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,
17 CHANGES IN APE VERSION 2.5-3
22 o The new function mixedFontLabel helps to make labels with bits of
23 text to be plotted in different fonts.
25 o There are now replacement operators for [, [[, and $ for the class
26 "multiPhylo" (i.e., TREES[11:20] <- rmtree(10, 100)). They possibly
27 check that the tip labels are the same in all trees.
29 o Objects of class "multiPhylo" can be built with c(): there are
30 methods for the classes "phylo" and "multiPhylo".
32 o The internal functions .compressTipLabel and .uncompressTipLabel are
38 o bind.tree(x, y, where, position = 0) did not work correctly if 'y'
39 was a single-edge tree and 'where' was a tip.
41 o rTraitCont() did not use the square-root of branch lengths when
42 simulating a Brownian motion model.
46 CHANGES IN APE VERSION 2.5-2
51 o There is now a print method for results from ace().
53 o There is a labels() method for objects of class "DNAbin".
55 o read.dna() has a new option 'as.matrix' to possibly force sequences
56 in a FASTA file to be stored in a matrix (see ?read.dna for details).
61 o as.phylo.hclust() used to multiply edge lengths by 2.
63 o A minor bug was fixed in rTraitDisc().
65 o ace() sometimes failed (parameter value was NaN and the optimisation
71 o evolve.phylo() and plot.ancestral() have been removed.
73 o chronogram(), ratogram(), and NPRS.criterion() have been removed.
78 o nj() has been improved and is now about 30% faster.
80 o The default option 'drop' of [.DNAbin has been changed to FALSE to
81 avoid dropping rownames when selecting a single sequence.
83 o print.DNAbin() has been changed to summary.DNAbin() which has been
88 CHANGES IN APE VERSION 2.5-1
93 o The new function stree generates trees with regular shapes.
95 o It is now possible to bind two trees with x + y (see ?bind.tree for
98 o drop.tip(), extract.clade(), root(), and bind.tree() now have an
99 'interactive' option to make the operation on a plotted tree.
101 o cophyloplot() gains two new arguments 'lwd' and 'lty' for the
102 association links; they are recycled like 'col' (which wasn't before).
107 o rTraitDisc() did not use its 'freq' argument correctly (it was
108 multiplied with the rate matrix column-wise instead of row-wise).
110 o [node|tip|edge]labels(thermo = ) used to draw empty thermometers
111 with NA values. Nothing is drawn now like with 'text' or 'pch'.
112 The same bug occurred with the 'pie' option.
114 o A bug was fixed in compar.ou() and the help page was clarified.
116 o bind.tree() has been rewritten fixing several bugs and making it
119 o plot.phylo(type = "p") sometimes failed to colour correctly the
120 vertical lines representing the nodes.
122 o plot.phylo(direction = "l", x.lim = 30) failed to plot the branches
123 in the correct direction though the tip labels were displayed
129 o The c, cbind, and rbind methods for "DNAbin" objetcs now check that
130 the sequences are correctly stored (in a list for c, in a matrix
131 for the two other functions).
135 CHANGES IN APE VERSION 2.5
140 o The new function parafit by Pierre Legendre tests for the
141 coevolution between hosts and parasites. It has a companion
142 function, pcoa, that does principal coordinate decomposition.
143 The latter has a biplot method.
145 o The new function lmorigin by Pierre Legendre performs multiple
146 regression through the origin with testing by permutation.
148 o The new functions rTraitCont and rTraitDisc simulate continuous and
149 discrete traits under a wide range of evolutionary models.
151 o The new function delta.plot does a delta plot following Holland et
152 al. (2002, Mol. Biol. Evol. 12:2051).
154 o The new function edges draws additional branches between any nodes
155 and/or tips on a plotted tree.
157 o The new function fancyarrows enhances arrows from graphics with
158 triangle and harpoon heads; it can be called from edges().
160 o add.scale.bar() has a new option 'ask' to draw interactively.
162 o The branch length score replaces the geodesic distance in dist.topo.
164 o Three new data sets are included: the gopher-lice data (gopher.D),
165 SO2 air pollution in 41 US cities (lmorigin.ex1, from Sokal &
166 Rohlf 1995), and some host-parasite specificity data
167 (lmorigin.ex2, from Legendre & Desdevises 2009).
172 o add.scale.bar() drew the bar outside the plotting region with the
173 default options with unrooted or radial trees.
175 o dist.topo() made R stuck when the trees had different sizes (thanks
176 to Otto Cordero for the fix).
181 o The geodesic distance has been replaced by the branch length score
186 CHANGES IN APE VERSION 2.4-1
191 o rtree() and rcoal() now accept a numeric vector for the 'br'
194 o vcv() is a new generic function with methods for the classes "phylo"
195 and "corPhyl" so that it is possible to calculate the var-cov matrix
196 for "transformation models". vcv.phylo() can still be used for trees
197 of class "phylo"; its argument 'cor' has been renamed 'corr'.
202 o bind.tree() failed when 'y' had no root edge.
204 o read.nexus() shuffled tip labels when the trees have no branch
205 lengths and there is a TRANSLATE block.
207 o read.nexus() does not try to translate node labels if there is a
208 translation table in the NEXUS file. See ?read.nexus for a
209 clarification on this behaviour.
211 o plot.multiPhylo() crashed R when plotting a list of trees with
212 compressed tip labels.
214 o write.nexus() did not translate the taxa names when asked for.
216 o plot.phylo(type = "fan") did not rotate the tip labels correctly
217 when the tree has branch lengths.
219 o ace(type = "continuous", method = "ML") now avoids sigma² being
220 negative (which resulted in an error).
222 o nj() crashed with NA/NaN in the distance matrix: an error in now
227 CHANGES IN APE VERSION 2.4
232 o base.freq() has a new option 'freq' to return the counts; the
233 default is still to return the proportions.
238 o seg.sites() did not handle ambiguous nucleotides correctly: they
241 o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
242 the tree: the argument is now ignored.
244 o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
250 o Trying to plot a tree with a single tip now returns NULL with a
251 warning (it returned an error previously).
253 o The way lines representing nodes are coloured in phylograms has
254 been modified (as well as their widths and types) following some
255 users' request; this is only for dichotomous nodes.
257 o The argument 'adj' in [node][tip][edge]labels() now works when
258 using 'pie' or 'thermo'.
260 o A more informative message error is now returned by dist.dna() when
261 'model' is badly specified (partial matching of this argument is
264 o Deprecated functions are now listed in a help page: see
265 help("ape-defunct") with the quotes.
270 o The functions heterozygosity, nuc.div, theta.h, theta.k and
271 theta.s have been moved from ape to pegas.
273 o The functions mlphylo, DNAmodel and sh.test have been removed.
