1 CHANGES IN APE VERSION 2.1-1
6 o The new function rmtree generates lists of random trees.
10 CHANGES IN APE VERSION 2.1
15 o The new function identify.phylo identifies clades on a plotted
18 o It is now possible to subset a list of trees (object of class
19 "multiPhylo") with "[" while keeping its class correct.
21 o The new function as.DNAbin.alignment converts DNA sequences
22 stored in the "alignment" format of the package seqinr into
23 an object of class "DNAbin".
25 o The new function weight.taxo2 helps to build similarity matrices
26 given two taxonomic levels (usually called by other functions).
28 o write.tree() can now take a list of trees (class "multiPhylo")
31 o plot.correlogram() and plot.correlogramList() have been
32 improved, and gain several options (see the help page for
33 details). A legend is now plotted by default.
38 o dist.dna() returned some incorrect values with `model = "JC69"'
39 and `pairwise.deletion = TRUE'. This affected only the
40 distances involving sequences with missing values. (Thanks
41 to Bruno Toupance for digging this bug out.)
43 o write.tree() failed with some trees: this is fixed by removing
44 the `multi.line' option (trees are now always printed on a
47 o read.nexus() did not correctly detect trees with multiple root
48 edges (see OTHER CHANGES).
53 o The code of mlphylo() has almost entirely rewritten, and should
54 much stabler now. The options have been also greatly simplified
55 (see ?mlphylo and ?DNAmodel for details).
57 o The internal function nTips has been renamed klastorin_nTips.
59 o The code of is.ultrametric() contained redundancies and has
62 o The code of Moran.I() and of correlogram.formula() have been
65 o read.tree() and read.nexus() now return an error when trying to
66 read a tree with multiple root edges (see BUG FIXES). The
67 correction applied in previous version did not work in all
70 o The class c("multi.tree", "phylo") has been renamed
76 o There is now a vignette in ape: see vignette("MoranI", "ape").
81 o as.matching() and as.phylo.matching() do not support branch
84 o correlogram.phylo() and discrete.dist() have been removed.
88 CHANGES IN APE VERSION 2.0-2
93 o The new function matexpo computes the exponential of a square
96 o The new function unique.multi.tree removes duplicate trees from
99 o yule() has a new option `use.root.edge = FALSE' that specifies
100 to ignore, by default, the root edge of the tree if it exists.
105 o which.edge() failed when the index of a single terminal edge was
108 o In diversi.time(), the values returned for model C were
111 o A bug was fixed in yule() that affected the calculation of the
112 likelihood in the presence of ties in the branching times.
114 o There was a bug in the C function mat_expo4x4 affecting the
115 calculations of the transition probabilities for models HKY and
118 o A small bug was fixed in as.matrix.DNAbin (thanks to James
121 o rtree() did not `shuffle' the tip labels by default, so only a
122 limited number of labelled topologies could be generated.
126 CHANGES IN APE VERSION 2.0-1
131 o The three new functions bionj, fastme.ols, and fastme.bal
132 perform phylogeny estimation by the BIONJ and fastME methods in
133 OLS and balanced versions. This is a port to R of previous
134 previous programs done by Vincent Lefort.
136 o The new function chronoMPL performs molecular dating with the
137 mean path lengths method of Britton et al. (2002, Mol. Phyl.
140 o The new function rotate, contributed by Christoph Heibl, swaps
141 two clades connected to the same node. It works also with
142 multichotomous nodes.
144 o The new `method' as.matrix.DNAbin() may be used to convert
145 easily DNA sequences stored in a list into a matrix while
146 keeping the names and the class.
151 o chronopl() failed when some branch lengths were equal to zero:
152 an error message is now returned.
154 o di2multi() failed when there was a series of consecutive edges
159 CHANGES IN APE VERSION 1.10-2
164 o plot.phylo() can now plot circular trees: the option is type =
165 "fan" or type = "f" (to avoid the ambiguity with type = "c").
167 o prop.part() has a new option `check.labels = FALSE' which allows
168 to considerably speed-up the calculations of bipartitions. As a
169 consequence, calculations of bootstrap values with boot.phylo()
170 should be much faster.
175 o read.GenBank() did not return correctly the list of species as
176 from ape 1.10: this is fixed in this version
178 o Applying as.phylo() on a tree of class "phylo" failed: the
179 object is now returned unchanged.
183 CHANGES IN APE VERSION 1.10-1
188 o The three new functions Ntip, Nnode, and Nedge return, for a
189 given tree, the number of tips, nodes, or edges, respectively.
194 o read.nexus() did not set correctly the class of the returned
195 object when reading multiple trees.
197 o mllt.plot() failed with objects of class c("multi.tree",
200 o unroot() did not work correctly in most cases.
