1 CHANGES IN APE VERSION 2.2-4
5 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
6 now fixed. (thanks to Peter Wragg for the fix!)
11 o There is now a general help page displayed with '?ape'
15 CHANGES IN APE VERSION 2.2-3
20 o The new function extract.clade extracts a clade from a tree by
21 specifying a node number or label.
23 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
24 operations of the same names.
26 o dist.dna() can now return the number of site differences by
32 o chronopl() did not work with CV = TRUE.
34 o read.nexus() did not work correctly in some situations (trees on
35 multiple lines with different numbers of lines and/or with
36 comments inserted within the trees).
38 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
39 the number of lineages with non-binary trees.
44 o ape has now a namespace.
46 o drip.tip() has been improved: it should be much faster and work
47 better in some cases (e.g., see the example in ?zoom).
51 CHANGES IN APE VERSION 2.2-2
56 o dist.gene() has been substantially improved and gains an option
59 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
65 o prop.part() failed with a single tree with the default option
66 'check.labels = TRUE'.
68 o summary.DNAbin() failed to display correctly the summary of
69 sequence lengths with lists of sequences of 10,000 bases or more
70 (because summary.default uses 4 significant digits by default).
72 o read.nexus() failed to read a file with a single tree with line
73 breaks in the Newick string.
75 o del.gaps() returned a list of empty sequences when there were no
81 o phymltest() has been updated for PhyML 3.0 and gains an option
82 'append', whereas the option 'path2exec' has been removed.
84 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
85 which is returned unchanged (instead of an error).
87 o The data sets bird.orders and bird.families are now stored as
88 Newick strings; i.e., the command data(bird.orders) calls
93 CHANGES IN APE VERSION 2.2-1
98 o The new function makeLabel() helps to modify labels of trees,
99 lists of trees, or DNA sequences, with several utilities to
100 truncate and/or make them unique, substituting some
101 characters, and so on.
103 o The new function del.gaps() removes insertion gaps ("-") in a
104 set of DNA sequences.
106 o read.dna() can now read Clustal files (*.aln).
111 o root() failed with 'resolve.root = TRUE' when the root was
112 already the specified root.
114 o Several bugs were fixed in mlphylo().
116 o collapsed.singles() did not propagate the 'Nnode' and
117 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
119 o read.nexus() failed to remove correctly the comments within
122 o read.nexus() failed to read a file with a single tree and no
123 translation of tip labels.
125 o read.nexus() failed to place correctly tip labels when reading
126 a single tree with no edge lengths.
128 o A bug was fixed in sh.test().
133 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
136 o The option 'check.labels' of consensus() and prop.part() is now
139 o write.dna() now does not truncate names to 10 characters with
144 CHANGES IN APE VERSION 2.2
149 o Four new functions have been written by Damien de Vienne for the
150 graphical exploration of large trees (cophyloplot, subtrees,
151 subtreeplot), and to return the graphical coordinates of tree
154 o The new functions corPagel and corBlomberg implement the Pagel's
155 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
157 o chronopl() has been improved and gains several options: see its
158 help page for details.
160 o boot.phylo() has now an option 'trees' to possibly return the
161 bootstraped trees (the default is FALSE).
163 o prop.part() has been improved and should now be faster in all
169 o read.dna() failed if "?" occurred in the first 10 sites of the
172 o The x/y aspect of the plot is now respected when plotting a
173 circular tree (type = "r" or "f").
175 o Drawing the tip labels sometimes failed when plotting circular
178 o zoom() failed when tip labels were used instead of their numbers
179 (thanks to Yan Wong for the fix).
181 o drop.tip() failed with some trees (fixed by Yan Wong).
183 o seg.sites() failed with a list.
185 o consensus() failed in some cases. The function has been improved
186 as well and is faster.
190 CHANGES IN APE VERSION 2.1-3
195 o A bug in read.nexus() made the Windows R-GUI crash.
197 o An error was fixed in the computation of ancestral character
198 states by generalized least squares in ace().
200 o di2multi() did not modify node labels correctly.
202 o multi2di() failed if the tree had its attribute "order" set to
207 CHANGES IN APE VERSION 2.1-2
212 o There three new methods for the "multiPhylo" class: str, $,
215 o root() gains the options 'node' and 'resolve.root'
216 (FALSE by default) as well as its code being improved.
218 o mltt.plot() has now an option 'log' used in the same way
219 than in plot.default().
224 o mltt.plot() failed to display the legend with an unnamed
227 o nodelabels() with pies now correcly uses the argument
228 'cex' to draw symbols of different sizes (which has
229 worked already for thermometers).
231 o read.nexus() generally failed to read very big files.
236 o The argument 'family' of compar.gee() can now be a function
237 as well as a character string.
239 o read.tree() and read.nexus() now return an unnamed list if
242 o read.nexus() now returns a modified object of class "multiPhylo"
243 when there is a TRANSLATE block in the NEXUS file: the individual
244 trees have no 'tip.label' vector, but the list has a 'TipLabel'
245 attribute. The new methods '$' and '[[' set these elements
246 correctly when extracting trees.
250 CHANGES IN APE VERSION 2.1-1
255 o The new function rmtree generates lists of random trees.
257 o rcoal() now generates a genuine coalescent tree by default
258 (thanks to Vladimir Minin for the code).
263 o nuc.div() returned an incorrect value with the default
264 pairwise.deletion = FALSE.
