1 CHANGES IN APE VERSION 2.2-3
6 o The new function extract.clade extracts a clade from a tree by
7 specifying a node number or label.
9 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
10 operations of the same names.
12 o dist.dna() can now return the number of site differences by
18 o chronopl() did not work with CV = TRUE.
20 o read.nexus() did not work correctly in some situations (trees on
21 multiple lines with different numbers of lines and/or with
22 comments inserted within the trees).
24 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
25 the number of lineages with non-binary trees.
30 o ape has now a namespace.
32 o drip.tip() has been improved: it should be much faster and work
33 better in some cases (e.g., see the example in ?zoom).
37 CHANGES IN APE VERSION 2.2-2
42 o dist.gene() has been substantially improved and gains an option
45 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
51 o prop.part() failed with a single tree with the default option
52 'check.labels = TRUE'.
54 o summary.DNAbin() failed to display correctly the summary of
55 sequence lengths with lists of sequences of 10,000 bases or more
56 (because summary.default uses 4 significant digits by default).
58 o read.nexus() failed to read a file with a single tree with line
59 breaks in the Newick string.
61 o del.gaps() returned a list of empty sequences when there were no
67 o phymltest() has been updated for PhyML 3.0 and gains an option
68 'append', whereas the option 'path2exec' has been removed.
70 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
71 which is returned unchanged (instead of an error).
73 o The data sets bird.orders and bird.families are now stored as
74 Newick strings; i.e., the command data(bird.orders) calls
79 CHANGES IN APE VERSION 2.2-1
84 o The new function makeLabel() helps to modify labels of trees,
85 lists of trees, or DNA sequences, with several utilities to
86 truncate and/or make them unique, substituting some
87 characters, and so on.
89 o The new function del.gaps() removes insertion gaps ("-") in a
92 o read.dna() can now read Clustal files (*.aln).
97 o root() failed with 'resolve.root = TRUE' when the root was
98 already the specified root.
100 o Several bugs were fixed in mlphylo().
102 o collapsed.singles() did not propagate the 'Nnode' and
103 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
105 o read.nexus() failed to remove correctly the comments within
108 o read.nexus() failed to read a file with a single tree and no
109 translation of tip labels.
111 o read.nexus() failed to place correctly tip labels when reading
112 a single tree with no edge lengths.
114 o A bug was fixed in sh.test().
119 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
122 o The option 'check.labels' of consensus() and prop.part() is now
125 o write.dna() now does not truncate names to 10 characters with
130 CHANGES IN APE VERSION 2.2
135 o Four new functions have been written by Damien de Vienne for the
136 graphical exploration of large trees (cophyloplot, subtrees,
137 subtreeplot), and to return the graphical coordinates of tree
140 o The new functions corPagel and corBlomberg implement the Pagel's
141 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
143 o chronopl() has been improved and gains several options: see its
144 help page for details.
146 o boot.phylo() has now an option 'trees' to possibly return the
147 bootstraped trees (the default is FALSE).
149 o prop.part() has been improved and should now be faster in all
155 o read.dna() failed if "?" occurred in the first 10 sites of the
158 o The x/y aspect of the plot is now respected when plotting a
159 circular tree (type = "r" or "f").
161 o Drawing the tip labels sometimes failed when plotting circular
164 o zoom() failed when tip labels were used instead of their numbers
165 (thanks to Yan Wong for the fix).
167 o drop.tip() failed with some trees (fixed by Yan Wong).
169 o seg.sites() failed with a list.
171 o consensus() failed in some cases. The function has been improved
172 as well and is faster.
176 CHANGES IN APE VERSION 2.1-3
181 o A bug in read.nexus() made the Windows R-GUI crash.
183 o An error was fixed in the computation of ancestral character
184 states by generalized least squares in ace().
186 o di2multi() did not modify node labels correctly.
188 o multi2di() failed if the tree had its attribute "order" set to
193 CHANGES IN APE VERSION 2.1-2
198 o There three new methods for the "multiPhylo" class: str, $,
201 o root() gains the options 'node' and 'resolve.root'
202 (FALSE by default) as well as its code being improved.
204 o mltt.plot() has now an option 'log' used in the same way
205 than in plot.default().
210 o mltt.plot() failed to display the legend with an unnamed
213 o nodelabels() with pies now correcly uses the argument
214 'cex' to draw symbols of different sizes (which has
215 worked already for thermometers).
217 o read.nexus() generally failed to read very big files.
222 o The argument 'family' of compar.gee() can now be a function
223 as well as a character string.
225 o read.tree() and read.nexus() now return an unnamed list if
228 o read.nexus() now returns a modified object of class "multiPhylo"
229 when there is a TRANSLATE block in the NEXUS file: the individual
230 trees have no 'tip.label' vector, but the list has a 'TipLabel'
231 attribute. The new methods '$' and '[[' set these elements
232 correctly when extracting trees.
236 CHANGES IN APE VERSION 2.1-1
241 o The new function rmtree generates lists of random trees.
243 o rcoal() now generates a genuine coalescent tree by default
244 (thanks to Vladimir Minin for the code).
249 o nuc.div() returned an incorrect value with the default
250 pairwise.deletion = FALSE.
255 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
256 have been improved so that they are stabler and faster.
258 o R packages used by ape are now loaded silently; lattice and gee
259 are loaded only when needed.
