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NEWS
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A revision history for the R package 'linkcomm'.
Author: Alex T. Kalinka (alex.t.kalinka@gmail.com).
linkcomm 1.0-14
===============
- Fixed doi format in DESCRIPTION file.
linkcomm 1.0-13
===============
- Fixed return() parenthesis issue in getOCG.clusters() and read.OCG().
- Fixed getCommunityCentrality() and getClusterRelatedness() issues.
- Updated README; vignette PDF now static.
linkcomm 1.0-12
===============
- Fixed class inherits issues.
linkcomm 1.0-11
===============
- Fixed downwards-incompatibility issue related to the "ward.D" clustering method name change.
linkcomm 1.0-10
===============
- Attempted to fix file access error relating to Sparc Solaris system.
linkcomm 1.0-9
==============
- Improved efficiency of edge.duplicates() function.
- Fixed a small memory-usage bug in linkdensities.cpp.
- Fixed memory leaks in OCG_algorithm.c.
linkcomm 1.0-8
==============
- Fixed a clang-specific bug affecting the calculation of edge similarities.
- Added dynamicTreeCut package to the imports field.
- Added function "meta.communities" to hierarchically cluster link communities and automatically identify clusters using dynamicTreeCut.
- Added function "get.community.overlaps" to find communities that share nodes.
- Added function "get.shared.nodes" to extract the shared nodes between specific sets of communities.
- Updated the vignette.
linkcomm 1.0-7
==============
- Changed dependency from "igraph0" to "igraph".
- Added support for bi-partite networks to "getLinkCommunities".
- Added argument "use.all.edges" to "getLinkCommunities" to allow edge similarities to be calculated for all pairs of edges, not just those sharing a node.
- Added function "linkcomm2clustnsee" to enable the export of clusters to Cytoscape and the Clust&See plug-in.
- Added function "integer.edgelist" to enable conversion of networks into integer edgelists.
- Fixed a bug in "newLinkCommsAt" which prevented the $edges output from being modified.
- Added "fastcluster" to the Suggests field.
- Changed function "getLinkDensities" to "LinkDensities".
linkcomm 1.0-6
==============
- Improved memory usage during the calculation of link densities.
- Added "node.pies" argument to "plotLinkCommGraph" to enable the visualization of nodes as pie charts of edge community membership.
- Included "edge.duplicates" function that finds loops, duplicate and bi-directional edges using a C++ function.
- Added "dist" argument to "getLinkCommunities" to allow the user to specify their own distance matrix.
- Fixed a bug that prevented link dendrograms from rendering correctly when trivial clusters are included.
- Fixed a bug that that led to summary plots rendering incorrectly if plotted sequentially on the same graphics device.
- Modified "plotOCGraph" so that node labels overlay node symbols.
- Changed Windows progress indicators to percentages.
- Updated vignette documentation to highlight node pie plots.
linkcomm 1.0-5
==============
- Added functions "getOCG.clusters", "plot.OCG", "read.OCG", "print.OCG", "numberEdgesIn", and "which.communities" to enable a port of the Overlapping Cluster Generator (OCG) algorithm into the linkcomm package.
- Fixed a bug that prevented linkcomm summary plots from rendering correctly on different sized graphics devices.
- Updated the vignette documentation to include information on the OCG algorithm and how to use it.
- Changed dependency from "igraph" to "igraph0" to avoid incompatibilites, and included "utils" in the imported package list.
linkcomm 1.0-4
==============
- Added functions "getEdgesIn" and "graph.feature" and modified "getNodesIn" to allow customization of network visualizations.
- Added "verbose" option to "getLinkCommunities", "plotLinkCommDend", and "plotLinkCommSummary".
- Added "directed" logical component to the "linkcomm" object.
- Fixed a bug that led to loss of the partition density axis in "summary" plots.
- Fixed a bug that prevented the correct colouring of dendrograms when several clusters merge at the same height.
- Updated vignette and manual documentation.
linkcomm 1.0-3
==============
- Fixed bug that prevented partition density summary plots from being saved correctly as PDFs or other file types.
- Updated citation information.
- Updated documentation.
linkcomm 1.0-2
==============
- Fixed Windows-specific bug that prevented progress indicators from working.
- Included a start-up message about documentation, demos, and read-write directory permissions.
- Added a note about bidirectional edges in directed networks to the documentation for "getLinkCommunities".
linkcomm 1.0-1
==============
- Windows binaries released after fixing bugs related to file reading and writing.
linkcomm 1.0-0
==============
- Function-complete version of linkcomm uploaded onto CRAN.