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).
11 o boot.phylo() now treats correctly data frames.
16 o [.multiPhylo and [.DNAbin now respect the original class.
18 o Instances of the form class(phy) == "phylo" have been replaced
19 by inherits(phy, "phylo").
23 CHANGES IN APE VERSION 2.3
28 o The new functions CADM.global and CADM.post, contributed by
29 Pierre Legendre, test the congruence among several distance
32 o The new function yule.time fits a user-defined time-dependent
33 Yule model by maximum likelihood.
35 o The new function makeNodeLabel creates and/or modifies node
36 labels in a flexible way.
38 o read.tree() and write.tree() have been modified so that they can
39 handle individual tree names.
41 o plot.phylo() has a new argument 'edge.lty' that specifies the
42 types of lines used for the edges (plain, dotted, dashed, ...)
44 o phymltest() has been updated to work with PhyML 3.0.1.
49 o drop.tip() shuffled tip labels in some cases.
51 o drop.tip() did not handle node.label correctly.
53 o is.ultrametric() now checks the ordering of the edge matrix.
55 o ace() sometimes returned negative values of likelihoods of
56 ancestral states (thanks to Dan Rabosky for solving this long
62 o The data set xenarthra has been removed.
66 CHANGES IN APE VERSION 2.2-4
70 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
71 now fixed. (Thanks to Peter Wragg for the fix!)
73 o A warning message occurred for no reason with ace(method="GLS").
78 o There is now a general help page displayed with '?ape'
82 CHANGES IN APE VERSION 2.2-3
87 o The new function extract.clade extracts a clade from a tree by
88 specifying a node number or label.
90 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
91 operations of the same names.
93 o dist.dna() can now return the number of site differences by
99 o chronopl() did not work with CV = TRUE.
101 o read.nexus() did not work correctly in some situations (trees on
102 multiple lines with different numbers of lines and/or with
103 comments inserted within the trees).
105 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
106 the number of lineages with non-binary trees.
111 o ape has now a namespace.
113 o drip.tip() has been improved: it should be much faster and work
114 better in some cases (e.g., see the example in ?zoom).
118 CHANGES IN APE VERSION 2.2-2
123 o dist.gene() has been substantially improved and gains an option
126 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
132 o prop.part() failed with a single tree with the default option
133 'check.labels = TRUE'.
135 o summary.DNAbin() failed to display correctly the summary of
136 sequence lengths with lists of sequences of 10,000 bases or more
137 (because summary.default uses 4 significant digits by default).
139 o read.nexus() failed to read a file with a single tree with line
140 breaks in the Newick string.
142 o del.gaps() returned a list of empty sequences when there were no
148 o phymltest() has been updated for PhyML 3.0 and gains an option
149 'append', whereas the option 'path2exec' has been removed.
151 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
152 which is returned unchanged (instead of an error).
154 o The data sets bird.orders and bird.families are now stored as
155 Newick strings; i.e., the command data(bird.orders) calls
160 CHANGES IN APE VERSION 2.2-1
165 o The new function makeLabel() helps to modify labels of trees,
166 lists of trees, or DNA sequences, with several utilities to
167 truncate and/or make them unique, substituting some
168 characters, and so on.
170 o The new function del.gaps() removes insertion gaps ("-") in a
171 set of DNA sequences.
173 o read.dna() can now read Clustal files (*.aln).
178 o root() failed with 'resolve.root = TRUE' when the root was
179 already the specified root.
181 o Several bugs were fixed in mlphylo().
183 o collapsed.singles() did not propagate the 'Nnode' and
184 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
186 o read.nexus() failed to remove correctly the comments within
189 o read.nexus() failed to read a file with a single tree and no
190 translation of tip labels.
192 o read.nexus() failed to place correctly tip labels when reading
193 a single tree with no edge lengths.
195 o A bug was fixed in sh.test().
200 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
203 o The option 'check.labels' of consensus() and prop.part() is now
206 o write.dna() now does not truncate names to 10 characters with
211 CHANGES IN APE VERSION 2.2
216 o Four new functions have been written by Damien de Vienne for the
217 graphical exploration of large trees (cophyloplot, subtrees,
218 subtreeplot), and to return the graphical coordinates of tree
221 o The new functions corPagel and corBlomberg implement the Pagel's
222 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
224 o chronopl() has been improved and gains several options: see its
225 help page for details.
227 o boot.phylo() has now an option 'trees' to possibly return the
228 bootstraped trees (the default is FALSE).
230 o prop.part() has been improved and should now be faster in all
236 o read.dna() failed if "?" occurred in the first 10 sites of the
239 o The x/y aspect of the plot is now respected when plotting a
240 circular tree (type = "r" or "f").
242 o Drawing the tip labels sometimes failed when plotting circular
245 o zoom() failed when tip labels were used instead of their numbers
246 (thanks to Yan Wong for the fix).
248 o drop.tip() failed with some trees (fixed by Yan Wong).
250 o seg.sites() failed with a list.
252 o consensus() failed in some cases. The function has been improved
253 as well and is faster.
257 CHANGES IN APE VERSION 2.1-3
262 o A bug in read.nexus() made the Windows R-GUI crash.
264 o An error was fixed in the computation of ancestral character
265 states by generalized least squares in ace().
267 o di2multi() did not modify node labels correctly.
269 o multi2di() failed if the tree had its attribute "order" set to
274 CHANGES IN APE VERSION 2.1-2
279 o There three new methods for the "multiPhylo" class: str, $,
282 o root() gains the options 'node' and 'resolve.root'
283 (FALSE by default) as well as its code being improved.
