1 CHANGES IN APE VERSION 2.5-2
6 o There is now a print method for results from ace().
11 o as.phylo.hclust() used to multiply edge lengths by 2.
13 o A minor bug was fixed in rTraitDisc().
15 o ace() sometimes failed (parameter value was NaN and the optimisation
21 o evolve.phylo() and plot.ancestral() have been removed.
23 o chronogram(), ratogram(), and NPRS.criterion() have been removed.
28 o nj() has been improved and is now about 30% faster.
32 CHANGES IN APE VERSION 2.5-1
37 o The new function stree generates trees with regular shapes.
39 o It is now possible to bind two trees with x + y (see ?bind.tree for
42 o drop.tip(), extract.clade(), root(), and bind.tree() now have an
43 'interactive' option to make the operation on a plotted tree.
45 o cophyloplot() gains two new arguments 'lwd' and 'lty' for the
46 association links; they are recycled like 'col' (which wasn't before).
51 o rTraitDisc() did not use its 'freq' argument correctly (it was
52 multiplied with the rate matrix column-wise instead of row-wise).
54 o [node|tip|edge]labels(thermo = ) used to draw empty thermometers
55 with NA values. Nothing is drawn now like with 'text' or 'pch'.
56 The same bug occurred with the 'pie' option.
58 o A bug was fixed in compar.ou() and the help page was clarified.
60 o bind.tree() has been rewritten fixing several bugs and making it
63 o plot.phylo(type = "p") sometimes failed to colour correctly the
64 vertical lines representing the nodes.
66 o plot.phylo(direction = "l", x.lim = 30) failed to plot the branches
67 in the correct direction though the tip labels were displayed
73 o The c, cbind, and rbind methods for "DNAbin" objetcs now check that
74 the sequences are correctly stored (in a list for c, in a matrix
75 for the two other functions).
79 CHANGES IN APE VERSION 2.5
84 o The new function parafit by Pierre Legendre tests for the
85 coevolution between hosts and parasites. It has a companion
86 function, pcoa, that does principal coordinate decomposition.
87 The latter has a biplot method.
89 o The new function lmorigin by Pierre Legendre performs multiple
90 regression through the origin with testing by permutation.
92 o The new functions rTraitCont and rTraitDisc simulate continuous and
93 discrete traits under a wide range of evolutionary models.
95 o The new function delta.plot does a delta plot following Holland et
96 al. (2002, Mol. Biol. Evol. 12:2051).
98 o The new function edges draws additional branches between any nodes
99 and/or tips on a plotted tree.
101 o The new function fancyarrows enhances arrows from graphics with
102 triangle and harpoon heads; it can be called from edges().
104 o add.scale.bar() has a new option 'ask' to draw interactively.
106 o The branch length score replaces the geodesic distance in dist.topo.
108 o Three new data sets are included: the gopher-lice data (gopher.D),
109 SO2 air pollution in 41 US cities (lmorigin.ex1, from Sokal &
110 Rohlf 1995), and some host-parasite specificity data
111 (lmorigin.ex2, from Legendre & Desdevises 2009).
116 o add.scale.bar() drew the bar outside the plotting region with the
117 default options with unrooted or radial trees.
119 o dist.topo() made R stuck when the trees had different sizes (thanks
120 to Otto Cordero for the fix).
125 o The geodesic distance has been replaced by the branch length score
130 CHANGES IN APE VERSION 2.4-1
135 o rtree() and rcoal() now accept a numeric vector for the 'br'
138 o vcv() is a new generic function with methods for the classes "phylo"
139 and "corPhyl" so that it is possible to calculate the var-cov matrix
140 for "transformation models". vcv.phylo() can still be used for trees
141 of class "phylo"; its argument 'cor' has been renamed 'corr'.
146 o bind.tree() failed when 'y' had no root edge.
148 o read.nexus() shuffled tip labels when the trees have no branch
149 lengths and there is a TRANSLATE block.
151 o read.nexus() does not try to translate node labels if there is a
152 translation table in the NEXUS file. See ?read.nexus for a
153 clarification on this behaviour.
155 o plot.multiPhylo() crashed R when plotting a list of trees with
156 compressed tip labels.
158 o write.nexus() did not translate the taxa names when asked for.
160 o plot.phylo(type = "fan") did not rotate the tip labels correctly
161 when the tree has branch lengths.
163 o ace(type = "continuous", method = "ML") now avoids sigma² being
164 negative (which resulted in an error).
166 o nj() crashed with NA/NaN in the distance matrix: an error in now
171 CHANGES IN APE VERSION 2.4
176 o base.freq() has a new option 'freq' to return the counts; the
177 default is still to return the proportions.
182 o seg.sites() did not handle ambiguous nucleotides correctly: they
185 o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
186 the tree: the argument is now ignored.
188 o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
194 o Trying to plot a tree with a single tip now returns NULL with a
195 warning (it returned an error previously).
197 o The way lines representing nodes are coloured in phylograms has
198 been modified (as well as their widths and types) following some
199 users' request; this is only for dichotomous nodes.
201 o The argument 'adj' in [node][tip][edge]labels() now works when
202 using 'pie' or 'thermo'.
204 o A more informative message error is now returned by dist.dna() when
205 'model' is badly specified (partial matching of this argument is
208 o Deprecated functions are now listed in a help page: see
209 help("ape-defunct") with the quotes.
214 o The functions heterozygosity, nuc.div, theta.h, theta.k and
215 theta.s have been moved from ape to pegas.
217 o The functions mlphylo, DNAmodel and sh.test have been removed.
221 CHANGES IN APE VERSION 2.3-3
226 o add.scale.bar() always drew a horizontal bar.
228 o zoom() shuffled tips with unrooted trees.
230 o write.nexus() failed to write correctly trees with a "TipLabel"
233 o rcoal() failed to compute branch lengths with very large n.
235 o A small bug was fixed in compar.cheverud() (thanks to Michael
238 o seg.sites() failed when passing a vector.
240 o drop.tip() sometimes shuffled tip labels.
242 o root() shuffled node labels with 'resolve.root = TRUE'.
246 CHANGES IN APE VERSION 2.3-2
251 o all.equal.phylo() did not compare unrooted trees correctly.
253 o dist.topo(... method = "PH85") did not treat unrooted trees
254 correctly (thanks to Tim Wallstrom for the fix).
256 o root() sometimes failed to test for the monophyly of the
259 o extract.clade() sometimes included too many edges.
261 o vcv.phylo() did not work correctly when the tree is in
264 o nj() did not handle correctly distance matrices with many 0's.
