1 CHANGES IN APE VERSION 2.1
6 o The new function identify.phylo identifies clades on a plotted
9 o It is now possible to subset a list of trees (object of class
10 "multiPhylo") with "[" while keeping its class correct.
12 o The new function as.DNAbin.alignment converts DNA sequences
13 stored in the "alignment" format of the package seqinr into
14 an object of class "DNAbin".
16 o The new function weight.taxo2 helps to build similarity matrices
17 given two taxonomic levels (usually called by other functions).
19 o write.tree() can now take a list of trees (class "multiPhylo")
22 o plot.correlogram() and plot.correlogramList() have been
23 improved, and gain several options (see the help page for
24 details). A legend is now plotted by default.
29 o dist.dna() returned some incorrect values with `model = "JC69"'
30 and `pairwise.deletion = TRUE'. This affected only the
31 distances involving sequences with missing values. (Thanks
32 to Bruno Toupance for digging this bug out.)
34 o write.tree() failed with some trees: this is fixed by removing
35 the `multi.line' option (trees are now always printed on a
38 o read.nexus() did not correctly detect trees with multiple root
39 edges (see OTHER CHANGES).
44 o The code of mlphylo() has almost entirely rewritten, and should
45 much stabler now. The options have been also greatly simplified
46 (see ?mlphylo and ?DNAmodel for details).
48 o The internal function nTips has been renamed klastorin_nTips.
50 o The code of is.ultrametric() contained redundancies and has
53 o The code of Moran.I() and of correlogram.formula() have been
56 o read.tree() and read.nexus() now return an error when trying to
57 read a tree with multiple root edges (see BUG FIXES). The
58 correction applied in previous version did not work in all
61 o The class c("multi.tree", "phylo") has been renamed
67 o There is now a vignette in ape: see vignette("MoranI", "ape").
72 o as.matching() and as.phylo.matching() do not support branch
75 o correlogram.phylo() and discrete.dist() have been removed.
79 CHANGES IN APE VERSION 2.0-2
84 o The new function matexpo computes the exponential of a square
87 o The new function unique.multi.tree removes duplicate trees from
90 o yule() has a new option `use.root.edge = FALSE' that specifies
91 to ignore, by default, the root edge of the tree if it exists.
96 o which.edge() failed when the index of a single terminal edge was
99 o In diversi.time(), the values returned for model C were
102 o A bug was fixed in yule() that affected the calculation of the
103 likelihood in the presence of ties in the branching times.
105 o There was a bug in the C function mat_expo4x4 affecting the
106 calculations of the transition probabilities for models HKY and
109 o A small bug was fixed in as.matrix.DNAbin (thanks to James
112 o rtree() did not `shuffle' the tip labels by default, so only a
113 limited number of labelled topologies could be generated.
117 CHANGES IN APE VERSION 2.0-1
122 o The three new functions bionj, fastme.ols, and fastme.bal
123 perform phylogeny estimation by the BIONJ and fastME methods in
124 OLS and balanced versions. This is a port to R of previous
125 previous programs done by Vincent Lefort.
127 o The new function chronoMPL performs molecular dating with the
128 mean path lengths method of Britton et al. (2002, Mol. Phyl.
131 o The new function rotate, contributed by Christoph Heibl, swaps
132 two clades connected to the same node. It works also with
133 multichotomous nodes.
135 o The new `method' as.matrix.DNAbin() may be used to convert
136 easily DNA sequences stored in a list into a matrix while
137 keeping the names and the class.
142 o chronopl() failed when some branch lengths were equal to zero:
143 an error message is now returned.
145 o di2multi() failed when there was a series of consecutive edges
150 CHANGES IN APE VERSION 1.10-2
155 o plot.phylo() can now plot circular trees: the option is type =
156 "fan" or type = "f" (to avoid the ambiguity with type = "c").
158 o prop.part() has a new option `check.labels = FALSE' which allows
159 to considerably speed-up the calculations of bipartitions. As a
160 consequence, calculations of bootstrap values with boot.phylo()
161 should be much faster.
166 o read.GenBank() did not return correctly the list of species as
167 from ape 1.10: this is fixed in this version
169 o Applying as.phylo() on a tree of class "phylo" failed: the
170 object is now returned unchanged.
174 CHANGES IN APE VERSION 1.10-1
179 o The three new functions Ntip, Nnode, and Nedge return, for a
180 given tree, the number of tips, nodes, or edges, respectively.
185 o read.nexus() did not set correctly the class of the returned
186 object when reading multiple trees.
188 o mllt.plot() failed with objects of class c("multi.tree",
191 o unroot() did not work correctly in most cases.
193 o reorder.phylo() made R freeze in some occasions.
