1 CHANGES IN APE VERSION 2.1-4
6 o Four new functions have been written by Damien de Vienne for the
7 graphical exploration of large trees (plot.cophylo, subtrees,
8 subtreeplot), and to return the graphical coordinates of tree
14 o read.dna() failed if "?" occurred in the first 10 sites of the
17 o The x/y aspect of the plot is now respected when plotting a
18 circular tree (type = "r" or "f").
20 o Drawing the tip labels sometimes failed when plotting circular
23 o zoom() failed when tip labels were used instead of their numbers
24 (thanks to Yan Wong for the fix).
26 o drop.tip() failed with some trees (fixed by Yan Wong).
31 o chronopl() has been improved and gains several options: see its
32 help page for details.
36 CHANGES IN APE VERSION 2.1-3
41 o A bug in read.nexus() made the Windows R-GUI crash.
43 o An error was fixed in the computation of ancestral character
44 states by generalized least squares in ace().
46 o di2multi() did not modify node labels correctly.
48 o multi2di() failed if the tree had its attribute "order" set to
53 CHANGES IN APE VERSION 2.1-2
58 o There three new methods for the "multiPhylo" class: str, $,
61 o root() gains the options 'node' and 'resolve.root'
62 (FALSE by default) as well as its code being improved.
64 o mltt.plot() has now an option 'log' used in the same way
65 than in plot.default().
70 o mltt.plot() failed to display the legend with an unnamed
73 o nodelabels() with pies now correcly uses the argument
74 'cex' to draw symbols of different sizes (which has
75 worked already for thermometers).
77 o read.nexus() generally failed to read very big files.
82 o The argument 'family' of compar.gee() can now be a function
83 as well as a character string.
85 o read.tree() and read.nexus() now return an unnamed list if
88 o read.nexus() now returns a modified object of class "multiPhylo"
89 when there is a TRANSLATE block in the NEXUS file: the individual
90 trees have no 'tip.label' vector, but the list has a 'TipLabel'
91 attribute. The new methods '$' and '[[' set these elements
92 correctly when extracting trees.
96 CHANGES IN APE VERSION 2.1-1
101 o The new function rmtree generates lists of random trees.
103 o rcoal() now generates a genuine coalescent tree by default
104 (thanks to Vladimir Minin for the code).
109 o nuc.div() returned an incorrect value with the default
110 pairwise.deletion = FALSE.
115 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
116 have been improved so that they are stabler and faster.
118 o R packages used by ape are now loaded silently; lattice and gee
119 are loaded only when needed.
123 CHANGES IN APE VERSION 2.1
128 o The new function identify.phylo identifies clades on a plotted
129 tree using the mouse.
131 o It is now possible to subset a list of trees (object of class
132 "multiPhylo") with "[" while keeping its class correct.
134 o The new function as.DNAbin.alignment converts DNA sequences
135 stored in the "alignment" format of the package seqinr into
136 an object of class "DNAbin".
138 o The new function weight.taxo2 helps to build similarity matrices
139 given two taxonomic levels (usually called by other functions).
141 o write.tree() can now take a list of trees (class "multiPhylo")
142 as its main argument.
144 o plot.correlogram() and plot.correlogramList() have been
145 improved, and gain several options (see the help page for
146 details). A legend is now plotted by default.
151 o dist.dna() returned some incorrect values with `model = "JC69"'
152 and `pairwise.deletion = TRUE'. This affected only the
153 distances involving sequences with missing values. (Thanks
154 to Bruno Toupance for digging this bug out.)
156 o write.tree() failed with some trees: this is fixed by removing
157 the `multi.line' option (trees are now always printed on a
160 o read.nexus() did not correctly detect trees with multiple root
161 edges (see OTHER CHANGES).
166 o The code of mlphylo() has almost entirely rewritten, and should
167 be much stabler. The options have been also greatly simplified
168 (see ?mlphylo and ?DNAmodel for details).
170 o The internal function nTips has been renamed klastorin_nTips.
172 o The code of is.ultrametric() contained redundancies and has
175 o The code of Moran.I() and of correlogram.formula() have been
178 o read.tree() and read.nexus() now return an error when trying to
179 read a tree with multiple root edges (see BUG FIXES). The
180 correction applied in previous version did not work in all
183 o The class c("multi.tree", "phylo") has been renamed
189 o There is now a vignette in ape: see vignette("MoranI", "ape").
194 o as.matching() and as.phylo.matching() do not support branch
197 o correlogram.phylo() and discrete.dist() have been removed.
201 CHANGES IN APE VERSION 2.0-2
206 o The new function matexpo computes the exponential of a square
209 o The new function unique.multi.tree removes duplicate trees from
212 o yule() has a new option `use.root.edge = FALSE' that specifies
213 to ignore, by default, the root edge of the tree if it exists.
218 o which.edge() failed when the index of a single terminal edge was
221 o In diversi.time(), the values returned for model C were
224 o A bug was fixed in yule() that affected the calculation of the
225 likelihood in the presence of ties in the branching times.
