1 CHANGES IN APE VERSION 2.2-1
6 o The new function del.gaps() removes insertion gaps ("-") in a
12 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
17 CHANGES IN APE VERSION 2.2
22 o Four new functions have been written by Damien de Vienne for the
23 graphical exploration of large trees (cophyloplot, subtrees,
24 subtreeplot), and to return the graphical coordinates of tree
27 o The new functions corPagel and corBlomberg implement the Pagel's
28 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
30 o chronopl() has been improved and gains several options: see its
31 help page for details.
33 o boot.phylo() has now an option 'trees' to possibly return the
34 bootstraped trees (the default is FALSE).
36 o prop.part() has been improved and should now be faster in all
42 o read.dna() failed if "?" occurred in the first 10 sites of the
45 o The x/y aspect of the plot is now respected when plotting a
46 circular tree (type = "r" or "f").
48 o Drawing the tip labels sometimes failed when plotting circular
51 o zoom() failed when tip labels were used instead of their numbers
52 (thanks to Yan Wong for the fix).
54 o drop.tip() failed with some trees (fixed by Yan Wong).
56 o seg.sites() failed with a list.
58 o consensus() failed in some cases. The function has been improved
59 as well and is faster.
63 CHANGES IN APE VERSION 2.1-3
68 o A bug in read.nexus() made the Windows R-GUI crash.
70 o An error was fixed in the computation of ancestral character
71 states by generalized least squares in ace().
73 o di2multi() did not modify node labels correctly.
75 o multi2di() failed if the tree had its attribute "order" set to
80 CHANGES IN APE VERSION 2.1-2
85 o There three new methods for the "multiPhylo" class: str, $,
88 o root() gains the options 'node' and 'resolve.root'
89 (FALSE by default) as well as its code being improved.
91 o mltt.plot() has now an option 'log' used in the same way
92 than in plot.default().
97 o mltt.plot() failed to display the legend with an unnamed
100 o nodelabels() with pies now correcly uses the argument
101 'cex' to draw symbols of different sizes (which has
102 worked already for thermometers).
104 o read.nexus() generally failed to read very big files.
109 o The argument 'family' of compar.gee() can now be a function
110 as well as a character string.
112 o read.tree() and read.nexus() now return an unnamed list if
115 o read.nexus() now returns a modified object of class "multiPhylo"
116 when there is a TRANSLATE block in the NEXUS file: the individual
117 trees have no 'tip.label' vector, but the list has a 'TipLabel'
118 attribute. The new methods '$' and '[[' set these elements
119 correctly when extracting trees.
123 CHANGES IN APE VERSION 2.1-1
128 o The new function rmtree generates lists of random trees.
130 o rcoal() now generates a genuine coalescent tree by default
131 (thanks to Vladimir Minin for the code).
136 o nuc.div() returned an incorrect value with the default
137 pairwise.deletion = FALSE.
142 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
143 have been improved so that they are stabler and faster.
145 o R packages used by ape are now loaded silently; lattice and gee
146 are loaded only when needed.
150 CHANGES IN APE VERSION 2.1
155 o The new function identify.phylo identifies clades on a plotted
156 tree using the mouse.
158 o It is now possible to subset a list of trees (object of class
159 "multiPhylo") with "[" while keeping its class correct.
161 o The new function as.DNAbin.alignment converts DNA sequences
162 stored in the "alignment" format of the package seqinr into
163 an object of class "DNAbin".
165 o The new function weight.taxo2 helps to build similarity matrices
166 given two taxonomic levels (usually called by other functions).
168 o write.tree() can now take a list of trees (class "multiPhylo")
169 as its main argument.
171 o plot.correlogram() and plot.correlogramList() have been
172 improved, and gain several options (see the help page for
173 details). A legend is now plotted by default.
178 o dist.dna() returned some incorrect values with `model = "JC69"'
179 and `pairwise.deletion = TRUE'. This affected only the
180 distances involving sequences with missing values. (Thanks
181 to Bruno Toupance for digging this bug out.)
183 o write.tree() failed with some trees: this is fixed by removing
184 the `multi.line' option (trees are now always printed on a
187 o read.nexus() did not correctly detect trees with multiple root
188 edges (see OTHER CHANGES).
193 o The code of mlphylo() has almost entirely rewritten, and should
194 be much stabler. The options have been also greatly simplified
195 (see ?mlphylo and ?DNAmodel for details).
197 o The internal function nTips has been renamed klastorin_nTips.
199 o The code of is.ultrametric() contained redundancies and has
202 o The code of Moran.I() and of correlogram.formula() have been
205 o read.tree() and read.nexus() now return an error when trying to
206 read a tree with multiple root edges (see BUG FIXES). The
207 correction applied in previous version did not work in all
210 o The class c("multi.tree", "phylo") has been renamed
216 o There is now a vignette in ape: see vignette("MoranI", "ape").
221 o as.matching() and as.phylo.matching() do not support branch
224 o correlogram.phylo() and discrete.dist() have been removed.
