1 CHANGES IN APE VERSION 2.6-1
6 o as.list.DNAbin() did not work correctly with vectors.
8 o as.hclust.phylo() failed with trees with node labels (thanks to
9 Filipe Vieira for the fix).
13 CHANGES IN APE VERSION 2.6
18 o The new functions rlineage and rbdtree simulate phylogenies under
19 any user-defined time-dependent speciation-extinction model. They
20 use continuous time algorithms.
22 o The new function drop.fossil removes the extinct species from a
25 o The new function bd.time fits a user-defined time-dependent
26 birth-death model. It is a generalization of yule.time() taking
27 extinction into account.
29 o The new function MPR does most parsimonious reconstruction of
32 o The new function Ftab computes the contingency table of base
33 frequencies from a pair of sequences.
35 o There is now an 'as.list' method for the class "DNAbin".
37 o dist.dna() can compute the number of transitions or transversions
38 with the option model = "Ts" or model = "Tv", respectively.
40 o [node|tip|edge]labels() gain three options with default values to
41 control the aspect of thermometers: horiz = TRUE, width = NULL,
44 o compar.gee() has been improved with the new option 'corStruct' as an
45 alternative to 'phy' to specify the correlation structure, and
46 calculation of the QIC (Pan 2001, Biometrics). The display of the
47 results has also been improved.
49 o read.GenBank() has a new option 'gene.names' to return the name of
50 the gene (FALSE by default).
55 o extract.clade() sometimes shuffled the tip labels.
57 o plot.phylo(type = "unrooted") did not force asp = 1 (thanks to Klaus
60 o dist.dna(model = "logdet") used to divide distances by 4. The
61 documentation has been clarified on the formulae used.
66 o rTraitCont(model = "OU") has an option 'linear = TRUE' to possibly
67 change the parameterisation (see ?rTraitCont for details).
69 o pic() now returns a vector with the node labels of the tree (if
72 o write.tree() and read.tree() have been substantially thanks to
73 contributions by Klaus Schliep.
77 CHANGES IN APE VERSION 2.5-3
82 o The new function mixedFontLabel helps to make labels with bits of
83 text to be plotted in different fonts.
85 o There are now replacement operators for [, [[, and $ for the class
86 "multiPhylo" (i.e., TREES[11:20] <- rmtree(10, 100)). They possibly
87 check that the tip labels are the same in all trees.
89 o Objects of class "multiPhylo" can be built with c(): there are
90 methods for the classes "phylo" and "multiPhylo".
92 o The internal functions .compressTipLabel and .uncompressTipLabel are
98 o bind.tree(x, y, where, position = 0) did not work correctly if 'y'
99 was a single-edge tree and 'where' was a tip.
101 o rTraitCont() did not use the square-root of branch lengths when
102 simulating a Brownian motion model.
106 CHANGES IN APE VERSION 2.5-2
111 o There is now a print method for results from ace().
113 o There is a labels() method for objects of class "DNAbin".
115 o read.dna() has a new option 'as.matrix' to possibly force sequences
116 in a FASTA file to be stored in a matrix (see ?read.dna for details).
121 o as.phylo.hclust() used to multiply edge lengths by 2.
123 o A minor bug was fixed in rTraitDisc().
125 o ace() sometimes failed (parameter value was NaN and the optimisation
131 o evolve.phylo() and plot.ancestral() have been removed.
133 o chronogram(), ratogram(), and NPRS.criterion() have been removed.
138 o nj() has been improved and is now about 30% faster.
140 o The default option 'drop' of [.DNAbin has been changed to FALSE to
141 avoid dropping rownames when selecting a single sequence.
143 o print.DNAbin() has been changed to summary.DNAbin() which has been
148 CHANGES IN APE VERSION 2.5-1
153 o The new function stree generates trees with regular shapes.
155 o It is now possible to bind two trees with x + y (see ?bind.tree for
158 o drop.tip(), extract.clade(), root(), and bind.tree() now have an
159 'interactive' option to make the operation on a plotted tree.
161 o cophyloplot() gains two new arguments 'lwd' and 'lty' for the
162 association links; they are recycled like 'col' (which wasn't before).
167 o rTraitDisc() did not use its 'freq' argument correctly (it was
168 multiplied with the rate matrix column-wise instead of row-wise).
170 o [node|tip|edge]labels(thermo = ) used to draw empty thermometers
171 with NA values. Nothing is drawn now like with 'text' or 'pch'.
172 The same bug occurred with the 'pie' option.
174 o A bug was fixed in compar.ou() and the help page was clarified.
176 o bind.tree() has been rewritten fixing several bugs and making it
179 o plot.phylo(type = "p") sometimes failed to colour correctly the
180 vertical lines representing the nodes.
182 o plot.phylo(direction = "l", x.lim = 30) failed to plot the branches
183 in the correct direction though the tip labels were displayed
189 o The c, cbind, and rbind methods for "DNAbin" objetcs now check that
190 the sequences are correctly stored (in a list for c, in a matrix
191 for the two other functions).
195 CHANGES IN APE VERSION 2.5
200 o The new function parafit by Pierre Legendre tests for the
201 coevolution between hosts and parasites. It has a companion
202 function, pcoa, that does principal coordinate decomposition.
203 The latter has a biplot method.
205 o The new function lmorigin by Pierre Legendre performs multiple
206 regression through the origin with testing by permutation.
208 o The new functions rTraitCont and rTraitDisc simulate continuous and
209 discrete traits under a wide range of evolutionary models.
211 o The new function delta.plot does a delta plot following Holland et
212 al. (2002, Mol. Biol. Evol. 12:2051).
214 o The new function edges draws additional branches between any nodes
215 and/or tips on a plotted tree.
217 o The new function fancyarrows enhances arrows from graphics with
218 triangle and harpoon heads; it can be called from edges().
220 o add.scale.bar() has a new option 'ask' to draw interactively.
222 o The branch length score replaces the geodesic distance in dist.topo.
224 o Three new data sets are included: the gopher-lice data (gopher.D),
225 SO2 air pollution in 41 US cities (lmorigin.ex1, from Sokal &
226 Rohlf 1995), and some host-parasite specificity data
227 (lmorigin.ex2, from Legendre & Desdevises 2009).
232 o add.scale.bar() drew the bar outside the plotting region with the
233 default options with unrooted or radial trees.
235 o dist.topo() made R stuck when the trees had different sizes (thanks
236 to Otto Cordero for the fix).
241 o The geodesic distance has been replaced by the branch length score
246 CHANGES IN APE VERSION 2.4-1
251 o rtree() and rcoal() now accept a numeric vector for the 'br'
254 o vcv() is a new generic function with methods for the classes "phylo"
255 and "corPhyl" so that it is possible to calculate the var-cov matrix
256 for "transformation models". vcv.phylo() can still be used for trees
257 of class "phylo"; its argument 'cor' has been renamed 'corr'.
262 o bind.tree() failed when 'y' had no root edge.