269 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
270 have been improved so that they are stabler and faster.
272 o R packages used by ape are now loaded silently; lattice and gee
273 are loaded only when needed.
277 CHANGES IN APE VERSION 2.1
282 o The new function identify.phylo identifies clades on a plotted
283 tree using the mouse.
285 o It is now possible to subset a list of trees (object of class
286 "multiPhylo") with "[" while keeping its class correct.
288 o The new function as.DNAbin.alignment converts DNA sequences
289 stored in the "alignment" format of the package seqinr into
290 an object of class "DNAbin".
292 o The new function weight.taxo2 helps to build similarity matrices
293 given two taxonomic levels (usually called by other functions).
295 o write.tree() can now take a list of trees (class "multiPhylo")
296 as its main argument.
298 o plot.correlogram() and plot.correlogramList() have been
299 improved, and gain several options (see the help page for
300 details). A legend is now plotted by default.
305 o dist.dna() returned some incorrect values with `model = "JC69"'
306 and `pairwise.deletion = TRUE'. This affected only the
307 distances involving sequences with missing values. (Thanks
308 to Bruno Toupance for digging this bug out.)
310 o write.tree() failed with some trees: this is fixed by removing
311 the `multi.line' option (trees are now always printed on a
314 o read.nexus() did not correctly detect trees with multiple root
315 edges (see OTHER CHANGES).
320 o The code of mlphylo() has been almost entirely rewritten, and
321 should be much stabler. The options have been also greatly
322 simplified (see ?mlphylo and ?DNAmodel for details).
324 o The internal function nTips has been renamed klastorin_nTips.
326 o The code of is.ultrametric() contained redundancies and has
329 o The code of Moran.I() and of correlogram.formula() have been
332 o read.tree() and read.nexus() now return an error when trying to
333 read a tree with multiple root edges (see BUG FIXES). The
334 correction applied in previous version did not work in all
337 o The class c("multi.tree", "phylo") has been renamed
343 o There is now a vignette in ape: see vignette("MoranI", "ape").
348 o as.matching() and as.phylo.matching() do not support branch
351 o correlogram.phylo() and discrete.dist() have been removed.
355 CHANGES IN APE VERSION 2.0-2
360 o The new function matexpo computes the exponential of a square
363 o The new function unique.multi.tree removes duplicate trees from
366 o yule() has a new option `use.root.edge = FALSE' that specifies
367 to ignore, by default, the root edge of the tree if it exists.
372 o which.edge() failed when the index of a single terminal edge was
375 o In diversi.time(), the values returned for model C were
378 o A bug was fixed in yule() that affected the calculation of the
379 likelihood in the presence of ties in the branching times.
381 o There was a bug in the C function mat_expo4x4 affecting the
382 calculations of the transition probabilities for models HKY and
385 o A small bug was fixed in as.matrix.DNAbin (thanks to James
388 o rtree() did not `shuffle' the tip labels by default, so only a
389 limited number of labelled topologies could be generated.
393 CHANGES IN APE VERSION 2.0-1
398 o The three new functions bionj, fastme.ols, and fastme.bal
399 perform phylogeny estimation by the BIONJ and fastME methods in
400 OLS and balanced versions. This is a port to R of previous
401 previous programs done by Vincent Lefort.
403 o The new function chronoMPL performs molecular dating with the
404 mean path lengths method of Britton et al. (2002, Mol. Phyl.
407 o The new function rotate, contributed by Christoph Heibl, swaps
408 two clades connected to the same node. It works also with
409 multichotomous nodes.
411 o The new `method' as.matrix.DNAbin() may be used to convert
412 easily DNA sequences stored in a list into a matrix while
413 keeping the names and the class.
418 o chronopl() failed when some branch lengths were equal to zero:
419 an error message is now returned.
421 o di2multi() failed when there was a series of consecutive edges
426 CHANGES IN APE VERSION 1.10-2
431 o plot.phylo() can now plot circular trees: the option is type =
432 "fan" or type = "f" (to avoid the ambiguity with type = "c").
434 o prop.part() has a new option `check.labels = FALSE' which allows
435 to considerably speed-up the calculations of bipartitions. As a
436 consequence, calculations of bootstrap values with boot.phylo()
437 should be much faster.
442 o read.GenBank() did not return correctly the list of species as
443 from ape 1.10: this is fixed in this version
445 o Applying as.phylo() on a tree of class "phylo" failed: the
446 object is now returned unchanged.
450 CHANGES IN APE VERSION 1.10-1
455 o The three new functions Ntip, Nnode, and Nedge return, for a
456 given tree, the number of tips, nodes, or edges, respectively.
461 o read.nexus() did not set correctly the class of the returned
462 object when reading multiple trees.
464 o mllt.plot() failed with objects of class c("multi.tree",
467 o unroot() did not work correctly in most cases.
469 o reorder.phylo() made R freeze in some occasions.
471 o Plotting a tree in pruningwise order failed.
473 o When plotting an unrooted tree, the tip labels where not all
474 correctly positioned if the option `cex' was used.
478 CHANGES IN APE VERSION 1.10
483 o Five new `method' functions have been introduced to manipulate
484 DNA sequences in binary format (see below).
486 o Three new functions have been introduced to convert between the
487 new binary and the character formats.
489 o The new function as.alignment converts DNA sequences stored as
490 single characters into the class "alignment" used by the package
493 o read.dna() and read.GenBank() have a new argument `as.character'
494 controlling whether the sequences are returned in binary format
500 o root() failed when the tree had node labels: this is fixed.
