1 CHANGES IN APE VERSION 2.2-1
6 o The new function del.gaps() removes insertion gaps ("-") in a
12 o root() failed with resolve.root = TRUE when the root was already
15 o Several bugs were fixed in mlphylo().
20 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
25 CHANGES IN APE VERSION 2.2
30 o Four new functions have been written by Damien de Vienne for the
31 graphical exploration of large trees (cophyloplot, subtrees,
32 subtreeplot), and to return the graphical coordinates of tree
35 o The new functions corPagel and corBlomberg implement the Pagel's
36 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
38 o chronopl() has been improved and gains several options: see its
39 help page for details.
41 o boot.phylo() has now an option 'trees' to possibly return the
42 bootstraped trees (the default is FALSE).
44 o prop.part() has been improved and should now be faster in all
50 o read.dna() failed if "?" occurred in the first 10 sites of the
53 o The x/y aspect of the plot is now respected when plotting a
54 circular tree (type = "r" or "f").
56 o Drawing the tip labels sometimes failed when plotting circular
59 o zoom() failed when tip labels were used instead of their numbers
60 (thanks to Yan Wong for the fix).
62 o drop.tip() failed with some trees (fixed by Yan Wong).
64 o seg.sites() failed with a list.
66 o consensus() failed in some cases. The function has been improved
67 as well and is faster.
71 CHANGES IN APE VERSION 2.1-3
76 o A bug in read.nexus() made the Windows R-GUI crash.
78 o An error was fixed in the computation of ancestral character
79 states by generalized least squares in ace().
81 o di2multi() did not modify node labels correctly.
83 o multi2di() failed if the tree had its attribute "order" set to
88 CHANGES IN APE VERSION 2.1-2
93 o There three new methods for the "multiPhylo" class: str, $,
96 o root() gains the options 'node' and 'resolve.root'
97 (FALSE by default) as well as its code being improved.
99 o mltt.plot() has now an option 'log' used in the same way
100 than in plot.default().
105 o mltt.plot() failed to display the legend with an unnamed
108 o nodelabels() with pies now correcly uses the argument
109 'cex' to draw symbols of different sizes (which has
110 worked already for thermometers).
112 o read.nexus() generally failed to read very big files.
117 o The argument 'family' of compar.gee() can now be a function
118 as well as a character string.
120 o read.tree() and read.nexus() now return an unnamed list if
123 o read.nexus() now returns a modified object of class "multiPhylo"
124 when there is a TRANSLATE block in the NEXUS file: the individual
125 trees have no 'tip.label' vector, but the list has a 'TipLabel'
126 attribute. The new methods '$' and '[[' set these elements
127 correctly when extracting trees.
131 CHANGES IN APE VERSION 2.1-1
136 o The new function rmtree generates lists of random trees.
138 o rcoal() now generates a genuine coalescent tree by default
139 (thanks to Vladimir Minin for the code).
144 o nuc.div() returned an incorrect value with the default
145 pairwise.deletion = FALSE.
150 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
151 have been improved so that they are stabler and faster.
153 o R packages used by ape are now loaded silently; lattice and gee
154 are loaded only when needed.
158 CHANGES IN APE VERSION 2.1
163 o The new function identify.phylo identifies clades on a plotted
164 tree using the mouse.
166 o It is now possible to subset a list of trees (object of class
167 "multiPhylo") with "[" while keeping its class correct.
169 o The new function as.DNAbin.alignment converts DNA sequences
170 stored in the "alignment" format of the package seqinr into
171 an object of class "DNAbin".
173 o The new function weight.taxo2 helps to build similarity matrices
174 given two taxonomic levels (usually called by other functions).
176 o write.tree() can now take a list of trees (class "multiPhylo")
177 as its main argument.
179 o plot.correlogram() and plot.correlogramList() have been
180 improved, and gain several options (see the help page for
181 details). A legend is now plotted by default.
186 o dist.dna() returned some incorrect values with `model = "JC69"'
187 and `pairwise.deletion = TRUE'. This affected only the
188 distances involving sequences with missing values. (Thanks
189 to Bruno Toupance for digging this bug out.)
191 o write.tree() failed with some trees: this is fixed by removing
192 the `multi.line' option (trees are now always printed on a
195 o read.nexus() did not correctly detect trees with multiple root
196 edges (see OTHER CHANGES).
201 o The code of mlphylo() has almost entirely rewritten, and should
202 be much stabler. The options have been also greatly simplified
203 (see ?mlphylo and ?DNAmodel for details).
205 o The internal function nTips has been renamed klastorin_nTips.
207 o The code of is.ultrametric() contained redundancies and has
210 o The code of Moran.I() and of correlogram.formula() have been
213 o read.tree() and read.nexus() now return an error when trying to
214 read a tree with multiple root edges (see BUG FIXES). The
215 correction applied in previous version did not work in all
218 o The class c("multi.tree", "phylo") has been renamed
224 o There is now a vignette in ape: see vignette("MoranI", "ape").
229 o as.matching() and as.phylo.matching() do not support branch
232 o correlogram.phylo() and discrete.dist() have been removed.
