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
 
 
                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
       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
 
 
 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.
 
       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.
 
     o The files ape-defunct.R and ape-defunct.Rd, which have not been
       modified for almost two years, have been removed.