1 CHANGES IN APE VERSION 2.2-5
6 o The new function yule.time fits a user-defined time-dependent
7 Yule model by maximum likelihood.
11 CHANGES IN APE VERSION 2.2-4
15 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
16 now fixed. (Thanks to Peter Wragg for the fix!)
18 o A warning message occurred for no reason with ace(method="GLS").
23 o There is now a general help page displayed with '?ape'
27 CHANGES IN APE VERSION 2.2-3
32 o The new function extract.clade extracts a clade from a tree by
33 specifying a node number or label.
35 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
36 operations of the same names.
38 o dist.dna() can now return the number of site differences by
44 o chronopl() did not work with CV = TRUE.
46 o read.nexus() did not work correctly in some situations (trees on
47 multiple lines with different numbers of lines and/or with
48 comments inserted within the trees).
50 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
51 the number of lineages with non-binary trees.
56 o ape has now a namespace.
58 o drip.tip() has been improved: it should be much faster and work
59 better in some cases (e.g., see the example in ?zoom).
63 CHANGES IN APE VERSION 2.2-2
68 o dist.gene() has been substantially improved and gains an option
71 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
77 o prop.part() failed with a single tree with the default option
78 'check.labels = TRUE'.
80 o summary.DNAbin() failed to display correctly the summary of
81 sequence lengths with lists of sequences of 10,000 bases or more
82 (because summary.default uses 4 significant digits by default).
84 o read.nexus() failed to read a file with a single tree with line
85 breaks in the Newick string.
87 o del.gaps() returned a list of empty sequences when there were no
93 o phymltest() has been updated for PhyML 3.0 and gains an option
94 'append', whereas the option 'path2exec' has been removed.
96 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
97 which is returned unchanged (instead of an error).
99 o The data sets bird.orders and bird.families are now stored as
100 Newick strings; i.e., the command data(bird.orders) calls
105 CHANGES IN APE VERSION 2.2-1
110 o The new function makeLabel() helps to modify labels of trees,
111 lists of trees, or DNA sequences, with several utilities to
112 truncate and/or make them unique, substituting some
113 characters, and so on.
115 o The new function del.gaps() removes insertion gaps ("-") in a
116 set of DNA sequences.
118 o read.dna() can now read Clustal files (*.aln).
123 o root() failed with 'resolve.root = TRUE' when the root was
124 already the specified root.
126 o Several bugs were fixed in mlphylo().
128 o collapsed.singles() did not propagate the 'Nnode' and
129 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
131 o read.nexus() failed to remove correctly the comments within
134 o read.nexus() failed to read a file with a single tree and no
135 translation of tip labels.
137 o read.nexus() failed to place correctly tip labels when reading
138 a single tree with no edge lengths.
140 o A bug was fixed in sh.test().
145 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
148 o The option 'check.labels' of consensus() and prop.part() is now
151 o write.dna() now does not truncate names to 10 characters with
156 CHANGES IN APE VERSION 2.2
161 o Four new functions have been written by Damien de Vienne for the
162 graphical exploration of large trees (cophyloplot, subtrees,
163 subtreeplot), and to return the graphical coordinates of tree
166 o The new functions corPagel and corBlomberg implement the Pagel's
167 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
169 o chronopl() has been improved and gains several options: see its
170 help page for details.
172 o boot.phylo() has now an option 'trees' to possibly return the
173 bootstraped trees (the default is FALSE).
175 o prop.part() has been improved and should now be faster in all
181 o read.dna() failed if "?" occurred in the first 10 sites of the
184 o The x/y aspect of the plot is now respected when plotting a
185 circular tree (type = "r" or "f").
187 o Drawing the tip labels sometimes failed when plotting circular
190 o zoom() failed when tip labels were used instead of their numbers
191 (thanks to Yan Wong for the fix).
193 o drop.tip() failed with some trees (fixed by Yan Wong).
195 o seg.sites() failed with a list.
197 o consensus() failed in some cases. The function has been improved
198 as well and is faster.
202 CHANGES IN APE VERSION 2.1-3
207 o A bug in read.nexus() made the Windows R-GUI crash.
209 o An error was fixed in the computation of ancestral character
210 states by generalized least squares in ace().
212 o di2multi() did not modify node labels correctly.
214 o multi2di() failed if the tree had its attribute "order" set to
219 CHANGES IN APE VERSION 2.1-2
224 o There three new methods for the "multiPhylo" class: str, $,
227 o root() gains the options 'node' and 'resolve.root'
228 (FALSE by default) as well as its code being improved.
230 o mltt.plot() has now an option 'log' used in the same way
231 than in plot.default().
236 o mltt.plot() failed to display the legend with an unnamed
239 o nodelabels() with pies now correcly uses the argument
240 'cex' to draw symbols of different sizes (which has
241 worked already for thermometers).
243 o read.nexus() generally failed to read very big files.
248 o The argument 'family' of compar.gee() can now be a function
249 as well as a character string.
251 o read.tree() and read.nexus() now return an unnamed list if
254 o read.nexus() now returns a modified object of class "multiPhylo"
255 when there is a TRANSLATE block in the NEXUS file: the individual
256 trees have no 'tip.label' vector, but the list has a 'TipLabel'
257 attribute. The new methods '$' and '[[' set these elements
258 correctly when extracting trees.
262 CHANGES IN APE VERSION 2.1-1
267 o The new function rmtree generates lists of random trees.
