1 CHANGES IN APE VERSION 2.2-1
6 o The new function del.gaps() removes insertion gaps ("-") in a
12 o root() failed with 'resolve.root = TRUE' when the root was
13 already the specified root.
15 o Several bugs were fixed in mlphylo().
17 o collapsed.singles() did not propagate the 'Nnode' and
18 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
20 o read.nexus failed to remove correctly the comments within trees.
25 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
30 CHANGES IN APE VERSION 2.2
35 o Four new functions have been written by Damien de Vienne for the
36 graphical exploration of large trees (cophyloplot, subtrees,
37 subtreeplot), and to return the graphical coordinates of tree
40 o The new functions corPagel and corBlomberg implement the Pagel's
41 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
43 o chronopl() has been improved and gains several options: see its
44 help page for details.
46 o boot.phylo() has now an option 'trees' to possibly return the
47 bootstraped trees (the default is FALSE).
49 o prop.part() has been improved and should now be faster in all
55 o read.dna() failed if "?" occurred in the first 10 sites of the
58 o The x/y aspect of the plot is now respected when plotting a
59 circular tree (type = "r" or "f").
61 o Drawing the tip labels sometimes failed when plotting circular
64 o zoom() failed when tip labels were used instead of their numbers
65 (thanks to Yan Wong for the fix).
67 o drop.tip() failed with some trees (fixed by Yan Wong).
69 o seg.sites() failed with a list.
71 o consensus() failed in some cases. The function has been improved
72 as well and is faster.
76 CHANGES IN APE VERSION 2.1-3
81 o A bug in read.nexus() made the Windows R-GUI crash.
83 o An error was fixed in the computation of ancestral character
84 states by generalized least squares in ace().
86 o di2multi() did not modify node labels correctly.
88 o multi2di() failed if the tree had its attribute "order" set to
93 CHANGES IN APE VERSION 2.1-2
98 o There three new methods for the "multiPhylo" class: str, $,
101 o root() gains the options 'node' and 'resolve.root'
102 (FALSE by default) as well as its code being improved.
104 o mltt.plot() has now an option 'log' used in the same way
105 than in plot.default().
110 o mltt.plot() failed to display the legend with an unnamed
113 o nodelabels() with pies now correcly uses the argument
114 'cex' to draw symbols of different sizes (which has
115 worked already for thermometers).
117 o read.nexus() generally failed to read very big files.
122 o The argument 'family' of compar.gee() can now be a function
123 as well as a character string.
125 o read.tree() and read.nexus() now return an unnamed list if
128 o read.nexus() now returns a modified object of class "multiPhylo"
129 when there is a TRANSLATE block in the NEXUS file: the individual
130 trees have no 'tip.label' vector, but the list has a 'TipLabel'
131 attribute. The new methods '$' and '[[' set these elements
132 correctly when extracting trees.
136 CHANGES IN APE VERSION 2.1-1
141 o The new function rmtree generates lists of random trees.
143 o rcoal() now generates a genuine coalescent tree by default
144 (thanks to Vladimir Minin for the code).
149 o nuc.div() returned an incorrect value with the default
150 pairwise.deletion = FALSE.
155 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
156 have been improved so that they are stabler and faster.
158 o R packages used by ape are now loaded silently; lattice and gee
159 are loaded only when needed.
163 CHANGES IN APE VERSION 2.1
168 o The new function identify.phylo identifies clades on a plotted
169 tree using the mouse.
171 o It is now possible to subset a list of trees (object of class
172 "multiPhylo") with "[" while keeping its class correct.
174 o The new function as.DNAbin.alignment converts DNA sequences
175 stored in the "alignment" format of the package seqinr into
176 an object of class "DNAbin".
178 o The new function weight.taxo2 helps to build similarity matrices
179 given two taxonomic levels (usually called by other functions).
181 o write.tree() can now take a list of trees (class "multiPhylo")
182 as its main argument.
184 o plot.correlogram() and plot.correlogramList() have been
185 improved, and gain several options (see the help page for
186 details). A legend is now plotted by default.
191 o dist.dna() returned some incorrect values with `model = "JC69"'
192 and `pairwise.deletion = TRUE'. This affected only the
193 distances involving sequences with missing values. (Thanks
194 to Bruno Toupance for digging this bug out.)
196 o write.tree() failed with some trees: this is fixed by removing
197 the `multi.line' option (trees are now always printed on a
200 o read.nexus() did not correctly detect trees with multiple root
201 edges (see OTHER CHANGES).
206 o The code of mlphylo() has almost entirely rewritten, and should
207 be much stabler. The options have been also greatly simplified
208 (see ?mlphylo and ?DNAmodel for details).
210 o The internal function nTips has been renamed klastorin_nTips.
212 o The code of is.ultrametric() contained redundancies and has
215 o The code of Moran.I() and of correlogram.formula() have been
218 o read.tree() and read.nexus() now return an error when trying to
219 read a tree with multiple root edges (see BUG FIXES). The
220 correction applied in previous version did not work in all
223 o The class c("multi.tree", "phylo") has been renamed
229 o There is now a vignette in ape: see vignette("MoranI", "ape").
