1 CHANGES IN APE VERSION 2.1-3
6 o An error was fixed in the computation of ancestral character
7 states by generalized least squares in ace().
11 CHANGES IN APE VERSION 2.1-2
16 o There three new methods for the "multiPhylo" class: str, $,
19 o root() gains the options 'node' and 'resolve.root'
20 (FALSE by default) as well as its code being improved.
22 o mltt.plot() has now an option 'log' used in the same way
23 than in plot.default().
28 o mltt.plot() failed to display the legend with an unnamed
31 o nodelabels() with pies now correcly uses the argument
32 'cex' to draw symbols of different sizes (which has
33 worked already for thermometers).
35 o read.nexus() generally failed to read very big files.
40 o The argument 'family' of compar.gee() can now be a function
41 as well as a character string.
43 o read.tree() and read.nexus() now return an unnamed list if
46 o read.nexus() now returns a modified object of class "multiPhylo"
47 when there is a TRANSLATE block in the NEXUS file: the individual
48 trees have no 'tip.label' vector, but the list has a 'TipLabel'
49 attribute. The new methods '$' and '[[' set these elements
50 correctly when extracting trees.
54 CHANGES IN APE VERSION 2.1-1
59 o The new function rmtree generates lists of random trees.
61 o rcoal() now generates a genuine coalescent tree by default
62 (thanks to Vladimir Minin for the code).
67 o nuc.div() returned an incorrect value with the default
68 pairwise.deletion = FALSE.
73 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
74 have been improved so that they are stabler and faster.
76 o R packages used by ape are now loaded silently; lattice and gee
77 are loaded only when needed.
81 CHANGES IN APE VERSION 2.1
86 o The new function identify.phylo identifies clades on a plotted
89 o It is now possible to subset a list of trees (object of class
90 "multiPhylo") with "[" while keeping its class correct.
92 o The new function as.DNAbin.alignment converts DNA sequences
93 stored in the "alignment" format of the package seqinr into
94 an object of class "DNAbin".
96 o The new function weight.taxo2 helps to build similarity matrices
97 given two taxonomic levels (usually called by other functions).
99 o write.tree() can now take a list of trees (class "multiPhylo")
100 as its main argument.
102 o plot.correlogram() and plot.correlogramList() have been
103 improved, and gain several options (see the help page for
104 details). A legend is now plotted by default.
109 o dist.dna() returned some incorrect values with `model = "JC69"'
110 and `pairwise.deletion = TRUE'. This affected only the
111 distances involving sequences with missing values. (Thanks
112 to Bruno Toupance for digging this bug out.)
114 o write.tree() failed with some trees: this is fixed by removing
115 the `multi.line' option (trees are now always printed on a
118 o read.nexus() did not correctly detect trees with multiple root
119 edges (see OTHER CHANGES).
124 o The code of mlphylo() has almost entirely rewritten, and should
125 much stabler now. The options have been also greatly simplified
126 (see ?mlphylo and ?DNAmodel for details).
128 o The internal function nTips has been renamed klastorin_nTips.
130 o The code of is.ultrametric() contained redundancies and has
133 o The code of Moran.I() and of correlogram.formula() have been
136 o read.tree() and read.nexus() now return an error when trying to
137 read a tree with multiple root edges (see BUG FIXES). The
138 correction applied in previous version did not work in all
141 o The class c("multi.tree", "phylo") has been renamed
147 o There is now a vignette in ape: see vignette("MoranI", "ape").
152 o as.matching() and as.phylo.matching() do not support branch
155 o correlogram.phylo() and discrete.dist() have been removed.
159 CHANGES IN APE VERSION 2.0-2
164 o The new function matexpo computes the exponential of a square
167 o The new function unique.multi.tree removes duplicate trees from
170 o yule() has a new option `use.root.edge = FALSE' that specifies
171 to ignore, by default, the root edge of the tree if it exists.
176 o which.edge() failed when the index of a single terminal edge was
179 o In diversi.time(), the values returned for model C were
182 o A bug was fixed in yule() that affected the calculation of the
183 likelihood in the presence of ties in the branching times.
185 o There was a bug in the C function mat_expo4x4 affecting the
186 calculations of the transition probabilities for models HKY and
189 o A small bug was fixed in as.matrix.DNAbin (thanks to James
192 o rtree() did not `shuffle' the tip labels by default, so only a
193 limited number of labelled topologies could be generated.
197 CHANGES IN APE VERSION 2.0-1
202 o The three new functions bionj, fastme.ols, and fastme.bal
203 perform phylogeny estimation by the BIONJ and fastME methods in
204 OLS and balanced versions. This is a port to R of previous
205 previous programs done by Vincent Lefort.
207 o The new function chronoMPL performs molecular dating with the
208 mean path lengths method of Britton et al. (2002, Mol. Phyl.
211 o The new function rotate, contributed by Christoph Heibl, swaps
212 two clades connected to the same node. It works also with
213 multichotomous nodes.
