+ CHANGES IN APE VERSION 3.0-7
+
+
+NEW FEATURES
+
+ o The new function 'where' searches patterns in DNA sequences.
+
+ o pic() gains an option 'rescaled.tree = FALSE' to return the tree
+ with its branch lengths rescaled for the PIC calculation.
+
+ o clustal(), muscle(), and tcoffee() gain an option
+ 'original.ordering = TRUE' to ease the comparisons of
+ alignments.
+
+ o plot.phylo() has a new option, open.angle, used when plotting
+ circular trees.
+
+ o The new function read.FASTA reads FASTA files much faster and
+ more efficiently. It is called internally by read.dna(, "fasta")
+ or can be called directly.
+
+
+BUG FIXES
+
+ o drop.tip() shuffled node labels on some trees.
+
+ o axisPhylo() now works correctly with circular trees, and gives a
+ sensible error message when type = "r" or "u".
+
+
+OTHER CHANGES
+
+ o .compressTipLabel() is 10 times faster thanks to Joseph Brown.
+
+ o base.freq() is now faster with lists.
+
+
+
+ CHANGES IN APE VERSION 3.0-6
+
+
+NEW FEATURES
+
+ o reorder.phylo() has a new order, "postorder", and a new option
+ index.only = TRUE to return only the vector of indices (the tree
+ is unmodified, see ?reorder.phylo for details).
+
+ o The three new functions node.depth.edgelength, node.height, and
+ node.height.clado make some internal code available from R. See
+ ?node.depth (which was already documented) for details.
+
+
+BUG FIXES
+
+ o reorder(, "pruningwise") made R crash if the rows of the edge
+ matrix are in random order: this is now fixed.
+
+ o drop.tip() sometimes shuffled node labels (thanks to Rebecca
+ Best for the report).
+
+ o drop.tip(phy, "") returned a tree with zero-length tip labels:
+ it now returns the tree unchanged (thanks to Brian Anacker for
+ the report).
+
+ o plot.phylo() made R crash if the tree has zero-length tip
+ labels: it now returns NULL (thanks again to Brian Anacker).
+
+
+OTHER CHANGES
+
+ o dist.nodes() is now 6 to 10 times faster.
+
+ o reorder(, "cladewise") is now faster. The change is not very
+ visible for small trees (n < 1000) but this can be more than
+ 1000 faster for big trees (n >= 1e4).
+
+ o The attribute "order" of the objects of class "phylo" is now
+ strongly recommended, though not mandatory. Most functions in
+ ape should return a tree with this attribute correctly set.
+
+ o dbd() is now vectorized on both arguments 'x' (number of species
+ in clade) and 't' (clade age) to make likelihood calculations
+ easier and faster.
+
+
+
+ CHANGES IN APE VERSION 3.0-5
+
+
+BUG FIXES
+
+ o ace() should better catch errors when SEs cannot be computed.
+
+
+OTHER CHANGES
+
+ o write.dna(format = "fasta") now conforms more closely to the
+ FASTA standard thanks to François Michonneau.
+
+ o print.DNAbin() does not print base compositions if there are more
+ than one million nucleotides.
+
+
+
+ CHANGES IN APE VERSION 3.0-4
+
+
+BUG FIXES
+
+ o read.dna() failed to read Phylip files if the first line used
+ tabulations instead of white spaces.
+
+ o read.dna() failed to read Phylip or Clustal files with less than
+ 10 nucleotides. (See other changes in this function below.)
+
+OTHER CHANGES
+
+ o read.dna() now requires at least one space (or tab) between the
+ taxa names and the sequences (whatever the length of taxa
+ names). write.dna() now follows the same rule.
+
+ o The option 'seq.names' of read.dna has been removed.
+
+ o The files ape-defunct.R and ape-defunct.Rd, which have not been
+ modified for almost two years, have been removed.
+
+ o The C code of bionj() has been reworked: it is more stable (by
+ avoiding passing character strings), slightly faster (by about
+ 20%), and numerically more accurate.
+
+ o The C code of fastme.*() has been slightly modified and should
+ be more stable by avoiding passing character strings (the
+ results are identical to the previous versions).
+
+ o The file src/newick.c has been removed.
+
+
+
+ CHANGES IN APE VERSION 3.0-3
+
+
+BUG FIXES
+
+ o birthdeath() now catches errors and warnings much better so that
+ a result is returned in most cases.
+
+
+OTHER CHANGES
+
+ o Because of problems with character string manipulation in C, the
+ examples in ?bionj and in ?fastme have been disallowed. In the
+ meantime, these functions might be unstable. This will be solved
+ for the next release.
+
+
+
CHANGES IN APE VERSION 3.0-2
o A bug was fixed in phymltest(): the executable couldn't be found
in some cases.
- o Three bug have been fixed in ace(): computing the likelihood of
+ o Three bugs have been fixed in ace(): computing the likelihood of
ancestral states of discrete characters failed, custom models
did not work, and the function failed with a null gradient (a
warning message is now returned; this latter bug was also
present in yule.cov() as well and is now fixed).
- o pic() hanged out when missing data were present: a message error
- is now returned.
+ o pic() hanged out when missing data were present: an error is now
+ returned.
o A small bug was fixed in dist.dna() where the gamma correction
was not always correctly dispatched.
DNA sequences by specifying model = "raw".
o dist.phylo() has a new option `full' to possibly compute the
- distances among all tips and nodes of the tree. The default if
+ distances among all tips and nodes of the tree. The default is
`full = FALSE'.
projects / ape.git / blobdiff