1 CHANGES IN APE VERSION 2.2-2
6 o dist.gene() has been substantially improved and gains an option
11 CHANGES IN APE VERSION 2.2-1
16 o The new function makeLabel() helps to modify labels of trees,
17 lists of trees, or DNA sequences, with several utilities to
18 truncate and/or make them unique, substituting some
19 characters, and so on.
21 o The new function del.gaps() removes insertion gaps ("-") in a
24 o read.dna() can now read Clustal files (*.aln).
29 o root() failed with 'resolve.root = TRUE' when the root was
30 already the specified root.
32 o Several bugs were fixed in mlphylo().
34 o collapsed.singles() did not propagate the 'Nnode' and
35 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
37 o read.nexus() failed to remove correctly the comments within
40 o read.nexus() failed to read a file with a single tree and no
41 translation of tip labels.
43 o read.nexus() failed to place correctly tip labels when reading
44 a single tree with no edge lengths.
46 o A bug was fixed in sh.test().
51 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
54 o The option 'check.labels' of consensus() and prop.part() is now
57 o write.dna() now does not truncate names to 10 characters with
62 CHANGES IN APE VERSION 2.2
67 o Four new functions have been written by Damien de Vienne for the
68 graphical exploration of large trees (cophyloplot, subtrees,
69 subtreeplot), and to return the graphical coordinates of tree
72 o The new functions corPagel and corBlomberg implement the Pagel's
73 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
75 o chronopl() has been improved and gains several options: see its
76 help page for details.
78 o boot.phylo() has now an option 'trees' to possibly return the
79 bootstraped trees (the default is FALSE).
81 o prop.part() has been improved and should now be faster in all
87 o read.dna() failed if "?" occurred in the first 10 sites of the
90 o The x/y aspect of the plot is now respected when plotting a
91 circular tree (type = "r" or "f").
93 o Drawing the tip labels sometimes failed when plotting circular
96 o zoom() failed when tip labels were used instead of their numbers
97 (thanks to Yan Wong for the fix).
99 o drop.tip() failed with some trees (fixed by Yan Wong).
101 o seg.sites() failed with a list.
103 o consensus() failed in some cases. The function has been improved
104 as well and is faster.
108 CHANGES IN APE VERSION 2.1-3
113 o A bug in read.nexus() made the Windows R-GUI crash.
115 o An error was fixed in the computation of ancestral character
116 states by generalized least squares in ace().
118 o di2multi() did not modify node labels correctly.
120 o multi2di() failed if the tree had its attribute "order" set to
125 CHANGES IN APE VERSION 2.1-2
130 o There three new methods for the "multiPhylo" class: str, $,
133 o root() gains the options 'node' and 'resolve.root'
134 (FALSE by default) as well as its code being improved.
136 o mltt.plot() has now an option 'log' used in the same way
137 than in plot.default().
142 o mltt.plot() failed to display the legend with an unnamed
145 o nodelabels() with pies now correcly uses the argument
146 'cex' to draw symbols of different sizes (which has
147 worked already for thermometers).
149 o read.nexus() generally failed to read very big files.
154 o The argument 'family' of compar.gee() can now be a function
155 as well as a character string.
157 o read.tree() and read.nexus() now return an unnamed list if
160 o read.nexus() now returns a modified object of class "multiPhylo"
161 when there is a TRANSLATE block in the NEXUS file: the individual
162 trees have no 'tip.label' vector, but the list has a 'TipLabel'
163 attribute. The new methods '$' and '[[' set these elements
164 correctly when extracting trees.
168 CHANGES IN APE VERSION 2.1-1
173 o The new function rmtree generates lists of random trees.
175 o rcoal() now generates a genuine coalescent tree by default
176 (thanks to Vladimir Minin for the code).
181 o nuc.div() returned an incorrect value with the default
182 pairwise.deletion = FALSE.
187 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
188 have been improved so that they are stabler and faster.
190 o R packages used by ape are now loaded silently; lattice and gee
191 are loaded only when needed.
195 CHANGES IN APE VERSION 2.1
200 o The new function identify.phylo identifies clades on a plotted
201 tree using the mouse.
203 o It is now possible to subset a list of trees (object of class
204 "multiPhylo") with "[" while keeping its class correct.
206 o The new function as.DNAbin.alignment converts DNA sequences
207 stored in the "alignment" format of the package seqinr into
208 an object of class "DNAbin".
210 o The new function weight.taxo2 helps to build similarity matrices
211 given two taxonomic levels (usually called by other functions).
213 o write.tree() can now take a list of trees (class "multiPhylo")
214 as its main argument.
216 o plot.correlogram() and plot.correlogramList() have been
217 improved, and gain several options (see the help page for
218 details). A legend is now plotted by default.
223 o dist.dna() returned some incorrect values with `model = "JC69"'
224 and `pairwise.deletion = TRUE'. This affected only the
225 distances involving sequences with missing values. (Thanks
226 to Bruno Toupance for digging this bug out.)
228 o write.tree() failed with some trees: this is fixed by removing
229 the `multi.line' option (trees are now always printed on a
232 o read.nexus() did not correctly detect trees with multiple root
233 edges (see OTHER CHANGES).
