+ CHANGES IN APE VERSION 3.0-5
+
+
+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
+
+
+NEW FEATURES
+
+ o The new function alex (alignment explorator) zooms in a DNA
+ alignment and opens the result in a new window.
+
+
+BUG FIXES
+
+ o compute.brtime() did not completely randomized the order of the
+ branching times.
+
+ o write.nexus() did not work correctly with rooted trees (thanks
+ to Matt Johnson for the fix).
+
+ o mltt.plot(, backward = FALSE) did not set the x-axis correctly.
+
+ 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.
+
+ 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).
+
+
+
+ CHANGES IN APE VERSION 3.0-1
+
+
+NEW FEATURES
+
+ o dist.dna() has two new models: "indel" and "indelblock".
+
+ o bind.tree() now accepts 'position' > 0 when the trees have no
+ banch length permitting to create a node in 'x' when grafting
+ 'y' (see ?bind.tree for details).
+
+
+BUG FIXES
+
+ o cophyloplot( , rotate = TRUE) made R hanged after a few clicks.
+ Also the tree is no more plotted twice.
+
+ o read.GenBank() has been updated to work with EFetch 2.0.
+
+ o unroot() on trees in "pruningwise" order did not respect this
+ attribute.
+
+
+
+ CHANGES IN APE VERSION 3.0
+
+
+NEW FEATURES
+
+ o The three functions dyule, dbd, and dbdTime calculate the
+ density probability (i.e., the distribution of the number of
+ species) for the Yule, the constant and the time-dependent
+ birth-beath models, respectively. These probabilities can be
+ conditional on no extinction and/or on a log-scale.
+
+ o plot.phylo() has a new option 'rotate.tree' to rotate unrooted,
+ fan, or radial trees around the center of the plot.
+
+ o boot.phylo() and prop.clades() have a new option rooted =
+ FALSE. Note that the behaviour of prop.part() is unchanged.
+
+ o edgelabels() has a new option 'date' to place labels on edges of
+ chronograms using the time scale (suggestion by Rob Lanfear).
+
+
+BUG FIXES
+
+ o In chronopl(), the code setting the initial dates failed in
+ complicated settings (several dates known within intervals).
+ This has been generally improved and should result in faster
+ and more efficient convergence even in simple settings.
+
+ o mantel.test() sometimes returned P-values > 1 with the default
+ two-tailed test.
+
+ o extract.clade() sometimes shuffled some tip labels (thanks to
+ Ludovic Mallet and Mahendra Mariadassou for the fix).
+
+ o clustal() should now find by default the executable under Windows.
+
+
+OTHER CHANGES
+
+ o The code of yule() has been simplified and is now much faster for
+ big trees.
+
+ o The code of mantel.test() has been adjusted to be consistent
+ with common permutation tests.
+
+ o The C code of base.freq() has been improved and is now nearly 8
+ times faster.
+
+ o The option 'original.data' of write.nexus() is now deprecated and
+ will be removed in a future release.
+
+ o The code of is.ultrametric() has been improved and is now 3 times
+ faster.
+
+ o The code of vcv.phylo() has been improved and is now 10 or 30
+ times faster for 100 or 1000 tips, respectively. Consequently,
+ fitting models with PGLS will be faster overall.
+
+
+
+ CHANGES IN APE VERSION 2.8
+
+
+NEW FEATURES
+
+ o Twelve new functions have been written by Andrei-Alin Popescu:
+ additive, ultrametric, is.compatible, arecompatible, mvr, mvrs,
+ njs, bionjs, SDM, treePop, triangMtd, triangMtd*.
+
+ o A new class "bitsplits" has been created by Andrei-Alin Popescu
+ to code splits (aka, bipartition).
+
+ o There is a new generic function as.bitsplits with a method to
+ convert from the class "prop.part" to the class "bitsplits".
+
+ o The new function ltt.coplot plots on the same scales a tree and
+ the derived LTT plot.
+
+ o ltt.plot() has two new options: backward and tol. It can now
+ handle non-ultrametic trees and its internal coding has been
+ improved. The coordinates of the plot can now be computed with
+ the new function ltt.plot.coords.
+
+
+BUG FIXES
+
+ o prop.part() crashed if some trees had some multichotomies.
+
+
+
CHANGES IN APE VERSION 2.7-3
incompatible splits occur in 50% of the trees (especially with
small number of trees).
- o c() with "multiPhylo" did not work correctly.
+ o c() with "multiPhylo" did not work correctly (thanks to Klaus
+ Schliep for the fix).
+
+ o root() failed in some cases with an outgroup made of several tips.
+ The help page has been clarified a bit.
OTHER CHANGES
- o identify.phylo() now returns NULL if the user right-(instead of
- left-)clicks (an error was returned previously).
+ o identify.phylo() now returns NULL if the user right- (instead of
+ left-) clicks (an error was returned previously).
o read.nexus() should be robust to commands inserted in the TREES
block.
projects / ape.git / blobdiff