1 CHANGES IN APE VERSION 2.3-1
6 o The new function is.monophyletic tests the monophyly of a group.
8 o There is now a c() method for lists of class "DNAbin".
10 o yule.cov() now fits the null model, and its help page has been
11 corrected with respect to this change.
16 o dist.gene() failed on most occasions with the default
17 pairwise.deletion = FALSE.
19 o read.tree() failed to read correctly the tree name(s).
21 o boot.phylo() now treats correctly data frames.
23 o del.gaps() did not copy the rownames of a matrix.
25 o A small bug was fixed in CDAM.global().
27 o ace() failed with large data sets. Thanks to Rich FitzJohn for
28 the fix. With other improvements, this function is now about 6
31 o write.tree() failed with objects of class "multiPhylo".
36 o [.multiPhylo and [.DNAbin now respect the original class.
38 o Instances of the form class(phy) == "phylo" have been replaced
39 by inherits(phy, "phylo").
41 o rcoal() is now faster.
46 o klastorin() has been removed.
50 CHANGES IN APE VERSION 2.3
55 o The new functions CADM.global and CADM.post, contributed by
56 Pierre Legendre, test the congruence among several distance
59 o The new function yule.time fits a user-defined time-dependent
60 Yule model by maximum likelihood.
62 o The new function makeNodeLabel creates and/or modifies node
63 labels in a flexible way.
65 o read.tree() and write.tree() have been modified so that they can
66 handle individual tree names.
68 o plot.phylo() has a new argument 'edge.lty' that specifies the
69 types of lines used for the edges (plain, dotted, dashed, ...)
71 o phymltest() has been updated to work with PhyML 3.0.1.
76 o drop.tip() shuffled tip labels in some cases.
78 o drop.tip() did not handle node.label correctly.
80 o is.ultrametric() now checks the ordering of the edge matrix.
82 o ace() sometimes returned negative values of likelihoods of
83 ancestral states (thanks to Dan Rabosky for solving this long
89 o The data set xenarthra has been removed.
93 CHANGES IN APE VERSION 2.2-4
97 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
98 now fixed. (Thanks to Peter Wragg for the fix!)
100 o A warning message occurred for no reason with ace(method="GLS").
105 o There is now a general help page displayed with '?ape'
109 CHANGES IN APE VERSION 2.2-3
114 o The new function extract.clade extracts a clade from a tree by
115 specifying a node number or label.
117 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
118 operations of the same names.
120 o dist.dna() can now return the number of site differences by
121 specifying model="N".
126 o chronopl() did not work with CV = TRUE.
128 o read.nexus() did not work correctly in some situations (trees on
129 multiple lines with different numbers of lines and/or with
130 comments inserted within the trees).
132 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
133 the number of lineages with non-binary trees.
138 o ape has now a namespace.
140 o drip.tip() has been improved: it should be much faster and work
141 better in some cases (e.g., see the example in ?zoom).
145 CHANGES IN APE VERSION 2.2-2
150 o dist.gene() has been substantially improved and gains an option
153 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
159 o prop.part() failed with a single tree with the default option
160 'check.labels = TRUE'.
162 o summary.DNAbin() failed to display correctly the summary of
163 sequence lengths with lists of sequences of 10,000 bases or more
164 (because summary.default uses 4 significant digits by default).
166 o read.nexus() failed to read a file with a single tree with line
167 breaks in the Newick string.
169 o del.gaps() returned a list of empty sequences when there were no
175 o phymltest() has been updated for PhyML 3.0 and gains an option
176 'append', whereas the option 'path2exec' has been removed.
178 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
179 which is returned unchanged (instead of an error).
181 o The data sets bird.orders and bird.families are now stored as
182 Newick strings; i.e., the command data(bird.orders) calls
187 CHANGES IN APE VERSION 2.2-1
192 o The new function makeLabel() helps to modify labels of trees,
193 lists of trees, or DNA sequences, with several utilities to
194 truncate and/or make them unique, substituting some
195 characters, and so on.
197 o The new function del.gaps() removes insertion gaps ("-") in a
198 set of DNA sequences.
200 o read.dna() can now read Clustal files (*.aln).
205 o root() failed with 'resolve.root = TRUE' when the root was
206 already the specified root.
208 o Several bugs were fixed in mlphylo().
210 o collapsed.singles() did not propagate the 'Nnode' and
211 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
213 o read.nexus() failed to remove correctly the comments within
216 o read.nexus() failed to read a file with a single tree and no
217 translation of tip labels.
219 o read.nexus() failed to place correctly tip labels when reading
220 a single tree with no edge lengths.
222 o A bug was fixed in sh.test().
227 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
230 o The option 'check.labels' of consensus() and prop.part() is now
233 o write.dna() now does not truncate names to 10 characters with
238 CHANGES IN APE VERSION 2.2
243 o Four new functions have been written by Damien de Vienne for the
244 graphical exploration of large trees (cophyloplot, subtrees,
245 subtreeplot), and to return the graphical coordinates of tree
248 o The new functions corPagel and corBlomberg implement the Pagel's
249 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
251 o chronopl() has been improved and gains several options: see its
252 help page for details.
254 o boot.phylo() has now an option 'trees' to possibly return the
255 bootstraped trees (the default is FALSE).
257 o prop.part() has been improved and should now be faster in all
263 o read.dna() failed if "?" occurred in the first 10 sites of the
266 o The x/y aspect of the plot is now respected when plotting a
267 circular tree (type = "r" or "f").
269 o Drawing the tip labels sometimes failed when plotting circular
272 o zoom() failed when tip labels were used instead of their numbers
273 (thanks to Yan Wong for the fix).
275 o drop.tip() failed with some trees (fixed by Yan Wong).
