1 CHANGES IN APE VERSION 2.3-1
6 o There is now a c() method for lists of class "DNAbin".
11 o dist.gene() failed on most occasions with the default
12 pairwise.deletion = FALSE.
14 o read.tree() failed to read correctly the tree name(s).
16 o boot.phylo() now treats correctly data frames.
21 o [.multiPhylo and [.DNAbin now respect the original class.
23 o Instances of the form class(phy) == "phylo" have been replaced
24 by inherits(phy, "phylo").
26 o rcoal() should be faster.
30 CHANGES IN APE VERSION 2.3
35 o The new functions CADM.global and CADM.post, contributed by
36 Pierre Legendre, test the congruence among several distance
39 o The new function yule.time fits a user-defined time-dependent
40 Yule model by maximum likelihood.
42 o The new function makeNodeLabel creates and/or modifies node
43 labels in a flexible way.
45 o read.tree() and write.tree() have been modified so that they can
46 handle individual tree names.
48 o plot.phylo() has a new argument 'edge.lty' that specifies the
49 types of lines used for the edges (plain, dotted, dashed, ...)
51 o phymltest() has been updated to work with PhyML 3.0.1.
56 o drop.tip() shuffled tip labels in some cases.
58 o drop.tip() did not handle node.label correctly.
60 o is.ultrametric() now checks the ordering of the edge matrix.
62 o ace() sometimes returned negative values of likelihoods of
63 ancestral states (thanks to Dan Rabosky for solving this long
69 o The data set xenarthra has been removed.
73 CHANGES IN APE VERSION 2.2-4
77 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
78 now fixed. (Thanks to Peter Wragg for the fix!)
80 o A warning message occurred for no reason with ace(method="GLS").
85 o There is now a general help page displayed with '?ape'
89 CHANGES IN APE VERSION 2.2-3
94 o The new function extract.clade extracts a clade from a tree by
95 specifying a node number or label.
97 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
98 operations of the same names.
100 o dist.dna() can now return the number of site differences by
101 specifying model="N".
106 o chronopl() did not work with CV = TRUE.
108 o read.nexus() did not work correctly in some situations (trees on
109 multiple lines with different numbers of lines and/or with
110 comments inserted within the trees).
112 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
113 the number of lineages with non-binary trees.
118 o ape has now a namespace.
120 o drip.tip() has been improved: it should be much faster and work
121 better in some cases (e.g., see the example in ?zoom).
125 CHANGES IN APE VERSION 2.2-2
130 o dist.gene() has been substantially improved and gains an option
133 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
139 o prop.part() failed with a single tree with the default option
140 'check.labels = TRUE'.
142 o summary.DNAbin() failed to display correctly the summary of
143 sequence lengths with lists of sequences of 10,000 bases or more
144 (because summary.default uses 4 significant digits by default).
146 o read.nexus() failed to read a file with a single tree with line
147 breaks in the Newick string.
149 o del.gaps() returned a list of empty sequences when there were no
155 o phymltest() has been updated for PhyML 3.0 and gains an option
156 'append', whereas the option 'path2exec' has been removed.
158 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
159 which is returned unchanged (instead of an error).
161 o The data sets bird.orders and bird.families are now stored as
162 Newick strings; i.e., the command data(bird.orders) calls
167 CHANGES IN APE VERSION 2.2-1
172 o The new function makeLabel() helps to modify labels of trees,
173 lists of trees, or DNA sequences, with several utilities to
174 truncate and/or make them unique, substituting some
175 characters, and so on.
177 o The new function del.gaps() removes insertion gaps ("-") in a
178 set of DNA sequences.
180 o read.dna() can now read Clustal files (*.aln).
185 o root() failed with 'resolve.root = TRUE' when the root was
186 already the specified root.
188 o Several bugs were fixed in mlphylo().
190 o collapsed.singles() did not propagate the 'Nnode' and
191 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
193 o read.nexus() failed to remove correctly the comments within
196 o read.nexus() failed to read a file with a single tree and no
197 translation of tip labels.
199 o read.nexus() failed to place correctly tip labels when reading
200 a single tree with no edge lengths.
202 o A bug was fixed in sh.test().
207 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
210 o The option 'check.labels' of consensus() and prop.part() is now
213 o write.dna() now does not truncate names to 10 characters with
218 CHANGES IN APE VERSION 2.2
223 o Four new functions have been written by Damien de Vienne for the
224 graphical exploration of large trees (cophyloplot, subtrees,
225 subtreeplot), and to return the graphical coordinates of tree
228 o The new functions corPagel and corBlomberg implement the Pagel's
229 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
231 o chronopl() has been improved and gains several options: see its
232 help page for details.
234 o boot.phylo() has now an option 'trees' to possibly return the
235 bootstraped trees (the default is FALSE).
237 o prop.part() has been improved and should now be faster in all
243 o read.dna() failed if "?" occurred in the first 10 sites of the
246 o The x/y aspect of the plot is now respected when plotting a
247 circular tree (type = "r" or "f").
249 o Drawing the tip labels sometimes failed when plotting circular
252 o zoom() failed when tip labels were used instead of their numbers
253 (thanks to Yan Wong for the fix).
255 o drop.tip() failed with some trees (fixed by Yan Wong).
257 o seg.sites() failed with a list.
259 o consensus() failed in some cases. The function has been improved
260 as well and is faster.
264 CHANGES IN APE VERSION 2.1-3
269 o A bug in read.nexus() made the Windows R-GUI crash.
271 o An error was fixed in the computation of ancestral character
272 states by generalized least squares in ace().
274 o di2multi() did not modify node labels correctly.
