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").
21 o rcoal() should be faster.
25 CHANGES IN APE VERSION 2.3
30 o The new functions CADM.global and CADM.post, contributed by
31 Pierre Legendre, test the congruence among several distance
34 o The new function yule.time fits a user-defined time-dependent
35 Yule model by maximum likelihood.
37 o The new function makeNodeLabel creates and/or modifies node
38 labels in a flexible way.
40 o read.tree() and write.tree() have been modified so that they can
41 handle individual tree names.
43 o plot.phylo() has a new argument 'edge.lty' that specifies the
44 types of lines used for the edges (plain, dotted, dashed, ...)
46 o phymltest() has been updated to work with PhyML 3.0.1.
51 o drop.tip() shuffled tip labels in some cases.
53 o drop.tip() did not handle node.label correctly.
55 o is.ultrametric() now checks the ordering of the edge matrix.
57 o ace() sometimes returned negative values of likelihoods of
58 ancestral states (thanks to Dan Rabosky for solving this long
64 o The data set xenarthra has been removed.
68 CHANGES IN APE VERSION 2.2-4
72 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
73 now fixed. (Thanks to Peter Wragg for the fix!)
75 o A warning message occurred for no reason with ace(method="GLS").
80 o There is now a general help page displayed with '?ape'
84 CHANGES IN APE VERSION 2.2-3
89 o The new function extract.clade extracts a clade from a tree by
90 specifying a node number or label.
92 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
93 operations of the same names.
95 o dist.dna() can now return the number of site differences by
101 o chronopl() did not work with CV = TRUE.
103 o read.nexus() did not work correctly in some situations (trees on
104 multiple lines with different numbers of lines and/or with
105 comments inserted within the trees).
107 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
108 the number of lineages with non-binary trees.
113 o ape has now a namespace.
115 o drip.tip() has been improved: it should be much faster and work
116 better in some cases (e.g., see the example in ?zoom).
120 CHANGES IN APE VERSION 2.2-2
125 o dist.gene() has been substantially improved and gains an option
128 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
134 o prop.part() failed with a single tree with the default option
135 'check.labels = TRUE'.
137 o summary.DNAbin() failed to display correctly the summary of
138 sequence lengths with lists of sequences of 10,000 bases or more
139 (because summary.default uses 4 significant digits by default).
141 o read.nexus() failed to read a file with a single tree with line
142 breaks in the Newick string.
144 o del.gaps() returned a list of empty sequences when there were no
150 o phymltest() has been updated for PhyML 3.0 and gains an option
151 'append', whereas the option 'path2exec' has been removed.
153 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
154 which is returned unchanged (instead of an error).
156 o The data sets bird.orders and bird.families are now stored as
157 Newick strings; i.e., the command data(bird.orders) calls
162 CHANGES IN APE VERSION 2.2-1
167 o The new function makeLabel() helps to modify labels of trees,
168 lists of trees, or DNA sequences, with several utilities to
169 truncate and/or make them unique, substituting some
170 characters, and so on.
172 o The new function del.gaps() removes insertion gaps ("-") in a
173 set of DNA sequences.
175 o read.dna() can now read Clustal files (*.aln).
180 o root() failed with 'resolve.root = TRUE' when the root was
181 already the specified root.
183 o Several bugs were fixed in mlphylo().
185 o collapsed.singles() did not propagate the 'Nnode' and
186 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
188 o read.nexus() failed to remove correctly the comments within
191 o read.nexus() failed to read a file with a single tree and no
192 translation of tip labels.
194 o read.nexus() failed to place correctly tip labels when reading
195 a single tree with no edge lengths.
197 o A bug was fixed in sh.test().
202 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
205 o The option 'check.labels' of consensus() and prop.part() is now
208 o write.dna() now does not truncate names to 10 characters with
213 CHANGES IN APE VERSION 2.2
218 o Four new functions have been written by Damien de Vienne for the
219 graphical exploration of large trees (cophyloplot, subtrees,
220 subtreeplot), and to return the graphical coordinates of tree
223 o The new functions corPagel and corBlomberg implement the Pagel's
224 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
226 o chronopl() has been improved and gains several options: see its
227 help page for details.
229 o boot.phylo() has now an option 'trees' to possibly return the
230 bootstraped trees (the default is FALSE).
232 o prop.part() has been improved and should now be faster in all
238 o read.dna() failed if "?" occurred in the first 10 sites of the
241 o The x/y aspect of the plot is now respected when plotting a
242 circular tree (type = "r" or "f").
244 o Drawing the tip labels sometimes failed when plotting circular
247 o zoom() failed when tip labels were used instead of their numbers
248 (thanks to Yan Wong for the fix).
250 o drop.tip() failed with some trees (fixed by Yan Wong).
252 o seg.sites() failed with a list.
254 o consensus() failed in some cases. The function has been improved
255 as well and is faster.
259 CHANGES IN APE VERSION 2.1-3
264 o A bug in read.nexus() made the Windows R-GUI crash.
266 o An error was fixed in the computation of ancestral character
267 states by generalized least squares in ace().
269 o di2multi() did not modify node labels correctly.
271 o multi2di() failed if the tree had its attribute "order" set to
276 CHANGES IN APE VERSION 2.1-2
281 o There three new methods for the "multiPhylo" class: str, $,
284 o root() gains the options 'node' and 'resolve.root'
285 (FALSE by default) as well as its code being improved.
287 o mltt.plot() has now an option 'log' used in the same way
288 than in plot.default().
