1 CHANGES IN APE VERSION 2.3-1
6 o dist.gene() failed on most occasions with the default
7 pairwise.deletion = FALSE.
9 o read.tree() failed to read correctly the tree name(s).
13 CHANGES IN APE VERSION 2.3
18 o The new functions CADM.global and CADM.post, contributed by
19 Pierre Legendre, test the congruence among several distance
22 o The new function yule.time fits a user-defined time-dependent
23 Yule model by maximum likelihood.
25 o The new function makeNodeLabel creates and/or modifies node
26 labels in a flexible way.
28 o read.tree() and write.tree() have been modified so that they can
29 handle individual tree names.
31 o plot.phylo() has a new argument 'edge.lty' that specifies the
32 types of lines used for the edges (plain, dotted, dashed, ...)
34 o phymltest() has been updated to work with PhyML 3.0.1.
39 o drop.tip() shuffled tip labels in some cases.
41 o drop.tip() did not handle node.label correctly.
43 o is.ultrametric() now checks the ordering of the edge matrix.
45 o ace() sometimes returned negative values of likelihoods of
46 ancestral states (thanks to Dan Rabosky for solving this long
52 o The data set xenarthra has been removed.
56 CHANGES IN APE VERSION 2.2-4
60 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
61 now fixed. (Thanks to Peter Wragg for the fix!)
63 o A warning message occurred for no reason with ace(method="GLS").
68 o There is now a general help page displayed with '?ape'
72 CHANGES IN APE VERSION 2.2-3
77 o The new function extract.clade extracts a clade from a tree by
78 specifying a node number or label.
80 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
81 operations of the same names.
83 o dist.dna() can now return the number of site differences by
89 o chronopl() did not work with CV = TRUE.
91 o read.nexus() did not work correctly in some situations (trees on
92 multiple lines with different numbers of lines and/or with
93 comments inserted within the trees).
95 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
96 the number of lineages with non-binary trees.
101 o ape has now a namespace.
103 o drip.tip() has been improved: it should be much faster and work
104 better in some cases (e.g., see the example in ?zoom).
108 CHANGES IN APE VERSION 2.2-2
113 o dist.gene() has been substantially improved and gains an option
116 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
122 o prop.part() failed with a single tree with the default option
123 'check.labels = TRUE'.
125 o summary.DNAbin() failed to display correctly the summary of
126 sequence lengths with lists of sequences of 10,000 bases or more
127 (because summary.default uses 4 significant digits by default).
129 o read.nexus() failed to read a file with a single tree with line
130 breaks in the Newick string.
132 o del.gaps() returned a list of empty sequences when there were no
138 o phymltest() has been updated for PhyML 3.0 and gains an option
139 'append', whereas the option 'path2exec' has been removed.
141 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
142 which is returned unchanged (instead of an error).
144 o The data sets bird.orders and bird.families are now stored as
145 Newick strings; i.e., the command data(bird.orders) calls
150 CHANGES IN APE VERSION 2.2-1
155 o The new function makeLabel() helps to modify labels of trees,
156 lists of trees, or DNA sequences, with several utilities to
157 truncate and/or make them unique, substituting some
158 characters, and so on.
160 o The new function del.gaps() removes insertion gaps ("-") in a
161 set of DNA sequences.
163 o read.dna() can now read Clustal files (*.aln).
168 o root() failed with 'resolve.root = TRUE' when the root was
169 already the specified root.
171 o Several bugs were fixed in mlphylo().
173 o collapsed.singles() did not propagate the 'Nnode' and
174 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
176 o read.nexus() failed to remove correctly the comments within
179 o read.nexus() failed to read a file with a single tree and no
180 translation of tip labels.
182 o read.nexus() failed to place correctly tip labels when reading
183 a single tree with no edge lengths.
185 o A bug was fixed in sh.test().
190 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
193 o The option 'check.labels' of consensus() and prop.part() is now
196 o write.dna() now does not truncate names to 10 characters with
201 CHANGES IN APE VERSION 2.2
206 o Four new functions have been written by Damien de Vienne for the
207 graphical exploration of large trees (cophyloplot, subtrees,
208 subtreeplot), and to return the graphical coordinates of tree
211 o The new functions corPagel and corBlomberg implement the Pagel's
212 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
214 o chronopl() has been improved and gains several options: see its
215 help page for details.
217 o boot.phylo() has now an option 'trees' to possibly return the
218 bootstraped trees (the default is FALSE).
220 o prop.part() has been improved and should now be faster in all
226 o read.dna() failed if "?" occurred in the first 10 sites of the
229 o The x/y aspect of the plot is now respected when plotting a
230 circular tree (type = "r" or "f").
232 o Drawing the tip labels sometimes failed when plotting circular
235 o zoom() failed when tip labels were used instead of their numbers
236 (thanks to Yan Wong for the fix).
238 o drop.tip() failed with some trees (fixed by Yan Wong).
240 o seg.sites() failed with a list.
242 o consensus() failed in some cases. The function has been improved
243 as well and is faster.
247 CHANGES IN APE VERSION 2.1-3
252 o A bug in read.nexus() made the Windows R-GUI crash.
254 o An error was fixed in the computation of ancestral character
255 states by generalized least squares in ace().
257 o di2multi() did not modify node labels correctly.
259 o multi2di() failed if the tree had its attribute "order" set to
264 CHANGES IN APE VERSION 2.1-2
269 o There three new methods for the "multiPhylo" class: str, $,
272 o root() gains the options 'node' and 'resolve.root'
273 (FALSE by default) as well as its code being improved.
