X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=ChangeLog;h=53f4a6209d15230d3dbb36932f60b65c3c173daa;hb=57c9d4fd10a4449c27c65873eaf9315b5b7ed874;hp=8db603f95885fcfddc68a3bc52b475f70953838c;hpb=071f848fadb1be486490a10f3de8324d3aaa5cb7;p=ape.git

diff --git a/ChangeLog b/ChangeLog
index 8db603f..53f4a62 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,21 +1,61 @@
+		CHANGES IN APE VERSION 2.6-3
+
+
+BUG FIXES
+
+    o as.hclust.phylo() now returns an error with unrooted trees.
+
+
+
 		CHANGES IN APE VERSION 2.6-2
 
 
 NEW FEATURES
 
+    o Two new functions, pic.ortho and varCompPhylip, implements the
+      orthonormal contrasts of Felsenstein (2008, Am Nat, 171:713). The
+      second function requires Phylip to be installed on the computer.
+
     o bd.ext() has a new option conditional = TRUE to use probabilities
       conditioned on no extinction for the taxonomic data.
 
 
+BUG FIXES
+
+    o write.tree() failed to output correctly tree names.
+
+    o dist.nodes() returned duplicated column(s) with unrooted and/or
+      multichotomous trees.
+
+    o mcmc.popsize() terminated unexpectedly if the progress bar was
+      turned off.
+
+    o prop.part(x) made R frozen if 'x' is of class "multiPhylo".
+
+    o Compilation under Mandriva failed (thanks to Jos Käfer for the fix).
+
+    o drop.tip() shuffled tip labels with subtree = TRUE or trim.internal
+      = FALSE.
+
+    o Objects returned by as.hclust.phylo() failed when analysed with
+      cutree() or rect.hclust().
+
+    o write.tree() did not output correctly node labels (thanks to Naim
+      Matasci and Jeremy Beaulieu for the fix).
+
+    o ace(type = "discrete") has been improved thanks to Naim Marasci and
+      Jeremy Beaulieu.
+
+
 
 		CHANGES IN APE VERSION 2.6-1
 
 
 NEW FEATURES
 
-    o The new speciesTree calculates the species tree from a set of gene
-      trees. Several methods are available including maximum tree and
-      shallowest divergence tree.
+    o The new function speciesTree calculates the species tree from a set
+      of gene trees. Several methods are available including maximum tree
+      and shallowest divergence tree.
 
 
 BUG FIXES