263 CHANGES IN APE VERSION 2.1
268 o The new function identify.phylo identifies clades on a plotted
269 tree using the mouse.
271 o It is now possible to subset a list of trees (object of class
272 "multiPhylo") with "[" while keeping its class correct.
274 o The new function as.DNAbin.alignment converts DNA sequences
275 stored in the "alignment" format of the package seqinr into
276 an object of class "DNAbin".
278 o The new function weight.taxo2 helps to build similarity matrices
279 given two taxonomic levels (usually called by other functions).
281 o write.tree() can now take a list of trees (class "multiPhylo")
282 as its main argument.
284 o plot.correlogram() and plot.correlogramList() have been
285 improved, and gain several options (see the help page for
286 details). A legend is now plotted by default.
291 o dist.dna() returned some incorrect values with `model = "JC69"'
292 and `pairwise.deletion = TRUE'. This affected only the
293 distances involving sequences with missing values. (Thanks
294 to Bruno Toupance for digging this bug out.)
296 o write.tree() failed with some trees: this is fixed by removing
297 the `multi.line' option (trees are now always printed on a
300 o read.nexus() did not correctly detect trees with multiple root
301 edges (see OTHER CHANGES).
306 o The code of mlphylo() has been almost entirely rewritten, and
307 should be much stabler. The options have been also greatly
308 simplified (see ?mlphylo and ?DNAmodel for details).
310 o The internal function nTips has been renamed klastorin_nTips.
312 o The code of is.ultrametric() contained redundancies and has
315 o The code of Moran.I() and of correlogram.formula() have been
318 o read.tree() and read.nexus() now return an error when trying to
319 read a tree with multiple root edges (see BUG FIXES). The
320 correction applied in previous version did not work in all
323 o The class c("multi.tree", "phylo") has been renamed
329 o There is now a vignette in ape: see vignette("MoranI", "ape").
334 o as.matching() and as.phylo.matching() do not support branch
337 o correlogram.phylo() and discrete.dist() have been removed.
341 CHANGES IN APE VERSION 2.0-2
346 o The new function matexpo computes the exponential of a square
349 o The new function unique.multi.tree removes duplicate trees from
352 o yule() has a new option `use.root.edge = FALSE' that specifies
353 to ignore, by default, the root edge of the tree if it exists.
358 o which.edge() failed when the index of a single terminal edge was
361 o In diversi.time(), the values returned for model C were
364 o A bug was fixed in yule() that affected the calculation of the
365 likelihood in the presence of ties in the branching times.
367 o There was a bug in the C function mat_expo4x4 affecting the
368 calculations of the transition probabilities for models HKY and
371 o A small bug was fixed in as.matrix.DNAbin (thanks to James
374 o rtree() did not `shuffle' the tip labels by default, so only a
375 limited number of labelled topologies could be generated.
379 CHANGES IN APE VERSION 2.0-1
384 o The three new functions bionj, fastme.ols, and fastme.bal
385 perform phylogeny estimation by the BIONJ and fastME methods in
386 OLS and balanced versions. This is a port to R of previous
387 previous programs done by Vincent Lefort.
389 o The new function chronoMPL performs molecular dating with the
390 mean path lengths method of Britton et al. (2002, Mol. Phyl.
393 o The new function rotate, contributed by Christoph Heibl, swaps
394 two clades connected to the same node. It works also with
395 multichotomous nodes.
397 o The new `method' as.matrix.DNAbin() may be used to convert
398 easily DNA sequences stored in a list into a matrix while
399 keeping the names and the class.
404 o chronopl() failed when some branch lengths were equal to zero:
405 an error message is now returned.
407 o di2multi() failed when there was a series of consecutive edges
412 CHANGES IN APE VERSION 1.10-2
417 o plot.phylo() can now plot circular trees: the option is type =
418 "fan" or type = "f" (to avoid the ambiguity with type = "c").
420 o prop.part() has a new option `check.labels = FALSE' which allows
421 to considerably speed-up the calculations of bipartitions. As a
422 consequence, calculations of bootstrap values with boot.phylo()
423 should be much faster.
428 o read.GenBank() did not return correctly the list of species as
429 from ape 1.10: this is fixed in this version
431 o Applying as.phylo() on a tree of class "phylo" failed: the
432 object is now returned unchanged.
436 CHANGES IN APE VERSION 1.10-1
441 o The three new functions Ntip, Nnode, and Nedge return, for a
442 given tree, the number of tips, nodes, or edges, respectively.
447 o read.nexus() did not set correctly the class of the returned
448 object when reading multiple trees.
450 o mllt.plot() failed with objects of class c("multi.tree",
453 o unroot() did not work correctly in most cases.
455 o reorder.phylo() made R freeze in some occasions.
457 o Plotting a tree in pruningwise order failed.
459 o When plotting an unrooted tree, the tip labels where not all
460 correctly positioned if the option `cex' was used.
464 CHANGES IN APE VERSION 1.10
469 o Five new `method' functions have been introduced to manipulate
470 DNA sequences in binary format (see below).
472 o Three new functions have been introduced to convert between the
473 new binary and the character formats.
475 o The new function as.alignment converts DNA sequences stored as
476 single characters into the class "alignment" used by the package
479 o read.dna() and read.GenBank() have a new argument `as.character'
480 controlling whether the sequences are returned in binary format
486 o root() failed when the tree had node labels: this is fixed.
