1 CHANGES IN APE VERSION 2.1-1
6 o The new function rmtree generates lists of random trees.
8 o rcoal() now generates a genuine coalescent tree by default
9 (thanks to Vladimir Minin for the code).
14 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
15 have been improved so that they are stabler and faster.
17 o R packages used by ape are now loaded silently; lattice and gee
18 are loaded only when needed.
22 CHANGES IN APE VERSION 2.1
27 o The new function identify.phylo identifies clades on a plotted
30 o It is now possible to subset a list of trees (object of class
31 "multiPhylo") with "[" while keeping its class correct.
33 o The new function as.DNAbin.alignment converts DNA sequences
34 stored in the "alignment" format of the package seqinr into
35 an object of class "DNAbin".
37 o The new function weight.taxo2 helps to build similarity matrices
38 given two taxonomic levels (usually called by other functions).
40 o write.tree() can now take a list of trees (class "multiPhylo")
43 o plot.correlogram() and plot.correlogramList() have been
44 improved, and gain several options (see the help page for
45 details). A legend is now plotted by default.
50 o dist.dna() returned some incorrect values with `model = "JC69"'
51 and `pairwise.deletion = TRUE'. This affected only the
52 distances involving sequences with missing values. (Thanks
53 to Bruno Toupance for digging this bug out.)
55 o write.tree() failed with some trees: this is fixed by removing
56 the `multi.line' option (trees are now always printed on a
59 o read.nexus() did not correctly detect trees with multiple root
60 edges (see OTHER CHANGES).
65 o The code of mlphylo() has almost entirely rewritten, and should
66 much stabler now. The options have been also greatly simplified
67 (see ?mlphylo and ?DNAmodel for details).
69 o The internal function nTips has been renamed klastorin_nTips.
71 o The code of is.ultrametric() contained redundancies and has
74 o The code of Moran.I() and of correlogram.formula() have been
77 o read.tree() and read.nexus() now return an error when trying to
78 read a tree with multiple root edges (see BUG FIXES). The
79 correction applied in previous version did not work in all
82 o The class c("multi.tree", "phylo") has been renamed
88 o There is now a vignette in ape: see vignette("MoranI", "ape").
93 o as.matching() and as.phylo.matching() do not support branch
96 o correlogram.phylo() and discrete.dist() have been removed.
100 CHANGES IN APE VERSION 2.0-2
105 o The new function matexpo computes the exponential of a square
108 o The new function unique.multi.tree removes duplicate trees from
111 o yule() has a new option `use.root.edge = FALSE' that specifies
112 to ignore, by default, the root edge of the tree if it exists.
117 o which.edge() failed when the index of a single terminal edge was
120 o In diversi.time(), the values returned for model C were
123 o A bug was fixed in yule() that affected the calculation of the
124 likelihood in the presence of ties in the branching times.
126 o There was a bug in the C function mat_expo4x4 affecting the
127 calculations of the transition probabilities for models HKY and
130 o A small bug was fixed in as.matrix.DNAbin (thanks to James
133 o rtree() did not `shuffle' the tip labels by default, so only a
134 limited number of labelled topologies could be generated.
138 CHANGES IN APE VERSION 2.0-1
143 o The three new functions bionj, fastme.ols, and fastme.bal
144 perform phylogeny estimation by the BIONJ and fastME methods in
145 OLS and balanced versions. This is a port to R of previous
146 previous programs done by Vincent Lefort.
148 o The new function chronoMPL performs molecular dating with the
149 mean path lengths method of Britton et al. (2002, Mol. Phyl.
152 o The new function rotate, contributed by Christoph Heibl, swaps
153 two clades connected to the same node. It works also with
154 multichotomous nodes.
156 o The new `method' as.matrix.DNAbin() may be used to convert
157 easily DNA sequences stored in a list into a matrix while
158 keeping the names and the class.
163 o chronopl() failed when some branch lengths were equal to zero:
164 an error message is now returned.
166 o di2multi() failed when there was a series of consecutive edges
171 CHANGES IN APE VERSION 1.10-2
176 o plot.phylo() can now plot circular trees: the option is type =
177 "fan" or type = "f" (to avoid the ambiguity with type = "c").
179 o prop.part() has a new option `check.labels = FALSE' which allows
180 to considerably speed-up the calculations of bipartitions. As a
181 consequence, calculations of bootstrap values with boot.phylo()
182 should be much faster.
187 o read.GenBank() did not return correctly the list of species as
188 from ape 1.10: this is fixed in this version
190 o Applying as.phylo() on a tree of class "phylo" failed: the
191 object is now returned unchanged.
195 CHANGES IN APE VERSION 1.10-1
200 o The three new functions Ntip, Nnode, and Nedge return, for a
201 given tree, the number of tips, nodes, or edges, respectively.
