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ChangeLog
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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().
o write.tree() did not output correctly node labels (thanks to Naim
Matasci for the fix).
o ace(type = "discrete") has been improved thanks to Naim Marasci.
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
NEW FEATURES
o The new function parafit by Pierre Legendre tests for the
coevolution between hosts and parasites. It has a companion
function, pcoa, that does principal coordinate decomposition.
The latter has a biplot method.
o The new function lmorigin by Pierre Legendre performs multiple
regression through the origin with testing by permutation.
o The new functions rTraitCont and rTraitDisc simulate continuous and
discrete traits under a wide range of evolutionary models.
o The new function delta.plot does a delta plot following Holland et
al. (2002, Mol. Biol. Evol. 12:2051).
o The new function edges draws additional branches between any nodes
and/or tips on a plotted tree.
o The new function fancyarrows enhances arrows from graphics with
triangle and harpoon heads; it can be called from edges().
o add.scale.bar() has a new option 'ask' to draw interactively.
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
o add.scale.bar() drew the bar outside the plotting region with the
default options with unrooted or radial trees.
o dist.topo() made R stuck when the trees had different sizes (thanks
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
NEW FEATURES
o rtree() and rcoal() now accept a numeric vector for the 'br'
argument.
o vcv() is a new generic function with methods for the classes "phylo"
and "corPhyl" so that it is possible to calculate the var-cov matrix
for "transformation models". vcv.phylo() can still be used for trees
of class "phylo"; its argument 'cor' has been renamed 'corr'.
BUG FIXES
o bind.tree() failed when 'y' had no root edge.
o read.nexus() shuffled tip labels when the trees have no branch
lengths and there is a TRANSLATE block.
o read.nexus() does not try to translate node labels if there is a
translation table in the NEXUS file. See ?read.nexus for a
clarification on this behaviour.
o plot.multiPhylo() crashed R when plotting a list of trees with
compressed tip labels.
o write.nexus() did not translate the taxa names when asked for.
o plot.phylo(type = "fan") did not rotate the tip labels correctly
when the tree has branch lengths.
o ace(type = "continuous", method = "ML") now avoids sigma² being
negative (which resulted in an error).
o nj() crashed with NA/NaN in the distance matrix: an error in now
returned.
CHANGES IN APE VERSION 2.4
NEW FEATURES
o base.freq() has a new option 'freq' to return the counts; the
default is still to return the proportions.
BUG FIXES
o seg.sites() did not handle ambiguous nucleotides correctly: they
are now ignored.
o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
the tree: the argument is now ignored.
o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
Young for the fix).
OTHER CHANGES
o Trying to plot a tree with a single tip now returns NULL with a
warning (it returned an error previously).
o The way lines representing nodes are coloured in phylograms has
been modified (as well as their widths and types) following some
users' request; this is only for dichotomous nodes.
o The argument 'adj' in [node][tip][edge]labels() now works when
using 'pie' or 'thermo'.
o A more informative message error is now returned by dist.dna() when
'model' is badly specified (partial matching of this argument is
done now).
o Deprecated functions are now listed in a help page: see
help("ape-defunct") with the quotes.
DEPRECATED & DEFUNCT
o The functions heterozygosity, nuc.div, theta.h, theta.k and
theta.s have been moved from ape to pegas.
o The functions mlphylo, DNAmodel and sh.test have been removed.
CHANGES IN APE VERSION 2.3-3
BUG FIXES
o add.scale.bar() always drew a horizontal bar.
o zoom() shuffled tips with unrooted trees.
o write.nexus() failed to write correctly trees with a "TipLabel"
attribute.
o rcoal() failed to compute branch lengths with very large n.
o A small bug was fixed in compar.cheverud() (thanks to Michael
Phelan for the fix).
o seg.sites() failed when passing a vector.
o drop.tip() sometimes shuffled tip labels.
o root() shuffled node labels with 'resolve.root = TRUE'.
CHANGES IN APE VERSION 2.3-2
BUG FIXES
o all.equal.phylo() did not compare unrooted trees correctly.
o dist.topo(... method = "PH85") did not treat unrooted trees
correctly (thanks to Tim Wallstrom for the fix).
o root() sometimes failed to test for the monophyly of the
outgroup correctly.
o extract.clade() sometimes included too many edges.
o vcv.phylo() did not work correctly when the tree is in
"pruningwise" order.
o nj() did not handle correctly distance matrices with many 0's.
