+ CHANGES IN APE VERSION 2.6-2
+
+
+NEW FEATURES
+
+ o Two new functions, pic.ortho and varCompPhylip, implements the
+ orthonormal contrasts of Felsenstein (2008, Am Nat, 171:713). The
+ second function requires Phylip to be installed on the computer.
+
+ o bd.ext() has a new option conditional = TRUE to use probabilities
+ conditioned on no extinction for the taxonomic data.
+
+
+BUG FIXES
+
+ o write.tree() failed to output correctly tree names.
+
+ o dist.nodes() returned duplicated column(s) with unrooted and/or
+ multichotomous trees.
+
+ o mcmc.popsize() terminated unexpectedly if the progress bar was
+ turned off.
+
+ o prop.part(x) made R frozen if 'x' is of class "multiPhylo".
+
+ o Compilation under Mandriva failed (thanks to Jos Käfer for the fix).
+
+ o drop.tip() shuffled tip labels with subtree = TRUE or trim.internal
+ = FALSE.
+
+ o Objects returned by as.hclust.phylo() failed when analysed with
+ cutree() or rect.hclust().
+
+
+
+ CHANGES IN APE VERSION 2.6-1
+
+
+NEW FEATURES
+
+ o The new function speciesTree calculates the species tree from a set
+ of gene trees. Several methods are available including maximum tree
+ and shallowest divergence tree.
+
+
+BUG FIXES
+
+ o A bug introduced in write.tree() with ape 2.6 has been fixed.
+
+ o as.list.DNAbin() did not work correctly with vectors.
+
+ o as.hclust.phylo() failed with trees with node labels (thanks to
+ Filipe Vieira for the fix).
+
+
+
+ CHANGES IN APE VERSION 2.6
+
+
+NEW FEATURES
+
+ o The new functions rlineage and rbdtree simulate phylogenies under
+ any user-defined time-dependent speciation-extinction model. They
+ use continuous time algorithms.
+
+ o The new function drop.fossil removes the extinct species from a
+ phylogeny.
+
+ o The new function bd.time fits a user-defined time-dependent
+ birth-death model. It is a generalization of yule.time() taking
+ extinction into account.
+
+ o The new function MPR does most parsimonious reconstruction of
+ discrete characters.
+
+ o The new function Ftab computes the contingency table of base
+ frequencies from a pair of sequences.
+
+ o There is now an 'as.list' method for the class "DNAbin".
+
+ o dist.dna() can compute the number of transitions or transversions
+ with the option model = "Ts" or model = "Tv", respectively.
+
+ o [node|tip|edge]labels() gain three options with default values to
+ control the aspect of thermometers: horiz = TRUE, width = NULL,
+ and height = NULL.
+
+ o compar.gee() has been improved with the new option 'corStruct' as an
+ alternative to 'phy' to specify the correlation structure, and
+ calculation of the QIC (Pan 2001, Biometrics). The display of the
+ results has also been improved.
+
+ o read.GenBank() has a new option 'gene.names' to return the name of
+ the gene (FALSE by default).
+
+
+BUG FIXES
+
+ o extract.clade() sometimes shuffled the tip labels.
+
+ o plot.phylo(type = "unrooted") did not force asp = 1 (thanks to Klaus
+ Schliep for the fix)
+
+ o dist.dna(model = "logdet") used to divide distances by 4. The
+ documentation has been clarified on the formulae used.
+
+
+OTHER CHANGES
+
+ o rTraitCont(model = "OU") has an option 'linear = TRUE' to possibly
+ change the parameterisation (see ?rTraitCont for details).
+
+ o pic() now returns a vector with the node labels of the tree (if
+ available) as names.
+
+ o write.tree() and read.tree() have been substantially improved thanks
+ to contributions by Klaus Schliep.
+
+
+
+ CHANGES IN APE VERSION 2.5-3
+
+
+NEW FEATURES
+
+ o The new function mixedFontLabel helps to make labels with bits of
+ text to be plotted in different fonts.
