add delta.plot + clarify doc in write.tree.Rd

[ape.git] / ChangeLog

diff --git a/ChangeLog b/ChangeLog
index 8b30895d882d170cbf02c92d11cc3db1a5ce12d3..0809491f4a2177b13b2a74e2711042de2e33df87 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,24 @@
+               CHANGES IN APE VERSION 2.5
+
+
+NEW FEATURES
+
+    o The new functions rTraitCont and rTraitDisc simulate continuous and
+      discrete traits under a wide range of evolutionary models.
+
+    o The new function delta.plot does a delta plot following Holland et
+      al. (2002, Mol. Biol. Evol. 12:2051).
+
+    o add.scale.bar() has a new option 'ask' to draw interactively.
+
+
+BUG FIXES
+
+    o add.scale.bar() drew the bar outside the plotting region with the
+      default options with unrooted or radial trees.
+
+
+
                CHANGES IN APE VERSION 2.4-1
 
 
@@ -6,6 +27,11 @@ NEW FEATURES
     o rtree() and rcoal() now accept a numeric vector for the 'br'
       argument.
 
+    o vcv() is a new generic function with methods for the classes "phylo"
+      and "corPhyl" so that it is possible to calculate the var-cov matrix
+      for "transformation models". vcv.phylo() can still be used for trees
+      of class "phylo"; its argument 'cor' has been renamed 'corr'.
+
 
 BUG FIXES
 
@@ -14,14 +40,24 @@ BUG FIXES
     o read.nexus() shuffled tip labels when the trees have no branch
       lengths and there is a TRANSLATE block.
 
+    o read.nexus() does not try to translate node labels if there is a
+      translation table in the NEXUS file. See ?read.nexus for a
+      clarification on this behaviour.
+
     o plot.multiPhylo() crashed R when plotting a list of trees with
-      "compressed tip labels".
+      compressed tip labels.
 
     o write.nexus() did not translate the taxa names when asked for.
 
     o plot.phylo(type = "fan") did not rotate the tip labels correctly
       when the tree has branch lengths.
 
+    o ace(type = "continuous", method = "ML") now avoids sigma² being
+      negative (which resulted in an error).
+
+    o nj() crashed with NA/NaN in the distance matrix: an error in now
+      returned.
+
 
 
                CHANGES IN APE VERSION 2.4