276 o multi2di() failed if the tree had its attribute "order" set to
281 CHANGES IN APE VERSION 2.1-2
286 o There three new methods for the "multiPhylo" class: str, $,
289 o root() gains the options 'node' and 'resolve.root'
290 (FALSE by default) as well as its code being improved.
292 o mltt.plot() has now an option 'log' used in the same way
293 than in plot.default().
298 o mltt.plot() failed to display the legend with an unnamed
301 o nodelabels() with pies now correcly uses the argument
302 'cex' to draw symbols of different sizes (which has
303 worked already for thermometers).
305 o read.nexus() generally failed to read very big files.
310 o The argument 'family' of compar.gee() can now be a function
311 as well as a character string.
313 o read.tree() and read.nexus() now return an unnamed list if
316 o read.nexus() now returns a modified object of class "multiPhylo"
317 when there is a TRANSLATE block in the NEXUS file: the individual
318 trees have no 'tip.label' vector, but the list has a 'TipLabel'
319 attribute. The new methods '$' and '[[' set these elements
320 correctly when extracting trees.
324 CHANGES IN APE VERSION 2.1-1
329 o The new function rmtree generates lists of random trees.
331 o rcoal() now generates a genuine coalescent tree by default
332 (thanks to Vladimir Minin for the code).
337 o nuc.div() returned an incorrect value with the default
338 pairwise.deletion = FALSE.
343 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
344 have been improved so that they are stabler and faster.
346 o R packages used by ape are now loaded silently; lattice and gee
347 are loaded only when needed.
351 CHANGES IN APE VERSION 2.1
356 o The new function identify.phylo identifies clades on a plotted
357 tree using the mouse.
359 o It is now possible to subset a list of trees (object of class
360 "multiPhylo") with "[" while keeping its class correct.
362 o The new function as.DNAbin.alignment converts DNA sequences
363 stored in the "alignment" format of the package seqinr into
364 an object of class "DNAbin".
366 o The new function weight.taxo2 helps to build similarity matrices
367 given two taxonomic levels (usually called by other functions).
369 o write.tree() can now take a list of trees (class "multiPhylo")
370 as its main argument.
372 o plot.correlogram() and plot.correlogramList() have been
373 improved, and gain several options (see the help page for
374 details). A legend is now plotted by default.
379 o dist.dna() returned some incorrect values with `model = "JC69"'
380 and `pairwise.deletion = TRUE'. This affected only the
381 distances involving sequences with missing values. (Thanks
382 to Bruno Toupance for digging this bug out.)
384 o write.tree() failed with some trees: this is fixed by removing
385 the `multi.line' option (trees are now always printed on a
388 o read.nexus() did not correctly detect trees with multiple root
389 edges (see OTHER CHANGES).
394 o The code of mlphylo() has been almost entirely rewritten, and
395 should be much stabler. The options have been also greatly
396 simplified (see ?mlphylo and ?DNAmodel for details).
398 o The internal function nTips has been renamed klastorin_nTips.
400 o The code of is.ultrametric() contained redundancies and has
403 o The code of Moran.I() and of correlogram.formula() have been
406 o read.tree() and read.nexus() now return an error when trying to
407 read a tree with multiple root edges (see BUG FIXES). The
408 correction applied in previous version did not work in all
411 o The class c("multi.tree", "phylo") has been renamed
417 o There is now a vignette in ape: see vignette("MoranI", "ape").
422 o as.matching() and as.phylo.matching() do not support branch
425 o correlogram.phylo() and discrete.dist() have been removed.
429 CHANGES IN APE VERSION 2.0-2
434 o The new function matexpo computes the exponential of a square
437 o The new function unique.multi.tree removes duplicate trees from
440 o yule() has a new option `use.root.edge = FALSE' that specifies
441 to ignore, by default, the root edge of the tree if it exists.
446 o which.edge() failed when the index of a single terminal edge was
449 o In diversi.time(), the values returned for model C were
452 o A bug was fixed in yule() that affected the calculation of the
453 likelihood in the presence of ties in the branching times.
455 o There was a bug in the C function mat_expo4x4 affecting the
456 calculations of the transition probabilities for models HKY and
459 o A small bug was fixed in as.matrix.DNAbin (thanks to James
462 o rtree() did not `shuffle' the tip labels by default, so only a
463 limited number of labelled topologies could be generated.
467 CHANGES IN APE VERSION 2.0-1
472 o The three new functions bionj, fastme.ols, and fastme.bal
473 perform phylogeny estimation by the BIONJ and fastME methods in
474 OLS and balanced versions. This is a port to R of previous
475 previous programs done by Vincent Lefort.
477 o The new function chronoMPL performs molecular dating with the
478 mean path lengths method of Britton et al. (2002, Mol. Phyl.
481 o The new function rotate, contributed by Christoph Heibl, swaps
482 two clades connected to the same node. It works also with
483 multichotomous nodes.
485 o The new `method' as.matrix.DNAbin() may be used to convert
486 easily DNA sequences stored in a list into a matrix while
487 keeping the names and the class.
492 o chronopl() failed when some branch lengths were equal to zero:
493 an error message is now returned.
495 o di2multi() failed when there was a series of consecutive edges
500 CHANGES IN APE VERSION 1.10-2
505 o plot.phylo() can now plot circular trees: the option is type =
506 "fan" or type = "f" (to avoid the ambiguity with type = "c").
508 o prop.part() has a new option `check.labels = FALSE' which allows
509 to considerably speed-up the calculations of bipartitions. As a
510 consequence, calculations of bootstrap values with boot.phylo()
511 should be much faster.
