final commit for ape 3.0-8

[ape.git] / NEWS

diff --git a/NEWS b/NEWS
index 59c6fede8764018d71cbc24b60051792ce803041..807a2e4fe3fc37650dc74b45bb914126c94cb59a 100644 (file)
--- a/NEWS
+++ b/NEWS
@@ -3,6 +3,11 @@
 
 NEW FEATURES
 
+    o The new function ewLasso tests whether an incomplete set of
+      distances uniquely determines the edge weights of a given
+      unrooted topology using the 'Lasso' method by Dress et
+      al. (2012, J. Math. Biol. 65:77).
+
     o ace() gains a new option 'use.expm' to use expm() from the
       package of the same name in place of matexpo().
 
@@ -15,6 +20,26 @@ BUG FIXES
       'phy' are not in the same order than the list of trees (thanks
       to Rupert Collins for the report).
 
+    o CADM.post() displayed "1" on the diagonal of the matrix of
+      Mantel p-values. It now displays "NA" on the diagonal,
+      indicating that no test of significance is computed between a
+      distance matrix and itself.
+
+    o rtree(n, rooted = FALSE) returned trees with an 'edge' matrix
+      stored as doubles instead of integers for n > 4.
+
+
+OTHER CHANGES
+
+    o The files CDAM.global.R and CDAM.post.R have been renamed
+      CADM.global.R and CADM.post.R.
+
+    o ace() has a new default for its option 'method': this is "REML"
+      for continuous characters and "ML" for discrete ones.
+
+    o ape does not import gee anymore so the latter doesn't need to
+      be installed.
+
 
 
                CHANGES IN APE VERSION 3.0-7