234 o as.matching() and as.phylo.matching() do not support branch
237 o correlogram.phylo() and discrete.dist() have been removed.
241 CHANGES IN APE VERSION 2.0-2
246 o The new function matexpo computes the exponential of a square
249 o The new function unique.multi.tree removes duplicate trees from
252 o yule() has a new option `use.root.edge = FALSE' that specifies
253 to ignore, by default, the root edge of the tree if it exists.
258 o which.edge() failed when the index of a single terminal edge was
261 o In diversi.time(), the values returned for model C were
264 o A bug was fixed in yule() that affected the calculation of the
265 likelihood in the presence of ties in the branching times.
267 o There was a bug in the C function mat_expo4x4 affecting the
268 calculations of the transition probabilities for models HKY and
271 o A small bug was fixed in as.matrix.DNAbin (thanks to James
274 o rtree() did not `shuffle' the tip labels by default, so only a
275 limited number of labelled topologies could be generated.
279 CHANGES IN APE VERSION 2.0-1
284 o The three new functions bionj, fastme.ols, and fastme.bal
285 perform phylogeny estimation by the BIONJ and fastME methods in
286 OLS and balanced versions. This is a port to R of previous
287 previous programs done by Vincent Lefort.
289 o The new function chronoMPL performs molecular dating with the
290 mean path lengths method of Britton et al. (2002, Mol. Phyl.
293 o The new function rotate, contributed by Christoph Heibl, swaps
294 two clades connected to the same node. It works also with
295 multichotomous nodes.
297 o The new `method' as.matrix.DNAbin() may be used to convert
298 easily DNA sequences stored in a list into a matrix while
299 keeping the names and the class.
304 o chronopl() failed when some branch lengths were equal to zero:
305 an error message is now returned.
307 o di2multi() failed when there was a series of consecutive edges
312 CHANGES IN APE VERSION 1.10-2
317 o plot.phylo() can now plot circular trees: the option is type =
318 "fan" or type = "f" (to avoid the ambiguity with type = "c").
320 o prop.part() has a new option `check.labels = FALSE' which allows
321 to considerably speed-up the calculations of bipartitions. As a
322 consequence, calculations of bootstrap values with boot.phylo()
323 should be much faster.
328 o read.GenBank() did not return correctly the list of species as
329 from ape 1.10: this is fixed in this version
331 o Applying as.phylo() on a tree of class "phylo" failed: the
332 object is now returned unchanged.
336 CHANGES IN APE VERSION 1.10-1
341 o The three new functions Ntip, Nnode, and Nedge return, for a
342 given tree, the number of tips, nodes, or edges, respectively.
347 o read.nexus() did not set correctly the class of the returned
348 object when reading multiple trees.
350 o mllt.plot() failed with objects of class c("multi.tree",
353 o unroot() did not work correctly in most cases.
355 o reorder.phylo() made R freeze in some occasions.
357 o Plotting a tree in pruningwise order failed.
359 o When plotting an unrooted tree, the tip labels where not all
360 correctly positioned if the option `cex' was used.
364 CHANGES IN APE VERSION 1.10
369 o Five new `method' functions have been introduced to manipulate
370 DNA sequences in binary format (see below).
372 o Three new functions have been introduced to convert between the
373 new binary and the character formats.
375 o The new function as.alignment converts DNA sequences stored as
376 single characters into the class "alignment" used by the package
379 o read.dna() and read.GenBank() have a new argument `as.character'
380 controlling whether the sequences are returned in binary format
386 o root() failed when the tree had node labels: this is fixed.
388 o plot.phylo() did not correctly set the limits on the y-axis with
389 the default setting: this is fixed.
391 o dist.dna() returned a wrong result for the LogDet, paralinear,
392 and BH87 models with `pairwise.deletion = TRUE'.
397 o DNA sequences are now internally stored in a binary format. See
398 the document "A Bit-Level Coding Scheme for Nucleotides" for the
399 details. Most functions analyzing DNA functions have been
400 modified accordingly and are now much faster (dist.dna is now
401 ca. 60 times faster).
405 CHANGES IN APE VERSION 1.9-4
410 o A bug was fixed in edgelabels().
412 o as.phylo.hclust() did not work correctly when the object of
413 class "hclust" has its labels set to NULL: the returned tree has
414 now its tip labels set to "1", "2", ...
416 o consensus could fail if some tip labels are a subset of others
417 (e.g., "a" and "a_1"): this is now fixed.
419 o mlphylo() failed in most cases if some branch lengths of the
420 initial tree were greater than one: an error message is now
423 o mlphylo() failed in most cases when estimating the proportion of
424 invariants: this is fixed.
428 CHANGES IN APE VERSION 1.9-3
433 o The new function edgelabels adds labels on the edge of the tree
434 in the same way than nodelabels or tiplabels.
439 o multi2di() did not handle correctly branch lengths with the
440 default option `random = TRUE': this is now fixed.
442 o A bug was fixed in nuc.div() when using pairwise deletions.
444 o A bug occurred in the analysis of bipartitions with large
445 numbers of large trees, with consequences on prop.part,
446 prop.clades, and boot.phylo.
