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This function finds communities in a (un)weighted undirected network based on the Louvain algorithm.

Usage

netclu_louvain(
  net,
  weight = TRUE,
  index = names(net)[3],
  lang = "Cpp",
  q = 0,
  c = 0.5,
  k = 1,
  bipartite = FALSE,
  site_col = 1,
  species_col = 2,
  return_node_type = "both",
  binpath = "tempdir",
  path_temp = "louvain_temp",
  delete_temp = TRUE,
  algorithm_in_output = TRUE
)

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.

lang

a string indicating what version of Louvain should be used (igraph or Cpp, see Details).

q

the quality function used to compute partition of the graph (modularity is chosen by default, see Details).

c

the parameter for the Owsinski-Zadrozny quality function (between 0 and 1, 0.5 is chosen by default).

k

the kappa_min value for the Shi-Malik quality function (it must be > 0, 1 is chosen by default).

bipartite

a boolean indicating if the network is bipartite (see Details).

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 (return_node_type = "both" by default).

binpath

a character indicating the path to the bin folder (see install_binaries and Details).

path_temp

a character indicating the path to the temporary folder (see Details).

delete_temp

a boolean indicating if the temporary folder should be removed (see Details).

algorithm_in_output

a boolean indicating if the original output of communities should be returned in the output (see Value). Default to TRUE.

Value

A list of class bioregion.clusters with five slots:

  1. name: character string containing the name of the algorithm

  2. args: list of input arguments as provided by the user

  3. inputs: list of characteristics of the clustering process

  4. algorithm: list of all objects associated with the clustering procedure, such as original cluster objects (only if algorithm_in_output = TRUE)

  5. clusters: data.frame containing the clustering results

In the algorithm slot, if algorithm_in_output = TRUE, users can find an "communities" object, output of cluster_louvain

if lang = "igraph" and the following element if lang = "Cpp":

  • cmd: the command line use to run Louvain

  • version: the Louvain version

  • web: Louvain's website

.

Details

Louvain is a network community detection algorithm proposed in (Blondel et al. 2008) . This function proposed two implementations of the function (parameter lang): the igraph implementation (cluster_louvain) and the C++ implementation (https://sourceforge.net/projects/louvain/, version 0.3). The latest offers the possibility to choose among several quality functions, q = 0 for the classical Newman-Girvan criterion (also called "Modularity"), 1 for the Zahn-Condorcet criterion, 2 for the Owsinski-Zadrozny criterion (you should specify the value of the parameter with the c argument), 3 for the Goldberg Density criterion, 4 for the A-weighted Condorcet criterion,5 for the Deviation to Indetermination criterion, 6 for the Deviation to Uniformity criterion, 7 for the Profile Difference criterion, 8 for the Shi-Malik criterion (you should specify the value of kappa_min with k argument) and 9 for the Balanced Modularity criterion.

The C++ version of Louvain is based on the version 0.3 (https://sourceforge.net/projects/louvain/). This function needs binary files to run. They can be installed with install_binaries.

If you changed the default path to the bin folder while running install_binaries PLEASE MAKE SURE to set binpath accordingly.

The C++ version of Louvain generates temporary folders and/or files that are stored in the path_temp folder ("louvain_temp" with an unique timestamp located in the bin folder in binpath by default). This temporary folder is removed by default (delete_temp = TRUE).

Note

Although this algorithm was not primarily designed to deal with bipartite network, it is possible to consider the bipartite network as unipartite network (bipartite = TRUE).

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.

References

Blondel VD, Guillaume JL, Lambiotte R, Mech ELJS (2008). “Fast unfolding of communities in large networks.” J. Stat. Mech, P10008.

Author

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

Examples

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_louvain(net, lang = "igraph")