Identify and Visualize Significantly Responsive Branches in a Phylogenetic Tree

Provides tools to identify and visualize branches in a phylogenetic tree that are significantly responsive to some intervention, taking as primary inputs a phylogenetic tree (of class phylo) and a data frame (or matrix) of corresponding tip (OTU) labels and p-values.


News

  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.

Reference manual

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install.packages("SigTree")

1.10.6 by John R. Stevens, a year ago


Browse source code at https://github.com/cran/SigTree


Authors: John R. Stevens and Todd R. Jones


Documentation:   PDF Manual  


Task views: Phylogenetics, Especially Comparative Methods


GPL-3 license


Imports ape, phylobase, phyext2, RColorBrewer, phyloseq, graphics, utils, stats, MASS, vegan


See at CRAN