run_infomap_multi: Run Infomap on Multilayer Networks with Intralayer Links

In lsaravia/EcoNetwork: Ecological network analyses including multiplex networks

Run Infomap on Multilayer Networks with Intralayer Links

Description

This function exports a multilayer network (as a list of igraph objects) into Infomap's required format, runs Infomap via an external binary, and imports the detected communities back into R as a data frame. It requires Infomap to be installed on the system. See installation instructions at Infomap.

Usage

run_infomap_multi(
  igraph_list,
  layer_names = NULL,
  infomap_path = "infomap",
  output_dir = tempdir(),
  directed = TRUE,
  two_level = TRUE,
  multilayer_relax_rate = 0.15,
  seed = 123
)

Arguments

igraph_list	A list of igraph objects, each representing a network layer.
layer_names	A character vector with layer names corresponding to each igraph object (default: NULL).
infomap_path	Character string specifying the path to the Infomap binary (default: "infomap", assumes it is in the system PATH).
output_dir	Character string specifying the directory for Infomap results (default: tempdir()).
directed	Logical; if TRUE, the network is treated as directed (default: TRUE).
two_level	Logical; if TRUE, uses two-level Infomap instead of hierarchical Infomap (default: TRUE).
multilayer_relax_rate	Numeric; relaxation rate for multilayer links (default: 0.15).
seed	Numeric; random seed for Infomap to ensure reproducibility (default: 123).

Details

If the network has the weight attribute, it will be used as the weight of the edges.

Value

A data frame containing the detected modules with columns:

module

Module/community assignment from Infomap.

node

The node name from the original igraph objects.

layer

The corresponding layer name from layer_names.

flow

The fraction of flow assigned to the module.

References

D. Edler, A. Holmgren and M. Rosvall, The MapEquation software package, available online at https://www.mapequation.org.

Examples

## Not run: 
# Load network data
fileName <- system.file("extdata", package = "multiweb")
dn <- list.files(fileName, pattern = "^Kefi2015.*\\.txt$")
g <- readNetwork(dn, fileName, skipColumn = 2)
class(g)
names(g) <- c("Negative", "Positive", "Trophic")

# Run Infomap
run_infomap_multi(g)

## End(Not run)

lsaravia/EcoNetwork documentation built on April 5, 2025, 1:51 p.m.