195 o Plotting a tree in pruningwise order failed.
197 o When plotting an unrooted tree, the tip labels where not all
198 correctly positioned if the option `cex' was used.
202 CHANGES IN APE VERSION 1.10
207 o Five new `method' functions have been introduced to manipulate
208 DNA sequences in binary format (see below).
210 o Three new functions have been introduced to convert between the
211 new binary and the character formats.
213 o The new function as.alignment converts DNA sequences stored as
214 single characters into the class "alignment" used by the package
217 o read.dna() and read.GenBank() have a new argument `as.character'
218 controlling whether the sequences are returned in binary format
224 o root() failed when the tree had node labels: this is fixed.
226 o plot.phylo() did not correctly set the limits on the y-axis with
227 the default setting: this is fixed.
229 o dist.dna() returned a wrong result for the LogDet, paralinear,
230 and BH87 models with `pairwise.deletion = TRUE'.
235 o DNA sequences are now internally stored in a binary format. See
236 the document "A Bit-Level Coding Scheme for Nucleotides" for the
237 details. Most functions analyzing DNA functions have been
238 modified accordingly and are now much faster (dist.dna is now
239 ca. 60 times faster).
243 CHANGES IN APE VERSION 1.9-4
248 o A bug was fixed in edgelabels().
250 o as.phylo.hclust() did not work correctly when the object of
251 class "hclust" has its labels set to NULL: the returned tree has
252 now its tip labels set to "1", "2", ...
254 o consensus could fail if some tip labels are a subset of others
255 (e.g., "a" and "a_1"): this is now fixed.
257 o mlphylo() failed in most cases if some branch lengths of the
258 initial tree were greater than one: an error message is now
261 o mlphylo() failed in most cases when estimating the proportion of
262 invariants: this is fixed.
266 CHANGES IN APE VERSION 1.9-3
271 o The new function edgelabels adds labels on the edge of the tree
272 in the same way than nodelabels or tiplabels.
277 o multi2di() did not handle correctly branch lengths with the
278 default option `random = TRUE': this is now fixed.
280 o A bug was fixed in nuc.div() when using pairwise deletions.
282 o A bug occurred in the analysis of bipartitions with large
283 numbers of large trees, with consequences on prop.part,
284 prop.clades, and boot.phylo.
286 o The calculation of the Billera-Holmes-Vogtmann distance in
287 dist.topo was wrong: this has been fixed.
291 CHANGES IN APE VERSION 1.9-2
296 o The new function ladderize reorganizes the internal structure of
297 a tree to plot them left- or right-ladderized.
299 o The new function dist.nodes computes the patristic distances
300 between all nodes, internal and terminal, of a tree. It replaces
301 the option `full = TRUE' of cophenetic.phylo (see below).
306 o A bug was fixed in old2new.phylo().
308 o Some bugs were fixed in chronopl().
310 o The edge colours were not correctly displayed by plot.phylo
311 (thank you to Li-San Wang for the fix).
313 o cophenetic.phylo() failed with multichotomous trees: this is
319 o read.dna() now returns the sequences in a matrix if they are
320 aligned (interleaved or sequential format). Sequences in FASTA
321 format are still returned in a list.
323 o The option `full' of cophenetic.phylo() has been removed because
324 it could not be used from the generic.
329 o rotate() has been removed; this function did not work correctly
334 CHANGES IN APE VERSION 1.9-1
339 o Trees with a single tip were not read correctly in R as the
340 element `Nnode' was not set: this is fixed.
342 o unroot() did not set correctly the number of nodes of the
343 unrooted tree in most cases.
345 o read.GenBank() failed when fetching very long sequences,
346 particularly of the BX-series.
348 o A bug was introduced in read.tree() with ape 1.9: it has been
353 CHANGES IN APE VERSION 1.9
358 o There are two new print `methods' for trees of class "phylo" and
359 lists of trees of class "multi.tree", so that they are now
360 displayed in a compact and informative way.
362 o There are two new functions, old2new.phylo and new2old.phylo,
363 for converting between the old and new coding of the class
366 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
367 LogDet ("logdet"), and paralinear ("paralin").
369 o compute.brlen() has been extended: several methods are now
370 available to compute branch lengths.
372 o write.dna() can now handle matrices as well as lists.
377 o cophenetic.phylo() sometimes returned a wrong result with
378 multichotomous trees: this is fixed.
380 o rotate() failed when a single tip was specified: the tree is now
383 o ace() did not return the correct index matrix with custom
384 models: this is fixed.
386 o multi2di() did not work correctly when resolving multichotomies
387 randomly: the topology was always the same, only the arrangement
388 of clades was randomized: this is fixed. This function now
389 accepts trees with no branch lengths.