265 The code has also been significantly improved: 7, 70, 160 times
266 faster with n = 100, 500, 1000, respectively.
270 CHANGES IN APE VERSION 2.3-1
275 o The new function is.monophyletic tests the monophyly of a group.
277 o There is now a c() method for lists of class "DNAbin".
279 o yule.cov() now fits the null model, and its help page has been
280 corrected with respect to this change.
282 o drop.tip() has a new option 'rooted' to force (or not) a tree
283 to be treated as (un)rooted.
288 o dist.gene() failed on most occasions with the default
289 pairwise.deletion = FALSE.
291 o read.tree() failed to read correctly the tree name(s).
293 o boot.phylo() now treats correctly data frames.
295 o del.gaps() did not copy the rownames of a matrix.
297 o A small bug was fixed in CDAM.global().
299 o ace() failed with large data sets. Thanks to Rich FitzJohn for
300 the fix. With other improvements, this function is now about 6
303 o write.tree() failed with objects of class "multiPhylo".
305 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
310 o [.multiPhylo and [.DNAbin now respect the original class.
312 o Instances of the form class(phy) == "phylo" have been replaced
313 by inherits(phy, "phylo").
315 o rcoal() is now faster.
320 o klastorin() has been removed.
324 CHANGES IN APE VERSION 2.3
329 o The new functions CADM.global and CADM.post, contributed by
330 Pierre Legendre, test the congruence among several distance
333 o The new function yule.time fits a user-defined time-dependent
334 Yule model by maximum likelihood.
336 o The new function makeNodeLabel creates and/or modifies node
337 labels in a flexible way.
339 o read.tree() and write.tree() have been modified so that they can
340 handle individual tree names.
342 o plot.phylo() has a new argument 'edge.lty' that specifies the
343 types of lines used for the edges (plain, dotted, dashed, ...)
345 o phymltest() has been updated to work with PhyML 3.0.1.
350 o drop.tip() shuffled tip labels in some cases.
352 o drop.tip() did not handle node.label correctly.
354 o is.ultrametric() now checks the ordering of the edge matrix.
356 o ace() sometimes returned negative values of likelihoods of
357 ancestral states (thanks to Dan Rabosky for solving this long
363 o The data set xenarthra has been removed.
367 CHANGES IN APE VERSION 2.2-4
371 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
372 now fixed. (Thanks to Peter Wragg for the fix!)
374 o A warning message occurred for no reason with ace(method="GLS").
379 o There is now a general help page displayed with '?ape'.
383 CHANGES IN APE VERSION 2.2-3
388 o The new function extract.clade extracts a clade from a tree by
389 specifying a node number or label.
391 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
392 operations of the same names.
394 o dist.dna() can now return the number of site differences by
395 specifying model="N".
400 o chronopl() did not work with CV = TRUE.
402 o read.nexus() did not work correctly in some situations (trees on
403 multiple lines with different numbers of lines and/or with
404 comments inserted within the trees).
406 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
407 the number of lineages with non-binary trees.
412 o ape has now a namespace.
414 o drop.tip() has been improved: it should be much faster and work
415 better in some cases (e.g., see the example in ?zoom).
419 CHANGES IN APE VERSION 2.2-2
424 o dist.gene() has been substantially improved and gains an option
427 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
433 o prop.part() failed with a single tree with the default option
434 'check.labels = TRUE'.
436 o summary.DNAbin() failed to display correctly the summary of
437 sequence lengths with lists of sequences of 10,000 bases or more
438 (because summary.default uses 4 significant digits by default).
440 o read.nexus() failed to read a file with a single tree with line
441 breaks in the Newick string.
443 o del.gaps() returned a list of empty sequences when there were no
449 o phymltest() has been updated for PhyML 3.0 and gains an option
450 'append', whereas the option 'path2exec' has been removed.
452 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
453 which is returned unchanged (instead of an error).
455 o The data sets bird.orders and bird.families are now stored as
456 Newick strings; i.e., the command data(bird.orders) calls
461 CHANGES IN APE VERSION 2.2-1
466 o The new function makeLabel() helps to modify labels of trees,
467 lists of trees, or DNA sequences, with several utilities to
468 truncate and/or make them unique, substituting some
469 characters, and so on.
471 o The new function del.gaps() removes insertion gaps ("-") in a
472 set of DNA sequences.
474 o read.dna() can now read Clustal files (*.aln).
479 o root() failed with 'resolve.root = TRUE' when the root was
480 already the specified root.
482 o Several bugs were fixed in mlphylo().
484 o collapsed.singles() did not propagate the 'Nnode' and
485 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
487 o read.nexus() failed to remove correctly the comments within
490 o read.nexus() failed to read a file with a single tree and no
491 translation of tip labels.
493 o read.nexus() failed to place correctly tip labels when reading
494 a single tree with no edge lengths.
496 o A bug was fixed in sh.test().
501 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
504 o The option 'check.labels' of consensus() and prop.part() is now
507 o write.dna() now does not truncate names to 10 characters with
512 CHANGES IN APE VERSION 2.2
517 o Four new functions have been written by Damien de Vienne for the
518 graphical exploration of large trees (cophyloplot, subtrees,
519 subtreeplot), and to return the graphical coordinates of tree
522 o The new functions corPagel and corBlomberg implement the Pagel's
523 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
525 o chronopl() has been improved and gains several options: see its
526 help page for details.
528 o boot.phylo() has now an option 'trees' to possibly return the
529 bootstraped trees (the default is FALSE).
531 o prop.part() has been improved and should now be faster in all
537 o read.dna() failed if "?" occurred in the first 10 sites of the
540 o The x/y aspect of the plot is now respected when plotting a
541 circular tree (type = "r" or "f").
543 o Drawing the tip labels sometimes failed when plotting circular
546 o zoom() failed when tip labels were used instead of their numbers
547 (thanks to Yan Wong for the fix).
549 o drop.tip() failed with some trees (fixed by Yan Wong).
551 o seg.sites() failed with a list.
553 o consensus() failed in some cases. The function has been improved
554 as well and is faster.
558 CHANGES IN APE VERSION 2.1-3
563 o A bug in read.nexus() made the Windows R-GUI crash.
565 o An error was fixed in the computation of ancestral character
566 states by generalized least squares in ace().
568 o di2multi() did not modify node labels correctly.
570 o multi2di() failed if the tree had its attribute "order" set to
575 CHANGES IN APE VERSION 2.1-2
580 o There three new methods for the "multiPhylo" class: str, $,
583 o root() gains the options 'node' and 'resolve.root'
584 (FALSE by default) as well as its code being improved.
