fix a bug in drop.tip + add new option 'rooted'

[ape.git] / ChangeLog

diff --git a/ChangeLog b/ChangeLog
index accd346a9138052ee8dac70c48ee7bc5addf9c77..98602f93fd35b93c2965986ebbc415dd68b2f902 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -3,8 +3,16 @@
 
 NEW FEATURES
 
+    o The new function is.monophyletic tests the monophyly of a group.
+
     o There is now a c() method for lists of class "DNAbin".
 
+    o yule.cov() now fits the null model, and its help page has been
+      corrected with respect to this change.
+
+    o drop.tip() has a new option 'rooted' to force (or not) a tree
+      to be treated as (un)rooted.
+
 
 BUG FIXES
 
@@ -15,6 +23,18 @@ BUG FIXES
 
     o boot.phylo() now treats correctly data frames.
 
+    o del.gaps() did not copy the rownames of a matrix.
+
+    o A small bug was fixed in CDAM.global().
+
+    o ace() failed with large data sets. Thanks to Rich FitzJohn for
+      the fix. With other improvements, this function is now about 6
+      times faster.
+
+    o write.tree() failed with objects of class "multiPhylo".
+
+    o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
+
 
 OTHER CHANGES
 
@@ -23,7 +43,12 @@ OTHER CHANGES
     o Instances of the form class(phy) == "phylo" have been replaced
       by inherits(phy, "phylo").
 
-    o rcoal() should be faster.
+    o rcoal() is now faster.
+
+
+DEPRECATED & DEFUNCT
+
+    o klastorin() has been removed.