new code from Pierre Legendre

[ape.git] / ChangeLog

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+               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 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 add.scale.bar() has a new option 'ask' to draw interactively.
+
+
+BUG FIXES
+
+    o add.scale.bar() drew the bar outside the plotting region with the
+      default options with unrooted or radial trees.
+
+
+
                CHANGES IN APE VERSION 2.4-1
 
 
@@ -34,6 +60,9 @@ BUG FIXES
     o ace(type = "continuous", method = "ML") now avoids sigma² being
       negative (which resulted in an error).
 
+    o nj() crashed with NA/NaN in the distance matrix: an error in now
+      returned.
+
 
 
                CHANGES IN APE VERSION 2.4