various changes to DNAbin functions + new labels.DNAbin()

[ape.git] / ChangeLog

diff --git a/ChangeLog b/ChangeLog
index c551deda10ce5fdb401272ecfa8a214adc31d645..229acbec29ae826afeb53fdf749dcc7e8540fe84 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,4 +1,46 @@
-               CHANGES IN APE VERSION 2.5-1
+               CHANGES IN APE VERSION 2.5-2
+
+
+NEW FEATURES
+
+    o There is now a print method for results from ace().
+
+    o There is a labels() method for objects of class "DNAbin".
+
+    o read.dna() has a new option 'as.matrix' to possibly force sequences
+      in a FASTA file to be stored in a matrix (see ?read.dna for details).
+
+
+BUG FIXES
+
+    o as.phylo.hclust() used to multiply edge lengths by 2.
+
+    o A minor bug was fixed in rTraitDisc().
+
+    o ace() sometimes failed (parameter value was NaN and the optimisation
+      failed).
+
+
+DEPRECATED & DEFUNCT
+
+    o evolve.phylo() and plot.ancestral() have been removed.
+
+    o chronogram(), ratogram(), and NPRS.criterion() have been removed.
+
+
+OTHER CHANGES
+
+    o nj() has been improved and is now about 30% faster.
+
+    o The default option 'drop' of [.DNAbin has been changed to FALSE to
+      avoid dropping rownames when selecting a single sequence.
+
+    o print.DNAbin() has been changed to summary.DNAbin() which has been
+      removed.
+
+
+
+               CHANGES IN APE VERSION 2.5-1
 
 
 NEW FEATURES
@@ -11,6 +53,9 @@ NEW FEATURES
     o drop.tip(), extract.clade(), root(), and bind.tree() now have an
       'interactive' option to make the operation on a plotted tree.
 
+    o cophyloplot() gains two new arguments 'lwd' and 'lty' for the
+      association links; they are recycled like 'col' (which wasn't before).
+
 
 BUG FIXES
 
@@ -29,6 +74,17 @@ BUG FIXES
     o plot.phylo(type = "p") sometimes failed to colour correctly the
       vertical lines representing the nodes.
 
+    o plot.phylo(direction = "l", x.lim = 30) failed to plot the branches
+      in the correct direction though the tip labels were displayed
+      correctly.
+
+
+OTHER CHANGES
+
+    o The c, cbind, and rbind methods for "DNAbin" objetcs now check that
+      the sequences are correctly stored (in a list for c, in a matrix
+      for the two other functions).
+
 
 
        CHANGES IN APE VERSION 2.5