1 CHANGES IN APE VERSION 2.6-1
6 o The new speciesTree calculates the species tree from a set of gene
7 trees. Two methods are currently available: maximum tree and
8 shallowest divergence tree.
13 o as.list.DNAbin() did not work correctly with vectors.
15 o as.hclust.phylo() failed with trees with node labels (thanks to
16 Filipe Vieira for the fix).
20 CHANGES IN APE VERSION 2.6
25 o The new functions rlineage and rbdtree simulate phylogenies under
26 any user-defined time-dependent speciation-extinction model. They
27 use continuous time algorithms.
29 o The new function drop.fossil removes the extinct species from a
32 o The new function bd.time fits a user-defined time-dependent
33 birth-death model. It is a generalization of yule.time() taking
34 extinction into account.
36 o The new function MPR does most parsimonious reconstruction of
39 o The new function Ftab computes the contingency table of base
40 frequencies from a pair of sequences.
42 o There is now an 'as.list' method for the class "DNAbin".
44 o dist.dna() can compute the number of transitions or transversions
45 with the option model = "Ts" or model = "Tv", respectively.
47 o [node|tip|edge]labels() gain three options with default values to
48 control the aspect of thermometers: horiz = TRUE, width = NULL,
51 o compar.gee() has been improved with the new option 'corStruct' as an
52 alternative to 'phy' to specify the correlation structure, and
53 calculation of the QIC (Pan 2001, Biometrics). The display of the
54 results has also been improved.
56 o read.GenBank() has a new option 'gene.names' to return the name of
57 the gene (FALSE by default).
62 o extract.clade() sometimes shuffled the tip labels.
64 o plot.phylo(type = "unrooted") did not force asp = 1 (thanks to Klaus
67 o dist.dna(model = "logdet") used to divide distances by 4. The
68 documentation has been clarified on the formulae used.
73 o rTraitCont(model = "OU") has an option 'linear = TRUE' to possibly
74 change the parameterisation (see ?rTraitCont for details).
76 o pic() now returns a vector with the node labels of the tree (if
79 o write.tree() and read.tree() have been substantially thanks to
80 contributions by Klaus Schliep.
84 CHANGES IN APE VERSION 2.5-3
89 o The new function mixedFontLabel helps to make labels with bits of
90 text to be plotted in different fonts.
92 o There are now replacement operators for [, [[, and $ for the class
93 "multiPhylo" (i.e., TREES[11:20] <- rmtree(10, 100)). They possibly
94 check that the tip labels are the same in all trees.
96 o Objects of class "multiPhylo" can be built with c(): there are
97 methods for the classes "phylo" and "multiPhylo".
99 o The internal functions .compressTipLabel and .uncompressTipLabel are
105 o bind.tree(x, y, where, position = 0) did not work correctly if 'y'
106 was a single-edge tree and 'where' was a tip.
108 o rTraitCont() did not use the square-root of branch lengths when
109 simulating a Brownian motion model.
113 CHANGES IN APE VERSION 2.5-2
118 o There is now a print method for results from ace().
120 o There is a labels() method for objects of class "DNAbin".
122 o read.dna() has a new option 'as.matrix' to possibly force sequences
123 in a FASTA file to be stored in a matrix (see ?read.dna for details).
128 o as.phylo.hclust() used to multiply edge lengths by 2.
130 o A minor bug was fixed in rTraitDisc().
132 o ace() sometimes failed (parameter value was NaN and the optimisation
138 o evolve.phylo() and plot.ancestral() have been removed.
140 o chronogram(), ratogram(), and NPRS.criterion() have been removed.
145 o nj() has been improved and is now about 30% faster.
147 o The default option 'drop' of [.DNAbin has been changed to FALSE to
148 avoid dropping rownames when selecting a single sequence.
150 o print.DNAbin() has been changed to summary.DNAbin() which has been
155 CHANGES IN APE VERSION 2.5-1
160 o The new function stree generates trees with regular shapes.
162 o It is now possible to bind two trees with x + y (see ?bind.tree for
165 o drop.tip(), extract.clade(), root(), and bind.tree() now have an
166 'interactive' option to make the operation on a plotted tree.
168 o cophyloplot() gains two new arguments 'lwd' and 'lty' for the
169 association links; they are recycled like 'col' (which wasn't before).
174 o rTraitDisc() did not use its 'freq' argument correctly (it was
175 multiplied with the rate matrix column-wise instead of row-wise).
177 o [node|tip|edge]labels(thermo = ) used to draw empty thermometers
178 with NA values. Nothing is drawn now like with 'text' or 'pch'.
179 The same bug occurred with the 'pie' option.
181 o A bug was fixed in compar.ou() and the help page was clarified.
183 o bind.tree() has been rewritten fixing several bugs and making it
186 o plot.phylo(type = "p") sometimes failed to colour correctly the
187 vertical lines representing the nodes.
189 o plot.phylo(direction = "l", x.lim = 30) failed to plot the branches
190 in the correct direction though the tip labels were displayed
196 o The c, cbind, and rbind methods for "DNAbin" objetcs now check that
197 the sequences are correctly stored (in a list for c, in a matrix
198 for the two other functions).
202 CHANGES IN APE VERSION 2.5
207 o The new function parafit by Pierre Legendre tests for the
208 coevolution between hosts and parasites. It has a companion
209 function, pcoa, that does principal coordinate decomposition.
210 The latter has a biplot method.
212 o The new function lmorigin by Pierre Legendre performs multiple
213 regression through the origin with testing by permutation.
215 o The new functions rTraitCont and rTraitDisc simulate continuous and
216 discrete traits under a wide range of evolutionary models.
218 o The new function delta.plot does a delta plot following Holland et
219 al. (2002, Mol. Biol. Evol. 12:2051).
221 o The new function edges draws additional branches between any nodes
222 and/or tips on a plotted tree.
224 o The new function fancyarrows enhances arrows from graphics with
225 triangle and harpoon heads; it can be called from edges().
227 o add.scale.bar() has a new option 'ask' to draw interactively.
229 o The branch length score replaces the geodesic distance in dist.topo.
231 o Three new data sets are included: the gopher-lice data (gopher.D),
232 SO2 air pollution in 41 US cities (lmorigin.ex1, from Sokal &
233 Rohlf 1995), and some host-parasite specificity data
234 (lmorigin.ex2, from Legendre & Desdevises 2009).
239 o add.scale.bar() drew the bar outside the plotting region with the
240 default options with unrooted or radial trees.
242 o dist.topo() made R stuck when the trees had different sizes (thanks
243 to Otto Cordero for the fix).
248 o The geodesic distance has been replaced by the branch length score
253 CHANGES IN APE VERSION 2.4-1
258 o rtree() and rcoal() now accept a numeric vector for the 'br'
261 o vcv() is a new generic function with methods for the classes "phylo"
262 and "corPhyl" so that it is possible to calculate the var-cov matrix
263 for "transformation models". vcv.phylo() can still be used for trees
264 of class "phylo"; its argument 'cor' has been renamed 'corr'.