227 o There was a bug in the C function mat_expo4x4 affecting the
228 calculations of the transition probabilities for models HKY and
231 o A small bug was fixed in as.matrix.DNAbin (thanks to James
234 o rtree() did not `shuffle' the tip labels by default, so only a
235 limited number of labelled topologies could be generated.
239 CHANGES IN APE VERSION 2.0-1
244 o The three new functions bionj, fastme.ols, and fastme.bal
245 perform phylogeny estimation by the BIONJ and fastME methods in
246 OLS and balanced versions. This is a port to R of previous
247 previous programs done by Vincent Lefort.
249 o The new function chronoMPL performs molecular dating with the
250 mean path lengths method of Britton et al. (2002, Mol. Phyl.
253 o The new function rotate, contributed by Christoph Heibl, swaps
254 two clades connected to the same node. It works also with
255 multichotomous nodes.
257 o The new `method' as.matrix.DNAbin() may be used to convert
258 easily DNA sequences stored in a list into a matrix while
259 keeping the names and the class.
264 o chronopl() failed when some branch lengths were equal to zero:
265 an error message is now returned.
267 o di2multi() failed when there was a series of consecutive edges
272 CHANGES IN APE VERSION 1.10-2
277 o plot.phylo() can now plot circular trees: the option is type =
278 "fan" or type = "f" (to avoid the ambiguity with type = "c").
280 o prop.part() has a new option `check.labels = FALSE' which allows
281 to considerably speed-up the calculations of bipartitions. As a
282 consequence, calculations of bootstrap values with boot.phylo()
283 should be much faster.
288 o read.GenBank() did not return correctly the list of species as
289 from ape 1.10: this is fixed in this version
291 o Applying as.phylo() on a tree of class "phylo" failed: the
292 object is now returned unchanged.
296 CHANGES IN APE VERSION 1.10-1
301 o The three new functions Ntip, Nnode, and Nedge return, for a
302 given tree, the number of tips, nodes, or edges, respectively.
307 o read.nexus() did not set correctly the class of the returned
308 object when reading multiple trees.
310 o mllt.plot() failed with objects of class c("multi.tree",
313 o unroot() did not work correctly in most cases.
315 o reorder.phylo() made R freeze in some occasions.
317 o Plotting a tree in pruningwise order failed.
319 o When plotting an unrooted tree, the tip labels where not all
320 correctly positioned if the option `cex' was used.
324 CHANGES IN APE VERSION 1.10
329 o Five new `method' functions have been introduced to manipulate
330 DNA sequences in binary format (see below).
332 o Three new functions have been introduced to convert between the
333 new binary and the character formats.
335 o The new function as.alignment converts DNA sequences stored as
336 single characters into the class "alignment" used by the package
339 o read.dna() and read.GenBank() have a new argument `as.character'
340 controlling whether the sequences are returned in binary format
346 o root() failed when the tree had node labels: this is fixed.
348 o plot.phylo() did not correctly set the limits on the y-axis with
349 the default setting: this is fixed.
351 o dist.dna() returned a wrong result for the LogDet, paralinear,
352 and BH87 models with `pairwise.deletion = TRUE'.
357 o DNA sequences are now internally stored in a binary format. See
358 the document "A Bit-Level Coding Scheme for Nucleotides" for the
359 details. Most functions analyzing DNA functions have been
360 modified accordingly and are now much faster (dist.dna is now
361 ca. 60 times faster).
365 CHANGES IN APE VERSION 1.9-4
370 o A bug was fixed in edgelabels().
372 o as.phylo.hclust() did not work correctly when the object of
373 class "hclust" has its labels set to NULL: the returned tree has
374 now its tip labels set to "1", "2", ...
376 o consensus could fail if some tip labels are a subset of others
377 (e.g., "a" and "a_1"): this is now fixed.
379 o mlphylo() failed in most cases if some branch lengths of the
380 initial tree were greater than one: an error message is now
383 o mlphylo() failed in most cases when estimating the proportion of
384 invariants: this is fixed.
388 CHANGES IN APE VERSION 1.9-3
393 o The new function edgelabels adds labels on the edge of the tree
394 in the same way than nodelabels or tiplabels.
399 o multi2di() did not handle correctly branch lengths with the
400 default option `random = TRUE': this is now fixed.
402 o A bug was fixed in nuc.div() when using pairwise deletions.
404 o A bug occurred in the analysis of bipartitions with large
405 numbers of large trees, with consequences on prop.part,
406 prop.clades, and boot.phylo.
408 o The calculation of the Billera-Holmes-Vogtmann distance in
409 dist.topo was wrong: this has been fixed.
413 CHANGES IN APE VERSION 1.9-2
418 o The new function ladderize reorganizes the internal structure of
419 a tree to plot them left- or right-ladderized.
421 o The new function dist.nodes computes the patristic distances
422 between all nodes, internal and terminal, of a tree. It replaces
423 the option `full = TRUE' of cophenetic.phylo (see below).
428 o A bug was fixed in old2new.phylo().