238 o The code of mlphylo() has almost entirely rewritten, and should
239 be much stabler. The options have been also greatly simplified
240 (see ?mlphylo and ?DNAmodel for details).
242 o The internal function nTips has been renamed klastorin_nTips.
244 o The code of is.ultrametric() contained redundancies and has
247 o The code of Moran.I() and of correlogram.formula() have been
250 o read.tree() and read.nexus() now return an error when trying to
251 read a tree with multiple root edges (see BUG FIXES). The
252 correction applied in previous version did not work in all
255 o The class c("multi.tree", "phylo") has been renamed
261 o There is now a vignette in ape: see vignette("MoranI", "ape").
266 o as.matching() and as.phylo.matching() do not support branch
269 o correlogram.phylo() and discrete.dist() have been removed.
273 CHANGES IN APE VERSION 2.0-2
278 o The new function matexpo computes the exponential of a square
281 o The new function unique.multi.tree removes duplicate trees from
284 o yule() has a new option `use.root.edge = FALSE' that specifies
285 to ignore, by default, the root edge of the tree if it exists.
290 o which.edge() failed when the index of a single terminal edge was
293 o In diversi.time(), the values returned for model C were
296 o A bug was fixed in yule() that affected the calculation of the
297 likelihood in the presence of ties in the branching times.
299 o There was a bug in the C function mat_expo4x4 affecting the
300 calculations of the transition probabilities for models HKY and
303 o A small bug was fixed in as.matrix.DNAbin (thanks to James
306 o rtree() did not `shuffle' the tip labels by default, so only a
307 limited number of labelled topologies could be generated.
311 CHANGES IN APE VERSION 2.0-1
316 o The three new functions bionj, fastme.ols, and fastme.bal
317 perform phylogeny estimation by the BIONJ and fastME methods in
318 OLS and balanced versions. This is a port to R of previous
319 previous programs done by Vincent Lefort.
321 o The new function chronoMPL performs molecular dating with the
322 mean path lengths method of Britton et al. (2002, Mol. Phyl.
325 o The new function rotate, contributed by Christoph Heibl, swaps
326 two clades connected to the same node. It works also with
327 multichotomous nodes.
329 o The new `method' as.matrix.DNAbin() may be used to convert
330 easily DNA sequences stored in a list into a matrix while
331 keeping the names and the class.
336 o chronopl() failed when some branch lengths were equal to zero:
337 an error message is now returned.
339 o di2multi() failed when there was a series of consecutive edges
344 CHANGES IN APE VERSION 1.10-2
349 o plot.phylo() can now plot circular trees: the option is type =
350 "fan" or type = "f" (to avoid the ambiguity with type = "c").
352 o prop.part() has a new option `check.labels = FALSE' which allows
353 to considerably speed-up the calculations of bipartitions. As a
354 consequence, calculations of bootstrap values with boot.phylo()
355 should be much faster.
360 o read.GenBank() did not return correctly the list of species as
361 from ape 1.10: this is fixed in this version
363 o Applying as.phylo() on a tree of class "phylo" failed: the
364 object is now returned unchanged.
368 CHANGES IN APE VERSION 1.10-1
373 o The three new functions Ntip, Nnode, and Nedge return, for a
374 given tree, the number of tips, nodes, or edges, respectively.
379 o read.nexus() did not set correctly the class of the returned
380 object when reading multiple trees.
382 o mllt.plot() failed with objects of class c("multi.tree",
385 o unroot() did not work correctly in most cases.
387 o reorder.phylo() made R freeze in some occasions.
389 o Plotting a tree in pruningwise order failed.
391 o When plotting an unrooted tree, the tip labels where not all
392 correctly positioned if the option `cex' was used.
396 CHANGES IN APE VERSION 1.10
401 o Five new `method' functions have been introduced to manipulate
402 DNA sequences in binary format (see below).
404 o Three new functions have been introduced to convert between the
405 new binary and the character formats.
407 o The new function as.alignment converts DNA sequences stored as
408 single characters into the class "alignment" used by the package
411 o read.dna() and read.GenBank() have a new argument `as.character'
412 controlling whether the sequences are returned in binary format
418 o root() failed when the tree had node labels: this is fixed.
420 o plot.phylo() did not correctly set the limits on the y-axis with
421 the default setting: this is fixed.
423 o dist.dna() returned a wrong result for the LogDet, paralinear,
424 and BH87 models with `pairwise.deletion = TRUE'.
429 o DNA sequences are now internally stored in a binary format. See
430 the document "A Bit-Level Coding Scheme for Nucleotides" for the
431 details. Most functions analyzing DNA functions have been
432 modified accordingly and are now much faster (dist.dna is now
433 ca. 60 times faster).
437 CHANGES IN APE VERSION 1.9-4
442 o A bug was fixed in edgelabels().
444 o as.phylo.hclust() did not work correctly when the object of
445 class "hclust" has its labels set to NULL: the returned tree has
446 now its tip labels set to "1", "2", ...
448 o consensus could fail if some tip labels are a subset of others
449 (e.g., "a" and "a_1"): this is now fixed.
451 o mlphylo() failed in most cases if some branch lengths of the
452 initial tree were greater than one: an error message is now
455 o mlphylo() failed in most cases when estimating the proportion of
456 invariants: this is fixed.
