1 CHANGES IN APE VERSION 2.1-4
6 o read.dna() failed if "?" occurred in the first 10 sites of the
9 o The x/y aspect of the plot is now respected when plotting a
10 circular tree (type = "r" or "f").
12 o Drawing the tip labels sometimes when plotting circular trees.
17 o chronopl() has been improved and gains several options: see its
18 help page for details.
22 CHANGES IN APE VERSION 2.1-3
27 o A bug in read.nexus() made the Windows R-GUI crash.
29 o An error was fixed in the computation of ancestral character
30 states by generalized least squares in ace().
32 o di2multi() did not modify node labels correctly.
34 o multi2di() failed if the tree had its attribute "order" set to
39 CHANGES IN APE VERSION 2.1-2
44 o There three new methods for the "multiPhylo" class: str, $,
47 o root() gains the options 'node' and 'resolve.root'
48 (FALSE by default) as well as its code being improved.
50 o mltt.plot() has now an option 'log' used in the same way
51 than in plot.default().
56 o mltt.plot() failed to display the legend with an unnamed
59 o nodelabels() with pies now correcly uses the argument
60 'cex' to draw symbols of different sizes (which has
61 worked already for thermometers).
63 o read.nexus() generally failed to read very big files.
68 o The argument 'family' of compar.gee() can now be a function
69 as well as a character string.
71 o read.tree() and read.nexus() now return an unnamed list if
74 o read.nexus() now returns a modified object of class "multiPhylo"
75 when there is a TRANSLATE block in the NEXUS file: the individual
76 trees have no 'tip.label' vector, but the list has a 'TipLabel'
77 attribute. The new methods '$' and '[[' set these elements
78 correctly when extracting trees.
82 CHANGES IN APE VERSION 2.1-1
87 o The new function rmtree generates lists of random trees.
89 o rcoal() now generates a genuine coalescent tree by default
90 (thanks to Vladimir Minin for the code).
95 o nuc.div() returned an incorrect value with the default
96 pairwise.deletion = FALSE.
101 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
102 have been improved so that they are stabler and faster.
104 o R packages used by ape are now loaded silently; lattice and gee
105 are loaded only when needed.
109 CHANGES IN APE VERSION 2.1
114 o The new function identify.phylo identifies clades on a plotted
115 tree using the mouse.
117 o It is now possible to subset a list of trees (object of class
118 "multiPhylo") with "[" while keeping its class correct.
120 o The new function as.DNAbin.alignment converts DNA sequences
121 stored in the "alignment" format of the package seqinr into
122 an object of class "DNAbin".
124 o The new function weight.taxo2 helps to build similarity matrices
125 given two taxonomic levels (usually called by other functions).
127 o write.tree() can now take a list of trees (class "multiPhylo")
128 as its main argument.
130 o plot.correlogram() and plot.correlogramList() have been
131 improved, and gain several options (see the help page for
132 details). A legend is now plotted by default.
137 o dist.dna() returned some incorrect values with `model = "JC69"'
138 and `pairwise.deletion = TRUE'. This affected only the
139 distances involving sequences with missing values. (Thanks
140 to Bruno Toupance for digging this bug out.)
142 o write.tree() failed with some trees: this is fixed by removing
143 the `multi.line' option (trees are now always printed on a
146 o read.nexus() did not correctly detect trees with multiple root
147 edges (see OTHER CHANGES).
152 o The code of mlphylo() has almost entirely rewritten, and should
153 be much stabler. The options have been also greatly simplified
154 (see ?mlphylo and ?DNAmodel for details).
156 o The internal function nTips has been renamed klastorin_nTips.
158 o The code of is.ultrametric() contained redundancies and has
161 o The code of Moran.I() and of correlogram.formula() have been
164 o read.tree() and read.nexus() now return an error when trying to
165 read a tree with multiple root edges (see BUG FIXES). The
166 correction applied in previous version did not work in all
169 o The class c("multi.tree", "phylo") has been renamed
175 o There is now a vignette in ape: see vignette("MoranI", "ape").
180 o as.matching() and as.phylo.matching() do not support branch
183 o correlogram.phylo() and discrete.dist() have been removed.
187 CHANGES IN APE VERSION 2.0-2
192 o The new function matexpo computes the exponential of a square
195 o The new function unique.multi.tree removes duplicate trees from
198 o yule() has a new option `use.root.edge = FALSE' that specifies
199 to ignore, by default, the root edge of the tree if it exists.
204 o which.edge() failed when the index of a single terminal edge was
207 o In diversi.time(), the values returned for model C were
210 o A bug was fixed in yule() that affected the calculation of the
211 likelihood in the presence of ties in the branching times.
213 o There was a bug in the C function mat_expo4x4 affecting the
214 calculations of the transition probabilities for models HKY and
217 o A small bug was fixed in as.matrix.DNAbin (thanks to James
220 o rtree() did not `shuffle' the tip labels by default, so only a
221 limited number of labelled topologies could be generated.