264 o read.nexus() shuffled tip labels when the trees have no branch
265 lengths and there is a TRANSLATE block.
267 o read.nexus() does not try to translate node labels if there is a
268 translation table in the NEXUS file. See ?read.nexus for a
269 clarification on this behaviour.
271 o plot.multiPhylo() crashed R when plotting a list of trees with
272 compressed tip labels.
274 o write.nexus() did not translate the taxa names when asked for.
276 o plot.phylo(type = "fan") did not rotate the tip labels correctly
277 when the tree has branch lengths.
279 o ace(type = "continuous", method = "ML") now avoids sigma² being
280 negative (which resulted in an error).
282 o nj() crashed with NA/NaN in the distance matrix: an error in now
287 CHANGES IN APE VERSION 2.4
292 o base.freq() has a new option 'freq' to return the counts; the
293 default is still to return the proportions.
298 o seg.sites() did not handle ambiguous nucleotides correctly: they
301 o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
302 the tree: the argument is now ignored.
304 o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
310 o Trying to plot a tree with a single tip now returns NULL with a
311 warning (it returned an error previously).
313 o The way lines representing nodes are coloured in phylograms has
314 been modified (as well as their widths and types) following some
315 users' request; this is only for dichotomous nodes.
317 o The argument 'adj' in [node][tip][edge]labels() now works when
318 using 'pie' or 'thermo'.
320 o A more informative message error is now returned by dist.dna() when
321 'model' is badly specified (partial matching of this argument is
324 o Deprecated functions are now listed in a help page: see
325 help("ape-defunct") with the quotes.
330 o The functions heterozygosity, nuc.div, theta.h, theta.k and
331 theta.s have been moved from ape to pegas.
333 o The functions mlphylo, DNAmodel and sh.test have been removed.
337 CHANGES IN APE VERSION 2.3-3
342 o add.scale.bar() always drew a horizontal bar.
344 o zoom() shuffled tips with unrooted trees.
346 o write.nexus() failed to write correctly trees with a "TipLabel"
349 o rcoal() failed to compute branch lengths with very large n.
351 o A small bug was fixed in compar.cheverud() (thanks to Michael
354 o seg.sites() failed when passing a vector.
356 o drop.tip() sometimes shuffled tip labels.
358 o root() shuffled node labels with 'resolve.root = TRUE'.
362 CHANGES IN APE VERSION 2.3-2
367 o all.equal.phylo() did not compare unrooted trees correctly.
369 o dist.topo(... method = "PH85") did not treat unrooted trees
370 correctly (thanks to Tim Wallstrom for the fix).
372 o root() sometimes failed to test for the monophyly of the
375 o extract.clade() sometimes included too many edges.
377 o vcv.phylo() did not work correctly when the tree is in
380 o nj() did not handle correctly distance matrices with many 0's.
381 The code has also been significantly improved: 7, 70, 160 times
382 faster with n = 100, 500, 1000, respectively.
386 CHANGES IN APE VERSION 2.3-1
391 o The new function is.monophyletic tests the monophyly of a group.
393 o There is now a c() method for lists of class "DNAbin".
395 o yule.cov() now fits the null model, and its help page has been
396 corrected with respect to this change.
398 o drop.tip() has a new option 'rooted' to force (or not) a tree
399 to be treated as (un)rooted.
404 o dist.gene() failed on most occasions with the default
405 pairwise.deletion = FALSE.
407 o read.tree() failed to read correctly the tree name(s).
409 o boot.phylo() now treats correctly data frames.
411 o del.gaps() did not copy the rownames of a matrix.
413 o A small bug was fixed in CDAM.global().
415 o ace() failed with large data sets. Thanks to Rich FitzJohn for
416 the fix. With other improvements, this function is now about 6
419 o write.tree() failed with objects of class "multiPhylo".
421 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
426 o [.multiPhylo and [.DNAbin now respect the original class.
428 o Instances of the form class(phy) == "phylo" have been replaced
429 by inherits(phy, "phylo").
431 o rcoal() is now faster.
436 o klastorin() has been removed.
440 CHANGES IN APE VERSION 2.3
445 o The new functions CADM.global and CADM.post, contributed by
446 Pierre Legendre, test the congruence among several distance
449 o The new function yule.time fits a user-defined time-dependent
450 Yule model by maximum likelihood.
452 o The new function makeNodeLabel creates and/or modifies node
453 labels in a flexible way.
455 o read.tree() and write.tree() have been modified so that they can
456 handle individual tree names.
458 o plot.phylo() has a new argument 'edge.lty' that specifies the
459 types of lines used for the edges (plain, dotted, dashed, ...)
461 o phymltest() has been updated to work with PhyML 3.0.1.
466 o drop.tip() shuffled tip labels in some cases.
468 o drop.tip() did not handle node.label correctly.
470 o is.ultrametric() now checks the ordering of the edge matrix.
472 o ace() sometimes returned negative values of likelihoods of
473 ancestral states (thanks to Dan Rabosky for solving this long
479 o The data set xenarthra has been removed.
483 CHANGES IN APE VERSION 2.2-4
487 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
488 now fixed. (Thanks to Peter Wragg for the fix!)
490 o A warning message occurred for no reason with ace(method="GLS").
495 o There is now a general help page displayed with '?ape'.
499 CHANGES IN APE VERSION 2.2-3
504 o The new function extract.clade extracts a clade from a tree by
505 specifying a node number or label.
507 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
508 operations of the same names.
510 o dist.dna() can now return the number of site differences by
511 specifying model="N".
516 o chronopl() did not work with CV = TRUE.
518 o read.nexus() did not work correctly in some situations (trees on
519 multiple lines with different numbers of lines and/or with
520 comments inserted within the trees).
522 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
523 the number of lineages with non-binary trees.
528 o ape has now a namespace.
530 o drop.tip() has been improved: it should be much faster and work
531 better in some cases (e.g., see the example in ?zoom).
535 CHANGES IN APE VERSION 2.2-2
540 o dist.gene() has been substantially improved and gains an option
543 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
549 o prop.part() failed with a single tree with the default option
550 'check.labels = TRUE'.
552 o summary.DNAbin() failed to display correctly the summary of
553 sequence lengths with lists of sequences of 10,000 bases or more
554 (because summary.default uses 4 significant digits by default).
556 o read.nexus() failed to read a file with a single tree with line
557 breaks in the Newick string.
559 o del.gaps() returned a list of empty sequences when there were no
565 o phymltest() has been updated for PhyML 3.0 and gains an option
566 'append', whereas the option 'path2exec' has been removed.
568 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
569 which is returned unchanged (instead of an error).
571 o The data sets bird.orders and bird.families are now stored as
572 Newick strings; i.e., the command data(bird.orders) calls
577 CHANGES IN APE VERSION 2.2-1
582 o The new function makeLabel() helps to modify labels of trees,
583 lists of trees, or DNA sequences, with several utilities to
584 truncate and/or make them unique, substituting some
585 characters, and so on.
587 o The new function del.gaps() removes insertion gaps ("-") in a
588 set of DNA sequences.
