1 CHANGES IN APE VERSION 2.3-2
6 o all.equal.phylo() did not compare unrooted trees correctly.
8 o dist.topo(... method = "PH85") did not treat unrooted trees
9 correctly (thanks to Tim Wallstrom for the fix).
11 o root() sometimes failed to test for the monophyly of the
14 o extract.clade() sometimes included too many edges.
16 o vcv.phylo() did not work correctly when the tree is in
21 CHANGES IN APE VERSION 2.3-1
26 o The new function is.monophyletic tests the monophyly of a group.
28 o There is now a c() method for lists of class "DNAbin".
30 o yule.cov() now fits the null model, and its help page has been
31 corrected with respect to this change.
33 o drop.tip() has a new option 'rooted' to force (or not) a tree
34 to be treated as (un)rooted.
39 o dist.gene() failed on most occasions with the default
40 pairwise.deletion = FALSE.
42 o read.tree() failed to read correctly the tree name(s).
44 o boot.phylo() now treats correctly data frames.
46 o del.gaps() did not copy the rownames of a matrix.
48 o A small bug was fixed in CDAM.global().
50 o ace() failed with large data sets. Thanks to Rich FitzJohn for
51 the fix. With other improvements, this function is now about 6
54 o write.tree() failed with objects of class "multiPhylo".
56 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
61 o [.multiPhylo and [.DNAbin now respect the original class.
63 o Instances of the form class(phy) == "phylo" have been replaced
64 by inherits(phy, "phylo").
66 o rcoal() is now faster.
71 o klastorin() has been removed.
75 CHANGES IN APE VERSION 2.3
80 o The new functions CADM.global and CADM.post, contributed by
81 Pierre Legendre, test the congruence among several distance
84 o The new function yule.time fits a user-defined time-dependent
85 Yule model by maximum likelihood.
87 o The new function makeNodeLabel creates and/or modifies node
88 labels in a flexible way.
90 o read.tree() and write.tree() have been modified so that they can
91 handle individual tree names.
93 o plot.phylo() has a new argument 'edge.lty' that specifies the
94 types of lines used for the edges (plain, dotted, dashed, ...)
96 o phymltest() has been updated to work with PhyML 3.0.1.
101 o drop.tip() shuffled tip labels in some cases.
103 o drop.tip() did not handle node.label correctly.
105 o is.ultrametric() now checks the ordering of the edge matrix.
107 o ace() sometimes returned negative values of likelihoods of
108 ancestral states (thanks to Dan Rabosky for solving this long
114 o The data set xenarthra has been removed.
118 CHANGES IN APE VERSION 2.2-4
122 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
123 now fixed. (Thanks to Peter Wragg for the fix!)
125 o A warning message occurred for no reason with ace(method="GLS").
130 o There is now a general help page displayed with '?ape'
134 CHANGES IN APE VERSION 2.2-3
139 o The new function extract.clade extracts a clade from a tree by
140 specifying a node number or label.
142 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
143 operations of the same names.
145 o dist.dna() can now return the number of site differences by
146 specifying model="N".
151 o chronopl() did not work with CV = TRUE.
153 o read.nexus() did not work correctly in some situations (trees on
154 multiple lines with different numbers of lines and/or with
155 comments inserted within the trees).
157 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
158 the number of lineages with non-binary trees.
163 o ape has now a namespace.
165 o drip.tip() has been improved: it should be much faster and work
166 better in some cases (e.g., see the example in ?zoom).
170 CHANGES IN APE VERSION 2.2-2
175 o dist.gene() has been substantially improved and gains an option
178 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
184 o prop.part() failed with a single tree with the default option
185 'check.labels = TRUE'.
187 o summary.DNAbin() failed to display correctly the summary of
188 sequence lengths with lists of sequences of 10,000 bases or more
189 (because summary.default uses 4 significant digits by default).
191 o read.nexus() failed to read a file with a single tree with line
192 breaks in the Newick string.
194 o del.gaps() returned a list of empty sequences when there were no
200 o phymltest() has been updated for PhyML 3.0 and gains an option
201 'append', whereas the option 'path2exec' has been removed.
203 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
204 which is returned unchanged (instead of an error).
206 o The data sets bird.orders and bird.families are now stored as
207 Newick strings; i.e., the command data(bird.orders) calls
212 CHANGES IN APE VERSION 2.2-1
217 o The new function makeLabel() helps to modify labels of trees,
218 lists of trees, or DNA sequences, with several utilities to
219 truncate and/or make them unique, substituting some
220 characters, and so on.
222 o The new function del.gaps() removes insertion gaps ("-") in a
223 set of DNA sequences.
225 o read.dna() can now read Clustal files (*.aln).
230 o root() failed with 'resolve.root = TRUE' when the root was
231 already the specified root.
233 o Several bugs were fixed in mlphylo().
235 o collapsed.singles() did not propagate the 'Nnode' and
236 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
238 o read.nexus() failed to remove correctly the comments within
241 o read.nexus() failed to read a file with a single tree and no
242 translation of tip labels.
244 o read.nexus() failed to place correctly tip labels when reading
245 a single tree with no edge lengths.
247 o A bug was fixed in sh.test().
252 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
255 o The option 'check.labels' of consensus() and prop.part() is now
258 o write.dna() now does not truncate names to 10 characters with
263 CHANGES IN APE VERSION 2.2
268 o Four new functions have been written by Damien de Vienne for the
269 graphical exploration of large trees (cophyloplot, subtrees,
270 subtreeplot), and to return the graphical coordinates of tree
273 o The new functions corPagel and corBlomberg implement the Pagel's
274 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
276 o chronopl() has been improved and gains several options: see its
277 help page for details.
279 o boot.phylo() has now an option 'trees' to possibly return the
280 bootstraped trees (the default is FALSE).