215 o The new `method' as.matrix.DNAbin() may be used to convert
216 easily DNA sequences stored in a list into a matrix while
217 keeping the names and the class.
222 o chronopl() failed when some branch lengths were equal to zero:
223 an error message is now returned.
225 o di2multi() failed when there was a series of consecutive edges
230 CHANGES IN APE VERSION 1.10-2
235 o plot.phylo() can now plot circular trees: the option is type =
236 "fan" or type = "f" (to avoid the ambiguity with type = "c").
238 o prop.part() has a new option `check.labels = FALSE' which allows
239 to considerably speed-up the calculations of bipartitions. As a
240 consequence, calculations of bootstrap values with boot.phylo()
241 should be much faster.
246 o read.GenBank() did not return correctly the list of species as
247 from ape 1.10: this is fixed in this version
249 o Applying as.phylo() on a tree of class "phylo" failed: the
250 object is now returned unchanged.
254 CHANGES IN APE VERSION 1.10-1
259 o The three new functions Ntip, Nnode, and Nedge return, for a
260 given tree, the number of tips, nodes, or edges, respectively.
265 o read.nexus() did not set correctly the class of the returned
266 object when reading multiple trees.
268 o mllt.plot() failed with objects of class c("multi.tree",
271 o unroot() did not work correctly in most cases.
273 o reorder.phylo() made R freeze in some occasions.
275 o Plotting a tree in pruningwise order failed.
277 o When plotting an unrooted tree, the tip labels where not all
278 correctly positioned if the option `cex' was used.
282 CHANGES IN APE VERSION 1.10
287 o Five new `method' functions have been introduced to manipulate
288 DNA sequences in binary format (see below).
290 o Three new functions have been introduced to convert between the
291 new binary and the character formats.
293 o The new function as.alignment converts DNA sequences stored as
294 single characters into the class "alignment" used by the package
297 o read.dna() and read.GenBank() have a new argument `as.character'
298 controlling whether the sequences are returned in binary format
304 o root() failed when the tree had node labels: this is fixed.
306 o plot.phylo() did not correctly set the limits on the y-axis with
307 the default setting: this is fixed.
309 o dist.dna() returned a wrong result for the LogDet, paralinear,
310 and BH87 models with `pairwise.deletion = TRUE'.
315 o DNA sequences are now internally stored in a binary format. See
316 the document "A Bit-Level Coding Scheme for Nucleotides" for the
317 details. Most functions analyzing DNA functions have been
318 modified accordingly and are now much faster (dist.dna is now
319 ca. 60 times faster).
323 CHANGES IN APE VERSION 1.9-4
328 o A bug was fixed in edgelabels().
330 o as.phylo.hclust() did not work correctly when the object of
331 class "hclust" has its labels set to NULL: the returned tree has
332 now its tip labels set to "1", "2", ...
334 o consensus could fail if some tip labels are a subset of others
335 (e.g., "a" and "a_1"): this is now fixed.
337 o mlphylo() failed in most cases if some branch lengths of the
338 initial tree were greater than one: an error message is now
341 o mlphylo() failed in most cases when estimating the proportion of
342 invariants: this is fixed.
346 CHANGES IN APE VERSION 1.9-3
351 o The new function edgelabels adds labels on the edge of the tree
352 in the same way than nodelabels or tiplabels.
357 o multi2di() did not handle correctly branch lengths with the
358 default option `random = TRUE': this is now fixed.
360 o A bug was fixed in nuc.div() when using pairwise deletions.
362 o A bug occurred in the analysis of bipartitions with large
363 numbers of large trees, with consequences on prop.part,
364 prop.clades, and boot.phylo.
366 o The calculation of the Billera-Holmes-Vogtmann distance in
367 dist.topo was wrong: this has been fixed.
371 CHANGES IN APE VERSION 1.9-2
376 o The new function ladderize reorganizes the internal structure of
377 a tree to plot them left- or right-ladderized.
379 o The new function dist.nodes computes the patristic distances
380 between all nodes, internal and terminal, of a tree. It replaces
381 the option `full = TRUE' of cophenetic.phylo (see below).
386 o A bug was fixed in old2new.phylo().
388 o Some bugs were fixed in chronopl().
390 o The edge colours were not correctly displayed by plot.phylo
391 (thank you to Li-San Wang for the fix).
393 o cophenetic.phylo() failed with multichotomous trees: this is
399 o read.dna() now returns the sequences in a matrix if they are
400 aligned (interleaved or sequential format). Sequences in FASTA
401 format are still returned in a list.
403 o The option `full' of cophenetic.phylo() has been removed because
404 it could not be used from the generic.
409 o rotate() has been removed; this function did not work correctly
414 CHANGES IN APE VERSION 1.9-1
419 o Trees with a single tip were not read correctly in R as the
420 element `Nnode' was not set: this is fixed.