236 CHANGES IN APE VERSION 2.0-2
241 o The new function matexpo computes the exponential of a square
244 o The new function unique.multi.tree removes duplicate trees from
247 o yule() has a new option `use.root.edge = FALSE' that specifies
248 to ignore, by default, the root edge of the tree if it exists.
253 o which.edge() failed when the index of a single terminal edge was
256 o In diversi.time(), the values returned for model C were
259 o A bug was fixed in yule() that affected the calculation of the
260 likelihood in the presence of ties in the branching times.
262 o There was a bug in the C function mat_expo4x4 affecting the
263 calculations of the transition probabilities for models HKY and
266 o A small bug was fixed in as.matrix.DNAbin (thanks to James
269 o rtree() did not `shuffle' the tip labels by default, so only a
270 limited number of labelled topologies could be generated.
274 CHANGES IN APE VERSION 2.0-1
279 o The three new functions bionj, fastme.ols, and fastme.bal
280 perform phylogeny estimation by the BIONJ and fastME methods in
281 OLS and balanced versions. This is a port to R of previous
282 previous programs done by Vincent Lefort.
284 o The new function chronoMPL performs molecular dating with the
285 mean path lengths method of Britton et al. (2002, Mol. Phyl.
288 o The new function rotate, contributed by Christoph Heibl, swaps
289 two clades connected to the same node. It works also with
290 multichotomous nodes.
292 o The new `method' as.matrix.DNAbin() may be used to convert
293 easily DNA sequences stored in a list into a matrix while
294 keeping the names and the class.
299 o chronopl() failed when some branch lengths were equal to zero:
300 an error message is now returned.
302 o di2multi() failed when there was a series of consecutive edges
307 CHANGES IN APE VERSION 1.10-2
312 o plot.phylo() can now plot circular trees: the option is type =
313 "fan" or type = "f" (to avoid the ambiguity with type = "c").
315 o prop.part() has a new option `check.labels = FALSE' which allows
316 to considerably speed-up the calculations of bipartitions. As a
317 consequence, calculations of bootstrap values with boot.phylo()
318 should be much faster.
323 o read.GenBank() did not return correctly the list of species as
324 from ape 1.10: this is fixed in this version
326 o Applying as.phylo() on a tree of class "phylo" failed: the
327 object is now returned unchanged.
331 CHANGES IN APE VERSION 1.10-1
336 o The three new functions Ntip, Nnode, and Nedge return, for a
337 given tree, the number of tips, nodes, or edges, respectively.
342 o read.nexus() did not set correctly the class of the returned
343 object when reading multiple trees.
345 o mllt.plot() failed with objects of class c("multi.tree",
348 o unroot() did not work correctly in most cases.
350 o reorder.phylo() made R freeze in some occasions.
352 o Plotting a tree in pruningwise order failed.
354 o When plotting an unrooted tree, the tip labels where not all
355 correctly positioned if the option `cex' was used.
359 CHANGES IN APE VERSION 1.10
364 o Five new `method' functions have been introduced to manipulate
365 DNA sequences in binary format (see below).
367 o Three new functions have been introduced to convert between the
368 new binary and the character formats.
370 o The new function as.alignment converts DNA sequences stored as
371 single characters into the class "alignment" used by the package
374 o read.dna() and read.GenBank() have a new argument `as.character'
375 controlling whether the sequences are returned in binary format
381 o root() failed when the tree had node labels: this is fixed.
383 o plot.phylo() did not correctly set the limits on the y-axis with
384 the default setting: this is fixed.
386 o dist.dna() returned a wrong result for the LogDet, paralinear,
387 and BH87 models with `pairwise.deletion = TRUE'.
392 o DNA sequences are now internally stored in a binary format. See
393 the document "A Bit-Level Coding Scheme for Nucleotides" for the
394 details. Most functions analyzing DNA functions have been
395 modified accordingly and are now much faster (dist.dna is now
396 ca. 60 times faster).
400 CHANGES IN APE VERSION 1.9-4
405 o A bug was fixed in edgelabels().
407 o as.phylo.hclust() did not work correctly when the object of
408 class "hclust" has its labels set to NULL: the returned tree has
409 now its tip labels set to "1", "2", ...
411 o consensus could fail if some tip labels are a subset of others
412 (e.g., "a" and "a_1"): this is now fixed.
414 o mlphylo() failed in most cases if some branch lengths of the
415 initial tree were greater than one: an error message is now
418 o mlphylo() failed in most cases when estimating the proportion of
419 invariants: this is fixed.
423 CHANGES IN APE VERSION 1.9-3
428 o The new function edgelabels adds labels on the edge of the tree
429 in the same way than nodelabels or tiplabels.
434 o multi2di() did not handle correctly branch lengths with the
435 default option `random = TRUE': this is now fixed.
437 o A bug was fixed in nuc.div() when using pairwise deletions.
439 o A bug occurred in the analysis of bipartitions with large
440 numbers of large trees, with consequences on prop.part,
441 prop.clades, and boot.phylo.
443 o The calculation of the Billera-Holmes-Vogtmann distance in
444 dist.topo was wrong: this has been fixed.
