new mixedFontLabel() + bug fix in rTraitCont.c

[ape.git] / ChangeLog

diff --git a/ChangeLog b/ChangeLog
index f59984ba0a79b20bbd2693075d1c0422eaa1aaf5..d1862f60b567b5ac81a855dbc0ddb53a86a9d0a0 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,74 @@
+               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 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
 
 
@@ -5,8 +76,14 @@ NEW FEATURES
 
     o The new function stree generates trees with regular shapes.
 
-    o drop.tip(), extract.clade(), and root() now have an 'interactive'
-      option to make the operation on a plotted tree.
+    o It is now possible to bind two trees with x + y (see ?bind.tree for
+      details).
+
+    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
@@ -18,9 +95,28 @@ BUG FIXES
       with NA values. Nothing is drawn now like with 'text' or 'pch'.
       The same bug occurred with the 'pie' option.
 
+    o A bug was fixed in compar.ou() and the help page was clarified.
+
+    o bind.tree() has been rewritten fixing several bugs and making it
+      more efficient.
+
+    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
+               CHANGES IN APE VERSION 2.5
 
 
 NEW FEATURES