391 o The output of diversi.gof() was blurred by useless prints when a
392 user distribution was specified. This has been corrected, and
393 the help page of this function has been expanded.
398 o The internal structure of the class "phylo" has been changed:
399 see the document "Definition of Formats for Coding Phylogenetic
400 Trees in R" for the details. In addition, the code of most
401 functions has been improved.
403 o Several functions have been improved by replacing some R codes
404 by C codes: pic, plot.phylo, and reorder.phylo.
406 o There is now a citation information: see citation("ape") in R.
408 o write.tree() now does not add extra 0's to branch lengths so
409 that 1.23 is printed "1.23" by default, not "1.2300000000".
411 o The syntax of bind.tree() has been simplified. This function now
412 accepts trees with no branch lengths, and handles correctly node
415 o The option `as.numeric' of mrca() has been removed.
417 o The unused options `format' and `rooted' of read.tree() have
420 o The unused option `format' of write.tree() has been removed.
422 o The use of node.depth() has been simplified.
426 CHANGES IN APE VERSION 1.8-5
431 o Two new functions read.nexus.data() and write.nexus.data(),
432 contributed by Johan Nylander, allow to read and write molecular
433 sequences in NEXUS files.
435 o The new function reorder.phylo() reorders the internal structure
436 of a tree of class "phylo". It is used as the generic, e.g.,
439 o read.tree() and read.nexus() can now read trees with a single
442 o The new data set `cynipids' supplies a set of protein sequences
448 o The code of all.equal.phylo() has been completely rewritten
449 (thanks to Benoît Durand) which fixes several bugs.
451 o read.tree() and read.nexus() now checks the labels of the tree
452 to remove or substitute any characters that are illegal in the
453 Newick format (parentheses, etc.)
455 o A negative P-value could be returned by mantel.test(): this is
460 CHANGES IN APE VERSION 1.8-4
465 o The new function sh.test() computes the Shimodaira-
468 o The new function collapse.singles() removes the nodes with a
469 single descendant from a tree.
471 o plot.phylo() has a new argument `tip.color' to specify the
474 o mlphylo() has now an option `quiet' to control the display of
475 the progress of the analysis (the default is FALSE).
480 o read.dna() did not read correctly sequences in sequential format
481 with leading alignment gaps "-": this is fixed.
483 o ace() returned a list with no class so that the generic
484 functions (anova, logLik, ...) could not be used directly. This
485 is fixed as ace() now returns an object of class "ace".
487 o anova.ace() had a small bug when computing the number of degrees
488 of freedom: this is fixed.
490 o mlphylo() did not work when the sequences were in a matrix or
491 a data frame: this is fixed.
493 o rtree() did not work correctly when trying to simulate an
494 unrooted tree with two tips: an error message is now issued.
499 o The algorithm of rtree() has been changed: it is now about 40,
500 100, and 130 times faster for 10, 100, and 1000 tips,
505 CHANGES IN APE VERSION 1.8-3
510 o There are four new `method' functions to be used with the
511 results of ace(): logLik(), deviance(), AIC(), and anova().
513 o The plot method of phymltest has two new arguments: `main' to
514 change the title, and `col' to control the colour of the
515 segments showing the AIC values.
517 o ace() has a new argument `ip' that gives the initial values used
518 in the ML estimation with discrete characters (see the examples
519 in ?ace). This function now returns a matrix giving the indices
520 of the estimated rates when analysing discrete characters.
522 o nodelabels() and tiplabels() have a new argument `pie' to
523 represent proportions, with any number of categories, as
524 piecharts. The use of the option `thermo' has been improved:
525 there is now no limitation on the number of categories.
530 o mlphylo() did not work with more than two partitions: this is
533 o root() failed if the proposed outgroup was already an outgroup
534 in the tree: this is fixed.
536 o The `col' argument in nodelabels() and tiplabels() was not
537 correctly passed when `text' was used: this is fixed.
539 o Two bugs were fixed in mlphylo(): parameters were not always
540 correctly output, and the estimation failed in some cases.
542 o plot.phylo() was stuck when given a tree with a single tip: this
543 is fixed and a message error is now returned.
545 o An error was corrected in the help page of gammaStat regarding
546 the calculation of P-values.
548 o Using gls() could crash R when the number of species in the tree
549 and in the variables were different: this is fixed.
553 CHANGES IN APE VERSION 1.8-2
558 o The new function mlphylo() fits a phylogenetic tree by maximum
559 likelihood from DNA sequences. Its companion function DNAmodel()
560 is used to define the substitution model which may include
561 partitioning. There are methods for logLik(), deviance(), and
562 AIC(), and the summary() method has been extended to display in
563 a friendly way the results of this model fitting. Currently, the
564 functionality is limited to estimating the substitution and
565 associated parameters and computing the likelihood.