228 CHANGES IN APE VERSION 2.0-2
233 o The new function matexpo computes the exponential of a square
236 o The new function unique.multi.tree removes duplicate trees from
239 o yule() has a new option `use.root.edge = FALSE' that specifies
240 to ignore, by default, the root edge of the tree if it exists.
245 o which.edge() failed when the index of a single terminal edge was
248 o In diversi.time(), the values returned for model C were
251 o A bug was fixed in yule() that affected the calculation of the
252 likelihood in the presence of ties in the branching times.
254 o There was a bug in the C function mat_expo4x4 affecting the
255 calculations of the transition probabilities for models HKY and
258 o A small bug was fixed in as.matrix.DNAbin (thanks to James
261 o rtree() did not `shuffle' the tip labels by default, so only a
262 limited number of labelled topologies could be generated.
266 CHANGES IN APE VERSION 2.0-1
271 o The three new functions bionj, fastme.ols, and fastme.bal
272 perform phylogeny estimation by the BIONJ and fastME methods in
273 OLS and balanced versions. This is a port to R of previous
274 previous programs done by Vincent Lefort.
276 o The new function chronoMPL performs molecular dating with the
277 mean path lengths method of Britton et al. (2002, Mol. Phyl.
280 o The new function rotate, contributed by Christoph Heibl, swaps
281 two clades connected to the same node. It works also with
282 multichotomous nodes.
284 o The new `method' as.matrix.DNAbin() may be used to convert
285 easily DNA sequences stored in a list into a matrix while
286 keeping the names and the class.
291 o chronopl() failed when some branch lengths were equal to zero:
292 an error message is now returned.
294 o di2multi() failed when there was a series of consecutive edges
299 CHANGES IN APE VERSION 1.10-2
304 o plot.phylo() can now plot circular trees: the option is type =
305 "fan" or type = "f" (to avoid the ambiguity with type = "c").
307 o prop.part() has a new option `check.labels = FALSE' which allows
308 to considerably speed-up the calculations of bipartitions. As a
309 consequence, calculations of bootstrap values with boot.phylo()
310 should be much faster.
315 o read.GenBank() did not return correctly the list of species as
316 from ape 1.10: this is fixed in this version
318 o Applying as.phylo() on a tree of class "phylo" failed: the
319 object is now returned unchanged.
323 CHANGES IN APE VERSION 1.10-1
328 o The three new functions Ntip, Nnode, and Nedge return, for a
329 given tree, the number of tips, nodes, or edges, respectively.
334 o read.nexus() did not set correctly the class of the returned
335 object when reading multiple trees.
337 o mllt.plot() failed with objects of class c("multi.tree",
340 o unroot() did not work correctly in most cases.
342 o reorder.phylo() made R freeze in some occasions.
344 o Plotting a tree in pruningwise order failed.
346 o When plotting an unrooted tree, the tip labels where not all
347 correctly positioned if the option `cex' was used.
351 CHANGES IN APE VERSION 1.10
356 o Five new `method' functions have been introduced to manipulate
357 DNA sequences in binary format (see below).
359 o Three new functions have been introduced to convert between the
360 new binary and the character formats.
362 o The new function as.alignment converts DNA sequences stored as
363 single characters into the class "alignment" used by the package
366 o read.dna() and read.GenBank() have a new argument `as.character'
367 controlling whether the sequences are returned in binary format
373 o root() failed when the tree had node labels: this is fixed.
375 o plot.phylo() did not correctly set the limits on the y-axis with
376 the default setting: this is fixed.
378 o dist.dna() returned a wrong result for the LogDet, paralinear,
379 and BH87 models with `pairwise.deletion = TRUE'.
384 o DNA sequences are now internally stored in a binary format. See
385 the document "A Bit-Level Coding Scheme for Nucleotides" for the
386 details. Most functions analyzing DNA functions have been
387 modified accordingly and are now much faster (dist.dna is now
388 ca. 60 times faster).
392 CHANGES IN APE VERSION 1.9-4
397 o A bug was fixed in edgelabels().
399 o as.phylo.hclust() did not work correctly when the object of
400 class "hclust" has its labels set to NULL: the returned tree has
401 now its tip labels set to "1", "2", ...
403 o consensus could fail if some tip labels are a subset of others
404 (e.g., "a" and "a_1"): this is now fixed.
406 o mlphylo() failed in most cases if some branch lengths of the
407 initial tree were greater than one: an error message is now
410 o mlphylo() failed in most cases when estimating the proportion of
411 invariants: this is fixed.
415 CHANGES IN APE VERSION 1.9-3
420 o The new function edgelabels adds labels on the edge of the tree
421 in the same way than nodelabels or tiplabels.
426 o multi2di() did not handle correctly branch lengths with the
427 default option `random = TRUE': this is now fixed.
429 o A bug was fixed in nuc.div() when using pairwise deletions.
431 o A bug occurred in the analysis of bipartitions with large
432 numbers of large trees, with consequences on prop.part,
433 prop.clades, and boot.phylo.
435 o The calculation of the Billera-Holmes-Vogtmann distance in
436 dist.topo was wrong: this has been fixed.