285 o mltt.plot() has now an option 'log' used in the same way
286 than in plot.default().
291 o mltt.plot() failed to display the legend with an unnamed
294 o nodelabels() with pies now correcly uses the argument
295 'cex' to draw symbols of different sizes (which has
296 worked already for thermometers).
298 o read.nexus() generally failed to read very big files.
303 o The argument 'family' of compar.gee() can now be a function
304 as well as a character string.
306 o read.tree() and read.nexus() now return an unnamed list if
309 o read.nexus() now returns a modified object of class "multiPhylo"
310 when there is a TRANSLATE block in the NEXUS file: the individual
311 trees have no 'tip.label' vector, but the list has a 'TipLabel'
312 attribute. The new methods '$' and '[[' set these elements
313 correctly when extracting trees.
317 CHANGES IN APE VERSION 2.1-1
322 o The new function rmtree generates lists of random trees.
324 o rcoal() now generates a genuine coalescent tree by default
325 (thanks to Vladimir Minin for the code).
330 o nuc.div() returned an incorrect value with the default
331 pairwise.deletion = FALSE.
336 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
337 have been improved so that they are stabler and faster.
339 o R packages used by ape are now loaded silently; lattice and gee
340 are loaded only when needed.
344 CHANGES IN APE VERSION 2.1
349 o The new function identify.phylo identifies clades on a plotted
350 tree using the mouse.
352 o It is now possible to subset a list of trees (object of class
353 "multiPhylo") with "[" while keeping its class correct.
355 o The new function as.DNAbin.alignment converts DNA sequences
356 stored in the "alignment" format of the package seqinr into
357 an object of class "DNAbin".
359 o The new function weight.taxo2 helps to build similarity matrices
360 given two taxonomic levels (usually called by other functions).
362 o write.tree() can now take a list of trees (class "multiPhylo")
363 as its main argument.
365 o plot.correlogram() and plot.correlogramList() have been
366 improved, and gain several options (see the help page for
367 details). A legend is now plotted by default.
372 o dist.dna() returned some incorrect values with `model = "JC69"'
373 and `pairwise.deletion = TRUE'. This affected only the
374 distances involving sequences with missing values. (Thanks
375 to Bruno Toupance for digging this bug out.)
377 o write.tree() failed with some trees: this is fixed by removing
378 the `multi.line' option (trees are now always printed on a
381 o read.nexus() did not correctly detect trees with multiple root
382 edges (see OTHER CHANGES).
387 o The code of mlphylo() has been almost entirely rewritten, and
388 should be much stabler. The options have been also greatly
389 simplified (see ?mlphylo and ?DNAmodel for details).
391 o The internal function nTips has been renamed klastorin_nTips.
393 o The code of is.ultrametric() contained redundancies and has
396 o The code of Moran.I() and of correlogram.formula() have been
399 o read.tree() and read.nexus() now return an error when trying to
400 read a tree with multiple root edges (see BUG FIXES). The
401 correction applied in previous version did not work in all
404 o The class c("multi.tree", "phylo") has been renamed
410 o There is now a vignette in ape: see vignette("MoranI", "ape").
415 o as.matching() and as.phylo.matching() do not support branch
418 o correlogram.phylo() and discrete.dist() have been removed.
422 CHANGES IN APE VERSION 2.0-2
427 o The new function matexpo computes the exponential of a square
430 o The new function unique.multi.tree removes duplicate trees from
433 o yule() has a new option `use.root.edge = FALSE' that specifies
434 to ignore, by default, the root edge of the tree if it exists.
439 o which.edge() failed when the index of a single terminal edge was
442 o In diversi.time(), the values returned for model C were
445 o A bug was fixed in yule() that affected the calculation of the
446 likelihood in the presence of ties in the branching times.
448 o There was a bug in the C function mat_expo4x4 affecting the
449 calculations of the transition probabilities for models HKY and
452 o A small bug was fixed in as.matrix.DNAbin (thanks to James
455 o rtree() did not `shuffle' the tip labels by default, so only a
456 limited number of labelled topologies could be generated.
460 CHANGES IN APE VERSION 2.0-1
465 o The three new functions bionj, fastme.ols, and fastme.bal
466 perform phylogeny estimation by the BIONJ and fastME methods in
467 OLS and balanced versions. This is a port to R of previous
468 previous programs done by Vincent Lefort.
470 o The new function chronoMPL performs molecular dating with the
471 mean path lengths method of Britton et al. (2002, Mol. Phyl.
474 o The new function rotate, contributed by Christoph Heibl, swaps
475 two clades connected to the same node. It works also with
476 multichotomous nodes.
478 o The new `method' as.matrix.DNAbin() may be used to convert
479 easily DNA sequences stored in a list into a matrix while
480 keeping the names and the class.
485 o chronopl() failed when some branch lengths were equal to zero:
486 an error message is now returned.
488 o di2multi() failed when there was a series of consecutive edges
493 CHANGES IN APE VERSION 1.10-2
498 o plot.phylo() can now plot circular trees: the option is type =
499 "fan" or type = "f" (to avoid the ambiguity with type = "c").
501 o prop.part() has a new option `check.labels = FALSE' which allows
502 to considerably speed-up the calculations of bipartitions. As a
503 consequence, calculations of bootstrap values with boot.phylo()
504 should be much faster.
509 o read.GenBank() did not return correctly the list of species as
510 from ape 1.10: this is fixed in this version
512 o Applying as.phylo() on a tree of class "phylo" failed: the
513 object is now returned unchanged.