293 o mltt.plot() failed to display the legend with an unnamed
296 o nodelabels() with pies now correcly uses the argument
297 'cex' to draw symbols of different sizes (which has
298 worked already for thermometers).
300 o read.nexus() generally failed to read very big files.
305 o The argument 'family' of compar.gee() can now be a function
306 as well as a character string.
308 o read.tree() and read.nexus() now return an unnamed list if
311 o read.nexus() now returns a modified object of class "multiPhylo"
312 when there is a TRANSLATE block in the NEXUS file: the individual
313 trees have no 'tip.label' vector, but the list has a 'TipLabel'
314 attribute. The new methods '$' and '[[' set these elements
315 correctly when extracting trees.
319 CHANGES IN APE VERSION 2.1-1
324 o The new function rmtree generates lists of random trees.
326 o rcoal() now generates a genuine coalescent tree by default
327 (thanks to Vladimir Minin for the code).
332 o nuc.div() returned an incorrect value with the default
333 pairwise.deletion = FALSE.
338 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
339 have been improved so that they are stabler and faster.
341 o R packages used by ape are now loaded silently; lattice and gee
342 are loaded only when needed.
346 CHANGES IN APE VERSION 2.1
351 o The new function identify.phylo identifies clades on a plotted
352 tree using the mouse.
354 o It is now possible to subset a list of trees (object of class
355 "multiPhylo") with "[" while keeping its class correct.
357 o The new function as.DNAbin.alignment converts DNA sequences
358 stored in the "alignment" format of the package seqinr into
359 an object of class "DNAbin".
361 o The new function weight.taxo2 helps to build similarity matrices
362 given two taxonomic levels (usually called by other functions).
364 o write.tree() can now take a list of trees (class "multiPhylo")
365 as its main argument.
367 o plot.correlogram() and plot.correlogramList() have been
368 improved, and gain several options (see the help page for
369 details). A legend is now plotted by default.
374 o dist.dna() returned some incorrect values with `model = "JC69"'
375 and `pairwise.deletion = TRUE'. This affected only the
376 distances involving sequences with missing values. (Thanks
377 to Bruno Toupance for digging this bug out.)
379 o write.tree() failed with some trees: this is fixed by removing
380 the `multi.line' option (trees are now always printed on a
383 o read.nexus() did not correctly detect trees with multiple root
384 edges (see OTHER CHANGES).
389 o The code of mlphylo() has been almost entirely rewritten, and
390 should be much stabler. The options have been also greatly
391 simplified (see ?mlphylo and ?DNAmodel for details).
393 o The internal function nTips has been renamed klastorin_nTips.
395 o The code of is.ultrametric() contained redundancies and has
398 o The code of Moran.I() and of correlogram.formula() have been
401 o read.tree() and read.nexus() now return an error when trying to
402 read a tree with multiple root edges (see BUG FIXES). The
403 correction applied in previous version did not work in all
406 o The class c("multi.tree", "phylo") has been renamed
412 o There is now a vignette in ape: see vignette("MoranI", "ape").
417 o as.matching() and as.phylo.matching() do not support branch
420 o correlogram.phylo() and discrete.dist() have been removed.
424 CHANGES IN APE VERSION 2.0-2
429 o The new function matexpo computes the exponential of a square
432 o The new function unique.multi.tree removes duplicate trees from
435 o yule() has a new option `use.root.edge = FALSE' that specifies
436 to ignore, by default, the root edge of the tree if it exists.
441 o which.edge() failed when the index of a single terminal edge was
444 o In diversi.time(), the values returned for model C were
447 o A bug was fixed in yule() that affected the calculation of the
448 likelihood in the presence of ties in the branching times.
450 o There was a bug in the C function mat_expo4x4 affecting the
451 calculations of the transition probabilities for models HKY and
454 o A small bug was fixed in as.matrix.DNAbin (thanks to James
457 o rtree() did not `shuffle' the tip labels by default, so only a
458 limited number of labelled topologies could be generated.
462 CHANGES IN APE VERSION 2.0-1
467 o The three new functions bionj, fastme.ols, and fastme.bal
468 perform phylogeny estimation by the BIONJ and fastME methods in
469 OLS and balanced versions. This is a port to R of previous
470 previous programs done by Vincent Lefort.
472 o The new function chronoMPL performs molecular dating with the
473 mean path lengths method of Britton et al. (2002, Mol. Phyl.
476 o The new function rotate, contributed by Christoph Heibl, swaps
477 two clades connected to the same node. It works also with
478 multichotomous nodes.
480 o The new `method' as.matrix.DNAbin() may be used to convert
481 easily DNA sequences stored in a list into a matrix while
482 keeping the names and the class.
487 o chronopl() failed when some branch lengths were equal to zero:
488 an error message is now returned.
490 o di2multi() failed when there was a series of consecutive edges
495 CHANGES IN APE VERSION 1.10-2
500 o plot.phylo() can now plot circular trees: the option is type =
501 "fan" or type = "f" (to avoid the ambiguity with type = "c").
503 o prop.part() has a new option `check.labels = FALSE' which allows
504 to considerably speed-up the calculations of bipartitions. As a
505 consequence, calculations of bootstrap values with boot.phylo()
506 should be much faster.
511 o read.GenBank() did not return correctly the list of species as
512 from ape 1.10: this is fixed in this version
514 o Applying as.phylo() on a tree of class "phylo" failed: the
515 object is now returned unchanged.
519 CHANGES IN APE VERSION 1.10-1
524 o The three new functions Ntip, Nnode, and Nedge return, for a
525 given tree, the number of tips, nodes, or edges, respectively.
