1 CHANGES IN APE VERSION 2.3
6 o The new functions CADM.global and CADM.post, contributed by
7 Pierre Legendre, test the congruence among several distance
10 o The new function yule.time fits a user-defined time-dependent
11 Yule model by maximum likelihood.
13 o The new function makeNodeLabel creates and/or modifies node
14 labels in a flexible way.
16 o read.tree() and write.tree() have been modified so that they can
17 handle individual tree names.
19 o plot.phylo() has a new argument 'edge.lty' that specifies the
20 types of lines used for the edges (plain, dotted, dashed, ...)
25 o drop.tip() shuffled tip labels in some cases.
27 o drop.tip() did not handle node.label correctly.
29 o is.ultrametric() now checks the ordering of the edge matrix.
31 o ace() sometimes returned negative values of likelihoods of
32 ancestral states (thanks to Dan Rabosky for solving this long
38 o The data set xenarthra has been removed.
42 CHANGES IN APE VERSION 2.2-4
46 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
47 now fixed. (Thanks to Peter Wragg for the fix!)
49 o A warning message occurred for no reason with ace(method="GLS").
54 o There is now a general help page displayed with '?ape'
58 CHANGES IN APE VERSION 2.2-3
63 o The new function extract.clade extracts a clade from a tree by
64 specifying a node number or label.
66 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
67 operations of the same names.
69 o dist.dna() can now return the number of site differences by
75 o chronopl() did not work with CV = TRUE.
77 o read.nexus() did not work correctly in some situations (trees on
78 multiple lines with different numbers of lines and/or with
79 comments inserted within the trees).
81 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
82 the number of lineages with non-binary trees.
87 o ape has now a namespace.
89 o drip.tip() has been improved: it should be much faster and work
90 better in some cases (e.g., see the example in ?zoom).
94 CHANGES IN APE VERSION 2.2-2
99 o dist.gene() has been substantially improved and gains an option
102 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
108 o prop.part() failed with a single tree with the default option
109 'check.labels = TRUE'.
111 o summary.DNAbin() failed to display correctly the summary of
112 sequence lengths with lists of sequences of 10,000 bases or more
113 (because summary.default uses 4 significant digits by default).
115 o read.nexus() failed to read a file with a single tree with line
116 breaks in the Newick string.
118 o del.gaps() returned a list of empty sequences when there were no
124 o phymltest() has been updated for PhyML 3.0 and gains an option
125 'append', whereas the option 'path2exec' has been removed.
127 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
128 which is returned unchanged (instead of an error).
130 o The data sets bird.orders and bird.families are now stored as
131 Newick strings; i.e., the command data(bird.orders) calls
136 CHANGES IN APE VERSION 2.2-1
141 o The new function makeLabel() helps to modify labels of trees,
142 lists of trees, or DNA sequences, with several utilities to
143 truncate and/or make them unique, substituting some
144 characters, and so on.
146 o The new function del.gaps() removes insertion gaps ("-") in a
147 set of DNA sequences.
149 o read.dna() can now read Clustal files (*.aln).
154 o root() failed with 'resolve.root = TRUE' when the root was
155 already the specified root.
157 o Several bugs were fixed in mlphylo().
159 o collapsed.singles() did not propagate the 'Nnode' and
160 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
162 o read.nexus() failed to remove correctly the comments within
165 o read.nexus() failed to read a file with a single tree and no
166 translation of tip labels.
168 o read.nexus() failed to place correctly tip labels when reading
169 a single tree with no edge lengths.
171 o A bug was fixed in sh.test().
176 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
179 o The option 'check.labels' of consensus() and prop.part() is now
182 o write.dna() now does not truncate names to 10 characters with
187 CHANGES IN APE VERSION 2.2
192 o Four new functions have been written by Damien de Vienne for the
193 graphical exploration of large trees (cophyloplot, subtrees,
194 subtreeplot), and to return the graphical coordinates of tree
197 o The new functions corPagel and corBlomberg implement the Pagel's
198 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
200 o chronopl() has been improved and gains several options: see its
201 help page for details.
203 o boot.phylo() has now an option 'trees' to possibly return the
204 bootstraped trees (the default is FALSE).
206 o prop.part() has been improved and should now be faster in all
212 o read.dna() failed if "?" occurred in the first 10 sites of the
215 o The x/y aspect of the plot is now respected when plotting a
216 circular tree (type = "r" or "f").
218 o Drawing the tip labels sometimes failed when plotting circular
221 o zoom() failed when tip labels were used instead of their numbers
222 (thanks to Yan Wong for the fix).
224 o drop.tip() failed with some trees (fixed by Yan Wong).
226 o seg.sites() failed with a list.
228 o consensus() failed in some cases. The function has been improved
229 as well and is faster.
233 CHANGES IN APE VERSION 2.1-3
238 o A bug in read.nexus() made the Windows R-GUI crash.
240 o An error was fixed in the computation of ancestral character
241 states by generalized least squares in ace().
243 o di2multi() did not modify node labels correctly.
245 o multi2di() failed if the tree had its attribute "order" set to
250 CHANGES IN APE VERSION 2.1-2
255 o There three new methods for the "multiPhylo" class: str, $,
258 o root() gains the options 'node' and 'resolve.root'
259 (FALSE by default) as well as its code being improved.
261 o mltt.plot() has now an option 'log' used in the same way
262 than in plot.default().
267 o mltt.plot() failed to display the legend with an unnamed
270 o nodelabels() with pies now correcly uses the argument
271 'cex' to draw symbols of different sizes (which has
272 worked already for thermometers).