430 o Some bugs were fixed in chronopl().
432 o The edge colours were not correctly displayed by plot.phylo
433 (thank you to Li-San Wang for the fix).
435 o cophenetic.phylo() failed with multichotomous trees: this is
441 o read.dna() now returns the sequences in a matrix if they are
442 aligned (interleaved or sequential format). Sequences in FASTA
443 format are still returned in a list.
445 o The option `full' of cophenetic.phylo() has been removed because
446 it could not be used from the generic.
451 o rotate() has been removed; this function did not work correctly
456 CHANGES IN APE VERSION 1.9-1
461 o Trees with a single tip were not read correctly in R as the
462 element `Nnode' was not set: this is fixed.
464 o unroot() did not set correctly the number of nodes of the
465 unrooted tree in most cases.
467 o read.GenBank() failed when fetching very long sequences,
468 particularly of the BX-series.
470 o A bug was introduced in read.tree() with ape 1.9: it has been
475 CHANGES IN APE VERSION 1.9
480 o There are two new print `methods' for trees of class "phylo" and
481 lists of trees of class "multi.tree", so that they are now
482 displayed in a compact and informative way.
484 o There are two new functions, old2new.phylo and new2old.phylo,
485 for converting between the old and new coding of the class
488 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
489 LogDet ("logdet"), and paralinear ("paralin").
491 o compute.brlen() has been extended: several methods are now
492 available to compute branch lengths.
494 o write.dna() can now handle matrices as well as lists.
499 o cophenetic.phylo() sometimes returned a wrong result with
500 multichotomous trees: this is fixed.
502 o rotate() failed when a single tip was specified: the tree is now
505 o ace() did not return the correct index matrix with custom
506 models: this is fixed.
508 o multi2di() did not work correctly when resolving multichotomies
509 randomly: the topology was always the same, only the arrangement
510 of clades was randomized: this is fixed. This function now
511 accepts trees with no branch lengths.
513 o The output of diversi.gof() was blurred by useless prints when a
514 user distribution was specified. This has been corrected, and
515 the help page of this function has been expanded.
520 o The internal structure of the class "phylo" has been changed:
521 see the document "Definition of Formats for Coding Phylogenetic
522 Trees in R" for the details. In addition, the code of most
523 functions has been improved.
525 o Several functions have been improved by replacing some R codes
526 by C codes: pic, plot.phylo, and reorder.phylo.
528 o There is now a citation information: see citation("ape") in R.
530 o write.tree() now does not add extra 0's to branch lengths so
531 that 1.23 is printed "1.23" by default, not "1.2300000000".
533 o The syntax of bind.tree() has been simplified. This function now
534 accepts trees with no branch lengths, and handles correctly node
537 o The option `as.numeric' of mrca() has been removed.
539 o The unused options `format' and `rooted' of read.tree() have
542 o The unused option `format' of write.tree() has been removed.
544 o The use of node.depth() has been simplified.
548 CHANGES IN APE VERSION 1.8-5
553 o Two new functions read.nexus.data() and write.nexus.data(),
554 contributed by Johan Nylander, allow to read and write molecular
555 sequences in NEXUS files.
557 o The new function reorder.phylo() reorders the internal structure
558 of a tree of class "phylo". It is used as the generic, e.g.,
561 o read.tree() and read.nexus() can now read trees with a single
564 o The new data set `cynipids' supplies a set of protein sequences
570 o The code of all.equal.phylo() has been completely rewritten
571 (thanks to Benoît Durand) which fixes several bugs.
573 o read.tree() and read.nexus() now checks the labels of the tree
574 to remove or substitute any characters that are illegal in the
575 Newick format (parentheses, etc.)
577 o A negative P-value could be returned by mantel.test(): this is
582 CHANGES IN APE VERSION 1.8-4
587 o The new function sh.test() computes the Shimodaira-
590 o The new function collapse.singles() removes the nodes with a
591 single descendant from a tree.
593 o plot.phylo() has a new argument `tip.color' to specify the
596 o mlphylo() has now an option `quiet' to control the display of
597 the progress of the analysis (the default is FALSE).
602 o read.dna() did not read correctly sequences in sequential format
603 with leading alignment gaps "-": this is fixed.
605 o ace() returned a list with no class so that the generic
606 functions (anova, logLik, ...) could not be used directly. This
607 is fixed as ace() now returns an object of class "ace".
609 o anova.ace() had a small bug when computing the number of degrees
610 of freedom: this is fixed.
612 o mlphylo() did not work when the sequences were in a matrix or
613 a data frame: this is fixed.
615 o rtree() did not work correctly when trying to simulate an
616 unrooted tree with two tips: an error message is now issued.
621 o The algorithm of rtree() has been changed: it is now about 40,
622 100, and 130 times faster for 10, 100, and 1000 tips,
627 CHANGES IN APE VERSION 1.8-3
632 o There are four new `method' functions to be used with the
633 results of ace(): logLik(), deviance(), AIC(), and anova().