269 o rcoal() now generates a genuine coalescent tree by default
270 (thanks to Vladimir Minin for the code).
275 o nuc.div() returned an incorrect value with the default
276 pairwise.deletion = FALSE.
281 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
282 have been improved so that they are stabler and faster.
284 o R packages used by ape are now loaded silently; lattice and gee
285 are loaded only when needed.
289 CHANGES IN APE VERSION 2.1
294 o The new function identify.phylo identifies clades on a plotted
295 tree using the mouse.
297 o It is now possible to subset a list of trees (object of class
298 "multiPhylo") with "[" while keeping its class correct.
300 o The new function as.DNAbin.alignment converts DNA sequences
301 stored in the "alignment" format of the package seqinr into
302 an object of class "DNAbin".
304 o The new function weight.taxo2 helps to build similarity matrices
305 given two taxonomic levels (usually called by other functions).
307 o write.tree() can now take a list of trees (class "multiPhylo")
308 as its main argument.
310 o plot.correlogram() and plot.correlogramList() have been
311 improved, and gain several options (see the help page for
312 details). A legend is now plotted by default.
317 o dist.dna() returned some incorrect values with `model = "JC69"'
318 and `pairwise.deletion = TRUE'. This affected only the
319 distances involving sequences with missing values. (Thanks
320 to Bruno Toupance for digging this bug out.)
322 o write.tree() failed with some trees: this is fixed by removing
323 the `multi.line' option (trees are now always printed on a
326 o read.nexus() did not correctly detect trees with multiple root
327 edges (see OTHER CHANGES).
332 o The code of mlphylo() has been almost entirely rewritten, and
333 should be much stabler. The options have been also greatly
334 simplified (see ?mlphylo and ?DNAmodel for details).
336 o The internal function nTips has been renamed klastorin_nTips.
338 o The code of is.ultrametric() contained redundancies and has
341 o The code of Moran.I() and of correlogram.formula() have been
344 o read.tree() and read.nexus() now return an error when trying to
345 read a tree with multiple root edges (see BUG FIXES). The
346 correction applied in previous version did not work in all
349 o The class c("multi.tree", "phylo") has been renamed
355 o There is now a vignette in ape: see vignette("MoranI", "ape").
360 o as.matching() and as.phylo.matching() do not support branch
363 o correlogram.phylo() and discrete.dist() have been removed.
367 CHANGES IN APE VERSION 2.0-2
372 o The new function matexpo computes the exponential of a square
375 o The new function unique.multi.tree removes duplicate trees from
378 o yule() has a new option `use.root.edge = FALSE' that specifies
379 to ignore, by default, the root edge of the tree if it exists.
384 o which.edge() failed when the index of a single terminal edge was
387 o In diversi.time(), the values returned for model C were
390 o A bug was fixed in yule() that affected the calculation of the
391 likelihood in the presence of ties in the branching times.
393 o There was a bug in the C function mat_expo4x4 affecting the
394 calculations of the transition probabilities for models HKY and
397 o A small bug was fixed in as.matrix.DNAbin (thanks to James
400 o rtree() did not `shuffle' the tip labels by default, so only a
401 limited number of labelled topologies could be generated.
405 CHANGES IN APE VERSION 2.0-1
410 o The three new functions bionj, fastme.ols, and fastme.bal
411 perform phylogeny estimation by the BIONJ and fastME methods in
412 OLS and balanced versions. This is a port to R of previous
413 previous programs done by Vincent Lefort.
415 o The new function chronoMPL performs molecular dating with the
416 mean path lengths method of Britton et al. (2002, Mol. Phyl.
419 o The new function rotate, contributed by Christoph Heibl, swaps
420 two clades connected to the same node. It works also with
421 multichotomous nodes.
423 o The new `method' as.matrix.DNAbin() may be used to convert
424 easily DNA sequences stored in a list into a matrix while
425 keeping the names and the class.
430 o chronopl() failed when some branch lengths were equal to zero:
431 an error message is now returned.
433 o di2multi() failed when there was a series of consecutive edges
438 CHANGES IN APE VERSION 1.10-2
443 o plot.phylo() can now plot circular trees: the option is type =
444 "fan" or type = "f" (to avoid the ambiguity with type = "c").
446 o prop.part() has a new option `check.labels = FALSE' which allows
447 to considerably speed-up the calculations of bipartitions. As a
448 consequence, calculations of bootstrap values with boot.phylo()
449 should be much faster.
454 o read.GenBank() did not return correctly the list of species as
455 from ape 1.10: this is fixed in this version
457 o Applying as.phylo() on a tree of class "phylo" failed: the
458 object is now returned unchanged.
462 CHANGES IN APE VERSION 1.10-1
467 o The three new functions Ntip, Nnode, and Nedge return, for a
468 given tree, the number of tips, nodes, or edges, respectively.
473 o read.nexus() did not set correctly the class of the returned
474 object when reading multiple trees.
476 o mllt.plot() failed with objects of class c("multi.tree",
479 o unroot() did not work correctly in most cases.
481 o reorder.phylo() made R freeze in some occasions.
483 o Plotting a tree in pruningwise order failed.
485 o When plotting an unrooted tree, the tip labels where not all
486 correctly positioned if the option `cex' was used.
490 CHANGES IN APE VERSION 1.10
495 o Five new `method' functions have been introduced to manipulate
496 DNA sequences in binary format (see below).
498 o Three new functions have been introduced to convert between the
499 new binary and the character formats.