516 o read.GenBank() did not return correctly the list of species as
517 from ape 1.10: this is fixed in this version
519 o Applying as.phylo() on a tree of class "phylo" failed: the
520 object is now returned unchanged.
524 CHANGES IN APE VERSION 1.10-1
529 o The three new functions Ntip, Nnode, and Nedge return, for a
530 given tree, the number of tips, nodes, or edges, respectively.
535 o read.nexus() did not set correctly the class of the returned
536 object when reading multiple trees.
538 o mllt.plot() failed with objects of class c("multi.tree",
541 o unroot() did not work correctly in most cases.
543 o reorder.phylo() made R freeze in some occasions.
545 o Plotting a tree in pruningwise order failed.
547 o When plotting an unrooted tree, the tip labels where not all
548 correctly positioned if the option `cex' was used.
552 CHANGES IN APE VERSION 1.10
557 o Five new `method' functions have been introduced to manipulate
558 DNA sequences in binary format (see below).
560 o Three new functions have been introduced to convert between the
561 new binary and the character formats.
563 o The new function as.alignment converts DNA sequences stored as
564 single characters into the class "alignment" used by the package
567 o read.dna() and read.GenBank() have a new argument `as.character'
568 controlling whether the sequences are returned in binary format
574 o root() failed when the tree had node labels: this is fixed.
576 o plot.phylo() did not correctly set the limits on the y-axis with
577 the default setting: this is fixed.
579 o dist.dna() returned a wrong result for the LogDet, paralinear,
580 and BH87 models with `pairwise.deletion = TRUE'.
585 o DNA sequences are now internally stored in a binary format. See
586 the document "A Bit-Level Coding Scheme for Nucleotides" for the
587 details. Most functions analyzing DNA functions have been
588 modified accordingly and are now much faster (dist.dna is now
589 ca. 60 times faster).
593 CHANGES IN APE VERSION 1.9-4
598 o A bug was fixed in edgelabels().
600 o as.phylo.hclust() did not work correctly when the object of
601 class "hclust" has its labels set to NULL: the returned tree has
602 now its tip labels set to "1", "2", ...
604 o consensus could fail if some tip labels are a subset of others
605 (e.g., "a" and "a_1"): this is now fixed.
607 o mlphylo() failed in most cases if some branch lengths of the
608 initial tree were greater than one: an error message is now
611 o mlphylo() failed in most cases when estimating the proportion of
612 invariants: this is fixed.
616 CHANGES IN APE VERSION 1.9-3
621 o The new function edgelabels adds labels on the edge of the tree
622 in the same way than nodelabels or tiplabels.
627 o multi2di() did not handle correctly branch lengths with the
628 default option `random = TRUE': this is now fixed.
630 o A bug was fixed in nuc.div() when using pairwise deletions.
632 o A bug occurred in the analysis of bipartitions with large
633 numbers of large trees, with consequences on prop.part,
634 prop.clades, and boot.phylo.
636 o The calculation of the Billera-Holmes-Vogtmann distance in
637 dist.topo was wrong: this has been fixed.
641 CHANGES IN APE VERSION 1.9-2
646 o The new function ladderize reorganizes the internal structure of
647 a tree to plot them left- or right-ladderized.
649 o The new function dist.nodes computes the patristic distances
650 between all nodes, internal and terminal, of a tree. It replaces
651 the option `full = TRUE' of cophenetic.phylo (see below).
656 o A bug was fixed in old2new.phylo().
658 o Some bugs were fixed in chronopl().
660 o The edge colours were not correctly displayed by plot.phylo
661 (thank you to Li-San Wang for the fix).
663 o cophenetic.phylo() failed with multichotomous trees: this is
669 o read.dna() now returns the sequences in a matrix if they are
670 aligned (interleaved or sequential format). Sequences in FASTA
671 format are still returned in a list.
673 o The option `full' of cophenetic.phylo() has been removed because
674 it could not be used from the generic.
679 o rotate() has been removed; this function did not work correctly
684 CHANGES IN APE VERSION 1.9-1
689 o Trees with a single tip were not read correctly in R as the
690 element `Nnode' was not set: this is fixed.
692 o unroot() did not set correctly the number of nodes of the
693 unrooted tree in most cases.
695 o read.GenBank() failed when fetching very long sequences,
696 particularly of the BX-series.
698 o A bug was introduced in read.tree() with ape 1.9: it has been
703 CHANGES IN APE VERSION 1.9
708 o There are two new print `methods' for trees of class "phylo" and
709 lists of trees of class "multi.tree", so that they are now
710 displayed in a compact and informative way.
712 o There are two new functions, old2new.phylo and new2old.phylo,
713 for converting between the old and new coding of the class
716 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
717 LogDet ("logdet"), and paralinear ("paralin").
719 o compute.brlen() has been extended: several methods are now
720 available to compute branch lengths.
722 o write.dna() can now handle matrices as well as lists.
727 o cophenetic.phylo() sometimes returned a wrong result with
728 multichotomous trees: this is fixed.
730 o rotate() failed when a single tip was specified: the tree is now
733 o ace() did not return the correct index matrix with custom
734 models: this is fixed.
736 o multi2di() did not work correctly when resolving multichotomies
737 randomly: the topology was always the same, only the arrangement
738 of clades was randomized: this is fixed. This function now
739 accepts trees with no branch lengths.
741 o The output of diversi.gof() was blurred by useless prints when a
742 user distribution was specified. This has been corrected, and
743 the help page of this function has been expanded.
748 o The internal structure of the class "phylo" has been changed:
749 see the document "Definition of Formats for Coding Phylogenetic
750 Trees in R" for the details. In addition, the code of most
751 functions has been improved.
