1 CHANGES IN APE VERSION 2.2-1
6 o The new function makeLabel() helps to modify labels of trees,
7 lists of trees, or DNA sequences, with several utilities to
8 truncate and/or make them unique, substituting some
11 o The new function del.gaps() removes insertion gaps ("-") in a
14 o read.dna() can now read Clustal files (*.aln).
19 o root() failed with 'resolve.root = TRUE' when the root was
20 already the specified root.
22 o Several bugs were fixed in mlphylo().
24 o collapsed.singles() did not propagate the 'Nnode' and
25 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
27 o read.nexus() failed to remove correctly the comments within
30 o read.nexus() failed to read a file with a single tree and no
31 translation of tip labels.
33 o read.nexus() failed to place correctly tip labels when reading
34 a single tree with no edge lengths.
36 o A bug was fixed in sh.test().
41 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
44 o The option 'check.labels' of consensus() and prop.part() is now
47 o write.dna() now does not truncate names to 10 characters with
52 CHANGES IN APE VERSION 2.2
57 o Four new functions have been written by Damien de Vienne for the
58 graphical exploration of large trees (cophyloplot, subtrees,
59 subtreeplot), and to return the graphical coordinates of tree
62 o The new functions corPagel and corBlomberg implement the Pagel's
63 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
65 o chronopl() has been improved and gains several options: see its
66 help page for details.
68 o boot.phylo() has now an option 'trees' to possibly return the
69 bootstraped trees (the default is FALSE).
71 o prop.part() has been improved and should now be faster in all
77 o read.dna() failed if "?" occurred in the first 10 sites of the
80 o The x/y aspect of the plot is now respected when plotting a
81 circular tree (type = "r" or "f").
83 o Drawing the tip labels sometimes failed when plotting circular
86 o zoom() failed when tip labels were used instead of their numbers
87 (thanks to Yan Wong for the fix).
89 o drop.tip() failed with some trees (fixed by Yan Wong).
91 o seg.sites() failed with a list.
93 o consensus() failed in some cases. The function has been improved
94 as well and is faster.
98 CHANGES IN APE VERSION 2.1-3
103 o A bug in read.nexus() made the Windows R-GUI crash.
105 o An error was fixed in the computation of ancestral character
106 states by generalized least squares in ace().
108 o di2multi() did not modify node labels correctly.
110 o multi2di() failed if the tree had its attribute "order" set to
115 CHANGES IN APE VERSION 2.1-2
120 o There three new methods for the "multiPhylo" class: str, $,
123 o root() gains the options 'node' and 'resolve.root'
124 (FALSE by default) as well as its code being improved.
126 o mltt.plot() has now an option 'log' used in the same way
127 than in plot.default().
132 o mltt.plot() failed to display the legend with an unnamed
135 o nodelabels() with pies now correcly uses the argument
136 'cex' to draw symbols of different sizes (which has
137 worked already for thermometers).
139 o read.nexus() generally failed to read very big files.
144 o The argument 'family' of compar.gee() can now be a function
145 as well as a character string.
147 o read.tree() and read.nexus() now return an unnamed list if
150 o read.nexus() now returns a modified object of class "multiPhylo"
151 when there is a TRANSLATE block in the NEXUS file: the individual
152 trees have no 'tip.label' vector, but the list has a 'TipLabel'
153 attribute. The new methods '$' and '[[' set these elements
154 correctly when extracting trees.
158 CHANGES IN APE VERSION 2.1-1
163 o The new function rmtree generates lists of random trees.
165 o rcoal() now generates a genuine coalescent tree by default
166 (thanks to Vladimir Minin for the code).
171 o nuc.div() returned an incorrect value with the default
172 pairwise.deletion = FALSE.
177 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
178 have been improved so that they are stabler and faster.
180 o R packages used by ape are now loaded silently; lattice and gee
181 are loaded only when needed.
185 CHANGES IN APE VERSION 2.1
190 o The new function identify.phylo identifies clades on a plotted
191 tree using the mouse.
193 o It is now possible to subset a list of trees (object of class
194 "multiPhylo") with "[" while keeping its class correct.
196 o The new function as.DNAbin.alignment converts DNA sequences
197 stored in the "alignment" format of the package seqinr into
198 an object of class "DNAbin".
200 o The new function weight.taxo2 helps to build similarity matrices
201 given two taxonomic levels (usually called by other functions).
203 o write.tree() can now take a list of trees (class "multiPhylo")
204 as its main argument.
206 o plot.correlogram() and plot.correlogramList() have been
207 improved, and gain several options (see the help page for
208 details). A legend is now plotted by default.
213 o dist.dna() returned some incorrect values with `model = "JC69"'
214 and `pairwise.deletion = TRUE'. This affected only the
215 distances involving sequences with missing values. (Thanks
216 to Bruno Toupance for digging this bug out.)
218 o write.tree() failed with some trees: this is fixed by removing
219 the `multi.line' option (trees are now always printed on a
222 o read.nexus() did not correctly detect trees with multiple root
223 edges (see OTHER CHANGES).
228 o The code of mlphylo() has almost entirely rewritten, and should
229 be much stabler. The options have been also greatly simplified
230 (see ?mlphylo and ?DNAmodel for details).