282 o prop.part() has been improved and should now be faster in all
288 o read.dna() failed if "?" occurred in the first 10 sites of the
291 o The x/y aspect of the plot is now respected when plotting a
292 circular tree (type = "r" or "f").
294 o Drawing the tip labels sometimes failed when plotting circular
297 o zoom() failed when tip labels were used instead of their numbers
298 (thanks to Yan Wong for the fix).
300 o drop.tip() failed with some trees (fixed by Yan Wong).
302 o seg.sites() failed with a list.
304 o consensus() failed in some cases. The function has been improved
305 as well and is faster.
309 CHANGES IN APE VERSION 2.1-3
314 o A bug in read.nexus() made the Windows R-GUI crash.
316 o An error was fixed in the computation of ancestral character
317 states by generalized least squares in ace().
319 o di2multi() did not modify node labels correctly.
321 o multi2di() failed if the tree had its attribute "order" set to
326 CHANGES IN APE VERSION 2.1-2
331 o There three new methods for the "multiPhylo" class: str, $,
334 o root() gains the options 'node' and 'resolve.root'
335 (FALSE by default) as well as its code being improved.
337 o mltt.plot() has now an option 'log' used in the same way
338 than in plot.default().
343 o mltt.plot() failed to display the legend with an unnamed
346 o nodelabels() with pies now correcly uses the argument
347 'cex' to draw symbols of different sizes (which has
348 worked already for thermometers).
350 o read.nexus() generally failed to read very big files.
355 o The argument 'family' of compar.gee() can now be a function
356 as well as a character string.
358 o read.tree() and read.nexus() now return an unnamed list if
361 o read.nexus() now returns a modified object of class "multiPhylo"
362 when there is a TRANSLATE block in the NEXUS file: the individual
363 trees have no 'tip.label' vector, but the list has a 'TipLabel'
364 attribute. The new methods '$' and '[[' set these elements
365 correctly when extracting trees.
369 CHANGES IN APE VERSION 2.1-1
374 o The new function rmtree generates lists of random trees.
376 o rcoal() now generates a genuine coalescent tree by default
377 (thanks to Vladimir Minin for the code).
382 o nuc.div() returned an incorrect value with the default
383 pairwise.deletion = FALSE.
388 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
389 have been improved so that they are stabler and faster.
391 o R packages used by ape are now loaded silently; lattice and gee
392 are loaded only when needed.
396 CHANGES IN APE VERSION 2.1
401 o The new function identify.phylo identifies clades on a plotted
402 tree using the mouse.
404 o It is now possible to subset a list of trees (object of class
405 "multiPhylo") with "[" while keeping its class correct.
407 o The new function as.DNAbin.alignment converts DNA sequences
408 stored in the "alignment" format of the package seqinr into
409 an object of class "DNAbin".
411 o The new function weight.taxo2 helps to build similarity matrices
412 given two taxonomic levels (usually called by other functions).
414 o write.tree() can now take a list of trees (class "multiPhylo")
415 as its main argument.
417 o plot.correlogram() and plot.correlogramList() have been
418 improved, and gain several options (see the help page for
419 details). A legend is now plotted by default.
424 o dist.dna() returned some incorrect values with `model = "JC69"'
425 and `pairwise.deletion = TRUE'. This affected only the
426 distances involving sequences with missing values. (Thanks
427 to Bruno Toupance for digging this bug out.)
429 o write.tree() failed with some trees: this is fixed by removing
430 the `multi.line' option (trees are now always printed on a
433 o read.nexus() did not correctly detect trees with multiple root
434 edges (see OTHER CHANGES).
439 o The code of mlphylo() has been almost entirely rewritten, and
440 should be much stabler. The options have been also greatly
441 simplified (see ?mlphylo and ?DNAmodel for details).
443 o The internal function nTips has been renamed klastorin_nTips.
445 o The code of is.ultrametric() contained redundancies and has
448 o The code of Moran.I() and of correlogram.formula() have been
451 o read.tree() and read.nexus() now return an error when trying to
452 read a tree with multiple root edges (see BUG FIXES). The
453 correction applied in previous version did not work in all
456 o The class c("multi.tree", "phylo") has been renamed
462 o There is now a vignette in ape: see vignette("MoranI", "ape").
467 o as.matching() and as.phylo.matching() do not support branch
470 o correlogram.phylo() and discrete.dist() have been removed.
474 CHANGES IN APE VERSION 2.0-2
479 o The new function matexpo computes the exponential of a square
482 o The new function unique.multi.tree removes duplicate trees from
485 o yule() has a new option `use.root.edge = FALSE' that specifies
486 to ignore, by default, the root edge of the tree if it exists.
491 o which.edge() failed when the index of a single terminal edge was
494 o In diversi.time(), the values returned for model C were
497 o A bug was fixed in yule() that affected the calculation of the
498 likelihood in the presence of ties in the branching times.
500 o There was a bug in the C function mat_expo4x4 affecting the
501 calculations of the transition probabilities for models HKY and
504 o A small bug was fixed in as.matrix.DNAbin (thanks to James
507 o rtree() did not `shuffle' the tip labels by default, so only a
508 limited number of labelled topologies could be generated.
512 CHANGES IN APE VERSION 2.0-1
517 o The three new functions bionj, fastme.ols, and fastme.bal
518 perform phylogeny estimation by the BIONJ and fastME methods in
519 OLS and balanced versions. This is a port to R of previous
520 previous programs done by Vincent Lefort.
522 o The new function chronoMPL performs molecular dating with the
523 mean path lengths method of Britton et al. (2002, Mol. Phyl.
526 o The new function rotate, contributed by Christoph Heibl, swaps
527 two clades connected to the same node. It works also with
528 multichotomous nodes.