277 CHANGES IN APE VERSION 2.3-3
282 o add.scale.bar() always drew a horizontal bar.
284 o zoom() shuffled tips with unrooted trees.
286 o write.nexus() failed to write correctly trees with a "TipLabel"
289 o rcoal() failed to compute branch lengths with very large n.
291 o A small bug was fixed in compar.cheverud() (thanks to Michael
294 o seg.sites() failed when passing a vector.
296 o drop.tip() sometimes shuffled tip labels.
298 o root() shuffled node labels with 'resolve.root = TRUE'.
302 CHANGES IN APE VERSION 2.3-2
307 o all.equal.phylo() did not compare unrooted trees correctly.
309 o dist.topo(... method = "PH85") did not treat unrooted trees
310 correctly (thanks to Tim Wallstrom for the fix).
312 o root() sometimes failed to test for the monophyly of the
315 o extract.clade() sometimes included too many edges.
317 o vcv.phylo() did not work correctly when the tree is in
320 o nj() did not handle correctly distance matrices with many 0's.
321 The code has also been significantly improved: 7, 70, 160 times
322 faster with n = 100, 500, 1000, respectively.
326 CHANGES IN APE VERSION 2.3-1
331 o The new function is.monophyletic tests the monophyly of a group.
333 o There is now a c() method for lists of class "DNAbin".
335 o yule.cov() now fits the null model, and its help page has been
336 corrected with respect to this change.
338 o drop.tip() has a new option 'rooted' to force (or not) a tree
339 to be treated as (un)rooted.
344 o dist.gene() failed on most occasions with the default
345 pairwise.deletion = FALSE.
347 o read.tree() failed to read correctly the tree name(s).
349 o boot.phylo() now treats correctly data frames.
351 o del.gaps() did not copy the rownames of a matrix.
353 o A small bug was fixed in CDAM.global().
355 o ace() failed with large data sets. Thanks to Rich FitzJohn for
356 the fix. With other improvements, this function is now about 6
359 o write.tree() failed with objects of class "multiPhylo".
361 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
366 o [.multiPhylo and [.DNAbin now respect the original class.
368 o Instances of the form class(phy) == "phylo" have been replaced
369 by inherits(phy, "phylo").
371 o rcoal() is now faster.
376 o klastorin() has been removed.
380 CHANGES IN APE VERSION 2.3
385 o The new functions CADM.global and CADM.post, contributed by
386 Pierre Legendre, test the congruence among several distance
389 o The new function yule.time fits a user-defined time-dependent
390 Yule model by maximum likelihood.
392 o The new function makeNodeLabel creates and/or modifies node
393 labels in a flexible way.
395 o read.tree() and write.tree() have been modified so that they can
396 handle individual tree names.
398 o plot.phylo() has a new argument 'edge.lty' that specifies the
399 types of lines used for the edges (plain, dotted, dashed, ...)
401 o phymltest() has been updated to work with PhyML 3.0.1.
406 o drop.tip() shuffled tip labels in some cases.
408 o drop.tip() did not handle node.label correctly.
410 o is.ultrametric() now checks the ordering of the edge matrix.
412 o ace() sometimes returned negative values of likelihoods of
413 ancestral states (thanks to Dan Rabosky for solving this long
419 o The data set xenarthra has been removed.
423 CHANGES IN APE VERSION 2.2-4
427 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
428 now fixed. (Thanks to Peter Wragg for the fix!)
430 o A warning message occurred for no reason with ace(method="GLS").
435 o There is now a general help page displayed with '?ape'.
439 CHANGES IN APE VERSION 2.2-3
444 o The new function extract.clade extracts a clade from a tree by
445 specifying a node number or label.
447 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
448 operations of the same names.
450 o dist.dna() can now return the number of site differences by
451 specifying model="N".
456 o chronopl() did not work with CV = TRUE.
458 o read.nexus() did not work correctly in some situations (trees on
459 multiple lines with different numbers of lines and/or with
460 comments inserted within the trees).
462 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
463 the number of lineages with non-binary trees.
468 o ape has now a namespace.
470 o drop.tip() has been improved: it should be much faster and work
471 better in some cases (e.g., see the example in ?zoom).
475 CHANGES IN APE VERSION 2.2-2
480 o dist.gene() has been substantially improved and gains an option
483 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
489 o prop.part() failed with a single tree with the default option
490 'check.labels = TRUE'.
492 o summary.DNAbin() failed to display correctly the summary of
493 sequence lengths with lists of sequences of 10,000 bases or more
494 (because summary.default uses 4 significant digits by default).
496 o read.nexus() failed to read a file with a single tree with line
497 breaks in the Newick string.
499 o del.gaps() returned a list of empty sequences when there were no
505 o phymltest() has been updated for PhyML 3.0 and gains an option
506 'append', whereas the option 'path2exec' has been removed.
508 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
509 which is returned unchanged (instead of an error).
511 o The data sets bird.orders and bird.families are now stored as
512 Newick strings; i.e., the command data(bird.orders) calls
517 CHANGES IN APE VERSION 2.2-1
522 o The new function makeLabel() helps to modify labels of trees,
523 lists of trees, or DNA sequences, with several utilities to
524 truncate and/or make them unique, substituting some
525 characters, and so on.
527 o The new function del.gaps() removes insertion gaps ("-") in a
528 set of DNA sequences.
530 o read.dna() can now read Clustal files (*.aln).
535 o root() failed with 'resolve.root = TRUE' when the root was
536 already the specified root.
538 o Several bugs were fixed in mlphylo().
540 o collapsed.singles() did not propagate the 'Nnode' and
541 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
543 o read.nexus() failed to remove correctly the comments within
546 o read.nexus() failed to read a file with a single tree and no
547 translation of tip labels.
549 o read.nexus() failed to place correctly tip labels when reading
550 a single tree with no edge lengths.
552 o A bug was fixed in sh.test().
557 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
560 o The option 'check.labels' of consensus() and prop.part() is now
563 o write.dna() now does not truncate names to 10 characters with
568 CHANGES IN APE VERSION 2.2
573 o Four new functions have been written by Damien de Vienne for the
574 graphical exploration of large trees (cophyloplot, subtrees,
575 subtreeplot), and to return the graphical coordinates of tree
578 o The new functions corPagel and corBlomberg implement the Pagel's
579 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
581 o chronopl() has been improved and gains several options: see its
582 help page for details.
584 o boot.phylo() has now an option 'trees' to possibly return the
585 bootstraped trees (the default is FALSE).
587 o prop.part() has been improved and should now be faster in all
593 o read.dna() failed if "?" occurred in the first 10 sites of the
596 o The x/y aspect of the plot is now respected when plotting a
597 circular tree (type = "r" or "f").
