BOTHlabels(... hozir = TRUE)

[ape.git] / ChangeLog

diff --git a/ChangeLog b/ChangeLog
index 430c21093791aab51038f32d86ce4575df8f8698..df3b32bc4fd721ecdac92e35d283d1c2b09e506b 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,23 +1,91 @@
+               CHANGES IN APE VERSION 2.5-4
+
+
+NEW FEATURES
+
+    o There is now an 'as.list' method for the class "DNAbin".
+
+    o dist.dna() can compute the number of transitions or transversions
+      with the option model = "Ts" or model = "Tv", respectively.
+
+    o [node|tip|edge]labels() gain three options with default values to
+      control the aspect of thermometers: horiz = TRUE, width = NULL,
+      and height = NULL.
+
+
+
+               CHANGES IN APE VERSION 2.5-3
+
+
+NEW FEATURES
+
+    o The new function mixedFontLabel helps to make labels with bits of
+      text to be plotted in different fonts.
+
+    o There are now replacement operators for [, [[, and $ for the class
+      "multiPhylo" (i.e., TREES[11:20] <- rmtree(10, 100)). They possibly
+      check that the tip labels are the same in all trees.
+
+    o Objects of class "multiPhylo" can be built with c(): there are
+      methods for the classes "phylo" and "multiPhylo".
+
+    o The internal functions .compressTipLabel and .uncompressTipLabel are
+      now documented.
+
+
+BUG FIXES
+
+    o bind.tree(x, y, where, position = 0) did not work correctly if 'y'
+      was a single-edge tree and 'where' was a tip.
+
+    o rTraitCont() did not use the square-root of branch lengths when
+      simulating a Brownian motion model.
+
+
+
                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
+               CHANGES IN APE VERSION 2.5-1
 
 
 NEW FEATURES
@@ -64,7 +132,7 @@ OTHER CHANGES
 
 
 
-       CHANGES IN APE VERSION 2.5
+               CHANGES IN APE VERSION 2.5
 
 
 NEW FEATURES