275 o mltt.plot() has now an option 'log' used in the same way
276 than in plot.default().
281 o mltt.plot() failed to display the legend with an unnamed
284 o nodelabels() with pies now correcly uses the argument
285 'cex' to draw symbols of different sizes (which has
286 worked already for thermometers).
288 o read.nexus() generally failed to read very big files.
293 o The argument 'family' of compar.gee() can now be a function
294 as well as a character string.
296 o read.tree() and read.nexus() now return an unnamed list if
299 o read.nexus() now returns a modified object of class "multiPhylo"
300 when there is a TRANSLATE block in the NEXUS file: the individual
301 trees have no 'tip.label' vector, but the list has a 'TipLabel'
302 attribute. The new methods '$' and '[[' set these elements
303 correctly when extracting trees.
307 CHANGES IN APE VERSION 2.1-1
312 o The new function rmtree generates lists of random trees.
314 o rcoal() now generates a genuine coalescent tree by default
315 (thanks to Vladimir Minin for the code).
320 o nuc.div() returned an incorrect value with the default
321 pairwise.deletion = FALSE.
326 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
327 have been improved so that they are stabler and faster.
329 o R packages used by ape are now loaded silently; lattice and gee
330 are loaded only when needed.
334 CHANGES IN APE VERSION 2.1
339 o The new function identify.phylo identifies clades on a plotted
340 tree using the mouse.
342 o It is now possible to subset a list of trees (object of class
343 "multiPhylo") with "[" while keeping its class correct.
345 o The new function as.DNAbin.alignment converts DNA sequences
346 stored in the "alignment" format of the package seqinr into
347 an object of class "DNAbin".
349 o The new function weight.taxo2 helps to build similarity matrices
350 given two taxonomic levels (usually called by other functions).
352 o write.tree() can now take a list of trees (class "multiPhylo")
353 as its main argument.
355 o plot.correlogram() and plot.correlogramList() have been
356 improved, and gain several options (see the help page for
357 details). A legend is now plotted by default.
362 o dist.dna() returned some incorrect values with `model = "JC69"'
363 and `pairwise.deletion = TRUE'. This affected only the
364 distances involving sequences with missing values. (Thanks
365 to Bruno Toupance for digging this bug out.)
367 o write.tree() failed with some trees: this is fixed by removing
368 the `multi.line' option (trees are now always printed on a
371 o read.nexus() did not correctly detect trees with multiple root
372 edges (see OTHER CHANGES).
377 o The code of mlphylo() has been almost entirely rewritten, and
378 should be much stabler. The options have been also greatly
379 simplified (see ?mlphylo and ?DNAmodel for details).
381 o The internal function nTips has been renamed klastorin_nTips.
383 o The code of is.ultrametric() contained redundancies and has
386 o The code of Moran.I() and of correlogram.formula() have been
389 o read.tree() and read.nexus() now return an error when trying to
390 read a tree with multiple root edges (see BUG FIXES). The
391 correction applied in previous version did not work in all
394 o The class c("multi.tree", "phylo") has been renamed
400 o There is now a vignette in ape: see vignette("MoranI", "ape").
405 o as.matching() and as.phylo.matching() do not support branch
408 o correlogram.phylo() and discrete.dist() have been removed.
412 CHANGES IN APE VERSION 2.0-2
417 o The new function matexpo computes the exponential of a square
420 o The new function unique.multi.tree removes duplicate trees from
423 o yule() has a new option `use.root.edge = FALSE' that specifies
424 to ignore, by default, the root edge of the tree if it exists.
429 o which.edge() failed when the index of a single terminal edge was
432 o In diversi.time(), the values returned for model C were
435 o A bug was fixed in yule() that affected the calculation of the
436 likelihood in the presence of ties in the branching times.
438 o There was a bug in the C function mat_expo4x4 affecting the
439 calculations of the transition probabilities for models HKY and
442 o A small bug was fixed in as.matrix.DNAbin (thanks to James
445 o rtree() did not `shuffle' the tip labels by default, so only a
446 limited number of labelled topologies could be generated.
450 CHANGES IN APE VERSION 2.0-1
455 o The three new functions bionj, fastme.ols, and fastme.bal
456 perform phylogeny estimation by the BIONJ and fastME methods in
457 OLS and balanced versions. This is a port to R of previous
458 previous programs done by Vincent Lefort.
460 o The new function chronoMPL performs molecular dating with the
461 mean path lengths method of Britton et al. (2002, Mol. Phyl.
464 o The new function rotate, contributed by Christoph Heibl, swaps
465 two clades connected to the same node. It works also with
466 multichotomous nodes.
468 o The new `method' as.matrix.DNAbin() may be used to convert
469 easily DNA sequences stored in a list into a matrix while
470 keeping the names and the class.
475 o chronopl() failed when some branch lengths were equal to zero:
476 an error message is now returned.
478 o di2multi() failed when there was a series of consecutive edges
483 CHANGES IN APE VERSION 1.10-2
488 o plot.phylo() can now plot circular trees: the option is type =
489 "fan" or type = "f" (to avoid the ambiguity with type = "c").
491 o prop.part() has a new option `check.labels = FALSE' which allows
492 to considerably speed-up the calculations of bipartitions. As a
493 consequence, calculations of bootstrap values with boot.phylo()
494 should be much faster.
499 o read.GenBank() did not return correctly the list of species as
500 from ape 1.10: this is fixed in this version
502 o Applying as.phylo() on a tree of class "phylo" failed: the
503 object is now returned unchanged.