440 CHANGES IN APE VERSION 1.9-2
445 o The new function ladderize reorganizes the internal structure of
446 a tree to plot them left- or right-ladderized.
448 o The new function dist.nodes computes the patristic distances
449 between all nodes, internal and terminal, of a tree. It replaces
450 the option `full = TRUE' of cophenetic.phylo (see below).
455 o A bug was fixed in old2new.phylo().
457 o Some bugs were fixed in chronopl().
459 o The edge colours were not correctly displayed by plot.phylo
460 (thank you to Li-San Wang for the fix).
462 o cophenetic.phylo() failed with multichotomous trees: this is
468 o read.dna() now returns the sequences in a matrix if they are
469 aligned (interleaved or sequential format). Sequences in FASTA
470 format are still returned in a list.
472 o The option `full' of cophenetic.phylo() has been removed because
473 it could not be used from the generic.
478 o rotate() has been removed; this function did not work correctly
483 CHANGES IN APE VERSION 1.9-1
488 o Trees with a single tip were not read correctly in R as the
489 element `Nnode' was not set: this is fixed.
491 o unroot() did not set correctly the number of nodes of the
492 unrooted tree in most cases.
494 o read.GenBank() failed when fetching very long sequences,
495 particularly of the BX-series.
497 o A bug was introduced in read.tree() with ape 1.9: it has been
502 CHANGES IN APE VERSION 1.9
507 o There are two new print `methods' for trees of class "phylo" and
508 lists of trees of class "multi.tree", so that they are now
509 displayed in a compact and informative way.
511 o There are two new functions, old2new.phylo and new2old.phylo,
512 for converting between the old and new coding of the class
515 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
516 LogDet ("logdet"), and paralinear ("paralin").
518 o compute.brlen() has been extended: several methods are now
519 available to compute branch lengths.
521 o write.dna() can now handle matrices as well as lists.
526 o cophenetic.phylo() sometimes returned a wrong result with
527 multichotomous trees: this is fixed.
529 o rotate() failed when a single tip was specified: the tree is now
532 o ace() did not return the correct index matrix with custom
533 models: this is fixed.
535 o multi2di() did not work correctly when resolving multichotomies
536 randomly: the topology was always the same, only the arrangement
537 of clades was randomized: this is fixed. This function now
538 accepts trees with no branch lengths.
540 o The output of diversi.gof() was blurred by useless prints when a
541 user distribution was specified. This has been corrected, and
542 the help page of this function has been expanded.
547 o The internal structure of the class "phylo" has been changed:
548 see the document "Definition of Formats for Coding Phylogenetic
549 Trees in R" for the details. In addition, the code of most
550 functions has been improved.
552 o Several functions have been improved by replacing some R codes
553 by C codes: pic, plot.phylo, and reorder.phylo.
555 o There is now a citation information: see citation("ape") in R.
557 o write.tree() now does not add extra 0's to branch lengths so
558 that 1.23 is printed "1.23" by default, not "1.2300000000".
560 o The syntax of bind.tree() has been simplified. This function now
561 accepts trees with no branch lengths, and handles correctly node
564 o The option `as.numeric' of mrca() has been removed.
566 o The unused options `format' and `rooted' of read.tree() have
569 o The unused option `format' of write.tree() has been removed.
571 o The use of node.depth() has been simplified.
575 CHANGES IN APE VERSION 1.8-5
580 o Two new functions read.nexus.data() and write.nexus.data(),
581 contributed by Johan Nylander, allow to read and write molecular
582 sequences in NEXUS files.
584 o The new function reorder.phylo() reorders the internal structure
585 of a tree of class "phylo". It is used as the generic, e.g.,
588 o read.tree() and read.nexus() can now read trees with a single
591 o The new data set `cynipids' supplies a set of protein sequences
597 o The code of all.equal.phylo() has been completely rewritten
598 (thanks to Benoît Durand) which fixes several bugs.
600 o read.tree() and read.nexus() now checks the labels of the tree
601 to remove or substitute any characters that are illegal in the
602 Newick format (parentheses, etc.)
604 o A negative P-value could be returned by mantel.test(): this is
609 CHANGES IN APE VERSION 1.8-4
614 o The new function sh.test() computes the Shimodaira-
617 o The new function collapse.singles() removes the nodes with a
618 single descendant from a tree.
620 o plot.phylo() has a new argument `tip.color' to specify the
623 o mlphylo() has now an option `quiet' to control the display of
624 the progress of the analysis (the default is FALSE).
629 o read.dna() did not read correctly sequences in sequential format
630 with leading alignment gaps "-": this is fixed.
632 o ace() returned a list with no class so that the generic
633 functions (anova, logLik, ...) could not be used directly. This
634 is fixed as ace() now returns an object of class "ace".
636 o anova.ace() had a small bug when computing the number of degrees
637 of freedom: this is fixed.
639 o mlphylo() did not work when the sequences were in a matrix or
640 a data frame: this is fixed.
642 o rtree() did not work correctly when trying to simulate an
643 unrooted tree with two tips: an error message is now issued.