635 o The plot method of phymltest has two new arguments: `main' to
636 change the title, and `col' to control the colour of the
637 segments showing the AIC values.
639 o ace() has a new argument `ip' that gives the initial values used
640 in the ML estimation with discrete characters (see the examples
641 in ?ace). This function now returns a matrix giving the indices
642 of the estimated rates when analysing discrete characters.
644 o nodelabels() and tiplabels() have a new argument `pie' to
645 represent proportions, with any number of categories, as
646 piecharts. The use of the option `thermo' has been improved:
647 there is now no limitation on the number of categories.
652 o mlphylo() did not work with more than two partitions: this is
655 o root() failed if the proposed outgroup was already an outgroup
656 in the tree: this is fixed.
658 o The `col' argument in nodelabels() and tiplabels() was not
659 correctly passed when `text' was used: this is fixed.
661 o Two bugs were fixed in mlphylo(): parameters were not always
662 correctly output, and the estimation failed in some cases.
664 o plot.phylo() was stuck when given a tree with a single tip: this
665 is fixed and a message error is now returned.
667 o An error was corrected in the help page of gammaStat regarding
668 the calculation of P-values.
670 o Using gls() could crash R when the number of species in the tree
671 and in the variables were different: this is fixed.
675 CHANGES IN APE VERSION 1.8-2
680 o The new function mlphylo() fits a phylogenetic tree by maximum
681 likelihood from DNA sequences. Its companion function DNAmodel()
682 is used to define the substitution model which may include
683 partitioning. There are methods for logLik(), deviance(), and
684 AIC(), and the summary() method has been extended to display in
685 a friendly way the results of this model fitting. Currently, the
686 functionality is limited to estimating the substitution and
687 associated parameters and computing the likelihood.
689 o The new function drop1.compar.gee (used as, e.g., drop1(m))
690 tests for single effects in GEE-based comparative method. A
691 warning message is printed if there is not enough degrees of
697 o An error message was sometimes issued by plot.multi.tree(),
698 though with no consequence.
702 CHANGES IN APE VERSION 1.8-1
707 o There is a new plot method for lists of trees (objects of class
708 "multi.tree"): it calls plot.phylo() internally and is
709 documented on the same help page.
714 o A bug was fixed in the C code that analyzes bipartitions: this
715 has impact on several functions like prop.part, prop.clades,
716 boot.phylo, or consensus.
718 o root() did not work correctly when the specified outgroup had
719 more than one element: this is fixed.
721 o dist.dna() sometimes returned a warning inappropriately: this
724 o If the distance object given to nj() had no rownames, nj()
725 returned a tree with no tip labels: it now returns tips labelled
726 "1", "2", ..., corresponding to the row numbers.
731 o nj() has been slightly changed so that tips with a zero distance
732 are first aggregated with zero-lengthed branches; the usual NJ
733 procedure is then performed on a distance matrix without 0's.
737 CHANGES IN APE VERSION 1.8
742 o The new function chronopl() estimates dates using the penalized
743 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
745 o The new function consensus() calculates the consensus tree of a
748 o The new function evolve.phylo() simulates the evolution of
749 continuous characters along a phylogeny under a Brownian model.
751 o The new plot method for objects of class "ancestral" displays a
752 tree together with ancestral values, as returned by the above
755 o The new function as.phylo.formula() returns a phylogeny from a
756 set of nested taxonomic variables given as a formula.
758 o The new function read.caic() reads trees in CAIC format.
760 o The new function tiplabels() allows to add labels to the tips
761 of a tree using text or plotting symbols in a flexible way.
763 o The new function unroot() unroots a phylogeny.
765 o multi2di() has a new option, `random', which specifies whether
766 to resolve the multichotomies randomly (the default) or not.
768 o prop.part() now returns an object of class "prop.part" for which
769 there are print (to display a partition in a more friendly way)
770 and summary (to extract the numbers) methods.
772 o plot.phylo() has a new option, `show.tip.label', specifying
773 whether to print the labels of the tips. The default is TRUE.
775 o The code of nj() has been replaced by a faster C code: it is now
776 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
779 o write.nexus() now writes whether a tree is rooted or not.
784 o Two bugs have been fixed in root(): unrooted trees are now
785 handled corretly, and node labels are now output normally.
787 o A bug was fixed in phymltest(): the executable couldn't be found
790 o Three bug have been fixed in ace(): computing the likelihood of
791 ancestral states of discrete characters failed, custom models
792 did not work, and the function failed with a null gradient (a
793 warning message is now returned; this latter bug was also
794 present in yule.cov() as well and is now fixed).
796 o pic() hanged out when missing data were present: a message error
799 o A small bug was fixed in dist.dna() where the gamma correction
800 was not always correctly dispatched.
802 o plot.phylo() plotted correctly the root edge only when the tree
803 was plotted rightwards: this works now for all directions.
808 o dist.taxo() has been renamed as weight.taxo().
810 o Various error and warning messages have been improved.
814 CHANGES IN APE VERSION 1.7
817 o The new function ace() estimates ancestral character states for
818 continuous characters (with ML, GLS, and contrasts methods), and
819 discrete characters (with ML only) for any number of states.
