fix rTraitDisc

[ape.git] / ChangeLog

diff --git a/ChangeLog b/ChangeLog
index fa764112a7ecaf1d4e58e05d273d2f0bf7999638..b1246e0e96a7e3be82c0fa2d4511cbbf36d8cd82 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,19 +1,62 @@
-               CHANGES IN APE VERSION 2.4-2
+               CHANGES IN APE VERSION 2.5-1
+
+
+BUG FIXES
+
+    o rTraitDisc() did not use its 'freq' argument correctly (it was
+      multiplied with the rate matrix column-wise instead of row-wise).
+
+
+
+       CHANGES IN APE VERSION 2.5
 
 
 NEW FEATURES
 
+    o The new function parafit by Pierre Legendre tests for the
+      coevolution between hosts and parasites. It has a companion
+      function, pcoa, that does principal coordinate decomposition.
+      The latter has a biplot method.
+
+    o The new function lmorigin by Pierre Legendre performs multiple
+      regression through the origin with testing by permutation.
+
     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 The new function edges draws additional branches between any nodes
+      and/or tips on a plotted tree.
+
+    o The new function fancyarrows enhances arrows from graphics with
+      triangle and harpoon heads; it can be called from edges().
+
     o add.scale.bar() has a new option 'ask' to draw interactively.
 
+    o The branch length score replaces the geodesic distance in dist.topo.
+
+    o Three new data sets are included: the gopher-lice data (gopher.D),
+      SO2 air pollution in 41 US cities (lmorigin.ex1, from Sokal &
+      Rohlf 1995), and some host-parasite specificity data
+      (lmorigin.ex2, from Legendre & Desdevises 2009).
+
 
 BUG FIXES
 
     o add.scale.bar() drew the bar outside the plotting region with the
       default options with unrooted or radial trees.
 
+    o dist.topo() made R stuck when the trees had different sizes (thanks
+      to Otto Cordero for the fix).
+
+
+OTHER CHANGES
+
+    o The geodesic distance has been replaced by the branch length score
+      in dist.topo().
+
 
 
                CHANGES IN APE VERSION 2.4-1
@@ -1218,6 +1261,8 @@ OTHER CHANGES
 
     o dist.taxo() has been renamed as weight.taxo().
 
+    o dist.phylo() has been replaced by the method cophenetic.phylo().
+
     o Various error and warning messages have been improved.