+ 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.
+
+
+
+ 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
+
+
+NEW FEATURES
+
+ o The new function compute.brtime computes and sets branching times.
+
+ o mantel.test() has a new argument 'alternative' which is
+ "two-sided" by default. Previously, this test was one-tailed
+ with no possibility to change.
+
+ o ace() can now do REML estimation with continuous characters,
+ giving better estimates of the variance of the Brownian motion
+ process.
+
+
+BUG FIXES
+
+ o Branch lengths were wrongly updated with bind.tree(, where = <tip>,
+ position = 0). (Thanks to Liam Revell for digging this bug out.)
+
+ o Simulation of OU process with rTraitCont() did not work correctly.
+ This now uses formula from Gillespie (1996) reduced to a BM
+ process when alpha = 0 to avoid division by zero. The option
+ 'linear' has been removed.
+
+ o Cross-validation in chronopl() did not work when 'age.max' was
+ used.
+
+ o consensus(, p = 0.5) could return an incorrect tree if some
+ incompatible splits occur in 50% of the trees (especially with
+ small number of trees).
+
+ 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.
+
+
+
CHANGES IN APE VERSION 2.7-2
NEW FEATURES
- o plot.phylo() has a new option 'draw = TRUE'. If FALSE, the tree
+ o There is a new class "evonet" to code evolutionary networks, with
+ a constructor function evonet(), a print() and a plot() methods,
+ and four conversion methods to the classes "phylo", "networx",
+ "network", and "igraph".
+
+ o The new function rTraitMult does multivariate traits simulation
+ with user-defined models.
+
+ o plot.phylo() has a new option 'plot = TRUE'. If FALSE, the tree
is not plotted but the graphical device is set and the
- coordinates are saved as normal.
+ coordinates are saved as usual.
+
+ o diversity.contrast.test() gains a fourth version of the test with
+ method = "logratio"; the literature citations have been clarified.
+
+ o add.scale.bar() has two new options, 'lwd' and 'lcol', to modify
+ the aspect of the bar.
+
+ o boot.phylo() now displays a progress bar by default (can be off
+ if 'quiet = TRUE').
+
+ o There is a new predict() method for compar.gee().
+
+
+BUG FIXES
+
+ o bionj() made R crash if distances were too large. It now returns
+ an error if at least one distance is greater than 100.
+
+ o drop.tip() returned a wrong tree if 'tip' was of zero length.
+
+ o read.nexus.data() failed with URLs.
+
+ o boot.phylo() returned overestimated support values in the
+ presence of identical or nearly identical sequences.
+
+
+OTHER CHANGES
+
+ o The data bird.families, bird.orders, cynipids, and woodmouse are
+ now provided as .rda files.
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