277 o seg.sites() failed with a list.
279 o consensus() failed in some cases. The function has been improved
280 as well and is faster.
284 CHANGES IN APE VERSION 2.1-3
289 o A bug in read.nexus() made the Windows R-GUI crash.
291 o An error was fixed in the computation of ancestral character
292 states by generalized least squares in ace().
294 o di2multi() did not modify node labels correctly.
296 o multi2di() failed if the tree had its attribute "order" set to
301 CHANGES IN APE VERSION 2.1-2
306 o There three new methods for the "multiPhylo" class: str, $,
309 o root() gains the options 'node' and 'resolve.root'
310 (FALSE by default) as well as its code being improved.
312 o mltt.plot() has now an option 'log' used in the same way
313 than in plot.default().
318 o mltt.plot() failed to display the legend with an unnamed
321 o nodelabels() with pies now correcly uses the argument
322 'cex' to draw symbols of different sizes (which has
323 worked already for thermometers).
325 o read.nexus() generally failed to read very big files.
330 o The argument 'family' of compar.gee() can now be a function
331 as well as a character string.
333 o read.tree() and read.nexus() now return an unnamed list if
336 o read.nexus() now returns a modified object of class "multiPhylo"
337 when there is a TRANSLATE block in the NEXUS file: the individual
338 trees have no 'tip.label' vector, but the list has a 'TipLabel'
339 attribute. The new methods '$' and '[[' set these elements
340 correctly when extracting trees.
344 CHANGES IN APE VERSION 2.1-1
349 o The new function rmtree generates lists of random trees.
351 o rcoal() now generates a genuine coalescent tree by default
352 (thanks to Vladimir Minin for the code).
357 o nuc.div() returned an incorrect value with the default
358 pairwise.deletion = FALSE.
363 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
364 have been improved so that they are stabler and faster.
366 o R packages used by ape are now loaded silently; lattice and gee
367 are loaded only when needed.
371 CHANGES IN APE VERSION 2.1
376 o The new function identify.phylo identifies clades on a plotted
377 tree using the mouse.
379 o It is now possible to subset a list of trees (object of class
380 "multiPhylo") with "[" while keeping its class correct.
382 o The new function as.DNAbin.alignment converts DNA sequences
383 stored in the "alignment" format of the package seqinr into
384 an object of class "DNAbin".
386 o The new function weight.taxo2 helps to build similarity matrices
387 given two taxonomic levels (usually called by other functions).
389 o write.tree() can now take a list of trees (class "multiPhylo")
390 as its main argument.
392 o plot.correlogram() and plot.correlogramList() have been
393 improved, and gain several options (see the help page for
394 details). A legend is now plotted by default.
399 o dist.dna() returned some incorrect values with `model = "JC69"'
400 and `pairwise.deletion = TRUE'. This affected only the
401 distances involving sequences with missing values. (Thanks
402 to Bruno Toupance for digging this bug out.)
404 o write.tree() failed with some trees: this is fixed by removing
405 the `multi.line' option (trees are now always printed on a
408 o read.nexus() did not correctly detect trees with multiple root
409 edges (see OTHER CHANGES).
414 o The code of mlphylo() has been almost entirely rewritten, and
415 should be much stabler. The options have been also greatly
416 simplified (see ?mlphylo and ?DNAmodel for details).
418 o The internal function nTips has been renamed klastorin_nTips.
420 o The code of is.ultrametric() contained redundancies and has
423 o The code of Moran.I() and of correlogram.formula() have been
426 o read.tree() and read.nexus() now return an error when trying to
427 read a tree with multiple root edges (see BUG FIXES). The
428 correction applied in previous version did not work in all
431 o The class c("multi.tree", "phylo") has been renamed
437 o There is now a vignette in ape: see vignette("MoranI", "ape").
442 o as.matching() and as.phylo.matching() do not support branch
445 o correlogram.phylo() and discrete.dist() have been removed.
449 CHANGES IN APE VERSION 2.0-2
454 o The new function matexpo computes the exponential of a square
457 o The new function unique.multi.tree removes duplicate trees from
460 o yule() has a new option `use.root.edge = FALSE' that specifies
461 to ignore, by default, the root edge of the tree if it exists.
466 o which.edge() failed when the index of a single terminal edge was
469 o In diversi.time(), the values returned for model C were
472 o A bug was fixed in yule() that affected the calculation of the
473 likelihood in the presence of ties in the branching times.
475 o There was a bug in the C function mat_expo4x4 affecting the
476 calculations of the transition probabilities for models HKY and
479 o A small bug was fixed in as.matrix.DNAbin (thanks to James
482 o rtree() did not `shuffle' the tip labels by default, so only a
483 limited number of labelled topologies could be generated.
487 CHANGES IN APE VERSION 2.0-1
492 o The three new functions bionj, fastme.ols, and fastme.bal
493 perform phylogeny estimation by the BIONJ and fastME methods in
494 OLS and balanced versions. This is a port to R of previous
495 previous programs done by Vincent Lefort.
497 o The new function chronoMPL performs molecular dating with the
498 mean path lengths method of Britton et al. (2002, Mol. Phyl.
501 o The new function rotate, contributed by Christoph Heibl, swaps
502 two clades connected to the same node. It works also with
503 multichotomous nodes.
505 o The new `method' as.matrix.DNAbin() may be used to convert
506 easily DNA sequences stored in a list into a matrix while
507 keeping the names and the class.
512 o chronopl() failed when some branch lengths were equal to zero:
513 an error message is now returned.
515 o di2multi() failed when there was a series of consecutive edges
520 CHANGES IN APE VERSION 1.10-2
525 o plot.phylo() can now plot circular trees: the option is type =
526 "fan" or type = "f" (to avoid the ambiguity with type = "c").
