Reference

Building multilayer networks Functions for buiding multilayer networks and/or its characterising matrices, and other basic functions
GetSampleMultiplex()	Get a sample of a Multiplex
BuildExtendedEdgelistFromSupraAdjacencyMatrix()	Builds extended edgelist from supra-adjacency matrix
BuildLayersTensor()	Build layers tensor
BuildSupraAdjacencyMatrixFromEdgeColoredMatrices()	Build supra-adjacency matrix from edge-colored matrices
BuildSupraAdjacencyMatrixFromExtendedEdgelist()	Build supra-adjacency matrix from edge lists
SupraAdjacencyToBlockTensor()	Return block tensor from supra-adjacency matrix
SupraAdjacencyToNetworkList()	Return a list of igraph objects corresponding to layers
SupraAdjacencyToNodesTensor()	Return nodes tensor from supra-adjacency matrix
buildMultilayerNetworkFromMuxvizFiles()	Return a Multilayer Network from Muxviz files
binarizeMatrix()	Binarize a matrix
Aggregation functions Obtaining aggregated networks from multilayes.
GetAggregateMatrix()	Get aggregate matrix from nodes tensor
GetAggregateMatrixFromNetworkList()	Get aggregate Matrix from network List
GetAggregateMatrixFromSupraAdjacencyMatrix()	Get aggregate matrix from supra-adjacency matrix
GetAggregateNetworkFromNetworkList()	Get aggregate Network from network List
GetAggregateNetworkFromSupraAdjacencyMatrix()	Get aggregate network from supra-adjacency matrix
Centralities Multilayer centralities.
GetMultiAuthCentrality()	Calculates Multi-Authority-Centrality
GetMultiClosenessCentrality()	Returns Multi Closeness Centrality
GetMultiDegree()	Return total multi-degree, not accounting for interlinks
GetMultiDegreeSum()	Return the Sum of total multi-degree, include multiple times the interlinks
GetMultiEigenvectorCentrality()	Calculates Multi-Eigenvector-Centrality
GetMultiHubCentrality()	Calculates Multi-Hub-Centrality
GetMultiInDegree()	Return the multi-in-degree, not accounting for interlinks
GetMultiInDegreeSum()	Return the Sum of multi-in-degree, include multiple times the interlinks
GetMultiInStrength()	Return the multi-in-Strength, not accounting for interlinks
GetMultiInStrengthSum()	Return the Sum of multi-in-Strength, include multiple times the interlinks
GetMultiKCoreCentrality()	Calculates Multi-KCore Centrality. Computes centrality in each layer separately and then get the max per node.
GetMultiKatzCentrality()	Calculates Multi-Katz Centrality
GetMultiOutDegree()	Return the multi-out-degree, not accounting for interlinks
GetMultiOutDegreeSum()	Return the Sum of multi-out-degree, include multiple times the interlinks
GetMultiOutStrength()	Return the multi-out-Strength, not accounting for interlinks
GetMultiOutStrengthSum()	Return the Sum of multi-out-Strength, include multiple times the interlinks
GetMultiPageRankCentrality()	Calculates Multi-PageRank-Centrality (based on Multi-RandomWalk-Centrality)
GetMultiPathStatistics()	Return statistics based on multilayer paths
GetMultiRWCentrality()	Returns Multi Random Walk Centrality
GetMultiStrength()	Return total multi-strength
GetMultiStrengthSum()	Return the Sum of total multi-Strength, include multiple times the interlinks
GetMultiplexityCentrality()	Calculates Multiplexity Centrality.
getVersatilityProfile()	Return the Versatility Profile for a given centrality
Mesoscale structures Describing and anlysis the mescoscale structure of multilayer networks.
GetConnectedComponents()	Return the component assignment for each node
GetGiantConnectedComponent()	Return the largest connected component
GetGiantIntersectionComponent()	Return the largest connected component obtained by intersecting LCC of each layer. Assumption: the network is an edge-colored multigraph
GetGiantIntersectionComponentFromNetworkList()	Return the largest connected component obtained by intersecting LCC of each layer. Assumption: the network is an edge-colored multigraph
GetGiantViableComponent()	Return the largest viable cluster
GetGiantViableComponentFromNetworkList()	Return the largest viable cluster from network list. Assumption: the network is an edge-colored multigraph
GetMultilayerCommunities_Infomap()	Return multilayer communities for interconnected multilayer networks
GetMultiplexCommunities_Infomap()	Return multilayer communities. INFOMAP wrapper
GetMultilayerMotifs()	Return the multilayer motifs. Note that even if inter-links are present, they will be neglected and the network treated as an edge-colored multigraph
GetMultilayerMotifsFromNetworkList()	Calculates the Motifs of a Multilayer from a network list
GetMonoplexTriads()	Return the closed triangles from a monoplex network
GetMultiplexTriads()	Return the closed triangles in single layers, aggregate and multilayer network, but working directly with tensors
GetMultiplexTriadsFromNetworkList()	Return the closed triangles in single layers, aggregate and multilayer network
Global Descriptors
GetGlobalNumberTriangles()	Calculate the global number of triangles
GetAverageGlobalClustering()	Calculate Global Clustering Coefficient
GetAverageGlobalNodeOverlappingMatrix()	Calculates the average global node overlap Matrix
GetAverageGlobalOverlapping()	Gets the average global edge overlap on the multilayer
GetAverageGlobalOverlappingMatrix()	Calculates the average global edge overlap Matrix
Dynamics & Co. Describing, evaluating, and anlysis dynamics on multilayer networks.
