1 CHANGES IN APE VERSION 2.6
6 o The new functions rlineage and rbdtree simulate phylogenies under
7 any user-defined time-dependent speciation-extinction model. They
8 use new continuous time algorithms.
10 o The new function drop.fossil removes the extinct species from a
13 o The new function MPR does most parsimonious reconstruction of
16 o The new function Ftab computes the contingency table of base
17 frequencies from a pair of sequences.
19 o There is now an 'as.list' method for the class "DNAbin".
21 o dist.dna() can compute the number of transitions or transversions
22 with the option model = "Ts" or model = "Tv", respectively.
24 o [node|tip|edge]labels() gain three options with default values to
25 control the aspect of thermometers: horiz = TRUE, width = NULL,
28 o compar.gee() has been improved with the new option 'corStruct' as an
29 alternative to 'phy' to specify the correlation structure, and
30 calculation of the QIC (Pan 2001, Biometrics). The display of the
31 results has also been improved.
33 o read.GenBank() has a new option 'gene.names' to return the name of
34 the gene (FALSE by default).
39 o extract.clade() sometimes shuffled the tip labels.
41 o plot.phylo(type = "unrooted") did not force asp = 1 (thanks to Klaus
44 o dist.dna(model = "logdet") used to divide distances by 4. The
45 documentation has been clarified on the formulae used.
50 o rTraitCont(model = "OU") has an option 'linear = TRUE' to possibly
51 change the parameterisation (see ?rTraitCont for details).
53 o pic() now returns a vector with the node labels of the tree (if
58 CHANGES IN APE VERSION 2.5-3
63 o The new function mixedFontLabel helps to make labels with bits of
64 text to be plotted in different fonts.
66 o There are now replacement operators for [, [[, and $ for the class
67 "multiPhylo" (i.e., TREES[11:20] <- rmtree(10, 100)). They possibly
68 check that the tip labels are the same in all trees.
70 o Objects of class "multiPhylo" can be built with c(): there are
71 methods for the classes "phylo" and "multiPhylo".
73 o The internal functions .compressTipLabel and .uncompressTipLabel are
79 o bind.tree(x, y, where, position = 0) did not work correctly if 'y'
80 was a single-edge tree and 'where' was a tip.
82 o rTraitCont() did not use the square-root of branch lengths when
83 simulating a Brownian motion model.
87 CHANGES IN APE VERSION 2.5-2
92 o There is now a print method for results from ace().
94 o There is a labels() method for objects of class "DNAbin".
96 o read.dna() has a new option 'as.matrix' to possibly force sequences
97 in a FASTA file to be stored in a matrix (see ?read.dna for details).
102 o as.phylo.hclust() used to multiply edge lengths by 2.
104 o A minor bug was fixed in rTraitDisc().
106 o ace() sometimes failed (parameter value was NaN and the optimisation
112 o evolve.phylo() and plot.ancestral() have been removed.
114 o chronogram(), ratogram(), and NPRS.criterion() have been removed.
119 o nj() has been improved and is now about 30% faster.
121 o The default option 'drop' of [.DNAbin has been changed to FALSE to
122 avoid dropping rownames when selecting a single sequence.
124 o print.DNAbin() has been changed to summary.DNAbin() which has been
129 CHANGES IN APE VERSION 2.5-1
134 o The new function stree generates trees with regular shapes.
136 o It is now possible to bind two trees with x + y (see ?bind.tree for
139 o drop.tip(), extract.clade(), root(), and bind.tree() now have an
140 'interactive' option to make the operation on a plotted tree.
142 o cophyloplot() gains two new arguments 'lwd' and 'lty' for the
143 association links; they are recycled like 'col' (which wasn't before).
148 o rTraitDisc() did not use its 'freq' argument correctly (it was
149 multiplied with the rate matrix column-wise instead of row-wise).
151 o [node|tip|edge]labels(thermo = ) used to draw empty thermometers
152 with NA values. Nothing is drawn now like with 'text' or 'pch'.
153 The same bug occurred with the 'pie' option.
155 o A bug was fixed in compar.ou() and the help page was clarified.
157 o bind.tree() has been rewritten fixing several bugs and making it
160 o plot.phylo(type = "p") sometimes failed to colour correctly the
161 vertical lines representing the nodes.
163 o plot.phylo(direction = "l", x.lim = 30) failed to plot the branches
164 in the correct direction though the tip labels were displayed
170 o The c, cbind, and rbind methods for "DNAbin" objetcs now check that
171 the sequences are correctly stored (in a list for c, in a matrix
172 for the two other functions).
176 CHANGES IN APE VERSION 2.5
181 o The new function parafit by Pierre Legendre tests for the
182 coevolution between hosts and parasites. It has a companion
183 function, pcoa, that does principal coordinate decomposition.
184 The latter has a biplot method.
186 o The new function lmorigin by Pierre Legendre performs multiple
187 regression through the origin with testing by permutation.
189 o The new functions rTraitCont and rTraitDisc simulate continuous and
190 discrete traits under a wide range of evolutionary models.
192 o The new function delta.plot does a delta plot following Holland et
193 al. (2002, Mol. Biol. Evol. 12:2051).
195 o The new function edges draws additional branches between any nodes
196 and/or tips on a plotted tree.
198 o The new function fancyarrows enhances arrows from graphics with
199 triangle and harpoon heads; it can be called from edges().
201 o add.scale.bar() has a new option 'ask' to draw interactively.
203 o The branch length score replaces the geodesic distance in dist.topo.
205 o Three new data sets are included: the gopher-lice data (gopher.D),
206 SO2 air pollution in 41 US cities (lmorigin.ex1, from Sokal &
207 Rohlf 1995), and some host-parasite specificity data
208 (lmorigin.ex2, from Legendre & Desdevises 2009).
213 o add.scale.bar() drew the bar outside the plotting region with the
214 default options with unrooted or radial trees.
216 o dist.topo() made R stuck when the trees had different sizes (thanks
217 to Otto Cordero for the fix).
222 o The geodesic distance has been replaced by the branch length score
227 CHANGES IN APE VERSION 2.4-1
232 o rtree() and rcoal() now accept a numeric vector for the 'br'
235 o vcv() is a new generic function with methods for the classes "phylo"
236 and "corPhyl" so that it is possible to calculate the var-cov matrix
237 for "transformation models". vcv.phylo() can still be used for trees
238 of class "phylo"; its argument 'cor' has been renamed 'corr'.
243 o bind.tree() failed when 'y' had no root edge.
245 o read.nexus() shuffled tip labels when the trees have no branch
246 lengths and there is a TRANSLATE block.
248 o read.nexus() does not try to translate node labels if there is a
249 translation table in the NEXUS file. See ?read.nexus for a
250 clarification on this behaviour.
252 o plot.multiPhylo() crashed R when plotting a list of trees with
253 compressed tip labels.
255 o write.nexus() did not translate the taxa names when asked for.