517 CHANGES IN APE VERSION 1.10-1
522 o The three new functions Ntip, Nnode, and Nedge return, for a
523 given tree, the number of tips, nodes, or edges, respectively.
528 o read.nexus() did not set correctly the class of the returned
529 object when reading multiple trees.
531 o mllt.plot() failed with objects of class c("multi.tree",
534 o unroot() did not work correctly in most cases.
536 o reorder.phylo() made R freeze in some occasions.
538 o Plotting a tree in pruningwise order failed.
540 o When plotting an unrooted tree, the tip labels where not all
541 correctly positioned if the option `cex' was used.
545 CHANGES IN APE VERSION 1.10
550 o Five new `method' functions have been introduced to manipulate
551 DNA sequences in binary format (see below).
553 o Three new functions have been introduced to convert between the
554 new binary and the character formats.
556 o The new function as.alignment converts DNA sequences stored as
557 single characters into the class "alignment" used by the package
560 o read.dna() and read.GenBank() have a new argument `as.character'
561 controlling whether the sequences are returned in binary format
567 o root() failed when the tree had node labels: this is fixed.
569 o plot.phylo() did not correctly set the limits on the y-axis with
570 the default setting: this is fixed.
572 o dist.dna() returned a wrong result for the LogDet, paralinear,
573 and BH87 models with `pairwise.deletion = TRUE'.
578 o DNA sequences are now internally stored in a binary format. See
579 the document "A Bit-Level Coding Scheme for Nucleotides" for the
580 details. Most functions analyzing DNA functions have been
581 modified accordingly and are now much faster (dist.dna is now
582 ca. 60 times faster).
586 CHANGES IN APE VERSION 1.9-4
591 o A bug was fixed in edgelabels().
593 o as.phylo.hclust() did not work correctly when the object of
594 class "hclust" has its labels set to NULL: the returned tree has
595 now its tip labels set to "1", "2", ...
597 o consensus could fail if some tip labels are a subset of others
598 (e.g., "a" and "a_1"): this is now fixed.
600 o mlphylo() failed in most cases if some branch lengths of the
601 initial tree were greater than one: an error message is now
604 o mlphylo() failed in most cases when estimating the proportion of
605 invariants: this is fixed.
609 CHANGES IN APE VERSION 1.9-3
614 o The new function edgelabels adds labels on the edge of the tree
615 in the same way than nodelabels or tiplabels.
620 o multi2di() did not handle correctly branch lengths with the
621 default option `random = TRUE': this is now fixed.
623 o A bug was fixed in nuc.div() when using pairwise deletions.
625 o A bug occurred in the analysis of bipartitions with large
626 numbers of large trees, with consequences on prop.part,
627 prop.clades, and boot.phylo.
629 o The calculation of the Billera-Holmes-Vogtmann distance in
630 dist.topo was wrong: this has been fixed.
634 CHANGES IN APE VERSION 1.9-2
639 o The new function ladderize reorganizes the internal structure of
640 a tree to plot them left- or right-ladderized.
642 o The new function dist.nodes computes the patristic distances
643 between all nodes, internal and terminal, of a tree. It replaces
644 the option `full = TRUE' of cophenetic.phylo (see below).
649 o A bug was fixed in old2new.phylo().
651 o Some bugs were fixed in chronopl().
653 o The edge colours were not correctly displayed by plot.phylo
654 (thank you to Li-San Wang for the fix).
656 o cophenetic.phylo() failed with multichotomous trees: this is
662 o read.dna() now returns the sequences in a matrix if they are
663 aligned (interleaved or sequential format). Sequences in FASTA
664 format are still returned in a list.
666 o The option `full' of cophenetic.phylo() has been removed because
667 it could not be used from the generic.
672 o rotate() has been removed; this function did not work correctly
677 CHANGES IN APE VERSION 1.9-1
682 o Trees with a single tip were not read correctly in R as the
683 element `Nnode' was not set: this is fixed.
685 o unroot() did not set correctly the number of nodes of the
686 unrooted tree in most cases.
688 o read.GenBank() failed when fetching very long sequences,
689 particularly of the BX-series.
691 o A bug was introduced in read.tree() with ape 1.9: it has been
696 CHANGES IN APE VERSION 1.9
701 o There are two new print `methods' for trees of class "phylo" and
702 lists of trees of class "multi.tree", so that they are now
703 displayed in a compact and informative way.
705 o There are two new functions, old2new.phylo and new2old.phylo,
706 for converting between the old and new coding of the class
709 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
710 LogDet ("logdet"), and paralinear ("paralin").
712 o compute.brlen() has been extended: several methods are now
713 available to compute branch lengths.
715 o write.dna() can now handle matrices as well as lists.
720 o cophenetic.phylo() sometimes returned a wrong result with
721 multichotomous trees: this is fixed.
723 o rotate() failed when a single tip was specified: the tree is now
726 o ace() did not return the correct index matrix with custom
727 models: this is fixed.
729 o multi2di() did not work correctly when resolving multichotomies
730 randomly: the topology was always the same, only the arrangement
731 of clades was randomized: this is fixed. This function now
732 accepts trees with no branch lengths.
734 o The output of diversi.gof() was blurred by useless prints when a
735 user distribution was specified. This has been corrected, and
736 the help page of this function has been expanded.
741 o The internal structure of the class "phylo" has been changed:
742 see the document "Definition of Formats for Coding Phylogenetic
743 Trees in R" for the details. In addition, the code of most
744 functions has been improved.
746 o Several functions have been improved by replacing some R codes
747 by C codes: pic, plot.phylo, and reorder.phylo.
749 o There is now a citation information: see citation("ape") in R.