202 o reorder.phylo() made R freeze in some occasions.
204 o Plotting a tree in pruningwise order failed.
206 o When plotting an unrooted tree, the tip labels where not all
207 correctly positioned if the option `cex' was used.
211 CHANGES IN APE VERSION 1.10
216 o Five new `method' functions have been introduced to manipulate
217 DNA sequences in binary format (see below).
219 o Three new functions have been introduced to convert between the
220 new binary and the character formats.
222 o The new function as.alignment converts DNA sequences stored as
223 single characters into the class "alignment" used by the package
226 o read.dna() and read.GenBank() have a new argument `as.character'
227 controlling whether the sequences are returned in binary format
233 o root() failed when the tree had node labels: this is fixed.
235 o plot.phylo() did not correctly set the limits on the y-axis with
236 the default setting: this is fixed.
238 o dist.dna() returned a wrong result for the LogDet, paralinear,
239 and BH87 models with `pairwise.deletion = TRUE'.
244 o DNA sequences are now internally stored in a binary format. See
245 the document "A Bit-Level Coding Scheme for Nucleotides" for the
246 details. Most functions analyzing DNA functions have been
247 modified accordingly and are now much faster (dist.dna is now
248 ca. 60 times faster).
252 CHANGES IN APE VERSION 1.9-4
257 o A bug was fixed in edgelabels().
259 o as.phylo.hclust() did not work correctly when the object of
260 class "hclust" has its labels set to NULL: the returned tree has
261 now its tip labels set to "1", "2", ...
263 o consensus could fail if some tip labels are a subset of others
264 (e.g., "a" and "a_1"): this is now fixed.
266 o mlphylo() failed in most cases if some branch lengths of the
267 initial tree were greater than one: an error message is now
270 o mlphylo() failed in most cases when estimating the proportion of
271 invariants: this is fixed.
275 CHANGES IN APE VERSION 1.9-3
280 o The new function edgelabels adds labels on the edge of the tree
281 in the same way than nodelabels or tiplabels.
286 o multi2di() did not handle correctly branch lengths with the
287 default option `random = TRUE': this is now fixed.
289 o A bug was fixed in nuc.div() when using pairwise deletions.
291 o A bug occurred in the analysis of bipartitions with large
292 numbers of large trees, with consequences on prop.part,
293 prop.clades, and boot.phylo.
295 o The calculation of the Billera-Holmes-Vogtmann distance in
296 dist.topo was wrong: this has been fixed.
300 CHANGES IN APE VERSION 1.9-2
305 o The new function ladderize reorganizes the internal structure of
306 a tree to plot them left- or right-ladderized.
308 o The new function dist.nodes computes the patristic distances
309 between all nodes, internal and terminal, of a tree. It replaces
310 the option `full = TRUE' of cophenetic.phylo (see below).
315 o A bug was fixed in old2new.phylo().
317 o Some bugs were fixed in chronopl().
319 o The edge colours were not correctly displayed by plot.phylo
320 (thank you to Li-San Wang for the fix).
322 o cophenetic.phylo() failed with multichotomous trees: this is
328 o read.dna() now returns the sequences in a matrix if they are
329 aligned (interleaved or sequential format). Sequences in FASTA
330 format are still returned in a list.
332 o The option `full' of cophenetic.phylo() has been removed because
333 it could not be used from the generic.
338 o rotate() has been removed; this function did not work correctly
343 CHANGES IN APE VERSION 1.9-1
348 o Trees with a single tip were not read correctly in R as the
349 element `Nnode' was not set: this is fixed.
351 o unroot() did not set correctly the number of nodes of the
352 unrooted tree in most cases.
354 o read.GenBank() failed when fetching very long sequences,
355 particularly of the BX-series.
357 o A bug was introduced in read.tree() with ape 1.9: it has been
362 CHANGES IN APE VERSION 1.9
367 o There are two new print `methods' for trees of class "phylo" and
368 lists of trees of class "multi.tree", so that they are now
369 displayed in a compact and informative way.
371 o There are two new functions, old2new.phylo and new2old.phylo,
372 for converting between the old and new coding of the class
375 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
376 LogDet ("logdet"), and paralinear ("paralin").
378 o compute.brlen() has been extended: several methods are now
379 available to compute branch lengths.
381 o write.dna() can now handle matrices as well as lists.
386 o cophenetic.phylo() sometimes returned a wrong result with
387 multichotomous trees: this is fixed.
389 o rotate() failed when a single tip was specified: the tree is now
392 o ace() did not return the correct index matrix with custom
393 models: this is fixed.
395 o multi2di() did not work correctly when resolving multichotomies
396 randomly: the topology was always the same, only the arrangement
397 of clades was randomized: this is fixed. This function now
398 accepts trees with no branch lengths.