460 CHANGES IN APE VERSION 1.9-3
465 o The new function edgelabels adds labels on the edge of the tree
466 in the same way than nodelabels or tiplabels.
471 o multi2di() did not handle correctly branch lengths with the
472 default option `random = TRUE': this is now fixed.
474 o A bug was fixed in nuc.div() when using pairwise deletions.
476 o A bug occurred in the analysis of bipartitions with large
477 numbers of large trees, with consequences on prop.part,
478 prop.clades, and boot.phylo.
480 o The calculation of the Billera-Holmes-Vogtmann distance in
481 dist.topo was wrong: this has been fixed.
485 CHANGES IN APE VERSION 1.9-2
490 o The new function ladderize reorganizes the internal structure of
491 a tree to plot them left- or right-ladderized.
493 o The new function dist.nodes computes the patristic distances
494 between all nodes, internal and terminal, of a tree. It replaces
495 the option `full = TRUE' of cophenetic.phylo (see below).
500 o A bug was fixed in old2new.phylo().
502 o Some bugs were fixed in chronopl().
504 o The edge colours were not correctly displayed by plot.phylo
505 (thank you to Li-San Wang for the fix).
507 o cophenetic.phylo() failed with multichotomous trees: this is
513 o read.dna() now returns the sequences in a matrix if they are
514 aligned (interleaved or sequential format). Sequences in FASTA
515 format are still returned in a list.
517 o The option `full' of cophenetic.phylo() has been removed because
518 it could not be used from the generic.
523 o rotate() has been removed; this function did not work correctly
528 CHANGES IN APE VERSION 1.9-1
533 o Trees with a single tip were not read correctly in R as the
534 element `Nnode' was not set: this is fixed.
536 o unroot() did not set correctly the number of nodes of the
537 unrooted tree in most cases.
539 o read.GenBank() failed when fetching very long sequences,
540 particularly of the BX-series.
542 o A bug was introduced in read.tree() with ape 1.9: it has been
547 CHANGES IN APE VERSION 1.9
552 o There are two new print `methods' for trees of class "phylo" and
553 lists of trees of class "multi.tree", so that they are now
554 displayed in a compact and informative way.
556 o There are two new functions, old2new.phylo and new2old.phylo,
557 for converting between the old and new coding of the class
560 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
561 LogDet ("logdet"), and paralinear ("paralin").
563 o compute.brlen() has been extended: several methods are now
564 available to compute branch lengths.
566 o write.dna() can now handle matrices as well as lists.
571 o cophenetic.phylo() sometimes returned a wrong result with
572 multichotomous trees: this is fixed.
574 o rotate() failed when a single tip was specified: the tree is now
577 o ace() did not return the correct index matrix with custom
578 models: this is fixed.
580 o multi2di() did not work correctly when resolving multichotomies
581 randomly: the topology was always the same, only the arrangement
582 of clades was randomized: this is fixed. This function now
583 accepts trees with no branch lengths.
585 o The output of diversi.gof() was blurred by useless prints when a
586 user distribution was specified. This has been corrected, and
587 the help page of this function has been expanded.
592 o The internal structure of the class "phylo" has been changed:
593 see the document "Definition of Formats for Coding Phylogenetic
594 Trees in R" for the details. In addition, the code of most
595 functions has been improved.
597 o Several functions have been improved by replacing some R codes
598 by C codes: pic, plot.phylo, and reorder.phylo.
600 o There is now a citation information: see citation("ape") in R.
602 o write.tree() now does not add extra 0's to branch lengths so
603 that 1.23 is printed "1.23" by default, not "1.2300000000".
605 o The syntax of bind.tree() has been simplified. This function now
606 accepts trees with no branch lengths, and handles correctly node
609 o The option `as.numeric' of mrca() has been removed.
611 o The unused options `format' and `rooted' of read.tree() have
614 o The unused option `format' of write.tree() has been removed.
616 o The use of node.depth() has been simplified.
620 CHANGES IN APE VERSION 1.8-5
625 o Two new functions read.nexus.data() and write.nexus.data(),
626 contributed by Johan Nylander, allow to read and write molecular
627 sequences in NEXUS files.
629 o The new function reorder.phylo() reorders the internal structure
630 of a tree of class "phylo". It is used as the generic, e.g.,
633 o read.tree() and read.nexus() can now read trees with a single
636 o The new data set `cynipids' supplies a set of protein sequences
642 o The code of all.equal.phylo() has been completely rewritten
643 (thanks to Benoît Durand) which fixes several bugs.
645 o read.tree() and read.nexus() now checks the labels of the tree
646 to remove or substitute any characters that are illegal in the
647 Newick format (parentheses, etc.)
649 o A negative P-value could be returned by mantel.test(): this is
654 CHANGES IN APE VERSION 1.8-4
659 o The new function sh.test() computes the Shimodaira-
662 o The new function collapse.singles() removes the nodes with a
663 single descendant from a tree.
665 o plot.phylo() has a new argument `tip.color' to specify the
668 o mlphylo() has now an option `quiet' to control the display of
669 the progress of the analysis (the default is FALSE).