530 o The new `method' as.matrix.DNAbin() may be used to convert
531 easily DNA sequences stored in a list into a matrix while
532 keeping the names and the class.
537 o chronopl() failed when some branch lengths were equal to zero:
538 an error message is now returned.
540 o di2multi() failed when there was a series of consecutive edges
545 CHANGES IN APE VERSION 1.10-2
550 o plot.phylo() can now plot circular trees: the option is type =
551 "fan" or type = "f" (to avoid the ambiguity with type = "c").
553 o prop.part() has a new option `check.labels = FALSE' which allows
554 to considerably speed-up the calculations of bipartitions. As a
555 consequence, calculations of bootstrap values with boot.phylo()
556 should be much faster.
561 o read.GenBank() did not return correctly the list of species as
562 from ape 1.10: this is fixed in this version
564 o Applying as.phylo() on a tree of class "phylo" failed: the
565 object is now returned unchanged.
569 CHANGES IN APE VERSION 1.10-1
574 o The three new functions Ntip, Nnode, and Nedge return, for a
575 given tree, the number of tips, nodes, or edges, respectively.
580 o read.nexus() did not set correctly the class of the returned
581 object when reading multiple trees.
583 o mllt.plot() failed with objects of class c("multi.tree",
586 o unroot() did not work correctly in most cases.
588 o reorder.phylo() made R freeze in some occasions.
590 o Plotting a tree in pruningwise order failed.
592 o When plotting an unrooted tree, the tip labels where not all
593 correctly positioned if the option `cex' was used.
597 CHANGES IN APE VERSION 1.10
602 o Five new `method' functions have been introduced to manipulate
603 DNA sequences in binary format (see below).
605 o Three new functions have been introduced to convert between the
606 new binary and the character formats.
608 o The new function as.alignment converts DNA sequences stored as
609 single characters into the class "alignment" used by the package
612 o read.dna() and read.GenBank() have a new argument `as.character'
613 controlling whether the sequences are returned in binary format
619 o root() failed when the tree had node labels: this is fixed.
621 o plot.phylo() did not correctly set the limits on the y-axis with
622 the default setting: this is fixed.
624 o dist.dna() returned a wrong result for the LogDet, paralinear,
625 and BH87 models with `pairwise.deletion = TRUE'.
630 o DNA sequences are now internally stored in a binary format. See
631 the document "A Bit-Level Coding Scheme for Nucleotides" for the
632 details. Most functions analyzing DNA functions have been
633 modified accordingly and are now much faster (dist.dna is now
634 ca. 60 times faster).
638 CHANGES IN APE VERSION 1.9-4
643 o A bug was fixed in edgelabels().
645 o as.phylo.hclust() did not work correctly when the object of
646 class "hclust" has its labels set to NULL: the returned tree has
647 now its tip labels set to "1", "2", ...
649 o consensus could fail if some tip labels are a subset of others
650 (e.g., "a" and "a_1"): this is now fixed.
652 o mlphylo() failed in most cases if some branch lengths of the
653 initial tree were greater than one: an error message is now
656 o mlphylo() failed in most cases when estimating the proportion of
657 invariants: this is fixed.
661 CHANGES IN APE VERSION 1.9-3
666 o The new function edgelabels adds labels on the edge of the tree
667 in the same way than nodelabels or tiplabels.
672 o multi2di() did not handle correctly branch lengths with the
673 default option `random = TRUE': this is now fixed.
675 o A bug was fixed in nuc.div() when using pairwise deletions.
677 o A bug occurred in the analysis of bipartitions with large
678 numbers of large trees, with consequences on prop.part,
679 prop.clades, and boot.phylo.
681 o The calculation of the Billera-Holmes-Vogtmann distance in
682 dist.topo was wrong: this has been fixed.
686 CHANGES IN APE VERSION 1.9-2
691 o The new function ladderize reorganizes the internal structure of
692 a tree to plot them left- or right-ladderized.
694 o The new function dist.nodes computes the patristic distances
695 between all nodes, internal and terminal, of a tree. It replaces
696 the option `full = TRUE' of cophenetic.phylo (see below).
701 o A bug was fixed in old2new.phylo().
703 o Some bugs were fixed in chronopl().
705 o The edge colours were not correctly displayed by plot.phylo
706 (thank you to Li-San Wang for the fix).
708 o cophenetic.phylo() failed with multichotomous trees: this is
714 o read.dna() now returns the sequences in a matrix if they are
715 aligned (interleaved or sequential format). Sequences in FASTA
716 format are still returned in a list.
718 o The option `full' of cophenetic.phylo() has been removed because
719 it could not be used from the generic.
724 o rotate() has been removed; this function did not work correctly
729 CHANGES IN APE VERSION 1.9-1
734 o Trees with a single tip were not read correctly in R as the
735 element `Nnode' was not set: this is fixed.
737 o unroot() did not set correctly the number of nodes of the
738 unrooted tree in most cases.
740 o read.GenBank() failed when fetching very long sequences,
741 particularly of the BX-series.
743 o A bug was introduced in read.tree() with ape 1.9: it has been
748 CHANGES IN APE VERSION 1.9
753 o There are two new print `methods' for trees of class "phylo" and
754 lists of trees of class "multi.tree", so that they are now
755 displayed in a compact and informative way.
757 o There are two new functions, old2new.phylo and new2old.phylo,
758 for converting between the old and new coding of the class
761 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
762 LogDet ("logdet"), and paralinear ("paralin").
764 o compute.brlen() has been extended: several methods are now
765 available to compute branch lengths.
767 o write.dna() can now handle matrices as well as lists.
772 o cophenetic.phylo() sometimes returned a wrong result with
773 multichotomous trees: this is fixed.