821 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
822 of directional evolution for continuous characters. The user
823 specifies the node(s) of the tree where the character optimum
826 o The new function is.rooted() tests whether a tree (of class
829 o The new function rcoal() generates random ultrametric trees with
830 the possibility to specify the function that generates the
831 inter-nodes distances.
833 o The new function mrca() gives for all pairs of tips in a tree
834 (and optionally nodes too) the most recent common ancestor.
836 o nodelabels() has a new option `thermo' to plot proportions (up
837 to three classes) on the nodes of a tree.
839 o rtree() has been improved: it can now generate rooted or
840 unrooted trees, and the mathematical function that generates the
841 branch lengths may be specified by the user. The tip labels may
842 be given directly in the call to rtree. The limit cases (n = 2,
843 3) are now handled correctly.
845 o dist.topo() has a new argument `method' with two choices: "PH85"
846 for Penny and Henny's method (already available before and now
847 the default), and "BHV01" for the geometric distance by Billera
848 et al. (2001, Adv. Appl. Math. 27:733).
850 o write.tree() has a new option, `digits', which specifies the
851 number of digits to be printed in the Newick tree. By default
852 digits = 10. The numbers are now always printed in decimal form
853 (i.e., 1.0e-1 is now avoided).
855 o dist.dna() can now compute the raw distances between pairs of
856 DNA sequences by specifying model = "raw".
858 o dist.phylo() has a new option `full' to possibly compute the
859 distances among all tips and nodes of the tree. The default if
865 o Several bugs were fixed in all.equal.phylo().
867 o dist.dna() did not handle correctly gaps ("-") in alignments:
868 they are now considered as missing data.
870 o rotate() did not work if the tips were not ordered: this is
873 o mantel.test() returned NA in some special cases: this is fixed
874 and the function has been improved and is now faster.
876 o A bug was fixed in diversi.gof() where the calculation of A² was
879 o cherry() did not work correctly under some OSs (mainly Linux):
882 o is.binary.tree() has been modified so that it works with both
883 rooted and unrooted trees.
885 o The documentation of theta.s() was not correct: this has been
888 o plot.mst() did not work correctly: this is fixed.
892 CHANGES IN APE VERSION 1.6
897 o The new function dist.topo() computes the topological distances
900 o The new function boot.phylo() performs a bootstrap analysis on
901 phylogeny estimation.
903 o The new functions prop.part() and prop.clades() analyse
904 bipartitions from a series of trees.
909 o read.GenBank() now uses the EFetch utility of NCBI instead of
910 the usual Web interface: it is now much faster (e.g., 12 times
911 faster to retrieve 8 sequences, 37 times for 60 sequences).
916 o Several bugs were fixed in read.dna().
918 o Several bugs were fixed in diversi.time().
920 o is.binary.tree() did not work correctly if the tree has no edge
921 lengths: this is fixed.
923 o drop.tip() did not correctly propagated the `node.label' of a
928 CHANGES IN APE VERSION 1.5
933 o Two new functions, as.matching.phylo() and as.phylo.matching(),
934 convert objects between the classes "phylo" and "matching". The
935 latter implements the representation of binary trees introduced by
936 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
937 as.matching() has been introduced as well.
939 o Two new functions, multi2di() and di2multi(), allow to resolve
940 and collapse multichotomies with branches of length zero.
942 o The new function nuc.div() computes the nucleotide diversity
943 from a sample a DNA sequences.
945 o dist.dna() has been completely rewritten with a much faster
946 (particularly for large data sets) C code. Eight models are
947 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
948 option `method' has been renamed `model'). Computation of variance
949 is available for all models. A gamma-correction is possible for
950 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
951 to remove sites with missing data on a pairwise basis. The option
952 `GCcontent' has been removed.
954 o read.GenBank() has a new option (species.names) which specifies
955 whether to return the species names of the organisms in addition
956 to the accession numbers of the sequences (this is the default
959 o write.nexus() can now write several trees in the same NEXUS file.
961 o drop.tip() has a new option `root.edge' that allows to specify the
962 new root edge if internal branches are trimmed.
967 o as.phylo.hclust() failed if some labels had parentheses: this
970 o Several bugs were fixed in all.equal.phylo(). This function now
971 returns the logical TRUE if the trees are identical but with
972 different representations (a report was printed previously).
974 o read.GenBank() did not correctly handle ambiguous base codes:
980 o birthdeath() now returns an object of class "birthdeath" for
981 which there is a print method.
985 CHANGES IN APE VERSION 1.4
990 o The new function nj() performs phylogeny estimation with the
991 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
994 o The new function which.edge() identifies the edges of a tree
995 that belong to a group specified as a set of tips.
997 o The new function as.phylo.phylog() converts an object of class
998 "phylog" (from the package ade4) into an object of class
1001 o The new function axisPhylo() draws axes on the side of a
1004 o The new function howmanytrees() calculates the number of trees
1005 in different cases and giving a number of tips.