751 o write.tree() now does not add extra 0's to branch lengths so
752 that 1.23 is printed "1.23" by default, not "1.2300000000".
754 o The syntax of bind.tree() has been simplified. This function now
755 accepts trees with no branch lengths, and handles correctly node
758 o The option `as.numeric' of mrca() has been removed.
760 o The unused options `format' and `rooted' of read.tree() have
763 o The unused option `format' of write.tree() has been removed.
765 o The use of node.depth() has been simplified.
769 CHANGES IN APE VERSION 1.8-5
774 o Two new functions read.nexus.data() and write.nexus.data(),
775 contributed by Johan Nylander, allow to read and write molecular
776 sequences in NEXUS files.
778 o The new function reorder.phylo() reorders the internal structure
779 of a tree of class "phylo". It is used as the generic, e.g.,
782 o read.tree() and read.nexus() can now read trees with a single
785 o The new data set `cynipids' supplies a set of protein sequences
791 o The code of all.equal.phylo() has been completely rewritten
792 (thanks to Benoît Durand) which fixes several bugs.
794 o read.tree() and read.nexus() now checks the labels of the tree
795 to remove or substitute any characters that are illegal in the
796 Newick format (parentheses, etc.)
798 o A negative P-value could be returned by mantel.test(): this is
803 CHANGES IN APE VERSION 1.8-4
808 o The new function sh.test() computes the Shimodaira-
811 o The new function collapse.singles() removes the nodes with a
812 single descendant from a tree.
814 o plot.phylo() has a new argument `tip.color' to specify the
817 o mlphylo() has now an option `quiet' to control the display of
818 the progress of the analysis (the default is FALSE).
823 o read.dna() did not read correctly sequences in sequential format
824 with leading alignment gaps "-": this is fixed.
826 o ace() returned a list with no class so that the generic
827 functions (anova, logLik, ...) could not be used directly. This
828 is fixed as ace() now returns an object of class "ace".
830 o anova.ace() had a small bug when computing the number of degrees
831 of freedom: this is fixed.
833 o mlphylo() did not work when the sequences were in a matrix or
834 a data frame: this is fixed.
836 o rtree() did not work correctly when trying to simulate an
837 unrooted tree with two tips: an error message is now issued.
842 o The algorithm of rtree() has been changed: it is now about 40,
843 100, and 130 times faster for 10, 100, and 1000 tips,
848 CHANGES IN APE VERSION 1.8-3
853 o There are four new `method' functions to be used with the
854 results of ace(): logLik(), deviance(), AIC(), and anova().
856 o The plot method of phymltest has two new arguments: `main' to
857 change the title, and `col' to control the colour of the
858 segments showing the AIC values.
860 o ace() has a new argument `ip' that gives the initial values used
861 in the ML estimation with discrete characters (see the examples
862 in ?ace). This function now returns a matrix giving the indices
863 of the estimated rates when analysing discrete characters.
865 o nodelabels() and tiplabels() have a new argument `pie' to
866 represent proportions, with any number of categories, as
867 piecharts. The use of the option `thermo' has been improved:
868 there is now no limitation on the number of categories.
873 o mlphylo() did not work with more than two partitions: this is
876 o root() failed if the proposed outgroup was already an outgroup
877 in the tree: this is fixed.
879 o The `col' argument in nodelabels() and tiplabels() was not
880 correctly passed when `text' was used: this is fixed.
882 o Two bugs were fixed in mlphylo(): parameters were not always
883 correctly output, and the estimation failed in some cases.
885 o plot.phylo() was stuck when given a tree with a single tip: this
886 is fixed and a message error is now returned.
888 o An error was corrected in the help page of gammaStat regarding
889 the calculation of P-values.
891 o Using gls() could crash R when the number of species in the tree
892 and in the variables were different: this is fixed.
896 CHANGES IN APE VERSION 1.8-2
901 o The new function mlphylo() fits a phylogenetic tree by maximum
902 likelihood from DNA sequences. Its companion function DNAmodel()
903 is used to define the substitution model which may include
904 partitioning. There are methods for logLik(), deviance(), and
905 AIC(), and the summary() method has been extended to display in
906 a friendly way the results of this model fitting. Currently, the
907 functionality is limited to estimating the substitution and
908 associated parameters and computing the likelihood.
910 o The new function drop1.compar.gee (used as, e.g., drop1(m))
911 tests for single effects in GEE-based comparative method. A
912 warning message is printed if there is not enough degrees of
918 o An error message was sometimes issued by plot.multi.tree(),
919 though with no consequence.
923 CHANGES IN APE VERSION 1.8-1
928 o There is a new plot method for lists of trees (objects of class
929 "multi.tree"): it calls plot.phylo() internally and is
930 documented on the same help page.
935 o A bug was fixed in the C code that analyzes bipartitions: this
936 has impact on several functions like prop.part, prop.clades,
937 boot.phylo, or consensus.
939 o root() did not work correctly when the specified outgroup had
940 more than one element: this is fixed.
942 o dist.dna() sometimes returned a warning inappropriately: this
945 o If the distance object given to nj() had no rownames, nj()
946 returned a tree with no tip labels: it now returns tips labelled
947 "1", "2", ..., corresponding to the row numbers.
952 o nj() has been slightly changed so that tips with a zero distance
953 are first aggregated with zero-lengthed branches; the usual NJ
954 procedure is then performed on a distance matrix without 0's.
958 CHANGES IN APE VERSION 1.8
963 o The new function chronopl() estimates dates using the penalized
964 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
966 o The new function consensus() calculates the consensus tree of a
969 o The new function evolve.phylo() simulates the evolution of
970 continuous characters along a phylogeny under a Brownian model.