448 o The calculation of the Billera-Holmes-Vogtmann distance in
449 dist.topo was wrong: this has been fixed.
453 CHANGES IN APE VERSION 1.9-2
458 o The new function ladderize reorganizes the internal structure of
459 a tree to plot them left- or right-ladderized.
461 o The new function dist.nodes computes the patristic distances
462 between all nodes, internal and terminal, of a tree. It replaces
463 the option `full = TRUE' of cophenetic.phylo (see below).
468 o A bug was fixed in old2new.phylo().
470 o Some bugs were fixed in chronopl().
472 o The edge colours were not correctly displayed by plot.phylo
473 (thank you to Li-San Wang for the fix).
475 o cophenetic.phylo() failed with multichotomous trees: this is
481 o read.dna() now returns the sequences in a matrix if they are
482 aligned (interleaved or sequential format). Sequences in FASTA
483 format are still returned in a list.
485 o The option `full' of cophenetic.phylo() has been removed because
486 it could not be used from the generic.
491 o rotate() has been removed; this function did not work correctly
496 CHANGES IN APE VERSION 1.9-1
501 o Trees with a single tip were not read correctly in R as the
502 element `Nnode' was not set: this is fixed.
504 o unroot() did not set correctly the number of nodes of the
505 unrooted tree in most cases.
507 o read.GenBank() failed when fetching very long sequences,
508 particularly of the BX-series.
510 o A bug was introduced in read.tree() with ape 1.9: it has been
515 CHANGES IN APE VERSION 1.9
520 o There are two new print `methods' for trees of class "phylo" and
521 lists of trees of class "multi.tree", so that they are now
522 displayed in a compact and informative way.
524 o There are two new functions, old2new.phylo and new2old.phylo,
525 for converting between the old and new coding of the class
528 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
529 LogDet ("logdet"), and paralinear ("paralin").
531 o compute.brlen() has been extended: several methods are now
532 available to compute branch lengths.
534 o write.dna() can now handle matrices as well as lists.
539 o cophenetic.phylo() sometimes returned a wrong result with
540 multichotomous trees: this is fixed.
542 o rotate() failed when a single tip was specified: the tree is now
545 o ace() did not return the correct index matrix with custom
546 models: this is fixed.
548 o multi2di() did not work correctly when resolving multichotomies
549 randomly: the topology was always the same, only the arrangement
550 of clades was randomized: this is fixed. This function now
551 accepts trees with no branch lengths.
553 o The output of diversi.gof() was blurred by useless prints when a
554 user distribution was specified. This has been corrected, and
555 the help page of this function has been expanded.
560 o The internal structure of the class "phylo" has been changed:
561 see the document "Definition of Formats for Coding Phylogenetic
562 Trees in R" for the details. In addition, the code of most
563 functions has been improved.
565 o Several functions have been improved by replacing some R codes
566 by C codes: pic, plot.phylo, and reorder.phylo.
568 o There is now a citation information: see citation("ape") in R.
570 o write.tree() now does not add extra 0's to branch lengths so
571 that 1.23 is printed "1.23" by default, not "1.2300000000".
573 o The syntax of bind.tree() has been simplified. This function now
574 accepts trees with no branch lengths, and handles correctly node
577 o The option `as.numeric' of mrca() has been removed.
579 o The unused options `format' and `rooted' of read.tree() have
582 o The unused option `format' of write.tree() has been removed.
584 o The use of node.depth() has been simplified.
588 CHANGES IN APE VERSION 1.8-5
593 o Two new functions read.nexus.data() and write.nexus.data(),
594 contributed by Johan Nylander, allow to read and write molecular
595 sequences in NEXUS files.
597 o The new function reorder.phylo() reorders the internal structure
598 of a tree of class "phylo". It is used as the generic, e.g.,
601 o read.tree() and read.nexus() can now read trees with a single
604 o The new data set `cynipids' supplies a set of protein sequences
610 o The code of all.equal.phylo() has been completely rewritten
611 (thanks to Benoît Durand) which fixes several bugs.
613 o read.tree() and read.nexus() now checks the labels of the tree
614 to remove or substitute any characters that are illegal in the
615 Newick format (parentheses, etc.)
617 o A negative P-value could be returned by mantel.test(): this is
622 CHANGES IN APE VERSION 1.8-4
627 o The new function sh.test() computes the Shimodaira-
630 o The new function collapse.singles() removes the nodes with a
631 single descendant from a tree.
633 o plot.phylo() has a new argument `tip.color' to specify the
636 o mlphylo() has now an option `quiet' to control the display of
637 the progress of the analysis (the default is FALSE).
642 o read.dna() did not read correctly sequences in sequential format
643 with leading alignment gaps "-": this is fixed.
645 o ace() returned a list with no class so that the generic
646 functions (anova, logLik, ...) could not be used directly. This
647 is fixed as ace() now returns an object of class "ace".
649 o anova.ace() had a small bug when computing the number of degrees
650 of freedom: this is fixed.
652 o mlphylo() did not work when the sequences were in a matrix or
653 a data frame: this is fixed.