586 o mltt.plot() has now an option 'log' used in the same way
587 than in plot.default().
592 o mltt.plot() failed to display the legend with an unnamed
595 o nodelabels() with pies now correcly uses the argument
596 'cex' to draw symbols of different sizes (which has
597 worked already for thermometers).
599 o read.nexus() generally failed to read very big files.
604 o The argument 'family' of compar.gee() can now be a function
605 as well as a character string.
607 o read.tree() and read.nexus() now return an unnamed list if
610 o read.nexus() now returns a modified object of class "multiPhylo"
611 when there is a TRANSLATE block in the NEXUS file: the individual
612 trees have no 'tip.label' vector, but the list has a 'TipLabel'
613 attribute. The new methods '$' and '[[' set these elements
614 correctly when extracting trees.
618 CHANGES IN APE VERSION 2.1-1
623 o The new function rmtree generates lists of random trees.
625 o rcoal() now generates a genuine coalescent tree by default
626 (thanks to Vladimir Minin for the code).
631 o nuc.div() returned an incorrect value with the default
632 pairwise.deletion = FALSE.
637 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
638 have been improved so that they are stabler and faster.
640 o R packages used by ape are now loaded silently; lattice and gee
641 are loaded only when needed.
645 CHANGES IN APE VERSION 2.1
650 o The new function identify.phylo identifies clades on a plotted
651 tree using the mouse.
653 o It is now possible to subset a list of trees (object of class
654 "multiPhylo") with "[" while keeping its class correct.
656 o The new function as.DNAbin.alignment converts DNA sequences
657 stored in the "alignment" format of the package seqinr into
658 an object of class "DNAbin".
660 o The new function weight.taxo2 helps to build similarity matrices
661 given two taxonomic levels (usually called by other functions).
663 o write.tree() can now take a list of trees (class "multiPhylo")
664 as its main argument.
666 o plot.correlogram() and plot.correlogramList() have been
667 improved, and gain several options (see the help page for
668 details). A legend is now plotted by default.
673 o dist.dna() returned some incorrect values with `model = "JC69"'
674 and `pairwise.deletion = TRUE'. This affected only the
675 distances involving sequences with missing values. (Thanks
676 to Bruno Toupance for digging this bug out.)
678 o write.tree() failed with some trees: this is fixed by removing
679 the `multi.line' option (trees are now always printed on a
682 o read.nexus() did not correctly detect trees with multiple root
683 edges (see OTHER CHANGES).
688 o The code of mlphylo() has been almost entirely rewritten, and
689 should be much stabler. The options have been also greatly
690 simplified (see ?mlphylo and ?DNAmodel for details).
692 o The internal function nTips has been renamed klastorin_nTips.
694 o The code of is.ultrametric() contained redundancies and has
697 o The code of Moran.I() and of correlogram.formula() have been
700 o read.tree() and read.nexus() now return an error when trying to
701 read a tree with multiple root edges (see BUG FIXES). The
702 correction applied in previous version did not work in all
705 o The class c("multi.tree", "phylo") has been renamed
711 o There is now a vignette in ape: see vignette("MoranI", "ape").
716 o as.matching() and as.phylo.matching() do not support branch
719 o correlogram.phylo() and discrete.dist() have been removed.
723 CHANGES IN APE VERSION 2.0-2
728 o The new function matexpo computes the exponential of a square
731 o The new function unique.multi.tree removes duplicate trees from
734 o yule() has a new option `use.root.edge = FALSE' that specifies
735 to ignore, by default, the root edge of the tree if it exists.
740 o which.edge() failed when the index of a single terminal edge was
743 o In diversi.time(), the values returned for model C were
746 o A bug was fixed in yule() that affected the calculation of the
747 likelihood in the presence of ties in the branching times.
749 o There was a bug in the C function mat_expo4x4 affecting the
750 calculations of the transition probabilities for models HKY and
753 o A small bug was fixed in as.matrix.DNAbin (thanks to James
756 o rtree() did not `shuffle' the tip labels by default, so only a
757 limited number of labelled topologies could be generated.
761 CHANGES IN APE VERSION 2.0-1
766 o The three new functions bionj, fastme.ols, and fastme.bal
767 perform phylogeny estimation by the BIONJ and fastME methods in
768 OLS and balanced versions. This is a port to R of previous
769 previous programs done by Vincent Lefort.
771 o The new function chronoMPL performs molecular dating with the
772 mean path lengths method of Britton et al. (2002, Mol. Phyl.
775 o The new function rotate, contributed by Christoph Heibl, swaps
776 two clades connected to the same node. It works also with
777 multichotomous nodes.
779 o The new `method' as.matrix.DNAbin() may be used to convert
780 easily DNA sequences stored in a list into a matrix while
781 keeping the names and the class.
786 o chronopl() failed when some branch lengths were equal to zero:
787 an error message is now returned.
789 o di2multi() failed when there was a series of consecutive edges
794 CHANGES IN APE VERSION 1.10-2
799 o plot.phylo() can now plot circular trees: the option is type =
800 "fan" or type = "f" (to avoid the ambiguity with type = "c").
802 o prop.part() has a new option `check.labels = FALSE' which allows
803 to considerably speed-up the calculations of bipartitions. As a
804 consequence, calculations of bootstrap values with boot.phylo()
805 should be much faster.
810 o read.GenBank() did not return correctly the list of species as
811 from ape 1.10: this is fixed in this version
813 o Applying as.phylo() on a tree of class "phylo" failed: the
814 object is now returned unchanged.
818 CHANGES IN APE VERSION 1.10-1
823 o The three new functions Ntip, Nnode, and Nedge return, for a
824 given tree, the number of tips, nodes, or edges, respectively.
829 o read.nexus() did not set correctly the class of the returned
830 object when reading multiple trees.
832 o mllt.plot() failed with objects of class c("multi.tree",
835 o unroot() did not work correctly in most cases.
837 o reorder.phylo() made R freeze in some occasions.
839 o Plotting a tree in pruningwise order failed.
841 o When plotting an unrooted tree, the tip labels where not all
842 correctly positioned if the option `cex' was used.
846 CHANGES IN APE VERSION 1.10
851 o Five new `method' functions have been introduced to manipulate
852 DNA sequences in binary format (see below).
854 o Three new functions have been introduced to convert between the
855 new binary and the character formats.
857 o The new function as.alignment converts DNA sequences stored as
858 single characters into the class "alignment" used by the package
861 o read.dna() and read.GenBank() have a new argument `as.character'
862 controlling whether the sequences are returned in binary format
868 o root() failed when the tree had node labels: this is fixed.
