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
19 o nj() did not handle correctly distance matrices with many 0's.
23 CHANGES IN APE VERSION 2.3-1
28 o The new function is.monophyletic tests the monophyly of a group.
30 o There is now a c() method for lists of class "DNAbin".
32 o yule.cov() now fits the null model, and its help page has been
33 corrected with respect to this change.
35 o drop.tip() has a new option 'rooted' to force (or not) a tree
36 to be treated as (un)rooted.
41 o dist.gene() failed on most occasions with the default
42 pairwise.deletion = FALSE.
44 o read.tree() failed to read correctly the tree name(s).
46 o boot.phylo() now treats correctly data frames.
48 o del.gaps() did not copy the rownames of a matrix.
50 o A small bug was fixed in CDAM.global().
52 o ace() failed with large data sets. Thanks to Rich FitzJohn for
53 the fix. With other improvements, this function is now about 6
56 o write.tree() failed with objects of class "multiPhylo".
58 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
63 o [.multiPhylo and [.DNAbin now respect the original class.
65 o Instances of the form class(phy) == "phylo" have been replaced
66 by inherits(phy, "phylo").
68 o rcoal() is now faster.
73 o klastorin() has been removed.
77 CHANGES IN APE VERSION 2.3
82 o The new functions CADM.global and CADM.post, contributed by
83 Pierre Legendre, test the congruence among several distance
86 o The new function yule.time fits a user-defined time-dependent
87 Yule model by maximum likelihood.
89 o The new function makeNodeLabel creates and/or modifies node
90 labels in a flexible way.
92 o read.tree() and write.tree() have been modified so that they can
93 handle individual tree names.
95 o plot.phylo() has a new argument 'edge.lty' that specifies the
96 types of lines used for the edges (plain, dotted, dashed, ...)
98 o phymltest() has been updated to work with PhyML 3.0.1.
103 o drop.tip() shuffled tip labels in some cases.
105 o drop.tip() did not handle node.label correctly.
107 o is.ultrametric() now checks the ordering of the edge matrix.
109 o ace() sometimes returned negative values of likelihoods of
110 ancestral states (thanks to Dan Rabosky for solving this long
116 o The data set xenarthra has been removed.
120 CHANGES IN APE VERSION 2.2-4
124 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
125 now fixed. (Thanks to Peter Wragg for the fix!)
127 o A warning message occurred for no reason with ace(method="GLS").
132 o There is now a general help page displayed with '?ape'
136 CHANGES IN APE VERSION 2.2-3
141 o The new function extract.clade extracts a clade from a tree by
142 specifying a node number or label.
144 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
145 operations of the same names.
147 o dist.dna() can now return the number of site differences by
148 specifying model="N".
153 o chronopl() did not work with CV = TRUE.
155 o read.nexus() did not work correctly in some situations (trees on
156 multiple lines with different numbers of lines and/or with
157 comments inserted within the trees).
159 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
160 the number of lineages with non-binary trees.
165 o ape has now a namespace.
167 o drip.tip() has been improved: it should be much faster and work
168 better in some cases (e.g., see the example in ?zoom).
172 CHANGES IN APE VERSION 2.2-2
177 o dist.gene() has been substantially improved and gains an option
180 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
186 o prop.part() failed with a single tree with the default option
187 'check.labels = TRUE'.
189 o summary.DNAbin() failed to display correctly the summary of
190 sequence lengths with lists of sequences of 10,000 bases or more
191 (because summary.default uses 4 significant digits by default).
193 o read.nexus() failed to read a file with a single tree with line
194 breaks in the Newick string.
196 o del.gaps() returned a list of empty sequences when there were no
202 o phymltest() has been updated for PhyML 3.0 and gains an option
203 'append', whereas the option 'path2exec' has been removed.
205 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
206 which is returned unchanged (instead of an error).
208 o The data sets bird.orders and bird.families are now stored as
209 Newick strings; i.e., the command data(bird.orders) calls
214 CHANGES IN APE VERSION 2.2-1
219 o The new function makeLabel() helps to modify labels of trees,
220 lists of trees, or DNA sequences, with several utilities to
221 truncate and/or make them unique, substituting some
222 characters, and so on.
224 o The new function del.gaps() removes insertion gaps ("-") in a
225 set of DNA sequences.
227 o read.dna() can now read Clustal files (*.aln).
232 o root() failed with 'resolve.root = TRUE' when the root was
233 already the specified root.
235 o Several bugs were fixed in mlphylo().
237 o collapsed.singles() did not propagate the 'Nnode' and
238 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
240 o read.nexus() failed to remove correctly the comments within
243 o read.nexus() failed to read a file with a single tree and no
244 translation of tip labels.
246 o read.nexus() failed to place correctly tip labels when reading
247 a single tree with no edge lengths.
249 o A bug was fixed in sh.test().
254 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
257 o The option 'check.labels' of consensus() and prop.part() is now
260 o write.dna() now does not truncate names to 10 characters with
265 CHANGES IN APE VERSION 2.2
270 o Four new functions have been written by Damien de Vienne for the
271 graphical exploration of large trees (cophyloplot, subtrees,
272 subtreeplot), and to return the graphical coordinates of tree
275 o The new functions corPagel and corBlomberg implement the Pagel's
276 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
278 o chronopl() has been improved and gains several options: see its
279 help page for details.
281 o boot.phylo() has now an option 'trees' to possibly return the
282 bootstraped trees (the default is FALSE).
284 o prop.part() has been improved and should now be faster in all
290 o read.dna() failed if "?" occurred in the first 10 sites of the
293 o The x/y aspect of the plot is now respected when plotting a
294 circular tree (type = "r" or "f").
