# Tools for Generating, Visualizing, and Analysing Link Communities in Networks

## Documentation for package ‘linkcomm’ version 1.0-12

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.

## Help Pages

linkcomm-package | The 'linkcomm' package
corLinkcommCentrality | Correlation of Community Centrality with Classic Centrality
cutDendrogramAt | Extract Meta-Communities
edge.duplicates | Find and Remove Edge Loops and Duplicates
get.community.overlaps | Find Node Overlaps between Communities
get.shared.nodes | Get Nodes Shared by Communities
getAllNestedComm | Find Nested Communities
getClusterRelatedness | Hierarchichal Clustering of Link Communities
getCommunityCentrality | Calculate Community Centrality Measures for Nodes
getCommunityConnectedness | Calculate Community Connectedness or Modularity
getCommunityMatrix | Construct a Community Membership Matrix
getEdgesIn | Extract Edge Indices from Communities
getLinkCommunities | Extract Link Communities from a Network
getNestedHierarchies | Find Nested Structures in Communities
getNodesIn | Extract Nodes from Communities
getOCG.clusters | Generate Overlapping Cluster Generator (OCG) Communities
graph.feature | Make Node or Edge Graph Features
human_pp | Sample Human Protein Interactome
integer.edgelist | Convert A Network to an Integer Edgelist
karate | Social Network in a Karate Club
layout.spencer.circle | Calculate Node Coordinates for a Spencer Circle
lesmiserables | Co-Appearance Network from Les Miserables
linkcomm | The 'linkcomm' package
linkcomm2clustnsee | Write a Partition File for Clust&See
linkcomm2cytoscape | Write an Edge Attribute File for Cytoscape
LinkDensities | Calculate Link Community Link Densities
meta.communities | Produce a Set of Meta-Communities
newLinkCommsAt | User-Defined Link Communities
numberEdgesIn | Extract Node Community Membership by Edges
orderCommunities | Order Link Communities According to the Dendrogram
plot.linkcomm | The 'linkcomm' Plotting Function
plot.OCG | The 'OCG' Plotting Function
plotLinkCommDend | Plot a Coloured Dendrogram of Link Communities
plotLinkCommGraph | Plot a Graph Layout of Link Communities
plotLinkCommMembers | Plot a Community Membership Matrix for Link Communities
plotLinkCommSumm | Plot a Summary of the Link Community Algorithm Output
plotLinkCommSummComm | Plot a Summary of the Link Communities
plotOCGraph | Plot a Graph Layout of OCG Communities
pp_rnapol | Sample Yeast Protein Interactome
print.linkcomm | Print a Summary of a 'linkcomm' Object
print.OCG | Print a Summary of an 'OCG' Object
read.OCG | Read an OCG Partition File into R
weighted | Sample Gene Co-Expression Network
which.communities | Extract Community Membership for Nodes