448 CHANGES IN APE VERSION 1.9-2
453 o The new function ladderize reorganizes the internal structure of
454 a tree to plot them left- or right-ladderized.
456 o The new function dist.nodes computes the patristic distances
457 between all nodes, internal and terminal, of a tree. It replaces
458 the option `full = TRUE' of cophenetic.phylo (see below).
463 o A bug was fixed in old2new.phylo().
465 o Some bugs were fixed in chronopl().
467 o The edge colours were not correctly displayed by plot.phylo
468 (thank you to Li-San Wang for the fix).
470 o cophenetic.phylo() failed with multichotomous trees: this is
476 o read.dna() now returns the sequences in a matrix if they are
477 aligned (interleaved or sequential format). Sequences in FASTA
478 format are still returned in a list.
480 o The option `full' of cophenetic.phylo() has been removed because
481 it could not be used from the generic.
486 o rotate() has been removed; this function did not work correctly
491 CHANGES IN APE VERSION 1.9-1
496 o Trees with a single tip were not read correctly in R as the
497 element `Nnode' was not set: this is fixed.
499 o unroot() did not set correctly the number of nodes of the
500 unrooted tree in most cases.
502 o read.GenBank() failed when fetching very long sequences,
503 particularly of the BX-series.
505 o A bug was introduced in read.tree() with ape 1.9: it has been
510 CHANGES IN APE VERSION 1.9
515 o There are two new print `methods' for trees of class "phylo" and
516 lists of trees of class "multi.tree", so that they are now
517 displayed in a compact and informative way.
519 o There are two new functions, old2new.phylo and new2old.phylo,
520 for converting between the old and new coding of the class
523 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
524 LogDet ("logdet"), and paralinear ("paralin").
526 o compute.brlen() has been extended: several methods are now
527 available to compute branch lengths.
529 o write.dna() can now handle matrices as well as lists.
534 o cophenetic.phylo() sometimes returned a wrong result with
535 multichotomous trees: this is fixed.
537 o rotate() failed when a single tip was specified: the tree is now
540 o ace() did not return the correct index matrix with custom
541 models: this is fixed.
543 o multi2di() did not work correctly when resolving multichotomies
544 randomly: the topology was always the same, only the arrangement
545 of clades was randomized: this is fixed. This function now
546 accepts trees with no branch lengths.
548 o The output of diversi.gof() was blurred by useless prints when a
549 user distribution was specified. This has been corrected, and
550 the help page of this function has been expanded.
555 o The internal structure of the class "phylo" has been changed:
556 see the document "Definition of Formats for Coding Phylogenetic
557 Trees in R" for the details. In addition, the code of most
558 functions has been improved.
560 o Several functions have been improved by replacing some R codes
561 by C codes: pic, plot.phylo, and reorder.phylo.
563 o There is now a citation information: see citation("ape") in R.
565 o write.tree() now does not add extra 0's to branch lengths so
566 that 1.23 is printed "1.23" by default, not "1.2300000000".
568 o The syntax of bind.tree() has been simplified. This function now
569 accepts trees with no branch lengths, and handles correctly node
572 o The option `as.numeric' of mrca() has been removed.
574 o The unused options `format' and `rooted' of read.tree() have
577 o The unused option `format' of write.tree() has been removed.
579 o The use of node.depth() has been simplified.
583 CHANGES IN APE VERSION 1.8-5
588 o Two new functions read.nexus.data() and write.nexus.data(),
589 contributed by Johan Nylander, allow to read and write molecular
590 sequences in NEXUS files.
592 o The new function reorder.phylo() reorders the internal structure
593 of a tree of class "phylo". It is used as the generic, e.g.,
596 o read.tree() and read.nexus() can now read trees with a single
599 o The new data set `cynipids' supplies a set of protein sequences
605 o The code of all.equal.phylo() has been completely rewritten
606 (thanks to Benoît Durand) which fixes several bugs.
608 o read.tree() and read.nexus() now checks the labels of the tree
609 to remove or substitute any characters that are illegal in the
610 Newick format (parentheses, etc.)
612 o A negative P-value could be returned by mantel.test(): this is
617 CHANGES IN APE VERSION 1.8-4
622 o The new function sh.test() computes the Shimodaira-
625 o The new function collapse.singles() removes the nodes with a
626 single descendant from a tree.
628 o plot.phylo() has a new argument `tip.color' to specify the
631 o mlphylo() has now an option `quiet' to control the display of
632 the progress of the analysis (the default is FALSE).
637 o read.dna() did not read correctly sequences in sequential format
638 with leading alignment gaps "-": this is fixed.
640 o ace() returned a list with no class so that the generic
641 functions (anova, logLik, ...) could not be used directly. This
642 is fixed as ace() now returns an object of class "ace".
644 o anova.ace() had a small bug when computing the number of degrees
645 of freedom: this is fixed.
647 o mlphylo() did not work when the sequences were in a matrix or
648 a data frame: this is fixed.
650 o rtree() did not work correctly when trying to simulate an
651 unrooted tree with two tips: an error message is now issued.