257 o plot.phylo(type = "fan") did not rotate the tip labels correctly
258 when the tree has branch lengths.
260 o ace(type = "continuous", method = "ML") now avoids sigma² being
261 negative (which resulted in an error).
263 o nj() crashed with NA/NaN in the distance matrix: an error in now
268 CHANGES IN APE VERSION 2.4
273 o base.freq() has a new option 'freq' to return the counts; the
274 default is still to return the proportions.
279 o seg.sites() did not handle ambiguous nucleotides correctly: they
282 o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
283 the tree: the argument is now ignored.
285 o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
291 o Trying to plot a tree with a single tip now returns NULL with a
292 warning (it returned an error previously).
294 o The way lines representing nodes are coloured in phylograms has
295 been modified (as well as their widths and types) following some
296 users' request; this is only for dichotomous nodes.
298 o The argument 'adj' in [node][tip][edge]labels() now works when
299 using 'pie' or 'thermo'.
301 o A more informative message error is now returned by dist.dna() when
302 'model' is badly specified (partial matching of this argument is
305 o Deprecated functions are now listed in a help page: see
306 help("ape-defunct") with the quotes.
311 o The functions heterozygosity, nuc.div, theta.h, theta.k and
312 theta.s have been moved from ape to pegas.
314 o The functions mlphylo, DNAmodel and sh.test have been removed.
318 CHANGES IN APE VERSION 2.3-3
323 o add.scale.bar() always drew a horizontal bar.
325 o zoom() shuffled tips with unrooted trees.
327 o write.nexus() failed to write correctly trees with a "TipLabel"
330 o rcoal() failed to compute branch lengths with very large n.
332 o A small bug was fixed in compar.cheverud() (thanks to Michael
335 o seg.sites() failed when passing a vector.
337 o drop.tip() sometimes shuffled tip labels.
339 o root() shuffled node labels with 'resolve.root = TRUE'.
343 CHANGES IN APE VERSION 2.3-2
348 o all.equal.phylo() did not compare unrooted trees correctly.
350 o dist.topo(... method = "PH85") did not treat unrooted trees
351 correctly (thanks to Tim Wallstrom for the fix).
353 o root() sometimes failed to test for the monophyly of the
356 o extract.clade() sometimes included too many edges.
358 o vcv.phylo() did not work correctly when the tree is in
361 o nj() did not handle correctly distance matrices with many 0's.
362 The code has also been significantly improved: 7, 70, 160 times
363 faster with n = 100, 500, 1000, respectively.
367 CHANGES IN APE VERSION 2.3-1
372 o The new function is.monophyletic tests the monophyly of a group.
374 o There is now a c() method for lists of class "DNAbin".
376 o yule.cov() now fits the null model, and its help page has been
377 corrected with respect to this change.
379 o drop.tip() has a new option 'rooted' to force (or not) a tree
380 to be treated as (un)rooted.
385 o dist.gene() failed on most occasions with the default
386 pairwise.deletion = FALSE.
388 o read.tree() failed to read correctly the tree name(s).
390 o boot.phylo() now treats correctly data frames.
392 o del.gaps() did not copy the rownames of a matrix.
394 o A small bug was fixed in CDAM.global().
396 o ace() failed with large data sets. Thanks to Rich FitzJohn for
397 the fix. With other improvements, this function is now about 6
400 o write.tree() failed with objects of class "multiPhylo".
402 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
407 o [.multiPhylo and [.DNAbin now respect the original class.
409 o Instances of the form class(phy) == "phylo" have been replaced
410 by inherits(phy, "phylo").
412 o rcoal() is now faster.
417 o klastorin() has been removed.
421 CHANGES IN APE VERSION 2.3
426 o The new functions CADM.global and CADM.post, contributed by
427 Pierre Legendre, test the congruence among several distance
430 o The new function yule.time fits a user-defined time-dependent
431 Yule model by maximum likelihood.
433 o The new function makeNodeLabel creates and/or modifies node
434 labels in a flexible way.
436 o read.tree() and write.tree() have been modified so that they can
437 handle individual tree names.
439 o plot.phylo() has a new argument 'edge.lty' that specifies the
440 types of lines used for the edges (plain, dotted, dashed, ...)
442 o phymltest() has been updated to work with PhyML 3.0.1.
447 o drop.tip() shuffled tip labels in some cases.
449 o drop.tip() did not handle node.label correctly.
451 o is.ultrametric() now checks the ordering of the edge matrix.
453 o ace() sometimes returned negative values of likelihoods of
454 ancestral states (thanks to Dan Rabosky for solving this long
460 o The data set xenarthra has been removed.
464 CHANGES IN APE VERSION 2.2-4
468 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
469 now fixed. (Thanks to Peter Wragg for the fix!)
471 o A warning message occurred for no reason with ace(method="GLS").
476 o There is now a general help page displayed with '?ape'.
480 CHANGES IN APE VERSION 2.2-3
485 o The new function extract.clade extracts a clade from a tree by
486 specifying a node number or label.
488 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
489 operations of the same names.
491 o dist.dna() can now return the number of site differences by
492 specifying model="N".
497 o chronopl() did not work with CV = TRUE.
499 o read.nexus() did not work correctly in some situations (trees on
500 multiple lines with different numbers of lines and/or with
501 comments inserted within the trees).
503 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
504 the number of lineages with non-binary trees.
509 o ape has now a namespace.
511 o drop.tip() has been improved: it should be much faster and work
512 better in some cases (e.g., see the example in ?zoom).
516 CHANGES IN APE VERSION 2.2-2
521 o dist.gene() has been substantially improved and gains an option
524 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
530 o prop.part() failed with a single tree with the default option
531 'check.labels = TRUE'.
533 o summary.DNAbin() failed to display correctly the summary of
534 sequence lengths with lists of sequences of 10,000 bases or more
535 (because summary.default uses 4 significant digits by default).
537 o read.nexus() failed to read a file with a single tree with line
538 breaks in the Newick string.
540 o del.gaps() returned a list of empty sequences when there were no
546 o phymltest() has been updated for PhyML 3.0 and gains an option
547 'append', whereas the option 'path2exec' has been removed.
549 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
550 which is returned unchanged (instead of an error).
552 o The data sets bird.orders and bird.families are now stored as
553 Newick strings; i.e., the command data(bird.orders) calls
558 CHANGES IN APE VERSION 2.2-1
563 o The new function makeLabel() helps to modify labels of trees,
564 lists of trees, or DNA sequences, with several utilities to
565 truncate and/or make them unique, substituting some
566 characters, and so on.
568 o The new function del.gaps() removes insertion gaps ("-") in a
569 set of DNA sequences.
571 o read.dna() can now read Clustal files (*.aln).
576 o root() failed with 'resolve.root = TRUE' when the root was
577 already the specified root.
579 o Several bugs were fixed in mlphylo().
