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Multiplex Recurrence Network

Source: R/mrn.R
mrn.Rd

This function will create a Multiplex Recurrence Network from a list of igraph objects that can be considered the layers of a network. The layers must have the same number of nodes. There are two modes of operation: Layer similarity (MRNweightedBy is set to "InterLayerMI", "InterLayerCor", "EdgeOvelap", or "JRP") and Layer importance (not implemented yet). The former generates weighted MRN based on Interlayer Mutual Information, Interlayer Correlation, Edge Overlap, Joint Recurrence Rate.

Usage

mrn(
  layers,
  MRNweightedBy = c("InterLayerMI", "InterLayerCor", "EdgeOverlap", "JRP")[1],
  jrp_measure = "RR",
  win = NA,
  step = NA,
  overlap = NA,
  alignment = "r",
  cumulative = FALSE,
  doPlot = FALSE,
  silent = TRUE
)

Arguments

layers

A list of igraph objects representing the layers of the multiplex network. The layer networks must all have the same number of vertices.

MRNweightedBy

The measure to be used to evaluate the average structural similarities between the layers of the network. Valid options are: "InterLayerMI" (Mutual information based on similarity of the vertex degree across layers), "InterLayerCor" (pearson correlation between vertex degree or strength of each layer pair), "EdgeOverlap" (proportion of vertices sharing the same edges across layers), or "JRP" which will calculate a joint recurrence plot for each layer pair and add the value passed to jrp_measure as the measure of association (default = InterLayerMI)

jrp_measure

Which JRP measure should be used to asses layer similarity. Use a column name of the data frame output by rp_measures (default = "RR")

win

The window size passed to ts_windower() in which to evaluate "InterLayerMI", "InterLayerCor", "EdgeOvelap", or "JRP". (default = NA).

step

The stepsize for the sliding window (default = NA).

overlap

The window overlap passed to ts_windower() if MRNweightedBy is "InterLayerMI" or "EdgeOvelap". The value of step will be ignored if overlap is not NA. (default = NA).

alignment

Whether to right ("r"), center ("c"), or left ("l") align the window.

cumulative

To make the network represent cumulative time, set directed = TRUE and cumulative = TRUE. This will set the upper triangle of the recurrence matrix to 0 and ensures that the network edges represent recurrent values that have occurred in the past relative to the current observed value (node). If directed = FALSE the argument is ignored (default = TRUE).

doPlot

Plot the multiplex recurrence network (default = FALSE).

silent

Silent-ish mode. (default = FALSE).

Value

A list object with a (windowed) Multiplex Recurrence Matrix based on MRNweightedBy:

  • interlayerMI - One or more matrices with edge weights between layers that represent the interlayer Mutual Information.

  • interlayerCor - One or more matrices with edge weights between layers that represent the Pearson correlation between vertex degrees (or strength if layers are weighted graphs) of layers.

  • edgeOverlap - One or more matrices with edge weights between layers that represent the overlapping edges between layers.

  • jointRP - One or more matrices with edge weights between layers that represent the value of the joint RP passed in jrp_measure. The default is the "RR" of joint Recurrence Plot of the two layers.

  • The field meanValues contains one or more matrices that represent the means and SDs of the weights requested inMRNweightedBy. The measure eo_joint (returned with "edgeOverlap") refers to the number of edges shared among all layers of the MRN.

Examples


# Create some layers
library(igraph)

layers <- list(g1 = igraph::sample_smallworld(1, 100, 5, 0.05),
g2 = igraph::sample_smallworld(1, 100, 5, 0.5),
g3 = igraph::sample_smallworld(1, 100, 5, 1))

mrn(layers = layers)