274 o read.nexus() generally failed to read very big files.
279 o The argument 'family' of compar.gee() can now be a function
280 as well as a character string.
282 o read.tree() and read.nexus() now return an unnamed list if
285 o read.nexus() now returns a modified object of class "multiPhylo"
286 when there is a TRANSLATE block in the NEXUS file: the individual
287 trees have no 'tip.label' vector, but the list has a 'TipLabel'
288 attribute. The new methods '$' and '[[' set these elements
289 correctly when extracting trees.
293 CHANGES IN APE VERSION 2.1-1
298 o The new function rmtree generates lists of random trees.
300 o rcoal() now generates a genuine coalescent tree by default
301 (thanks to Vladimir Minin for the code).
306 o nuc.div() returned an incorrect value with the default
307 pairwise.deletion = FALSE.
312 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
313 have been improved so that they are stabler and faster.
315 o R packages used by ape are now loaded silently; lattice and gee
316 are loaded only when needed.
320 CHANGES IN APE VERSION 2.1
325 o The new function identify.phylo identifies clades on a plotted
326 tree using the mouse.
328 o It is now possible to subset a list of trees (object of class
329 "multiPhylo") with "[" while keeping its class correct.
331 o The new function as.DNAbin.alignment converts DNA sequences
332 stored in the "alignment" format of the package seqinr into
333 an object of class "DNAbin".
335 o The new function weight.taxo2 helps to build similarity matrices
336 given two taxonomic levels (usually called by other functions).
338 o write.tree() can now take a list of trees (class "multiPhylo")
339 as its main argument.
341 o plot.correlogram() and plot.correlogramList() have been
342 improved, and gain several options (see the help page for
343 details). A legend is now plotted by default.
348 o dist.dna() returned some incorrect values with `model = "JC69"'
349 and `pairwise.deletion = TRUE'. This affected only the
350 distances involving sequences with missing values. (Thanks
351 to Bruno Toupance for digging this bug out.)
353 o write.tree() failed with some trees: this is fixed by removing
354 the `multi.line' option (trees are now always printed on a
357 o read.nexus() did not correctly detect trees with multiple root
358 edges (see OTHER CHANGES).
363 o The code of mlphylo() has been almost entirely rewritten, and
364 should be much stabler. The options have been also greatly
365 simplified (see ?mlphylo and ?DNAmodel for details).
367 o The internal function nTips has been renamed klastorin_nTips.
369 o The code of is.ultrametric() contained redundancies and has
372 o The code of Moran.I() and of correlogram.formula() have been
375 o read.tree() and read.nexus() now return an error when trying to
376 read a tree with multiple root edges (see BUG FIXES). The
377 correction applied in previous version did not work in all
380 o The class c("multi.tree", "phylo") has been renamed
386 o There is now a vignette in ape: see vignette("MoranI", "ape").
391 o as.matching() and as.phylo.matching() do not support branch
394 o correlogram.phylo() and discrete.dist() have been removed.
398 CHANGES IN APE VERSION 2.0-2
403 o The new function matexpo computes the exponential of a square
406 o The new function unique.multi.tree removes duplicate trees from
409 o yule() has a new option `use.root.edge = FALSE' that specifies
410 to ignore, by default, the root edge of the tree if it exists.
415 o which.edge() failed when the index of a single terminal edge was
418 o In diversi.time(), the values returned for model C were
421 o A bug was fixed in yule() that affected the calculation of the
422 likelihood in the presence of ties in the branching times.
424 o There was a bug in the C function mat_expo4x4 affecting the
425 calculations of the transition probabilities for models HKY and
428 o A small bug was fixed in as.matrix.DNAbin (thanks to James
431 o rtree() did not `shuffle' the tip labels by default, so only a
432 limited number of labelled topologies could be generated.
436 CHANGES IN APE VERSION 2.0-1
441 o The three new functions bionj, fastme.ols, and fastme.bal
442 perform phylogeny estimation by the BIONJ and fastME methods in
443 OLS and balanced versions. This is a port to R of previous
444 previous programs done by Vincent Lefort.
446 o The new function chronoMPL performs molecular dating with the
447 mean path lengths method of Britton et al. (2002, Mol. Phyl.
450 o The new function rotate, contributed by Christoph Heibl, swaps
451 two clades connected to the same node. It works also with
452 multichotomous nodes.
454 o The new `method' as.matrix.DNAbin() may be used to convert
455 easily DNA sequences stored in a list into a matrix while
456 keeping the names and the class.
461 o chronopl() failed when some branch lengths were equal to zero:
462 an error message is now returned.
464 o di2multi() failed when there was a series of consecutive edges
469 CHANGES IN APE VERSION 1.10-2
474 o plot.phylo() can now plot circular trees: the option is type =
475 "fan" or type = "f" (to avoid the ambiguity with type = "c").
477 o prop.part() has a new option `check.labels = FALSE' which allows
478 to considerably speed-up the calculations of bipartitions. As a
479 consequence, calculations of bootstrap values with boot.phylo()
480 should be much faster.
485 o read.GenBank() did not return correctly the list of species as
486 from ape 1.10: this is fixed in this version
488 o Applying as.phylo() on a tree of class "phylo" failed: the
489 object is now returned unchanged.
493 CHANGES IN APE VERSION 1.10-1
498 o The three new functions Ntip, Nnode, and Nedge return, for a
499 given tree, the number of tips, nodes, or edges, respectively.
504 o read.nexus() did not set correctly the class of the returned
505 object when reading multiple trees.