225 CHANGES IN APE VERSION 2.0-1
230 o The three new functions bionj, fastme.ols, and fastme.bal
231 perform phylogeny estimation by the BIONJ and fastME methods in
232 OLS and balanced versions. This is a port to R of previous
233 previous programs done by Vincent Lefort.
235 o The new function chronoMPL performs molecular dating with the
236 mean path lengths method of Britton et al. (2002, Mol. Phyl.
239 o The new function rotate, contributed by Christoph Heibl, swaps
240 two clades connected to the same node. It works also with
241 multichotomous nodes.
243 o The new `method' as.matrix.DNAbin() may be used to convert
244 easily DNA sequences stored in a list into a matrix while
245 keeping the names and the class.
250 o chronopl() failed when some branch lengths were equal to zero:
251 an error message is now returned.
253 o di2multi() failed when there was a series of consecutive edges
258 CHANGES IN APE VERSION 1.10-2
263 o plot.phylo() can now plot circular trees: the option is type =
264 "fan" or type = "f" (to avoid the ambiguity with type = "c").
266 o prop.part() has a new option `check.labels = FALSE' which allows
267 to considerably speed-up the calculations of bipartitions. As a
268 consequence, calculations of bootstrap values with boot.phylo()
269 should be much faster.
274 o read.GenBank() did not return correctly the list of species as
275 from ape 1.10: this is fixed in this version
277 o Applying as.phylo() on a tree of class "phylo" failed: the
278 object is now returned unchanged.
282 CHANGES IN APE VERSION 1.10-1
287 o The three new functions Ntip, Nnode, and Nedge return, for a
288 given tree, the number of tips, nodes, or edges, respectively.
293 o read.nexus() did not set correctly the class of the returned
294 object when reading multiple trees.
296 o mllt.plot() failed with objects of class c("multi.tree",
299 o unroot() did not work correctly in most cases.
301 o reorder.phylo() made R freeze in some occasions.
303 o Plotting a tree in pruningwise order failed.
305 o When plotting an unrooted tree, the tip labels where not all
306 correctly positioned if the option `cex' was used.
310 CHANGES IN APE VERSION 1.10
315 o Five new `method' functions have been introduced to manipulate
316 DNA sequences in binary format (see below).
318 o Three new functions have been introduced to convert between the
319 new binary and the character formats.
321 o The new function as.alignment converts DNA sequences stored as
322 single characters into the class "alignment" used by the package
325 o read.dna() and read.GenBank() have a new argument `as.character'
326 controlling whether the sequences are returned in binary format
332 o root() failed when the tree had node labels: this is fixed.
334 o plot.phylo() did not correctly set the limits on the y-axis with
335 the default setting: this is fixed.
337 o dist.dna() returned a wrong result for the LogDet, paralinear,
338 and BH87 models with `pairwise.deletion = TRUE'.
343 o DNA sequences are now internally stored in a binary format. See
344 the document "A Bit-Level Coding Scheme for Nucleotides" for the
345 details. Most functions analyzing DNA functions have been
346 modified accordingly and are now much faster (dist.dna is now
347 ca. 60 times faster).
351 CHANGES IN APE VERSION 1.9-4
356 o A bug was fixed in edgelabels().
358 o as.phylo.hclust() did not work correctly when the object of
359 class "hclust" has its labels set to NULL: the returned tree has
360 now its tip labels set to "1", "2", ...
362 o consensus could fail if some tip labels are a subset of others
363 (e.g., "a" and "a_1"): this is now fixed.
365 o mlphylo() failed in most cases if some branch lengths of the
366 initial tree were greater than one: an error message is now
369 o mlphylo() failed in most cases when estimating the proportion of
370 invariants: this is fixed.
374 CHANGES IN APE VERSION 1.9-3
379 o The new function edgelabels adds labels on the edge of the tree
380 in the same way than nodelabels or tiplabels.
385 o multi2di() did not handle correctly branch lengths with the
386 default option `random = TRUE': this is now fixed.
388 o A bug was fixed in nuc.div() when using pairwise deletions.
390 o A bug occurred in the analysis of bipartitions with large
391 numbers of large trees, with consequences on prop.part,
392 prop.clades, and boot.phylo.
394 o The calculation of the Billera-Holmes-Vogtmann distance in
395 dist.topo was wrong: this has been fixed.
399 CHANGES IN APE VERSION 1.9-2
404 o The new function ladderize reorganizes the internal structure of
405 a tree to plot them left- or right-ladderized.
407 o The new function dist.nodes computes the patristic distances
408 between all nodes, internal and terminal, of a tree. It replaces
409 the option `full = TRUE' of cophenetic.phylo (see below).
414 o A bug was fixed in old2new.phylo().
416 o Some bugs were fixed in chronopl().
418 o The edge colours were not correctly displayed by plot.phylo
419 (thank you to Li-San Wang for the fix).
421 o cophenetic.phylo() failed with multichotomous trees: this is
427 o read.dna() now returns the sequences in a matrix if they are
428 aligned (interleaved or sequential format). Sequences in FASTA
429 format are still returned in a list.