870 o plot.phylo() did not correctly set the limits on the y-axis with
871 the default setting: this is fixed.
873 o dist.dna() returned a wrong result for the LogDet, paralinear,
874 and BH87 models with `pairwise.deletion = TRUE'.
879 o DNA sequences are now internally stored in a binary format. See
880 the document "A Bit-Level Coding Scheme for Nucleotides" for the
881 details. Most functions analyzing DNA functions have been
882 modified accordingly and are now much faster (dist.dna is now
883 ca. 60 times faster).
887 CHANGES IN APE VERSION 1.9-4
892 o A bug was fixed in edgelabels().
894 o as.phylo.hclust() did not work correctly when the object of
895 class "hclust" has its labels set to NULL: the returned tree has
896 now its tip labels set to "1", "2", ...
898 o consensus could fail if some tip labels are a subset of others
899 (e.g., "a" and "a_1"): this is now fixed.
901 o mlphylo() failed in most cases if some branch lengths of the
902 initial tree were greater than one: an error message is now
905 o mlphylo() failed in most cases when estimating the proportion of
906 invariants: this is fixed.
910 CHANGES IN APE VERSION 1.9-3
915 o The new function edgelabels adds labels on the edge of the tree
916 in the same way than nodelabels or tiplabels.
921 o multi2di() did not handle correctly branch lengths with the
922 default option `random = TRUE': this is now fixed.
924 o A bug was fixed in nuc.div() when using pairwise deletions.
926 o A bug occurred in the analysis of bipartitions with large
927 numbers of large trees, with consequences on prop.part,
928 prop.clades, and boot.phylo.
930 o The calculation of the Billera-Holmes-Vogtmann distance in
931 dist.topo was wrong: this has been fixed.
935 CHANGES IN APE VERSION 1.9-2
940 o The new function ladderize reorganizes the internal structure of
941 a tree to plot them left- or right-ladderized.
943 o The new function dist.nodes computes the patristic distances
944 between all nodes, internal and terminal, of a tree. It replaces
945 the option `full = TRUE' of cophenetic.phylo (see below).
950 o A bug was fixed in old2new.phylo().
952 o Some bugs were fixed in chronopl().
954 o The edge colours were not correctly displayed by plot.phylo
955 (thank you to Li-San Wang for the fix).
957 o cophenetic.phylo() failed with multichotomous trees: this is
963 o read.dna() now returns the sequences in a matrix if they are
964 aligned (interleaved or sequential format). Sequences in FASTA
965 format are still returned in a list.
967 o The option `full' of cophenetic.phylo() has been removed because
968 it could not be used from the generic.
973 o rotate() has been removed; this function did not work correctly
978 CHANGES IN APE VERSION 1.9-1
983 o Trees with a single tip were not read correctly in R as the
984 element `Nnode' was not set: this is fixed.
986 o unroot() did not set correctly the number of nodes of the
987 unrooted tree in most cases.
989 o read.GenBank() failed when fetching very long sequences,
990 particularly of the BX-series.
992 o A bug was introduced in read.tree() with ape 1.9: it has been
997 CHANGES IN APE VERSION 1.9
1002 o There are two new print `methods' for trees of class "phylo" and
1003 lists of trees of class "multi.tree", so that they are now
1004 displayed in a compact and informative way.
1006 o There are two new functions, old2new.phylo and new2old.phylo,
1007 for converting between the old and new coding of the class
1010 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
1011 LogDet ("logdet"), and paralinear ("paralin").
1013 o compute.brlen() has been extended: several methods are now
1014 available to compute branch lengths.
1016 o write.dna() can now handle matrices as well as lists.
1021 o cophenetic.phylo() sometimes returned a wrong result with
1022 multichotomous trees: this is fixed.
1024 o rotate() failed when a single tip was specified: the tree is now
1027 o ace() did not return the correct index matrix with custom
1028 models: this is fixed.
1030 o multi2di() did not work correctly when resolving multichotomies
1031 randomly: the topology was always the same, only the arrangement
1032 of clades was randomized: this is fixed. This function now
1033 accepts trees with no branch lengths.
1035 o The output of diversi.gof() was blurred by useless prints when a
1036 user distribution was specified. This has been corrected, and
1037 the help page of this function has been expanded.
1042 o The internal structure of the class "phylo" has been changed:
1043 see the document "Definition of Formats for Coding Phylogenetic
1044 Trees in R" for the details. In addition, the code of most
1045 functions has been improved.
1047 o Several functions have been improved by replacing some R codes
1048 by C codes: pic, plot.phylo, and reorder.phylo.
1050 o There is now a citation information: see citation("ape") in R.
1052 o write.tree() now does not add extra 0's to branch lengths so
1053 that 1.23 is printed "1.23" by default, not "1.2300000000".
1055 o The syntax of bind.tree() has been simplified. This function now
1056 accepts trees with no branch lengths, and handles correctly node
1059 o The option `as.numeric' of mrca() has been removed.
1061 o The unused options `format' and `rooted' of read.tree() have
1064 o The unused option `format' of write.tree() has been removed.
1066 o The use of node.depth() has been simplified.
1070 CHANGES IN APE VERSION 1.8-5
1075 o Two new functions read.nexus.data() and write.nexus.data(),
1076 contributed by Johan Nylander, allow to read and write molecular
1077 sequences in NEXUS files.
1079 o The new function reorder.phylo() reorders the internal structure
1080 of a tree of class "phylo". It is used as the generic, e.g.,
1083 o read.tree() and read.nexus() can now read trees with a single
1086 o The new data set `cynipids' supplies a set of protein sequences
1092 o The code of all.equal.phylo() has been completely rewritten
1093 (thanks to Benoît Durand) which fixes several bugs.
1095 o read.tree() and read.nexus() now checks the labels of the tree
1096 to remove or substitute any characters that are illegal in the
1097 Newick format (parentheses, etc.)
1099 o A negative P-value could be returned by mantel.test(): this is
1104 CHANGES IN APE VERSION 1.8-4
1109 o The new function sh.test() computes the Shimodaira-
1112 o The new function collapse.singles() removes the nodes with a
1113 single descendant from a tree.
1115 o plot.phylo() has a new argument `tip.color' to specify the
1116 colours of the tips.
1118 o mlphylo() has now an option `quiet' to control the display of
1119 the progress of the analysis (the default is FALSE).
1124 o read.dna() did not read correctly sequences in sequential format
1125 with leading alignment gaps "-": this is fixed.