422 o unroot() did not set correctly the number of nodes of the
423 unrooted tree in most cases.
425 o read.GenBank() failed when fetching very long sequences,
426 particularly of the BX-series.
428 o A bug was introduced in read.tree() with ape 1.9: it has been
433 CHANGES IN APE VERSION 1.9
438 o There are two new print `methods' for trees of class "phylo" and
439 lists of trees of class "multi.tree", so that they are now
440 displayed in a compact and informative way.
442 o There are two new functions, old2new.phylo and new2old.phylo,
443 for converting between the old and new coding of the class
446 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
447 LogDet ("logdet"), and paralinear ("paralin").
449 o compute.brlen() has been extended: several methods are now
450 available to compute branch lengths.
452 o write.dna() can now handle matrices as well as lists.
457 o cophenetic.phylo() sometimes returned a wrong result with
458 multichotomous trees: this is fixed.
460 o rotate() failed when a single tip was specified: the tree is now
463 o ace() did not return the correct index matrix with custom
464 models: this is fixed.
466 o multi2di() did not work correctly when resolving multichotomies
467 randomly: the topology was always the same, only the arrangement
468 of clades was randomized: this is fixed. This function now
469 accepts trees with no branch lengths.
471 o The output of diversi.gof() was blurred by useless prints when a
472 user distribution was specified. This has been corrected, and
473 the help page of this function has been expanded.
478 o The internal structure of the class "phylo" has been changed:
479 see the document "Definition of Formats for Coding Phylogenetic
480 Trees in R" for the details. In addition, the code of most
481 functions has been improved.
483 o Several functions have been improved by replacing some R codes
484 by C codes: pic, plot.phylo, and reorder.phylo.
486 o There is now a citation information: see citation("ape") in R.
488 o write.tree() now does not add extra 0's to branch lengths so
489 that 1.23 is printed "1.23" by default, not "1.2300000000".
491 o The syntax of bind.tree() has been simplified. This function now
492 accepts trees with no branch lengths, and handles correctly node
495 o The option `as.numeric' of mrca() has been removed.
497 o The unused options `format' and `rooted' of read.tree() have
500 o The unused option `format' of write.tree() has been removed.
502 o The use of node.depth() has been simplified.
506 CHANGES IN APE VERSION 1.8-5
511 o Two new functions read.nexus.data() and write.nexus.data(),
512 contributed by Johan Nylander, allow to read and write molecular
513 sequences in NEXUS files.
515 o The new function reorder.phylo() reorders the internal structure
516 of a tree of class "phylo". It is used as the generic, e.g.,
519 o read.tree() and read.nexus() can now read trees with a single
522 o The new data set `cynipids' supplies a set of protein sequences
528 o The code of all.equal.phylo() has been completely rewritten
529 (thanks to Benoît Durand) which fixes several bugs.
531 o read.tree() and read.nexus() now checks the labels of the tree
532 to remove or substitute any characters that are illegal in the
533 Newick format (parentheses, etc.)
535 o A negative P-value could be returned by mantel.test(): this is
540 CHANGES IN APE VERSION 1.8-4
545 o The new function sh.test() computes the Shimodaira-
548 o The new function collapse.singles() removes the nodes with a
549 single descendant from a tree.
551 o plot.phylo() has a new argument `tip.color' to specify the
554 o mlphylo() has now an option `quiet' to control the display of
555 the progress of the analysis (the default is FALSE).
560 o read.dna() did not read correctly sequences in sequential format
561 with leading alignment gaps "-": this is fixed.
563 o ace() returned a list with no class so that the generic
564 functions (anova, logLik, ...) could not be used directly. This
565 is fixed as ace() now returns an object of class "ace".
567 o anova.ace() had a small bug when computing the number of degrees
568 of freedom: this is fixed.
570 o mlphylo() did not work when the sequences were in a matrix or
571 a data frame: this is fixed.
573 o rtree() did not work correctly when trying to simulate an
574 unrooted tree with two tips: an error message is now issued.
579 o The algorithm of rtree() has been changed: it is now about 40,
580 100, and 130 times faster for 10, 100, and 1000 tips,
585 CHANGES IN APE VERSION 1.8-3
590 o There are four new `method' functions to be used with the
591 results of ace(): logLik(), deviance(), AIC(), and anova().
593 o The plot method of phymltest has two new arguments: `main' to
594 change the title, and `col' to control the colour of the
595 segments showing the AIC values.
597 o ace() has a new argument `ip' that gives the initial values used
598 in the ML estimation with discrete characters (see the examples
599 in ?ace). This function now returns a matrix giving the indices
600 of the estimated rates when analysing discrete characters.
602 o nodelabels() and tiplabels() have a new argument `pie' to
603 represent proportions, with any number of categories, as
604 piecharts. The use of the option `thermo' has been improved:
605 there is now no limitation on the number of categories.