567 o The new function drop1.compar.gee (used as, e.g., drop1(m))
568 tests for single effects in GEE-based comparative method. A
569 warning message is printed if there is not enough degrees of
575 o An error message was sometimes issued by plot.multi.tree(),
576 though with no consequence.
580 CHANGES IN APE VERSION 1.8-1
585 o There is a new plot method for lists of trees (objects of class
586 "multi.tree"): it calls plot.phylo() internally and is
587 documented on the same help page.
592 o A bug was fixed in the C code that analyzes bipartitions: this
593 has impact on several functions like prop.part, prop.clades,
594 boot.phylo, or consensus.
596 o root() did not work correctly when the specified outgroup had
597 more than one element: this is fixed.
599 o dist.dna() sometimes returned a warning inappropriately: this
602 o If the distance object given to nj() had no rownames, nj()
603 returned a tree with no tip labels: it now returns tips labelled
604 "1", "2", ..., corresponding to the row numbers.
609 o nj() has been slightly changed so that tips with a zero distance
610 are first aggregated with zero-lengthed branches; the usual NJ
611 procedure is then performed on a distance matrix without 0's.
615 CHANGES IN APE VERSION 1.8
620 o The new function chronopl() estimates dates using the penalized
621 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
623 o The new function consensus() calculates the consensus tree of a
626 o The new function evolve.phylo() simulates the evolution of
627 continuous characters along a phylogeny under a Brownian model.
629 o The new plot method for objects of class "ancestral" displays a
630 tree together with ancestral values, as returned by the above
633 o The new function as.phylo.formula() returns a phylogeny from a
634 set of nested taxonomic variables given as a formula.
636 o The new function read.caic() reads trees in CAIC format.
638 o The new function tiplabels() allows to add labels to the tips
639 of a tree using text or plotting symbols in a flexible way.
641 o The new function unroot() unroots a phylogeny.
643 o multi2di() has a new option, `random', which specifies whether
644 to resolve the multichotomies randomly (the default) or not.
646 o prop.part() now returns an object of class "prop.part" for which
647 there are print (to display a partition in a more friendly way)
648 and summary (to extract the numbers) methods.
650 o plot.phylo() has a new option, `show.tip.label', specifying
651 whether to print the labels of the tips. The default is TRUE.
653 o The code of nj() has been replaced by a faster C code: it is now
654 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
657 o write.nexus() now writes whether a tree is rooted or not.
662 o Two bugs have been fixed in root(): unrooted trees are now
663 handled corretly, and node labels are now output normally.
665 o A bug was fixed in phymltest(): the executable couldn't be found
668 o Three bug have been fixed in ace(): computing the likelihood of
669 ancestral states of discrete characters failed, custom models
670 did not work, and the function failed with a null gradient (a
671 warning message is now returned; this latter bug was also
672 present in yule.cov() as well and is now fixed).
674 o pic() hanged out when missing data were present: a message error
677 o A small bug was fixed in dist.dna() where the gamma correction
678 was not always correctly dispatched.
680 o plot.phylo() plotted correctly the root edge only when the tree
681 was plotted rightwards: this works now for all directions.
686 o dist.taxo() has been renamed as weight.taxo().
688 o Various error and warning messages have been improved.
692 CHANGES IN APE VERSION 1.7
695 o The new function ace() estimates ancestral character states for
696 continuous characters (with ML, GLS, and contrasts methods), and
697 discrete characters (with ML only) for any number of states.
699 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
700 of directional evolution for continuous characters. The user
701 specifies the node(s) of the tree where the character optimum
704 o The new function is.rooted() tests whether a tree (of class
707 o The new function rcoal() generates random ultrametric trees with
708 the possibility to specify the function that generates the
709 inter-nodes distances.
711 o The new function mrca() gives for all pairs of tips in a tree
712 (and optionally nodes too) the most recent common ancestor.
714 o nodelabels() has a new option `thermo' to plot proportions (up
715 to three classes) on the nodes of a tree.
717 o rtree() has been improved: it can now generate rooted or
718 unrooted trees, and the mathematical function that generates the
719 branch lengths may be specified by the user. The tip labels may
720 be given directly in the call to rtree. The limit cases (n = 2,
721 3) are now handled correctly.
723 o dist.topo() has a new argument `method' with two choices: "PH85"
724 for Penny and Henny's method (already available before and now
725 the default), and "BHV01" for the geometric distance by Billera
726 et al. (2001, Adv. Appl. Math. 27:733).
