+ 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 mltt.plot(, backward = FALSE) did not set the x-axis correctly.
- o A bug was introduced in prop.clades() with ape 3.0.
+ o A bug was introduced in prop.clades() with ape 3.0. The help page
+ has been clarified relative to the use of the option 'rooted'.
o mantel.test() printed a useless warning message.
o plot.phylo(, direction = "downward") ignored 'y.lim'.
o is.monophyletic() did not work correctly if 'tips' was not stored
- as integers
+ as integers.
+
+ o prop.part() could make R crash if the first tree had many
+ multichotomies.
+
+ o njs(), bionjs(), and mvrs() now return an error if 'fs < 1'.
+
+ o SDM() did not work correctly. The code has also been generally
+ improved.
+
+
+OTHER CHANGES
+
+ o The DESCRIPTION file has been updated.
+
+ o The option 'original.data' of write.nexus() has been removed.
+
+ o The files bionjs.c, mvr.c, mvrs.c, njs.c, triangMtd.c, and
+ triangMtds.c have been improved which should fix some bugs in
+ the corresponding functions.
+
+ o dist.gene() now coerces input data frame as matrix resulting in
+ much faster calculations (thanks to a suggestion by Markus
+ Schlegel).
projects / ape.git / blobdiff