431 o The option `full' of cophenetic.phylo() has been removed because
432 it could not be used from the generic.
437 o rotate() has been removed; this function did not work correctly
442 CHANGES IN APE VERSION 1.9-1
447 o Trees with a single tip were not read correctly in R as the
448 element `Nnode' was not set: this is fixed.
450 o unroot() did not set correctly the number of nodes of the
451 unrooted tree in most cases.
453 o read.GenBank() failed when fetching very long sequences,
454 particularly of the BX-series.
456 o A bug was introduced in read.tree() with ape 1.9: it has been
461 CHANGES IN APE VERSION 1.9
466 o There are two new print `methods' for trees of class "phylo" and
467 lists of trees of class "multi.tree", so that they are now
468 displayed in a compact and informative way.
470 o There are two new functions, old2new.phylo and new2old.phylo,
471 for converting between the old and new coding of the class
474 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
475 LogDet ("logdet"), and paralinear ("paralin").
477 o compute.brlen() has been extended: several methods are now
478 available to compute branch lengths.
480 o write.dna() can now handle matrices as well as lists.
485 o cophenetic.phylo() sometimes returned a wrong result with
486 multichotomous trees: this is fixed.
488 o rotate() failed when a single tip was specified: the tree is now
491 o ace() did not return the correct index matrix with custom
492 models: this is fixed.
494 o multi2di() did not work correctly when resolving multichotomies
495 randomly: the topology was always the same, only the arrangement
496 of clades was randomized: this is fixed. This function now
497 accepts trees with no branch lengths.
499 o The output of diversi.gof() was blurred by useless prints when a
500 user distribution was specified. This has been corrected, and
501 the help page of this function has been expanded.
506 o The internal structure of the class "phylo" has been changed:
507 see the document "Definition of Formats for Coding Phylogenetic
508 Trees in R" for the details. In addition, the code of most
509 functions has been improved.
511 o Several functions have been improved by replacing some R codes
512 by C codes: pic, plot.phylo, and reorder.phylo.
514 o There is now a citation information: see citation("ape") in R.
516 o write.tree() now does not add extra 0's to branch lengths so
517 that 1.23 is printed "1.23" by default, not "1.2300000000".
519 o The syntax of bind.tree() has been simplified. This function now
520 accepts trees with no branch lengths, and handles correctly node
523 o The option `as.numeric' of mrca() has been removed.
525 o The unused options `format' and `rooted' of read.tree() have
528 o The unused option `format' of write.tree() has been removed.
530 o The use of node.depth() has been simplified.
534 CHANGES IN APE VERSION 1.8-5
539 o Two new functions read.nexus.data() and write.nexus.data(),
540 contributed by Johan Nylander, allow to read and write molecular
541 sequences in NEXUS files.
543 o The new function reorder.phylo() reorders the internal structure
544 of a tree of class "phylo". It is used as the generic, e.g.,
547 o read.tree() and read.nexus() can now read trees with a single
550 o The new data set `cynipids' supplies a set of protein sequences
556 o The code of all.equal.phylo() has been completely rewritten
557 (thanks to Benoît Durand) which fixes several bugs.
559 o read.tree() and read.nexus() now checks the labels of the tree
560 to remove or substitute any characters that are illegal in the
561 Newick format (parentheses, etc.)
563 o A negative P-value could be returned by mantel.test(): this is
568 CHANGES IN APE VERSION 1.8-4
573 o The new function sh.test() computes the Shimodaira-
576 o The new function collapse.singles() removes the nodes with a
577 single descendant from a tree.
579 o plot.phylo() has a new argument `tip.color' to specify the
582 o mlphylo() has now an option `quiet' to control the display of
583 the progress of the analysis (the default is FALSE).
588 o read.dna() did not read correctly sequences in sequential format
589 with leading alignment gaps "-": this is fixed.
591 o ace() returned a list with no class so that the generic
592 functions (anova, logLik, ...) could not be used directly. This
593 is fixed as ace() now returns an object of class "ace".
595 o anova.ace() had a small bug when computing the number of degrees
596 of freedom: this is fixed.
598 o mlphylo() did not work when the sequences were in a matrix or
599 a data frame: this is fixed.
601 o rtree() did not work correctly when trying to simulate an
602 unrooted tree with two tips: an error message is now issued.
607 o The algorithm of rtree() has been changed: it is now about 40,
608 100, and 130 times faster for 10, 100, and 1000 tips,
613 CHANGES IN APE VERSION 1.8-3
618 o There are four new `method' functions to be used with the
619 results of ace(): logLik(), deviance(), AIC(), and anova().
621 o The plot method of phymltest has two new arguments: `main' to
622 change the title, and `col' to control the colour of the
623 segments showing the AIC values.
625 o ace() has a new argument `ip' that gives the initial values used
626 in the ML estimation with discrete characters (see the examples
627 in ?ace). This function now returns a matrix giving the indices
628 of the estimated rates when analysing discrete characters.
