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Run Infomap on Multilayer Networks with Intralayer Links

Source: R/modularity.R
run_infomap_multi.Rd

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).

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.

Details

If the network has the weight attribute, it will be used as the weight of the edges. Since the exported multilayer network structure assumes only *Intra links (i.e., no explicit inter-layer links), Infomap internally constructs inter-layer connections for each physical node using the --multilayer-relax-rate parameter (default: 0.15). This creates inter-layer links between all instances of the same node across layers. The weights of these links are proportional to the weighted out-degree of the node in the target layer, resulting in non-uniform inter-layer transition probabilities.

This implicit construction of inter-layer links enables Infomap to model node-aligned multiplex dynamics without requiring an explicit *Inter section in the input file.

References

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

Examples

if (FALSE) { # \dontrun{
# 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)
} # }