+ 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
+
+
+NEW FEATURES
+
+ o base.freq() has a new option 'freq' to return the counts; the
+ default is still to return the proportions.
+
+
+BUG FIXES
+
+ o seg.sites() did not handle ambiguous nucleotides correctly: they
+ are now ignored.
+
+ o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
+ the tree: the argument is now ignored.
+
+ o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
+ Young for the fix).
+
+
+OTHER CHANGES
+
+ o Trying to plot a tree with a single tip now returns NULL with a
+ warning (it returned an error previously).
+
+ o The way lines representing nodes are coloured in phylograms has
+ been modified (as well as their widths and types) following some
+ users' request; this is only for dichotomous nodes.
+
+ o The argument 'adj' in [node][tip][edge]labels() now works when
+ using 'pie' or 'thermo'.
+
+ o A more informative message error is now returned by dist.dna() when
+ 'model' is badly specified (partial matching of this argument is
+ done now).
+
+ o Deprecated functions are now listed in a help page: see
+ help("ape-defunct") with the quotes.
+
+
+DEPRECATED & DEFUNCT
+
+ o The functions heterozygosity, nuc.div, theta.h, theta.k and
+ theta.s have been moved from ape to pegas.
+
+ o The functions mlphylo, DNAmodel and sh.test have been removed.
+
+
+
+ CHANGES IN APE VERSION 2.3-3
+
+
+BUG FIXES
+
+ o add.scale.bar() always drew a horizontal bar.
+
+ o zoom() shuffled tips with unrooted trees.
+
+ o write.nexus() failed to write correctly trees with a "TipLabel"
+ attribute.
+
+ o rcoal() failed to compute branch lengths with very large n.
+
+ o A small bug was fixed in compar.cheverud() (thanks to Michael
+ Phelan for the fix).
+
+ o seg.sites() failed when passing a vector.
+
+ o drop.tip() sometimes shuffled tip labels.
+
+ o root() shuffled node labels with 'resolve.root = TRUE'.
+
+
+
+ CHANGES IN APE VERSION 2.3-2
+
+
+BUG FIXES
+
+ o all.equal.phylo() did not compare unrooted trees correctly.
+
+ o dist.topo(... method = "PH85") did not treat unrooted trees
+ correctly (thanks to Tim Wallstrom for the fix).
+
+ o root() sometimes failed to test for the monophyly of the
+ outgroup correctly.
+
+ o extract.clade() sometimes included too many edges.
+
+ o vcv.phylo() did not work correctly when the tree is in
+ "pruningwise" order.
+
+ o nj() did not handle correctly distance matrices with many 0's.
+ The code has also been significantly improved: 7, 70, 160 times
+ faster with n = 100, 500, 1000, respectively.
+
+
+
CHANGES IN APE VERSION 2.3-1
NEW FEATURES
+ o The new function is.monophyletic tests the monophyly of a group.
+
o There is now a c() method for lists of class "DNAbin".
o yule.cov() now fits the null model, and its help page has been
corrected with respect to this change.
+ o drop.tip() has a new option 'rooted' to force (or not) a tree
+ to be treated as (un)rooted.
+
BUG FIXES
o A small bug was fixed in CDAM.global().
+ o ace() failed with large data sets. Thanks to Rich FitzJohn for
+ the fix. With other improvements, this function is now about 6
+ times faster.
+
+ o write.tree() failed with objects of class "multiPhylo".
+
+ o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
+
OTHER CHANGES
o rcoal() is now faster.
+DEPRECATED & DEFUNCT
+
+ o klastorin() has been removed.
+
+
CHANGES IN APE VERSION 2.3
OTHER CHANGES
- o There is now a general help page displayed with '?ape'
+ o There is now a general help page displayed with '?ape'.
o ape has now a namespace.
- o drip.tip() has been improved: it should be much faster and work
+ o drop.tip() has been improved: it should be much faster and work
better in some cases (e.g., see the example in ?zoom).