update for ape 2.1-2

[ape.git] / Changes

diff --git a/Changes b/Changes
index c488bf76b8cb1410cf2b74500298125f9fa4c1a4..9a33fa8598b4a3f768cf4386488e56a3cef97ae7 100644 (file)
--- a/Changes
+++ b/Changes
@@ -3,11 +3,14 @@
 
 NEW FEATURES
 
+    o There three new methods for the "multiPhylo" class: str, $,
+      and [[.
+
     o root() gains the options 'node' and 'resolve.root'
       (FALSE by default) as well as its code being improved.
 
     o mltt.plot() has now an option 'log' used in the same way
-      than in plot.default()
+      than in plot.default().
 
 
 BUG FIXES
@@ -19,12 +22,23 @@ BUG FIXES
       'cex' to draw symbols of different sizes (which has
       worked already for thermometers).
 
+    o read.nexus() generally failed to read very big files.
+
 
 OTHER CHANGES
 
     o The argument 'family' of compar.gee() can now be a function
       as well as a character string.
 
+    o read.tree() and read.nexus() now return an unnamed list if
+      'tree.names = NULL'.
+
+    o read.nexus() now returns a modified object of class "multiPhylo"
+      when there is a TRANSLATE block in the NEXUS file: the individual
+      trees have no 'tip.label' vector, but the list has a 'TipLabel'
+      attribute. The new methods '$' and '[[' set these elements
+      correctly when extracting trees.
+
 
 
                CHANGES IN APE VERSION 2.1-1