507 o mllt.plot() failed with objects of class c("multi.tree",
510 o unroot() did not work correctly in most cases.
512 o reorder.phylo() made R freeze in some occasions.
514 o Plotting a tree in pruningwise order failed.
516 o When plotting an unrooted tree, the tip labels where not all
517 correctly positioned if the option `cex' was used.
521 CHANGES IN APE VERSION 1.10
526 o Five new `method' functions have been introduced to manipulate
527 DNA sequences in binary format (see below).
529 o Three new functions have been introduced to convert between the
530 new binary and the character formats.
532 o The new function as.alignment converts DNA sequences stored as
533 single characters into the class "alignment" used by the package
536 o read.dna() and read.GenBank() have a new argument `as.character'
537 controlling whether the sequences are returned in binary format
543 o root() failed when the tree had node labels: this is fixed.
545 o plot.phylo() did not correctly set the limits on the y-axis with
546 the default setting: this is fixed.
548 o dist.dna() returned a wrong result for the LogDet, paralinear,
549 and BH87 models with `pairwise.deletion = TRUE'.
554 o DNA sequences are now internally stored in a binary format. See
555 the document "A Bit-Level Coding Scheme for Nucleotides" for the
556 details. Most functions analyzing DNA functions have been
557 modified accordingly and are now much faster (dist.dna is now
558 ca. 60 times faster).
562 CHANGES IN APE VERSION 1.9-4
567 o A bug was fixed in edgelabels().
569 o as.phylo.hclust() did not work correctly when the object of
570 class "hclust" has its labels set to NULL: the returned tree has
571 now its tip labels set to "1", "2", ...
573 o consensus could fail if some tip labels are a subset of others
574 (e.g., "a" and "a_1"): this is now fixed.
576 o mlphylo() failed in most cases if some branch lengths of the
577 initial tree were greater than one: an error message is now
580 o mlphylo() failed in most cases when estimating the proportion of
581 invariants: this is fixed.
585 CHANGES IN APE VERSION 1.9-3
590 o The new function edgelabels adds labels on the edge of the tree
591 in the same way than nodelabels or tiplabels.
596 o multi2di() did not handle correctly branch lengths with the
597 default option `random = TRUE': this is now fixed.
599 o A bug was fixed in nuc.div() when using pairwise deletions.
601 o A bug occurred in the analysis of bipartitions with large
602 numbers of large trees, with consequences on prop.part,
603 prop.clades, and boot.phylo.
605 o The calculation of the Billera-Holmes-Vogtmann distance in
606 dist.topo was wrong: this has been fixed.
610 CHANGES IN APE VERSION 1.9-2
615 o The new function ladderize reorganizes the internal structure of
616 a tree to plot them left- or right-ladderized.
618 o The new function dist.nodes computes the patristic distances
619 between all nodes, internal and terminal, of a tree. It replaces
620 the option `full = TRUE' of cophenetic.phylo (see below).
625 o A bug was fixed in old2new.phylo().
627 o Some bugs were fixed in chronopl().
629 o The edge colours were not correctly displayed by plot.phylo
630 (thank you to Li-San Wang for the fix).
632 o cophenetic.phylo() failed with multichotomous trees: this is
638 o read.dna() now returns the sequences in a matrix if they are
639 aligned (interleaved or sequential format). Sequences in FASTA
640 format are still returned in a list.
642 o The option `full' of cophenetic.phylo() has been removed because
643 it could not be used from the generic.
648 o rotate() has been removed; this function did not work correctly
653 CHANGES IN APE VERSION 1.9-1
658 o Trees with a single tip were not read correctly in R as the
659 element `Nnode' was not set: this is fixed.
661 o unroot() did not set correctly the number of nodes of the
662 unrooted tree in most cases.
664 o read.GenBank() failed when fetching very long sequences,
665 particularly of the BX-series.
667 o A bug was introduced in read.tree() with ape 1.9: it has been
672 CHANGES IN APE VERSION 1.9
677 o There are two new print `methods' for trees of class "phylo" and
678 lists of trees of class "multi.tree", so that they are now
679 displayed in a compact and informative way.
681 o There are two new functions, old2new.phylo and new2old.phylo,
682 for converting between the old and new coding of the class
685 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
686 LogDet ("logdet"), and paralinear ("paralin").
688 o compute.brlen() has been extended: several methods are now
689 available to compute branch lengths.
691 o write.dna() can now handle matrices as well as lists.
696 o cophenetic.phylo() sometimes returned a wrong result with
697 multichotomous trees: this is fixed.
699 o rotate() failed when a single tip was specified: the tree is now
702 o ace() did not return the correct index matrix with custom
703 models: this is fixed.
705 o multi2di() did not work correctly when resolving multichotomies
706 randomly: the topology was always the same, only the arrangement
707 of clades was randomized: this is fixed. This function now
708 accepts trees with no branch lengths.
710 o The output of diversi.gof() was blurred by useless prints when a
711 user distribution was specified. This has been corrected, and
712 the help page of this function has been expanded.
717 o The internal structure of the class "phylo" has been changed:
718 see the document "Definition of Formats for Coding Phylogenetic
719 Trees in R" for the details. In addition, the code of most
720 functions has been improved.
722 o Several functions have been improved by replacing some R codes
723 by C codes: pic, plot.phylo, and reorder.phylo.
725 o There is now a citation information: see citation("ape") in R.
727 o write.tree() now does not add extra 0's to branch lengths so
728 that 1.23 is printed "1.23" by default, not "1.2300000000".