232 o The internal function nTips has been renamed klastorin_nTips.
234 o The code of is.ultrametric() contained redundancies and has
237 o The code of Moran.I() and of correlogram.formula() have been
240 o read.tree() and read.nexus() now return an error when trying to
241 read a tree with multiple root edges (see BUG FIXES). The
242 correction applied in previous version did not work in all
245 o The class c("multi.tree", "phylo") has been renamed
251 o There is now a vignette in ape: see vignette("MoranI", "ape").
256 o as.matching() and as.phylo.matching() do not support branch
259 o correlogram.phylo() and discrete.dist() have been removed.
263 CHANGES IN APE VERSION 2.0-2
268 o The new function matexpo computes the exponential of a square
271 o The new function unique.multi.tree removes duplicate trees from
274 o yule() has a new option `use.root.edge = FALSE' that specifies
275 to ignore, by default, the root edge of the tree if it exists.
280 o which.edge() failed when the index of a single terminal edge was
283 o In diversi.time(), the values returned for model C were
286 o A bug was fixed in yule() that affected the calculation of the
287 likelihood in the presence of ties in the branching times.
289 o There was a bug in the C function mat_expo4x4 affecting the
290 calculations of the transition probabilities for models HKY and
293 o A small bug was fixed in as.matrix.DNAbin (thanks to James
296 o rtree() did not `shuffle' the tip labels by default, so only a
297 limited number of labelled topologies could be generated.
301 CHANGES IN APE VERSION 2.0-1
306 o The three new functions bionj, fastme.ols, and fastme.bal
307 perform phylogeny estimation by the BIONJ and fastME methods in
308 OLS and balanced versions. This is a port to R of previous
309 previous programs done by Vincent Lefort.
311 o The new function chronoMPL performs molecular dating with the
312 mean path lengths method of Britton et al. (2002, Mol. Phyl.
315 o The new function rotate, contributed by Christoph Heibl, swaps
316 two clades connected to the same node. It works also with
317 multichotomous nodes.
319 o The new `method' as.matrix.DNAbin() may be used to convert
320 easily DNA sequences stored in a list into a matrix while
321 keeping the names and the class.
326 o chronopl() failed when some branch lengths were equal to zero:
327 an error message is now returned.
329 o di2multi() failed when there was a series of consecutive edges
334 CHANGES IN APE VERSION 1.10-2
339 o plot.phylo() can now plot circular trees: the option is type =
340 "fan" or type = "f" (to avoid the ambiguity with type = "c").
342 o prop.part() has a new option `check.labels = FALSE' which allows
343 to considerably speed-up the calculations of bipartitions. As a
344 consequence, calculations of bootstrap values with boot.phylo()
345 should be much faster.
350 o read.GenBank() did not return correctly the list of species as
351 from ape 1.10: this is fixed in this version
353 o Applying as.phylo() on a tree of class "phylo" failed: the
354 object is now returned unchanged.
358 CHANGES IN APE VERSION 1.10-1
363 o The three new functions Ntip, Nnode, and Nedge return, for a
364 given tree, the number of tips, nodes, or edges, respectively.
369 o read.nexus() did not set correctly the class of the returned
370 object when reading multiple trees.
372 o mllt.plot() failed with objects of class c("multi.tree",
375 o unroot() did not work correctly in most cases.
377 o reorder.phylo() made R freeze in some occasions.
379 o Plotting a tree in pruningwise order failed.
381 o When plotting an unrooted tree, the tip labels where not all
382 correctly positioned if the option `cex' was used.
386 CHANGES IN APE VERSION 1.10
391 o Five new `method' functions have been introduced to manipulate
392 DNA sequences in binary format (see below).
394 o Three new functions have been introduced to convert between the
395 new binary and the character formats.
397 o The new function as.alignment converts DNA sequences stored as
398 single characters into the class "alignment" used by the package
401 o read.dna() and read.GenBank() have a new argument `as.character'
402 controlling whether the sequences are returned in binary format
408 o root() failed when the tree had node labels: this is fixed.
410 o plot.phylo() did not correctly set the limits on the y-axis with
411 the default setting: this is fixed.
413 o dist.dna() returned a wrong result for the LogDet, paralinear,
414 and BH87 models with `pairwise.deletion = TRUE'.
419 o DNA sequences are now internally stored in a binary format. See
420 the document "A Bit-Level Coding Scheme for Nucleotides" for the
421 details. Most functions analyzing DNA functions have been
422 modified accordingly and are now much faster (dist.dna is now
423 ca. 60 times faster).
427 CHANGES IN APE VERSION 1.9-4
432 o A bug was fixed in edgelabels().
434 o as.phylo.hclust() did not work correctly when the object of
435 class "hclust" has its labels set to NULL: the returned tree has
436 now its tip labels set to "1", "2", ...
438 o consensus could fail if some tip labels are a subset of others
439 (e.g., "a" and "a_1"): this is now fixed.
441 o mlphylo() failed in most cases if some branch lengths of the
442 initial tree were greater than one: an error message is now
445 o mlphylo() failed in most cases when estimating the proportion of
446 invariants: this is fixed.
