1 CHANGES IN APE VERSION 2.2-1
6 o The new function del.gaps() removes insertion gaps ("-") in a
11 CHANGES IN APE VERSION 2.2
16 o Four new functions have been written by Damien de Vienne for the
17 graphical exploration of large trees (cophyloplot, subtrees,
18 subtreeplot), and to return the graphical coordinates of tree
21 o The new functions corPagel and corBlomberg implement the Pagel's
22 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
24 o chronopl() has been improved and gains several options: see its
25 help page for details.
27 o boot.phylo() has now an option 'trees' to possibly return the
28 bootstraped trees (the default is FALSE).
30 o prop.part() has been improved and should now be faster in all
36 o read.dna() failed if "?" occurred in the first 10 sites of the
39 o The x/y aspect of the plot is now respected when plotting a
40 circular tree (type = "r" or "f").
42 o Drawing the tip labels sometimes failed when plotting circular
45 o zoom() failed when tip labels were used instead of their numbers
46 (thanks to Yan Wong for the fix).
48 o drop.tip() failed with some trees (fixed by Yan Wong).
50 o seg.sites() failed with a list.
52 o consensus() failed in some cases. The function has been improved
53 as well and is faster.
57 CHANGES IN APE VERSION 2.1-3
62 o A bug in read.nexus() made the Windows R-GUI crash.
64 o An error was fixed in the computation of ancestral character
65 states by generalized least squares in ace().
67 o di2multi() did not modify node labels correctly.
69 o multi2di() failed if the tree had its attribute "order" set to
74 CHANGES IN APE VERSION 2.1-2
79 o There three new methods for the "multiPhylo" class: str, $,
82 o root() gains the options 'node' and 'resolve.root'
83 (FALSE by default) as well as its code being improved.
85 o mltt.plot() has now an option 'log' used in the same way
86 than in plot.default().
91 o mltt.plot() failed to display the legend with an unnamed
94 o nodelabels() with pies now correcly uses the argument
95 'cex' to draw symbols of different sizes (which has
96 worked already for thermometers).
98 o read.nexus() generally failed to read very big files.
103 o The argument 'family' of compar.gee() can now be a function
104 as well as a character string.
106 o read.tree() and read.nexus() now return an unnamed list if
109 o read.nexus() now returns a modified object of class "multiPhylo"
110 when there is a TRANSLATE block in the NEXUS file: the individual
111 trees have no 'tip.label' vector, but the list has a 'TipLabel'
112 attribute. The new methods '$' and '[[' set these elements
113 correctly when extracting trees.
117 CHANGES IN APE VERSION 2.1-1
122 o The new function rmtree generates lists of random trees.
124 o rcoal() now generates a genuine coalescent tree by default
125 (thanks to Vladimir Minin for the code).
130 o nuc.div() returned an incorrect value with the default
131 pairwise.deletion = FALSE.
136 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
137 have been improved so that they are stabler and faster.
139 o R packages used by ape are now loaded silently; lattice and gee
140 are loaded only when needed.
144 CHANGES IN APE VERSION 2.1
149 o The new function identify.phylo identifies clades on a plotted
150 tree using the mouse.
152 o It is now possible to subset a list of trees (object of class
153 "multiPhylo") with "[" while keeping its class correct.
155 o The new function as.DNAbin.alignment converts DNA sequences
156 stored in the "alignment" format of the package seqinr into
157 an object of class "DNAbin".
159 o The new function weight.taxo2 helps to build similarity matrices
160 given two taxonomic levels (usually called by other functions).
162 o write.tree() can now take a list of trees (class "multiPhylo")
163 as its main argument.
165 o plot.correlogram() and plot.correlogramList() have been
166 improved, and gain several options (see the help page for
167 details). A legend is now plotted by default.
172 o dist.dna() returned some incorrect values with `model = "JC69"'
173 and `pairwise.deletion = TRUE'. This affected only the
174 distances involving sequences with missing values. (Thanks
175 to Bruno Toupance for digging this bug out.)
177 o write.tree() failed with some trees: this is fixed by removing
178 the `multi.line' option (trees are now always printed on a
181 o read.nexus() did not correctly detect trees with multiple root
182 edges (see OTHER CHANGES).
187 o The code of mlphylo() has almost entirely rewritten, and should
188 be much stabler. The options have been also greatly simplified
189 (see ?mlphylo and ?DNAmodel for details).
191 o The internal function nTips has been renamed klastorin_nTips.
193 o The code of is.ultrametric() contained redundancies and has
196 o The code of Moran.I() and of correlogram.formula() have been
199 o read.tree() and read.nexus() now return an error when trying to
200 read a tree with multiple root edges (see BUG FIXES). The
201 correction applied in previous version did not work in all
204 o The class c("multi.tree", "phylo") has been renamed
210 o There is now a vignette in ape: see vignette("MoranI", "ape").
215 o as.matching() and as.phylo.matching() do not support branch
218 o correlogram.phylo() and discrete.dist() have been removed.