972 o The new plot method for objects of class "ancestral" displays a
973 tree together with ancestral values, as returned by the above
976 o The new function as.phylo.formula() returns a phylogeny from a
977 set of nested taxonomic variables given as a formula.
979 o The new function read.caic() reads trees in CAIC format.
981 o The new function tiplabels() allows to add labels to the tips
982 of a tree using text or plotting symbols in a flexible way.
984 o The new function unroot() unroots a phylogeny.
986 o multi2di() has a new option, `random', which specifies whether
987 to resolve the multichotomies randomly (the default) or not.
989 o prop.part() now returns an object of class "prop.part" for which
990 there are print (to display a partition in a more friendly way)
991 and summary (to extract the numbers) methods.
993 o plot.phylo() has a new option, `show.tip.label', specifying
994 whether to print the labels of the tips. The default is TRUE.
996 o The code of nj() has been replaced by a faster C code: it is now
997 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1000 o write.nexus() now writes whether a tree is rooted or not.
1005 o Two bugs have been fixed in root(): unrooted trees are now
1006 handled corretly, and node labels are now output normally.
1008 o A bug was fixed in phymltest(): the executable couldn't be found
1011 o Three bug have been fixed in ace(): computing the likelihood of
1012 ancestral states of discrete characters failed, custom models
1013 did not work, and the function failed with a null gradient (a
1014 warning message is now returned; this latter bug was also
1015 present in yule.cov() as well and is now fixed).
1017 o pic() hanged out when missing data were present: a message error
1020 o A small bug was fixed in dist.dna() where the gamma correction
1021 was not always correctly dispatched.
1023 o plot.phylo() plotted correctly the root edge only when the tree
1024 was plotted rightwards: this works now for all directions.
1029 o dist.taxo() has been renamed as weight.taxo().
1031 o Various error and warning messages have been improved.
1035 CHANGES IN APE VERSION 1.7
1038 o The new function ace() estimates ancestral character states for
1039 continuous characters (with ML, GLS, and contrasts methods), and
1040 discrete characters (with ML only) for any number of states.
1042 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1043 of directional evolution for continuous characters. The user
1044 specifies the node(s) of the tree where the character optimum
1047 o The new function is.rooted() tests whether a tree (of class
1050 o The new function rcoal() generates random ultrametric trees with
1051 the possibility to specify the function that generates the
1052 inter-nodes distances.
1054 o The new function mrca() gives for all pairs of tips in a tree
1055 (and optionally nodes too) the most recent common ancestor.
1057 o nodelabels() has a new option `thermo' to plot proportions (up
1058 to three classes) on the nodes of a tree.
1060 o rtree() has been improved: it can now generate rooted or
1061 unrooted trees, and the mathematical function that generates the
1062 branch lengths may be specified by the user. The tip labels may
1063 be given directly in the call to rtree. The limit cases (n = 2,
1064 3) are now handled correctly.
1066 o dist.topo() has a new argument `method' with two choices: "PH85"
1067 for Penny and Henny's method (already available before and now
1068 the default), and "BHV01" for the geometric distance by Billera
1069 et al. (2001, Adv. Appl. Math. 27:733).
1071 o write.tree() has a new option, `digits', which specifies the
1072 number of digits to be printed in the Newick tree. By default
1073 digits = 10. The numbers are now always printed in decimal form
1074 (i.e., 1.0e-1 is now avoided).
1076 o dist.dna() can now compute the raw distances between pairs of
1077 DNA sequences by specifying model = "raw".
1079 o dist.phylo() has a new option `full' to possibly compute the
1080 distances among all tips and nodes of the tree. The default if
1086 o Several bugs were fixed in all.equal.phylo().
1088 o dist.dna() did not handle correctly gaps ("-") in alignments:
1089 they are now considered as missing data.
1091 o rotate() did not work if the tips were not ordered: this is
1094 o mantel.test() returned NA in some special cases: this is fixed
1095 and the function has been improved and is now faster.
1097 o A bug was fixed in diversi.gof() where the calculation of A² was
1100 o cherry() did not work correctly under some OSs (mainly Linux):
1103 o is.binary.tree() has been modified so that it works with both
1104 rooted and unrooted trees.
1106 o The documentation of theta.s() was not correct: this has been
1109 o plot.mst() did not work correctly: this is fixed.
1113 CHANGES IN APE VERSION 1.6
1118 o The new function dist.topo() computes the topological distances
1121 o The new function boot.phylo() performs a bootstrap analysis on
1122 phylogeny estimation.
1124 o The new functions prop.part() and prop.clades() analyse
1125 bipartitions from a series of trees.
1130 o read.GenBank() now uses the EFetch utility of NCBI instead of
1131 the usual Web interface: it is now much faster (e.g., 12 times
1132 faster to retrieve 8 sequences, 37 times for 60 sequences).
1137 o Several bugs were fixed in read.dna().
1139 o Several bugs were fixed in diversi.time().
1141 o is.binary.tree() did not work correctly if the tree has no edge
1142 lengths: this is fixed.
1144 o drop.tip() did not correctly propagated the `node.label' of a
1145 tree: this is fixed.
1149 CHANGES IN APE VERSION 1.5
1154 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1155 convert objects between the classes "phylo" and "matching". The
1156 latter implements the representation of binary trees introduced by
1157 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1158 as.matching() has been introduced as well.
1160 o Two new functions, multi2di() and di2multi(), allow to resolve
1161 and collapse multichotomies with branches of length zero.