674 o read.dna() did not read correctly sequences in sequential format
675 with leading alignment gaps "-": this is fixed.
677 o ace() returned a list with no class so that the generic
678 functions (anova, logLik, ...) could not be used directly. This
679 is fixed as ace() now returns an object of class "ace".
681 o anova.ace() had a small bug when computing the number of degrees
682 of freedom: this is fixed.
684 o mlphylo() did not work when the sequences were in a matrix or
685 a data frame: this is fixed.
687 o rtree() did not work correctly when trying to simulate an
688 unrooted tree with two tips: an error message is now issued.
693 o The algorithm of rtree() has been changed: it is now about 40,
694 100, and 130 times faster for 10, 100, and 1000 tips,
699 CHANGES IN APE VERSION 1.8-3
704 o There are four new `method' functions to be used with the
705 results of ace(): logLik(), deviance(), AIC(), and anova().
707 o The plot method of phymltest has two new arguments: `main' to
708 change the title, and `col' to control the colour of the
709 segments showing the AIC values.
711 o ace() has a new argument `ip' that gives the initial values used
712 in the ML estimation with discrete characters (see the examples
713 in ?ace). This function now returns a matrix giving the indices
714 of the estimated rates when analysing discrete characters.
716 o nodelabels() and tiplabels() have a new argument `pie' to
717 represent proportions, with any number of categories, as
718 piecharts. The use of the option `thermo' has been improved:
719 there is now no limitation on the number of categories.
724 o mlphylo() did not work with more than two partitions: this is
727 o root() failed if the proposed outgroup was already an outgroup
728 in the tree: this is fixed.
730 o The `col' argument in nodelabels() and tiplabels() was not
731 correctly passed when `text' was used: this is fixed.
733 o Two bugs were fixed in mlphylo(): parameters were not always
734 correctly output, and the estimation failed in some cases.
736 o plot.phylo() was stuck when given a tree with a single tip: this
737 is fixed and a message error is now returned.
739 o An error was corrected in the help page of gammaStat regarding
740 the calculation of P-values.
742 o Using gls() could crash R when the number of species in the tree
743 and in the variables were different: this is fixed.
747 CHANGES IN APE VERSION 1.8-2
752 o The new function mlphylo() fits a phylogenetic tree by maximum
753 likelihood from DNA sequences. Its companion function DNAmodel()
754 is used to define the substitution model which may include
755 partitioning. There are methods for logLik(), deviance(), and
756 AIC(), and the summary() method has been extended to display in
757 a friendly way the results of this model fitting. Currently, the
758 functionality is limited to estimating the substitution and
759 associated parameters and computing the likelihood.
761 o The new function drop1.compar.gee (used as, e.g., drop1(m))
762 tests for single effects in GEE-based comparative method. A
763 warning message is printed if there is not enough degrees of
769 o An error message was sometimes issued by plot.multi.tree(),
770 though with no consequence.
774 CHANGES IN APE VERSION 1.8-1
779 o There is a new plot method for lists of trees (objects of class
780 "multi.tree"): it calls plot.phylo() internally and is
781 documented on the same help page.
786 o A bug was fixed in the C code that analyzes bipartitions: this
787 has impact on several functions like prop.part, prop.clades,
788 boot.phylo, or consensus.
790 o root() did not work correctly when the specified outgroup had
791 more than one element: this is fixed.
793 o dist.dna() sometimes returned a warning inappropriately: this
796 o If the distance object given to nj() had no rownames, nj()
797 returned a tree with no tip labels: it now returns tips labelled
798 "1", "2", ..., corresponding to the row numbers.
803 o nj() has been slightly changed so that tips with a zero distance
804 are first aggregated with zero-lengthed branches; the usual NJ
805 procedure is then performed on a distance matrix without 0's.
809 CHANGES IN APE VERSION 1.8
814 o The new function chronopl() estimates dates using the penalized
815 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
817 o The new function consensus() calculates the consensus tree of a
820 o The new function evolve.phylo() simulates the evolution of
821 continuous characters along a phylogeny under a Brownian model.
823 o The new plot method for objects of class "ancestral" displays a
824 tree together with ancestral values, as returned by the above
827 o The new function as.phylo.formula() returns a phylogeny from a
828 set of nested taxonomic variables given as a formula.
830 o The new function read.caic() reads trees in CAIC format.
832 o The new function tiplabels() allows to add labels to the tips
833 of a tree using text or plotting symbols in a flexible way.
835 o The new function unroot() unroots a phylogeny.
837 o multi2di() has a new option, `random', which specifies whether
838 to resolve the multichotomies randomly (the default) or not.
840 o prop.part() now returns an object of class "prop.part" for which
841 there are print (to display a partition in a more friendly way)
842 and summary (to extract the numbers) methods.
844 o plot.phylo() has a new option, `show.tip.label', specifying
845 whether to print the labels of the tips. The default is TRUE.
847 o The code of nj() has been replaced by a faster C code: it is now
848 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
851 o write.nexus() now writes whether a tree is rooted or not.
856 o Two bugs have been fixed in root(): unrooted trees are now
857 handled corretly, and node labels are now output normally.