599 o Drawing the tip labels sometimes failed when plotting circular
602 o zoom() failed when tip labels were used instead of their numbers
603 (thanks to Yan Wong for the fix).
605 o drop.tip() failed with some trees (fixed by Yan Wong).
607 o seg.sites() failed with a list.
609 o consensus() failed in some cases. The function has been improved
610 as well and is faster.
614 CHANGES IN APE VERSION 2.1-3
619 o A bug in read.nexus() made the Windows R-GUI crash.
621 o An error was fixed in the computation of ancestral character
622 states by generalized least squares in ace().
624 o di2multi() did not modify node labels correctly.
626 o multi2di() failed if the tree had its attribute "order" set to
631 CHANGES IN APE VERSION 2.1-2
636 o There three new methods for the "multiPhylo" class: str, $,
639 o root() gains the options 'node' and 'resolve.root'
640 (FALSE by default) as well as its code being improved.
642 o mltt.plot() has now an option 'log' used in the same way
643 than in plot.default().
648 o mltt.plot() failed to display the legend with an unnamed
651 o nodelabels() with pies now correcly uses the argument
652 'cex' to draw symbols of different sizes (which has
653 worked already for thermometers).
655 o read.nexus() generally failed to read very big files.
660 o The argument 'family' of compar.gee() can now be a function
661 as well as a character string.
663 o read.tree() and read.nexus() now return an unnamed list if
666 o read.nexus() now returns a modified object of class "multiPhylo"
667 when there is a TRANSLATE block in the NEXUS file: the individual
668 trees have no 'tip.label' vector, but the list has a 'TipLabel'
669 attribute. The new methods '$' and '[[' set these elements
670 correctly when extracting trees.
674 CHANGES IN APE VERSION 2.1-1
679 o The new function rmtree generates lists of random trees.
681 o rcoal() now generates a genuine coalescent tree by default
682 (thanks to Vladimir Minin for the code).
687 o nuc.div() returned an incorrect value with the default
688 pairwise.deletion = FALSE.
693 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
694 have been improved so that they are stabler and faster.
696 o R packages used by ape are now loaded silently; lattice and gee
697 are loaded only when needed.
701 CHANGES IN APE VERSION 2.1
706 o The new function identify.phylo identifies clades on a plotted
707 tree using the mouse.
709 o It is now possible to subset a list of trees (object of class
710 "multiPhylo") with "[" while keeping its class correct.
712 o The new function as.DNAbin.alignment converts DNA sequences
713 stored in the "alignment" format of the package seqinr into
714 an object of class "DNAbin".
716 o The new function weight.taxo2 helps to build similarity matrices
717 given two taxonomic levels (usually called by other functions).
719 o write.tree() can now take a list of trees (class "multiPhylo")
720 as its main argument.
722 o plot.correlogram() and plot.correlogramList() have been
723 improved, and gain several options (see the help page for
724 details). A legend is now plotted by default.
729 o dist.dna() returned some incorrect values with `model = "JC69"'
730 and `pairwise.deletion = TRUE'. This affected only the
731 distances involving sequences with missing values. (Thanks
732 to Bruno Toupance for digging this bug out.)
734 o write.tree() failed with some trees: this is fixed by removing
735 the `multi.line' option (trees are now always printed on a
738 o read.nexus() did not correctly detect trees with multiple root
739 edges (see OTHER CHANGES).
744 o The code of mlphylo() has been almost entirely rewritten, and
745 should be much stabler. The options have been also greatly
746 simplified (see ?mlphylo and ?DNAmodel for details).
748 o The internal function nTips has been renamed klastorin_nTips.
750 o The code of is.ultrametric() contained redundancies and has
753 o The code of Moran.I() and of correlogram.formula() have been
756 o read.tree() and read.nexus() now return an error when trying to
757 read a tree with multiple root edges (see BUG FIXES). The
758 correction applied in previous version did not work in all
761 o The class c("multi.tree", "phylo") has been renamed
767 o There is now a vignette in ape: see vignette("MoranI", "ape").
772 o as.matching() and as.phylo.matching() do not support branch
775 o correlogram.phylo() and discrete.dist() have been removed.
779 CHANGES IN APE VERSION 2.0-2
784 o The new function matexpo computes the exponential of a square
787 o The new function unique.multi.tree removes duplicate trees from
790 o yule() has a new option `use.root.edge = FALSE' that specifies
791 to ignore, by default, the root edge of the tree if it exists.
796 o which.edge() failed when the index of a single terminal edge was
799 o In diversi.time(), the values returned for model C were
802 o A bug was fixed in yule() that affected the calculation of the
803 likelihood in the presence of ties in the branching times.
805 o There was a bug in the C function mat_expo4x4 affecting the
806 calculations of the transition probabilities for models HKY and
809 o A small bug was fixed in as.matrix.DNAbin (thanks to James
812 o rtree() did not `shuffle' the tip labels by default, so only a
813 limited number of labelled topologies could be generated.
817 CHANGES IN APE VERSION 2.0-1
822 o The three new functions bionj, fastme.ols, and fastme.bal
823 perform phylogeny estimation by the BIONJ and fastME methods in
824 OLS and balanced versions. This is a port to R of previous
825 previous programs done by Vincent Lefort.
827 o The new function chronoMPL performs molecular dating with the
828 mean path lengths method of Britton et al. (2002, Mol. Phyl.
831 o The new function rotate, contributed by Christoph Heibl, swaps
832 two clades connected to the same node. It works also with
833 multichotomous nodes.
835 o The new `method' as.matrix.DNAbin() may be used to convert
836 easily DNA sequences stored in a list into a matrix while
837 keeping the names and the class.
842 o chronopl() failed when some branch lengths were equal to zero:
843 an error message is now returned.
845 o di2multi() failed when there was a series of consecutive edges
850 CHANGES IN APE VERSION 1.10-2
855 o plot.phylo() can now plot circular trees: the option is type =
856 "fan" or type = "f" (to avoid the ambiguity with type = "c").
858 o prop.part() has a new option `check.labels = FALSE' which allows
859 to considerably speed-up the calculations of bipartitions. As a
860 consequence, calculations of bootstrap values with boot.phylo()
861 should be much faster.
866 o read.GenBank() did not return correctly the list of species as
867 from ape 1.10: this is fixed in this version
869 o Applying as.phylo() on a tree of class "phylo" failed: the
870 object is now returned unchanged.
874 CHANGES IN APE VERSION 1.10-1
879 o The three new functions Ntip, Nnode, and Nedge return, for a
880 given tree, the number of tips, nodes, or edges, respectively.
885 o read.nexus() did not set correctly the class of the returned
886 object when reading multiple trees.
888 o mllt.plot() failed with objects of class c("multi.tree",
891 o unroot() did not work correctly in most cases.
