- CHANGES IN APE VERSION 2.8-1
+ 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 'rooted' option.
+
+ 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'.
+
+
+OTHER CHANGES
+
+ o The DESCRIPTION file has been updated.
+
+ o The option 'original.data' of write.nexus() has been removed.
+
+
+
+ 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.
+ 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 mantel.test() could return P-values > 1 with the default
+ 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 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
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