296 o Drawing the tip labels sometimes failed when plotting circular
299 o zoom() failed when tip labels were used instead of their numbers
300 (thanks to Yan Wong for the fix).
302 o drop.tip() failed with some trees (fixed by Yan Wong).
304 o seg.sites() failed with a list.
306 o consensus() failed in some cases. The function has been improved
307 as well and is faster.
311 CHANGES IN APE VERSION 2.1-3
316 o A bug in read.nexus() made the Windows R-GUI crash.
318 o An error was fixed in the computation of ancestral character
319 states by generalized least squares in ace().
321 o di2multi() did not modify node labels correctly.
323 o multi2di() failed if the tree had its attribute "order" set to
328 CHANGES IN APE VERSION 2.1-2
333 o There three new methods for the "multiPhylo" class: str, $,
336 o root() gains the options 'node' and 'resolve.root'
337 (FALSE by default) as well as its code being improved.
339 o mltt.plot() has now an option 'log' used in the same way
340 than in plot.default().
345 o mltt.plot() failed to display the legend with an unnamed
348 o nodelabels() with pies now correcly uses the argument
349 'cex' to draw symbols of different sizes (which has
350 worked already for thermometers).
352 o read.nexus() generally failed to read very big files.
357 o The argument 'family' of compar.gee() can now be a function
358 as well as a character string.
360 o read.tree() and read.nexus() now return an unnamed list if
363 o read.nexus() now returns a modified object of class "multiPhylo"
364 when there is a TRANSLATE block in the NEXUS file: the individual
365 trees have no 'tip.label' vector, but the list has a 'TipLabel'
366 attribute. The new methods '$' and '[[' set these elements
367 correctly when extracting trees.
371 CHANGES IN APE VERSION 2.1-1
376 o The new function rmtree generates lists of random trees.
378 o rcoal() now generates a genuine coalescent tree by default
379 (thanks to Vladimir Minin for the code).
384 o nuc.div() returned an incorrect value with the default
385 pairwise.deletion = FALSE.
390 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
391 have been improved so that they are stabler and faster.
393 o R packages used by ape are now loaded silently; lattice and gee
394 are loaded only when needed.
398 CHANGES IN APE VERSION 2.1
403 o The new function identify.phylo identifies clades on a plotted
404 tree using the mouse.
406 o It is now possible to subset a list of trees (object of class
407 "multiPhylo") with "[" while keeping its class correct.
409 o The new function as.DNAbin.alignment converts DNA sequences
410 stored in the "alignment" format of the package seqinr into
411 an object of class "DNAbin".
413 o The new function weight.taxo2 helps to build similarity matrices
414 given two taxonomic levels (usually called by other functions).
416 o write.tree() can now take a list of trees (class "multiPhylo")
417 as its main argument.
419 o plot.correlogram() and plot.correlogramList() have been
420 improved, and gain several options (see the help page for
421 details). A legend is now plotted by default.
426 o dist.dna() returned some incorrect values with `model = "JC69"'
427 and `pairwise.deletion = TRUE'. This affected only the
428 distances involving sequences with missing values. (Thanks
429 to Bruno Toupance for digging this bug out.)
431 o write.tree() failed with some trees: this is fixed by removing
432 the `multi.line' option (trees are now always printed on a
435 o read.nexus() did not correctly detect trees with multiple root
436 edges (see OTHER CHANGES).
441 o The code of mlphylo() has been almost entirely rewritten, and
442 should be much stabler. The options have been also greatly
443 simplified (see ?mlphylo and ?DNAmodel for details).
445 o The internal function nTips has been renamed klastorin_nTips.
447 o The code of is.ultrametric() contained redundancies and has
450 o The code of Moran.I() and of correlogram.formula() have been
453 o read.tree() and read.nexus() now return an error when trying to
454 read a tree with multiple root edges (see BUG FIXES). The
455 correction applied in previous version did not work in all
458 o The class c("multi.tree", "phylo") has been renamed
464 o There is now a vignette in ape: see vignette("MoranI", "ape").
469 o as.matching() and as.phylo.matching() do not support branch
472 o correlogram.phylo() and discrete.dist() have been removed.
476 CHANGES IN APE VERSION 2.0-2
481 o The new function matexpo computes the exponential of a square
484 o The new function unique.multi.tree removes duplicate trees from
487 o yule() has a new option `use.root.edge = FALSE' that specifies
488 to ignore, by default, the root edge of the tree if it exists.
493 o which.edge() failed when the index of a single terminal edge was
496 o In diversi.time(), the values returned for model C were
499 o A bug was fixed in yule() that affected the calculation of the
500 likelihood in the presence of ties in the branching times.
502 o There was a bug in the C function mat_expo4x4 affecting the
503 calculations of the transition probabilities for models HKY and
506 o A small bug was fixed in as.matrix.DNAbin (thanks to James
509 o rtree() did not `shuffle' the tip labels by default, so only a
510 limited number of labelled topologies could be generated.
514 CHANGES IN APE VERSION 2.0-1
519 o The three new functions bionj, fastme.ols, and fastme.bal
520 perform phylogeny estimation by the BIONJ and fastME methods in
521 OLS and balanced versions. This is a port to R of previous
522 previous programs done by Vincent Lefort.
524 o The new function chronoMPL performs molecular dating with the
525 mean path lengths method of Britton et al. (2002, Mol. Phyl.
528 o The new function rotate, contributed by Christoph Heibl, swaps
529 two clades connected to the same node. It works also with
530 multichotomous nodes.
532 o The new `method' as.matrix.DNAbin() may be used to convert
533 easily DNA sequences stored in a list into a matrix while
534 keeping the names and the class.
539 o chronopl() failed when some branch lengths were equal to zero:
540 an error message is now returned.
