1 CHANGES IN APE VERSION 2.2
6 o Four new functions have been written by Damien de Vienne for the
7 graphical exploration of large trees (plot.cophylo, subtrees,
8 subtreeplot), and to return the graphical coordinates of tree
11 o The new function corPagel() implements the Pagel's "lambda"
12 correlation structure.
17 o read.dna() failed if "?" occurred in the first 10 sites of the
20 o The x/y aspect of the plot is now respected when plotting a
21 circular tree (type = "r" or "f").
23 o Drawing the tip labels sometimes failed when plotting circular
26 o zoom() failed when tip labels were used instead of their numbers
27 (thanks to Yan Wong for the fix).
29 o drop.tip() failed with some trees (fixed by Yan Wong).
34 o chronopl() has been improved and gains several options: see its
35 help page for details.
39 CHANGES IN APE VERSION 2.1-3
44 o A bug in read.nexus() made the Windows R-GUI crash.
46 o An error was fixed in the computation of ancestral character
47 states by generalized least squares in ace().
49 o di2multi() did not modify node labels correctly.
51 o multi2di() failed if the tree had its attribute "order" set to
56 CHANGES IN APE VERSION 2.1-2
61 o There three new methods for the "multiPhylo" class: str, $,
64 o root() gains the options 'node' and 'resolve.root'
65 (FALSE by default) as well as its code being improved.
67 o mltt.plot() has now an option 'log' used in the same way
68 than in plot.default().
73 o mltt.plot() failed to display the legend with an unnamed
76 o nodelabels() with pies now correcly uses the argument
77 'cex' to draw symbols of different sizes (which has
78 worked already for thermometers).
80 o read.nexus() generally failed to read very big files.
85 o The argument 'family' of compar.gee() can now be a function
86 as well as a character string.
88 o read.tree() and read.nexus() now return an unnamed list if
91 o read.nexus() now returns a modified object of class "multiPhylo"
92 when there is a TRANSLATE block in the NEXUS file: the individual
93 trees have no 'tip.label' vector, but the list has a 'TipLabel'
94 attribute. The new methods '$' and '[[' set these elements
95 correctly when extracting trees.
99 CHANGES IN APE VERSION 2.1-1
104 o The new function rmtree generates lists of random trees.
106 o rcoal() now generates a genuine coalescent tree by default
107 (thanks to Vladimir Minin for the code).
112 o nuc.div() returned an incorrect value with the default
113 pairwise.deletion = FALSE.
118 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
119 have been improved so that they are stabler and faster.
121 o R packages used by ape are now loaded silently; lattice and gee
122 are loaded only when needed.
126 CHANGES IN APE VERSION 2.1
131 o The new function identify.phylo identifies clades on a plotted
132 tree using the mouse.
134 o It is now possible to subset a list of trees (object of class
135 "multiPhylo") with "[" while keeping its class correct.
137 o The new function as.DNAbin.alignment converts DNA sequences
138 stored in the "alignment" format of the package seqinr into
139 an object of class "DNAbin".
141 o The new function weight.taxo2 helps to build similarity matrices
142 given two taxonomic levels (usually called by other functions).
144 o write.tree() can now take a list of trees (class "multiPhylo")
145 as its main argument.
147 o plot.correlogram() and plot.correlogramList() have been
148 improved, and gain several options (see the help page for
149 details). A legend is now plotted by default.
154 o dist.dna() returned some incorrect values with `model = "JC69"'
155 and `pairwise.deletion = TRUE'. This affected only the
156 distances involving sequences with missing values. (Thanks
157 to Bruno Toupance for digging this bug out.)
159 o write.tree() failed with some trees: this is fixed by removing
160 the `multi.line' option (trees are now always printed on a
163 o read.nexus() did not correctly detect trees with multiple root
164 edges (see OTHER CHANGES).
169 o The code of mlphylo() has almost entirely rewritten, and should
170 be much stabler. The options have been also greatly simplified
171 (see ?mlphylo and ?DNAmodel for details).
173 o The internal function nTips has been renamed klastorin_nTips.
175 o The code of is.ultrametric() contained redundancies and has
178 o The code of Moran.I() and of correlogram.formula() have been
181 o read.tree() and read.nexus() now return an error when trying to
182 read a tree with multiple root edges (see BUG FIXES). The
183 correction applied in previous version did not work in all
186 o The class c("multi.tree", "phylo") has been renamed
192 o There is now a vignette in ape: see vignette("MoranI", "ape").
197 o as.matching() and as.phylo.matching() do not support branch
200 o correlogram.phylo() and discrete.dist() have been removed.
204 CHANGES IN APE VERSION 2.0-2
209 o The new function matexpo computes the exponential of a square
212 o The new function unique.multi.tree removes duplicate trees from
215 o yule() has a new option `use.root.edge = FALSE' that specifies
216 to ignore, by default, the root edge of the tree if it exists.
221 o which.edge() failed when the index of a single terminal edge was
224 o In diversi.time(), the values returned for model C were
227 o A bug was fixed in yule() that affected the calculation of the
228 likelihood in the presence of ties in the branching times.
