1 CHANGES IN APE VERSION 2.6-1
6 o The new speciesTree calculates the species tree from a set of gene
7 trees. Several methods are available including maximum tree and
8 shallowest divergence tree.
13 o A bug introduced in write.tree() with ape 2.6 has been fixed.
15 o as.list.DNAbin() did not work correctly with vectors.
17 o as.hclust.phylo() failed with trees with node labels (thanks to
18 Filipe Vieira for the fix).
22 CHANGES IN APE VERSION 2.6
27 o The new functions rlineage and rbdtree simulate phylogenies under
28 any user-defined time-dependent speciation-extinction model. They
29 use continuous time algorithms.
31 o The new function drop.fossil removes the extinct species from a
34 o The new function bd.time fits a user-defined time-dependent
35 birth-death model. It is a generalization of yule.time() taking
36 extinction into account.
38 o The new function MPR does most parsimonious reconstruction of
41 o The new function Ftab computes the contingency table of base
42 frequencies from a pair of sequences.
44 o There is now an 'as.list' method for the class "DNAbin".
46 o dist.dna() can compute the number of transitions or transversions
47 with the option model = "Ts" or model = "Tv", respectively.
49 o [node|tip|edge]labels() gain three options with default values to
50 control the aspect of thermometers: horiz = TRUE, width = NULL,
53 o compar.gee() has been improved with the new option 'corStruct' as an
54 alternative to 'phy' to specify the correlation structure, and
55 calculation of the QIC (Pan 2001, Biometrics). The display of the
56 results has also been improved.
58 o read.GenBank() has a new option 'gene.names' to return the name of
59 the gene (FALSE by default).
64 o extract.clade() sometimes shuffled the tip labels.
66 o plot.phylo(type = "unrooted") did not force asp = 1 (thanks to Klaus
69 o dist.dna(model = "logdet") used to divide distances by 4. The
70 documentation has been clarified on the formulae used.
75 o rTraitCont(model = "OU") has an option 'linear = TRUE' to possibly
76 change the parameterisation (see ?rTraitCont for details).
78 o pic() now returns a vector with the node labels of the tree (if
81 o write.tree() and read.tree() have been substantially improved thanks
82 to contributions by Klaus Schliep.
86 CHANGES IN APE VERSION 2.5-3
91 o The new function mixedFontLabel helps to make labels with bits of
92 text to be plotted in different fonts.
94 o There are now replacement operators for [, [[, and $ for the class
95 "multiPhylo" (i.e., TREES[11:20] <- rmtree(10, 100)). They possibly
96 check that the tip labels are the same in all trees.
98 o Objects of class "multiPhylo" can be built with c(): there are
99 methods for the classes "phylo" and "multiPhylo".
101 o The internal functions .compressTipLabel and .uncompressTipLabel are
107 o bind.tree(x, y, where, position = 0) did not work correctly if 'y'
108 was a single-edge tree and 'where' was a tip.
110 o rTraitCont() did not use the square-root of branch lengths when
111 simulating a Brownian motion model.
115 CHANGES IN APE VERSION 2.5-2
120 o There is now a print method for results from ace().
122 o There is a labels() method for objects of class "DNAbin".
124 o read.dna() has a new option 'as.matrix' to possibly force sequences
125 in a FASTA file to be stored in a matrix (see ?read.dna for details).
130 o as.phylo.hclust() used to multiply edge lengths by 2.
132 o A minor bug was fixed in rTraitDisc().
134 o ace() sometimes failed (parameter value was NaN and the optimisation
140 o evolve.phylo() and plot.ancestral() have been removed.
142 o chronogram(), ratogram(), and NPRS.criterion() have been removed.
147 o nj() has been improved and is now about 30% faster.
149 o The default option 'drop' of [.DNAbin has been changed to FALSE to
150 avoid dropping rownames when selecting a single sequence.
152 o print.DNAbin() has been changed to summary.DNAbin() which has been
157 CHANGES IN APE VERSION 2.5-1
162 o The new function stree generates trees with regular shapes.
164 o It is now possible to bind two trees with x + y (see ?bind.tree for
167 o drop.tip(), extract.clade(), root(), and bind.tree() now have an
168 'interactive' option to make the operation on a plotted tree.
170 o cophyloplot() gains two new arguments 'lwd' and 'lty' for the
171 association links; they are recycled like 'col' (which wasn't before).
176 o rTraitDisc() did not use its 'freq' argument correctly (it was
177 multiplied with the rate matrix column-wise instead of row-wise).
179 o [node|tip|edge]labels(thermo = ) used to draw empty thermometers
180 with NA values. Nothing is drawn now like with 'text' or 'pch'.
181 The same bug occurred with the 'pie' option.
183 o A bug was fixed in compar.ou() and the help page was clarified.
185 o bind.tree() has been rewritten fixing several bugs and making it
188 o plot.phylo(type = "p") sometimes failed to colour correctly the
189 vertical lines representing the nodes.
191 o plot.phylo(direction = "l", x.lim = 30) failed to plot the branches
192 in the correct direction though the tip labels were displayed
198 o The c, cbind, and rbind methods for "DNAbin" objetcs now check that
199 the sequences are correctly stored (in a list for c, in a matrix
200 for the two other functions).
204 CHANGES IN APE VERSION 2.5
209 o The new function parafit by Pierre Legendre tests for the
210 coevolution between hosts and parasites. It has a companion
211 function, pcoa, that does principal coordinate decomposition.
212 The latter has a biplot method.
214 o The new function lmorigin by Pierre Legendre performs multiple
215 regression through the origin with testing by permutation.
217 o The new functions rTraitCont and rTraitDisc simulate continuous and
218 discrete traits under a wide range of evolutionary models.
220 o The new function delta.plot does a delta plot following Holland et
221 al. (2002, Mol. Biol. Evol. 12:2051).
223 o The new function edges draws additional branches between any nodes
224 and/or tips on a plotted tree.
226 o The new function fancyarrows enhances arrows from graphics with
227 triangle and harpoon heads; it can be called from edges().
229 o add.scale.bar() has a new option 'ask' to draw interactively.
231 o The branch length score replaces the geodesic distance in dist.topo.
233 o Three new data sets are included: the gopher-lice data (gopher.D),
234 SO2 air pollution in 41 US cities (lmorigin.ex1, from Sokal &
235 Rohlf 1995), and some host-parasite specificity data
236 (lmorigin.ex2, from Legendre & Desdevises 2009).
241 o add.scale.bar() drew the bar outside the plotting region with the
242 default options with unrooted or radial trees.
244 o dist.topo() made R stuck when the trees had different sizes (thanks
245 to Otto Cordero for the fix).
250 o The geodesic distance has been replaced by the branch length score
255 CHANGES IN APE VERSION 2.4-1
260 o rtree() and rcoal() now accept a numeric vector for the 'br'
263 o vcv() is a new generic function with methods for the classes "phylo"
264 and "corPhyl" so that it is possible to calculate the var-cov matrix
265 for "transformation models". vcv.phylo() can still be used for trees
266 of class "phylo"; its argument 'cor' has been renamed 'corr'.