753 o Several functions have been improved by replacing some R codes
754 by C codes: pic, plot.phylo, and reorder.phylo.
756 o There is now a citation information: see citation("ape") in R.
758 o write.tree() now does not add extra 0's to branch lengths so
759 that 1.23 is printed "1.23" by default, not "1.2300000000".
761 o The syntax of bind.tree() has been simplified. This function now
762 accepts trees with no branch lengths, and handles correctly node
765 o The option `as.numeric' of mrca() has been removed.
767 o The unused options `format' and `rooted' of read.tree() have
770 o The unused option `format' of write.tree() has been removed.
772 o The use of node.depth() has been simplified.
776 CHANGES IN APE VERSION 1.8-5
781 o Two new functions read.nexus.data() and write.nexus.data(),
782 contributed by Johan Nylander, allow to read and write molecular
783 sequences in NEXUS files.
785 o The new function reorder.phylo() reorders the internal structure
786 of a tree of class "phylo". It is used as the generic, e.g.,
789 o read.tree() and read.nexus() can now read trees with a single
792 o The new data set `cynipids' supplies a set of protein sequences
798 o The code of all.equal.phylo() has been completely rewritten
799 (thanks to Benoît Durand) which fixes several bugs.
801 o read.tree() and read.nexus() now checks the labels of the tree
802 to remove or substitute any characters that are illegal in the
803 Newick format (parentheses, etc.)
805 o A negative P-value could be returned by mantel.test(): this is
810 CHANGES IN APE VERSION 1.8-4
815 o The new function sh.test() computes the Shimodaira-
818 o The new function collapse.singles() removes the nodes with a
819 single descendant from a tree.
821 o plot.phylo() has a new argument `tip.color' to specify the
824 o mlphylo() has now an option `quiet' to control the display of
825 the progress of the analysis (the default is FALSE).
830 o read.dna() did not read correctly sequences in sequential format
831 with leading alignment gaps "-": this is fixed.
833 o ace() returned a list with no class so that the generic
834 functions (anova, logLik, ...) could not be used directly. This
835 is fixed as ace() now returns an object of class "ace".
837 o anova.ace() had a small bug when computing the number of degrees
838 of freedom: this is fixed.
840 o mlphylo() did not work when the sequences were in a matrix or
841 a data frame: this is fixed.
843 o rtree() did not work correctly when trying to simulate an
844 unrooted tree with two tips: an error message is now issued.
849 o The algorithm of rtree() has been changed: it is now about 40,
850 100, and 130 times faster for 10, 100, and 1000 tips,
855 CHANGES IN APE VERSION 1.8-3
860 o There are four new `method' functions to be used with the
861 results of ace(): logLik(), deviance(), AIC(), and anova().
863 o The plot method of phymltest has two new arguments: `main' to
864 change the title, and `col' to control the colour of the
865 segments showing the AIC values.
867 o ace() has a new argument `ip' that gives the initial values used
868 in the ML estimation with discrete characters (see the examples
869 in ?ace). This function now returns a matrix giving the indices
870 of the estimated rates when analysing discrete characters.
872 o nodelabels() and tiplabels() have a new argument `pie' to
873 represent proportions, with any number of categories, as
874 piecharts. The use of the option `thermo' has been improved:
875 there is now no limitation on the number of categories.
880 o mlphylo() did not work with more than two partitions: this is
883 o root() failed if the proposed outgroup was already an outgroup
884 in the tree: this is fixed.
886 o The `col' argument in nodelabels() and tiplabels() was not
887 correctly passed when `text' was used: this is fixed.
889 o Two bugs were fixed in mlphylo(): parameters were not always
890 correctly output, and the estimation failed in some cases.
892 o plot.phylo() was stuck when given a tree with a single tip: this
893 is fixed and a message error is now returned.
895 o An error was corrected in the help page of gammaStat regarding
896 the calculation of P-values.
898 o Using gls() could crash R when the number of species in the tree
899 and in the variables were different: this is fixed.
903 CHANGES IN APE VERSION 1.8-2
908 o The new function mlphylo() fits a phylogenetic tree by maximum
909 likelihood from DNA sequences. Its companion function DNAmodel()
910 is used to define the substitution model which may include
911 partitioning. There are methods for logLik(), deviance(), and
912 AIC(), and the summary() method has been extended to display in
913 a friendly way the results of this model fitting. Currently, the
914 functionality is limited to estimating the substitution and
915 associated parameters and computing the likelihood.
917 o The new function drop1.compar.gee (used as, e.g., drop1(m))
918 tests for single effects in GEE-based comparative method. A
919 warning message is printed if there is not enough degrees of
925 o An error message was sometimes issued by plot.multi.tree(),
926 though with no consequence.
930 CHANGES IN APE VERSION 1.8-1
935 o There is a new plot method for lists of trees (objects of class
936 "multi.tree"): it calls plot.phylo() internally and is
937 documented on the same help page.
942 o A bug was fixed in the C code that analyzes bipartitions: this
943 has impact on several functions like prop.part, prop.clades,
944 boot.phylo, or consensus.
946 o root() did not work correctly when the specified outgroup had
947 more than one element: this is fixed.
949 o dist.dna() sometimes returned a warning inappropriately: this
952 o If the distance object given to nj() had no rownames, nj()
953 returned a tree with no tip labels: it now returns tips labelled
954 "1", "2", ..., corresponding to the row numbers.
959 o nj() has been slightly changed so that tips with a zero distance
960 are first aggregated with zero-lengthed branches; the usual NJ
961 procedure is then performed on a distance matrix without 0's.