542 o di2multi() failed when there was a series of consecutive edges
547 CHANGES IN APE VERSION 1.10-2
552 o plot.phylo() can now plot circular trees: the option is type =
553 "fan" or type = "f" (to avoid the ambiguity with type = "c").
555 o prop.part() has a new option `check.labels = FALSE' which allows
556 to considerably speed-up the calculations of bipartitions. As a
557 consequence, calculations of bootstrap values with boot.phylo()
558 should be much faster.
563 o read.GenBank() did not return correctly the list of species as
564 from ape 1.10: this is fixed in this version
566 o Applying as.phylo() on a tree of class "phylo" failed: the
567 object is now returned unchanged.
571 CHANGES IN APE VERSION 1.10-1
576 o The three new functions Ntip, Nnode, and Nedge return, for a
577 given tree, the number of tips, nodes, or edges, respectively.
582 o read.nexus() did not set correctly the class of the returned
583 object when reading multiple trees.
585 o mllt.plot() failed with objects of class c("multi.tree",
588 o unroot() did not work correctly in most cases.
590 o reorder.phylo() made R freeze in some occasions.
592 o Plotting a tree in pruningwise order failed.
594 o When plotting an unrooted tree, the tip labels where not all
595 correctly positioned if the option `cex' was used.
599 CHANGES IN APE VERSION 1.10
604 o Five new `method' functions have been introduced to manipulate
605 DNA sequences in binary format (see below).
607 o Three new functions have been introduced to convert between the
608 new binary and the character formats.
610 o The new function as.alignment converts DNA sequences stored as
611 single characters into the class "alignment" used by the package
614 o read.dna() and read.GenBank() have a new argument `as.character'
615 controlling whether the sequences are returned in binary format
621 o root() failed when the tree had node labels: this is fixed.
623 o plot.phylo() did not correctly set the limits on the y-axis with
624 the default setting: this is fixed.
626 o dist.dna() returned a wrong result for the LogDet, paralinear,
627 and BH87 models with `pairwise.deletion = TRUE'.
632 o DNA sequences are now internally stored in a binary format. See
633 the document "A Bit-Level Coding Scheme for Nucleotides" for the
634 details. Most functions analyzing DNA functions have been
635 modified accordingly and are now much faster (dist.dna is now
636 ca. 60 times faster).
640 CHANGES IN APE VERSION 1.9-4
645 o A bug was fixed in edgelabels().
647 o as.phylo.hclust() did not work correctly when the object of
648 class "hclust" has its labels set to NULL: the returned tree has
649 now its tip labels set to "1", "2", ...
651 o consensus could fail if some tip labels are a subset of others
652 (e.g., "a" and "a_1"): this is now fixed.
654 o mlphylo() failed in most cases if some branch lengths of the
655 initial tree were greater than one: an error message is now
658 o mlphylo() failed in most cases when estimating the proportion of
659 invariants: this is fixed.
663 CHANGES IN APE VERSION 1.9-3
668 o The new function edgelabels adds labels on the edge of the tree
669 in the same way than nodelabels or tiplabels.
674 o multi2di() did not handle correctly branch lengths with the
675 default option `random = TRUE': this is now fixed.
677 o A bug was fixed in nuc.div() when using pairwise deletions.
679 o A bug occurred in the analysis of bipartitions with large
680 numbers of large trees, with consequences on prop.part,
681 prop.clades, and boot.phylo.
683 o The calculation of the Billera-Holmes-Vogtmann distance in
684 dist.topo was wrong: this has been fixed.
688 CHANGES IN APE VERSION 1.9-2
693 o The new function ladderize reorganizes the internal structure of
694 a tree to plot them left- or right-ladderized.
696 o The new function dist.nodes computes the patristic distances
697 between all nodes, internal and terminal, of a tree. It replaces
698 the option `full = TRUE' of cophenetic.phylo (see below).
703 o A bug was fixed in old2new.phylo().
705 o Some bugs were fixed in chronopl().
707 o The edge colours were not correctly displayed by plot.phylo
708 (thank you to Li-San Wang for the fix).
710 o cophenetic.phylo() failed with multichotomous trees: this is
716 o read.dna() now returns the sequences in a matrix if they are
717 aligned (interleaved or sequential format). Sequences in FASTA
718 format are still returned in a list.
720 o The option `full' of cophenetic.phylo() has been removed because
721 it could not be used from the generic.
726 o rotate() has been removed; this function did not work correctly
731 CHANGES IN APE VERSION 1.9-1
736 o Trees with a single tip were not read correctly in R as the
737 element `Nnode' was not set: this is fixed.
739 o unroot() did not set correctly the number of nodes of the
740 unrooted tree in most cases.
742 o read.GenBank() failed when fetching very long sequences,
743 particularly of the BX-series.
745 o A bug was introduced in read.tree() with ape 1.9: it has been
750 CHANGES IN APE VERSION 1.9
755 o There are two new print `methods' for trees of class "phylo" and
756 lists of trees of class "multi.tree", so that they are now
757 displayed in a compact and informative way.
759 o There are two new functions, old2new.phylo and new2old.phylo,
760 for converting between the old and new coding of the class
763 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
764 LogDet ("logdet"), and paralinear ("paralin").
766 o compute.brlen() has been extended: several methods are now
767 available to compute branch lengths.
769 o write.dna() can now handle matrices as well as lists.
774 o cophenetic.phylo() sometimes returned a wrong result with
775 multichotomous trees: this is fixed.
777 o rotate() failed when a single tip was specified: the tree is now
780 o ace() did not return the correct index matrix with custom
781 models: this is fixed.
783 o multi2di() did not work correctly when resolving multichotomies
784 randomly: the topology was always the same, only the arrangement
785 of clades was randomized: this is fixed. This function now
786 accepts trees with no branch lengths.