230 o There was a bug in the C function mat_expo4x4 affecting the
231 calculations of the transition probabilities for models HKY and
234 o A small bug was fixed in as.matrix.DNAbin (thanks to James
237 o rtree() did not `shuffle' the tip labels by default, so only a
238 limited number of labelled topologies could be generated.
242 CHANGES IN APE VERSION 2.0-1
247 o The three new functions bionj, fastme.ols, and fastme.bal
248 perform phylogeny estimation by the BIONJ and fastME methods in
249 OLS and balanced versions. This is a port to R of previous
250 previous programs done by Vincent Lefort.
252 o The new function chronoMPL performs molecular dating with the
253 mean path lengths method of Britton et al. (2002, Mol. Phyl.
256 o The new function rotate, contributed by Christoph Heibl, swaps
257 two clades connected to the same node. It works also with
258 multichotomous nodes.
260 o The new `method' as.matrix.DNAbin() may be used to convert
261 easily DNA sequences stored in a list into a matrix while
262 keeping the names and the class.
267 o chronopl() failed when some branch lengths were equal to zero:
268 an error message is now returned.
270 o di2multi() failed when there was a series of consecutive edges
275 CHANGES IN APE VERSION 1.10-2
280 o plot.phylo() can now plot circular trees: the option is type =
281 "fan" or type = "f" (to avoid the ambiguity with type = "c").
283 o prop.part() has a new option `check.labels = FALSE' which allows
284 to considerably speed-up the calculations of bipartitions. As a
285 consequence, calculations of bootstrap values with boot.phylo()
286 should be much faster.
291 o read.GenBank() did not return correctly the list of species as
292 from ape 1.10: this is fixed in this version
294 o Applying as.phylo() on a tree of class "phylo" failed: the
295 object is now returned unchanged.
299 CHANGES IN APE VERSION 1.10-1
304 o The three new functions Ntip, Nnode, and Nedge return, for a
305 given tree, the number of tips, nodes, or edges, respectively.
310 o read.nexus() did not set correctly the class of the returned
311 object when reading multiple trees.
313 o mllt.plot() failed with objects of class c("multi.tree",
316 o unroot() did not work correctly in most cases.
318 o reorder.phylo() made R freeze in some occasions.
320 o Plotting a tree in pruningwise order failed.
322 o When plotting an unrooted tree, the tip labels where not all
323 correctly positioned if the option `cex' was used.
327 CHANGES IN APE VERSION 1.10
332 o Five new `method' functions have been introduced to manipulate
333 DNA sequences in binary format (see below).
335 o Three new functions have been introduced to convert between the
336 new binary and the character formats.
338 o The new function as.alignment converts DNA sequences stored as
339 single characters into the class "alignment" used by the package
342 o read.dna() and read.GenBank() have a new argument `as.character'
343 controlling whether the sequences are returned in binary format
349 o root() failed when the tree had node labels: this is fixed.
351 o plot.phylo() did not correctly set the limits on the y-axis with
352 the default setting: this is fixed.
354 o dist.dna() returned a wrong result for the LogDet, paralinear,
355 and BH87 models with `pairwise.deletion = TRUE'.
360 o DNA sequences are now internally stored in a binary format. See
361 the document "A Bit-Level Coding Scheme for Nucleotides" for the
362 details. Most functions analyzing DNA functions have been
363 modified accordingly and are now much faster (dist.dna is now
364 ca. 60 times faster).
368 CHANGES IN APE VERSION 1.9-4
373 o A bug was fixed in edgelabels().
375 o as.phylo.hclust() did not work correctly when the object of
376 class "hclust" has its labels set to NULL: the returned tree has
377 now its tip labels set to "1", "2", ...
379 o consensus could fail if some tip labels are a subset of others
380 (e.g., "a" and "a_1"): this is now fixed.
382 o mlphylo() failed in most cases if some branch lengths of the
383 initial tree were greater than one: an error message is now
386 o mlphylo() failed in most cases when estimating the proportion of
387 invariants: this is fixed.
391 CHANGES IN APE VERSION 1.9-3
396 o The new function edgelabels adds labels on the edge of the tree
397 in the same way than nodelabels or tiplabels.
402 o multi2di() did not handle correctly branch lengths with the
403 default option `random = TRUE': this is now fixed.
405 o A bug was fixed in nuc.div() when using pairwise deletions.
407 o A bug occurred in the analysis of bipartitions with large
408 numbers of large trees, with consequences on prop.part,
409 prop.clades, and boot.phylo.
411 o The calculation of the Billera-Holmes-Vogtmann distance in
412 dist.topo was wrong: this has been fixed.
416 CHANGES IN APE VERSION 1.9-2
421 o The new function ladderize reorganizes the internal structure of
422 a tree to plot them left- or right-ladderized.
424 o The new function dist.nodes computes the patristic distances
425 between all nodes, internal and terminal, of a tree. It replaces
426 the option `full = TRUE' of cophenetic.phylo (see below).