501 o The new function as.alignment converts DNA sequences stored as
502 single characters into the class "alignment" used by the package
505 o read.dna() and read.GenBank() have a new argument `as.character'
506 controlling whether the sequences are returned in binary format
512 o root() failed when the tree had node labels: this is fixed.
514 o plot.phylo() did not correctly set the limits on the y-axis with
515 the default setting: this is fixed.
517 o dist.dna() returned a wrong result for the LogDet, paralinear,
518 and BH87 models with `pairwise.deletion = TRUE'.
523 o DNA sequences are now internally stored in a binary format. See
524 the document "A Bit-Level Coding Scheme for Nucleotides" for the
525 details. Most functions analyzing DNA functions have been
526 modified accordingly and are now much faster (dist.dna is now
527 ca. 60 times faster).
531 CHANGES IN APE VERSION 1.9-4
536 o A bug was fixed in edgelabels().
538 o as.phylo.hclust() did not work correctly when the object of
539 class "hclust" has its labels set to NULL: the returned tree has
540 now its tip labels set to "1", "2", ...
542 o consensus could fail if some tip labels are a subset of others
543 (e.g., "a" and "a_1"): this is now fixed.
545 o mlphylo() failed in most cases if some branch lengths of the
546 initial tree were greater than one: an error message is now
549 o mlphylo() failed in most cases when estimating the proportion of
550 invariants: this is fixed.
554 CHANGES IN APE VERSION 1.9-3
559 o The new function edgelabels adds labels on the edge of the tree
560 in the same way than nodelabels or tiplabels.
565 o multi2di() did not handle correctly branch lengths with the
566 default option `random = TRUE': this is now fixed.
568 o A bug was fixed in nuc.div() when using pairwise deletions.
570 o A bug occurred in the analysis of bipartitions with large
571 numbers of large trees, with consequences on prop.part,
572 prop.clades, and boot.phylo.
574 o The calculation of the Billera-Holmes-Vogtmann distance in
575 dist.topo was wrong: this has been fixed.
579 CHANGES IN APE VERSION 1.9-2
584 o The new function ladderize reorganizes the internal structure of
585 a tree to plot them left- or right-ladderized.
587 o The new function dist.nodes computes the patristic distances
588 between all nodes, internal and terminal, of a tree. It replaces
589 the option `full = TRUE' of cophenetic.phylo (see below).
594 o A bug was fixed in old2new.phylo().
596 o Some bugs were fixed in chronopl().
598 o The edge colours were not correctly displayed by plot.phylo
599 (thank you to Li-San Wang for the fix).
601 o cophenetic.phylo() failed with multichotomous trees: this is
607 o read.dna() now returns the sequences in a matrix if they are
608 aligned (interleaved or sequential format). Sequences in FASTA
609 format are still returned in a list.
611 o The option `full' of cophenetic.phylo() has been removed because
612 it could not be used from the generic.
617 o rotate() has been removed; this function did not work correctly
622 CHANGES IN APE VERSION 1.9-1
627 o Trees with a single tip were not read correctly in R as the
628 element `Nnode' was not set: this is fixed.
630 o unroot() did not set correctly the number of nodes of the
631 unrooted tree in most cases.
633 o read.GenBank() failed when fetching very long sequences,
634 particularly of the BX-series.
636 o A bug was introduced in read.tree() with ape 1.9: it has been
641 CHANGES IN APE VERSION 1.9
646 o There are two new print `methods' for trees of class "phylo" and
647 lists of trees of class "multi.tree", so that they are now
648 displayed in a compact and informative way.
650 o There are two new functions, old2new.phylo and new2old.phylo,
651 for converting between the old and new coding of the class
654 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
655 LogDet ("logdet"), and paralinear ("paralin").
657 o compute.brlen() has been extended: several methods are now
658 available to compute branch lengths.
660 o write.dna() can now handle matrices as well as lists.
665 o cophenetic.phylo() sometimes returned a wrong result with
666 multichotomous trees: this is fixed.
668 o rotate() failed when a single tip was specified: the tree is now
671 o ace() did not return the correct index matrix with custom
672 models: this is fixed.
674 o multi2di() did not work correctly when resolving multichotomies
675 randomly: the topology was always the same, only the arrangement
676 of clades was randomized: this is fixed. This function now
677 accepts trees with no branch lengths.
679 o The output of diversi.gof() was blurred by useless prints when a
680 user distribution was specified. This has been corrected, and
681 the help page of this function has been expanded.
686 o The internal structure of the class "phylo" has been changed:
687 see the document "Definition of Formats for Coding Phylogenetic
688 Trees in R" for the details. In addition, the code of most
689 functions has been improved.
691 o Several functions have been improved by replacing some R codes
692 by C codes: pic, plot.phylo, and reorder.phylo.
694 o There is now a citation information: see citation("ape") in R.
696 o write.tree() now does not add extra 0's to branch lengths so
697 that 1.23 is printed "1.23" by default, not "1.2300000000".
699 o The syntax of bind.tree() has been simplified. This function now
700 accepts trees with no branch lengths, and handles correctly node
703 o The option `as.numeric' of mrca() has been removed.
705 o The unused options `format' and `rooted' of read.tree() have
708 o The unused option `format' of write.tree() has been removed.
710 o The use of node.depth() has been simplified.
714 CHANGES IN APE VERSION 1.8-5
719 o Two new functions read.nexus.data() and write.nexus.data(),
720 contributed by Johan Nylander, allow to read and write molecular
721 sequences in NEXUS files.