775 o rotate() failed when a single tip was specified: the tree is now
778 o ace() did not return the correct index matrix with custom
779 models: this is fixed.
781 o multi2di() did not work correctly when resolving multichotomies
782 randomly: the topology was always the same, only the arrangement
783 of clades was randomized: this is fixed. This function now
784 accepts trees with no branch lengths.
786 o The output of diversi.gof() was blurred by useless prints when a
787 user distribution was specified. This has been corrected, and
788 the help page of this function has been expanded.
793 o The internal structure of the class "phylo" has been changed:
794 see the document "Definition of Formats for Coding Phylogenetic
795 Trees in R" for the details. In addition, the code of most
796 functions has been improved.
798 o Several functions have been improved by replacing some R codes
799 by C codes: pic, plot.phylo, and reorder.phylo.
801 o There is now a citation information: see citation("ape") in R.
803 o write.tree() now does not add extra 0's to branch lengths so
804 that 1.23 is printed "1.23" by default, not "1.2300000000".
806 o The syntax of bind.tree() has been simplified. This function now
807 accepts trees with no branch lengths, and handles correctly node
810 o The option `as.numeric' of mrca() has been removed.
812 o The unused options `format' and `rooted' of read.tree() have
815 o The unused option `format' of write.tree() has been removed.
817 o The use of node.depth() has been simplified.
821 CHANGES IN APE VERSION 1.8-5
826 o Two new functions read.nexus.data() and write.nexus.data(),
827 contributed by Johan Nylander, allow to read and write molecular
828 sequences in NEXUS files.
830 o The new function reorder.phylo() reorders the internal structure
831 of a tree of class "phylo". It is used as the generic, e.g.,
834 o read.tree() and read.nexus() can now read trees with a single
837 o The new data set `cynipids' supplies a set of protein sequences
843 o The code of all.equal.phylo() has been completely rewritten
844 (thanks to Benoît Durand) which fixes several bugs.
846 o read.tree() and read.nexus() now checks the labels of the tree
847 to remove or substitute any characters that are illegal in the
848 Newick format (parentheses, etc.)
850 o A negative P-value could be returned by mantel.test(): this is
855 CHANGES IN APE VERSION 1.8-4
860 o The new function sh.test() computes the Shimodaira-
863 o The new function collapse.singles() removes the nodes with a
864 single descendant from a tree.
866 o plot.phylo() has a new argument `tip.color' to specify the
869 o mlphylo() has now an option `quiet' to control the display of
870 the progress of the analysis (the default is FALSE).
875 o read.dna() did not read correctly sequences in sequential format
876 with leading alignment gaps "-": this is fixed.
878 o ace() returned a list with no class so that the generic
879 functions (anova, logLik, ...) could not be used directly. This
880 is fixed as ace() now returns an object of class "ace".
882 o anova.ace() had a small bug when computing the number of degrees
883 of freedom: this is fixed.
885 o mlphylo() did not work when the sequences were in a matrix or
886 a data frame: this is fixed.
888 o rtree() did not work correctly when trying to simulate an
889 unrooted tree with two tips: an error message is now issued.
894 o The algorithm of rtree() has been changed: it is now about 40,
895 100, and 130 times faster for 10, 100, and 1000 tips,
900 CHANGES IN APE VERSION 1.8-3
905 o There are four new `method' functions to be used with the
906 results of ace(): logLik(), deviance(), AIC(), and anova().
908 o The plot method of phymltest has two new arguments: `main' to
909 change the title, and `col' to control the colour of the
910 segments showing the AIC values.
912 o ace() has a new argument `ip' that gives the initial values used
913 in the ML estimation with discrete characters (see the examples
914 in ?ace). This function now returns a matrix giving the indices
915 of the estimated rates when analysing discrete characters.
917 o nodelabels() and tiplabels() have a new argument `pie' to
918 represent proportions, with any number of categories, as
919 piecharts. The use of the option `thermo' has been improved:
920 there is now no limitation on the number of categories.
925 o mlphylo() did not work with more than two partitions: this is
928 o root() failed if the proposed outgroup was already an outgroup
929 in the tree: this is fixed.
931 o The `col' argument in nodelabels() and tiplabels() was not
932 correctly passed when `text' was used: this is fixed.
934 o Two bugs were fixed in mlphylo(): parameters were not always
935 correctly output, and the estimation failed in some cases.
937 o plot.phylo() was stuck when given a tree with a single tip: this
938 is fixed and a message error is now returned.
940 o An error was corrected in the help page of gammaStat regarding
941 the calculation of P-values.
943 o Using gls() could crash R when the number of species in the tree
944 and in the variables were different: this is fixed.
948 CHANGES IN APE VERSION 1.8-2
953 o The new function mlphylo() fits a phylogenetic tree by maximum
954 likelihood from DNA sequences. Its companion function DNAmodel()
955 is used to define the substitution model which may include
956 partitioning. There are methods for logLik(), deviance(), and
957 AIC(), and the summary() method has been extended to display in
958 a friendly way the results of this model fitting. Currently, the
959 functionality is limited to estimating the substitution and
960 associated parameters and computing the likelihood.
962 o The new function drop1.compar.gee (used as, e.g., drop1(m))
963 tests for single effects in GEE-based comparative method. A
964 warning message is printed if there is not enough degrees of
970 o An error message was sometimes issued by plot.multi.tree(),
971 though with no consequence.
975 CHANGES IN APE VERSION 1.8-1
980 o There is a new plot method for lists of trees (objects of class
981 "multi.tree"): it calls plot.phylo() internally and is
982 documented on the same help page.
987 o A bug was fixed in the C code that analyzes bipartitions: this
988 has impact on several functions like prop.part, prop.clades,
989 boot.phylo, or consensus.