+
+ o There are now replacement operators for [, [[, and $ for the class
+ "multiPhylo" (i.e., TREES[11:20] <- rmtree(10, 100)). They possibly
+ check that the tip labels are the same in all trees.
+
+ o Objects of class "multiPhylo" can be built with c(): there are
+ methods for the classes "phylo" and "multiPhylo".
+
+ o The internal functions .compressTipLabel and .uncompressTipLabel are
+ now documented.
+
+
+BUG FIXES
+
+ o bind.tree(x, y, where, position = 0) did not work correctly if 'y'
+ was a single-edge tree and 'where' was a tip.
+
+ o rTraitCont() did not use the square-root of branch lengths when
+ simulating a Brownian motion model.
+
+
+
+ CHANGES IN APE VERSION 2.5-2
+
+
+NEW FEATURES
+
+ o There is now a print method for results from ace().
+
+ o There is a labels() method for objects of class "DNAbin".
+
+ o read.dna() has a new option 'as.matrix' to possibly force sequences
+ in a FASTA file to be stored in a matrix (see ?read.dna for details).
+
+
+BUG FIXES
+
+ o as.phylo.hclust() used to multiply edge lengths by 2.
+
+ o A minor bug was fixed in rTraitDisc().
+
+ o ace() sometimes failed (parameter value was NaN and the optimisation
+ failed).
+
+
+DEPRECATED & DEFUNCT
+
+ o evolve.phylo() and plot.ancestral() have been removed.
+
+ o chronogram(), ratogram(), and NPRS.criterion() have been removed.
+
+
+OTHER CHANGES
+
+ o nj() has been improved and is now about 30% faster.
+
+ o The default option 'drop' of [.DNAbin has been changed to FALSE to
+ avoid dropping rownames when selecting a single sequence.
+
+ o print.DNAbin() has been changed to summary.DNAbin() which has been
+ removed.
+
+
+
+ CHANGES IN APE VERSION 2.5-1
+
+
+NEW FEATURES
+
+ o The new function stree generates trees with regular shapes.
+
+ o It is now possible to bind two trees with x + y (see ?bind.tree for
+ details).
+
+ o drop.tip(), extract.clade(), root(), and bind.tree() now have an
+ 'interactive' option to make the operation on a plotted tree.
+
+ o cophyloplot() gains two new arguments 'lwd' and 'lty' for the
+ association links; they are recycled like 'col' (which wasn't before).
+
+
+BUG FIXES
+
+ o rTraitDisc() did not use its 'freq' argument correctly (it was
+ multiplied with the rate matrix column-wise instead of row-wise).
+
+ o [node|tip|edge]labels(thermo = ) used to draw empty thermometers
+ with NA values. Nothing is drawn now like with 'text' or 'pch'.
+ The same bug occurred with the 'pie' option.
+
+ o A bug was fixed in compar.ou() and the help page was clarified.
+
+ o bind.tree() has been rewritten fixing several bugs and making it
+ more efficient.
+
+ o plot.phylo(type = "p") sometimes failed to colour correctly the
+ vertical lines representing the nodes.
+
+ o plot.phylo(direction = "l", x.lim = 30) failed to plot the branches
+ in the correct direction though the tip labels were displayed
+ correctly.
+
+
+OTHER CHANGES
+
+ o The c, cbind, and rbind methods for "DNAbin" objetcs now check that
+ the sequences are correctly stored (in a list for c, in a matrix
+ for the two other functions).
+
+
+
CHANGES IN APE VERSION 2.5
o The branch length score replaces the geodesic distance in dist.topo.
+ o Three new data sets are included: the gopher-lice data (gopher.D),
+ SO2 air pollution in 41 US cities (lmorigin.ex1, from Sokal &
+ Rohlf 1995), and some host-parasite specificity data
+ (lmorigin.ex2, from Legendre & Desdevises 2009).
+
BUG FIXES
to Otto Cordero for the fix).
+OTHER CHANGES
+
+ o The geodesic distance has been replaced by the branch length score
+ in dist.topo().
+
+
CHANGES IN APE VERSION 2.4-1
projects / ape.git / blobdiff