610 o mlphylo() did not work with more than two partitions: this is
613 o root() failed if the proposed outgroup was already an outgroup
614 in the tree: this is fixed.
616 o The `col' argument in nodelabels() and tiplabels() was not
617 correctly passed when `text' was used: this is fixed.
619 o Two bugs were fixed in mlphylo(): parameters were not always
620 correctly output, and the estimation failed in some cases.
622 o plot.phylo() was stuck when given a tree with a single tip: this
623 is fixed and a message error is now returned.
625 o An error was corrected in the help page of gammaStat regarding
626 the calculation of P-values.
628 o Using gls() could crash R when the number of species in the tree
629 and in the variables were different: this is fixed.
633 CHANGES IN APE VERSION 1.8-2
638 o The new function mlphylo() fits a phylogenetic tree by maximum
639 likelihood from DNA sequences. Its companion function DNAmodel()
640 is used to define the substitution model which may include
641 partitioning. There are methods for logLik(), deviance(), and
642 AIC(), and the summary() method has been extended to display in
643 a friendly way the results of this model fitting. Currently, the
644 functionality is limited to estimating the substitution and
645 associated parameters and computing the likelihood.
647 o The new function drop1.compar.gee (used as, e.g., drop1(m))
648 tests for single effects in GEE-based comparative method. A
649 warning message is printed if there is not enough degrees of
655 o An error message was sometimes issued by plot.multi.tree(),
656 though with no consequence.
660 CHANGES IN APE VERSION 1.8-1
665 o There is a new plot method for lists of trees (objects of class
666 "multi.tree"): it calls plot.phylo() internally and is
667 documented on the same help page.
672 o A bug was fixed in the C code that analyzes bipartitions: this
673 has impact on several functions like prop.part, prop.clades,
674 boot.phylo, or consensus.
676 o root() did not work correctly when the specified outgroup had
677 more than one element: this is fixed.
679 o dist.dna() sometimes returned a warning inappropriately: this
682 o If the distance object given to nj() had no rownames, nj()
683 returned a tree with no tip labels: it now returns tips labelled
684 "1", "2", ..., corresponding to the row numbers.
689 o nj() has been slightly changed so that tips with a zero distance
690 are first aggregated with zero-lengthed branches; the usual NJ
691 procedure is then performed on a distance matrix without 0's.
695 CHANGES IN APE VERSION 1.8
700 o The new function chronopl() estimates dates using the penalized
701 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
703 o The new function consensus() calculates the consensus tree of a
706 o The new function evolve.phylo() simulates the evolution of
707 continuous characters along a phylogeny under a Brownian model.
709 o The new plot method for objects of class "ancestral" displays a
710 tree together with ancestral values, as returned by the above
713 o The new function as.phylo.formula() returns a phylogeny from a
714 set of nested taxonomic variables given as a formula.
716 o The new function read.caic() reads trees in CAIC format.
718 o The new function tiplabels() allows to add labels to the tips
719 of a tree using text or plotting symbols in a flexible way.
721 o The new function unroot() unroots a phylogeny.
723 o multi2di() has a new option, `random', which specifies whether
724 to resolve the multichotomies randomly (the default) or not.
726 o prop.part() now returns an object of class "prop.part" for which
727 there are print (to display a partition in a more friendly way)
728 and summary (to extract the numbers) methods.
730 o plot.phylo() has a new option, `show.tip.label', specifying
731 whether to print the labels of the tips. The default is TRUE.
733 o The code of nj() has been replaced by a faster C code: it is now
734 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
737 o write.nexus() now writes whether a tree is rooted or not.
742 o Two bugs have been fixed in root(): unrooted trees are now
743 handled corretly, and node labels are now output normally.
745 o A bug was fixed in phymltest(): the executable couldn't be found
748 o Three bug have been fixed in ace(): computing the likelihood of
749 ancestral states of discrete characters failed, custom models
750 did not work, and the function failed with a null gradient (a
751 warning message is now returned; this latter bug was also
752 present in yule.cov() as well and is now fixed).
754 o pic() hanged out when missing data were present: a message error
757 o A small bug was fixed in dist.dna() where the gamma correction
758 was not always correctly dispatched.
760 o plot.phylo() plotted correctly the root edge only when the tree
761 was plotted rightwards: this works now for all directions.
766 o dist.taxo() has been renamed as weight.taxo().
768 o Various error and warning messages have been improved.
772 CHANGES IN APE VERSION 1.7
775 o The new function ace() estimates ancestral character states for
776 continuous characters (with ML, GLS, and contrasts methods), and
777 discrete characters (with ML only) for any number of states.
779 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
780 of directional evolution for continuous characters. The user
781 specifies the node(s) of the tree where the character optimum
784 o The new function is.rooted() tests whether a tree (of class
787 o The new function rcoal() generates random ultrametric trees with
788 the possibility to specify the function that generates the
789 inter-nodes distances.
