a collection of bug fixes

[ape.git] / ChangeLog

diff --git a/ChangeLog b/ChangeLog
index dbe6fe09acbc5774976984d7345941ff816c3597..275ad2f7bd6dcd14f8d008e4515b8cb58bc9182c 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,28 @@
+               CHANGES IN APE VERSION 2.3-3
+
+
+BUG FIXES
+
+    o add.scale.bar() always drew a horizontal bar.
+
+    o zoom() shuffled tips with unrooted trees.
+
+    o write.nexus() failed to write correctly trees with a "TipLabel"
+      attribute.
+
+    o rcoal() failed to compute branch lengths with very large n.
+
+    o A small bug was fixed in compar.cheverud() (thanks to Michael
+      Phelan for the fix).
+
+    o seg.sites() failed when passing a vector.
+
+    o drop.tip() sometimes shuffled tip labels.
+
+    o root() shuffled node labels with 'resolve.root = TRUE'.
+
+
+
                CHANGES IN APE VERSION 2.3-2
 
 
@@ -16,6 +41,10 @@ BUG FIXES
     o vcv.phylo() did not work correctly when the tree is in
       "pruningwise" order.
 
+    o nj() did not handle correctly distance matrices with many 0's.
+      The code has also been significantly improved: 7, 70, 160 times
+      faster with n = 100, 500, 1000, respectively.
+
 
 
                CHANGES IN APE VERSION 2.3-1