269 o bind.tree() failed when 'y' had no root edge.
271 o read.nexus() shuffled tip labels when the trees have no branch
272 lengths and there is a TRANSLATE block.
274 o read.nexus() does not try to translate node labels if there is a
275 translation table in the NEXUS file. See ?read.nexus for a
276 clarification on this behaviour.
278 o plot.multiPhylo() crashed R when plotting a list of trees with
279 compressed tip labels.
281 o write.nexus() did not translate the taxa names when asked for.
283 o plot.phylo(type = "fan") did not rotate the tip labels correctly
284 when the tree has branch lengths.
286 o ace(type = "continuous", method = "ML") now avoids sigma² being
287 negative (which resulted in an error).
289 o nj() crashed with NA/NaN in the distance matrix: an error in now
294 CHANGES IN APE VERSION 2.4
299 o base.freq() has a new option 'freq' to return the counts; the
300 default is still to return the proportions.
305 o seg.sites() did not handle ambiguous nucleotides correctly: they
308 o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
309 the tree: the argument is now ignored.
311 o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
317 o Trying to plot a tree with a single tip now returns NULL with a
318 warning (it returned an error previously).
320 o The way lines representing nodes are coloured in phylograms has
321 been modified (as well as their widths and types) following some
322 users' request; this is only for dichotomous nodes.
324 o The argument 'adj' in [node][tip][edge]labels() now works when
325 using 'pie' or 'thermo'.
327 o A more informative message error is now returned by dist.dna() when
328 'model' is badly specified (partial matching of this argument is
331 o Deprecated functions are now listed in a help page: see
332 help("ape-defunct") with the quotes.
337 o The functions heterozygosity, nuc.div, theta.h, theta.k and
338 theta.s have been moved from ape to pegas.
340 o The functions mlphylo, DNAmodel and sh.test have been removed.
344 CHANGES IN APE VERSION 2.3-3
349 o add.scale.bar() always drew a horizontal bar.
351 o zoom() shuffled tips with unrooted trees.
353 o write.nexus() failed to write correctly trees with a "TipLabel"
356 o rcoal() failed to compute branch lengths with very large n.
358 o A small bug was fixed in compar.cheverud() (thanks to Michael
361 o seg.sites() failed when passing a vector.
363 o drop.tip() sometimes shuffled tip labels.
365 o root() shuffled node labels with 'resolve.root = TRUE'.
369 CHANGES IN APE VERSION 2.3-2
374 o all.equal.phylo() did not compare unrooted trees correctly.
376 o dist.topo(... method = "PH85") did not treat unrooted trees
377 correctly (thanks to Tim Wallstrom for the fix).
379 o root() sometimes failed to test for the monophyly of the
382 o extract.clade() sometimes included too many edges.
384 o vcv.phylo() did not work correctly when the tree is in
387 o nj() did not handle correctly distance matrices with many 0's.
388 The code has also been significantly improved: 7, 70, 160 times
389 faster with n = 100, 500, 1000, respectively.
393 CHANGES IN APE VERSION 2.3-1
398 o The new function is.monophyletic tests the monophyly of a group.
400 o There is now a c() method for lists of class "DNAbin".
402 o yule.cov() now fits the null model, and its help page has been
403 corrected with respect to this change.
405 o drop.tip() has a new option 'rooted' to force (or not) a tree
406 to be treated as (un)rooted.
411 o dist.gene() failed on most occasions with the default
412 pairwise.deletion = FALSE.
414 o read.tree() failed to read correctly the tree name(s).
416 o boot.phylo() now treats correctly data frames.
418 o del.gaps() did not copy the rownames of a matrix.
420 o A small bug was fixed in CDAM.global().
422 o ace() failed with large data sets. Thanks to Rich FitzJohn for
423 the fix. With other improvements, this function is now about 6
426 o write.tree() failed with objects of class "multiPhylo".
428 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
433 o [.multiPhylo and [.DNAbin now respect the original class.
435 o Instances of the form class(phy) == "phylo" have been replaced
436 by inherits(phy, "phylo").
438 o rcoal() is now faster.
443 o klastorin() has been removed.
447 CHANGES IN APE VERSION 2.3
452 o The new functions CADM.global and CADM.post, contributed by
453 Pierre Legendre, test the congruence among several distance
456 o The new function yule.time fits a user-defined time-dependent
457 Yule model by maximum likelihood.
459 o The new function makeNodeLabel creates and/or modifies node
460 labels in a flexible way.
462 o read.tree() and write.tree() have been modified so that they can
463 handle individual tree names.
465 o plot.phylo() has a new argument 'edge.lty' that specifies the
466 types of lines used for the edges (plain, dotted, dashed, ...)
468 o phymltest() has been updated to work with PhyML 3.0.1.
473 o drop.tip() shuffled tip labels in some cases.
475 o drop.tip() did not handle node.label correctly.
477 o is.ultrametric() now checks the ordering of the edge matrix.
479 o ace() sometimes returned negative values of likelihoods of
480 ancestral states (thanks to Dan Rabosky for solving this long
486 o The data set xenarthra has been removed.
490 CHANGES IN APE VERSION 2.2-4
494 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
495 now fixed. (Thanks to Peter Wragg for the fix!)
497 o A warning message occurred for no reason with ace(method="GLS").
502 o There is now a general help page displayed with '?ape'.
506 CHANGES IN APE VERSION 2.2-3
511 o The new function extract.clade extracts a clade from a tree by
512 specifying a node number or label.
514 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
515 operations of the same names.
517 o dist.dna() can now return the number of site differences by
518 specifying model="N".
523 o chronopl() did not work with CV = TRUE.
525 o read.nexus() did not work correctly in some situations (trees on
526 multiple lines with different numbers of lines and/or with
527 comments inserted within the trees).
529 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
530 the number of lineages with non-binary trees.
535 o ape has now a namespace.
537 o drop.tip() has been improved: it should be much faster and work
538 better in some cases (e.g., see the example in ?zoom).
542 CHANGES IN APE VERSION 2.2-2
547 o dist.gene() has been substantially improved and gains an option
550 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
556 o prop.part() failed with a single tree with the default option
557 'check.labels = TRUE'.
559 o summary.DNAbin() failed to display correctly the summary of
560 sequence lengths with lists of sequences of 10,000 bases or more
561 (because summary.default uses 4 significant digits by default).
563 o read.nexus() failed to read a file with a single tree with line
564 breaks in the Newick string.
566 o del.gaps() returned a list of empty sequences when there were no
572 o phymltest() has been updated for PhyML 3.0 and gains an option
573 'append', whereas the option 'path2exec' has been removed.
575 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
576 which is returned unchanged (instead of an error).
578 o The data sets bird.orders and bird.families are now stored as
579 Newick strings; i.e., the command data(bird.orders) calls
584 CHANGES IN APE VERSION 2.2-1
589 o The new function makeLabel() helps to modify labels of trees,
590 lists of trees, or DNA sequences, with several utilities to
591 truncate and/or make them unique, substituting some
592 characters, and so on.