791 o The new function mrca() gives for all pairs of tips in a tree
792 (and optionally nodes too) the most recent common ancestor.
794 o nodelabels() has a new option `thermo' to plot proportions (up
795 to three classes) on the nodes of a tree.
797 o rtree() has been improved: it can now generate rooted or
798 unrooted trees, and the mathematical function that generates the
799 branch lengths may be specified by the user. The tip labels may
800 be given directly in the call to rtree. The limit cases (n = 2,
801 3) are now handled correctly.
803 o dist.topo() has a new argument `method' with two choices: "PH85"
804 for Penny and Henny's method (already available before and now
805 the default), and "BHV01" for the geometric distance by Billera
806 et al. (2001, Adv. Appl. Math. 27:733).
808 o write.tree() has a new option, `digits', which specifies the
809 number of digits to be printed in the Newick tree. By default
810 digits = 10. The numbers are now always printed in decimal form
811 (i.e., 1.0e-1 is now avoided).
813 o dist.dna() can now compute the raw distances between pairs of
814 DNA sequences by specifying model = "raw".
816 o dist.phylo() has a new option `full' to possibly compute the
817 distances among all tips and nodes of the tree. The default if
823 o Several bugs were fixed in all.equal.phylo().
825 o dist.dna() did not handle correctly gaps ("-") in alignments:
826 they are now considered as missing data.
828 o rotate() did not work if the tips were not ordered: this is
831 o mantel.test() returned NA in some special cases: this is fixed
832 and the function has been improved and is now faster.
834 o A bug was fixed in diversi.gof() where the calculation of A² was
837 o cherry() did not work correctly under some OSs (mainly Linux):
840 o is.binary.tree() has been modified so that it works with both
841 rooted and unrooted trees.
843 o The documentation of theta.s() was not correct: this has been
846 o plot.mst() did not work correctly: this is fixed.
850 CHANGES IN APE VERSION 1.6
855 o The new function dist.topo() computes the topological distances
858 o The new function boot.phylo() performs a bootstrap analysis on
859 phylogeny estimation.
861 o The new functions prop.part() and prop.clades() analyse
862 bipartitions from a series of trees.
867 o read.GenBank() now uses the EFetch utility of NCBI instead of
868 the usual Web interface: it is now much faster (e.g., 12 times
869 faster to retrieve 8 sequences, 37 times for 60 sequences).
874 o Several bugs were fixed in read.dna().
876 o Several bugs were fixed in diversi.time().
878 o is.binary.tree() did not work correctly if the tree has no edge
879 lengths: this is fixed.
881 o drop.tip() did not correctly propagated the `node.label' of a
886 CHANGES IN APE VERSION 1.5
891 o Two new functions, as.matching.phylo() and as.phylo.matching(),
892 convert objects between the classes "phylo" and "matching". The
893 latter implements the representation of binary trees introduced by
894 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
895 as.matching() has been introduced as well.
897 o Two new functions, multi2di() and di2multi(), allow to resolve
898 and collapse multichotomies with branches of length zero.
900 o The new function nuc.div() computes the nucleotide diversity
901 from a sample a DNA sequences.
903 o dist.dna() has been completely rewritten with a much faster
904 (particularly for large data sets) C code. Eight models are
905 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
906 option `method' has been renamed `model'). Computation of variance
907 is available for all models. A gamma-correction is possible for
908 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
909 to remove sites with missing data on a pairwise basis. The option
910 `GCcontent' has been removed.
912 o read.GenBank() has a new option (species.names) which specifies
913 whether to return the species names of the organisms in addition
914 to the accession numbers of the sequences (this is the default
917 o write.nexus() can now write several trees in the same NEXUS file.
919 o drop.tip() has a new option `root.edge' that allows to specify the
920 new root edge if internal branches are trimmed.
925 o as.phylo.hclust() failed if some labels had parentheses: this
928 o Several bugs were fixed in all.equal.phylo(). This function now
929 returns the logical TRUE if the trees are identical but with
930 different representations (a report was printed previously).
932 o read.GenBank() did not correctly handle ambiguous base codes:
938 o birthdeath() now returns an object of class "birthdeath" for
939 which there is a print method.
943 CHANGES IN APE VERSION 1.4
948 o The new function nj() performs phylogeny estimation with the
949 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
952 o The new function which.edge() identifies the edges of a tree
953 that belong to a group specified as a set of tips.
955 o The new function as.phylo.phylog() converts an object of class
956 "phylog" (from the package ade4) into an object of class
959 o The new function axisPhylo() draws axes on the side of a
962 o The new function howmanytrees() calculates the number of trees
963 in different cases and giving a number of tips.
965 o write.tree() has a new option `multi.line' (TRUE by default) to
966 write a Newick tree on several lines rather than on a single
969 o The functionalities of zoom() have been extended. Several
970 subtrees can be visualized at the same time, and they are marked
971 on the main tree with colors. The context of the subtrees can be
972 marked with the option `subtree' (see below).