590 o read.dna() can now read Clustal files (*.aln).
595 o root() failed with 'resolve.root = TRUE' when the root was
596 already the specified root.
598 o Several bugs were fixed in mlphylo().
600 o collapsed.singles() did not propagate the 'Nnode' and
601 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
603 o read.nexus() failed to remove correctly the comments within
606 o read.nexus() failed to read a file with a single tree and no
607 translation of tip labels.
609 o read.nexus() failed to place correctly tip labels when reading
610 a single tree with no edge lengths.
612 o A bug was fixed in sh.test().
617 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
620 o The option 'check.labels' of consensus() and prop.part() is now
623 o write.dna() now does not truncate names to 10 characters with
628 CHANGES IN APE VERSION 2.2
633 o Four new functions have been written by Damien de Vienne for the
634 graphical exploration of large trees (cophyloplot, subtrees,
635 subtreeplot), and to return the graphical coordinates of tree
638 o The new functions corPagel and corBlomberg implement the Pagel's
639 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
641 o chronopl() has been improved and gains several options: see its
642 help page for details.
644 o boot.phylo() has now an option 'trees' to possibly return the
645 bootstraped trees (the default is FALSE).
647 o prop.part() has been improved and should now be faster in all
653 o read.dna() failed if "?" occurred in the first 10 sites of the
656 o The x/y aspect of the plot is now respected when plotting a
657 circular tree (type = "r" or "f").
659 o Drawing the tip labels sometimes failed when plotting circular
662 o zoom() failed when tip labels were used instead of their numbers
663 (thanks to Yan Wong for the fix).
665 o drop.tip() failed with some trees (fixed by Yan Wong).
667 o seg.sites() failed with a list.
669 o consensus() failed in some cases. The function has been improved
670 as well and is faster.
674 CHANGES IN APE VERSION 2.1-3
679 o A bug in read.nexus() made the Windows R-GUI crash.
681 o An error was fixed in the computation of ancestral character
682 states by generalized least squares in ace().
684 o di2multi() did not modify node labels correctly.
686 o multi2di() failed if the tree had its attribute "order" set to
691 CHANGES IN APE VERSION 2.1-2
696 o There three new methods for the "multiPhylo" class: str, $,
699 o root() gains the options 'node' and 'resolve.root'
700 (FALSE by default) as well as its code being improved.
702 o mltt.plot() has now an option 'log' used in the same way
703 than in plot.default().
708 o mltt.plot() failed to display the legend with an unnamed
711 o nodelabels() with pies now correcly uses the argument
712 'cex' to draw symbols of different sizes (which has
713 worked already for thermometers).
715 o read.nexus() generally failed to read very big files.
720 o The argument 'family' of compar.gee() can now be a function
721 as well as a character string.
723 o read.tree() and read.nexus() now return an unnamed list if
726 o read.nexus() now returns a modified object of class "multiPhylo"
727 when there is a TRANSLATE block in the NEXUS file: the individual
728 trees have no 'tip.label' vector, but the list has a 'TipLabel'
729 attribute. The new methods '$' and '[[' set these elements
730 correctly when extracting trees.
734 CHANGES IN APE VERSION 2.1-1
739 o The new function rmtree generates lists of random trees.
741 o rcoal() now generates a genuine coalescent tree by default
742 (thanks to Vladimir Minin for the code).
747 o nuc.div() returned an incorrect value with the default
748 pairwise.deletion = FALSE.
753 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
754 have been improved so that they are stabler and faster.
756 o R packages used by ape are now loaded silently; lattice and gee
757 are loaded only when needed.
761 CHANGES IN APE VERSION 2.1
766 o The new function identify.phylo identifies clades on a plotted
767 tree using the mouse.
769 o It is now possible to subset a list of trees (object of class
770 "multiPhylo") with "[" while keeping its class correct.
772 o The new function as.DNAbin.alignment converts DNA sequences
773 stored in the "alignment" format of the package seqinr into
774 an object of class "DNAbin".
776 o The new function weight.taxo2 helps to build similarity matrices
777 given two taxonomic levels (usually called by other functions).
779 o write.tree() can now take a list of trees (class "multiPhylo")
780 as its main argument.
782 o plot.correlogram() and plot.correlogramList() have been
783 improved, and gain several options (see the help page for
784 details). A legend is now plotted by default.
789 o dist.dna() returned some incorrect values with `model = "JC69"'
790 and `pairwise.deletion = TRUE'. This affected only the
791 distances involving sequences with missing values. (Thanks
792 to Bruno Toupance for digging this bug out.)
794 o write.tree() failed with some trees: this is fixed by removing
795 the `multi.line' option (trees are now always printed on a
798 o read.nexus() did not correctly detect trees with multiple root
799 edges (see OTHER CHANGES).
804 o The code of mlphylo() has been almost entirely rewritten, and
805 should be much stabler. The options have been also greatly
806 simplified (see ?mlphylo and ?DNAmodel for details).
808 o The internal function nTips has been renamed klastorin_nTips.
810 o The code of is.ultrametric() contained redundancies and has
813 o The code of Moran.I() and of correlogram.formula() have been
816 o read.tree() and read.nexus() now return an error when trying to
817 read a tree with multiple root edges (see BUG FIXES). The
818 correction applied in previous version did not work in all
821 o The class c("multi.tree", "phylo") has been renamed
827 o There is now a vignette in ape: see vignette("MoranI", "ape").
832 o as.matching() and as.phylo.matching() do not support branch
835 o correlogram.phylo() and discrete.dist() have been removed.
839 CHANGES IN APE VERSION 2.0-2
844 o The new function matexpo computes the exponential of a square
847 o The new function unique.multi.tree removes duplicate trees from
850 o yule() has a new option `use.root.edge = FALSE' that specifies
851 to ignore, by default, the root edge of the tree if it exists.
856 o which.edge() failed when the index of a single terminal edge was
859 o In diversi.time(), the values returned for model C were
862 o A bug was fixed in yule() that affected the calculation of the
863 likelihood in the presence of ties in the branching times.
865 o There was a bug in the C function mat_expo4x4 affecting the
866 calculations of the transition probabilities for models HKY and
869 o A small bug was fixed in as.matrix.DNAbin (thanks to James
872 o rtree() did not `shuffle' the tip labels by default, so only a
873 limited number of labelled topologies could be generated.
877 CHANGES IN APE VERSION 2.0-1
882 o The three new functions bionj, fastme.ols, and fastme.bal
883 perform phylogeny estimation by the BIONJ and fastME methods in
884 OLS and balanced versions. This is a port to R of previous
885 previous programs done by Vincent Lefort.
887 o The new function chronoMPL performs molecular dating with the
888 mean path lengths method of Britton et al. (2002, Mol. Phyl.
891 o The new function rotate, contributed by Christoph Heibl, swaps
892 two clades connected to the same node. It works also with
893 multichotomous nodes.