1007 o write.tree() has a new option `multi.line' (TRUE by default) to
1008 write a Newick tree on several lines rather than on a single
1011 o The functionalities of zoom() have been extended. Several
1012 subtrees can be visualized at the same time, and they are marked
1013 on the main tree with colors. The context of the subtrees can be
1014 marked with the option `subtree' (see below).
1016 o drop.tip() has a new option `subtree' (FALSE by default) which
1017 specifies whether to output in the tree how many tips have been
1020 o The arguments of add.scale.bar() have been redefined and have
1021 now default values (see ?add.scale.bar for details). This
1022 function now works even if the plotted tree has no edge length.
1024 o plot.phylo() can now plot radial trees, but this does not take
1025 edge lengths into account.
1027 o In plot.phylo() with `type = "phylogram"', if the values of
1028 `edge.color' and `edge.width' are identical for sister-branches,
1029 they are propagated to the vertical line that link them.
1034 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1035 crashing. This is fixed.
1037 o In plot.phylo(), the options `edge.color' and `edge.width' are
1038 now properly recycled; their default values are now "black" and
1041 o A bug has been fixed in write.nexus().
1046 o The function node.depth.edgelength() has been removed and
1047 replaced by a C code.
1051 CHANGES IN APE VERSION 1.3-1
1056 o The new function nodelabels() allows to add labels to the nodes
1057 of a tree using text or plotting symbols in a flexible way.
1059 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1060 numeric values specifying the lower and upper limits on the x-
1061 and y-axes. This allows to leave some space on any side of the
1062 tree. If a single value is given, this is taken as the upper
1067 CHANGES IN APE VERSION 1.3
1072 o The new function phymltest() calls the software PHYML and fits
1073 28 models of DNA sequence evolution. There are a print method to
1074 display likelihood and AIC values, a summary method to compute
1075 the hierarchical likelihood ratio tests, and a plot method to
1076 display graphically the AIC values of each model.
1078 o The new function yule.cov() fits the Yule model with covariates,
1079 a model where the speciation rate is affected by several species
1080 traits through a generalized linear model. The parameters are
1081 estimated by maximum likelihood.
1083 o Three new functions, corBrownian(), corGrafen(), and
1084 corMartins(), compute the expected correlation structures among
1085 species given a phylogeny under different models of evolution.
1086 These can be used for GLS comparative phylogenetic methods (see
1087 the examples). There are coef() and corMatrix() methods and an
1088 Initialize.corPhyl() function associated.
1090 o The new function compar.cheverud() implements Cheverud et al.'s
1091 (1985; Evolution 39:1335) phylogenetic comparative method.
1093 o The new function varcomp() estimates variance components; it has
1096 o Two new functions, panel.superpose.correlogram() and
1097 plot.correlogramList(), allow to plot several phylogenetic
1100 o The new function node.leafnumber() computes the number of leaves
1101 of a subtree defined by a particular node.
1103 o The new function node.sons() gets all tags of son nodes from a
1106 o The new function compute.brlen() computes the branch lengths of
1107 a tree according to a specified method.
1109 o plot.phylo() has three new options: "cex" controls the size of
1110 the (tip and node) labels (thus it is no more needed to change
1111 the global graphical parameter), "direction" which allows to
1112 plot the tree rightwards, leftwards, upwards, or downwards, and
1113 "y.lim" which sets the upper limit on the y-axis.
1118 o Some functions which try to match tip labels and names of
1119 additional data (e.g. vector) are likely to fail if there are
1120 typing or syntax errors. If both series of names do not perfectly
1121 match, they are ignored and a warning message is now issued.
1122 These functions are bd.ext, compar.gee, pic. Their help pages
1123 have been clarified on this point.
1127 CHANGES IN APE VERSION 1.2-7
1132 o The new function root() reroots a phylogenetic tree with respect
1133 to a specified outgroup.
1135 o The new function rotate() rotates an internal branch of a tree.
1137 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1138 trees) controls the display of the tip labels in unrooted trees.
1139 This display has been greatly improved: the tip labels are now not
1140 expected to overlap with the tree (particularly if lab4ut =
1141 "axial"). In all cases, combining appropriate values of "lab4ut"
1142 and the font size (via "par(cex = )") should result in readable
1143 unrooted trees. See ?plot.phylo for some examples.
1145 o In drop.tip(), the argument `tip' can now be numeric or character.
1150 o drop.tip() did not work correctly with trees with no branch
1151 lengths: this is fixed.
1153 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1154 plotted with some line crossings: this is now fixed.
1158 CHANGES IN APE VERSION 1.2-6
1163 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1164 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1165 to implement comparative methods with an autocorrelation approach.
1167 o A new data set describing some life history traits of Carnivores
1173 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1178 o When plotting a tree with plot.phylo(), the new default of the
1179 option `label.offset' is now 0, so the labels are always visible.
1183 CHANGES IN APE VERSION 1.2-5
1188 o The new function bd.ext() fits a birth-death model with combined
1189 phylogenetic and taxonomic data, and estimates the corresponding
1190 speciation and extinction rates.