974 o drop.tip() has a new option `subtree' (FALSE by default) which
975 specifies whether to output in the tree how many tips have been
978 o The arguments of add.scale.bar() have been redefined and have
979 now default values (see ?add.scale.bar for details). This
980 function now works even if the plotted tree has no edge length.
982 o plot.phylo() can now plot radial trees, but this does not take
983 edge lengths into account.
985 o In plot.phylo() with `type = "phylogram"', if the values of
986 `edge.color' and `edge.width' are identical for sister-branches,
987 they are propagated to the vertical line that link them.
992 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
993 crashing. This is fixed.
995 o In plot.phylo(), the options `edge.color' and `edge.width' are
996 now properly recycled; their default values are now "black" and
999 o A bug has been fixed in write.nexus().
1004 o The function node.depth.edgelength() has been removed and
1005 replaced by a C code.
1009 CHANGES IN APE VERSION 1.3-1
1014 o The new function nodelabels() allows to add labels to the nodes
1015 of a tree using text or plotting symbols in a flexible way.
1017 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1018 numeric values specifying the lower and upper limits on the x-
1019 and y-axes. This allows to leave some space on any side of the
1020 tree. If a single value is given, this is taken as the upper
1025 CHANGES IN APE VERSION 1.3
1030 o The new function phymltest() calls the software PHYML and fits
1031 28 models of DNA sequence evolution. There are a print method to
1032 display likelihood and AIC values, a summary method to compute
1033 the hierarchical likelihood ratio tests, and a plot method to
1034 display graphically the AIC values of each model.
1036 o The new function yule.cov() fits the Yule model with covariates,
1037 a model where the speciation rate is affected by several species
1038 traits through a generalized linear model. The parameters are
1039 estimated by maximum likelihood.
1041 o Three new functions, corBrownian(), corGrafen(), and
1042 corMartins(), compute the expected correlation structures among
1043 species given a phylogeny under different models of evolution.
1044 These can be used for GLS comparative phylogenetic methods (see
1045 the examples). There are coef() and corMatrix() methods and an
1046 Initialize.corPhyl() function associated.
1048 o The new function compar.cheverud() implements Cheverud et al.'s
1049 (1985; Evolution 39:1335) phylogenetic comparative method.
1051 o The new function varcomp() estimates variance components; it has
1054 o Two new functions, panel.superpose.correlogram() and
1055 plot.correlogramList(), allow to plot several phylogenetic
1058 o The new function node.leafnumber() computes the number of leaves
1059 of a subtree defined by a particular node.
1061 o The new function node.sons() gets all tags of son nodes from a
1064 o The new function compute.brlen() computes the branch lengths of
1065 a tree according to a specified method.
1067 o plot.phylo() has three new options: "cex" controls the size of
1068 the (tip and node) labels (thus it is no more needed to change
1069 the global graphical parameter), "direction" which allows to
1070 plot the tree rightwards, leftwards, upwards, or downwards, and
1071 "y.lim" which sets the upper limit on the y-axis.
1076 o Some functions which try to match tip labels and names of
1077 additional data (e.g. vector) are likely to fail if there are
1078 typing or syntax errors. If both series of names do not perfectly
1079 match, they are ignored and a warning message is now issued.
1080 These functions are bd.ext, compar.gee, pic. Their help pages
1081 have been clarified on this point.
1085 CHANGES IN APE VERSION 1.2-7
1090 o The new function root() reroots a phylogenetic tree with respect
1091 to a specified outgroup.
1093 o The new function rotate() rotates an internal branch of a tree.
1095 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1096 trees) controls the display of the tip labels in unrooted trees.
1097 This display has been greatly improved: the tip labels are now not
1098 expected to overlap with the tree (particularly if lab4ut =
1099 "axial"). In all cases, combining appropriate values of "lab4ut"
1100 and the font size (via "par(cex = )") should result in readable
1101 unrooted trees. See ?plot.phylo for some examples.
1103 o In drop.tip(), the argument `tip' can now be numeric or character.
1108 o drop.tip() did not work correctly with trees with no branch
1109 lengths: this is fixed.
1111 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1112 plotted with some line crossings: this is now fixed.
1116 CHANGES IN APE VERSION 1.2-6
1121 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1122 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1123 to implement comparative methods with an autocorrelation approach.
1125 o A new data set describing some life history traits of Carnivores
1131 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1136 o When plotting a tree with plot.phylo(), the new default of the
1137 option `label.offset' is now 0, so the labels are always visible.
1141 CHANGES IN APE VERSION 1.2-5
1146 o The new function bd.ext() fits a birth-death model with combined
1147 phylogenetic and taxonomic data, and estimates the corresponding
1148 speciation and extinction rates.
1153 o The package gee is no more required by ape but only suggested
1154 since only the function compar.gee() calls gee.
