1 CHANGES IN APE VERSION 2.5-4
6 o There is now an 'as.list' method for the class "DNAbin".
8 o dist.dna() can compute the number of transitions or transversions
9 with the option model = "Ts" or model = "Tv", respectively.
11 o [node|tip|edge]labels() gain three options with default values to
12 control the aspect of thermometers: horiz = TRUE, width = NULL,
15 o compar.gee() has been improved with the new option 'corStruct' as an
16 alternative to 'phy' to specify the correlation structure, and
17 calculation of the QIC (Pan 2001, Biometrics). The display of the
18 results have also been improved.
23 o extract.clade() sometimes shuffled the tip labels.
27 CHANGES IN APE VERSION 2.5-3
32 o The new function mixedFontLabel helps to make labels with bits of
33 text to be plotted in different fonts.
35 o There are now replacement operators for [, [[, and $ for the class
36 "multiPhylo" (i.e., TREES[11:20] <- rmtree(10, 100)). They possibly
37 check that the tip labels are the same in all trees.
39 o Objects of class "multiPhylo" can be built with c(): there are
40 methods for the classes "phylo" and "multiPhylo".
42 o The internal functions .compressTipLabel and .uncompressTipLabel are
48 o bind.tree(x, y, where, position = 0) did not work correctly if 'y'
49 was a single-edge tree and 'where' was a tip.
51 o rTraitCont() did not use the square-root of branch lengths when
52 simulating a Brownian motion model.
56 CHANGES IN APE VERSION 2.5-2
61 o There is now a print method for results from ace().
63 o There is a labels() method for objects of class "DNAbin".
65 o read.dna() has a new option 'as.matrix' to possibly force sequences
66 in a FASTA file to be stored in a matrix (see ?read.dna for details).
71 o as.phylo.hclust() used to multiply edge lengths by 2.
73 o A minor bug was fixed in rTraitDisc().
75 o ace() sometimes failed (parameter value was NaN and the optimisation
81 o evolve.phylo() and plot.ancestral() have been removed.
83 o chronogram(), ratogram(), and NPRS.criterion() have been removed.
88 o nj() has been improved and is now about 30% faster.
90 o The default option 'drop' of [.DNAbin has been changed to FALSE to
91 avoid dropping rownames when selecting a single sequence.
93 o print.DNAbin() has been changed to summary.DNAbin() which has been
98 CHANGES IN APE VERSION 2.5-1
103 o The new function stree generates trees with regular shapes.
105 o It is now possible to bind two trees with x + y (see ?bind.tree for
108 o drop.tip(), extract.clade(), root(), and bind.tree() now have an
109 'interactive' option to make the operation on a plotted tree.
111 o cophyloplot() gains two new arguments 'lwd' and 'lty' for the
112 association links; they are recycled like 'col' (which wasn't before).
117 o rTraitDisc() did not use its 'freq' argument correctly (it was
118 multiplied with the rate matrix column-wise instead of row-wise).
120 o [node|tip|edge]labels(thermo = ) used to draw empty thermometers
121 with NA values. Nothing is drawn now like with 'text' or 'pch'.
122 The same bug occurred with the 'pie' option.
124 o A bug was fixed in compar.ou() and the help page was clarified.
126 o bind.tree() has been rewritten fixing several bugs and making it
129 o plot.phylo(type = "p") sometimes failed to colour correctly the
130 vertical lines representing the nodes.
132 o plot.phylo(direction = "l", x.lim = 30) failed to plot the branches
133 in the correct direction though the tip labels were displayed
139 o The c, cbind, and rbind methods for "DNAbin" objetcs now check that
140 the sequences are correctly stored (in a list for c, in a matrix
141 for the two other functions).
145 CHANGES IN APE VERSION 2.5
150 o The new function parafit by Pierre Legendre tests for the
151 coevolution between hosts and parasites. It has a companion
152 function, pcoa, that does principal coordinate decomposition.
153 The latter has a biplot method.
155 o The new function lmorigin by Pierre Legendre performs multiple
156 regression through the origin with testing by permutation.
158 o The new functions rTraitCont and rTraitDisc simulate continuous and
159 discrete traits under a wide range of evolutionary models.
161 o The new function delta.plot does a delta plot following Holland et
162 al. (2002, Mol. Biol. Evol. 12:2051).
164 o The new function edges draws additional branches between any nodes
165 and/or tips on a plotted tree.
167 o The new function fancyarrows enhances arrows from graphics with
168 triangle and harpoon heads; it can be called from edges().
170 o add.scale.bar() has a new option 'ask' to draw interactively.
172 o The branch length score replaces the geodesic distance in dist.topo.
174 o Three new data sets are included: the gopher-lice data (gopher.D),
175 SO2 air pollution in 41 US cities (lmorigin.ex1, from Sokal &
176 Rohlf 1995), and some host-parasite specificity data
177 (lmorigin.ex2, from Legendre & Desdevises 2009).
182 o add.scale.bar() drew the bar outside the plotting region with the
183 default options with unrooted or radial trees.
185 o dist.topo() made R stuck when the trees had different sizes (thanks
186 to Otto Cordero for the fix).
191 o The geodesic distance has been replaced by the branch length score
196 CHANGES IN APE VERSION 2.4-1
201 o rtree() and rcoal() now accept a numeric vector for the 'br'
204 o vcv() is a new generic function with methods for the classes "phylo"
205 and "corPhyl" so that it is possible to calculate the var-cov matrix
206 for "transformation models". vcv.phylo() can still be used for trees
207 of class "phylo"; its argument 'cor' has been renamed 'corr'.
212 o bind.tree() failed when 'y' had no root edge.
214 o read.nexus() shuffled tip labels when the trees have no branch
215 lengths and there is a TRANSLATE block.
217 o read.nexus() does not try to translate node labels if there is a
218 translation table in the NEXUS file. See ?read.nexus for a
219 clarification on this behaviour.
221 o plot.multiPhylo() crashed R when plotting a list of trees with
222 compressed tip labels.
224 o write.nexus() did not translate the taxa names when asked for.
226 o plot.phylo(type = "fan") did not rotate the tip labels correctly
227 when the tree has branch lengths.
229 o ace(type = "continuous", method = "ML") now avoids sigma² being
230 negative (which resulted in an error).
232 o nj() crashed with NA/NaN in the distance matrix: an error in now
237 CHANGES IN APE VERSION 2.4
242 o base.freq() has a new option 'freq' to return the counts; the
243 default is still to return the proportions.
248 o seg.sites() did not handle ambiguous nucleotides correctly: they
251 o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
252 the tree: the argument is now ignored.
254 o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
260 o Trying to plot a tree with a single tip now returns NULL with a
261 warning (it returned an error previously).
263 o The way lines representing nodes are coloured in phylograms has
264 been modified (as well as their widths and types) following some
265 users' request; this is only for dichotomous nodes.