991 o root() did not work correctly when the specified outgroup had
992 more than one element: this is fixed.
994 o dist.dna() sometimes returned a warning inappropriately: this
997 o If the distance object given to nj() had no rownames, nj()
998 returned a tree with no tip labels: it now returns tips labelled
999 "1", "2", ..., corresponding to the row numbers.
1004 o nj() has been slightly changed so that tips with a zero distance
1005 are first aggregated with zero-lengthed branches; the usual NJ
1006 procedure is then performed on a distance matrix without 0's.
1010 CHANGES IN APE VERSION 1.8
1015 o The new function chronopl() estimates dates using the penalized
1016 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1018 o The new function consensus() calculates the consensus tree of a
1021 o The new function evolve.phylo() simulates the evolution of
1022 continuous characters along a phylogeny under a Brownian model.
1024 o The new plot method for objects of class "ancestral" displays a
1025 tree together with ancestral values, as returned by the above
1028 o The new function as.phylo.formula() returns a phylogeny from a
1029 set of nested taxonomic variables given as a formula.
1031 o The new function read.caic() reads trees in CAIC format.
1033 o The new function tiplabels() allows to add labels to the tips
1034 of a tree using text or plotting symbols in a flexible way.
1036 o The new function unroot() unroots a phylogeny.
1038 o multi2di() has a new option, `random', which specifies whether
1039 to resolve the multichotomies randomly (the default) or not.
1041 o prop.part() now returns an object of class "prop.part" for which
1042 there are print (to display a partition in a more friendly way)
1043 and summary (to extract the numbers) methods.
1045 o plot.phylo() has a new option, `show.tip.label', specifying
1046 whether to print the labels of the tips. The default is TRUE.
1048 o The code of nj() has been replaced by a faster C code: it is now
1049 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1052 o write.nexus() now writes whether a tree is rooted or not.
1057 o Two bugs have been fixed in root(): unrooted trees are now
1058 handled corretly, and node labels are now output normally.
1060 o A bug was fixed in phymltest(): the executable couldn't be found
1063 o Three bug have been fixed in ace(): computing the likelihood of
1064 ancestral states of discrete characters failed, custom models
1065 did not work, and the function failed with a null gradient (a
1066 warning message is now returned; this latter bug was also
1067 present in yule.cov() as well and is now fixed).
1069 o pic() hanged out when missing data were present: a message error
1072 o A small bug was fixed in dist.dna() where the gamma correction
1073 was not always correctly dispatched.
1075 o plot.phylo() plotted correctly the root edge only when the tree
1076 was plotted rightwards: this works now for all directions.
1081 o dist.taxo() has been renamed as weight.taxo().
1083 o Various error and warning messages have been improved.
1087 CHANGES IN APE VERSION 1.7
1090 o The new function ace() estimates ancestral character states for
1091 continuous characters (with ML, GLS, and contrasts methods), and
1092 discrete characters (with ML only) for any number of states.
1094 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1095 of directional evolution for continuous characters. The user
1096 specifies the node(s) of the tree where the character optimum
1099 o The new function is.rooted() tests whether a tree (of class
1102 o The new function rcoal() generates random ultrametric trees with
1103 the possibility to specify the function that generates the
1104 inter-nodes distances.
1106 o The new function mrca() gives for all pairs of tips in a tree
1107 (and optionally nodes too) the most recent common ancestor.
1109 o nodelabels() has a new option `thermo' to plot proportions (up
1110 to three classes) on the nodes of a tree.
1112 o rtree() has been improved: it can now generate rooted or
1113 unrooted trees, and the mathematical function that generates the
1114 branch lengths may be specified by the user. The tip labels may
1115 be given directly in the call to rtree. The limit cases (n = 2,
1116 3) are now handled correctly.
1118 o dist.topo() has a new argument `method' with two choices: "PH85"
1119 for Penny and Henny's method (already available before and now
1120 the default), and "BHV01" for the geometric distance by Billera
1121 et al. (2001, Adv. Appl. Math. 27:733).
1123 o write.tree() has a new option, `digits', which specifies the
1124 number of digits to be printed in the Newick tree. By default
1125 digits = 10. The numbers are now always printed in decimal form
1126 (i.e., 1.0e-1 is now avoided).
1128 o dist.dna() can now compute the raw distances between pairs of
1129 DNA sequences by specifying model = "raw".
1131 o dist.phylo() has a new option `full' to possibly compute the
1132 distances among all tips and nodes of the tree. The default if
1138 o Several bugs were fixed in all.equal.phylo().
1140 o dist.dna() did not handle correctly gaps ("-") in alignments:
1141 they are now considered as missing data.
1143 o rotate() did not work if the tips were not ordered: this is
1146 o mantel.test() returned NA in some special cases: this is fixed
1147 and the function has been improved and is now faster.
1149 o A bug was fixed in diversi.gof() where the calculation of A² was
1152 o cherry() did not work correctly under some OSs (mainly Linux):
1155 o is.binary.tree() has been modified so that it works with both
1156 rooted and unrooted trees.
1158 o The documentation of theta.s() was not correct: this has been
1161 o plot.mst() did not work correctly: this is fixed.
1165 CHANGES IN APE VERSION 1.6
1170 o The new function dist.topo() computes the topological distances
1173 o The new function boot.phylo() performs a bootstrap analysis on
1174 phylogeny estimation.
1176 o The new functions prop.part() and prop.clades() analyse
1177 bipartitions from a series of trees.
1182 o read.GenBank() now uses the EFetch utility of NCBI instead of
1183 the usual Web interface: it is now much faster (e.g., 12 times
1184 faster to retrieve 8 sequences, 37 times for 60 sequences).
1189 o Several bugs were fixed in read.dna().
1191 o Several bugs were fixed in diversi.time().
