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

[ape.git] / ChangeLog

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                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