267 o The argument 'adj' in [node][tip][edge]labels() now works when
268 using 'pie' or 'thermo'.
270 o A more informative message error is now returned by dist.dna() when
271 'model' is badly specified (partial matching of this argument is
274 o Deprecated functions are now listed in a help page: see
275 help("ape-defunct") with the quotes.
280 o The functions heterozygosity, nuc.div, theta.h, theta.k and
281 theta.s have been moved from ape to pegas.
283 o The functions mlphylo, DNAmodel and sh.test have been removed.
287 CHANGES IN APE VERSION 2.3-3
292 o add.scale.bar() always drew a horizontal bar.
294 o zoom() shuffled tips with unrooted trees.
296 o write.nexus() failed to write correctly trees with a "TipLabel"
299 o rcoal() failed to compute branch lengths with very large n.
301 o A small bug was fixed in compar.cheverud() (thanks to Michael
304 o seg.sites() failed when passing a vector.
306 o drop.tip() sometimes shuffled tip labels.
308 o root() shuffled node labels with 'resolve.root = TRUE'.
312 CHANGES IN APE VERSION 2.3-2
317 o all.equal.phylo() did not compare unrooted trees correctly.
319 o dist.topo(... method = "PH85") did not treat unrooted trees
320 correctly (thanks to Tim Wallstrom for the fix).
322 o root() sometimes failed to test for the monophyly of the
325 o extract.clade() sometimes included too many edges.
327 o vcv.phylo() did not work correctly when the tree is in
330 o nj() did not handle correctly distance matrices with many 0's.
331 The code has also been significantly improved: 7, 70, 160 times
332 faster with n = 100, 500, 1000, respectively.
336 CHANGES IN APE VERSION 2.3-1
341 o The new function is.monophyletic tests the monophyly of a group.
343 o There is now a c() method for lists of class "DNAbin".
345 o yule.cov() now fits the null model, and its help page has been
346 corrected with respect to this change.
348 o drop.tip() has a new option 'rooted' to force (or not) a tree
349 to be treated as (un)rooted.
354 o dist.gene() failed on most occasions with the default
355 pairwise.deletion = FALSE.
357 o read.tree() failed to read correctly the tree name(s).
359 o boot.phylo() now treats correctly data frames.
361 o del.gaps() did not copy the rownames of a matrix.
363 o A small bug was fixed in CDAM.global().
365 o ace() failed with large data sets. Thanks to Rich FitzJohn for
366 the fix. With other improvements, this function is now about 6
369 o write.tree() failed with objects of class "multiPhylo".
371 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
376 o [.multiPhylo and [.DNAbin now respect the original class.
378 o Instances of the form class(phy) == "phylo" have been replaced
379 by inherits(phy, "phylo").
381 o rcoal() is now faster.
386 o klastorin() has been removed.
390 CHANGES IN APE VERSION 2.3
395 o The new functions CADM.global and CADM.post, contributed by
396 Pierre Legendre, test the congruence among several distance
399 o The new function yule.time fits a user-defined time-dependent
400 Yule model by maximum likelihood.
402 o The new function makeNodeLabel creates and/or modifies node
403 labels in a flexible way.
405 o read.tree() and write.tree() have been modified so that they can
406 handle individual tree names.
408 o plot.phylo() has a new argument 'edge.lty' that specifies the
409 types of lines used for the edges (plain, dotted, dashed, ...)
411 o phymltest() has been updated to work with PhyML 3.0.1.
416 o drop.tip() shuffled tip labels in some cases.
418 o drop.tip() did not handle node.label correctly.
420 o is.ultrametric() now checks the ordering of the edge matrix.
422 o ace() sometimes returned negative values of likelihoods of
423 ancestral states (thanks to Dan Rabosky for solving this long
429 o The data set xenarthra has been removed.
433 CHANGES IN APE VERSION 2.2-4
437 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
438 now fixed. (Thanks to Peter Wragg for the fix!)
440 o A warning message occurred for no reason with ace(method="GLS").
445 o There is now a general help page displayed with '?ape'.
449 CHANGES IN APE VERSION 2.2-3
454 o The new function extract.clade extracts a clade from a tree by
455 specifying a node number or label.
457 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
458 operations of the same names.
460 o dist.dna() can now return the number of site differences by
461 specifying model="N".
466 o chronopl() did not work with CV = TRUE.
468 o read.nexus() did not work correctly in some situations (trees on
469 multiple lines with different numbers of lines and/or with
470 comments inserted within the trees).
472 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
473 the number of lineages with non-binary trees.
478 o ape has now a namespace.
480 o drop.tip() has been improved: it should be much faster and work
481 better in some cases (e.g., see the example in ?zoom).
485 CHANGES IN APE VERSION 2.2-2
490 o dist.gene() has been substantially improved and gains an option
493 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
499 o prop.part() failed with a single tree with the default option
500 'check.labels = TRUE'.
502 o summary.DNAbin() failed to display correctly the summary of
503 sequence lengths with lists of sequences of 10,000 bases or more
504 (because summary.default uses 4 significant digits by default).
506 o read.nexus() failed to read a file with a single tree with line
507 breaks in the Newick string.
509 o del.gaps() returned a list of empty sequences when there were no
515 o phymltest() has been updated for PhyML 3.0 and gains an option
516 'append', whereas the option 'path2exec' has been removed.
518 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
519 which is returned unchanged (instead of an error).
521 o The data sets bird.orders and bird.families are now stored as
522 Newick strings; i.e., the command data(bird.orders) calls
527 CHANGES IN APE VERSION 2.2-1
532 o The new function makeLabel() helps to modify labels of trees,
533 lists of trees, or DNA sequences, with several utilities to
534 truncate and/or make them unique, substituting some
535 characters, and so on.
537 o The new function del.gaps() removes insertion gaps ("-") in a
538 set of DNA sequences.
540 o read.dna() can now read Clustal files (*.aln).
545 o root() failed with 'resolve.root = TRUE' when the root was
546 already the specified root.
548 o Several bugs were fixed in mlphylo().
550 o collapsed.singles() did not propagate the 'Nnode' and
551 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
553 o read.nexus() failed to remove correctly the comments within
556 o read.nexus() failed to read a file with a single tree and no
557 translation of tip labels.
559 o read.nexus() failed to place correctly tip labels when reading
560 a single tree with no edge lengths.
562 o A bug was fixed in sh.test().
567 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
570 o The option 'check.labels' of consensus() and prop.part() is now
573 o write.dna() now does not truncate names to 10 characters with
578 CHANGES IN APE VERSION 2.2
583 o Four new functions have been written by Damien de Vienne for the
584 graphical exploration of large trees (cophyloplot, subtrees,
585 subtreeplot), and to return the graphical coordinates of tree
588 o The new functions corPagel and corBlomberg implement the Pagel's
589 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
591 o chronopl() has been improved and gains several options: see its
592 help page for details.
