read_infomap_communities.RdReads `Infomap` community structure for multiplex from two files. The first file contains `Infomap`-style multiplex structure and the second file is an output from the `Infomap` algorithm containing the communities. Function his returns data frame with nodes and their corresponding community.
read_infomap_communities( multiplex_file, clu_file, physical_nodes = FALSE, layer = NULL )
| multiplex_file | File with the `Infomap` structure of the multiplex. |
|---|---|
| clu_file | File with the communities obtained as output of the `Infomap` algorithm. |
| physical_nodes | Whether the `clu_file` contains physical of state nodes. Default to `FALSE`. |
| layer | The layer from which the community structure is obtained. Only used if `clu_file` contains state nodes. |
Data frame with two columns. The first column contains names of nodes and the second column contains corresponding `Infomap` community.
The first file can be obtained with `meMultiplex` function with the output type set to `"Infomap"`. The second file is a result of `Infomap` algorithm for community detection. `Infomap` algorithm finds community structure of the multiplex using `multiplex_file` and outputs it in `clu_file`. This function unites the two files in one tidy data frame with multiplex nodes and their corresponding community.
`Infomap` returns two different types of communities, communities based on physical nodes (normal nodes) and communities based on state nodes. State nodes are abstract nodes created by `Infomap` to label physical nodes which exist in multiple layers. For example, for a physical node which is shared between two layers, two state nodes are created. Thus community structure of the state nodes contains two community structures, one existing in each layer of multiplex and both od them influenced by the whole multiplex structure. If `physical_nodes` is `FALSE`, `clu_file` must contain state node output. In this case `layer` must be specified and the community structure is taken from that layer. If `physcal_nodes` is `TRUE`, `clu_file` must contain physical node output. This output overlaps two state node community structures existing in different layers and thus the same physical node can exist in multiple communities. For more information, visit `Infomap` website (De Domenico et al. 2015) .
De Domenico M, Lancichinetti A, Arenas A, Rosvall M (2015). “Identifying modular flows on multilayer networks reveals highly overlapping organization in interconnected systems.” Physical Review X, 5(1), 011027.