271 o bind.tree() failed when 'y' had no root edge.
273 o read.nexus() shuffled tip labels when the trees have no branch
274 lengths and there is a TRANSLATE block.
276 o read.nexus() does not try to translate node labels if there is a
277 translation table in the NEXUS file. See ?read.nexus for a
278 clarification on this behaviour.
280 o plot.multiPhylo() crashed R when plotting a list of trees with
281 compressed tip labels.
283 o write.nexus() did not translate the taxa names when asked for.
285 o plot.phylo(type = "fan") did not rotate the tip labels correctly
286 when the tree has branch lengths.
288 o ace(type = "continuous", method = "ML") now avoids sigma² being
289 negative (which resulted in an error).
291 o nj() crashed with NA/NaN in the distance matrix: an error in now
296 CHANGES IN APE VERSION 2.4
301 o base.freq() has a new option 'freq' to return the counts; the
302 default is still to return the proportions.
307 o seg.sites() did not handle ambiguous nucleotides correctly: they
310 o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
311 the tree: the argument is now ignored.
313 o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
319 o Trying to plot a tree with a single tip now returns NULL with a
320 warning (it returned an error previously).
322 o The way lines representing nodes are coloured in phylograms has
323 been modified (as well as their widths and types) following some
324 users' request; this is only for dichotomous nodes.
326 o The argument 'adj' in [node][tip][edge]labels() now works when
327 using 'pie' or 'thermo'.
329 o A more informative message error is now returned by dist.dna() when
330 'model' is badly specified (partial matching of this argument is
333 o Deprecated functions are now listed in a help page: see
334 help("ape-defunct") with the quotes.
339 o The functions heterozygosity, nuc.div, theta.h, theta.k and
340 theta.s have been moved from ape to pegas.
342 o The functions mlphylo, DNAmodel and sh.test have been removed.
346 CHANGES IN APE VERSION 2.3-3
351 o add.scale.bar() always drew a horizontal bar.
353 o zoom() shuffled tips with unrooted trees.
355 o write.nexus() failed to write correctly trees with a "TipLabel"
358 o rcoal() failed to compute branch lengths with very large n.
360 o A small bug was fixed in compar.cheverud() (thanks to Michael
363 o seg.sites() failed when passing a vector.
365 o drop.tip() sometimes shuffled tip labels.
367 o root() shuffled node labels with 'resolve.root = TRUE'.
371 CHANGES IN APE VERSION 2.3-2
376 o all.equal.phylo() did not compare unrooted trees correctly.
378 o dist.topo(... method = "PH85") did not treat unrooted trees
379 correctly (thanks to Tim Wallstrom for the fix).
381 o root() sometimes failed to test for the monophyly of the
384 o extract.clade() sometimes included too many edges.
386 o vcv.phylo() did not work correctly when the tree is in
389 o nj() did not handle correctly distance matrices with many 0's.
390 The code has also been significantly improved: 7, 70, 160 times
391 faster with n = 100, 500, 1000, respectively.
395 CHANGES IN APE VERSION 2.3-1
400 o The new function is.monophyletic tests the monophyly of a group.
402 o There is now a c() method for lists of class "DNAbin".
404 o yule.cov() now fits the null model, and its help page has been
405 corrected with respect to this change.
407 o drop.tip() has a new option 'rooted' to force (or not) a tree
408 to be treated as (un)rooted.
413 o dist.gene() failed on most occasions with the default
414 pairwise.deletion = FALSE.
416 o read.tree() failed to read correctly the tree name(s).
418 o boot.phylo() now treats correctly data frames.
420 o del.gaps() did not copy the rownames of a matrix.
422 o A small bug was fixed in CDAM.global().
424 o ace() failed with large data sets. Thanks to Rich FitzJohn for
425 the fix. With other improvements, this function is now about 6
428 o write.tree() failed with objects of class "multiPhylo".
430 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
435 o [.multiPhylo and [.DNAbin now respect the original class.
437 o Instances of the form class(phy) == "phylo" have been replaced
438 by inherits(phy, "phylo").
440 o rcoal() is now faster.
445 o klastorin() has been removed.
449 CHANGES IN APE VERSION 2.3
454 o The new functions CADM.global and CADM.post, contributed by
455 Pierre Legendre, test the congruence among several distance
458 o The new function yule.time fits a user-defined time-dependent
459 Yule model by maximum likelihood.
461 o The new function makeNodeLabel creates and/or modifies node
462 labels in a flexible way.
464 o read.tree() and write.tree() have been modified so that they can
465 handle individual tree names.
467 o plot.phylo() has a new argument 'edge.lty' that specifies the
468 types of lines used for the edges (plain, dotted, dashed, ...)
470 o phymltest() has been updated to work with PhyML 3.0.1.
475 o drop.tip() shuffled tip labels in some cases.
477 o drop.tip() did not handle node.label correctly.
479 o is.ultrametric() now checks the ordering of the edge matrix.
481 o ace() sometimes returned negative values of likelihoods of
482 ancestral states (thanks to Dan Rabosky for solving this long
488 o The data set xenarthra has been removed.
492 CHANGES IN APE VERSION 2.2-4
496 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
497 now fixed. (Thanks to Peter Wragg for the fix!)
499 o A warning message occurred for no reason with ace(method="GLS").
504 o There is now a general help page displayed with '?ape'.
508 CHANGES IN APE VERSION 2.2-3
513 o The new function extract.clade extracts a clade from a tree by
514 specifying a node number or label.
516 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
517 operations of the same names.
519 o dist.dna() can now return the number of site differences by
520 specifying model="N".
525 o chronopl() did not work with CV = TRUE.
527 o read.nexus() did not work correctly in some situations (trees on
528 multiple lines with different numbers of lines and/or with
529 comments inserted within the trees).
531 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
532 the number of lineages with non-binary trees.
537 o ape has now a namespace.
539 o drop.tip() has been improved: it should be much faster and work
540 better in some cases (e.g., see the example in ?zoom).
544 CHANGES IN APE VERSION 2.2-2
549 o dist.gene() has been substantially improved and gains an option
552 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
558 o prop.part() failed with a single tree with the default option
559 'check.labels = TRUE'.
561 o summary.DNAbin() failed to display correctly the summary of
562 sequence lengths with lists of sequences of 10,000 bases or more
563 (because summary.default uses 4 significant digits by default).
565 o read.nexus() failed to read a file with a single tree with line
566 breaks in the Newick string.
568 o del.gaps() returned a list of empty sequences when there were no
574 o phymltest() has been updated for PhyML 3.0 and gains an option
575 'append', whereas the option 'path2exec' has been removed.
577 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
578 which is returned unchanged (instead of an error).
580 o The data sets bird.orders and bird.families are now stored as
581 Newick strings; i.e., the command data(bird.orders) calls
586 CHANGES IN APE VERSION 2.2-1
591 o The new function makeLabel() helps to modify labels of trees,
592 lists of trees, or DNA sequences, with several utilities to
593 truncate and/or make them unique, substituting some
594 characters, and so on.
