[Phylobase-commits] r700 - pkg

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

Author: pdc
Date: 2009-10-31 02:44:53 +0100 (Sat, 31 Oct 2009)
New Revision: 700

Added:
   pkg/NEWS
Log:
Add a NEWS file

Added: pkg/NEWS
===================================================================
--- pkg/NEWS	                        (rev 0)
+++ pkg/NEWS	2009-10-31 01:44:53 UTC (rev 700)
@@ -0,0 +1,147 @@
+        *************************************************
+        *                                               *
+        *               0.5 SERIES NEWS                 *
+        *                                               *
+        *************************************************
+
+                CHANGES IN phylobase VERSION 0.5
+
+MAJOR CHANGES
+
+    *   A var-cov matrix tree class, phylo4vcov, and methods for converting to 
+        and from other classes now exists.
+
+    *   Replaced separate the tip.label and node.label slots with a unified 
+        label slot in the phylo4 class definition.
+
+    *   Replaced separate the tip.data and node.data into a single data slot in 
+        the phylo4d class definition.
+
+    *   The phylo4 class grew a annotate slot.
+
+    *   The phylo4d class grew a metadata slot.
+
+    *   Added an order slot to the phylo4 class definition and updated as()
+        methods to assign the proper order (if possible) when converting 
+        between ape and phylobase tree formats.
+
+    *   The Nnode slot was removed from the phylo4 class definition.
+
+    *   An explicit root edge has been added to the edge matrix with 0 as the 
+        ancestor and nTips(phy) + 1 as the rood node.
+
+    *   The edgeLabels() and edgeLength() accessors now return vectors with 
+        named elements in the same order as rows of the edge matrix, even when 
+        some/all values are missing.
+
+    *   The labels() accessor and nodeID() methods now always return labels in 
+        ascending order of node ID
+
+    *   Many function and argument names and defaults have been changed to make 
+        them more consistent most functions follow the getNode() pattern.
+
+    *   The plotting functions have been replaced (see below).
+
+    *   Now, data are matched against node numbers instead of node labels.
+
+    *   Tip and internal node labels have now internal names that are character 
+        strings of the node number they correspond to. Thus it is possible to 
+        store labels in any order and assignment of labels more robust.
+
+    *   We now use the RUnit package (not required for normal use) for adding 
+        unit tests.  Adding unit tests to inst/unitTests/ is now preferred over 
+        the tests/ directory.
+
+    *   Numerous changes to pruning and tree subsetting code.  It is 
+        considerably more robust and no longer relies on calls to APE.
+
+NEW FEATURES
+
+    *   Added a function nodeType() for identifying whether a node is root, 
+        tip or internal.
+
+    *   Changed nodeNumbers to nodeId() and extended it abilities.
+
+    *   Added method reorder() for converting edge matrices into preorder or 
+        postorder.
+
+    *   Added the edgeOrder accessor to get the order of a phylobase object.
+
+    *   Added a package help file accessible from ?phylobase.
+
+    *   Added labels()<- for assigning labels.
+
+    *   Added edgeLength()<- for assigning edgeLengths.
+
+    *   Added a phylo4() method for importing APE phylo objects.
+
+    *   Added a hasTipData() method.
+
+    *   Added a edgeId() method.
+
+    *   Created the addData() method for adding data to phylo4 objects.
+
+    *   Added tipData and nodeData getter/setter methods
+
+    *   If all node.labels are numerical values, they are automatically 
+        converted as data. Useful when importing consensus tree from MrBayes.
+
+    *   It is now possible to print tree objects in edge order using the 
+        edgeOrder argument in printphylo4().
+
+    *   reorder(), descendants(), ancestors(), and portions of the plotting code 
+        have been recoded in C to improve performance.
+
+    *   Added a developer vignette to document and guide development of the 
+        phylobase package.
+
+    *   The previous plotting functions, based on base graphics, have been 
+        replaced with function based on the grid graphics device.
+
+    *   A S4 generic plot() function, calling treePlot() has been added it 
+        dispatches a plotting function based on object class and arguments.
+
+    *   Plots using grid based code can be inserted at the tree tips using the 
+        tip.plot.fun argument in plot()
+
+    *   The getNode() method has been enhanced to allow matching against 
+        specific node types, and if the requested node is missing, all nodes of 
+        specified type are returned.
+
+    *   Changed getEdge() to allow no node argument, which returns all edges 
+        appropriate for the given type.
+
+CHANGES
+
+    *   Node labels are, if not supplied, a vector of NA.
+
+    *   printphylo() is now deprecated, print() and summary() now alsow work on 
+        empty objects.
+
+    *   phylo4() is now and S4 generic with signature "matrix".
+
+    *   phylobase now uses a NAMESPACE file.
+
+    *   Legacy plotting code (0.4) can be found in the SVN repo tags directory.
+
+    *   The tdata default "type" argument changed to 'all'.
+
+    *   Row names now stored internally as numeric, not character. 
+
+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.
+
+    *   The Nexus Class Library is build for the system default ARCH which may 
+        or may not be the architecture that R and the rest of the package is 
+        built with.  If this occurs the package will fail to load.
+
+    *   Unique labels are required for internal nodes, this behavior will be 
+        changed in the future.