2015-04-22: 1.63 . Bugfix fixes integer overflow problems with dendrograms that have more than aout 46k singletons . Bugfix makes handling externalBranchSplitFnc more robust . ExternalBranchSplitFnc can now be supplied as a simple vector of function names, rather than a list. . Fractional deepSplit is now accepted and will lead to linearly interpolated settings of minGap and maxCoreScatter 2014-05-07: 1.62 . New arguments minSplitHeight and minSplitAbsHeight allow the user to specify a height below which branches will automatically be merged. 2013-11-22: 1.61 . New argument externalSplitFncNeedsDistance can prevent unnecessary passing of the dissimilarity (distance) matrix to the external split functions (if they are used at all) 2013-11-19: 1.60-3 . A separate error/bug that could result in incorrectly interpreted cluster assignment fixed 2013-11-16: 1.60-2 . Occasional error fixed that occurred when only one cluster is present 2013-11-03: 1.60-1 . Occasional error crash in the function fixed (reported by Axel Kohei Glaubitz). 2013-08-20: 1.60 . Major clean-up: all expr- and stability-related merging criteria are removed. Instead, these should be supplied via the externalBranchSplitFnc. This cleans up the dynamic tree cut and puts the correlation network-specific criteria where they belong, namely into the WGCNA package. . Multiple externalBranchSplitFnc can be given. . Argument externalSplitThreshold is now called minExternalSplit. 2013-07-24: 1.55 . New arguments externalBranchSplitFnc, externalSplitThreshold, and externalSplitOptions let the users supply their own branch merging criterion for cutreeHybrid. 2011-01-26: 1.51 . Minor speed and efficiency gain via internal re-structuring . Bug fix: useMedoids = TRUE spurious error fixed 2010-12-10: 1.50 . Major new functionality: branch merging criteria expanded to include: 1. module split (a measure of separation between the two branches), 2. correlation of eigennodes, 3. similarity measure based on clustering of re-sampled data Criteria 1 and 2 are only applicable to correlation networks. Criterion 3 assumes that a stability study has been carried out before the final module identification. All three new criteria are optional and ignored if the requisite inputs are not supplied. 2009-11-22: 1.21 . new function merge2Clusters 2009-01-29: 1.20 . Support for cluster trimming has been dropped . New functionality: PAM stage can now optionally respect the dendrogram. If this option is set, for each object PAM stage will only consider those clusters that are on the same branch as the object being PAMed. In other words, an object can only be asigned by PAM to one of the clusters lying below the object on the branch on which the object is merged. Intuitively, this should produce a label assignment that is more compatible with the dendrogram. It will also prevent assignment of far outlying objects, resulting in more unassigned objects and cleaner, tighter clusters. 2008-06-12: . Changed verbose output from stage 1,2 to Tree Cut, PAM stage . distM is only modified (copied) if necessary 2008-06-03: 1.12 . labelUnlabeled is now deprecated and replaced by (renamed to) pamStage. . deepSplit range extended to 0 through 4 2008-04-03: cleanup: function .assignModuleColor commented out to remove a R CMD check warning. 2008-03-12: 1.11-3 another bug in interpretation of deepSplit fixed; in particular, the default now works. 2008-03-07: 1.11-2 bug in interpretation of deepSplit fixed 2008-03-05: 1.11-1 dynamicHybrid: When number of merges below the cut is smaller than minClusterSize, simply return with all labels=0 instead of throwing an error. 2008-02-19: 1.11 change default cutHeight from max(dendro$height) to 99% of the range of between maximum and 5th percentile (from minimum) of dendro$height change in printFlush: use cat, not print to get rid of the [1] " leading the output 2008-02-16: 1.10-02 cutreeDynamic: if method=="hybrid" and distM not given, issue a warning and default to method="tree" 2007-12-11: 1.10 cutreeHybrid: distM is a mandatory parameter now (no more NULL default) since it is used in stage 1 as well. 2007-11-22: 1.09 cutreeDynamicTree: bug where the last element on the dendrogram remained unlabeled is fixed by Bin Zhang. 2007-11-13: 1.09 Changes in Dynamic Tree: minimum significant forward runlength is now set as a fraction (1/3)+1 of the minimum cluster size; minAttachModuleSize is now 2*minModuleSize instead of a hardcoded number 100. 2007-09-17 Updated URL in description to http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting/