1 CHANGES IN APE VERSION 2.2-2
6 o dist.gene() has been substantially improved and gains an option
12 o prop.part() failed with a single tree with the default option
13 'check.labels = TRUE'.
15 o summary.DNAbin() failed to display correctly the summary of
16 sequence lengths with lists of sequences of 10,000 bases or more
17 (because summary.default uses 4 significant digits by default).
19 o read.nexus() failed to read a file with a single tree with line
20 breaks in the Newick string.
25 o The data sets bird.orders and bird.families are now stored as
26 Newick strings; i.e., the command data(bird.orders) calls
31 CHANGES IN APE VERSION 2.2-1
36 o The new function makeLabel() helps to modify labels of trees,
37 lists of trees, or DNA sequences, with several utilities to
38 truncate and/or make them unique, substituting some
39 characters, and so on.
41 o The new function del.gaps() removes insertion gaps ("-") in a
44 o read.dna() can now read Clustal files (*.aln).
49 o root() failed with 'resolve.root = TRUE' when the root was
50 already the specified root.
52 o Several bugs were fixed in mlphylo().
54 o collapsed.singles() did not propagate the 'Nnode' and
55 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
57 o read.nexus() failed to remove correctly the comments within
60 o read.nexus() failed to read a file with a single tree and no
61 translation of tip labels.
63 o read.nexus() failed to place correctly tip labels when reading
64 a single tree with no edge lengths.
66 o A bug was fixed in sh.test().
71 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
74 o The option 'check.labels' of consensus() and prop.part() is now
77 o write.dna() now does not truncate names to 10 characters with
82 CHANGES IN APE VERSION 2.2
87 o Four new functions have been written by Damien de Vienne for the
88 graphical exploration of large trees (cophyloplot, subtrees,
89 subtreeplot), and to return the graphical coordinates of tree
92 o The new functions corPagel and corBlomberg implement the Pagel's
93 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
95 o chronopl() has been improved and gains several options: see its
96 help page for details.
98 o boot.phylo() has now an option 'trees' to possibly return the
99 bootstraped trees (the default is FALSE).
101 o prop.part() has been improved and should now be faster in all
107 o read.dna() failed if "?" occurred in the first 10 sites of the
110 o The x/y aspect of the plot is now respected when plotting a
111 circular tree (type = "r" or "f").
113 o Drawing the tip labels sometimes failed when plotting circular
116 o zoom() failed when tip labels were used instead of their numbers
117 (thanks to Yan Wong for the fix).
119 o drop.tip() failed with some trees (fixed by Yan Wong).
121 o seg.sites() failed with a list.
123 o consensus() failed in some cases. The function has been improved
124 as well and is faster.
128 CHANGES IN APE VERSION 2.1-3
133 o A bug in read.nexus() made the Windows R-GUI crash.
135 o An error was fixed in the computation of ancestral character
136 states by generalized least squares in ace().
138 o di2multi() did not modify node labels correctly.
140 o multi2di() failed if the tree had its attribute "order" set to
145 CHANGES IN APE VERSION 2.1-2
150 o There three new methods for the "multiPhylo" class: str, $,
153 o root() gains the options 'node' and 'resolve.root'
154 (FALSE by default) as well as its code being improved.
156 o mltt.plot() has now an option 'log' used in the same way
157 than in plot.default().
162 o mltt.plot() failed to display the legend with an unnamed
165 o nodelabels() with pies now correcly uses the argument
166 'cex' to draw symbols of different sizes (which has
167 worked already for thermometers).
169 o read.nexus() generally failed to read very big files.
174 o The argument 'family' of compar.gee() can now be a function
175 as well as a character string.
177 o read.tree() and read.nexus() now return an unnamed list if
180 o read.nexus() now returns a modified object of class "multiPhylo"
181 when there is a TRANSLATE block in the NEXUS file: the individual
182 trees have no 'tip.label' vector, but the list has a 'TipLabel'
183 attribute. The new methods '$' and '[[' set these elements
184 correctly when extracting trees.
188 CHANGES IN APE VERSION 2.1-1
193 o The new function rmtree generates lists of random trees.
195 o rcoal() now generates a genuine coalescent tree by default
196 (thanks to Vladimir Minin for the code).
201 o nuc.div() returned an incorrect value with the default
202 pairwise.deletion = FALSE.
207 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
208 have been improved so that they are stabler and faster.
210 o R packages used by ape are now loaded silently; lattice and gee
211 are loaded only when needed.
215 CHANGES IN APE VERSION 2.1
220 o The new function identify.phylo identifies clades on a plotted
221 tree using the mouse.
223 o It is now possible to subset a list of trees (object of class
224 "multiPhylo") with "[" while keeping its class correct.
226 o The new function as.DNAbin.alignment converts DNA sequences
227 stored in the "alignment" format of the package seqinr into
228 an object of class "DNAbin".
230 o The new function weight.taxo2 helps to build similarity matrices
231 given two taxonomic levels (usually called by other functions).
233 o write.tree() can now take a list of trees (class "multiPhylo")
234 as its main argument.
236 o plot.correlogram() and plot.correlogramList() have been
237 improved, and gain several options (see the help page for
238 details). A legend is now plotted by default.
