code clean-up in DNA.R

[ape.git] / Changes

diff --git a/Changes b/Changes
index af1c2187083ded70f820c256c771674fcc0b6eba..aa313f07b306e42b7e1099614677d627a77a8324 100644 (file)
--- a/Changes
+++ b/Changes
@@ -1,3 +1,56 @@
+               CHANGES IN APE VERSION 2.1-3
+
+
+BUG FIXES
+
+    o An error was fixed in the computation of ancestral character
+      states by generalized least squares in ace().
+
+
+
+               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
 
 
@@ -9,6 +62,12 @@ NEW FEATURES
       (thanks to Vladimir Minin for the code).
 
 
+BUG FIXES
+
+    o nuc.div() returned an incorrect value with the default
+      pairwise.deletion = FALSE.
+
+
 OTHER CHANGES
 
     o The internal codes of bionj(), fastme.bal(), and fastme.ols()