+ CHANGES IN APE VERSION 2.2-2
+
+
+NEW FEATURES
+
+ o dist.gene() has been substantially improved and gains an option
+ 'pairwise.deletion'.
+
+
+BUG FIXES
+
+ o prop.part() failed with a single tree with the default option
+ 'check.labels = TRUE'.
+
+ o summary.DNAbin() failed to display correctly the summary of
+ sequence lengths with lists of sequences of 10,000 bases or more
+ (because summary.default uses 4 significant digits by default).
+
+ o read.nexus() failed to read a file with a single tree with line
+ breaks in the Newick string.
+
+ o del.gaps() returned a list of empty sequences when there were no
+ gaps.
+
+
+OTHER CHANGES
+
+ o The data sets bird.orders and bird.families are now stored as
+ Newick strings; i.e., the command data(bird.orders) calls
+ read.tree().
+
+
+
+ CHANGES IN APE VERSION 2.2-1
+
+
+NEW FEATURES
+
+ o The new function makeLabel() helps to modify labels of trees,
+ lists of trees, or DNA sequences, with several utilities to
+ truncate and/or make them unique, substituting some
+ characters, and so on.
+
+ o The new function del.gaps() removes insertion gaps ("-") in a
+ set of DNA sequences.
+
+ o read.dna() can now read Clustal files (*.aln).
+
+
+BUG FIXES
+
+ o root() failed with 'resolve.root = TRUE' when the root was
+ already the specified root.
+
+ o Several bugs were fixed in mlphylo().
+
+ o collapsed.singles() did not propagate the 'Nnode' and
+ 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
+
+ o read.nexus() failed to remove correctly the comments within
+ trees.
+
+ o read.nexus() failed to read a file with a single tree and no
+ translation of tip labels.
+
+ o read.nexus() failed to place correctly tip labels when reading
+ a single tree with no edge lengths.
+
+ o A bug was fixed in sh.test().
+
+
+OTHER CHANGES
+
+ o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
+ Minin.
+
+ o The option 'check.labels' of consensus() and prop.part() is now
+ TRUE by default.
+
+ o write.dna() now does not truncate names to 10 characters with
+ the Phylip formats.
+
+
+
+ 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
- (see ?mlphylo and ?DNAmodel for details).
+ o The code of mlphylo() has been almost entirely rewritten, and
+ should 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