1193 o is.binary.tree() did not work correctly if the tree has no edge
1194 lengths: this is fixed.
1196 o drop.tip() did not correctly propagated the `node.label' of a
1197 tree: this is fixed.
1201 CHANGES IN APE VERSION 1.5
1206 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1207 convert objects between the classes "phylo" and "matching". The
1208 latter implements the representation of binary trees introduced by
1209 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1210 as.matching() has been introduced as well.
1212 o Two new functions, multi2di() and di2multi(), allow to resolve
1213 and collapse multichotomies with branches of length zero.
1215 o The new function nuc.div() computes the nucleotide diversity
1216 from a sample a DNA sequences.
1218 o dist.dna() has been completely rewritten with a much faster
1219 (particularly for large data sets) C code. Eight models are
1220 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1221 option `method' has been renamed `model'). Computation of variance
1222 is available for all models. A gamma-correction is possible for
1223 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1224 to remove sites with missing data on a pairwise basis. The option
1225 `GCcontent' has been removed.
1227 o read.GenBank() has a new option (species.names) which specifies
1228 whether to return the species names of the organisms in addition
1229 to the accession numbers of the sequences (this is the default
1232 o write.nexus() can now write several trees in the same NEXUS file.
1234 o drop.tip() has a new option `root.edge' that allows to specify the
1235 new root edge if internal branches are trimmed.
1240 o as.phylo.hclust() failed if some labels had parentheses: this
1243 o Several bugs were fixed in all.equal.phylo(). This function now
1244 returns the logical TRUE if the trees are identical but with
1245 different representations (a report was printed previously).
1247 o read.GenBank() did not correctly handle ambiguous base codes:
1253 o birthdeath() now returns an object of class "birthdeath" for
1254 which there is a print method.
1258 CHANGES IN APE VERSION 1.4
1263 o The new function nj() performs phylogeny estimation with the
1264 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1267 o The new function which.edge() identifies the edges of a tree
1268 that belong to a group specified as a set of tips.
1270 o The new function as.phylo.phylog() converts an object of class
1271 "phylog" (from the package ade4) into an object of class
1274 o The new function axisPhylo() draws axes on the side of a
1277 o The new function howmanytrees() calculates the number of trees
1278 in different cases and giving a number of tips.
1280 o write.tree() has a new option `multi.line' (TRUE by default) to
1281 write a Newick tree on several lines rather than on a single
1284 o The functionalities of zoom() have been extended. Several
1285 subtrees can be visualized at the same time, and they are marked
1286 on the main tree with colors. The context of the subtrees can be
1287 marked with the option `subtree' (see below).
1289 o drop.tip() has a new option `subtree' (FALSE by default) which
1290 specifies whether to output in the tree how many tips have been
1293 o The arguments of add.scale.bar() have been redefined and have
1294 now default values (see ?add.scale.bar for details). This
1295 function now works even if the plotted tree has no edge length.
1297 o plot.phylo() can now plot radial trees, but this does not take
1298 edge lengths into account.
1300 o In plot.phylo() with `type = "phylogram"', if the values of
1301 `edge.color' and `edge.width' are identical for sister-branches,
1302 they are propagated to the vertical line that link them.
1307 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1308 crashing. This is fixed.
1310 o In plot.phylo(), the options `edge.color' and `edge.width' are
1311 now properly recycled; their default values are now "black" and
1314 o A bug has been fixed in write.nexus().
1319 o The function node.depth.edgelength() has been removed and
1320 replaced by a C code.
1324 CHANGES IN APE VERSION 1.3-1
1329 o The new function nodelabels() allows to add labels to the nodes
1330 of a tree using text or plotting symbols in a flexible way.
1332 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1333 numeric values specifying the lower and upper limits on the x-
1334 and y-axes. This allows to leave some space on any side of the
1335 tree. If a single value is given, this is taken as the upper
1340 CHANGES IN APE VERSION 1.3
1345 o The new function phymltest() calls the software PHYML and fits
1346 28 models of DNA sequence evolution. There are a print method to
1347 display likelihood and AIC values, a summary method to compute
1348 the hierarchical likelihood ratio tests, and a plot method to
1349 display graphically the AIC values of each model.
1351 o The new function yule.cov() fits the Yule model with covariates,
1352 a model where the speciation rate is affected by several species
1353 traits through a generalized linear model. The parameters are
1354 estimated by maximum likelihood.
1356 o Three new functions, corBrownian(), corGrafen(), and
1357 corMartins(), compute the expected correlation structures among
1358 species given a phylogeny under different models of evolution.
1359 These can be used for GLS comparative phylogenetic methods (see
1360 the examples). There are coef() and corMatrix() methods and an
1361 Initialize.corPhyl() function associated.
1363 o The new function compar.cheverud() implements Cheverud et al.'s
1364 (1985; Evolution 39:1335) phylogenetic comparative method.
1366 o The new function varcomp() estimates variance components; it has
1369 o Two new functions, panel.superpose.correlogram() and
1370 plot.correlogramList(), allow to plot several phylogenetic
1373 o The new function node.leafnumber() computes the number of leaves
1374 of a subtree defined by a particular node.
1376 o The new function node.sons() gets all tags of son nodes from a
1379 o The new function compute.brlen() computes the branch lengths of
1380 a tree according to a specified method.
1382 o plot.phylo() has three new options: "cex" controls the size of
1383 the (tip and node) labels (thus it is no more needed to change
1384 the global graphical parameter), "direction" which allows to
1385 plot the tree rightwards, leftwards, upwards, or downwards, and
1386 "y.lim" which sets the upper limit on the y-axis.
1391 o Some functions which try to match tip labels and names of
1392 additional data (e.g. vector) are likely to fail if there are
1393 typing or syntax errors. If both series of names do not perfectly
1394 match, they are ignored and a warning message is now issued.
