--- /dev/null
+ CHANGES IN APE VERSION 2.2-2
+
+
+NEW FEATURES
+
+ o dist.gene() has been substantially improved and gains an option
+ 'pairwise.deletion'.
+
+
+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() now accepts 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.
+
+ o reorder.phylo() made R freeze in some occasions.
+
+ o Plotting a tree in pruningwise order failed.
+
+ o When plotting an unrooted tree, the tip labels where not all
+ correctly positioned if the option `cex' was used.
+
+
+
+ CHANGES IN APE VERSION 1.10
+
+
+NEW FEATURES
+
+ o Five new `method' functions have been introduced to manipulate
+ DNA sequences in binary format (see below).
+
+ o Three new functions have been introduced to convert between the
+ new binary and the character formats.
+
+ o The new function as.alignment converts DNA sequences stored as
+ single characters into the class "alignment" used by the package
+ seqinr.
+
+ o read.dna() and read.GenBank() have a new argument `as.character'
+ controlling whether the sequences are returned in binary format
+ or as character.
+
+
+BUG FIXES
+
+ o root() failed when the tree had node labels: this is fixed.
+
+ o plot.phylo() did not correctly set the limits on the y-axis with
+ the default setting: this is fixed.
+
+ o dist.dna() returned a wrong result for the LogDet, paralinear,
+ and BH87 models with `pairwise.deletion = TRUE'.
+
+
+OTHER CHANGES
+
+ o DNA sequences are now internally stored in a binary format. See
+ the document "A Bit-Level Coding Scheme for Nucleotides" for the
+ details. Most functions analyzing DNA functions have been
+ modified accordingly and are now much faster (dist.dna is now
+ ca. 60 times faster).
+
+
+
+ CHANGES IN APE VERSION 1.9-4
+
+
+BUG FIXES
+
+ o A bug was fixed in edgelabels().
+
+ o as.phylo.hclust() did not work correctly when the object of
+ class "hclust" has its labels set to NULL: the returned tree has
+ now its tip labels set to "1", "2", ...
+
+ o consensus could fail if some tip labels are a subset of others
+ (e.g., "a" and "a_1"): this is now fixed.
+
+ o mlphylo() failed in most cases if some branch lengths of the
+ initial tree were greater than one: an error message is now
+ issued.
+
+ o mlphylo() failed in most cases when estimating the proportion of
+ invariants: this is fixed.
+
+
+
+ CHANGES IN APE VERSION 1.9-3
+
+
+NEW FEATURES
+
+ o The new function edgelabels adds labels on the edge of the tree
+ in the same way than nodelabels or tiplabels.
+
+
+BUG FIXES
+
+ o multi2di() did not handle correctly branch lengths with the
+ default option `random = TRUE': this is now fixed.
+
+ o A bug was fixed in nuc.div() when using pairwise deletions.
+
+ o A bug occurred in the analysis of bipartitions with large
+ numbers of large trees, with consequences on prop.part,
+ prop.clades, and boot.phylo.
+
+ o The calculation of the Billera-Holmes-Vogtmann distance in
+ dist.topo was wrong: this has been fixed.
+
+
+
+ CHANGES IN APE VERSION 1.9-2
+
+
+NEW FEATURES
+
+ o The new function ladderize reorganizes the internal structure of
+ a tree to plot them left- or right-ladderized.
+
+ o The new function dist.nodes computes the patristic distances
+ between all nodes, internal and terminal, of a tree. It replaces
+ the option `full = TRUE' of cophenetic.phylo (see below).
+
+
+BUG FIXES
+
+ o A bug was fixed in old2new.phylo().
+
+ o Some bugs were fixed in chronopl().
+
+ o The edge colours were not correctly displayed by plot.phylo
+ (thank you to Li-San Wang for the fix).
+
+ o cophenetic.phylo() failed with multichotomous trees: this is
+ fixed.
+
+
+OTHER CHANGES
+
+ o read.dna() now returns the sequences in a matrix if they are
+ aligned (interleaved or sequential format). Sequences in FASTA
+ format are still returned in a list.
+
+ o The option `full' of cophenetic.phylo() has been removed because
+ it could not be used from the generic.
+
+
+DEPRECATED & DEFUNCT
+
+ o rotate() has been removed; this function did not work correctly
+ since ape 1.9.
+
+
+
+ CHANGES IN APE VERSION 1.9-1
+
+
+BUG FIXES
+
+ o Trees with a single tip were not read correctly in R as the
+ element `Nnode' was not set: this is fixed.
+
+ o unroot() did not set correctly the number of nodes of the
+ unrooted tree in most cases.
+
+ o read.GenBank() failed when fetching very long sequences,
+ particularly of the BX-series.
+
+ o A bug was introduced in read.tree() with ape 1.9: it has been
+ fixed
+
+
+
+ CHANGES IN APE VERSION 1.9
+
+
+NEW FEATURES
+
+ o There are two new print `methods' for trees of class "phylo" and
+ lists of trees of class "multi.tree", so that they are now
+ displayed in a compact and informative way.
+
+ o There are two new functions, old2new.phylo and new2old.phylo,
+ for converting between the old and new coding of the class
+ "phylo".
+
+ o dist.dna() has three new models: Barry and Hartigan ("BH87"),
+ LogDet ("logdet"), and paralinear ("paralin").
+
+ o compute.brlen() has been extended: several methods are now
+ available to compute branch lengths.
+
+ o write.dna() can now handle matrices as well as lists.
+
+
+BUG FIXES
+
+ o cophenetic.phylo() sometimes returned a wrong result with
+ multichotomous trees: this is fixed.
+
+ o rotate() failed when a single tip was specified: the tree is now
+ returned unchanged.
+
+ o ace() did not return the correct index matrix with custom
+ models: this is fixed.
+
+ o multi2di() did not work correctly when resolving multichotomies
+ randomly: the topology was always the same, only the arrangement
+ of clades was randomized: this is fixed. This function now
+ accepts trees with no branch lengths.
+
+ o The output of diversi.gof() was blurred by useless prints when a
+ user distribution was specified. This has been corrected, and
+ the help page of this function has been expanded.
+
+
+OTHER CHANGES
+
+ o The internal structure of the class "phylo" has been changed:
+ see the document "Definition of Formats for Coding Phylogenetic
+ Trees in R" for the details. In addition, the code of most
+ functions has been improved.
+
+ o Several functions have been improved by replacing some R codes
+ by C codes: pic, plot.phylo, and reorder.phylo.
+
+ o There is now a citation information: see citation("ape") in R.