594 o boot.phylo() has now an option 'trees' to possibly return the
595 bootstraped trees (the default is FALSE).
597 o prop.part() has been improved and should now be faster in all
603 o read.dna() failed if "?" occurred in the first 10 sites of the
606 o The x/y aspect of the plot is now respected when plotting a
607 circular tree (type = "r" or "f").
609 o Drawing the tip labels sometimes failed when plotting circular
612 o zoom() failed when tip labels were used instead of their numbers
613 (thanks to Yan Wong for the fix).
615 o drop.tip() failed with some trees (fixed by Yan Wong).
617 o seg.sites() failed with a list.
619 o consensus() failed in some cases. The function has been improved
620 as well and is faster.
624 CHANGES IN APE VERSION 2.1-3
629 o A bug in read.nexus() made the Windows R-GUI crash.
631 o An error was fixed in the computation of ancestral character
632 states by generalized least squares in ace().
634 o di2multi() did not modify node labels correctly.
636 o multi2di() failed if the tree had its attribute "order" set to
641 CHANGES IN APE VERSION 2.1-2
646 o There three new methods for the "multiPhylo" class: str, $,
649 o root() gains the options 'node' and 'resolve.root'
650 (FALSE by default) as well as its code being improved.
652 o mltt.plot() has now an option 'log' used in the same way
653 than in plot.default().
658 o mltt.plot() failed to display the legend with an unnamed
661 o nodelabels() with pies now correcly uses the argument
662 'cex' to draw symbols of different sizes (which has
663 worked already for thermometers).
665 o read.nexus() generally failed to read very big files.
670 o The argument 'family' of compar.gee() can now be a function
671 as well as a character string.
673 o read.tree() and read.nexus() now return an unnamed list if
676 o read.nexus() now returns a modified object of class "multiPhylo"
677 when there is a TRANSLATE block in the NEXUS file: the individual
678 trees have no 'tip.label' vector, but the list has a 'TipLabel'
679 attribute. The new methods '$' and '[[' set these elements
680 correctly when extracting trees.
684 CHANGES IN APE VERSION 2.1-1
689 o The new function rmtree generates lists of random trees.
691 o rcoal() now generates a genuine coalescent tree by default
692 (thanks to Vladimir Minin for the code).
697 o nuc.div() returned an incorrect value with the default
698 pairwise.deletion = FALSE.
703 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
704 have been improved so that they are stabler and faster.
706 o R packages used by ape are now loaded silently; lattice and gee
707 are loaded only when needed.
711 CHANGES IN APE VERSION 2.1
716 o The new function identify.phylo identifies clades on a plotted
717 tree using the mouse.
719 o It is now possible to subset a list of trees (object of class
720 "multiPhylo") with "[" while keeping its class correct.
722 o The new function as.DNAbin.alignment converts DNA sequences
723 stored in the "alignment" format of the package seqinr into
724 an object of class "DNAbin".
726 o The new function weight.taxo2 helps to build similarity matrices
727 given two taxonomic levels (usually called by other functions).
729 o write.tree() can now take a list of trees (class "multiPhylo")
730 as its main argument.
732 o plot.correlogram() and plot.correlogramList() have been
733 improved, and gain several options (see the help page for
734 details). A legend is now plotted by default.
739 o dist.dna() returned some incorrect values with `model = "JC69"'
740 and `pairwise.deletion = TRUE'. This affected only the
741 distances involving sequences with missing values. (Thanks
742 to Bruno Toupance for digging this bug out.)
744 o write.tree() failed with some trees: this is fixed by removing
745 the `multi.line' option (trees are now always printed on a
748 o read.nexus() did not correctly detect trees with multiple root
749 edges (see OTHER CHANGES).
754 o The code of mlphylo() has been almost entirely rewritten, and
755 should be much stabler. The options have been also greatly
756 simplified (see ?mlphylo and ?DNAmodel for details).
758 o The internal function nTips has been renamed klastorin_nTips.
760 o The code of is.ultrametric() contained redundancies and has
763 o The code of Moran.I() and of correlogram.formula() have been
766 o read.tree() and read.nexus() now return an error when trying to
767 read a tree with multiple root edges (see BUG FIXES). The
768 correction applied in previous version did not work in all
771 o The class c("multi.tree", "phylo") has been renamed
777 o There is now a vignette in ape: see vignette("MoranI", "ape").
782 o as.matching() and as.phylo.matching() do not support branch
785 o correlogram.phylo() and discrete.dist() have been removed.
789 CHANGES IN APE VERSION 2.0-2
794 o The new function matexpo computes the exponential of a square
797 o The new function unique.multi.tree removes duplicate trees from
800 o yule() has a new option `use.root.edge = FALSE' that specifies
801 to ignore, by default, the root edge of the tree if it exists.
806 o which.edge() failed when the index of a single terminal edge was
809 o In diversi.time(), the values returned for model C were
812 o A bug was fixed in yule() that affected the calculation of the
813 likelihood in the presence of ties in the branching times.
815 o There was a bug in the C function mat_expo4x4 affecting the
816 calculations of the transition probabilities for models HKY and
819 o A small bug was fixed in as.matrix.DNAbin (thanks to James
822 o rtree() did not `shuffle' the tip labels by default, so only a
823 limited number of labelled topologies could be generated.
827 CHANGES IN APE VERSION 2.0-1
832 o The three new functions bionj, fastme.ols, and fastme.bal
833 perform phylogeny estimation by the BIONJ and fastME methods in
834 OLS and balanced versions. This is a port to R of previous
835 previous programs done by Vincent Lefort.
837 o The new function chronoMPL performs molecular dating with the
838 mean path lengths method of Britton et al. (2002, Mol. Phyl.
841 o The new function rotate, contributed by Christoph Heibl, swaps
842 two clades connected to the same node. It works also with
843 multichotomous nodes.
845 o The new `method' as.matrix.DNAbin() may be used to convert
846 easily DNA sequences stored in a list into a matrix while
847 keeping the names and the class.
852 o chronopl() failed when some branch lengths were equal to zero:
853 an error message is now returned.
855 o di2multi() failed when there was a series of consecutive edges
860 CHANGES IN APE VERSION 1.10-2
865 o plot.phylo() can now plot circular trees: the option is type =
866 "fan" or type = "f" (to avoid the ambiguity with type = "c").
868 o prop.part() has a new option `check.labels = FALSE' which allows
869 to considerably speed-up the calculations of bipartitions. As a
870 consequence, calculations of bootstrap values with boot.phylo()
871 should be much faster.
876 o read.GenBank() did not return correctly the list of species as
877 from ape 1.10: this is fixed in this version
879 o Applying as.phylo() on a tree of class "phylo" failed: the
880 object is now returned unchanged.