488 o plot.phylo() did not correctly set the limits on the y-axis with
489 the default setting: this is fixed.
491 o dist.dna() returned a wrong result for the LogDet, paralinear,
492 and BH87 models with `pairwise.deletion = TRUE'.
497 o DNA sequences are now internally stored in a binary format. See
498 the document "A Bit-Level Coding Scheme for Nucleotides" for the
499 details. Most functions analyzing DNA functions have been
500 modified accordingly and are now much faster (dist.dna is now
501 ca. 60 times faster).
505 CHANGES IN APE VERSION 1.9-4
510 o A bug was fixed in edgelabels().
512 o as.phylo.hclust() did not work correctly when the object of
513 class "hclust" has its labels set to NULL: the returned tree has
514 now its tip labels set to "1", "2", ...
516 o consensus could fail if some tip labels are a subset of others
517 (e.g., "a" and "a_1"): this is now fixed.
519 o mlphylo() failed in most cases if some branch lengths of the
520 initial tree were greater than one: an error message is now
523 o mlphylo() failed in most cases when estimating the proportion of
524 invariants: this is fixed.
528 CHANGES IN APE VERSION 1.9-3
533 o The new function edgelabels adds labels on the edge of the tree
534 in the same way than nodelabels or tiplabels.
539 o multi2di() did not handle correctly branch lengths with the
540 default option `random = TRUE': this is now fixed.
542 o A bug was fixed in nuc.div() when using pairwise deletions.
544 o A bug occurred in the analysis of bipartitions with large
545 numbers of large trees, with consequences on prop.part,
546 prop.clades, and boot.phylo.
548 o The calculation of the Billera-Holmes-Vogtmann distance in
549 dist.topo was wrong: this has been fixed.
553 CHANGES IN APE VERSION 1.9-2
558 o The new function ladderize reorganizes the internal structure of
559 a tree to plot them left- or right-ladderized.
561 o The new function dist.nodes computes the patristic distances
562 between all nodes, internal and terminal, of a tree. It replaces
563 the option `full = TRUE' of cophenetic.phylo (see below).
568 o A bug was fixed in old2new.phylo().
570 o Some bugs were fixed in chronopl().
572 o The edge colours were not correctly displayed by plot.phylo
573 (thank you to Li-San Wang for the fix).
575 o cophenetic.phylo() failed with multichotomous trees: this is
581 o read.dna() now returns the sequences in a matrix if they are
582 aligned (interleaved or sequential format). Sequences in FASTA
583 format are still returned in a list.
585 o The option `full' of cophenetic.phylo() has been removed because
586 it could not be used from the generic.
591 o rotate() has been removed; this function did not work correctly
596 CHANGES IN APE VERSION 1.9-1
601 o Trees with a single tip were not read correctly in R as the
602 element `Nnode' was not set: this is fixed.
604 o unroot() did not set correctly the number of nodes of the
605 unrooted tree in most cases.
607 o read.GenBank() failed when fetching very long sequences,
608 particularly of the BX-series.
610 o A bug was introduced in read.tree() with ape 1.9: it has been
615 CHANGES IN APE VERSION 1.9
620 o There are two new print `methods' for trees of class "phylo" and
621 lists of trees of class "multi.tree", so that they are now
622 displayed in a compact and informative way.
624 o There are two new functions, old2new.phylo and new2old.phylo,
625 for converting between the old and new coding of the class
628 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
629 LogDet ("logdet"), and paralinear ("paralin").
631 o compute.brlen() has been extended: several methods are now
632 available to compute branch lengths.
634 o write.dna() can now handle matrices as well as lists.
639 o cophenetic.phylo() sometimes returned a wrong result with
640 multichotomous trees: this is fixed.
642 o rotate() failed when a single tip was specified: the tree is now
645 o ace() did not return the correct index matrix with custom
646 models: this is fixed.
648 o multi2di() did not work correctly when resolving multichotomies
649 randomly: the topology was always the same, only the arrangement
650 of clades was randomized: this is fixed. This function now
651 accepts trees with no branch lengths.
653 o The output of diversi.gof() was blurred by useless prints when a
654 user distribution was specified. This has been corrected, and
655 the help page of this function has been expanded.
660 o The internal structure of the class "phylo" has been changed:
661 see the document "Definition of Formats for Coding Phylogenetic
662 Trees in R" for the details. In addition, the code of most
663 functions has been improved.
665 o Several functions have been improved by replacing some R codes
666 by C codes: pic, plot.phylo, and reorder.phylo.
668 o There is now a citation information: see citation("ape") in R.
670 o write.tree() now does not add extra 0's to branch lengths so
671 that 1.23 is printed "1.23" by default, not "1.2300000000".
673 o The syntax of bind.tree() has been simplified. This function now
674 accepts trees with no branch lengths, and handles correctly node
677 o The option `as.numeric' of mrca() has been removed.
679 o The unused options `format' and `rooted' of read.tree() have
682 o The unused option `format' of write.tree() has been removed.
684 o The use of node.depth() has been simplified.
688 CHANGES IN APE VERSION 1.8-5
693 o Two new functions read.nexus.data() and write.nexus.data(),
694 contributed by Johan Nylander, allow to read and write molecular
695 sequences in NEXUS files.
697 o The new function reorder.phylo() reorders the internal structure
698 of a tree of class "phylo". It is used as the generic, e.g.,
701 o read.tree() and read.nexus() can now read trees with a single
704 o The new data set `cynipids' supplies a set of protein sequences
710 o The code of all.equal.phylo() has been completely rewritten
711 (thanks to Benoît Durand) which fixes several bugs.