893 o reorder.phylo() made R freeze in some occasions.
895 o Plotting a tree in pruningwise order failed.
897 o When plotting an unrooted tree, the tip labels where not all
898 correctly positioned if the option `cex' was used.
902 CHANGES IN APE VERSION 1.10
907 o Five new `method' functions have been introduced to manipulate
908 DNA sequences in binary format (see below).
910 o Three new functions have been introduced to convert between the
911 new binary and the character formats.
913 o The new function as.alignment converts DNA sequences stored as
914 single characters into the class "alignment" used by the package
917 o read.dna() and read.GenBank() have a new argument `as.character'
918 controlling whether the sequences are returned in binary format
924 o root() failed when the tree had node labels: this is fixed.
926 o plot.phylo() did not correctly set the limits on the y-axis with
927 the default setting: this is fixed.
929 o dist.dna() returned a wrong result for the LogDet, paralinear,
930 and BH87 models with `pairwise.deletion = TRUE'.
935 o DNA sequences are now internally stored in a binary format. See
936 the document "A Bit-Level Coding Scheme for Nucleotides" for the
937 details. Most functions analyzing DNA functions have been
938 modified accordingly and are now much faster (dist.dna is now
939 ca. 60 times faster).
943 CHANGES IN APE VERSION 1.9-4
948 o A bug was fixed in edgelabels().
950 o as.phylo.hclust() did not work correctly when the object of
951 class "hclust" has its labels set to NULL: the returned tree has
952 now its tip labels set to "1", "2", ...
954 o consensus could fail if some tip labels are a subset of others
955 (e.g., "a" and "a_1"): this is now fixed.
957 o mlphylo() failed in most cases if some branch lengths of the
958 initial tree were greater than one: an error message is now
961 o mlphylo() failed in most cases when estimating the proportion of
962 invariants: this is fixed.
966 CHANGES IN APE VERSION 1.9-3
971 o The new function edgelabels adds labels on the edge of the tree
972 in the same way than nodelabels or tiplabels.
977 o multi2di() did not handle correctly branch lengths with the
978 default option `random = TRUE': this is now fixed.
980 o A bug was fixed in nuc.div() when using pairwise deletions.
982 o A bug occurred in the analysis of bipartitions with large
983 numbers of large trees, with consequences on prop.part,
984 prop.clades, and boot.phylo.
986 o The calculation of the Billera-Holmes-Vogtmann distance in
987 dist.topo was wrong: this has been fixed.
991 CHANGES IN APE VERSION 1.9-2
996 o The new function ladderize reorganizes the internal structure of
997 a tree to plot them left- or right-ladderized.
999 o The new function dist.nodes computes the patristic distances
1000 between all nodes, internal and terminal, of a tree. It replaces
1001 the option `full = TRUE' of cophenetic.phylo (see below).
1006 o A bug was fixed in old2new.phylo().
1008 o Some bugs were fixed in chronopl().
1010 o The edge colours were not correctly displayed by plot.phylo
1011 (thank you to Li-San Wang for the fix).
1013 o cophenetic.phylo() failed with multichotomous trees: this is
1019 o read.dna() now returns the sequences in a matrix if they are
1020 aligned (interleaved or sequential format). Sequences in FASTA
1021 format are still returned in a list.
1023 o The option `full' of cophenetic.phylo() has been removed because
1024 it could not be used from the generic.
1027 DEPRECATED & DEFUNCT
1029 o rotate() has been removed; this function did not work correctly
1034 CHANGES IN APE VERSION 1.9-1
1039 o Trees with a single tip were not read correctly in R as the
1040 element `Nnode' was not set: this is fixed.
1042 o unroot() did not set correctly the number of nodes of the
1043 unrooted tree in most cases.
1045 o read.GenBank() failed when fetching very long sequences,
1046 particularly of the BX-series.
1048 o A bug was introduced in read.tree() with ape 1.9: it has been
1053 CHANGES IN APE VERSION 1.9
1058 o There are two new print `methods' for trees of class "phylo" and
1059 lists of trees of class "multi.tree", so that they are now
1060 displayed in a compact and informative way.
1062 o There are two new functions, old2new.phylo and new2old.phylo,
1063 for converting between the old and new coding of the class
1066 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
1067 LogDet ("logdet"), and paralinear ("paralin").
1069 o compute.brlen() has been extended: several methods are now
1070 available to compute branch lengths.
1072 o write.dna() can now handle matrices as well as lists.
1077 o cophenetic.phylo() sometimes returned a wrong result with
1078 multichotomous trees: this is fixed.
1080 o rotate() failed when a single tip was specified: the tree is now
1083 o ace() did not return the correct index matrix with custom
1084 models: this is fixed.
1086 o multi2di() did not work correctly when resolving multichotomies
1087 randomly: the topology was always the same, only the arrangement
1088 of clades was randomized: this is fixed. This function now
1089 accepts trees with no branch lengths.
1091 o The output of diversi.gof() was blurred by useless prints when a
1092 user distribution was specified. This has been corrected, and
1093 the help page of this function has been expanded.
1098 o The internal structure of the class "phylo" has been changed:
1099 see the document "Definition of Formats for Coding Phylogenetic
1100 Trees in R" for the details. In addition, the code of most
1101 functions has been improved.
1103 o Several functions have been improved by replacing some R codes
1104 by C codes: pic, plot.phylo, and reorder.phylo.
1106 o There is now a citation information: see citation("ape") in R.
1108 o write.tree() now does not add extra 0's to branch lengths so
1109 that 1.23 is printed "1.23" by default, not "1.2300000000".
1111 o The syntax of bind.tree() has been simplified. This function now
1112 accepts trees with no branch lengths, and handles correctly node
1115 o The option `as.numeric' of mrca() has been removed.
1117 o The unused options `format' and `rooted' of read.tree() have
1120 o The unused option `format' of write.tree() has been removed.
1122 o The use of node.depth() has been simplified.
1126 CHANGES IN APE VERSION 1.8-5
1131 o Two new functions read.nexus.data() and write.nexus.data(),
1132 contributed by Johan Nylander, allow to read and write molecular
1133 sequences in NEXUS files.
1135 o The new function reorder.phylo() reorders the internal structure
1136 of a tree of class "phylo". It is used as the generic, e.g.,
1139 o read.tree() and read.nexus() can now read trees with a single
1142 o The new data set `cynipids' supplies a set of protein sequences
1148 o The code of all.equal.phylo() has been completely rewritten
1149 (thanks to Benoît Durand) which fixes several bugs.