The code has also been significantly improved: 7, 70, 160 times
faster with n = 100, 500, 1000, respectively.
CHANGES IN APE VERSION 2.3-1
NEW FEATURES
o The new function is.monophyletic tests the monophyly of a group.
o There is now a c() method for lists of class "DNAbin".
o yule.cov() now fits the null model, and its help page has been
corrected with respect to this change.
o drop.tip() has a new option 'rooted' to force (or not) a tree
to be treated as (un)rooted.
BUG FIXES
o dist.gene() failed on most occasions with the default
pairwise.deletion = FALSE.
o read.tree() failed to read correctly the tree name(s).
o boot.phylo() now treats correctly data frames.
o del.gaps() did not copy the rownames of a matrix.
o A small bug was fixed in CDAM.global().
o ace() failed with large data sets. Thanks to Rich FitzJohn for
the fix. With other improvements, this function is now about 6
times faster.
o write.tree() failed with objects of class "multiPhylo".
o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
OTHER CHANGES
o [.multiPhylo and [.DNAbin now respect the original class.
o Instances of the form class(phy) == "phylo" have been replaced
by inherits(phy, "phylo").
o rcoal() is now faster.
DEPRECATED & DEFUNCT
o klastorin() has been removed.
CHANGES IN APE VERSION 2.3
NEW FEATURES
o The new functions CADM.global and CADM.post, contributed by
Pierre Legendre, test the congruence among several distance
matrices.
o The new function yule.time fits a user-defined time-dependent
Yule model by maximum likelihood.
o The new function makeNodeLabel creates and/or modifies node
labels in a flexible way.
o read.tree() and write.tree() have been modified so that they can
handle individual tree names.
o plot.phylo() has a new argument 'edge.lty' that specifies the
types of lines used for the edges (plain, dotted, dashed, ...)
o phymltest() has been updated to work with PhyML 3.0.1.
BUG FIXES
o drop.tip() shuffled tip labels in some cases.
o drop.tip() did not handle node.label correctly.
o is.ultrametric() now checks the ordering of the edge matrix.
o ace() sometimes returned negative values of likelihoods of
ancestral states (thanks to Dan Rabosky for solving this long
lasting bug).
OTHER CHANGES
o The data set xenarthra has been removed.
CHANGES IN APE VERSION 2.2-4
BUG FIXES
o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
now fixed. (Thanks to Peter Wragg for the fix!)
o A warning message occurred for no reason with ace(method="GLS").
OTHER CHANGES
o There is now a general help page displayed with '?ape'.
CHANGES IN APE VERSION 2.2-3
NEW FEATURES
o The new function extract.clade extracts a clade from a tree by
specifying a node number or label.
o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
operations of the same names.
o dist.dna() can now return the number of site differences by
specifying model="N".
BUG FIXES
o chronopl() did not work with CV = TRUE.
o read.nexus() did not work correctly in some situations (trees on
multiple lines with different numbers of lines and/or with
comments inserted within the trees).
o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
the number of lineages with non-binary trees.
OTHER CHANGES
o ape has now a namespace.
o drop.tip() has been improved: it should be much faster and work
better in some cases (e.g., see the example in ?zoom).
CHANGES IN APE VERSION 2.2-2
NEW FEATURES
o dist.gene() has been substantially improved and gains an option
'pairwise.deletion'.
o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
more flexible.
BUG FIXES
o prop.part() failed with a single tree with the default option
'check.labels = TRUE'.
o summary.DNAbin() failed to display correctly the summary of
sequence lengths with lists of sequences of 10,000 bases or more
(because summary.default uses 4 significant digits by default).
o read.nexus() failed to read a file with a single tree with line
breaks in the Newick string.
o del.gaps() returned a list of empty sequences when there were no
gaps.
OTHER CHANGES
o phymltest() has been updated for PhyML 3.0 and gains an option
'append', whereas the option 'path2exec' has been removed.
o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
which is returned unchanged (instead of an error).
o The data sets bird.orders and bird.families are now stored as
Newick strings; i.e., the command data(bird.orders) calls
read.tree().
CHANGES IN APE VERSION 2.2-1
NEW FEATURES
o The new function makeLabel() helps to modify labels of trees,
lists of trees, or DNA sequences, with several utilities to
truncate and/or make them unique, substituting some
characters, and so on.
o The new function del.gaps() removes insertion gaps ("-") in a
set of DNA sequences.
o read.dna() can now read Clustal files (*.aln).
