https://github.com/cran/ape
Tip revision: 8b74fd1a33fc8f4447127946bf5ebdb6e4f367a4 authored by Emmanuel Paradis on 14 April 2005, 00:00:00 UTC
version 1.5
version 1.5
Tip revision: 8b74fd1
Changes
CHANGES IN APE VERSION 1.5
NEW FEATURES
o Two new functions, as.matching.phylo() and as.phylo.matching(),
convert objects between the classes "phylo" and "matching". The
latter implements the representation of binary trees introduced by
Diaconis and Holmes (1998; PNAS, 95:14600). The generic function
as.matching() has been introduced as well.
o Two new functions, multi2di() and di2multi(), allow to resolve
and collapse multichotomies with branches of length zero.
o The new function nuc.div() computes the nucleotide diversity
from a sample a DNA sequences.
o dist.dna() has been completely rewritten with a much faster
(particularly for large data sets) C code. Eight models are
available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
option `method' has been renamed `model'). Computation of variance
is available for all models. A gamma-correction is possible for
JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
to remove sites with missing data on a pairwise basis. The option
`GCcontent' has been removed.
o read.GenBank() has a new option (species.names) which specifies
whether to return the species names of the organisms in addition
to the accession numbers of the sequences (this is the default
behaviour).
o write.nexus() can now write several trees in the same NEXUS file.
o drop.tip() has a new option `root.edge' that allows to specify the
new root edge if internal branches are trimmed.
BUG FIXES
o as.phylo.hclust() failed if some labels had parentheses: this
is fixed.
o Several bugs were fixed in all.equal.phylo(). This function now
returns the logical TRUE if the trees are identical but with
different representations (a report was printed previously).
o read.GenBank() did not correctly handle ambiguous base codes:
this is fixed.
OTHER CHANGES
o birthdeath() now returns an object of class "birthdeath" for
which there is a print method.
CHANGES IN APE VERSION 1.4
NEW FEATURES
o The new function nj() performs phylogeny estimation with the
neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
Evol., 4:406).
o The new function which.edge() identifies the edges of a tree
that belong to a group specified as a set of tips.
o The new function as.phylo.phylog() converts an object of class
"phylog" (from the package ade4) into an object of class
"phylo".
o The new function axisPhylo() draws axes on the side of a
phylogeny plot.
o The new function howmanytrees() calculates the number of trees
in different cases and giving a number of tips.
o write.tree() has a new option `multi.line' (TRUE by default) to
write a Newick tree on several lines rather than on a single
line.
o The functionalities of zoom() have been extended. Several
subtrees can be visualized at the same time, and they are marked
on the main tree with colors. The context of the subtrees can be
marked with the option `subtree' (see below).
o drop.tip() has a new option `subtree' (FALSE by default) which
specifies whether to output in the tree how many tips have been
deleted and where.
o The arguments of add.scale.bar() have been redefined and have
now default values (see ?add.scale.bar for details). This
function now works even if the plotted tree has no edge length.
o plot.phylo() can now plot radial trees, but this does not take
edge lengths into account.
o In plot.phylo() with `type = "phylogram"', if the values of
`edge.color' and `edge.width' are identical for sister-branches,
they are propagated to the vertical line that link them.
BUG FIXES
o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
crashing. This is fixed.
o In plot.phylo(), the options `edge.color' and `edge.width' are
now properly recycled; their default values are now "black" and
1, respectively.
o A bug has been fixed in write.nexus().
OTHER CHANGES
o The function node.depth.edgelength() has been removed and
replaced by a C code.
CHANGES IN APE VERSION 1.3-1
NEW FEATURES
o The new function nodelabels() allows to add labels to the nodes
of a tree using text or plotting symbols in a flexible way.
o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
numeric values specifying the lower and upper limits on the x-
and y-axes. This allows to leave some space on any side of the
tree. If a single value is given, this is taken as the upper
limit (as before).
CHANGES IN APE VERSION 1.3
NEW FEATURES
o The new function phymltest() calls the software PHYML and fits
28 models of DNA sequence evolution. There are a print method to
display likelihood and AIC values, a summary method to compute
the hierarchical likelihood ratio tests, and a plot method to
display graphically the AIC values of each model.
o The new function yule.cov() fits the Yule model with covariates,
a model where the speciation rate is affected by several species
traits through a generalized linear model. The parameters are
estimated by maximum likelihood.
o Three new functions, corBrownian(), corGrafen(), and
corMartins(), compute the expected correlation structures among
species given a phylogeny under different models of evolution.