1127 o ace() returned a list with no class so that the generic
1128 functions (anova, logLik, ...) could not be used directly. This
1129 is fixed as ace() now returns an object of class "ace".
1131 o anova.ace() had a small bug when computing the number of degrees
1132 of freedom: this is fixed.
1134 o mlphylo() did not work when the sequences were in a matrix or
1135 a data frame: this is fixed.
1137 o rtree() did not work correctly when trying to simulate an
1138 unrooted tree with two tips: an error message is now issued.
1143 o The algorithm of rtree() has been changed: it is now about 40,
1144 100, and 130 times faster for 10, 100, and 1000 tips,
1149 CHANGES IN APE VERSION 1.8-3
1154 o There are four new `method' functions to be used with the
1155 results of ace(): logLik(), deviance(), AIC(), and anova().
1157 o The plot method of phymltest has two new arguments: `main' to
1158 change the title, and `col' to control the colour of the
1159 segments showing the AIC values.
1161 o ace() has a new argument `ip' that gives the initial values used
1162 in the ML estimation with discrete characters (see the examples
1163 in ?ace). This function now returns a matrix giving the indices
1164 of the estimated rates when analysing discrete characters.
1166 o nodelabels() and tiplabels() have a new argument `pie' to
1167 represent proportions, with any number of categories, as
1168 piecharts. The use of the option `thermo' has been improved:
1169 there is now no limitation on the number of categories.
1174 o mlphylo() did not work with more than two partitions: this is
1177 o root() failed if the proposed outgroup was already an outgroup
1178 in the tree: this is fixed.
1180 o The `col' argument in nodelabels() and tiplabels() was not
1181 correctly passed when `text' was used: this is fixed.
1183 o Two bugs were fixed in mlphylo(): parameters were not always
1184 correctly output, and the estimation failed in some cases.
1186 o plot.phylo() was stuck when given a tree with a single tip: this
1187 is fixed and a message error is now returned.
1189 o An error was corrected in the help page of gammaStat regarding
1190 the calculation of P-values.
1192 o Using gls() could crash R when the number of species in the tree
1193 and in the variables were different: this is fixed.
1197 CHANGES IN APE VERSION 1.8-2
1202 o The new function mlphylo() fits a phylogenetic tree by maximum
1203 likelihood from DNA sequences. Its companion function DNAmodel()
1204 is used to define the substitution model which may include
1205 partitioning. There are methods for logLik(), deviance(), and
1206 AIC(), and the summary() method has been extended to display in
1207 a friendly way the results of this model fitting. Currently, the
1208 functionality is limited to estimating the substitution and
1209 associated parameters and computing the likelihood.
1211 o The new function drop1.compar.gee (used as, e.g., drop1(m))
1212 tests for single effects in GEE-based comparative method. A
1213 warning message is printed if there is not enough degrees of
1219 o An error message was sometimes issued by plot.multi.tree(),
1220 though with no consequence.
1224 CHANGES IN APE VERSION 1.8-1
1229 o There is a new plot method for lists of trees (objects of class
1230 "multi.tree"): it calls plot.phylo() internally and is
1231 documented on the same help page.
1236 o A bug was fixed in the C code that analyzes bipartitions: this
1237 has impact on several functions like prop.part, prop.clades,
1238 boot.phylo, or consensus.
1240 o root() did not work correctly when the specified outgroup had
1241 more than one element: this is fixed.
1243 o dist.dna() sometimes returned a warning inappropriately: this
1246 o If the distance object given to nj() had no rownames, nj()
1247 returned a tree with no tip labels: it now returns tips labelled
1248 "1", "2", ..., corresponding to the row numbers.
1253 o nj() has been slightly changed so that tips with a zero distance
1254 are first aggregated with zero-lengthed branches; the usual NJ
1255 procedure is then performed on a distance matrix without 0's.
1259 CHANGES IN APE VERSION 1.8
1264 o The new function chronopl() estimates dates using the penalized
1265 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1267 o The new function consensus() calculates the consensus tree of a
1270 o The new function evolve.phylo() simulates the evolution of
1271 continuous characters along a phylogeny under a Brownian model.
1273 o The new plot method for objects of class "ancestral" displays a
1274 tree together with ancestral values, as returned by the above
1277 o The new function as.phylo.formula() returns a phylogeny from a
1278 set of nested taxonomic variables given as a formula.
1280 o The new function read.caic() reads trees in CAIC format.
1282 o The new function tiplabels() allows to add labels to the tips
1283 of a tree using text or plotting symbols in a flexible way.
1285 o The new function unroot() unroots a phylogeny.
1287 o multi2di() has a new option, `random', which specifies whether
1288 to resolve the multichotomies randomly (the default) or not.
1290 o prop.part() now returns an object of class "prop.part" for which
1291 there are print (to display a partition in a more friendly way)
1292 and summary (to extract the numbers) methods.
1294 o plot.phylo() has a new option, `show.tip.label', specifying
1295 whether to print the labels of the tips. The default is TRUE.
1297 o The code of nj() has been replaced by a faster C code: it is now
1298 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1301 o write.nexus() now writes whether a tree is rooted or not.
1306 o Two bugs have been fixed in root(): unrooted trees are now
1307 handled corretly, and node labels are now output normally.
1309 o A bug was fixed in phymltest(): the executable couldn't be found
1312 o Three bug have been fixed in ace(): computing the likelihood of
1313 ancestral states of discrete characters failed, custom models
1314 did not work, and the function failed with a null gradient (a
1315 warning message is now returned; this latter bug was also
1316 present in yule.cov() as well and is now fixed).
1318 o pic() hanged out when missing data were present: a message error
1321 o A small bug was fixed in dist.dna() where the gamma correction
1322 was not always correctly dispatched.
1324 o plot.phylo() plotted correctly the root edge only when the tree
1325 was plotted rightwards: this works now for all directions.
1330 o dist.taxo() has been renamed as weight.taxo().
1332 o dist.phylo() has been replaced by the method cophenetic.phylo().
1334 o Various error and warning messages have been improved.
1338 CHANGES IN APE VERSION 1.7
1341 o The new function ace() estimates ancestral character states for
1342 continuous characters (with ML, GLS, and contrasts methods), and
1343 discrete characters (with ML only) for any number of states.
1345 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1346 of directional evolution for continuous characters. The user
1347 specifies the node(s) of the tree where the character optimum
1350 o The new function is.rooted() tests whether a tree (of class
1353 o The new function rcoal() generates random ultrametric trees with
1354 the possibility to specify the function that generates the
1355 inter-nodes distances.