+
+ o write.tree() now does not add extra 0's to branch lengths so
+ that 1.23 is printed "1.23" by default, not "1.2300000000".
+
+ o The syntax of bind.tree() has been simplified. This function now
+ accepts trees with no branch lengths, and handles correctly node
+ labels.
+
+ o The option `as.numeric' of mrca() has been removed.
+
+ o The unused options `format' and `rooted' of read.tree() have
+ been removed.
+
+ o The unused option `format' of write.tree() has been removed.
+
+ o The use of node.depth() has been simplified.
+
+
+
+ CHANGES IN APE VERSION 1.8-5
+
+
+NEW FEATURES
+
+ o Two new functions read.nexus.data() and write.nexus.data(),
+ contributed by Johan Nylander, allow to read and write molecular
+ sequences in NEXUS files.
+
+ o The new function reorder.phylo() reorders the internal structure
+ of a tree of class "phylo". It is used as the generic, e.g.,
+ reorder(tr).
+
+ o read.tree() and read.nexus() can now read trees with a single
+ edge.
+
+ o The new data set `cynipids' supplies a set of protein sequences
+ in NEXUS format.
+
+
+BUG FIXES
+
+ o The code of all.equal.phylo() has been completely rewritten
+ (thanks to Benoît Durand) which fixes several bugs.
+
+ o read.tree() and read.nexus() now checks the labels of the tree
+ to remove or substitute any characters that are illegal in the
+ Newick format (parentheses, etc.)
+
+ o A negative P-value could be returned by mantel.test(): this is
+ now fixed.
+
+
+
+ CHANGES IN APE VERSION 1.8-4
+
+
+NEW FEATURES
+
+ o The new function sh.test() computes the Shimodaira-
+ Hasegawa test.
+
+ o The new function collapse.singles() removes the nodes with a
+ single descendant from a tree.
+
+ o plot.phylo() has a new argument `tip.color' to specify the
+ colours of the tips.
+
+ o mlphylo() has now an option `quiet' to control the display of
+ the progress of the analysis (the default is FALSE).
+
+
+BUG FIXES
+
+ o read.dna() did not read correctly sequences in sequential format
+ with leading alignment gaps "-": this is fixed.
+
+ o ace() returned a list with no class so that the generic
+ functions (anova, logLik, ...) could not be used directly. This
+ is fixed as ace() now returns an object of class "ace".
+
+ o anova.ace() had a small bug when computing the number of degrees
+ of freedom: this is fixed.
+
+ o mlphylo() did not work when the sequences were in a matrix or
+ a data frame: this is fixed.
+
+ o rtree() did not work correctly when trying to simulate an
+ unrooted tree with two tips: an error message is now issued.
+
+
+OTHER CHANGES
+
+ o The algorithm of rtree() has been changed: it is now about 40,
+ 100, and 130 times faster for 10, 100, and 1000 tips,
+ respectively.
+
+
+
+ CHANGES IN APE VERSION 1.8-3
+
+
+NEW FEATURES
+
+ o There are four new `method' functions to be used with the
+ results of ace(): logLik(), deviance(), AIC(), and anova().
+
+ o The plot method of phymltest has two new arguments: `main' to
+ change the title, and `col' to control the colour of the
+ segments showing the AIC values.
+
+ o ace() has a new argument `ip' that gives the initial values used
+ in the ML estimation with discrete characters (see the examples
+ in ?ace). This function now returns a matrix giving the indices
+ of the estimated rates when analysing discrete characters.
+
+ o nodelabels() and tiplabels() have a new argument `pie' to
+ represent proportions, with any number of categories, as
+ piecharts. The use of the option `thermo' has been improved:
+ there is now no limitation on the number of categories.
+
+
+BUG FIXES
+
+ o mlphylo() did not work with more than two partitions: this is
+ fixed.
+
+ o root() failed if the proposed outgroup was already an outgroup
+ in the tree: this is fixed.
+
+ o The `col' argument in nodelabels() and tiplabels() was not
+ correctly passed when `text' was used: this is fixed.
+
+ o Two bugs were fixed in mlphylo(): parameters were not always
+ correctly output, and the estimation failed in some cases.
+
+ o plot.phylo() was stuck when given a tree with a single tip: this
+ is fixed and a message error is now returned.
+
+ o An error was corrected in the help page of gammaStat regarding
+ the calculation of P-values.
+
+ o Using gls() could crash R when the number of species in the tree
+ and in the variables were different: this is fixed.
+
+
+
+ CHANGES IN APE VERSION 1.8-2
+
+
+NEW FEATURES
+
+ o The new function mlphylo() fits a phylogenetic tree by maximum
+ likelihood from DNA sequences. Its companion function DNAmodel()
+ is used to define the substitution model which may include
+ partitioning. There are methods for logLik(), deviance(), and
+ AIC(), and the summary() method has been extended to display in
+ a friendly way the results of this model fitting. Currently, the
+ functionality is limited to estimating the substitution and
+ associated parameters and computing the likelihood.
+
+ o The new function drop1.compar.gee (used as, e.g., drop1(m))
+ tests for single effects in GEE-based comparative method. A
+ warning message is printed if there is not enough degrees of
+ freedom.
+
+
+BUG FIXES
+
+ o An error message was sometimes issued by plot.multi.tree(),
+ though with no consequence.
+
+
+
+ CHANGES IN APE VERSION 1.8-1
+
+
+NEW FEATURES
+
+ o There is a new plot method for lists of trees (objects of class
+ "multi.tree"): it calls plot.phylo() internally and is
+ documented on the same help page.
+
+
+BUG FIXES
+
+ o A bug was fixed in the C code that analyzes bipartitions: this
+ has impact on several functions like prop.part, prop.clades,
+ boot.phylo, or consensus.
+
+ o root() did not work correctly when the specified outgroup had
+ more than one element: this is fixed.
+
+ o dist.dna() sometimes returned a warning inappropriately: this
+ has been corrected.
+
+ o If the distance object given to nj() had no rownames, nj()
+ returned a tree with no tip labels: it now returns tips labelled
+ "1", "2", ..., corresponding to the row numbers.
+
+
+OTHER CHANGES
+
+ o nj() has been slightly changed so that tips with a zero distance
+ are first aggregated with zero-lengthed branches; the usual NJ
+ procedure is then performed on a distance matrix without 0's.
+
+
+
+ CHANGES IN APE VERSION 1.8
+
+
+NEW FEATURES
+
+ o The new function chronopl() estimates dates using the penalized
+ likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
+
+ o The new function consensus() calculates the consensus tree of a
+ list of trees.
+
+ o The new function evolve.phylo() simulates the evolution of
+ continuous characters along a phylogeny under a Brownian model.