965 CHANGES IN APE VERSION 1.8
970 o The new function chronopl() estimates dates using the penalized
971 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
973 o The new function consensus() calculates the consensus tree of a
976 o The new function evolve.phylo() simulates the evolution of
977 continuous characters along a phylogeny under a Brownian model.
979 o The new plot method for objects of class "ancestral" displays a
980 tree together with ancestral values, as returned by the above
983 o The new function as.phylo.formula() returns a phylogeny from a
984 set of nested taxonomic variables given as a formula.
986 o The new function read.caic() reads trees in CAIC format.
988 o The new function tiplabels() allows to add labels to the tips
989 of a tree using text or plotting symbols in a flexible way.
991 o The new function unroot() unroots a phylogeny.
993 o multi2di() has a new option, `random', which specifies whether
994 to resolve the multichotomies randomly (the default) or not.
996 o prop.part() now returns an object of class "prop.part" for which
997 there are print (to display a partition in a more friendly way)
998 and summary (to extract the numbers) methods.
1000 o plot.phylo() has a new option, `show.tip.label', specifying
1001 whether to print the labels of the tips. The default is TRUE.
1003 o The code of nj() has been replaced by a faster C code: it is now
1004 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1007 o write.nexus() now writes whether a tree is rooted or not.
1012 o Two bugs have been fixed in root(): unrooted trees are now
1013 handled corretly, and node labels are now output normally.
1015 o A bug was fixed in phymltest(): the executable couldn't be found
1018 o Three bug have been fixed in ace(): computing the likelihood of
1019 ancestral states of discrete characters failed, custom models
1020 did not work, and the function failed with a null gradient (a
1021 warning message is now returned; this latter bug was also
1022 present in yule.cov() as well and is now fixed).
1024 o pic() hanged out when missing data were present: a message error
1027 o A small bug was fixed in dist.dna() where the gamma correction
1028 was not always correctly dispatched.
1030 o plot.phylo() plotted correctly the root edge only when the tree
1031 was plotted rightwards: this works now for all directions.
1036 o dist.taxo() has been renamed as weight.taxo().
1038 o Various error and warning messages have been improved.
1042 CHANGES IN APE VERSION 1.7
1045 o The new function ace() estimates ancestral character states for
1046 continuous characters (with ML, GLS, and contrasts methods), and
1047 discrete characters (with ML only) for any number of states.
1049 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1050 of directional evolution for continuous characters. The user
1051 specifies the node(s) of the tree where the character optimum
1054 o The new function is.rooted() tests whether a tree (of class
1057 o The new function rcoal() generates random ultrametric trees with
1058 the possibility to specify the function that generates the
1059 inter-nodes distances.
1061 o The new function mrca() gives for all pairs of tips in a tree
1062 (and optionally nodes too) the most recent common ancestor.
1064 o nodelabels() has a new option `thermo' to plot proportions (up
1065 to three classes) on the nodes of a tree.
1067 o rtree() has been improved: it can now generate rooted or
1068 unrooted trees, and the mathematical function that generates the
1069 branch lengths may be specified by the user. The tip labels may
1070 be given directly in the call to rtree. The limit cases (n = 2,
1071 3) are now handled correctly.
1073 o dist.topo() has a new argument `method' with two choices: "PH85"
1074 for Penny and Henny's method (already available before and now
1075 the default), and "BHV01" for the geometric distance by Billera
1076 et al. (2001, Adv. Appl. Math. 27:733).
1078 o write.tree() has a new option, `digits', which specifies the
1079 number of digits to be printed in the Newick tree. By default
1080 digits = 10. The numbers are now always printed in decimal form
1081 (i.e., 1.0e-1 is now avoided).
1083 o dist.dna() can now compute the raw distances between pairs of
1084 DNA sequences by specifying model = "raw".
1086 o dist.phylo() has a new option `full' to possibly compute the
1087 distances among all tips and nodes of the tree. The default if
1093 o Several bugs were fixed in all.equal.phylo().
1095 o dist.dna() did not handle correctly gaps ("-") in alignments:
1096 they are now considered as missing data.
1098 o rotate() did not work if the tips were not ordered: this is
1101 o mantel.test() returned NA in some special cases: this is fixed
1102 and the function has been improved and is now faster.
1104 o A bug was fixed in diversi.gof() where the calculation of A² was
1107 o cherry() did not work correctly under some OSs (mainly Linux):
1110 o is.binary.tree() has been modified so that it works with both
1111 rooted and unrooted trees.
1113 o The documentation of theta.s() was not correct: this has been
1116 o plot.mst() did not work correctly: this is fixed.
1120 CHANGES IN APE VERSION 1.6
1125 o The new function dist.topo() computes the topological distances
1128 o The new function boot.phylo() performs a bootstrap analysis on
1129 phylogeny estimation.
1131 o The new functions prop.part() and prop.clades() analyse
1132 bipartitions from a series of trees.
1137 o read.GenBank() now uses the EFetch utility of NCBI instead of
1138 the usual Web interface: it is now much faster (e.g., 12 times
1139 faster to retrieve 8 sequences, 37 times for 60 sequences).
1144 o Several bugs were fixed in read.dna().
1146 o Several bugs were fixed in diversi.time().
1148 o is.binary.tree() did not work correctly if the tree has no edge
1149 lengths: this is fixed.
1151 o drop.tip() did not correctly propagated the `node.label' of a
1152 tree: this is fixed.
1156 CHANGES IN APE VERSION 1.5
1161 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1162 convert objects between the classes "phylo" and "matching". The
1163 latter implements the representation of binary trees introduced by
1164 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1165 as.matching() has been introduced as well.