1395 These functions are bd.ext, compar.gee, pic. Their help pages
1396 have been clarified on this point.
1400 CHANGES IN APE VERSION 1.2-7
1405 o The new function root() reroots a phylogenetic tree with respect
1406 to a specified outgroup.
1408 o The new function rotate() rotates an internal branch of a tree.
1410 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1411 trees) controls the display of the tip labels in unrooted trees.
1412 This display has been greatly improved: the tip labels are now not
1413 expected to overlap with the tree (particularly if lab4ut =
1414 "axial"). In all cases, combining appropriate values of "lab4ut"
1415 and the font size (via "par(cex = )") should result in readable
1416 unrooted trees. See ?plot.phylo for some examples.
1418 o In drop.tip(), the argument `tip' can now be numeric or character.
1423 o drop.tip() did not work correctly with trees with no branch
1424 lengths: this is fixed.
1426 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1427 plotted with some line crossings: this is now fixed.
1431 CHANGES IN APE VERSION 1.2-6
1436 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1437 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1438 to implement comparative methods with an autocorrelation approach.
1440 o A new data set describing some life history traits of Carnivores
1446 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1451 o When plotting a tree with plot.phylo(), the new default of the
1452 option `label.offset' is now 0, so the labels are always visible.
1456 CHANGES IN APE VERSION 1.2-5
1461 o The new function bd.ext() fits a birth-death model with combined
1462 phylogenetic and taxonomic data, and estimates the corresponding
1463 speciation and extinction rates.
1468 o The package gee is no more required by ape but only suggested
1469 since only the function compar.gee() calls gee.
1473 CHANGES IN APE VERSION 1.2-4
1478 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1479 and lines.popsize) implementing a new approach for inferring the
1480 demographic history from genealogies using a reversible jump
1481 MCMC have been introduced.
1483 o The unit of time in the skyline plot and in the new plots can
1484 now be chosen to be actual years, rather than substitutions.
1488 CHANGES IN APE VERSION 1.2-3
1493 o The new function rtree() generates a random binary tree with or
1494 without branch lengths.
1496 o Two new functions for drawing lineages-through-time (LTT) plots
1497 are provided: ltt.lines() adds a LTT curve to an existing plot,
1498 and mltt.plot() does a multiple LTT plot giving several trees as
1499 arguments (see `?ltt.plot' for details).
1504 o Some taxon names made R crashing when calling as.phylo.hclust():
1507 o dist.dna() returned an error with two identical DNA sequences
1508 (only using the Jukes-Cantor method returned 0): this is fixed.
1513 o The function dist.phylo() has been re-written using a different
1514 algorithm: it is now about four times faster.
1516 o The code of branching.times() has been improved: it is now about
1521 CHANGES IN APE VERSION 1.2-2
1526 o The new function seg.sites() finds the segregating sites in a
1527 sample of DNA sequences.
1532 o A bug introduced in read.tree() and in read.nexus() with version
1535 o A few errors were corrected and a few examples were added in the
1540 CHANGES IN APE VERSION 1.2-1
1545 o plot.phylo() can now draw the edge of the root of a tree if it
1546 has one (see the new option `root.edge', its default is FALSE).
1551 o A bug was fixed in read.nexus(): files with semicolons inside
1552 comment blocks were not read correctly.
1554 o The behaviour of read.tree() and read.nexus() was corrected so
1555 that tree files with badly represented root edges (e.g., with
1556 an extra pair of parentheses, see the help pages for details)
1557 are now correctly represented in the object of class "phylo";
1558 a warning message is now issued.
1562 CHANGES IN APE VERSION 1.2
1567 o plot.phylo() has been completely re-written and offers several
1568 new functionalities. Three types of trees can now be drawn:
1569 phylogram (as previously), cladogram, and unrooted tree; in
1570 all three types the branch lengths can be drawn using the edge
1571 lengths of the phylogeny or not (e.g., if the latter is absent).
1572 The vertical position of the nodes can be adjusted with two
1573 choices (see option `node.pos'). The code has been re-structured,
1574 and two new functions (potentially useful for developpers) are
1575 documented separately: node.depth.edgelength() and node.depth();
1576 see the respective help pages for details.
1578 o The new function zoom() allows to explore very large trees by
1579 focusing on a small portion of it.
1581 o The new function yule() fits by maximum likelihood the Yule model
1582 (birth-only process) to a phylogenetic tree.
1584 o Support for writing DNA sequences in FASTA format has been
1585 introduced in write.dna() (support for reading sequences in
1586 this format was introduced in read.dna() in version 1.1-2).
1587 The function has been completely re-written, fixing some bugs
1588 (see below); the default behaviour is no more to display the
1589 sequences on the standard output. Several options have been
1590 introduced to control the sequence printing in a flexible
1591 way. The help page has been extended.
1593 o A new data set is included: a supertree of bats in NEXUS format.
1598 o In theta.s(), the default of the option `variance' has
1599 been changed to `FALSE' (as was indicated in the help page).
1601 o Several bugs were fixed in the code of all.equal.phylo().
1603 o Several bugs were fixed in write.dna(), particularly this
1604 function did not work with `format = "interleaved"'.
1606 o Various errors were corrected in the help pages.
1611 o The argument names of as.hclust.phylo() have been changed
1612 from "(phy)" to "(x, ...)" to conform to the definition of
1613 the corresponding generic function.
1615 o gamma.stat() has been renamed gammaStat() to avoid confusion
1616 since gamma() is a generic function.
1620 CHANGES IN APE VERSION 1.1-3
1625 o base.freq() previously did not return a value of 0 for
1626 bases absent in the data (e.g., a vector of length 3 was
1627 returned if one base was absent). This is now fixed (a
1628 vector of length 4 is always returned).