895 o The new `method' as.matrix.DNAbin() may be used to convert
896 easily DNA sequences stored in a list into a matrix while
897 keeping the names and the class.
902 o chronopl() failed when some branch lengths were equal to zero:
903 an error message is now returned.
905 o di2multi() failed when there was a series of consecutive edges
910 CHANGES IN APE VERSION 1.10-2
915 o plot.phylo() can now plot circular trees: the option is type =
916 "fan" or type = "f" (to avoid the ambiguity with type = "c").
918 o prop.part() has a new option `check.labels = FALSE' which allows
919 to considerably speed-up the calculations of bipartitions. As a
920 consequence, calculations of bootstrap values with boot.phylo()
921 should be much faster.
926 o read.GenBank() did not return correctly the list of species as
927 from ape 1.10: this is fixed in this version
929 o Applying as.phylo() on a tree of class "phylo" failed: the
930 object is now returned unchanged.
934 CHANGES IN APE VERSION 1.10-1
939 o The three new functions Ntip, Nnode, and Nedge return, for a
940 given tree, the number of tips, nodes, or edges, respectively.
945 o read.nexus() did not set correctly the class of the returned
946 object when reading multiple trees.
948 o mllt.plot() failed with objects of class c("multi.tree",
951 o unroot() did not work correctly in most cases.
953 o reorder.phylo() made R freeze in some occasions.
955 o Plotting a tree in pruningwise order failed.
957 o When plotting an unrooted tree, the tip labels where not all
958 correctly positioned if the option `cex' was used.
962 CHANGES IN APE VERSION 1.10
967 o Five new `method' functions have been introduced to manipulate
968 DNA sequences in binary format (see below).
970 o Three new functions have been introduced to convert between the
971 new binary and the character formats.
973 o The new function as.alignment converts DNA sequences stored as
974 single characters into the class "alignment" used by the package
977 o read.dna() and read.GenBank() have a new argument `as.character'
978 controlling whether the sequences are returned in binary format
984 o root() failed when the tree had node labels: this is fixed.
986 o plot.phylo() did not correctly set the limits on the y-axis with
987 the default setting: this is fixed.
989 o dist.dna() returned a wrong result for the LogDet, paralinear,
990 and BH87 models with `pairwise.deletion = TRUE'.
995 o DNA sequences are now internally stored in a binary format. See
996 the document "A Bit-Level Coding Scheme for Nucleotides" for the
997 details. Most functions analyzing DNA functions have been
998 modified accordingly and are now much faster (dist.dna is now
999 ca. 60 times faster).
1003 CHANGES IN APE VERSION 1.9-4
1008 o A bug was fixed in edgelabels().
1010 o as.phylo.hclust() did not work correctly when the object of
1011 class "hclust" has its labels set to NULL: the returned tree has
1012 now its tip labels set to "1", "2", ...
1014 o consensus could fail if some tip labels are a subset of others
1015 (e.g., "a" and "a_1"): this is now fixed.
1017 o mlphylo() failed in most cases if some branch lengths of the
1018 initial tree were greater than one: an error message is now
1021 o mlphylo() failed in most cases when estimating the proportion of
1022 invariants: this is fixed.
1026 CHANGES IN APE VERSION 1.9-3
1031 o The new function edgelabels adds labels on the edge of the tree
1032 in the same way than nodelabels or tiplabels.
1037 o multi2di() did not handle correctly branch lengths with the
1038 default option `random = TRUE': this is now fixed.
1040 o A bug was fixed in nuc.div() when using pairwise deletions.
1042 o A bug occurred in the analysis of bipartitions with large
1043 numbers of large trees, with consequences on prop.part,
1044 prop.clades, and boot.phylo.
1046 o The calculation of the Billera-Holmes-Vogtmann distance in
1047 dist.topo was wrong: this has been fixed.
1051 CHANGES IN APE VERSION 1.9-2
1056 o The new function ladderize reorganizes the internal structure of
1057 a tree to plot them left- or right-ladderized.
1059 o The new function dist.nodes computes the patristic distances
1060 between all nodes, internal and terminal, of a tree. It replaces
1061 the option `full = TRUE' of cophenetic.phylo (see below).
1066 o A bug was fixed in old2new.phylo().
1068 o Some bugs were fixed in chronopl().
1070 o The edge colours were not correctly displayed by plot.phylo
1071 (thank you to Li-San Wang for the fix).
1073 o cophenetic.phylo() failed with multichotomous trees: this is
1079 o read.dna() now returns the sequences in a matrix if they are
1080 aligned (interleaved or sequential format). Sequences in FASTA
1081 format are still returned in a list.
1083 o The option `full' of cophenetic.phylo() has been removed because
1084 it could not be used from the generic.
1087 DEPRECATED & DEFUNCT
1089 o rotate() has been removed; this function did not work correctly
1094 CHANGES IN APE VERSION 1.9-1
1099 o Trees with a single tip were not read correctly in R as the
1100 element `Nnode' was not set: this is fixed.
1102 o unroot() did not set correctly the number of nodes of the
1103 unrooted tree in most cases.
1105 o read.GenBank() failed when fetching very long sequences,
1106 particularly of the BX-series.
1108 o A bug was introduced in read.tree() with ape 1.9: it has been
1113 CHANGES IN APE VERSION 1.9
1118 o There are two new print `methods' for trees of class "phylo" and
1119 lists of trees of class "multi.tree", so that they are now
1120 displayed in a compact and informative way.
1122 o There are two new functions, old2new.phylo and new2old.phylo,
1123 for converting between the old and new coding of the class
1126 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
1127 LogDet ("logdet"), and paralinear ("paralin").
1129 o compute.brlen() has been extended: several methods are now
1130 available to compute branch lengths.
1132 o write.dna() can now handle matrices as well as lists.
1137 o cophenetic.phylo() sometimes returned a wrong result with
1138 multichotomous trees: this is fixed.
1140 o rotate() failed when a single tip was specified: the tree is now
1143 o ace() did not return the correct index matrix with custom
1144 models: this is fixed.
1146 o multi2di() did not work correctly when resolving multichotomies
1147 randomly: the topology was always the same, only the arrangement
1148 of clades was randomized: this is fixed. This function now
1149 accepts trees with no branch lengths.
1151 o The output of diversi.gof() was blurred by useless prints when a
1152 user distribution was specified. This has been corrected, and
1153 the help page of this function has been expanded.
1158 o The internal structure of the class "phylo" has been changed:
1159 see the document "Definition of Formats for Coding Phylogenetic
1160 Trees in R" for the details. In addition, the code of most
1161 functions has been improved.
1163 o Several functions have been improved by replacing some R codes
1164 by C codes: pic, plot.phylo, and reorder.phylo.
1166 o There is now a citation information: see citation("ape") in R.
1168 o write.tree() now does not add extra 0's to branch lengths so
1169 that 1.23 is printed "1.23" by default, not "1.2300000000".
1171 o The syntax of bind.tree() has been simplified. This function now
1172 accepts trees with no branch lengths, and handles correctly node
1175 o The option `as.numeric' of mrca() has been removed.