222 CHANGES IN APE VERSION 2.0-2
227 o The new function matexpo computes the exponential of a square
230 o The new function unique.multi.tree removes duplicate trees from
233 o yule() has a new option `use.root.edge = FALSE' that specifies
234 to ignore, by default, the root edge of the tree if it exists.
239 o which.edge() failed when the index of a single terminal edge was
242 o In diversi.time(), the values returned for model C were
245 o A bug was fixed in yule() that affected the calculation of the
246 likelihood in the presence of ties in the branching times.
248 o There was a bug in the C function mat_expo4x4 affecting the
249 calculations of the transition probabilities for models HKY and
252 o A small bug was fixed in as.matrix.DNAbin (thanks to James
255 o rtree() did not `shuffle' the tip labels by default, so only a
256 limited number of labelled topologies could be generated.
260 CHANGES IN APE VERSION 2.0-1
265 o The three new functions bionj, fastme.ols, and fastme.bal
266 perform phylogeny estimation by the BIONJ and fastME methods in
267 OLS and balanced versions. This is a port to R of previous
268 previous programs done by Vincent Lefort.
270 o The new function chronoMPL performs molecular dating with the
271 mean path lengths method of Britton et al. (2002, Mol. Phyl.
274 o The new function rotate, contributed by Christoph Heibl, swaps
275 two clades connected to the same node. It works also with
276 multichotomous nodes.
278 o The new `method' as.matrix.DNAbin() may be used to convert
279 easily DNA sequences stored in a list into a matrix while
280 keeping the names and the class.
285 o chronopl() failed when some branch lengths were equal to zero:
286 an error message is now returned.
288 o di2multi() failed when there was a series of consecutive edges
293 CHANGES IN APE VERSION 1.10-2
298 o plot.phylo() can now plot circular trees: the option is type =
299 "fan" or type = "f" (to avoid the ambiguity with type = "c").
301 o prop.part() has a new option `check.labels = FALSE' which allows
302 to considerably speed-up the calculations of bipartitions. As a
303 consequence, calculations of bootstrap values with boot.phylo()
304 should be much faster.
309 o read.GenBank() did not return correctly the list of species as
310 from ape 1.10: this is fixed in this version
312 o Applying as.phylo() on a tree of class "phylo" failed: the
313 object is now returned unchanged.
317 CHANGES IN APE VERSION 1.10-1
322 o The three new functions Ntip, Nnode, and Nedge return, for a
323 given tree, the number of tips, nodes, or edges, respectively.
328 o read.nexus() did not set correctly the class of the returned
329 object when reading multiple trees.
331 o mllt.plot() failed with objects of class c("multi.tree",
334 o unroot() did not work correctly in most cases.
336 o reorder.phylo() made R freeze in some occasions.
338 o Plotting a tree in pruningwise order failed.
340 o When plotting an unrooted tree, the tip labels where not all
341 correctly positioned if the option `cex' was used.
345 CHANGES IN APE VERSION 1.10
350 o Five new `method' functions have been introduced to manipulate
351 DNA sequences in binary format (see below).
353 o Three new functions have been introduced to convert between the
354 new binary and the character formats.
356 o The new function as.alignment converts DNA sequences stored as
357 single characters into the class "alignment" used by the package
360 o read.dna() and read.GenBank() have a new argument `as.character'
361 controlling whether the sequences are returned in binary format
367 o root() failed when the tree had node labels: this is fixed.
369 o plot.phylo() did not correctly set the limits on the y-axis with
370 the default setting: this is fixed.
372 o dist.dna() returned a wrong result for the LogDet, paralinear,
373 and BH87 models with `pairwise.deletion = TRUE'.
378 o DNA sequences are now internally stored in a binary format. See
379 the document "A Bit-Level Coding Scheme for Nucleotides" for the
380 details. Most functions analyzing DNA functions have been
381 modified accordingly and are now much faster (dist.dna is now
382 ca. 60 times faster).
386 CHANGES IN APE VERSION 1.9-4
391 o A bug was fixed in edgelabels().
393 o as.phylo.hclust() did not work correctly when the object of
394 class "hclust" has its labels set to NULL: the returned tree has
395 now its tip labels set to "1", "2", ...
397 o consensus could fail if some tip labels are a subset of others
398 (e.g., "a" and "a_1"): this is now fixed.
400 o mlphylo() failed in most cases if some branch lengths of the
401 initial tree were greater than one: an error message is now
404 o mlphylo() failed in most cases when estimating the proportion of
405 invariants: this is fixed.
409 CHANGES IN APE VERSION 1.9-3
414 o The new function edgelabels adds labels on the edge of the tree
415 in the same way than nodelabels or tiplabels.
420 o multi2di() did not handle correctly branch lengths with the
421 default option `random = TRUE': this is now fixed.
423 o A bug was fixed in nuc.div() when using pairwise deletions.
425 o A bug occurred in the analysis of bipartitions with large
426 numbers of large trees, with consequences on prop.part,
427 prop.clades, and boot.phylo.
429 o The calculation of the Billera-Holmes-Vogtmann distance in
430 dist.topo was wrong: this has been fixed.
