X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=ChangeLog;h=5a6817e06a65c287771809a14472393a88a7fe2c;hb=f295ab19440298e543db5a270e54f10a84382197;hp=df3b32bc4fd721ecdac92e35d283d1c2b09e506b;hpb=82dd3702485179ba5408f1e3e57eb856d025e16c;p=ape.git

diff --git a/ChangeLog b/ChangeLog
index df3b32b..5a6817e 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,8 +1,21 @@
-		CHANGES IN APE VERSION 2.5-4
+		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 new continuous time algorithms.
+
+    o The new function drop.fossil removes the extinct species from a
+      phylogeny.
+
+    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
@@ -12,6 +25,34 @@ NEW FEATURES
       control the aspect of thermometers: horiz = TRUE, width = NULL,
       and height = NULL.
 
+    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 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.
+
 
 
 		CHANGES IN APE VERSION 2.5-3