507 CHANGES IN APE VERSION 1.10-1
512 o The three new functions Ntip, Nnode, and Nedge return, for a
513 given tree, the number of tips, nodes, or edges, respectively.
518 o read.nexus() did not set correctly the class of the returned
519 object when reading multiple trees.
521 o mllt.plot() failed with objects of class c("multi.tree",
524 o unroot() did not work correctly in most cases.
526 o reorder.phylo() made R freeze in some occasions.
528 o Plotting a tree in pruningwise order failed.
530 o When plotting an unrooted tree, the tip labels where not all
531 correctly positioned if the option `cex' was used.
535 CHANGES IN APE VERSION 1.10
540 o Five new `method' functions have been introduced to manipulate
541 DNA sequences in binary format (see below).
543 o Three new functions have been introduced to convert between the
544 new binary and the character formats.
546 o The new function as.alignment converts DNA sequences stored as
547 single characters into the class "alignment" used by the package
550 o read.dna() and read.GenBank() have a new argument `as.character'
551 controlling whether the sequences are returned in binary format
557 o root() failed when the tree had node labels: this is fixed.
559 o plot.phylo() did not correctly set the limits on the y-axis with
560 the default setting: this is fixed.
562 o dist.dna() returned a wrong result for the LogDet, paralinear,
563 and BH87 models with `pairwise.deletion = TRUE'.
568 o DNA sequences are now internally stored in a binary format. See
569 the document "A Bit-Level Coding Scheme for Nucleotides" for the
570 details. Most functions analyzing DNA functions have been
571 modified accordingly and are now much faster (dist.dna is now
572 ca. 60 times faster).
576 CHANGES IN APE VERSION 1.9-4
581 o A bug was fixed in edgelabels().
583 o as.phylo.hclust() did not work correctly when the object of
584 class "hclust" has its labels set to NULL: the returned tree has
585 now its tip labels set to "1", "2", ...
587 o consensus could fail if some tip labels are a subset of others
588 (e.g., "a" and "a_1"): this is now fixed.
590 o mlphylo() failed in most cases if some branch lengths of the
591 initial tree were greater than one: an error message is now
594 o mlphylo() failed in most cases when estimating the proportion of
595 invariants: this is fixed.
599 CHANGES IN APE VERSION 1.9-3
604 o The new function edgelabels adds labels on the edge of the tree
605 in the same way than nodelabels or tiplabels.
610 o multi2di() did not handle correctly branch lengths with the
611 default option `random = TRUE': this is now fixed.
613 o A bug was fixed in nuc.div() when using pairwise deletions.
615 o A bug occurred in the analysis of bipartitions with large
616 numbers of large trees, with consequences on prop.part,
617 prop.clades, and boot.phylo.
619 o The calculation of the Billera-Holmes-Vogtmann distance in
620 dist.topo was wrong: this has been fixed.
624 CHANGES IN APE VERSION 1.9-2
629 o The new function ladderize reorganizes the internal structure of
630 a tree to plot them left- or right-ladderized.
632 o The new function dist.nodes computes the patristic distances
633 between all nodes, internal and terminal, of a tree. It replaces
634 the option `full = TRUE' of cophenetic.phylo (see below).
639 o A bug was fixed in old2new.phylo().
641 o Some bugs were fixed in chronopl().
643 o The edge colours were not correctly displayed by plot.phylo
644 (thank you to Li-San Wang for the fix).
646 o cophenetic.phylo() failed with multichotomous trees: this is
652 o read.dna() now returns the sequences in a matrix if they are
653 aligned (interleaved or sequential format). Sequences in FASTA
654 format are still returned in a list.
656 o The option `full' of cophenetic.phylo() has been removed because
657 it could not be used from the generic.
662 o rotate() has been removed; this function did not work correctly
667 CHANGES IN APE VERSION 1.9-1
672 o Trees with a single tip were not read correctly in R as the
673 element `Nnode' was not set: this is fixed.
675 o unroot() did not set correctly the number of nodes of the
676 unrooted tree in most cases.
678 o read.GenBank() failed when fetching very long sequences,
679 particularly of the BX-series.
681 o A bug was introduced in read.tree() with ape 1.9: it has been
686 CHANGES IN APE VERSION 1.9
691 o There are two new print `methods' for trees of class "phylo" and
692 lists of trees of class "multi.tree", so that they are now
693 displayed in a compact and informative way.
695 o There are two new functions, old2new.phylo and new2old.phylo,
696 for converting between the old and new coding of the class
699 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
700 LogDet ("logdet"), and paralinear ("paralin").
702 o compute.brlen() has been extended: several methods are now
703 available to compute branch lengths.
705 o write.dna() can now handle matrices as well as lists.
710 o cophenetic.phylo() sometimes returned a wrong result with
711 multichotomous trees: this is fixed.
713 o rotate() failed when a single tip was specified: the tree is now
716 o ace() did not return the correct index matrix with custom
717 models: this is fixed.
719 o multi2di() did not work correctly when resolving multichotomies
720 randomly: the topology was always the same, only the arrangement
721 of clades was randomized: this is fixed. This function now
722 accepts trees with no branch lengths.
724 o The output of diversi.gof() was blurred by useless prints when a
725 user distribution was specified. This has been corrected, and
726 the help page of this function has been expanded.
731 o The internal structure of the class "phylo" has been changed:
732 see the document "Definition of Formats for Coding Phylogenetic
733 Trees in R" for the details. In addition, the code of most
734 functions has been improved.
736 o Several functions have been improved by replacing some R codes
737 by C codes: pic, plot.phylo, and reorder.phylo.
739 o There is now a citation information: see citation("ape") in R.