243 o dist.dna() returned some incorrect values with `model = "JC69"'
244 and `pairwise.deletion = TRUE'. This affected only the
245 distances involving sequences with missing values. (Thanks
246 to Bruno Toupance for digging this bug out.)
248 o write.tree() failed with some trees: this is fixed by removing
249 the `multi.line' option (trees are now always printed on a
252 o read.nexus() did not correctly detect trees with multiple root
253 edges (see OTHER CHANGES).
258 o The code of mlphylo() has been almost entirely rewritten, and
259 should be much stabler. The options have been also greatly
260 simplified (see ?mlphylo and ?DNAmodel for details).
262 o The internal function nTips has been renamed klastorin_nTips.
264 o The code of is.ultrametric() contained redundancies and has
267 o The code of Moran.I() and of correlogram.formula() have been
270 o read.tree() and read.nexus() now return an error when trying to
271 read a tree with multiple root edges (see BUG FIXES). The
272 correction applied in previous version did not work in all
275 o The class c("multi.tree", "phylo") has been renamed
281 o There is now a vignette in ape: see vignette("MoranI", "ape").
286 o as.matching() and as.phylo.matching() do not support branch
289 o correlogram.phylo() and discrete.dist() have been removed.
293 CHANGES IN APE VERSION 2.0-2
298 o The new function matexpo computes the exponential of a square
301 o The new function unique.multi.tree removes duplicate trees from
304 o yule() has a new option `use.root.edge = FALSE' that specifies
305 to ignore, by default, the root edge of the tree if it exists.
310 o which.edge() failed when the index of a single terminal edge was
313 o In diversi.time(), the values returned for model C were
316 o A bug was fixed in yule() that affected the calculation of the
317 likelihood in the presence of ties in the branching times.
319 o There was a bug in the C function mat_expo4x4 affecting the
320 calculations of the transition probabilities for models HKY and
323 o A small bug was fixed in as.matrix.DNAbin (thanks to James
326 o rtree() did not `shuffle' the tip labels by default, so only a
327 limited number of labelled topologies could be generated.
331 CHANGES IN APE VERSION 2.0-1
336 o The three new functions bionj, fastme.ols, and fastme.bal
337 perform phylogeny estimation by the BIONJ and fastME methods in
338 OLS and balanced versions. This is a port to R of previous
339 previous programs done by Vincent Lefort.
341 o The new function chronoMPL performs molecular dating with the
342 mean path lengths method of Britton et al. (2002, Mol. Phyl.
345 o The new function rotate, contributed by Christoph Heibl, swaps
346 two clades connected to the same node. It works also with
347 multichotomous nodes.
349 o The new `method' as.matrix.DNAbin() may be used to convert
350 easily DNA sequences stored in a list into a matrix while
351 keeping the names and the class.
356 o chronopl() failed when some branch lengths were equal to zero:
357 an error message is now returned.
359 o di2multi() failed when there was a series of consecutive edges
364 CHANGES IN APE VERSION 1.10-2
369 o plot.phylo() can now plot circular trees: the option is type =
370 "fan" or type = "f" (to avoid the ambiguity with type = "c").
372 o prop.part() has a new option `check.labels = FALSE' which allows
373 to considerably speed-up the calculations of bipartitions. As a
374 consequence, calculations of bootstrap values with boot.phylo()
375 should be much faster.
380 o read.GenBank() did not return correctly the list of species as
381 from ape 1.10: this is fixed in this version
383 o Applying as.phylo() on a tree of class "phylo" failed: the
384 object is now returned unchanged.
388 CHANGES IN APE VERSION 1.10-1
393 o The three new functions Ntip, Nnode, and Nedge return, for a
394 given tree, the number of tips, nodes, or edges, respectively.
399 o read.nexus() did not set correctly the class of the returned
400 object when reading multiple trees.
402 o mllt.plot() failed with objects of class c("multi.tree",
405 o unroot() did not work correctly in most cases.
407 o reorder.phylo() made R freeze in some occasions.
409 o Plotting a tree in pruningwise order failed.
411 o When plotting an unrooted tree, the tip labels where not all
412 correctly positioned if the option `cex' was used.
416 CHANGES IN APE VERSION 1.10
421 o Five new `method' functions have been introduced to manipulate
422 DNA sequences in binary format (see below).
424 o Three new functions have been introduced to convert between the
425 new binary and the character formats.
427 o The new function as.alignment converts DNA sequences stored as
428 single characters into the class "alignment" used by the package
431 o read.dna() and read.GenBank() have a new argument `as.character'
432 controlling whether the sequences are returned in binary format
438 o root() failed when the tree had node labels: this is fixed.
440 o plot.phylo() did not correctly set the limits on the y-axis with
441 the default setting: this is fixed.
443 o dist.dna() returned a wrong result for the LogDet, paralinear,
444 and BH87 models with `pairwise.deletion = TRUE'.
449 o DNA sequences are now internally stored in a binary format. See
450 the document "A Bit-Level Coding Scheme for Nucleotides" for the
451 details. Most functions analyzing DNA functions have been
452 modified accordingly and are now much faster (dist.dna is now
453 ca. 60 times faster).
457 CHANGES IN APE VERSION 1.9-4
462 o A bug was fixed in edgelabels().