BUG FIXES
o root() failed with 'resolve.root = TRUE' when the root was
already the specified root.
o Several bugs were fixed in mlphylo().
o collapsed.singles() did not propagate the 'Nnode' and
'node.labels' elements (thanks to Elizabeth Purdom for the fix).
o read.nexus() failed to remove correctly the comments within
trees.
o read.nexus() failed to read a file with a single tree and no
translation of tip labels.
o read.nexus() failed to place correctly tip labels when reading
a single tree with no edge lengths.
o A bug was fixed in sh.test().
OTHER CHANGES
o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
Minin.
o The option 'check.labels' of consensus() and prop.part() is now
TRUE by default.
o write.dna() now does not truncate names to 10 characters with
the Phylip formats.
CHANGES IN APE VERSION 2.2
NEW FEATURES
o Four new functions have been written by Damien de Vienne for the
graphical exploration of large trees (cophyloplot, subtrees,
subtreeplot), and to return the graphical coordinates of tree
(without plotting).
o The new functions corPagel and corBlomberg implement the Pagel's
"lambda" and Blomberg et al.'s "ACDC" correlation structures.
o chronopl() has been improved and gains several options: see its
help page for details.
o boot.phylo() has now an option 'trees' to possibly return the
bootstraped trees (the default is FALSE).
o prop.part() has been improved and should now be faster in all
situations.
BUG FIXES
o read.dna() failed if "?" occurred in the first 10 sites of the
first sequence.
o The x/y aspect of the plot is now respected when plotting a
circular tree (type = "r" or "f").
o Drawing the tip labels sometimes failed when plotting circular
trees.
o zoom() failed when tip labels were used instead of their numbers
(thanks to Yan Wong for the fix).
o drop.tip() failed with some trees (fixed by Yan Wong).
o seg.sites() failed with a list.
o consensus() failed in some cases. The function has been improved
as well and is faster.
CHANGES IN APE VERSION 2.1-3
BUG FIXES
o A bug in read.nexus() made the Windows R-GUI crash.
o An error was fixed in the computation of ancestral character
states by generalized least squares in ace().
o di2multi() did not modify node labels correctly.
o multi2di() failed if the tree had its attribute "order" set to
"cladewise".
CHANGES IN APE VERSION 2.1-2
NEW FEATURES
o There three new methods for the "multiPhylo" class: str, $,
and [[.
o root() gains the options 'node' and 'resolve.root'
(FALSE by default) as well as its code being improved.
o mltt.plot() has now an option 'log' used in the same way
than in plot.default().
BUG FIXES
o mltt.plot() failed to display the legend with an unnamed
list of trees.
o nodelabels() with pies now correcly uses the argument
'cex' to draw symbols of different sizes (which has
worked already for thermometers).
o read.nexus() generally failed to read very big files.
OTHER CHANGES
o The argument 'family' of compar.gee() can now be a function
as well as a character string.
o read.tree() and read.nexus() now return an unnamed list if
'tree.names = NULL'.
o read.nexus() now returns a modified object of class "multiPhylo"
when there is a TRANSLATE block in the NEXUS file: the individual
trees have no 'tip.label' vector, but the list has a 'TipLabel'
attribute. The new methods '$' and '[[' set these elements
correctly when extracting trees.
CHANGES IN APE VERSION 2.1-1
NEW FEATURES
o The new function rmtree generates lists of random trees.
o rcoal() now generates a genuine coalescent tree by default
(thanks to Vladimir Minin for the code).
BUG FIXES
o nuc.div() returned an incorrect value with the default
pairwise.deletion = FALSE.
OTHER CHANGES
o The internal codes of bionj(), fastme.bal(), and fastme.ols()
have been improved so that they are stabler and faster.
o R packages used by ape are now loaded silently; lattice and gee
are loaded only when needed.
CHANGES IN APE VERSION 2.1
NEW FEATURES
o The new function identify.phylo identifies clades on a plotted
tree using the mouse.
o It is now possible to subset a list of trees (object of class
"multiPhylo") with "[" while keeping its class correct.
o The new function as.DNAbin.alignment converts DNA sequences
stored in the "alignment" format of the package seqinr into
an object of class "DNAbin".
o The new function weight.taxo2 helps to build similarity matrices
given two taxonomic levels (usually called by other functions).
o write.tree() can now take a list of trees (class "multiPhylo")
as its main argument.
o plot.correlogram() and plot.correlogramList() have been
improved, and gain several options (see the help page for
details). A legend is now plotted by default.