723 o The new function reorder.phylo() reorders the internal structure
724 of a tree of class "phylo". It is used as the generic, e.g.,
727 o read.tree() and read.nexus() can now read trees with a single
730 o The new data set `cynipids' supplies a set of protein sequences
736 o The code of all.equal.phylo() has been completely rewritten
737 (thanks to Benoît Durand) which fixes several bugs.
739 o read.tree() and read.nexus() now checks the labels of the tree
740 to remove or substitute any characters that are illegal in the
741 Newick format (parentheses, etc.)
743 o A negative P-value could be returned by mantel.test(): this is
748 CHANGES IN APE VERSION 1.8-4
753 o The new function sh.test() computes the Shimodaira-
756 o The new function collapse.singles() removes the nodes with a
757 single descendant from a tree.
759 o plot.phylo() has a new argument `tip.color' to specify the
762 o mlphylo() has now an option `quiet' to control the display of
763 the progress of the analysis (the default is FALSE).
768 o read.dna() did not read correctly sequences in sequential format
769 with leading alignment gaps "-": this is fixed.
771 o ace() returned a list with no class so that the generic
772 functions (anova, logLik, ...) could not be used directly. This
773 is fixed as ace() now returns an object of class "ace".
775 o anova.ace() had a small bug when computing the number of degrees
776 of freedom: this is fixed.
778 o mlphylo() did not work when the sequences were in a matrix or
779 a data frame: this is fixed.
781 o rtree() did not work correctly when trying to simulate an
782 unrooted tree with two tips: an error message is now issued.
787 o The algorithm of rtree() has been changed: it is now about 40,
788 100, and 130 times faster for 10, 100, and 1000 tips,
793 CHANGES IN APE VERSION 1.8-3
798 o There are four new `method' functions to be used with the
799 results of ace(): logLik(), deviance(), AIC(), and anova().
801 o The plot method of phymltest has two new arguments: `main' to
802 change the title, and `col' to control the colour of the
803 segments showing the AIC values.
805 o ace() has a new argument `ip' that gives the initial values used
806 in the ML estimation with discrete characters (see the examples
807 in ?ace). This function now returns a matrix giving the indices
808 of the estimated rates when analysing discrete characters.
810 o nodelabels() and tiplabels() have a new argument `pie' to
811 represent proportions, with any number of categories, as
812 piecharts. The use of the option `thermo' has been improved:
813 there is now no limitation on the number of categories.
818 o mlphylo() did not work with more than two partitions: this is
821 o root() failed if the proposed outgroup was already an outgroup
822 in the tree: this is fixed.
824 o The `col' argument in nodelabels() and tiplabels() was not
825 correctly passed when `text' was used: this is fixed.
827 o Two bugs were fixed in mlphylo(): parameters were not always
828 correctly output, and the estimation failed in some cases.
830 o plot.phylo() was stuck when given a tree with a single tip: this
831 is fixed and a message error is now returned.
833 o An error was corrected in the help page of gammaStat regarding
834 the calculation of P-values.
836 o Using gls() could crash R when the number of species in the tree
837 and in the variables were different: this is fixed.
841 CHANGES IN APE VERSION 1.8-2
846 o The new function mlphylo() fits a phylogenetic tree by maximum
847 likelihood from DNA sequences. Its companion function DNAmodel()
848 is used to define the substitution model which may include
849 partitioning. There are methods for logLik(), deviance(), and
850 AIC(), and the summary() method has been extended to display in
851 a friendly way the results of this model fitting. Currently, the
852 functionality is limited to estimating the substitution and
853 associated parameters and computing the likelihood.
855 o The new function drop1.compar.gee (used as, e.g., drop1(m))
856 tests for single effects in GEE-based comparative method. A
857 warning message is printed if there is not enough degrees of
863 o An error message was sometimes issued by plot.multi.tree(),
864 though with no consequence.
868 CHANGES IN APE VERSION 1.8-1
873 o There is a new plot method for lists of trees (objects of class
874 "multi.tree"): it calls plot.phylo() internally and is
875 documented on the same help page.
880 o A bug was fixed in the C code that analyzes bipartitions: this
881 has impact on several functions like prop.part, prop.clades,
882 boot.phylo, or consensus.
884 o root() did not work correctly when the specified outgroup had
885 more than one element: this is fixed.
887 o dist.dna() sometimes returned a warning inappropriately: this
890 o If the distance object given to nj() had no rownames, nj()
891 returned a tree with no tip labels: it now returns tips labelled
892 "1", "2", ..., corresponding to the row numbers.
897 o nj() has been slightly changed so that tips with a zero distance
898 are first aggregated with zero-lengthed branches; the usual NJ
899 procedure is then performed on a distance matrix without 0's.
903 CHANGES IN APE VERSION 1.8
908 o The new function chronopl() estimates dates using the penalized
909 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
911 o The new function consensus() calculates the consensus tree of a
914 o The new function evolve.phylo() simulates the evolution of
915 continuous characters along a phylogeny under a Brownian model.
917 o The new plot method for objects of class "ancestral" displays a
918 tree together with ancestral values, as returned by the above
921 o The new function as.phylo.formula() returns a phylogeny from a
922 set of nested taxonomic variables given as a formula.
924 o The new function read.caic() reads trees in CAIC format.
926 o The new function tiplabels() allows to add labels to the tips
927 of a tree using text or plotting symbols in a flexible way.