528 o prop.part() has a new option `check.labels = FALSE' which allows
529 to considerably speed-up the calculations of bipartitions. As a
530 consequence, calculations of bootstrap values with boot.phylo()
531 should be much faster.
536 o read.GenBank() did not return correctly the list of species as
537 from ape 1.10: this is fixed in this version
539 o Applying as.phylo() on a tree of class "phylo" failed: the
540 object is now returned unchanged.
544 CHANGES IN APE VERSION 1.10-1
549 o The three new functions Ntip, Nnode, and Nedge return, for a
550 given tree, the number of tips, nodes, or edges, respectively.
555 o read.nexus() did not set correctly the class of the returned
556 object when reading multiple trees.
558 o mllt.plot() failed with objects of class c("multi.tree",
561 o unroot() did not work correctly in most cases.
563 o reorder.phylo() made R freeze in some occasions.
565 o Plotting a tree in pruningwise order failed.
567 o When plotting an unrooted tree, the tip labels where not all
568 correctly positioned if the option `cex' was used.
572 CHANGES IN APE VERSION 1.10
577 o Five new `method' functions have been introduced to manipulate
578 DNA sequences in binary format (see below).
580 o Three new functions have been introduced to convert between the
581 new binary and the character formats.
583 o The new function as.alignment converts DNA sequences stored as
584 single characters into the class "alignment" used by the package
587 o read.dna() and read.GenBank() have a new argument `as.character'
588 controlling whether the sequences are returned in binary format
594 o root() failed when the tree had node labels: this is fixed.
596 o plot.phylo() did not correctly set the limits on the y-axis with
597 the default setting: this is fixed.
599 o dist.dna() returned a wrong result for the LogDet, paralinear,
600 and BH87 models with `pairwise.deletion = TRUE'.
605 o DNA sequences are now internally stored in a binary format. See
606 the document "A Bit-Level Coding Scheme for Nucleotides" for the
607 details. Most functions analyzing DNA functions have been
608 modified accordingly and are now much faster (dist.dna is now
609 ca. 60 times faster).
613 CHANGES IN APE VERSION 1.9-4
618 o A bug was fixed in edgelabels().
620 o as.phylo.hclust() did not work correctly when the object of
621 class "hclust" has its labels set to NULL: the returned tree has
622 now its tip labels set to "1", "2", ...
624 o consensus could fail if some tip labels are a subset of others
625 (e.g., "a" and "a_1"): this is now fixed.
627 o mlphylo() failed in most cases if some branch lengths of the
628 initial tree were greater than one: an error message is now
631 o mlphylo() failed in most cases when estimating the proportion of
632 invariants: this is fixed.
636 CHANGES IN APE VERSION 1.9-3
641 o The new function edgelabels adds labels on the edge of the tree
642 in the same way than nodelabels or tiplabels.
647 o multi2di() did not handle correctly branch lengths with the
648 default option `random = TRUE': this is now fixed.
650 o A bug was fixed in nuc.div() when using pairwise deletions.
652 o A bug occurred in the analysis of bipartitions with large
653 numbers of large trees, with consequences on prop.part,
654 prop.clades, and boot.phylo.
656 o The calculation of the Billera-Holmes-Vogtmann distance in
657 dist.topo was wrong: this has been fixed.
661 CHANGES IN APE VERSION 1.9-2
666 o The new function ladderize reorganizes the internal structure of
667 a tree to plot them left- or right-ladderized.
669 o The new function dist.nodes computes the patristic distances
670 between all nodes, internal and terminal, of a tree. It replaces
671 the option `full = TRUE' of cophenetic.phylo (see below).
676 o A bug was fixed in old2new.phylo().
678 o Some bugs were fixed in chronopl().
680 o The edge colours were not correctly displayed by plot.phylo
681 (thank you to Li-San Wang for the fix).
683 o cophenetic.phylo() failed with multichotomous trees: this is
689 o read.dna() now returns the sequences in a matrix if they are
690 aligned (interleaved or sequential format). Sequences in FASTA
691 format are still returned in a list.
693 o The option `full' of cophenetic.phylo() has been removed because
694 it could not be used from the generic.
699 o rotate() has been removed; this function did not work correctly
704 CHANGES IN APE VERSION 1.9-1
709 o Trees with a single tip were not read correctly in R as the
710 element `Nnode' was not set: this is fixed.
712 o unroot() did not set correctly the number of nodes of the
713 unrooted tree in most cases.
715 o read.GenBank() failed when fetching very long sequences,
716 particularly of the BX-series.
718 o A bug was introduced in read.tree() with ape 1.9: it has been
723 CHANGES IN APE VERSION 1.9
728 o There are two new print `methods' for trees of class "phylo" and
729 lists of trees of class "multi.tree", so that they are now
730 displayed in a compact and informative way.
732 o There are two new functions, old2new.phylo and new2old.phylo,
733 for converting between the old and new coding of the class
736 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
737 LogDet ("logdet"), and paralinear ("paralin").
739 o compute.brlen() has been extended: several methods are now
740 available to compute branch lengths.
742 o write.dna() can now handle matrices as well as lists.
747 o cophenetic.phylo() sometimes returned a wrong result with
748 multichotomous trees: this is fixed.
750 o rotate() failed when a single tip was specified: the tree is now
753 o ace() did not return the correct index matrix with custom
754 models: this is fixed.
756 o multi2di() did not work correctly when resolving multichotomies
757 randomly: the topology was always the same, only the arrangement
758 of clades was randomized: this is fixed. This function now
759 accepts trees with no branch lengths.
