+ CHANGES IN APE VERSION 2.2-1
+
+
+NEW FEATURES
+
+ o The new function del.gaps() removes insertion gaps ("-") in a
+ set of DNA sequences.
+
+
+BUG FIXES
+
+ o root() failed with resolve.root = TRUE when the root was already
+ the specified root.
+
+ o Several bugs were fixed in mlphylo().
+
+
+OTHER CHANGES
+
+ o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
+ Minin.
+
+
+
+ CHANGES IN APE VERSION 2.2
+
+
+NEW FEATURES
+
+ o Four new functions have been written by Damien de Vienne for the
+ graphical exploration of large trees (cophyloplot, subtrees,
+ subtreeplot), and to return the graphical coordinates of tree
+ (without plotting).
+
+ o The new functions corPagel and corBlomberg implement the Pagel's
+ "lambda" and Blomberg et al.'s "ACDC" correlation structures.
+
+ o chronopl() has been improved and gains several options: see its
+ help page for details.
+
+ o boot.phylo() has now an option 'trees' to possibly return the
+ bootstraped trees (the default is FALSE).
+
+ o prop.part() has been improved and should now be faster in all
+ situations.
+
+
+BUG FIXES
+
+ o read.dna() failed if "?" occurred in the first 10 sites of the
+ first sequence.
+
+ o The x/y aspect of the plot is now respected when plotting a
+ circular tree (type = "r" or "f").
+
+ o Drawing the tip labels sometimes failed when plotting circular
+ trees.
+
+ o zoom() failed when tip labels were used instead of their numbers
+ (thanks to Yan Wong for the fix).
+
+ o drop.tip() failed with some trees (fixed by Yan Wong).
+
+ o seg.sites() failed with a list.
+
+ o consensus() failed in some cases. The function has been improved
+ as well and is faster.
+
+
+
+ CHANGES IN APE VERSION 2.1-3
+
+
+BUG FIXES
+
+ o A bug in read.nexus() made the Windows R-GUI crash.
+
+ o An error was fixed in the computation of ancestral character
+ states by generalized least squares in ace().
+
+ o di2multi() did not modify node labels correctly.
+
+ o multi2di() failed if the tree had its attribute "order" set to
+ "cladewise".
+
+
+
+ CHANGES IN APE VERSION 2.1-2
+
+
+NEW FEATURES
+
+ o There three new methods for the "multiPhylo" class: str, $,
+ and [[.
+
+ o root() gains the options 'node' and 'resolve.root'
+ (FALSE by default) as well as its code being improved.
+
+ o mltt.plot() has now an option 'log' used in the same way
+ than in plot.default().
+
+
+BUG FIXES
+
+ o mltt.plot() failed to display the legend with an unnamed
+ list of trees.
+
+ o nodelabels() with pies now correcly uses the argument
+ 'cex' to draw symbols of different sizes (which has
+ worked already for thermometers).
+
+ o read.nexus() generally failed to read very big files.
+
+
+OTHER CHANGES
+
+ o The argument 'family' of compar.gee() can now be a function
+ as well as a character string.
+
+ o read.tree() and read.nexus() now return an unnamed list if
+ 'tree.names = NULL'.
+
+ o read.nexus() now returns a modified object of class "multiPhylo"
+ when there is a TRANSLATE block in the NEXUS file: the individual
+ trees have no 'tip.label' vector, but the list has a 'TipLabel'
+ attribute. The new methods '$' and '[[' set these elements
+ correctly when extracting trees.
+
+
+
CHANGES IN APE VERSION 2.1-1
OTHER CHANGES
o The code of mlphylo() has almost entirely rewritten, and should
- much stabler now. The options have been also greatly simplified
+ be much stabler. The options have been also greatly simplified
(see ?mlphylo and ?DNAmodel for details).
o The internal function nTips has been renamed klastorin_nTips.
projects / ape.git / blobdiff