+
+ o The new plot method for objects of class "ancestral" displays a
+ tree together with ancestral values, as returned by the above
+ function.
+
+ o The new function as.phylo.formula() returns a phylogeny from a
+ set of nested taxonomic variables given as a formula.
+
+ o The new function read.caic() reads trees in CAIC format.
+
+ o The new function tiplabels() allows to add labels to the tips
+ of a tree using text or plotting symbols in a flexible way.
+
+ o The new function unroot() unroots a phylogeny.
+
+ o multi2di() has a new option, `random', which specifies whether
+ to resolve the multichotomies randomly (the default) or not.
+
+ o prop.part() now returns an object of class "prop.part" for which
+ there are print (to display a partition in a more friendly way)
+ and summary (to extract the numbers) methods.
+
+ o plot.phylo() has a new option, `show.tip.label', specifying
+ whether to print the labels of the tips. The default is TRUE.
+
+ o The code of nj() has been replaced by a faster C code: it is now
+ about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
+ respectively.
+
+ o write.nexus() now writes whether a tree is rooted or not.
+
+
+BUG FIXES
+
+ o Two bugs have been fixed in root(): unrooted trees are now
+ handled corretly, and node labels are now output normally.
+
+ o A bug was fixed in phymltest(): the executable couldn't be found
+ in some cases.
+
+ o Three bug have been fixed in ace(): computing the likelihood of
+ ancestral states of discrete characters failed, custom models
+ did not work, and the function failed with a null gradient (a
+ warning message is now returned; this latter bug was also
+ present in yule.cov() as well and is now fixed).
+
+ o pic() hanged out when missing data were present: a message error
+ is now returned.
+
+ o A small bug was fixed in dist.dna() where the gamma correction
+ was not always correctly dispatched.
+
+ o plot.phylo() plotted correctly the root edge only when the tree
+ was plotted rightwards: this works now for all directions.
+
+
+OTHER CHANGES
+
+ o dist.taxo() has been renamed as weight.taxo().
+
+ o Various error and warning messages have been improved.
+
+
+
+ CHANGES IN APE VERSION 1.7
+NEW FEATURES
+
+ o The new function ace() estimates ancestral character states for
+ continuous characters (with ML, GLS, and contrasts methods), and
+ discrete characters (with ML only) for any number of states.
+
+ o The new function compar.ou() fits the Ornstein-Uhlenbeck model
+ of directional evolution for continuous characters. The user
+ specifies the node(s) of the tree where the character optimum
+ changes.
+
+ o The new function is.rooted() tests whether a tree (of class
+ "phylo") is rooted.
+
+ o The new function rcoal() generates random ultrametric trees with
+ the possibility to specify the function that generates the
+ inter-nodes distances.
+
+ o The new function mrca() gives for all pairs of tips in a tree
+ (and optionally nodes too) the most recent common ancestor.
+
+ o nodelabels() has a new option `thermo' to plot proportions (up
+ to three classes) on the nodes of a tree.
+
+ o rtree() has been improved: it can now generate rooted or
+ unrooted trees, and the mathematical function that generates the
+ branch lengths may be specified by the user. The tip labels may
+ be given directly in the call to rtree. The limit cases (n = 2,
+ 3) are now handled correctly.
+
+ o dist.topo() has a new argument `method' with two choices: "PH85"
+ for Penny and Henny's method (already available before and now
+ the default), and "BHV01" for the geometric distance by Billera
+ et al. (2001, Adv. Appl. Math. 27:733).
+
+ o write.tree() has a new option, `digits', which specifies the
+ number of digits to be printed in the Newick tree. By default
+ digits = 10. The numbers are now always printed in decimal form
+ (i.e., 1.0e-1 is now avoided).
+
+ o dist.dna() can now compute the raw distances between pairs of
+ DNA sequences by specifying model = "raw".
+
+ o dist.phylo() has a new option `full' to possibly compute the
+ distances among all tips and nodes of the tree. The default if
+ `full = FALSE'.
+
+
+BUG FIXES
+
+ o Several bugs were fixed in all.equal.phylo().
+
+ o dist.dna() did not handle correctly gaps ("-") in alignments:
+ they are now considered as missing data.
+
+ o rotate() did not work if the tips were not ordered: this is
+ fixed.
+
+ o mantel.test() returned NA in some special cases: this is fixed
+ and the function has been improved and is now faster.
+
+ o A bug was fixed in diversi.gof() where the calculation of A² was
+ incorrect.
+
+ o cherry() did not work correctly under some OSs (mainly Linux):
+ this is fixed.
+
+ o is.binary.tree() has been modified so that it works with both
+ rooted and unrooted trees.
+
+ o The documentation of theta.s() was not correct: this has been
+ fixed.
+
+ o plot.mst() did not work correctly: this is fixed.
+
+
+
+ CHANGES IN APE VERSION 1.6
+
+
+NEW FEATURES
+
+ o The new function dist.topo() computes the topological distances
+ between two trees.
+
+ o The new function boot.phylo() performs a bootstrap analysis on
+ phylogeny estimation.
+
+ o The new functions prop.part() and prop.clades() analyse
+ bipartitions from a series of trees.
+
+
+OTHER CHANGES
+
+ o read.GenBank() now uses the EFetch utility of NCBI instead of
+ the usual Web interface: it is now much faster (e.g., 12 times
+ faster to retrieve 8 sequences, 37 times for 60 sequences).
+
+
+BUG FIXES
+
+ o Several bugs were fixed in read.dna().
+
+ o Several bugs were fixed in diversi.time().
+
+ o is.binary.tree() did not work correctly if the tree has no edge
+ lengths: this is fixed.
+
+ o drop.tip() did not correctly propagated the `node.label' of a
+ tree: this is fixed.
+
+
+
+ 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.
+++ /dev/null
- CHANGES IN APE VERSION 2.2-2
-
-
-NEW FEATURES
-
- o dist.gene() has been substantially improved and gains an option
- 'pairwise.deletion'.
-
-
-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 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.
-
- o reorder.phylo() made R freeze in some occasions.
-
- o Plotting a tree in pruningwise order failed.
-
- o When plotting an unrooted tree, the tip labels where not all
- correctly positioned if the option `cex' was used.
-
-
-
- CHANGES IN APE VERSION 1.10
-
-
-NEW FEATURES
-
- o Five new `method' functions have been introduced to manipulate
- DNA sequences in binary format (see below).
-
- o Three new functions have been introduced to convert between the
- new binary and the character formats.
-
- o The new function as.alignment converts DNA sequences stored as
- single characters into the class "alignment" used by the package
- seqinr.