1195 o The package gee is no more required by ape but only suggested
1196 since only the function compar.gee() calls gee.
1200 CHANGES IN APE VERSION 1.2-4
1205 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1206 and lines.popsize) implementing a new approach for inferring the
1207 demographic history from genealogies using a reversible jump
1208 MCMC have been introduced.
1210 o The unit of time in the skyline plot and in the new plots can
1211 now be chosen to be actual years, rather than substitutions.
1215 CHANGES IN APE VERSION 1.2-3
1220 o The new function rtree() generates a random binary tree with or
1221 without branch lengths.
1223 o Two new functions for drawing lineages-through-time (LTT) plots
1224 are provided: ltt.lines() adds a LTT curve to an existing plot,
1225 and mltt.plot() does a multiple LTT plot giving several trees as
1226 arguments (see `?ltt.plot' for details).
1231 o Some taxon names made R crashing when calling as.phylo.hclust():
1234 o dist.dna() returned an error with two identical DNA sequences
1235 (only using the Jukes-Cantor method returned 0): this is fixed.
1240 o The function dist.phylo() has been re-written using a different
1241 algorithm: it is now about four times faster.
1243 o The code of branching.times() has been improved: it is now about
1248 CHANGES IN APE VERSION 1.2-2
1253 o The new function seg.sites() finds the segregating sites in a
1254 sample of DNA sequences.
1259 o A bug introduced in read.tree() and in read.nexus() with version
1262 o A few errors were corrected and a few examples were added in the
1267 CHANGES IN APE VERSION 1.2-1
1272 o plot.phylo() can now draw the edge of the root of a tree if it
1273 has one (see the new option `root.edge', its default is FALSE).
1278 o A bug was fixed in read.nexus(): files with semicolons inside
1279 comment blocks were not read correctly.
1281 o The behaviour of read.tree() and read.nexus() was corrected so
1282 that tree files with badly represented root edges (e.g., with
1283 an extra pair of parentheses, see the help pages for details)
1284 are now correctly represented in the object of class "phylo";
1285 a warning message is now issued.
1289 CHANGES IN APE VERSION 1.2
1294 o plot.phylo() has been completely re-written and offers several
1295 new functionalities. Three types of trees can now be drawn:
1296 phylogram (as previously), cladogram, and unrooted tree; in
1297 all three types the branch lengths can be drawn using the edge
1298 lengths of the phylogeny or not (e.g., if the latter is absent).
1299 The vertical position of the nodes can be adjusted with two
1300 choices (see option `node.pos'). The code has been re-structured,
1301 and two new functions (potentially useful for developpers) are
1302 documented separately: node.depth.edgelength() and node.depth();
1303 see the respective help pages for details.
1305 o The new function zoom() allows to explore very large trees by
1306 focusing on a small portion of it.
1308 o The new function yule() fits by maximum likelihood the Yule model
1309 (birth-only process) to a phylogenetic tree.
1311 o Support for writing DNA sequences in FASTA format has been
1312 introduced in write.dna() (support for reading sequences in
1313 this format was introduced in read.dna() in version 1.1-2).
1314 The function has been completely re-written, fixing some bugs
1315 (see below); the default behaviour is no more to display the
1316 sequences on the standard output. Several options have been
1317 introduced to control the sequence printing in a flexible
1318 way. The help page has been extended.
1320 o A new data set is included: a supertree of bats in NEXUS format.
1325 o In theta.s(), the default of the option `variance' has
1326 been changed to `FALSE' (as was indicated in the help page).
1328 o Several bugs were fixed in the code of all.equal.phylo().
1330 o Several bugs were fixed in write.dna(), particularly this
1331 function did not work with `format = "interleaved"'.
1333 o Various errors were corrected in the help pages.
1338 o The argument names of as.hclust.phylo() have been changed
1339 from "(phy)" to "(x, ...)" to conform to the definition of
1340 the corresponding generic function.
1342 o gamma.stat() has been renamed gammaStat() to avoid confusion
1343 since gamma() is a generic function.
1347 CHANGES IN APE VERSION 1.1-3
1352 o base.freq() previously did not return a value of 0 for
1353 bases absent in the data (e.g., a vector of length 3 was
1354 returned if one base was absent). This is now fixed (a
1355 vector of length 4 is always returned).
1357 o Several bugs were fixed in read.nexus(), including that this
1358 function did not work in this absence of a "TRANSLATE"
1359 command in the NEXUS file, and that the commands were
1364 CHANGES IN APE VERSION 1.1-2
1369 o The Tamura and Nei (1993) model of DNA distance is now implemented
1370 in dist.dna(): five models are now available in this function.
1372 o A new data set is included: a set of 15 sequences of the
1373 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1379 o A bug in read.nexus() was fixed.
1381 o read.dna() previously did not work correctly in most cases.
1382 The function has been completely re-written and its help page
1383 has been considerably extended (see ?read.dna for details).
1384 Underscores (_) in taxon names are no more replaced with
1385 spaces (this behaviour was undocumented).
