+ CHANGES IN APE VERSION 2.5
+
+
+NEW FEATURES
+
+ o The new function parafit by Pierre Legendre tests for the
+ coevolution between hosts and parasites. It has a companion
+ function, pcoa, that does principal coordinate decomposition. The
+ latter has a biplot method.
+
+ o The new functions rTraitCont and rTraitDisc simulate continuous and
+ discrete traits under a wide range of evolutionary models.
+
+ o The new function delta.plot does a delta plot following Holland et
+ al. (2002, Mol. Biol. Evol. 12:2051).
+
+ o add.scale.bar() has a new option 'ask' to draw interactively.
+
+
+BUG FIXES
+
+ o add.scale.bar() drew the bar outside the plotting region with the
+ default options with unrooted or radial trees.
+
+
+
+ CHANGES IN APE VERSION 2.4-1
+
+
+NEW FEATURES
+
+ o rtree() and rcoal() now accept a numeric vector for the 'br'
+ argument.
+
+ o vcv() is a new generic function with methods for the classes "phylo"
+ and "corPhyl" so that it is possible to calculate the var-cov matrix
+ for "transformation models". vcv.phylo() can still be used for trees
+ of class "phylo"; its argument 'cor' has been renamed 'corr'.
+
+
+BUG FIXES
+
+ o bind.tree() failed when 'y' had no root edge.
+
+ o read.nexus() shuffled tip labels when the trees have no branch
+ lengths and there is a TRANSLATE block.
+
+ o read.nexus() does not try to translate node labels if there is a
+ translation table in the NEXUS file. See ?read.nexus for a
+ clarification on this behaviour.
+
+ o plot.multiPhylo() crashed R when plotting a list of trees with
+ compressed tip labels.
+
+ o write.nexus() did not translate the taxa names when asked for.
+
+ o plot.phylo(type = "fan") did not rotate the tip labels correctly
+ when the tree has branch lengths.
+
+ o ace(type = "continuous", method = "ML") now avoids sigma² being
+ negative (which resulted in an error).
+
+ o nj() crashed with NA/NaN in the distance matrix: an error in now
+ returned.
+
+
+
CHANGES IN APE VERSION 2.4
OTHER CHANGES
- o There is now a general help page displayed with '?ape'
+ o There is now a general help page displayed with '?ape'.