431 o A bug was fixed in old2new.phylo().
433 o Some bugs were fixed in chronopl().
435 o The edge colours were not correctly displayed by plot.phylo
436 (thank you to Li-San Wang for the fix).
438 o cophenetic.phylo() failed with multichotomous trees: this is
444 o read.dna() now returns the sequences in a matrix if they are
445 aligned (interleaved or sequential format). Sequences in FASTA
446 format are still returned in a list.
448 o The option `full' of cophenetic.phylo() has been removed because
449 it could not be used from the generic.
454 o rotate() has been removed; this function did not work correctly
459 CHANGES IN APE VERSION 1.9-1
464 o Trees with a single tip were not read correctly in R as the
465 element `Nnode' was not set: this is fixed.
467 o unroot() did not set correctly the number of nodes of the
468 unrooted tree in most cases.
470 o read.GenBank() failed when fetching very long sequences,
471 particularly of the BX-series.
473 o A bug was introduced in read.tree() with ape 1.9: it has been
478 CHANGES IN APE VERSION 1.9
483 o There are two new print `methods' for trees of class "phylo" and
484 lists of trees of class "multi.tree", so that they are now
485 displayed in a compact and informative way.
487 o There are two new functions, old2new.phylo and new2old.phylo,
488 for converting between the old and new coding of the class
491 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
492 LogDet ("logdet"), and paralinear ("paralin").
494 o compute.brlen() has been extended: several methods are now
495 available to compute branch lengths.
497 o write.dna() can now handle matrices as well as lists.
502 o cophenetic.phylo() sometimes returned a wrong result with
503 multichotomous trees: this is fixed.
505 o rotate() failed when a single tip was specified: the tree is now
508 o ace() did not return the correct index matrix with custom
509 models: this is fixed.
511 o multi2di() did not work correctly when resolving multichotomies
512 randomly: the topology was always the same, only the arrangement
513 of clades was randomized: this is fixed. This function now
514 accepts trees with no branch lengths.
516 o The output of diversi.gof() was blurred by useless prints when a
517 user distribution was specified. This has been corrected, and
518 the help page of this function has been expanded.
523 o The internal structure of the class "phylo" has been changed:
524 see the document "Definition of Formats for Coding Phylogenetic
525 Trees in R" for the details. In addition, the code of most
526 functions has been improved.
528 o Several functions have been improved by replacing some R codes
529 by C codes: pic, plot.phylo, and reorder.phylo.
531 o There is now a citation information: see citation("ape") in R.
533 o write.tree() now does not add extra 0's to branch lengths so
534 that 1.23 is printed "1.23" by default, not "1.2300000000".
536 o The syntax of bind.tree() has been simplified. This function now
537 accepts trees with no branch lengths, and handles correctly node
540 o The option `as.numeric' of mrca() has been removed.
542 o The unused options `format' and `rooted' of read.tree() have
545 o The unused option `format' of write.tree() has been removed.
547 o The use of node.depth() has been simplified.
551 CHANGES IN APE VERSION 1.8-5
556 o Two new functions read.nexus.data() and write.nexus.data(),
557 contributed by Johan Nylander, allow to read and write molecular
558 sequences in NEXUS files.
560 o The new function reorder.phylo() reorders the internal structure
561 of a tree of class "phylo". It is used as the generic, e.g.,
564 o read.tree() and read.nexus() can now read trees with a single
567 o The new data set `cynipids' supplies a set of protein sequences
573 o The code of all.equal.phylo() has been completely rewritten
574 (thanks to Benoît Durand) which fixes several bugs.
576 o read.tree() and read.nexus() now checks the labels of the tree
577 to remove or substitute any characters that are illegal in the
578 Newick format (parentheses, etc.)
580 o A negative P-value could be returned by mantel.test(): this is
585 CHANGES IN APE VERSION 1.8-4
590 o The new function sh.test() computes the Shimodaira-
593 o The new function collapse.singles() removes the nodes with a
594 single descendant from a tree.
596 o plot.phylo() has a new argument `tip.color' to specify the
599 o mlphylo() has now an option `quiet' to control the display of
600 the progress of the analysis (the default is FALSE).
605 o read.dna() did not read correctly sequences in sequential format
606 with leading alignment gaps "-": this is fixed.
608 o ace() returned a list with no class so that the generic
609 functions (anova, logLik, ...) could not be used directly. This
610 is fixed as ace() now returns an object of class "ace".
612 o anova.ace() had a small bug when computing the number of degrees
613 of freedom: this is fixed.
615 o mlphylo() did not work when the sequences were in a matrix or
616 a data frame: this is fixed.
618 o rtree() did not work correctly when trying to simulate an
619 unrooted tree with two tips: an error message is now issued.
624 o The algorithm of rtree() has been changed: it is now about 40,
625 100, and 130 times faster for 10, 100, and 1000 tips,
630 CHANGES IN APE VERSION 1.8-3
635 o There are four new `method' functions to be used with the
636 results of ace(): logLik(), deviance(), AIC(), and anova().