859 o A bug was fixed in phymltest(): the executable couldn't be found
862 o Three bug have been fixed in ace(): computing the likelihood of
863 ancestral states of discrete characters failed, custom models
864 did not work, and the function failed with a null gradient (a
865 warning message is now returned; this latter bug was also
866 present in yule.cov() as well and is now fixed).
868 o pic() hanged out when missing data were present: a message error
871 o A small bug was fixed in dist.dna() where the gamma correction
872 was not always correctly dispatched.
874 o plot.phylo() plotted correctly the root edge only when the tree
875 was plotted rightwards: this works now for all directions.
880 o dist.taxo() has been renamed as weight.taxo().
882 o Various error and warning messages have been improved.
886 CHANGES IN APE VERSION 1.7
889 o The new function ace() estimates ancestral character states for
890 continuous characters (with ML, GLS, and contrasts methods), and
891 discrete characters (with ML only) for any number of states.
893 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
894 of directional evolution for continuous characters. The user
895 specifies the node(s) of the tree where the character optimum
898 o The new function is.rooted() tests whether a tree (of class
901 o The new function rcoal() generates random ultrametric trees with
902 the possibility to specify the function that generates the
903 inter-nodes distances.
905 o The new function mrca() gives for all pairs of tips in a tree
906 (and optionally nodes too) the most recent common ancestor.
908 o nodelabels() has a new option `thermo' to plot proportions (up
909 to three classes) on the nodes of a tree.
911 o rtree() has been improved: it can now generate rooted or
912 unrooted trees, and the mathematical function that generates the
913 branch lengths may be specified by the user. The tip labels may
914 be given directly in the call to rtree. The limit cases (n = 2,
915 3) are now handled correctly.
917 o dist.topo() has a new argument `method' with two choices: "PH85"
918 for Penny and Henny's method (already available before and now
919 the default), and "BHV01" for the geometric distance by Billera
920 et al. (2001, Adv. Appl. Math. 27:733).
922 o write.tree() has a new option, `digits', which specifies the
923 number of digits to be printed in the Newick tree. By default
924 digits = 10. The numbers are now always printed in decimal form
925 (i.e., 1.0e-1 is now avoided).
927 o dist.dna() can now compute the raw distances between pairs of
928 DNA sequences by specifying model = "raw".
930 o dist.phylo() has a new option `full' to possibly compute the
931 distances among all tips and nodes of the tree. The default if
937 o Several bugs were fixed in all.equal.phylo().
939 o dist.dna() did not handle correctly gaps ("-") in alignments:
940 they are now considered as missing data.
942 o rotate() did not work if the tips were not ordered: this is
945 o mantel.test() returned NA in some special cases: this is fixed
946 and the function has been improved and is now faster.
948 o A bug was fixed in diversi.gof() where the calculation of A² was
951 o cherry() did not work correctly under some OSs (mainly Linux):
954 o is.binary.tree() has been modified so that it works with both
955 rooted and unrooted trees.
957 o The documentation of theta.s() was not correct: this has been
960 o plot.mst() did not work correctly: this is fixed.
964 CHANGES IN APE VERSION 1.6
969 o The new function dist.topo() computes the topological distances
972 o The new function boot.phylo() performs a bootstrap analysis on
973 phylogeny estimation.
975 o The new functions prop.part() and prop.clades() analyse
976 bipartitions from a series of trees.
981 o read.GenBank() now uses the EFetch utility of NCBI instead of
982 the usual Web interface: it is now much faster (e.g., 12 times
983 faster to retrieve 8 sequences, 37 times for 60 sequences).
988 o Several bugs were fixed in read.dna().
990 o Several bugs were fixed in diversi.time().
992 o is.binary.tree() did not work correctly if the tree has no edge
993 lengths: this is fixed.
995 o drop.tip() did not correctly propagated the `node.label' of a
1000 CHANGES IN APE VERSION 1.5
1005 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1006 convert objects between the classes "phylo" and "matching". The
1007 latter implements the representation of binary trees introduced by
1008 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1009 as.matching() has been introduced as well.
1011 o Two new functions, multi2di() and di2multi(), allow to resolve
1012 and collapse multichotomies with branches of length zero.
1014 o The new function nuc.div() computes the nucleotide diversity
1015 from a sample a DNA sequences.
1017 o dist.dna() has been completely rewritten with a much faster
1018 (particularly for large data sets) C code. Eight models are
1019 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1020 option `method' has been renamed `model'). Computation of variance
1021 is available for all models. A gamma-correction is possible for
1022 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1023 to remove sites with missing data on a pairwise basis. The option
1024 `GCcontent' has been removed.
1026 o read.GenBank() has a new option (species.names) which specifies
1027 whether to return the species names of the organisms in addition
1028 to the accession numbers of the sequences (this is the default
1031 o write.nexus() can now write several trees in the same NEXUS file.
1033 o drop.tip() has a new option `root.edge' that allows to specify the
1034 new root edge if internal branches are trimmed.
1039 o as.phylo.hclust() failed if some labels had parentheses: this
1042 o Several bugs were fixed in all.equal.phylo(). This function now
1043 returns the logical TRUE if the trees are identical but with
1044 different representations (a report was printed previously).
1046 o read.GenBank() did not correctly handle ambiguous base codes:
1052 o birthdeath() now returns an object of class "birthdeath" for
1053 which there is a print method.
