bug fix in collapsed.singles()

[ape.git] / Changes

diff --git a/Changes b/Changes
index da98ec10377afbcdcce8cb4c9743e5ba871cb177..df065d469e97c0c7137e25500db9683358da3f92 100644 (file)
--- a/Changes
+++ b/Changes
@@ -1,15 +1,51 @@
+               CHANGES IN APE VERSION 2.2-1
+
+
+NEW FEATURES
+
+    o The new function del.gaps() removes insertion gaps ("-") in a
+      set of DNA sequences.
+
+
+BUG FIXES
+
+    o root() failed with 'resolve.root = TRUE' when the root was
+      already the specified root.
+
+    o Several bugs were fixed in mlphylo().
+
+    o collapsed.singles() did not propagate the 'Nnode' and
+      'node.labels' elements (thanks to Elizabeth Purdom for the fix.
+
+
+OTHER CHANGES
+
+    o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
+      Minin.
+
+
+
                CHANGES IN APE VERSION 2.2
 
 
 NEW FEATURES
 
     o Four new functions have been written by Damien de Vienne for the
-      graphical exploration of large trees (plot.cophylo, subtrees,
+      graphical exploration of large trees (cophyloplot, subtrees,
       subtreeplot), and to return the graphical coordinates of tree
       (without plotting).
 
-    o The new function corPagel() implements the Pagel's "lambda"
-      correlation structure.
+    o The new functions corPagel and corBlomberg implement the Pagel's
+      "lambda" and Blomberg et al.'s "ACDC" correlation structures.
+
+    o chronopl() has been improved and gains several options: see its
+      help page for details.
+
+    o boot.phylo() has now an option 'trees' to possibly return the
+      bootstraped trees (the default is FALSE).
+
+    o prop.part() has been improved and should now be faster in all
+      situations.
 
 
 BUG FIXES
@@ -26,15 +62,12 @@ BUG FIXES
     o zoom() failed when tip labels were used instead of their numbers
       (thanks to Yan Wong for the fix).
 
-    o drop.tip() failed with some trees  (fixed by Yan Wong).
+    o drop.tip() failed with some trees (fixed by Yan Wong).
 
     o seg.sites() failed with a list.
 
-
-OTHER CHANGES
-
-    o chronopl() has been improved and gains several options: see its
-      help page for details.
+    o consensus() failed in some cases. The function has been improved
+      as well and is faster.