630 o nodelabels() and tiplabels() have a new argument `pie' to
631 represent proportions, with any number of categories, as
632 piecharts. The use of the option `thermo' has been improved:
633 there is now no limitation on the number of categories.
638 o mlphylo() did not work with more than two partitions: this is
641 o root() failed if the proposed outgroup was already an outgroup
642 in the tree: this is fixed.
644 o The `col' argument in nodelabels() and tiplabels() was not
645 correctly passed when `text' was used: this is fixed.
647 o Two bugs were fixed in mlphylo(): parameters were not always
648 correctly output, and the estimation failed in some cases.
650 o plot.phylo() was stuck when given a tree with a single tip: this
651 is fixed and a message error is now returned.
653 o An error was corrected in the help page of gammaStat regarding
654 the calculation of P-values.
656 o Using gls() could crash R when the number of species in the tree
657 and in the variables were different: this is fixed.
661 CHANGES IN APE VERSION 1.8-2
666 o The new function mlphylo() fits a phylogenetic tree by maximum
667 likelihood from DNA sequences. Its companion function DNAmodel()
668 is used to define the substitution model which may include
669 partitioning. There are methods for logLik(), deviance(), and
670 AIC(), and the summary() method has been extended to display in
671 a friendly way the results of this model fitting. Currently, the
672 functionality is limited to estimating the substitution and
673 associated parameters and computing the likelihood.
675 o The new function drop1.compar.gee (used as, e.g., drop1(m))
676 tests for single effects in GEE-based comparative method. A
677 warning message is printed if there is not enough degrees of
683 o An error message was sometimes issued by plot.multi.tree(),
684 though with no consequence.
688 CHANGES IN APE VERSION 1.8-1
693 o There is a new plot method for lists of trees (objects of class
694 "multi.tree"): it calls plot.phylo() internally and is
695 documented on the same help page.
700 o A bug was fixed in the C code that analyzes bipartitions: this
701 has impact on several functions like prop.part, prop.clades,
702 boot.phylo, or consensus.
704 o root() did not work correctly when the specified outgroup had
705 more than one element: this is fixed.
707 o dist.dna() sometimes returned a warning inappropriately: this
710 o If the distance object given to nj() had no rownames, nj()
711 returned a tree with no tip labels: it now returns tips labelled
712 "1", "2", ..., corresponding to the row numbers.
717 o nj() has been slightly changed so that tips with a zero distance
718 are first aggregated with zero-lengthed branches; the usual NJ
719 procedure is then performed on a distance matrix without 0's.
723 CHANGES IN APE VERSION 1.8
728 o The new function chronopl() estimates dates using the penalized
729 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
731 o The new function consensus() calculates the consensus tree of a
734 o The new function evolve.phylo() simulates the evolution of
735 continuous characters along a phylogeny under a Brownian model.
737 o The new plot method for objects of class "ancestral" displays a
738 tree together with ancestral values, as returned by the above
741 o The new function as.phylo.formula() returns a phylogeny from a
742 set of nested taxonomic variables given as a formula.
744 o The new function read.caic() reads trees in CAIC format.
746 o The new function tiplabels() allows to add labels to the tips
747 of a tree using text or plotting symbols in a flexible way.
749 o The new function unroot() unroots a phylogeny.
751 o multi2di() has a new option, `random', which specifies whether
752 to resolve the multichotomies randomly (the default) or not.
754 o prop.part() now returns an object of class "prop.part" for which
755 there are print (to display a partition in a more friendly way)
756 and summary (to extract the numbers) methods.
758 o plot.phylo() has a new option, `show.tip.label', specifying
759 whether to print the labels of the tips. The default is TRUE.
761 o The code of nj() has been replaced by a faster C code: it is now
762 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
765 o write.nexus() now writes whether a tree is rooted or not.
770 o Two bugs have been fixed in root(): unrooted trees are now
771 handled corretly, and node labels are now output normally.
773 o A bug was fixed in phymltest(): the executable couldn't be found
776 o Three bug have been fixed in ace(): computing the likelihood of
777 ancestral states of discrete characters failed, custom models
778 did not work, and the function failed with a null gradient (a
779 warning message is now returned; this latter bug was also
780 present in yule.cov() as well and is now fixed).
782 o pic() hanged out when missing data were present: a message error
785 o A small bug was fixed in dist.dna() where the gamma correction
786 was not always correctly dispatched.
788 o plot.phylo() plotted correctly the root edge only when the tree
789 was plotted rightwards: this works now for all directions.
794 o dist.taxo() has been renamed as weight.taxo().
796 o Various error and warning messages have been improved.
800 CHANGES IN APE VERSION 1.7
803 o The new function ace() estimates ancestral character states for
804 continuous characters (with ML, GLS, and contrasts methods), and
805 discrete characters (with ML only) for any number of states.
