Threshold Edges by Weight, Count, Proportion or Density

Keeps the edges that satisfy every criterion supplied. The operation corresponds to qgraph's minimum argument and to tna::prune(). The result is a network that can be analysed and plotted.

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: Non-negative integer. Keep this many edges, the strongest first. top = 0 removes every edge.
absolute: Logical. Compare abs(weight) instead of the signed weight. Default TRUE, which suits correlation and partial-correlation networks. The minimum and maximum comparisons and the ranking used by proportion, density and top all 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.

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. A non-finite minimum or maximum, a proportion or density outside (0, 1], and a negative or fractional top raise a cograph_bad_selection error.

Details

Several criteria 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. When proportion, density and top are combined, the smallest of the implied edge counts is used.

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. The result therefore does not depend on the order in which the edges are stored.

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.

Examples

threshold_edges(regulation_net, minimum = 0.1)
#> Cograph network: 10 nodes, 27 edges ( directed )
#> Source: matrix 
#>   Nodes (10): Explore, Plan, Monitor, Adapt, Reflect, Discuss, ... +4 more
#>   Edges: 27 / 90 (density: 30.0%)
#>   Weights: [0.110, 0.490]  |  mean: 0.288
#>   Strongest edges:
#>     Share -> Monitor  0.490
#>     Plan -> Evaluate  0.490
#>     Evaluate -> Adapt  0.430
#>     Synthesize -> Reflect  0.420
#>     Plan -> Discuss  0.400
#> Layout: none 
#>   Use as.data.frame() for the edge table, as.data.frame(what = "nodes") for the nodes.