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/