various changes and fixes

[ape.git] / ChangeLog

diff --git a/ChangeLog b/ChangeLog
index 13751957239f34beb73b573549fa7c40ef51e7ba..402cf950ff587b3fb54fe40fb26c9f6e2e28f369 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -9,20 +9,41 @@ NEW FEATURES
 
 BUG FIXES
 
-    o seg.sites() did not handle ambiguous nucleotides correctly: they are
-      now ignored.
+    o seg.sites() did not handle ambiguous nucleotides correctly: they
+      are now ignored.
 
+    o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
+      the tree: the argument is now ignored.
 
-DEPRECATED & DEFUNCT
-
-    o The functions heterozygosity, nuc.div, theta.h, theta.k and
-      theta.s have been moved from ape to pegas.
+    o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
+      Young for the fix).
 
 
 OTHER CHANGES
 
+    o Trying to plot a tree with a single tip now returns NULL with a
+      warning (it returned an error previously).
+
+    o The way lines representing nodes are coloured in phylograms has
+      been modified (as well as their widths and types) following some
+      users' request; this is only for dichotomous nodes.
+
+    o The argument 'adj' in [node][tip][edge]labels() now works when
+      using 'pie' or 'thermo'.
+
+    o A more informative message error is now returned by dist.dna() when
+      'model' is badly specified (partial matching of this argument is
+      done now).
+
     o Deprecated functions are now listed in a help page: see
-      help("ape-defunct"), with the quotes!
+      help("ape-defunct") with the quotes.
+
+
+DEPRECATED & DEFUNCT
+
+    o The functions heterozygosity, nuc.div, theta.h, theta.k and
+      theta.s have been moved from ape to pegas.
+
 
 
                CHANGES IN APE VERSION 2.3-3