530 o read.nexus() did not set correctly the class of the returned
531 object when reading multiple trees.
533 o mllt.plot() failed with objects of class c("multi.tree",
536 o unroot() did not work correctly in most cases.
538 o reorder.phylo() made R freeze in some occasions.
540 o Plotting a tree in pruningwise order failed.
542 o When plotting an unrooted tree, the tip labels where not all
543 correctly positioned if the option `cex' was used.
547 CHANGES IN APE VERSION 1.10
552 o Five new `method' functions have been introduced to manipulate
553 DNA sequences in binary format (see below).
555 o Three new functions have been introduced to convert between the
556 new binary and the character formats.
558 o The new function as.alignment converts DNA sequences stored as
559 single characters into the class "alignment" used by the package
562 o read.dna() and read.GenBank() have a new argument `as.character'
563 controlling whether the sequences are returned in binary format
569 o root() failed when the tree had node labels: this is fixed.
571 o plot.phylo() did not correctly set the limits on the y-axis with
572 the default setting: this is fixed.
574 o dist.dna() returned a wrong result for the LogDet, paralinear,
575 and BH87 models with `pairwise.deletion = TRUE'.
580 o DNA sequences are now internally stored in a binary format. See
581 the document "A Bit-Level Coding Scheme for Nucleotides" for the
582 details. Most functions analyzing DNA functions have been
583 modified accordingly and are now much faster (dist.dna is now
584 ca. 60 times faster).
588 CHANGES IN APE VERSION 1.9-4
593 o A bug was fixed in edgelabels().
595 o as.phylo.hclust() did not work correctly when the object of
596 class "hclust" has its labels set to NULL: the returned tree has
597 now its tip labels set to "1", "2", ...
599 o consensus could fail if some tip labels are a subset of others
600 (e.g., "a" and "a_1"): this is now fixed.
602 o mlphylo() failed in most cases if some branch lengths of the
603 initial tree were greater than one: an error message is now
606 o mlphylo() failed in most cases when estimating the proportion of
607 invariants: this is fixed.
611 CHANGES IN APE VERSION 1.9-3
616 o The new function edgelabels adds labels on the edge of the tree
617 in the same way than nodelabels or tiplabels.
622 o multi2di() did not handle correctly branch lengths with the
623 default option `random = TRUE': this is now fixed.
625 o A bug was fixed in nuc.div() when using pairwise deletions.
627 o A bug occurred in the analysis of bipartitions with large
628 numbers of large trees, with consequences on prop.part,
629 prop.clades, and boot.phylo.
631 o The calculation of the Billera-Holmes-Vogtmann distance in
632 dist.topo was wrong: this has been fixed.
636 CHANGES IN APE VERSION 1.9-2
641 o The new function ladderize reorganizes the internal structure of
642 a tree to plot them left- or right-ladderized.
644 o The new function dist.nodes computes the patristic distances
645 between all nodes, internal and terminal, of a tree. It replaces
646 the option `full = TRUE' of cophenetic.phylo (see below).
651 o A bug was fixed in old2new.phylo().
653 o Some bugs were fixed in chronopl().
655 o The edge colours were not correctly displayed by plot.phylo
656 (thank you to Li-San Wang for the fix).
658 o cophenetic.phylo() failed with multichotomous trees: this is
664 o read.dna() now returns the sequences in a matrix if they are
665 aligned (interleaved or sequential format). Sequences in FASTA
666 format are still returned in a list.
668 o The option `full' of cophenetic.phylo() has been removed because
669 it could not be used from the generic.
674 o rotate() has been removed; this function did not work correctly
679 CHANGES IN APE VERSION 1.9-1
684 o Trees with a single tip were not read correctly in R as the
685 element `Nnode' was not set: this is fixed.
687 o unroot() did not set correctly the number of nodes of the
688 unrooted tree in most cases.
690 o read.GenBank() failed when fetching very long sequences,
691 particularly of the BX-series.
693 o A bug was introduced in read.tree() with ape 1.9: it has been
698 CHANGES IN APE VERSION 1.9
703 o There are two new print `methods' for trees of class "phylo" and
704 lists of trees of class "multi.tree", so that they are now
705 displayed in a compact and informative way.
707 o There are two new functions, old2new.phylo and new2old.phylo,
708 for converting between the old and new coding of the class
711 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
712 LogDet ("logdet"), and paralinear ("paralin").
714 o compute.brlen() has been extended: several methods are now
715 available to compute branch lengths.
717 o write.dna() can now handle matrices as well as lists.
722 o cophenetic.phylo() sometimes returned a wrong result with
723 multichotomous trees: this is fixed.
725 o rotate() failed when a single tip was specified: the tree is now
728 o ace() did not return the correct index matrix with custom
729 models: this is fixed.
731 o multi2di() did not work correctly when resolving multichotomies
732 randomly: the topology was always the same, only the arrangement
733 of clades was randomized: this is fixed. This function now
734 accepts trees with no branch lengths.
736 o The output of diversi.gof() was blurred by useless prints when a
737 user distribution was specified. This has been corrected, and
738 the help page of this function has been expanded.
743 o The internal structure of the class "phylo" has been changed:
744 see the document "Definition of Formats for Coding Phylogenetic
745 Trees in R" for the details. In addition, the code of most
746 functions has been improved.
748 o Several functions have been improved by replacing some R codes
749 by C codes: pic, plot.phylo, and reorder.phylo.
751 o There is now a citation information: see citation("ape") in R.
753 o write.tree() now does not add extra 0's to branch lengths so
754 that 1.23 is printed "1.23" by default, not "1.2300000000".
