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. 


