correcting a bug in write.tree + error in MPR examples

[ape.git] / ChangeLog

diff --git a/ChangeLog b/ChangeLog
index f92c51c79ab6a4b03291edf8ebd528884cd2884d..05ff24194a9cf674a7e75788a4e96ac75d1fd4be 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,8 +1,35 @@
-               CHANGES IN APE VERSION 2.5-4
+               CHANGES IN APE VERSION 2.6-1
+
+
+BUG FIXES
+
+    o as.hclust.phylo() failed with trees with node labels (thanks to
+      Filipe Vieira for the fix).
+
+
+
+               CHANGES IN APE VERSION 2.6
 
 
 NEW FEATURES
 
+    o The new functions rlineage and rbdtree simulate phylogenies under
+      any user-defined time-dependent speciation-extinction model. They
+      use continuous time algorithms.
+
+    o The new function drop.fossil removes the extinct species from a
+      phylogeny.
+
+    o The new function bd.time fits a user-defined time-dependent
+      birth-death model. It is a generalization of yule.time() taking
+      extinction into account.
+
+    o The new function MPR does most parsimonious reconstruction of
+      discrete characters.
+
+    o The new function Ftab computes the contingency table of base
+      frequencies from a pair of sequences.
+
     o There is now an 'as.list' method for the class "DNAbin".
 
     o dist.dna() can compute the number of transitions or transversions
@@ -15,13 +42,34 @@ NEW FEATURES
     o compar.gee() has been improved with the new option 'corStruct' as an
       alternative to 'phy' to specify the correlation structure, and
       calculation of the QIC (Pan 2001, Biometrics). The display of the
-      results have also been improved.
+      results has also been improved.
+
+    o read.GenBank() has a new option 'gene.names' to return the name of
+      the gene (FALSE by default).
 
 
 BUG FIXES
 
     o extract.clade() sometimes shuffled the tip labels.
 
+    o plot.phylo(type = "unrooted") did not force asp = 1 (thanks to Klaus
+      Schliep for the fix)
+
+    o dist.dna(model = "logdet") used to divide distances by 4. The
+      documentation has been clarified on the formulae used.
+
+
+OTHER CHANGES
+
+    o rTraitCont(model = "OU") has an option 'linear = TRUE' to possibly
+      change the parameterisation (see ?rTraitCont for details).
+
+    o pic() now returns a vector with the node labels of the tree (if
+      available) as names.
+
+    o write.tree() and read.tree() have been substantially thanks to
+      contributions by Klaus Schliep.
+
 
 
                CHANGES IN APE VERSION 2.5-3