464 o as.phylo.hclust() did not work correctly when the object of
465 class "hclust" has its labels set to NULL: the returned tree has
466 now its tip labels set to "1", "2", ...
468 o consensus could fail if some tip labels are a subset of others
469 (e.g., "a" and "a_1"): this is now fixed.
471 o mlphylo() failed in most cases if some branch lengths of the
472 initial tree were greater than one: an error message is now
475 o mlphylo() failed in most cases when estimating the proportion of
476 invariants: this is fixed.
480 CHANGES IN APE VERSION 1.9-3
485 o The new function edgelabels adds labels on the edge of the tree
486 in the same way than nodelabels or tiplabels.
491 o multi2di() did not handle correctly branch lengths with the
492 default option `random = TRUE': this is now fixed.
494 o A bug was fixed in nuc.div() when using pairwise deletions.
496 o A bug occurred in the analysis of bipartitions with large
497 numbers of large trees, with consequences on prop.part,
498 prop.clades, and boot.phylo.
500 o The calculation of the Billera-Holmes-Vogtmann distance in
501 dist.topo was wrong: this has been fixed.
505 CHANGES IN APE VERSION 1.9-2
510 o The new function ladderize reorganizes the internal structure of
511 a tree to plot them left- or right-ladderized.
513 o The new function dist.nodes computes the patristic distances
514 between all nodes, internal and terminal, of a tree. It replaces
515 the option `full = TRUE' of cophenetic.phylo (see below).
520 o A bug was fixed in old2new.phylo().
522 o Some bugs were fixed in chronopl().
524 o The edge colours were not correctly displayed by plot.phylo
525 (thank you to Li-San Wang for the fix).
527 o cophenetic.phylo() failed with multichotomous trees: this is
533 o read.dna() now returns the sequences in a matrix if they are
534 aligned (interleaved or sequential format). Sequences in FASTA
535 format are still returned in a list.
537 o The option `full' of cophenetic.phylo() has been removed because
538 it could not be used from the generic.
543 o rotate() has been removed; this function did not work correctly
548 CHANGES IN APE VERSION 1.9-1
553 o Trees with a single tip were not read correctly in R as the
554 element `Nnode' was not set: this is fixed.
556 o unroot() did not set correctly the number of nodes of the
557 unrooted tree in most cases.
559 o read.GenBank() failed when fetching very long sequences,
560 particularly of the BX-series.
562 o A bug was introduced in read.tree() with ape 1.9: it has been
567 CHANGES IN APE VERSION 1.9
572 o There are two new print `methods' for trees of class "phylo" and
573 lists of trees of class "multi.tree", so that they are now
574 displayed in a compact and informative way.
576 o There are two new functions, old2new.phylo and new2old.phylo,
577 for converting between the old and new coding of the class
580 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
581 LogDet ("logdet"), and paralinear ("paralin").
583 o compute.brlen() has been extended: several methods are now
584 available to compute branch lengths.
586 o write.dna() can now handle matrices as well as lists.
591 o cophenetic.phylo() sometimes returned a wrong result with
592 multichotomous trees: this is fixed.
594 o rotate() failed when a single tip was specified: the tree is now
597 o ace() did not return the correct index matrix with custom
598 models: this is fixed.
600 o multi2di() did not work correctly when resolving multichotomies
601 randomly: the topology was always the same, only the arrangement
602 of clades was randomized: this is fixed. This function now
603 accepts trees with no branch lengths.
605 o The output of diversi.gof() was blurred by useless prints when a
606 user distribution was specified. This has been corrected, and
607 the help page of this function has been expanded.
612 o The internal structure of the class "phylo" has been changed:
613 see the document "Definition of Formats for Coding Phylogenetic
614 Trees in R" for the details. In addition, the code of most
615 functions has been improved.
617 o Several functions have been improved by replacing some R codes
618 by C codes: pic, plot.phylo, and reorder.phylo.
620 o There is now a citation information: see citation("ape") in R.
622 o write.tree() now does not add extra 0's to branch lengths so
623 that 1.23 is printed "1.23" by default, not "1.2300000000".
625 o The syntax of bind.tree() has been simplified. This function now
626 accepts trees with no branch lengths, and handles correctly node
629 o The option `as.numeric' of mrca() has been removed.
631 o The unused options `format' and `rooted' of read.tree() have
634 o The unused option `format' of write.tree() has been removed.
636 o The use of node.depth() has been simplified.
640 CHANGES IN APE VERSION 1.8-5
645 o Two new functions read.nexus.data() and write.nexus.data(),
646 contributed by Johan Nylander, allow to read and write molecular
647 sequences in NEXUS files.
649 o The new function reorder.phylo() reorders the internal structure
650 of a tree of class "phylo". It is used as the generic, e.g.,
653 o read.tree() and read.nexus() can now read trees with a single
656 o The new data set `cynipids' supplies a set of protein sequences
662 o The code of all.equal.phylo() has been completely rewritten
663 (thanks to Benoît Durand) which fixes several bugs.
665 o read.tree() and read.nexus() now checks the labels of the tree
666 to remove or substitute any characters that are illegal in the
667 Newick format (parentheses, etc.)
669 o A negative P-value could be returned by mantel.test(): this is
674 CHANGES IN APE VERSION 1.8-4
679 o The new function sh.test() computes the Shimodaira-
682 o The new function collapse.singles() removes the nodes with a
683 single descendant from a tree.