638 o The plot method of phymltest has two new arguments: `main' to
639 change the title, and `col' to control the colour of the
640 segments showing the AIC values.
642 o ace() has a new argument `ip' that gives the initial values used
643 in the ML estimation with discrete characters (see the examples
644 in ?ace). This function now returns a matrix giving the indices
645 of the estimated rates when analysing discrete characters.
647 o nodelabels() and tiplabels() have a new argument `pie' to
648 represent proportions, with any number of categories, as
649 piecharts. The use of the option `thermo' has been improved:
650 there is now no limitation on the number of categories.
655 o mlphylo() did not work with more than two partitions: this is
658 o root() failed if the proposed outgroup was already an outgroup
659 in the tree: this is fixed.
661 o The `col' argument in nodelabels() and tiplabels() was not
662 correctly passed when `text' was used: this is fixed.
664 o Two bugs were fixed in mlphylo(): parameters were not always
665 correctly output, and the estimation failed in some cases.
667 o plot.phylo() was stuck when given a tree with a single tip: this
668 is fixed and a message error is now returned.
670 o An error was corrected in the help page of gammaStat regarding
671 the calculation of P-values.
673 o Using gls() could crash R when the number of species in the tree
674 and in the variables were different: this is fixed.
678 CHANGES IN APE VERSION 1.8-2
683 o The new function mlphylo() fits a phylogenetic tree by maximum
684 likelihood from DNA sequences. Its companion function DNAmodel()
685 is used to define the substitution model which may include
686 partitioning. There are methods for logLik(), deviance(), and
687 AIC(), and the summary() method has been extended to display in
688 a friendly way the results of this model fitting. Currently, the
689 functionality is limited to estimating the substitution and
690 associated parameters and computing the likelihood.
692 o The new function drop1.compar.gee (used as, e.g., drop1(m))
693 tests for single effects in GEE-based comparative method. A
694 warning message is printed if there is not enough degrees of
700 o An error message was sometimes issued by plot.multi.tree(),
701 though with no consequence.
705 CHANGES IN APE VERSION 1.8-1
710 o There is a new plot method for lists of trees (objects of class
711 "multi.tree"): it calls plot.phylo() internally and is
712 documented on the same help page.
717 o A bug was fixed in the C code that analyzes bipartitions: this
718 has impact on several functions like prop.part, prop.clades,
719 boot.phylo, or consensus.
721 o root() did not work correctly when the specified outgroup had
722 more than one element: this is fixed.
724 o dist.dna() sometimes returned a warning inappropriately: this
727 o If the distance object given to nj() had no rownames, nj()
728 returned a tree with no tip labels: it now returns tips labelled
729 "1", "2", ..., corresponding to the row numbers.
734 o nj() has been slightly changed so that tips with a zero distance
735 are first aggregated with zero-lengthed branches; the usual NJ
736 procedure is then performed on a distance matrix without 0's.
740 CHANGES IN APE VERSION 1.8
745 o The new function chronopl() estimates dates using the penalized
746 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
748 o The new function consensus() calculates the consensus tree of a
751 o The new function evolve.phylo() simulates the evolution of
752 continuous characters along a phylogeny under a Brownian model.
754 o The new plot method for objects of class "ancestral" displays a
755 tree together with ancestral values, as returned by the above
758 o The new function as.phylo.formula() returns a phylogeny from a
759 set of nested taxonomic variables given as a formula.
761 o The new function read.caic() reads trees in CAIC format.
763 o The new function tiplabels() allows to add labels to the tips
764 of a tree using text or plotting symbols in a flexible way.
766 o The new function unroot() unroots a phylogeny.
768 o multi2di() has a new option, `random', which specifies whether
769 to resolve the multichotomies randomly (the default) or not.
771 o prop.part() now returns an object of class "prop.part" for which
772 there are print (to display a partition in a more friendly way)
773 and summary (to extract the numbers) methods.
775 o plot.phylo() has a new option, `show.tip.label', specifying
776 whether to print the labels of the tips. The default is TRUE.
778 o The code of nj() has been replaced by a faster C code: it is now
779 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
782 o write.nexus() now writes whether a tree is rooted or not.
787 o Two bugs have been fixed in root(): unrooted trees are now
788 handled corretly, and node labels are now output normally.
790 o A bug was fixed in phymltest(): the executable couldn't be found
793 o Three bug have been fixed in ace(): computing the likelihood of
794 ancestral states of discrete characters failed, custom models
795 did not work, and the function failed with a null gradient (a
796 warning message is now returned; this latter bug was also
797 present in yule.cov() as well and is now fixed).
799 o pic() hanged out when missing data were present: a message error
802 o A small bug was fixed in dist.dna() where the gamma correction
803 was not always correctly dispatched.
805 o plot.phylo() plotted correctly the root edge only when the tree
806 was plotted rightwards: this works now for all directions.
811 o dist.taxo() has been renamed as weight.taxo().
813 o Various error and warning messages have been improved.
