a few changes...

[ape.git] / NEWS

diff --git a/NEWS b/NEWS
index a3aa8c97e7ab0d49d29f6711b1a41ed6b5b5a812..39b3905d1c4262bba55feec7f7fcf65f471c5ca6 100644 (file)
--- a/NEWS
+++ b/NEWS
@@ -1,12 +1,64 @@
+               CHANGES IN APE VERSION 2.8-1
+
+
+BUG FIXES
+
+    o mantel.test() could return P-values > 1 with the default
+      two-tailed test.
+
+
+OTHER CHANGES
+
+    o The code of yule() has been simplified and is now much faster for
+      big trees.
+
+
+
+               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
 
 
 NEW FEATURES
 
+    o The new function compute.brtime computes and sets branching times.
+
     o mantel.test() has a new argument 'alternative' which is
       "two-sided" by default. Previously, this test was one-tailed
       with no possibility to change.
 
+    o ace() can now do REML estimation with continuous characters,
+      giving better estimates of the variance of the Brownian motion
+      process.
+
 
 BUG FIXES
 
@@ -18,6 +70,19 @@ BUG FIXES
       process when alpha = 0 to avoid division by zero. The option
       'linear' has been removed.
 
+    o Cross-validation in chronopl() did not work when 'age.max' was
+      used.
+
+    o consensus(, p = 0.5) could return an incorrect tree if some
+      incompatible splits occur in 50% of the trees (especially with
+      small number of trees).
+
+    o c() with "multiPhylo" did not work correctly (thanks to Klaus
+      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.
+
 
 
                CHANGES IN APE VERSION 2.7-2