756 o The syntax of bind.tree() has been simplified. This function now
757 accepts trees with no branch lengths, and handles correctly node
760 o The option `as.numeric' of mrca() has been removed.
762 o The unused options `format' and `rooted' of read.tree() have
765 o The unused option `format' of write.tree() has been removed.
767 o The use of node.depth() has been simplified.
771 CHANGES IN APE VERSION 1.8-5
776 o Two new functions read.nexus.data() and write.nexus.data(),
777 contributed by Johan Nylander, allow to read and write molecular
778 sequences in NEXUS files.
780 o The new function reorder.phylo() reorders the internal structure
781 of a tree of class "phylo". It is used as the generic, e.g.,
784 o read.tree() and read.nexus() can now read trees with a single
787 o The new data set `cynipids' supplies a set of protein sequences
793 o The code of all.equal.phylo() has been completely rewritten
794 (thanks to Benoît Durand) which fixes several bugs.
796 o read.tree() and read.nexus() now checks the labels of the tree
797 to remove or substitute any characters that are illegal in the
798 Newick format (parentheses, etc.)
800 o A negative P-value could be returned by mantel.test(): this is
805 CHANGES IN APE VERSION 1.8-4
810 o The new function sh.test() computes the Shimodaira-
813 o The new function collapse.singles() removes the nodes with a
814 single descendant from a tree.
816 o plot.phylo() has a new argument `tip.color' to specify the
819 o mlphylo() has now an option `quiet' to control the display of
820 the progress of the analysis (the default is FALSE).
825 o read.dna() did not read correctly sequences in sequential format
826 with leading alignment gaps "-": this is fixed.
828 o ace() returned a list with no class so that the generic
829 functions (anova, logLik, ...) could not be used directly. This
830 is fixed as ace() now returns an object of class "ace".
832 o anova.ace() had a small bug when computing the number of degrees
833 of freedom: this is fixed.
835 o mlphylo() did not work when the sequences were in a matrix or
836 a data frame: this is fixed.
838 o rtree() did not work correctly when trying to simulate an
839 unrooted tree with two tips: an error message is now issued.
844 o The algorithm of rtree() has been changed: it is now about 40,
845 100, and 130 times faster for 10, 100, and 1000 tips,
850 CHANGES IN APE VERSION 1.8-3
855 o There are four new `method' functions to be used with the
856 results of ace(): logLik(), deviance(), AIC(), and anova().
858 o The plot method of phymltest has two new arguments: `main' to
859 change the title, and `col' to control the colour of the
860 segments showing the AIC values.
862 o ace() has a new argument `ip' that gives the initial values used
863 in the ML estimation with discrete characters (see the examples
864 in ?ace). This function now returns a matrix giving the indices
865 of the estimated rates when analysing discrete characters.
867 o nodelabels() and tiplabels() have a new argument `pie' to
868 represent proportions, with any number of categories, as
869 piecharts. The use of the option `thermo' has been improved:
870 there is now no limitation on the number of categories.
875 o mlphylo() did not work with more than two partitions: this is
878 o root() failed if the proposed outgroup was already an outgroup
879 in the tree: this is fixed.
881 o The `col' argument in nodelabels() and tiplabels() was not
882 correctly passed when `text' was used: this is fixed.
884 o Two bugs were fixed in mlphylo(): parameters were not always
885 correctly output, and the estimation failed in some cases.
887 o plot.phylo() was stuck when given a tree with a single tip: this
888 is fixed and a message error is now returned.
890 o An error was corrected in the help page of gammaStat regarding
891 the calculation of P-values.
893 o Using gls() could crash R when the number of species in the tree
894 and in the variables were different: this is fixed.
898 CHANGES IN APE VERSION 1.8-2
903 o The new function mlphylo() fits a phylogenetic tree by maximum
904 likelihood from DNA sequences. Its companion function DNAmodel()
905 is used to define the substitution model which may include
906 partitioning. There are methods for logLik(), deviance(), and
907 AIC(), and the summary() method has been extended to display in
908 a friendly way the results of this model fitting. Currently, the
909 functionality is limited to estimating the substitution and
910 associated parameters and computing the likelihood.
912 o The new function drop1.compar.gee (used as, e.g., drop1(m))
913 tests for single effects in GEE-based comparative method. A
914 warning message is printed if there is not enough degrees of
920 o An error message was sometimes issued by plot.multi.tree(),
921 though with no consequence.
925 CHANGES IN APE VERSION 1.8-1
930 o There is a new plot method for lists of trees (objects of class
931 "multi.tree"): it calls plot.phylo() internally and is
932 documented on the same help page.
937 o A bug was fixed in the C code that analyzes bipartitions: this
938 has impact on several functions like prop.part, prop.clades,
939 boot.phylo, or consensus.
941 o root() did not work correctly when the specified outgroup had
942 more than one element: this is fixed.
944 o dist.dna() sometimes returned a warning inappropriately: this
947 o If the distance object given to nj() had no rownames, nj()
948 returned a tree with no tip labels: it now returns tips labelled
949 "1", "2", ..., corresponding to the row numbers.
954 o nj() has been slightly changed so that tips with a zero distance
955 are first aggregated with zero-lengthed branches; the usual NJ
956 procedure is then performed on a distance matrix without 0's.
960 CHANGES IN APE VERSION 1.8
965 o The new function chronopl() estimates dates using the penalized
966 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
968 o The new function consensus() calculates the consensus tree of a
971 o The new function evolve.phylo() simulates the evolution of
972 continuous characters along a phylogeny under a Brownian model.