884 CHANGES IN APE VERSION 1.10-1
889 o The three new functions Ntip, Nnode, and Nedge return, for a
890 given tree, the number of tips, nodes, or edges, respectively.
895 o read.nexus() did not set correctly the class of the returned
896 object when reading multiple trees.
898 o mllt.plot() failed with objects of class c("multi.tree",
901 o unroot() did not work correctly in most cases.
903 o reorder.phylo() made R freeze in some occasions.
905 o Plotting a tree in pruningwise order failed.
907 o When plotting an unrooted tree, the tip labels where not all
908 correctly positioned if the option `cex' was used.
912 CHANGES IN APE VERSION 1.10
917 o Five new `method' functions have been introduced to manipulate
918 DNA sequences in binary format (see below).
920 o Three new functions have been introduced to convert between the
921 new binary and the character formats.
923 o The new function as.alignment converts DNA sequences stored as
924 single characters into the class "alignment" used by the package
927 o read.dna() and read.GenBank() have a new argument `as.character'
928 controlling whether the sequences are returned in binary format
934 o root() failed when the tree had node labels: this is fixed.
936 o plot.phylo() did not correctly set the limits on the y-axis with
937 the default setting: this is fixed.
939 o dist.dna() returned a wrong result for the LogDet, paralinear,
940 and BH87 models with `pairwise.deletion = TRUE'.
945 o DNA sequences are now internally stored in a binary format. See
946 the document "A Bit-Level Coding Scheme for Nucleotides" for the
947 details. Most functions analyzing DNA functions have been
948 modified accordingly and are now much faster (dist.dna is now
949 ca. 60 times faster).
953 CHANGES IN APE VERSION 1.9-4
958 o A bug was fixed in edgelabels().
960 o as.phylo.hclust() did not work correctly when the object of
961 class "hclust" has its labels set to NULL: the returned tree has
962 now its tip labels set to "1", "2", ...
964 o consensus could fail if some tip labels are a subset of others
965 (e.g., "a" and "a_1"): this is now fixed.
967 o mlphylo() failed in most cases if some branch lengths of the
968 initial tree were greater than one: an error message is now
971 o mlphylo() failed in most cases when estimating the proportion of
972 invariants: this is fixed.
976 CHANGES IN APE VERSION 1.9-3
981 o The new function edgelabels adds labels on the edge of the tree
982 in the same way than nodelabels or tiplabels.
987 o multi2di() did not handle correctly branch lengths with the
988 default option `random = TRUE': this is now fixed.
990 o A bug was fixed in nuc.div() when using pairwise deletions.
992 o A bug occurred in the analysis of bipartitions with large
993 numbers of large trees, with consequences on prop.part,
994 prop.clades, and boot.phylo.
996 o The calculation of the Billera-Holmes-Vogtmann distance in
997 dist.topo was wrong: this has been fixed.
1001 CHANGES IN APE VERSION 1.9-2
1006 o The new function ladderize reorganizes the internal structure of
1007 a tree to plot them left- or right-ladderized.
1009 o The new function dist.nodes computes the patristic distances
1010 between all nodes, internal and terminal, of a tree. It replaces
1011 the option `full = TRUE' of cophenetic.phylo (see below).
1016 o A bug was fixed in old2new.phylo().
1018 o Some bugs were fixed in chronopl().
1020 o The edge colours were not correctly displayed by plot.phylo
1021 (thank you to Li-San Wang for the fix).
1023 o cophenetic.phylo() failed with multichotomous trees: this is
1029 o read.dna() now returns the sequences in a matrix if they are
1030 aligned (interleaved or sequential format). Sequences in FASTA
1031 format are still returned in a list.
1033 o The option `full' of cophenetic.phylo() has been removed because
1034 it could not be used from the generic.
1037 DEPRECATED & DEFUNCT
1039 o rotate() has been removed; this function did not work correctly
1044 CHANGES IN APE VERSION 1.9-1
1049 o Trees with a single tip were not read correctly in R as the
1050 element `Nnode' was not set: this is fixed.
1052 o unroot() did not set correctly the number of nodes of the
1053 unrooted tree in most cases.
1055 o read.GenBank() failed when fetching very long sequences,
1056 particularly of the BX-series.
1058 o A bug was introduced in read.tree() with ape 1.9: it has been
1063 CHANGES IN APE VERSION 1.9
1068 o There are two new print `methods' for trees of class "phylo" and
1069 lists of trees of class "multi.tree", so that they are now
1070 displayed in a compact and informative way.
1072 o There are two new functions, old2new.phylo and new2old.phylo,
1073 for converting between the old and new coding of the class
1076 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
1077 LogDet ("logdet"), and paralinear ("paralin").
1079 o compute.brlen() has been extended: several methods are now
1080 available to compute branch lengths.
1082 o write.dna() can now handle matrices as well as lists.
1087 o cophenetic.phylo() sometimes returned a wrong result with
1088 multichotomous trees: this is fixed.
1090 o rotate() failed when a single tip was specified: the tree is now
1093 o ace() did not return the correct index matrix with custom
1094 models: this is fixed.
1096 o multi2di() did not work correctly when resolving multichotomies
1097 randomly: the topology was always the same, only the arrangement
1098 of clades was randomized: this is fixed. This function now
1099 accepts trees with no branch lengths.
1101 o The output of diversi.gof() was blurred by useless prints when a
1102 user distribution was specified. This has been corrected, and
1103 the help page of this function has been expanded.
1108 o The internal structure of the class "phylo" has been changed:
1109 see the document "Definition of Formats for Coding Phylogenetic
1110 Trees in R" for the details. In addition, the code of most
1111 functions has been improved.
1113 o Several functions have been improved by replacing some R codes
1114 by C codes: pic, plot.phylo, and reorder.phylo.
1116 o There is now a citation information: see citation("ape") in R.
1118 o write.tree() now does not add extra 0's to branch lengths so
1119 that 1.23 is printed "1.23" by default, not "1.2300000000".
1121 o The syntax of bind.tree() has been simplified. This function now
1122 accepts trees with no branch lengths, and handles correctly node
1125 o The option `as.numeric' of mrca() has been removed.
1127 o The unused options `format' and `rooted' of read.tree() have
1130 o The unused option `format' of write.tree() has been removed.
1132 o The use of node.depth() has been simplified.
1136 CHANGES IN APE VERSION 1.8-5
1141 o Two new functions read.nexus.data() and write.nexus.data(),
1142 contributed by Johan Nylander, allow to read and write molecular
1143 sequences in NEXUS files.
1145 o The new function reorder.phylo() reorders the internal structure
1146 of a tree of class "phylo". It is used as the generic, e.g.,
1149 o read.tree() and read.nexus() can now read trees with a single
1152 o The new data set `cynipids' supplies a set of protein sequences
1158 o The code of all.equal.phylo() has been completely rewritten
1159 (thanks to Benoît Durand) which fixes several bugs.