-
- o read.dna() and read.GenBank() have a new argument `as.character'
- controlling whether the sequences are returned in binary format
- or as character.
-
-
-BUG FIXES
-
- o root() failed when the tree had node labels: this is fixed.
-
- o plot.phylo() did not correctly set the limits on the y-axis with
- the default setting: this is fixed.
-
- o dist.dna() returned a wrong result for the LogDet, paralinear,
- and BH87 models with `pairwise.deletion = TRUE'.
-
-
-OTHER CHANGES
-
- o DNA sequences are now internally stored in a binary format. See
- the document "A Bit-Level Coding Scheme for Nucleotides" for the
- details. Most functions analyzing DNA functions have been
- modified accordingly and are now much faster (dist.dna is now
- ca. 60 times faster).
-
-
-
- CHANGES IN APE VERSION 1.9-4
-
-
-BUG FIXES
-
- o A bug was fixed in edgelabels().
-
- o as.phylo.hclust() did not work correctly when the object of
- class "hclust" has its labels set to NULL: the returned tree has
- now its tip labels set to "1", "2", ...
-
- o consensus could fail if some tip labels are a subset of others
- (e.g., "a" and "a_1"): this is now fixed.
-
- o mlphylo() failed in most cases if some branch lengths of the
- initial tree were greater than one: an error message is now
- issued.
-
- o mlphylo() failed in most cases when estimating the proportion of
- invariants: this is fixed.
-
-
-
- CHANGES IN APE VERSION 1.9-3
-
-
-NEW FEATURES
-
- o The new function edgelabels adds labels on the edge of the tree
- in the same way than nodelabels or tiplabels.
-
-
-BUG FIXES
-
- o multi2di() did not handle correctly branch lengths with the
- default option `random = TRUE': this is now fixed.
-
- o A bug was fixed in nuc.div() when using pairwise deletions.
-
- o A bug occurred in the analysis of bipartitions with large
- numbers of large trees, with consequences on prop.part,
- prop.clades, and boot.phylo.
-
- o The calculation of the Billera-Holmes-Vogtmann distance in
- dist.topo was wrong: this has been fixed.
-
-
-
- CHANGES IN APE VERSION 1.9-2
-
-
-NEW FEATURES
-
- o The new function ladderize reorganizes the internal structure of
- a tree to plot them left- or right-ladderized.
-
- o The new function dist.nodes computes the patristic distances
- between all nodes, internal and terminal, of a tree. It replaces
- the option `full = TRUE' of cophenetic.phylo (see below).
-
-
-BUG FIXES
-
- o A bug was fixed in old2new.phylo().
-
- o Some bugs were fixed in chronopl().
-
- o The edge colours were not correctly displayed by plot.phylo
- (thank you to Li-San Wang for the fix).
-
- o cophenetic.phylo() failed with multichotomous trees: this is
- fixed.
-
-
-OTHER CHANGES
-
- o read.dna() now returns the sequences in a matrix if they are
- aligned (interleaved or sequential format). Sequences in FASTA
- format are still returned in a list.
-
- o The option `full' of cophenetic.phylo() has been removed because
- it could not be used from the generic.
-
-
-DEPRECATED & DEFUNCT
-
- o rotate() has been removed; this function did not work correctly
- since ape 1.9.
-
-
-
- CHANGES IN APE VERSION 1.9-1
-
-
-BUG FIXES
-
- o Trees with a single tip were not read correctly in R as the
- element `Nnode' was not set: this is fixed.
-
- o unroot() did not set correctly the number of nodes of the
- unrooted tree in most cases.
-
- o read.GenBank() failed when fetching very long sequences,
- particularly of the BX-series.
-
- o A bug was introduced in read.tree() with ape 1.9: it has been
- fixed
-
-
-
- CHANGES IN APE VERSION 1.9
-
-
-NEW FEATURES
-
- o There are two new print `methods' for trees of class "phylo" and
- lists of trees of class "multi.tree", so that they are now
- displayed in a compact and informative way.
-
- o There are two new functions, old2new.phylo and new2old.phylo,
- for converting between the old and new coding of the class
- "phylo".
-
- o dist.dna() has three new models: Barry and Hartigan ("BH87"),
- LogDet ("logdet"), and paralinear ("paralin").
-
- o compute.brlen() has been extended: several methods are now
- available to compute branch lengths.
-
- o write.dna() can now handle matrices as well as lists.
-
-
-BUG FIXES
-
- o cophenetic.phylo() sometimes returned a wrong result with
- multichotomous trees: this is fixed.
-
- o rotate() failed when a single tip was specified: the tree is now
- returned unchanged.
-
- o ace() did not return the correct index matrix with custom
- models: this is fixed.
-
- o multi2di() did not work correctly when resolving multichotomies
- randomly: the topology was always the same, only the arrangement
- of clades was randomized: this is fixed. This function now
- accepts trees with no branch lengths.
-
- o The output of diversi.gof() was blurred by useless prints when a
- user distribution was specified. This has been corrected, and
- the help page of this function has been expanded.
-
-
-OTHER CHANGES
-
- o The internal structure of the class "phylo" has been changed:
- see the document "Definition of Formats for Coding Phylogenetic
- Trees in R" for the details. In addition, the code of most
- functions has been improved.
-
- o Several functions have been improved by replacing some R codes
- by C codes: pic, plot.phylo, and reorder.phylo.
-
- o There is now a citation information: see citation("ape") in R.
-
- o write.tree() now does not add extra 0's to branch lengths so
- that 1.23 is printed "1.23" by default, not "1.2300000000".
-
- o The syntax of bind.tree() has been simplified. This function now
- accepts trees with no branch lengths, and handles correctly node
- labels.
-
- o The option `as.numeric' of mrca() has been removed.
-
- o The unused options `format' and `rooted' of read.tree() have
- been removed.
-
- o The unused option `format' of write.tree() has been removed.
-
- o The use of node.depth() has been simplified.
-
-
-
- CHANGES IN APE VERSION 1.8-5
-
-
-NEW FEATURES
-
- o Two new functions read.nexus.data() and write.nexus.data(),
- contributed by Johan Nylander, allow to read and write molecular
- sequences in NEXUS files.
-
- o The new function reorder.phylo() reorders the internal structure
- of a tree of class "phylo". It is used as the generic, e.g.,
- reorder(tr).
-
- o read.tree() and read.nexus() can now read trees with a single
- edge.
-
- o The new data set `cynipids' supplies a set of protein sequences
- in NEXUS format.