596 o The new function del.gaps() removes insertion gaps ("-") in a
597 set of DNA sequences.
599 o read.dna() can now read Clustal files (*.aln).
604 o root() failed with 'resolve.root = TRUE' when the root was
605 already the specified root.
607 o Several bugs were fixed in mlphylo().
609 o collapsed.singles() did not propagate the 'Nnode' and
610 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
612 o read.nexus() failed to remove correctly the comments within
615 o read.nexus() failed to read a file with a single tree and no
616 translation of tip labels.
618 o read.nexus() failed to place correctly tip labels when reading
619 a single tree with no edge lengths.
621 o A bug was fixed in sh.test().
626 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
629 o The option 'check.labels' of consensus() and prop.part() is now
632 o write.dna() now does not truncate names to 10 characters with
637 CHANGES IN APE VERSION 2.2
642 o Four new functions have been written by Damien de Vienne for the
643 graphical exploration of large trees (cophyloplot, subtrees,
644 subtreeplot), and to return the graphical coordinates of tree
647 o The new functions corPagel and corBlomberg implement the Pagel's
648 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
650 o chronopl() has been improved and gains several options: see its
651 help page for details.
653 o boot.phylo() has now an option 'trees' to possibly return the
654 bootstraped trees (the default is FALSE).
656 o prop.part() has been improved and should now be faster in all
662 o read.dna() failed if "?" occurred in the first 10 sites of the
665 o The x/y aspect of the plot is now respected when plotting a
666 circular tree (type = "r" or "f").
668 o Drawing the tip labels sometimes failed when plotting circular
671 o zoom() failed when tip labels were used instead of their numbers
672 (thanks to Yan Wong for the fix).
674 o drop.tip() failed with some trees (fixed by Yan Wong).
676 o seg.sites() failed with a list.
678 o consensus() failed in some cases. The function has been improved
679 as well and is faster.
683 CHANGES IN APE VERSION 2.1-3
688 o A bug in read.nexus() made the Windows R-GUI crash.
690 o An error was fixed in the computation of ancestral character
691 states by generalized least squares in ace().
693 o di2multi() did not modify node labels correctly.
695 o multi2di() failed if the tree had its attribute "order" set to
700 CHANGES IN APE VERSION 2.1-2
705 o There three new methods for the "multiPhylo" class: str, $,
708 o root() gains the options 'node' and 'resolve.root'
709 (FALSE by default) as well as its code being improved.
711 o mltt.plot() has now an option 'log' used in the same way
712 than in plot.default().
717 o mltt.plot() failed to display the legend with an unnamed
720 o nodelabels() with pies now correcly uses the argument
721 'cex' to draw symbols of different sizes (which has
722 worked already for thermometers).
724 o read.nexus() generally failed to read very big files.
729 o The argument 'family' of compar.gee() can now be a function
730 as well as a character string.
732 o read.tree() and read.nexus() now return an unnamed list if
735 o read.nexus() now returns a modified object of class "multiPhylo"
736 when there is a TRANSLATE block in the NEXUS file: the individual
737 trees have no 'tip.label' vector, but the list has a 'TipLabel'
738 attribute. The new methods '$' and '[[' set these elements
739 correctly when extracting trees.
743 CHANGES IN APE VERSION 2.1-1
748 o The new function rmtree generates lists of random trees.
750 o rcoal() now generates a genuine coalescent tree by default
751 (thanks to Vladimir Minin for the code).
756 o nuc.div() returned an incorrect value with the default
757 pairwise.deletion = FALSE.
762 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
763 have been improved so that they are stabler and faster.
765 o R packages used by ape are now loaded silently; lattice and gee
766 are loaded only when needed.
770 CHANGES IN APE VERSION 2.1
775 o The new function identify.phylo identifies clades on a plotted
776 tree using the mouse.
778 o It is now possible to subset a list of trees (object of class
779 "multiPhylo") with "[" while keeping its class correct.
781 o The new function as.DNAbin.alignment converts DNA sequences
782 stored in the "alignment" format of the package seqinr into
783 an object of class "DNAbin".
785 o The new function weight.taxo2 helps to build similarity matrices
786 given two taxonomic levels (usually called by other functions).
788 o write.tree() can now take a list of trees (class "multiPhylo")
789 as its main argument.
791 o plot.correlogram() and plot.correlogramList() have been
792 improved, and gain several options (see the help page for
793 details). A legend is now plotted by default.
798 o dist.dna() returned some incorrect values with `model = "JC69"'
799 and `pairwise.deletion = TRUE'. This affected only the
800 distances involving sequences with missing values. (Thanks
801 to Bruno Toupance for digging this bug out.)
803 o write.tree() failed with some trees: this is fixed by removing
804 the `multi.line' option (trees are now always printed on a
807 o read.nexus() did not correctly detect trees with multiple root
808 edges (see OTHER CHANGES).
813 o The code of mlphylo() has been almost entirely rewritten, and
814 should be much stabler. The options have been also greatly
815 simplified (see ?mlphylo and ?DNAmodel for details).
817 o The internal function nTips has been renamed klastorin_nTips.
819 o The code of is.ultrametric() contained redundancies and has
822 o The code of Moran.I() and of correlogram.formula() have been
825 o read.tree() and read.nexus() now return an error when trying to
826 read a tree with multiple root edges (see BUG FIXES). The
827 correction applied in previous version did not work in all
830 o The class c("multi.tree", "phylo") has been renamed
836 o There is now a vignette in ape: see vignette("MoranI", "ape").
841 o as.matching() and as.phylo.matching() do not support branch
844 o correlogram.phylo() and discrete.dist() have been removed.
848 CHANGES IN APE VERSION 2.0-2
853 o The new function matexpo computes the exponential of a square
856 o The new function unique.multi.tree removes duplicate trees from
859 o yule() has a new option `use.root.edge = FALSE' that specifies
860 to ignore, by default, the root edge of the tree if it exists.
865 o which.edge() failed when the index of a single terminal edge was
868 o In diversi.time(), the values returned for model C were
871 o A bug was fixed in yule() that affected the calculation of the
872 likelihood in the presence of ties in the branching times.
874 o There was a bug in the C function mat_expo4x4 affecting the
875 calculations of the transition probabilities for models HKY and
878 o A small bug was fixed in as.matrix.DNAbin (thanks to James
881 o rtree() did not `shuffle' the tip labels by default, so only a
882 limited number of labelled topologies could be generated.
886 CHANGES IN APE VERSION 2.0-1
891 o The three new functions bionj, fastme.ols, and fastme.bal
892 perform phylogeny estimation by the BIONJ and fastME methods in
893 OLS and balanced versions. This is a port to R of previous
894 previous programs done by Vincent Lefort.
896 o The new function chronoMPL performs molecular dating with the
897 mean path lengths method of Britton et al. (2002, Mol. Phyl.
900 o The new function rotate, contributed by Christoph Heibl, swaps
901 two clades connected to the same node. It works also with
902 multichotomous nodes.