817 CHANGES IN APE VERSION 1.7
820 o The new function ace() estimates ancestral character states for
821 continuous characters (with ML, GLS, and contrasts methods), and
822 discrete characters (with ML only) for any number of states.
824 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
825 of directional evolution for continuous characters. The user
826 specifies the node(s) of the tree where the character optimum
829 o The new function is.rooted() tests whether a tree (of class
832 o The new function rcoal() generates random ultrametric trees with
833 the possibility to specify the function that generates the
834 inter-nodes distances.
836 o The new function mrca() gives for all pairs of tips in a tree
837 (and optionally nodes too) the most recent common ancestor.
839 o nodelabels() has a new option `thermo' to plot proportions (up
840 to three classes) on the nodes of a tree.
842 o rtree() has been improved: it can now generate rooted or
843 unrooted trees, and the mathematical function that generates the
844 branch lengths may be specified by the user. The tip labels may
845 be given directly in the call to rtree. The limit cases (n = 2,
846 3) are now handled correctly.
848 o dist.topo() has a new argument `method' with two choices: "PH85"
849 for Penny and Henny's method (already available before and now
850 the default), and "BHV01" for the geometric distance by Billera
851 et al. (2001, Adv. Appl. Math. 27:733).
853 o write.tree() has a new option, `digits', which specifies the
854 number of digits to be printed in the Newick tree. By default
855 digits = 10. The numbers are now always printed in decimal form
856 (i.e., 1.0e-1 is now avoided).
858 o dist.dna() can now compute the raw distances between pairs of
859 DNA sequences by specifying model = "raw".
861 o dist.phylo() has a new option `full' to possibly compute the
862 distances among all tips and nodes of the tree. The default if
868 o Several bugs were fixed in all.equal.phylo().
870 o dist.dna() did not handle correctly gaps ("-") in alignments:
871 they are now considered as missing data.
873 o rotate() did not work if the tips were not ordered: this is
876 o mantel.test() returned NA in some special cases: this is fixed
877 and the function has been improved and is now faster.
879 o A bug was fixed in diversi.gof() where the calculation of A² was
882 o cherry() did not work correctly under some OSs (mainly Linux):
885 o is.binary.tree() has been modified so that it works with both
886 rooted and unrooted trees.
888 o The documentation of theta.s() was not correct: this has been
891 o plot.mst() did not work correctly: this is fixed.
895 CHANGES IN APE VERSION 1.6
900 o The new function dist.topo() computes the topological distances
903 o The new function boot.phylo() performs a bootstrap analysis on
904 phylogeny estimation.
906 o The new functions prop.part() and prop.clades() analyse
907 bipartitions from a series of trees.
912 o read.GenBank() now uses the EFetch utility of NCBI instead of
913 the usual Web interface: it is now much faster (e.g., 12 times
914 faster to retrieve 8 sequences, 37 times for 60 sequences).
919 o Several bugs were fixed in read.dna().
921 o Several bugs were fixed in diversi.time().
923 o is.binary.tree() did not work correctly if the tree has no edge
924 lengths: this is fixed.
926 o drop.tip() did not correctly propagated the `node.label' of a
931 CHANGES IN APE VERSION 1.5
936 o Two new functions, as.matching.phylo() and as.phylo.matching(),
937 convert objects between the classes "phylo" and "matching". The
938 latter implements the representation of binary trees introduced by
939 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
940 as.matching() has been introduced as well.
942 o Two new functions, multi2di() and di2multi(), allow to resolve
943 and collapse multichotomies with branches of length zero.
945 o The new function nuc.div() computes the nucleotide diversity
946 from a sample a DNA sequences.
948 o dist.dna() has been completely rewritten with a much faster
949 (particularly for large data sets) C code. Eight models are
950 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
951 option `method' has been renamed `model'). Computation of variance
952 is available for all models. A gamma-correction is possible for
953 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
954 to remove sites with missing data on a pairwise basis. The option
955 `GCcontent' has been removed.
957 o read.GenBank() has a new option (species.names) which specifies
958 whether to return the species names of the organisms in addition
959 to the accession numbers of the sequences (this is the default
962 o write.nexus() can now write several trees in the same NEXUS file.
964 o drop.tip() has a new option `root.edge' that allows to specify the
965 new root edge if internal branches are trimmed.
970 o as.phylo.hclust() failed if some labels had parentheses: this
973 o Several bugs were fixed in all.equal.phylo(). This function now
974 returns the logical TRUE if the trees are identical but with
975 different representations (a report was printed previously).
977 o read.GenBank() did not correctly handle ambiguous base codes:
983 o birthdeath() now returns an object of class "birthdeath" for
984 which there is a print method.
988 CHANGES IN APE VERSION 1.4
993 o The new function nj() performs phylogeny estimation with the
994 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
997 o The new function which.edge() identifies the edges of a tree
998 that belong to a group specified as a set of tips.
1000 o The new function as.phylo.phylog() converts an object of class
1001 "phylog" (from the package ade4) into an object of class
1004 o The new function axisPhylo() draws axes on the side of a
1007 o The new function howmanytrees() calculates the number of trees
1008 in different cases and giving a number of tips.