-
-
-BUG FIXES
-
- o The code of all.equal.phylo() has been completely rewritten
- (thanks to Benoît Durand) which fixes several bugs.
-
- o read.tree() and read.nexus() now checks the labels of the tree
- to remove or substitute any characters that are illegal in the
- Newick format (parentheses, etc.)
-
- o A negative P-value could be returned by mantel.test(): this is
- now fixed.
-
-
-
- CHANGES IN APE VERSION 1.8-4
-
-
-NEW FEATURES
-
- o The new function sh.test() computes the Shimodaira-
- Hasegawa test.
-
- o The new function collapse.singles() removes the nodes with a
- single descendant from a tree.
-
- o plot.phylo() has a new argument `tip.color' to specify the
- colours of the tips.
-
- o mlphylo() has now an option `quiet' to control the display of
- the progress of the analysis (the default is FALSE).
-
-
-BUG FIXES
-
- o read.dna() did not read correctly sequences in sequential format
- with leading alignment gaps "-": this is fixed.
-
- o ace() returned a list with no class so that the generic
- functions (anova, logLik, ...) could not be used directly. This
- is fixed as ace() now returns an object of class "ace".
-
- o anova.ace() had a small bug when computing the number of degrees
- of freedom: this is fixed.
-
- o mlphylo() did not work when the sequences were in a matrix or
- a data frame: this is fixed.
-
- o rtree() did not work correctly when trying to simulate an
- unrooted tree with two tips: an error message is now issued.
-
-
-OTHER CHANGES
-
- o The algorithm of rtree() has been changed: it is now about 40,
- 100, and 130 times faster for 10, 100, and 1000 tips,
- respectively.
-
-
-
- CHANGES IN APE VERSION 1.8-3
-
-
-NEW FEATURES
-
- o There are four new `method' functions to be used with the
- results of ace(): logLik(), deviance(), AIC(), and anova().
-
- o The plot method of phymltest has two new arguments: `main' to
- change the title, and `col' to control the colour of the
- segments showing the AIC values.
-
- o ace() has a new argument `ip' that gives the initial values used
- in the ML estimation with discrete characters (see the examples
- in ?ace). This function now returns a matrix giving the indices
- of the estimated rates when analysing discrete characters.
-
- o nodelabels() and tiplabels() have a new argument `pie' to
- represent proportions, with any number of categories, as
- piecharts. The use of the option `thermo' has been improved:
- there is now no limitation on the number of categories.
-
-
-BUG FIXES
-
- o mlphylo() did not work with more than two partitions: this is
- fixed.
-
- o root() failed if the proposed outgroup was already an outgroup
- in the tree: this is fixed.
-
- o The `col' argument in nodelabels() and tiplabels() was not
- correctly passed when `text' was used: this is fixed.
-
- o Two bugs were fixed in mlphylo(): parameters were not always
- correctly output, and the estimation failed in some cases.
-
- o plot.phylo() was stuck when given a tree with a single tip: this
- is fixed and a message error is now returned.
-
- o An error was corrected in the help page of gammaStat regarding
- the calculation of P-values.
-
- o Using gls() could crash R when the number of species in the tree
- and in the variables were different: this is fixed.
-
-
-
- CHANGES IN APE VERSION 1.8-2
-
-
-NEW FEATURES
-
- o The new function mlphylo() fits a phylogenetic tree by maximum
- likelihood from DNA sequences. Its companion function DNAmodel()
- is used to define the substitution model which may include
- partitioning. There are methods for logLik(), deviance(), and
- AIC(), and the summary() method has been extended to display in
- a friendly way the results of this model fitting. Currently, the
- functionality is limited to estimating the substitution and
- associated parameters and computing the likelihood.
-
- o The new function drop1.compar.gee (used as, e.g., drop1(m))
- tests for single effects in GEE-based comparative method. A
- warning message is printed if there is not enough degrees of
- freedom.
-
-
-BUG FIXES
-
- o An error message was sometimes issued by plot.multi.tree(),
- though with no consequence.
-
-
-
- CHANGES IN APE VERSION 1.8-1
-
-
-NEW FEATURES
-
- o There is a new plot method for lists of trees (objects of class
- "multi.tree"): it calls plot.phylo() internally and is
- documented on the same help page.
-
-
-BUG FIXES
-
- o A bug was fixed in the C code that analyzes bipartitions: this
- has impact on several functions like prop.part, prop.clades,
- boot.phylo, or consensus.
-
- o root() did not work correctly when the specified outgroup had
- more than one element: this is fixed.
-
- o dist.dna() sometimes returned a warning inappropriately: this
- has been corrected.
-
- o If the distance object given to nj() had no rownames, nj()
- returned a tree with no tip labels: it now returns tips labelled
- "1", "2", ..., corresponding to the row numbers.
-
-
-OTHER CHANGES
-
- o nj() has been slightly changed so that tips with a zero distance
- are first aggregated with zero-lengthed branches; the usual NJ
- procedure is then performed on a distance matrix without 0's.
-
-
-
- CHANGES IN APE VERSION 1.8
-
-
-NEW FEATURES
-
- o The new function chronopl() estimates dates using the penalized
- likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
-
- o The new function consensus() calculates the consensus tree of a
- list of trees.
-
- o The new function evolve.phylo() simulates the evolution of
- continuous characters along a phylogeny under a Brownian model.
-
- o The new plot method for objects of class "ancestral" displays a
- tree together with ancestral values, as returned by the above
- function.
-
- o The new function as.phylo.formula() returns a phylogeny from a
- set of nested taxonomic variables given as a formula.
-
- o The new function read.caic() reads trees in CAIC format.
-
- o The new function tiplabels() allows to add labels to the tips
- of a tree using text or plotting symbols in a flexible way.
-
- o The new function unroot() unroots a phylogeny.
-
- o multi2di() has a new option, `random', which specifies whether
- to resolve the multichotomies randomly (the default) or not.
-
- o prop.part() now returns an object of class "prop.part" for which
- there are print (to display a partition in a more friendly way)
- and summary (to extract the numbers) methods.
-
- o plot.phylo() has a new option, `show.tip.label', specifying
- whether to print the labels of the tips. The default is TRUE.
-
- o The code of nj() has been replaced by a faster C code: it is now
- about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
- respectively.
-
- o write.nexus() now writes whether a tree is rooted or not.
-
-
-BUG FIXES
-
- o Two bugs have been fixed in root(): unrooted trees are now
- handled corretly, and node labels are now output normally.
-
- o A bug was fixed in phymltest(): the executable couldn't be found
- in some cases.