788 o The output of diversi.gof() was blurred by useless prints when a
789 user distribution was specified. This has been corrected, and
790 the help page of this function has been expanded.
795 o The internal structure of the class "phylo" has been changed:
796 see the document "Definition of Formats for Coding Phylogenetic
797 Trees in R" for the details. In addition, the code of most
798 functions has been improved.
800 o Several functions have been improved by replacing some R codes
801 by C codes: pic, plot.phylo, and reorder.phylo.
803 o There is now a citation information: see citation("ape") in R.
805 o write.tree() now does not add extra 0's to branch lengths so
806 that 1.23 is printed "1.23" by default, not "1.2300000000".
808 o The syntax of bind.tree() has been simplified. This function now
809 accepts trees with no branch lengths, and handles correctly node
812 o The option `as.numeric' of mrca() has been removed.
814 o The unused options `format' and `rooted' of read.tree() have
817 o The unused option `format' of write.tree() has been removed.
819 o The use of node.depth() has been simplified.
823 CHANGES IN APE VERSION 1.8-5
828 o Two new functions read.nexus.data() and write.nexus.data(),
829 contributed by Johan Nylander, allow to read and write molecular
830 sequences in NEXUS files.
832 o The new function reorder.phylo() reorders the internal structure
833 of a tree of class "phylo". It is used as the generic, e.g.,
836 o read.tree() and read.nexus() can now read trees with a single
839 o The new data set `cynipids' supplies a set of protein sequences
845 o The code of all.equal.phylo() has been completely rewritten
846 (thanks to Benoît Durand) which fixes several bugs.
848 o read.tree() and read.nexus() now checks the labels of the tree
849 to remove or substitute any characters that are illegal in the
850 Newick format (parentheses, etc.)
852 o A negative P-value could be returned by mantel.test(): this is
857 CHANGES IN APE VERSION 1.8-4
862 o The new function sh.test() computes the Shimodaira-
865 o The new function collapse.singles() removes the nodes with a
866 single descendant from a tree.
868 o plot.phylo() has a new argument `tip.color' to specify the
871 o mlphylo() has now an option `quiet' to control the display of
872 the progress of the analysis (the default is FALSE).
877 o read.dna() did not read correctly sequences in sequential format
878 with leading alignment gaps "-": this is fixed.
880 o ace() returned a list with no class so that the generic
881 functions (anova, logLik, ...) could not be used directly. This
882 is fixed as ace() now returns an object of class "ace".
884 o anova.ace() had a small bug when computing the number of degrees
885 of freedom: this is fixed.
887 o mlphylo() did not work when the sequences were in a matrix or
888 a data frame: this is fixed.
890 o rtree() did not work correctly when trying to simulate an
891 unrooted tree with two tips: an error message is now issued.
896 o The algorithm of rtree() has been changed: it is now about 40,
897 100, and 130 times faster for 10, 100, and 1000 tips,
902 CHANGES IN APE VERSION 1.8-3
907 o There are four new `method' functions to be used with the
908 results of ace(): logLik(), deviance(), AIC(), and anova().
910 o The plot method of phymltest has two new arguments: `main' to
911 change the title, and `col' to control the colour of the
912 segments showing the AIC values.
914 o ace() has a new argument `ip' that gives the initial values used
915 in the ML estimation with discrete characters (see the examples
916 in ?ace). This function now returns a matrix giving the indices
917 of the estimated rates when analysing discrete characters.
919 o nodelabels() and tiplabels() have a new argument `pie' to
920 represent proportions, with any number of categories, as
921 piecharts. The use of the option `thermo' has been improved:
922 there is now no limitation on the number of categories.
927 o mlphylo() did not work with more than two partitions: this is
930 o root() failed if the proposed outgroup was already an outgroup
931 in the tree: this is fixed.
933 o The `col' argument in nodelabels() and tiplabels() was not
934 correctly passed when `text' was used: this is fixed.
936 o Two bugs were fixed in mlphylo(): parameters were not always
937 correctly output, and the estimation failed in some cases.
939 o plot.phylo() was stuck when given a tree with a single tip: this
940 is fixed and a message error is now returned.
942 o An error was corrected in the help page of gammaStat regarding
943 the calculation of P-values.
945 o Using gls() could crash R when the number of species in the tree
946 and in the variables were different: this is fixed.
950 CHANGES IN APE VERSION 1.8-2
955 o The new function mlphylo() fits a phylogenetic tree by maximum
956 likelihood from DNA sequences. Its companion function DNAmodel()
957 is used to define the substitution model which may include
958 partitioning. There are methods for logLik(), deviance(), and
959 AIC(), and the summary() method has been extended to display in
960 a friendly way the results of this model fitting. Currently, the
961 functionality is limited to estimating the substitution and
962 associated parameters and computing the likelihood.
964 o The new function drop1.compar.gee (used as, e.g., drop1(m))
965 tests for single effects in GEE-based comparative method. A
966 warning message is printed if there is not enough degrees of
972 o An error message was sometimes issued by plot.multi.tree(),
973 though with no consequence.
977 CHANGES IN APE VERSION 1.8-1
982 o There is a new plot method for lists of trees (objects of class
983 "multi.tree"): it calls plot.phylo() internally and is
984 documented on the same help page.
989 o A bug was fixed in the C code that analyzes bipartitions: this
990 has impact on several functions like prop.part, prop.clades,
991 boot.phylo, or consensus.
993 o root() did not work correctly when the specified outgroup had
994 more than one element: this is fixed.
996 o dist.dna() sometimes returned a warning inappropriately: this
999 o If the distance object given to nj() had no rownames, nj()
1000 returned a tree with no tip labels: it now returns tips labelled
1001 "1", "2", ..., corresponding to the row numbers.
