CHANGES IN SigTree VERSION 1.10.6

BUG FIXES

    o Adjusted function export.inherit to handle trees with named nodes
	
    o Revised .C() calls to avoid fail check upon pending update to ape package.
	  No change in SigTree package functionality.


OTHER CHANGES

    o Updated citation and package vignette.


	  CHANGES IN SigTree VERSION 1.10.5

BUG FIXES

    o Added a numerical stability correction to adonis.tree

OTHER CHANGES

    o Updated citation and package vignette.


	  CHANGES IN SigTree VERSION 1.10.4

NEW FEATURES

    o Added ability to test for distance-based dependence
      (adonis.tree function), and account for dependence among
      p-values (test="Hartung" in main functions like plotSigTree).

    o Updated export.figtree function to use hexadecimal
      colors, based on changes to recent FigTree version.
      (Now fully compatible with FigTree version 1.4.3)

OTHER CHANGES

    o Updated citation and package vignette.



	  CHANGES IN SigTree VERSION 1.10.3

OTHER CHANGES

    o Updated citation and package vignette.


	  CHANGES IN SigTree VERSION 1.10.2

NEW FEATURES

    o Included package vignette (removed in version 1.8).
	


	  CHANGES IN SigTree VERSION 1.10.1

OTHER CHANGES

    o Formalized package dependence on the "phyext2" package,
	  which is now in CRAN.



	  CHANGES IN SigTree VERSION 1.9

OTHER CHANGES

    o With permission of phyext package's former maintainer,
	  made temporary copy package phyext2, and re-built package.



		CHANGES IN SigTree VERSION 1.8

NEW FEATURES

    o Removed package vignette, to provide faster package checking.
	
OTHER CHANGES

    o Minor updates to pass R CMD check


		CHANGES IN SigTree VERSION 1.7

NEW FEATURES

    o N/A
	
BUG FIXES

    o N/A

OTHER CHANGES

    o Updated vignette and citation information to reflect
	  submitted manuscript.  Also added brief discussion
	  of multiple treatment groups to vignette.
	



		CHANGES IN SigTree VERSION 1.6

NEW FEATURES

    o N/A
	
BUG FIXES

    o The ape package's which.edge() function was rewritten
	  in ape version 3.1-3 to allow trees not in clade-wise order,
	  and this new version caused SigTree's export.figtree() function
	  to stall.  The export.figtree(), plotSigTree(), and export.inherit()
	  functions of SigTree all now have an added step to reorder
	  the tree in clade-wise order, and rather than call the new
	  which.edge() function inside a loop (as before), 
	  export.figtree() instead accomplishes the same result (as the call
	  to the old which.edge() function) by an efficient call 
	  of the match() function.

OTHER CHANGES

    o N/A
	

		CHANGES IN SigTree VERSION 1.5

NEW FEATURES

    o N/A
	
BUG FIXES

    o N/A

OTHER CHANGES

    o Cleaned up NAMESPACE and DESCRIPTION files
	  (using Imports in DESCRIPTION and multiple import() 
	  in correct order in NAMESPACE to appease CRAN)

    o Updated SigTree.c to copy changes in plot_phylo.c from
	  ape package; also updated .C() calls in plotphylo2 function
	  to reflect these changes.  This was to appease CRAN,
	  as ape changes in R version 3.1.0 had caused problems
	  with SigTree.
	
	
		CHANGES IN SigTree VERSION 1.4

NEW FEATURES

    o N/A
	
BUG FIXES

    o N/A

OTHER CHANGES

    o Modified title in DESCRIPTION file
	
    o Moved vignette file to make compatible with CRAN
	
	
	

		CHANGES IN SigTree VERSION 1.3

NEW FEATURES

    o N/A
	
BUG FIXES

    o N/A

OTHER CHANGES

    o License is now GPL-3 rather than restricted
	  for non-academic or commercial users (to make
	  CRAN-compatible).

	o Included functions from ape package so that all 
	  .C calls remain within SigTree (to make CRAN-
	  compatible).
	
	
	  CHANGES IN SigTree VERSION 1.2

NEW FEATURES

    o Edge-specific coloring (as in FigTree) is now allowed
	  using the "branch='edge'" option in plotSigTree
	  and export.figtree.  Corresponding branch labels
	  (edge or node specific) added using "branch.label"
	  argument.

	o Root edge addition (and coloring) now allowed by
	  plotSigTree using "root.edge" argument.

	o Branch labels (for either edge or node, as controlled
	  by "branch" argument) made to agree between
	  plotSigTree and export.inherit functions.

BUG FIXES

    o N/A

OTHER CHANGES

    o For 1-sided p-values and a named color palette like 'RdBu',
	  the default mid-range color is now a medium grey for 
	  easier viewing (in plotSigTree and export.figtree).

	  

 	   CHANGES IN SigTree VERSION 1.1


NEW FEATURES

    o The default multiple testing adjustment is now 
	  "method='hommel'".

BUG FIXES

    o N/A

OTHER CHANGES

    o The package now has a tutorial vignette, accessible using
	  "vignette('SigTree')".
	 
	o The function 'plot.color' has been re-named 'plotSigTree'
	  to resolve S3 class issues.