1151 o read.tree() and read.nexus() now checks the labels of the tree
1152 to remove or substitute any characters that are illegal in the
1153 Newick format (parentheses, etc.)
1155 o A negative P-value could be returned by mantel.test(): this is
1160 CHANGES IN APE VERSION 1.8-4
1165 o The new function sh.test() computes the Shimodaira-
1168 o The new function collapse.singles() removes the nodes with a
1169 single descendant from a tree.
1171 o plot.phylo() has a new argument `tip.color' to specify the
1172 colours of the tips.
1174 o mlphylo() has now an option `quiet' to control the display of
1175 the progress of the analysis (the default is FALSE).
1180 o read.dna() did not read correctly sequences in sequential format
1181 with leading alignment gaps "-": this is fixed.
1183 o ace() returned a list with no class so that the generic
1184 functions (anova, logLik, ...) could not be used directly. This
1185 is fixed as ace() now returns an object of class "ace".
1187 o anova.ace() had a small bug when computing the number of degrees
1188 of freedom: this is fixed.
1190 o mlphylo() did not work when the sequences were in a matrix or
1191 a data frame: this is fixed.
1193 o rtree() did not work correctly when trying to simulate an
1194 unrooted tree with two tips: an error message is now issued.
1199 o The algorithm of rtree() has been changed: it is now about 40,
1200 100, and 130 times faster for 10, 100, and 1000 tips,
1205 CHANGES IN APE VERSION 1.8-3
1210 o There are four new `method' functions to be used with the
1211 results of ace(): logLik(), deviance(), AIC(), and anova().
1213 o The plot method of phymltest has two new arguments: `main' to
1214 change the title, and `col' to control the colour of the
1215 segments showing the AIC values.
1217 o ace() has a new argument `ip' that gives the initial values used
1218 in the ML estimation with discrete characters (see the examples
1219 in ?ace). This function now returns a matrix giving the indices
1220 of the estimated rates when analysing discrete characters.
1222 o nodelabels() and tiplabels() have a new argument `pie' to
1223 represent proportions, with any number of categories, as
1224 piecharts. The use of the option `thermo' has been improved:
1225 there is now no limitation on the number of categories.
1230 o mlphylo() did not work with more than two partitions: this is
1233 o root() failed if the proposed outgroup was already an outgroup
1234 in the tree: this is fixed.
1236 o The `col' argument in nodelabels() and tiplabels() was not
1237 correctly passed when `text' was used: this is fixed.
1239 o Two bugs were fixed in mlphylo(): parameters were not always
1240 correctly output, and the estimation failed in some cases.
1242 o plot.phylo() was stuck when given a tree with a single tip: this
1243 is fixed and a message error is now returned.
1245 o An error was corrected in the help page of gammaStat regarding
1246 the calculation of P-values.
1248 o Using gls() could crash R when the number of species in the tree
1249 and in the variables were different: this is fixed.
1253 CHANGES IN APE VERSION 1.8-2
1258 o The new function mlphylo() fits a phylogenetic tree by maximum
1259 likelihood from DNA sequences. Its companion function DNAmodel()
1260 is used to define the substitution model which may include
1261 partitioning. There are methods for logLik(), deviance(), and
1262 AIC(), and the summary() method has been extended to display in
1263 a friendly way the results of this model fitting. Currently, the
1264 functionality is limited to estimating the substitution and
1265 associated parameters and computing the likelihood.
1267 o The new function drop1.compar.gee (used as, e.g., drop1(m))
1268 tests for single effects in GEE-based comparative method. A
1269 warning message is printed if there is not enough degrees of
1275 o An error message was sometimes issued by plot.multi.tree(),
1276 though with no consequence.
1280 CHANGES IN APE VERSION 1.8-1
1285 o There is a new plot method for lists of trees (objects of class
1286 "multi.tree"): it calls plot.phylo() internally and is
1287 documented on the same help page.
1292 o A bug was fixed in the C code that analyzes bipartitions: this
1293 has impact on several functions like prop.part, prop.clades,
1294 boot.phylo, or consensus.
1296 o root() did not work correctly when the specified outgroup had
1297 more than one element: this is fixed.
1299 o dist.dna() sometimes returned a warning inappropriately: this
1302 o If the distance object given to nj() had no rownames, nj()
1303 returned a tree with no tip labels: it now returns tips labelled
1304 "1", "2", ..., corresponding to the row numbers.
1309 o nj() has been slightly changed so that tips with a zero distance
1310 are first aggregated with zero-lengthed branches; the usual NJ
1311 procedure is then performed on a distance matrix without 0's.
1315 CHANGES IN APE VERSION 1.8
1320 o The new function chronopl() estimates dates using the penalized
1321 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1323 o The new function consensus() calculates the consensus tree of a
1326 o The new function evolve.phylo() simulates the evolution of
1327 continuous characters along a phylogeny under a Brownian model.
1329 o The new plot method for objects of class "ancestral" displays a
1330 tree together with ancestral values, as returned by the above
1333 o The new function as.phylo.formula() returns a phylogeny from a
1334 set of nested taxonomic variables given as a formula.
1336 o The new function read.caic() reads trees in CAIC format.
1338 o The new function tiplabels() allows to add labels to the tips
1339 of a tree using text or plotting symbols in a flexible way.
1341 o The new function unroot() unroots a phylogeny.
1343 o multi2di() has a new option, `random', which specifies whether
1344 to resolve the multichotomies randomly (the default) or not.
1346 o prop.part() now returns an object of class "prop.part" for which
1347 there are print (to display a partition in a more friendly way)
1348 and summary (to extract the numbers) methods.
1350 o plot.phylo() has a new option, `show.tip.label', specifying
1351 whether to print the labels of the tips. The default is TRUE.
1353 o The code of nj() has been replaced by a faster C code: it is now
1354 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1357 o write.nexus() now writes whether a tree is rooted or not.
1362 o Two bugs have been fixed in root(): unrooted trees are now
1363 handled corretly, and node labels are now output normally.
1365 o A bug was fixed in phymltest(): the executable couldn't be found
1368 o Three bug have been fixed in ace(): computing the likelihood of
1369 ancestral states of discrete characters failed, custom models
1370 did not work, and the function failed with a null gradient (a
1371 warning message is now returned; this latter bug was also
1372 present in yule.cov() as well and is now fixed).
1374 o pic() hanged out when missing data were present: a message error
1377 o A small bug was fixed in dist.dna() where the gamma correction
1378 was not always correctly dispatched.
1380 o plot.phylo() plotted correctly the root edge only when the tree
1381 was plotted rightwards: this works now for all directions.
1386 o dist.taxo() has been renamed as weight.taxo().
1388 o dist.phylo() has been replaced by the method cophenetic.phylo().
1390 o Various error and warning messages have been improved.
1394 CHANGES IN APE VERSION 1.7
1397 o The new function ace() estimates ancestral character states for
1398 continuous characters (with ML, GLS, and contrasts methods), and
1399 discrete characters (with ML only) for any number of states.