1357 o The new function mrca() gives for all pairs of tips in a tree
1358 (and optionally nodes too) the most recent common ancestor.
1360 o nodelabels() has a new option `thermo' to plot proportions (up
1361 to three classes) on the nodes of a tree.
1363 o rtree() has been improved: it can now generate rooted or
1364 unrooted trees, and the mathematical function that generates the
1365 branch lengths may be specified by the user. The tip labels may
1366 be given directly in the call to rtree. The limit cases (n = 2,
1367 3) are now handled correctly.
1369 o dist.topo() has a new argument `method' with two choices: "PH85"
1370 for Penny and Henny's method (already available before and now
1371 the default), and "BHV01" for the geometric distance by Billera
1372 et al. (2001, Adv. Appl. Math. 27:733).
1374 o write.tree() has a new option, `digits', which specifies the
1375 number of digits to be printed in the Newick tree. By default
1376 digits = 10. The numbers are now always printed in decimal form
1377 (i.e., 1.0e-1 is now avoided).
1379 o dist.dna() can now compute the raw distances between pairs of
1380 DNA sequences by specifying model = "raw".
1382 o dist.phylo() has a new option `full' to possibly compute the
1383 distances among all tips and nodes of the tree. The default if
1389 o Several bugs were fixed in all.equal.phylo().
1391 o dist.dna() did not handle correctly gaps ("-") in alignments:
1392 they are now considered as missing data.
1394 o rotate() did not work if the tips were not ordered: this is
1397 o mantel.test() returned NA in some special cases: this is fixed
1398 and the function has been improved and is now faster.
1400 o A bug was fixed in diversi.gof() where the calculation of A² was
1403 o cherry() did not work correctly under some OSs (mainly Linux):
1406 o is.binary.tree() has been modified so that it works with both
1407 rooted and unrooted trees.
1409 o The documentation of theta.s() was not correct: this has been
1412 o plot.mst() did not work correctly: this is fixed.
1416 CHANGES IN APE VERSION 1.6
1421 o The new function dist.topo() computes the topological distances
1424 o The new function boot.phylo() performs a bootstrap analysis on
1425 phylogeny estimation.
1427 o The new functions prop.part() and prop.clades() analyse
1428 bipartitions from a series of trees.
1433 o read.GenBank() now uses the EFetch utility of NCBI instead of
1434 the usual Web interface: it is now much faster (e.g., 12 times
1435 faster to retrieve 8 sequences, 37 times for 60 sequences).
1440 o Several bugs were fixed in read.dna().
1442 o Several bugs were fixed in diversi.time().
1444 o is.binary.tree() did not work correctly if the tree has no edge
1445 lengths: this is fixed.
1447 o drop.tip() did not correctly propagated the `node.label' of a
1448 tree: this is fixed.
1452 CHANGES IN APE VERSION 1.5
1457 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1458 convert objects between the classes "phylo" and "matching". The
1459 latter implements the representation of binary trees introduced by
1460 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1461 as.matching() has been introduced as well.
1463 o Two new functions, multi2di() and di2multi(), allow to resolve
1464 and collapse multichotomies with branches of length zero.
1466 o The new function nuc.div() computes the nucleotide diversity
1467 from a sample a DNA sequences.
1469 o dist.dna() has been completely rewritten with a much faster
1470 (particularly for large data sets) C code. Eight models are
1471 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1472 option `method' has been renamed `model'). Computation of variance
1473 is available for all models. A gamma-correction is possible for
1474 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1475 to remove sites with missing data on a pairwise basis. The option
1476 `GCcontent' has been removed.
1478 o read.GenBank() has a new option (species.names) which specifies
1479 whether to return the species names of the organisms in addition
1480 to the accession numbers of the sequences (this is the default
1483 o write.nexus() can now write several trees in the same NEXUS file.
1485 o drop.tip() has a new option `root.edge' that allows to specify the
1486 new root edge if internal branches are trimmed.
1491 o as.phylo.hclust() failed if some labels had parentheses: this
1494 o Several bugs were fixed in all.equal.phylo(). This function now
1495 returns the logical TRUE if the trees are identical but with
1496 different representations (a report was printed previously).
1498 o read.GenBank() did not correctly handle ambiguous base codes:
1504 o birthdeath() now returns an object of class "birthdeath" for
1505 which there is a print method.
1509 CHANGES IN APE VERSION 1.4
1514 o The new function nj() performs phylogeny estimation with the
1515 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1518 o The new function which.edge() identifies the edges of a tree
1519 that belong to a group specified as a set of tips.
1521 o The new function as.phylo.phylog() converts an object of class
1522 "phylog" (from the package ade4) into an object of class
1525 o The new function axisPhylo() draws axes on the side of a
1528 o The new function howmanytrees() calculates the number of trees
1529 in different cases and giving a number of tips.
1531 o write.tree() has a new option `multi.line' (TRUE by default) to
1532 write a Newick tree on several lines rather than on a single
1535 o The functionalities of zoom() have been extended. Several
1536 subtrees can be visualized at the same time, and they are marked
1537 on the main tree with colors. The context of the subtrees can be
1538 marked with the option `subtree' (see below).
1540 o drop.tip() has a new option `subtree' (FALSE by default) which
1541 specifies whether to output in the tree how many tips have been
1544 o The arguments of add.scale.bar() have been redefined and have
1545 now default values (see ?add.scale.bar for details). This
1546 function now works even if the plotted tree has no edge length.
1548 o plot.phylo() can now plot radial trees, but this does not take
1549 edge lengths into account.
1551 o In plot.phylo() with `type = "phylogram"', if the values of
1552 `edge.color' and `edge.width' are identical for sister-branches,
1553 they are propagated to the vertical line that link them.
1558 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1559 crashing. This is fixed.
1561 o In plot.phylo(), the options `edge.color' and `edge.width' are
1562 now properly recycled; their default values are now "black" and
1565 o A bug has been fixed in write.nexus().
1570 o The function node.depth.edgelength() has been removed and
1571 replaced by a C code.
1575 CHANGES IN APE VERSION 1.3-1
1580 o The new function nodelabels() allows to add labels to the nodes
1581 of a tree using text or plotting symbols in a flexible way.
1583 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1584 numeric values specifying the lower and upper limits on the x-
1585 and y-axes. This allows to leave some space on any side of the
1586 tree. If a single value is given, this is taken as the upper
1591 CHANGES IN APE VERSION 1.3
1596 o The new function phymltest() calls the software PHYML and fits
1597 28 models of DNA sequence evolution. There are a print method to
1598 display likelihood and AIC values, a summary method to compute
1599 the hierarchical likelihood ratio tests, and a plot method to
1600 display graphically the AIC values of each model.