-
- o Three bug have been fixed in ace(): computing the likelihood of
- ancestral states of discrete characters failed, custom models
- did not work, and the function failed with a null gradient (a
- warning message is now returned; this latter bug was also
- present in yule.cov() as well and is now fixed).
-
- o pic() hanged out when missing data were present: a message error
- is now returned.
-
- o A small bug was fixed in dist.dna() where the gamma correction
- was not always correctly dispatched.
-
- o plot.phylo() plotted correctly the root edge only when the tree
- was plotted rightwards: this works now for all directions.
-
-
-OTHER CHANGES
-
- o dist.taxo() has been renamed as weight.taxo().
-
- o Various error and warning messages have been improved.
-
-
-
- CHANGES IN APE VERSION 1.7
-NEW FEATURES
-
- o The new function ace() estimates ancestral character states for
- continuous characters (with ML, GLS, and contrasts methods), and
- discrete characters (with ML only) for any number of states.
-
- o The new function compar.ou() fits the Ornstein-Uhlenbeck model
- of directional evolution for continuous characters. The user
- specifies the node(s) of the tree where the character optimum
- changes.
-
- o The new function is.rooted() tests whether a tree (of class
- "phylo") is rooted.
-
- o The new function rcoal() generates random ultrametric trees with
- the possibility to specify the function that generates the
- inter-nodes distances.
-
- o The new function mrca() gives for all pairs of tips in a tree
- (and optionally nodes too) the most recent common ancestor.
-
- o nodelabels() has a new option `thermo' to plot proportions (up
- to three classes) on the nodes of a tree.
-
- o rtree() has been improved: it can now generate rooted or
- unrooted trees, and the mathematical function that generates the
- branch lengths may be specified by the user. The tip labels may
- be given directly in the call to rtree. The limit cases (n = 2,
- 3) are now handled correctly.
-
- o dist.topo() has a new argument `method' with two choices: "PH85"
- for Penny and Henny's method (already available before and now
- the default), and "BHV01" for the geometric distance by Billera
- et al. (2001, Adv. Appl. Math. 27:733).
-
- o write.tree() has a new option, `digits', which specifies the
- number of digits to be printed in the Newick tree. By default
- digits = 10. The numbers are now always printed in decimal form
- (i.e., 1.0e-1 is now avoided).
-
- o dist.dna() can now compute the raw distances between pairs of
- DNA sequences by specifying model = "raw".
-
- o dist.phylo() has a new option `full' to possibly compute the
- distances among all tips and nodes of the tree. The default if
- `full = FALSE'.
-
-
-BUG FIXES
-
- o Several bugs were fixed in all.equal.phylo().
-
- o dist.dna() did not handle correctly gaps ("-") in alignments:
- they are now considered as missing data.
-
- o rotate() did not work if the tips were not ordered: this is
- fixed.
-
- o mantel.test() returned NA in some special cases: this is fixed
- and the function has been improved and is now faster.
-
- o A bug was fixed in diversi.gof() where the calculation of A² was
- incorrect.
-
- o cherry() did not work correctly under some OSs (mainly Linux):
- this is fixed.
-
- o is.binary.tree() has been modified so that it works with both
- rooted and unrooted trees.
-
- o The documentation of theta.s() was not correct: this has been
- fixed.
-
- o plot.mst() did not work correctly: this is fixed.
-
-
-
- CHANGES IN APE VERSION 1.6
-
-
-NEW FEATURES
-
- o The new function dist.topo() computes the topological distances
- between two trees.
-
- o The new function boot.phylo() performs a bootstrap analysis on
- phylogeny estimation.
-
- o The new functions prop.part() and prop.clades() analyse
- bipartitions from a series of trees.
-
-
-OTHER CHANGES
-
- o read.GenBank() now uses the EFetch utility of NCBI instead of
- the usual Web interface: it is now much faster (e.g., 12 times
- faster to retrieve 8 sequences, 37 times for 60 sequences).
-
-
-BUG FIXES
-
- o Several bugs were fixed in read.dna().
-
- o Several bugs were fixed in diversi.time().
-
- o is.binary.tree() did not work correctly if the tree has no edge
- lengths: this is fixed.
-
- o drop.tip() did not correctly propagated the `node.label' of a
- tree: this is fixed.
-
-
-
- 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.
Package: ape
Version: 2.2-2
-Date: 2008-10-02
+Date: 2008-10-08
Title: Analyses of Phylogenetics and Evolution
Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong,
Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel,
Gangolf Jobb, Christoph Heibl, Vincent Lefort, Jim Lemon,
Yvonnick Noel, Johan Nylander, Rainer Opgen-Rhein, Korbinian Strimmer,
Damien de Vienne
-Maintainer: Emmanuel Paradis <Emmanuel.Paradis@mpl.ird.fr>
+Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
Depends: R (>= 2.6.0)
Suggests: gee, nlme, lattice
ZipData: no
-## DNA.R (2008-10-02)
+## DNA.R (2008-10-08)
## Manipulations and Comparisons of DNA Sequences
### works only with matrices for the moment
{
obj <- list(...)
- nobj <- length(obj)
- if (nobj == 1) stop("only one matrix to bind.")
- NC <- ncol(obj[[1]])
- for (i in 2:nobj)
- if(ncol(obj[[i]]) != NC)
+ n <- length(obj)
+ if (n == 1) return(obj[[1]])
+ NC <- unlist(lapply(obj, ncol))
+ if (length(unique(NC)) > 1)
stop("matrices do not have the same number of columns.")
- for (i in 1:nobj) class(obj[[i]]) <- NULL
- ans <- obj[[1]]
- for (i in 2:nobj) ans <- rbind(ans, obj[[i]])
- structure(ans, class = "DNAbin")
+ for (i in 1:n) class(obj[[i]]) <- NULL
+ for (i in 2:n) obj[[1]] <- rbind(obj[[1]], obj[[i]])
+ structure(obj[[1]], class = "DNAbin")
}
-cbind.DNAbin <- function(..., check.names = TRUE)
+cbind.DNAbin <- function(..., check.names = TRUE, fill.with.gaps = FALSE,
+ quiet = TRUE)
### works only with matrices for the moment
{
obj <- list(...)
- nobj <- length(obj)
- if (nobj == 1) stop("only one matrix to bind.")
- NR <- nrow(obj[[1]])
- for (i in 2:nobj)
- if(nrow(obj[[i]]) != NR)
+ n <- length(obj)
+ if (n == 1) return(obj[[1]])
+ NR <- unlist(lapply(obj, nrow))
+ if (length(unique(NR)) > 1)
stop("matrices do not have the same number of rows.")