713 o read.tree() and read.nexus() now checks the labels of the tree
714 to remove or substitute any characters that are illegal in the
715 Newick format (parentheses, etc.)
717 o A negative P-value could be returned by mantel.test(): this is
722 CHANGES IN APE VERSION 1.8-4
727 o The new function sh.test() computes the Shimodaira-
730 o The new function collapse.singles() removes the nodes with a
731 single descendant from a tree.
733 o plot.phylo() has a new argument `tip.color' to specify the
736 o mlphylo() has now an option `quiet' to control the display of
737 the progress of the analysis (the default is FALSE).
742 o read.dna() did not read correctly sequences in sequential format
743 with leading alignment gaps "-": this is fixed.
745 o ace() returned a list with no class so that the generic
746 functions (anova, logLik, ...) could not be used directly. This
747 is fixed as ace() now returns an object of class "ace".
749 o anova.ace() had a small bug when computing the number of degrees
750 of freedom: this is fixed.
752 o mlphylo() did not work when the sequences were in a matrix or
753 a data frame: this is fixed.
755 o rtree() did not work correctly when trying to simulate an
756 unrooted tree with two tips: an error message is now issued.
761 o The algorithm of rtree() has been changed: it is now about 40,
762 100, and 130 times faster for 10, 100, and 1000 tips,
767 CHANGES IN APE VERSION 1.8-3
772 o There are four new `method' functions to be used with the
773 results of ace(): logLik(), deviance(), AIC(), and anova().
775 o The plot method of phymltest has two new arguments: `main' to
776 change the title, and `col' to control the colour of the
777 segments showing the AIC values.
779 o ace() has a new argument `ip' that gives the initial values used
780 in the ML estimation with discrete characters (see the examples
781 in ?ace). This function now returns a matrix giving the indices
782 of the estimated rates when analysing discrete characters.
784 o nodelabels() and tiplabels() have a new argument `pie' to
785 represent proportions, with any number of categories, as
786 piecharts. The use of the option `thermo' has been improved:
787 there is now no limitation on the number of categories.
792 o mlphylo() did not work with more than two partitions: this is
795 o root() failed if the proposed outgroup was already an outgroup
796 in the tree: this is fixed.
798 o The `col' argument in nodelabels() and tiplabels() was not
799 correctly passed when `text' was used: this is fixed.
801 o Two bugs were fixed in mlphylo(): parameters were not always
802 correctly output, and the estimation failed in some cases.
804 o plot.phylo() was stuck when given a tree with a single tip: this
805 is fixed and a message error is now returned.
807 o An error was corrected in the help page of gammaStat regarding
808 the calculation of P-values.
810 o Using gls() could crash R when the number of species in the tree
811 and in the variables were different: this is fixed.
815 CHANGES IN APE VERSION 1.8-2
820 o The new function mlphylo() fits a phylogenetic tree by maximum
821 likelihood from DNA sequences. Its companion function DNAmodel()
822 is used to define the substitution model which may include
823 partitioning. There are methods for logLik(), deviance(), and
824 AIC(), and the summary() method has been extended to display in
825 a friendly way the results of this model fitting. Currently, the
826 functionality is limited to estimating the substitution and
827 associated parameters and computing the likelihood.
829 o The new function drop1.compar.gee (used as, e.g., drop1(m))
830 tests for single effects in GEE-based comparative method. A
831 warning message is printed if there is not enough degrees of
837 o An error message was sometimes issued by plot.multi.tree(),
838 though with no consequence.
842 CHANGES IN APE VERSION 1.8-1
847 o There is a new plot method for lists of trees (objects of class
848 "multi.tree"): it calls plot.phylo() internally and is
849 documented on the same help page.
854 o A bug was fixed in the C code that analyzes bipartitions: this
855 has impact on several functions like prop.part, prop.clades,
856 boot.phylo, or consensus.
858 o root() did not work correctly when the specified outgroup had
859 more than one element: this is fixed.
861 o dist.dna() sometimes returned a warning inappropriately: this
864 o If the distance object given to nj() had no rownames, nj()
865 returned a tree with no tip labels: it now returns tips labelled
866 "1", "2", ..., corresponding to the row numbers.
871 o nj() has been slightly changed so that tips with a zero distance
872 are first aggregated with zero-lengthed branches; the usual NJ
873 procedure is then performed on a distance matrix without 0's.
877 CHANGES IN APE VERSION 1.8
882 o The new function chronopl() estimates dates using the penalized
883 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
885 o The new function consensus() calculates the consensus tree of a
888 o The new function evolve.phylo() simulates the evolution of
889 continuous characters along a phylogeny under a Brownian model.
891 o The new plot method for objects of class "ancestral" displays a
892 tree together with ancestral values, as returned by the above
895 o The new function as.phylo.formula() returns a phylogeny from a
896 set of nested taxonomic variables given as a formula.
898 o The new function read.caic() reads trees in CAIC format.
900 o The new function tiplabels() allows to add labels to the tips
901 of a tree using text or plotting symbols in a flexible way.
903 o The new function unroot() unroots a phylogeny.
905 o multi2di() has a new option, `random', which specifies whether
906 to resolve the multichotomies randomly (the default) or not.