655 o rtree() did not work correctly when trying to simulate an
656 unrooted tree with two tips: an error message is now issued.
661 o The algorithm of rtree() has been changed: it is now about 40,
662 100, and 130 times faster for 10, 100, and 1000 tips,
667 CHANGES IN APE VERSION 1.8-3
672 o There are four new `method' functions to be used with the
673 results of ace(): logLik(), deviance(), AIC(), and anova().
675 o The plot method of phymltest has two new arguments: `main' to
676 change the title, and `col' to control the colour of the
677 segments showing the AIC values.
679 o ace() has a new argument `ip' that gives the initial values used
680 in the ML estimation with discrete characters (see the examples
681 in ?ace). This function now returns a matrix giving the indices
682 of the estimated rates when analysing discrete characters.
684 o nodelabels() and tiplabels() have a new argument `pie' to
685 represent proportions, with any number of categories, as
686 piecharts. The use of the option `thermo' has been improved:
687 there is now no limitation on the number of categories.
692 o mlphylo() did not work with more than two partitions: this is
695 o root() failed if the proposed outgroup was already an outgroup
696 in the tree: this is fixed.
698 o The `col' argument in nodelabels() and tiplabels() was not
699 correctly passed when `text' was used: this is fixed.
701 o Two bugs were fixed in mlphylo(): parameters were not always
702 correctly output, and the estimation failed in some cases.
704 o plot.phylo() was stuck when given a tree with a single tip: this
705 is fixed and a message error is now returned.
707 o An error was corrected in the help page of gammaStat regarding
708 the calculation of P-values.
710 o Using gls() could crash R when the number of species in the tree
711 and in the variables were different: this is fixed.
715 CHANGES IN APE VERSION 1.8-2
720 o The new function mlphylo() fits a phylogenetic tree by maximum
721 likelihood from DNA sequences. Its companion function DNAmodel()
722 is used to define the substitution model which may include
723 partitioning. There are methods for logLik(), deviance(), and
724 AIC(), and the summary() method has been extended to display in
725 a friendly way the results of this model fitting. Currently, the
726 functionality is limited to estimating the substitution and
727 associated parameters and computing the likelihood.
729 o The new function drop1.compar.gee (used as, e.g., drop1(m))
730 tests for single effects in GEE-based comparative method. A
731 warning message is printed if there is not enough degrees of
737 o An error message was sometimes issued by plot.multi.tree(),
738 though with no consequence.
742 CHANGES IN APE VERSION 1.8-1
747 o There is a new plot method for lists of trees (objects of class
748 "multi.tree"): it calls plot.phylo() internally and is
749 documented on the same help page.
754 o A bug was fixed in the C code that analyzes bipartitions: this
755 has impact on several functions like prop.part, prop.clades,
756 boot.phylo, or consensus.
758 o root() did not work correctly when the specified outgroup had
759 more than one element: this is fixed.
761 o dist.dna() sometimes returned a warning inappropriately: this
764 o If the distance object given to nj() had no rownames, nj()
765 returned a tree with no tip labels: it now returns tips labelled
766 "1", "2", ..., corresponding to the row numbers.
771 o nj() has been slightly changed so that tips with a zero distance
772 are first aggregated with zero-lengthed branches; the usual NJ
773 procedure is then performed on a distance matrix without 0's.
777 CHANGES IN APE VERSION 1.8
782 o The new function chronopl() estimates dates using the penalized
783 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
785 o The new function consensus() calculates the consensus tree of a
788 o The new function evolve.phylo() simulates the evolution of
789 continuous characters along a phylogeny under a Brownian model.
791 o The new plot method for objects of class "ancestral" displays a
792 tree together with ancestral values, as returned by the above
795 o The new function as.phylo.formula() returns a phylogeny from a
796 set of nested taxonomic variables given as a formula.
798 o The new function read.caic() reads trees in CAIC format.
800 o The new function tiplabels() allows to add labels to the tips
801 of a tree using text or plotting symbols in a flexible way.
803 o The new function unroot() unroots a phylogeny.
805 o multi2di() has a new option, `random', which specifies whether
806 to resolve the multichotomies randomly (the default) or not.
808 o prop.part() now returns an object of class "prop.part" for which
809 there are print (to display a partition in a more friendly way)
810 and summary (to extract the numbers) methods.
812 o plot.phylo() has a new option, `show.tip.label', specifying
813 whether to print the labels of the tips. The default is TRUE.
815 o The code of nj() has been replaced by a faster C code: it is now
816 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
819 o write.nexus() now writes whether a tree is rooted or not.
824 o Two bugs have been fixed in root(): unrooted trees are now
825 handled corretly, and node labels are now output normally.
827 o A bug was fixed in phymltest(): the executable couldn't be found
830 o Three bug have been fixed in ace(): computing the likelihood of
831 ancestral states of discrete characters failed, custom models
832 did not work, and the function failed with a null gradient (a
833 warning message is now returned; this latter bug was also
834 present in yule.cov() as well and is now fixed).
836 o pic() hanged out when missing data were present: a message error
839 o A small bug was fixed in dist.dna() where the gamma correction
840 was not always correctly dispatched.
