make_DD {netcom}

Makes a Duplication and Divergence Network

Description

Makes a network according to the Duplication and Divergence mechanism.

Usage

make_DD(size, net_kind, divergence, directed = TRUE)

Arguments

size

Number of nodes in the network.

net_kind

If the network is an adjacency matrix ("matrix") or an edge list ("list").

divergence

Probability that the new node loses edges associated with the node it duplicates. Needs to be between zero and one.

directed

Whether the target network is directed. Defaults to TRUE.

Details

Different from Duplication & Mutation models in that edges can only be lost.

Value

An adjacency matrix.

References

Ispolatov, I., Krapivsky, P. L., & Yuryev, A. (2005). Duplication-divergence model of protein interaction network. Physical review E, 71(6), 061911.

Examples

# Import netcom
library(netcom)

# Network size (number of nodes)
size <- 10

# Divergence parameter
divergence <- 0.237

# Make network according to the Duplication & Divergence mechanism
make_DD(size = size, net_kind = "matrix", divergence = divergence)