1057 CHANGES IN APE VERSION 1.4
1062 o The new function nj() performs phylogeny estimation with the
1063 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1066 o The new function which.edge() identifies the edges of a tree
1067 that belong to a group specified as a set of tips.
1069 o The new function as.phylo.phylog() converts an object of class
1070 "phylog" (from the package ade4) into an object of class
1073 o The new function axisPhylo() draws axes on the side of a
1076 o The new function howmanytrees() calculates the number of trees
1077 in different cases and giving a number of tips.
1079 o write.tree() has a new option `multi.line' (TRUE by default) to
1080 write a Newick tree on several lines rather than on a single
1083 o The functionalities of zoom() have been extended. Several
1084 subtrees can be visualized at the same time, and they are marked
1085 on the main tree with colors. The context of the subtrees can be
1086 marked with the option `subtree' (see below).
1088 o drop.tip() has a new option `subtree' (FALSE by default) which
1089 specifies whether to output in the tree how many tips have been
1092 o The arguments of add.scale.bar() have been redefined and have
1093 now default values (see ?add.scale.bar for details). This
1094 function now works even if the plotted tree has no edge length.
1096 o plot.phylo() can now plot radial trees, but this does not take
1097 edge lengths into account.
1099 o In plot.phylo() with `type = "phylogram"', if the values of
1100 `edge.color' and `edge.width' are identical for sister-branches,
1101 they are propagated to the vertical line that link them.
1106 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1107 crashing. This is fixed.
1109 o In plot.phylo(), the options `edge.color' and `edge.width' are
1110 now properly recycled; their default values are now "black" and
1113 o A bug has been fixed in write.nexus().
1118 o The function node.depth.edgelength() has been removed and
1119 replaced by a C code.
1123 CHANGES IN APE VERSION 1.3-1
1128 o The new function nodelabels() allows to add labels to the nodes
1129 of a tree using text or plotting symbols in a flexible way.
1131 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1132 numeric values specifying the lower and upper limits on the x-
1133 and y-axes. This allows to leave some space on any side of the
1134 tree. If a single value is given, this is taken as the upper
1139 CHANGES IN APE VERSION 1.3
1144 o The new function phymltest() calls the software PHYML and fits
1145 28 models of DNA sequence evolution. There are a print method to
1146 display likelihood and AIC values, a summary method to compute
1147 the hierarchical likelihood ratio tests, and a plot method to
1148 display graphically the AIC values of each model.
1150 o The new function yule.cov() fits the Yule model with covariates,
1151 a model where the speciation rate is affected by several species
1152 traits through a generalized linear model. The parameters are
1153 estimated by maximum likelihood.
1155 o Three new functions, corBrownian(), corGrafen(), and
1156 corMartins(), compute the expected correlation structures among
1157 species given a phylogeny under different models of evolution.
1158 These can be used for GLS comparative phylogenetic methods (see
1159 the examples). There are coef() and corMatrix() methods and an
1160 Initialize.corPhyl() function associated.
1162 o The new function compar.cheverud() implements Cheverud et al.'s
1163 (1985; Evolution 39:1335) phylogenetic comparative method.
1165 o The new function varcomp() estimates variance components; it has
1168 o Two new functions, panel.superpose.correlogram() and
1169 plot.correlogramList(), allow to plot several phylogenetic
1172 o The new function node.leafnumber() computes the number of leaves
1173 of a subtree defined by a particular node.
1175 o The new function node.sons() gets all tags of son nodes from a
1178 o The new function compute.brlen() computes the branch lengths of
1179 a tree according to a specified method.
1181 o plot.phylo() has three new options: "cex" controls the size of
1182 the (tip and node) labels (thus it is no more needed to change
1183 the global graphical parameter), "direction" which allows to
1184 plot the tree rightwards, leftwards, upwards, or downwards, and
1185 "y.lim" which sets the upper limit on the y-axis.
1190 o Some functions which try to match tip labels and names of
1191 additional data (e.g. vector) are likely to fail if there are
1192 typing or syntax errors. If both series of names do not perfectly
1193 match, they are ignored and a warning message is now issued.
1194 These functions are bd.ext, compar.gee, pic. Their help pages
1195 have been clarified on this point.
1199 CHANGES IN APE VERSION 1.2-7
1204 o The new function root() reroots a phylogenetic tree with respect
1205 to a specified outgroup.
1207 o The new function rotate() rotates an internal branch of a tree.
1209 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1210 trees) controls the display of the tip labels in unrooted trees.
1211 This display has been greatly improved: the tip labels are now not
1212 expected to overlap with the tree (particularly if lab4ut =
1213 "axial"). In all cases, combining appropriate values of "lab4ut"
1214 and the font size (via "par(cex = )") should result in readable
1215 unrooted trees. See ?plot.phylo for some examples.
1217 o In drop.tip(), the argument `tip' can now be numeric or character.
1222 o drop.tip() did not work correctly with trees with no branch
1223 lengths: this is fixed.
1225 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1226 plotted with some line crossings: this is now fixed.
1230 CHANGES IN APE VERSION 1.2-6
1235 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1236 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1237 to implement comparative methods with an autocorrelation approach.