581 o collapsed.singles() did not propagate the 'Nnode' and
582 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
584 o read.nexus() failed to remove correctly the comments within
587 o read.nexus() failed to read a file with a single tree and no
588 translation of tip labels.
590 o read.nexus() failed to place correctly tip labels when reading
591 a single tree with no edge lengths.
593 o A bug was fixed in sh.test().
598 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
601 o The option 'check.labels' of consensus() and prop.part() is now
604 o write.dna() now does not truncate names to 10 characters with
609 CHANGES IN APE VERSION 2.2
614 o Four new functions have been written by Damien de Vienne for the
615 graphical exploration of large trees (cophyloplot, subtrees,
616 subtreeplot), and to return the graphical coordinates of tree
619 o The new functions corPagel and corBlomberg implement the Pagel's
620 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
622 o chronopl() has been improved and gains several options: see its
623 help page for details.
625 o boot.phylo() has now an option 'trees' to possibly return the
626 bootstraped trees (the default is FALSE).
628 o prop.part() has been improved and should now be faster in all
634 o read.dna() failed if "?" occurred in the first 10 sites of the
637 o The x/y aspect of the plot is now respected when plotting a
638 circular tree (type = "r" or "f").
640 o Drawing the tip labels sometimes failed when plotting circular
643 o zoom() failed when tip labels were used instead of their numbers
644 (thanks to Yan Wong for the fix).
646 o drop.tip() failed with some trees (fixed by Yan Wong).
648 o seg.sites() failed with a list.
650 o consensus() failed in some cases. The function has been improved
651 as well and is faster.
655 CHANGES IN APE VERSION 2.1-3
660 o A bug in read.nexus() made the Windows R-GUI crash.
662 o An error was fixed in the computation of ancestral character
663 states by generalized least squares in ace().
665 o di2multi() did not modify node labels correctly.
667 o multi2di() failed if the tree had its attribute "order" set to
672 CHANGES IN APE VERSION 2.1-2
677 o There three new methods for the "multiPhylo" class: str, $,
680 o root() gains the options 'node' and 'resolve.root'
681 (FALSE by default) as well as its code being improved.
683 o mltt.plot() has now an option 'log' used in the same way
684 than in plot.default().
689 o mltt.plot() failed to display the legend with an unnamed
692 o nodelabels() with pies now correcly uses the argument
693 'cex' to draw symbols of different sizes (which has
694 worked already for thermometers).
696 o read.nexus() generally failed to read very big files.
701 o The argument 'family' of compar.gee() can now be a function
702 as well as a character string.
704 o read.tree() and read.nexus() now return an unnamed list if
707 o read.nexus() now returns a modified object of class "multiPhylo"
708 when there is a TRANSLATE block in the NEXUS file: the individual
709 trees have no 'tip.label' vector, but the list has a 'TipLabel'
710 attribute. The new methods '$' and '[[' set these elements
711 correctly when extracting trees.
715 CHANGES IN APE VERSION 2.1-1
720 o The new function rmtree generates lists of random trees.
722 o rcoal() now generates a genuine coalescent tree by default
723 (thanks to Vladimir Minin for the code).
728 o nuc.div() returned an incorrect value with the default
729 pairwise.deletion = FALSE.
734 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
735 have been improved so that they are stabler and faster.
737 o R packages used by ape are now loaded silently; lattice and gee
738 are loaded only when needed.
742 CHANGES IN APE VERSION 2.1
747 o The new function identify.phylo identifies clades on a plotted
748 tree using the mouse.
750 o It is now possible to subset a list of trees (object of class
751 "multiPhylo") with "[" while keeping its class correct.
753 o The new function as.DNAbin.alignment converts DNA sequences
754 stored in the "alignment" format of the package seqinr into
755 an object of class "DNAbin".
757 o The new function weight.taxo2 helps to build similarity matrices
758 given two taxonomic levels (usually called by other functions).
760 o write.tree() can now take a list of trees (class "multiPhylo")
761 as its main argument.
763 o plot.correlogram() and plot.correlogramList() have been
764 improved, and gain several options (see the help page for
765 details). A legend is now plotted by default.
770 o dist.dna() returned some incorrect values with `model = "JC69"'
771 and `pairwise.deletion = TRUE'. This affected only the
772 distances involving sequences with missing values. (Thanks
773 to Bruno Toupance for digging this bug out.)
775 o write.tree() failed with some trees: this is fixed by removing
776 the `multi.line' option (trees are now always printed on a
779 o read.nexus() did not correctly detect trees with multiple root
780 edges (see OTHER CHANGES).
785 o The code of mlphylo() has been almost entirely rewritten, and
786 should be much stabler. The options have been also greatly
787 simplified (see ?mlphylo and ?DNAmodel for details).
789 o The internal function nTips has been renamed klastorin_nTips.
791 o The code of is.ultrametric() contained redundancies and has
794 o The code of Moran.I() and of correlogram.formula() have been
797 o read.tree() and read.nexus() now return an error when trying to
798 read a tree with multiple root edges (see BUG FIXES). The
799 correction applied in previous version did not work in all
802 o The class c("multi.tree", "phylo") has been renamed
808 o There is now a vignette in ape: see vignette("MoranI", "ape").
813 o as.matching() and as.phylo.matching() do not support branch
816 o correlogram.phylo() and discrete.dist() have been removed.
820 CHANGES IN APE VERSION 2.0-2
825 o The new function matexpo computes the exponential of a square
828 o The new function unique.multi.tree removes duplicate trees from
831 o yule() has a new option `use.root.edge = FALSE' that specifies
832 to ignore, by default, the root edge of the tree if it exists.
837 o which.edge() failed when the index of a single terminal edge was
840 o In diversi.time(), the values returned for model C were
843 o A bug was fixed in yule() that affected the calculation of the
844 likelihood in the presence of ties in the branching times.
846 o There was a bug in the C function mat_expo4x4 affecting the
847 calculations of the transition probabilities for models HKY and
850 o A small bug was fixed in as.matrix.DNAbin (thanks to James
853 o rtree() did not `shuffle' the tip labels by default, so only a
854 limited number of labelled topologies could be generated.
858 CHANGES IN APE VERSION 2.0-1
863 o The three new functions bionj, fastme.ols, and fastme.bal
864 perform phylogeny estimation by the BIONJ and fastME methods in
865 OLS and balanced versions. This is a port to R of previous
866 previous programs done by Vincent Lefort.
868 o The new function chronoMPL performs molecular dating with the
869 mean path lengths method of Britton et al. (2002, Mol. Phyl.
872 o The new function rotate, contributed by Christoph Heibl, swaps
873 two clades connected to the same node. It works also with
874 multichotomous nodes.
876 o The new `method' as.matrix.DNAbin() may be used to convert
877 easily DNA sequences stored in a list into a matrix while
878 keeping the names and the class.
883 o chronopl() failed when some branch lengths were equal to zero:
884 an error message is now returned.