842 o plot.phylo() plotted correctly the root edge only when the tree
843 was plotted rightwards: this works now for all directions.
848 o dist.taxo() has been renamed as weight.taxo().
850 o Various error and warning messages have been improved.
854 CHANGES IN APE VERSION 1.7
857 o The new function ace() estimates ancestral character states for
858 continuous characters (with ML, GLS, and contrasts methods), and
859 discrete characters (with ML only) for any number of states.
861 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
862 of directional evolution for continuous characters. The user
863 specifies the node(s) of the tree where the character optimum
866 o The new function is.rooted() tests whether a tree (of class
869 o The new function rcoal() generates random ultrametric trees with
870 the possibility to specify the function that generates the
871 inter-nodes distances.
873 o The new function mrca() gives for all pairs of tips in a tree
874 (and optionally nodes too) the most recent common ancestor.
876 o nodelabels() has a new option `thermo' to plot proportions (up
877 to three classes) on the nodes of a tree.
879 o rtree() has been improved: it can now generate rooted or
880 unrooted trees, and the mathematical function that generates the
881 branch lengths may be specified by the user. The tip labels may
882 be given directly in the call to rtree. The limit cases (n = 2,
883 3) are now handled correctly.
885 o dist.topo() has a new argument `method' with two choices: "PH85"
886 for Penny and Henny's method (already available before and now
887 the default), and "BHV01" for the geometric distance by Billera
888 et al. (2001, Adv. Appl. Math. 27:733).
890 o write.tree() has a new option, `digits', which specifies the
891 number of digits to be printed in the Newick tree. By default
892 digits = 10. The numbers are now always printed in decimal form
893 (i.e., 1.0e-1 is now avoided).
895 o dist.dna() can now compute the raw distances between pairs of
896 DNA sequences by specifying model = "raw".
898 o dist.phylo() has a new option `full' to possibly compute the
899 distances among all tips and nodes of the tree. The default if
905 o Several bugs were fixed in all.equal.phylo().
907 o dist.dna() did not handle correctly gaps ("-") in alignments:
908 they are now considered as missing data.
910 o rotate() did not work if the tips were not ordered: this is
913 o mantel.test() returned NA in some special cases: this is fixed
914 and the function has been improved and is now faster.
916 o A bug was fixed in diversi.gof() where the calculation of A² was
919 o cherry() did not work correctly under some OSs (mainly Linux):
922 o is.binary.tree() has been modified so that it works with both
923 rooted and unrooted trees.
925 o The documentation of theta.s() was not correct: this has been
928 o plot.mst() did not work correctly: this is fixed.
932 CHANGES IN APE VERSION 1.6
937 o The new function dist.topo() computes the topological distances
940 o The new function boot.phylo() performs a bootstrap analysis on
941 phylogeny estimation.
943 o The new functions prop.part() and prop.clades() analyse
944 bipartitions from a series of trees.
949 o read.GenBank() now uses the EFetch utility of NCBI instead of
950 the usual Web interface: it is now much faster (e.g., 12 times
951 faster to retrieve 8 sequences, 37 times for 60 sequences).
956 o Several bugs were fixed in read.dna().
958 o Several bugs were fixed in diversi.time().
960 o is.binary.tree() did not work correctly if the tree has no edge
961 lengths: this is fixed.
963 o drop.tip() did not correctly propagated the `node.label' of a
968 CHANGES IN APE VERSION 1.5
973 o Two new functions, as.matching.phylo() and as.phylo.matching(),
974 convert objects between the classes "phylo" and "matching". The
975 latter implements the representation of binary trees introduced by
976 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
977 as.matching() has been introduced as well.
979 o Two new functions, multi2di() and di2multi(), allow to resolve
980 and collapse multichotomies with branches of length zero.
982 o The new function nuc.div() computes the nucleotide diversity
983 from a sample a DNA sequences.
985 o dist.dna() has been completely rewritten with a much faster
986 (particularly for large data sets) C code. Eight models are
987 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
988 option `method' has been renamed `model'). Computation of variance
989 is available for all models. A gamma-correction is possible for
990 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
991 to remove sites with missing data on a pairwise basis. The option
992 `GCcontent' has been removed.
994 o read.GenBank() has a new option (species.names) which specifies
995 whether to return the species names of the organisms in addition
996 to the accession numbers of the sequences (this is the default
999 o write.nexus() can now write several trees in the same NEXUS file.
1001 o drop.tip() has a new option `root.edge' that allows to specify the
1002 new root edge if internal branches are trimmed.
1007 o as.phylo.hclust() failed if some labels had parentheses: this
1010 o Several bugs were fixed in all.equal.phylo(). This function now
1011 returns the logical TRUE if the trees are identical but with
1012 different representations (a report was printed previously).
1014 o read.GenBank() did not correctly handle ambiguous base codes:
1020 o birthdeath() now returns an object of class "birthdeath" for
1021 which there is a print method.
1025 CHANGES IN APE VERSION 1.4
1030 o The new function nj() performs phylogeny estimation with the
1031 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1034 o The new function which.edge() identifies the edges of a tree
1035 that belong to a group specified as a set of tips.