1010 o write.tree() has a new option `multi.line' (TRUE by default) to
1011 write a Newick tree on several lines rather than on a single
1014 o The functionalities of zoom() have been extended. Several
1015 subtrees can be visualized at the same time, and they are marked
1016 on the main tree with colors. The context of the subtrees can be
1017 marked with the option `subtree' (see below).
1019 o drop.tip() has a new option `subtree' (FALSE by default) which
1020 specifies whether to output in the tree how many tips have been
1023 o The arguments of add.scale.bar() have been redefined and have
1024 now default values (see ?add.scale.bar for details). This
1025 function now works even if the plotted tree has no edge length.
1027 o plot.phylo() can now plot radial trees, but this does not take
1028 edge lengths into account.
1030 o In plot.phylo() with `type = "phylogram"', if the values of
1031 `edge.color' and `edge.width' are identical for sister-branches,
1032 they are propagated to the vertical line that link them.
1037 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1038 crashing. This is fixed.
1040 o In plot.phylo(), the options `edge.color' and `edge.width' are
1041 now properly recycled; their default values are now "black" and
1044 o A bug has been fixed in write.nexus().
1049 o The function node.depth.edgelength() has been removed and
1050 replaced by a C code.
1054 CHANGES IN APE VERSION 1.3-1
1059 o The new function nodelabels() allows to add labels to the nodes
1060 of a tree using text or plotting symbols in a flexible way.
1062 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1063 numeric values specifying the lower and upper limits on the x-
1064 and y-axes. This allows to leave some space on any side of the
1065 tree. If a single value is given, this is taken as the upper
1070 CHANGES IN APE VERSION 1.3
1075 o The new function phymltest() calls the software PHYML and fits
1076 28 models of DNA sequence evolution. There are a print method to
1077 display likelihood and AIC values, a summary method to compute
1078 the hierarchical likelihood ratio tests, and a plot method to
1079 display graphically the AIC values of each model.
1081 o The new function yule.cov() fits the Yule model with covariates,
1082 a model where the speciation rate is affected by several species
1083 traits through a generalized linear model. The parameters are
1084 estimated by maximum likelihood.
1086 o Three new functions, corBrownian(), corGrafen(), and
1087 corMartins(), compute the expected correlation structures among
1088 species given a phylogeny under different models of evolution.
1089 These can be used for GLS comparative phylogenetic methods (see
1090 the examples). There are coef() and corMatrix() methods and an
1091 Initialize.corPhyl() function associated.
1093 o The new function compar.cheverud() implements Cheverud et al.'s
1094 (1985; Evolution 39:1335) phylogenetic comparative method.
1096 o The new function varcomp() estimates variance components; it has
1099 o Two new functions, panel.superpose.correlogram() and
1100 plot.correlogramList(), allow to plot several phylogenetic
1103 o The new function node.leafnumber() computes the number of leaves
1104 of a subtree defined by a particular node.
1106 o The new function node.sons() gets all tags of son nodes from a
1109 o The new function compute.brlen() computes the branch lengths of
1110 a tree according to a specified method.
1112 o plot.phylo() has three new options: "cex" controls the size of
1113 the (tip and node) labels (thus it is no more needed to change
1114 the global graphical parameter), "direction" which allows to
1115 plot the tree rightwards, leftwards, upwards, or downwards, and
1116 "y.lim" which sets the upper limit on the y-axis.
1121 o Some functions which try to match tip labels and names of
1122 additional data (e.g. vector) are likely to fail if there are
1123 typing or syntax errors. If both series of names do not perfectly
1124 match, they are ignored and a warning message is now issued.
1125 These functions are bd.ext, compar.gee, pic. Their help pages
1126 have been clarified on this point.
1130 CHANGES IN APE VERSION 1.2-7
1135 o The new function root() reroots a phylogenetic tree with respect
1136 to a specified outgroup.
1138 o The new function rotate() rotates an internal branch of a tree.
1140 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1141 trees) controls the display of the tip labels in unrooted trees.
1142 This display has been greatly improved: the tip labels are now not
1143 expected to overlap with the tree (particularly if lab4ut =
1144 "axial"). In all cases, combining appropriate values of "lab4ut"
1145 and the font size (via "par(cex = )") should result in readable
1146 unrooted trees. See ?plot.phylo for some examples.
1148 o In drop.tip(), the argument `tip' can now be numeric or character.
1153 o drop.tip() did not work correctly with trees with no branch
1154 lengths: this is fixed.
1156 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1157 plotted with some line crossings: this is now fixed.
1161 CHANGES IN APE VERSION 1.2-6
1166 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1167 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1168 to implement comparative methods with an autocorrelation approach.
1170 o A new data set describing some life history traits of Carnivores
1176 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1181 o When plotting a tree with plot.phylo(), the new default of the
1182 option `label.offset' is now 0, so the labels are always visible.
1186 CHANGES IN APE VERSION 1.2-5
1191 o The new function bd.ext() fits a birth-death model with combined
1192 phylogenetic and taxonomic data, and estimates the corresponding
1193 speciation and extinction rates.