1177 o The unused options `format' and `rooted' of read.tree() have
1180 o The unused option `format' of write.tree() has been removed.
1182 o The use of node.depth() has been simplified.
1186 CHANGES IN APE VERSION 1.8-5
1191 o Two new functions read.nexus.data() and write.nexus.data(),
1192 contributed by Johan Nylander, allow to read and write molecular
1193 sequences in NEXUS files.
1195 o The new function reorder.phylo() reorders the internal structure
1196 of a tree of class "phylo". It is used as the generic, e.g.,
1199 o read.tree() and read.nexus() can now read trees with a single
1202 o The new data set `cynipids' supplies a set of protein sequences
1208 o The code of all.equal.phylo() has been completely rewritten
1209 (thanks to Benoît Durand) which fixes several bugs.
1211 o read.tree() and read.nexus() now checks the labels of the tree
1212 to remove or substitute any characters that are illegal in the
1213 Newick format (parentheses, etc.)
1215 o A negative P-value could be returned by mantel.test(): this is
1220 CHANGES IN APE VERSION 1.8-4
1225 o The new function sh.test() computes the Shimodaira-
1228 o The new function collapse.singles() removes the nodes with a
1229 single descendant from a tree.
1231 o plot.phylo() has a new argument `tip.color' to specify the
1232 colours of the tips.
1234 o mlphylo() has now an option `quiet' to control the display of
1235 the progress of the analysis (the default is FALSE).
1240 o read.dna() did not read correctly sequences in sequential format
1241 with leading alignment gaps "-": this is fixed.
1243 o ace() returned a list with no class so that the generic
1244 functions (anova, logLik, ...) could not be used directly. This
1245 is fixed as ace() now returns an object of class "ace".
1247 o anova.ace() had a small bug when computing the number of degrees
1248 of freedom: this is fixed.
1250 o mlphylo() did not work when the sequences were in a matrix or
1251 a data frame: this is fixed.
1253 o rtree() did not work correctly when trying to simulate an
1254 unrooted tree with two tips: an error message is now issued.
1259 o The algorithm of rtree() has been changed: it is now about 40,
1260 100, and 130 times faster for 10, 100, and 1000 tips,
1265 CHANGES IN APE VERSION 1.8-3
1270 o There are four new `method' functions to be used with the
1271 results of ace(): logLik(), deviance(), AIC(), and anova().
1273 o The plot method of phymltest has two new arguments: `main' to
1274 change the title, and `col' to control the colour of the
1275 segments showing the AIC values.
1277 o ace() has a new argument `ip' that gives the initial values used
1278 in the ML estimation with discrete characters (see the examples
1279 in ?ace). This function now returns a matrix giving the indices
1280 of the estimated rates when analysing discrete characters.
1282 o nodelabels() and tiplabels() have a new argument `pie' to
1283 represent proportions, with any number of categories, as
1284 piecharts. The use of the option `thermo' has been improved:
1285 there is now no limitation on the number of categories.
1290 o mlphylo() did not work with more than two partitions: this is
1293 o root() failed if the proposed outgroup was already an outgroup
1294 in the tree: this is fixed.
1296 o The `col' argument in nodelabels() and tiplabels() was not
1297 correctly passed when `text' was used: this is fixed.
1299 o Two bugs were fixed in mlphylo(): parameters were not always
1300 correctly output, and the estimation failed in some cases.
1302 o plot.phylo() was stuck when given a tree with a single tip: this
1303 is fixed and a message error is now returned.
1305 o An error was corrected in the help page of gammaStat regarding
1306 the calculation of P-values.
1308 o Using gls() could crash R when the number of species in the tree
1309 and in the variables were different: this is fixed.
1313 CHANGES IN APE VERSION 1.8-2
1318 o The new function mlphylo() fits a phylogenetic tree by maximum
1319 likelihood from DNA sequences. Its companion function DNAmodel()
1320 is used to define the substitution model which may include
1321 partitioning. There are methods for logLik(), deviance(), and
1322 AIC(), and the summary() method has been extended to display in
1323 a friendly way the results of this model fitting. Currently, the
1324 functionality is limited to estimating the substitution and
1325 associated parameters and computing the likelihood.
1327 o The new function drop1.compar.gee (used as, e.g., drop1(m))
1328 tests for single effects in GEE-based comparative method. A
1329 warning message is printed if there is not enough degrees of
1335 o An error message was sometimes issued by plot.multi.tree(),
1336 though with no consequence.
1340 CHANGES IN APE VERSION 1.8-1
1345 o There is a new plot method for lists of trees (objects of class
1346 "multi.tree"): it calls plot.phylo() internally and is
1347 documented on the same help page.
1352 o A bug was fixed in the C code that analyzes bipartitions: this
1353 has impact on several functions like prop.part, prop.clades,
1354 boot.phylo, or consensus.
1356 o root() did not work correctly when the specified outgroup had
1357 more than one element: this is fixed.
1359 o dist.dna() sometimes returned a warning inappropriately: this
1362 o If the distance object given to nj() had no rownames, nj()
1363 returned a tree with no tip labels: it now returns tips labelled
1364 "1", "2", ..., corresponding to the row numbers.
1369 o nj() has been slightly changed so that tips with a zero distance
1370 are first aggregated with zero-lengthed branches; the usual NJ
1371 procedure is then performed on a distance matrix without 0's.
1375 CHANGES IN APE VERSION 1.8
1380 o The new function chronopl() estimates dates using the penalized
1381 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1383 o The new function consensus() calculates the consensus tree of a
1386 o The new function evolve.phylo() simulates the evolution of
1387 continuous characters along a phylogeny under a Brownian model.
1389 o The new plot method for objects of class "ancestral" displays a
1390 tree together with ancestral values, as returned by the above
1393 o The new function as.phylo.formula() returns a phylogeny from a
1394 set of nested taxonomic variables given as a formula.
1396 o The new function read.caic() reads trees in CAIC format.
1398 o The new function tiplabels() allows to add labels to the tips
1399 of a tree using text or plotting symbols in a flexible way.
1401 o The new function unroot() unroots a phylogeny.
1403 o multi2di() has a new option, `random', which specifies whether
1404 to resolve the multichotomies randomly (the default) or not.
1406 o prop.part() now returns an object of class "prop.part" for which
1407 there are print (to display a partition in a more friendly way)
1408 and summary (to extract the numbers) methods.
1410 o plot.phylo() has a new option, `show.tip.label', specifying
1411 whether to print the labels of the tips. The default is TRUE.
1413 o The code of nj() has been replaced by a faster C code: it is now
1414 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1417 o write.nexus() now writes whether a tree is rooted or not.
1422 o Two bugs have been fixed in root(): unrooted trees are now
1423 handled corretly, and node labels are now output normally.
1425 o A bug was fixed in phymltest(): the executable couldn't be found
1428 o Three bug have been fixed in ace(): computing the likelihood of
1429 ancestral states of discrete characters failed, custom models
1430 did not work, and the function failed with a null gradient (a
1431 warning message is now returned; this latter bug was also
1432 present in yule.cov() as well and is now fixed).