206 o read.nexus() did not set correctly the class of the returned
207 object when reading multiple trees.
209 o mllt.plot() failed with objects of class c("multi.tree",
212 o unroot() did not work correctly in most cases.
214 o reorder.phylo() made R freeze in some occasions.
216 o Plotting a tree in pruningwise order failed.
218 o When plotting an unrooted tree, the tip labels where not all
219 correctly positioned if the option `cex' was used.
223 CHANGES IN APE VERSION 1.10
228 o Five new `method' functions have been introduced to manipulate
229 DNA sequences in binary format (see below).
231 o Three new functions have been introduced to convert between the
232 new binary and the character formats.
234 o The new function as.alignment converts DNA sequences stored as
235 single characters into the class "alignment" used by the package
238 o read.dna() and read.GenBank() have a new argument `as.character'
239 controlling whether the sequences are returned in binary format
245 o root() failed when the tree had node labels: this is fixed.
247 o plot.phylo() did not correctly set the limits on the y-axis with
248 the default setting: this is fixed.
250 o dist.dna() returned a wrong result for the LogDet, paralinear,
251 and BH87 models with `pairwise.deletion = TRUE'.
256 o DNA sequences are now internally stored in a binary format. See
257 the document "A Bit-Level Coding Scheme for Nucleotides" for the
258 details. Most functions analyzing DNA functions have been
259 modified accordingly and are now much faster (dist.dna is now
260 ca. 60 times faster).
264 CHANGES IN APE VERSION 1.9-4
269 o A bug was fixed in edgelabels().
271 o as.phylo.hclust() did not work correctly when the object of
272 class "hclust" has its labels set to NULL: the returned tree has
273 now its tip labels set to "1", "2", ...
275 o consensus could fail if some tip labels are a subset of others
276 (e.g., "a" and "a_1"): this is now fixed.
278 o mlphylo() failed in most cases if some branch lengths of the
279 initial tree were greater than one: an error message is now
282 o mlphylo() failed in most cases when estimating the proportion of
283 invariants: this is fixed.
287 CHANGES IN APE VERSION 1.9-3
292 o The new function edgelabels adds labels on the edge of the tree
293 in the same way than nodelabels or tiplabels.
298 o multi2di() did not handle correctly branch lengths with the
299 default option `random = TRUE': this is now fixed.
301 o A bug was fixed in nuc.div() when using pairwise deletions.
303 o A bug occurred in the analysis of bipartitions with large
304 numbers of large trees, with consequences on prop.part,
305 prop.clades, and boot.phylo.
307 o The calculation of the Billera-Holmes-Vogtmann distance in
308 dist.topo was wrong: this has been fixed.
312 CHANGES IN APE VERSION 1.9-2
317 o The new function ladderize reorganizes the internal structure of
318 a tree to plot them left- or right-ladderized.
320 o The new function dist.nodes computes the patristic distances
321 between all nodes, internal and terminal, of a tree. It replaces
322 the option `full = TRUE' of cophenetic.phylo (see below).
327 o A bug was fixed in old2new.phylo().
329 o Some bugs were fixed in chronopl().
331 o The edge colours were not correctly displayed by plot.phylo
332 (thank you to Li-San Wang for the fix).
334 o cophenetic.phylo() failed with multichotomous trees: this is
340 o read.dna() now returns the sequences in a matrix if they are
341 aligned (interleaved or sequential format). Sequences in FASTA
342 format are still returned in a list.
344 o The option `full' of cophenetic.phylo() has been removed because
345 it could not be used from the generic.
350 o rotate() has been removed; this function did not work correctly
355 CHANGES IN APE VERSION 1.9-1
360 o Trees with a single tip were not read correctly in R as the
361 element `Nnode' was not set: this is fixed.
363 o unroot() did not set correctly the number of nodes of the
364 unrooted tree in most cases.
366 o read.GenBank() failed when fetching very long sequences,
367 particularly of the BX-series.
369 o A bug was introduced in read.tree() with ape 1.9: it has been
374 CHANGES IN APE VERSION 1.9
379 o There are two new print `methods' for trees of class "phylo" and
380 lists of trees of class "multi.tree", so that they are now
381 displayed in a compact and informative way.
383 o There are two new functions, old2new.phylo and new2old.phylo,
384 for converting between the old and new coding of the class
387 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
388 LogDet ("logdet"), and paralinear ("paralin").
390 o compute.brlen() has been extended: several methods are now
391 available to compute branch lengths.
393 o write.dna() can now handle matrices as well as lists.
398 o cophenetic.phylo() sometimes returned a wrong result with
399 multichotomous trees: this is fixed.