807 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
808 of directional evolution for continuous characters. The user
809 specifies the node(s) of the tree where the character optimum
812 o The new function is.rooted() tests whether a tree (of class
815 o The new function rcoal() generates random ultrametric trees with
816 the possibility to specify the function that generates the
817 inter-nodes distances.
819 o The new function mrca() gives for all pairs of tips in a tree
820 (and optionally nodes too) the most recent common ancestor.
822 o nodelabels() has a new option `thermo' to plot proportions (up
823 to three classes) on the nodes of a tree.
825 o rtree() has been improved: it can now generate rooted or
826 unrooted trees, and the mathematical function that generates the
827 branch lengths may be specified by the user. The tip labels may
828 be given directly in the call to rtree. The limit cases (n = 2,
829 3) are now handled correctly.
831 o dist.topo() has a new argument `method' with two choices: "PH85"
832 for Penny and Henny's method (already available before and now
833 the default), and "BHV01" for the geometric distance by Billera
834 et al. (2001, Adv. Appl. Math. 27:733).
836 o write.tree() has a new option, `digits', which specifies the
837 number of digits to be printed in the Newick tree. By default
838 digits = 10. The numbers are now always printed in decimal form
839 (i.e., 1.0e-1 is now avoided).
841 o dist.dna() can now compute the raw distances between pairs of
842 DNA sequences by specifying model = "raw".
844 o dist.phylo() has a new option `full' to possibly compute the
845 distances among all tips and nodes of the tree. The default if
851 o Several bugs were fixed in all.equal.phylo().
853 o dist.dna() did not handle correctly gaps ("-") in alignments:
854 they are now considered as missing data.
856 o rotate() did not work if the tips were not ordered: this is
859 o mantel.test() returned NA in some special cases: this is fixed
860 and the function has been improved and is now faster.
862 o A bug was fixed in diversi.gof() where the calculation of A² was
865 o cherry() did not work correctly under some OSs (mainly Linux):
868 o is.binary.tree() has been modified so that it works with both
869 rooted and unrooted trees.
871 o The documentation of theta.s() was not correct: this has been
874 o plot.mst() did not work correctly: this is fixed.
878 CHANGES IN APE VERSION 1.6
883 o The new function dist.topo() computes the topological distances
886 o The new function boot.phylo() performs a bootstrap analysis on
887 phylogeny estimation.
889 o The new functions prop.part() and prop.clades() analyse
890 bipartitions from a series of trees.
895 o read.GenBank() now uses the EFetch utility of NCBI instead of
896 the usual Web interface: it is now much faster (e.g., 12 times
897 faster to retrieve 8 sequences, 37 times for 60 sequences).
902 o Several bugs were fixed in read.dna().
904 o Several bugs were fixed in diversi.time().
906 o is.binary.tree() did not work correctly if the tree has no edge
907 lengths: this is fixed.
909 o drop.tip() did not correctly propagated the `node.label' of a
914 CHANGES IN APE VERSION 1.5
919 o Two new functions, as.matching.phylo() and as.phylo.matching(),
920 convert objects between the classes "phylo" and "matching". The
921 latter implements the representation of binary trees introduced by
922 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
923 as.matching() has been introduced as well.
925 o Two new functions, multi2di() and di2multi(), allow to resolve
926 and collapse multichotomies with branches of length zero.
928 o The new function nuc.div() computes the nucleotide diversity
929 from a sample a DNA sequences.
931 o dist.dna() has been completely rewritten with a much faster
932 (particularly for large data sets) C code. Eight models are
933 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
934 option `method' has been renamed `model'). Computation of variance
935 is available for all models. A gamma-correction is possible for
936 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
937 to remove sites with missing data on a pairwise basis. The option
938 `GCcontent' has been removed.
940 o read.GenBank() has a new option (species.names) which specifies
941 whether to return the species names of the organisms in addition
942 to the accession numbers of the sequences (this is the default
945 o write.nexus() can now write several trees in the same NEXUS file.
947 o drop.tip() has a new option `root.edge' that allows to specify the
948 new root edge if internal branches are trimmed.
953 o as.phylo.hclust() failed if some labels had parentheses: this
956 o Several bugs were fixed in all.equal.phylo(). This function now
957 returns the logical TRUE if the trees are identical but with
958 different representations (a report was printed previously).
960 o read.GenBank() did not correctly handle ambiguous base codes:
966 o birthdeath() now returns an object of class "birthdeath" for
967 which there is a print method.
971 CHANGES IN APE VERSION 1.4
976 o The new function nj() performs phylogeny estimation with the
977 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
980 o The new function which.edge() identifies the edges of a tree
981 that belong to a group specified as a set of tips.
983 o The new function as.phylo.phylog() converts an object of class
984 "phylog" (from the package ade4) into an object of class
987 o The new function axisPhylo() draws axes on the side of a
990 o The new function howmanytrees() calculates the number of trees
991 in different cases and giving a number of tips.
