Skip to contents

Calculate Topological Roles Within Network Modules

Source: R/calcTopologicalIndices.r
calc_topological_roles.Rd

This function identifies the topological roles of nodes (e.g., species) in an ecological or interaction network based on their position within and among modules. Modules (or communities) are detected using the cluster_spinglass algorithm by default, unless an alternative community object is provided.

Usage

calc_topological_roles(g, nsim = 1, ncores = 0, community = NULL)

Arguments

g

An igraph object representing the network.

nsim

Integer. Number of independent runs of the Spinglass community detection algorithm (default is 1).

ncores

Integer. Number of cores to use for parallel computation. Set to 0 for sequential processing.

community

Optional. A community detection object (class communities) from an alternative algorithm. If NULL, cluster_spinglass is used.

Value

A data frame with the following columns:

node

Node ID.

within_module_degree

Within-module degree z-score (\(z\)).

among_module_conn

Participation coefficient (\(PC\)).

Details

Topological roles are quantified using two parameters:

  • \(z\) (within-module degree z-score): quantifies how well-connected a node is to others within its own module, relative to other members of the same module.

  • \(PC\) (participation coefficient): quantifies how evenly a node’s links are distributed across different modules.

When using the Spinglass algorithm, which is stochastic, multiple runs can be performed by setting the nsim parameter to repeat the procedure.

References

  1. Guimerà, R. & Nunes Amaral, L.A. (2005). Functional cartography of complex metabolic networks. Nature, 433, 895–900.

  2. Kortsch, S., Primicerio, R., Fossheim, M., Dolgov, A.V., & Aschan, M. (2015). Climate change alters the structure of Arctic marine food webs due to poleward shifts of boreal generalists. Proceedings of the Royal Society B: Biological Sciences, 282(1814), 20151546. doi:10.1098/rspb.2015.1546

Examples