450 CHANGES IN APE VERSION 1.9-3
455 o The new function edgelabels adds labels on the edge of the tree
456 in the same way than nodelabels or tiplabels.
461 o multi2di() did not handle correctly branch lengths with the
462 default option `random = TRUE': this is now fixed.
464 o A bug was fixed in nuc.div() when using pairwise deletions.
466 o A bug occurred in the analysis of bipartitions with large
467 numbers of large trees, with consequences on prop.part,
468 prop.clades, and boot.phylo.
470 o The calculation of the Billera-Holmes-Vogtmann distance in
471 dist.topo was wrong: this has been fixed.
475 CHANGES IN APE VERSION 1.9-2
480 o The new function ladderize reorganizes the internal structure of
481 a tree to plot them left- or right-ladderized.
483 o The new function dist.nodes computes the patristic distances
484 between all nodes, internal and terminal, of a tree. It replaces
485 the option `full = TRUE' of cophenetic.phylo (see below).
490 o A bug was fixed in old2new.phylo().
492 o Some bugs were fixed in chronopl().
494 o The edge colours were not correctly displayed by plot.phylo
495 (thank you to Li-San Wang for the fix).
497 o cophenetic.phylo() failed with multichotomous trees: this is
503 o read.dna() now returns the sequences in a matrix if they are
504 aligned (interleaved or sequential format). Sequences in FASTA
505 format are still returned in a list.
507 o The option `full' of cophenetic.phylo() has been removed because
508 it could not be used from the generic.
513 o rotate() has been removed; this function did not work correctly
518 CHANGES IN APE VERSION 1.9-1
523 o Trees with a single tip were not read correctly in R as the
524 element `Nnode' was not set: this is fixed.
526 o unroot() did not set correctly the number of nodes of the
527 unrooted tree in most cases.
529 o read.GenBank() failed when fetching very long sequences,
530 particularly of the BX-series.
532 o A bug was introduced in read.tree() with ape 1.9: it has been
537 CHANGES IN APE VERSION 1.9
542 o There are two new print `methods' for trees of class "phylo" and
543 lists of trees of class "multi.tree", so that they are now
544 displayed in a compact and informative way.
546 o There are two new functions, old2new.phylo and new2old.phylo,
547 for converting between the old and new coding of the class
550 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
551 LogDet ("logdet"), and paralinear ("paralin").
553 o compute.brlen() has been extended: several methods are now
554 available to compute branch lengths.
556 o write.dna() can now handle matrices as well as lists.
561 o cophenetic.phylo() sometimes returned a wrong result with
562 multichotomous trees: this is fixed.
564 o rotate() failed when a single tip was specified: the tree is now
567 o ace() did not return the correct index matrix with custom
568 models: this is fixed.
570 o multi2di() did not work correctly when resolving multichotomies
571 randomly: the topology was always the same, only the arrangement
572 of clades was randomized: this is fixed. This function now
573 accepts trees with no branch lengths.
575 o The output of diversi.gof() was blurred by useless prints when a
576 user distribution was specified. This has been corrected, and
577 the help page of this function has been expanded.
582 o The internal structure of the class "phylo" has been changed:
583 see the document "Definition of Formats for Coding Phylogenetic
584 Trees in R" for the details. In addition, the code of most
585 functions has been improved.
587 o Several functions have been improved by replacing some R codes
588 by C codes: pic, plot.phylo, and reorder.phylo.
590 o There is now a citation information: see citation("ape") in R.
592 o write.tree() now does not add extra 0's to branch lengths so
593 that 1.23 is printed "1.23" by default, not "1.2300000000".
595 o The syntax of bind.tree() has been simplified. This function now
596 accepts trees with no branch lengths, and handles correctly node
599 o The option `as.numeric' of mrca() has been removed.
601 o The unused options `format' and `rooted' of read.tree() have
604 o The unused option `format' of write.tree() has been removed.
606 o The use of node.depth() has been simplified.
610 CHANGES IN APE VERSION 1.8-5
615 o Two new functions read.nexus.data() and write.nexus.data(),
616 contributed by Johan Nylander, allow to read and write molecular
617 sequences in NEXUS files.
619 o The new function reorder.phylo() reorders the internal structure
620 of a tree of class "phylo". It is used as the generic, e.g.,
623 o read.tree() and read.nexus() can now read trees with a single
626 o The new data set `cynipids' supplies a set of protein sequences
632 o The code of all.equal.phylo() has been completely rewritten
633 (thanks to Benoît Durand) which fixes several bugs.
635 o read.tree() and read.nexus() now checks the labels of the tree
636 to remove or substitute any characters that are illegal in the
637 Newick format (parentheses, etc.)
639 o A negative P-value could be returned by mantel.test(): this is
644 CHANGES IN APE VERSION 1.8-4
649 o The new function sh.test() computes the Shimodaira-
652 o The new function collapse.singles() removes the nodes with a
653 single descendant from a tree.
655 o plot.phylo() has a new argument `tip.color' to specify the
658 o mlphylo() has now an option `quiet' to control the display of
659 the progress of the analysis (the default is FALSE).
664 o read.dna() did not read correctly sequences in sequential format
665 with leading alignment gaps "-": this is fixed.
