getCommunityConnectedness function

Calculate Community Connectedness or Modularity

This function returns a measure of how relatively outwardly or inwardly connected a community is.

getCommunityConnectedness(x, clusterids = 1:x$numbers[3], conn = "conn", 
                          normalise = TRUE, verbose = FALSE)

Arguments

• x: An object of class linkcomm.
• clusterids: An integer vector of community IDs. Defaults to all communities.
• conn: A character string naming the connectedness measure to use. Can be one of "conn" or "mod" (see Details below). Defaults to "conn".
• normalise: Logical, whether to normalise community connectedness measures by the number of nodes in individual communities. Defaults to TRUE.
• verbose: Logical, whether to display the progress of the calculation on the screen. Defaults to FALSE.

Details

The connectedness and modularity of different communities indicates whether a particular community is bridging several other communities, or existing as a relatively isolated module. The modularity of community i is

where $e_{w}(i)$ is the number of edges within community i, $e_{b}(i)$ is the number of edges community i makes to other communities, $n_{i}$ is the number of nodes in community i, and $\hat{d}$ is the average degree in the network. Community connectedness is the inverse of this value.

Returns

A named numerical vector, where the names are community IDs and the numbers are community connectedness or modularity scores.

References

Kalinka, A.T. and Tomancak, P. (2011). linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type. Bioinformatics 27 , 2011-2012.

Author(s)

Alex T. Kalinka alex.t.kalinka@gmail.com

See Also

getCommunityCentrality

Examples

## Generate graph and extract link communities.
g <- swiss[,3:4]
lc <- getLinkCommunities(g)

## Get community connectedness.
cc <- getCommunityConnectedness(lc, normalise = FALSE)