908 o prop.part() now returns an object of class "prop.part" for which
909 there are print (to display a partition in a more friendly way)
910 and summary (to extract the numbers) methods.
912 o plot.phylo() has a new option, `show.tip.label', specifying
913 whether to print the labels of the tips. The default is TRUE.
915 o The code of nj() has been replaced by a faster C code: it is now
916 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
919 o write.nexus() now writes whether a tree is rooted or not.
924 o Two bugs have been fixed in root(): unrooted trees are now
925 handled corretly, and node labels are now output normally.
927 o A bug was fixed in phymltest(): the executable couldn't be found
930 o Three bug have been fixed in ace(): computing the likelihood of
931 ancestral states of discrete characters failed, custom models
932 did not work, and the function failed with a null gradient (a
933 warning message is now returned; this latter bug was also
934 present in yule.cov() as well and is now fixed).
936 o pic() hanged out when missing data were present: a message error
939 o A small bug was fixed in dist.dna() where the gamma correction
940 was not always correctly dispatched.
942 o plot.phylo() plotted correctly the root edge only when the tree
943 was plotted rightwards: this works now for all directions.
948 o dist.taxo() has been renamed as weight.taxo().
950 o Various error and warning messages have been improved.
954 CHANGES IN APE VERSION 1.7
957 o The new function ace() estimates ancestral character states for
958 continuous characters (with ML, GLS, and contrasts methods), and
959 discrete characters (with ML only) for any number of states.
961 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
962 of directional evolution for continuous characters. The user
963 specifies the node(s) of the tree where the character optimum
966 o The new function is.rooted() tests whether a tree (of class
969 o The new function rcoal() generates random ultrametric trees with
970 the possibility to specify the function that generates the
971 inter-nodes distances.
973 o The new function mrca() gives for all pairs of tips in a tree
974 (and optionally nodes too) the most recent common ancestor.
976 o nodelabels() has a new option `thermo' to plot proportions (up
977 to three classes) on the nodes of a tree.
979 o rtree() has been improved: it can now generate rooted or
980 unrooted trees, and the mathematical function that generates the
981 branch lengths may be specified by the user. The tip labels may
982 be given directly in the call to rtree. The limit cases (n = 2,
983 3) are now handled correctly.
985 o dist.topo() has a new argument `method' with two choices: "PH85"
986 for Penny and Henny's method (already available before and now
987 the default), and "BHV01" for the geometric distance by Billera
988 et al. (2001, Adv. Appl. Math. 27:733).
990 o write.tree() has a new option, `digits', which specifies the
991 number of digits to be printed in the Newick tree. By default
992 digits = 10. The numbers are now always printed in decimal form
993 (i.e., 1.0e-1 is now avoided).
995 o dist.dna() can now compute the raw distances between pairs of
996 DNA sequences by specifying model = "raw".
998 o dist.phylo() has a new option `full' to possibly compute the
999 distances among all tips and nodes of the tree. The default if
1005 o Several bugs were fixed in all.equal.phylo().
1007 o dist.dna() did not handle correctly gaps ("-") in alignments:
1008 they are now considered as missing data.
1010 o rotate() did not work if the tips were not ordered: this is
1013 o mantel.test() returned NA in some special cases: this is fixed
1014 and the function has been improved and is now faster.
1016 o A bug was fixed in diversi.gof() where the calculation of A² was
1019 o cherry() did not work correctly under some OSs (mainly Linux):
1022 o is.binary.tree() has been modified so that it works with both
1023 rooted and unrooted trees.
1025 o The documentation of theta.s() was not correct: this has been
1028 o plot.mst() did not work correctly: this is fixed.
1032 CHANGES IN APE VERSION 1.6
1037 o The new function dist.topo() computes the topological distances
1040 o The new function boot.phylo() performs a bootstrap analysis on
1041 phylogeny estimation.
1043 o The new functions prop.part() and prop.clades() analyse
1044 bipartitions from a series of trees.
1049 o read.GenBank() now uses the EFetch utility of NCBI instead of
1050 the usual Web interface: it is now much faster (e.g., 12 times
1051 faster to retrieve 8 sequences, 37 times for 60 sequences).
1056 o Several bugs were fixed in read.dna().
1058 o Several bugs were fixed in diversi.time().
1060 o is.binary.tree() did not work correctly if the tree has no edge
1061 lengths: this is fixed.
1063 o drop.tip() did not correctly propagated the `node.label' of a
1064 tree: this is fixed.
1068 CHANGES IN APE VERSION 1.5
1073 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1074 convert objects between the classes "phylo" and "matching". The
1075 latter implements the representation of binary trees introduced by
1076 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1077 as.matching() has been introduced as well.
1079 o Two new functions, multi2di() and di2multi(), allow to resolve
1080 and collapse multichotomies with branches of length zero.
1082 o The new function nuc.div() computes the nucleotide diversity
1083 from a sample a DNA sequences.
1085 o dist.dna() has been completely rewritten with a much faster
1086 (particularly for large data sets) C code. Eight models are
1087 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1088 option `method' has been renamed `model'). Computation of variance
1089 is available for all models. A gamma-correction is possible for
1090 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1091 to remove sites with missing data on a pairwise basis. The option
1092 `GCcontent' has been removed.
1094 o read.GenBank() has a new option (species.names) which specifies
1095 whether to return the species names of the organisms in addition
1096 to the accession numbers of the sequences (this is the default
1099 o write.nexus() can now write several trees in the same NEXUS file.