993 o write.tree() has a new option `multi.line' (TRUE by default) to
994 write a Newick tree on several lines rather than on a single
997 o The functionalities of zoom() have been extended. Several
998 subtrees can be visualized at the same time, and they are marked
999 on the main tree with colors. The context of the subtrees can be
1000 marked with the option `subtree' (see below).
1002 o drop.tip() has a new option `subtree' (FALSE by default) which
1003 specifies whether to output in the tree how many tips have been
1006 o The arguments of add.scale.bar() have been redefined and have
1007 now default values (see ?add.scale.bar for details). This
1008 function now works even if the plotted tree has no edge length.
1010 o plot.phylo() can now plot radial trees, but this does not take
1011 edge lengths into account.
1013 o In plot.phylo() with `type = "phylogram"', if the values of
1014 `edge.color' and `edge.width' are identical for sister-branches,
1015 they are propagated to the vertical line that link them.
1020 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1021 crashing. This is fixed.
1023 o In plot.phylo(), the options `edge.color' and `edge.width' are
1024 now properly recycled; their default values are now "black" and
1027 o A bug has been fixed in write.nexus().
1032 o The function node.depth.edgelength() has been removed and
1033 replaced by a C code.
1037 CHANGES IN APE VERSION 1.3-1
1042 o The new function nodelabels() allows to add labels to the nodes
1043 of a tree using text or plotting symbols in a flexible way.
1045 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1046 numeric values specifying the lower and upper limits on the x-
1047 and y-axes. This allows to leave some space on any side of the
1048 tree. If a single value is given, this is taken as the upper
1053 CHANGES IN APE VERSION 1.3
1058 o The new function phymltest() calls the software PHYML and fits
1059 28 models of DNA sequence evolution. There are a print method to
1060 display likelihood and AIC values, a summary method to compute
1061 the hierarchical likelihood ratio tests, and a plot method to
1062 display graphically the AIC values of each model.
1064 o The new function yule.cov() fits the Yule model with covariates,
1065 a model where the speciation rate is affected by several species
1066 traits through a generalized linear model. The parameters are
1067 estimated by maximum likelihood.
1069 o Three new functions, corBrownian(), corGrafen(), and
1070 corMartins(), compute the expected correlation structures among
1071 species given a phylogeny under different models of evolution.
1072 These can be used for GLS comparative phylogenetic methods (see
1073 the examples). There are coef() and corMatrix() methods and an
1074 Initialize.corPhyl() function associated.
1076 o The new function compar.cheverud() implements Cheverud et al.'s
1077 (1985; Evolution 39:1335) phylogenetic comparative method.
1079 o The new function varcomp() estimates variance components; it has
1082 o Two new functions, panel.superpose.correlogram() and
1083 plot.correlogramList(), allow to plot several phylogenetic
1086 o The new function node.leafnumber() computes the number of leaves
1087 of a subtree defined by a particular node.
1089 o The new function node.sons() gets all tags of son nodes from a
1092 o The new function compute.brlen() computes the branch lengths of
1093 a tree according to a specified method.
1095 o plot.phylo() has three new options: "cex" controls the size of
1096 the (tip and node) labels (thus it is no more needed to change
1097 the global graphical parameter), "direction" which allows to
1098 plot the tree rightwards, leftwards, upwards, or downwards, and
1099 "y.lim" which sets the upper limit on the y-axis.
1104 o Some functions which try to match tip labels and names of
1105 additional data (e.g. vector) are likely to fail if there are
1106 typing or syntax errors. If both series of names do not perfectly
1107 match, they are ignored and a warning message is now issued.
1108 These functions are bd.ext, compar.gee, pic. Their help pages
1109 have been clarified on this point.
1113 CHANGES IN APE VERSION 1.2-7
1118 o The new function root() reroots a phylogenetic tree with respect
1119 to a specified outgroup.
1121 o The new function rotate() rotates an internal branch of a tree.
1123 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1124 trees) controls the display of the tip labels in unrooted trees.
1125 This display has been greatly improved: the tip labels are now not
1126 expected to overlap with the tree (particularly if lab4ut =
1127 "axial"). In all cases, combining appropriate values of "lab4ut"
1128 and the font size (via "par(cex = )") should result in readable
1129 unrooted trees. See ?plot.phylo for some examples.
1131 o In drop.tip(), the argument `tip' can now be numeric or character.
1136 o drop.tip() did not work correctly with trees with no branch
1137 lengths: this is fixed.
1139 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1140 plotted with some line crossings: this is now fixed.
1144 CHANGES IN APE VERSION 1.2-6
1149 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1150 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1151 to implement comparative methods with an autocorrelation approach.
1153 o A new data set describing some life history traits of Carnivores
1159 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1164 o When plotting a tree with plot.phylo(), the new default of the
1165 option `label.offset' is now 0, so the labels are always visible.
1169 CHANGES IN APE VERSION 1.2-5
1174 o The new function bd.ext() fits a birth-death model with combined
1175 phylogenetic and taxonomic data, and estimates the corresponding
1176 speciation and extinction rates.