741 o write.tree() now does not add extra 0's to branch lengths so
742 that 1.23 is printed "1.23" by default, not "1.2300000000".
744 o The syntax of bind.tree() has been simplified. This function now
745 accepts trees with no branch lengths, and handles correctly node
748 o The option `as.numeric' of mrca() has been removed.
750 o The unused options `format' and `rooted' of read.tree() have
753 o The unused option `format' of write.tree() has been removed.
755 o The use of node.depth() has been simplified.
759 CHANGES IN APE VERSION 1.8-5
764 o Two new functions read.nexus.data() and write.nexus.data(),
765 contributed by Johan Nylander, allow to read and write molecular
766 sequences in NEXUS files.
768 o The new function reorder.phylo() reorders the internal structure
769 of a tree of class "phylo". It is used as the generic, e.g.,
772 o read.tree() and read.nexus() can now read trees with a single
775 o The new data set `cynipids' supplies a set of protein sequences
781 o The code of all.equal.phylo() has been completely rewritten
782 (thanks to Benoît Durand) which fixes several bugs.
784 o read.tree() and read.nexus() now checks the labels of the tree
785 to remove or substitute any characters that are illegal in the
786 Newick format (parentheses, etc.)
788 o A negative P-value could be returned by mantel.test(): this is
793 CHANGES IN APE VERSION 1.8-4
798 o The new function sh.test() computes the Shimodaira-
801 o The new function collapse.singles() removes the nodes with a
802 single descendant from a tree.
804 o plot.phylo() has a new argument `tip.color' to specify the
807 o mlphylo() has now an option `quiet' to control the display of
808 the progress of the analysis (the default is FALSE).
813 o read.dna() did not read correctly sequences in sequential format
814 with leading alignment gaps "-": this is fixed.
816 o ace() returned a list with no class so that the generic
817 functions (anova, logLik, ...) could not be used directly. This
818 is fixed as ace() now returns an object of class "ace".
820 o anova.ace() had a small bug when computing the number of degrees
821 of freedom: this is fixed.
823 o mlphylo() did not work when the sequences were in a matrix or
824 a data frame: this is fixed.
826 o rtree() did not work correctly when trying to simulate an
827 unrooted tree with two tips: an error message is now issued.
832 o The algorithm of rtree() has been changed: it is now about 40,
833 100, and 130 times faster for 10, 100, and 1000 tips,
838 CHANGES IN APE VERSION 1.8-3
843 o There are four new `method' functions to be used with the
844 results of ace(): logLik(), deviance(), AIC(), and anova().
846 o The plot method of phymltest has two new arguments: `main' to
847 change the title, and `col' to control the colour of the
848 segments showing the AIC values.
850 o ace() has a new argument `ip' that gives the initial values used
851 in the ML estimation with discrete characters (see the examples
852 in ?ace). This function now returns a matrix giving the indices
853 of the estimated rates when analysing discrete characters.
855 o nodelabels() and tiplabels() have a new argument `pie' to
856 represent proportions, with any number of categories, as
857 piecharts. The use of the option `thermo' has been improved:
858 there is now no limitation on the number of categories.
863 o mlphylo() did not work with more than two partitions: this is
866 o root() failed if the proposed outgroup was already an outgroup
867 in the tree: this is fixed.
869 o The `col' argument in nodelabels() and tiplabels() was not
870 correctly passed when `text' was used: this is fixed.
872 o Two bugs were fixed in mlphylo(): parameters were not always
873 correctly output, and the estimation failed in some cases.
875 o plot.phylo() was stuck when given a tree with a single tip: this
876 is fixed and a message error is now returned.
878 o An error was corrected in the help page of gammaStat regarding
879 the calculation of P-values.
881 o Using gls() could crash R when the number of species in the tree
882 and in the variables were different: this is fixed.
886 CHANGES IN APE VERSION 1.8-2
891 o The new function mlphylo() fits a phylogenetic tree by maximum
892 likelihood from DNA sequences. Its companion function DNAmodel()
893 is used to define the substitution model which may include
894 partitioning. There are methods for logLik(), deviance(), and
895 AIC(), and the summary() method has been extended to display in
896 a friendly way the results of this model fitting. Currently, the
897 functionality is limited to estimating the substitution and
898 associated parameters and computing the likelihood.
900 o The new function drop1.compar.gee (used as, e.g., drop1(m))
901 tests for single effects in GEE-based comparative method. A
902 warning message is printed if there is not enough degrees of
908 o An error message was sometimes issued by plot.multi.tree(),
909 though with no consequence.
913 CHANGES IN APE VERSION 1.8-1
918 o There is a new plot method for lists of trees (objects of class
919 "multi.tree"): it calls plot.phylo() internally and is
920 documented on the same help page.
925 o A bug was fixed in the C code that analyzes bipartitions: this
926 has impact on several functions like prop.part, prop.clades,
927 boot.phylo, or consensus.
929 o root() did not work correctly when the specified outgroup had
930 more than one element: this is fixed.
932 o dist.dna() sometimes returned a warning inappropriately: this
935 o If the distance object given to nj() had no rownames, nj()
936 returned a tree with no tip labels: it now returns tips labelled
937 "1", "2", ..., corresponding to the row numbers.
942 o nj() has been slightly changed so that tips with a zero distance
943 are first aggregated with zero-lengthed branches; the usual NJ
944 procedure is then performed on a distance matrix without 0's.
948 CHANGES IN APE VERSION 1.8
953 o The new function chronopl() estimates dates using the penalized
954 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
956 o The new function consensus() calculates the consensus tree of a
959 o The new function evolve.phylo() simulates the evolution of
960 continuous characters along a phylogeny under a Brownian model.