594 o The new function del.gaps() removes insertion gaps ("-") in a
595 set of DNA sequences.
597 o read.dna() can now read Clustal files (*.aln).
602 o root() failed with 'resolve.root = TRUE' when the root was
603 already the specified root.
605 o Several bugs were fixed in mlphylo().
607 o collapsed.singles() did not propagate the 'Nnode' and
608 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
610 o read.nexus() failed to remove correctly the comments within
613 o read.nexus() failed to read a file with a single tree and no
614 translation of tip labels.
616 o read.nexus() failed to place correctly tip labels when reading
617 a single tree with no edge lengths.
619 o A bug was fixed in sh.test().
624 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
627 o The option 'check.labels' of consensus() and prop.part() is now
630 o write.dna() now does not truncate names to 10 characters with
635 CHANGES IN APE VERSION 2.2
640 o Four new functions have been written by Damien de Vienne for the
641 graphical exploration of large trees (cophyloplot, subtrees,
642 subtreeplot), and to return the graphical coordinates of tree
645 o The new functions corPagel and corBlomberg implement the Pagel's
646 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
648 o chronopl() has been improved and gains several options: see its
649 help page for details.
651 o boot.phylo() has now an option 'trees' to possibly return the
652 bootstraped trees (the default is FALSE).
654 o prop.part() has been improved and should now be faster in all
660 o read.dna() failed if "?" occurred in the first 10 sites of the
663 o The x/y aspect of the plot is now respected when plotting a
664 circular tree (type = "r" or "f").
666 o Drawing the tip labels sometimes failed when plotting circular
669 o zoom() failed when tip labels were used instead of their numbers
670 (thanks to Yan Wong for the fix).
672 o drop.tip() failed with some trees (fixed by Yan Wong).
674 o seg.sites() failed with a list.
676 o consensus() failed in some cases. The function has been improved
677 as well and is faster.
681 CHANGES IN APE VERSION 2.1-3
686 o A bug in read.nexus() made the Windows R-GUI crash.
688 o An error was fixed in the computation of ancestral character
689 states by generalized least squares in ace().
691 o di2multi() did not modify node labels correctly.
693 o multi2di() failed if the tree had its attribute "order" set to
698 CHANGES IN APE VERSION 2.1-2
703 o There three new methods for the "multiPhylo" class: str, $,
706 o root() gains the options 'node' and 'resolve.root'
707 (FALSE by default) as well as its code being improved.
709 o mltt.plot() has now an option 'log' used in the same way
710 than in plot.default().
715 o mltt.plot() failed to display the legend with an unnamed
718 o nodelabels() with pies now correcly uses the argument
719 'cex' to draw symbols of different sizes (which has
720 worked already for thermometers).
722 o read.nexus() generally failed to read very big files.
727 o The argument 'family' of compar.gee() can now be a function
728 as well as a character string.
730 o read.tree() and read.nexus() now return an unnamed list if
733 o read.nexus() now returns a modified object of class "multiPhylo"
734 when there is a TRANSLATE block in the NEXUS file: the individual
735 trees have no 'tip.label' vector, but the list has a 'TipLabel'
736 attribute. The new methods '$' and '[[' set these elements
737 correctly when extracting trees.
741 CHANGES IN APE VERSION 2.1-1
746 o The new function rmtree generates lists of random trees.
748 o rcoal() now generates a genuine coalescent tree by default
749 (thanks to Vladimir Minin for the code).
754 o nuc.div() returned an incorrect value with the default
755 pairwise.deletion = FALSE.
760 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
761 have been improved so that they are stabler and faster.
763 o R packages used by ape are now loaded silently; lattice and gee
764 are loaded only when needed.
768 CHANGES IN APE VERSION 2.1
773 o The new function identify.phylo identifies clades on a plotted
774 tree using the mouse.
776 o It is now possible to subset a list of trees (object of class
777 "multiPhylo") with "[" while keeping its class correct.
779 o The new function as.DNAbin.alignment converts DNA sequences
780 stored in the "alignment" format of the package seqinr into
781 an object of class "DNAbin".
783 o The new function weight.taxo2 helps to build similarity matrices
784 given two taxonomic levels (usually called by other functions).
786 o write.tree() can now take a list of trees (class "multiPhylo")
787 as its main argument.
789 o plot.correlogram() and plot.correlogramList() have been
790 improved, and gain several options (see the help page for
791 details). A legend is now plotted by default.
796 o dist.dna() returned some incorrect values with `model = "JC69"'
797 and `pairwise.deletion = TRUE'. This affected only the
798 distances involving sequences with missing values. (Thanks
799 to Bruno Toupance for digging this bug out.)
801 o write.tree() failed with some trees: this is fixed by removing
802 the `multi.line' option (trees are now always printed on a
805 o read.nexus() did not correctly detect trees with multiple root
806 edges (see OTHER CHANGES).
811 o The code of mlphylo() has been almost entirely rewritten, and
812 should be much stabler. The options have been also greatly
813 simplified (see ?mlphylo and ?DNAmodel for details).
815 o The internal function nTips has been renamed klastorin_nTips.
817 o The code of is.ultrametric() contained redundancies and has
820 o The code of Moran.I() and of correlogram.formula() have been
823 o read.tree() and read.nexus() now return an error when trying to
824 read a tree with multiple root edges (see BUG FIXES). The
825 correction applied in previous version did not work in all
828 o The class c("multi.tree", "phylo") has been renamed
834 o There is now a vignette in ape: see vignette("MoranI", "ape").
839 o as.matching() and as.phylo.matching() do not support branch
842 o correlogram.phylo() and discrete.dist() have been removed.
846 CHANGES IN APE VERSION 2.0-2
851 o The new function matexpo computes the exponential of a square
854 o The new function unique.multi.tree removes duplicate trees from
857 o yule() has a new option `use.root.edge = FALSE' that specifies
858 to ignore, by default, the root edge of the tree if it exists.
863 o which.edge() failed when the index of a single terminal edge was
866 o In diversi.time(), the values returned for model C were
869 o A bug was fixed in yule() that affected the calculation of the
870 likelihood in the presence of ties in the branching times.
872 o There was a bug in the C function mat_expo4x4 affecting the
873 calculations of the transition probabilities for models HKY and
876 o A small bug was fixed in as.matrix.DNAbin (thanks to James
879 o rtree() did not `shuffle' the tip labels by default, so only a
880 limited number of labelled topologies could be generated.
884 CHANGES IN APE VERSION 2.0-1
889 o The three new functions bionj, fastme.ols, and fastme.bal
890 perform phylogeny estimation by the BIONJ and fastME methods in
891 OLS and balanced versions. This is a port to R of previous
892 previous programs done by Vincent Lefort.
894 o The new function chronoMPL performs molecular dating with the
895 mean path lengths method of Britton et al. (2002, Mol. Phyl.
898 o The new function rotate, contributed by Christoph Heibl, swaps
899 two clades connected to the same node. It works also with
900 multichotomous nodes.