667 o ace() returned a list with no class so that the generic
668 functions (anova, logLik, ...) could not be used directly. This
669 is fixed as ace() now returns an object of class "ace".
671 o anova.ace() had a small bug when computing the number of degrees
672 of freedom: this is fixed.
674 o mlphylo() did not work when the sequences were in a matrix or
675 a data frame: this is fixed.
677 o rtree() did not work correctly when trying to simulate an
678 unrooted tree with two tips: an error message is now issued.
683 o The algorithm of rtree() has been changed: it is now about 40,
684 100, and 130 times faster for 10, 100, and 1000 tips,
689 CHANGES IN APE VERSION 1.8-3
694 o There are four new `method' functions to be used with the
695 results of ace(): logLik(), deviance(), AIC(), and anova().
697 o The plot method of phymltest has two new arguments: `main' to
698 change the title, and `col' to control the colour of the
699 segments showing the AIC values.
701 o ace() has a new argument `ip' that gives the initial values used
702 in the ML estimation with discrete characters (see the examples
703 in ?ace). This function now returns a matrix giving the indices
704 of the estimated rates when analysing discrete characters.
706 o nodelabels() and tiplabels() have a new argument `pie' to
707 represent proportions, with any number of categories, as
708 piecharts. The use of the option `thermo' has been improved:
709 there is now no limitation on the number of categories.
714 o mlphylo() did not work with more than two partitions: this is
717 o root() failed if the proposed outgroup was already an outgroup
718 in the tree: this is fixed.
720 o The `col' argument in nodelabels() and tiplabels() was not
721 correctly passed when `text' was used: this is fixed.
723 o Two bugs were fixed in mlphylo(): parameters were not always
724 correctly output, and the estimation failed in some cases.
726 o plot.phylo() was stuck when given a tree with a single tip: this
727 is fixed and a message error is now returned.
729 o An error was corrected in the help page of gammaStat regarding
730 the calculation of P-values.
732 o Using gls() could crash R when the number of species in the tree
733 and in the variables were different: this is fixed.
737 CHANGES IN APE VERSION 1.8-2
742 o The new function mlphylo() fits a phylogenetic tree by maximum
743 likelihood from DNA sequences. Its companion function DNAmodel()
744 is used to define the substitution model which may include
745 partitioning. There are methods for logLik(), deviance(), and
746 AIC(), and the summary() method has been extended to display in
747 a friendly way the results of this model fitting. Currently, the
748 functionality is limited to estimating the substitution and
749 associated parameters and computing the likelihood.
751 o The new function drop1.compar.gee (used as, e.g., drop1(m))
752 tests for single effects in GEE-based comparative method. A
753 warning message is printed if there is not enough degrees of
759 o An error message was sometimes issued by plot.multi.tree(),
760 though with no consequence.
764 CHANGES IN APE VERSION 1.8-1
769 o There is a new plot method for lists of trees (objects of class
770 "multi.tree"): it calls plot.phylo() internally and is
771 documented on the same help page.
776 o A bug was fixed in the C code that analyzes bipartitions: this
777 has impact on several functions like prop.part, prop.clades,
778 boot.phylo, or consensus.
780 o root() did not work correctly when the specified outgroup had
781 more than one element: this is fixed.
783 o dist.dna() sometimes returned a warning inappropriately: this
786 o If the distance object given to nj() had no rownames, nj()
787 returned a tree with no tip labels: it now returns tips labelled
788 "1", "2", ..., corresponding to the row numbers.
793 o nj() has been slightly changed so that tips with a zero distance
794 are first aggregated with zero-lengthed branches; the usual NJ
795 procedure is then performed on a distance matrix without 0's.
799 CHANGES IN APE VERSION 1.8
804 o The new function chronopl() estimates dates using the penalized
805 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
807 o The new function consensus() calculates the consensus tree of a
810 o The new function evolve.phylo() simulates the evolution of
811 continuous characters along a phylogeny under a Brownian model.
813 o The new plot method for objects of class "ancestral" displays a
814 tree together with ancestral values, as returned by the above
817 o The new function as.phylo.formula() returns a phylogeny from a
818 set of nested taxonomic variables given as a formula.
820 o The new function read.caic() reads trees in CAIC format.
822 o The new function tiplabels() allows to add labels to the tips
823 of a tree using text or plotting symbols in a flexible way.
825 o The new function unroot() unroots a phylogeny.
827 o multi2di() has a new option, `random', which specifies whether
828 to resolve the multichotomies randomly (the default) or not.
830 o prop.part() now returns an object of class "prop.part" for which
831 there are print (to display a partition in a more friendly way)
832 and summary (to extract the numbers) methods.
834 o plot.phylo() has a new option, `show.tip.label', specifying
835 whether to print the labels of the tips. The default is TRUE.
837 o The code of nj() has been replaced by a faster C code: it is now
838 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
841 o write.nexus() now writes whether a tree is rooted or not.
846 o Two bugs have been fixed in root(): unrooted trees are now
847 handled corretly, and node labels are now output normally.
849 o A bug was fixed in phymltest(): the executable couldn't be found
852 o Three bug have been fixed in ace(): computing the likelihood of
853 ancestral states of discrete characters failed, custom models
854 did not work, and the function failed with a null gradient (a
855 warning message is now returned; this latter bug was also
856 present in yule.cov() as well and is now fixed).