1167 o Two new functions, multi2di() and di2multi(), allow to resolve
1168 and collapse multichotomies with branches of length zero.
1170 o The new function nuc.div() computes the nucleotide diversity
1171 from a sample a DNA sequences.
1173 o dist.dna() has been completely rewritten with a much faster
1174 (particularly for large data sets) C code. Eight models are
1175 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1176 option `method' has been renamed `model'). Computation of variance
1177 is available for all models. A gamma-correction is possible for
1178 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1179 to remove sites with missing data on a pairwise basis. The option
1180 `GCcontent' has been removed.
1182 o read.GenBank() has a new option (species.names) which specifies
1183 whether to return the species names of the organisms in addition
1184 to the accession numbers of the sequences (this is the default
1187 o write.nexus() can now write several trees in the same NEXUS file.
1189 o drop.tip() has a new option `root.edge' that allows to specify the
1190 new root edge if internal branches are trimmed.
1195 o as.phylo.hclust() failed if some labels had parentheses: this
1198 o Several bugs were fixed in all.equal.phylo(). This function now
1199 returns the logical TRUE if the trees are identical but with
1200 different representations (a report was printed previously).
1202 o read.GenBank() did not correctly handle ambiguous base codes:
1208 o birthdeath() now returns an object of class "birthdeath" for
1209 which there is a print method.
1213 CHANGES IN APE VERSION 1.4
1218 o The new function nj() performs phylogeny estimation with the
1219 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1222 o The new function which.edge() identifies the edges of a tree
1223 that belong to a group specified as a set of tips.
1225 o The new function as.phylo.phylog() converts an object of class
1226 "phylog" (from the package ade4) into an object of class
1229 o The new function axisPhylo() draws axes on the side of a
1232 o The new function howmanytrees() calculates the number of trees
1233 in different cases and giving a number of tips.
1235 o write.tree() has a new option `multi.line' (TRUE by default) to
1236 write a Newick tree on several lines rather than on a single
1239 o The functionalities of zoom() have been extended. Several
1240 subtrees can be visualized at the same time, and they are marked
1241 on the main tree with colors. The context of the subtrees can be
1242 marked with the option `subtree' (see below).
1244 o drop.tip() has a new option `subtree' (FALSE by default) which
1245 specifies whether to output in the tree how many tips have been
1248 o The arguments of add.scale.bar() have been redefined and have
1249 now default values (see ?add.scale.bar for details). This
1250 function now works even if the plotted tree has no edge length.
1252 o plot.phylo() can now plot radial trees, but this does not take
1253 edge lengths into account.
1255 o In plot.phylo() with `type = "phylogram"', if the values of
1256 `edge.color' and `edge.width' are identical for sister-branches,
1257 they are propagated to the vertical line that link them.
1262 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1263 crashing. This is fixed.
1265 o In plot.phylo(), the options `edge.color' and `edge.width' are
1266 now properly recycled; their default values are now "black" and
1269 o A bug has been fixed in write.nexus().
1274 o The function node.depth.edgelength() has been removed and
1275 replaced by a C code.
1279 CHANGES IN APE VERSION 1.3-1
1284 o The new function nodelabels() allows to add labels to the nodes
1285 of a tree using text or plotting symbols in a flexible way.
1287 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1288 numeric values specifying the lower and upper limits on the x-
1289 and y-axes. This allows to leave some space on any side of the
1290 tree. If a single value is given, this is taken as the upper
1295 CHANGES IN APE VERSION 1.3
1300 o The new function phymltest() calls the software PHYML and fits
1301 28 models of DNA sequence evolution. There are a print method to
1302 display likelihood and AIC values, a summary method to compute
1303 the hierarchical likelihood ratio tests, and a plot method to
1304 display graphically the AIC values of each model.
1306 o The new function yule.cov() fits the Yule model with covariates,
1307 a model where the speciation rate is affected by several species
1308 traits through a generalized linear model. The parameters are
1309 estimated by maximum likelihood.
1311 o Three new functions, corBrownian(), corGrafen(), and
1312 corMartins(), compute the expected correlation structures among
1313 species given a phylogeny under different models of evolution.
1314 These can be used for GLS comparative phylogenetic methods (see
1315 the examples). There are coef() and corMatrix() methods and an
1316 Initialize.corPhyl() function associated.
1318 o The new function compar.cheverud() implements Cheverud et al.'s
1319 (1985; Evolution 39:1335) phylogenetic comparative method.
1321 o The new function varcomp() estimates variance components; it has
1324 o Two new functions, panel.superpose.correlogram() and
1325 plot.correlogramList(), allow to plot several phylogenetic
1328 o The new function node.leafnumber() computes the number of leaves
1329 of a subtree defined by a particular node.
1331 o The new function node.sons() gets all tags of son nodes from a
1334 o The new function compute.brlen() computes the branch lengths of
1335 a tree according to a specified method.
1337 o plot.phylo() has three new options: "cex" controls the size of
1338 the (tip and node) labels (thus it is no more needed to change
1339 the global graphical parameter), "direction" which allows to
1340 plot the tree rightwards, leftwards, upwards, or downwards, and
1341 "y.lim" which sets the upper limit on the y-axis.
1346 o Some functions which try to match tip labels and names of
1347 additional data (e.g. vector) are likely to fail if there are
1348 typing or syntax errors. If both series of names do not perfectly
1349 match, they are ignored and a warning message is now issued.
1350 These functions are bd.ext, compar.gee, pic. Their help pages
1351 have been clarified on this point.
1355 CHANGES IN APE VERSION 1.2-7
1360 o The new function root() reroots a phylogenetic tree with respect
1361 to a specified outgroup.