1401 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1402 of directional evolution for continuous characters. The user
1403 specifies the node(s) of the tree where the character optimum
1406 o The new function is.rooted() tests whether a tree (of class
1409 o The new function rcoal() generates random ultrametric trees with
1410 the possibility to specify the function that generates the
1411 inter-nodes distances.
1413 o The new function mrca() gives for all pairs of tips in a tree
1414 (and optionally nodes too) the most recent common ancestor.
1416 o nodelabels() has a new option `thermo' to plot proportions (up
1417 to three classes) on the nodes of a tree.
1419 o rtree() has been improved: it can now generate rooted or
1420 unrooted trees, and the mathematical function that generates the
1421 branch lengths may be specified by the user. The tip labels may
1422 be given directly in the call to rtree. The limit cases (n = 2,
1423 3) are now handled correctly.
1425 o dist.topo() has a new argument `method' with two choices: "PH85"
1426 for Penny and Henny's method (already available before and now
1427 the default), and "BHV01" for the geometric distance by Billera
1428 et al. (2001, Adv. Appl. Math. 27:733).
1430 o write.tree() has a new option, `digits', which specifies the
1431 number of digits to be printed in the Newick tree. By default
1432 digits = 10. The numbers are now always printed in decimal form
1433 (i.e., 1.0e-1 is now avoided).
1435 o dist.dna() can now compute the raw distances between pairs of
1436 DNA sequences by specifying model = "raw".
1438 o dist.phylo() has a new option `full' to possibly compute the
1439 distances among all tips and nodes of the tree. The default if
1445 o Several bugs were fixed in all.equal.phylo().
1447 o dist.dna() did not handle correctly gaps ("-") in alignments:
1448 they are now considered as missing data.
1450 o rotate() did not work if the tips were not ordered: this is
1453 o mantel.test() returned NA in some special cases: this is fixed
1454 and the function has been improved and is now faster.
1456 o A bug was fixed in diversi.gof() where the calculation of A² was
1459 o cherry() did not work correctly under some OSs (mainly Linux):
1462 o is.binary.tree() has been modified so that it works with both
1463 rooted and unrooted trees.
1465 o The documentation of theta.s() was not correct: this has been
1468 o plot.mst() did not work correctly: this is fixed.
1472 CHANGES IN APE VERSION 1.6
1477 o The new function dist.topo() computes the topological distances
1480 o The new function boot.phylo() performs a bootstrap analysis on
1481 phylogeny estimation.
1483 o The new functions prop.part() and prop.clades() analyse
1484 bipartitions from a series of trees.
1489 o read.GenBank() now uses the EFetch utility of NCBI instead of
1490 the usual Web interface: it is now much faster (e.g., 12 times
1491 faster to retrieve 8 sequences, 37 times for 60 sequences).
1496 o Several bugs were fixed in read.dna().
1498 o Several bugs were fixed in diversi.time().
1500 o is.binary.tree() did not work correctly if the tree has no edge
1501 lengths: this is fixed.
1503 o drop.tip() did not correctly propagated the `node.label' of a
1504 tree: this is fixed.
1508 CHANGES IN APE VERSION 1.5
1513 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1514 convert objects between the classes "phylo" and "matching". The
1515 latter implements the representation of binary trees introduced by
1516 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1517 as.matching() has been introduced as well.
1519 o Two new functions, multi2di() and di2multi(), allow to resolve
1520 and collapse multichotomies with branches of length zero.
1522 o The new function nuc.div() computes the nucleotide diversity
1523 from a sample a DNA sequences.
1525 o dist.dna() has been completely rewritten with a much faster
1526 (particularly for large data sets) C code. Eight models are
1527 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1528 option `method' has been renamed `model'). Computation of variance
1529 is available for all models. A gamma-correction is possible for
1530 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1531 to remove sites with missing data on a pairwise basis. The option
1532 `GCcontent' has been removed.
1534 o read.GenBank() has a new option (species.names) which specifies
1535 whether to return the species names of the organisms in addition
1536 to the accession numbers of the sequences (this is the default
1539 o write.nexus() can now write several trees in the same NEXUS file.
1541 o drop.tip() has a new option `root.edge' that allows to specify the
1542 new root edge if internal branches are trimmed.
1547 o as.phylo.hclust() failed if some labels had parentheses: this
1550 o Several bugs were fixed in all.equal.phylo(). This function now
1551 returns the logical TRUE if the trees are identical but with
1552 different representations (a report was printed previously).
1554 o read.GenBank() did not correctly handle ambiguous base codes:
1560 o birthdeath() now returns an object of class "birthdeath" for
1561 which there is a print method.
1565 CHANGES IN APE VERSION 1.4
1570 o The new function nj() performs phylogeny estimation with the
1571 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1574 o The new function which.edge() identifies the edges of a tree
1575 that belong to a group specified as a set of tips.
1577 o The new function as.phylo.phylog() converts an object of class
1578 "phylog" (from the package ade4) into an object of class
1581 o The new function axisPhylo() draws axes on the side of a
1584 o The new function howmanytrees() calculates the number of trees
1585 in different cases and giving a number of tips.
1587 o write.tree() has a new option `multi.line' (TRUE by default) to
1588 write a Newick tree on several lines rather than on a single
1591 o The functionalities of zoom() have been extended. Several
1592 subtrees can be visualized at the same time, and they are marked
1593 on the main tree with colors. The context of the subtrees can be
1594 marked with the option `subtree' (see below).
1596 o drop.tip() has a new option `subtree' (FALSE by default) which
1597 specifies whether to output in the tree how many tips have been
1600 o The arguments of add.scale.bar() have been redefined and have
1601 now default values (see ?add.scale.bar for details). This
1602 function now works even if the plotted tree has no edge length.
1604 o plot.phylo() can now plot radial trees, but this does not take
1605 edge lengths into account.
1607 o In plot.phylo() with `type = "phylogram"', if the values of
1608 `edge.color' and `edge.width' are identical for sister-branches,
1609 they are propagated to the vertical line that link them.
1614 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1615 crashing. This is fixed.
1617 o In plot.phylo(), the options `edge.color' and `edge.width' are
1618 now properly recycled; their default values are now "black" and
1621 o A bug has been fixed in write.nexus().
1626 o The function node.depth.edgelength() has been removed and
1627 replaced by a C code.
1631 CHANGES IN APE VERSION 1.3-1
1636 o The new function nodelabels() allows to add labels to the nodes
1637 of a tree using text or plotting symbols in a flexible way.
