improvements to compar.gee + bug fix in extract.clade

[ape.git] / ChangeLog

diff --git a/ChangeLog b/ChangeLog
index 229acbec29ae826afeb53fdf749dcc7e8540fe84..f92c51c79ab6a4b03291edf8ebd528884cd2884d 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,58 @@
+               CHANGES IN APE VERSION 2.5-4
+
+
+NEW FEATURES
+
+    o There is now an 'as.list' method for the class "DNAbin".
+
+    o dist.dna() can compute the number of transitions or transversions
+      with the option model = "Ts" or model = "Tv", respectively.
+
+    o [node|tip|edge]labels() gain three options with default values to
+      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 have also been improved.
+
+
+BUG FIXES
+
+    o extract.clade() sometimes shuffled the tip labels.
+
+
+
+               CHANGES IN APE VERSION 2.5-3
+
+
+NEW FEATURES
+
+    o The new function mixedFontLabel helps to make labels with bits of
+      text to be plotted in different fonts.
+
+    o There are now replacement operators for [, [[, and $ for the class
+      "multiPhylo" (i.e., TREES[11:20] <- rmtree(10, 100)). They possibly
+      check that the tip labels are the same in all trees.
+
+    o Objects of class "multiPhylo" can be built with c(): there are
+      methods for the classes "phylo" and "multiPhylo".
+
+    o The internal functions .compressTipLabel and .uncompressTipLabel are
+      now documented.
+
+
+BUG FIXES
+
+    o bind.tree(x, y, where, position = 0) did not work correctly if 'y'
+      was a single-edge tree and 'where' was a tip.
+
+    o rTraitCont() did not use the square-root of branch lengths when
+      simulating a Brownian motion model.
+
+
+
                CHANGES IN APE VERSION 2.5-2
 
 
@@ -40,7 +95,7 @@ OTHER CHANGES
 
 
 
-               CHANGES IN APE VERSION 2.5-1
+               CHANGES IN APE VERSION 2.5-1
 
 
 NEW FEATURES
@@ -87,7 +142,7 @@ OTHER CHANGES
 
 
 
-       CHANGES IN APE VERSION 2.5
+               CHANGES IN APE VERSION 2.5
 
 
 NEW FEATURES