902 o The new `method' as.matrix.DNAbin() may be used to convert
903 easily DNA sequences stored in a list into a matrix while
904 keeping the names and the class.
909 o chronopl() failed when some branch lengths were equal to zero:
910 an error message is now returned.
912 o di2multi() failed when there was a series of consecutive edges
917 CHANGES IN APE VERSION 1.10-2
922 o plot.phylo() can now plot circular trees: the option is type =
923 "fan" or type = "f" (to avoid the ambiguity with type = "c").
925 o prop.part() has a new option `check.labels = FALSE' which allows
926 to considerably speed-up the calculations of bipartitions. As a
927 consequence, calculations of bootstrap values with boot.phylo()
928 should be much faster.
933 o read.GenBank() did not return correctly the list of species as
934 from ape 1.10: this is fixed in this version
936 o Applying as.phylo() on a tree of class "phylo" failed: the
937 object is now returned unchanged.
941 CHANGES IN APE VERSION 1.10-1
946 o The three new functions Ntip, Nnode, and Nedge return, for a
947 given tree, the number of tips, nodes, or edges, respectively.
952 o read.nexus() did not set correctly the class of the returned
953 object when reading multiple trees.
955 o mllt.plot() failed with objects of class c("multi.tree",
958 o unroot() did not work correctly in most cases.
960 o reorder.phylo() made R freeze in some occasions.
962 o Plotting a tree in pruningwise order failed.
964 o When plotting an unrooted tree, the tip labels where not all
965 correctly positioned if the option `cex' was used.
969 CHANGES IN APE VERSION 1.10
974 o Five new `method' functions have been introduced to manipulate
975 DNA sequences in binary format (see below).
977 o Three new functions have been introduced to convert between the
978 new binary and the character formats.
980 o The new function as.alignment converts DNA sequences stored as
981 single characters into the class "alignment" used by the package
984 o read.dna() and read.GenBank() have a new argument `as.character'
985 controlling whether the sequences are returned in binary format
991 o root() failed when the tree had node labels: this is fixed.
993 o plot.phylo() did not correctly set the limits on the y-axis with
994 the default setting: this is fixed.
996 o dist.dna() returned a wrong result for the LogDet, paralinear,
997 and BH87 models with `pairwise.deletion = TRUE'.
1002 o DNA sequences are now internally stored in a binary format. See
1003 the document "A Bit-Level Coding Scheme for Nucleotides" for the
1004 details. Most functions analyzing DNA functions have been
1005 modified accordingly and are now much faster (dist.dna is now
1006 ca. 60 times faster).
1010 CHANGES IN APE VERSION 1.9-4
1015 o A bug was fixed in edgelabels().
1017 o as.phylo.hclust() did not work correctly when the object of
1018 class "hclust" has its labels set to NULL: the returned tree has
1019 now its tip labels set to "1", "2", ...
1021 o consensus could fail if some tip labels are a subset of others
1022 (e.g., "a" and "a_1"): this is now fixed.
1024 o mlphylo() failed in most cases if some branch lengths of the
1025 initial tree were greater than one: an error message is now
1028 o mlphylo() failed in most cases when estimating the proportion of
1029 invariants: this is fixed.
1033 CHANGES IN APE VERSION 1.9-3
1038 o The new function edgelabels adds labels on the edge of the tree
1039 in the same way than nodelabels or tiplabels.
1044 o multi2di() did not handle correctly branch lengths with the
1045 default option `random = TRUE': this is now fixed.
1047 o A bug was fixed in nuc.div() when using pairwise deletions.
1049 o A bug occurred in the analysis of bipartitions with large
1050 numbers of large trees, with consequences on prop.part,
1051 prop.clades, and boot.phylo.
1053 o The calculation of the Billera-Holmes-Vogtmann distance in
1054 dist.topo was wrong: this has been fixed.
1058 CHANGES IN APE VERSION 1.9-2
1063 o The new function ladderize reorganizes the internal structure of
1064 a tree to plot them left- or right-ladderized.
1066 o The new function dist.nodes computes the patristic distances
1067 between all nodes, internal and terminal, of a tree. It replaces
1068 the option `full = TRUE' of cophenetic.phylo (see below).
1073 o A bug was fixed in old2new.phylo().
1075 o Some bugs were fixed in chronopl().
1077 o The edge colours were not correctly displayed by plot.phylo
1078 (thank you to Li-San Wang for the fix).
1080 o cophenetic.phylo() failed with multichotomous trees: this is
1086 o read.dna() now returns the sequences in a matrix if they are
1087 aligned (interleaved or sequential format). Sequences in FASTA
1088 format are still returned in a list.
1090 o The option `full' of cophenetic.phylo() has been removed because
1091 it could not be used from the generic.
1094 DEPRECATED & DEFUNCT
1096 o rotate() has been removed; this function did not work correctly
1101 CHANGES IN APE VERSION 1.9-1
1106 o Trees with a single tip were not read correctly in R as the
1107 element `Nnode' was not set: this is fixed.
1109 o unroot() did not set correctly the number of nodes of the
1110 unrooted tree in most cases.
1112 o read.GenBank() failed when fetching very long sequences,
1113 particularly of the BX-series.
1115 o A bug was introduced in read.tree() with ape 1.9: it has been
1120 CHANGES IN APE VERSION 1.9
1125 o There are two new print `methods' for trees of class "phylo" and
1126 lists of trees of class "multi.tree", so that they are now
1127 displayed in a compact and informative way.
1129 o There are two new functions, old2new.phylo and new2old.phylo,
1130 for converting between the old and new coding of the class
1133 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
1134 LogDet ("logdet"), and paralinear ("paralin").
1136 o compute.brlen() has been extended: several methods are now
1137 available to compute branch lengths.
1139 o write.dna() can now handle matrices as well as lists.
1144 o cophenetic.phylo() sometimes returned a wrong result with
1145 multichotomous trees: this is fixed.
1147 o rotate() failed when a single tip was specified: the tree is now
1150 o ace() did not return the correct index matrix with custom
1151 models: this is fixed.
1153 o multi2di() did not work correctly when resolving multichotomies
1154 randomly: the topology was always the same, only the arrangement
1155 of clades was randomized: this is fixed. This function now
1156 accepts trees with no branch lengths.
1158 o The output of diversi.gof() was blurred by useless prints when a
1159 user distribution was specified. This has been corrected, and
1160 the help page of this function has been expanded.
1165 o The internal structure of the class "phylo" has been changed:
1166 see the document "Definition of Formats for Coding Phylogenetic
1167 Trees in R" for the details. In addition, the code of most
1168 functions has been improved.
1170 o Several functions have been improved by replacing some R codes
1171 by C codes: pic, plot.phylo, and reorder.phylo.
1173 o There is now a citation information: see citation("ape") in R.
1175 o write.tree() now does not add extra 0's to branch lengths so
1176 that 1.23 is printed "1.23" by default, not "1.2300000000".