1639 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1640 numeric values specifying the lower and upper limits on the x-
1641 and y-axes. This allows to leave some space on any side of the
1642 tree. If a single value is given, this is taken as the upper
1647 CHANGES IN APE VERSION 1.3
1652 o The new function phymltest() calls the software PHYML and fits
1653 28 models of DNA sequence evolution. There are a print method to
1654 display likelihood and AIC values, a summary method to compute
1655 the hierarchical likelihood ratio tests, and a plot method to
1656 display graphically the AIC values of each model.
1658 o The new function yule.cov() fits the Yule model with covariates,
1659 a model where the speciation rate is affected by several species
1660 traits through a generalized linear model. The parameters are
1661 estimated by maximum likelihood.
1663 o Three new functions, corBrownian(), corGrafen(), and
1664 corMartins(), compute the expected correlation structures among
1665 species given a phylogeny under different models of evolution.
1666 These can be used for GLS comparative phylogenetic methods (see
1667 the examples). There are coef() and corMatrix() methods and an
1668 Initialize.corPhyl() function associated.
1670 o The new function compar.cheverud() implements Cheverud et al.'s
1671 (1985; Evolution 39:1335) phylogenetic comparative method.
1673 o The new function varcomp() estimates variance components; it has
1676 o Two new functions, panel.superpose.correlogram() and
1677 plot.correlogramList(), allow to plot several phylogenetic
1680 o The new function node.leafnumber() computes the number of leaves
1681 of a subtree defined by a particular node.
1683 o The new function node.sons() gets all tags of son nodes from a
1686 o The new function compute.brlen() computes the branch lengths of
1687 a tree according to a specified method.
1689 o plot.phylo() has three new options: "cex" controls the size of
1690 the (tip and node) labels (thus it is no more needed to change
1691 the global graphical parameter), "direction" which allows to
1692 plot the tree rightwards, leftwards, upwards, or downwards, and
1693 "y.lim" which sets the upper limit on the y-axis.
1698 o Some functions which try to match tip labels and names of
1699 additional data (e.g. vector) are likely to fail if there are
1700 typing or syntax errors. If both series of names do not perfectly
1701 match, they are ignored and a warning message is now issued.
1702 These functions are bd.ext, compar.gee, pic. Their help pages
1703 have been clarified on this point.
1707 CHANGES IN APE VERSION 1.2-7
1712 o The new function root() reroots a phylogenetic tree with respect
1713 to a specified outgroup.
1715 o The new function rotate() rotates an internal branch of a tree.
1717 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1718 trees) controls the display of the tip labels in unrooted trees.
1719 This display has been greatly improved: the tip labels are now not
1720 expected to overlap with the tree (particularly if lab4ut =
1721 "axial"). In all cases, combining appropriate values of "lab4ut"
1722 and the font size (via "par(cex = )") should result in readable
1723 unrooted trees. See ?plot.phylo for some examples.
1725 o In drop.tip(), the argument `tip' can now be numeric or character.
1730 o drop.tip() did not work correctly with trees with no branch
1731 lengths: this is fixed.
1733 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1734 plotted with some line crossings: this is now fixed.
1738 CHANGES IN APE VERSION 1.2-6
1743 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1744 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1745 to implement comparative methods with an autocorrelation approach.
1747 o A new data set describing some life history traits of Carnivores
1753 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1758 o When plotting a tree with plot.phylo(), the new default of the
1759 option `label.offset' is now 0, so the labels are always visible.
1763 CHANGES IN APE VERSION 1.2-5
1768 o The new function bd.ext() fits a birth-death model with combined
1769 phylogenetic and taxonomic data, and estimates the corresponding
1770 speciation and extinction rates.
1775 o The package gee is no more required by ape but only suggested
1776 since only the function compar.gee() calls gee.
1780 CHANGES IN APE VERSION 1.2-4
1785 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1786 and lines.popsize) implementing a new approach for inferring the
1787 demographic history from genealogies using a reversible jump
1788 MCMC have been introduced.
1790 o The unit of time in the skyline plot and in the new plots can
1791 now be chosen to be actual years, rather than substitutions.
1795 CHANGES IN APE VERSION 1.2-3
1800 o The new function rtree() generates a random binary tree with or
1801 without branch lengths.
1803 o Two new functions for drawing lineages-through-time (LTT) plots
1804 are provided: ltt.lines() adds a LTT curve to an existing plot,
1805 and mltt.plot() does a multiple LTT plot giving several trees as
1806 arguments (see `?ltt.plot' for details).
1811 o Some taxon names made R crashing when calling as.phylo.hclust():
1814 o dist.dna() returned an error with two identical DNA sequences
1815 (only using the Jukes-Cantor method returned 0): this is fixed.
1820 o The function dist.phylo() has been re-written using a different
1821 algorithm: it is now about four times faster.
1823 o The code of branching.times() has been improved: it is now about
1828 CHANGES IN APE VERSION 1.2-2
1833 o The new function seg.sites() finds the segregating sites in a
1834 sample of DNA sequences.
1839 o A bug introduced in read.tree() and in read.nexus() with version
1842 o A few errors were corrected and a few examples were added in the
1847 CHANGES IN APE VERSION 1.2-1
1852 o plot.phylo() can now draw the edge of the root of a tree if it
1853 has one (see the new option `root.edge', its default is FALSE).
1858 o A bug was fixed in read.nexus(): files with semicolons inside
1859 comment blocks were not read correctly.
1861 o The behaviour of read.tree() and read.nexus() was corrected so
1862 that tree files with badly represented root edges (e.g., with
1863 an extra pair of parentheses, see the help pages for details)
1864 are now correctly represented in the object of class "phylo";
1865 a warning message is now issued.
1869 CHANGES IN APE VERSION 1.2
1874 o plot.phylo() has been completely re-written and offers several
1875 new functionalities. Three types of trees can now be drawn:
1876 phylogram (as previously), cladogram, and unrooted tree; in
1877 all three types the branch lengths can be drawn using the edge
1878 lengths of the phylogeny or not (e.g., if the latter is absent).
1879 The vertical position of the nodes can be adjusted with two
1880 choices (see option `node.pos'). The code has been re-structured,
1881 and two new functions (potentially useful for developpers) are
1882 documented separately: node.depth.edgelength() and node.depth();
1883 see the respective help pages for details.
1885 o The new function zoom() allows to explore very large trees by
1886 focusing on a small portion of it.
1888 o The new function yule() fits by maximum likelihood the Yule model
1889 (birth-only process) to a phylogenetic tree.
1891 o Support for writing DNA sequences in FASTA format has been
1892 introduced in write.dna() (support for reading sequences in
1893 this format was introduced in read.dna() in version 1.1-2).
1894 The function has been completely re-written, fixing some bugs
1895 (see below); the default behaviour is no more to display the
1896 sequences on the standard output. Several options have been
1897 introduced to control the sequence printing in a flexible
1898 way. The help page has been extended.