1037 o The new function as.phylo.phylog() converts an object of class
1038 "phylog" (from the package ade4) into an object of class
1041 o The new function axisPhylo() draws axes on the side of a
1044 o The new function howmanytrees() calculates the number of trees
1045 in different cases and giving a number of tips.
1047 o write.tree() has a new option `multi.line' (TRUE by default) to
1048 write a Newick tree on several lines rather than on a single
1051 o The functionalities of zoom() have been extended. Several
1052 subtrees can be visualized at the same time, and they are marked
1053 on the main tree with colors. The context of the subtrees can be
1054 marked with the option `subtree' (see below).
1056 o drop.tip() has a new option `subtree' (FALSE by default) which
1057 specifies whether to output in the tree how many tips have been
1060 o The arguments of add.scale.bar() have been redefined and have
1061 now default values (see ?add.scale.bar for details). This
1062 function now works even if the plotted tree has no edge length.
1064 o plot.phylo() can now plot radial trees, but this does not take
1065 edge lengths into account.
1067 o In plot.phylo() with `type = "phylogram"', if the values of
1068 `edge.color' and `edge.width' are identical for sister-branches,
1069 they are propagated to the vertical line that link them.
1074 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1075 crashing. This is fixed.
1077 o In plot.phylo(), the options `edge.color' and `edge.width' are
1078 now properly recycled; their default values are now "black" and
1081 o A bug has been fixed in write.nexus().
1086 o The function node.depth.edgelength() has been removed and
1087 replaced by a C code.
1091 CHANGES IN APE VERSION 1.3-1
1096 o The new function nodelabels() allows to add labels to the nodes
1097 of a tree using text or plotting symbols in a flexible way.
1099 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1100 numeric values specifying the lower and upper limits on the x-
1101 and y-axes. This allows to leave some space on any side of the
1102 tree. If a single value is given, this is taken as the upper
1107 CHANGES IN APE VERSION 1.3
1112 o The new function phymltest() calls the software PHYML and fits
1113 28 models of DNA sequence evolution. There are a print method to
1114 display likelihood and AIC values, a summary method to compute
1115 the hierarchical likelihood ratio tests, and a plot method to
1116 display graphically the AIC values of each model.
1118 o The new function yule.cov() fits the Yule model with covariates,
1119 a model where the speciation rate is affected by several species
1120 traits through a generalized linear model. The parameters are
1121 estimated by maximum likelihood.
1123 o Three new functions, corBrownian(), corGrafen(), and
1124 corMartins(), compute the expected correlation structures among
1125 species given a phylogeny under different models of evolution.
1126 These can be used for GLS comparative phylogenetic methods (see
1127 the examples). There are coef() and corMatrix() methods and an
1128 Initialize.corPhyl() function associated.
1130 o The new function compar.cheverud() implements Cheverud et al.'s
1131 (1985; Evolution 39:1335) phylogenetic comparative method.
1133 o The new function varcomp() estimates variance components; it has
1136 o Two new functions, panel.superpose.correlogram() and
1137 plot.correlogramList(), allow to plot several phylogenetic
1140 o The new function node.leafnumber() computes the number of leaves
1141 of a subtree defined by a particular node.
1143 o The new function node.sons() gets all tags of son nodes from a
1146 o The new function compute.brlen() computes the branch lengths of
1147 a tree according to a specified method.
1149 o plot.phylo() has three new options: "cex" controls the size of
1150 the (tip and node) labels (thus it is no more needed to change
1151 the global graphical parameter), "direction" which allows to
1152 plot the tree rightwards, leftwards, upwards, or downwards, and
1153 "y.lim" which sets the upper limit on the y-axis.
1158 o Some functions which try to match tip labels and names of
1159 additional data (e.g. vector) are likely to fail if there are
1160 typing or syntax errors. If both series of names do not perfectly
1161 match, they are ignored and a warning message is now issued.
1162 These functions are bd.ext, compar.gee, pic. Their help pages
1163 have been clarified on this point.
1167 CHANGES IN APE VERSION 1.2-7
1172 o The new function root() reroots a phylogenetic tree with respect
1173 to a specified outgroup.
1175 o The new function rotate() rotates an internal branch of a tree.
1177 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1178 trees) controls the display of the tip labels in unrooted trees.
1179 This display has been greatly improved: the tip labels are now not
1180 expected to overlap with the tree (particularly if lab4ut =
1181 "axial"). In all cases, combining appropriate values of "lab4ut"
1182 and the font size (via "par(cex = )") should result in readable
1183 unrooted trees. See ?plot.phylo for some examples.
1185 o In drop.tip(), the argument `tip' can now be numeric or character.
1190 o drop.tip() did not work correctly with trees with no branch
1191 lengths: this is fixed.
1193 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1194 plotted with some line crossings: this is now fixed.
1198 CHANGES IN APE VERSION 1.2-6
1203 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1204 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1205 to implement comparative methods with an autocorrelation approach.
1207 o A new data set describing some life history traits of Carnivores
1213 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1218 o When plotting a tree with plot.phylo(), the new default of the
1219 option `label.offset' is now 0, so the labels are always visible.