502 o plot.phylo() did not correctly set the limits on the y-axis with
503 the default setting: this is fixed.
505 o dist.dna() returned a wrong result for the LogDet, paralinear,
506 and BH87 models with `pairwise.deletion = TRUE'.
511 o DNA sequences are now internally stored in a binary format. See
512 the document "A Bit-Level Coding Scheme for Nucleotides" for the
513 details. Most functions analyzing DNA functions have been
514 modified accordingly and are now much faster (dist.dna is now
515 ca. 60 times faster).
519 CHANGES IN APE VERSION 1.9-4
524 o A bug was fixed in edgelabels().
526 o as.phylo.hclust() did not work correctly when the object of
527 class "hclust" has its labels set to NULL: the returned tree has
528 now its tip labels set to "1", "2", ...
530 o consensus could fail if some tip labels are a subset of others
531 (e.g., "a" and "a_1"): this is now fixed.
533 o mlphylo() failed in most cases if some branch lengths of the
534 initial tree were greater than one: an error message is now
537 o mlphylo() failed in most cases when estimating the proportion of
538 invariants: this is fixed.
542 CHANGES IN APE VERSION 1.9-3
547 o The new function edgelabels adds labels on the edge of the tree
548 in the same way than nodelabels or tiplabels.
553 o multi2di() did not handle correctly branch lengths with the
554 default option `random = TRUE': this is now fixed.
556 o A bug was fixed in nuc.div() when using pairwise deletions.
558 o A bug occurred in the analysis of bipartitions with large
559 numbers of large trees, with consequences on prop.part,
560 prop.clades, and boot.phylo.
562 o The calculation of the Billera-Holmes-Vogtmann distance in
563 dist.topo was wrong: this has been fixed.
567 CHANGES IN APE VERSION 1.9-2
572 o The new function ladderize reorganizes the internal structure of
573 a tree to plot them left- or right-ladderized.
575 o The new function dist.nodes computes the patristic distances
576 between all nodes, internal and terminal, of a tree. It replaces
577 the option `full = TRUE' of cophenetic.phylo (see below).
582 o A bug was fixed in old2new.phylo().
584 o Some bugs were fixed in chronopl().
586 o The edge colours were not correctly displayed by plot.phylo
587 (thank you to Li-San Wang for the fix).
589 o cophenetic.phylo() failed with multichotomous trees: this is
595 o read.dna() now returns the sequences in a matrix if they are
596 aligned (interleaved or sequential format). Sequences in FASTA
597 format are still returned in a list.
599 o The option `full' of cophenetic.phylo() has been removed because
600 it could not be used from the generic.
605 o rotate() has been removed; this function did not work correctly
610 CHANGES IN APE VERSION 1.9-1
615 o Trees with a single tip were not read correctly in R as the
616 element `Nnode' was not set: this is fixed.
618 o unroot() did not set correctly the number of nodes of the
619 unrooted tree in most cases.
621 o read.GenBank() failed when fetching very long sequences,
622 particularly of the BX-series.
624 o A bug was introduced in read.tree() with ape 1.9: it has been
629 CHANGES IN APE VERSION 1.9
634 o There are two new print `methods' for trees of class "phylo" and
635 lists of trees of class "multi.tree", so that they are now
636 displayed in a compact and informative way.
638 o There are two new functions, old2new.phylo and new2old.phylo,
639 for converting between the old and new coding of the class
642 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
643 LogDet ("logdet"), and paralinear ("paralin").
645 o compute.brlen() has been extended: several methods are now
646 available to compute branch lengths.
648 o write.dna() can now handle matrices as well as lists.
653 o cophenetic.phylo() sometimes returned a wrong result with
654 multichotomous trees: this is fixed.
656 o rotate() failed when a single tip was specified: the tree is now
659 o ace() did not return the correct index matrix with custom
660 models: this is fixed.
662 o multi2di() did not work correctly when resolving multichotomies
663 randomly: the topology was always the same, only the arrangement
664 of clades was randomized: this is fixed. This function now
665 accepts trees with no branch lengths.
667 o The output of diversi.gof() was blurred by useless prints when a
668 user distribution was specified. This has been corrected, and
669 the help page of this function has been expanded.
674 o The internal structure of the class "phylo" has been changed:
675 see the document "Definition of Formats for Coding Phylogenetic
676 Trees in R" for the details. In addition, the code of most
677 functions has been improved.
679 o Several functions have been improved by replacing some R codes
680 by C codes: pic, plot.phylo, and reorder.phylo.
682 o There is now a citation information: see citation("ape") in R.
684 o write.tree() now does not add extra 0's to branch lengths so
685 that 1.23 is printed "1.23" by default, not "1.2300000000".
687 o The syntax of bind.tree() has been simplified. This function now
688 accepts trees with no branch lengths, and handles correctly node
691 o The option `as.numeric' of mrca() has been removed.
693 o The unused options `format' and `rooted' of read.tree() have
696 o The unused option `format' of write.tree() has been removed.
698 o The use of node.depth() has been simplified.
702 CHANGES IN APE VERSION 1.8-5
707 o Two new functions read.nexus.data() and write.nexus.data(),
708 contributed by Johan Nylander, allow to read and write molecular
709 sequences in NEXUS files.