761 o The output of diversi.gof() was blurred by useless prints when a
762 user distribution was specified. This has been corrected, and
763 the help page of this function has been expanded.
768 o The internal structure of the class "phylo" has been changed:
769 see the document "Definition of Formats for Coding Phylogenetic
770 Trees in R" for the details. In addition, the code of most
771 functions has been improved.
773 o Several functions have been improved by replacing some R codes
774 by C codes: pic, plot.phylo, and reorder.phylo.
776 o There is now a citation information: see citation("ape") in R.
778 o write.tree() now does not add extra 0's to branch lengths so
779 that 1.23 is printed "1.23" by default, not "1.2300000000".
781 o The syntax of bind.tree() has been simplified. This function now
782 accepts trees with no branch lengths, and handles correctly node
785 o The option `as.numeric' of mrca() has been removed.
787 o The unused options `format' and `rooted' of read.tree() have
790 o The unused option `format' of write.tree() has been removed.
792 o The use of node.depth() has been simplified.
796 CHANGES IN APE VERSION 1.8-5
801 o Two new functions read.nexus.data() and write.nexus.data(),
802 contributed by Johan Nylander, allow to read and write molecular
803 sequences in NEXUS files.
805 o The new function reorder.phylo() reorders the internal structure
806 of a tree of class "phylo". It is used as the generic, e.g.,
809 o read.tree() and read.nexus() can now read trees with a single
812 o The new data set `cynipids' supplies a set of protein sequences
818 o The code of all.equal.phylo() has been completely rewritten
819 (thanks to Benoît Durand) which fixes several bugs.
821 o read.tree() and read.nexus() now checks the labels of the tree
822 to remove or substitute any characters that are illegal in the
823 Newick format (parentheses, etc.)
825 o A negative P-value could be returned by mantel.test(): this is
830 CHANGES IN APE VERSION 1.8-4
835 o The new function sh.test() computes the Shimodaira-
838 o The new function collapse.singles() removes the nodes with a
839 single descendant from a tree.
841 o plot.phylo() has a new argument `tip.color' to specify the
844 o mlphylo() has now an option `quiet' to control the display of
845 the progress of the analysis (the default is FALSE).
850 o read.dna() did not read correctly sequences in sequential format
851 with leading alignment gaps "-": this is fixed.
853 o ace() returned a list with no class so that the generic
854 functions (anova, logLik, ...) could not be used directly. This
855 is fixed as ace() now returns an object of class "ace".
857 o anova.ace() had a small bug when computing the number of degrees
858 of freedom: this is fixed.
860 o mlphylo() did not work when the sequences were in a matrix or
861 a data frame: this is fixed.
863 o rtree() did not work correctly when trying to simulate an
864 unrooted tree with two tips: an error message is now issued.
869 o The algorithm of rtree() has been changed: it is now about 40,
870 100, and 130 times faster for 10, 100, and 1000 tips,
875 CHANGES IN APE VERSION 1.8-3
880 o There are four new `method' functions to be used with the
881 results of ace(): logLik(), deviance(), AIC(), and anova().
883 o The plot method of phymltest has two new arguments: `main' to
884 change the title, and `col' to control the colour of the
885 segments showing the AIC values.
887 o ace() has a new argument `ip' that gives the initial values used
888 in the ML estimation with discrete characters (see the examples
889 in ?ace). This function now returns a matrix giving the indices
890 of the estimated rates when analysing discrete characters.
892 o nodelabels() and tiplabels() have a new argument `pie' to
893 represent proportions, with any number of categories, as
894 piecharts. The use of the option `thermo' has been improved:
895 there is now no limitation on the number of categories.
900 o mlphylo() did not work with more than two partitions: this is
903 o root() failed if the proposed outgroup was already an outgroup
904 in the tree: this is fixed.
906 o The `col' argument in nodelabels() and tiplabels() was not
907 correctly passed when `text' was used: this is fixed.
909 o Two bugs were fixed in mlphylo(): parameters were not always
910 correctly output, and the estimation failed in some cases.
912 o plot.phylo() was stuck when given a tree with a single tip: this
913 is fixed and a message error is now returned.
915 o An error was corrected in the help page of gammaStat regarding
916 the calculation of P-values.
918 o Using gls() could crash R when the number of species in the tree
919 and in the variables were different: this is fixed.
923 CHANGES IN APE VERSION 1.8-2
928 o The new function mlphylo() fits a phylogenetic tree by maximum
929 likelihood from DNA sequences. Its companion function DNAmodel()
930 is used to define the substitution model which may include
931 partitioning. There are methods for logLik(), deviance(), and
932 AIC(), and the summary() method has been extended to display in
933 a friendly way the results of this model fitting. Currently, the
934 functionality is limited to estimating the substitution and
935 associated parameters and computing the likelihood.
937 o The new function drop1.compar.gee (used as, e.g., drop1(m))
938 tests for single effects in GEE-based comparative method. A
939 warning message is printed if there is not enough degrees of
945 o An error message was sometimes issued by plot.multi.tree(),
946 though with no consequence.
950 CHANGES IN APE VERSION 1.8-1
955 o There is a new plot method for lists of trees (objects of class
956 "multi.tree"): it calls plot.phylo() internally and is
957 documented on the same help page.
962 o A bug was fixed in the C code that analyzes bipartitions: this
963 has impact on several functions like prop.part, prop.clades,
964 boot.phylo, or consensus.
966 o root() did not work correctly when the specified outgroup had
967 more than one element: this is fixed.
969 o dist.dna() sometimes returned a warning inappropriately: this
972 o If the distance object given to nj() had no rownames, nj()
973 returned a tree with no tip labels: it now returns tips labelled
974 "1", "2", ..., corresponding to the row numbers.