1602 o The new function yule.cov() fits the Yule model with covariates,
1603 a model where the speciation rate is affected by several species
1604 traits through a generalized linear model. The parameters are
1605 estimated by maximum likelihood.
1607 o Three new functions, corBrownian(), corGrafen(), and
1608 corMartins(), compute the expected correlation structures among
1609 species given a phylogeny under different models of evolution.
1610 These can be used for GLS comparative phylogenetic methods (see
1611 the examples). There are coef() and corMatrix() methods and an
1612 Initialize.corPhyl() function associated.
1614 o The new function compar.cheverud() implements Cheverud et al.'s
1615 (1985; Evolution 39:1335) phylogenetic comparative method.
1617 o The new function varcomp() estimates variance components; it has
1620 o Two new functions, panel.superpose.correlogram() and
1621 plot.correlogramList(), allow to plot several phylogenetic
1624 o The new function node.leafnumber() computes the number of leaves
1625 of a subtree defined by a particular node.
1627 o The new function node.sons() gets all tags of son nodes from a
1630 o The new function compute.brlen() computes the branch lengths of
1631 a tree according to a specified method.
1633 o plot.phylo() has three new options: "cex" controls the size of
1634 the (tip and node) labels (thus it is no more needed to change
1635 the global graphical parameter), "direction" which allows to
1636 plot the tree rightwards, leftwards, upwards, or downwards, and
1637 "y.lim" which sets the upper limit on the y-axis.
1642 o Some functions which try to match tip labels and names of
1643 additional data (e.g. vector) are likely to fail if there are
1644 typing or syntax errors. If both series of names do not perfectly
1645 match, they are ignored and a warning message is now issued.
1646 These functions are bd.ext, compar.gee, pic. Their help pages
1647 have been clarified on this point.
1651 CHANGES IN APE VERSION 1.2-7
1656 o The new function root() reroots a phylogenetic tree with respect
1657 to a specified outgroup.
1659 o The new function rotate() rotates an internal branch of a tree.
1661 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1662 trees) controls the display of the tip labels in unrooted trees.
1663 This display has been greatly improved: the tip labels are now not
1664 expected to overlap with the tree (particularly if lab4ut =
1665 "axial"). In all cases, combining appropriate values of "lab4ut"
1666 and the font size (via "par(cex = )") should result in readable
1667 unrooted trees. See ?plot.phylo for some examples.
1669 o In drop.tip(), the argument `tip' can now be numeric or character.
1674 o drop.tip() did not work correctly with trees with no branch
1675 lengths: this is fixed.
1677 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1678 plotted with some line crossings: this is now fixed.
1682 CHANGES IN APE VERSION 1.2-6
1687 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1688 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1689 to implement comparative methods with an autocorrelation approach.
1691 o A new data set describing some life history traits of Carnivores
1697 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1702 o When plotting a tree with plot.phylo(), the new default of the
1703 option `label.offset' is now 0, so the labels are always visible.
1707 CHANGES IN APE VERSION 1.2-5
1712 o The new function bd.ext() fits a birth-death model with combined
1713 phylogenetic and taxonomic data, and estimates the corresponding
1714 speciation and extinction rates.
1719 o The package gee is no more required by ape but only suggested
1720 since only the function compar.gee() calls gee.
1724 CHANGES IN APE VERSION 1.2-4
1729 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1730 and lines.popsize) implementing a new approach for inferring the
1731 demographic history from genealogies using a reversible jump
1732 MCMC have been introduced.
1734 o The unit of time in the skyline plot and in the new plots can
1735 now be chosen to be actual years, rather than substitutions.
1739 CHANGES IN APE VERSION 1.2-3
1744 o The new function rtree() generates a random binary tree with or
1745 without branch lengths.
1747 o Two new functions for drawing lineages-through-time (LTT) plots
1748 are provided: ltt.lines() adds a LTT curve to an existing plot,
1749 and mltt.plot() does a multiple LTT plot giving several trees as
1750 arguments (see `?ltt.plot' for details).
1755 o Some taxon names made R crashing when calling as.phylo.hclust():
1758 o dist.dna() returned an error with two identical DNA sequences
1759 (only using the Jukes-Cantor method returned 0): this is fixed.
1764 o The function dist.phylo() has been re-written using a different
1765 algorithm: it is now about four times faster.
1767 o The code of branching.times() has been improved: it is now about
1772 CHANGES IN APE VERSION 1.2-2
1777 o The new function seg.sites() finds the segregating sites in a
1778 sample of DNA sequences.
1783 o A bug introduced in read.tree() and in read.nexus() with version
1786 o A few errors were corrected and a few examples were added in the
1791 CHANGES IN APE VERSION 1.2-1
1796 o plot.phylo() can now draw the edge of the root of a tree if it
1797 has one (see the new option `root.edge', its default is FALSE).
1802 o A bug was fixed in read.nexus(): files with semicolons inside
1803 comment blocks were not read correctly.
1805 o The behaviour of read.tree() and read.nexus() was corrected so
1806 that tree files with badly represented root edges (e.g., with
1807 an extra pair of parentheses, see the help pages for details)
1808 are now correctly represented in the object of class "phylo";
1809 a warning message is now issued.
1813 CHANGES IN APE VERSION 1.2
1818 o plot.phylo() has been completely re-written and offers several
1819 new functionalities. Three types of trees can now be drawn:
1820 phylogram (as previously), cladogram, and unrooted tree; in
1821 all three types the branch lengths can be drawn using the edge
1822 lengths of the phylogeny or not (e.g., if the latter is absent).
1823 The vertical position of the nodes can be adjusted with two
1824 choices (see option `node.pos'). The code has been re-structured,
1825 and two new functions (potentially useful for developpers) are
1826 documented separately: node.depth.edgelength() and node.depth();
1827 see the respective help pages for details.
1829 o The new function zoom() allows to explore very large trees by
1830 focusing on a small portion of it.
1832 o The new function yule() fits by maximum likelihood the Yule model
1833 (birth-only process) to a phylogenetic tree.
1835 o Support for writing DNA sequences in FASTA format has been
1836 introduced in write.dna() (support for reading sequences in
1837 this format was introduced in read.dna() in version 1.1-2).
1838 The function has been completely re-written, fixing some bugs
1839 (see below); the default behaviour is no more to display the
1840 sequences on the standard output. Several options have been
1841 introduced to control the sequence printing in a flexible
1842 way. The help page has been extended.
1844 o A new data set is included: a supertree of bats in NEXUS format.