1161 o read.tree() and read.nexus() now checks the labels of the tree
1162 to remove or substitute any characters that are illegal in the
1163 Newick format (parentheses, etc.)
1165 o A negative P-value could be returned by mantel.test(): this is
1170 CHANGES IN APE VERSION 1.8-4
1175 o The new function sh.test() computes the Shimodaira-
1178 o The new function collapse.singles() removes the nodes with a
1179 single descendant from a tree.
1181 o plot.phylo() has a new argument `tip.color' to specify the
1182 colours of the tips.
1184 o mlphylo() has now an option `quiet' to control the display of
1185 the progress of the analysis (the default is FALSE).
1190 o read.dna() did not read correctly sequences in sequential format
1191 with leading alignment gaps "-": this is fixed.
1193 o ace() returned a list with no class so that the generic
1194 functions (anova, logLik, ...) could not be used directly. This
1195 is fixed as ace() now returns an object of class "ace".
1197 o anova.ace() had a small bug when computing the number of degrees
1198 of freedom: this is fixed.
1200 o mlphylo() did not work when the sequences were in a matrix or
1201 a data frame: this is fixed.
1203 o rtree() did not work correctly when trying to simulate an
1204 unrooted tree with two tips: an error message is now issued.
1209 o The algorithm of rtree() has been changed: it is now about 40,
1210 100, and 130 times faster for 10, 100, and 1000 tips,
1215 CHANGES IN APE VERSION 1.8-3
1220 o There are four new `method' functions to be used with the
1221 results of ace(): logLik(), deviance(), AIC(), and anova().
1223 o The plot method of phymltest has two new arguments: `main' to
1224 change the title, and `col' to control the colour of the
1225 segments showing the AIC values.
1227 o ace() has a new argument `ip' that gives the initial values used
1228 in the ML estimation with discrete characters (see the examples
1229 in ?ace). This function now returns a matrix giving the indices
1230 of the estimated rates when analysing discrete characters.
1232 o nodelabels() and tiplabels() have a new argument `pie' to
1233 represent proportions, with any number of categories, as
1234 piecharts. The use of the option `thermo' has been improved:
1235 there is now no limitation on the number of categories.
1240 o mlphylo() did not work with more than two partitions: this is
1243 o root() failed if the proposed outgroup was already an outgroup
1244 in the tree: this is fixed.
1246 o The `col' argument in nodelabels() and tiplabels() was not
1247 correctly passed when `text' was used: this is fixed.
1249 o Two bugs were fixed in mlphylo(): parameters were not always
1250 correctly output, and the estimation failed in some cases.
1252 o plot.phylo() was stuck when given a tree with a single tip: this
1253 is fixed and a message error is now returned.
1255 o An error was corrected in the help page of gammaStat regarding
1256 the calculation of P-values.
1258 o Using gls() could crash R when the number of species in the tree
1259 and in the variables were different: this is fixed.
1263 CHANGES IN APE VERSION 1.8-2
1268 o The new function mlphylo() fits a phylogenetic tree by maximum
1269 likelihood from DNA sequences. Its companion function DNAmodel()
1270 is used to define the substitution model which may include
1271 partitioning. There are methods for logLik(), deviance(), and
1272 AIC(), and the summary() method has been extended to display in
1273 a friendly way the results of this model fitting. Currently, the
1274 functionality is limited to estimating the substitution and
1275 associated parameters and computing the likelihood.
1277 o The new function drop1.compar.gee (used as, e.g., drop1(m))
1278 tests for single effects in GEE-based comparative method. A
1279 warning message is printed if there is not enough degrees of
1285 o An error message was sometimes issued by plot.multi.tree(),
1286 though with no consequence.
1290 CHANGES IN APE VERSION 1.8-1
1295 o There is a new plot method for lists of trees (objects of class
1296 "multi.tree"): it calls plot.phylo() internally and is
1297 documented on the same help page.
1302 o A bug was fixed in the C code that analyzes bipartitions: this
1303 has impact on several functions like prop.part, prop.clades,
1304 boot.phylo, or consensus.
1306 o root() did not work correctly when the specified outgroup had
1307 more than one element: this is fixed.
1309 o dist.dna() sometimes returned a warning inappropriately: this
1312 o If the distance object given to nj() had no rownames, nj()
1313 returned a tree with no tip labels: it now returns tips labelled
1314 "1", "2", ..., corresponding to the row numbers.
1319 o nj() has been slightly changed so that tips with a zero distance
1320 are first aggregated with zero-lengthed branches; the usual NJ
1321 procedure is then performed on a distance matrix without 0's.
1325 CHANGES IN APE VERSION 1.8
1330 o The new function chronopl() estimates dates using the penalized
1331 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1333 o The new function consensus() calculates the consensus tree of a
1336 o The new function evolve.phylo() simulates the evolution of
1337 continuous characters along a phylogeny under a Brownian model.
1339 o The new plot method for objects of class "ancestral" displays a
1340 tree together with ancestral values, as returned by the above
1343 o The new function as.phylo.formula() returns a phylogeny from a
1344 set of nested taxonomic variables given as a formula.
1346 o The new function read.caic() reads trees in CAIC format.
1348 o The new function tiplabels() allows to add labels to the tips
1349 of a tree using text or plotting symbols in a flexible way.
1351 o The new function unroot() unroots a phylogeny.
1353 o multi2di() has a new option, `random', which specifies whether
1354 to resolve the multichotomies randomly (the default) or not.
1356 o prop.part() now returns an object of class "prop.part" for which
1357 there are print (to display a partition in a more friendly way)
1358 and summary (to extract the numbers) methods.
1360 o plot.phylo() has a new option, `show.tip.label', specifying
1361 whether to print the labels of the tips. The default is TRUE.
1363 o The code of nj() has been replaced by a faster C code: it is now
1364 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1367 o write.nexus() now writes whether a tree is rooted or not.
1372 o Two bugs have been fixed in root(): unrooted trees are now
1373 handled corretly, and node labels are now output normally.
1375 o A bug was fixed in phymltest(): the executable couldn't be found
1378 o Three bug have been fixed in ace(): computing the likelihood of
1379 ancestral states of discrete characters failed, custom models
1380 did not work, and the function failed with a null gradient (a
1381 warning message is now returned; this latter bug was also
1382 present in yule.cov() as well and is now fixed).
1384 o pic() hanged out when missing data were present: a message error
1387 o A small bug was fixed in dist.dna() where the gamma correction
1388 was not always correctly dispatched.
1390 o plot.phylo() plotted correctly the root edge only when the tree
1391 was plotted rightwards: this works now for all directions.
1396 o dist.taxo() has been renamed as weight.taxo().