929 o The new function unroot() unroots a phylogeny.
931 o multi2di() has a new option, `random', which specifies whether
932 to resolve the multichotomies randomly (the default) or not.
934 o prop.part() now returns an object of class "prop.part" for which
935 there are print (to display a partition in a more friendly way)
936 and summary (to extract the numbers) methods.
938 o plot.phylo() has a new option, `show.tip.label', specifying
939 whether to print the labels of the tips. The default is TRUE.
941 o The code of nj() has been replaced by a faster C code: it is now
942 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
945 o write.nexus() now writes whether a tree is rooted or not.
950 o Two bugs have been fixed in root(): unrooted trees are now
951 handled corretly, and node labels are now output normally.
953 o A bug was fixed in phymltest(): the executable couldn't be found
956 o Three bug have been fixed in ace(): computing the likelihood of
957 ancestral states of discrete characters failed, custom models
958 did not work, and the function failed with a null gradient (a
959 warning message is now returned; this latter bug was also
960 present in yule.cov() as well and is now fixed).
962 o pic() hanged out when missing data were present: a message error
965 o A small bug was fixed in dist.dna() where the gamma correction
966 was not always correctly dispatched.
968 o plot.phylo() plotted correctly the root edge only when the tree
969 was plotted rightwards: this works now for all directions.
974 o dist.taxo() has been renamed as weight.taxo().
976 o Various error and warning messages have been improved.
980 CHANGES IN APE VERSION 1.7
983 o The new function ace() estimates ancestral character states for
984 continuous characters (with ML, GLS, and contrasts methods), and
985 discrete characters (with ML only) for any number of states.
987 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
988 of directional evolution for continuous characters. The user
989 specifies the node(s) of the tree where the character optimum
992 o The new function is.rooted() tests whether a tree (of class
995 o The new function rcoal() generates random ultrametric trees with
996 the possibility to specify the function that generates the
997 inter-nodes distances.
999 o The new function mrca() gives for all pairs of tips in a tree
1000 (and optionally nodes too) the most recent common ancestor.
1002 o nodelabels() has a new option `thermo' to plot proportions (up
1003 to three classes) on the nodes of a tree.
1005 o rtree() has been improved: it can now generate rooted or
1006 unrooted trees, and the mathematical function that generates the
1007 branch lengths may be specified by the user. The tip labels may
1008 be given directly in the call to rtree. The limit cases (n = 2,
1009 3) are now handled correctly.
1011 o dist.topo() has a new argument `method' with two choices: "PH85"
1012 for Penny and Henny's method (already available before and now
1013 the default), and "BHV01" for the geometric distance by Billera
1014 et al. (2001, Adv. Appl. Math. 27:733).
1016 o write.tree() has a new option, `digits', which specifies the
1017 number of digits to be printed in the Newick tree. By default
1018 digits = 10. The numbers are now always printed in decimal form
1019 (i.e., 1.0e-1 is now avoided).
1021 o dist.dna() can now compute the raw distances between pairs of
1022 DNA sequences by specifying model = "raw".
1024 o dist.phylo() has a new option `full' to possibly compute the
1025 distances among all tips and nodes of the tree. The default if
1031 o Several bugs were fixed in all.equal.phylo().
1033 o dist.dna() did not handle correctly gaps ("-") in alignments:
1034 they are now considered as missing data.
1036 o rotate() did not work if the tips were not ordered: this is
1039 o mantel.test() returned NA in some special cases: this is fixed
1040 and the function has been improved and is now faster.
1042 o A bug was fixed in diversi.gof() where the calculation of A² was
1045 o cherry() did not work correctly under some OSs (mainly Linux):
1048 o is.binary.tree() has been modified so that it works with both
1049 rooted and unrooted trees.
1051 o The documentation of theta.s() was not correct: this has been
1054 o plot.mst() did not work correctly: this is fixed.
1058 CHANGES IN APE VERSION 1.6
1063 o The new function dist.topo() computes the topological distances
1066 o The new function boot.phylo() performs a bootstrap analysis on
1067 phylogeny estimation.
1069 o The new functions prop.part() and prop.clades() analyse
1070 bipartitions from a series of trees.
1075 o read.GenBank() now uses the EFetch utility of NCBI instead of
1076 the usual Web interface: it is now much faster (e.g., 12 times
1077 faster to retrieve 8 sequences, 37 times for 60 sequences).
1082 o Several bugs were fixed in read.dna().
1084 o Several bugs were fixed in diversi.time().
1086 o is.binary.tree() did not work correctly if the tree has no edge
1087 lengths: this is fixed.
1089 o drop.tip() did not correctly propagated the `node.label' of a
1090 tree: this is fixed.
1094 CHANGES IN APE VERSION 1.5
1099 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1100 convert objects between the classes "phylo" and "matching". The
1101 latter implements the representation of binary trees introduced by
1102 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1103 as.matching() has been introduced as well.
1105 o Two new functions, multi2di() and di2multi(), allow to resolve
1106 and collapse multichotomies with branches of length zero.
1108 o The new function nuc.div() computes the nucleotide diversity
1109 from a sample a DNA sequences.
1111 o dist.dna() has been completely rewritten with a much faster
1112 (particularly for large data sets) C code. Eight models are
1113 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1114 option `method' has been renamed `model'). Computation of variance
1115 is available for all models. A gamma-correction is possible for
1116 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1117 to remove sites with missing data on a pairwise basis. The option
1118 `GCcontent' has been removed.