1630 o Several bugs were fixed in read.nexus(), including that this
1631 function did not work in this absence of a "TRANSLATE"
1632 command in the NEXUS file, and that the commands were
1637 CHANGES IN APE VERSION 1.1-2
1642 o The Tamura and Nei (1993) model of DNA distance is now implemented
1643 in dist.dna(): five models are now available in this function.
1645 o A new data set is included: a set of 15 sequences of the
1646 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1652 o A bug in read.nexus() was fixed.
1654 o read.dna() previously did not work correctly in most cases.
1655 The function has been completely re-written and its help page
1656 has been considerably extended (see ?read.dna for details).
1657 Underscores (_) in taxon names are no more replaced with
1658 spaces (this behaviour was undocumented).
1660 o A bug was fixed in write.dna().
1664 CHANGES IN APE VERSION 1.1-1
1669 o A bug in read.tree() introduced in APE 1.1 was fixed.
1671 o A bug in compar.gee() resulted in an error when trying to fit
1672 a model with `family = "binomial"'. This is now fixed.
1676 CHANGES IN APE VERSION 1.1
1681 o The Klastorin (1982) method as suggested by Misawa and Tajima
1682 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1683 on the basis of phylogenetic trees has been implemented (see
1684 the function klastorin()).
1686 o Functions have been added to convert APE's "phylo" objects in
1687 "hclust" cluster objects and vice versa (see the help page of
1688 as.phylo for details).
1690 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1691 are introduced for the estimation of absolute evolutionary rates
1692 (ratogram) and dated clock-like trees (chronogram) from
1693 phylogenetic trees using the non-parametric rate smoothing approach
1694 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1696 o A summary method is now provided printing a summary information on a
1697 phylogenetic tree with, for instance, `summary(tree)'.
1699 o The behaviour of read.tree() was changed so that all spaces and
1700 tabulations in tree files are now ignored. Consequently, spaces in tip
1701 labels are no more allowed. Another side effect is that read.nexus()
1702 now does not replace the underscores (_) in tip labels with spaces
1703 (this behaviour was undocumented).
1705 o The function plot.phylo() has a new option (`underscore') which
1706 specifies whether the underscores in tip labels should be written on
1707 the plot as such or replaced with spaces (the default).
1709 o The function birthdeath() now computes 95% confidence intervals of
1710 the estimated parameters using profile likelihood.
1712 o Three new data sets are included: a gene tree estimated from 36
1713 landplant rbcL sequences, a gene tree estimated from 32 opsin
1714 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1719 o A bug was fixed in dist.gene() where nothing was returned.
1721 o A bug in plot.mst() was fixed.
1723 o A bug in vcv.phylo() resulted in false correlations when the
1724 option `cor = TRUE' was used (now fixed).
1728 CHANGES IN APE VERSION 1.0
1733 o Two new functions, read.dna() and write.dna(), read/write in a file
1734 DNA sequences in interleaved or in sequential format.
1736 o Two new functions, read.nexus() and write.nexus(), read/write trees
1739 o The new function bind.tree() allows to bind two trees together,
1740 possibly handling root edges to give internal branches.
1742 o The new function drop.tip() removes the tips in a phylogenetic tree,
1743 and trims (or not) the corresponding internal branches.
1745 o The new function is.ultrametric() tests if a tree is ultrametric.
1747 o The function plot.phylo() has more functionalities such as drawing the
1748 branches with different colours and/or different widths, showing the
1749 node labels, controling the position and font of the labels, rotating
1750 the labels, and controling the space around the plot.
1752 o The function read.tree() can now read trees with no branch length,
1753 such as "(a,b),c);". Consequently, the element `edge.length' in
1754 objects of class "phylo" is now optional.
1756 o The function write.tree() has a new default behaviour: if the default
1757 for the option `file' is used (i.e. file = ""), then a variable of
1758 mode character containing the tree in Newick format is returned which
1759 can thus be assigned (e.g., tree <- write.tree(phy)).
1761 o The function read.tree() has a new argument `text' which allows
1762 to read the tree in a variable of mode character.
1764 o A new data set is included: the phylogenetic relationships among
1765 the orders of birds from Sibley and Ahlquist (1990).
1769 CHANGES IN APE VERSION 0.2-1
1774 o Several bugs were fixed in the help pages.
1778 CHANGES IN APE VERSION 0.2
1783 o The function write.tree() writes phylogenetic trees (objects of class
1784 "phylo") in an ASCII file using the Newick parenthetic format.
1786 o The function birthdeath() fits a birth-death model to branching times
1787 by maximum likelihood, and estimates the corresponding speciation and
1790 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1793 o The function is.binary.tree() tests whether a phylogeny is binary.
1795 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1796 as well as some methods are introduced.
1798 o Several functions, including some generics and methods, for computing
1799 skyline plot estimates (classic and generalized) of effective
1800 population size through time are introduced and replace the function
1801 skyline.plot() in version 0.1.
1803 o Two data sets are now included: the phylogenetic relationships among
1804 the families of birds from Sibley and Ahlquist (1990), and an
1805 estimated clock-like phylogeny of HIV sequences sampled in the
1806 Democratic Republic of Congo.
1809 DEPRECATED & DEFUNCT
1811 o The function skyline.plot() in ape 0.1 has been deprecated and
1812 replaced by more elaborate functions (see above).
1817 o Two important bugs were fixed in plot.phylo(): phylogenies with
1818 multichotomies not at the root or not with only terminal branches,
1819 and phylogenies with a single node (i.e. only terminal branches)
1820 did not plot. These trees should be plotted correctly now.
1822 o Several bugs were fixed in diversi.time() in the computation of
1825 o Various errors were corrected in the help pages.