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.length, node.height, and
+ node.height.clado make some internal code available from R. See
+ ?node.depth (which was already available and 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.
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