858 o pic() hanged out when missing data were present: a message error
861 o A small bug was fixed in dist.dna() where the gamma correction
862 was not always correctly dispatched.
864 o plot.phylo() plotted correctly the root edge only when the tree
865 was plotted rightwards: this works now for all directions.
870 o dist.taxo() has been renamed as weight.taxo().
872 o Various error and warning messages have been improved.
876 CHANGES IN APE VERSION 1.7
879 o The new function ace() estimates ancestral character states for
880 continuous characters (with ML, GLS, and contrasts methods), and
881 discrete characters (with ML only) for any number of states.
883 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
884 of directional evolution for continuous characters. The user
885 specifies the node(s) of the tree where the character optimum
888 o The new function is.rooted() tests whether a tree (of class
891 o The new function rcoal() generates random ultrametric trees with
892 the possibility to specify the function that generates the
893 inter-nodes distances.
895 o The new function mrca() gives for all pairs of tips in a tree
896 (and optionally nodes too) the most recent common ancestor.
898 o nodelabels() has a new option `thermo' to plot proportions (up
899 to three classes) on the nodes of a tree.
901 o rtree() has been improved: it can now generate rooted or
902 unrooted trees, and the mathematical function that generates the
903 branch lengths may be specified by the user. The tip labels may
904 be given directly in the call to rtree. The limit cases (n = 2,
905 3) are now handled correctly.
907 o dist.topo() has a new argument `method' with two choices: "PH85"
908 for Penny and Henny's method (already available before and now
909 the default), and "BHV01" for the geometric distance by Billera
910 et al. (2001, Adv. Appl. Math. 27:733).
912 o write.tree() has a new option, `digits', which specifies the
913 number of digits to be printed in the Newick tree. By default
914 digits = 10. The numbers are now always printed in decimal form
915 (i.e., 1.0e-1 is now avoided).
917 o dist.dna() can now compute the raw distances between pairs of
918 DNA sequences by specifying model = "raw".
920 o dist.phylo() has a new option `full' to possibly compute the
921 distances among all tips and nodes of the tree. The default if
927 o Several bugs were fixed in all.equal.phylo().
929 o dist.dna() did not handle correctly gaps ("-") in alignments:
930 they are now considered as missing data.
932 o rotate() did not work if the tips were not ordered: this is
935 o mantel.test() returned NA in some special cases: this is fixed
936 and the function has been improved and is now faster.
938 o A bug was fixed in diversi.gof() where the calculation of A² was
941 o cherry() did not work correctly under some OSs (mainly Linux):
944 o is.binary.tree() has been modified so that it works with both
945 rooted and unrooted trees.
947 o The documentation of theta.s() was not correct: this has been
950 o plot.mst() did not work correctly: this is fixed.
954 CHANGES IN APE VERSION 1.6
959 o The new function dist.topo() computes the topological distances
962 o The new function boot.phylo() performs a bootstrap analysis on
963 phylogeny estimation.
965 o The new functions prop.part() and prop.clades() analyse
966 bipartitions from a series of trees.
971 o read.GenBank() now uses the EFetch utility of NCBI instead of
972 the usual Web interface: it is now much faster (e.g., 12 times
973 faster to retrieve 8 sequences, 37 times for 60 sequences).
978 o Several bugs were fixed in read.dna().
980 o Several bugs were fixed in diversi.time().
982 o is.binary.tree() did not work correctly if the tree has no edge
983 lengths: this is fixed.
985 o drop.tip() did not correctly propagated the `node.label' of a
990 CHANGES IN APE VERSION 1.5
995 o Two new functions, as.matching.phylo() and as.phylo.matching(),
996 convert objects between the classes "phylo" and "matching". The
997 latter implements the representation of binary trees introduced by
998 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
999 as.matching() has been introduced as well.
1001 o Two new functions, multi2di() and di2multi(), allow to resolve
1002 and collapse multichotomies with branches of length zero.
1004 o The new function nuc.div() computes the nucleotide diversity
1005 from a sample a DNA sequences.
1007 o dist.dna() has been completely rewritten with a much faster
1008 (particularly for large data sets) C code. Eight models are
1009 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1010 option `method' has been renamed `model'). Computation of variance
1011 is available for all models. A gamma-correction is possible for
1012 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1013 to remove sites with missing data on a pairwise basis. The option
1014 `GCcontent' has been removed.
1016 o read.GenBank() has a new option (species.names) which specifies
1017 whether to return the species names of the organisms in addition
1018 to the accession numbers of the sequences (this is the default
1021 o write.nexus() can now write several trees in the same NEXUS file.
1023 o drop.tip() has a new option `root.edge' that allows to specify the
1024 new root edge if internal branches are trimmed.
1029 o as.phylo.hclust() failed if some labels had parentheses: this
1032 o Several bugs were fixed in all.equal.phylo(). This function now
1033 returns the logical TRUE if the trees are identical but with
1034 different representations (a report was printed previously).
1036 o read.GenBank() did not correctly handle ambiguous base codes:
1042 o birthdeath() now returns an object of class "birthdeath" for
1043 which there is a print method.
