X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Changes;h=3d1da0783a81034682838af2c211a3aa44cfbf4e;hb=99df51c79eb9c42eaffff0694b3b07e42282217f;hp=58e0ddbd99fee2c39750d7e59e7923d6369b7fd9;hpb=6dfbab243973c0c3fa2e6d02b190aefbe5a67280;p=ape.git

diff --git a/Changes b/Changes
index 58e0ddb..3d1da07 100644
--- a/Changes
+++ b/Changes
@@ -1,3 +1,133 @@
+		CHANGES IN APE VERSION 2.2-1
+
+
+NEW FEATURES
+
+    o The new function del.gaps() removes insertion gaps ("-") in a
+      set of DNA sequences.
+
+
+BUG FIXES
+
+    o root() failed with resolve.root = TRUE when the root was already
+      the specified root.
+
+    o Several bugs were fixed in mlphylo().
+
+
+OTHER CHANGES
+
+    o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
+      Minin.
+
+
+
+		CHANGES IN APE VERSION 2.2
+
+
+NEW FEATURES
+
+    o Four new functions have been written by Damien de Vienne for the
+      graphical exploration of large trees (cophyloplot, subtrees,
+      subtreeplot), and to return the graphical coordinates of tree
+      (without plotting).
+
+    o The new functions corPagel and corBlomberg implement the Pagel's
+      "lambda" and Blomberg et al.'s "ACDC" correlation structures.
+
+    o chronopl() has been improved and gains several options: see its
+      help page for details.
+
+    o boot.phylo() has now an option 'trees' to possibly return the
+      bootstraped trees (the default is FALSE).
+
+    o prop.part() has been improved and should now be faster in all
+      situations.
+
+
+BUG FIXES
+
+    o read.dna() failed if "?" occurred in the first 10 sites of the
+      first sequence.
+
+    o The x/y aspect of the plot is now respected when plotting a
+      circular tree (type = "r" or "f").
+
+    o Drawing the tip labels sometimes failed when plotting circular
+      trees.
+
+    o zoom() failed when tip labels were used instead of their numbers
+      (thanks to Yan Wong for the fix).
+
+    o drop.tip() failed with some trees (fixed by Yan Wong).
+
+    o seg.sites() failed with a list.
+
+    o consensus() failed in some cases. The function has been improved
+      as well and is faster.
+
+
+
+		CHANGES IN APE VERSION 2.1-3
+
+
+BUG FIXES
+
+    o A bug in read.nexus() made the Windows R-GUI crash.
+
+    o An error was fixed in the computation of ancestral character
+      states by generalized least squares in ace().
+
+    o di2multi() did not modify node labels correctly.
+
+    o multi2di() failed if the tree had its attribute "order" set to
+      "cladewise".
+
+
+
+		CHANGES IN APE VERSION 2.1-2
+
+
+NEW FEATURES
+
+    o There three new methods for the "multiPhylo" class: str, $,
+      and [[.
+
+    o root() gains the options 'node' and 'resolve.root'
+      (FALSE by default) as well as its code being improved.
+
+    o mltt.plot() has now an option 'log' used in the same way
+      than in plot.default().
+
+
+BUG FIXES
+
+    o mltt.plot() failed to display the legend with an unnamed
+      list of trees.
+
+    o nodelabels() with pies now correcly uses the argument
+      'cex' to draw symbols of different sizes (which has
+      worked already for thermometers).
+
+    o read.nexus() generally failed to read very big files.
+
+
+OTHER CHANGES
+
+    o The argument 'family' of compar.gee() can now be a function
+      as well as a character string.
+
+    o read.tree() and read.nexus() now return an unnamed list if
+      'tree.names = NULL'.
+
+    o read.nexus() now returns a modified object of class "multiPhylo"
+      when there is a TRANSLATE block in the NEXUS file: the individual
+      trees have no 'tip.label' vector, but the list has a 'TipLabel'
+      attribute. The new methods '$' and '[[' set these elements
+      correctly when extracting trees.
+
+
+
 		CHANGES IN APE VERSION 2.1-1
 
 
@@ -69,7 +199,7 @@ BUG FIXES
 OTHER CHANGES
 
     o The code of mlphylo() has almost entirely rewritten, and should
-      much stabler now. The options have been also greatly simplified
+      be much stabler. The options have been also greatly simplified
       (see ?mlphylo and ?DNAmodel for details).
 
     o The internal function nTips has been renamed klastorin_nTips.