1101 o drop.tip() has a new option `root.edge' that allows to specify the
1102 new root edge if internal branches are trimmed.
1107 o as.phylo.hclust() failed if some labels had parentheses: this
1110 o Several bugs were fixed in all.equal.phylo(). This function now
1111 returns the logical TRUE if the trees are identical but with
1112 different representations (a report was printed previously).
1114 o read.GenBank() did not correctly handle ambiguous base codes:
1120 o birthdeath() now returns an object of class "birthdeath" for
1121 which there is a print method.
1125 CHANGES IN APE VERSION 1.4
1130 o The new function nj() performs phylogeny estimation with the
1131 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1134 o The new function which.edge() identifies the edges of a tree
1135 that belong to a group specified as a set of tips.
1137 o The new function as.phylo.phylog() converts an object of class
1138 "phylog" (from the package ade4) into an object of class
1141 o The new function axisPhylo() draws axes on the side of a
1144 o The new function howmanytrees() calculates the number of trees
1145 in different cases and giving a number of tips.
1147 o write.tree() has a new option `multi.line' (TRUE by default) to
1148 write a Newick tree on several lines rather than on a single
1151 o The functionalities of zoom() have been extended. Several
1152 subtrees can be visualized at the same time, and they are marked
1153 on the main tree with colors. The context of the subtrees can be
1154 marked with the option `subtree' (see below).
1156 o drop.tip() has a new option `subtree' (FALSE by default) which
1157 specifies whether to output in the tree how many tips have been
1160 o The arguments of add.scale.bar() have been redefined and have
1161 now default values (see ?add.scale.bar for details). This
1162 function now works even if the plotted tree has no edge length.
1164 o plot.phylo() can now plot radial trees, but this does not take
1165 edge lengths into account.
1167 o In plot.phylo() with `type = "phylogram"', if the values of
1168 `edge.color' and `edge.width' are identical for sister-branches,
1169 they are propagated to the vertical line that link them.
1174 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1175 crashing. This is fixed.
1177 o In plot.phylo(), the options `edge.color' and `edge.width' are
1178 now properly recycled; their default values are now "black" and
1181 o A bug has been fixed in write.nexus().
1186 o The function node.depth.edgelength() has been removed and
1187 replaced by a C code.
1191 CHANGES IN APE VERSION 1.3-1
1196 o The new function nodelabels() allows to add labels to the nodes
1197 of a tree using text or plotting symbols in a flexible way.
1199 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1200 numeric values specifying the lower and upper limits on the x-
1201 and y-axes. This allows to leave some space on any side of the
1202 tree. If a single value is given, this is taken as the upper
1207 CHANGES IN APE VERSION 1.3
1212 o The new function phymltest() calls the software PHYML and fits
1213 28 models of DNA sequence evolution. There are a print method to
1214 display likelihood and AIC values, a summary method to compute
1215 the hierarchical likelihood ratio tests, and a plot method to
1216 display graphically the AIC values of each model.
1218 o The new function yule.cov() fits the Yule model with covariates,
1219 a model where the speciation rate is affected by several species
1220 traits through a generalized linear model. The parameters are
1221 estimated by maximum likelihood.
1223 o Three new functions, corBrownian(), corGrafen(), and
1224 corMartins(), compute the expected correlation structures among
1225 species given a phylogeny under different models of evolution.
1226 These can be used for GLS comparative phylogenetic methods (see
1227 the examples). There are coef() and corMatrix() methods and an
1228 Initialize.corPhyl() function associated.
1230 o The new function compar.cheverud() implements Cheverud et al.'s
1231 (1985; Evolution 39:1335) phylogenetic comparative method.
1233 o The new function varcomp() estimates variance components; it has
1236 o Two new functions, panel.superpose.correlogram() and
1237 plot.correlogramList(), allow to plot several phylogenetic
1240 o The new function node.leafnumber() computes the number of leaves
1241 of a subtree defined by a particular node.
1243 o The new function node.sons() gets all tags of son nodes from a
1246 o The new function compute.brlen() computes the branch lengths of
1247 a tree according to a specified method.
1249 o plot.phylo() has three new options: "cex" controls the size of
1250 the (tip and node) labels (thus it is no more needed to change
1251 the global graphical parameter), "direction" which allows to
1252 plot the tree rightwards, leftwards, upwards, or downwards, and
1253 "y.lim" which sets the upper limit on the y-axis.
1258 o Some functions which try to match tip labels and names of
1259 additional data (e.g. vector) are likely to fail if there are
1260 typing or syntax errors. If both series of names do not perfectly
1261 match, they are ignored and a warning message is now issued.
1262 These functions are bd.ext, compar.gee, pic. Their help pages
1263 have been clarified on this point.
1267 CHANGES IN APE VERSION 1.2-7
1272 o The new function root() reroots a phylogenetic tree with respect
1273 to a specified outgroup.
1275 o The new function rotate() rotates an internal branch of a tree.
1277 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1278 trees) controls the display of the tip labels in unrooted trees.
1279 This display has been greatly improved: the tip labels are now not
1280 expected to overlap with the tree (particularly if lab4ut =
1281 "axial"). In all cases, combining appropriate values of "lab4ut"
1282 and the font size (via "par(cex = )") should result in readable
1283 unrooted trees. See ?plot.phylo for some examples.
