Calculate Link Community Link Densities
LinkDensities.RdThis function calculates link densities for link communities.
LinkDensities(x, clusterids = 1:x$numbers[3])
Arguments
| x | An object of class |
|---|---|
| clusterids | An integer vector of community IDs. Defaults to all communities. |
Details
The link density of community i is $$D_{i}=\frac{e_{i}-n_{i}+1}{(n_{i}(n_{i}-1)/2)-n_{i}+1}$$ where \(e_{i}\) is the number of edges in community i and \(n_{i}\) is the number of nodes in community i.
Value
A named numerical vector, where the names are community IDs and the numbers are link densities.
References
Ahn, Y.Y., Bagrow, J.P., and Lehmann, S. (2010). Link communities reveal multiscale complexity in networks. Nature 466, 761-764.
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
Alex T. Kalinka alex.t.kalinka@gmail.com
See also
Examples
#> Checking for loops and duplicate edges... 0.000% Checking for loops and duplicate edges... 2.174% Checking for loops and duplicate edges... 4.348% Checking for loops and duplicate edges... 6.522% Checking for loops and duplicate edges... 8.696% Checking for loops and duplicate edges... 10.870% Checking for loops and duplicate edges... 13.043% Checking for loops and duplicate edges... 15.217% Checking for loops and duplicate edges... 17.391% Checking for loops and duplicate edges... 19.565% Checking for loops and duplicate edges... 21.739% Checking for loops and duplicate edges... 23.913% Checking for loops and duplicate edges... 26.087% Checking for loops and duplicate edges... 28.261% Checking for loops and duplicate edges... 30.435% Checking for loops and duplicate edges... 32.609% Checking for loops and duplicate edges... 34.783% Checking for loops and duplicate edges... 36.957% Checking for loops and duplicate edges... 39.130% Checking for loops and duplicate edges... 41.304% Checking for loops and duplicate edges... 43.478% Checking for loops and duplicate edges... 45.652% Checking for loops and duplicate edges... 47.826% Checking for loops and duplicate edges... 50.000% Checking for loops and duplicate edges... 52.174% Checking for loops and duplicate edges... 54.348% Checking for loops and duplicate edges... 56.522% Checking for loops and duplicate edges... 58.696% Checking for loops and duplicate edges... 60.870% Checking for loops and duplicate edges... 63.043% Checking for loops and duplicate edges... 65.217% Checking for loops and duplicate edges... 67.391% Checking for loops and duplicate edges... 69.565% Checking for loops and duplicate edges... 71.739% Checking for loops and duplicate edges... 73.913% Checking for loops and duplicate edges... 76.087% Checking for loops and duplicate edges... 78.261% Checking for loops and duplicate edges... 80.435% Checking for loops and duplicate edges... 82.609% Checking for loops and duplicate edges... 84.783% Checking for loops and duplicate edges... 86.957% Checking for loops and duplicate edges... 89.130% Checking for loops and duplicate edges... 91.304% Checking for loops and duplicate edges... 93.478% Checking for loops and duplicate edges... 95.652% Checking for loops and duplicate edges... 97.826% Checking for loops and duplicate edges... 100.000% #> Found and removed 4 loop(s) #> Found and removed 2 duplicate edge(s) #> Calculating edge similarities for 41 edges... 0.00% Calculating edge similarities for 41 edges... 2.56% Calculating edge similarities for 41 edges... 5.13% Calculating edge similarities for 41 edges... 7.69% Calculating edge similarities for 41 edges... 10.26% Calculating edge similarities for 41 edges... 12.82% Calculating edge similarities for 41 edges... 15.38% Calculating edge similarities for 41 edges... 17.95% Calculating edge similarities for 41 edges... 20.51% Calculating edge similarities for 41 edges... 23.08% Calculating edge similarities for 41 edges... 25.64% Calculating edge similarities for 41 edges... 28.21% Calculating edge similarities for 41 edges... 30.77% Calculating edge similarities for 41 edges... 33.33% Calculating edge similarities for 41 edges... 35.90% Calculating edge similarities for 41 edges... 38.46% Calculating edge similarities for 41 edges... 41.03% Calculating edge similarities for 41 edges... 43.59% Calculating edge similarities for 41 edges... 46.15% Calculating edge similarities for 41 edges... 48.72% Calculating edge similarities for 41 edges... 51.28% Calculating edge similarities for 41 edges... 53.85% Calculating edge similarities for 41 edges... 56.41% Calculating edge similarities for 41 edges... 58.97% Calculating edge similarities for 41 edges... 61.54% Calculating edge similarities for 41 edges... 64.10% Calculating edge similarities for 41 edges... 66.67% Calculating edge similarities for 41 edges... 69.23% Calculating edge similarities for 41 edges... 71.79% Calculating edge similarities for 41 edges... 74.36% Calculating edge similarities for 41 edges... 76.92% Calculating edge similarities for 41 edges... 79.49% Calculating edge similarities for 41 edges... 82.05% Calculating edge similarities for 41 edges... 84.62% Calculating edge similarities for 41 edges... 87.18% Calculating edge similarities for 41 edges... 89.74% Calculating edge similarities for 41 edges... 92.31% Calculating edge similarities for 41 edges... 