linkcomm: Tools for Generating, Visualizing, and Analysing Link Communities in Networks
Version 1.0-11

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.

Browse man pages Browse package API and functions Browse package files

AuthorAlex T. Kalinka <alex.t.kalinka@gmail.com>, with contributions from Alain Guenoche
Date of publication2014-08-13 19:00:50
MaintainerAlex T. Kalinka <alex.t.kalinka@gmail.com>
LicenseGPL (>= 2)
Version1.0-11
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("linkcomm")

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

Functions

LinkDensities Man page Source code
corLinkcommCentrality Man page Source code
cutDendrogramAt Man page Source code
edge.duplicates Man page Source code
get.community.overlaps Man page Source code
get.shared.nodes Man page Source code
getAllNestedComm Man page Source code
getClusterRelatedness Man page Source code
getCommunityCentrality Man page Source code
getCommunityConnectedness Man page Source code
getCommunityMatrix Man page Source code
getEdgesIn Man page Source code
getLinkCommunities Man page Source code
getNestedHierarchies Man page Source code
getNodesIn Man page Source code
getOCG.clusters Man page Source code
getUpperTriIndices Source code
graph.feature Man page Source code
human_pp Man page
integer.edgelist Man page Source code
karate Man page
layout.spencer.circle Man page Source code
lesmiserables Man page
linkcomm Man page
linkcomm-package Man page
linkcomm2clustnsee Man page Source code
linkcomm2cytoscape Man page Source code
meta.communities Man page Source code
newLinkCommsAt Man page Source code
nodePie Source code
numberEdgesIn Man page Source code
onAttach Source code
orderCommunities Man page Source code
plot.OCG Man page Source code
plot.linkcomm Man page Source code
plotLinkCommDend Man page Source code
plotLinkCommGraph Man page Source code
plotLinkCommMembers Man page Source code
plotLinkCommSumm Man page Source code
plotLinkCommSummComm Man page Source code
plotOCGraph Man page Source code
pp_rnapol Man page
print.OCG Man page Source code
print.linkcomm Man page Source code
read.OCG Man page Source code
weighted Man page
which.communities Man page Source code

Files

inst
inst/CITATION
inst/doc
inst/doc/linkcomm.Rnw
inst/doc/linkcomm.R
inst/doc/linkcomm.pdf
src
src/linkcomm_functions.cpp
src/linkcommhclust_order.cpp
src/linkcomm_linkdensities.cpp
src/linkcomm_hclust.cpp
src/OCG_algorithm.c
src/edge_duplicates.cpp
src/read_OCG.cpp
src/linkcomm_edgesims_all.cpp
src/linkcomm_edgesims.cpp
NAMESPACE
demo
demo/linkcomm.R
demo/00Index
NEWS
data
data/networks.rda
R
R/linkcomm_plotting.R
R/linkcomm_misc.R
R/linkcomm_main.R
R/OCG_main.R
vignettes
vignettes/nodepie_linkcomm.pdf
vignettes/graph_layout_examples.pdf
vignettes/custom_graphs.pdf
vignettes/linkcomm.Rnw
vignettes/networks.rda
vignettes/cluster_relatedness.pdf
vignettes/ocg_lesmis.pdf
vignettes/fig1_vignette.pdf
MD5
build
build/vignette.rds
DESCRIPTION
man
man/getOCG.clusters.Rd
man/edge.duplicates.Rd
man/getLinkCommunities.Rd
man/getNodesIn.Rd
man/linkcomm2cytoscape.Rd
man/which.communities.Rd
man/layout.spencer.circle.Rd
man/getCommunityMatrix.Rd
man/linkcomm-package.Rd
man/graph.feature.Rd
man/karate.Rd
man/pp_rnapol.Rd
man/print.OCG.Rd
man/newLinkCommsAt.Rd
man/integer.edgelist.Rd
man/weighted.Rd
man/read.OCG.Rd
man/getNestedHierarchies.Rd
man/LinkDensities.Rd
man/plotOCGraph.Rd
man/getAllNestedComm.Rd
man/lesmiserables.Rd
man/plotLinkCommSumm.Rd
man/human_pp.Rd
man/plotLinkCommSummComm.Rd
man/plotLinkCommDend.Rd
man/linkcomm2clustnsee.Rd
man/get.community.overlaps.Rd
man/meta.communities.Rd
man/plotLinkCommMembers.Rd
man/getClusterRelatedness.Rd
man/get.shared.nodes.Rd
man/plot.linkcomm.Rd
man/getCommunityConnectedness.Rd
man/numberEdgesIn.Rd
man/plot.OCG.Rd
man/print.linkcomm.Rd
man/plotLinkCommGraph.Rd
man/corLinkcommCentrality.Rd
man/getEdgesIn.Rd
man/cutDendrogramAt.Rd
man/orderCommunities.Rd
man/getCommunityCentrality.Rd
linkcomm documentation built on May 19, 2017, 7:04 p.m.