netclu_infomap: Infomap community finding
In bioRgeo/bioRgeo: Bioregionalisation Methods in R

netclu_infomap

R Documentation

Infomap community finding

Description

This function finds communities in a (un)weighted (un)directed network based on the Infomap algorithm (https://github.com/mapequation/infomap).

Usage

netclu_infomap(
  net,
  weight = TRUE,
  index = names(net)[3],
  nbmod = 0,
  markovtime = 1,
  seed = 0,
  numtrials = 1,
  twolevel = FALSE,
  show_hierarchy = FALSE,
  directed = FALSE,
  bipartite_version = FALSE,
  bipartite = FALSE,
  site_col = 1,
  species_col = 2,
  return_node_type = "both",
  version = "2.6.0",
  delete_temp = TRUE,
  path_temp = "infomap_temp",
  binpath = NULL
)

Arguments

`net`	the output object from `similarity()` or `dissimilarity_to_similarity()`. If a `data.frame` is used, the first two columns represent pairs of sites (or any pair of nodes), and the next column(s) are the similarity indices.
`weight`	a `boolean` indicating if the weights should be considered if there are more than two columns.
`index`	name or number of the column to use as weight. By default, the third column name of `net` is used.
`nbmod`	penalize solutions the more they differ from this number (0 by default for no preferred number of modules).
`markovtime`	scales link flow to change the cost of moving between modules, higher values results in fewer modules (default is 1).
`seed`	for the random number generator (0 for random by default).
`numtrials`	for the number of trials before picking up the best solution.
`twolevel`	a `boolean` indicating if the algorithm should optimize a two-level partition of the network (default is multi-level).
`show_hierarchy`	a `boolean` specifying if the hierarchy of community should be identifiable in the outputs (FALSE by default).
`directed`	a `boolean` indicating if the network is directed (from column 1 to column 2).
`bipartite_version`	a `boolean` indicating if the bipartite version of Infomap should be used (see Note).
`bipartite`	a `boolean` indicating if the network is bipartite (see Note).
`site_col`	name or number for the column of site nodes (i.e. primary nodes).
`species_col`	name or number for the column of species nodes (i.e. feature nodes).
`return_node_type`	a `character` indicating what types of nodes ("sites", "species" or "both") should be returned in the output (`keep_nodes_type="both"` by default).
`version`	a `character` indicating the Infomap version to use.
`delete_temp`	a `boolean` indicating if the temporary folder should be removed (see Details).
`path_temp`	a `character` indicating the path to the temporary folder (see Details).
`binpath`	a `character` indicating the path to the bin folder (see install_binaries and Details).

Details

Infomap is a network clustering algorithm based on the Map equation proposed in \insertCiteRosvall2008bioRgeo that finds communities in (un)weighted and (un)directed networks.

This function is based on the C++ version of Infomap (https://github.com/mapequation/infomap/releases). This function needs binary files to run. They can be installed with install_binaries(). If you set the path to the folder that will host the bin folder manually while running install_binaries please make sure to set binpath accordingly.

The C++ version of Infomap generates temporary folders and/or files that are stored in the path_temp folder ("infomap_temp" with an unique time stamp located in the working directory by default). This temporary folder is removed by default (delete_temp = TRUE).

Several version of Infomap are available in the package. See install_binaries() for more details.

Value

A list of class bioRgeo.clusters with five slots:

name: character string containing the name of the algorithm
args: list of input arguments as provided by the user
inputs: list of characteristics of the input dataset
algorithm: list of all objects associated with the clustering procedure, such as original cluster objects
clusters: data.frame containing the clustering results

In the algorithm slot, users can find the following elements:

cmd: the command line use to run Infomap
version: the Infomap version
web: Infomap's GitHub repository

Note

Infomap has been designed to deal with bipartite networks. To use this functionality set the bipartite_version argument to TRUE in order to approximate a two-step random walker (see https://www.mapequation.org/infomap/ for more information). Note that a bipartite network can also be considered as unipartite network (bipartite = TRUE).

In both cases do not forget to indicate which of the first two columns is dedicated to the site nodes (i.e. primary nodes) and species nodes (i.e. feature nodes) using the arguments site_col and species_col. The type of nodes returned in the output can be chosen with the argument return_node_type equal to "both" to keep both types of nodes, "sites" to preserve only the sites nodes and "species" to preserve only the species nodes.

Author(s)

Maxime Lenormand (maxime.lenormand@inrae.fr), Pierre Denelle (pierre.denelle@gmail.com) and Boris Leroy (leroy.boris@gmail.com)

References

\insertRef

Rosvall2008bioRgeo

Examples

## Not run: 
comat <- matrix(sample(1000, 50), 5, 10)
rownames(comat) <- paste0("Site", 1:5)
colnames(comat) <- paste0("Species", 1:10)

net <- similarity(comat, metric = "Simpson")
com <- netclu_infomap(net)

## End(Not run)

bioRgeo/bioRgeo documentation built on March 10, 2023, 9:48 p.m.