new files by Damien + a few bug fixes

[ape.git] / Changes

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@@ -1,3 +1,123 @@
+               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
+
+
+NEW FEATURES
+
+    o There three new methods for the "multiPhylo" class: str, $,
+      and [[.
+
+    o root() gains the options 'node' and 'resolve.root'
+      (FALSE by default) as well as its code being improved.
+
+    o mltt.plot() has now an option 'log' used in the same way
+      than in plot.default().
+
+
+BUG FIXES
+
+    o mltt.plot() failed to display the legend with an unnamed
+      list of trees.
+
+    o nodelabels() with pies now correcly uses the argument
+      'cex' to draw symbols of different sizes (which has
+      worked already for thermometers).
+
+    o read.nexus() generally failed to read very big files.
+
+
+OTHER CHANGES
+
+    o The argument 'family' of compar.gee() can now be a function
+      as well as a character string.
+
+    o read.tree() and read.nexus() now return an unnamed list if
+      'tree.names = NULL'.
+
+    o read.nexus() now returns a modified object of class "multiPhylo"
+      when there is a TRANSLATE block in the NEXUS file: the individual
+      trees have no 'tip.label' vector, but the list has a 'TipLabel'
+      attribute. The new methods '$' and '[[' set these elements
+      correctly when extracting trees.
+
+
+
+               CHANGES IN APE VERSION 2.1-1
+
+
+NEW FEATURES
+
+    o The new function rmtree generates lists of random trees.
+
+    o rcoal() now generates a genuine coalescent tree by default
+      (thanks to Vladimir Minin for the code).
+
+
+BUG FIXES
+
+    o nuc.div() returned an incorrect value with the default
+      pairwise.deletion = FALSE.
+
+
+OTHER CHANGES
+
+    o The internal codes of bionj(), fastme.bal(), and fastme.ols()
+      have been improved so that they are stabler and faster.
+
+    o R packages used by ape are now loaded silently; lattice and gee
+      are loaded only when needed.
+
+
+
                CHANGES IN APE VERSION 2.1
 
 
@@ -42,7 +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.