X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=NEWS;h=807a2e4fe3fc37650dc74b45bb914126c94cb59a;hb=refs%2Fheads%2Fmaster;hp=1f2cd220f396a79f3bc7b53b25555fa3bf2a683c;hpb=a0436318d70829a2d16134be7ca1d6d454613a20;p=ape.git

diff --git a/NEWS b/NEWS
index 1f2cd22..807a2e4 100644
--- a/NEWS
+++ b/NEWS
@@ -1,9 +1,57 @@
+		CHANGES IN APE VERSION 3.0-8
+
+
+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().
+
+
+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.
+
+    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
 
 
 NEW FEATURES
 
-      The new function chronos ..........
+    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.
 
@@ -36,9 +84,8 @@ OTHER CHANGES
 
     o base.freq() is now faster with lists.
 
-      as.matrix.DNAbin() ............ should be faster.... now accepts vectors,
-
-      read.dna() has a new for FASTA files............. faster C code.
+    o as.matrix.DNAbin() should be faster and more efficient with
+      lists; it now accepts vectors.
 
 
 
@@ -480,7 +527,7 @@ 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.