1398 o dist.phylo() has been replaced by the method cophenetic.phylo().
1400 o Various error and warning messages have been improved.
1404 CHANGES IN APE VERSION 1.7
1407 o The new function ace() estimates ancestral character states for
1408 continuous characters (with ML, GLS, and contrasts methods), and
1409 discrete characters (with ML only) for any number of states.
1411 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1412 of directional evolution for continuous characters. The user
1413 specifies the node(s) of the tree where the character optimum
1416 o The new function is.rooted() tests whether a tree (of class
1419 o The new function rcoal() generates random ultrametric trees with
1420 the possibility to specify the function that generates the
1421 inter-nodes distances.
1423 o The new function mrca() gives for all pairs of tips in a tree
1424 (and optionally nodes too) the most recent common ancestor.
1426 o nodelabels() has a new option `thermo' to plot proportions (up
1427 to three classes) on the nodes of a tree.
1429 o rtree() has been improved: it can now generate rooted or
1430 unrooted trees, and the mathematical function that generates the
1431 branch lengths may be specified by the user. The tip labels may
1432 be given directly in the call to rtree. The limit cases (n = 2,
1433 3) are now handled correctly.
1435 o dist.topo() has a new argument `method' with two choices: "PH85"
1436 for Penny and Henny's method (already available before and now
1437 the default), and "BHV01" for the geometric distance by Billera
1438 et al. (2001, Adv. Appl. Math. 27:733).
1440 o write.tree() has a new option, `digits', which specifies the
1441 number of digits to be printed in the Newick tree. By default
1442 digits = 10. The numbers are now always printed in decimal form
1443 (i.e., 1.0e-1 is now avoided).
1445 o dist.dna() can now compute the raw distances between pairs of
1446 DNA sequences by specifying model = "raw".
1448 o dist.phylo() has a new option `full' to possibly compute the
1449 distances among all tips and nodes of the tree. The default if
1455 o Several bugs were fixed in all.equal.phylo().
1457 o dist.dna() did not handle correctly gaps ("-") in alignments:
1458 they are now considered as missing data.
1460 o rotate() did not work if the tips were not ordered: this is
1463 o mantel.test() returned NA in some special cases: this is fixed
1464 and the function has been improved and is now faster.
1466 o A bug was fixed in diversi.gof() where the calculation of A² was
1469 o cherry() did not work correctly under some OSs (mainly Linux):
1472 o is.binary.tree() has been modified so that it works with both
1473 rooted and unrooted trees.
1475 o The documentation of theta.s() was not correct: this has been
1478 o plot.mst() did not work correctly: this is fixed.
1482 CHANGES IN APE VERSION 1.6
1487 o The new function dist.topo() computes the topological distances
1490 o The new function boot.phylo() performs a bootstrap analysis on
1491 phylogeny estimation.
1493 o The new functions prop.part() and prop.clades() analyse
1494 bipartitions from a series of trees.
1499 o read.GenBank() now uses the EFetch utility of NCBI instead of
1500 the usual Web interface: it is now much faster (e.g., 12 times
1501 faster to retrieve 8 sequences, 37 times for 60 sequences).
1506 o Several bugs were fixed in read.dna().
1508 o Several bugs were fixed in diversi.time().
1510 o is.binary.tree() did not work correctly if the tree has no edge
1511 lengths: this is fixed.
1513 o drop.tip() did not correctly propagated the `node.label' of a
1514 tree: this is fixed.
1518 CHANGES IN APE VERSION 1.5
1523 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1524 convert objects between the classes "phylo" and "matching". The
1525 latter implements the representation of binary trees introduced by
1526 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1527 as.matching() has been introduced as well.
1529 o Two new functions, multi2di() and di2multi(), allow to resolve
1530 and collapse multichotomies with branches of length zero.
1532 o The new function nuc.div() computes the nucleotide diversity
1533 from a sample a DNA sequences.
1535 o dist.dna() has been completely rewritten with a much faster
1536 (particularly for large data sets) C code. Eight models are
1537 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1538 option `method' has been renamed `model'). Computation of variance
1539 is available for all models. A gamma-correction is possible for
1540 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1541 to remove sites with missing data on a pairwise basis. The option
1542 `GCcontent' has been removed.
1544 o read.GenBank() has a new option (species.names) which specifies
1545 whether to return the species names of the organisms in addition
1546 to the accession numbers of the sequences (this is the default
1549 o write.nexus() can now write several trees in the same NEXUS file.
1551 o drop.tip() has a new option `root.edge' that allows to specify the
1552 new root edge if internal branches are trimmed.
1557 o as.phylo.hclust() failed if some labels had parentheses: this
1560 o Several bugs were fixed in all.equal.phylo(). This function now
1561 returns the logical TRUE if the trees are identical but with
1562 different representations (a report was printed previously).
1564 o read.GenBank() did not correctly handle ambiguous base codes:
1570 o birthdeath() now returns an object of class "birthdeath" for
1571 which there is a print method.
1575 CHANGES IN APE VERSION 1.4
1580 o The new function nj() performs phylogeny estimation with the
1581 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1584 o The new function which.edge() identifies the edges of a tree
1585 that belong to a group specified as a set of tips.
1587 o The new function as.phylo.phylog() converts an object of class
1588 "phylog" (from the package ade4) into an object of class
1591 o The new function axisPhylo() draws axes on the side of a
1594 o The new function howmanytrees() calculates the number of trees
1595 in different cases and giving a number of tips.
1597 o write.tree() has a new option `multi.line' (TRUE by default) to
1598 write a Newick tree on several lines rather than on a single
1601 o The functionalities of zoom() have been extended. Several
1602 subtrees can be visualized at the same time, and they are marked
1603 on the main tree with colors. The context of the subtrees can be
1604 marked with the option `subtree' (see below).
1606 o drop.tip() has a new option `subtree' (FALSE by default) which
1607 specifies whether to output in the tree how many tips have been
1610 o The arguments of add.scale.bar() have been redefined and have
1611 now default values (see ?add.scale.bar for details). This
1612 function now works even if the plotted tree has no edge length.
1614 o plot.phylo() can now plot radial trees, but this does not take
1615 edge lengths into account.
1617 o In plot.phylo() with `type = "phylogram"', if the values of
1618 `edge.color' and `edge.width' are identical for sister-branches,
1619 they are propagated to the vertical line that link them.
1624 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1625 crashing. This is fixed.
1627 o In plot.phylo(), the options `edge.color' and `edge.width' are
1628 now properly recycled; their default values are now "black" and
1631 o A bug has been fixed in write.nexus().
1636 o The function node.depth.edgelength() has been removed and
1637 replaced by a C code.
1641 CHANGES IN APE VERSION 1.3-1
1646 o The new function nodelabels() allows to add labels to the nodes
1647 of a tree using text or plotting symbols in a flexible way.