648 o The algorithm of rtree() has been changed: it is now about 40,
649 100, and 130 times faster for 10, 100, and 1000 tips,
654 CHANGES IN APE VERSION 1.8-3
659 o There are four new `method' functions to be used with the
660 results of ace(): logLik(), deviance(), AIC(), and anova().
662 o The plot method of phymltest has two new arguments: `main' to
663 change the title, and `col' to control the colour of the
664 segments showing the AIC values.
666 o ace() has a new argument `ip' that gives the initial values used
667 in the ML estimation with discrete characters (see the examples
668 in ?ace). This function now returns a matrix giving the indices
669 of the estimated rates when analysing discrete characters.
671 o nodelabels() and tiplabels() have a new argument `pie' to
672 represent proportions, with any number of categories, as
673 piecharts. The use of the option `thermo' has been improved:
674 there is now no limitation on the number of categories.
679 o mlphylo() did not work with more than two partitions: this is
682 o root() failed if the proposed outgroup was already an outgroup
683 in the tree: this is fixed.
685 o The `col' argument in nodelabels() and tiplabels() was not
686 correctly passed when `text' was used: this is fixed.
688 o Two bugs were fixed in mlphylo(): parameters were not always
689 correctly output, and the estimation failed in some cases.
691 o plot.phylo() was stuck when given a tree with a single tip: this
692 is fixed and a message error is now returned.
694 o An error was corrected in the help page of gammaStat regarding
695 the calculation of P-values.
697 o Using gls() could crash R when the number of species in the tree
698 and in the variables were different: this is fixed.
702 CHANGES IN APE VERSION 1.8-2
707 o The new function mlphylo() fits a phylogenetic tree by maximum
708 likelihood from DNA sequences. Its companion function DNAmodel()
709 is used to define the substitution model which may include
710 partitioning. There are methods for logLik(), deviance(), and
711 AIC(), and the summary() method has been extended to display in
712 a friendly way the results of this model fitting. Currently, the
713 functionality is limited to estimating the substitution and
714 associated parameters and computing the likelihood.
716 o The new function drop1.compar.gee (used as, e.g., drop1(m))
717 tests for single effects in GEE-based comparative method. A
718 warning message is printed if there is not enough degrees of
724 o An error message was sometimes issued by plot.multi.tree(),
725 though with no consequence.
729 CHANGES IN APE VERSION 1.8-1
734 o There is a new plot method for lists of trees (objects of class
735 "multi.tree"): it calls plot.phylo() internally and is
736 documented on the same help page.
741 o A bug was fixed in the C code that analyzes bipartitions: this
742 has impact on several functions like prop.part, prop.clades,
743 boot.phylo, or consensus.
745 o root() did not work correctly when the specified outgroup had
746 more than one element: this is fixed.
748 o dist.dna() sometimes returned a warning inappropriately: this
751 o If the distance object given to nj() had no rownames, nj()
752 returned a tree with no tip labels: it now returns tips labelled
753 "1", "2", ..., corresponding to the row numbers.
758 o nj() has been slightly changed so that tips with a zero distance
759 are first aggregated with zero-lengthed branches; the usual NJ
760 procedure is then performed on a distance matrix without 0's.
764 CHANGES IN APE VERSION 1.8
769 o The new function chronopl() estimates dates using the penalized
770 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
772 o The new function consensus() calculates the consensus tree of a
775 o The new function evolve.phylo() simulates the evolution of
776 continuous characters along a phylogeny under a Brownian model.
778 o The new plot method for objects of class "ancestral" displays a
779 tree together with ancestral values, as returned by the above
782 o The new function as.phylo.formula() returns a phylogeny from a
783 set of nested taxonomic variables given as a formula.
785 o The new function read.caic() reads trees in CAIC format.
787 o The new function tiplabels() allows to add labels to the tips
788 of a tree using text or plotting symbols in a flexible way.
790 o The new function unroot() unroots a phylogeny.
792 o multi2di() has a new option, `random', which specifies whether
793 to resolve the multichotomies randomly (the default) or not.
795 o prop.part() now returns an object of class "prop.part" for which
796 there are print (to display a partition in a more friendly way)
797 and summary (to extract the numbers) methods.
799 o plot.phylo() has a new option, `show.tip.label', specifying
800 whether to print the labels of the tips. The default is TRUE.
802 o The code of nj() has been replaced by a faster C code: it is now
803 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
806 o write.nexus() now writes whether a tree is rooted or not.
811 o Two bugs have been fixed in root(): unrooted trees are now
812 handled corretly, and node labels are now output normally.
814 o A bug was fixed in phymltest(): the executable couldn't be found
817 o Three bug have been fixed in ace(): computing the likelihood of
818 ancestral states of discrete characters failed, custom models
819 did not work, and the function failed with a null gradient (a
820 warning message is now returned; this latter bug was also
821 present in yule.cov() as well and is now fixed).
823 o pic() hanged out when missing data were present: a message error
826 o A small bug was fixed in dist.dna() where the gamma correction
827 was not always correctly dispatched.
829 o plot.phylo() plotted correctly the root edge only when the tree
830 was plotted rightwards: this works now for all directions.