434 CHANGES IN APE VERSION 1.9-2
439 o The new function ladderize reorganizes the internal structure of
440 a tree to plot them left- or right-ladderized.
442 o The new function dist.nodes computes the patristic distances
443 between all nodes, internal and terminal, of a tree. It replaces
444 the option `full = TRUE' of cophenetic.phylo (see below).
449 o A bug was fixed in old2new.phylo().
451 o Some bugs were fixed in chronopl().
453 o The edge colours were not correctly displayed by plot.phylo
454 (thank you to Li-San Wang for the fix).
456 o cophenetic.phylo() failed with multichotomous trees: this is
462 o read.dna() now returns the sequences in a matrix if they are
463 aligned (interleaved or sequential format). Sequences in FASTA
464 format are still returned in a list.
466 o The option `full' of cophenetic.phylo() has been removed because
467 it could not be used from the generic.
472 o rotate() has been removed; this function did not work correctly
477 CHANGES IN APE VERSION 1.9-1
482 o Trees with a single tip were not read correctly in R as the
483 element `Nnode' was not set: this is fixed.
485 o unroot() did not set correctly the number of nodes of the
486 unrooted tree in most cases.
488 o read.GenBank() failed when fetching very long sequences,
489 particularly of the BX-series.
491 o A bug was introduced in read.tree() with ape 1.9: it has been
496 CHANGES IN APE VERSION 1.9
501 o There are two new print `methods' for trees of class "phylo" and
502 lists of trees of class "multi.tree", so that they are now
503 displayed in a compact and informative way.
505 o There are two new functions, old2new.phylo and new2old.phylo,
506 for converting between the old and new coding of the class
509 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
510 LogDet ("logdet"), and paralinear ("paralin").
512 o compute.brlen() has been extended: several methods are now
513 available to compute branch lengths.
515 o write.dna() can now handle matrices as well as lists.
520 o cophenetic.phylo() sometimes returned a wrong result with
521 multichotomous trees: this is fixed.
523 o rotate() failed when a single tip was specified: the tree is now
526 o ace() did not return the correct index matrix with custom
527 models: this is fixed.
529 o multi2di() did not work correctly when resolving multichotomies
530 randomly: the topology was always the same, only the arrangement
531 of clades was randomized: this is fixed. This function now
532 accepts trees with no branch lengths.
534 o The output of diversi.gof() was blurred by useless prints when a
535 user distribution was specified. This has been corrected, and
536 the help page of this function has been expanded.
541 o The internal structure of the class "phylo" has been changed:
542 see the document "Definition of Formats for Coding Phylogenetic
543 Trees in R" for the details. In addition, the code of most
544 functions has been improved.
546 o Several functions have been improved by replacing some R codes
547 by C codes: pic, plot.phylo, and reorder.phylo.
549 o There is now a citation information: see citation("ape") in R.
551 o write.tree() now does not add extra 0's to branch lengths so
552 that 1.23 is printed "1.23" by default, not "1.2300000000".
554 o The syntax of bind.tree() has been simplified. This function now
555 accepts trees with no branch lengths, and handles correctly node
558 o The option `as.numeric' of mrca() has been removed.
560 o The unused options `format' and `rooted' of read.tree() have
563 o The unused option `format' of write.tree() has been removed.
565 o The use of node.depth() has been simplified.
569 CHANGES IN APE VERSION 1.8-5
574 o Two new functions read.nexus.data() and write.nexus.data(),
575 contributed by Johan Nylander, allow to read and write molecular
576 sequences in NEXUS files.
578 o The new function reorder.phylo() reorders the internal structure
579 of a tree of class "phylo". It is used as the generic, e.g.,
582 o read.tree() and read.nexus() can now read trees with a single
585 o The new data set `cynipids' supplies a set of protein sequences
591 o The code of all.equal.phylo() has been completely rewritten
592 (thanks to Benoît Durand) which fixes several bugs.
594 o read.tree() and read.nexus() now checks the labels of the tree
595 to remove or substitute any characters that are illegal in the
596 Newick format (parentheses, etc.)
598 o A negative P-value could be returned by mantel.test(): this is
603 CHANGES IN APE VERSION 1.8-4
608 o The new function sh.test() computes the Shimodaira-
611 o The new function collapse.singles() removes the nodes with a
612 single descendant from a tree.
614 o plot.phylo() has a new argument `tip.color' to specify the
617 o mlphylo() has now an option `quiet' to control the display of
618 the progress of the analysis (the default is FALSE).
623 o read.dna() did not read correctly sequences in sequential format
624 with leading alignment gaps "-": this is fixed.
626 o ace() returned a list with no class so that the generic
627 functions (anova, logLik, ...) could not be used directly. This
628 is fixed as ace() now returns an object of class "ace".
630 o anova.ace() had a small bug when computing the number of degrees
631 of freedom: this is fixed.
633 o mlphylo() did not work when the sequences were in a matrix or
634 a data frame: this is fixed.
636 o rtree() did not work correctly when trying to simulate an
637 unrooted tree with two tips: an error message is now issued.
