[Phylobase-commits] r799 - pkg

[noreply at r-forge.r-project.org]

Author: francois
Date: 2010-07-15 11:08:14 +0200 (Thu, 15 Jul 2010)
New Revision: 799

Modified:
   pkg/DESCRIPTION
   pkg/NEWS
Log:
updated DESCRIPTION and NEWS in preparation of 0.6 release


Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2010-07-15 08:40:04 UTC (rev 798)
+++ pkg/DESCRIPTION	2010-07-15 09:08:14 UTC (rev 799)
@@ -3,7 +3,7 @@
 Title: Base package for phylogenetic structures and comparative data
 Version: 0.6.0
 Date: 2010-07-15
-Depends: methods, grid, ape(>= 2.1), Rcpp (>= 0.7.4)
+Depends: methods, grid, ape(>= 2.1), Rcpp (>= 0.8.3)
 Suggests: ade4, MASS
 Author: R Hackathon et al. (alphabetically: Ben Bolker, Marguerite Butler, Peter Cowan,  Damien de Vienne, Dirk Eddelbuettel, Mark Holder, Thibaut Jombart, Steve Kembel, Francois Michonneau, David Orme, Brian O'Meara, Emmanuel Paradis, Jim Regetz, Derrick Zwickl)
 Maintainer:  Ben Bolker <bolker at ufl.edu>

Modified: pkg/NEWS
===================================================================
--- pkg/NEWS	2010-07-15 08:40:04 UTC (rev 798)
+++ pkg/NEWS	2010-07-15 09:08:14 UTC (rev 799)
@@ -1,5 +1,64 @@
         *************************************************
         *                                               *
+        *               0.6 SERIES NEWS                 *
+        *                                               *
+        *************************************************
+
+                CHANGES IN phylobase VERSION 0.6
+                
+MAJOR CHANGES
+
+    *   Updated to the Nexus Class Library (NCL) 2.1.12.
+    
+    *   Changed the way NCL is built during the installation process.
+    
+    *   Complete rewrite of the function readNexus which brings many new
+        functionalities.
+        
+    *   Nodes labels do not have to be unique.
+    
+        
+NEW FEATURES
+   
+    *   In readNexus, the option return.labels gives the state labels of the
+        characters.
+        
+    *   It is now possible to import several types of  data blocks in a single
+        NEXUS file with readNexus.
+        
+    *   The function phylobase.options() provides global options to control the
+        behavior of the phylo4/phylo4d validator.
+        
+    *   The new method hasDuplicatedLabels() indicates whether any node labels
+        are duplicated.
+        
+    *   The new method nData() returns the number of datasets associated with
+        a tree.
+        
+    *   The column that contains the labels can now be specified by its name in
+        the function formatData()
+     
+CHANGES
+
+    *   The function getNode() has been modified to allow node matching in the
+        case of non-unique labels.
+        
+    *   Many new unit tests.
+    
+BUG FIXES
+
+    *   Far too many to document.  See the SVN log for details.
+
+KNOWN ISSUES
+
+    *   Unrooted trees are not supported by all functions, e.g. plot() and 
+        reorder().
+
+    *   Factors are not supported by the default plotting method.
+
+
+        *************************************************
+        *                                               *
         *               0.5 SERIES NEWS                 *
         *                                               *
         *************************************************