835 o dist.taxo() has been renamed as weight.taxo().
837 o Various error and warning messages have been improved.
841 CHANGES IN APE VERSION 1.7
844 o The new function ace() estimates ancestral character states for
845 continuous characters (with ML, GLS, and contrasts methods), and
846 discrete characters (with ML only) for any number of states.
848 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
849 of directional evolution for continuous characters. The user
850 specifies the node(s) of the tree where the character optimum
853 o The new function is.rooted() tests whether a tree (of class
856 o The new function rcoal() generates random ultrametric trees with
857 the possibility to specify the function that generates the
858 inter-nodes distances.
860 o The new function mrca() gives for all pairs of tips in a tree
861 (and optionally nodes too) the most recent common ancestor.
863 o nodelabels() has a new option `thermo' to plot proportions (up
864 to three classes) on the nodes of a tree.
866 o rtree() has been improved: it can now generate rooted or
867 unrooted trees, and the mathematical function that generates the
868 branch lengths may be specified by the user. The tip labels may
869 be given directly in the call to rtree. The limit cases (n = 2,
870 3) are now handled correctly.
872 o dist.topo() has a new argument `method' with two choices: "PH85"
873 for Penny and Henny's method (already available before and now
874 the default), and "BHV01" for the geometric distance by Billera
875 et al. (2001, Adv. Appl. Math. 27:733).
877 o write.tree() has a new option, `digits', which specifies the
878 number of digits to be printed in the Newick tree. By default
879 digits = 10. The numbers are now always printed in decimal form
880 (i.e., 1.0e-1 is now avoided).
882 o dist.dna() can now compute the raw distances between pairs of
883 DNA sequences by specifying model = "raw".
885 o dist.phylo() has a new option `full' to possibly compute the
886 distances among all tips and nodes of the tree. The default if
892 o Several bugs were fixed in all.equal.phylo().
894 o dist.dna() did not handle correctly gaps ("-") in alignments:
895 they are now considered as missing data.
897 o rotate() did not work if the tips were not ordered: this is
900 o mantel.test() returned NA in some special cases: this is fixed
901 and the function has been improved and is now faster.
903 o A bug was fixed in diversi.gof() where the calculation of A² was
906 o cherry() did not work correctly under some OSs (mainly Linux):
909 o is.binary.tree() has been modified so that it works with both
910 rooted and unrooted trees.
912 o The documentation of theta.s() was not correct: this has been
915 o plot.mst() did not work correctly: this is fixed.
919 CHANGES IN APE VERSION 1.6
924 o The new function dist.topo() computes the topological distances
927 o The new function boot.phylo() performs a bootstrap analysis on
928 phylogeny estimation.
930 o The new functions prop.part() and prop.clades() analyse
931 bipartitions from a series of trees.
936 o read.GenBank() now uses the EFetch utility of NCBI instead of
937 the usual Web interface: it is now much faster (e.g., 12 times
938 faster to retrieve 8 sequences, 37 times for 60 sequences).
943 o Several bugs were fixed in read.dna().
945 o Several bugs were fixed in diversi.time().
947 o is.binary.tree() did not work correctly if the tree has no edge
948 lengths: this is fixed.
950 o drop.tip() did not correctly propagated the `node.label' of a
955 CHANGES IN APE VERSION 1.5
960 o Two new functions, as.matching.phylo() and as.phylo.matching(),
961 convert objects between the classes "phylo" and "matching". The
962 latter implements the representation of binary trees introduced by
963 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
964 as.matching() has been introduced as well.
966 o Two new functions, multi2di() and di2multi(), allow to resolve
967 and collapse multichotomies with branches of length zero.
969 o The new function nuc.div() computes the nucleotide diversity
970 from a sample a DNA sequences.
972 o dist.dna() has been completely rewritten with a much faster
973 (particularly for large data sets) C code. Eight models are
974 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
975 option `method' has been renamed `model'). Computation of variance
976 is available for all models. A gamma-correction is possible for
977 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
978 to remove sites with missing data on a pairwise basis. The option
979 `GCcontent' has been removed.
981 o read.GenBank() has a new option (species.names) which specifies
982 whether to return the species names of the organisms in addition
983 to the accession numbers of the sequences (this is the default
986 o write.nexus() can now write several trees in the same NEXUS file.
988 o drop.tip() has a new option `root.edge' that allows to specify the
989 new root edge if internal branches are trimmed.
994 o as.phylo.hclust() failed if some labels had parentheses: this
997 o Several bugs were fixed in all.equal.phylo(). This function now
998 returns the logical TRUE if the trees are identical but with
999 different representations (a report was printed previously).
1001 o read.GenBank() did not correctly handle ambiguous base codes:
1007 o birthdeath() now returns an object of class "birthdeath" for
1008 which there is a print method.
1012 CHANGES IN APE VERSION 1.4
1017 o The new function nj() performs phylogeny estimation with the
1018 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1021 o The new function which.edge() identifies the edges of a tree
1022 that belong to a group specified as a set of tips.