730 o The syntax of bind.tree() has been simplified. This function now
731 accepts trees with no branch lengths, and handles correctly node
734 o The option `as.numeric' of mrca() has been removed.
736 o The unused options `format' and `rooted' of read.tree() have
739 o The unused option `format' of write.tree() has been removed.
741 o The use of node.depth() has been simplified.
745 CHANGES IN APE VERSION 1.8-5
750 o Two new functions read.nexus.data() and write.nexus.data(),
751 contributed by Johan Nylander, allow to read and write molecular
752 sequences in NEXUS files.
754 o The new function reorder.phylo() reorders the internal structure
755 of a tree of class "phylo". It is used as the generic, e.g.,
758 o read.tree() and read.nexus() can now read trees with a single
761 o The new data set `cynipids' supplies a set of protein sequences
767 o The code of all.equal.phylo() has been completely rewritten
768 (thanks to Benoît Durand) which fixes several bugs.
770 o read.tree() and read.nexus() now checks the labels of the tree
771 to remove or substitute any characters that are illegal in the
772 Newick format (parentheses, etc.)
774 o A negative P-value could be returned by mantel.test(): this is
779 CHANGES IN APE VERSION 1.8-4
784 o The new function sh.test() computes the Shimodaira-
787 o The new function collapse.singles() removes the nodes with a
788 single descendant from a tree.
790 o plot.phylo() has a new argument `tip.color' to specify the
793 o mlphylo() has now an option `quiet' to control the display of
794 the progress of the analysis (the default is FALSE).
799 o read.dna() did not read correctly sequences in sequential format
800 with leading alignment gaps "-": this is fixed.
802 o ace() returned a list with no class so that the generic
803 functions (anova, logLik, ...) could not be used directly. This
804 is fixed as ace() now returns an object of class "ace".
806 o anova.ace() had a small bug when computing the number of degrees
807 of freedom: this is fixed.
809 o mlphylo() did not work when the sequences were in a matrix or
810 a data frame: this is fixed.
812 o rtree() did not work correctly when trying to simulate an
813 unrooted tree with two tips: an error message is now issued.
818 o The algorithm of rtree() has been changed: it is now about 40,
819 100, and 130 times faster for 10, 100, and 1000 tips,
824 CHANGES IN APE VERSION 1.8-3
829 o There are four new `method' functions to be used with the
830 results of ace(): logLik(), deviance(), AIC(), and anova().
832 o The plot method of phymltest has two new arguments: `main' to
833 change the title, and `col' to control the colour of the
834 segments showing the AIC values.
836 o ace() has a new argument `ip' that gives the initial values used
837 in the ML estimation with discrete characters (see the examples
838 in ?ace). This function now returns a matrix giving the indices
839 of the estimated rates when analysing discrete characters.
841 o nodelabels() and tiplabels() have a new argument `pie' to
842 represent proportions, with any number of categories, as
843 piecharts. The use of the option `thermo' has been improved:
844 there is now no limitation on the number of categories.
849 o mlphylo() did not work with more than two partitions: this is
852 o root() failed if the proposed outgroup was already an outgroup
853 in the tree: this is fixed.
855 o The `col' argument in nodelabels() and tiplabels() was not
856 correctly passed when `text' was used: this is fixed.
858 o Two bugs were fixed in mlphylo(): parameters were not always
859 correctly output, and the estimation failed in some cases.
861 o plot.phylo() was stuck when given a tree with a single tip: this
862 is fixed and a message error is now returned.
864 o An error was corrected in the help page of gammaStat regarding
865 the calculation of P-values.
867 o Using gls() could crash R when the number of species in the tree
868 and in the variables were different: this is fixed.
872 CHANGES IN APE VERSION 1.8-2
877 o The new function mlphylo() fits a phylogenetic tree by maximum
878 likelihood from DNA sequences. Its companion function DNAmodel()
879 is used to define the substitution model which may include
880 partitioning. There are methods for logLik(), deviance(), and
881 AIC(), and the summary() method has been extended to display in
882 a friendly way the results of this model fitting. Currently, the
883 functionality is limited to estimating the substitution and
884 associated parameters and computing the likelihood.
886 o The new function drop1.compar.gee (used as, e.g., drop1(m))
887 tests for single effects in GEE-based comparative method. A
888 warning message is printed if there is not enough degrees of
894 o An error message was sometimes issued by plot.multi.tree(),
895 though with no consequence.
899 CHANGES IN APE VERSION 1.8-1
904 o There is a new plot method for lists of trees (objects of class
905 "multi.tree"): it calls plot.phylo() internally and is
906 documented on the same help page.
911 o A bug was fixed in the C code that analyzes bipartitions: this
912 has impact on several functions like prop.part, prop.clades,
913 boot.phylo, or consensus.
915 o root() did not work correctly when the specified outgroup had
916 more than one element: this is fixed.
918 o dist.dna() sometimes returned a warning inappropriately: this
921 o If the distance object given to nj() had no rownames, nj()
922 returned a tree with no tip labels: it now returns tips labelled
923 "1", "2", ..., corresponding to the row numbers.
928 o nj() has been slightly changed so that tips with a zero distance
929 are first aggregated with zero-lengthed branches; the usual NJ
930 procedure is then performed on a distance matrix without 0's.
934 CHANGES IN APE VERSION 1.8
939 o The new function chronopl() estimates dates using the penalized
940 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
942 o The new function consensus() calculates the consensus tree of a
945 o The new function evolve.phylo() simulates the evolution of
946 continuous characters along a phylogeny under a Brownian model.