685 o plot.phylo() has a new argument `tip.color' to specify the
688 o mlphylo() has now an option `quiet' to control the display of
689 the progress of the analysis (the default is FALSE).
694 o read.dna() did not read correctly sequences in sequential format
695 with leading alignment gaps "-": this is fixed.
697 o ace() returned a list with no class so that the generic
698 functions (anova, logLik, ...) could not be used directly. This
699 is fixed as ace() now returns an object of class "ace".
701 o anova.ace() had a small bug when computing the number of degrees
702 of freedom: this is fixed.
704 o mlphylo() did not work when the sequences were in a matrix or
705 a data frame: this is fixed.
707 o rtree() did not work correctly when trying to simulate an
708 unrooted tree with two tips: an error message is now issued.
713 o The algorithm of rtree() has been changed: it is now about 40,
714 100, and 130 times faster for 10, 100, and 1000 tips,
719 CHANGES IN APE VERSION 1.8-3
724 o There are four new `method' functions to be used with the
725 results of ace(): logLik(), deviance(), AIC(), and anova().
727 o The plot method of phymltest has two new arguments: `main' to
728 change the title, and `col' to control the colour of the
729 segments showing the AIC values.
731 o ace() has a new argument `ip' that gives the initial values used
732 in the ML estimation with discrete characters (see the examples
733 in ?ace). This function now returns a matrix giving the indices
734 of the estimated rates when analysing discrete characters.
736 o nodelabels() and tiplabels() have a new argument `pie' to
737 represent proportions, with any number of categories, as
738 piecharts. The use of the option `thermo' has been improved:
739 there is now no limitation on the number of categories.
744 o mlphylo() did not work with more than two partitions: this is
747 o root() failed if the proposed outgroup was already an outgroup
748 in the tree: this is fixed.
750 o The `col' argument in nodelabels() and tiplabels() was not
751 correctly passed when `text' was used: this is fixed.
753 o Two bugs were fixed in mlphylo(): parameters were not always
754 correctly output, and the estimation failed in some cases.
756 o plot.phylo() was stuck when given a tree with a single tip: this
757 is fixed and a message error is now returned.
759 o An error was corrected in the help page of gammaStat regarding
760 the calculation of P-values.
762 o Using gls() could crash R when the number of species in the tree
763 and in the variables were different: this is fixed.
767 CHANGES IN APE VERSION 1.8-2
772 o The new function mlphylo() fits a phylogenetic tree by maximum
773 likelihood from DNA sequences. Its companion function DNAmodel()
774 is used to define the substitution model which may include
775 partitioning. There are methods for logLik(), deviance(), and
776 AIC(), and the summary() method has been extended to display in
777 a friendly way the results of this model fitting. Currently, the
778 functionality is limited to estimating the substitution and
779 associated parameters and computing the likelihood.
781 o The new function drop1.compar.gee (used as, e.g., drop1(m))
782 tests for single effects in GEE-based comparative method. A
783 warning message is printed if there is not enough degrees of
789 o An error message was sometimes issued by plot.multi.tree(),
790 though with no consequence.
794 CHANGES IN APE VERSION 1.8-1
799 o There is a new plot method for lists of trees (objects of class
800 "multi.tree"): it calls plot.phylo() internally and is
801 documented on the same help page.
806 o A bug was fixed in the C code that analyzes bipartitions: this
807 has impact on several functions like prop.part, prop.clades,
808 boot.phylo, or consensus.
810 o root() did not work correctly when the specified outgroup had
811 more than one element: this is fixed.
813 o dist.dna() sometimes returned a warning inappropriately: this
816 o If the distance object given to nj() had no rownames, nj()
817 returned a tree with no tip labels: it now returns tips labelled
818 "1", "2", ..., corresponding to the row numbers.
823 o nj() has been slightly changed so that tips with a zero distance
824 are first aggregated with zero-lengthed branches; the usual NJ
825 procedure is then performed on a distance matrix without 0's.
829 CHANGES IN APE VERSION 1.8
834 o The new function chronopl() estimates dates using the penalized
835 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
837 o The new function consensus() calculates the consensus tree of a
840 o The new function evolve.phylo() simulates the evolution of
841 continuous characters along a phylogeny under a Brownian model.
843 o The new plot method for objects of class "ancestral" displays a
844 tree together with ancestral values, as returned by the above
847 o The new function as.phylo.formula() returns a phylogeny from a
848 set of nested taxonomic variables given as a formula.
850 o The new function read.caic() reads trees in CAIC format.
852 o The new function tiplabels() allows to add labels to the tips
853 of a tree using text or plotting symbols in a flexible way.
855 o The new function unroot() unroots a phylogeny.
857 o multi2di() has a new option, `random', which specifies whether
858 to resolve the multichotomies randomly (the default) or not.
860 o prop.part() now returns an object of class "prop.part" for which
861 there are print (to display a partition in a more friendly way)
862 and summary (to extract the numbers) methods.
864 o plot.phylo() has a new option, `show.tip.label', specifying
865 whether to print the labels of the tips. The default is TRUE.
867 o The code of nj() has been replaced by a faster C code: it is now
868 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
871 o write.nexus() now writes whether a tree is rooted or not.