904 o The new `method' as.matrix.DNAbin() may be used to convert
905 easily DNA sequences stored in a list into a matrix while
906 keeping the names and the class.
911 o chronopl() failed when some branch lengths were equal to zero:
912 an error message is now returned.
914 o di2multi() failed when there was a series of consecutive edges
919 CHANGES IN APE VERSION 1.10-2
924 o plot.phylo() can now plot circular trees: the option is type =
925 "fan" or type = "f" (to avoid the ambiguity with type = "c").
927 o prop.part() has a new option `check.labels = FALSE' which allows
928 to considerably speed-up the calculations of bipartitions. As a
929 consequence, calculations of bootstrap values with boot.phylo()
930 should be much faster.
935 o read.GenBank() did not return correctly the list of species as
936 from ape 1.10: this is fixed in this version
938 o Applying as.phylo() on a tree of class "phylo" failed: the
939 object is now returned unchanged.
943 CHANGES IN APE VERSION 1.10-1
948 o The three new functions Ntip, Nnode, and Nedge return, for a
949 given tree, the number of tips, nodes, or edges, respectively.
954 o read.nexus() did not set correctly the class of the returned
955 object when reading multiple trees.
957 o mllt.plot() failed with objects of class c("multi.tree",
960 o unroot() did not work correctly in most cases.
962 o reorder.phylo() made R freeze in some occasions.
964 o Plotting a tree in pruningwise order failed.
966 o When plotting an unrooted tree, the tip labels where not all
967 correctly positioned if the option `cex' was used.
971 CHANGES IN APE VERSION 1.10
976 o Five new `method' functions have been introduced to manipulate
977 DNA sequences in binary format (see below).
979 o Three new functions have been introduced to convert between the
980 new binary and the character formats.
982 o The new function as.alignment converts DNA sequences stored as
983 single characters into the class "alignment" used by the package
986 o read.dna() and read.GenBank() have a new argument `as.character'
987 controlling whether the sequences are returned in binary format
993 o root() failed when the tree had node labels: this is fixed.
995 o plot.phylo() did not correctly set the limits on the y-axis with
996 the default setting: this is fixed.
998 o dist.dna() returned a wrong result for the LogDet, paralinear,
999 and BH87 models with `pairwise.deletion = TRUE'.
1004 o DNA sequences are now internally stored in a binary format. See
1005 the document "A Bit-Level Coding Scheme for Nucleotides" for the
1006 details. Most functions analyzing DNA functions have been
1007 modified accordingly and are now much faster (dist.dna is now
1008 ca. 60 times faster).
1012 CHANGES IN APE VERSION 1.9-4
1017 o A bug was fixed in edgelabels().
1019 o as.phylo.hclust() did not work correctly when the object of
1020 class "hclust" has its labels set to NULL: the returned tree has
1021 now its tip labels set to "1", "2", ...
1023 o consensus could fail if some tip labels are a subset of others
1024 (e.g., "a" and "a_1"): this is now fixed.
1026 o mlphylo() failed in most cases if some branch lengths of the
1027 initial tree were greater than one: an error message is now
1030 o mlphylo() failed in most cases when estimating the proportion of
1031 invariants: this is fixed.
1035 CHANGES IN APE VERSION 1.9-3
1040 o The new function edgelabels adds labels on the edge of the tree
1041 in the same way than nodelabels or tiplabels.
1046 o multi2di() did not handle correctly branch lengths with the
1047 default option `random = TRUE': this is now fixed.
1049 o A bug was fixed in nuc.div() when using pairwise deletions.
1051 o A bug occurred in the analysis of bipartitions with large
1052 numbers of large trees, with consequences on prop.part,
1053 prop.clades, and boot.phylo.
1055 o The calculation of the Billera-Holmes-Vogtmann distance in
1056 dist.topo was wrong: this has been fixed.
1060 CHANGES IN APE VERSION 1.9-2
1065 o The new function ladderize reorganizes the internal structure of
1066 a tree to plot them left- or right-ladderized.
1068 o The new function dist.nodes computes the patristic distances
1069 between all nodes, internal and terminal, of a tree. It replaces
1070 the option `full = TRUE' of cophenetic.phylo (see below).
1075 o A bug was fixed in old2new.phylo().
1077 o Some bugs were fixed in chronopl().
1079 o The edge colours were not correctly displayed by plot.phylo
1080 (thank you to Li-San Wang for the fix).
1082 o cophenetic.phylo() failed with multichotomous trees: this is
1088 o read.dna() now returns the sequences in a matrix if they are
1089 aligned (interleaved or sequential format). Sequences in FASTA
1090 format are still returned in a list.
1092 o The option `full' of cophenetic.phylo() has been removed because
1093 it could not be used from the generic.
1096 DEPRECATED & DEFUNCT
1098 o rotate() has been removed; this function did not work correctly
1103 CHANGES IN APE VERSION 1.9-1
1108 o Trees with a single tip were not read correctly in R as the
1109 element `Nnode' was not set: this is fixed.
1111 o unroot() did not set correctly the number of nodes of the
1112 unrooted tree in most cases.
1114 o read.GenBank() failed when fetching very long sequences,
1115 particularly of the BX-series.
1117 o A bug was introduced in read.tree() with ape 1.9: it has been
1122 CHANGES IN APE VERSION 1.9
1127 o There are two new print `methods' for trees of class "phylo" and
1128 lists of trees of class "multi.tree", so that they are now
1129 displayed in a compact and informative way.
1131 o There are two new functions, old2new.phylo and new2old.phylo,
1132 for converting between the old and new coding of the class
1135 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
1136 LogDet ("logdet"), and paralinear ("paralin").
1138 o compute.brlen() has been extended: several methods are now
1139 available to compute branch lengths.
1141 o write.dna() can now handle matrices as well as lists.
1146 o cophenetic.phylo() sometimes returned a wrong result with
1147 multichotomous trees: this is fixed.
1149 o rotate() failed when a single tip was specified: the tree is now
1152 o ace() did not return the correct index matrix with custom
1153 models: this is fixed.
1155 o multi2di() did not work correctly when resolving multichotomies
1156 randomly: the topology was always the same, only the arrangement
1157 of clades was randomized: this is fixed. This function now
1158 accepts trees with no branch lengths.
1160 o The output of diversi.gof() was blurred by useless prints when a
1161 user distribution was specified. This has been corrected, and
1162 the help page of this function has been expanded.
1167 o The internal structure of the class "phylo" has been changed:
1168 see the document "Definition of Formats for Coding Phylogenetic
1169 Trees in R" for the details. In addition, the code of most
1170 functions has been improved.
1172 o Several functions have been improved by replacing some R codes
1173 by C codes: pic, plot.phylo, and reorder.phylo.
1175 o There is now a citation information: see citation("ape") in R.
1177 o write.tree() now does not add extra 0's to branch lengths so
1178 that 1.23 is printed "1.23" by default, not "1.2300000000".