1024 o The new function as.phylo.phylog() converts an object of class
1025 "phylog" (from the package ade4) into an object of class
1028 o The new function axisPhylo() draws axes on the side of a
1031 o The new function howmanytrees() calculates the number of trees
1032 in different cases and giving a number of tips.
1034 o write.tree() has a new option `multi.line' (TRUE by default) to
1035 write a Newick tree on several lines rather than on a single
1038 o The functionalities of zoom() have been extended. Several
1039 subtrees can be visualized at the same time, and they are marked
1040 on the main tree with colors. The context of the subtrees can be
1041 marked with the option `subtree' (see below).
1043 o drop.tip() has a new option `subtree' (FALSE by default) which
1044 specifies whether to output in the tree how many tips have been
1047 o The arguments of add.scale.bar() have been redefined and have
1048 now default values (see ?add.scale.bar for details). This
1049 function now works even if the plotted tree has no edge length.
1051 o plot.phylo() can now plot radial trees, but this does not take
1052 edge lengths into account.
1054 o In plot.phylo() with `type = "phylogram"', if the values of
1055 `edge.color' and `edge.width' are identical for sister-branches,
1056 they are propagated to the vertical line that link them.
1061 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1062 crashing. This is fixed.
1064 o In plot.phylo(), the options `edge.color' and `edge.width' are
1065 now properly recycled; their default values are now "black" and
1068 o A bug has been fixed in write.nexus().
1073 o The function node.depth.edgelength() has been removed and
1074 replaced by a C code.
1078 CHANGES IN APE VERSION 1.3-1
1083 o The new function nodelabels() allows to add labels to the nodes
1084 of a tree using text or plotting symbols in a flexible way.
1086 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1087 numeric values specifying the lower and upper limits on the x-
1088 and y-axes. This allows to leave some space on any side of the
1089 tree. If a single value is given, this is taken as the upper
1094 CHANGES IN APE VERSION 1.3
1099 o The new function phymltest() calls the software PHYML and fits
1100 28 models of DNA sequence evolution. There are a print method to
1101 display likelihood and AIC values, a summary method to compute
1102 the hierarchical likelihood ratio tests, and a plot method to
1103 display graphically the AIC values of each model.
1105 o The new function yule.cov() fits the Yule model with covariates,
1106 a model where the speciation rate is affected by several species
1107 traits through a generalized linear model. The parameters are
1108 estimated by maximum likelihood.
1110 o Three new functions, corBrownian(), corGrafen(), and
1111 corMartins(), compute the expected correlation structures among
1112 species given a phylogeny under different models of evolution.
1113 These can be used for GLS comparative phylogenetic methods (see
1114 the examples). There are coef() and corMatrix() methods and an
1115 Initialize.corPhyl() function associated.
1117 o The new function compar.cheverud() implements Cheverud et al.'s
1118 (1985; Evolution 39:1335) phylogenetic comparative method.
1120 o The new function varcomp() estimates variance components; it has
1123 o Two new functions, panel.superpose.correlogram() and
1124 plot.correlogramList(), allow to plot several phylogenetic
1127 o The new function node.leafnumber() computes the number of leaves
1128 of a subtree defined by a particular node.
1130 o The new function node.sons() gets all tags of son nodes from a
1133 o The new function compute.brlen() computes the branch lengths of
1134 a tree according to a specified method.
1136 o plot.phylo() has three new options: "cex" controls the size of
1137 the (tip and node) labels (thus it is no more needed to change
1138 the global graphical parameter), "direction" which allows to
1139 plot the tree rightwards, leftwards, upwards, or downwards, and
1140 "y.lim" which sets the upper limit on the y-axis.
1145 o Some functions which try to match tip labels and names of
1146 additional data (e.g. vector) are likely to fail if there are
1147 typing or syntax errors. If both series of names do not perfectly
1148 match, they are ignored and a warning message is now issued.
1149 These functions are bd.ext, compar.gee, pic. Their help pages
1150 have been clarified on this point.
1154 CHANGES IN APE VERSION 1.2-7
1159 o The new function root() reroots a phylogenetic tree with respect
1160 to a specified outgroup.
1162 o The new function rotate() rotates an internal branch of a tree.
1164 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1165 trees) controls the display of the tip labels in unrooted trees.
1166 This display has been greatly improved: the tip labels are now not
1167 expected to overlap with the tree (particularly if lab4ut =
1168 "axial"). In all cases, combining appropriate values of "lab4ut"
1169 and the font size (via "par(cex = )") should result in readable
1170 unrooted trees. See ?plot.phylo for some examples.
1172 o In drop.tip(), the argument `tip' can now be numeric or character.
1177 o drop.tip() did not work correctly with trees with no branch
1178 lengths: this is fixed.
1180 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1181 plotted with some line crossings: this is now fixed.
1185 CHANGES IN APE VERSION 1.2-6
1190 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1191 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1192 to implement comparative methods with an autocorrelation approach.
1194 o A new data set describing some life history traits of Carnivores
1200 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1205 o When plotting a tree with plot.phylo(), the new default of the
1206 option `label.offset' is now 0, so the labels are always visible.