656 o The algorithm of rtree() has been changed: it is now about 40,
657 100, and 130 times faster for 10, 100, and 1000 tips,
662 CHANGES IN APE VERSION 1.8-3
667 o There are four new `method' functions to be used with the
668 results of ace(): logLik(), deviance(), AIC(), and anova().
670 o The plot method of phymltest has two new arguments: `main' to
671 change the title, and `col' to control the colour of the
672 segments showing the AIC values.
674 o ace() has a new argument `ip' that gives the initial values used
675 in the ML estimation with discrete characters (see the examples
676 in ?ace). This function now returns a matrix giving the indices
677 of the estimated rates when analysing discrete characters.
679 o nodelabels() and tiplabels() have a new argument `pie' to
680 represent proportions, with any number of categories, as
681 piecharts. The use of the option `thermo' has been improved:
682 there is now no limitation on the number of categories.
687 o mlphylo() did not work with more than two partitions: this is
690 o root() failed if the proposed outgroup was already an outgroup
691 in the tree: this is fixed.
693 o The `col' argument in nodelabels() and tiplabels() was not
694 correctly passed when `text' was used: this is fixed.
696 o Two bugs were fixed in mlphylo(): parameters were not always
697 correctly output, and the estimation failed in some cases.
699 o plot.phylo() was stuck when given a tree with a single tip: this
700 is fixed and a message error is now returned.
702 o An error was corrected in the help page of gammaStat regarding
703 the calculation of P-values.
705 o Using gls() could crash R when the number of species in the tree
706 and in the variables were different: this is fixed.
710 CHANGES IN APE VERSION 1.8-2
715 o The new function mlphylo() fits a phylogenetic tree by maximum
716 likelihood from DNA sequences. Its companion function DNAmodel()
717 is used to define the substitution model which may include
718 partitioning. There are methods for logLik(), deviance(), and
719 AIC(), and the summary() method has been extended to display in
720 a friendly way the results of this model fitting. Currently, the
721 functionality is limited to estimating the substitution and
722 associated parameters and computing the likelihood.
724 o The new function drop1.compar.gee (used as, e.g., drop1(m))
725 tests for single effects in GEE-based comparative method. A
726 warning message is printed if there is not enough degrees of
732 o An error message was sometimes issued by plot.multi.tree(),
733 though with no consequence.
737 CHANGES IN APE VERSION 1.8-1
742 o There is a new plot method for lists of trees (objects of class
743 "multi.tree"): it calls plot.phylo() internally and is
744 documented on the same help page.
749 o A bug was fixed in the C code that analyzes bipartitions: this
750 has impact on several functions like prop.part, prop.clades,
751 boot.phylo, or consensus.
753 o root() did not work correctly when the specified outgroup had
754 more than one element: this is fixed.
756 o dist.dna() sometimes returned a warning inappropriately: this
759 o If the distance object given to nj() had no rownames, nj()
760 returned a tree with no tip labels: it now returns tips labelled
761 "1", "2", ..., corresponding to the row numbers.
766 o nj() has been slightly changed so that tips with a zero distance
767 are first aggregated with zero-lengthed branches; the usual NJ
768 procedure is then performed on a distance matrix without 0's.
772 CHANGES IN APE VERSION 1.8
777 o The new function chronopl() estimates dates using the penalized
778 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
780 o The new function consensus() calculates the consensus tree of a
783 o The new function evolve.phylo() simulates the evolution of
784 continuous characters along a phylogeny under a Brownian model.
786 o The new plot method for objects of class "ancestral" displays a
787 tree together with ancestral values, as returned by the above
790 o The new function as.phylo.formula() returns a phylogeny from a
791 set of nested taxonomic variables given as a formula.
793 o The new function read.caic() reads trees in CAIC format.
795 o The new function tiplabels() allows to add labels to the tips
796 of a tree using text or plotting symbols in a flexible way.
798 o The new function unroot() unroots a phylogeny.
800 o multi2di() has a new option, `random', which specifies whether
801 to resolve the multichotomies randomly (the default) or not.
803 o prop.part() now returns an object of class "prop.part" for which
804 there are print (to display a partition in a more friendly way)
805 and summary (to extract the numbers) methods.
807 o plot.phylo() has a new option, `show.tip.label', specifying
808 whether to print the labels of the tips. The default is TRUE.
810 o The code of nj() has been replaced by a faster C code: it is now
811 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
814 o write.nexus() now writes whether a tree is rooted or not.
819 o Two bugs have been fixed in root(): unrooted trees are now
820 handled corretly, and node labels are now output normally.
822 o A bug was fixed in phymltest(): the executable couldn't be found
825 o Three bug have been fixed in ace(): computing the likelihood of
826 ancestral states of discrete characters failed, custom models
827 did not work, and the function failed with a null gradient (a
828 warning message is now returned; this latter bug was also
829 present in yule.cov() as well and is now fixed).
831 o pic() hanged out when missing data were present: a message error
834 o A small bug was fixed in dist.dna() where the gamma correction
835 was not always correctly dispatched.
837 o plot.phylo() plotted correctly the root edge only when the tree
838 was plotted rightwards: this works now for all directions.