1649 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1650 numeric values specifying the lower and upper limits on the x-
1651 and y-axes. This allows to leave some space on any side of the
1652 tree. If a single value is given, this is taken as the upper
1657 CHANGES IN APE VERSION 1.3
1662 o The new function phymltest() calls the software PHYML and fits
1663 28 models of DNA sequence evolution. There are a print method to
1664 display likelihood and AIC values, a summary method to compute
1665 the hierarchical likelihood ratio tests, and a plot method to
1666 display graphically the AIC values of each model.
1668 o The new function yule.cov() fits the Yule model with covariates,
1669 a model where the speciation rate is affected by several species
1670 traits through a generalized linear model. The parameters are
1671 estimated by maximum likelihood.
1673 o Three new functions, corBrownian(), corGrafen(), and
1674 corMartins(), compute the expected correlation structures among
1675 species given a phylogeny under different models of evolution.
1676 These can be used for GLS comparative phylogenetic methods (see
1677 the examples). There are coef() and corMatrix() methods and an
1678 Initialize.corPhyl() function associated.
1680 o The new function compar.cheverud() implements Cheverud et al.'s
1681 (1985; Evolution 39:1335) phylogenetic comparative method.
1683 o The new function varcomp() estimates variance components; it has
1686 o Two new functions, panel.superpose.correlogram() and
1687 plot.correlogramList(), allow to plot several phylogenetic
1690 o The new function node.leafnumber() computes the number of leaves
1691 of a subtree defined by a particular node.
1693 o The new function node.sons() gets all tags of son nodes from a
1696 o The new function compute.brlen() computes the branch lengths of
1697 a tree according to a specified method.
1699 o plot.phylo() has three new options: "cex" controls the size of
1700 the (tip and node) labels (thus it is no more needed to change
1701 the global graphical parameter), "direction" which allows to
1702 plot the tree rightwards, leftwards, upwards, or downwards, and
1703 "y.lim" which sets the upper limit on the y-axis.
1708 o Some functions which try to match tip labels and names of
1709 additional data (e.g. vector) are likely to fail if there are
1710 typing or syntax errors. If both series of names do not perfectly
1711 match, they are ignored and a warning message is now issued.
1712 These functions are bd.ext, compar.gee, pic. Their help pages
1713 have been clarified on this point.
1717 CHANGES IN APE VERSION 1.2-7
1722 o The new function root() reroots a phylogenetic tree with respect
1723 to a specified outgroup.
1725 o The new function rotate() rotates an internal branch of a tree.
1727 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1728 trees) controls the display of the tip labels in unrooted trees.
1729 This display has been greatly improved: the tip labels are now not
1730 expected to overlap with the tree (particularly if lab4ut =
1731 "axial"). In all cases, combining appropriate values of "lab4ut"
1732 and the font size (via "par(cex = )") should result in readable
1733 unrooted trees. See ?plot.phylo for some examples.
1735 o In drop.tip(), the argument `tip' can now be numeric or character.
1740 o drop.tip() did not work correctly with trees with no branch
1741 lengths: this is fixed.
1743 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1744 plotted with some line crossings: this is now fixed.
1748 CHANGES IN APE VERSION 1.2-6
1753 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1754 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1755 to implement comparative methods with an autocorrelation approach.
1757 o A new data set describing some life history traits of Carnivores
1763 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1768 o When plotting a tree with plot.phylo(), the new default of the
1769 option `label.offset' is now 0, so the labels are always visible.
1773 CHANGES IN APE VERSION 1.2-5
1778 o The new function bd.ext() fits a birth-death model with combined
1779 phylogenetic and taxonomic data, and estimates the corresponding
1780 speciation and extinction rates.
1785 o The package gee is no more required by ape but only suggested
1786 since only the function compar.gee() calls gee.
1790 CHANGES IN APE VERSION 1.2-4
1795 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1796 and lines.popsize) implementing a new approach for inferring the
1797 demographic history from genealogies using a reversible jump
1798 MCMC have been introduced.
1800 o The unit of time in the skyline plot and in the new plots can
1801 now be chosen to be actual years, rather than substitutions.
1805 CHANGES IN APE VERSION 1.2-3
1810 o The new function rtree() generates a random binary tree with or
1811 without branch lengths.
1813 o Two new functions for drawing lineages-through-time (LTT) plots
1814 are provided: ltt.lines() adds a LTT curve to an existing plot,
1815 and mltt.plot() does a multiple LTT plot giving several trees as
1816 arguments (see `?ltt.plot' for details).
1821 o Some taxon names made R crashing when calling as.phylo.hclust():
1824 o dist.dna() returned an error with two identical DNA sequences
1825 (only using the Jukes-Cantor method returned 0): this is fixed.
1830 o The function dist.phylo() has been re-written using a different
1831 algorithm: it is now about four times faster.
1833 o The code of branching.times() has been improved: it is now about
1838 CHANGES IN APE VERSION 1.2-2
1843 o The new function seg.sites() finds the segregating sites in a
1844 sample of DNA sequences.
1849 o A bug introduced in read.tree() and in read.nexus() with version
1852 o A few errors were corrected and a few examples were added in the
1857 CHANGES IN APE VERSION 1.2-1
1862 o plot.phylo() can now draw the edge of the root of a tree if it
1863 has one (see the new option `root.edge', its default is FALSE).
1868 o A bug was fixed in read.nexus(): files with semicolons inside
1869 comment blocks were not read correctly.
1871 o The behaviour of read.tree() and read.nexus() was corrected so
1872 that tree files with badly represented root edges (e.g., with
1873 an extra pair of parentheses, see the help pages for details)
1874 are now correctly represented in the object of class "phylo";
1875 a warning message is now issued.
1879 CHANGES IN APE VERSION 1.2
1884 o plot.phylo() has been completely re-written and offers several
1885 new functionalities. Three types of trees can now be drawn:
1886 phylogram (as previously), cladogram, and unrooted tree; in
1887 all three types the branch lengths can be drawn using the edge
1888 lengths of the phylogeny or not (e.g., if the latter is absent).
1889 The vertical position of the nodes can be adjusted with two
1890 choices (see option `node.pos'). The code has been re-structured,
1891 and two new functions (potentially useful for developpers) are
1892 documented separately: node.depth.edgelength() and node.depth();
1893 see the respective help pages for details.
1895 o The new function zoom() allows to explore very large trees by
1896 focusing on a small portion of it.
1898 o The new function yule() fits by maximum likelihood the Yule model
1899 (birth-only process) to a phylogenetic tree.
1901 o Support for writing DNA sequences in FASTA format has been
1902 introduced in write.dna() (support for reading sequences in
1903 this format was introduced in read.dna() in version 1.1-2).