1849 o In theta.s(), the default of the option `variance' has
1850 been changed to `FALSE' (as was indicated in the help page).
1852 o Several bugs were fixed in the code of all.equal.phylo().
1854 o Several bugs were fixed in write.dna(), particularly this
1855 function did not work with `format = "interleaved"'.
1857 o Various errors were corrected in the help pages.
1862 o The argument names of as.hclust.phylo() have been changed
1863 from "(phy)" to "(x, ...)" to conform to the definition of
1864 the corresponding generic function.
1866 o gamma.stat() has been renamed gammaStat() to avoid confusion
1867 since gamma() is a generic function.
1871 CHANGES IN APE VERSION 1.1-3
1876 o base.freq() previously did not return a value of 0 for
1877 bases absent in the data (e.g., a vector of length 3 was
1878 returned if one base was absent). This is now fixed (a
1879 vector of length 4 is always returned).
1881 o Several bugs were fixed in read.nexus(), including that this
1882 function did not work in this absence of a "TRANSLATE"
1883 command in the NEXUS file, and that the commands were
1888 CHANGES IN APE VERSION 1.1-2
1893 o The Tamura and Nei (1993) model of DNA distance is now implemented
1894 in dist.dna(): five models are now available in this function.
1896 o A new data set is included: a set of 15 sequences of the
1897 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1903 o A bug in read.nexus() was fixed.
1905 o read.dna() previously did not work correctly in most cases.
1906 The function has been completely re-written and its help page
1907 has been considerably extended (see ?read.dna for details).
1908 Underscores (_) in taxon names are no more replaced with
1909 spaces (this behaviour was undocumented).
1911 o A bug was fixed in write.dna().
1915 CHANGES IN APE VERSION 1.1-1
1920 o A bug in read.tree() introduced in APE 1.1 was fixed.
1922 o A bug in compar.gee() resulted in an error when trying to fit
1923 a model with `family = "binomial"'. This is now fixed.
1927 CHANGES IN APE VERSION 1.1
1932 o The Klastorin (1982) method as suggested by Misawa and Tajima
1933 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1934 on the basis of phylogenetic trees has been implemented (see
1935 the function klastorin()).
1937 o Functions have been added to convert APE's "phylo" objects in
1938 "hclust" cluster objects and vice versa (see the help page of
1939 as.phylo for details).
1941 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1942 are introduced for the estimation of absolute evolutionary rates
1943 (ratogram) and dated clock-like trees (chronogram) from
1944 phylogenetic trees using the non-parametric rate smoothing approach
1945 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1947 o A summary method is now provided printing a summary information on a
1948 phylogenetic tree with, for instance, `summary(tree)'.
1950 o The behaviour of read.tree() was changed so that all spaces and
1951 tabulations in tree files are now ignored. Consequently, spaces in tip
1952 labels are no more allowed. Another side effect is that read.nexus()
1953 now does not replace the underscores (_) in tip labels with spaces
1954 (this behaviour was undocumented).
1956 o The function plot.phylo() has a new option (`underscore') which
1957 specifies whether the underscores in tip labels should be written on
1958 the plot as such or replaced with spaces (the default).
1960 o The function birthdeath() now computes 95% confidence intervals of
1961 the estimated parameters using profile likelihood.
1963 o Three new data sets are included: a gene tree estimated from 36
1964 landplant rbcL sequences, a gene tree estimated from 32 opsin
1965 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1970 o A bug was fixed in dist.gene() where nothing was returned.
1972 o A bug in plot.mst() was fixed.
1974 o A bug in vcv.phylo() resulted in false correlations when the
1975 option `cor = TRUE' was used (now fixed).
1979 CHANGES IN APE VERSION 1.0
1984 o Two new functions, read.dna() and write.dna(), read/write in a file
1985 DNA sequences in interleaved or in sequential format.
1987 o Two new functions, read.nexus() and write.nexus(), read/write trees
1990 o The new function bind.tree() allows to bind two trees together,
1991 possibly handling root edges to give internal branches.
1993 o The new function drop.tip() removes the tips in a phylogenetic tree,
1994 and trims (or not) the corresponding internal branches.
1996 o The new function is.ultrametric() tests if a tree is ultrametric.
1998 o The function plot.phylo() has more functionalities such as drawing the
1999 branches with different colours and/or different widths, showing the
2000 node labels, controling the position and font of the labels, rotating
2001 the labels, and controling the space around the plot.
2003 o The function read.tree() can now read trees with no branch length,
2004 such as "(a,b),c);". Consequently, the element `edge.length' in
2005 objects of class "phylo" is now optional.
2007 o The function write.tree() has a new default behaviour: if the default
2008 for the option `file' is used (i.e. file = ""), then a variable of
2009 mode character containing the tree in Newick format is returned which
2010 can thus be assigned (e.g., tree <- write.tree(phy)).
2012 o The function read.tree() has a new argument `text' which allows
2013 to read the tree in a variable of mode character.
2015 o A new data set is included: the phylogenetic relationships among
2016 the orders of birds from Sibley and Ahlquist (1990).
2020 CHANGES IN APE VERSION 0.2-1
2025 o Several bugs were fixed in the help pages.
2029 CHANGES IN APE VERSION 0.2
2034 o The function write.tree() writes phylogenetic trees (objects of class
2035 "phylo") in an ASCII file using the Newick parenthetic format.
2037 o The function birthdeath() fits a birth-death model to branching times
2038 by maximum likelihood, and estimates the corresponding speciation and
2041 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
2044 o The function is.binary.tree() tests whether a phylogeny is binary.
2046 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
2047 as well as some methods are introduced.
2049 o Several functions, including some generics and methods, for computing
2050 skyline plot estimates (classic and generalized) of effective
2051 population size through time are introduced and replace the function
2052 skyline.plot() in version 0.1.
2054 o Two data sets are now included: the phylogenetic relationships among
2055 the families of birds from Sibley and Ahlquist (1990), and an
2056 estimated clock-like phylogeny of HIV sequences sampled in the
2057 Democratic Republic of Congo.
2060 DEPRECATED & DEFUNCT
2062 o The function skyline.plot() in ape 0.1 has been deprecated and
2063 replaced by more elaborate functions (see above).
2068 o Two important bugs were fixed in plot.phylo(): phylogenies with
2069 multichotomies not at the root or not with only terminal branches,
2070 and phylogenies with a single node (i.e. only terminal branches)
2071 did not plot. These trees should be plotted correctly now.
2073 o Several bugs were fixed in diversi.time() in the computation of
2076 o Various errors were corrected in the help pages.