843 o dist.taxo() has been renamed as weight.taxo().
845 o Various error and warning messages have been improved.
849 CHANGES IN APE VERSION 1.7
852 o The new function ace() estimates ancestral character states for
853 continuous characters (with ML, GLS, and contrasts methods), and
854 discrete characters (with ML only) for any number of states.
856 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
857 of directional evolution for continuous characters. The user
858 specifies the node(s) of the tree where the character optimum
861 o The new function is.rooted() tests whether a tree (of class
864 o The new function rcoal() generates random ultrametric trees with
865 the possibility to specify the function that generates the
866 inter-nodes distances.
868 o The new function mrca() gives for all pairs of tips in a tree
869 (and optionally nodes too) the most recent common ancestor.
871 o nodelabels() has a new option `thermo' to plot proportions (up
872 to three classes) on the nodes of a tree.
874 o rtree() has been improved: it can now generate rooted or
875 unrooted trees, and the mathematical function that generates the
876 branch lengths may be specified by the user. The tip labels may
877 be given directly in the call to rtree. The limit cases (n = 2,
878 3) are now handled correctly.
880 o dist.topo() has a new argument `method' with two choices: "PH85"
881 for Penny and Henny's method (already available before and now
882 the default), and "BHV01" for the geometric distance by Billera
883 et al. (2001, Adv. Appl. Math. 27:733).
885 o write.tree() has a new option, `digits', which specifies the
886 number of digits to be printed in the Newick tree. By default
887 digits = 10. The numbers are now always printed in decimal form
888 (i.e., 1.0e-1 is now avoided).
890 o dist.dna() can now compute the raw distances between pairs of
891 DNA sequences by specifying model = "raw".
893 o dist.phylo() has a new option `full' to possibly compute the
894 distances among all tips and nodes of the tree. The default if
900 o Several bugs were fixed in all.equal.phylo().
902 o dist.dna() did not handle correctly gaps ("-") in alignments:
903 they are now considered as missing data.
905 o rotate() did not work if the tips were not ordered: this is
908 o mantel.test() returned NA in some special cases: this is fixed
909 and the function has been improved and is now faster.
911 o A bug was fixed in diversi.gof() where the calculation of A² was
914 o cherry() did not work correctly under some OSs (mainly Linux):
917 o is.binary.tree() has been modified so that it works with both
918 rooted and unrooted trees.
920 o The documentation of theta.s() was not correct: this has been
923 o plot.mst() did not work correctly: this is fixed.
927 CHANGES IN APE VERSION 1.6
932 o The new function dist.topo() computes the topological distances
935 o The new function boot.phylo() performs a bootstrap analysis on
936 phylogeny estimation.
938 o The new functions prop.part() and prop.clades() analyse
939 bipartitions from a series of trees.
944 o read.GenBank() now uses the EFetch utility of NCBI instead of
945 the usual Web interface: it is now much faster (e.g., 12 times
946 faster to retrieve 8 sequences, 37 times for 60 sequences).
951 o Several bugs were fixed in read.dna().
953 o Several bugs were fixed in diversi.time().
955 o is.binary.tree() did not work correctly if the tree has no edge
956 lengths: this is fixed.
958 o drop.tip() did not correctly propagated the `node.label' of a
963 CHANGES IN APE VERSION 1.5
968 o Two new functions, as.matching.phylo() and as.phylo.matching(),
969 convert objects between the classes "phylo" and "matching". The
970 latter implements the representation of binary trees introduced by
971 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
972 as.matching() has been introduced as well.
974 o Two new functions, multi2di() and di2multi(), allow to resolve
975 and collapse multichotomies with branches of length zero.
977 o The new function nuc.div() computes the nucleotide diversity
978 from a sample a DNA sequences.
980 o dist.dna() has been completely rewritten with a much faster
981 (particularly for large data sets) C code. Eight models are
982 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
983 option `method' has been renamed `model'). Computation of variance
984 is available for all models. A gamma-correction is possible for
985 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
986 to remove sites with missing data on a pairwise basis. The option
987 `GCcontent' has been removed.
989 o read.GenBank() has a new option (species.names) which specifies
990 whether to return the species names of the organisms in addition
991 to the accession numbers of the sequences (this is the default
994 o write.nexus() can now write several trees in the same NEXUS file.
996 o drop.tip() has a new option `root.edge' that allows to specify the
997 new root edge if internal branches are trimmed.
1002 o as.phylo.hclust() failed if some labels had parentheses: this
1005 o Several bugs were fixed in all.equal.phylo(). This function now
1006 returns the logical TRUE if the trees are identical but with
1007 different representations (a report was printed previously).
1009 o read.GenBank() did not correctly handle ambiguous base codes:
1015 o birthdeath() now returns an object of class "birthdeath" for
1016 which there is a print method.
1020 CHANGES IN APE VERSION 1.4
1025 o The new function nj() performs phylogeny estimation with the
1026 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1029 o The new function which.edge() identifies the edges of a tree
1030 that belong to a group specified as a set of tips.