GetLaplacianMatrix()	Network combinatorial Laplacian
GetNormalizedLaplacianMatrix()	Network normalized Laplacian
BuildSupraTransitionMatrixFromSupraAdjacencyMatrix()	Build the supra-transition matrix for a multilayer network
BuildTransitionMatrixFromEdgeColoredMatrices()	Random walk transition matrix for an edge-coloured network. Given the node tensor for the edge-coloured multi-layer network the function builds the supra transition matrix for a discrete time RW.
BuildTransitionMatrixFromSingleLayer()	Returns a Transition Matrix from a single Layer
GetCoverageEvolutionMultilayer()	Get the Coverage Evolution of a Multilayer Network
GetCoverageEvolutionEdgeColored()	Get the Coverage Evolution of an edge-colored network
GetCoverageEvolutionSingleLayer()	Get the Coverage Evolution of a single-layer network
Plotting Plotting routines (documentation is poor, sorry).
plot_multiplex() plot.multiplex()	Plot a multiplex
plot_multiplex3D() plot.multiplex3D()	3D plot of a multiplex
multiplot() multiplot.col() multiplot.row()	Multiplot
layoutMultiplex()	layoutMultiplex
plot_multimotif() plot.multimotif()	Plot multilayer motifs Plot a motif from a motifs table returned by GetMultilayerMotifs.
plot_multimodules() plot.multimodules()	Plot modules
Others Other functions for building a Configuration Model, for evaluating entropy, for solving the eigenvalue problem, for finding shortest paths, etc.
CanonicalVector()	Return the ith canonical vector of a N-dimesnion basis
GetConfigurationModelTypeIFromNetworkList()	Generate random multiplex networks with fixed degree sequences, while destroying intra-layer degree correlations, but not inter-layer ones
GetConfigurationModelTypeIIFromNetworkList()	Generate random multiplex networks with fixed degree sequences, while destroying both intra- and inter-layer degree correlations
BuildDensityMatrixBGS()	Calculate the density matrix from an adjacency matrix
GetEigenvaluesOfDensityMatrix()	Calculate the eigenvalues of a density matrix
GetEigenvaluesOfDensityMatrixFromAdjacencyMatrix()	Calculate the eigenvalues of a density matrix from an adjacency matrix
GetInterAssortativityTensor()	Return Assortativity Inter-layer values
GetJensenShannonDivergence()	Calculate the Jensen-Shannon Divergence of two networks
GetLargestEigenv()	Gets the largest Eigenvalue from a Matrix. A warning is raised if complex numbers emerge.
GetLocalClustering()	Calculate Local Clustering Coefficient
GetMultilayerReducibility()	Calculate the Reducibility of a multilayer network
GetRenyiEntropyFromAdjacencyMatrix()	Calculate the quantum Renyi entropy of a network
GetRewiredLayerWithOverlappingEdges()	Generate multiplex networks with given amount of edge overlapping
GetSPSimilarityMatrix()	Returns pairwise similarity based on Frobenius norm
MultiShortestPathFromNode()	Return the Shortest-Path from given node to other nodes, with option for counting replicates
ShortestPathFromNode()	Return the Shortest-Path from the given node to other nodes
SolveEigenvalueProblem()	Return the matrix of eigenvectors (Q) and the diagonal matrix of eigenvalues (L) as well as a vector with ordered eigenvalues (E)
Auxiliary functions MATLAB-like functions that help building multilayers from diagonal, blockdiagonal… matrices.
blkdiag()	Return a list of matrices in block diagonal form
reshapeR()	Return a matrix reshaped according to dimension n and m
diagR()	Return a matrix with elements on a diagonal specified by offset
traceR()	Return the trace of input matrix
modR()	Return the remainder of x divided by y
sumR()	Return the sum across rows (n=1) or columns (n=2) of a matrix
binarizeMatrix()	Binarize a matrix