1163 o The new function nuc.div() computes the nucleotide diversity
1164 from a sample a DNA sequences.
1166 o dist.dna() has been completely rewritten with a much faster
1167 (particularly for large data sets) C code. Eight models are
1168 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1169 option `method' has been renamed `model'). Computation of variance
1170 is available for all models. A gamma-correction is possible for
1171 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1172 to remove sites with missing data on a pairwise basis. The option
1173 `GCcontent' has been removed.
1175 o read.GenBank() has a new option (species.names) which specifies
1176 whether to return the species names of the organisms in addition
1177 to the accession numbers of the sequences (this is the default
1180 o write.nexus() can now write several trees in the same NEXUS file.
1182 o drop.tip() has a new option `root.edge' that allows to specify the
1183 new root edge if internal branches are trimmed.
1188 o as.phylo.hclust() failed if some labels had parentheses: this
1191 o Several bugs were fixed in all.equal.phylo(). This function now
1192 returns the logical TRUE if the trees are identical but with
1193 different representations (a report was printed previously).
1195 o read.GenBank() did not correctly handle ambiguous base codes:
1201 o birthdeath() now returns an object of class "birthdeath" for
1202 which there is a print method.
1206 CHANGES IN APE VERSION 1.4
1211 o The new function nj() performs phylogeny estimation with the
1212 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1215 o The new function which.edge() identifies the edges of a tree
1216 that belong to a group specified as a set of tips.
1218 o The new function as.phylo.phylog() converts an object of class
1219 "phylog" (from the package ade4) into an object of class
1222 o The new function axisPhylo() draws axes on the side of a
1225 o The new function howmanytrees() calculates the number of trees
1226 in different cases and giving a number of tips.
1228 o write.tree() has a new option `multi.line' (TRUE by default) to
1229 write a Newick tree on several lines rather than on a single
1232 o The functionalities of zoom() have been extended. Several
1233 subtrees can be visualized at the same time, and they are marked
1234 on the main tree with colors. The context of the subtrees can be
1235 marked with the option `subtree' (see below).
1237 o drop.tip() has a new option `subtree' (FALSE by default) which
1238 specifies whether to output in the tree how many tips have been
1241 o The arguments of add.scale.bar() have been redefined and have
1242 now default values (see ?add.scale.bar for details). This
1243 function now works even if the plotted tree has no edge length.
1245 o plot.phylo() can now plot radial trees, but this does not take
1246 edge lengths into account.
1248 o In plot.phylo() with `type = "phylogram"', if the values of
1249 `edge.color' and `edge.width' are identical for sister-branches,
1250 they are propagated to the vertical line that link them.
1255 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1256 crashing. This is fixed.
1258 o In plot.phylo(), the options `edge.color' and `edge.width' are
1259 now properly recycled; their default values are now "black" and
1262 o A bug has been fixed in write.nexus().
1267 o The function node.depth.edgelength() has been removed and
1268 replaced by a C code.
1272 CHANGES IN APE VERSION 1.3-1
1277 o The new function nodelabels() allows to add labels to the nodes
1278 of a tree using text or plotting symbols in a flexible way.
1280 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1281 numeric values specifying the lower and upper limits on the x-
1282 and y-axes. This allows to leave some space on any side of the
1283 tree. If a single value is given, this is taken as the upper
1288 CHANGES IN APE VERSION 1.3
1293 o The new function phymltest() calls the software PHYML and fits
1294 28 models of DNA sequence evolution. There are a print method to
1295 display likelihood and AIC values, a summary method to compute
1296 the hierarchical likelihood ratio tests, and a plot method to
1297 display graphically the AIC values of each model.
1299 o The new function yule.cov() fits the Yule model with covariates,
1300 a model where the speciation rate is affected by several species
1301 traits through a generalized linear model. The parameters are
1302 estimated by maximum likelihood.
1304 o Three new functions, corBrownian(), corGrafen(), and
1305 corMartins(), compute the expected correlation structures among
1306 species given a phylogeny under different models of evolution.
1307 These can be used for GLS comparative phylogenetic methods (see
1308 the examples). There are coef() and corMatrix() methods and an
1309 Initialize.corPhyl() function associated.
1311 o The new function compar.cheverud() implements Cheverud et al.'s
1312 (1985; Evolution 39:1335) phylogenetic comparative method.
1314 o The new function varcomp() estimates variance components; it has
1317 o Two new functions, panel.superpose.correlogram() and
1318 plot.correlogramList(), allow to plot several phylogenetic
1321 o The new function node.leafnumber() computes the number of leaves
1322 of a subtree defined by a particular node.
1324 o The new function node.sons() gets all tags of son nodes from a
1327 o The new function compute.brlen() computes the branch lengths of
1328 a tree according to a specified method.
1330 o plot.phylo() has three new options: "cex" controls the size of
1331 the (tip and node) labels (thus it is no more needed to change
1332 the global graphical parameter), "direction" which allows to
1333 plot the tree rightwards, leftwards, upwards, or downwards, and
1334 "y.lim" which sets the upper limit on the y-axis.
1339 o Some functions which try to match tip labels and names of
1340 additional data (e.g. vector) are likely to fail if there are
1341 typing or syntax errors. If both series of names do not perfectly
1342 match, they are ignored and a warning message is now issued.
1343 These functions are bd.ext, compar.gee, pic. Their help pages
1344 have been clarified on this point.
1348 CHANGES IN APE VERSION 1.2-7
1353 o The new function root() reroots a phylogenetic tree with respect
1354 to a specified outgroup.
1356 o The new function rotate() rotates an internal branch of a tree.