1178 o The syntax of bind.tree() has been simplified. This function now
1179 accepts trees with no branch lengths, and handles correctly node
1182 o The option `as.numeric' of mrca() has been removed.
1184 o The unused options `format' and `rooted' of read.tree() have
1187 o The unused option `format' of write.tree() has been removed.
1189 o The use of node.depth() has been simplified.
1193 CHANGES IN APE VERSION 1.8-5
1198 o Two new functions read.nexus.data() and write.nexus.data(),
1199 contributed by Johan Nylander, allow to read and write molecular
1200 sequences in NEXUS files.
1202 o The new function reorder.phylo() reorders the internal structure
1203 of a tree of class "phylo". It is used as the generic, e.g.,
1206 o read.tree() and read.nexus() can now read trees with a single
1209 o The new data set `cynipids' supplies a set of protein sequences
1215 o The code of all.equal.phylo() has been completely rewritten
1216 (thanks to Benoît Durand) which fixes several bugs.
1218 o read.tree() and read.nexus() now checks the labels of the tree
1219 to remove or substitute any characters that are illegal in the
1220 Newick format (parentheses, etc.)
1222 o A negative P-value could be returned by mantel.test(): this is
1227 CHANGES IN APE VERSION 1.8-4
1232 o The new function sh.test() computes the Shimodaira-
1235 o The new function collapse.singles() removes the nodes with a
1236 single descendant from a tree.
1238 o plot.phylo() has a new argument `tip.color' to specify the
1239 colours of the tips.
1241 o mlphylo() has now an option `quiet' to control the display of
1242 the progress of the analysis (the default is FALSE).
1247 o read.dna() did not read correctly sequences in sequential format
1248 with leading alignment gaps "-": this is fixed.
1250 o ace() returned a list with no class so that the generic
1251 functions (anova, logLik, ...) could not be used directly. This
1252 is fixed as ace() now returns an object of class "ace".
1254 o anova.ace() had a small bug when computing the number of degrees
1255 of freedom: this is fixed.
1257 o mlphylo() did not work when the sequences were in a matrix or
1258 a data frame: this is fixed.
1260 o rtree() did not work correctly when trying to simulate an
1261 unrooted tree with two tips: an error message is now issued.
1266 o The algorithm of rtree() has been changed: it is now about 40,
1267 100, and 130 times faster for 10, 100, and 1000 tips,
1272 CHANGES IN APE VERSION 1.8-3
1277 o There are four new `method' functions to be used with the
1278 results of ace(): logLik(), deviance(), AIC(), and anova().
1280 o The plot method of phymltest has two new arguments: `main' to
1281 change the title, and `col' to control the colour of the
1282 segments showing the AIC values.
1284 o ace() has a new argument `ip' that gives the initial values used
1285 in the ML estimation with discrete characters (see the examples
1286 in ?ace). This function now returns a matrix giving the indices
1287 of the estimated rates when analysing discrete characters.
1289 o nodelabels() and tiplabels() have a new argument `pie' to
1290 represent proportions, with any number of categories, as
1291 piecharts. The use of the option `thermo' has been improved:
1292 there is now no limitation on the number of categories.
1297 o mlphylo() did not work with more than two partitions: this is
1300 o root() failed if the proposed outgroup was already an outgroup
1301 in the tree: this is fixed.
1303 o The `col' argument in nodelabels() and tiplabels() was not
1304 correctly passed when `text' was used: this is fixed.
1306 o Two bugs were fixed in mlphylo(): parameters were not always
1307 correctly output, and the estimation failed in some cases.
1309 o plot.phylo() was stuck when given a tree with a single tip: this
1310 is fixed and a message error is now returned.
1312 o An error was corrected in the help page of gammaStat regarding
1313 the calculation of P-values.
1315 o Using gls() could crash R when the number of species in the tree
1316 and in the variables were different: this is fixed.
1320 CHANGES IN APE VERSION 1.8-2
1325 o The new function mlphylo() fits a phylogenetic tree by maximum
1326 likelihood from DNA sequences. Its companion function DNAmodel()
1327 is used to define the substitution model which may include
1328 partitioning. There are methods for logLik(), deviance(), and
1329 AIC(), and the summary() method has been extended to display in
1330 a friendly way the results of this model fitting. Currently, the
1331 functionality is limited to estimating the substitution and
1332 associated parameters and computing the likelihood.
1334 o The new function drop1.compar.gee (used as, e.g., drop1(m))
1335 tests for single effects in GEE-based comparative method. A
1336 warning message is printed if there is not enough degrees of
1342 o An error message was sometimes issued by plot.multi.tree(),
1343 though with no consequence.
1347 CHANGES IN APE VERSION 1.8-1
1352 o There is a new plot method for lists of trees (objects of class
1353 "multi.tree"): it calls plot.phylo() internally and is
1354 documented on the same help page.
1359 o A bug was fixed in the C code that analyzes bipartitions: this
1360 has impact on several functions like prop.part, prop.clades,
1361 boot.phylo, or consensus.
1363 o root() did not work correctly when the specified outgroup had
1364 more than one element: this is fixed.
1366 o dist.dna() sometimes returned a warning inappropriately: this
1369 o If the distance object given to nj() had no rownames, nj()
1370 returned a tree with no tip labels: it now returns tips labelled
1371 "1", "2", ..., corresponding to the row numbers.
1376 o nj() has been slightly changed so that tips with a zero distance
1377 are first aggregated with zero-lengthed branches; the usual NJ
1378 procedure is then performed on a distance matrix without 0's.
1382 CHANGES IN APE VERSION 1.8
1387 o The new function chronopl() estimates dates using the penalized
1388 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1390 o The new function consensus() calculates the consensus tree of a
1393 o The new function evolve.phylo() simulates the evolution of
1394 continuous characters along a phylogeny under a Brownian model.
1396 o The new plot method for objects of class "ancestral" displays a
1397 tree together with ancestral values, as returned by the above
1400 o The new function as.phylo.formula() returns a phylogeny from a
1401 set of nested taxonomic variables given as a formula.
1403 o The new function read.caic() reads trees in CAIC format.
1405 o The new function tiplabels() allows to add labels to the tips
1406 of a tree using text or plotting symbols in a flexible way.
1408 o The new function unroot() unroots a phylogeny.
1410 o multi2di() has a new option, `random', which specifies whether
1411 to resolve the multichotomies randomly (the default) or not.
1413 o prop.part() now returns an object of class "prop.part" for which
1414 there are print (to display a partition in a more friendly way)
1415 and summary (to extract the numbers) methods.
1417 o plot.phylo() has a new option, `show.tip.label', specifying
1418 whether to print the labels of the tips. The default is TRUE.
1420 o The code of nj() has been replaced by a faster C code: it is now
1421 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1424 o write.nexus() now writes whether a tree is rooted or not.
1429 o Two bugs have been fixed in root(): unrooted trees are now
1430 handled corretly, and node labels are now output normally.
