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/