979 o nj() has been slightly changed so that tips with a zero distance
980 are first aggregated with zero-lengthed branches; the usual NJ
981 procedure is then performed on a distance matrix without 0's.
985 CHANGES IN APE VERSION 1.8
990 o The new function chronopl() estimates dates using the penalized
991 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
993 o The new function consensus() calculates the consensus tree of a
996 o The new function evolve.phylo() simulates the evolution of
997 continuous characters along a phylogeny under a Brownian model.
999 o The new plot method for objects of class "ancestral" displays a
1000 tree together with ancestral values, as returned by the above
1003 o The new function as.phylo.formula() returns a phylogeny from a
1004 set of nested taxonomic variables given as a formula.
1006 o The new function read.caic() reads trees in CAIC format.
1008 o The new function tiplabels() allows to add labels to the tips
1009 of a tree using text or plotting symbols in a flexible way.
1011 o The new function unroot() unroots a phylogeny.
1013 o multi2di() has a new option, `random', which specifies whether
1014 to resolve the multichotomies randomly (the default) or not.
1016 o prop.part() now returns an object of class "prop.part" for which
1017 there are print (to display a partition in a more friendly way)
1018 and summary (to extract the numbers) methods.
1020 o plot.phylo() has a new option, `show.tip.label', specifying
1021 whether to print the labels of the tips. The default is TRUE.
1023 o The code of nj() has been replaced by a faster C code: it is now
1024 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1027 o write.nexus() now writes whether a tree is rooted or not.
1032 o Two bugs have been fixed in root(): unrooted trees are now
1033 handled corretly, and node labels are now output normally.
1035 o A bug was fixed in phymltest(): the executable couldn't be found
1038 o Three bug have been fixed in ace(): computing the likelihood of
1039 ancestral states of discrete characters failed, custom models
1040 did not work, and the function failed with a null gradient (a
1041 warning message is now returned; this latter bug was also
1042 present in yule.cov() as well and is now fixed).
1044 o pic() hanged out when missing data were present: a message error
1047 o A small bug was fixed in dist.dna() where the gamma correction
1048 was not always correctly dispatched.
1050 o plot.phylo() plotted correctly the root edge only when the tree
1051 was plotted rightwards: this works now for all directions.
1056 o dist.taxo() has been renamed as weight.taxo().
1058 o Various error and warning messages have been improved.
1062 CHANGES IN APE VERSION 1.7
1065 o The new function ace() estimates ancestral character states for
1066 continuous characters (with ML, GLS, and contrasts methods), and
1067 discrete characters (with ML only) for any number of states.
1069 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1070 of directional evolution for continuous characters. The user
1071 specifies the node(s) of the tree where the character optimum
1074 o The new function is.rooted() tests whether a tree (of class
1077 o The new function rcoal() generates random ultrametric trees with
1078 the possibility to specify the function that generates the
1079 inter-nodes distances.
1081 o The new function mrca() gives for all pairs of tips in a tree
1082 (and optionally nodes too) the most recent common ancestor.
1084 o nodelabels() has a new option `thermo' to plot proportions (up
1085 to three classes) on the nodes of a tree.
1087 o rtree() has been improved: it can now generate rooted or
1088 unrooted trees, and the mathematical function that generates the
1089 branch lengths may be specified by the user. The tip labels may
1090 be given directly in the call to rtree. The limit cases (n = 2,
1091 3) are now handled correctly.
1093 o dist.topo() has a new argument `method' with two choices: "PH85"
1094 for Penny and Henny's method (already available before and now
1095 the default), and "BHV01" for the geometric distance by Billera
1096 et al. (2001, Adv. Appl. Math. 27:733).
1098 o write.tree() has a new option, `digits', which specifies the
1099 number of digits to be printed in the Newick tree. By default
1100 digits = 10. The numbers are now always printed in decimal form
1101 (i.e., 1.0e-1 is now avoided).
1103 o dist.dna() can now compute the raw distances between pairs of
1104 DNA sequences by specifying model = "raw".
1106 o dist.phylo() has a new option `full' to possibly compute the
1107 distances among all tips and nodes of the tree. The default if
1113 o Several bugs were fixed in all.equal.phylo().
1115 o dist.dna() did not handle correctly gaps ("-") in alignments:
1116 they are now considered as missing data.
1118 o rotate() did not work if the tips were not ordered: this is
1121 o mantel.test() returned NA in some special cases: this is fixed
1122 and the function has been improved and is now faster.
1124 o A bug was fixed in diversi.gof() where the calculation of A² was
1127 o cherry() did not work correctly under some OSs (mainly Linux):
1130 o is.binary.tree() has been modified so that it works with both
1131 rooted and unrooted trees.
1133 o The documentation of theta.s() was not correct: this has been
1136 o plot.mst() did not work correctly: this is fixed.
1140 CHANGES IN APE VERSION 1.6
1145 o The new function dist.topo() computes the topological distances
1148 o The new function boot.phylo() performs a bootstrap analysis on
1149 phylogeny estimation.
1151 o The new functions prop.part() and prop.clades() analyse
1152 bipartitions from a series of trees.
1157 o read.GenBank() now uses the EFetch utility of NCBI instead of
1158 the usual Web interface: it is now much faster (e.g., 12 times
1159 faster to retrieve 8 sequences, 37 times for 60 sequences).
1164 o Several bugs were fixed in read.dna().
1166 o Several bugs were fixed in diversi.time().
1168 o is.binary.tree() did not work correctly if the tree has no edge
1169 lengths: this is fixed.
1171 o drop.tip() did not correctly propagated the `node.label' of a
1172 tree: this is fixed.
