final corrections for ape 3.0-6

[ape.git] / NEWS

diff --git a/NEWS b/NEWS
index 46af03fc06ef1fcf9e8a61d37760c26251265397..e90cec15c61f7d4d1bae3e76033142edcfac8b3d 100644 (file)
--- a/NEWS
+++ b/NEWS
@@ -5,13 +5,27 @@ NEW FEATURES
 
     o reorder.phylo() has a new order, "postorder", and a new option
       index.only = TRUE to return only the vector of indices (the tree
-      is unmodified; see ?reorder.phylo for details).
+      is unmodified, see ?reorder.phylo for details).
+
+    o The three new functions node.depth.edgelength, node.height, and
+      node.height.clado make some internal code available from R. See
+      ?node.depth (which was already documented) for details.
 
 
 BUG FIXES
 
     o reorder(, "pruningwise") made R crash if the rows of the edge
-      matrix are in random order.
+      matrix are in random order: this is now fixed.
+
+    o drop.tip() sometimes shuffled node labels (thanks to Rebecca
+      Best for the report).
+
+    o drop.tip(phy, "") returned a tree with zero-length tip labels:
+      it now returns the tree unchanged (thanks to Brian Anacker for
+      the report).
+
+    o plot.phylo() made R crash if the tree has zero-length tip
+      labels: it now returns NULL (thanks again to Brian Anacker).
 
 
 OTHER CHANGES
@@ -22,6 +36,14 @@ OTHER CHANGES
       visible for small trees (n < 1000) but this can be more than
       1000 faster for big trees (n >= 1e4).
 
+    o The attribute "order" of the objects of class "phylo" is now
+      strongly recommended, though not mandatory. Most functions in
+      ape should return a tree with this attribute correctly set.
+
+    o dbd() is now vectorized on both arguments 'x' (number of species
+      in clade) and 't' (clade age) to make likelihood calculations
+      easier and faster.
+
 
 
                CHANGES IN APE VERSION 3.0-5