fix from Pierre Legendre

[ape.git] / NEWS

diff --git a/NEWS b/NEWS
index 57d1924cccdeffb9e41b43d9a2934a04ebe6aa68..9bc3f6c8c56effb85d22da07d4d5fed2f086ee8d 100644 (file)
--- a/NEWS
+++ b/NEWS
@@ -1,8 +1,38 @@
+               CHANGES IN APE VERSION 3.0-8
+
+
+NEW FEATURES
+
+    o ace() gains a new option 'use.expm' to use expm() from the
+      package of the same name in place of matexpo().
+
+
+BUG FIXES
+
+    o read.dna(, "fasta") may add '\r' in labels: this is fixed.
+
+    o prop.clades() returned wrong numbers when the tip labels of
+      '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.
+
+
+
                CHANGES IN APE VERSION 3.0-7
 
 
 NEW FEATURES
 
+    o The new function chronos estimates chronograms by penalised
+      likelihood and maximum likelihood with a completely reworked
+      code and interface. There is a new function makeChronosCalib to
+      set the calibration points easily. chronos() will eventually
+      replace chronopl().
+
     o The new function 'where' searches patterns in DNA sequences.
 
     o pic() gains an option 'rescaled.tree = FALSE' to return the tree
@@ -34,6 +64,9 @@ OTHER CHANGES
 
     o base.freq() is now faster with lists.
 
+    o as.matrix.DNAbin() should be faster and more efficient with
+      lists; it now accepts vectors.
+
 
 
                CHANGES IN APE VERSION 3.0-6
@@ -474,7 +507,7 @@ NEW FEATURES
     o base.freq() gains an option 'all' to count all the possible bases
       including the ambiguous ones (defaults to FALSE).
 
-    o read.nexus() now writes tree names in the NEXUS file if given a
+    o write.nexus() now writes tree names in the NEXUS file if given a
       list of trees with names.