642 o The algorithm of rtree() has been changed: it is now about 40,
643 100, and 130 times faster for 10, 100, and 1000 tips,
648 CHANGES IN APE VERSION 1.8-3
653 o There are four new `method' functions to be used with the
654 results of ace(): logLik(), deviance(), AIC(), and anova().
656 o The plot method of phymltest has two new arguments: `main' to
657 change the title, and `col' to control the colour of the
658 segments showing the AIC values.
660 o ace() has a new argument `ip' that gives the initial values used
661 in the ML estimation with discrete characters (see the examples
662 in ?ace). This function now returns a matrix giving the indices
663 of the estimated rates when analysing discrete characters.
665 o nodelabels() and tiplabels() have a new argument `pie' to
666 represent proportions, with any number of categories, as
667 piecharts. The use of the option `thermo' has been improved:
668 there is now no limitation on the number of categories.
673 o mlphylo() did not work with more than two partitions: this is
676 o root() failed if the proposed outgroup was already an outgroup
677 in the tree: this is fixed.
679 o The `col' argument in nodelabels() and tiplabels() was not
680 correctly passed when `text' was used: this is fixed.
682 o Two bugs were fixed in mlphylo(): parameters were not always
683 correctly output, and the estimation failed in some cases.
685 o plot.phylo() was stuck when given a tree with a single tip: this
686 is fixed and a message error is now returned.
688 o An error was corrected in the help page of gammaStat regarding
689 the calculation of P-values.
691 o Using gls() could crash R when the number of species in the tree
692 and in the variables were different: this is fixed.
696 CHANGES IN APE VERSION 1.8-2
701 o The new function mlphylo() fits a phylogenetic tree by maximum
702 likelihood from DNA sequences. Its companion function DNAmodel()
703 is used to define the substitution model which may include
704 partitioning. There are methods for logLik(), deviance(), and
705 AIC(), and the summary() method has been extended to display in
706 a friendly way the results of this model fitting. Currently, the
707 functionality is limited to estimating the substitution and
708 associated parameters and computing the likelihood.
710 o The new function drop1.compar.gee (used as, e.g., drop1(m))
711 tests for single effects in GEE-based comparative method. A
712 warning message is printed if there is not enough degrees of
718 o An error message was sometimes issued by plot.multi.tree(),
719 though with no consequence.
723 CHANGES IN APE VERSION 1.8-1
728 o There is a new plot method for lists of trees (objects of class
729 "multi.tree"): it calls plot.phylo() internally and is
730 documented on the same help page.
735 o A bug was fixed in the C code that analyzes bipartitions: this
736 has impact on several functions like prop.part, prop.clades,
737 boot.phylo, or consensus.
739 o root() did not work correctly when the specified outgroup had
740 more than one element: this is fixed.
742 o dist.dna() sometimes returned a warning inappropriately: this
745 o If the distance object given to nj() had no rownames, nj()
746 returned a tree with no tip labels: it now returns tips labelled
747 "1", "2", ..., corresponding to the row numbers.
752 o nj() has been slightly changed so that tips with a zero distance
753 are first aggregated with zero-lengthed branches; the usual NJ
754 procedure is then performed on a distance matrix without 0's.
758 CHANGES IN APE VERSION 1.8
763 o The new function chronopl() estimates dates using the penalized
764 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
766 o The new function consensus() calculates the consensus tree of a
769 o The new function evolve.phylo() simulates the evolution of
770 continuous characters along a phylogeny under a Brownian model.
772 o The new plot method for objects of class "ancestral" displays a
773 tree together with ancestral values, as returned by the above
776 o The new function as.phylo.formula() returns a phylogeny from a
777 set of nested taxonomic variables given as a formula.
779 o The new function read.caic() reads trees in CAIC format.
781 o The new function tiplabels() allows to add labels to the tips
782 of a tree using text or plotting symbols in a flexible way.
784 o The new function unroot() unroots a phylogeny.
786 o multi2di() has a new option, `random', which specifies whether
787 to resolve the multichotomies randomly (the default) or not.
789 o prop.part() now returns an object of class "prop.part" for which
790 there are print (to display a partition in a more friendly way)
791 and summary (to extract the numbers) methods.
793 o plot.phylo() has a new option, `show.tip.label', specifying
794 whether to print the labels of the tips. The default is TRUE.
796 o The code of nj() has been replaced by a faster C code: it is now
797 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
800 o write.nexus() now writes whether a tree is rooted or not.
805 o Two bugs have been fixed in root(): unrooted trees are now
806 handled corretly, and node labels are now output normally.
808 o A bug was fixed in phymltest(): the executable couldn't be found
811 o Three bug have been fixed in ace(): computing the likelihood of
812 ancestral states of discrete characters failed, custom models
813 did not work, and the function failed with a null gradient (a
814 warning message is now returned; this latter bug was also
815 present in yule.cov() as well and is now fixed).
817 o pic() hanged out when missing data were present: a message error
820 o A small bug was fixed in dist.dna() where the gamma correction
821 was not always correctly dispatched.
823 o plot.phylo() plotted correctly the root edge only when the tree
824 was plotted rightwards: this works now for all directions.