1006 o nj() has been slightly changed so that tips with a zero distance
1007 are first aggregated with zero-lengthed branches; the usual NJ
1008 procedure is then performed on a distance matrix without 0's.
1012 CHANGES IN APE VERSION 1.8
1017 o The new function chronopl() estimates dates using the penalized
1018 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1020 o The new function consensus() calculates the consensus tree of a
1023 o The new function evolve.phylo() simulates the evolution of
1024 continuous characters along a phylogeny under a Brownian model.
1026 o The new plot method for objects of class "ancestral" displays a
1027 tree together with ancestral values, as returned by the above
1030 o The new function as.phylo.formula() returns a phylogeny from a
1031 set of nested taxonomic variables given as a formula.
1033 o The new function read.caic() reads trees in CAIC format.
1035 o The new function tiplabels() allows to add labels to the tips
1036 of a tree using text or plotting symbols in a flexible way.
1038 o The new function unroot() unroots a phylogeny.
1040 o multi2di() has a new option, `random', which specifies whether
1041 to resolve the multichotomies randomly (the default) or not.
1043 o prop.part() now returns an object of class "prop.part" for which
1044 there are print (to display a partition in a more friendly way)
1045 and summary (to extract the numbers) methods.
1047 o plot.phylo() has a new option, `show.tip.label', specifying
1048 whether to print the labels of the tips. The default is TRUE.
1050 o The code of nj() has been replaced by a faster C code: it is now
1051 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1054 o write.nexus() now writes whether a tree is rooted or not.
1059 o Two bugs have been fixed in root(): unrooted trees are now
1060 handled corretly, and node labels are now output normally.
1062 o A bug was fixed in phymltest(): the executable couldn't be found
1065 o Three bug have been fixed in ace(): computing the likelihood of
1066 ancestral states of discrete characters failed, custom models
1067 did not work, and the function failed with a null gradient (a
1068 warning message is now returned; this latter bug was also
1069 present in yule.cov() as well and is now fixed).
1071 o pic() hanged out when missing data were present: a message error
1074 o A small bug was fixed in dist.dna() where the gamma correction
1075 was not always correctly dispatched.
1077 o plot.phylo() plotted correctly the root edge only when the tree
1078 was plotted rightwards: this works now for all directions.
1083 o dist.taxo() has been renamed as weight.taxo().
1085 o Various error and warning messages have been improved.
1089 CHANGES IN APE VERSION 1.7
1092 o The new function ace() estimates ancestral character states for
1093 continuous characters (with ML, GLS, and contrasts methods), and
1094 discrete characters (with ML only) for any number of states.
1096 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1097 of directional evolution for continuous characters. The user
1098 specifies the node(s) of the tree where the character optimum
1101 o The new function is.rooted() tests whether a tree (of class
1104 o The new function rcoal() generates random ultrametric trees with
1105 the possibility to specify the function that generates the
1106 inter-nodes distances.
1108 o The new function mrca() gives for all pairs of tips in a tree
1109 (and optionally nodes too) the most recent common ancestor.
1111 o nodelabels() has a new option `thermo' to plot proportions (up
1112 to three classes) on the nodes of a tree.
1114 o rtree() has been improved: it can now generate rooted or
1115 unrooted trees, and the mathematical function that generates the
1116 branch lengths may be specified by the user. The tip labels may
1117 be given directly in the call to rtree. The limit cases (n = 2,
1118 3) are now handled correctly.
1120 o dist.topo() has a new argument `method' with two choices: "PH85"
1121 for Penny and Henny's method (already available before and now
1122 the default), and "BHV01" for the geometric distance by Billera
1123 et al. (2001, Adv. Appl. Math. 27:733).
1125 o write.tree() has a new option, `digits', which specifies the
1126 number of digits to be printed in the Newick tree. By default
1127 digits = 10. The numbers are now always printed in decimal form
1128 (i.e., 1.0e-1 is now avoided).
1130 o dist.dna() can now compute the raw distances between pairs of
1131 DNA sequences by specifying model = "raw".
1133 o dist.phylo() has a new option `full' to possibly compute the
1134 distances among all tips and nodes of the tree. The default if
1140 o Several bugs were fixed in all.equal.phylo().
1142 o dist.dna() did not handle correctly gaps ("-") in alignments:
1143 they are now considered as missing data.
1145 o rotate() did not work if the tips were not ordered: this is
1148 o mantel.test() returned NA in some special cases: this is fixed
1149 and the function has been improved and is now faster.
1151 o A bug was fixed in diversi.gof() where the calculation of A² was
1154 o cherry() did not work correctly under some OSs (mainly Linux):
1157 o is.binary.tree() has been modified so that it works with both
1158 rooted and unrooted trees.
1160 o The documentation of theta.s() was not correct: this has been
1163 o plot.mst() did not work correctly: this is fixed.
1167 CHANGES IN APE VERSION 1.6
1172 o The new function dist.topo() computes the topological distances
1175 o The new function boot.phylo() performs a bootstrap analysis on
1176 phylogeny estimation.
1178 o The new functions prop.part() and prop.clades() analyse
1179 bipartitions from a series of trees.
1184 o read.GenBank() now uses the EFetch utility of NCBI instead of
1185 the usual Web interface: it is now much faster (e.g., 12 times
1186 faster to retrieve 8 sequences, 37 times for 60 sequences).
1191 o Several bugs were fixed in read.dna().
1193 o Several bugs were fixed in diversi.time().
1195 o is.binary.tree() did not work correctly if the tree has no edge
1196 lengths: this is fixed.
1198 o drop.tip() did not correctly propagated the `node.label' of a
1199 tree: this is fixed.