1434 o pic() hanged out when missing data were present: a message error
1437 o A small bug was fixed in dist.dna() where the gamma correction
1438 was not always correctly dispatched.
1440 o plot.phylo() plotted correctly the root edge only when the tree
1441 was plotted rightwards: this works now for all directions.
1446 o dist.taxo() has been renamed as weight.taxo().
1448 o dist.phylo() has been replaced by the method cophenetic.phylo().
1450 o Various error and warning messages have been improved.
1454 CHANGES IN APE VERSION 1.7
1457 o The new function ace() estimates ancestral character states for
1458 continuous characters (with ML, GLS, and contrasts methods), and
1459 discrete characters (with ML only) for any number of states.
1461 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1462 of directional evolution for continuous characters. The user
1463 specifies the node(s) of the tree where the character optimum
1466 o The new function is.rooted() tests whether a tree (of class
1469 o The new function rcoal() generates random ultrametric trees with
1470 the possibility to specify the function that generates the
1471 inter-nodes distances.
1473 o The new function mrca() gives for all pairs of tips in a tree
1474 (and optionally nodes too) the most recent common ancestor.
1476 o nodelabels() has a new option `thermo' to plot proportions (up
1477 to three classes) on the nodes of a tree.
1479 o rtree() has been improved: it can now generate rooted or
1480 unrooted trees, and the mathematical function that generates the
1481 branch lengths may be specified by the user. The tip labels may
1482 be given directly in the call to rtree. The limit cases (n = 2,
1483 3) are now handled correctly.
1485 o dist.topo() has a new argument `method' with two choices: "PH85"
1486 for Penny and Henny's method (already available before and now
1487 the default), and "BHV01" for the geometric distance by Billera
1488 et al. (2001, Adv. Appl. Math. 27:733).
1490 o write.tree() has a new option, `digits', which specifies the
1491 number of digits to be printed in the Newick tree. By default
1492 digits = 10. The numbers are now always printed in decimal form
1493 (i.e., 1.0e-1 is now avoided).
1495 o dist.dna() can now compute the raw distances between pairs of
1496 DNA sequences by specifying model = "raw".
1498 o dist.phylo() has a new option `full' to possibly compute the
1499 distances among all tips and nodes of the tree. The default if
1505 o Several bugs were fixed in all.equal.phylo().
1507 o dist.dna() did not handle correctly gaps ("-") in alignments:
1508 they are now considered as missing data.
1510 o rotate() did not work if the tips were not ordered: this is
1513 o mantel.test() returned NA in some special cases: this is fixed
1514 and the function has been improved and is now faster.
1516 o A bug was fixed in diversi.gof() where the calculation of A² was
1519 o cherry() did not work correctly under some OSs (mainly Linux):
1522 o is.binary.tree() has been modified so that it works with both
1523 rooted and unrooted trees.
1525 o The documentation of theta.s() was not correct: this has been
1528 o plot.mst() did not work correctly: this is fixed.
1532 CHANGES IN APE VERSION 1.6
1537 o The new function dist.topo() computes the topological distances
1540 o The new function boot.phylo() performs a bootstrap analysis on
1541 phylogeny estimation.
1543 o The new functions prop.part() and prop.clades() analyse
1544 bipartitions from a series of trees.
1549 o read.GenBank() now uses the EFetch utility of NCBI instead of
1550 the usual Web interface: it is now much faster (e.g., 12 times
1551 faster to retrieve 8 sequences, 37 times for 60 sequences).
1556 o Several bugs were fixed in read.dna().
1558 o Several bugs were fixed in diversi.time().
1560 o is.binary.tree() did not work correctly if the tree has no edge
1561 lengths: this is fixed.
1563 o drop.tip() did not correctly propagated the `node.label' of a
1564 tree: this is fixed.
1568 CHANGES IN APE VERSION 1.5
1573 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1574 convert objects between the classes "phylo" and "matching". The
1575 latter implements the representation of binary trees introduced by
1576 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1577 as.matching() has been introduced as well.
1579 o Two new functions, multi2di() and di2multi(), allow to resolve
1580 and collapse multichotomies with branches of length zero.
1582 o The new function nuc.div() computes the nucleotide diversity
1583 from a sample a DNA sequences.
1585 o dist.dna() has been completely rewritten with a much faster
1586 (particularly for large data sets) C code. Eight models are
1587 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1588 option `method' has been renamed `model'). Computation of variance
1589 is available for all models. A gamma-correction is possible for
1590 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1591 to remove sites with missing data on a pairwise basis. The option
1592 `GCcontent' has been removed.
1594 o read.GenBank() has a new option (species.names) which specifies
1595 whether to return the species names of the organisms in addition
1596 to the accession numbers of the sequences (this is the default
1599 o write.nexus() can now write several trees in the same NEXUS file.
1601 o drop.tip() has a new option `root.edge' that allows to specify the
1602 new root edge if internal branches are trimmed.
1607 o as.phylo.hclust() failed if some labels had parentheses: this
1610 o Several bugs were fixed in all.equal.phylo(). This function now
1611 returns the logical TRUE if the trees are identical but with
1612 different representations (a report was printed previously).
1614 o read.GenBank() did not correctly handle ambiguous base codes:
1620 o birthdeath() now returns an object of class "birthdeath" for
1621 which there is a print method.
1625 CHANGES IN APE VERSION 1.4
1630 o The new function nj() performs phylogeny estimation with the
1631 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1634 o The new function which.edge() identifies the edges of a tree
1635 that belong to a group specified as a set of tips.
1637 o The new function as.phylo.phylog() converts an object of class
1638 "phylog" (from the package ade4) into an object of class
1641 o The new function axisPhylo() draws axes on the side of a
1644 o The new function howmanytrees() calculates the number of trees
1645 in different cases and giving a number of tips.
1647 o write.tree() has a new option `multi.line' (TRUE by default) to
1648 write a Newick tree on several lines rather than on a single
1651 o The functionalities of zoom() have been extended. Several
1652 subtrees can be visualized at the same time, and they are marked
1653 on the main tree with colors. The context of the subtrees can be
1654 marked with the option `subtree' (see below).
1656 o drop.tip() has a new option `subtree' (FALSE by default) which
1657 specifies whether to output in the tree how many tips have been
1660 o The arguments of add.scale.bar() have been redefined and have
1661 now default values (see ?add.scale.bar for details). This
1662 function now works even if the plotted tree has no edge length.
1664 o plot.phylo() can now plot radial trees, but this does not take
1665 edge lengths into account.
1667 o In plot.phylo() with `type = "phylogram"', if the values of
1668 `edge.color' and `edge.width' are identical for sister-branches,
1669 they are propagated to the vertical line that link them.
1674 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1675 crashing. This is fixed.
1677 o In plot.phylo(), the options `edge.color' and `edge.width' are
1678 now properly recycled; their default values are now "black" and
1681 o A bug has been fixed in write.nexus().
