bug fix in read.nexus + new ?ape man page

[ape.git] / ChangeLog

diff --git a/ChangeLog b/ChangeLog
index a3923a68c8dbcc4856a24e6622e1a5076cdba634..6e2f4f15ac1ac7ee4619f2f18504019c1227f0b3 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,53 @@
+               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!)
+
+
+OTHER CHANGES
+
+    o There is now a general help page displayed with '?ape' 
+
+
+
+               CHANGES IN APE VERSION 2.2-3
+
+
+NEW FEATURES
+
+    o The new function extract.clade extracts a clade from a tree by
+      specifying a node number or label.
+
+    o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
+      operations of the same names.
+
+    o dist.dna() can now return the number of site differences by
+      specifying model="N".
+
+
+BUG FIXES
+
+    o chronopl() did not work with CV = TRUE.
+
+    o read.nexus() did not work correctly in some situations (trees on
+      multiple lines with different numbers of lines and/or with
+      comments inserted within the trees).
+
+    o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
+      the number of lineages with non-binary trees.
+
+
+OTHER CHANGES
+
+    o ape has now a namespace.
+
+    o drip.tip() has been improved: it should be much faster and work
+      better in some cases (e.g., see the example in ?zoom).
+
+
+
                CHANGES IN APE VERSION 2.2-2
 
 
@@ -6,6 +56,9 @@ NEW FEATURES
     o dist.gene() has been substantially improved and gains an option
       'pairwise.deletion'.
 
+    o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
+      more flexible.
+
 
 BUG FIXES
 
@@ -28,8 +81,8 @@ OTHER CHANGES
     o phymltest() has been updated for PhyML 3.0 and gains an option
       'append', whereas the option 'path2exec' has been removed.
 
-    o rbind.DNAbin() now accepts a single matrix which is returned
-      unchanged instead of an error.
+    o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
+      which is returned unchanged (instead of an error).
 
     o The data sets bird.orders and bird.families are now stored as
       Newick strings; i.e., the command data(bird.orders) calls