886 o di2multi() failed when there was a series of consecutive edges
891 CHANGES IN APE VERSION 1.10-2
896 o plot.phylo() can now plot circular trees: the option is type =
897 "fan" or type = "f" (to avoid the ambiguity with type = "c").
899 o prop.part() has a new option `check.labels = FALSE' which allows
900 to considerably speed-up the calculations of bipartitions. As a
901 consequence, calculations of bootstrap values with boot.phylo()
902 should be much faster.
907 o read.GenBank() did not return correctly the list of species as
908 from ape 1.10: this is fixed in this version
910 o Applying as.phylo() on a tree of class "phylo" failed: the
911 object is now returned unchanged.
915 CHANGES IN APE VERSION 1.10-1
920 o The three new functions Ntip, Nnode, and Nedge return, for a
921 given tree, the number of tips, nodes, or edges, respectively.
926 o read.nexus() did not set correctly the class of the returned
927 object when reading multiple trees.
929 o mllt.plot() failed with objects of class c("multi.tree",
932 o unroot() did not work correctly in most cases.
934 o reorder.phylo() made R freeze in some occasions.
936 o Plotting a tree in pruningwise order failed.
938 o When plotting an unrooted tree, the tip labels where not all
939 correctly positioned if the option `cex' was used.
943 CHANGES IN APE VERSION 1.10
948 o Five new `method' functions have been introduced to manipulate
949 DNA sequences in binary format (see below).
951 o Three new functions have been introduced to convert between the
952 new binary and the character formats.
954 o The new function as.alignment converts DNA sequences stored as
955 single characters into the class "alignment" used by the package
958 o read.dna() and read.GenBank() have a new argument `as.character'
959 controlling whether the sequences are returned in binary format
965 o root() failed when the tree had node labels: this is fixed.
967 o plot.phylo() did not correctly set the limits on the y-axis with
968 the default setting: this is fixed.
970 o dist.dna() returned a wrong result for the LogDet, paralinear,
971 and BH87 models with `pairwise.deletion = TRUE'.
976 o DNA sequences are now internally stored in a binary format. See
977 the document "A Bit-Level Coding Scheme for Nucleotides" for the
978 details. Most functions analyzing DNA functions have been
979 modified accordingly and are now much faster (dist.dna is now
980 ca. 60 times faster).
984 CHANGES IN APE VERSION 1.9-4
989 o A bug was fixed in edgelabels().
991 o as.phylo.hclust() did not work correctly when the object of
992 class "hclust" has its labels set to NULL: the returned tree has
993 now its tip labels set to "1", "2", ...
995 o consensus could fail if some tip labels are a subset of others
996 (e.g., "a" and "a_1"): this is now fixed.
998 o mlphylo() failed in most cases if some branch lengths of the
999 initial tree were greater than one: an error message is now
1002 o mlphylo() failed in most cases when estimating the proportion of
1003 invariants: this is fixed.
1007 CHANGES IN APE VERSION 1.9-3
1012 o The new function edgelabels adds labels on the edge of the tree
1013 in the same way than nodelabels or tiplabels.
1018 o multi2di() did not handle correctly branch lengths with the
1019 default option `random = TRUE': this is now fixed.
1021 o A bug was fixed in nuc.div() when using pairwise deletions.
1023 o A bug occurred in the analysis of bipartitions with large
1024 numbers of large trees, with consequences on prop.part,
1025 prop.clades, and boot.phylo.
1027 o The calculation of the Billera-Holmes-Vogtmann distance in
1028 dist.topo was wrong: this has been fixed.
1032 CHANGES IN APE VERSION 1.9-2
1037 o The new function ladderize reorganizes the internal structure of
1038 a tree to plot them left- or right-ladderized.
1040 o The new function dist.nodes computes the patristic distances
1041 between all nodes, internal and terminal, of a tree. It replaces
1042 the option `full = TRUE' of cophenetic.phylo (see below).
1047 o A bug was fixed in old2new.phylo().
1049 o Some bugs were fixed in chronopl().
1051 o The edge colours were not correctly displayed by plot.phylo
1052 (thank you to Li-San Wang for the fix).
1054 o cophenetic.phylo() failed with multichotomous trees: this is
1060 o read.dna() now returns the sequences in a matrix if they are
1061 aligned (interleaved or sequential format). Sequences in FASTA
1062 format are still returned in a list.
1064 o The option `full' of cophenetic.phylo() has been removed because
1065 it could not be used from the generic.
1068 DEPRECATED & DEFUNCT
1070 o rotate() has been removed; this function did not work correctly
1075 CHANGES IN APE VERSION 1.9-1
1080 o Trees with a single tip were not read correctly in R as the
1081 element `Nnode' was not set: this is fixed.
1083 o unroot() did not set correctly the number of nodes of the
1084 unrooted tree in most cases.
1086 o read.GenBank() failed when fetching very long sequences,
1087 particularly of the BX-series.
1089 o A bug was introduced in read.tree() with ape 1.9: it has been
1094 CHANGES IN APE VERSION 1.9
1099 o There are two new print `methods' for trees of class "phylo" and
1100 lists of trees of class "multi.tree", so that they are now
1101 displayed in a compact and informative way.
1103 o There are two new functions, old2new.phylo and new2old.phylo,
1104 for converting between the old and new coding of the class
1107 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
1108 LogDet ("logdet"), and paralinear ("paralin").
1110 o compute.brlen() has been extended: several methods are now
1111 available to compute branch lengths.
1113 o write.dna() can now handle matrices as well as lists.
1118 o cophenetic.phylo() sometimes returned a wrong result with
1119 multichotomous trees: this is fixed.
1121 o rotate() failed when a single tip was specified: the tree is now
1124 o ace() did not return the correct index matrix with custom
1125 models: this is fixed.
1127 o multi2di() did not work correctly when resolving multichotomies
1128 randomly: the topology was always the same, only the arrangement
1129 of clades was randomized: this is fixed. This function now
1130 accepts trees with no branch lengths.
1132 o The output of diversi.gof() was blurred by useless prints when a
1133 user distribution was specified. This has been corrected, and
1134 the help page of this function has been expanded.
1139 o The internal structure of the class "phylo" has been changed:
1140 see the document "Definition of Formats for Coding Phylogenetic
1141 Trees in R" for the details. In addition, the code of most
1142 functions has been improved.
1144 o Several functions have been improved by replacing some R codes
1145 by C codes: pic, plot.phylo, and reorder.phylo.
1147 o There is now a citation information: see citation("ape") in R.
1149 o write.tree() now does not add extra 0's to branch lengths so
1150 that 1.23 is printed "1.23" by default, not "1.2300000000".
1152 o The syntax of bind.tree() has been simplified. This function now
1153 accepts trees with no branch lengths, and handles correctly node
1156 o The option `as.numeric' of mrca() has been removed.
1158 o The unused options `format' and `rooted' of read.tree() have
1161 o The unused option `format' of write.tree() has been removed.
1163 o The use of node.depth() has been simplified.
