updated reorder.phylo.Rd

[ape.git] / NEWS

diff --git a/NEWS b/NEWS
index e4235a9a0cf397de73f5f19215f6401525e98f96..46af03fc06ef1fcf9e8a61d37760c26251265397 100644 (file)
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,47 @@
+               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).
+
+
+BUG FIXES
+
+    o reorder(, "pruningwise") made R crash if the rows of the edge
+      matrix are in random order.
+
+
+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).
+
+
+
+               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 +51,7 @@ 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 +59,8 @@ 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.