1180 o The syntax of bind.tree() has been simplified. This function now
1181 accepts trees with no branch lengths, and handles correctly node
1184 o The option `as.numeric' of mrca() has been removed.
1186 o The unused options `format' and `rooted' of read.tree() have
1189 o The unused option `format' of write.tree() has been removed.
1191 o The use of node.depth() has been simplified.
1195 CHANGES IN APE VERSION 1.8-5
1200 o Two new functions read.nexus.data() and write.nexus.data(),
1201 contributed by Johan Nylander, allow to read and write molecular
1202 sequences in NEXUS files.
1204 o The new function reorder.phylo() reorders the internal structure
1205 of a tree of class "phylo". It is used as the generic, e.g.,
1208 o read.tree() and read.nexus() can now read trees with a single
1211 o The new data set `cynipids' supplies a set of protein sequences
1217 o The code of all.equal.phylo() has been completely rewritten
1218 (thanks to Benoît Durand) which fixes several bugs.
1220 o read.tree() and read.nexus() now checks the labels of the tree
1221 to remove or substitute any characters that are illegal in the
1222 Newick format (parentheses, etc.)
1224 o A negative P-value could be returned by mantel.test(): this is
1229 CHANGES IN APE VERSION 1.8-4
1234 o The new function sh.test() computes the Shimodaira-
1237 o The new function collapse.singles() removes the nodes with a
1238 single descendant from a tree.
1240 o plot.phylo() has a new argument `tip.color' to specify the
1241 colours of the tips.
1243 o mlphylo() has now an option `quiet' to control the display of
1244 the progress of the analysis (the default is FALSE).
1249 o read.dna() did not read correctly sequences in sequential format
1250 with leading alignment gaps "-": this is fixed.
1252 o ace() returned a list with no class so that the generic
1253 functions (anova, logLik, ...) could not be used directly. This
1254 is fixed as ace() now returns an object of class "ace".
1256 o anova.ace() had a small bug when computing the number of degrees
1257 of freedom: this is fixed.
1259 o mlphylo() did not work when the sequences were in a matrix or
1260 a data frame: this is fixed.
1262 o rtree() did not work correctly when trying to simulate an
1263 unrooted tree with two tips: an error message is now issued.
1268 o The algorithm of rtree() has been changed: it is now about 40,
1269 100, and 130 times faster for 10, 100, and 1000 tips,
1274 CHANGES IN APE VERSION 1.8-3
1279 o There are four new `method' functions to be used with the
1280 results of ace(): logLik(), deviance(), AIC(), and anova().
1282 o The plot method of phymltest has two new arguments: `main' to
1283 change the title, and `col' to control the colour of the
1284 segments showing the AIC values.
1286 o ace() has a new argument `ip' that gives the initial values used
1287 in the ML estimation with discrete characters (see the examples
1288 in ?ace). This function now returns a matrix giving the indices
1289 of the estimated rates when analysing discrete characters.
1291 o nodelabels() and tiplabels() have a new argument `pie' to
1292 represent proportions, with any number of categories, as
1293 piecharts. The use of the option `thermo' has been improved:
1294 there is now no limitation on the number of categories.
1299 o mlphylo() did not work with more than two partitions: this is
1302 o root() failed if the proposed outgroup was already an outgroup
1303 in the tree: this is fixed.
1305 o The `col' argument in nodelabels() and tiplabels() was not
1306 correctly passed when `text' was used: this is fixed.
1308 o Two bugs were fixed in mlphylo(): parameters were not always
1309 correctly output, and the estimation failed in some cases.
1311 o plot.phylo() was stuck when given a tree with a single tip: this
1312 is fixed and a message error is now returned.
1314 o An error was corrected in the help page of gammaStat regarding
1315 the calculation of P-values.
1317 o Using gls() could crash R when the number of species in the tree
1318 and in the variables were different: this is fixed.
1322 CHANGES IN APE VERSION 1.8-2
1327 o The new function mlphylo() fits a phylogenetic tree by maximum
1328 likelihood from DNA sequences. Its companion function DNAmodel()
1329 is used to define the substitution model which may include
1330 partitioning. There are methods for logLik(), deviance(), and
1331 AIC(), and the summary() method has been extended to display in
1332 a friendly way the results of this model fitting. Currently, the
1333 functionality is limited to estimating the substitution and
1334 associated parameters and computing the likelihood.
1336 o The new function drop1.compar.gee (used as, e.g., drop1(m))
1337 tests for single effects in GEE-based comparative method. A
1338 warning message is printed if there is not enough degrees of
1344 o An error message was sometimes issued by plot.multi.tree(),
1345 though with no consequence.
1349 CHANGES IN APE VERSION 1.8-1
1354 o There is a new plot method for lists of trees (objects of class
1355 "multi.tree"): it calls plot.phylo() internally and is
1356 documented on the same help page.
1361 o A bug was fixed in the C code that analyzes bipartitions: this
1362 has impact on several functions like prop.part, prop.clades,
1363 boot.phylo, or consensus.
1365 o root() did not work correctly when the specified outgroup had
1366 more than one element: this is fixed.
1368 o dist.dna() sometimes returned a warning inappropriately: this
1371 o If the distance object given to nj() had no rownames, nj()
1372 returned a tree with no tip labels: it now returns tips labelled
1373 "1", "2", ..., corresponding to the row numbers.
1378 o nj() has been slightly changed so that tips with a zero distance
1379 are first aggregated with zero-lengthed branches; the usual NJ
1380 procedure is then performed on a distance matrix without 0's.
1384 CHANGES IN APE VERSION 1.8
1389 o The new function chronopl() estimates dates using the penalized
1390 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1392 o The new function consensus() calculates the consensus tree of a
1395 o The new function evolve.phylo() simulates the evolution of
1396 continuous characters along a phylogeny under a Brownian model.
1398 o The new plot method for objects of class "ancestral" displays a
1399 tree together with ancestral values, as returned by the above
1402 o The new function as.phylo.formula() returns a phylogeny from a
1403 set of nested taxonomic variables given as a formula.
1405 o The new function read.caic() reads trees in CAIC format.
1407 o The new function tiplabels() allows to add labels to the tips
1408 of a tree using text or plotting symbols in a flexible way.
1410 o The new function unroot() unroots a phylogeny.
1412 o multi2di() has a new option, `random', which specifies whether
1413 to resolve the multichotomies randomly (the default) or not.
1415 o prop.part() now returns an object of class "prop.part" for which
1416 there are print (to display a partition in a more friendly way)
1417 and summary (to extract the numbers) methods.
1419 o plot.phylo() has a new option, `show.tip.label', specifying
1420 whether to print the labels of the tips. The default is TRUE.
1422 o The code of nj() has been replaced by a faster C code: it is now
1423 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1426 o write.nexus() now writes whether a tree is rooted or not.
1431 o Two bugs have been fixed in root(): unrooted trees are now
1432 handled corretly, and node labels are now output normally.