1181 o The package gee is no more required by ape but only suggested
1182 since only the function compar.gee() calls gee.
1186 CHANGES IN APE VERSION 1.2-4
1191 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1192 and lines.popsize) implementing a new approach for inferring the
1193 demographic history from genealogies using a reversible jump
1194 MCMC have been introduced.
1196 o The unit of time in the skyline plot and in the new plots can
1197 now be chosen to be actual years, rather than substitutions.
1201 CHANGES IN APE VERSION 1.2-3
1206 o The new function rtree() generates a random binary tree with or
1207 without branch lengths.
1209 o Two new functions for drawing lineages-through-time (LTT) plots
1210 are provided: ltt.lines() adds a LTT curve to an existing plot,
1211 and mltt.plot() does a multiple LTT plot giving several trees as
1212 arguments (see `?ltt.plot' for details).
1217 o Some taxon names made R crashing when calling as.phylo.hclust():
1220 o dist.dna() returned an error with two identical DNA sequences
1221 (only using the Jukes-Cantor method returned 0): this is fixed.
1226 o The function dist.phylo() has been re-written using a different
1227 algorithm: it is now about four times faster.
1229 o The code of branching.times() has been improved: it is now about
1234 CHANGES IN APE VERSION 1.2-2
1239 o The new function seg.sites() finds the segregating sites in a
1240 sample of DNA sequences.
1245 o A bug introduced in read.tree() and in read.nexus() with version
1248 o A few errors were corrected and a few examples were added in the
1253 CHANGES IN APE VERSION 1.2-1
1258 o plot.phylo() can now draw the edge of the root of a tree if it
1259 has one (see the new option `root.edge', its default is FALSE).
1264 o A bug was fixed in read.nexus(): files with semicolons inside
1265 comment blocks were not read correctly.
1267 o The behaviour of read.tree() and read.nexus() was corrected so
1268 that tree files with badly represented root edges (e.g., with
1269 an extra pair of parentheses, see the help pages for details)
1270 are now correctly represented in the object of class "phylo";
1271 a warning message is now issued.
1275 CHANGES IN APE VERSION 1.2
1280 o plot.phylo() has been completely re-written and offers several
1281 new functionalities. Three types of trees can now be drawn:
1282 phylogram (as previously), cladogram, and unrooted tree; in
1283 all three types the branch lengths can be drawn using the edge
1284 lengths of the phylogeny or not (e.g., if the latter is absent).
1285 The vertical position of the nodes can be adjusted with two
1286 choices (see option `node.pos'). The code has been re-structured,
1287 and two new functions (potentially useful for developpers) are
1288 documented separately: node.depth.edgelength() and node.depth();
1289 see the respective help pages for details.
1291 o The new function zoom() allows to explore very large trees by
1292 focusing on a small portion of it.
1294 o The new function yule() fits by maximum likelihood the Yule model
1295 (birth-only process) to a phylogenetic tree.
1297 o Support for writing DNA sequences in FASTA format has been
1298 introduced in write.dna() (support for reading sequences in
1299 this format was introduced in read.dna() in version 1.1-2).
1300 The function has been completely re-written, fixing some bugs
1301 (see below); the default behaviour is no more to display the
1302 sequences on the standard output. Several options have been
1303 introduced to control the sequence printing in a flexible
1304 way. The help page has been extended.
1306 o A new data set is included: a supertree of bats in NEXUS format.
1311 o In theta.s(), the default of the option `variance' has
1312 been changed to `FALSE' (as was indicated in the help page).
1314 o Several bugs were fixed in the code of all.equal.phylo().
1316 o Several bugs were fixed in write.dna(), particularly this
1317 function did not work with `format = "interleaved"'.
1319 o Various errors were corrected in the help pages.
1324 o The argument names of as.hclust.phylo() have been changed
1325 from "(phy)" to "(x, ...)" to conform to the definition of
1326 the corresponding generic function.
1328 o gamma.stat() has been renamed gammaStat() to avoid confusion
1329 since gamma() is a generic function.
1333 CHANGES IN APE VERSION 1.1-3
1338 o base.freq() previously did not return a value of 0 for
1339 bases absent in the data (e.g., a vector of length 3 was
1340 returned if one base was absent). This is now fixed (a
1341 vector of length 4 is always returned).
1343 o Several bugs were fixed in read.nexus(), including that this
1344 function did not work in this absence of a "TRANSLATE"
1345 command in the NEXUS file, and that the commands were
1350 CHANGES IN APE VERSION 1.1-2
1355 o The Tamura and Nei (1993) model of DNA distance is now implemented
1356 in dist.dna(): five models are now available in this function.
1358 o A new data set is included: a set of 15 sequences of the
1359 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1365 o A bug in read.nexus() was fixed.
1367 o read.dna() previously did not work correctly in most cases.
1368 The function has been completely re-written and its help page
1369 has been considerably extended (see ?read.dna for details).
1370 Underscores (_) in taxon names are no more replaced with
1371 spaces (this behaviour was undocumented).