1176 CHANGES IN APE VERSION 1.5
1181 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1182 convert objects between the classes "phylo" and "matching". The
1183 latter implements the representation of binary trees introduced by
1184 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1185 as.matching() has been introduced as well.
1187 o Two new functions, multi2di() and di2multi(), allow to resolve
1188 and collapse multichotomies with branches of length zero.
1190 o The new function nuc.div() computes the nucleotide diversity
1191 from a sample a DNA sequences.
1193 o dist.dna() has been completely rewritten with a much faster
1194 (particularly for large data sets) C code. Eight models are
1195 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1196 option `method' has been renamed `model'). Computation of variance
1197 is available for all models. A gamma-correction is possible for
1198 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1199 to remove sites with missing data on a pairwise basis. The option
1200 `GCcontent' has been removed.
1202 o read.GenBank() has a new option (species.names) which specifies
1203 whether to return the species names of the organisms in addition
1204 to the accession numbers of the sequences (this is the default
1207 o write.nexus() can now write several trees in the same NEXUS file.
1209 o drop.tip() has a new option `root.edge' that allows to specify the
1210 new root edge if internal branches are trimmed.
1215 o as.phylo.hclust() failed if some labels had parentheses: this
1218 o Several bugs were fixed in all.equal.phylo(). This function now
1219 returns the logical TRUE if the trees are identical but with
1220 different representations (a report was printed previously).
1222 o read.GenBank() did not correctly handle ambiguous base codes:
1228 o birthdeath() now returns an object of class "birthdeath" for
1229 which there is a print method.
1233 CHANGES IN APE VERSION 1.4
1238 o The new function nj() performs phylogeny estimation with the
1239 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1242 o The new function which.edge() identifies the edges of a tree
1243 that belong to a group specified as a set of tips.
1245 o The new function as.phylo.phylog() converts an object of class
1246 "phylog" (from the package ade4) into an object of class
1249 o The new function axisPhylo() draws axes on the side of a
1252 o The new function howmanytrees() calculates the number of trees
1253 in different cases and giving a number of tips.
1255 o write.tree() has a new option `multi.line' (TRUE by default) to
1256 write a Newick tree on several lines rather than on a single
1259 o The functionalities of zoom() have been extended. Several
1260 subtrees can be visualized at the same time, and they are marked
1261 on the main tree with colors. The context of the subtrees can be
1262 marked with the option `subtree' (see below).
1264 o drop.tip() has a new option `subtree' (FALSE by default) which
1265 specifies whether to output in the tree how many tips have been
1268 o The arguments of add.scale.bar() have been redefined and have
1269 now default values (see ?add.scale.bar for details). This
1270 function now works even if the plotted tree has no edge length.
1272 o plot.phylo() can now plot radial trees, but this does not take
1273 edge lengths into account.
1275 o In plot.phylo() with `type = "phylogram"', if the values of
1276 `edge.color' and `edge.width' are identical for sister-branches,
1277 they are propagated to the vertical line that link them.
1282 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1283 crashing. This is fixed.
1285 o In plot.phylo(), the options `edge.color' and `edge.width' are
1286 now properly recycled; their default values are now "black" and
1289 o A bug has been fixed in write.nexus().
1294 o The function node.depth.edgelength() has been removed and
1295 replaced by a C code.
1299 CHANGES IN APE VERSION 1.3-1
1304 o The new function nodelabels() allows to add labels to the nodes
1305 of a tree using text or plotting symbols in a flexible way.
1307 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1308 numeric values specifying the lower and upper limits on the x-
1309 and y-axes. This allows to leave some space on any side of the
1310 tree. If a single value is given, this is taken as the upper
1315 CHANGES IN APE VERSION 1.3
1320 o The new function phymltest() calls the software PHYML and fits
1321 28 models of DNA sequence evolution. There are a print method to
1322 display likelihood and AIC values, a summary method to compute
1323 the hierarchical likelihood ratio tests, and a plot method to
1324 display graphically the AIC values of each model.
1326 o The new function yule.cov() fits the Yule model with covariates,
1327 a model where the speciation rate is affected by several species
1328 traits through a generalized linear model. The parameters are
1329 estimated by maximum likelihood.
1331 o Three new functions, corBrownian(), corGrafen(), and
1332 corMartins(), compute the expected correlation structures among
1333 species given a phylogeny under different models of evolution.
1334 These can be used for GLS comparative phylogenetic methods (see
1335 the examples). There are coef() and corMatrix() methods and an
1336 Initialize.corPhyl() function associated.
1338 o The new function compar.cheverud() implements Cheverud et al.'s
1339 (1985; Evolution 39:1335) phylogenetic comparative method.
1341 o The new function varcomp() estimates variance components; it has
1344 o Two new functions, panel.superpose.correlogram() and
1345 plot.correlogramList(), allow to plot several phylogenetic
1348 o The new function node.leafnumber() computes the number of leaves
1349 of a subtree defined by a particular node.
1351 o The new function node.sons() gets all tags of son nodes from a
1354 o The new function compute.brlen() computes the branch lengths of
1355 a tree according to a specified method.
1357 o plot.phylo() has three new options: "cex" controls the size of
1358 the (tip and node) labels (thus it is no more needed to change
1359 the global graphical parameter), "direction" which allows to
1360 plot the tree rightwards, leftwards, upwards, or downwards, and
1361 "y.lim" which sets the upper limit on the y-axis.
1366 o Some functions which try to match tip labels and names of
1367 additional data (e.g. vector) are likely to fail if there are
1368 typing or syntax errors. If both series of names do not perfectly
1369 match, they are ignored and a warning message is now issued.
1370 These functions are bd.ext, compar.gee, pic. Their help pages
1371 have been clarified on this point.