1900 o A new data set is included: a supertree of bats in NEXUS format.
1905 o In theta.s(), the default of the option `variance' has
1906 been changed to `FALSE' (as was indicated in the help page).
1908 o Several bugs were fixed in the code of all.equal.phylo().
1910 o Several bugs were fixed in write.dna(), particularly this
1911 function did not work with `format = "interleaved"'.
1913 o Various errors were corrected in the help pages.
1918 o The argument names of as.hclust.phylo() have been changed
1919 from "(phy)" to "(x, ...)" to conform to the definition of
1920 the corresponding generic function.
1922 o gamma.stat() has been renamed gammaStat() to avoid confusion
1923 since gamma() is a generic function.
1927 CHANGES IN APE VERSION 1.1-3
1932 o base.freq() previously did not return a value of 0 for
1933 bases absent in the data (e.g., a vector of length 3 was
1934 returned if one base was absent). This is now fixed (a
1935 vector of length 4 is always returned).
1937 o Several bugs were fixed in read.nexus(), including that this
1938 function did not work in this absence of a "TRANSLATE"
1939 command in the NEXUS file, and that the commands were
1944 CHANGES IN APE VERSION 1.1-2
1949 o The Tamura and Nei (1993) model of DNA distance is now implemented
1950 in dist.dna(): five models are now available in this function.
1952 o A new data set is included: a set of 15 sequences of the
1953 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1959 o A bug in read.nexus() was fixed.
1961 o read.dna() previously did not work correctly in most cases.
1962 The function has been completely re-written and its help page
1963 has been considerably extended (see ?read.dna for details).
1964 Underscores (_) in taxon names are no more replaced with
1965 spaces (this behaviour was undocumented).
1967 o A bug was fixed in write.dna().
1971 CHANGES IN APE VERSION 1.1-1
1976 o A bug in read.tree() introduced in APE 1.1 was fixed.
1978 o A bug in compar.gee() resulted in an error when trying to fit
1979 a model with `family = "binomial"'. This is now fixed.
1983 CHANGES IN APE VERSION 1.1
1988 o The Klastorin (1982) method as suggested by Misawa and Tajima
1989 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1990 on the basis of phylogenetic trees has been implemented (see
1991 the function klastorin()).
1993 o Functions have been added to convert APE's "phylo" objects in
1994 "hclust" cluster objects and vice versa (see the help page of
1995 as.phylo for details).
1997 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1998 are introduced for the estimation of absolute evolutionary rates
1999 (ratogram) and dated clock-like trees (chronogram) from
2000 phylogenetic trees using the non-parametric rate smoothing approach
2001 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
2003 o A summary method is now provided printing a summary information on a
2004 phylogenetic tree with, for instance, `summary(tree)'.
2006 o The behaviour of read.tree() was changed so that all spaces and
2007 tabulations in tree files are now ignored. Consequently, spaces in tip
2008 labels are no more allowed. Another side effect is that read.nexus()
2009 now does not replace the underscores (_) in tip labels with spaces
2010 (this behaviour was undocumented).
2012 o The function plot.phylo() has a new option (`underscore') which
2013 specifies whether the underscores in tip labels should be written on
2014 the plot as such or replaced with spaces (the default).
2016 o The function birthdeath() now computes 95% confidence intervals of
2017 the estimated parameters using profile likelihood.
2019 o Three new data sets are included: a gene tree estimated from 36
2020 landplant rbcL sequences, a gene tree estimated from 32 opsin
2021 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
2026 o A bug was fixed in dist.gene() where nothing was returned.
2028 o A bug in plot.mst() was fixed.
2030 o A bug in vcv.phylo() resulted in false correlations when the
2031 option `cor = TRUE' was used (now fixed).
2035 CHANGES IN APE VERSION 1.0
2040 o Two new functions, read.dna() and write.dna(), read/write in a file
2041 DNA sequences in interleaved or in sequential format.
2043 o Two new functions, read.nexus() and write.nexus(), read/write trees
2046 o The new function bind.tree() allows to bind two trees together,
2047 possibly handling root edges to give internal branches.
2049 o The new function drop.tip() removes the tips in a phylogenetic tree,
2050 and trims (or not) the corresponding internal branches.
2052 o The new function is.ultrametric() tests if a tree is ultrametric.
2054 o The function plot.phylo() has more functionalities such as drawing the
2055 branches with different colours and/or different widths, showing the
2056 node labels, controling the position and font of the labels, rotating
2057 the labels, and controling the space around the plot.
2059 o The function read.tree() can now read trees with no branch length,
2060 such as "(a,b),c);". Consequently, the element `edge.length' in
2061 objects of class "phylo" is now optional.
2063 o The function write.tree() has a new default behaviour: if the default
2064 for the option `file' is used (i.e. file = ""), then a variable of
2065 mode character containing the tree in Newick format is returned which
2066 can thus be assigned (e.g., tree <- write.tree(phy)).
2068 o The function read.tree() has a new argument `text' which allows
2069 to read the tree in a variable of mode character.
2071 o A new data set is included: the phylogenetic relationships among
2072 the orders of birds from Sibley and Ahlquist (1990).
2076 CHANGES IN APE VERSION 0.2-1
2081 o Several bugs were fixed in the help pages.
2085 CHANGES IN APE VERSION 0.2
2090 o The function write.tree() writes phylogenetic trees (objects of class
2091 "phylo") in an ASCII file using the Newick parenthetic format.
2093 o The function birthdeath() fits a birth-death model to branching times
2094 by maximum likelihood, and estimates the corresponding speciation and
2097 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
2100 o The function is.binary.tree() tests whether a phylogeny is binary.
2102 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
2103 as well as some methods are introduced.
2105 o Several functions, including some generics and methods, for computing
2106 skyline plot estimates (classic and generalized) of effective
2107 population size through time are introduced and replace the function
2108 skyline.plot() in version 0.1.
2110 o Two data sets are now included: the phylogenetic relationships among
2111 the families of birds from Sibley and Ahlquist (1990), and an
2112 estimated clock-like phylogeny of HIV sequences sampled in the
2113 Democratic Republic of Congo.
2116 DEPRECATED & DEFUNCT
2118 o The function skyline.plot() in ape 0.1 has been deprecated and
2119 replaced by more elaborate functions (see above).
2124 o Two important bugs were fixed in plot.phylo(): phylogenies with
2125 multichotomies not at the root or not with only terminal branches,
2126 and phylogenies with a single node (i.e. only terminal branches)
2127 did not plot. These trees should be plotted correctly now.
2129 o Several bugs were fixed in diversi.time() in the computation of
2132 o Various errors were corrected in the help pages.
projects / ape.git / blob