1047 CHANGES IN APE VERSION 1.4
1052 o The new function nj() performs phylogeny estimation with the
1053 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1056 o The new function which.edge() identifies the edges of a tree
1057 that belong to a group specified as a set of tips.
1059 o The new function as.phylo.phylog() converts an object of class
1060 "phylog" (from the package ade4) into an object of class
1063 o The new function axisPhylo() draws axes on the side of a
1066 o The new function howmanytrees() calculates the number of trees
1067 in different cases and giving a number of tips.
1069 o write.tree() has a new option `multi.line' (TRUE by default) to
1070 write a Newick tree on several lines rather than on a single
1073 o The functionalities of zoom() have been extended. Several
1074 subtrees can be visualized at the same time, and they are marked
1075 on the main tree with colors. The context of the subtrees can be
1076 marked with the option `subtree' (see below).
1078 o drop.tip() has a new option `subtree' (FALSE by default) which
1079 specifies whether to output in the tree how many tips have been
1082 o The arguments of add.scale.bar() have been redefined and have
1083 now default values (see ?add.scale.bar for details). This
1084 function now works even if the plotted tree has no edge length.
1086 o plot.phylo() can now plot radial trees, but this does not take
1087 edge lengths into account.
1089 o In plot.phylo() with `type = "phylogram"', if the values of
1090 `edge.color' and `edge.width' are identical for sister-branches,
1091 they are propagated to the vertical line that link them.
1096 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1097 crashing. This is fixed.
1099 o In plot.phylo(), the options `edge.color' and `edge.width' are
1100 now properly recycled; their default values are now "black" and
1103 o A bug has been fixed in write.nexus().
1108 o The function node.depth.edgelength() has been removed and
1109 replaced by a C code.
1113 CHANGES IN APE VERSION 1.3-1
1118 o The new function nodelabels() allows to add labels to the nodes
1119 of a tree using text or plotting symbols in a flexible way.
1121 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1122 numeric values specifying the lower and upper limits on the x-
1123 and y-axes. This allows to leave some space on any side of the
1124 tree. If a single value is given, this is taken as the upper
1129 CHANGES IN APE VERSION 1.3
1134 o The new function phymltest() calls the software PHYML and fits
1135 28 models of DNA sequence evolution. There are a print method to
1136 display likelihood and AIC values, a summary method to compute
1137 the hierarchical likelihood ratio tests, and a plot method to
1138 display graphically the AIC values of each model.
1140 o The new function yule.cov() fits the Yule model with covariates,
1141 a model where the speciation rate is affected by several species
1142 traits through a generalized linear model. The parameters are
1143 estimated by maximum likelihood.
1145 o Three new functions, corBrownian(), corGrafen(), and
1146 corMartins(), compute the expected correlation structures among
1147 species given a phylogeny under different models of evolution.
1148 These can be used for GLS comparative phylogenetic methods (see
1149 the examples). There are coef() and corMatrix() methods and an
1150 Initialize.corPhyl() function associated.
1152 o The new function compar.cheverud() implements Cheverud et al.'s
1153 (1985; Evolution 39:1335) phylogenetic comparative method.
1155 o The new function varcomp() estimates variance components; it has
1158 o Two new functions, panel.superpose.correlogram() and
1159 plot.correlogramList(), allow to plot several phylogenetic
1162 o The new function node.leafnumber() computes the number of leaves
1163 of a subtree defined by a particular node.
1165 o The new function node.sons() gets all tags of son nodes from a
1168 o The new function compute.brlen() computes the branch lengths of
1169 a tree according to a specified method.
1171 o plot.phylo() has three new options: "cex" controls the size of
1172 the (tip and node) labels (thus it is no more needed to change
1173 the global graphical parameter), "direction" which allows to
1174 plot the tree rightwards, leftwards, upwards, or downwards, and
1175 "y.lim" which sets the upper limit on the y-axis.
1180 o Some functions which try to match tip labels and names of
1181 additional data (e.g. vector) are likely to fail if there are
1182 typing or syntax errors. If both series of names do not perfectly
1183 match, they are ignored and a warning message is now issued.
1184 These functions are bd.ext, compar.gee, pic. Their help pages
1185 have been clarified on this point.
1189 CHANGES IN APE VERSION 1.2-7
1194 o The new function root() reroots a phylogenetic tree with respect
1195 to a specified outgroup.
1197 o The new function rotate() rotates an internal branch of a tree.
1199 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1200 trees) controls the display of the tip labels in unrooted trees.
1201 This display has been greatly improved: the tip labels are now not
1202 expected to overlap with the tree (particularly if lab4ut =
1203 "axial"). In all cases, combining appropriate values of "lab4ut"
1204 and the font size (via "par(cex = )") should result in readable
1205 unrooted trees. See ?plot.phylo for some examples.
1207 o In drop.tip(), the argument `tip' can now be numeric or character.
1212 o drop.tip() did not work correctly with trees with no branch
1213 lengths: this is fixed.
1215 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1216 plotted with some line crossings: this is now fixed.
1220 CHANGES IN APE VERSION 1.2-6
1225 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1226 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1227 to implement comparative methods with an autocorrelation approach.
