add delta.plot + clarify doc in write.tree.Rd

[ape.git] / ChangeLog

diff --git a/ChangeLog b/ChangeLog
index 13751957239f34beb73b573549fa7c40ef51e7ba..0809491f4a2177b13b2a74e2711042de2e33df87 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,65 @@
+               CHANGES IN APE VERSION 2.5
+
+
+NEW FEATURES
+
+    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
 
 
@@ -9,8 +71,34 @@ NEW FEATURES
 
 BUG FIXES
 
-    o seg.sites() did not handle ambiguous nucleotides correctly: they are
-      now ignored.
+    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
@@ -18,11 +106,8 @@ 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.
 
-OTHER CHANGES
-
-    o Deprecated functions are now listed in a help page: see
-      help("ape-defunct"), with the quotes!
 
 
                CHANGES IN APE VERSION 2.3-3
@@ -183,7 +268,7 @@ BUG FIXES
 
 OTHER CHANGES
 
-    o There is now a general help page displayed with '?ape' 
+    o There is now a general help page displayed with '?ape'.