1120 o read.GenBank() has a new option (species.names) which specifies
1121 whether to return the species names of the organisms in addition
1122 to the accession numbers of the sequences (this is the default
1125 o write.nexus() can now write several trees in the same NEXUS file.
1127 o drop.tip() has a new option `root.edge' that allows to specify the
1128 new root edge if internal branches are trimmed.
1133 o as.phylo.hclust() failed if some labels had parentheses: this
1136 o Several bugs were fixed in all.equal.phylo(). This function now
1137 returns the logical TRUE if the trees are identical but with
1138 different representations (a report was printed previously).
1140 o read.GenBank() did not correctly handle ambiguous base codes:
1146 o birthdeath() now returns an object of class "birthdeath" for
1147 which there is a print method.
1151 CHANGES IN APE VERSION 1.4
1156 o The new function nj() performs phylogeny estimation with the
1157 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1160 o The new function which.edge() identifies the edges of a tree
1161 that belong to a group specified as a set of tips.
1163 o The new function as.phylo.phylog() converts an object of class
1164 "phylog" (from the package ade4) into an object of class
1167 o The new function axisPhylo() draws axes on the side of a
1170 o The new function howmanytrees() calculates the number of trees
1171 in different cases and giving a number of tips.
1173 o write.tree() has a new option `multi.line' (TRUE by default) to
1174 write a Newick tree on several lines rather than on a single
1177 o The functionalities of zoom() have been extended. Several
1178 subtrees can be visualized at the same time, and they are marked
1179 on the main tree with colors. The context of the subtrees can be
1180 marked with the option `subtree' (see below).
1182 o drop.tip() has a new option `subtree' (FALSE by default) which
1183 specifies whether to output in the tree how many tips have been
1186 o The arguments of add.scale.bar() have been redefined and have
1187 now default values (see ?add.scale.bar for details). This
1188 function now works even if the plotted tree has no edge length.
1190 o plot.phylo() can now plot radial trees, but this does not take
1191 edge lengths into account.
1193 o In plot.phylo() with `type = "phylogram"', if the values of
1194 `edge.color' and `edge.width' are identical for sister-branches,
1195 they are propagated to the vertical line that link them.
1200 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1201 crashing. This is fixed.
1203 o In plot.phylo(), the options `edge.color' and `edge.width' are
1204 now properly recycled; their default values are now "black" and
1207 o A bug has been fixed in write.nexus().
1212 o The function node.depth.edgelength() has been removed and
1213 replaced by a C code.
1217 CHANGES IN APE VERSION 1.3-1
1222 o The new function nodelabels() allows to add labels to the nodes
1223 of a tree using text or plotting symbols in a flexible way.
1225 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1226 numeric values specifying the lower and upper limits on the x-
1227 and y-axes. This allows to leave some space on any side of the
1228 tree. If a single value is given, this is taken as the upper
1233 CHANGES IN APE VERSION 1.3
1238 o The new function phymltest() calls the software PHYML and fits
1239 28 models of DNA sequence evolution. There are a print method to
1240 display likelihood and AIC values, a summary method to compute
1241 the hierarchical likelihood ratio tests, and a plot method to
1242 display graphically the AIC values of each model.
1244 o The new function yule.cov() fits the Yule model with covariates,
1245 a model where the speciation rate is affected by several species
1246 traits through a generalized linear model. The parameters are
1247 estimated by maximum likelihood.
1249 o Three new functions, corBrownian(), corGrafen(), and
1250 corMartins(), compute the expected correlation structures among
1251 species given a phylogeny under different models of evolution.
1252 These can be used for GLS comparative phylogenetic methods (see
1253 the examples). There are coef() and corMatrix() methods and an
1254 Initialize.corPhyl() function associated.
1256 o The new function compar.cheverud() implements Cheverud et al.'s
1257 (1985; Evolution 39:1335) phylogenetic comparative method.
1259 o The new function varcomp() estimates variance components; it has
1262 o Two new functions, panel.superpose.correlogram() and
1263 plot.correlogramList(), allow to plot several phylogenetic
1266 o The new function node.leafnumber() computes the number of leaves
1267 of a subtree defined by a particular node.
1269 o The new function node.sons() gets all tags of son nodes from a
1272 o The new function compute.brlen() computes the branch lengths of
1273 a tree according to a specified method.
1275 o plot.phylo() has three new options: "cex" controls the size of
1276 the (tip and node) labels (thus it is no more needed to change
1277 the global graphical parameter), "direction" which allows to
1278 plot the tree rightwards, leftwards, upwards, or downwards, and
1279 "y.lim" which sets the upper limit on the y-axis.
1284 o Some functions which try to match tip labels and names of
1285 additional data (e.g. vector) are likely to fail if there are
1286 typing or syntax errors. If both series of names do not perfectly
1287 match, they are ignored and a warning message is now issued.
1288 These functions are bd.ext, compar.gee, pic. Their help pages
1289 have been clarified on this point.
1293 CHANGES IN APE VERSION 1.2-7
1298 o The new function root() reroots a phylogenetic tree with respect
1299 to a specified outgroup.
1301 o The new function rotate() rotates an internal branch of a tree.
1303 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1304 trees) controls the display of the tip labels in unrooted trees.
1305 This display has been greatly improved: the tip labels are now not
1306 expected to overlap with the tree (particularly if lab4ut =
1307 "axial"). In all cases, combining appropriate values of "lab4ut"
1308 and the font size (via "par(cex = )") should result in readable
1309 unrooted trees. See ?plot.phylo for some examples.