401 o rotate() failed when a single tip was specified: the tree is now
404 o ace() did not return the correct index matrix with custom
405 models: this is fixed.
407 o multi2di() did not work correctly when resolving multichotomies
408 randomly: the topology was always the same, only the arrangement
409 of clades was randomized: this is fixed. This function now
410 accepts trees with no branch lengths.
412 o The output of diversi.gof() was blurred by useless prints when a
413 user distribution was specified. This has been corrected, and
414 the help page of this function has been expanded.
419 o The internal structure of the class "phylo" has been changed:
420 see the document "Definition of Formats for Coding Phylogenetic
421 Trees in R" for the details. In addition, the code of most
422 functions has been improved.
424 o Several functions have been improved by replacing some R codes
425 by C codes: pic, plot.phylo, and reorder.phylo.
427 o There is now a citation information: see citation("ape") in R.
429 o write.tree() now does not add extra 0's to branch lengths so
430 that 1.23 is printed "1.23" by default, not "1.2300000000".
432 o The syntax of bind.tree() has been simplified. This function now
433 accepts trees with no branch lengths, and handles correctly node
436 o The option `as.numeric' of mrca() has been removed.
438 o The unused options `format' and `rooted' of read.tree() have
441 o The unused option `format' of write.tree() has been removed.
443 o The use of node.depth() has been simplified.
447 CHANGES IN APE VERSION 1.8-5
452 o Two new functions read.nexus.data() and write.nexus.data(),
453 contributed by Johan Nylander, allow to read and write molecular
454 sequences in NEXUS files.
456 o The new function reorder.phylo() reorders the internal structure
457 of a tree of class "phylo". It is used as the generic, e.g.,
460 o read.tree() and read.nexus() can now read trees with a single
463 o The new data set `cynipids' supplies a set of protein sequences
469 o The code of all.equal.phylo() has been completely rewritten
470 (thanks to Benoît Durand) which fixes several bugs.
472 o read.tree() and read.nexus() now checks the labels of the tree
473 to remove or substitute any characters that are illegal in the
474 Newick format (parentheses, etc.)
476 o A negative P-value could be returned by mantel.test(): this is
481 CHANGES IN APE VERSION 1.8-4
486 o The new function sh.test() computes the Shimodaira-
489 o The new function collapse.singles() removes the nodes with a
490 single descendant from a tree.
492 o plot.phylo() has a new argument `tip.color' to specify the
495 o mlphylo() has now an option `quiet' to control the display of
496 the progress of the analysis (the default is FALSE).
501 o read.dna() did not read correctly sequences in sequential format
502 with leading alignment gaps "-": this is fixed.
504 o ace() returned a list with no class so that the generic
505 functions (anova, logLik, ...) could not be used directly. This
506 is fixed as ace() now returns an object of class "ace".
508 o anova.ace() had a small bug when computing the number of degrees
509 of freedom: this is fixed.
511 o mlphylo() did not work when the sequences were in a matrix or
512 a data frame: this is fixed.
514 o rtree() did not work correctly when trying to simulate an
515 unrooted tree with two tips: an error message is now issued.
520 o The algorithm of rtree() has been changed: it is now about 40,
521 100, and 130 times faster for 10, 100, and 1000 tips,
526 CHANGES IN APE VERSION 1.8-3
531 o There are four new `method' functions to be used with the
532 results of ace(): logLik(), deviance(), AIC(), and anova().
534 o The plot method of phymltest has two new arguments: `main' to
535 change the title, and `col' to control the colour of the
536 segments showing the AIC values.
538 o ace() has a new argument `ip' that gives the initial values used
539 in the ML estimation with discrete characters (see the examples
540 in ?ace). This function now returns a matrix giving the indices
541 of the estimated rates when analysing discrete characters.
543 o nodelabels() and tiplabels() have a new argument `pie' to
544 represent proportions, with any number of categories, as
545 piecharts. The use of the option `thermo' has been improved:
546 there is now no limitation on the number of categories.
551 o mlphylo() did not work with more than two partitions: this is
554 o root() failed if the proposed outgroup was already an outgroup
555 in the tree: this is fixed.
557 o The `col' argument in nodelabels() and tiplabels() was not
558 correctly passed when `text' was used: this is fixed.
560 o Two bugs were fixed in mlphylo(): parameters were not always
561 correctly output, and the estimation failed in some cases.
563 o plot.phylo() was stuck when given a tree with a single tip: this
564 is fixed and a message error is now returned.
566 o An error was corrected in the help page of gammaStat regarding
567 the calculation of P-values.
569 o Using gls() could crash R when the number of species in the tree
570 and in the variables were different: this is fixed.