1032 o The new function as.phylo.phylog() converts an object of class
1033 "phylog" (from the package ade4) into an object of class
1036 o The new function axisPhylo() draws axes on the side of a
1039 o The new function howmanytrees() calculates the number of trees
1040 in different cases and giving a number of tips.
1042 o write.tree() has a new option `multi.line' (TRUE by default) to
1043 write a Newick tree on several lines rather than on a single
1046 o The functionalities of zoom() have been extended. Several
1047 subtrees can be visualized at the same time, and they are marked
1048 on the main tree with colors. The context of the subtrees can be
1049 marked with the option `subtree' (see below).
1051 o drop.tip() has a new option `subtree' (FALSE by default) which
1052 specifies whether to output in the tree how many tips have been
1055 o The arguments of add.scale.bar() have been redefined and have
1056 now default values (see ?add.scale.bar for details). This
1057 function now works even if the plotted tree has no edge length.
1059 o plot.phylo() can now plot radial trees, but this does not take
1060 edge lengths into account.
1062 o In plot.phylo() with `type = "phylogram"', if the values of
1063 `edge.color' and `edge.width' are identical for sister-branches,
1064 they are propagated to the vertical line that link them.
1069 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1070 crashing. This is fixed.
1072 o In plot.phylo(), the options `edge.color' and `edge.width' are
1073 now properly recycled; their default values are now "black" and
1076 o A bug has been fixed in write.nexus().
1081 o The function node.depth.edgelength() has been removed and
1082 replaced by a C code.
1086 CHANGES IN APE VERSION 1.3-1
1091 o The new function nodelabels() allows to add labels to the nodes
1092 of a tree using text or plotting symbols in a flexible way.
1094 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1095 numeric values specifying the lower and upper limits on the x-
1096 and y-axes. This allows to leave some space on any side of the
1097 tree. If a single value is given, this is taken as the upper
1102 CHANGES IN APE VERSION 1.3
1107 o The new function phymltest() calls the software PHYML and fits
1108 28 models of DNA sequence evolution. There are a print method to
1109 display likelihood and AIC values, a summary method to compute
1110 the hierarchical likelihood ratio tests, and a plot method to
1111 display graphically the AIC values of each model.
1113 o The new function yule.cov() fits the Yule model with covariates,
1114 a model where the speciation rate is affected by several species
1115 traits through a generalized linear model. The parameters are
1116 estimated by maximum likelihood.
1118 o Three new functions, corBrownian(), corGrafen(), and
1119 corMartins(), compute the expected correlation structures among
1120 species given a phylogeny under different models of evolution.
1121 These can be used for GLS comparative phylogenetic methods (see
1122 the examples). There are coef() and corMatrix() methods and an
1123 Initialize.corPhyl() function associated.
1125 o The new function compar.cheverud() implements Cheverud et al.'s
1126 (1985; Evolution 39:1335) phylogenetic comparative method.
1128 o The new function varcomp() estimates variance components; it has
1131 o Two new functions, panel.superpose.correlogram() and
1132 plot.correlogramList(), allow to plot several phylogenetic
1135 o The new function node.leafnumber() computes the number of leaves
1136 of a subtree defined by a particular node.
1138 o The new function node.sons() gets all tags of son nodes from a
1141 o The new function compute.brlen() computes the branch lengths of
1142 a tree according to a specified method.
1144 o plot.phylo() has three new options: "cex" controls the size of
1145 the (tip and node) labels (thus it is no more needed to change
1146 the global graphical parameter), "direction" which allows to
1147 plot the tree rightwards, leftwards, upwards, or downwards, and
1148 "y.lim" which sets the upper limit on the y-axis.
1153 o Some functions which try to match tip labels and names of
1154 additional data (e.g. vector) are likely to fail if there are
1155 typing or syntax errors. If both series of names do not perfectly
1156 match, they are ignored and a warning message is now issued.
1157 These functions are bd.ext, compar.gee, pic. Their help pages
1158 have been clarified on this point.
1162 CHANGES IN APE VERSION 1.2-7
1167 o The new function root() reroots a phylogenetic tree with respect
1168 to a specified outgroup.
1170 o The new function rotate() rotates an internal branch of a tree.
1172 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1173 trees) controls the display of the tip labels in unrooted trees.
1174 This display has been greatly improved: the tip labels are now not
1175 expected to overlap with the tree (particularly if lab4ut =
1176 "axial"). In all cases, combining appropriate values of "lab4ut"
1177 and the font size (via "par(cex = )") should result in readable
1178 unrooted trees. See ?plot.phylo for some examples.
1180 o In drop.tip(), the argument `tip' can now be numeric or character.
1185 o drop.tip() did not work correctly with trees with no branch
1186 lengths: this is fixed.
1188 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1189 plotted with some line crossings: this is now fixed.
1193 CHANGES IN APE VERSION 1.2-6
1198 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1199 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1200 to implement comparative methods with an autocorrelation approach.
1202 o A new data set describing some life history traits of Carnivores
1208 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1213 o When plotting a tree with plot.phylo(), the new default of the
1214 option `label.offset' is now 0, so the labels are always visible.