711 o The new function reorder.phylo() reorders the internal structure
712 of a tree of class "phylo". It is used as the generic, e.g.,
715 o read.tree() and read.nexus() can now read trees with a single
718 o The new data set `cynipids' supplies a set of protein sequences
724 o The code of all.equal.phylo() has been completely rewritten
725 (thanks to Benoît Durand) which fixes several bugs.
727 o read.tree() and read.nexus() now checks the labels of the tree
728 to remove or substitute any characters that are illegal in the
729 Newick format (parentheses, etc.)
731 o A negative P-value could be returned by mantel.test(): this is
736 CHANGES IN APE VERSION 1.8-4
741 o The new function sh.test() computes the Shimodaira-
744 o The new function collapse.singles() removes the nodes with a
745 single descendant from a tree.
747 o plot.phylo() has a new argument `tip.color' to specify the
750 o mlphylo() has now an option `quiet' to control the display of
751 the progress of the analysis (the default is FALSE).
756 o read.dna() did not read correctly sequences in sequential format
757 with leading alignment gaps "-": this is fixed.
759 o ace() returned a list with no class so that the generic
760 functions (anova, logLik, ...) could not be used directly. This
761 is fixed as ace() now returns an object of class "ace".
763 o anova.ace() had a small bug when computing the number of degrees
764 of freedom: this is fixed.
766 o mlphylo() did not work when the sequences were in a matrix or
767 a data frame: this is fixed.
769 o rtree() did not work correctly when trying to simulate an
770 unrooted tree with two tips: an error message is now issued.
775 o The algorithm of rtree() has been changed: it is now about 40,
776 100, and 130 times faster for 10, 100, and 1000 tips,
781 CHANGES IN APE VERSION 1.8-3
786 o There are four new `method' functions to be used with the
787 results of ace(): logLik(), deviance(), AIC(), and anova().
789 o The plot method of phymltest has two new arguments: `main' to
790 change the title, and `col' to control the colour of the
791 segments showing the AIC values.
793 o ace() has a new argument `ip' that gives the initial values used
794 in the ML estimation with discrete characters (see the examples
795 in ?ace). This function now returns a matrix giving the indices
796 of the estimated rates when analysing discrete characters.
798 o nodelabels() and tiplabels() have a new argument `pie' to
799 represent proportions, with any number of categories, as
800 piecharts. The use of the option `thermo' has been improved:
801 there is now no limitation on the number of categories.
806 o mlphylo() did not work with more than two partitions: this is
809 o root() failed if the proposed outgroup was already an outgroup
810 in the tree: this is fixed.
812 o The `col' argument in nodelabels() and tiplabels() was not
813 correctly passed when `text' was used: this is fixed.
815 o Two bugs were fixed in mlphylo(): parameters were not always
816 correctly output, and the estimation failed in some cases.
818 o plot.phylo() was stuck when given a tree with a single tip: this
819 is fixed and a message error is now returned.
821 o An error was corrected in the help page of gammaStat regarding
822 the calculation of P-values.
824 o Using gls() could crash R when the number of species in the tree
825 and in the variables were different: this is fixed.
829 CHANGES IN APE VERSION 1.8-2
834 o The new function mlphylo() fits a phylogenetic tree by maximum
835 likelihood from DNA sequences. Its companion function DNAmodel()
836 is used to define the substitution model which may include
837 partitioning. There are methods for logLik(), deviance(), and
838 AIC(), and the summary() method has been extended to display in
839 a friendly way the results of this model fitting. Currently, the
840 functionality is limited to estimating the substitution and
841 associated parameters and computing the likelihood.
843 o The new function drop1.compar.gee (used as, e.g., drop1(m))
844 tests for single effects in GEE-based comparative method. A
845 warning message is printed if there is not enough degrees of
851 o An error message was sometimes issued by plot.multi.tree(),
852 though with no consequence.
856 CHANGES IN APE VERSION 1.8-1
861 o There is a new plot method for lists of trees (objects of class
862 "multi.tree"): it calls plot.phylo() internally and is
863 documented on the same help page.
868 o A bug was fixed in the C code that analyzes bipartitions: this
869 has impact on several functions like prop.part, prop.clades,
870 boot.phylo, or consensus.
872 o root() did not work correctly when the specified outgroup had
873 more than one element: this is fixed.
875 o dist.dna() sometimes returned a warning inappropriately: this
878 o If the distance object given to nj() had no rownames, nj()
879 returned a tree with no tip labels: it now returns tips labelled
880 "1", "2", ..., corresponding to the row numbers.
885 o nj() has been slightly changed so that tips with a zero distance
886 are first aggregated with zero-lengthed branches; the usual NJ
887 procedure is then performed on a distance matrix without 0's.
891 CHANGES IN APE VERSION 1.8
896 o The new function chronopl() estimates dates using the penalized
897 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
899 o The new function consensus() calculates the consensus tree of a
902 o The new function evolve.phylo() simulates the evolution of
903 continuous characters along a phylogeny under a Brownian model.
905 o The new plot method for objects of class "ancestral" displays a
906 tree together with ancestral values, as returned by the above
909 o The new function as.phylo.formula() returns a phylogeny from a
910 set of nested taxonomic variables given as a formula.
912 o The new function read.caic() reads trees in CAIC format.
914 o The new function tiplabels() allows to add labels to the tips
915 of a tree using text or plotting symbols in a flexible way.
917 o The new function unroot() unroots a phylogeny.