974 o The new plot method for objects of class "ancestral" displays a
975 tree together with ancestral values, as returned by the above
978 o The new function as.phylo.formula() returns a phylogeny from a
979 set of nested taxonomic variables given as a formula.
981 o The new function read.caic() reads trees in CAIC format.
983 o The new function tiplabels() allows to add labels to the tips
984 of a tree using text or plotting symbols in a flexible way.
986 o The new function unroot() unroots a phylogeny.
988 o multi2di() has a new option, `random', which specifies whether
989 to resolve the multichotomies randomly (the default) or not.
991 o prop.part() now returns an object of class "prop.part" for which
992 there are print (to display a partition in a more friendly way)
993 and summary (to extract the numbers) methods.
995 o plot.phylo() has a new option, `show.tip.label', specifying
996 whether to print the labels of the tips. The default is TRUE.
998 o The code of nj() has been replaced by a faster C code: it is now
999 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1002 o write.nexus() now writes whether a tree is rooted or not.
1007 o Two bugs have been fixed in root(): unrooted trees are now
1008 handled corretly, and node labels are now output normally.
1010 o A bug was fixed in phymltest(): the executable couldn't be found
1013 o Three bug have been fixed in ace(): computing the likelihood of
1014 ancestral states of discrete characters failed, custom models
1015 did not work, and the function failed with a null gradient (a
1016 warning message is now returned; this latter bug was also
1017 present in yule.cov() as well and is now fixed).
1019 o pic() hanged out when missing data were present: a message error
1022 o A small bug was fixed in dist.dna() where the gamma correction
1023 was not always correctly dispatched.
1025 o plot.phylo() plotted correctly the root edge only when the tree
1026 was plotted rightwards: this works now for all directions.
1031 o dist.taxo() has been renamed as weight.taxo().
1033 o Various error and warning messages have been improved.
1037 CHANGES IN APE VERSION 1.7
1040 o The new function ace() estimates ancestral character states for
1041 continuous characters (with ML, GLS, and contrasts methods), and
1042 discrete characters (with ML only) for any number of states.
1044 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1045 of directional evolution for continuous characters. The user
1046 specifies the node(s) of the tree where the character optimum
1049 o The new function is.rooted() tests whether a tree (of class
1052 o The new function rcoal() generates random ultrametric trees with
1053 the possibility to specify the function that generates the
1054 inter-nodes distances.
1056 o The new function mrca() gives for all pairs of tips in a tree
1057 (and optionally nodes too) the most recent common ancestor.
1059 o nodelabels() has a new option `thermo' to plot proportions (up
1060 to three classes) on the nodes of a tree.
1062 o rtree() has been improved: it can now generate rooted or
1063 unrooted trees, and the mathematical function that generates the
1064 branch lengths may be specified by the user. The tip labels may
1065 be given directly in the call to rtree. The limit cases (n = 2,
1066 3) are now handled correctly.
1068 o dist.topo() has a new argument `method' with two choices: "PH85"
1069 for Penny and Henny's method (already available before and now
1070 the default), and "BHV01" for the geometric distance by Billera
1071 et al. (2001, Adv. Appl. Math. 27:733).
1073 o write.tree() has a new option, `digits', which specifies the
1074 number of digits to be printed in the Newick tree. By default
1075 digits = 10. The numbers are now always printed in decimal form
1076 (i.e., 1.0e-1 is now avoided).
1078 o dist.dna() can now compute the raw distances between pairs of
1079 DNA sequences by specifying model = "raw".
1081 o dist.phylo() has a new option `full' to possibly compute the
1082 distances among all tips and nodes of the tree. The default if
1088 o Several bugs were fixed in all.equal.phylo().
1090 o dist.dna() did not handle correctly gaps ("-") in alignments:
1091 they are now considered as missing data.
1093 o rotate() did not work if the tips were not ordered: this is
1096 o mantel.test() returned NA in some special cases: this is fixed
1097 and the function has been improved and is now faster.
1099 o A bug was fixed in diversi.gof() where the calculation of A² was
1102 o cherry() did not work correctly under some OSs (mainly Linux):
1105 o is.binary.tree() has been modified so that it works with both
1106 rooted and unrooted trees.
1108 o The documentation of theta.s() was not correct: this has been
1111 o plot.mst() did not work correctly: this is fixed.
1115 CHANGES IN APE VERSION 1.6
1120 o The new function dist.topo() computes the topological distances
1123 o The new function boot.phylo() performs a bootstrap analysis on
1124 phylogeny estimation.
1126 o The new functions prop.part() and prop.clades() analyse
1127 bipartitions from a series of trees.
1132 o read.GenBank() now uses the EFetch utility of NCBI instead of
1133 the usual Web interface: it is now much faster (e.g., 12 times
1134 faster to retrieve 8 sequences, 37 times for 60 sequences).
1139 o Several bugs were fixed in read.dna().
1141 o Several bugs were fixed in diversi.time().
1143 o is.binary.tree() did not work correctly if the tree has no edge
1144 lengths: this is fixed.
1146 o drop.tip() did not correctly propagated the `node.label' of a
1147 tree: this is fixed.
1151 CHANGES IN APE VERSION 1.5
1156 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1157 convert objects between the classes "phylo" and "matching". The
1158 latter implements the representation of binary trees introduced by
1159 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1160 as.matching() has been introduced as well.
1162 o Two new functions, multi2di() and di2multi(), allow to resolve
1163 and collapse multichotomies with branches of length zero.
1165 o The new function nuc.div() computes the nucleotide diversity
1166 from a sample a DNA sequences.
