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
 
 
 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().
 
     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).
 
       '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
 
 
                CHANGES IN APE VERSION 3.0-7