1375 CHANGES IN APE VERSION 1.2-7
1380 o The new function root() reroots a phylogenetic tree with respect
1381 to a specified outgroup.
1383 o The new function rotate() rotates an internal branch of a tree.
1385 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1386 trees) controls the display of the tip labels in unrooted trees.
1387 This display has been greatly improved: the tip labels are now not
1388 expected to overlap with the tree (particularly if lab4ut =
1389 "axial"). In all cases, combining appropriate values of "lab4ut"
1390 and the font size (via "par(cex = )") should result in readable
1391 unrooted trees. See ?plot.phylo for some examples.
1393 o In drop.tip(), the argument `tip' can now be numeric or character.
1398 o drop.tip() did not work correctly with trees with no branch
1399 lengths: this is fixed.
1401 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1402 plotted with some line crossings: this is now fixed.
1406 CHANGES IN APE VERSION 1.2-6
1411 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1412 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1413 to implement comparative methods with an autocorrelation approach.
1415 o A new data set describing some life history traits of Carnivores
1421 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1426 o When plotting a tree with plot.phylo(), the new default of the
1427 option `label.offset' is now 0, so the labels are always visible.
1431 CHANGES IN APE VERSION 1.2-5
1436 o The new function bd.ext() fits a birth-death model with combined
1437 phylogenetic and taxonomic data, and estimates the corresponding
1438 speciation and extinction rates.
1443 o The package gee is no more required by ape but only suggested
1444 since only the function compar.gee() calls gee.
1448 CHANGES IN APE VERSION 1.2-4
1453 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1454 and lines.popsize) implementing a new approach for inferring the
1455 demographic history from genealogies using a reversible jump
1456 MCMC have been introduced.
1458 o The unit of time in the skyline plot and in the new plots can
1459 now be chosen to be actual years, rather than substitutions.
1463 CHANGES IN APE VERSION 1.2-3
1468 o The new function rtree() generates a random binary tree with or
1469 without branch lengths.
1471 o Two new functions for drawing lineages-through-time (LTT) plots
1472 are provided: ltt.lines() adds a LTT curve to an existing plot,
1473 and mltt.plot() does a multiple LTT plot giving several trees as
1474 arguments (see `?ltt.plot' for details).
1479 o Some taxon names made R crashing when calling as.phylo.hclust():
1482 o dist.dna() returned an error with two identical DNA sequences
1483 (only using the Jukes-Cantor method returned 0): this is fixed.
1488 o The function dist.phylo() has been re-written using a different
1489 algorithm: it is now about four times faster.
1491 o The code of branching.times() has been improved: it is now about
1496 CHANGES IN APE VERSION 1.2-2
1501 o The new function seg.sites() finds the segregating sites in a
1502 sample of DNA sequences.
1507 o A bug introduced in read.tree() and in read.nexus() with version
1510 o A few errors were corrected and a few examples were added in the
1515 CHANGES IN APE VERSION 1.2-1
1520 o plot.phylo() can now draw the edge of the root of a tree if it
1521 has one (see the new option `root.edge', its default is FALSE).
1526 o A bug was fixed in read.nexus(): files with semicolons inside
1527 comment blocks were not read correctly.
1529 o The behaviour of read.tree() and read.nexus() was corrected so
1530 that tree files with badly represented root edges (e.g., with
1531 an extra pair of parentheses, see the help pages for details)
1532 are now correctly represented in the object of class "phylo";
1533 a warning message is now issued.
1537 CHANGES IN APE VERSION 1.2
1542 o plot.phylo() has been completely re-written and offers several
1543 new functionalities. Three types of trees can now be drawn:
1544 phylogram (as previously), cladogram, and unrooted tree; in
1545 all three types the branch lengths can be drawn using the edge
1546 lengths of the phylogeny or not (e.g., if the latter is absent).
1547 The vertical position of the nodes can be adjusted with two
1548 choices (see option `node.pos'). The code has been re-structured,
1549 and two new functions (potentially useful for developpers) are
1550 documented separately: node.depth.edgelength() and node.depth();
1551 see the respective help pages for details.
1553 o The new function zoom() allows to explore very large trees by
1554 focusing on a small portion of it.
1556 o The new function yule() fits by maximum likelihood the Yule model
1557 (birth-only process) to a phylogenetic tree.
1559 o Support for writing DNA sequences in FASTA format has been
1560 introduced in write.dna() (support for reading sequences in
1561 this format was introduced in read.dna() in version 1.1-2).
1562 The function has been completely re-written, fixing some bugs
1563 (see below); the default behaviour is no more to display the
1564 sequences on the standard output. Several options have been
1565 introduced to control the sequence printing in a flexible
1566 way. The help page has been extended.
1568 o A new data set is included: a supertree of bats in NEXUS format.
1573 o In theta.s(), the default of the option `variance' has
1574 been changed to `FALSE' (as was indicated in the help page).
1576 o Several bugs were fixed in the code of all.equal.phylo().
1578 o Several bugs were fixed in write.dna(), particularly this
1579 function did not work with `format = "interleaved"'.
1581 o Various errors were corrected in the help pages.
1586 o The argument names of as.hclust.phylo() have been changed
1587 from "(phy)" to "(x, ...)" to conform to the definition of
1588 the corresponding generic function.
1590 o gamma.stat() has been renamed gammaStat() to avoid confusion
1591 since gamma() is a generic function.
1595 CHANGES IN APE VERSION 1.1-3
1600 o base.freq() previously did not return a value of 0 for
1601 bases absent in the data (e.g., a vector of length 3 was
1602 returned if one base was absent). This is now fixed (a
1603 vector of length 4 is always returned).