1168 o dist.dna() has been completely rewritten with a much faster
1169 (particularly for large data sets) C code. Eight models are
1170 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1171 option `method' has been renamed `model'). Computation of variance
1172 is available for all models. A gamma-correction is possible for
1173 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1174 to remove sites with missing data on a pairwise basis. The option
1175 `GCcontent' has been removed.
1177 o read.GenBank() has a new option (species.names) which specifies
1178 whether to return the species names of the organisms in addition
1179 to the accession numbers of the sequences (this is the default
1182 o write.nexus() can now write several trees in the same NEXUS file.
1184 o drop.tip() has a new option `root.edge' that allows to specify the
1185 new root edge if internal branches are trimmed.
1190 o as.phylo.hclust() failed if some labels had parentheses: this
1193 o Several bugs were fixed in all.equal.phylo(). This function now
1194 returns the logical TRUE if the trees are identical but with
1195 different representations (a report was printed previously).
1197 o read.GenBank() did not correctly handle ambiguous base codes:
1203 o birthdeath() now returns an object of class "birthdeath" for
1204 which there is a print method.
1208 CHANGES IN APE VERSION 1.4
1213 o The new function nj() performs phylogeny estimation with the
1214 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1217 o The new function which.edge() identifies the edges of a tree
1218 that belong to a group specified as a set of tips.
1220 o The new function as.phylo.phylog() converts an object of class
1221 "phylog" (from the package ade4) into an object of class
1224 o The new function axisPhylo() draws axes on the side of a
1227 o The new function howmanytrees() calculates the number of trees
1228 in different cases and giving a number of tips.
1230 o write.tree() has a new option `multi.line' (TRUE by default) to
1231 write a Newick tree on several lines rather than on a single
1234 o The functionalities of zoom() have been extended. Several
1235 subtrees can be visualized at the same time, and they are marked
1236 on the main tree with colors. The context of the subtrees can be
1237 marked with the option `subtree' (see below).
1239 o drop.tip() has a new option `subtree' (FALSE by default) which
1240 specifies whether to output in the tree how many tips have been
1243 o The arguments of add.scale.bar() have been redefined and have
1244 now default values (see ?add.scale.bar for details). This
1245 function now works even if the plotted tree has no edge length.
1247 o plot.phylo() can now plot radial trees, but this does not take
1248 edge lengths into account.
1250 o In plot.phylo() with `type = "phylogram"', if the values of
1251 `edge.color' and `edge.width' are identical for sister-branches,
1252 they are propagated to the vertical line that link them.
1257 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1258 crashing. This is fixed.
1260 o In plot.phylo(), the options `edge.color' and `edge.width' are
1261 now properly recycled; their default values are now "black" and
1264 o A bug has been fixed in write.nexus().
1269 o The function node.depth.edgelength() has been removed and
1270 replaced by a C code.
1274 CHANGES IN APE VERSION 1.3-1
1279 o The new function nodelabels() allows to add labels to the nodes
1280 of a tree using text or plotting symbols in a flexible way.
1282 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1283 numeric values specifying the lower and upper limits on the x-
1284 and y-axes. This allows to leave some space on any side of the
1285 tree. If a single value is given, this is taken as the upper
1290 CHANGES IN APE VERSION 1.3
1295 o The new function phymltest() calls the software PHYML and fits
1296 28 models of DNA sequence evolution. There are a print method to
1297 display likelihood and AIC values, a summary method to compute
1298 the hierarchical likelihood ratio tests, and a plot method to
1299 display graphically the AIC values of each model.
1301 o The new function yule.cov() fits the Yule model with covariates,
1302 a model where the speciation rate is affected by several species
1303 traits through a generalized linear model. The parameters are
1304 estimated by maximum likelihood.
1306 o Three new functions, corBrownian(), corGrafen(), and
1307 corMartins(), compute the expected correlation structures among
1308 species given a phylogeny under different models of evolution.
1309 These can be used for GLS comparative phylogenetic methods (see
1310 the examples). There are coef() and corMatrix() methods and an
1311 Initialize.corPhyl() function associated.
1313 o The new function compar.cheverud() implements Cheverud et al.'s
1314 (1985; Evolution 39:1335) phylogenetic comparative method.
1316 o The new function varcomp() estimates variance components; it has
1319 o Two new functions, panel.superpose.correlogram() and
1320 plot.correlogramList(), allow to plot several phylogenetic
1323 o The new function node.leafnumber() computes the number of leaves
1324 of a subtree defined by a particular node.
1326 o The new function node.sons() gets all tags of son nodes from a
1329 o The new function compute.brlen() computes the branch lengths of
1330 a tree according to a specified method.
1332 o plot.phylo() has three new options: "cex" controls the size of
1333 the (tip and node) labels (thus it is no more needed to change
1334 the global graphical parameter), "direction" which allows to
1335 plot the tree rightwards, leftwards, upwards, or downwards, and
1336 "y.lim" which sets the upper limit on the y-axis.
1341 o Some functions which try to match tip labels and names of
1342 additional data (e.g. vector) are likely to fail if there are
1343 typing or syntax errors. If both series of names do not perfectly
1344 match, they are ignored and a warning message is now issued.
1345 These functions are bd.ext, compar.gee, pic. Their help pages
1346 have been clarified on this point.
1350 CHANGES IN APE VERSION 1.2-7
1355 o The new function root() reroots a phylogenetic tree with respect
1356 to a specified outgroup.
1358 o The new function rotate() rotates an internal branch of a tree.