962 o The new plot method for objects of class "ancestral" displays a
963 tree together with ancestral values, as returned by the above
966 o The new function as.phylo.formula() returns a phylogeny from a
967 set of nested taxonomic variables given as a formula.
969 o The new function read.caic() reads trees in CAIC format.
971 o The new function tiplabels() allows to add labels to the tips
972 of a tree using text or plotting symbols in a flexible way.
974 o The new function unroot() unroots a phylogeny.
976 o multi2di() has a new option, `random', which specifies whether
977 to resolve the multichotomies randomly (the default) or not.
979 o prop.part() now returns an object of class "prop.part" for which
980 there are print (to display a partition in a more friendly way)
981 and summary (to extract the numbers) methods.
983 o plot.phylo() has a new option, `show.tip.label', specifying
984 whether to print the labels of the tips. The default is TRUE.
986 o The code of nj() has been replaced by a faster C code: it is now
987 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
990 o write.nexus() now writes whether a tree is rooted or not.
995 o Two bugs have been fixed in root(): unrooted trees are now
996 handled corretly, and node labels are now output normally.
998 o A bug was fixed in phymltest(): the executable couldn't be found
1001 o Three bug have been fixed in ace(): computing the likelihood of
1002 ancestral states of discrete characters failed, custom models
1003 did not work, and the function failed with a null gradient (a
1004 warning message is now returned; this latter bug was also
1005 present in yule.cov() as well and is now fixed).
1007 o pic() hanged out when missing data were present: a message error
1010 o A small bug was fixed in dist.dna() where the gamma correction
1011 was not always correctly dispatched.
1013 o plot.phylo() plotted correctly the root edge only when the tree
1014 was plotted rightwards: this works now for all directions.
1019 o dist.taxo() has been renamed as weight.taxo().
1021 o Various error and warning messages have been improved.
1025 CHANGES IN APE VERSION 1.7
1028 o The new function ace() estimates ancestral character states for
1029 continuous characters (with ML, GLS, and contrasts methods), and
1030 discrete characters (with ML only) for any number of states.
1032 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1033 of directional evolution for continuous characters. The user
1034 specifies the node(s) of the tree where the character optimum
1037 o The new function is.rooted() tests whether a tree (of class
1040 o The new function rcoal() generates random ultrametric trees with
1041 the possibility to specify the function that generates the
1042 inter-nodes distances.
1044 o The new function mrca() gives for all pairs of tips in a tree
1045 (and optionally nodes too) the most recent common ancestor.
1047 o nodelabels() has a new option `thermo' to plot proportions (up
1048 to three classes) on the nodes of a tree.
1050 o rtree() has been improved: it can now generate rooted or
1051 unrooted trees, and the mathematical function that generates the
1052 branch lengths may be specified by the user. The tip labels may
1053 be given directly in the call to rtree. The limit cases (n = 2,
1054 3) are now handled correctly.
1056 o dist.topo() has a new argument `method' with two choices: "PH85"
1057 for Penny and Henny's method (already available before and now
1058 the default), and "BHV01" for the geometric distance by Billera
1059 et al. (2001, Adv. Appl. Math. 27:733).
1061 o write.tree() has a new option, `digits', which specifies the
1062 number of digits to be printed in the Newick tree. By default
1063 digits = 10. The numbers are now always printed in decimal form
1064 (i.e., 1.0e-1 is now avoided).
1066 o dist.dna() can now compute the raw distances between pairs of
1067 DNA sequences by specifying model = "raw".
1069 o dist.phylo() has a new option `full' to possibly compute the
1070 distances among all tips and nodes of the tree. The default if
1076 o Several bugs were fixed in all.equal.phylo().
1078 o dist.dna() did not handle correctly gaps ("-") in alignments:
1079 they are now considered as missing data.
1081 o rotate() did not work if the tips were not ordered: this is
1084 o mantel.test() returned NA in some special cases: this is fixed
1085 and the function has been improved and is now faster.
1087 o A bug was fixed in diversi.gof() where the calculation of A² was
1090 o cherry() did not work correctly under some OSs (mainly Linux):
1093 o is.binary.tree() has been modified so that it works with both
1094 rooted and unrooted trees.
1096 o The documentation of theta.s() was not correct: this has been
1099 o plot.mst() did not work correctly: this is fixed.
1103 CHANGES IN APE VERSION 1.6
1108 o The new function dist.topo() computes the topological distances
1111 o The new function boot.phylo() performs a bootstrap analysis on
1112 phylogeny estimation.
1114 o The new functions prop.part() and prop.clades() analyse
1115 bipartitions from a series of trees.
1120 o read.GenBank() now uses the EFetch utility of NCBI instead of
1121 the usual Web interface: it is now much faster (e.g., 12 times
1122 faster to retrieve 8 sequences, 37 times for 60 sequences).
1127 o Several bugs were fixed in read.dna().
1129 o Several bugs were fixed in diversi.time().
1131 o is.binary.tree() did not work correctly if the tree has no edge
1132 lengths: this is fixed.
1134 o drop.tip() did not correctly propagated the `node.label' of a
1135 tree: this is fixed.
1139 CHANGES IN APE VERSION 1.5
1144 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1145 convert objects between the classes "phylo" and "matching". The
1146 latter implements the representation of binary trees introduced by
1147 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1148 as.matching() has been introduced as well.
1150 o Two new functions, multi2di() and di2multi(), allow to resolve
1151 and collapse multichotomies with branches of length zero.