919 o multi2di() has a new option, `random', which specifies whether
920 to resolve the multichotomies randomly (the default) or not.
922 o prop.part() now returns an object of class "prop.part" for which
923 there are print (to display a partition in a more friendly way)
924 and summary (to extract the numbers) methods.
926 o plot.phylo() has a new option, `show.tip.label', specifying
927 whether to print the labels of the tips. The default is TRUE.
929 o The code of nj() has been replaced by a faster C code: it is now
930 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
933 o write.nexus() now writes whether a tree is rooted or not.
938 o Two bugs have been fixed in root(): unrooted trees are now
939 handled corretly, and node labels are now output normally.
941 o A bug was fixed in phymltest(): the executable couldn't be found
944 o Three bug have been fixed in ace(): computing the likelihood of
945 ancestral states of discrete characters failed, custom models
946 did not work, and the function failed with a null gradient (a
947 warning message is now returned; this latter bug was also
948 present in yule.cov() as well and is now fixed).
950 o pic() hanged out when missing data were present: a message error
953 o A small bug was fixed in dist.dna() where the gamma correction
954 was not always correctly dispatched.
956 o plot.phylo() plotted correctly the root edge only when the tree
957 was plotted rightwards: this works now for all directions.
962 o dist.taxo() has been renamed as weight.taxo().
964 o Various error and warning messages have been improved.
968 CHANGES IN APE VERSION 1.7
971 o The new function ace() estimates ancestral character states for
972 continuous characters (with ML, GLS, and contrasts methods), and
973 discrete characters (with ML only) for any number of states.
975 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
976 of directional evolution for continuous characters. The user
977 specifies the node(s) of the tree where the character optimum
980 o The new function is.rooted() tests whether a tree (of class
983 o The new function rcoal() generates random ultrametric trees with
984 the possibility to specify the function that generates the
985 inter-nodes distances.
987 o The new function mrca() gives for all pairs of tips in a tree
988 (and optionally nodes too) the most recent common ancestor.
990 o nodelabels() has a new option `thermo' to plot proportions (up
991 to three classes) on the nodes of a tree.
993 o rtree() has been improved: it can now generate rooted or
994 unrooted trees, and the mathematical function that generates the
995 branch lengths may be specified by the user. The tip labels may
996 be given directly in the call to rtree. The limit cases (n = 2,
997 3) are now handled correctly.
999 o dist.topo() has a new argument `method' with two choices: "PH85"
1000 for Penny and Henny's method (already available before and now
1001 the default), and "BHV01" for the geometric distance by Billera
1002 et al. (2001, Adv. Appl. Math. 27:733).
1004 o write.tree() has a new option, `digits', which specifies the
1005 number of digits to be printed in the Newick tree. By default
1006 digits = 10. The numbers are now always printed in decimal form
1007 (i.e., 1.0e-1 is now avoided).
1009 o dist.dna() can now compute the raw distances between pairs of
1010 DNA sequences by specifying model = "raw".
1012 o dist.phylo() has a new option `full' to possibly compute the
1013 distances among all tips and nodes of the tree. The default if
1019 o Several bugs were fixed in all.equal.phylo().
1021 o dist.dna() did not handle correctly gaps ("-") in alignments:
1022 they are now considered as missing data.
1024 o rotate() did not work if the tips were not ordered: this is
1027 o mantel.test() returned NA in some special cases: this is fixed
1028 and the function has been improved and is now faster.
1030 o A bug was fixed in diversi.gof() where the calculation of A² was
1033 o cherry() did not work correctly under some OSs (mainly Linux):
1036 o is.binary.tree() has been modified so that it works with both
1037 rooted and unrooted trees.
1039 o The documentation of theta.s() was not correct: this has been
1042 o plot.mst() did not work correctly: this is fixed.
1046 CHANGES IN APE VERSION 1.6
1051 o The new function dist.topo() computes the topological distances
1054 o The new function boot.phylo() performs a bootstrap analysis on
1055 phylogeny estimation.
1057 o The new functions prop.part() and prop.clades() analyse
1058 bipartitions from a series of trees.
1063 o read.GenBank() now uses the EFetch utility of NCBI instead of
1064 the usual Web interface: it is now much faster (e.g., 12 times
1065 faster to retrieve 8 sequences, 37 times for 60 sequences).
1070 o Several bugs were fixed in read.dna().
1072 o Several bugs were fixed in diversi.time().
1074 o is.binary.tree() did not work correctly if the tree has no edge
1075 lengths: this is fixed.
1077 o drop.tip() did not correctly propagated the `node.label' of a
1078 tree: this is fixed.
1082 CHANGES IN APE VERSION 1.5
1087 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1088 convert objects between the classes "phylo" and "matching". The
1089 latter implements the representation of binary trees introduced by
1090 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1091 as.matching() has been introduced as well.
1093 o Two new functions, multi2di() and di2multi(), allow to resolve
1094 and collapse multichotomies with branches of length zero.
1096 o The new function nuc.div() computes the nucleotide diversity
1097 from a sample a DNA sequences.
1099 o dist.dna() has been completely rewritten with a much faster
1100 (particularly for large data sets) C code. Eight models are
1101 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1102 option `method' has been renamed `model'). Computation of variance
1103 is available for all models. A gamma-correction is possible for
1104 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1105 to remove sites with missing data on a pairwise basis. The option
1106 `GCcontent' has been removed.