1158 CHANGES IN APE VERSION 1.2-4
1163 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1164 and lines.popsize) implementing a new approach for inferring the
1165 demographic history from genealogies using a reversible jump
1166 MCMC have been introduced.
1168 o The unit of time in the skyline plot and in the new plots can
1169 now be chosen to be actual years, rather than substitutions.
1173 CHANGES IN APE VERSION 1.2-3
1178 o The new function rtree() generates a random binary tree with or
1179 without branch lengths.
1181 o Two new functions for drawing lineages-through-time (LTT) plots
1182 are provided: ltt.lines() adds a LTT curve to an existing plot,
1183 and mltt.plot() does a multiple LTT plot giving several trees as
1184 arguments (see `?ltt.plot' for details).
1189 o Some taxon names made R crashing when calling as.phylo.hclust():
1192 o dist.dna() returned an error with two identical DNA sequences
1193 (only using the Jukes-Cantor method returned 0): this is fixed.
1198 o The function dist.phylo() has been re-written using a different
1199 algorithm: it is now about four times faster.
1201 o The code of branching.times() has been improved: it is now about
1206 CHANGES IN APE VERSION 1.2-2
1211 o The new function seg.sites() finds the segregating sites in a
1212 sample of DNA sequences.
1217 o A bug introduced in read.tree() and in read.nexus() with version
1220 o A few errors were corrected and a few examples were added in the
1225 CHANGES IN APE VERSION 1.2-1
1230 o plot.phylo() can now draw the edge of the root of a tree if it
1231 has one (see the new option `root.edge', its default is FALSE).
1236 o A bug was fixed in read.nexus(): files with semicolons inside
1237 comment blocks were not read correctly.
1239 o The behaviour of read.tree() and read.nexus() was corrected so
1240 that tree files with badly represented root edges (e.g., with
1241 an extra pair of parentheses, see the help pages for details)
1242 are now correctly represented in the object of class "phylo";
1243 a warning message is now issued.
1247 CHANGES IN APE VERSION 1.2
1252 o plot.phylo() has been completely re-written and offers several
1253 new functionalities. Three types of trees can now be drawn:
1254 phylogram (as previously), cladogram, and unrooted tree; in
1255 all three types the branch lengths can be drawn using the edge
1256 lengths of the phylogeny or not (e.g., if the latter is absent).
1257 The vertical position of the nodes can be adjusted with two
1258 choices (see option `node.pos'). The code has been re-structured,
1259 and two new functions (potentially useful for developpers) are
1260 documented separately: node.depth.edgelength() and node.depth();
1261 see the respective help pages for details.
1263 o The new function zoom() allows to explore very large trees by
1264 focusing on a small portion of it.
1266 o The new function yule() fits by maximum likelihood the Yule model
1267 (birth-only process) to a phylogenetic tree.
1269 o Support for writing DNA sequences in FASTA format has been
1270 introduced in write.dna() (support for reading sequences in
1271 this format was introduced in read.dna() in version 1.1-2).
1272 The function has been completely re-written, fixing some bugs
1273 (see below); the default behaviour is no more to display the
1274 sequences on the standard output. Several options have been
1275 introduced to control the sequence printing in a flexible
1276 way. The help page has been extended.
1278 o A new data set is included: a supertree of bats in NEXUS format.
1283 o In theta.s(), the default of the option `variance' has
1284 been changed to `FALSE' (as was indicated in the help page).
1286 o Several bugs were fixed in the code of all.equal.phylo().
1288 o Several bugs were fixed in write.dna(), particularly this
1289 function did not work with `format = "interleaved"'.
1291 o Various errors were corrected in the help pages.
1296 o The argument names of as.hclust.phylo() have been changed
1297 from "(phy)" to "(x, ...)" to conform to the definition of
1298 the corresponding generic function.
1300 o gamma.stat() has been renamed gammaStat() to avoid confusion
1301 since gamma() is a generic function.
1305 CHANGES IN APE VERSION 1.1-3
1310 o base.freq() previously did not return a value of 0 for
1311 bases absent in the data (e.g., a vector of length 3 was
1312 returned if one base was absent). This is now fixed (a
1313 vector of length 4 is always returned).
1315 o Several bugs were fixed in read.nexus(), including that this
1316 function did not work in this absence of a "TRANSLATE"
1317 command in the NEXUS file, and that the commands were
1322 CHANGES IN APE VERSION 1.1-2
1327 o The Tamura and Nei (1993) model of DNA distance is now implemented
1328 in dist.dna(): five models are now available in this function.
1330 o A new data set is included: a set of 15 sequences of the
1331 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1337 o A bug in read.nexus() was fixed.
1339 o read.dna() previously did not work correctly in most cases.
1340 The function has been completely re-written and its help page
1341 has been considerably extended (see ?read.dna for details).
1342 Underscores (_) in taxon names are no more replaced with
1343 spaces (this behaviour was undocumented).
1345 o A bug was fixed in write.dna().