1203 CHANGES IN APE VERSION 1.5
1208 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1209 convert objects between the classes "phylo" and "matching". The
1210 latter implements the representation of binary trees introduced by
1211 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1212 as.matching() has been introduced as well.
1214 o Two new functions, multi2di() and di2multi(), allow to resolve
1215 and collapse multichotomies with branches of length zero.
1217 o The new function nuc.div() computes the nucleotide diversity
1218 from a sample a DNA sequences.
1220 o dist.dna() has been completely rewritten with a much faster
1221 (particularly for large data sets) C code. Eight models are
1222 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1223 option `method' has been renamed `model'). Computation of variance
1224 is available for all models. A gamma-correction is possible for
1225 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1226 to remove sites with missing data on a pairwise basis. The option
1227 `GCcontent' has been removed.
1229 o read.GenBank() has a new option (species.names) which specifies
1230 whether to return the species names of the organisms in addition
1231 to the accession numbers of the sequences (this is the default
1234 o write.nexus() can now write several trees in the same NEXUS file.
1236 o drop.tip() has a new option `root.edge' that allows to specify the
1237 new root edge if internal branches are trimmed.
1242 o as.phylo.hclust() failed if some labels had parentheses: this
1245 o Several bugs were fixed in all.equal.phylo(). This function now
1246 returns the logical TRUE if the trees are identical but with
1247 different representations (a report was printed previously).
1249 o read.GenBank() did not correctly handle ambiguous base codes:
1255 o birthdeath() now returns an object of class "birthdeath" for
1256 which there is a print method.
1260 CHANGES IN APE VERSION 1.4
1265 o The new function nj() performs phylogeny estimation with the
1266 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1269 o The new function which.edge() identifies the edges of a tree
1270 that belong to a group specified as a set of tips.
1272 o The new function as.phylo.phylog() converts an object of class
1273 "phylog" (from the package ade4) into an object of class
1276 o The new function axisPhylo() draws axes on the side of a
1279 o The new function howmanytrees() calculates the number of trees
1280 in different cases and giving a number of tips.
1282 o write.tree() has a new option `multi.line' (TRUE by default) to
1283 write a Newick tree on several lines rather than on a single
1286 o The functionalities of zoom() have been extended. Several
1287 subtrees can be visualized at the same time, and they are marked
1288 on the main tree with colors. The context of the subtrees can be
1289 marked with the option `subtree' (see below).
1291 o drop.tip() has a new option `subtree' (FALSE by default) which
1292 specifies whether to output in the tree how many tips have been
1295 o The arguments of add.scale.bar() have been redefined and have
1296 now default values (see ?add.scale.bar for details). This
1297 function now works even if the plotted tree has no edge length.
1299 o plot.phylo() can now plot radial trees, but this does not take
1300 edge lengths into account.
1302 o In plot.phylo() with `type = "phylogram"', if the values of
1303 `edge.color' and `edge.width' are identical for sister-branches,
1304 they are propagated to the vertical line that link them.
1309 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1310 crashing. This is fixed.
1312 o In plot.phylo(), the options `edge.color' and `edge.width' are
1313 now properly recycled; their default values are now "black" and
1316 o A bug has been fixed in write.nexus().
1321 o The function node.depth.edgelength() has been removed and
1322 replaced by a C code.
1326 CHANGES IN APE VERSION 1.3-1
1331 o The new function nodelabels() allows to add labels to the nodes
1332 of a tree using text or plotting symbols in a flexible way.
1334 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1335 numeric values specifying the lower and upper limits on the x-
1336 and y-axes. This allows to leave some space on any side of the
1337 tree. If a single value is given, this is taken as the upper
1342 CHANGES IN APE VERSION 1.3
1347 o The new function phymltest() calls the software PHYML and fits
1348 28 models of DNA sequence evolution. There are a print method to
1349 display likelihood and AIC values, a summary method to compute
1350 the hierarchical likelihood ratio tests, and a plot method to
1351 display graphically the AIC values of each model.
1353 o The new function yule.cov() fits the Yule model with covariates,
1354 a model where the speciation rate is affected by several species
1355 traits through a generalized linear model. The parameters are
1356 estimated by maximum likelihood.
1358 o Three new functions, corBrownian(), corGrafen(), and
1359 corMartins(), compute the expected correlation structures among
1360 species given a phylogeny under different models of evolution.
1361 These can be used for GLS comparative phylogenetic methods (see
1362 the examples). There are coef() and corMatrix() methods and an
1363 Initialize.corPhyl() function associated.
1365 o The new function compar.cheverud() implements Cheverud et al.'s
1366 (1985; Evolution 39:1335) phylogenetic comparative method.
1368 o The new function varcomp() estimates variance components; it has
1371 o Two new functions, panel.superpose.correlogram() and
1372 plot.correlogramList(), allow to plot several phylogenetic
1375 o The new function node.leafnumber() computes the number of leaves
1376 of a subtree defined by a particular node.
1378 o The new function node.sons() gets all tags of son nodes from a
1381 o The new function compute.brlen() computes the branch lengths of
1382 a tree according to a specified method.
1384 o plot.phylo() has three new options: "cex" controls the size of
1385 the (tip and node) labels (thus it is no more needed to change
1386 the global graphical parameter), "direction" which allows to
1387 plot the tree rightwards, leftwards, upwards, or downwards, and
1388 "y.lim" which sets the upper limit on the y-axis.
1393 o Some functions which try to match tip labels and names of
1394 additional data (e.g. vector) are likely to fail if there are
1395 typing or syntax errors. If both series of names do not perfectly
1396 match, they are ignored and a warning message is now issued.