These can be used for GLS comparative phylogenetic methods (see
the examples). There are coef() and corMatrix() methods and an
Initialize.corPhyl() function associated.
o The new function compar.cheverud() implements Cheverud et al.'s
(1985; Evolution 39:1335) phylogenetic comparative method.
o The new function varcomp() estimates variance components; it has
a plot method.
o Two new functions, panel.superpose.correlogram() and
plot.correlogramList(), allow to plot several phylogenetic
correlograms.
o The new function node.leafnumber() computes the number of leaves
of a subtree defined by a particular node.
o The new function node.sons() gets all tags of son nodes from a
given parent node.
o The new function compute.brlen() computes the branch lengths of
a tree according to a specified method.
o plot.phylo() has three new options: "cex" controls the size of
the (tip and node) labels (thus it is no more needed to change
the global graphical parameter), "direction" which allows to
plot the tree rightwards, leftwards, upwards, or downwards, and
"y.lim" which sets the upper limit on the y-axis.
BUG FIXES
o Some functions which try to match tip labels and names of
additional data (e.g. vector) are likely to fail if there are
typing or syntax errors. If both series of names do not perfectly
match, they are ignored and a warning message is now issued.
These functions are bd.ext, compar.gee, pic. Their help pages
have been clarified on this point.
CHANGES IN APE VERSION 1.2-7
NEW FEATURES
o The new function root() reroots a phylogenetic tree with respect
to a specified outgroup.
o The new function rotate() rotates an internal branch of a tree.
o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
trees) controls the display of the tip labels in unrooted trees.
This display has been greatly improved: the tip labels are now not
expected to overlap with the tree (particularly if lab4ut =
"axial"). In all cases, combining appropriate values of "lab4ut"
and the font size (via "par(cex = )") should result in readable
unrooted trees. See ?plot.phylo for some examples.
o In drop.tip(), the argument `tip' can now be numeric or character.
BUG FIXES
o drop.tip() did not work correctly with trees with no branch
lengths: this is fixed.
o A bug in plot.phylo(..., type = "unrooted") made some trees being
plotted with some line crossings: this is now fixed.
CHANGES IN APE VERSION 1.2-6
NEW FEATURES
o Six new functions (Moran.I, correlogram.formula, discrete.dist,
correlogram.phylo, dist.taxo, plot.correlogram) have been added
to implement comparative methods with an autocorrelation approach.
o A new data set describing some life history traits of Carnivores
has been included.
BUG FIXES
o A fix was made on mcmc.popsize() to conform to R 2.0.0.
OTHER CHANGES
o When plotting a tree with plot.phylo(), the new default of the
option `label.offset' is now 0, so the labels are always visible.
CHANGES IN APE VERSION 1.2-5
NEW FEATURES
o The new function bd.ext() fits a birth-death model with combined
phylogenetic and taxonomic data, and estimates the corresponding
speciation and extinction rates.
OTHER CHANGES
o The package gee is no more required by ape but only suggested
since only the function compar.gee() calls gee.
CHANGES IN APE VERSION 1.2-4
NEW FEATURES
o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
and lines.popsize) implementing a new approach for inferring the
demographic history from genealogies using a reversible jump
MCMC have been introduced.
o The unit of time in the skyline plot and in the new plots can
now be chosen to be actual years, rather than substitutions.
CHANGES IN APE VERSION 1.2-3
NEW FEATURES
o The new function rtree() generates a random binary tree with or
without branch lengths.
o Two new functions for drawing lineages-through-time (LTT) plots
are provided: ltt.lines() adds a LTT curve to an existing plot,
and mltt.plot() does a multiple LTT plot giving several trees as
arguments (see `?ltt.plot' for details).
BUG FIXES
o Some taxon names made R crashing when calling as.phylo.hclust():
this is fixed.
o dist.dna() returned an error with two identical DNA sequences
(only using the Jukes-Cantor method returned 0): this is fixed.