1108 o read.GenBank() has a new option (species.names) which specifies
1109 whether to return the species names of the organisms in addition
1110 to the accession numbers of the sequences (this is the default
1113 o write.nexus() can now write several trees in the same NEXUS file.
1115 o drop.tip() has a new option `root.edge' that allows to specify the
1116 new root edge if internal branches are trimmed.
1121 o as.phylo.hclust() failed if some labels had parentheses: this
1124 o Several bugs were fixed in all.equal.phylo(). This function now
1125 returns the logical TRUE if the trees are identical but with
1126 different representations (a report was printed previously).
1128 o read.GenBank() did not correctly handle ambiguous base codes:
1134 o birthdeath() now returns an object of class "birthdeath" for
1135 which there is a print method.
1139 CHANGES IN APE VERSION 1.4
1144 o The new function nj() performs phylogeny estimation with the
1145 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1148 o The new function which.edge() identifies the edges of a tree
1149 that belong to a group specified as a set of tips.
1151 o The new function as.phylo.phylog() converts an object of class
1152 "phylog" (from the package ade4) into an object of class
1155 o The new function axisPhylo() draws axes on the side of a
1158 o The new function howmanytrees() calculates the number of trees
1159 in different cases and giving a number of tips.
1161 o write.tree() has a new option `multi.line' (TRUE by default) to
1162 write a Newick tree on several lines rather than on a single
1165 o The functionalities of zoom() have been extended. Several
1166 subtrees can be visualized at the same time, and they are marked
1167 on the main tree with colors. The context of the subtrees can be
1168 marked with the option `subtree' (see below).
1170 o drop.tip() has a new option `subtree' (FALSE by default) which
1171 specifies whether to output in the tree how many tips have been
1174 o The arguments of add.scale.bar() have been redefined and have
1175 now default values (see ?add.scale.bar for details). This
1176 function now works even if the plotted tree has no edge length.
1178 o plot.phylo() can now plot radial trees, but this does not take
1179 edge lengths into account.
1181 o In plot.phylo() with `type = "phylogram"', if the values of
1182 `edge.color' and `edge.width' are identical for sister-branches,
1183 they are propagated to the vertical line that link them.
1188 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1189 crashing. This is fixed.
1191 o In plot.phylo(), the options `edge.color' and `edge.width' are
1192 now properly recycled; their default values are now "black" and
1195 o A bug has been fixed in write.nexus().
1200 o The function node.depth.edgelength() has been removed and
1201 replaced by a C code.
1205 CHANGES IN APE VERSION 1.3-1
1210 o The new function nodelabels() allows to add labels to the nodes
1211 of a tree using text or plotting symbols in a flexible way.
1213 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1214 numeric values specifying the lower and upper limits on the x-
1215 and y-axes. This allows to leave some space on any side of the
1216 tree. If a single value is given, this is taken as the upper
1221 CHANGES IN APE VERSION 1.3
1226 o The new function phymltest() calls the software PHYML and fits
1227 28 models of DNA sequence evolution. There are a print method to
1228 display likelihood and AIC values, a summary method to compute
1229 the hierarchical likelihood ratio tests, and a plot method to
1230 display graphically the AIC values of each model.
1232 o The new function yule.cov() fits the Yule model with covariates,
1233 a model where the speciation rate is affected by several species
1234 traits through a generalized linear model. The parameters are
1235 estimated by maximum likelihood.
1237 o Three new functions, corBrownian(), corGrafen(), and
1238 corMartins(), compute the expected correlation structures among
1239 species given a phylogeny under different models of evolution.
1240 These can be used for GLS comparative phylogenetic methods (see
1241 the examples). There are coef() and corMatrix() methods and an
1242 Initialize.corPhyl() function associated.
1244 o The new function compar.cheverud() implements Cheverud et al.'s
1245 (1985; Evolution 39:1335) phylogenetic comparative method.
1247 o The new function varcomp() estimates variance components; it has
1250 o Two new functions, panel.superpose.correlogram() and
1251 plot.correlogramList(), allow to plot several phylogenetic
1254 o The new function node.leafnumber() computes the number of leaves
1255 of a subtree defined by a particular node.
1257 o The new function node.sons() gets all tags of son nodes from a
1260 o The new function compute.brlen() computes the branch lengths of
1261 a tree according to a specified method.
1263 o plot.phylo() has three new options: "cex" controls the size of
1264 the (tip and node) labels (thus it is no more needed to change
1265 the global graphical parameter), "direction" which allows to
1266 plot the tree rightwards, leftwards, upwards, or downwards, and
1267 "y.lim" which sets the upper limit on the y-axis.
1272 o Some functions which try to match tip labels and names of
1273 additional data (e.g. vector) are likely to fail if there are
1274 typing or syntax errors. If both series of names do not perfectly
1275 match, they are ignored and a warning message is now issued.
1276 These functions are bd.ext, compar.gee, pic. Their help pages
1277 have been clarified on this point.
1281 CHANGES IN APE VERSION 1.2-7
1286 o The new function root() reroots a phylogenetic tree with respect
1287 to a specified outgroup.
1289 o The new function rotate() rotates an internal branch of a tree.
1291 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1292 trees) controls the display of the tip labels in unrooted trees.
1293 This display has been greatly improved: the tip labels are now not
1294 expected to overlap with the tree (particularly if lab4ut =
1295 "axial"). In all cases, combining appropriate values of "lab4ut"
1296 and the font size (via "par(cex = )") should result in readable
1297 unrooted trees. See ?plot.phylo for some examples.