574 CHANGES IN APE VERSION 1.8-2
579 o The new function mlphylo() fits a phylogenetic tree by maximum
580 likelihood from DNA sequences. Its companion function DNAmodel()
581 is used to define the substitution model which may include
582 partitioning. There are methods for logLik(), deviance(), and
583 AIC(), and the summary() method has been extended to display in
584 a friendly way the results of this model fitting. Currently, the
585 functionality is limited to estimating the substitution and
586 associated parameters and computing the likelihood.
588 o The new function drop1.compar.gee (used as, e.g., drop1(m))
589 tests for single effects in GEE-based comparative method. A
590 warning message is printed if there is not enough degrees of
596 o An error message was sometimes issued by plot.multi.tree(),
597 though with no consequence.
601 CHANGES IN APE VERSION 1.8-1
606 o There is a new plot method for lists of trees (objects of class
607 "multi.tree"): it calls plot.phylo() internally and is
608 documented on the same help page.
613 o A bug was fixed in the C code that analyzes bipartitions: this
614 has impact on several functions like prop.part, prop.clades,
615 boot.phylo, or consensus.
617 o root() did not work correctly when the specified outgroup had
618 more than one element: this is fixed.
620 o dist.dna() sometimes returned a warning inappropriately: this
623 o If the distance object given to nj() had no rownames, nj()
624 returned a tree with no tip labels: it now returns tips labelled
625 "1", "2", ..., corresponding to the row numbers.
630 o nj() has been slightly changed so that tips with a zero distance
631 are first aggregated with zero-lengthed branches; the usual NJ
632 procedure is then performed on a distance matrix without 0's.
636 CHANGES IN APE VERSION 1.8
641 o The new function chronopl() estimates dates using the penalized
642 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
644 o The new function consensus() calculates the consensus tree of a
647 o The new function evolve.phylo() simulates the evolution of
648 continuous characters along a phylogeny under a Brownian model.
650 o The new plot method for objects of class "ancestral" displays a
651 tree together with ancestral values, as returned by the above
654 o The new function as.phylo.formula() returns a phylogeny from a
655 set of nested taxonomic variables given as a formula.
657 o The new function read.caic() reads trees in CAIC format.
659 o The new function tiplabels() allows to add labels to the tips
660 of a tree using text or plotting symbols in a flexible way.
662 o The new function unroot() unroots a phylogeny.
664 o multi2di() has a new option, `random', which specifies whether
665 to resolve the multichotomies randomly (the default) or not.
667 o prop.part() now returns an object of class "prop.part" for which
668 there are print (to display a partition in a more friendly way)
669 and summary (to extract the numbers) methods.
671 o plot.phylo() has a new option, `show.tip.label', specifying
672 whether to print the labels of the tips. The default is TRUE.
674 o The code of nj() has been replaced by a faster C code: it is now
675 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
678 o write.nexus() now writes whether a tree is rooted or not.
683 o Two bugs have been fixed in root(): unrooted trees are now
684 handled corretly, and node labels are now output normally.
686 o A bug was fixed in phymltest(): the executable couldn't be found
689 o Three bug have been fixed in ace(): computing the likelihood of
690 ancestral states of discrete characters failed, custom models
691 did not work, and the function failed with a null gradient (a
692 warning message is now returned; this latter bug was also
693 present in yule.cov() as well and is now fixed).
695 o pic() hanged out when missing data were present: a message error
698 o A small bug was fixed in dist.dna() where the gamma correction
699 was not always correctly dispatched.
701 o plot.phylo() plotted correctly the root edge only when the tree
702 was plotted rightwards: this works now for all directions.
707 o dist.taxo() has been renamed as weight.taxo().
709 o Various error and warning messages have been improved.
713 CHANGES IN APE VERSION 1.7
716 o The new function ace() estimates ancestral character states for
717 continuous characters (with ML, GLS, and contrasts methods), and
718 discrete characters (with ML only) for any number of states.
720 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
721 of directional evolution for continuous characters. The user
722 specifies the node(s) of the tree where the character optimum
725 o The new function is.rooted() tests whether a tree (of class
728 o The new function rcoal() generates random ultrametric trees with
729 the possibility to specify the function that generates the
730 inter-nodes distances.
732 o The new function mrca() gives for all pairs of tips in a tree
733 (and optionally nodes too) the most recent common ancestor.
735 o nodelabels() has a new option `thermo' to plot proportions (up
736 to three classes) on the nodes of a tree.
738 o rtree() has been improved: it can now generate rooted or
739 unrooted trees, and the mathematical function that generates the
740 branch lengths may be specified by the user. The tip labels may
741 be given directly in the call to rtree. The limit cases (n = 2,
742 3) are now handled correctly.
744 o dist.topo() has a new argument `method' with two choices: "PH85"
745 for Penny and Henny's method (already available before and now
746 the default), and "BHV01" for the geometric distance by Billera
747 et al. (2001, Adv. Appl. Math. 27:733).
