Lists the triads of a network that contain at least one edge, with the labels of their nodes, so that the node combinations forming each motif pattern can be identified.
Usage
extract_triads(
x,
type = NULL,
involving = NULL,
threshold = 0,
min_total = 5,
directed = NULL
)Arguments
- x
A matrix, igraph object, tna, or cograph_network.
- type
Character vector of MAN codes to filter by (e.g., "030T", "030C"). Default NULL returns all types.
- involving
Character vector of node labels. Only return triads involving at least one of these nodes. Default NULL returns all triads.
- threshold
Edge weight threshold. An edge counts as present for the triad type when its weight is greater than
threshold. Default 0.- min_total
Minimum total weight across all 6 edges. Excludes trivial triads with low overall activity. Default 5.
- directed
Logical or NULL. Whether the network is treated as directed. NULL (default) detects it from the input.
Value
A data frame with one row per triad, in node index order, and the columns:
- A, B, C
Labels of the three nodes in the triad.
- type
MAN code (012, ..., 300). Triads of type 003 have no edge and are not returned.
- weight_AB, weight_BA, weight_AC, weight_CA, weight_BC, weight_CB
Edge weights of the 6 possible directed edges.
- total_weight
Sum of the 6 edge weights.
A network with fewer than 3 nodes gives a data frame with no rows.
Details
The function complements motif_census() by showing the node combinations
that form each motif pattern. The triad type is determined by edge presence
(weight greater than threshold). The weight columns hold the edge
weights themselves, which measure the strength of each triad.
Examples
extract_triads(regulation_net, type = "030T", min_total = 0)
#> A B C type weight_AB weight_BA weight_AC weight_CA
#> 1 Explore Adapt Discuss 030T 0.00 0.28 0.00 0.30
#> 2 Explore Discuss Create 030T 0.00 0.30 0.00 0.14
#> 3 Explore Create Share 030T 0.00 0.14 0.27 0.00
#> 4 Plan Monitor Synthesize 030T 0.13 0.00 0.00 0.11
#> 5 Plan Monitor Evaluate 030T 0.13 0.00 0.49 0.00
#> 6 Plan Discuss Create 030T 0.40 0.00 0.20 0.00
#> 7 Plan Evaluate Create 030T 0.49 0.00 0.20 0.00
#> 8 Monitor Adapt Evaluate 030T 0.16 0.00 0.00 0.33
#> 9 Monitor Adapt Share 030T 0.16 0.00 0.00 0.49
#> 10 Monitor Reflect Synthesize 030T 0.00 0.15 0.00 0.07
#> 11 Monitor Reflect Evaluate 030T 0.00 0.15 0.00 0.33
#> weight_BC weight_CB total_weight
#> 1 0.34 0.00 0.92
#> 2 0.14 0.00 0.58
#> 3 0.23 0.00 0.64
#> 4 0.00 0.07 0.31
#> 5 0.00 0.33 0.95
#> 6 0.14 0.00 0.74
#> 7 0.00 0.39 1.08
#> 8 0.00 0.43 0.92
#> 9 0.00 0.39 1.04
#> 10 0.00 0.42 0.64
#> 11 0.00 0.07 0.55