1363 o The new function rotate() rotates an internal branch of a tree.
1365 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1366 trees) controls the display of the tip labels in unrooted trees.
1367 This display has been greatly improved: the tip labels are now not
1368 expected to overlap with the tree (particularly if lab4ut =
1369 "axial"). In all cases, combining appropriate values of "lab4ut"
1370 and the font size (via "par(cex = )") should result in readable
1371 unrooted trees. See ?plot.phylo for some examples.
1373 o In drop.tip(), the argument `tip' can now be numeric or character.
1378 o drop.tip() did not work correctly with trees with no branch
1379 lengths: this is fixed.
1381 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1382 plotted with some line crossings: this is now fixed.
1386 CHANGES IN APE VERSION 1.2-6
1391 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1392 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1393 to implement comparative methods with an autocorrelation approach.
1395 o A new data set describing some life history traits of Carnivores
1401 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1406 o When plotting a tree with plot.phylo(), the new default of the
1407 option `label.offset' is now 0, so the labels are always visible.
1411 CHANGES IN APE VERSION 1.2-5
1416 o The new function bd.ext() fits a birth-death model with combined
1417 phylogenetic and taxonomic data, and estimates the corresponding
1418 speciation and extinction rates.
1423 o The package gee is no more required by ape but only suggested
1424 since only the function compar.gee() calls gee.
1428 CHANGES IN APE VERSION 1.2-4
1433 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1434 and lines.popsize) implementing a new approach for inferring the
1435 demographic history from genealogies using a reversible jump
1436 MCMC have been introduced.
1438 o The unit of time in the skyline plot and in the new plots can
1439 now be chosen to be actual years, rather than substitutions.
1443 CHANGES IN APE VERSION 1.2-3
1448 o The new function rtree() generates a random binary tree with or
1449 without branch lengths.
1451 o Two new functions for drawing lineages-through-time (LTT) plots
1452 are provided: ltt.lines() adds a LTT curve to an existing plot,
1453 and mltt.plot() does a multiple LTT plot giving several trees as
1454 arguments (see `?ltt.plot' for details).
1459 o Some taxon names made R crashing when calling as.phylo.hclust():
1462 o dist.dna() returned an error with two identical DNA sequences
1463 (only using the Jukes-Cantor method returned 0): this is fixed.
1468 o The function dist.phylo() has been re-written using a different
1469 algorithm: it is now about four times faster.
1471 o The code of branching.times() has been improved: it is now about
1476 CHANGES IN APE VERSION 1.2-2
1481 o The new function seg.sites() finds the segregating sites in a
1482 sample of DNA sequences.
1487 o A bug introduced in read.tree() and in read.nexus() with version
1490 o A few errors were corrected and a few examples were added in the
1495 CHANGES IN APE VERSION 1.2-1
1500 o plot.phylo() can now draw the edge of the root of a tree if it
1501 has one (see the new option `root.edge', its default is FALSE).
1506 o A bug was fixed in read.nexus(): files with semicolons inside
1507 comment blocks were not read correctly.
1509 o The behaviour of read.tree() and read.nexus() was corrected so
1510 that tree files with badly represented root edges (e.g., with
1511 an extra pair of parentheses, see the help pages for details)
1512 are now correctly represented in the object of class "phylo";
1513 a warning message is now issued.
1517 CHANGES IN APE VERSION 1.2
1522 o plot.phylo() has been completely re-written and offers several
1523 new functionalities. Three types of trees can now be drawn:
1524 phylogram (as previously), cladogram, and unrooted tree; in
1525 all three types the branch lengths can be drawn using the edge
1526 lengths of the phylogeny or not (e.g., if the latter is absent).
1527 The vertical position of the nodes can be adjusted with two
1528 choices (see option `node.pos'). The code has been re-structured,
1529 and two new functions (potentially useful for developpers) are
1530 documented separately: node.depth.edgelength() and node.depth();
1531 see the respective help pages for details.
1533 o The new function zoom() allows to explore very large trees by
1534 focusing on a small portion of it.
1536 o The new function yule() fits by maximum likelihood the Yule model
1537 (birth-only process) to a phylogenetic tree.
1539 o Support for writing DNA sequences in FASTA format has been
1540 introduced in write.dna() (support for reading sequences in
1541 this format was introduced in read.dna() in version 1.1-2).
1542 The function has been completely re-written, fixing some bugs
1543 (see below); the default behaviour is no more to display the
1544 sequences on the standard output. Several options have been
1545 introduced to control the sequence printing in a flexible
1546 way. The help page has been extended.
1548 o A new data set is included: a supertree of bats in NEXUS format.
1553 o In theta.s(), the default of the option `variance' has
1554 been changed to `FALSE' (as was indicated in the help page).
1556 o Several bugs were fixed in the code of all.equal.phylo().
1558 o Several bugs were fixed in write.dna(), particularly this
1559 function did not work with `format = "interleaved"'.
1561 o Various errors were corrected in the help pages.
1566 o The argument names of as.hclust.phylo() have been changed
1567 from "(phy)" to "(x, ...)" to conform to the definition of
1568 the corresponding generic function.
1570 o gamma.stat() has been renamed gammaStat() to avoid confusion
1571 since gamma() is a generic function.
1575 CHANGES IN APE VERSION 1.1-3
1580 o base.freq() previously did not return a value of 0 for
1581 bases absent in the data (e.g., a vector of length 3 was
1582 returned if one base was absent). This is now fixed (a
1583 vector of length 4 is always returned).