94.87% Calculating edge similarities for 41 edges... 97.44% Calculating edge similarities for 41 edges... 100.00% #> Hierarchical clustering of edges... #> Calculating link densities... 0.00% Calculating link densities... 2.56% Calculating link densities... 5.13% Calculating link densities... 7.69% Calculating link densities... 10.26% Calculating link densities... 12.82% Calculating link densities... 15.38% Calculating link densities... 17.95% Calculating link densities... 20.51% Calculating link densities... 23.08% Calculating link densities... 25.64% Calculating link densities... 28.21% Calculating link densities... 30.77% Calculating link densities... 33.33% Calculating link densities... 35.90% Calculating link densities... 38.46% Calculating link densities... 41.03% Calculating link densities... 43.59% Calculating link densities... 46.15% Calculating link densities... 48.72% Calculating link densities... 51.28% Calculating link densities... 53.85% Calculating link densities... 56.41% Calculating link densities... 58.97% Calculating link densities... 61.54% Calculating link densities... 64.10% Calculating link densities... 66.67% Calculating link densities... 69.23% Calculating link densities... 71.79% Calculating link densities... 74.36% Calculating link densities... 76.92% Calculating link densities... 79.49% Calculating link densities... 82.05% Calculating link densities... 84.62% Calculating link densities... 87.18% Calculating link densities... 89.74% Calculating link densities... 92.31% Calculating link densities... 94.87% Calculating link densities... 97.44% Calculating link densities... 100.00% #> Maximum partition density = 0.2601626 #> Finishing up...1/4... 12% Finishing up...1/4... 25% Finishing up...1/4... 37% Finishing up...1/4... 50% Finishing up...1/4... 62% Finishing up...1/4... 75% Finishing up...1/4... 87% Finishing up...1/4... 100% Finishing up...2/4... 12% Finishing up...2/4... 25% Finishing up...2/4... 37% Finishing up...2/4... 50% Finishing up...2/4... 62% Finishing up...2/4... 75% Finishing up...2/4... 87% Finishing up...2/4... 100% Finishing up...3/4... 12% Finishing up...3/4... 25% Finishing up...3/4... 37% Finishing up...3/4... 50% Finishing up...3/4... 62% Finishing up...3/4... 75% Finishing up...3/4... 87% Finishing up...3/4... 100% Finishing up...4/4... 0.00% Finishing up...4/4... 4.76% Finishing up...4/4... 9.52% Finishing up...4/4... 14.29% Finishing up...4/4... 19.05% Finishing up...4/4... 23.81% Finishing up...4/4... 28.57% Finishing up...4/4... 33.33% Finishing up...4/4... 38.10% Finishing up...4/4... 42.86% Finishing up...4/4... 47.62% Finishing up...4/4... 52.38% Finishing up...4/4... 57.14% Finishing up...4/4... 61.90% Finishing up...4/4... 66.67% Finishing up...4/4... 71.43% Finishing up...4/4... 76.19% Finishing up...4/4... 80.95% Finishing up...4/4... 85.71% Finishing up...4/4... 90.48% Finishing up...4/4... 95.24% Finishing up...4/4... 100.00% #> Plotting... #> Colouring dendrogram... 1% Colouring dendrogram... 2% Colouring dendrogram... 3% Colouring dendrogram... 4% Colouring dendrogram... 6% Colouring dendrogram... 7% Colouring dendrogram... 8% Colouring dendrogram... 9% Colouring dendrogram... 11% Colouring dendrogram... 12% Colouring dendrogram... 13% Colouring dendrogram... 14% Colouring dendrogram... 16% Colouring dendrogram... 17% Colouring dendrogram... 18% Colouring dendrogram... 19% Colouring dendrogram... 20% Colouring dendrogram... 22% Colouring dendrogram... 23% Colouring dendrogram... 24% Colouring dendrogram... 25% Colouring dendrogram... 27% Colouring dendrogram... 28% Colouring dendrogram... 29% Colouring dendrogram... 30% Colouring dendrogram... 32% Colouring dendrogram... 33% Colouring dendrogram... 34% Colouring dendrogram... 35% Colouring dendrogram... 37% Colouring dendrogram... 38% Colouring dendrogram... 39% Colouring dendrogram... 40% Colouring dendrogram... 41% Colouring dendrogram... 43% Colouring dendrogram... 44% Colouring dendrogram... 45% Colouring dendrogram... 46% Colouring dendrogram... 48% Colouring dendrogram... 49% Colouring dendrogram... 50% Colouring dendrogram... 51% Colouring dendrogram... 53% Colouring dendrogram... 54% Colouring dendrogram... 55% Colouring dendrogram... 56% Colouring dendrogram... 58% Colouring dendrogram... 59% Colouring dendrogram... 60% Colouring dendrogram... 61% Colouring dendrogram... 62% Colouring dendrogram... 64% Colouring dendrogram... 65% Colouring dendrogram... 66% Colouring dendrogram... 67% Colouring dendrogram... 69% Colouring dendrogram... 70% Colouring dendrogram... 71% Colouring dendrogram... 72% Colouring dendrogram... 74% Colouring dendrogram... 75% Colouring dendrogram... 76% Colouring dendrogram... 77% Colouring dendrogram... 79% Colouring dendrogram... 80% Colouring dendrogram... 81% Colouring dendrogram... 82% Colouring dendrogram... 83% Colouring dendrogram... 85% Colouring dendrogram... 86% Colouring dendrogram... 87% Colouring dendrogram... 88% Colouring dendrogram... 90% Colouring dendrogram... 91% Colouring dendrogram... 92% Colouring dendrogram... 93% Colouring dendrogram... 95% Colouring dendrogram... 96% Colouring dendrogram... 97% Colouring dendrogram... 98% Colouring dendrogram... 100%## Calculate link densities. ld <- LinkDensities(lc)
