changed rtree and rcoal

[ape.git] / ChangeLog

diff --git a/ChangeLog b/ChangeLog
index 4f860f9260e7a1a132c40f8bc280b3a6174ae14c..46aa1e3b065d760852511aa9ecfcea8b573e1f01 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,26 @@
+               CHANGES IN APE VERSION 2.4-1
+
+
+NEW FEATURES
+
+    o rtree() and rcoal() now accept a numeric vector for the 'br'
+      argument.
+
+
+BUG FIXES
+
+    o bind.tree() failed when 'y' had no root edge.
+
+    o read.nexus() shuffled tip labels when the trees have no branch
+      lengths and there is a TRANSLATE block.
+
+    o plot.multiPhylo() crashed R when plotting a list of trees with
+      "compressed tip labels".
+
+    o write.nexus() did not translate the taxa names when asked for.
+
+
+
                CHANGES IN APE VERSION 2.4
 
 
@@ -15,6 +38,9 @@ BUG FIXES
     o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
       the tree: the argument is now ignored.
 
+    o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
+      Young for the fix).
+
 
 OTHER CHANGES
 
@@ -28,6 +54,10 @@ OTHER CHANGES
     o The argument 'adj' in [node][tip][edge]labels() now works when
       using 'pie' or 'thermo'.
 
+    o A more informative message error is now returned by dist.dna() when
+      'model' is badly specified (partial matching of this argument is
+      done now).
+
     o Deprecated functions are now listed in a help page: see
       help("ape-defunct") with the quotes.
 
@@ -37,6 +67,8 @@ DEPRECATED & DEFUNCT
     o The functions heterozygosity, nuc.div, theta.h, theta.k and
       theta.s have been moved from ape to pegas.
 
+    o The functions mlphylo, DNAmodel and sh.test have been removed.
+
 
 
                CHANGES IN APE VERSION 2.3-3
@@ -197,7 +229,7 @@ BUG FIXES
 
 OTHER CHANGES
 
-    o There is now a general help page displayed with '?ape' 
+    o There is now a general help page displayed with '?ape'.