1198 o The package gee is no more required by ape but only suggested
1199 since only the function compar.gee() calls gee.
1203 CHANGES IN APE VERSION 1.2-4
1208 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1209 and lines.popsize) implementing a new approach for inferring the
1210 demographic history from genealogies using a reversible jump
1211 MCMC have been introduced.
1213 o The unit of time in the skyline plot and in the new plots can
1214 now be chosen to be actual years, rather than substitutions.
1218 CHANGES IN APE VERSION 1.2-3
1223 o The new function rtree() generates a random binary tree with or
1224 without branch lengths.
1226 o Two new functions for drawing lineages-through-time (LTT) plots
1227 are provided: ltt.lines() adds a LTT curve to an existing plot,
1228 and mltt.plot() does a multiple LTT plot giving several trees as
1229 arguments (see `?ltt.plot' for details).
1234 o Some taxon names made R crashing when calling as.phylo.hclust():
1237 o dist.dna() returned an error with two identical DNA sequences
1238 (only using the Jukes-Cantor method returned 0): this is fixed.
1243 o The function dist.phylo() has been re-written using a different
1244 algorithm: it is now about four times faster.
1246 o The code of branching.times() has been improved: it is now about
1251 CHANGES IN APE VERSION 1.2-2
1256 o The new function seg.sites() finds the segregating sites in a
1257 sample of DNA sequences.
1262 o A bug introduced in read.tree() and in read.nexus() with version
1265 o A few errors were corrected and a few examples were added in the
1270 CHANGES IN APE VERSION 1.2-1
1275 o plot.phylo() can now draw the edge of the root of a tree if it
1276 has one (see the new option `root.edge', its default is FALSE).
1281 o A bug was fixed in read.nexus(): files with semicolons inside
1282 comment blocks were not read correctly.
1284 o The behaviour of read.tree() and read.nexus() was corrected so
1285 that tree files with badly represented root edges (e.g., with
1286 an extra pair of parentheses, see the help pages for details)
1287 are now correctly represented in the object of class "phylo";
1288 a warning message is now issued.
1292 CHANGES IN APE VERSION 1.2
1297 o plot.phylo() has been completely re-written and offers several
1298 new functionalities. Three types of trees can now be drawn:
1299 phylogram (as previously), cladogram, and unrooted tree; in
1300 all three types the branch lengths can be drawn using the edge
1301 lengths of the phylogeny or not (e.g., if the latter is absent).
1302 The vertical position of the nodes can be adjusted with two
1303 choices (see option `node.pos'). The code has been re-structured,
1304 and two new functions (potentially useful for developpers) are
1305 documented separately: node.depth.edgelength() and node.depth();
1306 see the respective help pages for details.
1308 o The new function zoom() allows to explore very large trees by
1309 focusing on a small portion of it.
1311 o The new function yule() fits by maximum likelihood the Yule model
1312 (birth-only process) to a phylogenetic tree.
1314 o Support for writing DNA sequences in FASTA format has been
1315 introduced in write.dna() (support for reading sequences in
1316 this format was introduced in read.dna() in version 1.1-2).
1317 The function has been completely re-written, fixing some bugs
1318 (see below); the default behaviour is no more to display the
1319 sequences on the standard output. Several options have been
1320 introduced to control the sequence printing in a flexible
1321 way. The help page has been extended.
1323 o A new data set is included: a supertree of bats in NEXUS format.
1328 o In theta.s(), the default of the option `variance' has
1329 been changed to `FALSE' (as was indicated in the help page).
1331 o Several bugs were fixed in the code of all.equal.phylo().
1333 o Several bugs were fixed in write.dna(), particularly this
1334 function did not work with `format = "interleaved"'.
1336 o Various errors were corrected in the help pages.
1341 o The argument names of as.hclust.phylo() have been changed
1342 from "(phy)" to "(x, ...)" to conform to the definition of
1343 the corresponding generic function.
1345 o gamma.stat() has been renamed gammaStat() to avoid confusion
1346 since gamma() is a generic function.
1350 CHANGES IN APE VERSION 1.1-3
1355 o base.freq() previously did not return a value of 0 for
1356 bases absent in the data (e.g., a vector of length 3 was
1357 returned if one base was absent). This is now fixed (a
1358 vector of length 4 is always returned).
1360 o Several bugs were fixed in read.nexus(), including that this
1361 function did not work in this absence of a "TRANSLATE"
1362 command in the NEXUS file, and that the commands were
1367 CHANGES IN APE VERSION 1.1-2
1372 o The Tamura and Nei (1993) model of DNA distance is now implemented
1373 in dist.dna(): five models are now available in this function.
1375 o A new data set is included: a set of 15 sequences of the
1376 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1382 o A bug in read.nexus() was fixed.
1384 o read.dna() previously did not work correctly in most cases.
1385 The function has been completely re-written and its help page
1386 has been considerably extended (see ?read.dna for details).
1387 Underscores (_) in taxon names are no more replaced with
1388 spaces (this behaviour was undocumented).
