linkcomm: Tools for Generating, Visualizing, and Analysing Link Communities in Networks

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Link communities reveal the nested and overlapping structure in networks, and uncover the key nodes that form connections to multiple communities. linkcomm provides a set of tools for generating, visualizing, and analysing link communities in networks of arbitrary size and type. The linkcomm package also includes tools for generating, visualizing, and analysing Overlapping Cluster Generator (OCG) communities.

Author
Alex T. Kalinka <alex.t.kalinka@gmail.com>, with contributions from Alain Guenoche
Date of publication
2014-08-13 19:00:50
Maintainer
Alex T. Kalinka <alex.t.kalinka@gmail.com>
License
GPL (>= 2)
Version
1.0-11

View on CRAN

Man pages

corLinkcommCentrality
Correlation of Community Centrality with Classic Centrality
cutDendrogramAt
Extract Meta-Communities
edge.duplicates
Find and Remove Edge Loops and Duplicates
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
get.community.overlaps
Find Node Overlaps between Communities
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
get.shared.nodes
Get Nodes Shared by 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
linkcomm2clustnsee
Write a Partition File for Clust&See
linkcomm2cytoscape
Write an Edge Attribute File for Cytoscape
linkcomm-package
The 'linkcomm' package
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
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
plot.OCG
The 'OCG' Plotting Function
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

Files in this package

linkcomm
linkcomm/inst
linkcomm/inst/CITATION
linkcomm/inst/doc
linkcomm/inst/doc/linkcomm.Rnw
linkcomm/inst/doc/linkcomm.R
linkcomm/inst/doc/linkcomm.pdf
linkcomm/src
linkcomm/src/linkcomm_functions.cpp
linkcomm/src/linkcommhclust_order.cpp
linkcomm/src/linkcomm_linkdensities.cpp
linkcomm/src/linkcomm_hclust.cpp
linkcomm/src/OCG_algorithm.c
linkcomm/src/edge_duplicates.cpp
linkcomm/src/read_OCG.cpp
linkcomm/src/linkcomm_edgesims_all.cpp
linkcomm/src/linkcomm_edgesims.cpp
linkcomm/NAMESPACE
linkcomm/demo
linkcomm/demo/linkcomm.R
linkcomm/demo/00Index
linkcomm/NEWS
linkcomm/data
linkcomm/data/networks.rda
linkcomm/R
linkcomm/R/linkcomm_plotting.R
linkcomm/R/linkcomm_misc.R
linkcomm/R/linkcomm_main.R
linkcomm/R/OCG_main.R
linkcomm/vignettes
linkcomm/vignettes/nodepie_linkcomm.pdf
linkcomm/vignettes/graph_layout_examples.pdf
linkcomm/vignettes/custom_graphs.pdf
linkcomm/vignettes/linkcomm.Rnw
linkcomm/vignettes/networks.rda
linkcomm/vignettes/cluster_relatedness.pdf
linkcomm/vignettes/ocg_lesmis.pdf
linkcomm/vignettes/fig1_vignette.pdf
linkcomm/MD5
linkcomm/build
linkcomm/build/vignette.rds
linkcomm/DESCRIPTION
linkcomm/man
linkcomm/man/getOCG.clusters.Rd
linkcomm/man/edge.duplicates.Rd
linkcomm/man/getLinkCommunities.Rd
linkcomm/man/getNodesIn.Rd
linkcomm/man/linkcomm2cytoscape.Rd
linkcomm/man/which.communities.Rd
linkcomm/man/layout.spencer.circle.Rd
linkcomm/man/getCommunityMatrix.Rd
linkcomm/man/linkcomm-package.Rd
linkcomm/man/graph.feature.Rd
linkcomm/man/karate.Rd
linkcomm/man/pp_rnapol.Rd
linkcomm/man/print.OCG.Rd
linkcomm/man/newLinkCommsAt.Rd
linkcomm/man/integer.edgelist.Rd
linkcomm/man/weighted.Rd
linkcomm/man/read.OCG.Rd
linkcomm/man/getNestedHierarchies.Rd
linkcomm/man/LinkDensities.Rd
linkcomm/man/plotOCGraph.Rd
linkcomm/man/getAllNestedComm.Rd
linkcomm/man/lesmiserables.Rd
linkcomm/man/plotLinkCommSumm.Rd
linkcomm/man/human_pp.Rd
linkcomm/man/plotLinkCommSummComm.Rd
linkcomm/man/plotLinkCommDend.Rd
linkcomm/man/linkcomm2clustnsee.Rd
linkcomm/man/get.community.overlaps.Rd
linkcomm/man/meta.communities.Rd
linkcomm/man/plotLinkCommMembers.Rd
linkcomm/man/getClusterRelatedness.Rd
linkcomm/man/get.shared.nodes.Rd
linkcomm/man/plot.linkcomm.Rd
linkcomm/man/getCommunityConnectedness.Rd
linkcomm/man/numberEdgesIn.Rd
linkcomm/man/plot.OCG.Rd
linkcomm/man/print.linkcomm.Rd
linkcomm/man/plotLinkCommGraph.Rd
linkcomm/man/corLinkcommCentrality.Rd
linkcomm/man/getEdgesIn.Rd
linkcomm/man/cutDendrogramAt.Rd
linkcomm/man/orderCommunities.Rd
linkcomm/man/getCommunityCentrality.Rd