BUG FIXES
o dist.dna() returned some incorrect values with `model = "JC69"'
and `pairwise.deletion = TRUE'. This affected only the
distances involving sequences with missing values. (Thanks
to Bruno Toupance for digging this bug out.)
o write.tree() failed with some trees: this is fixed by removing
the `multi.line' option (trees are now always printed on a
single line).
o read.nexus() did not correctly detect trees with multiple root
edges (see OTHER CHANGES).
OTHER CHANGES
o The code of mlphylo() has been almost entirely rewritten, and
should be much stabler. The options have been also greatly
simplified (see ?mlphylo and ?DNAmodel for details).
o The internal function nTips has been renamed klastorin_nTips.
o The code of is.ultrametric() contained redundancies and has
been cleaned-up.
o The code of Moran.I() and of correlogram.formula() have been
improved.
o read.tree() and read.nexus() now return an error when trying to
read a tree with multiple root edges (see BUG FIXES). The
correction applied in previous version did not work in all
situations.
o The class c("multi.tree", "phylo") has been renamed
"multiPhylo".
DOCUMENTATION
o There is now a vignette in ape: see vignette("MoranI", "ape").
DEPRECATED & DEFUNCT
o as.matching() and as.phylo.matching() do not support branch
lengths.
o correlogram.phylo() and discrete.dist() have been removed.
CHANGES IN APE VERSION 2.0-2
NEW FEATURES
o The new function matexpo computes the exponential of a square
matrix.
o The new function unique.multi.tree removes duplicate trees from
a list.
o yule() has a new option `use.root.edge = FALSE' that specifies
to ignore, by default, the root edge of the tree if it exists.
BUG FIXES
o which.edge() failed when the index of a single terminal edge was
looked for.
o In diversi.time(), the values returned for model C were
incorrect.
o A bug was fixed in yule() that affected the calculation of the
likelihood in the presence of ties in the branching times.
o There was a bug in the C function mat_expo4x4 affecting the
calculations of the transition probabilities for models HKY and
GTR in mlphylo().
o A small bug was fixed in as.matrix.DNAbin (thanks to James
Bullard).
o rtree() did not `shuffle' the tip labels by default, so only a
limited number of labelled topologies could be generated.
CHANGES IN APE VERSION 2.0-1
NEW FEATURES
o The three new functions bionj, fastme.ols, and fastme.bal
perform phylogeny estimation by the BIONJ and fastME methods in
OLS and balanced versions. This is a port to R of previous
previous programs done by Vincent Lefort.
o The new function chronoMPL performs molecular dating with the
mean path lengths method of Britton et al. (2002, Mol. Phyl.
Evol. 24: 58).
o The new function rotate, contributed by Christoph Heibl, swaps
two clades connected to the same node. It works also with
multichotomous nodes.
o The new `method' as.matrix.DNAbin() may be used to convert
easily DNA sequences stored in a list into a matrix while
keeping the names and the class.
BUG FIXES
o chronopl() failed when some branch lengths were equal to zero:
an error message is now returned.
o di2multi() failed when there was a series of consecutive edges
to remove.
CHANGES IN APE VERSION 1.10-2
NEW FEATURES
o plot.phylo() can now plot circular trees: the option is type =
"fan" or type = "f" (to avoid the ambiguity with type = "c").
o prop.part() has a new option `check.labels = FALSE' which allows
to considerably speed-up the calculations of bipartitions. As a
consequence, calculations of bootstrap values with boot.phylo()
should be much faster.
BUG FIXES
o read.GenBank() did not return correctly the list of species as
from ape 1.10: this is fixed in this version
o Applying as.phylo() on a tree of class "phylo" failed: the
object is now returned unchanged.
CHANGES IN APE VERSION 1.10-1
NEW FEATURES
o The three new functions Ntip, Nnode, and Nedge return, for a
given tree, the number of tips, nodes, or edges, respectively.
BUG FIXES
o read.nexus() did not set correctly the class of the returned
object when reading multiple trees.
o mllt.plot() failed with objects of class c("multi.tree",
"phylo").
o unroot() did not work correctly in most cases.