1210 CHANGES IN APE VERSION 1.2-5
1215 o The new function bd.ext() fits a birth-death model with combined
1216 phylogenetic and taxonomic data, and estimates the corresponding
1217 speciation and extinction rates.
1222 o The package gee is no more required by ape but only suggested
1223 since only the function compar.gee() calls gee.
1227 CHANGES IN APE VERSION 1.2-4
1232 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1233 and lines.popsize) implementing a new approach for inferring the
1234 demographic history from genealogies using a reversible jump
1235 MCMC have been introduced.
1237 o The unit of time in the skyline plot and in the new plots can
1238 now be chosen to be actual years, rather than substitutions.
1242 CHANGES IN APE VERSION 1.2-3
1247 o The new function rtree() generates a random binary tree with or
1248 without branch lengths.
1250 o Two new functions for drawing lineages-through-time (LTT) plots
1251 are provided: ltt.lines() adds a LTT curve to an existing plot,
1252 and mltt.plot() does a multiple LTT plot giving several trees as
1253 arguments (see `?ltt.plot' for details).
1258 o Some taxon names made R crashing when calling as.phylo.hclust():
1261 o dist.dna() returned an error with two identical DNA sequences
1262 (only using the Jukes-Cantor method returned 0): this is fixed.
1267 o The function dist.phylo() has been re-written using a different
1268 algorithm: it is now about four times faster.
1270 o The code of branching.times() has been improved: it is now about
1275 CHANGES IN APE VERSION 1.2-2
1280 o The new function seg.sites() finds the segregating sites in a
1281 sample of DNA sequences.
1286 o A bug introduced in read.tree() and in read.nexus() with version
1289 o A few errors were corrected and a few examples were added in the
1294 CHANGES IN APE VERSION 1.2-1
1299 o plot.phylo() can now draw the edge of the root of a tree if it
1300 has one (see the new option `root.edge', its default is FALSE).
1305 o A bug was fixed in read.nexus(): files with semicolons inside
1306 comment blocks were not read correctly.
1308 o The behaviour of read.tree() and read.nexus() was corrected so
1309 that tree files with badly represented root edges (e.g., with
1310 an extra pair of parentheses, see the help pages for details)
1311 are now correctly represented in the object of class "phylo";
1312 a warning message is now issued.
1316 CHANGES IN APE VERSION 1.2
1321 o plot.phylo() has been completely re-written and offers several
1322 new functionalities. Three types of trees can now be drawn:
1323 phylogram (as previously), cladogram, and unrooted tree; in
1324 all three types the branch lengths can be drawn using the edge
1325 lengths of the phylogeny or not (e.g., if the latter is absent).
1326 The vertical position of the nodes can be adjusted with two
1327 choices (see option `node.pos'). The code has been re-structured,
1328 and two new functions (potentially useful for developpers) are
1329 documented separately: node.depth.edgelength() and node.depth();
1330 see the respective help pages for details.
1332 o The new function zoom() allows to explore very large trees by
1333 focusing on a small portion of it.
1335 o The new function yule() fits by maximum likelihood the Yule model
1336 (birth-only process) to a phylogenetic tree.
1338 o Support for writing DNA sequences in FASTA format has been
1339 introduced in write.dna() (support for reading sequences in
1340 this format was introduced in read.dna() in version 1.1-2).
1341 The function has been completely re-written, fixing some bugs
1342 (see below); the default behaviour is no more to display the
1343 sequences on the standard output. Several options have been
1344 introduced to control the sequence printing in a flexible
1345 way. The help page has been extended.
1347 o A new data set is included: a supertree of bats in NEXUS format.
1352 o In theta.s(), the default of the option `variance' has
1353 been changed to `FALSE' (as was indicated in the help page).
1355 o Several bugs were fixed in the code of all.equal.phylo().
1357 o Several bugs were fixed in write.dna(), particularly this
1358 function did not work with `format = "interleaved"'.
1360 o Various errors were corrected in the help pages.
1365 o The argument names of as.hclust.phylo() have been changed
1366 from "(phy)" to "(x, ...)" to conform to the definition of
1367 the corresponding generic function.
1369 o gamma.stat() has been renamed gammaStat() to avoid confusion
1370 since gamma() is a generic function.
1374 CHANGES IN APE VERSION 1.1-3
1379 o base.freq() previously did not return a value of 0 for
1380 bases absent in the data (e.g., a vector of length 3 was
1381 returned if one base was absent). This is now fixed (a
1382 vector of length 4 is always returned).
1384 o Several bugs were fixed in read.nexus(), including that this
1385 function did not work in this absence of a "TRANSLATE"
1386 command in the NEXUS file, and that the commands were
1391 CHANGES IN APE VERSION 1.1-2
1396 o The Tamura and Nei (1993) model of DNA distance is now implemented
1397 in dist.dna(): five models are now available in this function.
1399 o A new data set is included: a set of 15 sequences of the
1400 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1406 o A bug in read.nexus() was fixed.
1408 o read.dna() previously did not work correctly in most cases.
1409 The function has been completely re-written and its help page
1410 has been considerably extended (see ?read.dna for details).