- for (i in 1:nobj) class(obj[[i]]) <- NULL
+ for (i in 1:n) class(obj[[i]]) <- NULL
nms <- rownames(obj[[1]])
if (check.names) {
- for (i in 2:nobj)
+ for (i in 2:n)
if (all(rownames(obj[[i]]) %in% nms))
obj[[i]] <- obj[[i]][nms, ]
else stop("rownames do not match among matrices.")
-## phymltest.R (2005-11-10)
+## phymltest.R (2008-10-08)
-## Fits a Bunch of Models with PHYML
+## Fits a Bunch of Models with PhyML
-## Copyright 2004-2005 Emmanuel Paradis
+## Copyright 2004-2008 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
-.phymltest.model <- c("JC69", "JC69+I", "JC69+G", "JC69+I+G",
- "K80", "K80+I", "K80+G", "K80+I+G",
- "F81", "F81+I", "F81+G", "F81+I+G",
- "F84", "F84+I", "F84+G", "F84+I+G",
- "HKY85", "HKY85+I", "HKY85+G", "HKY85+I+G",
- "TN93", "TN93+I", "TN93+G", "TN93+I+G",
- "GTR", "GTR+I", "GTR+G", "GTR+I+G")
+.phymltest.model <-
+ c("JC69", "JC69+I", "JC69+G", "JC69+I+G",
+ "K80", "K80+I", "K80+G", "K80+I+G",
+ "F81", "F81+I", "F81+G", "F81+I+G",
+ "F84", "F84+I", "F84+G", "F84+I+G",
+ "HKY85", "HKY85+I", "HKY85+G", "HKY85+I+G",
+ "TN93", "TN93+I", "TN93+G", "TN93+I+G",
+ "GTR", "GTR+I", "GTR+G", "GTR+I+G")
-.phymltest.nfp <- c(1, 2, 2, 3, 2, 3, 3, 4, 4, 5, 5, 6, 5, 6, 6, 7,
- 5, 6, 6, 7, 6, 7, 7, 8, 9, 10, 10, 11)
+.phymltest.nfp <-
+ c(1, 2, 2, 3, 2, 3, 3, 4, 4, 5, 5, 6, 5, 6, 6, 7,
+ 5, 6, 6, 7, 6, 7, 7, 8, 9, 10, 10, 11)
phymltest <- function(seqfile, format = "interleaved", itree = NULL,
- exclude = NULL, execname, path2exec = NULL)
+ exclude = NULL, execname = NULL, append = TRUE)
{
- windoz <- .Platform$OS.type == "windows"
- if (missing(execname)) {
- if (windoz) execname <- "phyml_w32"
- else stop("you must give an executable file name for PHYML")
+ os <- Sys.info()[1]
+ ## default names of PhyML:
+ if (is.null(execname)) {
+ if (os == "Linux") execname <- "phyml_3.0_linux32"
+ if (os == "Darwin") execname <- "phyml_3.0_macintel"
+ if (os == "Windows") execname <- "phyml_3.0_win32"
}
- outfile <- paste(seqfile, "_phyml_stat.txt", sep = "")
- inp <- seqfile
- if (file.exists(outfile)) inp <- c(inp, "A")
- if (file.exists(paste(seqfile, "_phyml_tree.txt", sep = "")))
- inp <- c(inp, "A")
- if (format != "interleaved") inp <- c(inp, "I")
- if (!is.null(itree)) inp <- c(inp, "U", itree)
+ if (is.null(execname))
+ stop("you must give an executable file name for PHYML")
N <- length(.phymltest.model)
- input.model <- list(c(rep("M", 5), "Y"),
- c(rep("M", 5), "V", rep("Y", 2)),
- c(rep("M", 5), "R", "A", rep("Y", 2)),
- c(rep("M", 5), "R", "A", "Y", "V", rep("Y", 2)),
- c(rep("M", 6), "T", rep("Y", 2)),
- c(rep("M", 6), "T", "Y", "V", rep("Y", 2)),
- c(rep("M", 6), "T", "Y", "R", "A", rep("Y", 2)),
- c(rep("M", 6), "T", "Y", "R", "A", "Y", "V", rep("Y", 2)),
- c(rep("M", 7), "Y"),
- c(rep("M", 7), "V", rep("Y", 2)),
- c(rep("M", 7), "R", "A", rep("Y", 2)),
- c(rep("M", 7), "V", "Y", "R", "A", rep("Y", 2)),
- c("M", "T", rep("Y", 2)),
- c("M", "T", "Y", "V", rep("Y", 2)),
- c("M", "T", "Y", "R", "A", rep("Y", 2)),
- c("M", "T", "Y", "V", "Y", "R", "A", rep("Y", 2)),
- c("T", rep("Y", 2)),
- c("T", "Y", "V", rep("Y", 2)),
- c("T", "Y", "R", "A", rep("Y", 2)),
- c("T", "Y", "V", "Y", "R", "A", rep("Y", 2)),
- c(rep("M", 2), "T", rep("Y", 2)),
- c(rep("M", 2), "T", "Y", "V", rep("Y", 2)),
- c(rep("M", 2), "T", "Y", "R", "A", rep("Y", 2)),
- c(rep("M", 2), "T", "Y", "R", "A", "Y", "V", rep("Y", 2)),
- c(rep("M", 3), "Y"),
- c(rep("M", 3), "V", rep("Y", 2)),
- c(rep("M", 3), "R", "A", rep("Y", 2)),
- c(rep("M", 3), "V", "Y", "R", "A", rep("Y", 2)))
- loglik <- numeric(N)
- names(input.model) <- names(loglik) <- .phymltest.model
- if (is.null(path2exec)) exec <- execname
- else exec <- paste(path2exec, execname, sep = "/")
- imod <- if (is.null(exclude)) 1:N else (1:N)[!.phymltest.model %in% exclude]
- for (i in imod) {
- if (i == 2) {
- if (length(inp) == 1) inp <- c(inp, rep("A", 2))
- else if (inp[2] != "A") inp <- c(inp[1], rep("A", 2), inp[2:length(inp)])
- }
- if (windoz) system(exec, input = c(inp, input.model[[i]]))
- else {
- cat(c(inp, input.model[[i]]), file = "f", sep = "\n")
- system(paste(exec, "f", sep = " < "))
- }
- loglik[i] <- scan(paste(seqfile, "_phyml_lk.txt", sep = ""), quiet = TRUE)
+ format <- match.arg(format, c("interleaved", "sequential"))
+ fmt <- rep("", N)
+ if (format != "interleaved") fmt[] <- "-q"
+ boot <- rep("-b 0", N) # to avoid any testing
+ mdl <- paste("-m", rep(c("JC69", "K80", "F81", "HKY85", "F84", "TN93", "GTR"), each = 4))
+ tstv <- rep("-t e", N) # ignored by PhyML with JC69 or F81
+ inv <- rep(c("", "-v e"), length.out = N)
+ ## no need to use the -c option of PhyML (4 categories by default if '-a e' is set):
+ alpha <- rep(rep(c("", "-a e"), each = 2), length.out = N)
+ tree <- rep("", N)
+ if (!is.null(itree)) tree[] <- paste("-u ", itree)
+
+ cmd <- paste(execname, "-i", seqfile, fmt, boot, mdl, tstv, inv, alpha, tree, "--append ")
+ outfile <- paste(seqfile, "_phyml_stats.txt", sep = "")
+ if (!append) {
+ unlink(outfile)
+ unlink(paste(seqfile, "_phyml_tree.txt", sep = ""))
}
- unlink("f")
- loglik <- loglik[imod]
+ imod <- 1:N
+ if (!is.null(exclude)) imod <- imod[!.phymltest.model %in% exclude]
+
+ for (i in imod) system(cmd[i])
+
+ l <- readLines(outfile)
+ l <- grep("Log-likelihood:", l, value = TRUE)
+ ## in case there were already some results in the output file:
+ if (dd <- length(l) - length(imod)) l <- l[-(1:dd)]
+ loglik <- as.numeric(sub(". Log-likelihood:", "", l))
+ names(loglik) <- .phymltest.model[imod]