1218 CHANGES IN APE VERSION 1.2-5
1223 o The new function bd.ext() fits a birth-death model with combined
1224 phylogenetic and taxonomic data, and estimates the corresponding
1225 speciation and extinction rates.
1230 o The package gee is no more required by ape but only suggested
1231 since only the function compar.gee() calls gee.
1235 CHANGES IN APE VERSION 1.2-4
1240 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1241 and lines.popsize) implementing a new approach for inferring the
1242 demographic history from genealogies using a reversible jump
1243 MCMC have been introduced.
1245 o The unit of time in the skyline plot and in the new plots can
1246 now be chosen to be actual years, rather than substitutions.
1250 CHANGES IN APE VERSION 1.2-3
1255 o The new function rtree() generates a random binary tree with or
1256 without branch lengths.
1258 o Two new functions for drawing lineages-through-time (LTT) plots
1259 are provided: ltt.lines() adds a LTT curve to an existing plot,
1260 and mltt.plot() does a multiple LTT plot giving several trees as
1261 arguments (see `?ltt.plot' for details).
1266 o Some taxon names made R crashing when calling as.phylo.hclust():
1269 o dist.dna() returned an error with two identical DNA sequences
1270 (only using the Jukes-Cantor method returned 0): this is fixed.
1275 o The function dist.phylo() has been re-written using a different
1276 algorithm: it is now about four times faster.
1278 o The code of branching.times() has been improved: it is now about
1283 CHANGES IN APE VERSION 1.2-2
1288 o The new function seg.sites() finds the segregating sites in a
1289 sample of DNA sequences.
1294 o A bug introduced in read.tree() and in read.nexus() with version
1297 o A few errors were corrected and a few examples were added in the
1302 CHANGES IN APE VERSION 1.2-1
1307 o plot.phylo() can now draw the edge of the root of a tree if it
1308 has one (see the new option `root.edge', its default is FALSE).
1313 o A bug was fixed in read.nexus(): files with semicolons inside
1314 comment blocks were not read correctly.
1316 o The behaviour of read.tree() and read.nexus() was corrected so
1317 that tree files with badly represented root edges (e.g., with
1318 an extra pair of parentheses, see the help pages for details)
1319 are now correctly represented in the object of class "phylo";
1320 a warning message is now issued.
1324 CHANGES IN APE VERSION 1.2
1329 o plot.phylo() has been completely re-written and offers several
1330 new functionalities. Three types of trees can now be drawn:
1331 phylogram (as previously), cladogram, and unrooted tree; in
1332 all three types the branch lengths can be drawn using the edge
1333 lengths of the phylogeny or not (e.g., if the latter is absent).
1334 The vertical position of the nodes can be adjusted with two
1335 choices (see option `node.pos'). The code has been re-structured,
1336 and two new functions (potentially useful for developpers) are
1337 documented separately: node.depth.edgelength() and node.depth();
1338 see the respective help pages for details.
1340 o The new function zoom() allows to explore very large trees by
1341 focusing on a small portion of it.
1343 o The new function yule() fits by maximum likelihood the Yule model
1344 (birth-only process) to a phylogenetic tree.
1346 o Support for writing DNA sequences in FASTA format has been
1347 introduced in write.dna() (support for reading sequences in
1348 this format was introduced in read.dna() in version 1.1-2).
1349 The function has been completely re-written, fixing some bugs
1350 (see below); the default behaviour is no more to display the
1351 sequences on the standard output. Several options have been
1352 introduced to control the sequence printing in a flexible
1353 way. The help page has been extended.
1355 o A new data set is included: a supertree of bats in NEXUS format.
1360 o In theta.s(), the default of the option `variance' has
1361 been changed to `FALSE' (as was indicated in the help page).
1363 o Several bugs were fixed in the code of all.equal.phylo().
1365 o Several bugs were fixed in write.dna(), particularly this
1366 function did not work with `format = "interleaved"'.
1368 o Various errors were corrected in the help pages.
1373 o The argument names of as.hclust.phylo() have been changed
1374 from "(phy)" to "(x, ...)" to conform to the definition of
1375 the corresponding generic function.
1377 o gamma.stat() has been renamed gammaStat() to avoid confusion
1378 since gamma() is a generic function.
1382 CHANGES IN APE VERSION 1.1-3
1387 o base.freq() previously did not return a value of 0 for
1388 bases absent in the data (e.g., a vector of length 3 was
1389 returned if one base was absent). This is now fixed (a
1390 vector of length 4 is always returned).
1392 o Several bugs were fixed in read.nexus(), including that this
1393 function did not work in this absence of a "TRANSLATE"
1394 command in the NEXUS file, and that the commands were
1399 CHANGES IN APE VERSION 1.1-2
1404 o The Tamura and Nei (1993) model of DNA distance is now implemented
1405 in dist.dna(): five models are now available in this function.
1407 o A new data set is included: a set of 15 sequences of the
1408 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1414 o A bug in read.nexus() was fixed.
1416 o read.dna() previously did not work correctly in most cases.
1417 The function has been completely re-written and its help page
1418 has been considerably extended (see ?read.dna for details).