400 o The output of diversi.gof() was blurred by useless prints when a
401 user distribution was specified. This has been corrected, and
402 the help page of this function has been expanded.
407 o The internal structure of the class "phylo" has been changed:
408 see the document "Definition of Formats for Coding Phylogenetic
409 Trees in R" for the details. In addition, the code of most
410 functions has been improved.
412 o Several functions have been improved by replacing some R codes
413 by C codes: pic, plot.phylo, and reorder.phylo.
415 o There is now a citation information: see citation("ape") in R.
417 o write.tree() now does not add extra 0's to branch lengths so
418 that 1.23 is printed "1.23" by default, not "1.2300000000".
420 o The syntax of bind.tree() has been simplified. This function now
421 accepts trees with no branch lengths, and handles correctly node
424 o The option `as.numeric' of mrca() has been removed.
426 o The unused options `format' and `rooted' of read.tree() have
429 o The unused option `format' of write.tree() has been removed.
431 o The use of node.depth() has been simplified.
435 CHANGES IN APE VERSION 1.8-5
440 o Two new functions read.nexus.data() and write.nexus.data(),
441 contributed by Johan Nylander, allow to read and write molecular
442 sequences in NEXUS files.
444 o The new function reorder.phylo() reorders the internal structure
445 of a tree of class "phylo". It is used as the generic, e.g.,
448 o read.tree() and read.nexus() can now read trees with a single
451 o The new data set `cynipids' supplies a set of protein sequences
457 o The code of all.equal.phylo() has been completely rewritten
458 (thanks to Benoît Durand) which fixes several bugs.
460 o read.tree() and read.nexus() now checks the labels of the tree
461 to remove or substitute any characters that are illegal in the
462 Newick format (parentheses, etc.)
464 o A negative P-value could be returned by mantel.test(): this is
469 CHANGES IN APE VERSION 1.8-4
474 o The new function sh.test() computes the Shimodaira-
477 o The new function collapse.singles() removes the nodes with a
478 single descendant from a tree.
480 o plot.phylo() has a new argument `tip.color' to specify the
483 o mlphylo() has now an option `quiet' to control the display of
484 the progress of the analysis (the default is FALSE).
489 o read.dna() did not read correctly sequences in sequential format
490 with leading alignment gaps "-": this is fixed.
492 o ace() returned a list with no class so that the generic
493 functions (anova, logLik, ...) could not be used directly. This
494 is fixed as ace() now returns an object of class "ace".
496 o anova.ace() had a small bug when computing the number of degrees
497 of freedom: this is fixed.
499 o mlphylo() did not work when the sequences were in a matrix or
500 a data frame: this is fixed.
502 o rtree() did not work correctly when trying to simulate an
503 unrooted tree with two tips: an error message is now issued.
508 o The algorithm of rtree() has been changed: it is now about 40,
509 100, and 130 times faster for 10, 100, and 1000 tips,
514 CHANGES IN APE VERSION 1.8-3
519 o There are four new `method' functions to be used with the
520 results of ace(): logLik(), deviance(), AIC(), and anova().
522 o The plot method of phymltest has two new arguments: `main' to
523 change the title, and `col' to control the colour of the
524 segments showing the AIC values.
526 o ace() has a new argument `ip' that gives the initial values used
527 in the ML estimation with discrete characters (see the examples
528 in ?ace). This function now returns a matrix giving the indices
529 of the estimated rates when analysing discrete characters.
531 o nodelabels() and tiplabels() have a new argument `pie' to
532 represent proportions, with any number of categories, as
533 piecharts. The use of the option `thermo' has been improved:
534 there is now no limitation on the number of categories.
539 o mlphylo() did not work with more than two partitions: this is
542 o root() failed if the proposed outgroup was already an outgroup
543 in the tree: this is fixed.
545 o The `col' argument in nodelabels() and tiplabels() was not
546 correctly passed when `text' was used: this is fixed.
548 o Two bugs were fixed in mlphylo(): parameters were not always
549 correctly output, and the estimation failed in some cases.
551 o plot.phylo() was stuck when given a tree with a single tip: this
552 is fixed and a message error is now returned.
554 o An error was corrected in the help page of gammaStat regarding
555 the calculation of P-values.
557 o Using gls() could crash R when the number of species in the tree
558 and in the variables were different: this is fixed.
562 CHANGES IN APE VERSION 1.8-2
567 o The new function mlphylo() fits a phylogenetic tree by maximum
568 likelihood from DNA sequences. Its companion function DNAmodel()
569 is used to define the substitution model which may include
570 partitioning. There are methods for logLik(), deviance(), and
571 AIC(), and the summary() method has been extended to display in
572 a friendly way the results of this model fitting. Currently, the
573 functionality is limited to estimating the substitution and
574 associated parameters and computing the likelihood.
