X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=ChangeLog;h=275ad2f7bd6dcd14f8d008e4515b8cb58bc9182c;hb=3ad385892d75db5c646c92f0f631ae9c5e3da4f6;hp=accd346a9138052ee8dac70c48ee7bc5addf9c77;hpb=5b88d637fc5ae12085847b35271ffa82ccc3b221;p=ape.git

diff --git a/ChangeLog b/ChangeLog
index accd346..275ad2f 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,10 +1,67 @@
+		CHANGES IN APE VERSION 2.3-3
+
+
+BUG FIXES
+
+    o add.scale.bar() always drew a horizontal bar.
+
+    o zoom() shuffled tips with unrooted trees.
+
+    o write.nexus() failed to write correctly trees with a "TipLabel"
+      attribute.
+
+    o rcoal() failed to compute branch lengths with very large n.
+
+    o A small bug was fixed in compar.cheverud() (thanks to Michael
+      Phelan for the fix).
+
+    o seg.sites() failed when passing a vector.
+
+    o drop.tip() sometimes shuffled tip labels.
+
+    o root() shuffled node labels with 'resolve.root = TRUE'.
+
+
+
+		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
 
@@ -15,6 +72,18 @@ 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
 
@@ -23,7 +92,12 @@ OTHER CHANGES
     o Instances of the form class(phy) == "phylo" have been replaced
       by inherits(phy, "phylo").
 
-    o rcoal() should be faster.
+    o rcoal() is now faster.
+
+
+DEPRECATED & DEFUNCT
+
+    o klastorin() has been removed.