749 o write.tree() has a new option, `digits', which specifies the
750 number of digits to be printed in the Newick tree. By default
751 digits = 10. The numbers are now always printed in decimal form
752 (i.e., 1.0e-1 is now avoided).
754 o dist.dna() can now compute the raw distances between pairs of
755 DNA sequences by specifying model = "raw".
757 o dist.phylo() has a new option `full' to possibly compute the
758 distances among all tips and nodes of the tree. The default if
764 o Several bugs were fixed in all.equal.phylo().
766 o dist.dna() did not handle correctly gaps ("-") in alignments:
767 they are now considered as missing data.
769 o rotate() did not work if the tips were not ordered: this is
772 o mantel.test() returned NA in some special cases: this is fixed
773 and the function has been improved and is now faster.
775 o A bug was fixed in diversi.gof() where the calculation of A² was
778 o cherry() did not work correctly under some OSs (mainly Linux):
781 o is.binary.tree() has been modified so that it works with both
782 rooted and unrooted trees.
784 o The documentation of theta.s() was not correct: this has been
787 o plot.mst() did not work correctly: this is fixed.
791 CHANGES IN APE VERSION 1.6
796 o The new function dist.topo() computes the topological distances
799 o The new function boot.phylo() performs a bootstrap analysis on
800 phylogeny estimation.
802 o The new functions prop.part() and prop.clades() analyse
803 bipartitions from a series of trees.
808 o read.GenBank() now uses the EFetch utility of NCBI instead of
809 the usual Web interface: it is now much faster (e.g., 12 times
810 faster to retrieve 8 sequences, 37 times for 60 sequences).
815 o Several bugs were fixed in read.dna().
817 o Several bugs were fixed in diversi.time().
819 o is.binary.tree() did not work correctly if the tree has no edge
820 lengths: this is fixed.
822 o drop.tip() did not correctly propagated the `node.label' of a
827 CHANGES IN APE VERSION 1.5
832 o Two new functions, as.matching.phylo() and as.phylo.matching(),
833 convert objects between the classes "phylo" and "matching". The
834 latter implements the representation of binary trees introduced by
835 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
836 as.matching() has been introduced as well.
838 o Two new functions, multi2di() and di2multi(), allow to resolve
839 and collapse multichotomies with branches of length zero.
841 o The new function nuc.div() computes the nucleotide diversity
842 from a sample a DNA sequences.
844 o dist.dna() has been completely rewritten with a much faster
845 (particularly for large data sets) C code. Eight models are
846 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
847 option `method' has been renamed `model'). Computation of variance
848 is available for all models. A gamma-correction is possible for
849 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
850 to remove sites with missing data on a pairwise basis. The option
851 `GCcontent' has been removed.
853 o read.GenBank() has a new option (species.names) which specifies
854 whether to return the species names of the organisms in addition
855 to the accession numbers of the sequences (this is the default
858 o write.nexus() can now write several trees in the same NEXUS file.
860 o drop.tip() has a new option `root.edge' that allows to specify the
861 new root edge if internal branches are trimmed.
866 o as.phylo.hclust() failed if some labels had parentheses: this
869 o Several bugs were fixed in all.equal.phylo(). This function now
870 returns the logical TRUE if the trees are identical but with
871 different representations (a report was printed previously).
873 o read.GenBank() did not correctly handle ambiguous base codes:
879 o birthdeath() now returns an object of class "birthdeath" for
880 which there is a print method.
884 CHANGES IN APE VERSION 1.4
889 o The new function nj() performs phylogeny estimation with the
890 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
893 o The new function which.edge() identifies the edges of a tree
894 that belong to a group specified as a set of tips.
896 o The new function as.phylo.phylog() converts an object of class
897 "phylog" (from the package ade4) into an object of class
900 o The new function axisPhylo() draws axes on the side of a
903 o The new function howmanytrees() calculates the number of trees
904 in different cases and giving a number of tips.
906 o write.tree() has a new option `multi.line' (TRUE by default) to
907 write a Newick tree on several lines rather than on a single
910 o The functionalities of zoom() have been extended. Several
911 subtrees can be visualized at the same time, and they are marked
912 on the main tree with colors. The context of the subtrees can be
913 marked with the option `subtree' (see below).
915 o drop.tip() has a new option `subtree' (FALSE by default) which
916 specifies whether to output in the tree how many tips have been
919 o The arguments of add.scale.bar() have been redefined and have
920 now default values (see ?add.scale.bar for details). This
921 function now works even if the plotted tree has no edge length.
923 o plot.phylo() can now plot radial trees, but this does not take
924 edge lengths into account.