1153 o The new function nuc.div() computes the nucleotide diversity
1154 from a sample a DNA sequences.
1156 o dist.dna() has been completely rewritten with a much faster
1157 (particularly for large data sets) C code. Eight models are
1158 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1159 option `method' has been renamed `model'). Computation of variance
1160 is available for all models. A gamma-correction is possible for
1161 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1162 to remove sites with missing data on a pairwise basis. The option
1163 `GCcontent' has been removed.
1165 o read.GenBank() has a new option (species.names) which specifies
1166 whether to return the species names of the organisms in addition
1167 to the accession numbers of the sequences (this is the default
1170 o write.nexus() can now write several trees in the same NEXUS file.
1172 o drop.tip() has a new option `root.edge' that allows to specify the
1173 new root edge if internal branches are trimmed.
1178 o as.phylo.hclust() failed if some labels had parentheses: this
1181 o Several bugs were fixed in all.equal.phylo(). This function now
1182 returns the logical TRUE if the trees are identical but with
1183 different representations (a report was printed previously).
1185 o read.GenBank() did not correctly handle ambiguous base codes:
1191 o birthdeath() now returns an object of class "birthdeath" for
1192 which there is a print method.
1196 CHANGES IN APE VERSION 1.4
1201 o The new function nj() performs phylogeny estimation with the
1202 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1205 o The new function which.edge() identifies the edges of a tree
1206 that belong to a group specified as a set of tips.
1208 o The new function as.phylo.phylog() converts an object of class
1209 "phylog" (from the package ade4) into an object of class
1212 o The new function axisPhylo() draws axes on the side of a
1215 o The new function howmanytrees() calculates the number of trees
1216 in different cases and giving a number of tips.
1218 o write.tree() has a new option `multi.line' (TRUE by default) to
1219 write a Newick tree on several lines rather than on a single
1222 o The functionalities of zoom() have been extended. Several
1223 subtrees can be visualized at the same time, and they are marked
1224 on the main tree with colors. The context of the subtrees can be
1225 marked with the option `subtree' (see below).
1227 o drop.tip() has a new option `subtree' (FALSE by default) which
1228 specifies whether to output in the tree how many tips have been
1231 o The arguments of add.scale.bar() have been redefined and have
1232 now default values (see ?add.scale.bar for details). This
1233 function now works even if the plotted tree has no edge length.
1235 o plot.phylo() can now plot radial trees, but this does not take
1236 edge lengths into account.
1238 o In plot.phylo() with `type = "phylogram"', if the values of
1239 `edge.color' and `edge.width' are identical for sister-branches,
1240 they are propagated to the vertical line that link them.
1245 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1246 crashing. This is fixed.
1248 o In plot.phylo(), the options `edge.color' and `edge.width' are
1249 now properly recycled; their default values are now "black" and
1252 o A bug has been fixed in write.nexus().
1257 o The function node.depth.edgelength() has been removed and
1258 replaced by a C code.
1262 CHANGES IN APE VERSION 1.3-1
1267 o The new function nodelabels() allows to add labels to the nodes
1268 of a tree using text or plotting symbols in a flexible way.
1270 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1271 numeric values specifying the lower and upper limits on the x-
1272 and y-axes. This allows to leave some space on any side of the
1273 tree. If a single value is given, this is taken as the upper
1278 CHANGES IN APE VERSION 1.3
1283 o The new function phymltest() calls the software PHYML and fits
1284 28 models of DNA sequence evolution. There are a print method to
1285 display likelihood and AIC values, a summary method to compute
1286 the hierarchical likelihood ratio tests, and a plot method to
1287 display graphically the AIC values of each model.
1289 o The new function yule.cov() fits the Yule model with covariates,
1290 a model where the speciation rate is affected by several species
1291 traits through a generalized linear model. The parameters are
1292 estimated by maximum likelihood.
1294 o Three new functions, corBrownian(), corGrafen(), and
1295 corMartins(), compute the expected correlation structures among
1296 species given a phylogeny under different models of evolution.
1297 These can be used for GLS comparative phylogenetic methods (see
1298 the examples). There are coef() and corMatrix() methods and an
1299 Initialize.corPhyl() function associated.
1301 o The new function compar.cheverud() implements Cheverud et al.'s
1302 (1985; Evolution 39:1335) phylogenetic comparative method.
1304 o The new function varcomp() estimates variance components; it has
1307 o Two new functions, panel.superpose.correlogram() and
1308 plot.correlogramList(), allow to plot several phylogenetic
1311 o The new function node.leafnumber() computes the number of leaves
1312 of a subtree defined by a particular node.
1314 o The new function node.sons() gets all tags of son nodes from a
1317 o The new function compute.brlen() computes the branch lengths of
1318 a tree according to a specified method.
1320 o plot.phylo() has three new options: "cex" controls the size of
1321 the (tip and node) labels (thus it is no more needed to change
1322 the global graphical parameter), "direction" which allows to
1323 plot the tree rightwards, leftwards, upwards, or downwards, and
1324 "y.lim" which sets the upper limit on the y-axis.
1329 o Some functions which try to match tip labels and names of
1330 additional data (e.g. vector) are likely to fail if there are
1331 typing or syntax errors. If both series of names do not perfectly
1332 match, they are ignored and a warning message is now issued.
1333 These functions are bd.ext, compar.gee, pic. Their help pages
1334 have been clarified on this point.
1338 CHANGES IN APE VERSION 1.2-7
1343 o The new function root() reroots a phylogenetic tree with respect
1344 to a specified outgroup.
1346 o The new function rotate() rotates an internal branch of a tree.