829 o dist.taxo() has been renamed as weight.taxo().
831 o Various error and warning messages have been improved.
835 CHANGES IN APE VERSION 1.7
838 o The new function ace() estimates ancestral character states for
839 continuous characters (with ML, GLS, and contrasts methods), and
840 discrete characters (with ML only) for any number of states.
842 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
843 of directional evolution for continuous characters. The user
844 specifies the node(s) of the tree where the character optimum
847 o The new function is.rooted() tests whether a tree (of class
850 o The new function rcoal() generates random ultrametric trees with
851 the possibility to specify the function that generates the
852 inter-nodes distances.
854 o The new function mrca() gives for all pairs of tips in a tree
855 (and optionally nodes too) the most recent common ancestor.
857 o nodelabels() has a new option `thermo' to plot proportions (up
858 to three classes) on the nodes of a tree.
860 o rtree() has been improved: it can now generate rooted or
861 unrooted trees, and the mathematical function that generates the
862 branch lengths may be specified by the user. The tip labels may
863 be given directly in the call to rtree. The limit cases (n = 2,
864 3) are now handled correctly.
866 o dist.topo() has a new argument `method' with two choices: "PH85"
867 for Penny and Henny's method (already available before and now
868 the default), and "BHV01" for the geometric distance by Billera
869 et al. (2001, Adv. Appl. Math. 27:733).
871 o write.tree() has a new option, `digits', which specifies the
872 number of digits to be printed in the Newick tree. By default
873 digits = 10. The numbers are now always printed in decimal form
874 (i.e., 1.0e-1 is now avoided).
876 o dist.dna() can now compute the raw distances between pairs of
877 DNA sequences by specifying model = "raw".
879 o dist.phylo() has a new option `full' to possibly compute the
880 distances among all tips and nodes of the tree. The default if
886 o Several bugs were fixed in all.equal.phylo().
888 o dist.dna() did not handle correctly gaps ("-") in alignments:
889 they are now considered as missing data.
891 o rotate() did not work if the tips were not ordered: this is
894 o mantel.test() returned NA in some special cases: this is fixed
895 and the function has been improved and is now faster.
897 o A bug was fixed in diversi.gof() where the calculation of A² was
900 o cherry() did not work correctly under some OSs (mainly Linux):
903 o is.binary.tree() has been modified so that it works with both
904 rooted and unrooted trees.
906 o The documentation of theta.s() was not correct: this has been
909 o plot.mst() did not work correctly: this is fixed.
913 CHANGES IN APE VERSION 1.6
918 o The new function dist.topo() computes the topological distances
921 o The new function boot.phylo() performs a bootstrap analysis on
922 phylogeny estimation.
924 o The new functions prop.part() and prop.clades() analyse
925 bipartitions from a series of trees.
930 o read.GenBank() now uses the EFetch utility of NCBI instead of
931 the usual Web interface: it is now much faster (e.g., 12 times
932 faster to retrieve 8 sequences, 37 times for 60 sequences).
937 o Several bugs were fixed in read.dna().
939 o Several bugs were fixed in diversi.time().
941 o is.binary.tree() did not work correctly if the tree has no edge
942 lengths: this is fixed.
944 o drop.tip() did not correctly propagated the `node.label' of a
949 CHANGES IN APE VERSION 1.5
954 o Two new functions, as.matching.phylo() and as.phylo.matching(),
955 convert objects between the classes "phylo" and "matching". The
956 latter implements the representation of binary trees introduced by
957 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
958 as.matching() has been introduced as well.
960 o Two new functions, multi2di() and di2multi(), allow to resolve
961 and collapse multichotomies with branches of length zero.
963 o The new function nuc.div() computes the nucleotide diversity
964 from a sample a DNA sequences.
966 o dist.dna() has been completely rewritten with a much faster
967 (particularly for large data sets) C code. Eight models are
968 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
969 option `method' has been renamed `model'). Computation of variance
970 is available for all models. A gamma-correction is possible for
971 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
972 to remove sites with missing data on a pairwise basis. The option
973 `GCcontent' has been removed.
975 o read.GenBank() has a new option (species.names) which specifies
976 whether to return the species names of the organisms in addition
977 to the accession numbers of the sequences (this is the default
980 o write.nexus() can now write several trees in the same NEXUS file.
982 o drop.tip() has a new option `root.edge' that allows to specify the
983 new root edge if internal branches are trimmed.
988 o as.phylo.hclust() failed if some labels had parentheses: this
991 o Several bugs were fixed in all.equal.phylo(). This function now
992 returns the logical TRUE if the trees are identical but with
993 different representations (a report was printed previously).
995 o read.GenBank() did not correctly handle ambiguous base codes:
1001 o birthdeath() now returns an object of class "birthdeath" for
1002 which there is a print method.
1006 CHANGES IN APE VERSION 1.4
1011 o The new function nj() performs phylogeny estimation with the
1012 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1015 o The new function which.edge() identifies the edges of a tree
1016 that belong to a group specified as a set of tips.