576 o The new function drop1.compar.gee (used as, e.g., drop1(m))
577 tests for single effects in GEE-based comparative method. A
578 warning message is printed if there is not enough degrees of
584 o An error message was sometimes issued by plot.multi.tree(),
585 though with no consequence.
589 CHANGES IN APE VERSION 1.8-1
594 o There is a new plot method for lists of trees (objects of class
595 "multi.tree"): it calls plot.phylo() internally and is
596 documented on the same help page.
601 o A bug was fixed in the C code that analyzes bipartitions: this
602 has impact on several functions like prop.part, prop.clades,
603 boot.phylo, or consensus.
605 o root() did not work correctly when the specified outgroup had
606 more than one element: this is fixed.
608 o dist.dna() sometimes returned a warning inappropriately: this
611 o If the distance object given to nj() had no rownames, nj()
612 returned a tree with no tip labels: it now returns tips labelled
613 "1", "2", ..., corresponding to the row numbers.
618 o nj() has been slightly changed so that tips with a zero distance
619 are first aggregated with zero-lengthed branches; the usual NJ
620 procedure is then performed on a distance matrix without 0's.
624 CHANGES IN APE VERSION 1.8
629 o The new function chronopl() estimates dates using the penalized
630 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
632 o The new function consensus() calculates the consensus tree of a
635 o The new function evolve.phylo() simulates the evolution of
636 continuous characters along a phylogeny under a Brownian model.
638 o The new plot method for objects of class "ancestral" displays a
639 tree together with ancestral values, as returned by the above
642 o The new function as.phylo.formula() returns a phylogeny from a
643 set of nested taxonomic variables given as a formula.
645 o The new function read.caic() reads trees in CAIC format.
647 o The new function tiplabels() allows to add labels to the tips
648 of a tree using text or plotting symbols in a flexible way.
650 o The new function unroot() unroots a phylogeny.
652 o multi2di() has a new option, `random', which specifies whether
653 to resolve the multichotomies randomly (the default) or not.
655 o prop.part() now returns an object of class "prop.part" for which
656 there are print (to display a partition in a more friendly way)
657 and summary (to extract the numbers) methods.
659 o plot.phylo() has a new option, `show.tip.label', specifying
660 whether to print the labels of the tips. The default is TRUE.
662 o The code of nj() has been replaced by a faster C code: it is now
663 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
666 o write.nexus() now writes whether a tree is rooted or not.
671 o Two bugs have been fixed in root(): unrooted trees are now
672 handled corretly, and node labels are now output normally.
674 o A bug was fixed in phymltest(): the executable couldn't be found
677 o Three bug have been fixed in ace(): computing the likelihood of
678 ancestral states of discrete characters failed, custom models
679 did not work, and the function failed with a null gradient (a
680 warning message is now returned; this latter bug was also
681 present in yule.cov() as well and is now fixed).
683 o pic() hanged out when missing data were present: a message error
686 o A small bug was fixed in dist.dna() where the gamma correction
687 was not always correctly dispatched.
689 o plot.phylo() plotted correctly the root edge only when the tree
690 was plotted rightwards: this works now for all directions.
695 o dist.taxo() has been renamed as weight.taxo().
697 o Various error and warning messages have been improved.
701 CHANGES IN APE VERSION 1.7
704 o The new function ace() estimates ancestral character states for
705 continuous characters (with ML, GLS, and contrasts methods), and
706 discrete characters (with ML only) for any number of states.
708 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
709 of directional evolution for continuous characters. The user
710 specifies the node(s) of the tree where the character optimum
713 o The new function is.rooted() tests whether a tree (of class
716 o The new function rcoal() generates random ultrametric trees with
717 the possibility to specify the function that generates the
718 inter-nodes distances.
720 o The new function mrca() gives for all pairs of tips in a tree
721 (and optionally nodes too) the most recent common ancestor.
723 o nodelabels() has a new option `thermo' to plot proportions (up
724 to three classes) on the nodes of a tree.
726 o rtree() has been improved: it can now generate rooted or
727 unrooted trees, and the mathematical function that generates the
728 branch lengths may be specified by the user. The tip labels may
729 be given directly in the call to rtree. The limit cases (n = 2,
730 3) are now handled correctly.
732 o dist.topo() has a new argument `method' with two choices: "PH85"
733 for Penny and Henny's method (already available before and now
734 the default), and "BHV01" for the geometric distance by Billera
735 et al. (2001, Adv. Appl. Math. 27:733).