876 o Two bugs have been fixed in root(): unrooted trees are now
877 handled corretly, and node labels are now output normally.
879 o A bug was fixed in phymltest(): the executable couldn't be found
882 o Three bug have been fixed in ace(): computing the likelihood of
883 ancestral states of discrete characters failed, custom models
884 did not work, and the function failed with a null gradient (a
885 warning message is now returned; this latter bug was also
886 present in yule.cov() as well and is now fixed).
888 o pic() hanged out when missing data were present: a message error
891 o A small bug was fixed in dist.dna() where the gamma correction
892 was not always correctly dispatched.
894 o plot.phylo() plotted correctly the root edge only when the tree
895 was plotted rightwards: this works now for all directions.
900 o dist.taxo() has been renamed as weight.taxo().
902 o Various error and warning messages have been improved.
906 CHANGES IN APE VERSION 1.7
909 o The new function ace() estimates ancestral character states for
910 continuous characters (with ML, GLS, and contrasts methods), and
911 discrete characters (with ML only) for any number of states.
913 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
914 of directional evolution for continuous characters. The user
915 specifies the node(s) of the tree where the character optimum
918 o The new function is.rooted() tests whether a tree (of class
921 o The new function rcoal() generates random ultrametric trees with
922 the possibility to specify the function that generates the
923 inter-nodes distances.
925 o The new function mrca() gives for all pairs of tips in a tree
926 (and optionally nodes too) the most recent common ancestor.
928 o nodelabels() has a new option `thermo' to plot proportions (up
929 to three classes) on the nodes of a tree.
931 o rtree() has been improved: it can now generate rooted or
932 unrooted trees, and the mathematical function that generates the
933 branch lengths may be specified by the user. The tip labels may
934 be given directly in the call to rtree. The limit cases (n = 2,
935 3) are now handled correctly.
937 o dist.topo() has a new argument `method' with two choices: "PH85"
938 for Penny and Henny's method (already available before and now
939 the default), and "BHV01" for the geometric distance by Billera
940 et al. (2001, Adv. Appl. Math. 27:733).
942 o write.tree() has a new option, `digits', which specifies the
943 number of digits to be printed in the Newick tree. By default
944 digits = 10. The numbers are now always printed in decimal form
945 (i.e., 1.0e-1 is now avoided).
947 o dist.dna() can now compute the raw distances between pairs of
948 DNA sequences by specifying model = "raw".
950 o dist.phylo() has a new option `full' to possibly compute the
951 distances among all tips and nodes of the tree. The default if
957 o Several bugs were fixed in all.equal.phylo().
959 o dist.dna() did not handle correctly gaps ("-") in alignments:
960 they are now considered as missing data.
962 o rotate() did not work if the tips were not ordered: this is
965 o mantel.test() returned NA in some special cases: this is fixed
966 and the function has been improved and is now faster.
968 o A bug was fixed in diversi.gof() where the calculation of A² was
971 o cherry() did not work correctly under some OSs (mainly Linux):
974 o is.binary.tree() has been modified so that it works with both
975 rooted and unrooted trees.
977 o The documentation of theta.s() was not correct: this has been
980 o plot.mst() did not work correctly: this is fixed.
984 CHANGES IN APE VERSION 1.6
989 o The new function dist.topo() computes the topological distances
992 o The new function boot.phylo() performs a bootstrap analysis on
993 phylogeny estimation.
995 o The new functions prop.part() and prop.clades() analyse
996 bipartitions from a series of trees.
1001 o read.GenBank() now uses the EFetch utility of NCBI instead of
1002 the usual Web interface: it is now much faster (e.g., 12 times
1003 faster to retrieve 8 sequences, 37 times for 60 sequences).
1008 o Several bugs were fixed in read.dna().
1010 o Several bugs were fixed in diversi.time().
1012 o is.binary.tree() did not work correctly if the tree has no edge
1013 lengths: this is fixed.
1015 o drop.tip() did not correctly propagated the `node.label' of a
1016 tree: this is fixed.
1020 CHANGES IN APE VERSION 1.5
1025 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1026 convert objects between the classes "phylo" and "matching". The
1027 latter implements the representation of binary trees introduced by
1028 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1029 as.matching() has been introduced as well.
1031 o Two new functions, multi2di() and di2multi(), allow to resolve
1032 and collapse multichotomies with branches of length zero.
1034 o The new function nuc.div() computes the nucleotide diversity
1035 from a sample a DNA sequences.
1037 o dist.dna() has been completely rewritten with a much faster
1038 (particularly for large data sets) C code. Eight models are
1039 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1040 option `method' has been renamed `model'). Computation of variance
1041 is available for all models. A gamma-correction is possible for
1042 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1043 to remove sites with missing data on a pairwise basis. The option
1044 `GCcontent' has been removed.
1046 o read.GenBank() has a new option (species.names) which specifies
1047 whether to return the species names of the organisms in addition
1048 to the accession numbers of the sequences (this is the default
1051 o write.nexus() can now write several trees in the same NEXUS file.
1053 o drop.tip() has a new option `root.edge' that allows to specify the
1054 new root edge if internal branches are trimmed.
1059 o as.phylo.hclust() failed if some labels had parentheses: this
1062 o Several bugs were fixed in all.equal.phylo(). This function now
1063 returns the logical TRUE if the trees are identical but with
1064 different representations (a report was printed previously).