1349 CHANGES IN APE VERSION 1.1-1
1354 o A bug in read.tree() introduced in APE 1.1 was fixed.
1356 o A bug in compar.gee() resulted in an error when trying to fit
1357 a model with `family = "binomial"'. This is now fixed.
1361 CHANGES IN APE VERSION 1.1
1366 o The Klastorin (1982) method as suggested by Misawa and Tajima
1367 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1368 on the basis of phylogenetic trees has been implemented (see
1369 the function klastorin()).
1371 o Functions have been added to convert APE's "phylo" objects in
1372 "hclust" cluster objects and vice versa (see the help page of
1373 as.phylo for details).
1375 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1376 are introduced for the estimation of absolute evolutionary rates
1377 (ratogram) and dated clock-like trees (chronogram) from
1378 phylogenetic trees using the non-parametric rate smoothing approach
1379 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1381 o A summary method is now provided printing a summary information on a
1382 phylogenetic tree with, for instance, `summary(tree)'.
1384 o The behaviour of read.tree() was changed so that all spaces and
1385 tabulations in tree files are now ignored. Consequently, spaces in tip
1386 labels are no more allowed. Another side effect is that read.nexus()
1387 now does not replace the underscores (_) in tip labels with spaces
1388 (this behaviour was undocumented).
1390 o The function plot.phylo() has a new option (`underscore') which
1391 specifies whether the underscores in tip labels should be written on
1392 the plot as such or replaced with spaces (the default).
1394 o The function birthdeath() now computes 95% confidence intervals of
1395 the estimated parameters using profile likelihood.
1397 o Three new data sets are included: a gene tree estimated from 36
1398 landplant rbcL sequences, a gene tree estimated from 32 opsin
1399 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1404 o A bug was fixed in dist.gene() where nothing was returned.
1406 o A bug in plot.mst() was fixed.
1408 o A bug in vcv.phylo() resulted in false correlations when the
1409 option `cor = TRUE' was used (now fixed).
1413 CHANGES IN APE VERSION 1.0
1418 o Two new functions, read.dna() and write.dna(), read/write in a file
1419 DNA sequences in interleaved or in sequential format.
1421 o Two new functions, read.nexus() and write.nexus(), read/write trees
1424 o The new function bind.tree() allows to bind two trees together,
1425 possibly handling root edges to give internal branches.
1427 o The new function drop.tip() removes the tips in a phylogenetic tree,
1428 and trims (or not) the corresponding internal branches.
1430 o The new function is.ultrametric() tests if a tree is ultrametric.
1432 o The function plot.phylo() has more functionalities such as drawing the
1433 branches with different colours and/or different widths, showing the
1434 node labels, controling the position and font of the labels, rotating
1435 the labels, and controling the space around the plot.
1437 o The function read.tree() can now read trees with no branch length,
1438 such as "(a,b),c);". Consequently, the element `edge.length' in
1439 objects of class "phylo" is now optional.
1441 o The function write.tree() has a new default behaviour: if the default
1442 for the option `file' is used (i.e. file = ""), then a variable of
1443 mode character containing the tree in Newick format is returned which
1444 can thus be assigned (e.g., tree <- write.tree(phy)).
1446 o The function read.tree() has a new argument `text' which allows
1447 to read the tree in a variable of mode character.
1449 o A new data set is included: the phylogenetic relationships among
1450 the orders of birds from Sibley and Ahlquist (1990).
1454 CHANGES IN APE VERSION 0.2-1
1459 o Several bugs were fixed in the help pages.
1463 CHANGES IN APE VERSION 0.2
1468 o The function write.tree() writes phylogenetic trees (objects of class
1469 "phylo") in an ASCII file using the Newick parenthetic format.
1471 o The function birthdeath() fits a birth-death model to branching times
1472 by maximum likelihood, and estimates the corresponding speciation and
1475 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1478 o The function is.binary.tree() tests whether a phylogeny is binary.
1480 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1481 as well as some methods are introduced.
1483 o Several functions, including some generics and methods, for computing
1484 skyline plot estimates (classic and generalized) of effective
1485 population size through time are introduced and replace the function
1486 skyline.plot() in version 0.1.
1488 o Two data sets are now included: the phylogenetic relationships among
1489 the families of birds from Sibley and Ahlquist (1990), and an
1490 estimated clock-like phylogeny of HIV sequences sampled in the
1491 Democratic Republic of Congo.
1494 DEPRECATED & DEFUNCT
1496 o The function skyline.plot() in ape 0.1 has been deprecated and
1497 replaced by more elaborate functions (see above).
1502 o Two important bugs were fixed in plot.phylo(): phylogenies with
1503 multichotomies not at the root or not with only terminal branches,
1504 and phylogenies with a single node (i.e. only terminal branches)
1505 did not plot. These trees should be plotted correctly now.
1507 o Several bugs were fixed in diversi.time() in the computation of
1510 o Various errors were corrected in the help pages.