1348 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1349 trees) controls the display of the tip labels in unrooted trees.
1350 This display has been greatly improved: the tip labels are now not
1351 expected to overlap with the tree (particularly if lab4ut =
1352 "axial"). In all cases, combining appropriate values of "lab4ut"
1353 and the font size (via "par(cex = )") should result in readable
1354 unrooted trees. See ?plot.phylo for some examples.
1356 o In drop.tip(), the argument `tip' can now be numeric or character.
1361 o drop.tip() did not work correctly with trees with no branch
1362 lengths: this is fixed.
1364 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1365 plotted with some line crossings: this is now fixed.
1369 CHANGES IN APE VERSION 1.2-6
1374 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1375 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1376 to implement comparative methods with an autocorrelation approach.
1378 o A new data set describing some life history traits of Carnivores
1384 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1389 o When plotting a tree with plot.phylo(), the new default of the
1390 option `label.offset' is now 0, so the labels are always visible.
1394 CHANGES IN APE VERSION 1.2-5
1399 o The new function bd.ext() fits a birth-death model with combined
1400 phylogenetic and taxonomic data, and estimates the corresponding
1401 speciation and extinction rates.
1406 o The package gee is no more required by ape but only suggested
1407 since only the function compar.gee() calls gee.
1411 CHANGES IN APE VERSION 1.2-4
1416 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1417 and lines.popsize) implementing a new approach for inferring the
1418 demographic history from genealogies using a reversible jump
1419 MCMC have been introduced.
1421 o The unit of time in the skyline plot and in the new plots can
1422 now be chosen to be actual years, rather than substitutions.
1426 CHANGES IN APE VERSION 1.2-3
1431 o The new function rtree() generates a random binary tree with or
1432 without branch lengths.
1434 o Two new functions for drawing lineages-through-time (LTT) plots
1435 are provided: ltt.lines() adds a LTT curve to an existing plot,
1436 and mltt.plot() does a multiple LTT plot giving several trees as
1437 arguments (see `?ltt.plot' for details).
1442 o Some taxon names made R crashing when calling as.phylo.hclust():
1445 o dist.dna() returned an error with two identical DNA sequences
1446 (only using the Jukes-Cantor method returned 0): this is fixed.
1451 o The function dist.phylo() has been re-written using a different
1452 algorithm: it is now about four times faster.
1454 o The code of branching.times() has been improved: it is now about
1459 CHANGES IN APE VERSION 1.2-2
1464 o The new function seg.sites() finds the segregating sites in a
1465 sample of DNA sequences.
1470 o A bug introduced in read.tree() and in read.nexus() with version
1473 o A few errors were corrected and a few examples were added in the
1478 CHANGES IN APE VERSION 1.2-1
1483 o plot.phylo() can now draw the edge of the root of a tree if it
1484 has one (see the new option `root.edge', its default is FALSE).
1489 o A bug was fixed in read.nexus(): files with semicolons inside
1490 comment blocks were not read correctly.
1492 o The behaviour of read.tree() and read.nexus() was corrected so
1493 that tree files with badly represented root edges (e.g., with
1494 an extra pair of parentheses, see the help pages for details)
1495 are now correctly represented in the object of class "phylo";
1496 a warning message is now issued.
1500 CHANGES IN APE VERSION 1.2
1505 o plot.phylo() has been completely re-written and offers several
1506 new functionalities. Three types of trees can now be drawn:
1507 phylogram (as previously), cladogram, and unrooted tree; in
1508 all three types the branch lengths can be drawn using the edge
1509 lengths of the phylogeny or not (e.g., if the latter is absent).
1510 The vertical position of the nodes can be adjusted with two
1511 choices (see option `node.pos'). The code has been re-structured,
1512 and two new functions (potentially useful for developpers) are
1513 documented separately: node.depth.edgelength() and node.depth();
1514 see the respective help pages for details.
1516 o The new function zoom() allows to explore very large trees by
1517 focusing on a small portion of it.
1519 o The new function yule() fits by maximum likelihood the Yule model
1520 (birth-only process) to a phylogenetic tree.
1522 o Support for writing DNA sequences in FASTA format has been
1523 introduced in write.dna() (support for reading sequences in
1524 this format was introduced in read.dna() in version 1.1-2).
1525 The function has been completely re-written, fixing some bugs
1526 (see below); the default behaviour is no more to display the
1527 sequences on the standard output. Several options have been
1528 introduced to control the sequence printing in a flexible
1529 way. The help page has been extended.
1531 o A new data set is included: a supertree of bats in NEXUS format.
1536 o In theta.s(), the default of the option `variance' has
1537 been changed to `FALSE' (as was indicated in the help page).
1539 o Several bugs were fixed in the code of all.equal.phylo().
1541 o Several bugs were fixed in write.dna(), particularly this
1542 function did not work with `format = "interleaved"'.
1544 o Various errors were corrected in the help pages.
1549 o The argument names of as.hclust.phylo() have been changed
1550 from "(phy)" to "(x, ...)" to conform to the definition of
1551 the corresponding generic function.
1553 o gamma.stat() has been renamed gammaStat() to avoid confusion
1554 since gamma() is a generic function.
1558 CHANGES IN APE VERSION 1.1-3
1563 o base.freq() previously did not return a value of 0 for
1564 bases absent in the data (e.g., a vector of length 3 was
1565 returned if one base was absent). This is now fixed (a
1566 vector of length 4 is always returned).