OTHER CHANGES
o The function dist.phylo() has been re-written using a different
algorithm: it is now about four times faster.
o The code of branching.times() has been improved: it is now about
twice faster.
CHANGES IN APE VERSION 1.2-2
NEW FEATURES
o The new function seg.sites() finds the segregating sites in a
sample of DNA sequences.
BUG FIXES
o A bug introduced in read.tree() and in read.nexus() with version
1.2-1 was fixed.
o A few errors were corrected and a few examples were added in the
help pages.
CHANGES IN APE VERSION 1.2-1
NEW FEATURES
o plot.phylo() can now draw the edge of the root of a tree if it
has one (see the new option `root.edge', its default is FALSE).
BUG FIXES
o A bug was fixed in read.nexus(): files with semicolons inside
comment blocks were not read correctly.
o The behaviour of read.tree() and read.nexus() was corrected so
that tree files with badly represented root edges (e.g., with
an extra pair of parentheses, see the help pages for details)
are now correctly represented in the object of class "phylo";
a warning message is now issued.
CHANGES IN APE VERSION 1.2
NEW FEATURES
o plot.phylo() has been completely re-written and offers several
new functionalities. Three types of trees can now be drawn:
phylogram (as previously), cladogram, and unrooted tree; in
all three types the branch lengths can be drawn using the edge
lengths of the phylogeny or not (e.g., if the latter is absent).
The vertical position of the nodes can be adjusted with two
choices (see option `node.pos'). The code has been re-structured,
and two new functions (potentially useful for developpers) are
documented separately: node.depth.edgelength() and node.depth();
see the respective help pages for details.
o The new function zoom() allows to explore very large trees by
focusing on a small portion of it.
o The new function yule() fits by maximum likelihood the Yule model
(birth-only process) to a phylogenetic tree.
o Support for writing DNA sequences in FASTA format has been
introduced in write.dna() (support for reading sequences in
this format was introduced in read.dna() in version 1.1-2).
The function has been completely re-written, fixing some bugs
(see below); the default behaviour is no more to display the
sequences on the standard output. Several options have been
introduced to control the sequence printing in a flexible
way. The help page has been extended.
o A new data set is included: a supertree of bats in NEXUS format.
BUG FIXES
o In theta.s(), the default of the option `variance' has
been changed to `FALSE' (as was indicated in the help page).
o Several bugs were fixed in the code of all.equal.phylo().
o Several bugs were fixed in write.dna(), particularly this
function did not work with `format = "interleaved"'.
o Various errors were corrected in the help pages.
OTHER CHANGES
o The argument names of as.hclust.phylo() have been changed
from "(phy)" to "(x, ...)" to conform to the definition of
the corresponding generic function.
o gamma.stat() has been renamed gammaStat() to avoid confusion
since gamma() is a generic function.
CHANGES IN APE VERSION 1.1-3
BUG FIXES
o base.freq() previously did not return a value of 0 for
bases absent in the data (e.g., a vector of length 3 was
returned if one base was absent). This is now fixed (a
vector of length 4 is always returned).
o Several bugs were fixed in read.nexus(), including that this
function did not work in this absence of a "TRANSLATE"
command in the NEXUS file, and that the commands were
case-sensitive.
CHANGES IN APE VERSION 1.1-2
NEW FEATURES
o The Tamura and Nei (1993) model of DNA distance is now implemented
in dist.dna(): five models are now available in this function.
o A new data set is included: a set of 15 sequences of the
cytochrome b mitochondrial gene of the woodmouse (Apodemus
sylvaticus).
BUG FIXES
o A bug in read.nexus() was fixed.
o read.dna() previously did not work correctly in most cases.
The function has been completely re-written and its help page
has been considerably extended (see ?read.dna for details).
Underscores (_) in taxon names are no more replaced with
spaces (this behaviour was undocumented).
o A bug was fixed in write.dna().
CHANGES IN APE VERSION 1.1-1
BUG FIXES
o A bug in read.tree() introduced in APE 1.1 was fixed.
o A bug in compar.gee() resulted in an error when trying to fit
a model with `family = "binomial"'. This is now fixed.
