new faster nj.c

[ape.git] / ChangeLog

diff --git a/ChangeLog b/ChangeLog
index b1246e0e96a7e3be82c0fa2d4511cbbf36d8cd82..430c21093791aab51038f32d86ce4575df8f8698 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,4 +1,37 @@
-               CHANGES IN APE VERSION 2.5-1
+               CHANGES IN APE VERSION 2.5-2
+
+
+BUG FIXES
+
+    o as.phylo.hclust() used to multiply edge lengths by 2.
+
+
+DEPRECATED & DEFUNCT
+
+    o evolve.phylo() and plot.ancestral() have been removed.
+
+
+OTHER CHANGES
+
+    o nj() has been improved and is now about 30% faster.
+
+
+
+               CHANGES IN APE VERSION 2.5-1
+
+
+NEW FEATURES
+
+    o The new function stree generates trees with regular shapes.
+
+    o It is now possible to bind two trees with x + y (see ?bind.tree for
+      details).
+
+    o drop.tip(), extract.clade(), root(), and bind.tree() now have an
+      'interactive' option to make the operation on a plotted tree.
+
+    o cophyloplot() gains two new arguments 'lwd' and 'lty' for the
+      association links; they are recycled like 'col' (which wasn't before).
 
 
 BUG FIXES
@@ -6,6 +39,29 @@ BUG FIXES
     o rTraitDisc() did not use its 'freq' argument correctly (it was
       multiplied with the rate matrix column-wise instead of row-wise).
 
+    o [node|tip|edge]labels(thermo = ) used to draw empty thermometers
+      with NA values. Nothing is drawn now like with 'text' or 'pch'.
+      The same bug occurred with the 'pie' option.
+
+    o A bug was fixed in compar.ou() and the help page was clarified.
+
+    o bind.tree() has been rewritten fixing several bugs and making it
+      more efficient.
+
+    o plot.phylo(type = "p") sometimes failed to colour correctly the
+      vertical lines representing the nodes.
+
+    o plot.phylo(direction = "l", x.lim = 30) failed to plot the branches
+      in the correct direction though the tip labels were displayed
+      correctly.
+
+
+OTHER CHANGES
+
+    o The c, cbind, and rbind methods for "DNAbin" objetcs now check that
+      the sequences are correctly stored (in a list for c, in a matrix
+      for the two other functions).
+
 
 
        CHANGES IN APE VERSION 2.5