1358 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1359 trees) controls the display of the tip labels in unrooted trees.
1360 This display has been greatly improved: the tip labels are now not
1361 expected to overlap with the tree (particularly if lab4ut =
1362 "axial"). In all cases, combining appropriate values of "lab4ut"
1363 and the font size (via "par(cex = )") should result in readable
1364 unrooted trees. See ?plot.phylo for some examples.
1366 o In drop.tip(), the argument `tip' can now be numeric or character.
1371 o drop.tip() did not work correctly with trees with no branch
1372 lengths: this is fixed.
1374 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1375 plotted with some line crossings: this is now fixed.
1379 CHANGES IN APE VERSION 1.2-6
1384 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1385 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1386 to implement comparative methods with an autocorrelation approach.
1388 o A new data set describing some life history traits of Carnivores
1394 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1399 o When plotting a tree with plot.phylo(), the new default of the
1400 option `label.offset' is now 0, so the labels are always visible.
1404 CHANGES IN APE VERSION 1.2-5
1409 o The new function bd.ext() fits a birth-death model with combined
1410 phylogenetic and taxonomic data, and estimates the corresponding
1411 speciation and extinction rates.
1416 o The package gee is no more required by ape but only suggested
1417 since only the function compar.gee() calls gee.
1421 CHANGES IN APE VERSION 1.2-4
1426 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1427 and lines.popsize) implementing a new approach for inferring the
1428 demographic history from genealogies using a reversible jump
1429 MCMC have been introduced.
1431 o The unit of time in the skyline plot and in the new plots can
1432 now be chosen to be actual years, rather than substitutions.
1436 CHANGES IN APE VERSION 1.2-3
1441 o The new function rtree() generates a random binary tree with or
1442 without branch lengths.
1444 o Two new functions for drawing lineages-through-time (LTT) plots
1445 are provided: ltt.lines() adds a LTT curve to an existing plot,
1446 and mltt.plot() does a multiple LTT plot giving several trees as
1447 arguments (see `?ltt.plot' for details).
1452 o Some taxon names made R crashing when calling as.phylo.hclust():
1455 o dist.dna() returned an error with two identical DNA sequences
1456 (only using the Jukes-Cantor method returned 0): this is fixed.
1461 o The function dist.phylo() has been re-written using a different
1462 algorithm: it is now about four times faster.
1464 o The code of branching.times() has been improved: it is now about
1469 CHANGES IN APE VERSION 1.2-2
1474 o The new function seg.sites() finds the segregating sites in a
1475 sample of DNA sequences.
1480 o A bug introduced in read.tree() and in read.nexus() with version
1483 o A few errors were corrected and a few examples were added in the
1488 CHANGES IN APE VERSION 1.2-1
1493 o plot.phylo() can now draw the edge of the root of a tree if it
1494 has one (see the new option `root.edge', its default is FALSE).
1499 o A bug was fixed in read.nexus(): files with semicolons inside
1500 comment blocks were not read correctly.
1502 o The behaviour of read.tree() and read.nexus() was corrected so
1503 that tree files with badly represented root edges (e.g., with
1504 an extra pair of parentheses, see the help pages for details)
1505 are now correctly represented in the object of class "phylo";
1506 a warning message is now issued.
1510 CHANGES IN APE VERSION 1.2
1515 o plot.phylo() has been completely re-written and offers several
1516 new functionalities. Three types of trees can now be drawn:
1517 phylogram (as previously), cladogram, and unrooted tree; in
1518 all three types the branch lengths can be drawn using the edge
1519 lengths of the phylogeny or not (e.g., if the latter is absent).
1520 The vertical position of the nodes can be adjusted with two
1521 choices (see option `node.pos'). The code has been re-structured,
1522 and two new functions (potentially useful for developpers) are
1523 documented separately: node.depth.edgelength() and node.depth();
1524 see the respective help pages for details.
1526 o The new function zoom() allows to explore very large trees by
1527 focusing on a small portion of it.
1529 o The new function yule() fits by maximum likelihood the Yule model
1530 (birth-only process) to a phylogenetic tree.
1532 o Support for writing DNA sequences in FASTA format has been
1533 introduced in write.dna() (support for reading sequences in
1534 this format was introduced in read.dna() in version 1.1-2).
1535 The function has been completely re-written, fixing some bugs
1536 (see below); the default behaviour is no more to display the
1537 sequences on the standard output. Several options have been
1538 introduced to control the sequence printing in a flexible
1539 way. The help page has been extended.
1541 o A new data set is included: a supertree of bats in NEXUS format.
1546 o In theta.s(), the default of the option `variance' has
1547 been changed to `FALSE' (as was indicated in the help page).
1549 o Several bugs were fixed in the code of all.equal.phylo().
1551 o Several bugs were fixed in write.dna(), particularly this
1552 function did not work with `format = "interleaved"'.
1554 o Various errors were corrected in the help pages.
1559 o The argument names of as.hclust.phylo() have been changed
1560 from "(phy)" to "(x, ...)" to conform to the definition of
1561 the corresponding generic function.
1563 o gamma.stat() has been renamed gammaStat() to avoid confusion
1564 since gamma() is a generic function.
1568 CHANGES IN APE VERSION 1.1-3
1573 o base.freq() previously did not return a value of 0 for
1574 bases absent in the data (e.g., a vector of length 3 was
1575 returned if one base was absent). This is now fixed (a
1576 vector of length 4 is always returned).