CHANGES IN APE VERSION 1.1
NEW FEATURES
o The Klastorin (1982) method as suggested by Misawa and Tajima
(2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
on the basis of phylogenetic trees has been implemented (see
the function klastorin()).
o Functions have been added to convert APE's "phylo" objects in
"hclust" cluster objects and vice versa (see the help page of
as.phylo for details).
o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
are introduced for the estimation of absolute evolutionary rates
(ratogram) and dated clock-like trees (chronogram) from
phylogenetic trees using the non-parametric rate smoothing approach
by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
o A summary method is now provided printing a summary information on a
phylogenetic tree with, for instance, `summary(tree)'.
o The behaviour of read.tree() was changed so that all spaces and
tabulations in tree files are now ignored. Consequently, spaces in tip
labels are no more allowed. Another side effect is that read.nexus()
now does not replace the underscores (_) in tip labels with spaces
(this behaviour was undocumented).
o The function plot.phylo() has a new option (`underscore') which
specifies whether the underscores in tip labels should be written on
the plot as such or replaced with spaces (the default).
o The function birthdeath() now computes 95% confidence intervals of
the estimated parameters using profile likelihood.
o Three new data sets are included: a gene tree estimated from 36
landplant rbcL sequences, a gene tree estimated from 32 opsin
sequences, and a gene tree for 50 BRCA1 mammalian sequences.
BUG FIXES
o A bug was fixed in dist.gene() where nothing was returned.
o A bug in plot.mst() was fixed.
o A bug in vcv.phylo() resulted in false correlations when the
option `cor = TRUE' was used (now fixed).
CHANGES IN APE VERSION 1.0
NEW FEATURES
o Two new functions, read.dna() and write.dna(), read/write in a file
DNA sequences in interleaved or in sequential format.
o Two new functions, read.nexus() and write.nexus(), read/write trees
in a NEXUS file.
o The new function bind.tree() allows to bind two trees together,
possibly handling root edges to give internal branches.
o The new function drop.tip() removes the tips in a phylogenetic tree,
and trims (or not) the corresponding internal branches.
o The new function is.ultrametric() tests if a tree is ultrametric.
o The function plot.phylo() has more functionalities such as drawing the
branches with different colours and/or different widths, showing the
node labels, controling the position and font of the labels, rotating
the labels, and controling the space around the plot.
o The function read.tree() can now read trees with no branch length,
such as "(a,b),c);". Consequently, the element `edge.length' in
objects of class "phylo" is now optional.
o The function write.tree() has a new default behaviour: if the default
for the option `file' is used (i.e. file = ""), then a variable of
mode character containing the tree in Newick format is returned which
can thus be assigned (e.g., tree <- write.tree(phy)).
o The function read.tree() has a new argument `text' which allows
to read the tree in a variable of mode character.
o A new data set is included: the phylogenetic relationships among
the orders of birds from Sibley and Ahlquist (1990).
CHANGES IN APE VERSION 0.2-1
BUG FIXES
o Several bugs were fixed in the help pages.
CHANGES IN APE VERSION 0.2
NEW FEATURES
o The function write.tree() writes phylogenetic trees (objects of class
"phylo") in an ASCII file using the Newick parenthetic format.
o The function birthdeath() fits a birth-death model to branching times
by maximum likelihood, and estimates the corresponding speciation and
extinction rates.
o The function scale.bar() adds a scale bar to a plot of a phylogenetic
tree.
o The function is.binary.tree() tests whether a phylogeny is binary.
o Two generic functions, coalescent.intervals() and collapsed.intervals(),
as well as some methods are introduced.
o Several functions, including some generics and methods, for computing
skyline plot estimates (classic and generalized) of effective
population size through time are introduced and replace the function
skyline.plot() in version 0.1.
o Two data sets are now included: the phylogenetic relationships among
the families of birds from Sibley and Ahlquist (1990), and an
estimated clock-like phylogeny of HIV sequences sampled in the
Democratic Republic of Congo.
DEPRECATED & DEFUNCT
o The function skyline.plot() in ape 0.1 has been deprecated and
replaced by more elaborate functions (see above).
BUG FIXES
o Two important bugs were fixed in plot.phylo(): phylogenies with
multichotomies not at the root or not with only terminal branches,
and phylogenies with a single node (i.e. only terminal branches)
did not plot. These trees should be plotted correctly now.
o Several bugs were fixed in diversi.time() in the computation of
AICs and LRTs.
o Various errors were corrected in the help pages.