1432 o A bug was fixed in phymltest(): the executable couldn't be found
1435 o Three bug have been fixed in ace(): computing the likelihood of
1436 ancestral states of discrete characters failed, custom models
1437 did not work, and the function failed with a null gradient (a
1438 warning message is now returned; this latter bug was also
1439 present in yule.cov() as well and is now fixed).
1441 o pic() hanged out when missing data were present: a message error
1444 o A small bug was fixed in dist.dna() where the gamma correction
1445 was not always correctly dispatched.
1447 o plot.phylo() plotted correctly the root edge only when the tree
1448 was plotted rightwards: this works now for all directions.
1453 o dist.taxo() has been renamed as weight.taxo().
1455 o dist.phylo() has been replaced by the method cophenetic.phylo().
1457 o Various error and warning messages have been improved.
1461 CHANGES IN APE VERSION 1.7
1464 o The new function ace() estimates ancestral character states for
1465 continuous characters (with ML, GLS, and contrasts methods), and
1466 discrete characters (with ML only) for any number of states.
1468 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1469 of directional evolution for continuous characters. The user
1470 specifies the node(s) of the tree where the character optimum
1473 o The new function is.rooted() tests whether a tree (of class
1476 o The new function rcoal() generates random ultrametric trees with
1477 the possibility to specify the function that generates the
1478 inter-nodes distances.
1480 o The new function mrca() gives for all pairs of tips in a tree
1481 (and optionally nodes too) the most recent common ancestor.
1483 o nodelabels() has a new option `thermo' to plot proportions (up
1484 to three classes) on the nodes of a tree.
1486 o rtree() has been improved: it can now generate rooted or
1487 unrooted trees, and the mathematical function that generates the
1488 branch lengths may be specified by the user. The tip labels may
1489 be given directly in the call to rtree. The limit cases (n = 2,
1490 3) are now handled correctly.
1492 o dist.topo() has a new argument `method' with two choices: "PH85"
1493 for Penny and Henny's method (already available before and now
1494 the default), and "BHV01" for the geometric distance by Billera
1495 et al. (2001, Adv. Appl. Math. 27:733).
1497 o write.tree() has a new option, `digits', which specifies the
1498 number of digits to be printed in the Newick tree. By default
1499 digits = 10. The numbers are now always printed in decimal form
1500 (i.e., 1.0e-1 is now avoided).
1502 o dist.dna() can now compute the raw distances between pairs of
1503 DNA sequences by specifying model = "raw".
1505 o dist.phylo() has a new option `full' to possibly compute the
1506 distances among all tips and nodes of the tree. The default if
1512 o Several bugs were fixed in all.equal.phylo().
1514 o dist.dna() did not handle correctly gaps ("-") in alignments:
1515 they are now considered as missing data.
1517 o rotate() did not work if the tips were not ordered: this is
1520 o mantel.test() returned NA in some special cases: this is fixed
1521 and the function has been improved and is now faster.
1523 o A bug was fixed in diversi.gof() where the calculation of A² was
1526 o cherry() did not work correctly under some OSs (mainly Linux):
1529 o is.binary.tree() has been modified so that it works with both
1530 rooted and unrooted trees.
1532 o The documentation of theta.s() was not correct: this has been
1535 o plot.mst() did not work correctly: this is fixed.
1539 CHANGES IN APE VERSION 1.6
1544 o The new function dist.topo() computes the topological distances
1547 o The new function boot.phylo() performs a bootstrap analysis on
1548 phylogeny estimation.
1550 o The new functions prop.part() and prop.clades() analyse
1551 bipartitions from a series of trees.
1556 o read.GenBank() now uses the EFetch utility of NCBI instead of
1557 the usual Web interface: it is now much faster (e.g., 12 times
1558 faster to retrieve 8 sequences, 37 times for 60 sequences).
1563 o Several bugs were fixed in read.dna().
1565 o Several bugs were fixed in diversi.time().
1567 o is.binary.tree() did not work correctly if the tree has no edge
1568 lengths: this is fixed.
1570 o drop.tip() did not correctly propagated the `node.label' of a
1571 tree: this is fixed.
1575 CHANGES IN APE VERSION 1.5
1580 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1581 convert objects between the classes "phylo" and "matching". The
1582 latter implements the representation of binary trees introduced by
1583 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1584 as.matching() has been introduced as well.
1586 o Two new functions, multi2di() and di2multi(), allow to resolve
1587 and collapse multichotomies with branches of length zero.
1589 o The new function nuc.div() computes the nucleotide diversity
1590 from a sample a DNA sequences.
1592 o dist.dna() has been completely rewritten with a much faster
1593 (particularly for large data sets) C code. Eight models are
1594 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1595 option `method' has been renamed `model'). Computation of variance
1596 is available for all models. A gamma-correction is possible for
1597 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1598 to remove sites with missing data on a pairwise basis. The option
1599 `GCcontent' has been removed.
1601 o read.GenBank() has a new option (species.names) which specifies
1602 whether to return the species names of the organisms in addition
1603 to the accession numbers of the sequences (this is the default
1606 o write.nexus() can now write several trees in the same NEXUS file.
1608 o drop.tip() has a new option `root.edge' that allows to specify the
1609 new root edge if internal branches are trimmed.
1614 o as.phylo.hclust() failed if some labels had parentheses: this
1617 o Several bugs were fixed in all.equal.phylo(). This function now
1618 returns the logical TRUE if the trees are identical but with
1619 different representations (a report was printed previously).
1621 o read.GenBank() did not correctly handle ambiguous base codes:
1627 o birthdeath() now returns an object of class "birthdeath" for
1628 which there is a print method.
1632 CHANGES IN APE VERSION 1.4
1637 o The new function nj() performs phylogeny estimation with the
1638 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1641 o The new function which.edge() identifies the edges of a tree
1642 that belong to a group specified as a set of tips.
1644 o The new function as.phylo.phylog() converts an object of class
1645 "phylog" (from the package ade4) into an object of class
1648 o The new function axisPhylo() draws axes on the side of a
1651 o The new function howmanytrees() calculates the number of trees
1652 in different cases and giving a number of tips.
1654 o write.tree() has a new option `multi.line' (TRUE by default) to
1655 write a Newick tree on several lines rather than on a single
1658 o The functionalities of zoom() have been extended. Several
1659 subtrees can be visualized at the same time, and they are marked
1660 on the main tree with colors. The context of the subtrees can be
1661 marked with the option `subtree' (see below).
1663 o drop.tip() has a new option `subtree' (FALSE by default) which
1664 specifies whether to output in the tree how many tips have been
1667 o The arguments of add.scale.bar() have been redefined and have
1668 now default values (see ?add.scale.bar for details). This
1669 function now works even if the plotted tree has no edge length.
1671 o plot.phylo() can now plot radial trees, but this does not take
1672 edge lengths into account.
1674 o In plot.phylo() with `type = "phylogram"', if the values of
1675 `edge.color' and `edge.width' are identical for sister-branches,
1676 they are propagated to the vertical line that link them.
1681 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1682 crashing. This is fixed.