1239 o A new data set describing some life history traits of Carnivores
1245 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1250 o When plotting a tree with plot.phylo(), the new default of the
1251 option `label.offset' is now 0, so the labels are always visible.
1255 CHANGES IN APE VERSION 1.2-5
1260 o The new function bd.ext() fits a birth-death model with combined
1261 phylogenetic and taxonomic data, and estimates the corresponding
1262 speciation and extinction rates.
1267 o The package gee is no more required by ape but only suggested
1268 since only the function compar.gee() calls gee.
1272 CHANGES IN APE VERSION 1.2-4
1277 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1278 and lines.popsize) implementing a new approach for inferring the
1279 demographic history from genealogies using a reversible jump
1280 MCMC have been introduced.
1282 o The unit of time in the skyline plot and in the new plots can
1283 now be chosen to be actual years, rather than substitutions.
1287 CHANGES IN APE VERSION 1.2-3
1292 o The new function rtree() generates a random binary tree with or
1293 without branch lengths.
1295 o Two new functions for drawing lineages-through-time (LTT) plots
1296 are provided: ltt.lines() adds a LTT curve to an existing plot,
1297 and mltt.plot() does a multiple LTT plot giving several trees as
1298 arguments (see `?ltt.plot' for details).
1303 o Some taxon names made R crashing when calling as.phylo.hclust():
1306 o dist.dna() returned an error with two identical DNA sequences
1307 (only using the Jukes-Cantor method returned 0): this is fixed.
1312 o The function dist.phylo() has been re-written using a different
1313 algorithm: it is now about four times faster.
1315 o The code of branching.times() has been improved: it is now about
1320 CHANGES IN APE VERSION 1.2-2
1325 o The new function seg.sites() finds the segregating sites in a
1326 sample of DNA sequences.
1331 o A bug introduced in read.tree() and in read.nexus() with version
1334 o A few errors were corrected and a few examples were added in the
1339 CHANGES IN APE VERSION 1.2-1
1344 o plot.phylo() can now draw the edge of the root of a tree if it
1345 has one (see the new option `root.edge', its default is FALSE).
1350 o A bug was fixed in read.nexus(): files with semicolons inside
1351 comment blocks were not read correctly.
1353 o The behaviour of read.tree() and read.nexus() was corrected so
1354 that tree files with badly represented root edges (e.g., with
1355 an extra pair of parentheses, see the help pages for details)
1356 are now correctly represented in the object of class "phylo";
1357 a warning message is now issued.
1361 CHANGES IN APE VERSION 1.2
1366 o plot.phylo() has been completely re-written and offers several
1367 new functionalities. Three types of trees can now be drawn:
1368 phylogram (as previously), cladogram, and unrooted tree; in
1369 all three types the branch lengths can be drawn using the edge
1370 lengths of the phylogeny or not (e.g., if the latter is absent).
1371 The vertical position of the nodes can be adjusted with two
1372 choices (see option `node.pos'). The code has been re-structured,
1373 and two new functions (potentially useful for developpers) are
1374 documented separately: node.depth.edgelength() and node.depth();
1375 see the respective help pages for details.
1377 o The new function zoom() allows to explore very large trees by
1378 focusing on a small portion of it.
1380 o The new function yule() fits by maximum likelihood the Yule model
1381 (birth-only process) to a phylogenetic tree.
1383 o Support for writing DNA sequences in FASTA format has been
1384 introduced in write.dna() (support for reading sequences in
1385 this format was introduced in read.dna() in version 1.1-2).
1386 The function has been completely re-written, fixing some bugs
1387 (see below); the default behaviour is no more to display the
1388 sequences on the standard output. Several options have been
1389 introduced to control the sequence printing in a flexible
1390 way. The help page has been extended.
1392 o A new data set is included: a supertree of bats in NEXUS format.
1397 o In theta.s(), the default of the option `variance' has
1398 been changed to `FALSE' (as was indicated in the help page).
1400 o Several bugs were fixed in the code of all.equal.phylo().
1402 o Several bugs were fixed in write.dna(), particularly this
1403 function did not work with `format = "interleaved"'.
1405 o Various errors were corrected in the help pages.
1410 o The argument names of as.hclust.phylo() have been changed
1411 from "(phy)" to "(x, ...)" to conform to the definition of
1412 the corresponding generic function.
1414 o gamma.stat() has been renamed gammaStat() to avoid confusion
1415 since gamma() is a generic function.
1419 CHANGES IN APE VERSION 1.1-3
1424 o base.freq() previously did not return a value of 0 for
1425 bases absent in the data (e.g., a vector of length 3 was
1426 returned if one base was absent). This is now fixed (a
1427 vector of length 4 is always returned).
1429 o Several bugs were fixed in read.nexus(), including that this
1430 function did not work in this absence of a "TRANSLATE"
1431 command in the NEXUS file, and that the commands were
1436 CHANGES IN APE VERSION 1.1-2
1441 o The Tamura and Nei (1993) model of DNA distance is now implemented
1442 in dist.dna(): five models are now available in this function.
1444 o A new data set is included: a set of 15 sequences of the
1445 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1451 o A bug in read.nexus() was fixed.