737 o write.tree() has a new option, `digits', which specifies the
738 number of digits to be printed in the Newick tree. By default
739 digits = 10. The numbers are now always printed in decimal form
740 (i.e., 1.0e-1 is now avoided).
742 o dist.dna() can now compute the raw distances between pairs of
743 DNA sequences by specifying model = "raw".
745 o dist.phylo() has a new option `full' to possibly compute the
746 distances among all tips and nodes of the tree. The default if
752 o Several bugs were fixed in all.equal.phylo().
754 o dist.dna() did not handle correctly gaps ("-") in alignments:
755 they are now considered as missing data.
757 o rotate() did not work if the tips were not ordered: this is
760 o mantel.test() returned NA in some special cases: this is fixed
761 and the function has been improved and is now faster.
763 o A bug was fixed in diversi.gof() where the calculation of A² was
766 o cherry() did not work correctly under some OSs (mainly Linux):
769 o is.binary.tree() has been modified so that it works with both
770 rooted and unrooted trees.
772 o The documentation of theta.s() was not correct: this has been
775 o plot.mst() did not work correctly: this is fixed.
779 CHANGES IN APE VERSION 1.6
784 o The new function dist.topo() computes the topological distances
787 o The new function boot.phylo() performs a bootstrap analysis on
788 phylogeny estimation.
790 o The new functions prop.part() and prop.clades() analyse
791 bipartitions from a series of trees.
796 o read.GenBank() now uses the EFetch utility of NCBI instead of
797 the usual Web interface: it is now much faster (e.g., 12 times
798 faster to retrieve 8 sequences, 37 times for 60 sequences).
803 o Several bugs were fixed in read.dna().
805 o Several bugs were fixed in diversi.time().
807 o is.binary.tree() did not work correctly if the tree has no edge
808 lengths: this is fixed.
810 o drop.tip() did not correctly propagated the `node.label' of a
815 CHANGES IN APE VERSION 1.5
820 o Two new functions, as.matching.phylo() and as.phylo.matching(),
821 convert objects between the classes "phylo" and "matching". The
822 latter implements the representation of binary trees introduced by
823 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
824 as.matching() has been introduced as well.
826 o Two new functions, multi2di() and di2multi(), allow to resolve
827 and collapse multichotomies with branches of length zero.
829 o The new function nuc.div() computes the nucleotide diversity
830 from a sample a DNA sequences.
832 o dist.dna() has been completely rewritten with a much faster
833 (particularly for large data sets) C code. Eight models are
834 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
835 option `method' has been renamed `model'). Computation of variance
836 is available for all models. A gamma-correction is possible for
837 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
838 to remove sites with missing data on a pairwise basis. The option
839 `GCcontent' has been removed.
841 o read.GenBank() has a new option (species.names) which specifies
842 whether to return the species names of the organisms in addition
843 to the accession numbers of the sequences (this is the default
846 o write.nexus() can now write several trees in the same NEXUS file.
848 o drop.tip() has a new option `root.edge' that allows to specify the
849 new root edge if internal branches are trimmed.
854 o as.phylo.hclust() failed if some labels had parentheses: this
857 o Several bugs were fixed in all.equal.phylo(). This function now
858 returns the logical TRUE if the trees are identical but with
859 different representations (a report was printed previously).
861 o read.GenBank() did not correctly handle ambiguous base codes:
867 o birthdeath() now returns an object of class "birthdeath" for
868 which there is a print method.
872 CHANGES IN APE VERSION 1.4
877 o The new function nj() performs phylogeny estimation with the
878 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
881 o The new function which.edge() identifies the edges of a tree
882 that belong to a group specified as a set of tips.
884 o The new function as.phylo.phylog() converts an object of class
885 "phylog" (from the package ade4) into an object of class
888 o The new function axisPhylo() draws axes on the side of a
891 o The new function howmanytrees() calculates the number of trees
892 in different cases and giving a number of tips.
894 o write.tree() has a new option `multi.line' (TRUE by default) to
895 write a Newick tree on several lines rather than on a single
898 o The functionalities of zoom() have been extended. Several
899 subtrees can be visualized at the same time, and they are marked
900 on the main tree with colors. The context of the subtrees can be
901 marked with the option `subtree' (see below).
903 o drop.tip() has a new option `subtree' (FALSE by default) which
904 specifies whether to output in the tree how many tips have been
907 o The arguments of add.scale.bar() have been redefined and have
908 now default values (see ?add.scale.bar for details). This
909 function now works even if the plotted tree has no edge length.
911 o plot.phylo() can now plot radial trees, but this does not take
912 edge lengths into account.
914 o In plot.phylo() with `type = "phylogram"', if the values of
915 `edge.color' and `edge.width' are identical for sister-branches,
916 they are propagated to the vertical line that link them.