1018 o The new function as.phylo.phylog() converts an object of class
1019 "phylog" (from the package ade4) into an object of class
1022 o The new function axisPhylo() draws axes on the side of a
1025 o The new function howmanytrees() calculates the number of trees
1026 in different cases and giving a number of tips.
1028 o write.tree() has a new option `multi.line' (TRUE by default) to
1029 write a Newick tree on several lines rather than on a single
1032 o The functionalities of zoom() have been extended. Several
1033 subtrees can be visualized at the same time, and they are marked
1034 on the main tree with colors. The context of the subtrees can be
1035 marked with the option `subtree' (see below).
1037 o drop.tip() has a new option `subtree' (FALSE by default) which
1038 specifies whether to output in the tree how many tips have been
1041 o The arguments of add.scale.bar() have been redefined and have
1042 now default values (see ?add.scale.bar for details). This
1043 function now works even if the plotted tree has no edge length.
1045 o plot.phylo() can now plot radial trees, but this does not take
1046 edge lengths into account.
1048 o In plot.phylo() with `type = "phylogram"', if the values of
1049 `edge.color' and `edge.width' are identical for sister-branches,
1050 they are propagated to the vertical line that link them.
1055 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1056 crashing. This is fixed.
1058 o In plot.phylo(), the options `edge.color' and `edge.width' are
1059 now properly recycled; their default values are now "black" and
1062 o A bug has been fixed in write.nexus().
1067 o The function node.depth.edgelength() has been removed and
1068 replaced by a C code.
1072 CHANGES IN APE VERSION 1.3-1
1077 o The new function nodelabels() allows to add labels to the nodes
1078 of a tree using text or plotting symbols in a flexible way.
1080 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1081 numeric values specifying the lower and upper limits on the x-
1082 and y-axes. This allows to leave some space on any side of the
1083 tree. If a single value is given, this is taken as the upper
1088 CHANGES IN APE VERSION 1.3
1093 o The new function phymltest() calls the software PHYML and fits
1094 28 models of DNA sequence evolution. There are a print method to
1095 display likelihood and AIC values, a summary method to compute
1096 the hierarchical likelihood ratio tests, and a plot method to
1097 display graphically the AIC values of each model.
1099 o The new function yule.cov() fits the Yule model with covariates,
1100 a model where the speciation rate is affected by several species
1101 traits through a generalized linear model. The parameters are
1102 estimated by maximum likelihood.
1104 o Three new functions, corBrownian(), corGrafen(), and
1105 corMartins(), compute the expected correlation structures among
1106 species given a phylogeny under different models of evolution.
1107 These can be used for GLS comparative phylogenetic methods (see
1108 the examples). There are coef() and corMatrix() methods and an
1109 Initialize.corPhyl() function associated.
1111 o The new function compar.cheverud() implements Cheverud et al.'s
1112 (1985; Evolution 39:1335) phylogenetic comparative method.
1114 o The new function varcomp() estimates variance components; it has
1117 o Two new functions, panel.superpose.correlogram() and
1118 plot.correlogramList(), allow to plot several phylogenetic
1121 o The new function node.leafnumber() computes the number of leaves
1122 of a subtree defined by a particular node.
1124 o The new function node.sons() gets all tags of son nodes from a
1127 o The new function compute.brlen() computes the branch lengths of
1128 a tree according to a specified method.
1130 o plot.phylo() has three new options: "cex" controls the size of
1131 the (tip and node) labels (thus it is no more needed to change
1132 the global graphical parameter), "direction" which allows to
1133 plot the tree rightwards, leftwards, upwards, or downwards, and
1134 "y.lim" which sets the upper limit on the y-axis.
1139 o Some functions which try to match tip labels and names of
1140 additional data (e.g. vector) are likely to fail if there are
1141 typing or syntax errors. If both series of names do not perfectly
1142 match, they are ignored and a warning message is now issued.
1143 These functions are bd.ext, compar.gee, pic. Their help pages
1144 have been clarified on this point.
1148 CHANGES IN APE VERSION 1.2-7
1153 o The new function root() reroots a phylogenetic tree with respect
1154 to a specified outgroup.
1156 o The new function rotate() rotates an internal branch of a tree.
1158 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1159 trees) controls the display of the tip labels in unrooted trees.
1160 This display has been greatly improved: the tip labels are now not
1161 expected to overlap with the tree (particularly if lab4ut =
1162 "axial"). In all cases, combining appropriate values of "lab4ut"
1163 and the font size (via "par(cex = )") should result in readable
1164 unrooted trees. See ?plot.phylo for some examples.
1166 o In drop.tip(), the argument `tip' can now be numeric or character.
1171 o drop.tip() did not work correctly with trees with no branch
1172 lengths: this is fixed.
1174 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1175 plotted with some line crossings: this is now fixed.
1179 CHANGES IN APE VERSION 1.2-6
1184 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1185 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1186 to implement comparative methods with an autocorrelation approach.
1188 o A new data set describing some life history traits of Carnivores
1194 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1199 o When plotting a tree with plot.phylo(), the new default of the
1200 option `label.offset' is now 0, so the labels are always visible.