1684 o In plot.phylo(), the options `edge.color' and `edge.width' are
1685 now properly recycled; their default values are now "black" and
1688 o A bug has been fixed in write.nexus().
1693 o The function node.depth.edgelength() has been removed and
1694 replaced by a C code.
1698 CHANGES IN APE VERSION 1.3-1
1703 o The new function nodelabels() allows to add labels to the nodes
1704 of a tree using text or plotting symbols in a flexible way.
1706 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1707 numeric values specifying the lower and upper limits on the x-
1708 and y-axes. This allows to leave some space on any side of the
1709 tree. If a single value is given, this is taken as the upper
1714 CHANGES IN APE VERSION 1.3
1719 o The new function phymltest() calls the software PHYML and fits
1720 28 models of DNA sequence evolution. There are a print method to
1721 display likelihood and AIC values, a summary method to compute
1722 the hierarchical likelihood ratio tests, and a plot method to
1723 display graphically the AIC values of each model.
1725 o The new function yule.cov() fits the Yule model with covariates,
1726 a model where the speciation rate is affected by several species
1727 traits through a generalized linear model. The parameters are
1728 estimated by maximum likelihood.
1730 o Three new functions, corBrownian(), corGrafen(), and
1731 corMartins(), compute the expected correlation structures among
1732 species given a phylogeny under different models of evolution.
1733 These can be used for GLS comparative phylogenetic methods (see
1734 the examples). There are coef() and corMatrix() methods and an
1735 Initialize.corPhyl() function associated.
1737 o The new function compar.cheverud() implements Cheverud et al.'s
1738 (1985; Evolution 39:1335) phylogenetic comparative method.
1740 o The new function varcomp() estimates variance components; it has
1743 o Two new functions, panel.superpose.correlogram() and
1744 plot.correlogramList(), allow to plot several phylogenetic
1747 o The new function node.leafnumber() computes the number of leaves
1748 of a subtree defined by a particular node.
1750 o The new function node.sons() gets all tags of son nodes from a
1753 o The new function compute.brlen() computes the branch lengths of
1754 a tree according to a specified method.
1756 o plot.phylo() has three new options: "cex" controls the size of
1757 the (tip and node) labels (thus it is no more needed to change
1758 the global graphical parameter), "direction" which allows to
1759 plot the tree rightwards, leftwards, upwards, or downwards, and
1760 "y.lim" which sets the upper limit on the y-axis.
1765 o Some functions which try to match tip labels and names of
1766 additional data (e.g. vector) are likely to fail if there are
1767 typing or syntax errors. If both series of names do not perfectly
1768 match, they are ignored and a warning message is now issued.
1769 These functions are bd.ext, compar.gee, pic. Their help pages
1770 have been clarified on this point.
1774 CHANGES IN APE VERSION 1.2-7
1779 o The new function root() reroots a phylogenetic tree with respect
1780 to a specified outgroup.
1782 o The new function rotate() rotates an internal branch of a tree.
1784 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1785 trees) controls the display of the tip labels in unrooted trees.
1786 This display has been greatly improved: the tip labels are now not
1787 expected to overlap with the tree (particularly if lab4ut =
1788 "axial"). In all cases, combining appropriate values of "lab4ut"
1789 and the font size (via "par(cex = )") should result in readable
1790 unrooted trees. See ?plot.phylo for some examples.
1792 o In drop.tip(), the argument `tip' can now be numeric or character.
1797 o drop.tip() did not work correctly with trees with no branch
1798 lengths: this is fixed.
1800 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1801 plotted with some line crossings: this is now fixed.
1805 CHANGES IN APE VERSION 1.2-6
1810 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1811 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1812 to implement comparative methods with an autocorrelation approach.
1814 o A new data set describing some life history traits of Carnivores
1820 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1825 o When plotting a tree with plot.phylo(), the new default of the
1826 option `label.offset' is now 0, so the labels are always visible.
1830 CHANGES IN APE VERSION 1.2-5
1835 o The new function bd.ext() fits a birth-death model with combined
1836 phylogenetic and taxonomic data, and estimates the corresponding
1837 speciation and extinction rates.
1842 o The package gee is no more required by ape but only suggested
1843 since only the function compar.gee() calls gee.
1847 CHANGES IN APE VERSION 1.2-4
1852 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1853 and lines.popsize) implementing a new approach for inferring the
1854 demographic history from genealogies using a reversible jump
1855 MCMC have been introduced.
1857 o The unit of time in the skyline plot and in the new plots can
1858 now be chosen to be actual years, rather than substitutions.
1862 CHANGES IN APE VERSION 1.2-3
1867 o The new function rtree() generates a random binary tree with or
1868 without branch lengths.
1870 o Two new functions for drawing lineages-through-time (LTT) plots
1871 are provided: ltt.lines() adds a LTT curve to an existing plot,
1872 and mltt.plot() does a multiple LTT plot giving several trees as
1873 arguments (see `?ltt.plot' for details).
1878 o Some taxon names made R crashing when calling as.phylo.hclust():
1881 o dist.dna() returned an error with two identical DNA sequences
1882 (only using the Jukes-Cantor method returned 0): this is fixed.
1887 o The function dist.phylo() has been re-written using a different
1888 algorithm: it is now about four times faster.
1890 o The code of branching.times() has been improved: it is now about
1895 CHANGES IN APE VERSION 1.2-2
1900 o The new function seg.sites() finds the segregating sites in a
1901 sample of DNA sequences.
1906 o A bug introduced in read.tree() and in read.nexus() with version
1909 o A few errors were corrected and a few examples were added in the
1914 CHANGES IN APE VERSION 1.2-1
1919 o plot.phylo() can now draw the edge of the root of a tree if it
1920 has one (see the new option `root.edge', its default is FALSE).
1925 o A bug was fixed in read.nexus(): files with semicolons inside
1926 comment blocks were not read correctly.
1928 o The behaviour of read.tree() and read.nexus() was corrected so
1929 that tree files with badly represented root edges (e.g., with
1930 an extra pair of parentheses, see the help pages for details)
1931 are now correctly represented in the object of class "phylo";
1932 a warning message is now issued.
1936 CHANGES IN APE VERSION 1.2
1941 o plot.phylo() has been completely re-written and offers several
1942 new functionalities. Three types of trees can now be drawn:
1943 phylogram (as previously), cladogram, and unrooted tree; in
1944 all three types the branch lengths can be drawn using the edge
1945 lengths of the phylogeny or not (e.g., if the latter is absent).
1946 The vertical position of the nodes can be adjusted with two
1947 choices (see option `node.pos'). The code has been re-structured,
1948 and two new functions (potentially useful for developpers) are
1949 documented separately: node.depth.edgelength() and node.depth();
1950 see the respective help pages for details.
1952 o The new function zoom() allows to explore very large trees by
1953 focusing on a small portion of it.
1955 o The new function yule() fits by maximum likelihood the Yule model
1956 (birth-only process) to a phylogenetic tree.
1958 o Support for writing DNA sequences in FASTA format has been
1959 introduced in write.dna() (support for reading sequences in
1960 this format was introduced in read.dna() in version 1.1-2).