1311 o In drop.tip(), the argument `tip' can now be numeric or character.
1316 o drop.tip() did not work correctly with trees with no branch
1317 lengths: this is fixed.
1319 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1320 plotted with some line crossings: this is now fixed.
1324 CHANGES IN APE VERSION 1.2-6
1329 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1330 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1331 to implement comparative methods with an autocorrelation approach.
1333 o A new data set describing some life history traits of Carnivores
1339 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1344 o When plotting a tree with plot.phylo(), the new default of the
1345 option `label.offset' is now 0, so the labels are always visible.
1349 CHANGES IN APE VERSION 1.2-5
1354 o The new function bd.ext() fits a birth-death model with combined
1355 phylogenetic and taxonomic data, and estimates the corresponding
1356 speciation and extinction rates.
1361 o The package gee is no more required by ape but only suggested
1362 since only the function compar.gee() calls gee.
1366 CHANGES IN APE VERSION 1.2-4
1371 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1372 and lines.popsize) implementing a new approach for inferring the
1373 demographic history from genealogies using a reversible jump
1374 MCMC have been introduced.
1376 o The unit of time in the skyline plot and in the new plots can
1377 now be chosen to be actual years, rather than substitutions.
1381 CHANGES IN APE VERSION 1.2-3
1386 o The new function rtree() generates a random binary tree with or
1387 without branch lengths.
1389 o Two new functions for drawing lineages-through-time (LTT) plots
1390 are provided: ltt.lines() adds a LTT curve to an existing plot,
1391 and mltt.plot() does a multiple LTT plot giving several trees as
1392 arguments (see `?ltt.plot' for details).
1397 o Some taxon names made R crashing when calling as.phylo.hclust():
1400 o dist.dna() returned an error with two identical DNA sequences
1401 (only using the Jukes-Cantor method returned 0): this is fixed.
1406 o The function dist.phylo() has been re-written using a different
1407 algorithm: it is now about four times faster.
1409 o The code of branching.times() has been improved: it is now about
1414 CHANGES IN APE VERSION 1.2-2
1419 o The new function seg.sites() finds the segregating sites in a
1420 sample of DNA sequences.
1425 o A bug introduced in read.tree() and in read.nexus() with version
1428 o A few errors were corrected and a few examples were added in the
1433 CHANGES IN APE VERSION 1.2-1
1438 o plot.phylo() can now draw the edge of the root of a tree if it
1439 has one (see the new option `root.edge', its default is FALSE).
1444 o A bug was fixed in read.nexus(): files with semicolons inside
1445 comment blocks were not read correctly.
1447 o The behaviour of read.tree() and read.nexus() was corrected so
1448 that tree files with badly represented root edges (e.g., with
1449 an extra pair of parentheses, see the help pages for details)
1450 are now correctly represented in the object of class "phylo";
1451 a warning message is now issued.
1455 CHANGES IN APE VERSION 1.2
1460 o plot.phylo() has been completely re-written and offers several
1461 new functionalities. Three types of trees can now be drawn:
1462 phylogram (as previously), cladogram, and unrooted tree; in
1463 all three types the branch lengths can be drawn using the edge
1464 lengths of the phylogeny or not (e.g., if the latter is absent).
1465 The vertical position of the nodes can be adjusted with two
1466 choices (see option `node.pos'). The code has been re-structured,
1467 and two new functions (potentially useful for developpers) are
1468 documented separately: node.depth.edgelength() and node.depth();
1469 see the respective help pages for details.
1471 o The new function zoom() allows to explore very large trees by
1472 focusing on a small portion of it.
1474 o The new function yule() fits by maximum likelihood the Yule model
1475 (birth-only process) to a phylogenetic tree.
1477 o Support for writing DNA sequences in FASTA format has been
1478 introduced in write.dna() (support for reading sequences in
1479 this format was introduced in read.dna() in version 1.1-2).
1480 The function has been completely re-written, fixing some bugs
1481 (see below); the default behaviour is no more to display the
1482 sequences on the standard output. Several options have been
1483 introduced to control the sequence printing in a flexible
1484 way. The help page has been extended.
1486 o A new data set is included: a supertree of bats in NEXUS format.
1491 o In theta.s(), the default of the option `variance' has
1492 been changed to `FALSE' (as was indicated in the help page).
1494 o Several bugs were fixed in the code of all.equal.phylo().
1496 o Several bugs were fixed in write.dna(), particularly this
1497 function did not work with `format = "interleaved"'.
1499 o Various errors were corrected in the help pages.
1504 o The argument names of as.hclust.phylo() have been changed
1505 from "(phy)" to "(x, ...)" to conform to the definition of
1506 the corresponding generic function.
1508 o gamma.stat() has been renamed gammaStat() to avoid confusion
1509 since gamma() is a generic function.
1513 CHANGES IN APE VERSION 1.1-3
1518 o base.freq() previously did not return a value of 0 for
1519 bases absent in the data (e.g., a vector of length 3 was
1520 returned if one base was absent). This is now fixed (a
1521 vector of length 4 is always returned).
1523 o Several bugs were fixed in read.nexus(), including that this
1524 function did not work in this absence of a "TRANSLATE"
1525 command in the NEXUS file, and that the commands were
1530 CHANGES IN APE VERSION 1.1-2
1535 o The Tamura and Nei (1993) model of DNA distance is now implemented
1536 in dist.dna(): five models are now available in this function.