1453 o read.dna() previously did not work correctly in most cases.
1454 The function has been completely re-written and its help page
1455 has been considerably extended (see ?read.dna for details).
1456 Underscores (_) in taxon names are no more replaced with
1457 spaces (this behaviour was undocumented).
1459 o A bug was fixed in write.dna().
1463 CHANGES IN APE VERSION 1.1-1
1468 o A bug in read.tree() introduced in APE 1.1 was fixed.
1470 o A bug in compar.gee() resulted in an error when trying to fit
1471 a model with `family = "binomial"'. This is now fixed.
1475 CHANGES IN APE VERSION 1.1
1480 o The Klastorin (1982) method as suggested by Misawa and Tajima
1481 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1482 on the basis of phylogenetic trees has been implemented (see
1483 the function klastorin()).
1485 o Functions have been added to convert APE's "phylo" objects in
1486 "hclust" cluster objects and vice versa (see the help page of
1487 as.phylo for details).
1489 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1490 are introduced for the estimation of absolute evolutionary rates
1491 (ratogram) and dated clock-like trees (chronogram) from
1492 phylogenetic trees using the non-parametric rate smoothing approach
1493 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1495 o A summary method is now provided printing a summary information on a
1496 phylogenetic tree with, for instance, `summary(tree)'.
1498 o The behaviour of read.tree() was changed so that all spaces and
1499 tabulations in tree files are now ignored. Consequently, spaces in tip
1500 labels are no more allowed. Another side effect is that read.nexus()
1501 now does not replace the underscores (_) in tip labels with spaces
1502 (this behaviour was undocumented).
1504 o The function plot.phylo() has a new option (`underscore') which
1505 specifies whether the underscores in tip labels should be written on
1506 the plot as such or replaced with spaces (the default).
1508 o The function birthdeath() now computes 95% confidence intervals of
1509 the estimated parameters using profile likelihood.
1511 o Three new data sets are included: a gene tree estimated from 36
1512 landplant rbcL sequences, a gene tree estimated from 32 opsin
1513 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1518 o A bug was fixed in dist.gene() where nothing was returned.
1520 o A bug in plot.mst() was fixed.
1522 o A bug in vcv.phylo() resulted in false correlations when the
1523 option `cor = TRUE' was used (now fixed).
1527 CHANGES IN APE VERSION 1.0
1532 o Two new functions, read.dna() and write.dna(), read/write in a file
1533 DNA sequences in interleaved or in sequential format.
1535 o Two new functions, read.nexus() and write.nexus(), read/write trees
1538 o The new function bind.tree() allows to bind two trees together,
1539 possibly handling root edges to give internal branches.
1541 o The new function drop.tip() removes the tips in a phylogenetic tree,
1542 and trims (or not) the corresponding internal branches.
1544 o The new function is.ultrametric() tests if a tree is ultrametric.
1546 o The function plot.phylo() has more functionalities such as drawing the
1547 branches with different colours and/or different widths, showing the
1548 node labels, controling the position and font of the labels, rotating
1549 the labels, and controling the space around the plot.
1551 o The function read.tree() can now read trees with no branch length,
1552 such as "(a,b),c);". Consequently, the element `edge.length' in
1553 objects of class "phylo" is now optional.
1555 o The function write.tree() has a new default behaviour: if the default
1556 for the option `file' is used (i.e. file = ""), then a variable of
1557 mode character containing the tree in Newick format is returned which
1558 can thus be assigned (e.g., tree <- write.tree(phy)).
1560 o The function read.tree() has a new argument `text' which allows
1561 to read the tree in a variable of mode character.
1563 o A new data set is included: the phylogenetic relationships among
1564 the orders of birds from Sibley and Ahlquist (1990).
1568 CHANGES IN APE VERSION 0.2-1
1573 o Several bugs were fixed in the help pages.
1577 CHANGES IN APE VERSION 0.2
1582 o The function write.tree() writes phylogenetic trees (objects of class
1583 "phylo") in an ASCII file using the Newick parenthetic format.
1585 o The function birthdeath() fits a birth-death model to branching times
1586 by maximum likelihood, and estimates the corresponding speciation and
1589 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1592 o The function is.binary.tree() tests whether a phylogeny is binary.
1594 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1595 as well as some methods are introduced.
1597 o Several functions, including some generics and methods, for computing
1598 skyline plot estimates (classic and generalized) of effective
1599 population size through time are introduced and replace the function
1600 skyline.plot() in version 0.1.
1602 o Two data sets are now included: the phylogenetic relationships among
1603 the families of birds from Sibley and Ahlquist (1990), and an
1604 estimated clock-like phylogeny of HIV sequences sampled in the
1605 Democratic Republic of Congo.
1608 DEPRECATED & DEFUNCT
1610 o The function skyline.plot() in ape 0.1 has been deprecated and
1611 replaced by more elaborate functions (see above).
1616 o Two important bugs were fixed in plot.phylo(): phylogenies with
1617 multichotomies not at the root or not with only terminal branches,
1618 and phylogenies with a single node (i.e. only terminal branches)
1619 did not plot. These trees should be plotted correctly now.
1621 o Several bugs were fixed in diversi.time() in the computation of
1624 o Various errors were corrected in the help pages.