1904 The function has been completely re-written, fixing some bugs
1905 (see below); the default behaviour is no more to display the
1906 sequences on the standard output. Several options have been
1907 introduced to control the sequence printing in a flexible
1908 way. The help page has been extended.
1910 o A new data set is included: a supertree of bats in NEXUS format.
1915 o In theta.s(), the default of the option `variance' has
1916 been changed to `FALSE' (as was indicated in the help page).
1918 o Several bugs were fixed in the code of all.equal.phylo().
1920 o Several bugs were fixed in write.dna(), particularly this
1921 function did not work with `format = "interleaved"'.
1923 o Various errors were corrected in the help pages.
1928 o The argument names of as.hclust.phylo() have been changed
1929 from "(phy)" to "(x, ...)" to conform to the definition of
1930 the corresponding generic function.
1932 o gamma.stat() has been renamed gammaStat() to avoid confusion
1933 since gamma() is a generic function.
1937 CHANGES IN APE VERSION 1.1-3
1942 o base.freq() previously did not return a value of 0 for
1943 bases absent in the data (e.g., a vector of length 3 was
1944 returned if one base was absent). This is now fixed (a
1945 vector of length 4 is always returned).
1947 o Several bugs were fixed in read.nexus(), including that this
1948 function did not work in this absence of a "TRANSLATE"
1949 command in the NEXUS file, and that the commands were
1954 CHANGES IN APE VERSION 1.1-2
1959 o The Tamura and Nei (1993) model of DNA distance is now implemented
1960 in dist.dna(): five models are now available in this function.
1962 o A new data set is included: a set of 15 sequences of the
1963 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1969 o A bug in read.nexus() was fixed.
1971 o read.dna() previously did not work correctly in most cases.
1972 The function has been completely re-written and its help page
1973 has been considerably extended (see ?read.dna for details).
1974 Underscores (_) in taxon names are no more replaced with
1975 spaces (this behaviour was undocumented).
1977 o A bug was fixed in write.dna().
1981 CHANGES IN APE VERSION 1.1-1
1986 o A bug in read.tree() introduced in APE 1.1 was fixed.
1988 o A bug in compar.gee() resulted in an error when trying to fit
1989 a model with `family = "binomial"'. This is now fixed.
1993 CHANGES IN APE VERSION 1.1
1998 o The Klastorin (1982) method as suggested by Misawa and Tajima
1999 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
2000 on the basis of phylogenetic trees has been implemented (see
2001 the function klastorin()).
2003 o Functions have been added to convert APE's "phylo" objects in
2004 "hclust" cluster objects and vice versa (see the help page of
2005 as.phylo for details).
2007 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
2008 are introduced for the estimation of absolute evolutionary rates
2009 (ratogram) and dated clock-like trees (chronogram) from
2010 phylogenetic trees using the non-parametric rate smoothing approach
2011 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
2013 o A summary method is now provided printing a summary information on a
2014 phylogenetic tree with, for instance, `summary(tree)'.
2016 o The behaviour of read.tree() was changed so that all spaces and
2017 tabulations in tree files are now ignored. Consequently, spaces in tip
2018 labels are no more allowed. Another side effect is that read.nexus()
2019 now does not replace the underscores (_) in tip labels with spaces
2020 (this behaviour was undocumented).
2022 o The function plot.phylo() has a new option (`underscore') which
2023 specifies whether the underscores in tip labels should be written on
2024 the plot as such or replaced with spaces (the default).
2026 o The function birthdeath() now computes 95% confidence intervals of
2027 the estimated parameters using profile likelihood.
2029 o Three new data sets are included: a gene tree estimated from 36
2030 landplant rbcL sequences, a gene tree estimated from 32 opsin
2031 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
2036 o A bug was fixed in dist.gene() where nothing was returned.
2038 o A bug in plot.mst() was fixed.
2040 o A bug in vcv.phylo() resulted in false correlations when the
2041 option `cor = TRUE' was used (now fixed).
2045 CHANGES IN APE VERSION 1.0
2050 o Two new functions, read.dna() and write.dna(), read/write in a file
2051 DNA sequences in interleaved or in sequential format.
2053 o Two new functions, read.nexus() and write.nexus(), read/write trees
2056 o The new function bind.tree() allows to bind two trees together,
2057 possibly handling root edges to give internal branches.
2059 o The new function drop.tip() removes the tips in a phylogenetic tree,
2060 and trims (or not) the corresponding internal branches.
2062 o The new function is.ultrametric() tests if a tree is ultrametric.
2064 o The function plot.phylo() has more functionalities such as drawing the
2065 branches with different colours and/or different widths, showing the
2066 node labels, controling the position and font of the labels, rotating
2067 the labels, and controling the space around the plot.
2069 o The function read.tree() can now read trees with no branch length,
2070 such as "(a,b),c);". Consequently, the element `edge.length' in
2071 objects of class "phylo" is now optional.
2073 o The function write.tree() has a new default behaviour: if the default
2074 for the option `file' is used (i.e. file = ""), then a variable of
2075 mode character containing the tree in Newick format is returned which
2076 can thus be assigned (e.g., tree <- write.tree(phy)).
2078 o The function read.tree() has a new argument `text' which allows
2079 to read the tree in a variable of mode character.
2081 o A new data set is included: the phylogenetic relationships among
2082 the orders of birds from Sibley and Ahlquist (1990).
2086 CHANGES IN APE VERSION 0.2-1
2091 o Several bugs were fixed in the help pages.
2095 CHANGES IN APE VERSION 0.2
2100 o The function write.tree() writes phylogenetic trees (objects of class
2101 "phylo") in an ASCII file using the Newick parenthetic format.
2103 o The function birthdeath() fits a birth-death model to branching times
2104 by maximum likelihood, and estimates the corresponding speciation and
2107 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
2110 o The function is.binary.tree() tests whether a phylogeny is binary.
2112 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
2113 as well as some methods are introduced.
2115 o Several functions, including some generics and methods, for computing
2116 skyline plot estimates (classic and generalized) of effective
2117 population size through time are introduced and replace the function
2118 skyline.plot() in version 0.1.
2120 o Two data sets are now included: the phylogenetic relationships among
2121 the families of birds from Sibley and Ahlquist (1990), and an
2122 estimated clock-like phylogeny of HIV sequences sampled in the
2123 Democratic Republic of Congo.
2126 DEPRECATED & DEFUNCT
2128 o The function skyline.plot() in ape 0.1 has been deprecated and
2129 replaced by more elaborate functions (see above).
2134 o Two important bugs were fixed in plot.phylo(): phylogenies with
2135 multichotomies not at the root or not with only terminal branches,
2136 and phylogenies with a single node (i.e. only terminal branches)
2137 did not plot. These trees should be plotted correctly now.
2139 o Several bugs were fixed in diversi.time() in the computation of
2142 o Various errors were corrected in the help pages.