921 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
922 crashing. This is fixed.
924 o In plot.phylo(), the options `edge.color' and `edge.width' are
925 now properly recycled; their default values are now "black" and
928 o A bug has been fixed in write.nexus().
933 o The function node.depth.edgelength() has been removed and
934 replaced by a C code.
938 CHANGES IN APE VERSION 1.3-1
943 o The new function nodelabels() allows to add labels to the nodes
944 of a tree using text or plotting symbols in a flexible way.
946 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
947 numeric values specifying the lower and upper limits on the x-
948 and y-axes. This allows to leave some space on any side of the
949 tree. If a single value is given, this is taken as the upper
954 CHANGES IN APE VERSION 1.3
959 o The new function phymltest() calls the software PHYML and fits
960 28 models of DNA sequence evolution. There are a print method to
961 display likelihood and AIC values, a summary method to compute
962 the hierarchical likelihood ratio tests, and a plot method to
963 display graphically the AIC values of each model.
965 o The new function yule.cov() fits the Yule model with covariates,
966 a model where the speciation rate is affected by several species
967 traits through a generalized linear model. The parameters are
968 estimated by maximum likelihood.
970 o Three new functions, corBrownian(), corGrafen(), and
971 corMartins(), compute the expected correlation structures among
972 species given a phylogeny under different models of evolution.
973 These can be used for GLS comparative phylogenetic methods (see
974 the examples). There are coef() and corMatrix() methods and an
975 Initialize.corPhyl() function associated.
977 o The new function compar.cheverud() implements Cheverud et al.'s
978 (1985; Evolution 39:1335) phylogenetic comparative method.
980 o The new function varcomp() estimates variance components; it has
983 o Two new functions, panel.superpose.correlogram() and
984 plot.correlogramList(), allow to plot several phylogenetic
987 o The new function node.leafnumber() computes the number of leaves
988 of a subtree defined by a particular node.
990 o The new function node.sons() gets all tags of son nodes from a
993 o The new function compute.brlen() computes the branch lengths of
994 a tree according to a specified method.
996 o plot.phylo() has three new options: "cex" controls the size of
997 the (tip and node) labels (thus it is no more needed to change
998 the global graphical parameter), "direction" which allows to
999 plot the tree rightwards, leftwards, upwards, or downwards, and
1000 "y.lim" which sets the upper limit on the y-axis.
1005 o Some functions which try to match tip labels and names of
1006 additional data (e.g. vector) are likely to fail if there are
1007 typing or syntax errors. If both series of names do not perfectly
1008 match, they are ignored and a warning message is now issued.
1009 These functions are bd.ext, compar.gee, pic. Their help pages
1010 have been clarified on this point.
1014 CHANGES IN APE VERSION 1.2-7
1019 o The new function root() reroots a phylogenetic tree with respect
1020 to a specified outgroup.
1022 o The new function rotate() rotates an internal branch of a tree.
1024 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1025 trees) controls the display of the tip labels in unrooted trees.
1026 This display has been greatly improved: the tip labels are now not
1027 expected to overlap with the tree (particularly if lab4ut =
1028 "axial"). In all cases, combining appropriate values of "lab4ut"
1029 and the font size (via "par(cex = )") should result in readable
1030 unrooted trees. See ?plot.phylo for some examples.
1032 o In drop.tip(), the argument `tip' can now be numeric or character.
1037 o drop.tip() did not work correctly with trees with no branch
1038 lengths: this is fixed.
1040 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1041 plotted with some line crossings: this is now fixed.
1045 CHANGES IN APE VERSION 1.2-6
1050 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1051 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1052 to implement comparative methods with an autocorrelation approach.
1054 o A new data set describing some life history traits of Carnivores
1060 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1065 o When plotting a tree with plot.phylo(), the new default of the
1066 option `label.offset' is now 0, so the labels are always visible.
1070 CHANGES IN APE VERSION 1.2-5
1075 o The new function bd.ext() fits a birth-death model with combined
1076 phylogenetic and taxonomic data, and estimates the corresponding
1077 speciation and extinction rates.
1082 o The package gee is no more required by ape but only suggested
1083 since only the function compar.gee() calls gee.
1087 CHANGES IN APE VERSION 1.2-4
1092 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1093 and lines.popsize) implementing a new approach for inferring the
1094 demographic history from genealogies using a reversible jump
1095 MCMC have been introduced.
1097 o The unit of time in the skyline plot and in the new plots can
1098 now be chosen to be actual years, rather than substitutions.
1102 CHANGES IN APE VERSION 1.2-3
1107 o The new function rtree() generates a random binary tree with or
1108 without branch lengths.