1578 o Several bugs were fixed in read.nexus(), including that this
1579 function did not work in this absence of a "TRANSLATE"
1580 command in the NEXUS file, and that the commands were
1585 CHANGES IN APE VERSION 1.1-2
1590 o The Tamura and Nei (1993) model of DNA distance is now implemented
1591 in dist.dna(): five models are now available in this function.
1593 o A new data set is included: a set of 15 sequences of the
1594 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1600 o A bug in read.nexus() was fixed.
1602 o read.dna() previously did not work correctly in most cases.
1603 The function has been completely re-written and its help page
1604 has been considerably extended (see ?read.dna for details).
1605 Underscores (_) in taxon names are no more replaced with
1606 spaces (this behaviour was undocumented).
1608 o A bug was fixed in write.dna().
1612 CHANGES IN APE VERSION 1.1-1
1617 o A bug in read.tree() introduced in APE 1.1 was fixed.
1619 o A bug in compar.gee() resulted in an error when trying to fit
1620 a model with `family = "binomial"'. This is now fixed.
1624 CHANGES IN APE VERSION 1.1
1629 o The Klastorin (1982) method as suggested by Misawa and Tajima
1630 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1631 on the basis of phylogenetic trees has been implemented (see
1632 the function klastorin()).
1634 o Functions have been added to convert APE's "phylo" objects in
1635 "hclust" cluster objects and vice versa (see the help page of
1636 as.phylo for details).
1638 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1639 are introduced for the estimation of absolute evolutionary rates
1640 (ratogram) and dated clock-like trees (chronogram) from
1641 phylogenetic trees using the non-parametric rate smoothing approach
1642 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1644 o A summary method is now provided printing a summary information on a
1645 phylogenetic tree with, for instance, `summary(tree)'.
1647 o The behaviour of read.tree() was changed so that all spaces and
1648 tabulations in tree files are now ignored. Consequently, spaces in tip
1649 labels are no more allowed. Another side effect is that read.nexus()
1650 now does not replace the underscores (_) in tip labels with spaces
1651 (this behaviour was undocumented).
1653 o The function plot.phylo() has a new option (`underscore') which
1654 specifies whether the underscores in tip labels should be written on
1655 the plot as such or replaced with spaces (the default).
1657 o The function birthdeath() now computes 95% confidence intervals of
1658 the estimated parameters using profile likelihood.
1660 o Three new data sets are included: a gene tree estimated from 36
1661 landplant rbcL sequences, a gene tree estimated from 32 opsin
1662 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1667 o A bug was fixed in dist.gene() where nothing was returned.
1669 o A bug in plot.mst() was fixed.
1671 o A bug in vcv.phylo() resulted in false correlations when the
1672 option `cor = TRUE' was used (now fixed).
1676 CHANGES IN APE VERSION 1.0
1681 o Two new functions, read.dna() and write.dna(), read/write in a file
1682 DNA sequences in interleaved or in sequential format.
1684 o Two new functions, read.nexus() and write.nexus(), read/write trees
1687 o The new function bind.tree() allows to bind two trees together,
1688 possibly handling root edges to give internal branches.
1690 o The new function drop.tip() removes the tips in a phylogenetic tree,
1691 and trims (or not) the corresponding internal branches.
1693 o The new function is.ultrametric() tests if a tree is ultrametric.
1695 o The function plot.phylo() has more functionalities such as drawing the
1696 branches with different colours and/or different widths, showing the
1697 node labels, controling the position and font of the labels, rotating
1698 the labels, and controling the space around the plot.
1700 o The function read.tree() can now read trees with no branch length,
1701 such as "(a,b),c);". Consequently, the element `edge.length' in
1702 objects of class "phylo" is now optional.
1704 o The function write.tree() has a new default behaviour: if the default
1705 for the option `file' is used (i.e. file = ""), then a variable of
1706 mode character containing the tree in Newick format is returned which
1707 can thus be assigned (e.g., tree <- write.tree(phy)).
1709 o The function read.tree() has a new argument `text' which allows
1710 to read the tree in a variable of mode character.
1712 o A new data set is included: the phylogenetic relationships among
1713 the orders of birds from Sibley and Ahlquist (1990).
1717 CHANGES IN APE VERSION 0.2-1
1722 o Several bugs were fixed in the help pages.
1726 CHANGES IN APE VERSION 0.2
1731 o The function write.tree() writes phylogenetic trees (objects of class
1732 "phylo") in an ASCII file using the Newick parenthetic format.
1734 o The function birthdeath() fits a birth-death model to branching times
1735 by maximum likelihood, and estimates the corresponding speciation and
1738 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1741 o The function is.binary.tree() tests whether a phylogeny is binary.
1743 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1744 as well as some methods are introduced.
1746 o Several functions, including some generics and methods, for computing
1747 skyline plot estimates (classic and generalized) of effective
1748 population size through time are introduced and replace the function
1749 skyline.plot() in version 0.1.
1751 o Two data sets are now included: the phylogenetic relationships among
1752 the families of birds from Sibley and Ahlquist (1990), and an
1753 estimated clock-like phylogeny of HIV sequences sampled in the
1754 Democratic Republic of Congo.
1757 DEPRECATED & DEFUNCT
1759 o The function skyline.plot() in ape 0.1 has been deprecated and
1760 replaced by more elaborate functions (see above).
1765 o Two important bugs were fixed in plot.phylo(): phylogenies with
1766 multichotomies not at the root or not with only terminal branches,
1767 and phylogenies with a single node (i.e. only terminal branches)
1768 did not plot. These trees should be plotted correctly now.
1770 o Several bugs were fixed in diversi.time() in the computation of
1773 o Various errors were corrected in the help pages.
projects / ape.git / blob