1434 o A bug was fixed in phymltest(): the executable couldn't be found
1437 o Three bug have been fixed in ace(): computing the likelihood of
1438 ancestral states of discrete characters failed, custom models
1439 did not work, and the function failed with a null gradient (a
1440 warning message is now returned; this latter bug was also
1441 present in yule.cov() as well and is now fixed).
1443 o pic() hanged out when missing data were present: a message error
1446 o A small bug was fixed in dist.dna() where the gamma correction
1447 was not always correctly dispatched.
1449 o plot.phylo() plotted correctly the root edge only when the tree
1450 was plotted rightwards: this works now for all directions.
1455 o dist.taxo() has been renamed as weight.taxo().
1457 o dist.phylo() has been replaced by the method cophenetic.phylo().
1459 o Various error and warning messages have been improved.
1463 CHANGES IN APE VERSION 1.7
1466 o The new function ace() estimates ancestral character states for
1467 continuous characters (with ML, GLS, and contrasts methods), and
1468 discrete characters (with ML only) for any number of states.
1470 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1471 of directional evolution for continuous characters. The user
1472 specifies the node(s) of the tree where the character optimum
1475 o The new function is.rooted() tests whether a tree (of class
1478 o The new function rcoal() generates random ultrametric trees with
1479 the possibility to specify the function that generates the
1480 inter-nodes distances.
1482 o The new function mrca() gives for all pairs of tips in a tree
1483 (and optionally nodes too) the most recent common ancestor.
1485 o nodelabels() has a new option `thermo' to plot proportions (up
1486 to three classes) on the nodes of a tree.
1488 o rtree() has been improved: it can now generate rooted or
1489 unrooted trees, and the mathematical function that generates the
1490 branch lengths may be specified by the user. The tip labels may
1491 be given directly in the call to rtree. The limit cases (n = 2,
1492 3) are now handled correctly.
1494 o dist.topo() has a new argument `method' with two choices: "PH85"
1495 for Penny and Henny's method (already available before and now
1496 the default), and "BHV01" for the geometric distance by Billera
1497 et al. (2001, Adv. Appl. Math. 27:733).
1499 o write.tree() has a new option, `digits', which specifies the
1500 number of digits to be printed in the Newick tree. By default
1501 digits = 10. The numbers are now always printed in decimal form
1502 (i.e., 1.0e-1 is now avoided).
1504 o dist.dna() can now compute the raw distances between pairs of
1505 DNA sequences by specifying model = "raw".
1507 o dist.phylo() has a new option `full' to possibly compute the
1508 distances among all tips and nodes of the tree. The default if
1514 o Several bugs were fixed in all.equal.phylo().
1516 o dist.dna() did not handle correctly gaps ("-") in alignments:
1517 they are now considered as missing data.
1519 o rotate() did not work if the tips were not ordered: this is
1522 o mantel.test() returned NA in some special cases: this is fixed
1523 and the function has been improved and is now faster.
1525 o A bug was fixed in diversi.gof() where the calculation of A² was
1528 o cherry() did not work correctly under some OSs (mainly Linux):
1531 o is.binary.tree() has been modified so that it works with both
1532 rooted and unrooted trees.
1534 o The documentation of theta.s() was not correct: this has been
1537 o plot.mst() did not work correctly: this is fixed.
1541 CHANGES IN APE VERSION 1.6
1546 o The new function dist.topo() computes the topological distances
1549 o The new function boot.phylo() performs a bootstrap analysis on
1550 phylogeny estimation.
1552 o The new functions prop.part() and prop.clades() analyse
1553 bipartitions from a series of trees.
1558 o read.GenBank() now uses the EFetch utility of NCBI instead of
1559 the usual Web interface: it is now much faster (e.g., 12 times
1560 faster to retrieve 8 sequences, 37 times for 60 sequences).
1565 o Several bugs were fixed in read.dna().
1567 o Several bugs were fixed in diversi.time().
1569 o is.binary.tree() did not work correctly if the tree has no edge
1570 lengths: this is fixed.
1572 o drop.tip() did not correctly propagated the `node.label' of a
1573 tree: this is fixed.
1577 CHANGES IN APE VERSION 1.5
1582 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1583 convert objects between the classes "phylo" and "matching". The
1584 latter implements the representation of binary trees introduced by
1585 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1586 as.matching() has been introduced as well.
1588 o Two new functions, multi2di() and di2multi(), allow to resolve
1589 and collapse multichotomies with branches of length zero.
1591 o The new function nuc.div() computes the nucleotide diversity
1592 from a sample a DNA sequences.
1594 o dist.dna() has been completely rewritten with a much faster
1595 (particularly for large data sets) C code. Eight models are
1596 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1597 option `method' has been renamed `model'). Computation of variance
1598 is available for all models. A gamma-correction is possible for
1599 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1600 to remove sites with missing data on a pairwise basis. The option
1601 `GCcontent' has been removed.
1603 o read.GenBank() has a new option (species.names) which specifies
1604 whether to return the species names of the organisms in addition
1605 to the accession numbers of the sequences (this is the default
1608 o write.nexus() can now write several trees in the same NEXUS file.
1610 o drop.tip() has a new option `root.edge' that allows to specify the
1611 new root edge if internal branches are trimmed.
1616 o as.phylo.hclust() failed if some labels had parentheses: this
1619 o Several bugs were fixed in all.equal.phylo(). This function now
1620 returns the logical TRUE if the trees are identical but with
1621 different representations (a report was printed previously).
1623 o read.GenBank() did not correctly handle ambiguous base codes:
1629 o birthdeath() now returns an object of class "birthdeath" for
1630 which there is a print method.
1634 CHANGES IN APE VERSION 1.4
1639 o The new function nj() performs phylogeny estimation with the
1640 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1643 o The new function which.edge() identifies the edges of a tree
1644 that belong to a group specified as a set of tips.
1646 o The new function as.phylo.phylog() converts an object of class
1647 "phylog" (from the package ade4) into an object of class
1650 o The new function axisPhylo() draws axes on the side of a
1653 o The new function howmanytrees() calculates the number of trees
1654 in different cases and giving a number of tips.
1656 o write.tree() has a new option `multi.line' (TRUE by default) to
1657 write a Newick tree on several lines rather than on a single
1660 o The functionalities of zoom() have been extended. Several
1661 subtrees can be visualized at the same time, and they are marked
1662 on the main tree with colors. The context of the subtrees can be
1663 marked with the option `subtree' (see below).
1665 o drop.tip() has a new option `subtree' (FALSE by default) which
1666 specifies whether to output in the tree how many tips have been
1669 o The arguments of add.scale.bar() have been redefined and have
1670 now default values (see ?add.scale.bar for details). This
1671 function now works even if the plotted tree has no edge length.
1673 o plot.phylo() can now plot radial trees, but this does not take
1674 edge lengths into account.
1676 o In plot.phylo() with `type = "phylogram"', if the values of
1677 `edge.color' and `edge.width' are identical for sister-branches,
1678 they are propagated to the vertical line that link them.
1683 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1684 crashing. This is fixed.