1387 o A bug was fixed in write.dna().
1391 CHANGES IN APE VERSION 1.1-1
1396 o A bug in read.tree() introduced in APE 1.1 was fixed.
1398 o A bug in compar.gee() resulted in an error when trying to fit
1399 a model with `family = "binomial"'. This is now fixed.
1403 CHANGES IN APE VERSION 1.1
1408 o The Klastorin (1982) method as suggested by Misawa and Tajima
1409 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1410 on the basis of phylogenetic trees has been implemented (see
1411 the function klastorin()).
1413 o Functions have been added to convert APE's "phylo" objects in
1414 "hclust" cluster objects and vice versa (see the help page of
1415 as.phylo for details).
1417 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1418 are introduced for the estimation of absolute evolutionary rates
1419 (ratogram) and dated clock-like trees (chronogram) from
1420 phylogenetic trees using the non-parametric rate smoothing approach
1421 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1423 o A summary method is now provided printing a summary information on a
1424 phylogenetic tree with, for instance, `summary(tree)'.
1426 o The behaviour of read.tree() was changed so that all spaces and
1427 tabulations in tree files are now ignored. Consequently, spaces in tip
1428 labels are no more allowed. Another side effect is that read.nexus()
1429 now does not replace the underscores (_) in tip labels with spaces
1430 (this behaviour was undocumented).
1432 o The function plot.phylo() has a new option (`underscore') which
1433 specifies whether the underscores in tip labels should be written on
1434 the plot as such or replaced with spaces (the default).
1436 o The function birthdeath() now computes 95% confidence intervals of
1437 the estimated parameters using profile likelihood.
1439 o Three new data sets are included: a gene tree estimated from 36
1440 landplant rbcL sequences, a gene tree estimated from 32 opsin
1441 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1446 o A bug was fixed in dist.gene() where nothing was returned.
1448 o A bug in plot.mst() was fixed.
1450 o A bug in vcv.phylo() resulted in false correlations when the
1451 option `cor = TRUE' was used (now fixed).
1455 CHANGES IN APE VERSION 1.0
1460 o Two new functions, read.dna() and write.dna(), read/write in a file
1461 DNA sequences in interleaved or in sequential format.
1463 o Two new functions, read.nexus() and write.nexus(), read/write trees
1466 o The new function bind.tree() allows to bind two trees together,
1467 possibly handling root edges to give internal branches.
1469 o The new function drop.tip() removes the tips in a phylogenetic tree,
1470 and trims (or not) the corresponding internal branches.
1472 o The new function is.ultrametric() tests if a tree is ultrametric.
1474 o The function plot.phylo() has more functionalities such as drawing the
1475 branches with different colours and/or different widths, showing the
1476 node labels, controling the position and font of the labels, rotating
1477 the labels, and controling the space around the plot.
1479 o The function read.tree() can now read trees with no branch length,
1480 such as "(a,b),c);". Consequently, the element `edge.length' in
1481 objects of class "phylo" is now optional.
1483 o The function write.tree() has a new default behaviour: if the default
1484 for the option `file' is used (i.e. file = ""), then a variable of
1485 mode character containing the tree in Newick format is returned which
1486 can thus be assigned (e.g., tree <- write.tree(phy)).
1488 o The function read.tree() has a new argument `text' which allows
1489 to read the tree in a variable of mode character.
1491 o A new data set is included: the phylogenetic relationships among
1492 the orders of birds from Sibley and Ahlquist (1990).
1496 CHANGES IN APE VERSION 0.2-1
1501 o Several bugs were fixed in the help pages.
1505 CHANGES IN APE VERSION 0.2
1510 o The function write.tree() writes phylogenetic trees (objects of class
1511 "phylo") in an ASCII file using the Newick parenthetic format.
1513 o The function birthdeath() fits a birth-death model to branching times
1514 by maximum likelihood, and estimates the corresponding speciation and
1517 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1520 o The function is.binary.tree() tests whether a phylogeny is binary.
1522 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1523 as well as some methods are introduced.
1525 o Several functions, including some generics and methods, for computing
1526 skyline plot estimates (classic and generalized) of effective
1527 population size through time are introduced and replace the function
1528 skyline.plot() in version 0.1.
1530 o Two data sets are now included: the phylogenetic relationships among
1531 the families of birds from Sibley and Ahlquist (1990), and an
1532 estimated clock-like phylogeny of HIV sequences sampled in the
1533 Democratic Republic of Congo.
1536 DEPRECATED & DEFUNCT
1538 o The function skyline.plot() in ape 0.1 has been deprecated and
1539 replaced by more elaborate functions (see above).
1544 o Two important bugs were fixed in plot.phylo(): phylogenies with
1545 multichotomies not at the root or not with only terminal branches,
1546 and phylogenies with a single node (i.e. only terminal branches)
1547 did not plot. These trees should be plotted correctly now.
1549 o Several bugs were fixed in diversi.time() in the computation of
1552 o Various errors were corrected in the help pages.