1229 o A new data set describing some life history traits of Carnivores
1235 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1240 o When plotting a tree with plot.phylo(), the new default of the
1241 option `label.offset' is now 0, so the labels are always visible.
1245 CHANGES IN APE VERSION 1.2-5
1250 o The new function bd.ext() fits a birth-death model with combined
1251 phylogenetic and taxonomic data, and estimates the corresponding
1252 speciation and extinction rates.
1257 o The package gee is no more required by ape but only suggested
1258 since only the function compar.gee() calls gee.
1262 CHANGES IN APE VERSION 1.2-4
1267 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1268 and lines.popsize) implementing a new approach for inferring the
1269 demographic history from genealogies using a reversible jump
1270 MCMC have been introduced.
1272 o The unit of time in the skyline plot and in the new plots can
1273 now be chosen to be actual years, rather than substitutions.
1277 CHANGES IN APE VERSION 1.2-3
1282 o The new function rtree() generates a random binary tree with or
1283 without branch lengths.
1285 o Two new functions for drawing lineages-through-time (LTT) plots
1286 are provided: ltt.lines() adds a LTT curve to an existing plot,
1287 and mltt.plot() does a multiple LTT plot giving several trees as
1288 arguments (see `?ltt.plot' for details).
1293 o Some taxon names made R crashing when calling as.phylo.hclust():
1296 o dist.dna() returned an error with two identical DNA sequences
1297 (only using the Jukes-Cantor method returned 0): this is fixed.
1302 o The function dist.phylo() has been re-written using a different
1303 algorithm: it is now about four times faster.
1305 o The code of branching.times() has been improved: it is now about
1310 CHANGES IN APE VERSION 1.2-2
1315 o The new function seg.sites() finds the segregating sites in a
1316 sample of DNA sequences.
1321 o A bug introduced in read.tree() and in read.nexus() with version
1324 o A few errors were corrected and a few examples were added in the
1329 CHANGES IN APE VERSION 1.2-1
1334 o plot.phylo() can now draw the edge of the root of a tree if it
1335 has one (see the new option `root.edge', its default is FALSE).
1340 o A bug was fixed in read.nexus(): files with semicolons inside
1341 comment blocks were not read correctly.
1343 o The behaviour of read.tree() and read.nexus() was corrected so
1344 that tree files with badly represented root edges (e.g., with
1345 an extra pair of parentheses, see the help pages for details)
1346 are now correctly represented in the object of class "phylo";
1347 a warning message is now issued.
1351 CHANGES IN APE VERSION 1.2
1356 o plot.phylo() has been completely re-written and offers several
1357 new functionalities. Three types of trees can now be drawn:
1358 phylogram (as previously), cladogram, and unrooted tree; in
1359 all three types the branch lengths can be drawn using the edge
1360 lengths of the phylogeny or not (e.g., if the latter is absent).
1361 The vertical position of the nodes can be adjusted with two
1362 choices (see option `node.pos'). The code has been re-structured,
1363 and two new functions (potentially useful for developpers) are
1364 documented separately: node.depth.edgelength() and node.depth();
1365 see the respective help pages for details.
1367 o The new function zoom() allows to explore very large trees by
1368 focusing on a small portion of it.
1370 o The new function yule() fits by maximum likelihood the Yule model
1371 (birth-only process) to a phylogenetic tree.
1373 o Support for writing DNA sequences in FASTA format has been
1374 introduced in write.dna() (support for reading sequences in
1375 this format was introduced in read.dna() in version 1.1-2).
1376 The function has been completely re-written, fixing some bugs
1377 (see below); the default behaviour is no more to display the
1378 sequences on the standard output. Several options have been
1379 introduced to control the sequence printing in a flexible
1380 way. The help page has been extended.
1382 o A new data set is included: a supertree of bats in NEXUS format.
1387 o In theta.s(), the default of the option `variance' has
1388 been changed to `FALSE' (as was indicated in the help page).
1390 o Several bugs were fixed in the code of all.equal.phylo().
1392 o Several bugs were fixed in write.dna(), particularly this
1393 function did not work with `format = "interleaved"'.
1395 o Various errors were corrected in the help pages.
1400 o The argument names of as.hclust.phylo() have been changed
1401 from "(phy)" to "(x, ...)" to conform to the definition of
1402 the corresponding generic function.
1404 o gamma.stat() has been renamed gammaStat() to avoid confusion
1405 since gamma() is a generic function.
1409 CHANGES IN APE VERSION 1.1-3
1414 o base.freq() previously did not return a value of 0 for
1415 bases absent in the data (e.g., a vector of length 3 was
1416 returned if one base was absent). This is now fixed (a
1417 vector of length 4 is always returned).
1419 o Several bugs were fixed in read.nexus(), including that this
1420 function did not work in this absence of a "TRANSLATE"
1421 command in the NEXUS file, and that the commands were
1426 CHANGES IN APE VERSION 1.1-2
1431 o The Tamura and Nei (1993) model of DNA distance is now implemented
1432 in dist.dna(): five models are now available in this function.
1434 o A new data set is included: a set of 15 sequences of the
1435 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1441 o A bug in read.nexus() was fixed.
1443 o read.dna() previously did not work correctly in most cases.
