
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/