1390 o A bug was fixed in write.dna().
1394 CHANGES IN APE VERSION 1.1-1
1399 o A bug in read.tree() introduced in APE 1.1 was fixed.
1401 o A bug in compar.gee() resulted in an error when trying to fit
1402 a model with `family = "binomial"'. This is now fixed.
1406 CHANGES IN APE VERSION 1.1
1411 o The Klastorin (1982) method as suggested by Misawa and Tajima
1412 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1413 on the basis of phylogenetic trees has been implemented (see
1414 the function klastorin()).
1416 o Functions have been added to convert APE's "phylo" objects in
1417 "hclust" cluster objects and vice versa (see the help page of
1418 as.phylo for details).
1420 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1421 are introduced for the estimation of absolute evolutionary rates
1422 (ratogram) and dated clock-like trees (chronogram) from
1423 phylogenetic trees using the non-parametric rate smoothing approach
1424 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1426 o A summary method is now provided printing a summary information on a
1427 phylogenetic tree with, for instance, `summary(tree)'.
1429 o The behaviour of read.tree() was changed so that all spaces and
1430 tabulations in tree files are now ignored. Consequently, spaces in tip
1431 labels are no more allowed. Another side effect is that read.nexus()
1432 now does not replace the underscores (_) in tip labels with spaces
1433 (this behaviour was undocumented).
1435 o The function plot.phylo() has a new option (`underscore') which
1436 specifies whether the underscores in tip labels should be written on
1437 the plot as such or replaced with spaces (the default).
1439 o The function birthdeath() now computes 95% confidence intervals of
1440 the estimated parameters using profile likelihood.
1442 o Three new data sets are included: a gene tree estimated from 36
1443 landplant rbcL sequences, a gene tree estimated from 32 opsin
1444 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1449 o A bug was fixed in dist.gene() where nothing was returned.
1451 o A bug in plot.mst() was fixed.
1453 o A bug in vcv.phylo() resulted in false correlations when the
1454 option `cor = TRUE' was used (now fixed).
1458 CHANGES IN APE VERSION 1.0
1463 o Two new functions, read.dna() and write.dna(), read/write in a file
1464 DNA sequences in interleaved or in sequential format.
1466 o Two new functions, read.nexus() and write.nexus(), read/write trees
1469 o The new function bind.tree() allows to bind two trees together,
1470 possibly handling root edges to give internal branches.
1472 o The new function drop.tip() removes the tips in a phylogenetic tree,
1473 and trims (or not) the corresponding internal branches.
1475 o The new function is.ultrametric() tests if a tree is ultrametric.
1477 o The function plot.phylo() has more functionalities such as drawing the
1478 branches with different colours and/or different widths, showing the
1479 node labels, controling the position and font of the labels, rotating
1480 the labels, and controling the space around the plot.
1482 o The function read.tree() can now read trees with no branch length,
1483 such as "(a,b),c);". Consequently, the element `edge.length' in
1484 objects of class "phylo" is now optional.
1486 o The function write.tree() has a new default behaviour: if the default
1487 for the option `file' is used (i.e. file = ""), then a variable of
1488 mode character containing the tree in Newick format is returned which
1489 can thus be assigned (e.g., tree <- write.tree(phy)).
1491 o The function read.tree() has a new argument `text' which allows
1492 to read the tree in a variable of mode character.
1494 o A new data set is included: the phylogenetic relationships among
1495 the orders of birds from Sibley and Ahlquist (1990).
1499 CHANGES IN APE VERSION 0.2-1
1504 o Several bugs were fixed in the help pages.
1508 CHANGES IN APE VERSION 0.2
1513 o The function write.tree() writes phylogenetic trees (objects of class
1514 "phylo") in an ASCII file using the Newick parenthetic format.
1516 o The function birthdeath() fits a birth-death model to branching times
1517 by maximum likelihood, and estimates the corresponding speciation and
1520 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1523 o The function is.binary.tree() tests whether a phylogeny is binary.
1525 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1526 as well as some methods are introduced.
1528 o Several functions, including some generics and methods, for computing
1529 skyline plot estimates (classic and generalized) of effective
1530 population size through time are introduced and replace the function
1531 skyline.plot() in version 0.1.
1533 o Two data sets are now included: the phylogenetic relationships among
1534 the families of birds from Sibley and Ahlquist (1990), and an
1535 estimated clock-like phylogeny of HIV sequences sampled in the
1536 Democratic Republic of Congo.
1539 DEPRECATED & DEFUNCT
1541 o The function skyline.plot() in ape 0.1 has been deprecated and
1542 replaced by more elaborate functions (see above).
1547 o Two important bugs were fixed in plot.phylo(): phylogenies with
1548 multichotomies not at the root or not with only terminal branches,
1549 and phylogenies with a single node (i.e. only terminal branches)
1550 did not plot. These trees should be plotted correctly now.
1552 o Several bugs were fixed in diversi.time() in the computation of
1555 o Various errors were corrected in the help pages.
projects / ape.git / blob