stir_DD | R Documentation |
Stirs an already existing network by rewiring a node according to the Duplication and Divergence mechanism.
stir_DD( matrix, x, divergence, directed = TRUE, link = 0, force_connected = FALSE )
matrix |
Existing network to be rewired (stirred). |
x |
The ID of the node to be grown. |
divergence |
Probability that the new node loses edges associated with the node it duplicates. Needs to be between zero and one. |
directed |
Binary variable determining if the network is directed, resulting in off-diagonal asymmetry in the adjacency matrix. |
link |
Probability that the new node attaches to the node it duplicates. Defaults to 0. |
force_connected |
Binary argument determining if the newly grown node has to be connected to the existing network. Defaults to FALSE, to prevent rare computational slow-downs when it is unlikely to create a connected network. Defaults to FALSE. |
Different from Duplication & Mutation models in that edges can only be lost.
An adjacency matrix.
Ispolatov, I., Krapivsky, P. L., & Yuryev, A. (2005). Duplication-divergence model of protein interaction network. Physical review E, 71(6), 061911.
# Import netcom library(netcom) size <- 10 existing_network <- matrix(sample(c(0,1), size = size^2, replace = TRUE), nrow = size, ncol = size) new_network_prep <- matrix(0, nrow = size + 1, ncol = size + 1) new_network_prep[1:size, 1:size] = existing_network new_network <- stir_DD(matrix = new_network_prep, x = size + 1, divergence = 0.5)
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