new LTT plot functions + updated reference in yule.time.Rd

[ape.git] / NEWS

diff --git a/NEWS b/NEWS
index 9e66a45982269e849ce15198fc94c2813a598e50..776fd4ae533120c384bbe3cfca87a8bbac66b698 100644 (file)
--- a/NEWS
+++ b/NEWS
@@ -1,12 +1,33 @@
+               CHANGES IN APE VERSION 2.8
+
+
+NEW FEATURES
+
+    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.
+
+    o The new function ltt.coplot plots on the same scales a tree and
+      its LTT plot.
+
+
+
                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
 
@@ -21,6 +42,16 @@ BUG FIXES
     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