1204 CHANGES IN APE VERSION 1.2-5
1209 o The new function bd.ext() fits a birth-death model with combined
1210 phylogenetic and taxonomic data, and estimates the corresponding
1211 speciation and extinction rates.
1216 o The package gee is no more required by ape but only suggested
1217 since only the function compar.gee() calls gee.
1221 CHANGES IN APE VERSION 1.2-4
1226 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1227 and lines.popsize) implementing a new approach for inferring the
1228 demographic history from genealogies using a reversible jump
1229 MCMC have been introduced.
1231 o The unit of time in the skyline plot and in the new plots can
1232 now be chosen to be actual years, rather than substitutions.
1236 CHANGES IN APE VERSION 1.2-3
1241 o The new function rtree() generates a random binary tree with or
1242 without branch lengths.
1244 o Two new functions for drawing lineages-through-time (LTT) plots
1245 are provided: ltt.lines() adds a LTT curve to an existing plot,
1246 and mltt.plot() does a multiple LTT plot giving several trees as
1247 arguments (see `?ltt.plot' for details).
1252 o Some taxon names made R crashing when calling as.phylo.hclust():
1255 o dist.dna() returned an error with two identical DNA sequences
1256 (only using the Jukes-Cantor method returned 0): this is fixed.
1261 o The function dist.phylo() has been re-written using a different
1262 algorithm: it is now about four times faster.
1264 o The code of branching.times() has been improved: it is now about
1269 CHANGES IN APE VERSION 1.2-2
1274 o The new function seg.sites() finds the segregating sites in a
1275 sample of DNA sequences.
1280 o A bug introduced in read.tree() and in read.nexus() with version
1283 o A few errors were corrected and a few examples were added in the
1288 CHANGES IN APE VERSION 1.2-1
1293 o plot.phylo() can now draw the edge of the root of a tree if it
1294 has one (see the new option `root.edge', its default is FALSE).
1299 o A bug was fixed in read.nexus(): files with semicolons inside
1300 comment blocks were not read correctly.
1302 o The behaviour of read.tree() and read.nexus() was corrected so
1303 that tree files with badly represented root edges (e.g., with
1304 an extra pair of parentheses, see the help pages for details)
1305 are now correctly represented in the object of class "phylo";
1306 a warning message is now issued.
1310 CHANGES IN APE VERSION 1.2
1315 o plot.phylo() has been completely re-written and offers several
1316 new functionalities. Three types of trees can now be drawn:
1317 phylogram (as previously), cladogram, and unrooted tree; in
1318 all three types the branch lengths can be drawn using the edge
1319 lengths of the phylogeny or not (e.g., if the latter is absent).
1320 The vertical position of the nodes can be adjusted with two
1321 choices (see option `node.pos'). The code has been re-structured,
1322 and two new functions (potentially useful for developpers) are
1323 documented separately: node.depth.edgelength() and node.depth();
1324 see the respective help pages for details.
1326 o The new function zoom() allows to explore very large trees by
1327 focusing on a small portion of it.
1329 o The new function yule() fits by maximum likelihood the Yule model
1330 (birth-only process) to a phylogenetic tree.
1332 o Support for writing DNA sequences in FASTA format has been
1333 introduced in write.dna() (support for reading sequences in
1334 this format was introduced in read.dna() in version 1.1-2).
1335 The function has been completely re-written, fixing some bugs
1336 (see below); the default behaviour is no more to display the
1337 sequences on the standard output. Several options have been
1338 introduced to control the sequence printing in a flexible
1339 way. The help page has been extended.
1341 o A new data set is included: a supertree of bats in NEXUS format.
1346 o In theta.s(), the default of the option `variance' has
1347 been changed to `FALSE' (as was indicated in the help page).
1349 o Several bugs were fixed in the code of all.equal.phylo().
1351 o Several bugs were fixed in write.dna(), particularly this
1352 function did not work with `format = "interleaved"'.
1354 o Various errors were corrected in the help pages.
1359 o The argument names of as.hclust.phylo() have been changed
1360 from "(phy)" to "(x, ...)" to conform to the definition of
1361 the corresponding generic function.
1363 o gamma.stat() has been renamed gammaStat() to avoid confusion
1364 since gamma() is a generic function.
1368 CHANGES IN APE VERSION 1.1-3
1373 o base.freq() previously did not return a value of 0 for
1374 bases absent in the data (e.g., a vector of length 3 was
1375 returned if one base was absent). This is now fixed (a
1376 vector of length 4 is always returned).
1378 o Several bugs were fixed in read.nexus(), including that this
1379 function did not work in this absence of a "TRANSLATE"
1380 command in the NEXUS file, and that the commands were
1385 CHANGES IN APE VERSION 1.1-2
1390 o The Tamura and Nei (1993) model of DNA distance is now implemented
1391 in dist.dna(): five models are now available in this function.
1393 o A new data set is included: a set of 15 sequences of the
1394 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1400 o A bug in read.nexus() was fixed.
1402 o read.dna() previously did not work correctly in most cases.
1403 The function has been completely re-written and its help page
1404 has been considerably extended (see ?read.dna for details).