1223 CHANGES IN APE VERSION 1.2-5
1228 o The new function bd.ext() fits a birth-death model with combined
1229 phylogenetic and taxonomic data, and estimates the corresponding
1230 speciation and extinction rates.
1235 o The package gee is no more required by ape but only suggested
1236 since only the function compar.gee() calls gee.
1240 CHANGES IN APE VERSION 1.2-4
1245 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1246 and lines.popsize) implementing a new approach for inferring the
1247 demographic history from genealogies using a reversible jump
1248 MCMC have been introduced.
1250 o The unit of time in the skyline plot and in the new plots can
1251 now be chosen to be actual years, rather than substitutions.
1255 CHANGES IN APE VERSION 1.2-3
1260 o The new function rtree() generates a random binary tree with or
1261 without branch lengths.
1263 o Two new functions for drawing lineages-through-time (LTT) plots
1264 are provided: ltt.lines() adds a LTT curve to an existing plot,
1265 and mltt.plot() does a multiple LTT plot giving several trees as
1266 arguments (see `?ltt.plot' for details).
1271 o Some taxon names made R crashing when calling as.phylo.hclust():
1274 o dist.dna() returned an error with two identical DNA sequences
1275 (only using the Jukes-Cantor method returned 0): this is fixed.
1280 o The function dist.phylo() has been re-written using a different
1281 algorithm: it is now about four times faster.
1283 o The code of branching.times() has been improved: it is now about
1288 CHANGES IN APE VERSION 1.2-2
1293 o The new function seg.sites() finds the segregating sites in a
1294 sample of DNA sequences.
1299 o A bug introduced in read.tree() and in read.nexus() with version
1302 o A few errors were corrected and a few examples were added in the
1307 CHANGES IN APE VERSION 1.2-1
1312 o plot.phylo() can now draw the edge of the root of a tree if it
1313 has one (see the new option `root.edge', its default is FALSE).
1318 o A bug was fixed in read.nexus(): files with semicolons inside
1319 comment blocks were not read correctly.
1321 o The behaviour of read.tree() and read.nexus() was corrected so
1322 that tree files with badly represented root edges (e.g., with
1323 an extra pair of parentheses, see the help pages for details)
1324 are now correctly represented in the object of class "phylo";
1325 a warning message is now issued.
1329 CHANGES IN APE VERSION 1.2
1334 o plot.phylo() has been completely re-written and offers several
1335 new functionalities. Three types of trees can now be drawn:
1336 phylogram (as previously), cladogram, and unrooted tree; in
1337 all three types the branch lengths can be drawn using the edge
1338 lengths of the phylogeny or not (e.g., if the latter is absent).
1339 The vertical position of the nodes can be adjusted with two
1340 choices (see option `node.pos'). The code has been re-structured,
1341 and two new functions (potentially useful for developpers) are
1342 documented separately: node.depth.edgelength() and node.depth();
1343 see the respective help pages for details.
1345 o The new function zoom() allows to explore very large trees by
1346 focusing on a small portion of it.
1348 o The new function yule() fits by maximum likelihood the Yule model
1349 (birth-only process) to a phylogenetic tree.
1351 o Support for writing DNA sequences in FASTA format has been
1352 introduced in write.dna() (support for reading sequences in
1353 this format was introduced in read.dna() in version 1.1-2).
1354 The function has been completely re-written, fixing some bugs
1355 (see below); the default behaviour is no more to display the
1356 sequences on the standard output. Several options have been
1357 introduced to control the sequence printing in a flexible
1358 way. The help page has been extended.
1360 o A new data set is included: a supertree of bats in NEXUS format.
1365 o In theta.s(), the default of the option `variance' has
1366 been changed to `FALSE' (as was indicated in the help page).
1368 o Several bugs were fixed in the code of all.equal.phylo().
1370 o Several bugs were fixed in write.dna(), particularly this
1371 function did not work with `format = "interleaved"'.
1373 o Various errors were corrected in the help pages.
1378 o The argument names of as.hclust.phylo() have been changed
1379 from "(phy)" to "(x, ...)" to conform to the definition of
1380 the corresponding generic function.
1382 o gamma.stat() has been renamed gammaStat() to avoid confusion
1383 since gamma() is a generic function.
1387 CHANGES IN APE VERSION 1.1-3
1392 o base.freq() previously did not return a value of 0 for
1393 bases absent in the data (e.g., a vector of length 3 was
1394 returned if one base was absent). This is now fixed (a
1395 vector of length 4 is always returned).
1397 o Several bugs were fixed in read.nexus(), including that this
1398 function did not work in this absence of a "TRANSLATE"
1399 command in the NEXUS file, and that the commands were
1404 CHANGES IN APE VERSION 1.1-2
1409 o The Tamura and Nei (1993) model of DNA distance is now implemented
1410 in dist.dna(): five models are now available in this function.
1412 o A new data set is included: a set of 15 sequences of the
1413 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1419 o A bug in read.nexus() was fixed.
1421 o read.dna() previously did not work correctly in most cases.
1422 The function has been completely re-written and its help page
1423 has been considerably extended (see ?read.dna for details).