1397 These functions are bd.ext, compar.gee, pic. Their help pages
1398 have been clarified on this point.
1402 CHANGES IN APE VERSION 1.2-7
1407 o The new function root() reroots a phylogenetic tree with respect
1408 to a specified outgroup.
1410 o The new function rotate() rotates an internal branch of a tree.
1412 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1413 trees) controls the display of the tip labels in unrooted trees.
1414 This display has been greatly improved: the tip labels are now not
1415 expected to overlap with the tree (particularly if lab4ut =
1416 "axial"). In all cases, combining appropriate values of "lab4ut"
1417 and the font size (via "par(cex = )") should result in readable
1418 unrooted trees. See ?plot.phylo for some examples.
1420 o In drop.tip(), the argument `tip' can now be numeric or character.
1425 o drop.tip() did not work correctly with trees with no branch
1426 lengths: this is fixed.
1428 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1429 plotted with some line crossings: this is now fixed.
1433 CHANGES IN APE VERSION 1.2-6
1438 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1439 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1440 to implement comparative methods with an autocorrelation approach.
1442 o A new data set describing some life history traits of Carnivores
1448 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1453 o When plotting a tree with plot.phylo(), the new default of the
1454 option `label.offset' is now 0, so the labels are always visible.
1458 CHANGES IN APE VERSION 1.2-5
1463 o The new function bd.ext() fits a birth-death model with combined
1464 phylogenetic and taxonomic data, and estimates the corresponding
1465 speciation and extinction rates.
1470 o The package gee is no more required by ape but only suggested
1471 since only the function compar.gee() calls gee.
1475 CHANGES IN APE VERSION 1.2-4
1480 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1481 and lines.popsize) implementing a new approach for inferring the
1482 demographic history from genealogies using a reversible jump
1483 MCMC have been introduced.
1485 o The unit of time in the skyline plot and in the new plots can
1486 now be chosen to be actual years, rather than substitutions.
1490 CHANGES IN APE VERSION 1.2-3
1495 o The new function rtree() generates a random binary tree with or
1496 without branch lengths.
1498 o Two new functions for drawing lineages-through-time (LTT) plots
1499 are provided: ltt.lines() adds a LTT curve to an existing plot,
1500 and mltt.plot() does a multiple LTT plot giving several trees as
1501 arguments (see `?ltt.plot' for details).
1506 o Some taxon names made R crashing when calling as.phylo.hclust():
1509 o dist.dna() returned an error with two identical DNA sequences
1510 (only using the Jukes-Cantor method returned 0): this is fixed.
1515 o The function dist.phylo() has been re-written using a different
1516 algorithm: it is now about four times faster.
1518 o The code of branching.times() has been improved: it is now about
1523 CHANGES IN APE VERSION 1.2-2
1528 o The new function seg.sites() finds the segregating sites in a
1529 sample of DNA sequences.
1534 o A bug introduced in read.tree() and in read.nexus() with version
1537 o A few errors were corrected and a few examples were added in the
1542 CHANGES IN APE VERSION 1.2-1
1547 o plot.phylo() can now draw the edge of the root of a tree if it
1548 has one (see the new option `root.edge', its default is FALSE).
1553 o A bug was fixed in read.nexus(): files with semicolons inside
1554 comment blocks were not read correctly.
1556 o The behaviour of read.tree() and read.nexus() was corrected so
1557 that tree files with badly represented root edges (e.g., with
1558 an extra pair of parentheses, see the help pages for details)
1559 are now correctly represented in the object of class "phylo";
1560 a warning message is now issued.
1564 CHANGES IN APE VERSION 1.2
1569 o plot.phylo() has been completely re-written and offers several
1570 new functionalities. Three types of trees can now be drawn:
1571 phylogram (as previously), cladogram, and unrooted tree; in
1572 all three types the branch lengths can be drawn using the edge
1573 lengths of the phylogeny or not (e.g., if the latter is absent).
1574 The vertical position of the nodes can be adjusted with two
1575 choices (see option `node.pos'). The code has been re-structured,
1576 and two new functions (potentially useful for developpers) are
1577 documented separately: node.depth.edgelength() and node.depth();
1578 see the respective help pages for details.
1580 o The new function zoom() allows to explore very large trees by
1581 focusing on a small portion of it.
1583 o The new function yule() fits by maximum likelihood the Yule model
1584 (birth-only process) to a phylogenetic tree.
1586 o Support for writing DNA sequences in FASTA format has been
1587 introduced in write.dna() (support for reading sequences in
1588 this format was introduced in read.dna() in version 1.1-2).
1589 The function has been completely re-written, fixing some bugs
1590 (see below); the default behaviour is no more to display the
1591 sequences on the standard output. Several options have been
1592 introduced to control the sequence printing in a flexible
1593 way. The help page has been extended.
1595 o A new data set is included: a supertree of bats in NEXUS format.
1600 o In theta.s(), the default of the option `variance' has
1601 been changed to `FALSE' (as was indicated in the help page).
1603 o Several bugs were fixed in the code of all.equal.phylo().
1605 o Several bugs were fixed in write.dna(), particularly this
1606 function did not work with `format = "interleaved"'.
1608 o Various errors were corrected in the help pages.
1613 o The argument names of as.hclust.phylo() have been changed
1614 from "(phy)" to "(x, ...)" to conform to the definition of
1615 the corresponding generic function.
1617 o gamma.stat() has been renamed gammaStat() to avoid confusion
1618 since gamma() is a generic function.
1622 CHANGES IN APE VERSION 1.1-3
1627 o base.freq() previously did not return a value of 0 for
1628 bases absent in the data (e.g., a vector of length 3 was
1629 returned if one base was absent). This is now fixed (a
1630 vector of length 4 is always returned).
