fixed null model in yule.cov + various things

[ape.git] / ChangeLog

diff --git a/ChangeLog b/ChangeLog
index d659113a7cd989de0357b1303000d0a47674b66b..8ad799a009ac2d7c8469030d915b855691453cfa 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,39 @@
+               CHANGES IN APE VERSION 2.3-1
+
+
+NEW FEATURES
+
+    o There is now a c() method for lists of class "DNAbin".
+
+    o yule.cov() now fits the null model, and its help page has been
+      corrected with respect to this change.
+
+
+BUG FIXES
+
+    o dist.gene() failed on most occasions with the default
+      pairwise.deletion = FALSE.
+
+    o read.tree() failed to read correctly the tree name(s).
+
+    o boot.phylo() now treats correctly data frames.
+
+    o del.gaps() did not copy the rownames of a matrix.
+
+    o A small bug was fixed in CDAM.global().
+
+
+OTHER CHANGES
+
+    o [.multiPhylo and [.DNAbin now respect the original class.
+
+    o Instances of the form class(phy) == "phylo" have been replaced
+      by inherits(phy, "phylo").
+
+    o rcoal() is now faster.
+
+
+
                CHANGES IN APE VERSION 2.3
 
 
@@ -13,6 +49,14 @@ NEW FEATURES
     o The new function makeNodeLabel creates and/or modifies node
       labels in a flexible way.
 
+    o read.tree() and write.tree() have been modified so that they can
+      handle individual tree names.
+
+    o plot.phylo() has a new argument 'edge.lty' that specifies the
+      types of lines used for the edges (plain, dotted, dashed, ...)
+
+    o phymltest() has been updated to work with PhyML 3.0.1.
+
 
 BUG FIXES