1360 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1361 trees) controls the display of the tip labels in unrooted trees.
1362 This display has been greatly improved: the tip labels are now not
1363 expected to overlap with the tree (particularly if lab4ut =
1364 "axial"). In all cases, combining appropriate values of "lab4ut"
1365 and the font size (via "par(cex = )") should result in readable
1366 unrooted trees. See ?plot.phylo for some examples.
1368 o In drop.tip(), the argument `tip' can now be numeric or character.
1373 o drop.tip() did not work correctly with trees with no branch
1374 lengths: this is fixed.
1376 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1377 plotted with some line crossings: this is now fixed.
1381 CHANGES IN APE VERSION 1.2-6
1386 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1387 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1388 to implement comparative methods with an autocorrelation approach.
1390 o A new data set describing some life history traits of Carnivores
1396 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1401 o When plotting a tree with plot.phylo(), the new default of the
1402 option `label.offset' is now 0, so the labels are always visible.
1406 CHANGES IN APE VERSION 1.2-5
1411 o The new function bd.ext() fits a birth-death model with combined
1412 phylogenetic and taxonomic data, and estimates the corresponding
1413 speciation and extinction rates.
1418 o The package gee is no more required by ape but only suggested
1419 since only the function compar.gee() calls gee.
1423 CHANGES IN APE VERSION 1.2-4
1428 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1429 and lines.popsize) implementing a new approach for inferring the
1430 demographic history from genealogies using a reversible jump
1431 MCMC have been introduced.
1433 o The unit of time in the skyline plot and in the new plots can
1434 now be chosen to be actual years, rather than substitutions.
1438 CHANGES IN APE VERSION 1.2-3
1443 o The new function rtree() generates a random binary tree with or
1444 without branch lengths.
1446 o Two new functions for drawing lineages-through-time (LTT) plots
1447 are provided: ltt.lines() adds a LTT curve to an existing plot,
1448 and mltt.plot() does a multiple LTT plot giving several trees as
1449 arguments (see `?ltt.plot' for details).
1454 o Some taxon names made R crashing when calling as.phylo.hclust():
1457 o dist.dna() returned an error with two identical DNA sequences
1458 (only using the Jukes-Cantor method returned 0): this is fixed.
1463 o The function dist.phylo() has been re-written using a different
1464 algorithm: it is now about four times faster.
1466 o The code of branching.times() has been improved: it is now about
1471 CHANGES IN APE VERSION 1.2-2
1476 o The new function seg.sites() finds the segregating sites in a
1477 sample of DNA sequences.
1482 o A bug introduced in read.tree() and in read.nexus() with version
1485 o A few errors were corrected and a few examples were added in the
1490 CHANGES IN APE VERSION 1.2-1
1495 o plot.phylo() can now draw the edge of the root of a tree if it
1496 has one (see the new option `root.edge', its default is FALSE).
1501 o A bug was fixed in read.nexus(): files with semicolons inside
1502 comment blocks were not read correctly.
1504 o The behaviour of read.tree() and read.nexus() was corrected so
1505 that tree files with badly represented root edges (e.g., with
1506 an extra pair of parentheses, see the help pages for details)
1507 are now correctly represented in the object of class "phylo";
1508 a warning message is now issued.
1512 CHANGES IN APE VERSION 1.2
1517 o plot.phylo() has been completely re-written and offers several
1518 new functionalities. Three types of trees can now be drawn:
1519 phylogram (as previously), cladogram, and unrooted tree; in
1520 all three types the branch lengths can be drawn using the edge
1521 lengths of the phylogeny or not (e.g., if the latter is absent).
1522 The vertical position of the nodes can be adjusted with two
1523 choices (see option `node.pos'). The code has been re-structured,
1524 and two new functions (potentially useful for developpers) are
1525 documented separately: node.depth.edgelength() and node.depth();
1526 see the respective help pages for details.
1528 o The new function zoom() allows to explore very large trees by
1529 focusing on a small portion of it.
1531 o The new function yule() fits by maximum likelihood the Yule model
1532 (birth-only process) to a phylogenetic tree.
1534 o Support for writing DNA sequences in FASTA format has been
1535 introduced in write.dna() (support for reading sequences in
1536 this format was introduced in read.dna() in version 1.1-2).
1537 The function has been completely re-written, fixing some bugs
1538 (see below); the default behaviour is no more to display the
1539 sequences on the standard output. Several options have been
1540 introduced to control the sequence printing in a flexible
1541 way. The help page has been extended.
1543 o A new data set is included: a supertree of bats in NEXUS format.
1548 o In theta.s(), the default of the option `variance' has
1549 been changed to `FALSE' (as was indicated in the help page).
1551 o Several bugs were fixed in the code of all.equal.phylo().
1553 o Several bugs were fixed in write.dna(), particularly this
1554 function did not work with `format = "interleaved"'.
1556 o Various errors were corrected in the help pages.
1561 o The argument names of as.hclust.phylo() have been changed
1562 from "(phy)" to "(x, ...)" to conform to the definition of
1563 the corresponding generic function.
1565 o gamma.stat() has been renamed gammaStat() to avoid confusion
1566 since gamma() is a generic function.
1570 CHANGES IN APE VERSION 1.1-3
1575 o base.freq() previously did not return a value of 0 for
1576 bases absent in the data (e.g., a vector of length 3 was
1577 returned if one base was absent). This is now fixed (a
1578 vector of length 4 is always returned).