1686 o The function node.depth.edgelength() has been removed and
1687 replaced by a C code.
1691 CHANGES IN APE VERSION 1.3-1
1696 o The new function nodelabels() allows to add labels to the nodes
1697 of a tree using text or plotting symbols in a flexible way.
1699 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1700 numeric values specifying the lower and upper limits on the x-
1701 and y-axes. This allows to leave some space on any side of the
1702 tree. If a single value is given, this is taken as the upper
1707 CHANGES IN APE VERSION 1.3
1712 o The new function phymltest() calls the software PHYML and fits
1713 28 models of DNA sequence evolution. There are a print method to
1714 display likelihood and AIC values, a summary method to compute
1715 the hierarchical likelihood ratio tests, and a plot method to
1716 display graphically the AIC values of each model.
1718 o The new function yule.cov() fits the Yule model with covariates,
1719 a model where the speciation rate is affected by several species
1720 traits through a generalized linear model. The parameters are
1721 estimated by maximum likelihood.
1723 o Three new functions, corBrownian(), corGrafen(), and
1724 corMartins(), compute the expected correlation structures among
1725 species given a phylogeny under different models of evolution.
1726 These can be used for GLS comparative phylogenetic methods (see
1727 the examples). There are coef() and corMatrix() methods and an
1728 Initialize.corPhyl() function associated.
1730 o The new function compar.cheverud() implements Cheverud et al.'s
1731 (1985; Evolution 39:1335) phylogenetic comparative method.
1733 o The new function varcomp() estimates variance components; it has
1736 o Two new functions, panel.superpose.correlogram() and
1737 plot.correlogramList(), allow to plot several phylogenetic
1740 o The new function node.leafnumber() computes the number of leaves
1741 of a subtree defined by a particular node.
1743 o The new function node.sons() gets all tags of son nodes from a
1746 o The new function compute.brlen() computes the branch lengths of
1747 a tree according to a specified method.
1749 o plot.phylo() has three new options: "cex" controls the size of
1750 the (tip and node) labels (thus it is no more needed to change
1751 the global graphical parameter), "direction" which allows to
1752 plot the tree rightwards, leftwards, upwards, or downwards, and
1753 "y.lim" which sets the upper limit on the y-axis.
1758 o Some functions which try to match tip labels and names of
1759 additional data (e.g. vector) are likely to fail if there are
1760 typing or syntax errors. If both series of names do not perfectly
1761 match, they are ignored and a warning message is now issued.
1762 These functions are bd.ext, compar.gee, pic. Their help pages
1763 have been clarified on this point.
1767 CHANGES IN APE VERSION 1.2-7
1772 o The new function root() reroots a phylogenetic tree with respect
1773 to a specified outgroup.
1775 o The new function rotate() rotates an internal branch of a tree.
1777 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1778 trees) controls the display of the tip labels in unrooted trees.
1779 This display has been greatly improved: the tip labels are now not
1780 expected to overlap with the tree (particularly if lab4ut =
1781 "axial"). In all cases, combining appropriate values of "lab4ut"
1782 and the font size (via "par(cex = )") should result in readable
1783 unrooted trees. See ?plot.phylo for some examples.
1785 o In drop.tip(), the argument `tip' can now be numeric or character.
1790 o drop.tip() did not work correctly with trees with no branch
1791 lengths: this is fixed.
1793 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1794 plotted with some line crossings: this is now fixed.
1798 CHANGES IN APE VERSION 1.2-6
1803 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1804 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1805 to implement comparative methods with an autocorrelation approach.
1807 o A new data set describing some life history traits of Carnivores
1813 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1818 o When plotting a tree with plot.phylo(), the new default of the
1819 option `label.offset' is now 0, so the labels are always visible.
1823 CHANGES IN APE VERSION 1.2-5
1828 o The new function bd.ext() fits a birth-death model with combined
1829 phylogenetic and taxonomic data, and estimates the corresponding
1830 speciation and extinction rates.
1835 o The package gee is no more required by ape but only suggested
1836 since only the function compar.gee() calls gee.
1840 CHANGES IN APE VERSION 1.2-4
1845 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1846 and lines.popsize) implementing a new approach for inferring the
1847 demographic history from genealogies using a reversible jump
1848 MCMC have been introduced.
1850 o The unit of time in the skyline plot and in the new plots can
1851 now be chosen to be actual years, rather than substitutions.
1855 CHANGES IN APE VERSION 1.2-3
1860 o The new function rtree() generates a random binary tree with or
1861 without branch lengths.
1863 o Two new functions for drawing lineages-through-time (LTT) plots
1864 are provided: ltt.lines() adds a LTT curve to an existing plot,
1865 and mltt.plot() does a multiple LTT plot giving several trees as
1866 arguments (see `?ltt.plot' for details).
1871 o Some taxon names made R crashing when calling as.phylo.hclust():
1874 o dist.dna() returned an error with two identical DNA sequences
1875 (only using the Jukes-Cantor method returned 0): this is fixed.
1880 o The function dist.phylo() has been re-written using a different
1881 algorithm: it is now about four times faster.
1883 o The code of branching.times() has been improved: it is now about
1888 CHANGES IN APE VERSION 1.2-2
1893 o The new function seg.sites() finds the segregating sites in a
1894 sample of DNA sequences.
1899 o A bug introduced in read.tree() and in read.nexus() with version
1902 o A few errors were corrected and a few examples were added in the
1907 CHANGES IN APE VERSION 1.2-1
1912 o plot.phylo() can now draw the edge of the root of a tree if it
1913 has one (see the new option `root.edge', its default is FALSE).
1918 o A bug was fixed in read.nexus(): files with semicolons inside
1919 comment blocks were not read correctly.
1921 o The behaviour of read.tree() and read.nexus() was corrected so
1922 that tree files with badly represented root edges (e.g., with
1923 an extra pair of parentheses, see the help pages for details)
1924 are now correctly represented in the object of class "phylo";
1925 a warning message is now issued.
1929 CHANGES IN APE VERSION 1.2
1934 o plot.phylo() has been completely re-written and offers several
1935 new functionalities. Three types of trees can now be drawn:
1936 phylogram (as previously), cladogram, and unrooted tree; in
1937 all three types the branch lengths can be drawn using the edge
1938 lengths of the phylogeny or not (e.g., if the latter is absent).
1939 The vertical position of the nodes can be adjusted with two
1940 choices (see option `node.pos'). The code has been re-structured,
1941 and two new functions (potentially useful for developpers) are
1942 documented separately: node.depth.edgelength() and node.depth();
1943 see the respective help pages for details.
1945 o The new function zoom() allows to explore very large trees by
1946 focusing on a small portion of it.
1948 o The new function yule() fits by maximum likelihood the Yule model
1949 (birth-only process) to a phylogenetic tree.
1951 o Support for writing DNA sequences in FASTA format has been
1952 introduced in write.dna() (support for reading sequences in
1953 this format was introduced in read.dna() in version 1.1-2).