1110 o Two new functions for drawing lineages-through-time (LTT) plots
1111 are provided: ltt.lines() adds a LTT curve to an existing plot,
1112 and mltt.plot() does a multiple LTT plot giving several trees as
1113 arguments (see `?ltt.plot' for details).
1118 o Some taxon names made R crashing when calling as.phylo.hclust():
1121 o dist.dna() returned an error with two identical DNA sequences
1122 (only using the Jukes-Cantor method returned 0): this is fixed.
1127 o The function dist.phylo() has been re-written using a different
1128 algorithm: it is now about four times faster.
1130 o The code of branching.times() has been improved: it is now about
1135 CHANGES IN APE VERSION 1.2-2
1140 o The new function seg.sites() finds the segregating sites in a
1141 sample of DNA sequences.
1146 o A bug introduced in read.tree() and in read.nexus() with version
1149 o A few errors were corrected and a few examples were added in the
1154 CHANGES IN APE VERSION 1.2-1
1159 o plot.phylo() can now draw the edge of the root of a tree if it
1160 has one (see the new option `root.edge', its default is FALSE).
1165 o A bug was fixed in read.nexus(): files with semicolons inside
1166 comment blocks were not read correctly.
1168 o The behaviour of read.tree() and read.nexus() was corrected so
1169 that tree files with badly represented root edges (e.g., with
1170 an extra pair of parentheses, see the help pages for details)
1171 are now correctly represented in the object of class "phylo";
1172 a warning message is now issued.
1176 CHANGES IN APE VERSION 1.2
1181 o plot.phylo() has been completely re-written and offers several
1182 new functionalities. Three types of trees can now be drawn:
1183 phylogram (as previously), cladogram, and unrooted tree; in
1184 all three types the branch lengths can be drawn using the edge
1185 lengths of the phylogeny or not (e.g., if the latter is absent).
1186 The vertical position of the nodes can be adjusted with two
1187 choices (see option `node.pos'). The code has been re-structured,
1188 and two new functions (potentially useful for developpers) are
1189 documented separately: node.depth.edgelength() and node.depth();
1190 see the respective help pages for details.
1192 o The new function zoom() allows to explore very large trees by
1193 focusing on a small portion of it.
1195 o The new function yule() fits by maximum likelihood the Yule model
1196 (birth-only process) to a phylogenetic tree.
1198 o Support for writing DNA sequences in FASTA format has been
1199 introduced in write.dna() (support for reading sequences in
1200 this format was introduced in read.dna() in version 1.1-2).
1201 The function has been completely re-written, fixing some bugs
1202 (see below); the default behaviour is no more to display the
1203 sequences on the standard output. Several options have been
1204 introduced to control the sequence printing in a flexible
1205 way. The help page has been extended.
1207 o A new data set is included: a supertree of bats in NEXUS format.
1212 o In theta.s(), the default of the option `variance' has
1213 been changed to `FALSE' (as was indicated in the help page).
1215 o Several bugs were fixed in the code of all.equal.phylo().
1217 o Several bugs were fixed in write.dna(), particularly this
1218 function did not work with `format = "interleaved"'.
1220 o Various errors were corrected in the help pages.
1225 o The argument names of as.hclust.phylo() have been changed
1226 from "(phy)" to "(x, ...)" to conform to the definition of
1227 the corresponding generic function.
1229 o gamma.stat() has been renamed gammaStat() to avoid confusion
1230 since gamma() is a generic function.
1234 CHANGES IN APE VERSION 1.1-3
1239 o base.freq() previously did not return a value of 0 for
1240 bases absent in the data (e.g., a vector of length 3 was
1241 returned if one base was absent). This is now fixed (a
1242 vector of length 4 is always returned).
1244 o Several bugs were fixed in read.nexus(), including that this
1245 function did not work in this absence of a "TRANSLATE"
1246 command in the NEXUS file, and that the commands were
1251 CHANGES IN APE VERSION 1.1-2
1256 o The Tamura and Nei (1993) model of DNA distance is now implemented
1257 in dist.dna(): five models are now available in this function.
1259 o A new data set is included: a set of 15 sequences of the
1260 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1266 o A bug in read.nexus() was fixed.
1268 o read.dna() previously did not work correctly in most cases.
1269 The function has been completely re-written and its help page
1270 has been considerably extended (see ?read.dna for details).
1271 Underscores (_) in taxon names are no more replaced with
1272 spaces (this behaviour was undocumented).
1274 o A bug was fixed in write.dna().
1278 CHANGES IN APE VERSION 1.1-1
1283 o A bug in read.tree() introduced in APE 1.1 was fixed.
1285 o A bug in compar.gee() resulted in an error when trying to fit
1286 a model with `family = "binomial"'. This is now fixed.