728 o write.tree() has a new option, `digits', which specifies the
729 number of digits to be printed in the Newick tree. By default
730 digits = 10. The numbers are now always printed in decimal form
731 (i.e., 1.0e-1 is now avoided).
733 o dist.dna() can now compute the raw distances between pairs of
734 DNA sequences by specifying model = "raw".
736 o dist.phylo() has a new option `full' to possibly compute the
737 distances among all tips and nodes of the tree. The default if
743 o Several bugs were fixed in all.equal.phylo().
745 o dist.dna() did not handle correctly gaps ("-") in alignments:
746 they are now considered as missing data.
748 o rotate() did not work if the tips were not ordered: this is
751 o mantel.test() returned NA in some special cases: this is fixed
752 and the function has been improved and is now faster.
754 o A bug was fixed in diversi.gof() where the calculation of A² was
757 o cherry() did not work correctly under some OSs (mainly Linux):
760 o is.binary.tree() has been modified so that it works with both
761 rooted and unrooted trees.
763 o The documentation of theta.s() was not correct: this has been
766 o plot.mst() did not work correctly: this is fixed.
770 CHANGES IN APE VERSION 1.6
775 o The new function dist.topo() computes the topological distances
778 o The new function boot.phylo() performs a bootstrap analysis on
779 phylogeny estimation.
781 o The new functions prop.part() and prop.clades() analyse
782 bipartitions from a series of trees.
787 o read.GenBank() now uses the EFetch utility of NCBI instead of
788 the usual Web interface: it is now much faster (e.g., 12 times
789 faster to retrieve 8 sequences, 37 times for 60 sequences).
794 o Several bugs were fixed in read.dna().
796 o Several bugs were fixed in diversi.time().
798 o is.binary.tree() did not work correctly if the tree has no edge
799 lengths: this is fixed.
801 o drop.tip() did not correctly propagated the `node.label' of a
806 CHANGES IN APE VERSION 1.5
811 o Two new functions, as.matching.phylo() and as.phylo.matching(),
812 convert objects between the classes "phylo" and "matching". The
813 latter implements the representation of binary trees introduced by
814 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
815 as.matching() has been introduced as well.
817 o Two new functions, multi2di() and di2multi(), allow to resolve
818 and collapse multichotomies with branches of length zero.
820 o The new function nuc.div() computes the nucleotide diversity
821 from a sample a DNA sequences.
823 o dist.dna() has been completely rewritten with a much faster
824 (particularly for large data sets) C code. Eight models are
825 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
826 option `method' has been renamed `model'). Computation of variance
827 is available for all models. A gamma-correction is possible for
828 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
829 to remove sites with missing data on a pairwise basis. The option
830 `GCcontent' has been removed.
832 o read.GenBank() has a new option (species.names) which specifies
833 whether to return the species names of the organisms in addition
834 to the accession numbers of the sequences (this is the default
837 o write.nexus() can now write several trees in the same NEXUS file.
839 o drop.tip() has a new option `root.edge' that allows to specify the
840 new root edge if internal branches are trimmed.
845 o as.phylo.hclust() failed if some labels had parentheses: this
848 o Several bugs were fixed in all.equal.phylo(). This function now
849 returns the logical TRUE if the trees are identical but with
850 different representations (a report was printed previously).
852 o read.GenBank() did not correctly handle ambiguous base codes:
858 o birthdeath() now returns an object of class "birthdeath" for
859 which there is a print method.
863 CHANGES IN APE VERSION 1.4
868 o The new function nj() performs phylogeny estimation with the
869 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
872 o The new function which.edge() identifies the edges of a tree
873 that belong to a group specified as a set of tips.
875 o The new function as.phylo.phylog() converts an object of class
876 "phylog" (from the package ade4) into an object of class
879 o The new function axisPhylo() draws axes on the side of a
882 o The new function howmanytrees() calculates the number of trees
883 in different cases and giving a number of tips.
885 o write.tree() has a new option `multi.line' (TRUE by default) to
886 write a Newick tree on several lines rather than on a single
889 o The functionalities of zoom() have been extended. Several
890 subtrees can be visualized at the same time, and they are marked
891 on the main tree with colors. The context of the subtrees can be
892 marked with the option `subtree' (see below).
894 o drop.tip() has a new option `subtree' (FALSE by default) which
895 specifies whether to output in the tree how many tips have been
898 o The arguments of add.scale.bar() have been redefined and have
899 now default values (see ?add.scale.bar for details). This
900 function now works even if the plotted tree has no edge length.
902 o plot.phylo() can now plot radial trees, but this does not take
903 edge lengths into account.
905 o In plot.phylo() with `type = "phylogram"', if the values of
906 `edge.color' and `edge.width' are identical for sister-branches,
907 they are propagated to the vertical line that link them.
