fixes in mantel.test() and extract.clade()

[ape.git] / NEWS

diff --git a/NEWS b/NEWS
index 7b43668c946918a267b1a726a6bd4b73aeff8b2a..223169c57b1ff73d0570cb0d5c62f033d8900881 100644 (file)
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,55 @@
+               CHANGES IN APE VERSION 2.8-1
+
+
+BUG FIXES
+
+    o mantel.test() could return P-values > 1 with the default
+      two-tailed test.
+
+    o extract.clade() sometimes shuffled some tip labels (thanks to
+      Ludovic Mallet and Mahendra Mariadassou for the fix).
+
+
+OTHER CHANGES
+
+    o The code of yule() has been simplified and is now much faster for
+      big trees.
+
+    o The code of mantel.test() has been adjusted to be consistent
+      with common permutation tests.
+
+
+
+               CHANGES IN APE VERSION 2.8
+
+
+NEW FEATURES
+
+    o Twelve new functions have been written by Andrei-Alin Popescu:
+      additive, ultrametric, is.compatible, arecompatible, mvr, mvrs,
+      njs, bionjs, SDM, treePop, triangMtd, triangMtd*.
+
+    o A new class "bitsplits" has been created by Andrei-Alin Popescu
+      to code splits (aka, bipartition).
+
+    o There is a new generic function as.bitsplits with a method to
+      convert from the class "prop.part" to the class "bitsplits".
+
+    o The new function ltt.coplot plots on the same scales a tree and
+      the derived LTT plot.
+
+    o ltt.plot() has two new options: backward and tol. It can now
+      handle non-ultrametic trees and its internal coding has been
+      improved. The coordinates of the plot can now be computed with
+      the new function ltt.plot.coords.
+
+
+BUG FIXES
+
+    o prop.part() crashed if some trees had some multichotomies.
+
+
+
                CHANGES IN APE VERSION 2.7-3
 
 
@@ -35,6 +87,7 @@ BUG FIXES
       Schliep for the fix).
 
     o root() failed in some cases with an outgroup made of several tips.
+      The help page has been clarified a bit.