1580 o Several bugs were fixed in read.nexus(), including that this
1581 function did not work in this absence of a "TRANSLATE"
1582 command in the NEXUS file, and that the commands were
1587 CHANGES IN APE VERSION 1.1-2
1592 o The Tamura and Nei (1993) model of DNA distance is now implemented
1593 in dist.dna(): five models are now available in this function.
1595 o A new data set is included: a set of 15 sequences of the
1596 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1602 o A bug in read.nexus() was fixed.
1604 o read.dna() previously did not work correctly in most cases.
1605 The function has been completely re-written and its help page
1606 has been considerably extended (see ?read.dna for details).
1607 Underscores (_) in taxon names are no more replaced with
1608 spaces (this behaviour was undocumented).
1610 o A bug was fixed in write.dna().
1614 CHANGES IN APE VERSION 1.1-1
1619 o A bug in read.tree() introduced in APE 1.1 was fixed.
1621 o A bug in compar.gee() resulted in an error when trying to fit
1622 a model with `family = "binomial"'. This is now fixed.
1626 CHANGES IN APE VERSION 1.1
1631 o The Klastorin (1982) method as suggested by Misawa and Tajima
1632 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1633 on the basis of phylogenetic trees has been implemented (see
1634 the function klastorin()).
1636 o Functions have been added to convert APE's "phylo" objects in
1637 "hclust" cluster objects and vice versa (see the help page of
1638 as.phylo for details).
1640 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1641 are introduced for the estimation of absolute evolutionary rates
1642 (ratogram) and dated clock-like trees (chronogram) from
1643 phylogenetic trees using the non-parametric rate smoothing approach
1644 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1646 o A summary method is now provided printing a summary information on a
1647 phylogenetic tree with, for instance, `summary(tree)'.
1649 o The behaviour of read.tree() was changed so that all spaces and
1650 tabulations in tree files are now ignored. Consequently, spaces in tip
1651 labels are no more allowed. Another side effect is that read.nexus()
1652 now does not replace the underscores (_) in tip labels with spaces
1653 (this behaviour was undocumented).
1655 o The function plot.phylo() has a new option (`underscore') which
1656 specifies whether the underscores in tip labels should be written on
1657 the plot as such or replaced with spaces (the default).
1659 o The function birthdeath() now computes 95% confidence intervals of
1660 the estimated parameters using profile likelihood.
1662 o Three new data sets are included: a gene tree estimated from 36
1663 landplant rbcL sequences, a gene tree estimated from 32 opsin
1664 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1669 o A bug was fixed in dist.gene() where nothing was returned.
1671 o A bug in plot.mst() was fixed.
1673 o A bug in vcv.phylo() resulted in false correlations when the
1674 option `cor = TRUE' was used (now fixed).
1678 CHANGES IN APE VERSION 1.0
1683 o Two new functions, read.dna() and write.dna(), read/write in a file
1684 DNA sequences in interleaved or in sequential format.
1686 o Two new functions, read.nexus() and write.nexus(), read/write trees
1689 o The new function bind.tree() allows to bind two trees together,
1690 possibly handling root edges to give internal branches.
1692 o The new function drop.tip() removes the tips in a phylogenetic tree,
1693 and trims (or not) the corresponding internal branches.
1695 o The new function is.ultrametric() tests if a tree is ultrametric.
1697 o The function plot.phylo() has more functionalities such as drawing the
1698 branches with different colours and/or different widths, showing the
1699 node labels, controling the position and font of the labels, rotating
1700 the labels, and controling the space around the plot.
1702 o The function read.tree() can now read trees with no branch length,
1703 such as "(a,b),c);". Consequently, the element `edge.length' in
1704 objects of class "phylo" is now optional.
1706 o The function write.tree() has a new default behaviour: if the default
1707 for the option `file' is used (i.e. file = ""), then a variable of
1708 mode character containing the tree in Newick format is returned which
1709 can thus be assigned (e.g., tree <- write.tree(phy)).
1711 o The function read.tree() has a new argument `text' which allows
1712 to read the tree in a variable of mode character.
1714 o A new data set is included: the phylogenetic relationships among
1715 the orders of birds from Sibley and Ahlquist (1990).
1719 CHANGES IN APE VERSION 0.2-1
1724 o Several bugs were fixed in the help pages.
1728 CHANGES IN APE VERSION 0.2
1733 o The function write.tree() writes phylogenetic trees (objects of class
1734 "phylo") in an ASCII file using the Newick parenthetic format.
1736 o The function birthdeath() fits a birth-death model to branching times
1737 by maximum likelihood, and estimates the corresponding speciation and
1740 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1743 o The function is.binary.tree() tests whether a phylogeny is binary.
1745 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1746 as well as some methods are introduced.
1748 o Several functions, including some generics and methods, for computing
1749 skyline plot estimates (classic and generalized) of effective
1750 population size through time are introduced and replace the function
1751 skyline.plot() in version 0.1.
1753 o Two data sets are now included: the phylogenetic relationships among
1754 the families of birds from Sibley and Ahlquist (1990), and an
1755 estimated clock-like phylogeny of HIV sequences sampled in the
1756 Democratic Republic of Congo.
1759 DEPRECATED & DEFUNCT
1761 o The function skyline.plot() in ape 0.1 has been deprecated and
1762 replaced by more elaborate functions (see above).
1767 o Two important bugs were fixed in plot.phylo(): phylogenies with
1768 multichotomies not at the root or not with only terminal branches,
1769 and phylogenies with a single node (i.e. only terminal branches)
1770 did not plot. These trees should be plotted correctly now.
1772 o Several bugs were fixed in diversi.time() in the computation of
1775 o Various errors were corrected in the help pages.
projects / ape.git / blob