new files by Damien + a few bug fixes

[ape.git] / Changes

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+++ b/Changes
@@ -1,11 +1,51 @@
+               CHANGES IN APE VERSION 2.1-4
+
+
+NEW FEATURES
+
+    o Four new functions have been written by Damien de Vienne for the
+      graphical exploration of large trees (plot.cophylo, subtrees,
+      subtreeplot), and to return the graphical coordinates of tree
+      (without plotting).
+
+
+BUG FIXES
+
+    o read.dna() failed if "?" occurred in the first 10 sites of the
+      first sequence.
+
+    o The x/y aspect of the plot is now respected when plotting a
+      circular tree (type = "r" or "f").
+
+    o Drawing the tip labels sometimes failed when plotting circular
+      trees.
+
+    o zoom() failed when tip labels were used instead of their numbers
+      (thanks to Yan Wong for the fix).
+
+
+OTHER CHANGES
+
+    o chronopl() has been improved and gains several options: see its
+      help page for details.
+
+
+
                CHANGES IN APE VERSION 2.1-3
 
 
 BUG FIXES
 
+    o A bug in read.nexus() made the Windows R-GUI crash.
+
     o An error was fixed in the computation of ancestral character
       states by generalized least squares in ace().
 
+    o di2multi() did not modify node labels correctly.
+
+    o multi2di() failed if the tree had its attribute "order" set to
+      "cladewise".
+
 
 
                CHANGES IN APE VERSION 2.1-2
@@ -122,7 +162,7 @@ BUG FIXES
 OTHER CHANGES
 
     o The code of mlphylo() has almost entirely rewritten, and should
-      much stabler now. The options have been also greatly simplified
+      be much stabler. The options have been also greatly simplified
       (see ?mlphylo and ?DNAmodel for details).
 
     o The internal function nTips has been renamed klastorin_nTips.