926 o In plot.phylo() with `type = "phylogram"', if the values of
927 `edge.color' and `edge.width' are identical for sister-branches,
928 they are propagated to the vertical line that link them.
933 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
934 crashing. This is fixed.
936 o In plot.phylo(), the options `edge.color' and `edge.width' are
937 now properly recycled; their default values are now "black" and
940 o A bug has been fixed in write.nexus().
945 o The function node.depth.edgelength() has been removed and
946 replaced by a C code.
950 CHANGES IN APE VERSION 1.3-1
955 o The new function nodelabels() allows to add labels to the nodes
956 of a tree using text or plotting symbols in a flexible way.
958 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
959 numeric values specifying the lower and upper limits on the x-
960 and y-axes. This allows to leave some space on any side of the
961 tree. If a single value is given, this is taken as the upper
966 CHANGES IN APE VERSION 1.3
971 o The new function phymltest() calls the software PHYML and fits
972 28 models of DNA sequence evolution. There are a print method to
973 display likelihood and AIC values, a summary method to compute
974 the hierarchical likelihood ratio tests, and a plot method to
975 display graphically the AIC values of each model.
977 o The new function yule.cov() fits the Yule model with covariates,
978 a model where the speciation rate is affected by several species
979 traits through a generalized linear model. The parameters are
980 estimated by maximum likelihood.
982 o Three new functions, corBrownian(), corGrafen(), and
983 corMartins(), compute the expected correlation structures among
984 species given a phylogeny under different models of evolution.
985 These can be used for GLS comparative phylogenetic methods (see
986 the examples). There are coef() and corMatrix() methods and an
987 Initialize.corPhyl() function associated.
989 o The new function compar.cheverud() implements Cheverud et al.'s
990 (1985; Evolution 39:1335) phylogenetic comparative method.
992 o The new function varcomp() estimates variance components; it has
995 o Two new functions, panel.superpose.correlogram() and
996 plot.correlogramList(), allow to plot several phylogenetic
999 o The new function node.leafnumber() computes the number of leaves
1000 of a subtree defined by a particular node.
1002 o The new function node.sons() gets all tags of son nodes from a
1005 o The new function compute.brlen() computes the branch lengths of
1006 a tree according to a specified method.
1008 o plot.phylo() has three new options: "cex" controls the size of
1009 the (tip and node) labels (thus it is no more needed to change
1010 the global graphical parameter), "direction" which allows to
1011 plot the tree rightwards, leftwards, upwards, or downwards, and
1012 "y.lim" which sets the upper limit on the y-axis.
1017 o Some functions which try to match tip labels and names of
1018 additional data (e.g. vector) are likely to fail if there are
1019 typing or syntax errors. If both series of names do not perfectly
1020 match, they are ignored and a warning message is now issued.
1021 These functions are bd.ext, compar.gee, pic. Their help pages
1022 have been clarified on this point.
1026 CHANGES IN APE VERSION 1.2-7
1031 o The new function root() reroots a phylogenetic tree with respect
1032 to a specified outgroup.
1034 o The new function rotate() rotates an internal branch of a tree.
1036 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1037 trees) controls the display of the tip labels in unrooted trees.
1038 This display has been greatly improved: the tip labels are now not
1039 expected to overlap with the tree (particularly if lab4ut =
1040 "axial"). In all cases, combining appropriate values of "lab4ut"
1041 and the font size (via "par(cex = )") should result in readable
1042 unrooted trees. See ?plot.phylo for some examples.
1044 o In drop.tip(), the argument `tip' can now be numeric or character.
1049 o drop.tip() did not work correctly with trees with no branch
1050 lengths: this is fixed.
1052 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1053 plotted with some line crossings: this is now fixed.
1057 CHANGES IN APE VERSION 1.2-6
1062 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1063 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1064 to implement comparative methods with an autocorrelation approach.
1066 o A new data set describing some life history traits of Carnivores
1072 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1077 o When plotting a tree with plot.phylo(), the new default of the
1078 option `label.offset' is now 0, so the labels are always visible.
1082 CHANGES IN APE VERSION 1.2-5
1087 o The new function bd.ext() fits a birth-death model with combined
1088 phylogenetic and taxonomic data, and estimates the corresponding
1089 speciation and extinction rates.
1094 o The package gee is no more required by ape but only suggested
1095 since only the function compar.gee() calls gee.
1099 CHANGES IN APE VERSION 1.2-4
1104 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1105 and lines.popsize) implementing a new approach for inferring the
1106 demographic history from genealogies using a reversible jump
1107 MCMC have been introduced.
1109 o The unit of time in the skyline plot and in the new plots can
1110 now be chosen to be actual years, rather than substitutions.
1114 CHANGES IN APE VERSION 1.2-3
1119 o The new function rtree() generates a random binary tree with or
1120 without branch lengths.