1961 The function has been completely re-written, fixing some bugs
1962 (see below); the default behaviour is no more to display the
1963 sequences on the standard output. Several options have been
1964 introduced to control the sequence printing in a flexible
1965 way. The help page has been extended.
1967 o A new data set is included: a supertree of bats in NEXUS format.
1972 o In theta.s(), the default of the option `variance' has
1973 been changed to `FALSE' (as was indicated in the help page).
1975 o Several bugs were fixed in the code of all.equal.phylo().
1977 o Several bugs were fixed in write.dna(), particularly this
1978 function did not work with `format = "interleaved"'.
1980 o Various errors were corrected in the help pages.
1985 o The argument names of as.hclust.phylo() have been changed
1986 from "(phy)" to "(x, ...)" to conform to the definition of
1987 the corresponding generic function.
1989 o gamma.stat() has been renamed gammaStat() to avoid confusion
1990 since gamma() is a generic function.
1994 CHANGES IN APE VERSION 1.1-3
1999 o base.freq() previously did not return a value of 0 for
2000 bases absent in the data (e.g., a vector of length 3 was
2001 returned if one base was absent). This is now fixed (a
2002 vector of length 4 is always returned).
2004 o Several bugs were fixed in read.nexus(), including that this
2005 function did not work in this absence of a "TRANSLATE"
2006 command in the NEXUS file, and that the commands were
2011 CHANGES IN APE VERSION 1.1-2
2016 o The Tamura and Nei (1993) model of DNA distance is now implemented
2017 in dist.dna(): five models are now available in this function.
2019 o A new data set is included: a set of 15 sequences of the
2020 cytochrome b mitochondrial gene of the woodmouse (Apodemus
2026 o A bug in read.nexus() was fixed.
2028 o read.dna() previously did not work correctly in most cases.
2029 The function has been completely re-written and its help page
2030 has been considerably extended (see ?read.dna for details).
2031 Underscores (_) in taxon names are no more replaced with
2032 spaces (this behaviour was undocumented).
2034 o A bug was fixed in write.dna().
2038 CHANGES IN APE VERSION 1.1-1
2043 o A bug in read.tree() introduced in APE 1.1 was fixed.
2045 o A bug in compar.gee() resulted in an error when trying to fit
2046 a model with `family = "binomial"'. This is now fixed.
2050 CHANGES IN APE VERSION 1.1
2055 o The Klastorin (1982) method as suggested by Misawa and Tajima
2056 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
2057 on the basis of phylogenetic trees has been implemented (see
2058 the function klastorin()).
2060 o Functions have been added to convert APE's "phylo" objects in
2061 "hclust" cluster objects and vice versa (see the help page of
2062 as.phylo for details).
2064 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
2065 are introduced for the estimation of absolute evolutionary rates
2066 (ratogram) and dated clock-like trees (chronogram) from
2067 phylogenetic trees using the non-parametric rate smoothing approach
2068 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
2070 o A summary method is now provided printing a summary information on a
2071 phylogenetic tree with, for instance, `summary(tree)'.
2073 o The behaviour of read.tree() was changed so that all spaces and
2074 tabulations in tree files are now ignored. Consequently, spaces in tip
2075 labels are no more allowed. Another side effect is that read.nexus()
2076 now does not replace the underscores (_) in tip labels with spaces
2077 (this behaviour was undocumented).
2079 o The function plot.phylo() has a new option (`underscore') which
2080 specifies whether the underscores in tip labels should be written on
2081 the plot as such or replaced with spaces (the default).
2083 o The function birthdeath() now computes 95% confidence intervals of
2084 the estimated parameters using profile likelihood.
2086 o Three new data sets are included: a gene tree estimated from 36
2087 landplant rbcL sequences, a gene tree estimated from 32 opsin
2088 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
2093 o A bug was fixed in dist.gene() where nothing was returned.
2095 o A bug in plot.mst() was fixed.
2097 o A bug in vcv.phylo() resulted in false correlations when the
2098 option `cor = TRUE' was used (now fixed).
2102 CHANGES IN APE VERSION 1.0
2107 o Two new functions, read.dna() and write.dna(), read/write in a file
2108 DNA sequences in interleaved or in sequential format.
2110 o Two new functions, read.nexus() and write.nexus(), read/write trees
2113 o The new function bind.tree() allows to bind two trees together,
2114 possibly handling root edges to give internal branches.
2116 o The new function drop.tip() removes the tips in a phylogenetic tree,
2117 and trims (or not) the corresponding internal branches.
2119 o The new function is.ultrametric() tests if a tree is ultrametric.
2121 o The function plot.phylo() has more functionalities such as drawing the
2122 branches with different colours and/or different widths, showing the
2123 node labels, controling the position and font of the labels, rotating
2124 the labels, and controling the space around the plot.
2126 o The function read.tree() can now read trees with no branch length,
2127 such as "(a,b),c);". Consequently, the element `edge.length' in
2128 objects of class "phylo" is now optional.
2130 o The function write.tree() has a new default behaviour: if the default
2131 for the option `file' is used (i.e. file = ""), then a variable of
2132 mode character containing the tree in Newick format is returned which
2133 can thus be assigned (e.g., tree <- write.tree(phy)).
2135 o The function read.tree() has a new argument `text' which allows
2136 to read the tree in a variable of mode character.
2138 o A new data set is included: the phylogenetic relationships among
2139 the orders of birds from Sibley and Ahlquist (1990).
2143 CHANGES IN APE VERSION 0.2-1
2148 o Several bugs were fixed in the help pages.
2152 CHANGES IN APE VERSION 0.2
2157 o The function write.tree() writes phylogenetic trees (objects of class
2158 "phylo") in an ASCII file using the Newick parenthetic format.
2160 o The function birthdeath() fits a birth-death model to branching times
2161 by maximum likelihood, and estimates the corresponding speciation and
2164 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
2167 o The function is.binary.tree() tests whether a phylogeny is binary.
2169 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
2170 as well as some methods are introduced.
2172 o Several functions, including some generics and methods, for computing
2173 skyline plot estimates (classic and generalized) of effective
2174 population size through time are introduced and replace the function
2175 skyline.plot() in version 0.1.
2177 o Two data sets are now included: the phylogenetic relationships among
2178 the families of birds from Sibley and Ahlquist (1990), and an
2179 estimated clock-like phylogeny of HIV sequences sampled in the
2180 Democratic Republic of Congo.
2183 DEPRECATED & DEFUNCT
2185 o The function skyline.plot() in ape 0.1 has been deprecated and
2186 replaced by more elaborate functions (see above).
2191 o Two important bugs were fixed in plot.phylo(): phylogenies with
2192 multichotomies not at the root or not with only terminal branches,
2193 and phylogenies with a single node (i.e. only terminal branches)
2194 did not plot. These trees should be plotted correctly now.
2196 o Several bugs were fixed in diversi.time() in the computation of
2199 o Various errors were corrected in the help pages.
projects / ape.git / blob