912 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
913 crashing. This is fixed.
915 o In plot.phylo(), the options `edge.color' and `edge.width' are
916 now properly recycled; their default values are now "black" and
919 o A bug has been fixed in write.nexus().
924 o The function node.depth.edgelength() has been removed and
925 replaced by a C code.
929 CHANGES IN APE VERSION 1.3-1
934 o The new function nodelabels() allows to add labels to the nodes
935 of a tree using text or plotting symbols in a flexible way.
937 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
938 numeric values specifying the lower and upper limits on the x-
939 and y-axes. This allows to leave some space on any side of the
940 tree. If a single value is given, this is taken as the upper
945 CHANGES IN APE VERSION 1.3
950 o The new function phymltest() calls the software PHYML and fits
951 28 models of DNA sequence evolution. There are a print method to
952 display likelihood and AIC values, a summary method to compute
953 the hierarchical likelihood ratio tests, and a plot method to
954 display graphically the AIC values of each model.
956 o The new function yule.cov() fits the Yule model with covariates,
957 a model where the speciation rate is affected by several species
958 traits through a generalized linear model. The parameters are
959 estimated by maximum likelihood.
961 o Three new functions, corBrownian(), corGrafen(), and
962 corMartins(), compute the expected correlation structures among
963 species given a phylogeny under different models of evolution.
964 These can be used for GLS comparative phylogenetic methods (see
965 the examples). There are coef() and corMatrix() methods and an
966 Initialize.corPhyl() function associated.
968 o The new function compar.cheverud() implements Cheverud et al.'s
969 (1985; Evolution 39:1335) phylogenetic comparative method.
971 o The new function varcomp() estimates variance components; it has
974 o Two new functions, panel.superpose.correlogram() and
975 plot.correlogramList(), allow to plot several phylogenetic
978 o The new function node.leafnumber() computes the number of leaves
979 of a subtree defined by a particular node.
981 o The new function node.sons() gets all tags of son nodes from a
984 o The new function compute.brlen() computes the branch lengths of
985 a tree according to a specified method.
987 o plot.phylo() has three new options: "cex" controls the size of
988 the (tip and node) labels (thus it is no more needed to change
989 the global graphical parameter), "direction" which allows to
990 plot the tree rightwards, leftwards, upwards, or downwards, and
991 "y.lim" which sets the upper limit on the y-axis.
996 o Some functions which try to match tip labels and names of
997 additional data (e.g. vector) are likely to fail if there are
998 typing or syntax errors. If both series of names do not perfectly
999 match, they are ignored and a warning message is now issued.
1000 These functions are bd.ext, compar.gee, pic. Their help pages
1001 have been clarified on this point.
1005 CHANGES IN APE VERSION 1.2-7
1010 o The new function root() reroots a phylogenetic tree with respect
1011 to a specified outgroup.
1013 o The new function rotate() rotates an internal branch of a tree.
1015 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1016 trees) controls the display of the tip labels in unrooted trees.
1017 This display has been greatly improved: the tip labels are now not
1018 expected to overlap with the tree (particularly if lab4ut =
1019 "axial"). In all cases, combining appropriate values of "lab4ut"
1020 and the font size (via "par(cex = )") should result in readable
1021 unrooted trees. See ?plot.phylo for some examples.
1023 o In drop.tip(), the argument `tip' can now be numeric or character.
1028 o drop.tip() did not work correctly with trees with no branch
1029 lengths: this is fixed.
1031 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1032 plotted with some line crossings: this is now fixed.
1036 CHANGES IN APE VERSION 1.2-6
1041 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1042 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1043 to implement comparative methods with an autocorrelation approach.
1045 o A new data set describing some life history traits of Carnivores
1051 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1056 o When plotting a tree with plot.phylo(), the new default of the
1057 option `label.offset' is now 0, so the labels are always visible.
1061 CHANGES IN APE VERSION 1.2-5
1066 o The new function bd.ext() fits a birth-death model with combined
1067 phylogenetic and taxonomic data, and estimates the corresponding
1068 speciation and extinction rates.
1073 o The package gee is no more required by ape but only suggested
1074 since only the function compar.gee() calls gee.
1078 CHANGES IN APE VERSION 1.2-4
1083 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1084 and lines.popsize) implementing a new approach for inferring the
1085 demographic history from genealogies using a reversible jump
1086 MCMC have been introduced.
1088 o The unit of time in the skyline plot and in the new plots can
1089 now be chosen to be actual years, rather than substitutions.
1093 CHANGES IN APE VERSION 1.2-3
1098 o The new function rtree() generates a random binary tree with or
1099 without branch lengths.