1122 o Two new functions for drawing lineages-through-time (LTT) plots
1123 are provided: ltt.lines() adds a LTT curve to an existing plot,
1124 and mltt.plot() does a multiple LTT plot giving several trees as
1125 arguments (see `?ltt.plot' for details).
1130 o Some taxon names made R crashing when calling as.phylo.hclust():
1133 o dist.dna() returned an error with two identical DNA sequences
1134 (only using the Jukes-Cantor method returned 0): this is fixed.
1139 o The function dist.phylo() has been re-written using a different
1140 algorithm: it is now about four times faster.
1142 o The code of branching.times() has been improved: it is now about
1147 CHANGES IN APE VERSION 1.2-2
1152 o The new function seg.sites() finds the segregating sites in a
1153 sample of DNA sequences.
1158 o A bug introduced in read.tree() and in read.nexus() with version
1161 o A few errors were corrected and a few examples were added in the
1166 CHANGES IN APE VERSION 1.2-1
1171 o plot.phylo() can now draw the edge of the root of a tree if it
1172 has one (see the new option `root.edge', its default is FALSE).
1177 o A bug was fixed in read.nexus(): files with semicolons inside
1178 comment blocks were not read correctly.
1180 o The behaviour of read.tree() and read.nexus() was corrected so
1181 that tree files with badly represented root edges (e.g., with
1182 an extra pair of parentheses, see the help pages for details)
1183 are now correctly represented in the object of class "phylo";
1184 a warning message is now issued.
1188 CHANGES IN APE VERSION 1.2
1193 o plot.phylo() has been completely re-written and offers several
1194 new functionalities. Three types of trees can now be drawn:
1195 phylogram (as previously), cladogram, and unrooted tree; in
1196 all three types the branch lengths can be drawn using the edge
1197 lengths of the phylogeny or not (e.g., if the latter is absent).
1198 The vertical position of the nodes can be adjusted with two
1199 choices (see option `node.pos'). The code has been re-structured,
1200 and two new functions (potentially useful for developpers) are
1201 documented separately: node.depth.edgelength() and node.depth();
1202 see the respective help pages for details.
1204 o The new function zoom() allows to explore very large trees by
1205 focusing on a small portion of it.
1207 o The new function yule() fits by maximum likelihood the Yule model
1208 (birth-only process) to a phylogenetic tree.
1210 o Support for writing DNA sequences in FASTA format has been
1211 introduced in write.dna() (support for reading sequences in
1212 this format was introduced in read.dna() in version 1.1-2).
1213 The function has been completely re-written, fixing some bugs
1214 (see below); the default behaviour is no more to display the
1215 sequences on the standard output. Several options have been
1216 introduced to control the sequence printing in a flexible
1217 way. The help page has been extended.
1219 o A new data set is included: a supertree of bats in NEXUS format.
1224 o In theta.s(), the default of the option `variance' has
1225 been changed to `FALSE' (as was indicated in the help page).
1227 o Several bugs were fixed in the code of all.equal.phylo().
1229 o Several bugs were fixed in write.dna(), particularly this
1230 function did not work with `format = "interleaved"'.
1232 o Various errors were corrected in the help pages.
1237 o The argument names of as.hclust.phylo() have been changed
1238 from "(phy)" to "(x, ...)" to conform to the definition of
1239 the corresponding generic function.
1241 o gamma.stat() has been renamed gammaStat() to avoid confusion
1242 since gamma() is a generic function.
1246 CHANGES IN APE VERSION 1.1-3
1251 o base.freq() previously did not return a value of 0 for
1252 bases absent in the data (e.g., a vector of length 3 was
1253 returned if one base was absent). This is now fixed (a
1254 vector of length 4 is always returned).
1256 o Several bugs were fixed in read.nexus(), including that this
1257 function did not work in this absence of a "TRANSLATE"
1258 command in the NEXUS file, and that the commands were
1263 CHANGES IN APE VERSION 1.1-2
1268 o The Tamura and Nei (1993) model of DNA distance is now implemented
1269 in dist.dna(): five models are now available in this function.
1271 o A new data set is included: a set of 15 sequences of the
1272 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1278 o A bug in read.nexus() was fixed.
1280 o read.dna() previously did not work correctly in most cases.
1281 The function has been completely re-written and its help page
1282 has been considerably extended (see ?read.dna for details).
1283 Underscores (_) in taxon names are no more replaced with
1284 spaces (this behaviour was undocumented).
1286 o A bug was fixed in write.dna().
1290 CHANGES IN APE VERSION 1.1-1
1295 o A bug in read.tree() introduced in APE 1.1 was fixed.
1297 o A bug in compar.gee() resulted in an error when trying to fit
1298 a model with `family = "binomial"'. This is now fixed.