1167 CHANGES IN APE VERSION 1.8-5
1172 o Two new functions read.nexus.data() and write.nexus.data(),
1173 contributed by Johan Nylander, allow to read and write molecular
1174 sequences in NEXUS files.
1176 o The new function reorder.phylo() reorders the internal structure
1177 of a tree of class "phylo". It is used as the generic, e.g.,
1180 o read.tree() and read.nexus() can now read trees with a single
1183 o The new data set `cynipids' supplies a set of protein sequences
1189 o The code of all.equal.phylo() has been completely rewritten
1190 (thanks to Benoît Durand) which fixes several bugs.
1192 o read.tree() and read.nexus() now checks the labels of the tree
1193 to remove or substitute any characters that are illegal in the
1194 Newick format (parentheses, etc.)
1196 o A negative P-value could be returned by mantel.test(): this is
1201 CHANGES IN APE VERSION 1.8-4
1206 o The new function sh.test() computes the Shimodaira-
1209 o The new function collapse.singles() removes the nodes with a
1210 single descendant from a tree.
1212 o plot.phylo() has a new argument `tip.color' to specify the
1213 colours of the tips.
1215 o mlphylo() has now an option `quiet' to control the display of
1216 the progress of the analysis (the default is FALSE).
1221 o read.dna() did not read correctly sequences in sequential format
1222 with leading alignment gaps "-": this is fixed.
1224 o ace() returned a list with no class so that the generic
1225 functions (anova, logLik, ...) could not be used directly. This
1226 is fixed as ace() now returns an object of class "ace".
1228 o anova.ace() had a small bug when computing the number of degrees
1229 of freedom: this is fixed.
1231 o mlphylo() did not work when the sequences were in a matrix or
1232 a data frame: this is fixed.
1234 o rtree() did not work correctly when trying to simulate an
1235 unrooted tree with two tips: an error message is now issued.
1240 o The algorithm of rtree() has been changed: it is now about 40,
1241 100, and 130 times faster for 10, 100, and 1000 tips,
1246 CHANGES IN APE VERSION 1.8-3
1251 o There are four new `method' functions to be used with the
1252 results of ace(): logLik(), deviance(), AIC(), and anova().
1254 o The plot method of phymltest has two new arguments: `main' to
1255 change the title, and `col' to control the colour of the
1256 segments showing the AIC values.
1258 o ace() has a new argument `ip' that gives the initial values used
1259 in the ML estimation with discrete characters (see the examples
1260 in ?ace). This function now returns a matrix giving the indices
1261 of the estimated rates when analysing discrete characters.
1263 o nodelabels() and tiplabels() have a new argument `pie' to
1264 represent proportions, with any number of categories, as
1265 piecharts. The use of the option `thermo' has been improved:
1266 there is now no limitation on the number of categories.
1271 o mlphylo() did not work with more than two partitions: this is
1274 o root() failed if the proposed outgroup was already an outgroup
1275 in the tree: this is fixed.
1277 o The `col' argument in nodelabels() and tiplabels() was not
1278 correctly passed when `text' was used: this is fixed.
1280 o Two bugs were fixed in mlphylo(): parameters were not always
1281 correctly output, and the estimation failed in some cases.
1283 o plot.phylo() was stuck when given a tree with a single tip: this
1284 is fixed and a message error is now returned.
1286 o An error was corrected in the help page of gammaStat regarding
1287 the calculation of P-values.
1289 o Using gls() could crash R when the number of species in the tree
1290 and in the variables were different: this is fixed.
1294 CHANGES IN APE VERSION 1.8-2
1299 o The new function mlphylo() fits a phylogenetic tree by maximum
1300 likelihood from DNA sequences. Its companion function DNAmodel()
1301 is used to define the substitution model which may include
1302 partitioning. There are methods for logLik(), deviance(), and
1303 AIC(), and the summary() method has been extended to display in
1304 a friendly way the results of this model fitting. Currently, the
1305 functionality is limited to estimating the substitution and
1306 associated parameters and computing the likelihood.
1308 o The new function drop1.compar.gee (used as, e.g., drop1(m))
1309 tests for single effects in GEE-based comparative method. A
1310 warning message is printed if there is not enough degrees of
1316 o An error message was sometimes issued by plot.multi.tree(),
1317 though with no consequence.
1321 CHANGES IN APE VERSION 1.8-1
1326 o There is a new plot method for lists of trees (objects of class
1327 "multi.tree"): it calls plot.phylo() internally and is
1328 documented on the same help page.
1333 o A bug was fixed in the C code that analyzes bipartitions: this
1334 has impact on several functions like prop.part, prop.clades,
1335 boot.phylo, or consensus.
1337 o root() did not work correctly when the specified outgroup had
1338 more than one element: this is fixed.
1340 o dist.dna() sometimes returned a warning inappropriately: this
1343 o If the distance object given to nj() had no rownames, nj()
1344 returned a tree with no tip labels: it now returns tips labelled
1345 "1", "2", ..., corresponding to the row numbers.
1350 o nj() has been slightly changed so that tips with a zero distance
1351 are first aggregated with zero-lengthed branches; the usual NJ
1352 procedure is then performed on a distance matrix without 0's.
1356 CHANGES IN APE VERSION 1.8
1361 o The new function chronopl() estimates dates using the penalized
1362 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1364 o The new function consensus() calculates the consensus tree of a
1367 o The new function evolve.phylo() simulates the evolution of
1368 continuous characters along a phylogeny under a Brownian model.
1370 o The new plot method for objects of class "ancestral" displays a
1371 tree together with ancestral values, as returned by the above
1374 o The new function as.phylo.formula() returns a phylogeny from a
1375 set of nested taxonomic variables given as a formula.
1377 o The new function read.caic() reads trees in CAIC format.
1379 o The new function tiplabels() allows to add labels to the tips
1380 of a tree using text or plotting symbols in a flexible way.
1382 o The new function unroot() unroots a phylogeny.
1384 o multi2di() has a new option, `random', which specifies whether
1385 to resolve the multichotomies randomly (the default) or not.
1387 o prop.part() now returns an object of class "prop.part" for which
1388 there are print (to display a partition in a more friendly way)
1389 and summary (to extract the numbers) methods.
1391 o plot.phylo() has a new option, `show.tip.label', specifying
1392 whether to print the labels of the tips. The default is TRUE.
1394 o The code of nj() has been replaced by a faster C code: it is now
1395 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1398 o write.nexus() now writes whether a tree is rooted or not.
1403 o Two bugs have been fixed in root(): unrooted trees are now
1404 handled corretly, and node labels are now output normally.
1406 o A bug was fixed in phymltest(): the executable couldn't be found
1409 o Three bug have been fixed in ace(): computing the likelihood of
1410 ancestral states of discrete characters failed, custom models
1411 did not work, and the function failed with a null gradient (a
1412 warning message is now returned; this latter bug was also
1413 present in yule.cov() as well and is now fixed).
