faster nj()!!!

[ape.git] / ChangeLog

diff --git a/ChangeLog b/ChangeLog
index d76cb8db266152314af17f8b51b17a2239a74428..c3a2a844a0e098a57e65e6d93e27e1ce3439377b 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,6 +1,43 @@
+               CHANGES IN APE VERSION 2.3-2
+
+
+BUG FIXES
+
+    o all.equal.phylo() did not compare unrooted trees correctly.
+
+    o dist.topo(... method = "PH85") did not treat unrooted trees
+      correctly (thanks to Tim Wallstrom for the fix).
+
+    o root() sometimes failed to test for the monophyly of the
+      outgroup correctly.
+
+    o extract.clade() sometimes included too many edges.
+
+    o vcv.phylo() did not work correctly when the tree is in
+      "pruningwise" order.
+
+    o nj() did not handle correctly distance matrices with many 0's.
+      The code has also been significantly improved: 7, 70, 160 times
+      faster with n = 100, 500, 1000, respectively.
+
+
+
                CHANGES IN APE VERSION 2.3-1
 
 
+NEW FEATURES
+
+    o The new function is.monophyletic tests the monophyly of a group.
+
+    o There is now a c() method for lists of class "DNAbin".
+
+    o yule.cov() now fits the null model, and its help page has been
+      corrected with respect to this change.
+
+    o drop.tip() has a new option 'rooted' to force (or not) a tree
+      to be treated as (un)rooted.
+
+
 BUG FIXES
 
     o dist.gene() failed on most occasions with the default
@@ -10,6 +47,18 @@ BUG FIXES
 
     o boot.phylo() now treats correctly data frames.
 
+    o del.gaps() did not copy the rownames of a matrix.
+
+    o A small bug was fixed in CDAM.global().
+
+    o ace() failed with large data sets. Thanks to Rich FitzJohn for
+      the fix. With other improvements, this function is now about 6
+      times faster.
+
+    o write.tree() failed with objects of class "multiPhylo".
+
+    o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
+
 
 OTHER CHANGES
 
@@ -18,6 +67,13 @@ OTHER CHANGES
     o Instances of the form class(phy) == "phylo" have been replaced
       by inherits(phy, "phylo").
 
+    o rcoal() is now faster.
+
+
+DEPRECATED & DEFUNCT
+
+    o klastorin() has been removed.
+
 
 
                CHANGES IN APE VERSION 2.3