1419 Underscores (_) in taxon names are no more replaced with
1420 spaces (this behaviour was undocumented).
1422 o A bug was fixed in write.dna().
1426 CHANGES IN APE VERSION 1.1-1
1431 o A bug in read.tree() introduced in APE 1.1 was fixed.
1433 o A bug in compar.gee() resulted in an error when trying to fit
1434 a model with `family = "binomial"'. This is now fixed.
1438 CHANGES IN APE VERSION 1.1
1443 o The Klastorin (1982) method as suggested by Misawa and Tajima
1444 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1445 on the basis of phylogenetic trees has been implemented (see
1446 the function klastorin()).
1448 o Functions have been added to convert APE's "phylo" objects in
1449 "hclust" cluster objects and vice versa (see the help page of
1450 as.phylo for details).
1452 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1453 are introduced for the estimation of absolute evolutionary rates
1454 (ratogram) and dated clock-like trees (chronogram) from
1455 phylogenetic trees using the non-parametric rate smoothing approach
1456 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1458 o A summary method is now provided printing a summary information on a
1459 phylogenetic tree with, for instance, `summary(tree)'.
1461 o The behaviour of read.tree() was changed so that all spaces and
1462 tabulations in tree files are now ignored. Consequently, spaces in tip
1463 labels are no more allowed. Another side effect is that read.nexus()
1464 now does not replace the underscores (_) in tip labels with spaces
1465 (this behaviour was undocumented).
1467 o The function plot.phylo() has a new option (`underscore') which
1468 specifies whether the underscores in tip labels should be written on
1469 the plot as such or replaced with spaces (the default).
1471 o The function birthdeath() now computes 95% confidence intervals of
1472 the estimated parameters using profile likelihood.
1474 o Three new data sets are included: a gene tree estimated from 36
1475 landplant rbcL sequences, a gene tree estimated from 32 opsin
1476 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1481 o A bug was fixed in dist.gene() where nothing was returned.
1483 o A bug in plot.mst() was fixed.
1485 o A bug in vcv.phylo() resulted in false correlations when the
1486 option `cor = TRUE' was used (now fixed).
1490 CHANGES IN APE VERSION 1.0
1495 o Two new functions, read.dna() and write.dna(), read/write in a file
1496 DNA sequences in interleaved or in sequential format.
1498 o Two new functions, read.nexus() and write.nexus(), read/write trees
1501 o The new function bind.tree() allows to bind two trees together,
1502 possibly handling root edges to give internal branches.
1504 o The new function drop.tip() removes the tips in a phylogenetic tree,
1505 and trims (or not) the corresponding internal branches.
1507 o The new function is.ultrametric() tests if a tree is ultrametric.
1509 o The function plot.phylo() has more functionalities such as drawing the
1510 branches with different colours and/or different widths, showing the
1511 node labels, controling the position and font of the labels, rotating
1512 the labels, and controling the space around the plot.
1514 o The function read.tree() can now read trees with no branch length,
1515 such as "(a,b),c);". Consequently, the element `edge.length' in
1516 objects of class "phylo" is now optional.
1518 o The function write.tree() has a new default behaviour: if the default
1519 for the option `file' is used (i.e. file = ""), then a variable of
1520 mode character containing the tree in Newick format is returned which
1521 can thus be assigned (e.g., tree <- write.tree(phy)).
1523 o The function read.tree() has a new argument `text' which allows
1524 to read the tree in a variable of mode character.
1526 o A new data set is included: the phylogenetic relationships among
1527 the orders of birds from Sibley and Ahlquist (1990).
1531 CHANGES IN APE VERSION 0.2-1
1536 o Several bugs were fixed in the help pages.
1540 CHANGES IN APE VERSION 0.2
1545 o The function write.tree() writes phylogenetic trees (objects of class
1546 "phylo") in an ASCII file using the Newick parenthetic format.
1548 o The function birthdeath() fits a birth-death model to branching times
1549 by maximum likelihood, and estimates the corresponding speciation and
1552 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1555 o The function is.binary.tree() tests whether a phylogeny is binary.
1557 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1558 as well as some methods are introduced.
1560 o Several functions, including some generics and methods, for computing
1561 skyline plot estimates (classic and generalized) of effective
1562 population size through time are introduced and replace the function
1563 skyline.plot() in version 0.1.
1565 o Two data sets are now included: the phylogenetic relationships among
1566 the families of birds from Sibley and Ahlquist (1990), and an
1567 estimated clock-like phylogeny of HIV sequences sampled in the
1568 Democratic Republic of Congo.
1571 DEPRECATED & DEFUNCT
1573 o The function skyline.plot() in ape 0.1 has been deprecated and
1574 replaced by more elaborate functions (see above).
1579 o Two important bugs were fixed in plot.phylo(): phylogenies with
1580 multichotomies not at the root or not with only terminal branches,
1581 and phylogenies with a single node (i.e. only terminal branches)
1582 did not plot. These trees should be plotted correctly now.
1584 o Several bugs were fixed in diversi.time() in the computation of
1587 o Various errors were corrected in the help pages.