1415 o pic() hanged out when missing data were present: a message error
1418 o A small bug was fixed in dist.dna() where the gamma correction
1419 was not always correctly dispatched.
1421 o plot.phylo() plotted correctly the root edge only when the tree
1422 was plotted rightwards: this works now for all directions.
1427 o dist.taxo() has been renamed as weight.taxo().
1429 o dist.phylo() has been replaced by the method cophenetic.phylo().
1431 o Various error and warning messages have been improved.
1435 CHANGES IN APE VERSION 1.7
1438 o The new function ace() estimates ancestral character states for
1439 continuous characters (with ML, GLS, and contrasts methods), and
1440 discrete characters (with ML only) for any number of states.
1442 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1443 of directional evolution for continuous characters. The user
1444 specifies the node(s) of the tree where the character optimum
1447 o The new function is.rooted() tests whether a tree (of class
1450 o The new function rcoal() generates random ultrametric trees with
1451 the possibility to specify the function that generates the
1452 inter-nodes distances.
1454 o The new function mrca() gives for all pairs of tips in a tree
1455 (and optionally nodes too) the most recent common ancestor.
1457 o nodelabels() has a new option `thermo' to plot proportions (up
1458 to three classes) on the nodes of a tree.
1460 o rtree() has been improved: it can now generate rooted or
1461 unrooted trees, and the mathematical function that generates the
1462 branch lengths may be specified by the user. The tip labels may
1463 be given directly in the call to rtree. The limit cases (n = 2,
1464 3) are now handled correctly.
1466 o dist.topo() has a new argument `method' with two choices: "PH85"
1467 for Penny and Henny's method (already available before and now
1468 the default), and "BHV01" for the geometric distance by Billera
1469 et al. (2001, Adv. Appl. Math. 27:733).
1471 o write.tree() has a new option, `digits', which specifies the
1472 number of digits to be printed in the Newick tree. By default
1473 digits = 10. The numbers are now always printed in decimal form
1474 (i.e., 1.0e-1 is now avoided).
1476 o dist.dna() can now compute the raw distances between pairs of
1477 DNA sequences by specifying model = "raw".
1479 o dist.phylo() has a new option `full' to possibly compute the
1480 distances among all tips and nodes of the tree. The default if
1486 o Several bugs were fixed in all.equal.phylo().
1488 o dist.dna() did not handle correctly gaps ("-") in alignments:
1489 they are now considered as missing data.
1491 o rotate() did not work if the tips were not ordered: this is
1494 o mantel.test() returned NA in some special cases: this is fixed
1495 and the function has been improved and is now faster.
1497 o A bug was fixed in diversi.gof() where the calculation of A² was
1500 o cherry() did not work correctly under some OSs (mainly Linux):
1503 o is.binary.tree() has been modified so that it works with both
1504 rooted and unrooted trees.
1506 o The documentation of theta.s() was not correct: this has been
1509 o plot.mst() did not work correctly: this is fixed.
1513 CHANGES IN APE VERSION 1.6
1518 o The new function dist.topo() computes the topological distances
1521 o The new function boot.phylo() performs a bootstrap analysis on
1522 phylogeny estimation.
1524 o The new functions prop.part() and prop.clades() analyse
1525 bipartitions from a series of trees.
1530 o read.GenBank() now uses the EFetch utility of NCBI instead of
1531 the usual Web interface: it is now much faster (e.g., 12 times
1532 faster to retrieve 8 sequences, 37 times for 60 sequences).
1537 o Several bugs were fixed in read.dna().
1539 o Several bugs were fixed in diversi.time().
1541 o is.binary.tree() did not work correctly if the tree has no edge
1542 lengths: this is fixed.
1544 o drop.tip() did not correctly propagated the `node.label' of a
1545 tree: this is fixed.
1549 CHANGES IN APE VERSION 1.5
1554 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1555 convert objects between the classes "phylo" and "matching". The
1556 latter implements the representation of binary trees introduced by
1557 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1558 as.matching() has been introduced as well.
1560 o Two new functions, multi2di() and di2multi(), allow to resolve
1561 and collapse multichotomies with branches of length zero.
1563 o The new function nuc.div() computes the nucleotide diversity
1564 from a sample a DNA sequences.
1566 o dist.dna() has been completely rewritten with a much faster
1567 (particularly for large data sets) C code. Eight models are
1568 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1569 option `method' has been renamed `model'). Computation of variance
1570 is available for all models. A gamma-correction is possible for
1571 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1572 to remove sites with missing data on a pairwise basis. The option
1573 `GCcontent' has been removed.
1575 o read.GenBank() has a new option (species.names) which specifies
1576 whether to return the species names of the organisms in addition
1577 to the accession numbers of the sequences (this is the default
1580 o write.nexus() can now write several trees in the same NEXUS file.
1582 o drop.tip() has a new option `root.edge' that allows to specify the
1583 new root edge if internal branches are trimmed.
1588 o as.phylo.hclust() failed if some labels had parentheses: this
1591 o Several bugs were fixed in all.equal.phylo(). This function now
1592 returns the logical TRUE if the trees are identical but with
1593 different representations (a report was printed previously).
1595 o read.GenBank() did not correctly handle ambiguous base codes:
1601 o birthdeath() now returns an object of class "birthdeath" for
1602 which there is a print method.
1606 CHANGES IN APE VERSION 1.4
1611 o The new function nj() performs phylogeny estimation with the
1612 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1615 o The new function which.edge() identifies the edges of a tree
1616 that belong to a group specified as a set of tips.
1618 o The new function as.phylo.phylog() converts an object of class
1619 "phylog" (from the package ade4) into an object of class
1622 o The new function axisPhylo() draws axes on the side of a
1625 o The new function howmanytrees() calculates the number of trees
1626 in different cases and giving a number of tips.
1628 o write.tree() has a new option `multi.line' (TRUE by default) to
1629 write a Newick tree on several lines rather than on a single
1632 o The functionalities of zoom() have been extended. Several
1633 subtrees can be visualized at the same time, and they are marked
1634 on the main tree with colors. The context of the subtrees can be
1635 marked with the option `subtree' (see below).
1637 o drop.tip() has a new option `subtree' (FALSE by default) which
1638 specifies whether to output in the tree how many tips have been
1641 o The arguments of add.scale.bar() have been redefined and have
1642 now default values (see ?add.scale.bar for details). This
1643 function now works even if the plotted tree has no edge length.
1645 o plot.phylo() can now plot radial trees, but this does not take
1646 edge lengths into account.
1648 o In plot.phylo() with `type = "phylogram"', if the values of
1649 `edge.color' and `edge.width' are identical for sister-branches,
1650 they are propagated to the vertical line that link them.
1655 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1656 crashing. This is fixed.
1658 o In plot.phylo(), the options `edge.color' and `edge.width' are
1659 now properly recycled; their default values are now "black" and
1662 o A bug has been fixed in write.nexus().
1667 o The function node.depth.edgelength() has been removed and
1668 replaced by a C code.