1605 o Several bugs were fixed in read.nexus(), including that this
1606 function did not work in this absence of a "TRANSLATE"
1607 command in the NEXUS file, and that the commands were
1612 CHANGES IN APE VERSION 1.1-2
1617 o The Tamura and Nei (1993) model of DNA distance is now implemented
1618 in dist.dna(): five models are now available in this function.
1620 o A new data set is included: a set of 15 sequences of the
1621 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1627 o A bug in read.nexus() was fixed.
1629 o read.dna() previously did not work correctly in most cases.
1630 The function has been completely re-written and its help page
1631 has been considerably extended (see ?read.dna for details).
1632 Underscores (_) in taxon names are no more replaced with
1633 spaces (this behaviour was undocumented).
1635 o A bug was fixed in write.dna().
1639 CHANGES IN APE VERSION 1.1-1
1644 o A bug in read.tree() introduced in APE 1.1 was fixed.
1646 o A bug in compar.gee() resulted in an error when trying to fit
1647 a model with `family = "binomial"'. This is now fixed.
1651 CHANGES IN APE VERSION 1.1
1656 o The Klastorin (1982) method as suggested by Misawa and Tajima
1657 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1658 on the basis of phylogenetic trees has been implemented (see
1659 the function klastorin()).
1661 o Functions have been added to convert APE's "phylo" objects in
1662 "hclust" cluster objects and vice versa (see the help page of
1663 as.phylo for details).
1665 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1666 are introduced for the estimation of absolute evolutionary rates
1667 (ratogram) and dated clock-like trees (chronogram) from
1668 phylogenetic trees using the non-parametric rate smoothing approach
1669 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1671 o A summary method is now provided printing a summary information on a
1672 phylogenetic tree with, for instance, `summary(tree)'.
1674 o The behaviour of read.tree() was changed so that all spaces and
1675 tabulations in tree files are now ignored. Consequently, spaces in tip
1676 labels are no more allowed. Another side effect is that read.nexus()
1677 now does not replace the underscores (_) in tip labels with spaces
1678 (this behaviour was undocumented).
1680 o The function plot.phylo() has a new option (`underscore') which
1681 specifies whether the underscores in tip labels should be written on
1682 the plot as such or replaced with spaces (the default).
1684 o The function birthdeath() now computes 95% confidence intervals of
1685 the estimated parameters using profile likelihood.
1687 o Three new data sets are included: a gene tree estimated from 36
1688 landplant rbcL sequences, a gene tree estimated from 32 opsin
1689 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1694 o A bug was fixed in dist.gene() where nothing was returned.
1696 o A bug in plot.mst() was fixed.
1698 o A bug in vcv.phylo() resulted in false correlations when the
1699 option `cor = TRUE' was used (now fixed).
1703 CHANGES IN APE VERSION 1.0
1708 o Two new functions, read.dna() and write.dna(), read/write in a file
1709 DNA sequences in interleaved or in sequential format.
1711 o Two new functions, read.nexus() and write.nexus(), read/write trees
1714 o The new function bind.tree() allows to bind two trees together,
1715 possibly handling root edges to give internal branches.
1717 o The new function drop.tip() removes the tips in a phylogenetic tree,
1718 and trims (or not) the corresponding internal branches.
1720 o The new function is.ultrametric() tests if a tree is ultrametric.
1722 o The function plot.phylo() has more functionalities such as drawing the
1723 branches with different colours and/or different widths, showing the
1724 node labels, controling the position and font of the labels, rotating
1725 the labels, and controling the space around the plot.
1727 o The function read.tree() can now read trees with no branch length,
1728 such as "(a,b),c);". Consequently, the element `edge.length' in
1729 objects of class "phylo" is now optional.
1731 o The function write.tree() has a new default behaviour: if the default
1732 for the option `file' is used (i.e. file = ""), then a variable of
1733 mode character containing the tree in Newick format is returned which
1734 can thus be assigned (e.g., tree <- write.tree(phy)).
1736 o The function read.tree() has a new argument `text' which allows
1737 to read the tree in a variable of mode character.
1739 o A new data set is included: the phylogenetic relationships among
1740 the orders of birds from Sibley and Ahlquist (1990).
1744 CHANGES IN APE VERSION 0.2-1
1749 o Several bugs were fixed in the help pages.
1753 CHANGES IN APE VERSION 0.2
1758 o The function write.tree() writes phylogenetic trees (objects of class
1759 "phylo") in an ASCII file using the Newick parenthetic format.
1761 o The function birthdeath() fits a birth-death model to branching times
1762 by maximum likelihood, and estimates the corresponding speciation and
1765 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1768 o The function is.binary.tree() tests whether a phylogeny is binary.
1770 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1771 as well as some methods are introduced.
1773 o Several functions, including some generics and methods, for computing
1774 skyline plot estimates (classic and generalized) of effective
1775 population size through time are introduced and replace the function
1776 skyline.plot() in version 0.1.
1778 o Two data sets are now included: the phylogenetic relationships among
1779 the families of birds from Sibley and Ahlquist (1990), and an
1780 estimated clock-like phylogeny of HIV sequences sampled in the
1781 Democratic Republic of Congo.
1784 DEPRECATED & DEFUNCT
1786 o The function skyline.plot() in ape 0.1 has been deprecated and
1787 replaced by more elaborate functions (see above).
1792 o Two important bugs were fixed in plot.phylo(): phylogenies with
1793 multichotomies not at the root or not with only terminal branches,
1794 and phylogenies with a single node (i.e. only terminal branches)
1795 did not plot. These trees should be plotted correctly now.
1797 o Several bugs were fixed in diversi.time() in the computation of
1800 o Various errors were corrected in the help pages.