1444 The function has been completely re-written and its help page
1445 has been considerably extended (see ?read.dna for details).
1446 Underscores (_) in taxon names are no more replaced with
1447 spaces (this behaviour was undocumented).
1449 o A bug was fixed in write.dna().
1453 CHANGES IN APE VERSION 1.1-1
1458 o A bug in read.tree() introduced in APE 1.1 was fixed.
1460 o A bug in compar.gee() resulted in an error when trying to fit
1461 a model with `family = "binomial"'. This is now fixed.
1465 CHANGES IN APE VERSION 1.1
1470 o The Klastorin (1982) method as suggested by Misawa and Tajima
1471 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1472 on the basis of phylogenetic trees has been implemented (see
1473 the function klastorin()).
1475 o Functions have been added to convert APE's "phylo" objects in
1476 "hclust" cluster objects and vice versa (see the help page of
1477 as.phylo for details).
1479 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1480 are introduced for the estimation of absolute evolutionary rates
1481 (ratogram) and dated clock-like trees (chronogram) from
1482 phylogenetic trees using the non-parametric rate smoothing approach
1483 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1485 o A summary method is now provided printing a summary information on a
1486 phylogenetic tree with, for instance, `summary(tree)'.
1488 o The behaviour of read.tree() was changed so that all spaces and
1489 tabulations in tree files are now ignored. Consequently, spaces in tip
1490 labels are no more allowed. Another side effect is that read.nexus()
1491 now does not replace the underscores (_) in tip labels with spaces
1492 (this behaviour was undocumented).
1494 o The function plot.phylo() has a new option (`underscore') which
1495 specifies whether the underscores in tip labels should be written on
1496 the plot as such or replaced with spaces (the default).
1498 o The function birthdeath() now computes 95% confidence intervals of
1499 the estimated parameters using profile likelihood.
1501 o Three new data sets are included: a gene tree estimated from 36
1502 landplant rbcL sequences, a gene tree estimated from 32 opsin
1503 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1508 o A bug was fixed in dist.gene() where nothing was returned.
1510 o A bug in plot.mst() was fixed.
1512 o A bug in vcv.phylo() resulted in false correlations when the
1513 option `cor = TRUE' was used (now fixed).
1517 CHANGES IN APE VERSION 1.0
1522 o Two new functions, read.dna() and write.dna(), read/write in a file
1523 DNA sequences in interleaved or in sequential format.
1525 o Two new functions, read.nexus() and write.nexus(), read/write trees
1528 o The new function bind.tree() allows to bind two trees together,
1529 possibly handling root edges to give internal branches.
1531 o The new function drop.tip() removes the tips in a phylogenetic tree,
1532 and trims (or not) the corresponding internal branches.
1534 o The new function is.ultrametric() tests if a tree is ultrametric.
1536 o The function plot.phylo() has more functionalities such as drawing the
1537 branches with different colours and/or different widths, showing the
1538 node labels, controling the position and font of the labels, rotating
1539 the labels, and controling the space around the plot.
1541 o The function read.tree() can now read trees with no branch length,
1542 such as "(a,b),c);". Consequently, the element `edge.length' in
1543 objects of class "phylo" is now optional.
1545 o The function write.tree() has a new default behaviour: if the default
1546 for the option `file' is used (i.e. file = ""), then a variable of
1547 mode character containing the tree in Newick format is returned which
1548 can thus be assigned (e.g., tree <- write.tree(phy)).
1550 o The function read.tree() has a new argument `text' which allows
1551 to read the tree in a variable of mode character.
1553 o A new data set is included: the phylogenetic relationships among
1554 the orders of birds from Sibley and Ahlquist (1990).
1558 CHANGES IN APE VERSION 0.2-1
1563 o Several bugs were fixed in the help pages.
1567 CHANGES IN APE VERSION 0.2
1572 o The function write.tree() writes phylogenetic trees (objects of class
1573 "phylo") in an ASCII file using the Newick parenthetic format.
1575 o The function birthdeath() fits a birth-death model to branching times
1576 by maximum likelihood, and estimates the corresponding speciation and
1579 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1582 o The function is.binary.tree() tests whether a phylogeny is binary.
1584 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1585 as well as some methods are introduced.
1587 o Several functions, including some generics and methods, for computing
1588 skyline plot estimates (classic and generalized) of effective
1589 population size through time are introduced and replace the function
1590 skyline.plot() in version 0.1.
1592 o Two data sets are now included: the phylogenetic relationships among
1593 the families of birds from Sibley and Ahlquist (1990), and an
1594 estimated clock-like phylogeny of HIV sequences sampled in the
1595 Democratic Republic of Congo.
1598 DEPRECATED & DEFUNCT
1600 o The function skyline.plot() in ape 0.1 has been deprecated and
1601 replaced by more elaborate functions (see above).
1606 o Two important bugs were fixed in plot.phylo(): phylogenies with
1607 multichotomies not at the root or not with only terminal branches,
1608 and phylogenies with a single node (i.e. only terminal branches)
1609 did not plot. These trees should be plotted correctly now.
1611 o Several bugs were fixed in diversi.time() in the computation of
1614 o Various errors were corrected in the help pages.