948 o The new plot method for objects of class "ancestral" displays a
949 tree together with ancestral values, as returned by the above
952 o The new function as.phylo.formula() returns a phylogeny from a
953 set of nested taxonomic variables given as a formula.
955 o The new function read.caic() reads trees in CAIC format.
957 o The new function tiplabels() allows to add labels to the tips
958 of a tree using text or plotting symbols in a flexible way.
960 o The new function unroot() unroots a phylogeny.
962 o multi2di() has a new option, `random', which specifies whether
963 to resolve the multichotomies randomly (the default) or not.
965 o prop.part() now returns an object of class "prop.part" for which
966 there are print (to display a partition in a more friendly way)
967 and summary (to extract the numbers) methods.
969 o plot.phylo() has a new option, `show.tip.label', specifying
970 whether to print the labels of the tips. The default is TRUE.
972 o The code of nj() has been replaced by a faster C code: it is now
973 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
976 o write.nexus() now writes whether a tree is rooted or not.
981 o Two bugs have been fixed in root(): unrooted trees are now
982 handled corretly, and node labels are now output normally.
984 o A bug was fixed in phymltest(): the executable couldn't be found
987 o Three bug have been fixed in ace(): computing the likelihood of
988 ancestral states of discrete characters failed, custom models
989 did not work, and the function failed with a null gradient (a
990 warning message is now returned; this latter bug was also
991 present in yule.cov() as well and is now fixed).
993 o pic() hanged out when missing data were present: a message error
996 o A small bug was fixed in dist.dna() where the gamma correction
997 was not always correctly dispatched.
999 o plot.phylo() plotted correctly the root edge only when the tree
1000 was plotted rightwards: this works now for all directions.
1005 o dist.taxo() has been renamed as weight.taxo().
1007 o Various error and warning messages have been improved.
1011 CHANGES IN APE VERSION 1.7
1014 o The new function ace() estimates ancestral character states for
1015 continuous characters (with ML, GLS, and contrasts methods), and
1016 discrete characters (with ML only) for any number of states.
1018 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1019 of directional evolution for continuous characters. The user
1020 specifies the node(s) of the tree where the character optimum
1023 o The new function is.rooted() tests whether a tree (of class
1026 o The new function rcoal() generates random ultrametric trees with
1027 the possibility to specify the function that generates the
1028 inter-nodes distances.
1030 o The new function mrca() gives for all pairs of tips in a tree
1031 (and optionally nodes too) the most recent common ancestor.
1033 o nodelabels() has a new option `thermo' to plot proportions (up
1034 to three classes) on the nodes of a tree.
1036 o rtree() has been improved: it can now generate rooted or
1037 unrooted trees, and the mathematical function that generates the
1038 branch lengths may be specified by the user. The tip labels may
1039 be given directly in the call to rtree. The limit cases (n = 2,
1040 3) are now handled correctly.
1042 o dist.topo() has a new argument `method' with two choices: "PH85"
1043 for Penny and Henny's method (already available before and now
1044 the default), and "BHV01" for the geometric distance by Billera
1045 et al. (2001, Adv. Appl. Math. 27:733).
1047 o write.tree() has a new option, `digits', which specifies the
1048 number of digits to be printed in the Newick tree. By default
1049 digits = 10. The numbers are now always printed in decimal form
1050 (i.e., 1.0e-1 is now avoided).
1052 o dist.dna() can now compute the raw distances between pairs of
1053 DNA sequences by specifying model = "raw".
1055 o dist.phylo() has a new option `full' to possibly compute the
1056 distances among all tips and nodes of the tree. The default if
1062 o Several bugs were fixed in all.equal.phylo().
1064 o dist.dna() did not handle correctly gaps ("-") in alignments:
1065 they are now considered as missing data.
1067 o rotate() did not work if the tips were not ordered: this is
1070 o mantel.test() returned NA in some special cases: this is fixed
1071 and the function has been improved and is now faster.
1073 o A bug was fixed in diversi.gof() where the calculation of A² was
1076 o cherry() did not work correctly under some OSs (mainly Linux):
1079 o is.binary.tree() has been modified so that it works with both
1080 rooted and unrooted trees.
1082 o The documentation of theta.s() was not correct: this has been
1085 o plot.mst() did not work correctly: this is fixed.
1089 CHANGES IN APE VERSION 1.6
1094 o The new function dist.topo() computes the topological distances
1097 o The new function boot.phylo() performs a bootstrap analysis on
1098 phylogeny estimation.
1100 o The new functions prop.part() and prop.clades() analyse
1101 bipartitions from a series of trees.
1106 o read.GenBank() now uses the EFetch utility of NCBI instead of
1107 the usual Web interface: it is now much faster (e.g., 12 times
1108 faster to retrieve 8 sequences, 37 times for 60 sequences).
1113 o Several bugs were fixed in read.dna().
1115 o Several bugs were fixed in diversi.time().
1117 o is.binary.tree() did not work correctly if the tree has no edge
1118 lengths: this is fixed.
1120 o drop.tip() did not correctly propagated the `node.label' of a
1121 tree: this is fixed.
1125 CHANGES IN APE VERSION 1.5
1130 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1131 convert objects between the classes "phylo" and "matching". The
1132 latter implements the representation of binary trees introduced by
1133 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1134 as.matching() has been introduced as well.
1136 o Two new functions, multi2di() and di2multi(), allow to resolve
1137 and collapse multichotomies with branches of length zero.
1139 o The new function nuc.div() computes the nucleotide diversity
1140 from a sample a DNA sequences.