1066 o read.GenBank() did not correctly handle ambiguous base codes:
1072 o birthdeath() now returns an object of class "birthdeath" for
1073 which there is a print method.
1077 CHANGES IN APE VERSION 1.4
1082 o The new function nj() performs phylogeny estimation with the
1083 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1086 o The new function which.edge() identifies the edges of a tree
1087 that belong to a group specified as a set of tips.
1089 o The new function as.phylo.phylog() converts an object of class
1090 "phylog" (from the package ade4) into an object of class
1093 o The new function axisPhylo() draws axes on the side of a
1096 o The new function howmanytrees() calculates the number of trees
1097 in different cases and giving a number of tips.
1099 o write.tree() has a new option `multi.line' (TRUE by default) to
1100 write a Newick tree on several lines rather than on a single
1103 o The functionalities of zoom() have been extended. Several
1104 subtrees can be visualized at the same time, and they are marked
1105 on the main tree with colors. The context of the subtrees can be
1106 marked with the option `subtree' (see below).
1108 o drop.tip() has a new option `subtree' (FALSE by default) which
1109 specifies whether to output in the tree how many tips have been
1112 o The arguments of add.scale.bar() have been redefined and have
1113 now default values (see ?add.scale.bar for details). This
1114 function now works even if the plotted tree has no edge length.
1116 o plot.phylo() can now plot radial trees, but this does not take
1117 edge lengths into account.
1119 o In plot.phylo() with `type = "phylogram"', if the values of
1120 `edge.color' and `edge.width' are identical for sister-branches,
1121 they are propagated to the vertical line that link them.
1126 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1127 crashing. This is fixed.
1129 o In plot.phylo(), the options `edge.color' and `edge.width' are
1130 now properly recycled; their default values are now "black" and
1133 o A bug has been fixed in write.nexus().
1138 o The function node.depth.edgelength() has been removed and
1139 replaced by a C code.
1143 CHANGES IN APE VERSION 1.3-1
1148 o The new function nodelabels() allows to add labels to the nodes
1149 of a tree using text or plotting symbols in a flexible way.
1151 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1152 numeric values specifying the lower and upper limits on the x-
1153 and y-axes. This allows to leave some space on any side of the
1154 tree. If a single value is given, this is taken as the upper
1159 CHANGES IN APE VERSION 1.3
1164 o The new function phymltest() calls the software PHYML and fits
1165 28 models of DNA sequence evolution. There are a print method to
1166 display likelihood and AIC values, a summary method to compute
1167 the hierarchical likelihood ratio tests, and a plot method to
1168 display graphically the AIC values of each model.
1170 o The new function yule.cov() fits the Yule model with covariates,
1171 a model where the speciation rate is affected by several species
1172 traits through a generalized linear model. The parameters are
1173 estimated by maximum likelihood.
1175 o Three new functions, corBrownian(), corGrafen(), and
1176 corMartins(), compute the expected correlation structures among
1177 species given a phylogeny under different models of evolution.
1178 These can be used for GLS comparative phylogenetic methods (see
1179 the examples). There are coef() and corMatrix() methods and an
1180 Initialize.corPhyl() function associated.
1182 o The new function compar.cheverud() implements Cheverud et al.'s
1183 (1985; Evolution 39:1335) phylogenetic comparative method.
1185 o The new function varcomp() estimates variance components; it has
1188 o Two new functions, panel.superpose.correlogram() and
1189 plot.correlogramList(), allow to plot several phylogenetic
1192 o The new function node.leafnumber() computes the number of leaves
1193 of a subtree defined by a particular node.
1195 o The new function node.sons() gets all tags of son nodes from a
1198 o The new function compute.brlen() computes the branch lengths of
1199 a tree according to a specified method.
1201 o plot.phylo() has three new options: "cex" controls the size of
1202 the (tip and node) labels (thus it is no more needed to change
1203 the global graphical parameter), "direction" which allows to
1204 plot the tree rightwards, leftwards, upwards, or downwards, and
1205 "y.lim" which sets the upper limit on the y-axis.
1210 o Some functions which try to match tip labels and names of
1211 additional data (e.g. vector) are likely to fail if there are
1212 typing or syntax errors. If both series of names do not perfectly
1213 match, they are ignored and a warning message is now issued.
1214 These functions are bd.ext, compar.gee, pic. Their help pages
1215 have been clarified on this point.
1219 CHANGES IN APE VERSION 1.2-7
1224 o The new function root() reroots a phylogenetic tree with respect
1225 to a specified outgroup.
1227 o The new function rotate() rotates an internal branch of a tree.
1229 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1230 trees) controls the display of the tip labels in unrooted trees.
1231 This display has been greatly improved: the tip labels are now not
1232 expected to overlap with the tree (particularly if lab4ut =
1233 "axial"). In all cases, combining appropriate values of "lab4ut"
1234 and the font size (via "par(cex = )") should result in readable
1235 unrooted trees. See ?plot.phylo for some examples.
1237 o In drop.tip(), the argument `tip' can now be numeric or character.
1242 o drop.tip() did not work correctly with trees with no branch
1243 lengths: this is fixed.
1245 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1246 plotted with some line crossings: this is now fixed.