1585 o Several bugs were fixed in read.nexus(), including that this
1586 function did not work in this absence of a "TRANSLATE"
1587 command in the NEXUS file, and that the commands were
1592 CHANGES IN APE VERSION 1.1-2
1597 o The Tamura and Nei (1993) model of DNA distance is now implemented
1598 in dist.dna(): five models are now available in this function.
1600 o A new data set is included: a set of 15 sequences of the
1601 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1607 o A bug in read.nexus() was fixed.
1609 o read.dna() previously did not work correctly in most cases.
1610 The function has been completely re-written and its help page
1611 has been considerably extended (see ?read.dna for details).
1612 Underscores (_) in taxon names are no more replaced with
1613 spaces (this behaviour was undocumented).
1615 o A bug was fixed in write.dna().
1619 CHANGES IN APE VERSION 1.1-1
1624 o A bug in read.tree() introduced in APE 1.1 was fixed.
1626 o A bug in compar.gee() resulted in an error when trying to fit
1627 a model with `family = "binomial"'. This is now fixed.
1631 CHANGES IN APE VERSION 1.1
1636 o The Klastorin (1982) method as suggested by Misawa and Tajima
1637 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1638 on the basis of phylogenetic trees has been implemented (see
1639 the function klastorin()).
1641 o Functions have been added to convert APE's "phylo" objects in
1642 "hclust" cluster objects and vice versa (see the help page of
1643 as.phylo for details).
1645 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1646 are introduced for the estimation of absolute evolutionary rates
1647 (ratogram) and dated clock-like trees (chronogram) from
1648 phylogenetic trees using the non-parametric rate smoothing approach
1649 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1651 o A summary method is now provided printing a summary information on a
1652 phylogenetic tree with, for instance, `summary(tree)'.
1654 o The behaviour of read.tree() was changed so that all spaces and
1655 tabulations in tree files are now ignored. Consequently, spaces in tip
1656 labels are no more allowed. Another side effect is that read.nexus()
1657 now does not replace the underscores (_) in tip labels with spaces
1658 (this behaviour was undocumented).
1660 o The function plot.phylo() has a new option (`underscore') which
1661 specifies whether the underscores in tip labels should be written on
1662 the plot as such or replaced with spaces (the default).
1664 o The function birthdeath() now computes 95% confidence intervals of
1665 the estimated parameters using profile likelihood.
1667 o Three new data sets are included: a gene tree estimated from 36
1668 landplant rbcL sequences, a gene tree estimated from 32 opsin
1669 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1674 o A bug was fixed in dist.gene() where nothing was returned.
1676 o A bug in plot.mst() was fixed.
1678 o A bug in vcv.phylo() resulted in false correlations when the
1679 option `cor = TRUE' was used (now fixed).
1683 CHANGES IN APE VERSION 1.0
1688 o Two new functions, read.dna() and write.dna(), read/write in a file
1689 DNA sequences in interleaved or in sequential format.
1691 o Two new functions, read.nexus() and write.nexus(), read/write trees
1694 o The new function bind.tree() allows to bind two trees together,
1695 possibly handling root edges to give internal branches.
1697 o The new function drop.tip() removes the tips in a phylogenetic tree,
1698 and trims (or not) the corresponding internal branches.
1700 o The new function is.ultrametric() tests if a tree is ultrametric.
1702 o The function plot.phylo() has more functionalities such as drawing the
1703 branches with different colours and/or different widths, showing the
1704 node labels, controling the position and font of the labels, rotating
1705 the labels, and controling the space around the plot.
1707 o The function read.tree() can now read trees with no branch length,
1708 such as "(a,b),c);". Consequently, the element `edge.length' in
1709 objects of class "phylo" is now optional.
1711 o The function write.tree() has a new default behaviour: if the default
1712 for the option `file' is used (i.e. file = ""), then a variable of
1713 mode character containing the tree in Newick format is returned which
1714 can thus be assigned (e.g., tree <- write.tree(phy)).
1716 o The function read.tree() has a new argument `text' which allows
1717 to read the tree in a variable of mode character.
1719 o A new data set is included: the phylogenetic relationships among
1720 the orders of birds from Sibley and Ahlquist (1990).
1724 CHANGES IN APE VERSION 0.2-1
1729 o Several bugs were fixed in the help pages.
1733 CHANGES IN APE VERSION 0.2
1738 o The function write.tree() writes phylogenetic trees (objects of class
1739 "phylo") in an ASCII file using the Newick parenthetic format.
1741 o The function birthdeath() fits a birth-death model to branching times
1742 by maximum likelihood, and estimates the corresponding speciation and
1745 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1748 o The function is.binary.tree() tests whether a phylogeny is binary.
1750 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1751 as well as some methods are introduced.
1753 o Several functions, including some generics and methods, for computing
1754 skyline plot estimates (classic and generalized) of effective
1755 population size through time are introduced and replace the function
1756 skyline.plot() in version 0.1.
1758 o Two data sets are now included: the phylogenetic relationships among
1759 the families of birds from Sibley and Ahlquist (1990), and an
1760 estimated clock-like phylogeny of HIV sequences sampled in the
1761 Democratic Republic of Congo.
1764 DEPRECATED & DEFUNCT
1766 o The function skyline.plot() in ape 0.1 has been deprecated and
1767 replaced by more elaborate functions (see above).
1772 o Two important bugs were fixed in plot.phylo(): phylogenies with
1773 multichotomies not at the root or not with only terminal branches,
1774 and phylogenies with a single node (i.e. only terminal branches)
1775 did not plot. These trees should be plotted correctly now.
1777 o Several bugs were fixed in diversi.time() in the computation of
1780 o Various errors were corrected in the help pages.