1142 o dist.dna() has been completely rewritten with a much faster
1143 (particularly for large data sets) C code. Eight models are
1144 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1145 option `method' has been renamed `model'). Computation of variance
1146 is available for all models. A gamma-correction is possible for
1147 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1148 to remove sites with missing data on a pairwise basis. The option
1149 `GCcontent' has been removed.
1151 o read.GenBank() has a new option (species.names) which specifies
1152 whether to return the species names of the organisms in addition
1153 to the accession numbers of the sequences (this is the default
1156 o write.nexus() can now write several trees in the same NEXUS file.
1158 o drop.tip() has a new option `root.edge' that allows to specify the
1159 new root edge if internal branches are trimmed.
1164 o as.phylo.hclust() failed if some labels had parentheses: this
1167 o Several bugs were fixed in all.equal.phylo(). This function now
1168 returns the logical TRUE if the trees are identical but with
1169 different representations (a report was printed previously).
1171 o read.GenBank() did not correctly handle ambiguous base codes:
1177 o birthdeath() now returns an object of class "birthdeath" for
1178 which there is a print method.
1182 CHANGES IN APE VERSION 1.4
1187 o The new function nj() performs phylogeny estimation with the
1188 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1191 o The new function which.edge() identifies the edges of a tree
1192 that belong to a group specified as a set of tips.
1194 o The new function as.phylo.phylog() converts an object of class
1195 "phylog" (from the package ade4) into an object of class
1198 o The new function axisPhylo() draws axes on the side of a
1201 o The new function howmanytrees() calculates the number of trees
1202 in different cases and giving a number of tips.
1204 o write.tree() has a new option `multi.line' (TRUE by default) to
1205 write a Newick tree on several lines rather than on a single
1208 o The functionalities of zoom() have been extended. Several
1209 subtrees can be visualized at the same time, and they are marked
1210 on the main tree with colors. The context of the subtrees can be
1211 marked with the option `subtree' (see below).
1213 o drop.tip() has a new option `subtree' (FALSE by default) which
1214 specifies whether to output in the tree how many tips have been
1217 o The arguments of add.scale.bar() have been redefined and have
1218 now default values (see ?add.scale.bar for details). This
1219 function now works even if the plotted tree has no edge length.
1221 o plot.phylo() can now plot radial trees, but this does not take
1222 edge lengths into account.
1224 o In plot.phylo() with `type = "phylogram"', if the values of
1225 `edge.color' and `edge.width' are identical for sister-branches,
1226 they are propagated to the vertical line that link them.
1231 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1232 crashing. This is fixed.
1234 o In plot.phylo(), the options `edge.color' and `edge.width' are
1235 now properly recycled; their default values are now "black" and
1238 o A bug has been fixed in write.nexus().
1243 o The function node.depth.edgelength() has been removed and
1244 replaced by a C code.
1248 CHANGES IN APE VERSION 1.3-1
1253 o The new function nodelabels() allows to add labels to the nodes
1254 of a tree using text or plotting symbols in a flexible way.
1256 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1257 numeric values specifying the lower and upper limits on the x-
1258 and y-axes. This allows to leave some space on any side of the
1259 tree. If a single value is given, this is taken as the upper
1264 CHANGES IN APE VERSION 1.3
1269 o The new function phymltest() calls the software PHYML and fits
1270 28 models of DNA sequence evolution. There are a print method to
1271 display likelihood and AIC values, a summary method to compute
1272 the hierarchical likelihood ratio tests, and a plot method to
1273 display graphically the AIC values of each model.
1275 o The new function yule.cov() fits the Yule model with covariates,
1276 a model where the speciation rate is affected by several species
1277 traits through a generalized linear model. The parameters are
1278 estimated by maximum likelihood.
1280 o Three new functions, corBrownian(), corGrafen(), and
1281 corMartins(), compute the expected correlation structures among
1282 species given a phylogeny under different models of evolution.
1283 These can be used for GLS comparative phylogenetic methods (see
1284 the examples). There are coef() and corMatrix() methods and an
1285 Initialize.corPhyl() function associated.
1287 o The new function compar.cheverud() implements Cheverud et al.'s
1288 (1985; Evolution 39:1335) phylogenetic comparative method.
1290 o The new function varcomp() estimates variance components; it has
1293 o Two new functions, panel.superpose.correlogram() and
1294 plot.correlogramList(), allow to plot several phylogenetic
1297 o The new function node.leafnumber() computes the number of leaves
1298 of a subtree defined by a particular node.
1300 o The new function node.sons() gets all tags of son nodes from a
1303 o The new function compute.brlen() computes the branch lengths of
1304 a tree according to a specified method.
1306 o plot.phylo() has three new options: "cex" controls the size of
1307 the (tip and node) labels (thus it is no more needed to change
1308 the global graphical parameter), "direction" which allows to
1309 plot the tree rightwards, leftwards, upwards, or downwards, and
1310 "y.lim" which sets the upper limit on the y-axis.
1315 o Some functions which try to match tip labels and names of
1316 additional data (e.g. vector) are likely to fail if there are
1317 typing or syntax errors. If both series of names do not perfectly
1318 match, they are ignored and a warning message is now issued.
1319 These functions are bd.ext, compar.gee, pic. Their help pages
1320 have been clarified on this point.
1324 CHANGES IN APE VERSION 1.2-7
1329 o The new function root() reroots a phylogenetic tree with respect
1330 to a specified outgroup.
1332 o The new function rotate() rotates an internal branch of a tree.
1334 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1335 trees) controls the display of the tip labels in unrooted trees.