class(loglik) <- "phymltest"
loglik
}
\alias{print.phymltest}
\alias{summary.phymltest}
\alias{plot.phymltest}
-\title{Fits a Bunch of Models with PHYML}
+\title{Fits a Bunch of Models with PhyML}
\usage{
phymltest(seqfile, format = "interleaved", itree = NULL,
- exclude = NULL, execname, path2exec = NULL)
+ exclude = NULL, execname = NULL, append = TRUE)
\method{print}{phymltest}(x, ...)
\method{summary}{phymltest}(object, ...)
\method{plot}{phymltest}(x, main = NULL, col = "blue", ...)
}
\arguments{
\item{seqfile}{a character string giving the name of the file that
- contains the DNA sequences to be analysed by PHYML.}
+ contains the DNA sequences to be analysed by PhyML.}
\item{format}{a character string specifying the format of the DNA
sequences: either \code{"interleaved"} (the default), or
\code{"sequential"}.}
\item{itree}{a character string giving the name of a file with a tree
- in Newick format to be used as an initial tree by PHYML. If
- \code{NULL} (the default), PHYML uses a ``BIONJ'' tree.}
+ in Newick format to be used as an initial tree by PhyML. If
+ \code{NULL} (the default), PhyML uses a ``BIONJ'' tree.}
\item{exclude}{a vector of mode character giving the models to be
excluded from the analysis. These must be among those below, and
follow the same syntax.}
- \item{execname}{a character string specifying the name of the PHYML
- binary file. This argument can be left missing under Windows: the
- default name \code{"phyml_w32"} will then be used.}
- \item{path2exec}{a character string giving the path to the PHYML
- binary file. If \code{NULL} the file must be accessible to R (either
- it is in the computer path, or it is in R's working directory).}
+ \item{execname}{a character string specifying the name of the PhyML
+ executable. This argument can be left as \code{NULL} if PhyML's
+ default names are used: \code{"phyml_3.0_linux32"},
+ \code{"phyml_3.0_macintel"}, or \code{"phyml_3.0_win32.exe"}, under
+ Linux, MacOS, or Windows respectively.}
+ \item{append}{a logical indicating whether to erase previous PhyML
+ output files if present; the default is to not erase.}
\item{x}{an object of class \code{"phymltest"}.}
\item{object}{an object of class \code{"phymltest"}.}
\item{main}{a title for the plot; if left \code{NULL}, a title is made
\item{...}{further arguments passed to or from other methods.}
}
\description{
- This function calls the software PHYML and fits successively 28 models
- of DNA evolution. The results are saved on disk, as PHYML usually
- does, and returned in R as a vector with the log-likelihood value of
- each model.
+ This function calls PhyML and fits successively 28 models of DNA
+ evolution. The results are saved on disk, as PhyML usually does, and
+ returned in R as a vector with the log-likelihood value of each model.
}
\details{
- The present function has been tested with version 2.4 of PHYML; it
- should also work with version 2.3, but it won't work with version 2.1.
-
- Under unix-like systems, it seems necessary to run R from csh or a
- similar shell (sh might not work).
+ The present function requires version 3.0 of PhyML; it won't work with
+ older versions.
The user must take care to set correctly the three different paths
- involved here: the path to PHYML's binary, the path to the sequence
+ involved here: the path to PhyML's binary, the path to the sequence
file, and the path to R's working directory. The function should work
if all three paths are different. Obviously, there should be no problem
if they are all the same.
- If the usual output files of PHYML already exist, they are not
- deleted and PHYML's results are appended.
-
The following syntax is used for the models:
"X[Y][Z]00[+I][+G]"
are described in the help page of \code{\link{dist.dna}}.
When a gamma distribution of substitution rates is specified, four
- categories are used (which is PHYML's default behaviour), and the
+ categories are used (which is PhyML's default behaviour), and the
``alpha'' parameter is estimated from the data.
For the models with a different substition rate for transitions and
transversions, these rates are left free and estimated from the data
- (and not constrained with a ratio of 4 as in PHYML's default).
+ (and not constrained with a ratio of 4 as in PhyML's default).
+
+ The option \code{path2exec} has been removed in the present version:
+ the path to PhyML's executable can be specified with the option
+ \code{execname}.
}
\note{
It is important to note that the models fitted by this function is
- only a small fraction of the models possible with PHYML. For instance,
+ only a small fraction of the models possible with PhyML. For instance,
it is possible to vary the number of categories in the (discretized)
gamma distribution of substitution rates, and many parameters can be
fixed by the user. The results from the present function should rather
}
\examples{
### A `fake' example with random likelihood values: it does not
-### make sense, but does not need PHYML and gives you a flavour
+### make sense, but does not need PhyML and gives you a flavour
### of what the output looks like:
x <- runif(28, -100, -50)
names(x) <- .phymltest.model
summary(x)
plot(x)
plot(x, main = "", col = "red")
-### This example needs PHYML, copy/paste or type the
+### This example needs PhyML, copy/paste or type the
### following commands if you want to try them, eventually
### changing setwd() and the options of phymltest()
\dontrun{
projects / ape.git / commitdiff