1568 o Several bugs were fixed in read.nexus(), including that this
1569 function did not work in this absence of a "TRANSLATE"
1570 command in the NEXUS file, and that the commands were
1575 CHANGES IN APE VERSION 1.1-2
1580 o The Tamura and Nei (1993) model of DNA distance is now implemented
1581 in dist.dna(): five models are now available in this function.
1583 o A new data set is included: a set of 15 sequences of the
1584 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1590 o A bug in read.nexus() was fixed.
1592 o read.dna() previously did not work correctly in most cases.
1593 The function has been completely re-written and its help page
1594 has been considerably extended (see ?read.dna for details).
1595 Underscores (_) in taxon names are no more replaced with
1596 spaces (this behaviour was undocumented).
1598 o A bug was fixed in write.dna().
1602 CHANGES IN APE VERSION 1.1-1
1607 o A bug in read.tree() introduced in APE 1.1 was fixed.
1609 o A bug in compar.gee() resulted in an error when trying to fit
1610 a model with `family = "binomial"'. This is now fixed.
1614 CHANGES IN APE VERSION 1.1
1619 o The Klastorin (1982) method as suggested by Misawa and Tajima
1620 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1621 on the basis of phylogenetic trees has been implemented (see
1622 the function klastorin()).
1624 o Functions have been added to convert APE's "phylo" objects in
1625 "hclust" cluster objects and vice versa (see the help page of
1626 as.phylo for details).
1628 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1629 are introduced for the estimation of absolute evolutionary rates
1630 (ratogram) and dated clock-like trees (chronogram) from
1631 phylogenetic trees using the non-parametric rate smoothing approach
1632 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1634 o A summary method is now provided printing a summary information on a
1635 phylogenetic tree with, for instance, `summary(tree)'.
1637 o The behaviour of read.tree() was changed so that all spaces and
1638 tabulations in tree files are now ignored. Consequently, spaces in tip
1639 labels are no more allowed. Another side effect is that read.nexus()
1640 now does not replace the underscores (_) in tip labels with spaces
1641 (this behaviour was undocumented).
1643 o The function plot.phylo() has a new option (`underscore') which
1644 specifies whether the underscores in tip labels should be written on
1645 the plot as such or replaced with spaces (the default).
1647 o The function birthdeath() now computes 95% confidence intervals of
1648 the estimated parameters using profile likelihood.
1650 o Three new data sets are included: a gene tree estimated from 36
1651 landplant rbcL sequences, a gene tree estimated from 32 opsin
1652 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1657 o A bug was fixed in dist.gene() where nothing was returned.
1659 o A bug in plot.mst() was fixed.
1661 o A bug in vcv.phylo() resulted in false correlations when the
1662 option `cor = TRUE' was used (now fixed).
1666 CHANGES IN APE VERSION 1.0
1671 o Two new functions, read.dna() and write.dna(), read/write in a file
1672 DNA sequences in interleaved or in sequential format.
1674 o Two new functions, read.nexus() and write.nexus(), read/write trees
1677 o The new function bind.tree() allows to bind two trees together,
1678 possibly handling root edges to give internal branches.
1680 o The new function drop.tip() removes the tips in a phylogenetic tree,
1681 and trims (or not) the corresponding internal branches.
1683 o The new function is.ultrametric() tests if a tree is ultrametric.
1685 o The function plot.phylo() has more functionalities such as drawing the
1686 branches with different colours and/or different widths, showing the
1687 node labels, controling the position and font of the labels, rotating
1688 the labels, and controling the space around the plot.
1690 o The function read.tree() can now read trees with no branch length,
1691 such as "(a,b),c);". Consequently, the element `edge.length' in
1692 objects of class "phylo" is now optional.
1694 o The function write.tree() has a new default behaviour: if the default
1695 for the option `file' is used (i.e. file = ""), then a variable of
1696 mode character containing the tree in Newick format is returned which
1697 can thus be assigned (e.g., tree <- write.tree(phy)).
1699 o The function read.tree() has a new argument `text' which allows
1700 to read the tree in a variable of mode character.
1702 o A new data set is included: the phylogenetic relationships among
1703 the orders of birds from Sibley and Ahlquist (1990).
1707 CHANGES IN APE VERSION 0.2-1
1712 o Several bugs were fixed in the help pages.
1716 CHANGES IN APE VERSION 0.2
1721 o The function write.tree() writes phylogenetic trees (objects of class
1722 "phylo") in an ASCII file using the Newick parenthetic format.
1724 o The function birthdeath() fits a birth-death model to branching times
1725 by maximum likelihood, and estimates the corresponding speciation and
1728 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1731 o The function is.binary.tree() tests whether a phylogeny is binary.
1733 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1734 as well as some methods are introduced.
1736 o Several functions, including some generics and methods, for computing
1737 skyline plot estimates (classic and generalized) of effective
1738 population size through time are introduced and replace the function
1739 skyline.plot() in version 0.1.
1741 o Two data sets are now included: the phylogenetic relationships among
1742 the families of birds from Sibley and Ahlquist (1990), and an
1743 estimated clock-like phylogeny of HIV sequences sampled in the
1744 Democratic Republic of Congo.
1747 DEPRECATED & DEFUNCT
1749 o The function skyline.plot() in ape 0.1 has been deprecated and
1750 replaced by more elaborate functions (see above).
1755 o Two important bugs were fixed in plot.phylo(): phylogenies with
1756 multichotomies not at the root or not with only terminal branches,
1757 and phylogenies with a single node (i.e. only terminal branches)
1758 did not plot. These trees should be plotted correctly now.
1760 o Several bugs were fixed in diversi.time() in the computation of
1763 o Various errors were corrected in the help pages.