1336 This display has been greatly improved: the tip labels are now not
1337 expected to overlap with the tree (particularly if lab4ut =
1338 "axial"). In all cases, combining appropriate values of "lab4ut"
1339 and the font size (via "par(cex = )") should result in readable
1340 unrooted trees. See ?plot.phylo for some examples.
1342 o In drop.tip(), the argument `tip' can now be numeric or character.
1347 o drop.tip() did not work correctly with trees with no branch
1348 lengths: this is fixed.
1350 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1351 plotted with some line crossings: this is now fixed.
1355 CHANGES IN APE VERSION 1.2-6
1360 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1361 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1362 to implement comparative methods with an autocorrelation approach.
1364 o A new data set describing some life history traits of Carnivores
1370 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1375 o When plotting a tree with plot.phylo(), the new default of the
1376 option `label.offset' is now 0, so the labels are always visible.
1380 CHANGES IN APE VERSION 1.2-5
1385 o The new function bd.ext() fits a birth-death model with combined
1386 phylogenetic and taxonomic data, and estimates the corresponding
1387 speciation and extinction rates.
1392 o The package gee is no more required by ape but only suggested
1393 since only the function compar.gee() calls gee.
1397 CHANGES IN APE VERSION 1.2-4
1402 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1403 and lines.popsize) implementing a new approach for inferring the
1404 demographic history from genealogies using a reversible jump
1405 MCMC have been introduced.
1407 o The unit of time in the skyline plot and in the new plots can
1408 now be chosen to be actual years, rather than substitutions.
1412 CHANGES IN APE VERSION 1.2-3
1417 o The new function rtree() generates a random binary tree with or
1418 without branch lengths.
1420 o Two new functions for drawing lineages-through-time (LTT) plots
1421 are provided: ltt.lines() adds a LTT curve to an existing plot,
1422 and mltt.plot() does a multiple LTT plot giving several trees as
1423 arguments (see `?ltt.plot' for details).
1428 o Some taxon names made R crashing when calling as.phylo.hclust():
1431 o dist.dna() returned an error with two identical DNA sequences
1432 (only using the Jukes-Cantor method returned 0): this is fixed.
1437 o The function dist.phylo() has been re-written using a different
1438 algorithm: it is now about four times faster.
1440 o The code of branching.times() has been improved: it is now about
1445 CHANGES IN APE VERSION 1.2-2
1450 o The new function seg.sites() finds the segregating sites in a
1451 sample of DNA sequences.
1456 o A bug introduced in read.tree() and in read.nexus() with version
1459 o A few errors were corrected and a few examples were added in the
1464 CHANGES IN APE VERSION 1.2-1
1469 o plot.phylo() can now draw the edge of the root of a tree if it
1470 has one (see the new option `root.edge', its default is FALSE).
1475 o A bug was fixed in read.nexus(): files with semicolons inside
1476 comment blocks were not read correctly.
1478 o The behaviour of read.tree() and read.nexus() was corrected so
1479 that tree files with badly represented root edges (e.g., with
1480 an extra pair of parentheses, see the help pages for details)
1481 are now correctly represented in the object of class "phylo";
1482 a warning message is now issued.
1486 CHANGES IN APE VERSION 1.2
1491 o plot.phylo() has been completely re-written and offers several
1492 new functionalities. Three types of trees can now be drawn:
1493 phylogram (as previously), cladogram, and unrooted tree; in
1494 all three types the branch lengths can be drawn using the edge
1495 lengths of the phylogeny or not (e.g., if the latter is absent).
1496 The vertical position of the nodes can be adjusted with two
1497 choices (see option `node.pos'). The code has been re-structured,
1498 and two new functions (potentially useful for developpers) are
1499 documented separately: node.depth.edgelength() and node.depth();
1500 see the respective help pages for details.
1502 o The new function zoom() allows to explore very large trees by
1503 focusing on a small portion of it.
1505 o The new function yule() fits by maximum likelihood the Yule model
1506 (birth-only process) to a phylogenetic tree.
1508 o Support for writing DNA sequences in FASTA format has been
1509 introduced in write.dna() (support for reading sequences in
1510 this format was introduced in read.dna() in version 1.1-2).
1511 The function has been completely re-written, fixing some bugs
1512 (see below); the default behaviour is no more to display the
1513 sequences on the standard output. Several options have been
1514 introduced to control the sequence printing in a flexible
1515 way. The help page has been extended.
1517 o A new data set is included: a supertree of bats in NEXUS format.
1522 o In theta.s(), the default of the option `variance' has
1523 been changed to `FALSE' (as was indicated in the help page).
1525 o Several bugs were fixed in the code of all.equal.phylo().
1527 o Several bugs were fixed in write.dna(), particularly this
1528 function did not work with `format = "interleaved"'.
1530 o Various errors were corrected in the help pages.
1535 o The argument names of as.hclust.phylo() have been changed
1536 from "(phy)" to "(x, ...)" to conform to the definition of
1537 the corresponding generic function.
1539 o gamma.stat() has been renamed gammaStat() to avoid confusion
1540 since gamma() is a generic function.
1544 CHANGES IN APE VERSION 1.1-3
1549 o base.freq() previously did not return a value of 0 for
1550 bases absent in the data (e.g., a vector of length 3 was
1551 returned if one base was absent). This is now fixed (a
1552 vector of length 4 is always returned).
1554 o Several bugs were fixed in read.nexus(), including that this
1555 function did not work in this absence of a "TRANSLATE"
1556 command in the NEXUS file, and that the commands were
1561 CHANGES IN APE VERSION 1.1-2
1566 o The Tamura and Nei (1993) model of DNA distance is now implemented
1567 in dist.dna(): five models are now available in this function.