1672 CHANGES IN APE VERSION 1.3-1
1677 o The new function nodelabels() allows to add labels to the nodes
1678 of a tree using text or plotting symbols in a flexible way.
1680 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1681 numeric values specifying the lower and upper limits on the x-
1682 and y-axes. This allows to leave some space on any side of the
1683 tree. If a single value is given, this is taken as the upper
1688 CHANGES IN APE VERSION 1.3
1693 o The new function phymltest() calls the software PHYML and fits
1694 28 models of DNA sequence evolution. There are a print method to
1695 display likelihood and AIC values, a summary method to compute
1696 the hierarchical likelihood ratio tests, and a plot method to
1697 display graphically the AIC values of each model.
1699 o The new function yule.cov() fits the Yule model with covariates,
1700 a model where the speciation rate is affected by several species
1701 traits through a generalized linear model. The parameters are
1702 estimated by maximum likelihood.
1704 o Three new functions, corBrownian(), corGrafen(), and
1705 corMartins(), compute the expected correlation structures among
1706 species given a phylogeny under different models of evolution.
1707 These can be used for GLS comparative phylogenetic methods (see
1708 the examples). There are coef() and corMatrix() methods and an
1709 Initialize.corPhyl() function associated.
1711 o The new function compar.cheverud() implements Cheverud et al.'s
1712 (1985; Evolution 39:1335) phylogenetic comparative method.
1714 o The new function varcomp() estimates variance components; it has
1717 o Two new functions, panel.superpose.correlogram() and
1718 plot.correlogramList(), allow to plot several phylogenetic
1721 o The new function node.leafnumber() computes the number of leaves
1722 of a subtree defined by a particular node.
1724 o The new function node.sons() gets all tags of son nodes from a
1727 o The new function compute.brlen() computes the branch lengths of
1728 a tree according to a specified method.
1730 o plot.phylo() has three new options: "cex" controls the size of
1731 the (tip and node) labels (thus it is no more needed to change
1732 the global graphical parameter), "direction" which allows to
1733 plot the tree rightwards, leftwards, upwards, or downwards, and
1734 "y.lim" which sets the upper limit on the y-axis.
1739 o Some functions which try to match tip labels and names of
1740 additional data (e.g. vector) are likely to fail if there are
1741 typing or syntax errors. If both series of names do not perfectly
1742 match, they are ignored and a warning message is now issued.
1743 These functions are bd.ext, compar.gee, pic. Their help pages
1744 have been clarified on this point.
1748 CHANGES IN APE VERSION 1.2-7
1753 o The new function root() reroots a phylogenetic tree with respect
1754 to a specified outgroup.
1756 o The new function rotate() rotates an internal branch of a tree.
1758 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1759 trees) controls the display of the tip labels in unrooted trees.
1760 This display has been greatly improved: the tip labels are now not
1761 expected to overlap with the tree (particularly if lab4ut =
1762 "axial"). In all cases, combining appropriate values of "lab4ut"
1763 and the font size (via "par(cex = )") should result in readable
1764 unrooted trees. See ?plot.phylo for some examples.
1766 o In drop.tip(), the argument `tip' can now be numeric or character.
1771 o drop.tip() did not work correctly with trees with no branch
1772 lengths: this is fixed.
1774 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1775 plotted with some line crossings: this is now fixed.
1779 CHANGES IN APE VERSION 1.2-6
1784 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1785 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1786 to implement comparative methods with an autocorrelation approach.
1788 o A new data set describing some life history traits of Carnivores
1794 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1799 o When plotting a tree with plot.phylo(), the new default of the
1800 option `label.offset' is now 0, so the labels are always visible.
1804 CHANGES IN APE VERSION 1.2-5
1809 o The new function bd.ext() fits a birth-death model with combined
1810 phylogenetic and taxonomic data, and estimates the corresponding
1811 speciation and extinction rates.
1816 o The package gee is no more required by ape but only suggested
1817 since only the function compar.gee() calls gee.
1821 CHANGES IN APE VERSION 1.2-4
1826 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1827 and lines.popsize) implementing a new approach for inferring the
1828 demographic history from genealogies using a reversible jump
1829 MCMC have been introduced.
1831 o The unit of time in the skyline plot and in the new plots can
1832 now be chosen to be actual years, rather than substitutions.
1836 CHANGES IN APE VERSION 1.2-3
1841 o The new function rtree() generates a random binary tree with or
1842 without branch lengths.
1844 o Two new functions for drawing lineages-through-time (LTT) plots
1845 are provided: ltt.lines() adds a LTT curve to an existing plot,
1846 and mltt.plot() does a multiple LTT plot giving several trees as
1847 arguments (see `?ltt.plot' for details).
1852 o Some taxon names made R crashing when calling as.phylo.hclust():
1855 o dist.dna() returned an error with two identical DNA sequences
1856 (only using the Jukes-Cantor method returned 0): this is fixed.
1861 o The function dist.phylo() has been re-written using a different
1862 algorithm: it is now about four times faster.
1864 o The code of branching.times() has been improved: it is now about
1869 CHANGES IN APE VERSION 1.2-2
1874 o The new function seg.sites() finds the segregating sites in a
1875 sample of DNA sequences.
1880 o A bug introduced in read.tree() and in read.nexus() with version
1883 o A few errors were corrected and a few examples were added in the
1888 CHANGES IN APE VERSION 1.2-1
1893 o plot.phylo() can now draw the edge of the root of a tree if it
1894 has one (see the new option `root.edge', its default is FALSE).
1899 o A bug was fixed in read.nexus(): files with semicolons inside
1900 comment blocks were not read correctly.
1902 o The behaviour of read.tree() and read.nexus() was corrected so
1903 that tree files with badly represented root edges (e.g., with
1904 an extra pair of parentheses, see the help pages for details)
1905 are now correctly represented in the object of class "phylo";
1906 a warning message is now issued.
1910 CHANGES IN APE VERSION 1.2
1915 o plot.phylo() has been completely re-written and offers several
1916 new functionalities. Three types of trees can now be drawn:
1917 phylogram (as previously), cladogram, and unrooted tree; in
1918 all three types the branch lengths can be drawn using the edge
1919 lengths of the phylogeny or not (e.g., if the latter is absent).
1920 The vertical position of the nodes can be adjusted with two
1921 choices (see option `node.pos'). The code has been re-structured,
1922 and two new functions (potentially useful for developpers) are
1923 documented separately: node.depth.edgelength() and node.depth();
1924 see the respective help pages for details.
1926 o The new function zoom() allows to explore very large trees by
1927 focusing on a small portion of it.
1929 o The new function yule() fits by maximum likelihood the Yule model
1930 (birth-only process) to a phylogenetic tree.
1932 o Support for writing DNA sequences in FASTA format has been
1933 introduced in write.dna() (support for reading sequences in
1934 this format was introduced in read.dna() in version 1.1-2).