1632 o Several bugs were fixed in read.nexus(), including that this
1633 function did not work in this absence of a "TRANSLATE"
1634 command in the NEXUS file, and that the commands were
1639 CHANGES IN APE VERSION 1.1-2
1644 o The Tamura and Nei (1993) model of DNA distance is now implemented
1645 in dist.dna(): five models are now available in this function.
1647 o A new data set is included: a set of 15 sequences of the
1648 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1654 o A bug in read.nexus() was fixed.
1656 o read.dna() previously did not work correctly in most cases.
1657 The function has been completely re-written and its help page
1658 has been considerably extended (see ?read.dna for details).
1659 Underscores (_) in taxon names are no more replaced with
1660 spaces (this behaviour was undocumented).
1662 o A bug was fixed in write.dna().
1666 CHANGES IN APE VERSION 1.1-1
1671 o A bug in read.tree() introduced in APE 1.1 was fixed.
1673 o A bug in compar.gee() resulted in an error when trying to fit
1674 a model with `family = "binomial"'. This is now fixed.
1678 CHANGES IN APE VERSION 1.1
1683 o The Klastorin (1982) method as suggested by Misawa and Tajima
1684 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1685 on the basis of phylogenetic trees has been implemented (see
1686 the function klastorin()).
1688 o Functions have been added to convert APE's "phylo" objects in
1689 "hclust" cluster objects and vice versa (see the help page of
1690 as.phylo for details).
1692 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1693 are introduced for the estimation of absolute evolutionary rates
1694 (ratogram) and dated clock-like trees (chronogram) from
1695 phylogenetic trees using the non-parametric rate smoothing approach
1696 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1698 o A summary method is now provided printing a summary information on a
1699 phylogenetic tree with, for instance, `summary(tree)'.
1701 o The behaviour of read.tree() was changed so that all spaces and
1702 tabulations in tree files are now ignored. Consequently, spaces in tip
1703 labels are no more allowed. Another side effect is that read.nexus()
1704 now does not replace the underscores (_) in tip labels with spaces
1705 (this behaviour was undocumented).
1707 o The function plot.phylo() has a new option (`underscore') which
1708 specifies whether the underscores in tip labels should be written on
1709 the plot as such or replaced with spaces (the default).
1711 o The function birthdeath() now computes 95% confidence intervals of
1712 the estimated parameters using profile likelihood.
1714 o Three new data sets are included: a gene tree estimated from 36
1715 landplant rbcL sequences, a gene tree estimated from 32 opsin
1716 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1721 o A bug was fixed in dist.gene() where nothing was returned.
1723 o A bug in plot.mst() was fixed.
1725 o A bug in vcv.phylo() resulted in false correlations when the
1726 option `cor = TRUE' was used (now fixed).
1730 CHANGES IN APE VERSION 1.0
1735 o Two new functions, read.dna() and write.dna(), read/write in a file
1736 DNA sequences in interleaved or in sequential format.
1738 o Two new functions, read.nexus() and write.nexus(), read/write trees
1741 o The new function bind.tree() allows to bind two trees together,
1742 possibly handling root edges to give internal branches.
1744 o The new function drop.tip() removes the tips in a phylogenetic tree,
1745 and trims (or not) the corresponding internal branches.
1747 o The new function is.ultrametric() tests if a tree is ultrametric.
1749 o The function plot.phylo() has more functionalities such as drawing the
1750 branches with different colours and/or different widths, showing the
1751 node labels, controling the position and font of the labels, rotating
1752 the labels, and controling the space around the plot.
1754 o The function read.tree() can now read trees with no branch length,
1755 such as "(a,b),c);". Consequently, the element `edge.length' in
1756 objects of class "phylo" is now optional.
1758 o The function write.tree() has a new default behaviour: if the default
1759 for the option `file' is used (i.e. file = ""), then a variable of
1760 mode character containing the tree in Newick format is returned which
1761 can thus be assigned (e.g., tree <- write.tree(phy)).
1763 o The function read.tree() has a new argument `text' which allows
1764 to read the tree in a variable of mode character.
1766 o A new data set is included: the phylogenetic relationships among
1767 the orders of birds from Sibley and Ahlquist (1990).
1771 CHANGES IN APE VERSION 0.2-1
1776 o Several bugs were fixed in the help pages.
1780 CHANGES IN APE VERSION 0.2
1785 o The function write.tree() writes phylogenetic trees (objects of class
1786 "phylo") in an ASCII file using the Newick parenthetic format.
1788 o The function birthdeath() fits a birth-death model to branching times
1789 by maximum likelihood, and estimates the corresponding speciation and
1792 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1795 o The function is.binary.tree() tests whether a phylogeny is binary.
1797 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1798 as well as some methods are introduced.
1800 o Several functions, including some generics and methods, for computing
1801 skyline plot estimates (classic and generalized) of effective
1802 population size through time are introduced and replace the function
1803 skyline.plot() in version 0.1.
1805 o Two data sets are now included: the phylogenetic relationships among
1806 the families of birds from Sibley and Ahlquist (1990), and an
1807 estimated clock-like phylogeny of HIV sequences sampled in the
1808 Democratic Republic of Congo.
1811 DEPRECATED & DEFUNCT
1813 o The function skyline.plot() in ape 0.1 has been deprecated and
1814 replaced by more elaborate functions (see above).
1819 o Two important bugs were fixed in plot.phylo(): phylogenies with
1820 multichotomies not at the root or not with only terminal branches,
1821 and phylogenies with a single node (i.e. only terminal branches)
1822 did not plot. These trees should be plotted correctly now.
1824 o Several bugs were fixed in diversi.time() in the computation of
1827 o Various errors were corrected in the help pages.
projects / ape.git / blob