1569 o A new data set is included: a set of 15 sequences of the
1570 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1576 o A bug in read.nexus() was fixed.
1578 o read.dna() previously did not work correctly in most cases.
1579 The function has been completely re-written and its help page
1580 has been considerably extended (see ?read.dna for details).
1581 Underscores (_) in taxon names are no more replaced with
1582 spaces (this behaviour was undocumented).
1584 o A bug was fixed in write.dna().
1588 CHANGES IN APE VERSION 1.1-1
1593 o A bug in read.tree() introduced in APE 1.1 was fixed.
1595 o A bug in compar.gee() resulted in an error when trying to fit
1596 a model with `family = "binomial"'. This is now fixed.
1600 CHANGES IN APE VERSION 1.1
1605 o The Klastorin (1982) method as suggested by Misawa and Tajima
1606 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1607 on the basis of phylogenetic trees has been implemented (see
1608 the function klastorin()).
1610 o Functions have been added to convert APE's "phylo" objects in
1611 "hclust" cluster objects and vice versa (see the help page of
1612 as.phylo for details).
1614 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1615 are introduced for the estimation of absolute evolutionary rates
1616 (ratogram) and dated clock-like trees (chronogram) from
1617 phylogenetic trees using the non-parametric rate smoothing approach
1618 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1620 o A summary method is now provided printing a summary information on a
1621 phylogenetic tree with, for instance, `summary(tree)'.
1623 o The behaviour of read.tree() was changed so that all spaces and
1624 tabulations in tree files are now ignored. Consequently, spaces in tip
1625 labels are no more allowed. Another side effect is that read.nexus()
1626 now does not replace the underscores (_) in tip labels with spaces
1627 (this behaviour was undocumented).
1629 o The function plot.phylo() has a new option (`underscore') which
1630 specifies whether the underscores in tip labels should be written on
1631 the plot as such or replaced with spaces (the default).
1633 o The function birthdeath() now computes 95% confidence intervals of
1634 the estimated parameters using profile likelihood.
1636 o Three new data sets are included: a gene tree estimated from 36
1637 landplant rbcL sequences, a gene tree estimated from 32 opsin
1638 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1643 o A bug was fixed in dist.gene() where nothing was returned.
1645 o A bug in plot.mst() was fixed.
1647 o A bug in vcv.phylo() resulted in false correlations when the
1648 option `cor = TRUE' was used (now fixed).
1652 CHANGES IN APE VERSION 1.0
1657 o Two new functions, read.dna() and write.dna(), read/write in a file
1658 DNA sequences in interleaved or in sequential format.
1660 o Two new functions, read.nexus() and write.nexus(), read/write trees
1663 o The new function bind.tree() allows to bind two trees together,
1664 possibly handling root edges to give internal branches.
1666 o The new function drop.tip() removes the tips in a phylogenetic tree,
1667 and trims (or not) the corresponding internal branches.
1669 o The new function is.ultrametric() tests if a tree is ultrametric.
1671 o The function plot.phylo() has more functionalities such as drawing the
1672 branches with different colours and/or different widths, showing the
1673 node labels, controling the position and font of the labels, rotating
1674 the labels, and controling the space around the plot.
1676 o The function read.tree() can now read trees with no branch length,
1677 such as "(a,b),c);". Consequently, the element `edge.length' in
1678 objects of class "phylo" is now optional.
1680 o The function write.tree() has a new default behaviour: if the default
1681 for the option `file' is used (i.e. file = ""), then a variable of
1682 mode character containing the tree in Newick format is returned which
1683 can thus be assigned (e.g., tree <- write.tree(phy)).
1685 o The function read.tree() has a new argument `text' which allows
1686 to read the tree in a variable of mode character.
1688 o A new data set is included: the phylogenetic relationships among
1689 the orders of birds from Sibley and Ahlquist (1990).
1693 CHANGES IN APE VERSION 0.2-1
1698 o Several bugs were fixed in the help pages.
1702 CHANGES IN APE VERSION 0.2
1707 o The function write.tree() writes phylogenetic trees (objects of class
1708 "phylo") in an ASCII file using the Newick parenthetic format.
1710 o The function birthdeath() fits a birth-death model to branching times
1711 by maximum likelihood, and estimates the corresponding speciation and
1714 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1717 o The function is.binary.tree() tests whether a phylogeny is binary.
1719 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1720 as well as some methods are introduced.
1722 o Several functions, including some generics and methods, for computing
1723 skyline plot estimates (classic and generalized) of effective
1724 population size through time are introduced and replace the function
1725 skyline.plot() in version 0.1.
1727 o Two data sets are now included: the phylogenetic relationships among
1728 the families of birds from Sibley and Ahlquist (1990), and an
1729 estimated clock-like phylogeny of HIV sequences sampled in the
1730 Democratic Republic of Congo.
1733 DEPRECATED & DEFUNCT
1735 o The function skyline.plot() in ape 0.1 has been deprecated and
1736 replaced by more elaborate functions (see above).
1741 o Two important bugs were fixed in plot.phylo(): phylogenies with
1742 multichotomies not at the root or not with only terminal branches,
1743 and phylogenies with a single node (i.e. only terminal branches)
1744 did not plot. These trees should be plotted correctly now.
1746 o Several bugs were fixed in diversi.time() in the computation of
1749 o Various errors were corrected in the help pages.
projects / ape.git / blob