1373 o A bug was fixed in write.dna().
1377 CHANGES IN APE VERSION 1.1-1
1382 o A bug in read.tree() introduced in APE 1.1 was fixed.
1384 o A bug in compar.gee() resulted in an error when trying to fit
1385 a model with `family = "binomial"'. This is now fixed.
1389 CHANGES IN APE VERSION 1.1
1394 o The Klastorin (1982) method as suggested by Misawa and Tajima
1395 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1396 on the basis of phylogenetic trees has been implemented (see
1397 the function klastorin()).
1399 o Functions have been added to convert APE's "phylo" objects in
1400 "hclust" cluster objects and vice versa (see the help page of
1401 as.phylo for details).
1403 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1404 are introduced for the estimation of absolute evolutionary rates
1405 (ratogram) and dated clock-like trees (chronogram) from
1406 phylogenetic trees using the non-parametric rate smoothing approach
1407 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1409 o A summary method is now provided printing a summary information on a
1410 phylogenetic tree with, for instance, `summary(tree)'.
1412 o The behaviour of read.tree() was changed so that all spaces and
1413 tabulations in tree files are now ignored. Consequently, spaces in tip
1414 labels are no more allowed. Another side effect is that read.nexus()
1415 now does not replace the underscores (_) in tip labels with spaces
1416 (this behaviour was undocumented).
1418 o The function plot.phylo() has a new option (`underscore') which
1419 specifies whether the underscores in tip labels should be written on
1420 the plot as such or replaced with spaces (the default).
1422 o The function birthdeath() now computes 95% confidence intervals of
1423 the estimated parameters using profile likelihood.
1425 o Three new data sets are included: a gene tree estimated from 36
1426 landplant rbcL sequences, a gene tree estimated from 32 opsin
1427 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1432 o A bug was fixed in dist.gene() where nothing was returned.
1434 o A bug in plot.mst() was fixed.
1436 o A bug in vcv.phylo() resulted in false correlations when the
1437 option `cor = TRUE' was used (now fixed).
1441 CHANGES IN APE VERSION 1.0
1446 o Two new functions, read.dna() and write.dna(), read/write in a file
1447 DNA sequences in interleaved or in sequential format.
1449 o Two new functions, read.nexus() and write.nexus(), read/write trees
1452 o The new function bind.tree() allows to bind two trees together,
1453 possibly handling root edges to give internal branches.
1455 o The new function drop.tip() removes the tips in a phylogenetic tree,
1456 and trims (or not) the corresponding internal branches.
1458 o The new function is.ultrametric() tests if a tree is ultrametric.
1460 o The function plot.phylo() has more functionalities such as drawing the
1461 branches with different colours and/or different widths, showing the
1462 node labels, controling the position and font of the labels, rotating
1463 the labels, and controling the space around the plot.
1465 o The function read.tree() can now read trees with no branch length,
1466 such as "(a,b),c);". Consequently, the element `edge.length' in
1467 objects of class "phylo" is now optional.
1469 o The function write.tree() has a new default behaviour: if the default
1470 for the option `file' is used (i.e. file = ""), then a variable of
1471 mode character containing the tree in Newick format is returned which
1472 can thus be assigned (e.g., tree <- write.tree(phy)).
1474 o The function read.tree() has a new argument `text' which allows
1475 to read the tree in a variable of mode character.
1477 o A new data set is included: the phylogenetic relationships among
1478 the orders of birds from Sibley and Ahlquist (1990).
1482 CHANGES IN APE VERSION 0.2-1
1487 o Several bugs were fixed in the help pages.
1491 CHANGES IN APE VERSION 0.2
1496 o The function write.tree() writes phylogenetic trees (objects of class
1497 "phylo") in an ASCII file using the Newick parenthetic format.
1499 o The function birthdeath() fits a birth-death model to branching times
1500 by maximum likelihood, and estimates the corresponding speciation and
1503 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1506 o The function is.binary.tree() tests whether a phylogeny is binary.
1508 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1509 as well as some methods are introduced.
1511 o Several functions, including some generics and methods, for computing
1512 skyline plot estimates (classic and generalized) of effective
1513 population size through time are introduced and replace the function
1514 skyline.plot() in version 0.1.
1516 o Two data sets are now included: the phylogenetic relationships among
1517 the families of birds from Sibley and Ahlquist (1990), and an
1518 estimated clock-like phylogeny of HIV sequences sampled in the
1519 Democratic Republic of Congo.
1522 DEPRECATED & DEFUNCT
1524 o The function skyline.plot() in ape 0.1 has been deprecated and
1525 replaced by more elaborate functions (see above).
1530 o Two important bugs were fixed in plot.phylo(): phylogenies with
1531 multichotomies not at the root or not with only terminal branches,
1532 and phylogenies with a single node (i.e. only terminal branches)
1533 did not plot. These trees should be plotted correctly now.
1535 o Several bugs were fixed in diversi.time() in the computation of
1538 o Various errors were corrected in the help pages.