1285 o In drop.tip(), the argument `tip' can now be numeric or character.
1290 o drop.tip() did not work correctly with trees with no branch
1291 lengths: this is fixed.
1293 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1294 plotted with some line crossings: this is now fixed.
1298 CHANGES IN APE VERSION 1.2-6
1303 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1304 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1305 to implement comparative methods with an autocorrelation approach.
1307 o A new data set describing some life history traits of Carnivores
1313 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1318 o When plotting a tree with plot.phylo(), the new default of the
1319 option `label.offset' is now 0, so the labels are always visible.
1323 CHANGES IN APE VERSION 1.2-5
1328 o The new function bd.ext() fits a birth-death model with combined
1329 phylogenetic and taxonomic data, and estimates the corresponding
1330 speciation and extinction rates.
1335 o The package gee is no more required by ape but only suggested
1336 since only the function compar.gee() calls gee.
1340 CHANGES IN APE VERSION 1.2-4
1345 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1346 and lines.popsize) implementing a new approach for inferring the
1347 demographic history from genealogies using a reversible jump
1348 MCMC have been introduced.
1350 o The unit of time in the skyline plot and in the new plots can
1351 now be chosen to be actual years, rather than substitutions.
1355 CHANGES IN APE VERSION 1.2-3
1360 o The new function rtree() generates a random binary tree with or
1361 without branch lengths.
1363 o Two new functions for drawing lineages-through-time (LTT) plots
1364 are provided: ltt.lines() adds a LTT curve to an existing plot,
1365 and mltt.plot() does a multiple LTT plot giving several trees as
1366 arguments (see `?ltt.plot' for details).
1371 o Some taxon names made R crashing when calling as.phylo.hclust():
1374 o dist.dna() returned an error with two identical DNA sequences
1375 (only using the Jukes-Cantor method returned 0): this is fixed.
1380 o The function dist.phylo() has been re-written using a different
1381 algorithm: it is now about four times faster.
1383 o The code of branching.times() has been improved: it is now about
1388 CHANGES IN APE VERSION 1.2-2
1393 o The new function seg.sites() finds the segregating sites in a
1394 sample of DNA sequences.
1399 o A bug introduced in read.tree() and in read.nexus() with version
1402 o A few errors were corrected and a few examples were added in the
1407 CHANGES IN APE VERSION 1.2-1
1412 o plot.phylo() can now draw the edge of the root of a tree if it
1413 has one (see the new option `root.edge', its default is FALSE).
1418 o A bug was fixed in read.nexus(): files with semicolons inside
1419 comment blocks were not read correctly.
1421 o The behaviour of read.tree() and read.nexus() was corrected so
1422 that tree files with badly represented root edges (e.g., with
1423 an extra pair of parentheses, see the help pages for details)
1424 are now correctly represented in the object of class "phylo";
1425 a warning message is now issued.
1429 CHANGES IN APE VERSION 1.2
1434 o plot.phylo() has been completely re-written and offers several
1435 new functionalities. Three types of trees can now be drawn:
1436 phylogram (as previously), cladogram, and unrooted tree; in
1437 all three types the branch lengths can be drawn using the edge
1438 lengths of the phylogeny or not (e.g., if the latter is absent).
1439 The vertical position of the nodes can be adjusted with two
1440 choices (see option `node.pos'). The code has been re-structured,
1441 and two new functions (potentially useful for developpers) are
1442 documented separately: node.depth.edgelength() and node.depth();
1443 see the respective help pages for details.
1445 o The new function zoom() allows to explore very large trees by
1446 focusing on a small portion of it.
1448 o The new function yule() fits by maximum likelihood the Yule model
1449 (birth-only process) to a phylogenetic tree.
1451 o Support for writing DNA sequences in FASTA format has been
1452 introduced in write.dna() (support for reading sequences in
1453 this format was introduced in read.dna() in version 1.1-2).
1454 The function has been completely re-written, fixing some bugs
1455 (see below); the default behaviour is no more to display the
1456 sequences on the standard output. Several options have been
1457 introduced to control the sequence printing in a flexible
1458 way. The help page has been extended.
1460 o A new data set is included: a supertree of bats in NEXUS format.
1465 o In theta.s(), the default of the option `variance' has
1466 been changed to `FALSE' (as was indicated in the help page).
1468 o Several bugs were fixed in the code of all.equal.phylo().
1470 o Several bugs were fixed in write.dna(), particularly this
1471 function did not work with `format = "interleaved"'.
1473 o Various errors were corrected in the help pages.
1478 o The argument names of as.hclust.phylo() have been changed
1479 from "(phy)" to "(x, ...)" to conform to the definition of
1480 the corresponding generic function.
1482 o gamma.stat() has been renamed gammaStat() to avoid confusion
1483 since gamma() is a generic function.
1487 CHANGES IN APE VERSION 1.1-3
1492 o base.freq() previously did not return a value of 0 for
1493 bases absent in the data (e.g., a vector of length 3 was
1494 returned if one base was absent). This is now fixed (a
1495 vector of length 4 is always returned).
1497 o Several bugs were fixed in read.nexus(), including that this
1498 function did not work in this absence of a "TRANSLATE"
1499 command in the NEXUS file, and that the commands were
1504 CHANGES IN APE VERSION 1.1-2
1509 o The Tamura and Nei (1993) model of DNA distance is now implemented
1510 in dist.dna(): five models are now available in this function.