1405 Underscores (_) in taxon names are no more replaced with
1406 spaces (this behaviour was undocumented).
1408 o A bug was fixed in write.dna().
1412 CHANGES IN APE VERSION 1.1-1
1417 o A bug in read.tree() introduced in APE 1.1 was fixed.
1419 o A bug in compar.gee() resulted in an error when trying to fit
1420 a model with `family = "binomial"'. This is now fixed.
1424 CHANGES IN APE VERSION 1.1
1429 o The Klastorin (1982) method as suggested by Misawa and Tajima
1430 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1431 on the basis of phylogenetic trees has been implemented (see
1432 the function klastorin()).
1434 o Functions have been added to convert APE's "phylo" objects in
1435 "hclust" cluster objects and vice versa (see the help page of
1436 as.phylo for details).
1438 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1439 are introduced for the estimation of absolute evolutionary rates
1440 (ratogram) and dated clock-like trees (chronogram) from
1441 phylogenetic trees using the non-parametric rate smoothing approach
1442 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1444 o A summary method is now provided printing a summary information on a
1445 phylogenetic tree with, for instance, `summary(tree)'.
1447 o The behaviour of read.tree() was changed so that all spaces and
1448 tabulations in tree files are now ignored. Consequently, spaces in tip
1449 labels are no more allowed. Another side effect is that read.nexus()
1450 now does not replace the underscores (_) in tip labels with spaces
1451 (this behaviour was undocumented).
1453 o The function plot.phylo() has a new option (`underscore') which
1454 specifies whether the underscores in tip labels should be written on
1455 the plot as such or replaced with spaces (the default).
1457 o The function birthdeath() now computes 95% confidence intervals of
1458 the estimated parameters using profile likelihood.
1460 o Three new data sets are included: a gene tree estimated from 36
1461 landplant rbcL sequences, a gene tree estimated from 32 opsin
1462 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1467 o A bug was fixed in dist.gene() where nothing was returned.
1469 o A bug in plot.mst() was fixed.
1471 o A bug in vcv.phylo() resulted in false correlations when the
1472 option `cor = TRUE' was used (now fixed).
1476 CHANGES IN APE VERSION 1.0
1481 o Two new functions, read.dna() and write.dna(), read/write in a file
1482 DNA sequences in interleaved or in sequential format.
1484 o Two new functions, read.nexus() and write.nexus(), read/write trees
1487 o The new function bind.tree() allows to bind two trees together,
1488 possibly handling root edges to give internal branches.
1490 o The new function drop.tip() removes the tips in a phylogenetic tree,
1491 and trims (or not) the corresponding internal branches.
1493 o The new function is.ultrametric() tests if a tree is ultrametric.
1495 o The function plot.phylo() has more functionalities such as drawing the
1496 branches with different colours and/or different widths, showing the
1497 node labels, controling the position and font of the labels, rotating
1498 the labels, and controling the space around the plot.
1500 o The function read.tree() can now read trees with no branch length,
1501 such as "(a,b),c);". Consequently, the element `edge.length' in
1502 objects of class "phylo" is now optional.
1504 o The function write.tree() has a new default behaviour: if the default
1505 for the option `file' is used (i.e. file = ""), then a variable of
1506 mode character containing the tree in Newick format is returned which
1507 can thus be assigned (e.g., tree <- write.tree(phy)).
1509 o The function read.tree() has a new argument `text' which allows
1510 to read the tree in a variable of mode character.
1512 o A new data set is included: the phylogenetic relationships among
1513 the orders of birds from Sibley and Ahlquist (1990).
1517 CHANGES IN APE VERSION 0.2-1
1522 o Several bugs were fixed in the help pages.
1526 CHANGES IN APE VERSION 0.2
1531 o The function write.tree() writes phylogenetic trees (objects of class
1532 "phylo") in an ASCII file using the Newick parenthetic format.
1534 o The function birthdeath() fits a birth-death model to branching times
1535 by maximum likelihood, and estimates the corresponding speciation and
1538 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1541 o The function is.binary.tree() tests whether a phylogeny is binary.
1543 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1544 as well as some methods are introduced.
1546 o Several functions, including some generics and methods, for computing
1547 skyline plot estimates (classic and generalized) of effective
1548 population size through time are introduced and replace the function
1549 skyline.plot() in version 0.1.
1551 o Two data sets are now included: the phylogenetic relationships among
1552 the families of birds from Sibley and Ahlquist (1990), and an
1553 estimated clock-like phylogeny of HIV sequences sampled in the
1554 Democratic Republic of Congo.
1557 DEPRECATED & DEFUNCT
1559 o The function skyline.plot() in ape 0.1 has been deprecated and
1560 replaced by more elaborate functions (see above).
1565 o Two important bugs were fixed in plot.phylo(): phylogenies with
1566 multichotomies not at the root or not with only terminal branches,
1567 and phylogenies with a single node (i.e. only terminal branches)
1568 did not plot. These trees should be plotted correctly now.
1570 o Several bugs were fixed in diversi.time() in the computation of
1573 o Various errors were corrected in the help pages.
projects / ape.git / blob