site_species_subset: Extract a subset of sites or species from a...

In bioregion: Comparison of Bioregionalisation Methods

Extract a subset of sites or species from a bioregion.clusters object

Description

This function extracts a subset of nodes based on their type ("site" or "species") from a bioregion.clusters object, which contains both types of nodes (sites and species).

Usage

site_species_subset(clusters, node_type = "site")

Arguments

clusters	An object of class bioregion.clusters.
node_type	A character string indicating the type of nodes to extract. Possible values are "site" or "species". The default is "site".

Value

An object of class bioregion.clusters containing only the specified node type (sites or species).

Note

Network clustering functions (prefixed with netclu_) may return both types of nodes (sites and species) when applied to bipartite networks (using the bipartite argument). In such cases, the type of nodes included in the output can be specified with the return_node_type argument. This function allows you to extract a particular type of nodes (sites or species) from the output and adjust the return_node_type attribute accordingly.

Author(s)

Maxime Lenormand ([e-mail])
Pierre Denelle ([e-mail])
Boris Leroy ([e-mail])

Examples

net <- data.frame(
  Site = c(rep("A", 2), rep("B", 3), rep("C", 2)),
  Species = c("a", "b", "a", "c", "d", "b", "d"),
  Weight = c(10, 100, 1, 20, 50, 10, 20)
)

clusters <- netclu_louvain(net, lang = "igraph", bipartite = TRUE)

clusters_sites <- site_species_subset(clusters, node_type = "site")

bioregion documentation built on April 12, 2025, 9:13 a.m.