change nlm to nlminb in ace() + new makeNodeLabel + fixed drop.tip

[ape.git] / ChangeLog

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index 5aab9bdf0da3824e12300e0419b913fc164b8fb4..d659113a7cd989de0357b1303000d0a47674b66b 100644 (file)
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+               CHANGES IN APE VERSION 2.3
+
+
+NEW FEATURES
+
+    o The new functions CADM.global and CADM.post, contributed by
+      Pierre Legendre, test the congruence among several distance
+      matrices.
+
+    o The new function yule.time fits a user-defined time-dependent
+      Yule model by maximum likelihood.
+
+    o The new function makeNodeLabel creates and/or modifies node
+      labels in a flexible way.
+
+
+BUG FIXES
+
+    o drop.tip() shuffled tip labels in some cases.
+
+    o drop.tip() did not handle node.label correctly.
+
+    o is.ultrametric() now checks the ordering of the edge matrix.
+
+    o ace() sometimes returned negative values of likelihoods of
+      ancestral states (thanks to Dan Rabosky for solving this long
+      lasting bug).
+
+
+OTHER CHANGES
+
+    o The data set xenarthra has been removed.
+
+
+
+               CHANGES IN APE VERSION 2.2-4
+
+BUG FIXES
+
+    o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
+      now fixed. (Thanks to Peter Wragg for the fix!)
+
+    o A warning message occurred for no reason with ace(method="GLS").
+
+
+OTHER CHANGES
+
+    o There is now a general help page displayed with '?ape' 
+
+
+
                CHANGES IN APE VERSION 2.2-3