Keep this many edges, the strongest first.
absolute	Logical. Compare abs(weight) rather than the signed weight. Default TRUE, which is what correlation and partial-correlation networks need. minimum/maximum and the ranking used by proportion, density and top both follow this flag.
keep_isolates	Logical. Keep nodes that end up with no edges? Default TRUE. Set FALSE, or call remove_isolates(), to drop them.
keep_format	Logical. Return the input format when TRUE.
directed	Logical or NULL. If NULL (default), auto-detect.

Details

When several criteria are given they are combined with AND: for example threshold_edges(x, minimum = 0.2, top = 20) keeps the twenty strongest edges among those of weight at least 0.2.

Ties at the cut point are all kept, so top = 10 can return more than ten edges when the tenth and eleventh weights are equal. This is deliberate: breaking ties on edge order would make the result depend on how the network was built.

Value

A cograph_network with the surviving edges, or the input format when keep_format = TRUE. Every node is kept unless keep_isolates = FALSE; nodes the threshold stranded are reported in a cograph_isolates_created warning. An out-of-range minimum, maximum, proportion, density or top raises a cograph_bad_selection error.

References

Epskamp, S., Cramer, A. O. J., Waldorp, L. J., Schmittmann, V. D., & Borsboom, D. (2012). qgraph: Network visualizations of relationships in psychometric data. Journal of Statistical Software, 48(4), 1–18.

See Also

binarize, filter_edges, disparity_filter, remove_isolates

Examples

adj <- matrix(c(0, .5, .8, 0,
                .5, 0, .3, .6,
                .8, .3, 0, .4,
                 0, .6, .4, 0), 4, 4, byrow = TRUE)
rownames(adj) <- colnames(adj) <- c("A", "B", "C", "D")

threshold_edges(adj, minimum = 0.5)
threshold_edges(adj, top = 2)
threshold_edges(adj, density = 0.5)

cograph documentation built on Sept. 30, 2026, 5:08 p.m.