1299 o In drop.tip(), the argument `tip' can now be numeric or character.
1304 o drop.tip() did not work correctly with trees with no branch
1305 lengths: this is fixed.
1307 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1308 plotted with some line crossings: this is now fixed.
1312 CHANGES IN APE VERSION 1.2-6
1317 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1318 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1319 to implement comparative methods with an autocorrelation approach.
1321 o A new data set describing some life history traits of Carnivores
1327 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1332 o When plotting a tree with plot.phylo(), the new default of the
1333 option `label.offset' is now 0, so the labels are always visible.
1337 CHANGES IN APE VERSION 1.2-5
1342 o The new function bd.ext() fits a birth-death model with combined
1343 phylogenetic and taxonomic data, and estimates the corresponding
1344 speciation and extinction rates.
1349 o The package gee is no more required by ape but only suggested
1350 since only the function compar.gee() calls gee.
1354 CHANGES IN APE VERSION 1.2-4
1359 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1360 and lines.popsize) implementing a new approach for inferring the
1361 demographic history from genealogies using a reversible jump
1362 MCMC have been introduced.
1364 o The unit of time in the skyline plot and in the new plots can
1365 now be chosen to be actual years, rather than substitutions.
1369 CHANGES IN APE VERSION 1.2-3
1374 o The new function rtree() generates a random binary tree with or
1375 without branch lengths.
1377 o Two new functions for drawing lineages-through-time (LTT) plots
1378 are provided: ltt.lines() adds a LTT curve to an existing plot,
1379 and mltt.plot() does a multiple LTT plot giving several trees as
1380 arguments (see `?ltt.plot' for details).
1385 o Some taxon names made R crashing when calling as.phylo.hclust():
1388 o dist.dna() returned an error with two identical DNA sequences
1389 (only using the Jukes-Cantor method returned 0): this is fixed.
1394 o The function dist.phylo() has been re-written using a different
1395 algorithm: it is now about four times faster.
1397 o The code of branching.times() has been improved: it is now about
1402 CHANGES IN APE VERSION 1.2-2
1407 o The new function seg.sites() finds the segregating sites in a
1408 sample of DNA sequences.
1413 o A bug introduced in read.tree() and in read.nexus() with version
1416 o A few errors were corrected and a few examples were added in the
1421 CHANGES IN APE VERSION 1.2-1
1426 o plot.phylo() can now draw the edge of the root of a tree if it
1427 has one (see the new option `root.edge', its default is FALSE).
1432 o A bug was fixed in read.nexus(): files with semicolons inside
1433 comment blocks were not read correctly.
1435 o The behaviour of read.tree() and read.nexus() was corrected so
1436 that tree files with badly represented root edges (e.g., with
1437 an extra pair of parentheses, see the help pages for details)
1438 are now correctly represented in the object of class "phylo";
1439 a warning message is now issued.
1443 CHANGES IN APE VERSION 1.2
1448 o plot.phylo() has been completely re-written and offers several
1449 new functionalities. Three types of trees can now be drawn:
1450 phylogram (as previously), cladogram, and unrooted tree; in
1451 all three types the branch lengths can be drawn using the edge
1452 lengths of the phylogeny or not (e.g., if the latter is absent).
1453 The vertical position of the nodes can be adjusted with two
1454 choices (see option `node.pos'). The code has been re-structured,
1455 and two new functions (potentially useful for developpers) are
1456 documented separately: node.depth.edgelength() and node.depth();
1457 see the respective help pages for details.
1459 o The new function zoom() allows to explore very large trees by
1460 focusing on a small portion of it.
1462 o The new function yule() fits by maximum likelihood the Yule model
1463 (birth-only process) to a phylogenetic tree.
1465 o Support for writing DNA sequences in FASTA format has been
1466 introduced in write.dna() (support for reading sequences in
1467 this format was introduced in read.dna() in version 1.1-2).
1468 The function has been completely re-written, fixing some bugs
1469 (see below); the default behaviour is no more to display the
1470 sequences on the standard output. Several options have been
1471 introduced to control the sequence printing in a flexible
1472 way. The help page has been extended.
1474 o A new data set is included: a supertree of bats in NEXUS format.
1479 o In theta.s(), the default of the option `variance' has
1480 been changed to `FALSE' (as was indicated in the help page).
1482 o Several bugs were fixed in the code of all.equal.phylo().
1484 o Several bugs were fixed in write.dna(), particularly this
1485 function did not work with `format = "interleaved"'.
1487 o Various errors were corrected in the help pages.
1492 o The argument names of as.hclust.phylo() have been changed
1493 from "(phy)" to "(x, ...)" to conform to the definition of
1494 the corresponding generic function.
1496 o gamma.stat() has been renamed gammaStat() to avoid confusion
1497 since gamma() is a generic function.
1501 CHANGES IN APE VERSION 1.1-3
1506 o base.freq() previously did not return a value of 0 for
1507 bases absent in the data (e.g., a vector of length 3 was
1508 returned if one base was absent). This is now fixed (a
1509 vector of length 4 is always returned).
1511 o Several bugs were fixed in read.nexus(), including that this
1512 function did not work in this absence of a "TRANSLATE"
1513 command in the NEXUS file, and that the commands were
1518 CHANGES IN APE VERSION 1.1-2
1523 o The Tamura and Nei (1993) model of DNA distance is now implemented
1524 in dist.dna(): five models are now available in this function.