1512 o A new data set is included: a set of 15 sequences of the
1513 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1519 o A bug in read.nexus() was fixed.
1521 o read.dna() previously did not work correctly in most cases.
1522 The function has been completely re-written and its help page
1523 has been considerably extended (see ?read.dna for details).
1524 Underscores (_) in taxon names are no more replaced with
1525 spaces (this behaviour was undocumented).
1527 o A bug was fixed in write.dna().
1531 CHANGES IN APE VERSION 1.1-1
1536 o A bug in read.tree() introduced in APE 1.1 was fixed.
1538 o A bug in compar.gee() resulted in an error when trying to fit
1539 a model with `family = "binomial"'. This is now fixed.
1543 CHANGES IN APE VERSION 1.1
1548 o The Klastorin (1982) method as suggested by Misawa and Tajima
1549 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1550 on the basis of phylogenetic trees has been implemented (see
1551 the function klastorin()).
1553 o Functions have been added to convert APE's "phylo" objects in
1554 "hclust" cluster objects and vice versa (see the help page of
1555 as.phylo for details).
1557 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1558 are introduced for the estimation of absolute evolutionary rates
1559 (ratogram) and dated clock-like trees (chronogram) from
1560 phylogenetic trees using the non-parametric rate smoothing approach
1561 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1563 o A summary method is now provided printing a summary information on a
1564 phylogenetic tree with, for instance, `summary(tree)'.
1566 o The behaviour of read.tree() was changed so that all spaces and
1567 tabulations in tree files are now ignored. Consequently, spaces in tip
1568 labels are no more allowed. Another side effect is that read.nexus()
1569 now does not replace the underscores (_) in tip labels with spaces
1570 (this behaviour was undocumented).
1572 o The function plot.phylo() has a new option (`underscore') which
1573 specifies whether the underscores in tip labels should be written on
1574 the plot as such or replaced with spaces (the default).
1576 o The function birthdeath() now computes 95% confidence intervals of
1577 the estimated parameters using profile likelihood.
1579 o Three new data sets are included: a gene tree estimated from 36
1580 landplant rbcL sequences, a gene tree estimated from 32 opsin
1581 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1586 o A bug was fixed in dist.gene() where nothing was returned.
1588 o A bug in plot.mst() was fixed.
1590 o A bug in vcv.phylo() resulted in false correlations when the
1591 option `cor = TRUE' was used (now fixed).
1595 CHANGES IN APE VERSION 1.0
1600 o Two new functions, read.dna() and write.dna(), read/write in a file
1601 DNA sequences in interleaved or in sequential format.
1603 o Two new functions, read.nexus() and write.nexus(), read/write trees
1606 o The new function bind.tree() allows to bind two trees together,
1607 possibly handling root edges to give internal branches.
1609 o The new function drop.tip() removes the tips in a phylogenetic tree,
1610 and trims (or not) the corresponding internal branches.
1612 o The new function is.ultrametric() tests if a tree is ultrametric.
1614 o The function plot.phylo() has more functionalities such as drawing the
1615 branches with different colours and/or different widths, showing the
1616 node labels, controling the position and font of the labels, rotating
1617 the labels, and controling the space around the plot.
1619 o The function read.tree() can now read trees with no branch length,
1620 such as "(a,b),c);". Consequently, the element `edge.length' in
1621 objects of class "phylo" is now optional.
1623 o The function write.tree() has a new default behaviour: if the default
1624 for the option `file' is used (i.e. file = ""), then a variable of
1625 mode character containing the tree in Newick format is returned which
1626 can thus be assigned (e.g., tree <- write.tree(phy)).
1628 o The function read.tree() has a new argument `text' which allows
1629 to read the tree in a variable of mode character.
1631 o A new data set is included: the phylogenetic relationships among
1632 the orders of birds from Sibley and Ahlquist (1990).
1636 CHANGES IN APE VERSION 0.2-1
1641 o Several bugs were fixed in the help pages.
1645 CHANGES IN APE VERSION 0.2
1650 o The function write.tree() writes phylogenetic trees (objects of class
1651 "phylo") in an ASCII file using the Newick parenthetic format.
1653 o The function birthdeath() fits a birth-death model to branching times
1654 by maximum likelihood, and estimates the corresponding speciation and
1657 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1660 o The function is.binary.tree() tests whether a phylogeny is binary.
1662 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1663 as well as some methods are introduced.
1665 o Several functions, including some generics and methods, for computing
1666 skyline plot estimates (classic and generalized) of effective
1667 population size through time are introduced and replace the function
1668 skyline.plot() in version 0.1.
1670 o Two data sets are now included: the phylogenetic relationships among
1671 the families of birds from Sibley and Ahlquist (1990), and an
1672 estimated clock-like phylogeny of HIV sequences sampled in the
1673 Democratic Republic of Congo.
1676 DEPRECATED & DEFUNCT
1678 o The function skyline.plot() in ape 0.1 has been deprecated and
1679 replaced by more elaborate functions (see above).
1684 o Two important bugs were fixed in plot.phylo(): phylogenies with
1685 multichotomies not at the root or not with only terminal branches,
1686 and phylogenies with a single node (i.e. only terminal branches)
1687 did not plot. These trees should be plotted correctly now.
1689 o Several bugs were fixed in diversi.time() in the computation of
1692 o Various errors were corrected in the help pages.
projects / ape.git / blob