1538 o A new data set is included: a set of 15 sequences of the
1539 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1545 o A bug in read.nexus() was fixed.
1547 o read.dna() previously did not work correctly in most cases.
1548 The function has been completely re-written and its help page
1549 has been considerably extended (see ?read.dna for details).
1550 Underscores (_) in taxon names are no more replaced with
1551 spaces (this behaviour was undocumented).
1553 o A bug was fixed in write.dna().
1557 CHANGES IN APE VERSION 1.1-1
1562 o A bug in read.tree() introduced in APE 1.1 was fixed.
1564 o A bug in compar.gee() resulted in an error when trying to fit
1565 a model with `family = "binomial"'. This is now fixed.
1569 CHANGES IN APE VERSION 1.1
1574 o The Klastorin (1982) method as suggested by Misawa and Tajima
1575 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1576 on the basis of phylogenetic trees has been implemented (see
1577 the function klastorin()).
1579 o Functions have been added to convert APE's "phylo" objects in
1580 "hclust" cluster objects and vice versa (see the help page of
1581 as.phylo for details).
1583 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1584 are introduced for the estimation of absolute evolutionary rates
1585 (ratogram) and dated clock-like trees (chronogram) from
1586 phylogenetic trees using the non-parametric rate smoothing approach
1587 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1589 o A summary method is now provided printing a summary information on a
1590 phylogenetic tree with, for instance, `summary(tree)'.
1592 o The behaviour of read.tree() was changed so that all spaces and
1593 tabulations in tree files are now ignored. Consequently, spaces in tip
1594 labels are no more allowed. Another side effect is that read.nexus()
1595 now does not replace the underscores (_) in tip labels with spaces
1596 (this behaviour was undocumented).
1598 o The function plot.phylo() has a new option (`underscore') which
1599 specifies whether the underscores in tip labels should be written on
1600 the plot as such or replaced with spaces (the default).
1602 o The function birthdeath() now computes 95% confidence intervals of
1603 the estimated parameters using profile likelihood.
1605 o Three new data sets are included: a gene tree estimated from 36
1606 landplant rbcL sequences, a gene tree estimated from 32 opsin
1607 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1612 o A bug was fixed in dist.gene() where nothing was returned.
1614 o A bug in plot.mst() was fixed.
1616 o A bug in vcv.phylo() resulted in false correlations when the
1617 option `cor = TRUE' was used (now fixed).
1621 CHANGES IN APE VERSION 1.0
1626 o Two new functions, read.dna() and write.dna(), read/write in a file
1627 DNA sequences in interleaved or in sequential format.
1629 o Two new functions, read.nexus() and write.nexus(), read/write trees
1632 o The new function bind.tree() allows to bind two trees together,
1633 possibly handling root edges to give internal branches.
1635 o The new function drop.tip() removes the tips in a phylogenetic tree,
1636 and trims (or not) the corresponding internal branches.
1638 o The new function is.ultrametric() tests if a tree is ultrametric.
1640 o The function plot.phylo() has more functionalities such as drawing the
1641 branches with different colours and/or different widths, showing the
1642 node labels, controling the position and font of the labels, rotating
1643 the labels, and controling the space around the plot.
1645 o The function read.tree() can now read trees with no branch length,
1646 such as "(a,b),c);". Consequently, the element `edge.length' in
1647 objects of class "phylo" is now optional.
1649 o The function write.tree() has a new default behaviour: if the default
1650 for the option `file' is used (i.e. file = ""), then a variable of
1651 mode character containing the tree in Newick format is returned which
1652 can thus be assigned (e.g., tree <- write.tree(phy)).
1654 o The function read.tree() has a new argument `text' which allows
1655 to read the tree in a variable of mode character.
1657 o A new data set is included: the phylogenetic relationships among
1658 the orders of birds from Sibley and Ahlquist (1990).
1662 CHANGES IN APE VERSION 0.2-1
1667 o Several bugs were fixed in the help pages.
1671 CHANGES IN APE VERSION 0.2
1676 o The function write.tree() writes phylogenetic trees (objects of class
1677 "phylo") in an ASCII file using the Newick parenthetic format.
1679 o The function birthdeath() fits a birth-death model to branching times
1680 by maximum likelihood, and estimates the corresponding speciation and
1683 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1686 o The function is.binary.tree() tests whether a phylogeny is binary.
1688 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1689 as well as some methods are introduced.
1691 o Several functions, including some generics and methods, for computing
1692 skyline plot estimates (classic and generalized) of effective
1693 population size through time are introduced and replace the function
1694 skyline.plot() in version 0.1.
1696 o Two data sets are now included: the phylogenetic relationships among
1697 the families of birds from Sibley and Ahlquist (1990), and an
1698 estimated clock-like phylogeny of HIV sequences sampled in the
1699 Democratic Republic of Congo.
1702 DEPRECATED & DEFUNCT
1704 o The function skyline.plot() in ape 0.1 has been deprecated and
1705 replaced by more elaborate functions (see above).
1710 o Two important bugs were fixed in plot.phylo(): phylogenies with
1711 multichotomies not at the root or not with only terminal branches,
1712 and phylogenies with a single node (i.e. only terminal branches)
1713 did not plot. These trees should be plotted correctly now.
1715 o Several bugs were fixed in diversi.time() in the computation of
1718 o Various errors were corrected in the help pages.
projects / ape.git / blob