evolqg (version 0.3-4)

LModularity: L Modularity

Description

Calculates the L-Modularity (Newman-type modularity) and the partition of traits that minimizes L-Modularity. Wrapper for using correlations matrices in community detection algorithms from igraph.

Usage

LModularity(cor.matrix, method = optimal.community, ...)

Value

List with L-Modularity value and trait partition

Arguments

cor.matrix

correlation matrix

method

community detection function

...

Additional arguments to igraph community detection function

Details

Warning: Using modularity maximization is almost always a terrible idea. See: https://skewed.de/tiago/blog/modularity-harmful

References

Modularity and community structure in networks (2006) M. E. J. Newman, 8577-8582, doi: 10.1073/pnas.0601602103

Examples

if (FALSE) {
# A modular matrix:
modules = matrix(c(rep(c(1, 0, 0), each = 5),
rep(c(0, 1, 0), each = 5),
rep(c(0, 0, 1), each = 5)), 15)
cor.hypot = CreateHypotMatrix(modules)[[4]]
hypot.mask = matrix(as.logical(cor.hypot), 15, 15)
mod.cor = matrix(NA, 15, 15)
mod.cor[ hypot.mask] = runif(length(mod.cor[ hypot.mask]), 0.8, 0.9) # within-modules
mod.cor[!hypot.mask] = runif(length(mod.cor[!hypot.mask]), 0.3, 0.4) # between-modules
diag(mod.cor) = 1
mod.cor = (mod.cor + t(mod.cor))/2 # correlation matrices should be symmetric

# requires a custom igraph installation with GLPK installed in the system
LModularity(mod.cor)}