1101 o Two new functions for drawing lineages-through-time (LTT) plots
1102 are provided: ltt.lines() adds a LTT curve to an existing plot,
1103 and mltt.plot() does a multiple LTT plot giving several trees as
1104 arguments (see `?ltt.plot' for details).
1109 o Some taxon names made R crashing when calling as.phylo.hclust():
1112 o dist.dna() returned an error with two identical DNA sequences
1113 (only using the Jukes-Cantor method returned 0): this is fixed.
1118 o The function dist.phylo() has been re-written using a different
1119 algorithm: it is now about four times faster.
1121 o The code of branching.times() has been improved: it is now about
1126 CHANGES IN APE VERSION 1.2-2
1131 o The new function seg.sites() finds the segregating sites in a
1132 sample of DNA sequences.
1137 o A bug introduced in read.tree() and in read.nexus() with version
1140 o A few errors were corrected and a few examples were added in the
1145 CHANGES IN APE VERSION 1.2-1
1150 o plot.phylo() can now draw the edge of the root of a tree if it
1151 has one (see the new option `root.edge', its default is FALSE).
1156 o A bug was fixed in read.nexus(): files with semicolons inside
1157 comment blocks were not read correctly.
1159 o The behaviour of read.tree() and read.nexus() was corrected so
1160 that tree files with badly represented root edges (e.g., with
1161 an extra pair of parentheses, see the help pages for details)
1162 are now correctly represented in the object of class "phylo";
1163 a warning message is now issued.
1167 CHANGES IN APE VERSION 1.2
1172 o plot.phylo() has been completely re-written and offers several
1173 new functionalities. Three types of trees can now be drawn:
1174 phylogram (as previously), cladogram, and unrooted tree; in
1175 all three types the branch lengths can be drawn using the edge
1176 lengths of the phylogeny or not (e.g., if the latter is absent).
1177 The vertical position of the nodes can be adjusted with two
1178 choices (see option `node.pos'). The code has been re-structured,
1179 and two new functions (potentially useful for developpers) are
1180 documented separately: node.depth.edgelength() and node.depth();
1181 see the respective help pages for details.
1183 o The new function zoom() allows to explore very large trees by
1184 focusing on a small portion of it.
1186 o The new function yule() fits by maximum likelihood the Yule model
1187 (birth-only process) to a phylogenetic tree.
1189 o Support for writing DNA sequences in FASTA format has been
1190 introduced in write.dna() (support for reading sequences in
1191 this format was introduced in read.dna() in version 1.1-2).
1192 The function has been completely re-written, fixing some bugs
1193 (see below); the default behaviour is no more to display the
1194 sequences on the standard output. Several options have been
1195 introduced to control the sequence printing in a flexible
1196 way. The help page has been extended.
1198 o A new data set is included: a supertree of bats in NEXUS format.
1203 o In theta.s(), the default of the option `variance' has
1204 been changed to `FALSE' (as was indicated in the help page).
1206 o Several bugs were fixed in the code of all.equal.phylo().
1208 o Several bugs were fixed in write.dna(), particularly this
1209 function did not work with `format = "interleaved"'.
1211 o Various errors were corrected in the help pages.
1216 o The argument names of as.hclust.phylo() have been changed
1217 from "(phy)" to "(x, ...)" to conform to the definition of
1218 the corresponding generic function.
1220 o gamma.stat() has been renamed gammaStat() to avoid confusion
1221 since gamma() is a generic function.
1225 CHANGES IN APE VERSION 1.1-3
1230 o base.freq() previously did not return a value of 0 for
1231 bases absent in the data (e.g., a vector of length 3 was
1232 returned if one base was absent). This is now fixed (a
1233 vector of length 4 is always returned).
1235 o Several bugs were fixed in read.nexus(), including that this
1236 function did not work in this absence of a "TRANSLATE"
1237 command in the NEXUS file, and that the commands were
1242 CHANGES IN APE VERSION 1.1-2
1247 o The Tamura and Nei (1993) model of DNA distance is now implemented
1248 in dist.dna(): five models are now available in this function.
1250 o A new data set is included: a set of 15 sequences of the
1251 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1257 o A bug in read.nexus() was fixed.
1259 o read.dna() previously did not work correctly in most cases.
1260 The function has been completely re-written and its help page
1261 has been considerably extended (see ?read.dna for details).
1262 Underscores (_) in taxon names are no more replaced with
1263 spaces (this behaviour was undocumented).
1265 o A bug was fixed in write.dna().
1269 CHANGES IN APE VERSION 1.1-1
1274 o A bug in read.tree() introduced in APE 1.1 was fixed.
1276 o A bug in compar.gee() resulted in an error when trying to fit
1277 a model with `family = "binomial"'. This is now fixed.