1424 Underscores (_) in taxon names are no more replaced with
1425 spaces (this behaviour was undocumented).
1427 o A bug was fixed in write.dna().
1431 CHANGES IN APE VERSION 1.1-1
1436 o A bug in read.tree() introduced in APE 1.1 was fixed.
1438 o A bug in compar.gee() resulted in an error when trying to fit
1439 a model with `family = "binomial"'. This is now fixed.
1443 CHANGES IN APE VERSION 1.1
1448 o The Klastorin (1982) method as suggested by Misawa and Tajima
1449 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1450 on the basis of phylogenetic trees has been implemented (see
1451 the function klastorin()).
1453 o Functions have been added to convert APE's "phylo" objects in
1454 "hclust" cluster objects and vice versa (see the help page of
1455 as.phylo for details).
1457 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1458 are introduced for the estimation of absolute evolutionary rates
1459 (ratogram) and dated clock-like trees (chronogram) from
1460 phylogenetic trees using the non-parametric rate smoothing approach
1461 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1463 o A summary method is now provided printing a summary information on a
1464 phylogenetic tree with, for instance, `summary(tree)'.
1466 o The behaviour of read.tree() was changed so that all spaces and
1467 tabulations in tree files are now ignored. Consequently, spaces in tip
1468 labels are no more allowed. Another side effect is that read.nexus()
1469 now does not replace the underscores (_) in tip labels with spaces
1470 (this behaviour was undocumented).
1472 o The function plot.phylo() has a new option (`underscore') which
1473 specifies whether the underscores in tip labels should be written on
1474 the plot as such or replaced with spaces (the default).
1476 o The function birthdeath() now computes 95% confidence intervals of
1477 the estimated parameters using profile likelihood.
1479 o Three new data sets are included: a gene tree estimated from 36
1480 landplant rbcL sequences, a gene tree estimated from 32 opsin
1481 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1486 o A bug was fixed in dist.gene() where nothing was returned.
1488 o A bug in plot.mst() was fixed.
1490 o A bug in vcv.phylo() resulted in false correlations when the
1491 option `cor = TRUE' was used (now fixed).
1495 CHANGES IN APE VERSION 1.0
1500 o Two new functions, read.dna() and write.dna(), read/write in a file
1501 DNA sequences in interleaved or in sequential format.
1503 o Two new functions, read.nexus() and write.nexus(), read/write trees
1506 o The new function bind.tree() allows to bind two trees together,
1507 possibly handling root edges to give internal branches.
1509 o The new function drop.tip() removes the tips in a phylogenetic tree,
1510 and trims (or not) the corresponding internal branches.
1512 o The new function is.ultrametric() tests if a tree is ultrametric.
1514 o The function plot.phylo() has more functionalities such as drawing the
1515 branches with different colours and/or different widths, showing the
1516 node labels, controling the position and font of the labels, rotating
1517 the labels, and controling the space around the plot.
1519 o The function read.tree() can now read trees with no branch length,
1520 such as "(a,b),c);". Consequently, the element `edge.length' in
1521 objects of class "phylo" is now optional.
1523 o The function write.tree() has a new default behaviour: if the default
1524 for the option `file' is used (i.e. file = ""), then a variable of
1525 mode character containing the tree in Newick format is returned which
1526 can thus be assigned (e.g., tree <- write.tree(phy)).
1528 o The function read.tree() has a new argument `text' which allows
1529 to read the tree in a variable of mode character.
1531 o A new data set is included: the phylogenetic relationships among
1532 the orders of birds from Sibley and Ahlquist (1990).
1536 CHANGES IN APE VERSION 0.2-1
1541 o Several bugs were fixed in the help pages.
1545 CHANGES IN APE VERSION 0.2
1550 o The function write.tree() writes phylogenetic trees (objects of class
1551 "phylo") in an ASCII file using the Newick parenthetic format.
1553 o The function birthdeath() fits a birth-death model to branching times
1554 by maximum likelihood, and estimates the corresponding speciation and
1557 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1560 o The function is.binary.tree() tests whether a phylogeny is binary.
1562 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1563 as well as some methods are introduced.
1565 o Several functions, including some generics and methods, for computing
1566 skyline plot estimates (classic and generalized) of effective
1567 population size through time are introduced and replace the function
1568 skyline.plot() in version 0.1.
1570 o Two data sets are now included: the phylogenetic relationships among
1571 the families of birds from Sibley and Ahlquist (1990), and an
1572 estimated clock-like phylogeny of HIV sequences sampled in the
1573 Democratic Republic of Congo.
1576 DEPRECATED & DEFUNCT
1578 o The function skyline.plot() in ape 0.1 has been deprecated and
1579 replaced by more elaborate functions (see above).
1584 o Two important bugs were fixed in plot.phylo(): phylogenies with
1585 multichotomies not at the root or not with only terminal branches,
1586 and phylogenies with a single node (i.e. only terminal branches)
1587 did not plot. These trees should be plotted correctly now.
1589 o Several bugs were fixed in diversi.time() in the computation of
1592 o Various errors were corrected in the help pages.