1290 CHANGES IN APE VERSION 1.1
1295 o The Klastorin (1982) method as suggested by Misawa and Tajima
1296 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1297 on the basis of phylogenetic trees has been implemented (see
1298 the function klastorin()).
1300 o Functions have been added to convert APE's "phylo" objects in
1301 "hclust" cluster objects and vice versa (see the help page of
1302 as.phylo for details).
1304 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1305 are introduced for the estimation of absolute evolutionary rates
1306 (ratogram) and dated clock-like trees (chronogram) from
1307 phylogenetic trees using the non-parametric rate smoothing approach
1308 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1310 o A summary method is now provided printing a summary information on a
1311 phylogenetic tree with, for instance, `summary(tree)'.
1313 o The behaviour of read.tree() was changed so that all spaces and
1314 tabulations in tree files are now ignored. Consequently, spaces in tip
1315 labels are no more allowed. Another side effect is that read.nexus()
1316 now does not replace the underscores (_) in tip labels with spaces
1317 (this behaviour was undocumented).
1319 o The function plot.phylo() has a new option (`underscore') which
1320 specifies whether the underscores in tip labels should be written on
1321 the plot as such or replaced with spaces (the default).
1323 o The function birthdeath() now computes 95% confidence intervals of
1324 the estimated parameters using profile likelihood.
1326 o Three new data sets are included: a gene tree estimated from 36
1327 landplant rbcL sequences, a gene tree estimated from 32 opsin
1328 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1333 o A bug was fixed in dist.gene() where nothing was returned.
1335 o A bug in plot.mst() was fixed.
1337 o A bug in vcv.phylo() resulted in false correlations when the
1338 option `cor = TRUE' was used (now fixed).
1342 CHANGES IN APE VERSION 1.0
1347 o Two new functions, read.dna() and write.dna(), read/write in a file
1348 DNA sequences in interleaved or in sequential format.
1350 o Two new functions, read.nexus() and write.nexus(), read/write trees
1353 o The new function bind.tree() allows to bind two trees together,
1354 possibly handling root edges to give internal branches.
1356 o The new function drop.tip() removes the tips in a phylogenetic tree,
1357 and trims (or not) the corresponding internal branches.
1359 o The new function is.ultrametric() tests if a tree is ultrametric.
1361 o The function plot.phylo() has more functionalities such as drawing the
1362 branches with different colours and/or different widths, showing the
1363 node labels, controling the position and font of the labels, rotating
1364 the labels, and controling the space around the plot.
1366 o The function read.tree() can now read trees with no branch length,
1367 such as "(a,b),c);". Consequently, the element `edge.length' in
1368 objects of class "phylo" is now optional.
1370 o The function write.tree() has a new default behaviour: if the default
1371 for the option `file' is used (i.e. file = ""), then a variable of
1372 mode character containing the tree in Newick format is returned which
1373 can thus be assigned (e.g., tree <- write.tree(phy)).
1375 o The function read.tree() has a new argument `text' which allows
1376 to read the tree in a variable of mode character.
1378 o A new data set is included: the phylogenetic relationships among
1379 the orders of birds from Sibley and Ahlquist (1990).
1383 CHANGES IN APE VERSION 0.2-1
1388 o Several bugs were fixed in the help pages.
1392 CHANGES IN APE VERSION 0.2
1397 o The function write.tree() writes phylogenetic trees (objects of class
1398 "phylo") in an ASCII file using the Newick parenthetic format.
1400 o The function birthdeath() fits a birth-death model to branching times
1401 by maximum likelihood, and estimates the corresponding speciation and
1404 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1407 o The function is.binary.tree() tests whether a phylogeny is binary.
1409 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1410 as well as some methods are introduced.
1412 o Several functions, including some generics and methods, for computing
1413 skyline plot estimates (classic and generalized) of effective
1414 population size through time are introduced and replace the function
1415 skyline.plot() in version 0.1.
1417 o Two data sets are now included: the phylogenetic relationships among
1418 the families of birds from Sibley and Ahlquist (1990), and an
1419 estimated clock-like phylogeny of HIV sequences sampled in the
1420 Democratic Republic of Congo.
1423 DEPRECATED & DEFUNCT
1425 o The function skyline.plot() in ape 0.1 has been deprecated and
1426 replaced by more elaborate functions (see above).
1431 o Two important bugs were fixed in plot.phylo(): phylogenies with
1432 multichotomies not at the root or not with only terminal branches,
1433 and phylogenies with a single node (i.e. only terminal branches)
1434 did not plot. These trees should be plotted correctly now.
1436 o Several bugs were fixed in diversi.time() in the computation of
1439 o Various errors were corrected in the help pages.
projects / ape.git / blob