1250 CHANGES IN APE VERSION 1.2-6
1255 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1256 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1257 to implement comparative methods with an autocorrelation approach.
1259 o A new data set describing some life history traits of Carnivores
1265 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1270 o When plotting a tree with plot.phylo(), the new default of the
1271 option `label.offset' is now 0, so the labels are always visible.
1275 CHANGES IN APE VERSION 1.2-5
1280 o The new function bd.ext() fits a birth-death model with combined
1281 phylogenetic and taxonomic data, and estimates the corresponding
1282 speciation and extinction rates.
1287 o The package gee is no more required by ape but only suggested
1288 since only the function compar.gee() calls gee.
1292 CHANGES IN APE VERSION 1.2-4
1297 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1298 and lines.popsize) implementing a new approach for inferring the
1299 demographic history from genealogies using a reversible jump
1300 MCMC have been introduced.
1302 o The unit of time in the skyline plot and in the new plots can
1303 now be chosen to be actual years, rather than substitutions.
1307 CHANGES IN APE VERSION 1.2-3
1312 o The new function rtree() generates a random binary tree with or
1313 without branch lengths.
1315 o Two new functions for drawing lineages-through-time (LTT) plots
1316 are provided: ltt.lines() adds a LTT curve to an existing plot,
1317 and mltt.plot() does a multiple LTT plot giving several trees as
1318 arguments (see `?ltt.plot' for details).
1323 o Some taxon names made R crashing when calling as.phylo.hclust():
1326 o dist.dna() returned an error with two identical DNA sequences
1327 (only using the Jukes-Cantor method returned 0): this is fixed.
1332 o The function dist.phylo() has been re-written using a different
1333 algorithm: it is now about four times faster.
1335 o The code of branching.times() has been improved: it is now about
1340 CHANGES IN APE VERSION 1.2-2
1345 o The new function seg.sites() finds the segregating sites in a
1346 sample of DNA sequences.
1351 o A bug introduced in read.tree() and in read.nexus() with version
1354 o A few errors were corrected and a few examples were added in the
1359 CHANGES IN APE VERSION 1.2-1
1364 o plot.phylo() can now draw the edge of the root of a tree if it
1365 has one (see the new option `root.edge', its default is FALSE).
1370 o A bug was fixed in read.nexus(): files with semicolons inside
1371 comment blocks were not read correctly.
1373 o The behaviour of read.tree() and read.nexus() was corrected so
1374 that tree files with badly represented root edges (e.g., with
1375 an extra pair of parentheses, see the help pages for details)
1376 are now correctly represented in the object of class "phylo";
1377 a warning message is now issued.
1381 CHANGES IN APE VERSION 1.2
1386 o plot.phylo() has been completely re-written and offers several
1387 new functionalities. Three types of trees can now be drawn:
1388 phylogram (as previously), cladogram, and unrooted tree; in
1389 all three types the branch lengths can be drawn using the edge
1390 lengths of the phylogeny or not (e.g., if the latter is absent).
1391 The vertical position of the nodes can be adjusted with two
1392 choices (see option `node.pos'). The code has been re-structured,
1393 and two new functions (potentially useful for developpers) are
1394 documented separately: node.depth.edgelength() and node.depth();
1395 see the respective help pages for details.
1397 o The new function zoom() allows to explore very large trees by
1398 focusing on a small portion of it.
1400 o The new function yule() fits by maximum likelihood the Yule model
1401 (birth-only process) to a phylogenetic tree.
1403 o Support for writing DNA sequences in FASTA format has been
1404 introduced in write.dna() (support for reading sequences in
1405 this format was introduced in read.dna() in version 1.1-2).
1406 The function has been completely re-written, fixing some bugs
1407 (see below); the default behaviour is no more to display the
1408 sequences on the standard output. Several options have been
1409 introduced to control the sequence printing in a flexible
1410 way. The help page has been extended.
1412 o A new data set is included: a supertree of bats in NEXUS format.
1417 o In theta.s(), the default of the option `variance' has
1418 been changed to `FALSE' (as was indicated in the help page).
1420 o Several bugs were fixed in the code of all.equal.phylo().
1422 o Several bugs were fixed in write.dna(), particularly this
1423 function did not work with `format = "interleaved"'.
1425 o Various errors were corrected in the help pages.
1430 o The argument names of as.hclust.phylo() have been changed
1431 from "(phy)" to "(x, ...)" to conform to the definition of
1432 the corresponding generic function.
1434 o gamma.stat() has been renamed gammaStat() to avoid confusion
1435 since gamma() is a generic function.
1439 CHANGES IN APE VERSION 1.1-3
1444 o base.freq() previously did not return a value of 0 for
1445 bases absent in the data (e.g., a vector of length 3 was
1446 returned if one base was absent). This is now fixed (a
1447 vector of length 4 is always returned).
1449 o Several bugs were fixed in read.nexus(), including that this
1450 function did not work in this absence of a "TRANSLATE"
1451 command in the NEXUS file, and that the commands were
1456 CHANGES IN APE VERSION 1.1-2
1461 o The Tamura and Nei (1993) model of DNA distance is now implemented
1462 in dist.dna(): five models are now available in this function.
1464 o A new data set is included: a set of 15 sequences of the
1465 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1471 o A bug in read.nexus() was fixed.