1954 The function has been completely re-written, fixing some bugs
1955 (see below); the default behaviour is no more to display the
1956 sequences on the standard output. Several options have been
1957 introduced to control the sequence printing in a flexible
1958 way. The help page has been extended.
1960 o A new data set is included: a supertree of bats in NEXUS format.
1965 o In theta.s(), the default of the option `variance' has
1966 been changed to `FALSE' (as was indicated in the help page).
1968 o Several bugs were fixed in the code of all.equal.phylo().
1970 o Several bugs were fixed in write.dna(), particularly this
1971 function did not work with `format = "interleaved"'.
1973 o Various errors were corrected in the help pages.
1978 o The argument names of as.hclust.phylo() have been changed
1979 from "(phy)" to "(x, ...)" to conform to the definition of
1980 the corresponding generic function.
1982 o gamma.stat() has been renamed gammaStat() to avoid confusion
1983 since gamma() is a generic function.
1987 CHANGES IN APE VERSION 1.1-3
1992 o base.freq() previously did not return a value of 0 for
1993 bases absent in the data (e.g., a vector of length 3 was
1994 returned if one base was absent). This is now fixed (a
1995 vector of length 4 is always returned).
1997 o Several bugs were fixed in read.nexus(), including that this
1998 function did not work in this absence of a "TRANSLATE"
1999 command in the NEXUS file, and that the commands were
2004 CHANGES IN APE VERSION 1.1-2
2009 o The Tamura and Nei (1993) model of DNA distance is now implemented
2010 in dist.dna(): five models are now available in this function.
2012 o A new data set is included: a set of 15 sequences of the
2013 cytochrome b mitochondrial gene of the woodmouse (Apodemus
2019 o A bug in read.nexus() was fixed.
2021 o read.dna() previously did not work correctly in most cases.
2022 The function has been completely re-written and its help page
2023 has been considerably extended (see ?read.dna for details).
2024 Underscores (_) in taxon names are no more replaced with
2025 spaces (this behaviour was undocumented).
2027 o A bug was fixed in write.dna().
2031 CHANGES IN APE VERSION 1.1-1
2036 o A bug in read.tree() introduced in APE 1.1 was fixed.
2038 o A bug in compar.gee() resulted in an error when trying to fit
2039 a model with `family = "binomial"'. This is now fixed.
2043 CHANGES IN APE VERSION 1.1
2048 o The Klastorin (1982) method as suggested by Misawa and Tajima
2049 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
2050 on the basis of phylogenetic trees has been implemented (see
2051 the function klastorin()).
2053 o Functions have been added to convert APE's "phylo" objects in
2054 "hclust" cluster objects and vice versa (see the help page of
2055 as.phylo for details).
2057 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
2058 are introduced for the estimation of absolute evolutionary rates
2059 (ratogram) and dated clock-like trees (chronogram) from
2060 phylogenetic trees using the non-parametric rate smoothing approach
2061 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
2063 o A summary method is now provided printing a summary information on a
2064 phylogenetic tree with, for instance, `summary(tree)'.
2066 o The behaviour of read.tree() was changed so that all spaces and
2067 tabulations in tree files are now ignored. Consequently, spaces in tip
2068 labels are no more allowed. Another side effect is that read.nexus()
2069 now does not replace the underscores (_) in tip labels with spaces
2070 (this behaviour was undocumented).
2072 o The function plot.phylo() has a new option (`underscore') which
2073 specifies whether the underscores in tip labels should be written on
2074 the plot as such or replaced with spaces (the default).
2076 o The function birthdeath() now computes 95% confidence intervals of
2077 the estimated parameters using profile likelihood.
2079 o Three new data sets are included: a gene tree estimated from 36
2080 landplant rbcL sequences, a gene tree estimated from 32 opsin
2081 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
2086 o A bug was fixed in dist.gene() where nothing was returned.
2088 o A bug in plot.mst() was fixed.
2090 o A bug in vcv.phylo() resulted in false correlations when the
2091 option `cor = TRUE' was used (now fixed).
2095 CHANGES IN APE VERSION 1.0
2100 o Two new functions, read.dna() and write.dna(), read/write in a file
2101 DNA sequences in interleaved or in sequential format.
2103 o Two new functions, read.nexus() and write.nexus(), read/write trees
2106 o The new function bind.tree() allows to bind two trees together,
2107 possibly handling root edges to give internal branches.
2109 o The new function drop.tip() removes the tips in a phylogenetic tree,
2110 and trims (or not) the corresponding internal branches.
2112 o The new function is.ultrametric() tests if a tree is ultrametric.
2114 o The function plot.phylo() has more functionalities such as drawing the
2115 branches with different colours and/or different widths, showing the
2116 node labels, controling the position and font of the labels, rotating
2117 the labels, and controling the space around the plot.
2119 o The function read.tree() can now read trees with no branch length,
2120 such as "(a,b),c);". Consequently, the element `edge.length' in
2121 objects of class "phylo" is now optional.
2123 o The function write.tree() has a new default behaviour: if the default
2124 for the option `file' is used (i.e. file = ""), then a variable of
2125 mode character containing the tree in Newick format is returned which
2126 can thus be assigned (e.g., tree <- write.tree(phy)).
2128 o The function read.tree() has a new argument `text' which allows
2129 to read the tree in a variable of mode character.
2131 o A new data set is included: the phylogenetic relationships among
2132 the orders of birds from Sibley and Ahlquist (1990).
2136 CHANGES IN APE VERSION 0.2-1
2141 o Several bugs were fixed in the help pages.
2145 CHANGES IN APE VERSION 0.2
2150 o The function write.tree() writes phylogenetic trees (objects of class
2151 "phylo") in an ASCII file using the Newick parenthetic format.
2153 o The function birthdeath() fits a birth-death model to branching times
2154 by maximum likelihood, and estimates the corresponding speciation and
2157 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
2160 o The function is.binary.tree() tests whether a phylogeny is binary.
2162 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
2163 as well as some methods are introduced.
2165 o Several functions, including some generics and methods, for computing
2166 skyline plot estimates (classic and generalized) of effective
2167 population size through time are introduced and replace the function
2168 skyline.plot() in version 0.1.
2170 o Two data sets are now included: the phylogenetic relationships among
2171 the families of birds from Sibley and Ahlquist (1990), and an
2172 estimated clock-like phylogeny of HIV sequences sampled in the
2173 Democratic Republic of Congo.
2176 DEPRECATED & DEFUNCT
2178 o The function skyline.plot() in ape 0.1 has been deprecated and
2179 replaced by more elaborate functions (see above).
2184 o Two important bugs were fixed in plot.phylo(): phylogenies with
2185 multichotomies not at the root or not with only terminal branches,
2186 and phylogenies with a single node (i.e. only terminal branches)
2187 did not plot. These trees should be plotted correctly now.
2189 o Several bugs were fixed in diversi.time() in the computation of
2192 o Various errors were corrected in the help pages.