1526 o A new data set is included: a set of 15 sequences of the
1527 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1533 o A bug in read.nexus() was fixed.
1535 o read.dna() previously did not work correctly in most cases.
1536 The function has been completely re-written and its help page
1537 has been considerably extended (see ?read.dna for details).
1538 Underscores (_) in taxon names are no more replaced with
1539 spaces (this behaviour was undocumented).
1541 o A bug was fixed in write.dna().
1545 CHANGES IN APE VERSION 1.1-1
1550 o A bug in read.tree() introduced in APE 1.1 was fixed.
1552 o A bug in compar.gee() resulted in an error when trying to fit
1553 a model with `family = "binomial"'. This is now fixed.
1557 CHANGES IN APE VERSION 1.1
1562 o The Klastorin (1982) method as suggested by Misawa and Tajima
1563 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1564 on the basis of phylogenetic trees has been implemented (see
1565 the function klastorin()).
1567 o Functions have been added to convert APE's "phylo" objects in
1568 "hclust" cluster objects and vice versa (see the help page of
1569 as.phylo for details).
1571 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1572 are introduced for the estimation of absolute evolutionary rates
1573 (ratogram) and dated clock-like trees (chronogram) from
1574 phylogenetic trees using the non-parametric rate smoothing approach
1575 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1577 o A summary method is now provided printing a summary information on a
1578 phylogenetic tree with, for instance, `summary(tree)'.
1580 o The behaviour of read.tree() was changed so that all spaces and
1581 tabulations in tree files are now ignored. Consequently, spaces in tip
1582 labels are no more allowed. Another side effect is that read.nexus()
1583 now does not replace the underscores (_) in tip labels with spaces
1584 (this behaviour was undocumented).
1586 o The function plot.phylo() has a new option (`underscore') which
1587 specifies whether the underscores in tip labels should be written on
1588 the plot as such or replaced with spaces (the default).
1590 o The function birthdeath() now computes 95% confidence intervals of
1591 the estimated parameters using profile likelihood.
1593 o Three new data sets are included: a gene tree estimated from 36
1594 landplant rbcL sequences, a gene tree estimated from 32 opsin
1595 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1600 o A bug was fixed in dist.gene() where nothing was returned.
1602 o A bug in plot.mst() was fixed.
1604 o A bug in vcv.phylo() resulted in false correlations when the
1605 option `cor = TRUE' was used (now fixed).
1609 CHANGES IN APE VERSION 1.0
1614 o Two new functions, read.dna() and write.dna(), read/write in a file
1615 DNA sequences in interleaved or in sequential format.
1617 o Two new functions, read.nexus() and write.nexus(), read/write trees
1620 o The new function bind.tree() allows to bind two trees together,
1621 possibly handling root edges to give internal branches.
1623 o The new function drop.tip() removes the tips in a phylogenetic tree,
1624 and trims (or not) the corresponding internal branches.
1626 o The new function is.ultrametric() tests if a tree is ultrametric.
1628 o The function plot.phylo() has more functionalities such as drawing the
1629 branches with different colours and/or different widths, showing the
1630 node labels, controling the position and font of the labels, rotating
1631 the labels, and controling the space around the plot.
1633 o The function read.tree() can now read trees with no branch length,
1634 such as "(a,b),c);". Consequently, the element `edge.length' in
1635 objects of class "phylo" is now optional.
1637 o The function write.tree() has a new default behaviour: if the default
1638 for the option `file' is used (i.e. file = ""), then a variable of
1639 mode character containing the tree in Newick format is returned which
1640 can thus be assigned (e.g., tree <- write.tree(phy)).
1642 o The function read.tree() has a new argument `text' which allows
1643 to read the tree in a variable of mode character.
1645 o A new data set is included: the phylogenetic relationships among
1646 the orders of birds from Sibley and Ahlquist (1990).
1650 CHANGES IN APE VERSION 0.2-1
1655 o Several bugs were fixed in the help pages.
1659 CHANGES IN APE VERSION 0.2
1664 o The function write.tree() writes phylogenetic trees (objects of class
1665 "phylo") in an ASCII file using the Newick parenthetic format.
1667 o The function birthdeath() fits a birth-death model to branching times
1668 by maximum likelihood, and estimates the corresponding speciation and
1671 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1674 o The function is.binary.tree() tests whether a phylogeny is binary.
1676 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1677 as well as some methods are introduced.
1679 o Several functions, including some generics and methods, for computing
1680 skyline plot estimates (classic and generalized) of effective
1681 population size through time are introduced and replace the function
1682 skyline.plot() in version 0.1.
1684 o Two data sets are now included: the phylogenetic relationships among
1685 the families of birds from Sibley and Ahlquist (1990), and an
1686 estimated clock-like phylogeny of HIV sequences sampled in the
1687 Democratic Republic of Congo.
1690 DEPRECATED & DEFUNCT
1692 o The function skyline.plot() in ape 0.1 has been deprecated and
1693 replaced by more elaborate functions (see above).
1698 o Two important bugs were fixed in plot.phylo(): phylogenies with
1699 multichotomies not at the root or not with only terminal branches,
1700 and phylogenies with a single node (i.e. only terminal branches)
1701 did not plot. These trees should be plotted correctly now.
1703 o Several bugs were fixed in diversi.time() in the computation of
1706 o Various errors were corrected in the help pages.