1686 o In plot.phylo(), the options `edge.color' and `edge.width' are
1687 now properly recycled; their default values are now "black" and
1690 o A bug has been fixed in write.nexus().
1695 o The function node.depth.edgelength() has been removed and
1696 replaced by a C code.
1700 CHANGES IN APE VERSION 1.3-1
1705 o The new function nodelabels() allows to add labels to the nodes
1706 of a tree using text or plotting symbols in a flexible way.
1708 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1709 numeric values specifying the lower and upper limits on the x-
1710 and y-axes. This allows to leave some space on any side of the
1711 tree. If a single value is given, this is taken as the upper
1716 CHANGES IN APE VERSION 1.3
1721 o The new function phymltest() calls the software PHYML and fits
1722 28 models of DNA sequence evolution. There are a print method to
1723 display likelihood and AIC values, a summary method to compute
1724 the hierarchical likelihood ratio tests, and a plot method to
1725 display graphically the AIC values of each model.
1727 o The new function yule.cov() fits the Yule model with covariates,
1728 a model where the speciation rate is affected by several species
1729 traits through a generalized linear model. The parameters are
1730 estimated by maximum likelihood.
1732 o Three new functions, corBrownian(), corGrafen(), and
1733 corMartins(), compute the expected correlation structures among
1734 species given a phylogeny under different models of evolution.
1735 These can be used for GLS comparative phylogenetic methods (see
1736 the examples). There are coef() and corMatrix() methods and an
1737 Initialize.corPhyl() function associated.
1739 o The new function compar.cheverud() implements Cheverud et al.'s
1740 (1985; Evolution 39:1335) phylogenetic comparative method.
1742 o The new function varcomp() estimates variance components; it has
1745 o Two new functions, panel.superpose.correlogram() and
1746 plot.correlogramList(), allow to plot several phylogenetic
1749 o The new function node.leafnumber() computes the number of leaves
1750 of a subtree defined by a particular node.
1752 o The new function node.sons() gets all tags of son nodes from a
1755 o The new function compute.brlen() computes the branch lengths of
1756 a tree according to a specified method.
1758 o plot.phylo() has three new options: "cex" controls the size of
1759 the (tip and node) labels (thus it is no more needed to change
1760 the global graphical parameter), "direction" which allows to
1761 plot the tree rightwards, leftwards, upwards, or downwards, and
1762 "y.lim" which sets the upper limit on the y-axis.
1767 o Some functions which try to match tip labels and names of
1768 additional data (e.g. vector) are likely to fail if there are
1769 typing or syntax errors. If both series of names do not perfectly
1770 match, they are ignored and a warning message is now issued.
1771 These functions are bd.ext, compar.gee, pic. Their help pages
1772 have been clarified on this point.
1776 CHANGES IN APE VERSION 1.2-7
1781 o The new function root() reroots a phylogenetic tree with respect
1782 to a specified outgroup.
1784 o The new function rotate() rotates an internal branch of a tree.
1786 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1787 trees) controls the display of the tip labels in unrooted trees.
1788 This display has been greatly improved: the tip labels are now not
1789 expected to overlap with the tree (particularly if lab4ut =
1790 "axial"). In all cases, combining appropriate values of "lab4ut"
1791 and the font size (via "par(cex = )") should result in readable
1792 unrooted trees. See ?plot.phylo for some examples.
1794 o In drop.tip(), the argument `tip' can now be numeric or character.
1799 o drop.tip() did not work correctly with trees with no branch
1800 lengths: this is fixed.
1802 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1803 plotted with some line crossings: this is now fixed.
1807 CHANGES IN APE VERSION 1.2-6
1812 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1813 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1814 to implement comparative methods with an autocorrelation approach.
1816 o A new data set describing some life history traits of Carnivores
1822 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1827 o When plotting a tree with plot.phylo(), the new default of the
1828 option `label.offset' is now 0, so the labels are always visible.
1832 CHANGES IN APE VERSION 1.2-5
1837 o The new function bd.ext() fits a birth-death model with combined
1838 phylogenetic and taxonomic data, and estimates the corresponding
1839 speciation and extinction rates.
1844 o The package gee is no more required by ape but only suggested
1845 since only the function compar.gee() calls gee.
1849 CHANGES IN APE VERSION 1.2-4
1854 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1855 and lines.popsize) implementing a new approach for inferring the
1856 demographic history from genealogies using a reversible jump
1857 MCMC have been introduced.
1859 o The unit of time in the skyline plot and in the new plots can
1860 now be chosen to be actual years, rather than substitutions.
1864 CHANGES IN APE VERSION 1.2-3
1869 o The new function rtree() generates a random binary tree with or
1870 without branch lengths.
1872 o Two new functions for drawing lineages-through-time (LTT) plots
1873 are provided: ltt.lines() adds a LTT curve to an existing plot,
1874 and mltt.plot() does a multiple LTT plot giving several trees as
1875 arguments (see `?ltt.plot' for details).
1880 o Some taxon names made R crashing when calling as.phylo.hclust():
1883 o dist.dna() returned an error with two identical DNA sequences
1884 (only using the Jukes-Cantor method returned 0): this is fixed.
1889 o The function dist.phylo() has been re-written using a different
1890 algorithm: it is now about four times faster.
1892 o The code of branching.times() has been improved: it is now about
1897 CHANGES IN APE VERSION 1.2-2
1902 o The new function seg.sites() finds the segregating sites in a
1903 sample of DNA sequences.
1908 o A bug introduced in read.tree() and in read.nexus() with version
1911 o A few errors were corrected and a few examples were added in the
1916 CHANGES IN APE VERSION 1.2-1
1921 o plot.phylo() can now draw the edge of the root of a tree if it
1922 has one (see the new option `root.edge', its default is FALSE).
1927 o A bug was fixed in read.nexus(): files with semicolons inside
1928 comment blocks were not read correctly.
1930 o The behaviour of read.tree() and read.nexus() was corrected so
1931 that tree files with badly represented root edges (e.g., with
1932 an extra pair of parentheses, see the help pages for details)
1933 are now correctly represented in the object of class "phylo";
1934 a warning message is now issued.
1938 CHANGES IN APE VERSION 1.2
1943 o plot.phylo() has been completely re-written and offers several
1944 new functionalities. Three types of trees can now be drawn:
1945 phylogram (as previously), cladogram, and unrooted tree; in
1946 all three types the branch lengths can be drawn using the edge
1947 lengths of the phylogeny or not (e.g., if the latter is absent).
1948 The vertical position of the nodes can be adjusted with two
1949 choices (see option `node.pos'). The code has been re-structured,
1950 and two new functions (potentially useful for developpers) are
1951 documented separately: node.depth.edgelength() and node.depth();
1952 see the respective help pages for details.
1954 o The new function zoom() allows to explore very large trees by
1955 focusing on a small portion of it.
1957 o The new function yule() fits by maximum likelihood the Yule model
1958 (birth-only process) to a phylogenetic tree.
1960 o Support for writing DNA sequences in FASTA format has been
1961 introduced in write.dna() (support for reading sequences in
1962 this format was introduced in read.dna() in version 1.1-2).
