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Classify and plot topological roles

Source: R/calcTopologicalIndices.r
classify_topological_roles.Rd

This function classifies species into four topological roles based on their within-module degree (dz) and among-module connectivity (PC), following the approach of Kortsch (2015). The classification is as follows:

  • modhub: Species with high within-module degree (dz >= 2.5) and low among-module connectivity (PC < 0.625).

  • hubcon: Species with high within-module degree (dz >= 2.5) and high among-module connectivity (PC >= 0.625).

  • modspe: Species with low within-module degree (dz < 2.5) and low among-module connectivity (PC < 0.625).

  • modcon: Species with low within-module degree (dz < 2.5) and high among-module connectivity (PC >= 0.625).

Usage

classify_topological_roles(tRoles, g, community = NULL)

Arguments

tRoles

A data frame of calculated topological roles obtained from calc_topological_roles().

g

An igraph network object.

community

An igraph community object used to determine module membership for plotting. If NULL, the function calculates community structure using cluster_spinglass().

Value

A list containing:

  • hub_conn: A data frame with node classifications and topological role values.

  • gp: A ggplot object visualizing the topological roles.

Details

The function also generates a ggplot visualization of the species' topological roles, with nodes colored according to their module membership.

References

  1. 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. https://doi.org/10.1098/rspb.2015.1546

  2. Saravia, L. A., Marina, T. I., Kristensen, N. P., De Troch, M., & Momo, F. R. (2022). Ecological network assembly: How the regional metaweb influences local food webs. Journal of Animal Ecology, 91(3), 630–642. https://doi.org/10.1111/1365-2656.13652

Examples

if (FALSE) { # \dontrun{

g <- netData[[2]]

tp <- calc_topological_roles(g,nsim=10)

classify_topological_roles(tp,g)
} # }