1935 The function has been completely re-written, fixing some bugs
1936 (see below); the default behaviour is no more to display the
1937 sequences on the standard output. Several options have been
1938 introduced to control the sequence printing in a flexible
1939 way. The help page has been extended.
1941 o A new data set is included: a supertree of bats in NEXUS format.
1946 o In theta.s(), the default of the option `variance' has
1947 been changed to `FALSE' (as was indicated in the help page).
1949 o Several bugs were fixed in the code of all.equal.phylo().
1951 o Several bugs were fixed in write.dna(), particularly this
1952 function did not work with `format = "interleaved"'.
1954 o Various errors were corrected in the help pages.
1959 o The argument names of as.hclust.phylo() have been changed
1960 from "(phy)" to "(x, ...)" to conform to the definition of
1961 the corresponding generic function.
1963 o gamma.stat() has been renamed gammaStat() to avoid confusion
1964 since gamma() is a generic function.
1968 CHANGES IN APE VERSION 1.1-3
1973 o base.freq() previously did not return a value of 0 for
1974 bases absent in the data (e.g., a vector of length 3 was
1975 returned if one base was absent). This is now fixed (a
1976 vector of length 4 is always returned).
1978 o Several bugs were fixed in read.nexus(), including that this
1979 function did not work in this absence of a "TRANSLATE"
1980 command in the NEXUS file, and that the commands were
1985 CHANGES IN APE VERSION 1.1-2
1990 o The Tamura and Nei (1993) model of DNA distance is now implemented
1991 in dist.dna(): five models are now available in this function.
1993 o A new data set is included: a set of 15 sequences of the
1994 cytochrome b mitochondrial gene of the woodmouse (Apodemus
2000 o A bug in read.nexus() was fixed.
2002 o read.dna() previously did not work correctly in most cases.
2003 The function has been completely re-written and its help page
2004 has been considerably extended (see ?read.dna for details).
2005 Underscores (_) in taxon names are no more replaced with
2006 spaces (this behaviour was undocumented).
2008 o A bug was fixed in write.dna().
2012 CHANGES IN APE VERSION 1.1-1
2017 o A bug in read.tree() introduced in APE 1.1 was fixed.
2019 o A bug in compar.gee() resulted in an error when trying to fit
2020 a model with `family = "binomial"'. This is now fixed.
2024 CHANGES IN APE VERSION 1.1
2029 o The Klastorin (1982) method as suggested by Misawa and Tajima
2030 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
2031 on the basis of phylogenetic trees has been implemented (see
2032 the function klastorin()).
2034 o Functions have been added to convert APE's "phylo" objects in
2035 "hclust" cluster objects and vice versa (see the help page of
2036 as.phylo for details).
2038 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
2039 are introduced for the estimation of absolute evolutionary rates
2040 (ratogram) and dated clock-like trees (chronogram) from
2041 phylogenetic trees using the non-parametric rate smoothing approach
2042 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
2044 o A summary method is now provided printing a summary information on a
2045 phylogenetic tree with, for instance, `summary(tree)'.
2047 o The behaviour of read.tree() was changed so that all spaces and
2048 tabulations in tree files are now ignored. Consequently, spaces in tip
2049 labels are no more allowed. Another side effect is that read.nexus()
2050 now does not replace the underscores (_) in tip labels with spaces
2051 (this behaviour was undocumented).
2053 o The function plot.phylo() has a new option (`underscore') which
2054 specifies whether the underscores in tip labels should be written on
2055 the plot as such or replaced with spaces (the default).
2057 o The function birthdeath() now computes 95% confidence intervals of
2058 the estimated parameters using profile likelihood.
2060 o Three new data sets are included: a gene tree estimated from 36
2061 landplant rbcL sequences, a gene tree estimated from 32 opsin
2062 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
2067 o A bug was fixed in dist.gene() where nothing was returned.
2069 o A bug in plot.mst() was fixed.
2071 o A bug in vcv.phylo() resulted in false correlations when the
2072 option `cor = TRUE' was used (now fixed).
2076 CHANGES IN APE VERSION 1.0
2081 o Two new functions, read.dna() and write.dna(), read/write in a file
2082 DNA sequences in interleaved or in sequential format.
2084 o Two new functions, read.nexus() and write.nexus(), read/write trees
2087 o The new function bind.tree() allows to bind two trees together,
2088 possibly handling root edges to give internal branches.
2090 o The new function drop.tip() removes the tips in a phylogenetic tree,
2091 and trims (or not) the corresponding internal branches.
2093 o The new function is.ultrametric() tests if a tree is ultrametric.
2095 o The function plot.phylo() has more functionalities such as drawing the
2096 branches with different colours and/or different widths, showing the
2097 node labels, controling the position and font of the labels, rotating
2098 the labels, and controling the space around the plot.
2100 o The function read.tree() can now read trees with no branch length,
2101 such as "(a,b),c);". Consequently, the element `edge.length' in
2102 objects of class "phylo" is now optional.
2104 o The function write.tree() has a new default behaviour: if the default
2105 for the option `file' is used (i.e. file = ""), then a variable of
2106 mode character containing the tree in Newick format is returned which
2107 can thus be assigned (e.g., tree <- write.tree(phy)).
2109 o The function read.tree() has a new argument `text' which allows
2110 to read the tree in a variable of mode character.
2112 o A new data set is included: the phylogenetic relationships among
2113 the orders of birds from Sibley and Ahlquist (1990).
2117 CHANGES IN APE VERSION 0.2-1
2122 o Several bugs were fixed in the help pages.
2126 CHANGES IN APE VERSION 0.2
2131 o The function write.tree() writes phylogenetic trees (objects of class
2132 "phylo") in an ASCII file using the Newick parenthetic format.
2134 o The function birthdeath() fits a birth-death model to branching times
2135 by maximum likelihood, and estimates the corresponding speciation and
2138 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
2141 o The function is.binary.tree() tests whether a phylogeny is binary.
2143 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
2144 as well as some methods are introduced.
2146 o Several functions, including some generics and methods, for computing
2147 skyline plot estimates (classic and generalized) of effective
2148 population size through time are introduced and replace the function
2149 skyline.plot() in version 0.1.
2151 o Two data sets are now included: the phylogenetic relationships among
2152 the families of birds from Sibley and Ahlquist (1990), and an
2153 estimated clock-like phylogeny of HIV sequences sampled in the
2154 Democratic Republic of Congo.
2157 DEPRECATED & DEFUNCT
2159 o The function skyline.plot() in ape 0.1 has been deprecated and
2160 replaced by more elaborate functions (see above).
2165 o Two important bugs were fixed in plot.phylo(): phylogenies with
2166 multichotomies not at the root or not with only terminal branches,
2167 and phylogenies with a single node (i.e. only terminal branches)
2168 did not plot. These trees should be plotted correctly now.
2170 o Several bugs were fixed in diversi.time() in the computation of
2173 o Various errors were corrected in the help pages.