1302 CHANGES IN APE VERSION 1.1
1307 o The Klastorin (1982) method as suggested by Misawa and Tajima
1308 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1309 on the basis of phylogenetic trees has been implemented (see
1310 the function klastorin()).
1312 o Functions have been added to convert APE's "phylo" objects in
1313 "hclust" cluster objects and vice versa (see the help page of
1314 as.phylo for details).
1316 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1317 are introduced for the estimation of absolute evolutionary rates
1318 (ratogram) and dated clock-like trees (chronogram) from
1319 phylogenetic trees using the non-parametric rate smoothing approach
1320 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1322 o A summary method is now provided printing a summary information on a
1323 phylogenetic tree with, for instance, `summary(tree)'.
1325 o The behaviour of read.tree() was changed so that all spaces and
1326 tabulations in tree files are now ignored. Consequently, spaces in tip
1327 labels are no more allowed. Another side effect is that read.nexus()
1328 now does not replace the underscores (_) in tip labels with spaces
1329 (this behaviour was undocumented).
1331 o The function plot.phylo() has a new option (`underscore') which
1332 specifies whether the underscores in tip labels should be written on
1333 the plot as such or replaced with spaces (the default).
1335 o The function birthdeath() now computes 95% confidence intervals of
1336 the estimated parameters using profile likelihood.
1338 o Three new data sets are included: a gene tree estimated from 36
1339 landplant rbcL sequences, a gene tree estimated from 32 opsin
1340 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1345 o A bug was fixed in dist.gene() where nothing was returned.
1347 o A bug in plot.mst() was fixed.
1349 o A bug in vcv.phylo() resulted in false correlations when the
1350 option `cor = TRUE' was used (now fixed).
1354 CHANGES IN APE VERSION 1.0
1359 o Two new functions, read.dna() and write.dna(), read/write in a file
1360 DNA sequences in interleaved or in sequential format.
1362 o Two new functions, read.nexus() and write.nexus(), read/write trees
1365 o The new function bind.tree() allows to bind two trees together,
1366 possibly handling root edges to give internal branches.
1368 o The new function drop.tip() removes the tips in a phylogenetic tree,
1369 and trims (or not) the corresponding internal branches.
1371 o The new function is.ultrametric() tests if a tree is ultrametric.
1373 o The function plot.phylo() has more functionalities such as drawing the
1374 branches with different colours and/or different widths, showing the
1375 node labels, controling the position and font of the labels, rotating
1376 the labels, and controling the space around the plot.
1378 o The function read.tree() can now read trees with no branch length,
1379 such as "(a,b),c);". Consequently, the element `edge.length' in
1380 objects of class "phylo" is now optional.
1382 o The function write.tree() has a new default behaviour: if the default
1383 for the option `file' is used (i.e. file = ""), then a variable of
1384 mode character containing the tree in Newick format is returned which
1385 can thus be assigned (e.g., tree <- write.tree(phy)).
1387 o The function read.tree() has a new argument `text' which allows
1388 to read the tree in a variable of mode character.
1390 o A new data set is included: the phylogenetic relationships among
1391 the orders of birds from Sibley and Ahlquist (1990).
1395 CHANGES IN APE VERSION 0.2-1
1400 o Several bugs were fixed in the help pages.
1404 CHANGES IN APE VERSION 0.2
1409 o The function write.tree() writes phylogenetic trees (objects of class
1410 "phylo") in an ASCII file using the Newick parenthetic format.
1412 o The function birthdeath() fits a birth-death model to branching times
1413 by maximum likelihood, and estimates the corresponding speciation and
1416 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1419 o The function is.binary.tree() tests whether a phylogeny is binary.
1421 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1422 as well as some methods are introduced.
1424 o Several functions, including some generics and methods, for computing
1425 skyline plot estimates (classic and generalized) of effective
1426 population size through time are introduced and replace the function
1427 skyline.plot() in version 0.1.
1429 o Two data sets are now included: the phylogenetic relationships among
1430 the families of birds from Sibley and Ahlquist (1990), and an
1431 estimated clock-like phylogeny of HIV sequences sampled in the
1432 Democratic Republic of Congo.
1435 DEPRECATED & DEFUNCT
1437 o The function skyline.plot() in ape 0.1 has been deprecated and
1438 replaced by more elaborate functions (see above).
1443 o Two important bugs were fixed in plot.phylo(): phylogenies with
1444 multichotomies not at the root or not with only terminal branches,
1445 and phylogenies with a single node (i.e. only terminal branches)
1446 did not plot. These trees should be plotted correctly now.
1448 o Several bugs were fixed in diversi.time() in the computation of
1451 o Various errors were corrected in the help pages.
projects / ape.git / blob