X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=ChangeLog;h=efef3ba6cedea36dba17a9e51cb601bab081a324;hb=7e78dcfcf1bca3d6aaca7ae92ab0f4fb3d9cc711;hp=6e2f4f15ac1ac7ee4619f2f18504019c1227f0b3;hpb=34f56710584c96664cbdcc2f9586af02b6e849bd;p=ape.git

diff --git a/ChangeLog b/ChangeLog
index 6e2f4f1..efef3ba 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,9 +1,96 @@
+		CHANGES IN APE VERSION 2.3-1
+
+
+NEW FEATURES
+
+    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.
+
+
+BUG FIXES
+
+    o dist.gene() failed on most occasions with the default
+      pairwise.deletion = FALSE.
+
+    o read.tree() failed to read correctly the tree name(s).
+
+    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.
+
+
+OTHER CHANGES
+
+    o [.multiPhylo and [.DNAbin now respect the original class.
+
+    o Instances of the form class(phy) == "phylo" have been replaced
+      by inherits(phy, "phylo").
+
+    o rcoal() is now faster.
+
+    o klastorin() has been removed.
+
+
+
+		CHANGES IN APE VERSION 2.3
+
+
+NEW FEATURES
+
+    o The new functions CADM.global and CADM.post, contributed by
+      Pierre Legendre, test the congruence among several distance
+      matrices.
+
+    o The new function yule.time fits a user-defined time-dependent
+      Yule model by maximum likelihood.
+
+    o The new function makeNodeLabel creates and/or modifies node
+      labels in a flexible way.
+
+    o read.tree() and write.tree() have been modified so that they can
+      handle individual tree names.
+
+    o plot.phylo() has a new argument 'edge.lty' that specifies the
+      types of lines used for the edges (plain, dotted, dashed, ...)
+
+    o phymltest() has been updated to work with PhyML 3.0.1.
+
+
+BUG FIXES
+
+    o drop.tip() shuffled tip labels in some cases.
+
+    o drop.tip() did not handle node.label correctly.
+
+    o is.ultrametric() now checks the ordering of the edge matrix.
+
+    o ace() sometimes returned negative values of likelihoods of
+      ancestral states (thanks to Dan Rabosky for solving this long
+      lasting bug).
+
+
+OTHER CHANGES
+
+    o The data set xenarthra has been removed.
+
+
+
 		CHANGES IN APE VERSION 2.2-4
 
 BUG FIXES
 
     o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
-      now fixed. (thanks to Peter Wragg for the fix!)
+      now fixed. (Thanks to Peter Wragg for the fix!)
+
+    o A warning message occurred for no reason with ace(method="GLS").
 
 
 OTHER CHANGES