1281 CHANGES IN APE VERSION 1.1
1286 o The Klastorin (1982) method as suggested by Misawa and Tajima
1287 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1288 on the basis of phylogenetic trees has been implemented (see
1289 the function klastorin()).
1291 o Functions have been added to convert APE's "phylo" objects in
1292 "hclust" cluster objects and vice versa (see the help page of
1293 as.phylo for details).
1295 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1296 are introduced for the estimation of absolute evolutionary rates
1297 (ratogram) and dated clock-like trees (chronogram) from
1298 phylogenetic trees using the non-parametric rate smoothing approach
1299 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1301 o A summary method is now provided printing a summary information on a
1302 phylogenetic tree with, for instance, `summary(tree)'.
1304 o The behaviour of read.tree() was changed so that all spaces and
1305 tabulations in tree files are now ignored. Consequently, spaces in tip
1306 labels are no more allowed. Another side effect is that read.nexus()
1307 now does not replace the underscores (_) in tip labels with spaces
1308 (this behaviour was undocumented).
1310 o The function plot.phylo() has a new option (`underscore') which
1311 specifies whether the underscores in tip labels should be written on
1312 the plot as such or replaced with spaces (the default).
1314 o The function birthdeath() now computes 95% confidence intervals of
1315 the estimated parameters using profile likelihood.
1317 o Three new data sets are included: a gene tree estimated from 36
1318 landplant rbcL sequences, a gene tree estimated from 32 opsin
1319 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1324 o A bug was fixed in dist.gene() where nothing was returned.
1326 o A bug in plot.mst() was fixed.
1328 o A bug in vcv.phylo() resulted in false correlations when the
1329 option `cor = TRUE' was used (now fixed).
1333 CHANGES IN APE VERSION 1.0
1338 o Two new functions, read.dna() and write.dna(), read/write in a file
1339 DNA sequences in interleaved or in sequential format.
1341 o Two new functions, read.nexus() and write.nexus(), read/write trees
1344 o The new function bind.tree() allows to bind two trees together,
1345 possibly handling root edges to give internal branches.
1347 o The new function drop.tip() removes the tips in a phylogenetic tree,
1348 and trims (or not) the corresponding internal branches.
1350 o The new function is.ultrametric() tests if a tree is ultrametric.
1352 o The function plot.phylo() has more functionalities such as drawing the
1353 branches with different colours and/or different widths, showing the
1354 node labels, controling the position and font of the labels, rotating
1355 the labels, and controling the space around the plot.
1357 o The function read.tree() can now read trees with no branch length,
1358 such as "(a,b),c);". Consequently, the element `edge.length' in
1359 objects of class "phylo" is now optional.
1361 o The function write.tree() has a new default behaviour: if the default
1362 for the option `file' is used (i.e. file = ""), then a variable of
1363 mode character containing the tree in Newick format is returned which
1364 can thus be assigned (e.g., tree <- write.tree(phy)).
1366 o The function read.tree() has a new argument `text' which allows
1367 to read the tree in a variable of mode character.
1369 o A new data set is included: the phylogenetic relationships among
1370 the orders of birds from Sibley and Ahlquist (1990).
1374 CHANGES IN APE VERSION 0.2-1
1379 o Several bugs were fixed in the help pages.
1383 CHANGES IN APE VERSION 0.2
1388 o The function write.tree() writes phylogenetic trees (objects of class
1389 "phylo") in an ASCII file using the Newick parenthetic format.
1391 o The function birthdeath() fits a birth-death model to branching times
1392 by maximum likelihood, and estimates the corresponding speciation and
1395 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1398 o The function is.binary.tree() tests whether a phylogeny is binary.
1400 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1401 as well as some methods are introduced.
1403 o Several functions, including some generics and methods, for computing
1404 skyline plot estimates (classic and generalized) of effective
1405 population size through time are introduced and replace the function
1406 skyline.plot() in version 0.1.
1408 o Two data sets are now included: the phylogenetic relationships among
1409 the families of birds from Sibley and Ahlquist (1990), and an
1410 estimated clock-like phylogeny of HIV sequences sampled in the
1411 Democratic Republic of Congo.
1414 DEPRECATED & DEFUNCT
1416 o The function skyline.plot() in ape 0.1 has been deprecated and
1417 replaced by more elaborate functions (see above).
1422 o Two important bugs were fixed in plot.phylo(): phylogenies with
1423 multichotomies not at the root or not with only terminal branches,
1424 and phylogenies with a single node (i.e. only terminal branches)
1425 did not plot. These trees should be plotted correctly now.
1427 o Several bugs were fixed in diversi.time() in the computation of
1430 o Various errors were corrected in the help pages.
projects / ape.git / blob