1963 The function has been completely re-written, fixing some bugs
1964 (see below); the default behaviour is no more to display the
1965 sequences on the standard output. Several options have been
1966 introduced to control the sequence printing in a flexible
1967 way. The help page has been extended.
1969 o A new data set is included: a supertree of bats in NEXUS format.
1974 o In theta.s(), the default of the option `variance' has
1975 been changed to `FALSE' (as was indicated in the help page).
1977 o Several bugs were fixed in the code of all.equal.phylo().
1979 o Several bugs were fixed in write.dna(), particularly this
1980 function did not work with `format = "interleaved"'.
1982 o Various errors were corrected in the help pages.
1987 o The argument names of as.hclust.phylo() have been changed
1988 from "(phy)" to "(x, ...)" to conform to the definition of
1989 the corresponding generic function.
1991 o gamma.stat() has been renamed gammaStat() to avoid confusion
1992 since gamma() is a generic function.
1996 CHANGES IN APE VERSION 1.1-3
2001 o base.freq() previously did not return a value of 0 for
2002 bases absent in the data (e.g., a vector of length 3 was
2003 returned if one base was absent). This is now fixed (a
2004 vector of length 4 is always returned).
2006 o Several bugs were fixed in read.nexus(), including that this
2007 function did not work in this absence of a "TRANSLATE"
2008 command in the NEXUS file, and that the commands were
2013 CHANGES IN APE VERSION 1.1-2
2018 o The Tamura and Nei (1993) model of DNA distance is now implemented
2019 in dist.dna(): five models are now available in this function.
2021 o A new data set is included: a set of 15 sequences of the
2022 cytochrome b mitochondrial gene of the woodmouse (Apodemus
2028 o A bug in read.nexus() was fixed.
2030 o read.dna() previously did not work correctly in most cases.
2031 The function has been completely re-written and its help page
2032 has been considerably extended (see ?read.dna for details).
2033 Underscores (_) in taxon names are no more replaced with
2034 spaces (this behaviour was undocumented).
2036 o A bug was fixed in write.dna().
2040 CHANGES IN APE VERSION 1.1-1
2045 o A bug in read.tree() introduced in APE 1.1 was fixed.
2047 o A bug in compar.gee() resulted in an error when trying to fit
2048 a model with `family = "binomial"'. This is now fixed.
2052 CHANGES IN APE VERSION 1.1
2057 o The Klastorin (1982) method as suggested by Misawa and Tajima
2058 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
2059 on the basis of phylogenetic trees has been implemented (see
2060 the function klastorin()).
2062 o Functions have been added to convert APE's "phylo" objects in
2063 "hclust" cluster objects and vice versa (see the help page of
2064 as.phylo for details).
2066 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
2067 are introduced for the estimation of absolute evolutionary rates
2068 (ratogram) and dated clock-like trees (chronogram) from
2069 phylogenetic trees using the non-parametric rate smoothing approach
2070 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
2072 o A summary method is now provided printing a summary information on a
2073 phylogenetic tree with, for instance, `summary(tree)'.
2075 o The behaviour of read.tree() was changed so that all spaces and
2076 tabulations in tree files are now ignored. Consequently, spaces in tip
2077 labels are no more allowed. Another side effect is that read.nexus()
2078 now does not replace the underscores (_) in tip labels with spaces
2079 (this behaviour was undocumented).
2081 o The function plot.phylo() has a new option (`underscore') which
2082 specifies whether the underscores in tip labels should be written on
2083 the plot as such or replaced with spaces (the default).
2085 o The function birthdeath() now computes 95% confidence intervals of
2086 the estimated parameters using profile likelihood.
2088 o Three new data sets are included: a gene tree estimated from 36
2089 landplant rbcL sequences, a gene tree estimated from 32 opsin
2090 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
2095 o A bug was fixed in dist.gene() where nothing was returned.
2097 o A bug in plot.mst() was fixed.
2099 o A bug in vcv.phylo() resulted in false correlations when the
2100 option `cor = TRUE' was used (now fixed).
2104 CHANGES IN APE VERSION 1.0
2109 o Two new functions, read.dna() and write.dna(), read/write in a file
2110 DNA sequences in interleaved or in sequential format.
2112 o Two new functions, read.nexus() and write.nexus(), read/write trees
2115 o The new function bind.tree() allows to bind two trees together,
2116 possibly handling root edges to give internal branches.
2118 o The new function drop.tip() removes the tips in a phylogenetic tree,
2119 and trims (or not) the corresponding internal branches.
2121 o The new function is.ultrametric() tests if a tree is ultrametric.
2123 o The function plot.phylo() has more functionalities such as drawing the
2124 branches with different colours and/or different widths, showing the
2125 node labels, controling the position and font of the labels, rotating
2126 the labels, and controling the space around the plot.
2128 o The function read.tree() can now read trees with no branch length,
2129 such as "(a,b),c);". Consequently, the element `edge.length' in
2130 objects of class "phylo" is now optional.
2132 o The function write.tree() has a new default behaviour: if the default
2133 for the option `file' is used (i.e. file = ""), then a variable of
2134 mode character containing the tree in Newick format is returned which
2135 can thus be assigned (e.g., tree <- write.tree(phy)).
2137 o The function read.tree() has a new argument `text' which allows
2138 to read the tree in a variable of mode character.
2140 o A new data set is included: the phylogenetic relationships among
2141 the orders of birds from Sibley and Ahlquist (1990).
2145 CHANGES IN APE VERSION 0.2-1
2150 o Several bugs were fixed in the help pages.
2154 CHANGES IN APE VERSION 0.2
2159 o The function write.tree() writes phylogenetic trees (objects of class
2160 "phylo") in an ASCII file using the Newick parenthetic format.
2162 o The function birthdeath() fits a birth-death model to branching times
2163 by maximum likelihood, and estimates the corresponding speciation and
2166 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
2169 o The function is.binary.tree() tests whether a phylogeny is binary.
2171 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
2172 as well as some methods are introduced.
2174 o Several functions, including some generics and methods, for computing
2175 skyline plot estimates (classic and generalized) of effective
2176 population size through time are introduced and replace the function
2177 skyline.plot() in version 0.1.
2179 o Two data sets are now included: the phylogenetic relationships among
2180 the families of birds from Sibley and Ahlquist (1990), and an
2181 estimated clock-like phylogeny of HIV sequences sampled in the
2182 Democratic Republic of Congo.
2185 DEPRECATED & DEFUNCT
2187 o The function skyline.plot() in ape 0.1 has been deprecated and
2188 replaced by more elaborate functions (see above).
2193 o Two important bugs were fixed in plot.phylo(): phylogenies with
2194 multichotomies not at the root or not with only terminal branches,
2195 and phylogenies with a single node (i.e. only terminal branches)
2196 did not plot. These trees should be plotted correctly now.
2198 o Several bugs were fixed in diversi.time() in the computation of
2201 o Various errors were corrected in the help pages.
projects / ape.git / blob