1411 Underscores (_) in taxon names are no more replaced with
1412 spaces (this behaviour was undocumented).
1414 o A bug was fixed in write.dna().
1418 CHANGES IN APE VERSION 1.1-1
1423 o A bug in read.tree() introduced in APE 1.1 was fixed.
1425 o A bug in compar.gee() resulted in an error when trying to fit
1426 a model with `family = "binomial"'. This is now fixed.
1430 CHANGES IN APE VERSION 1.1
1435 o The Klastorin (1982) method as suggested by Misawa and Tajima
1436 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1437 on the basis of phylogenetic trees has been implemented (see
1438 the function klastorin()).
1440 o Functions have been added to convert APE's "phylo" objects in
1441 "hclust" cluster objects and vice versa (see the help page of
1442 as.phylo for details).
1444 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1445 are introduced for the estimation of absolute evolutionary rates
1446 (ratogram) and dated clock-like trees (chronogram) from
1447 phylogenetic trees using the non-parametric rate smoothing approach
1448 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1450 o A summary method is now provided printing a summary information on a
1451 phylogenetic tree with, for instance, `summary(tree)'.
1453 o The behaviour of read.tree() was changed so that all spaces and
1454 tabulations in tree files are now ignored. Consequently, spaces in tip
1455 labels are no more allowed. Another side effect is that read.nexus()
1456 now does not replace the underscores (_) in tip labels with spaces
1457 (this behaviour was undocumented).
1459 o The function plot.phylo() has a new option (`underscore') which
1460 specifies whether the underscores in tip labels should be written on
1461 the plot as such or replaced with spaces (the default).
1463 o The function birthdeath() now computes 95% confidence intervals of
1464 the estimated parameters using profile likelihood.
1466 o Three new data sets are included: a gene tree estimated from 36
1467 landplant rbcL sequences, a gene tree estimated from 32 opsin
1468 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1473 o A bug was fixed in dist.gene() where nothing was returned.
1475 o A bug in plot.mst() was fixed.
1477 o A bug in vcv.phylo() resulted in false correlations when the
1478 option `cor = TRUE' was used (now fixed).
1482 CHANGES IN APE VERSION 1.0
1487 o Two new functions, read.dna() and write.dna(), read/write in a file
1488 DNA sequences in interleaved or in sequential format.
1490 o Two new functions, read.nexus() and write.nexus(), read/write trees
1493 o The new function bind.tree() allows to bind two trees together,
1494 possibly handling root edges to give internal branches.
1496 o The new function drop.tip() removes the tips in a phylogenetic tree,
1497 and trims (or not) the corresponding internal branches.
1499 o The new function is.ultrametric() tests if a tree is ultrametric.
1501 o The function plot.phylo() has more functionalities such as drawing the
1502 branches with different colours and/or different widths, showing the
1503 node labels, controling the position and font of the labels, rotating
1504 the labels, and controling the space around the plot.
1506 o The function read.tree() can now read trees with no branch length,
1507 such as "(a,b),c);". Consequently, the element `edge.length' in
1508 objects of class "phylo" is now optional.
1510 o The function write.tree() has a new default behaviour: if the default
1511 for the option `file' is used (i.e. file = ""), then a variable of
1512 mode character containing the tree in Newick format is returned which
1513 can thus be assigned (e.g., tree <- write.tree(phy)).
1515 o The function read.tree() has a new argument `text' which allows
1516 to read the tree in a variable of mode character.
1518 o A new data set is included: the phylogenetic relationships among
1519 the orders of birds from Sibley and Ahlquist (1990).
1523 CHANGES IN APE VERSION 0.2-1
1528 o Several bugs were fixed in the help pages.
1532 CHANGES IN APE VERSION 0.2
1537 o The function write.tree() writes phylogenetic trees (objects of class
1538 "phylo") in an ASCII file using the Newick parenthetic format.
1540 o The function birthdeath() fits a birth-death model to branching times
1541 by maximum likelihood, and estimates the corresponding speciation and
1544 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1547 o The function is.binary.tree() tests whether a phylogeny is binary.
1549 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1550 as well as some methods are introduced.
1552 o Several functions, including some generics and methods, for computing
1553 skyline plot estimates (classic and generalized) of effective
1554 population size through time are introduced and replace the function
1555 skyline.plot() in version 0.1.
1557 o Two data sets are now included: the phylogenetic relationships among
1558 the families of birds from Sibley and Ahlquist (1990), and an
1559 estimated clock-like phylogeny of HIV sequences sampled in the
1560 Democratic Republic of Congo.
1563 DEPRECATED & DEFUNCT
1565 o The function skyline.plot() in ape 0.1 has been deprecated and
1566 replaced by more elaborate functions (see above).
1571 o Two important bugs were fixed in plot.phylo(): phylogenies with
1572 multichotomies not at the root or not with only terminal branches,
1573 and phylogenies with a single node (i.e. only terminal branches)
1574 did not plot. These trees should be plotted correctly now.
1576 o Several bugs were fixed in diversi.time() in the computation of
1579 o Various errors were corrected in the help pages.
projects / ape.git / blob