1473 o read.dna() previously did not work correctly in most cases.
1474 The function has been completely re-written and its help page
1475 has been considerably extended (see ?read.dna for details).
1476 Underscores (_) in taxon names are no more replaced with
1477 spaces (this behaviour was undocumented).
1479 o A bug was fixed in write.dna().
1483 CHANGES IN APE VERSION 1.1-1
1488 o A bug in read.tree() introduced in APE 1.1 was fixed.
1490 o A bug in compar.gee() resulted in an error when trying to fit
1491 a model with `family = "binomial"'. This is now fixed.
1495 CHANGES IN APE VERSION 1.1
1500 o The Klastorin (1982) method as suggested by Misawa and Tajima
1501 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1502 on the basis of phylogenetic trees has been implemented (see
1503 the function klastorin()).
1505 o Functions have been added to convert APE's "phylo" objects in
1506 "hclust" cluster objects and vice versa (see the help page of
1507 as.phylo for details).
1509 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1510 are introduced for the estimation of absolute evolutionary rates
1511 (ratogram) and dated clock-like trees (chronogram) from
1512 phylogenetic trees using the non-parametric rate smoothing approach
1513 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1515 o A summary method is now provided printing a summary information on a
1516 phylogenetic tree with, for instance, `summary(tree)'.
1518 o The behaviour of read.tree() was changed so that all spaces and
1519 tabulations in tree files are now ignored. Consequently, spaces in tip
1520 labels are no more allowed. Another side effect is that read.nexus()
1521 now does not replace the underscores (_) in tip labels with spaces
1522 (this behaviour was undocumented).
1524 o The function plot.phylo() has a new option (`underscore') which
1525 specifies whether the underscores in tip labels should be written on
1526 the plot as such or replaced with spaces (the default).
1528 o The function birthdeath() now computes 95% confidence intervals of
1529 the estimated parameters using profile likelihood.
1531 o Three new data sets are included: a gene tree estimated from 36
1532 landplant rbcL sequences, a gene tree estimated from 32 opsin
1533 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1538 o A bug was fixed in dist.gene() where nothing was returned.
1540 o A bug in plot.mst() was fixed.
1542 o A bug in vcv.phylo() resulted in false correlations when the
1543 option `cor = TRUE' was used (now fixed).
1547 CHANGES IN APE VERSION 1.0
1552 o Two new functions, read.dna() and write.dna(), read/write in a file
1553 DNA sequences in interleaved or in sequential format.
1555 o Two new functions, read.nexus() and write.nexus(), read/write trees
1558 o The new function bind.tree() allows to bind two trees together,
1559 possibly handling root edges to give internal branches.
1561 o The new function drop.tip() removes the tips in a phylogenetic tree,
1562 and trims (or not) the corresponding internal branches.
1564 o The new function is.ultrametric() tests if a tree is ultrametric.
1566 o The function plot.phylo() has more functionalities such as drawing the
1567 branches with different colours and/or different widths, showing the
1568 node labels, controling the position and font of the labels, rotating
1569 the labels, and controling the space around the plot.
1571 o The function read.tree() can now read trees with no branch length,
1572 such as "(a,b),c);". Consequently, the element `edge.length' in
1573 objects of class "phylo" is now optional.
1575 o The function write.tree() has a new default behaviour: if the default
1576 for the option `file' is used (i.e. file = ""), then a variable of
1577 mode character containing the tree in Newick format is returned which
1578 can thus be assigned (e.g., tree <- write.tree(phy)).
1580 o The function read.tree() has a new argument `text' which allows
1581 to read the tree in a variable of mode character.
1583 o A new data set is included: the phylogenetic relationships among
1584 the orders of birds from Sibley and Ahlquist (1990).
1588 CHANGES IN APE VERSION 0.2-1
1593 o Several bugs were fixed in the help pages.
1597 CHANGES IN APE VERSION 0.2
1602 o The function write.tree() writes phylogenetic trees (objects of class
1603 "phylo") in an ASCII file using the Newick parenthetic format.
1605 o The function birthdeath() fits a birth-death model to branching times
1606 by maximum likelihood, and estimates the corresponding speciation and
1609 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1612 o The function is.binary.tree() tests whether a phylogeny is binary.
1614 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1615 as well as some methods are introduced.
1617 o Several functions, including some generics and methods, for computing
1618 skyline plot estimates (classic and generalized) of effective
1619 population size through time are introduced and replace the function
1620 skyline.plot() in version 0.1.
1622 o Two data sets are now included: the phylogenetic relationships among
1623 the families of birds from Sibley and Ahlquist (1990), and an
1624 estimated clock-like phylogeny of HIV sequences sampled in the
1625 Democratic Republic of Congo.
1628 DEPRECATED & DEFUNCT
1630 o The function skyline.plot() in ape 0.1 has been deprecated and
1631 replaced by more elaborate functions (see above).
1636 o Two important bugs were fixed in plot.phylo(): phylogenies with
1637 multichotomies not at the root or not with only terminal branches,
1638 and phylogenies with a single node (i.e. only terminal branches)
1639 did not plot. These trees should be plotted correctly now.
1641 o Several bugs were fixed in diversi.time() in the computation of
1644 o Various errors were corrected in the help pages.