final corrections for ape 3.0-6

[ape.git] / NEWS

diff --git a/NEWS b/NEWS
index e4235a9a0cf397de73f5f19215f6401525e98f96..e90cec15c61f7d4d1bae3e76033142edcfac8b3d 100644 (file)
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,69 @@
+               CHANGES IN APE VERSION 3.0-6
+
+
+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).
+
+    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: 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
+
+    o dist.nodes() is now 6 to 10 times faster.
+
+    o reorder(, "cladewise") is now faster. The change is not very
+      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
+
+
+BUG FIXES
+
+    o ace() should better catch errors when SEs cannot be computed.
+
+
+OTHER CHANGES
+
+    o write.dna(format = "fasta") now conforms more closely to the
+      FASTA standard thanks to François Michonneau.
+
+    o print.DNAbin() does not print base compositions if there are more
+      than one million nucleotides.
+
+
+
                CHANGES IN APE VERSION 3.0-4
 
 
@@ -7,8 +73,7 @@ BUG FIXES
       tabulations instead of white spaces.
 
     o read.dna() failed to read Phylip or Clustal files with less than
-      10 nucleotides failed. (See other changes in this function
-      below.)
+      10 nucleotides. (See other changes in this function below.)
 
 OTHER CHANGES
 
@@ -16,6 +81,8 @@ OTHER CHANGES
       taxa names and the sequences (whatever the length of taxa
       names). write.dna() now follows the same rule.
 
+    o The option 'seq.names' of read.dna has been removed.
+
     o The files ape-defunct.R and ape-defunct.Rd, which have not been
       modified for almost two years, have been removed.