1 CHANGES IN APE VERSION 2.5-2
6 o as.phylo.hclust() used to multiply edge lengths by 2.
11 o evolve.phylo() and plot.ancestral() have been removed.
15 CHANGES IN APE VERSION 2.5-1
20 o The new function stree generates trees with regular shapes.
22 o It is now possible to bind two trees with x + y (see ?bind.tree for
25 o drop.tip(), extract.clade(), root(), and bind.tree() now have an
26 'interactive' option to make the operation on a plotted tree.
28 o cophyloplot() gains two new arguments 'lwd' and 'lty' for the
29 association links; they are recycled like 'col' (which wasn't before).
34 o rTraitDisc() did not use its 'freq' argument correctly (it was
35 multiplied with the rate matrix column-wise instead of row-wise).
37 o [node|tip|edge]labels(thermo = ) used to draw empty thermometers
38 with NA values. Nothing is drawn now like with 'text' or 'pch'.
39 The same bug occurred with the 'pie' option.
41 o A bug was fixed in compar.ou() and the help page was clarified.
43 o bind.tree() has been rewritten fixing several bugs and making it
46 o plot.phylo(type = "p") sometimes failed to colour correctly the
47 vertical lines representing the nodes.
49 o plot.phylo(direction = "l", x.lim = 30) failed to plot the branches
50 in the correct direction though the tip labels were displayed
56 o The c, cbind, and rbind methods for "DNAbin" objetcs now check that
57 the sequences are correctly stored (in a list for c, in a matrix
58 for the two other functions).
62 CHANGES IN APE VERSION 2.5
67 o The new function parafit by Pierre Legendre tests for the
68 coevolution between hosts and parasites. It has a companion
69 function, pcoa, that does principal coordinate decomposition.
70 The latter has a biplot method.
72 o The new function lmorigin by Pierre Legendre performs multiple
73 regression through the origin with testing by permutation.
75 o The new functions rTraitCont and rTraitDisc simulate continuous and
76 discrete traits under a wide range of evolutionary models.
78 o The new function delta.plot does a delta plot following Holland et
79 al. (2002, Mol. Biol. Evol. 12:2051).
81 o The new function edges draws additional branches between any nodes
82 and/or tips on a plotted tree.
84 o The new function fancyarrows enhances arrows from graphics with
85 triangle and harpoon heads; it can be called from edges().
87 o add.scale.bar() has a new option 'ask' to draw interactively.
89 o The branch length score replaces the geodesic distance in dist.topo.
91 o Three new data sets are included: the gopher-lice data (gopher.D),
92 SO2 air pollution in 41 US cities (lmorigin.ex1, from Sokal &
93 Rohlf 1995), and some host-parasite specificity data
94 (lmorigin.ex2, from Legendre & Desdevises 2009).
99 o add.scale.bar() drew the bar outside the plotting region with the
100 default options with unrooted or radial trees.
102 o dist.topo() made R stuck when the trees had different sizes (thanks
103 to Otto Cordero for the fix).
108 o The geodesic distance has been replaced by the branch length score
113 CHANGES IN APE VERSION 2.4-1
118 o rtree() and rcoal() now accept a numeric vector for the 'br'
121 o vcv() is a new generic function with methods for the classes "phylo"
122 and "corPhyl" so that it is possible to calculate the var-cov matrix
123 for "transformation models". vcv.phylo() can still be used for trees
124 of class "phylo"; its argument 'cor' has been renamed 'corr'.
129 o bind.tree() failed when 'y' had no root edge.
131 o read.nexus() shuffled tip labels when the trees have no branch
132 lengths and there is a TRANSLATE block.
134 o read.nexus() does not try to translate node labels if there is a
135 translation table in the NEXUS file. See ?read.nexus for a
136 clarification on this behaviour.
138 o plot.multiPhylo() crashed R when plotting a list of trees with
139 compressed tip labels.
141 o write.nexus() did not translate the taxa names when asked for.
143 o plot.phylo(type = "fan") did not rotate the tip labels correctly
144 when the tree has branch lengths.
146 o ace(type = "continuous", method = "ML") now avoids sigma² being
147 negative (which resulted in an error).
149 o nj() crashed with NA/NaN in the distance matrix: an error in now
154 CHANGES IN APE VERSION 2.4
159 o base.freq() has a new option 'freq' to return the counts; the
160 default is still to return the proportions.
165 o seg.sites() did not handle ambiguous nucleotides correctly: they
168 o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
169 the tree: the argument is now ignored.
171 o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
177 o Trying to plot a tree with a single tip now returns NULL with a
178 warning (it returned an error previously).
180 o The way lines representing nodes are coloured in phylograms has
181 been modified (as well as their widths and types) following some
182 users' request; this is only for dichotomous nodes.
184 o The argument 'adj' in [node][tip][edge]labels() now works when
185 using 'pie' or 'thermo'.
187 o A more informative message error is now returned by dist.dna() when
188 'model' is badly specified (partial matching of this argument is
191 o Deprecated functions are now listed in a help page: see
192 help("ape-defunct") with the quotes.
197 o The functions heterozygosity, nuc.div, theta.h, theta.k and
198 theta.s have been moved from ape to pegas.
200 o The functions mlphylo, DNAmodel and sh.test have been removed.
204 CHANGES IN APE VERSION 2.3-3
209 o add.scale.bar() always drew a horizontal bar.
211 o zoom() shuffled tips with unrooted trees.
213 o write.nexus() failed to write correctly trees with a "TipLabel"
216 o rcoal() failed to compute branch lengths with very large n.
218 o A small bug was fixed in compar.cheverud() (thanks to Michael
221 o seg.sites() failed when passing a vector.
223 o drop.tip() sometimes shuffled tip labels.
225 o root() shuffled node labels with 'resolve.root = TRUE'.
229 CHANGES IN APE VERSION 2.3-2
234 o all.equal.phylo() did not compare unrooted trees correctly.
236 o dist.topo(... method = "PH85") did not treat unrooted trees
237 correctly (thanks to Tim Wallstrom for the fix).
239 o root() sometimes failed to test for the monophyly of the
242 o extract.clade() sometimes included too many edges.
244 o vcv.phylo() did not work correctly when the tree is in
247 o nj() did not handle correctly distance matrices with many 0's.
248 The code has also been significantly improved: 7, 70, 160 times
249 faster with n = 100, 500, 1000, respectively.
253 CHANGES IN APE VERSION 2.3-1
258 o The new function is.monophyletic tests the monophyly of a group.
260 o There is now a c() method for lists of class "DNAbin".
262 o yule.cov() now fits the null model, and its help page has been
263 corrected with respect to this change.
265 o drop.tip() has a new option 'rooted' to force (or not) a tree
266 to be treated as (un)rooted.
271 o dist.gene() failed on most occasions with the default
272 pairwise.deletion = FALSE.
274 o read.tree() failed to read correctly the tree name(s).
276 o boot.phylo() now treats correctly data frames.
278 o del.gaps() did not copy the rownames of a matrix.
280 o A small bug was fixed in CDAM.global().
282 o ace() failed with large data sets. Thanks to Rich FitzJohn for
283 the fix. With other improvements, this function is now about 6
286 o write.tree() failed with objects of class "multiPhylo".
288 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
293 o [.multiPhylo and [.DNAbin now respect the original class.
295 o Instances of the form class(phy) == "phylo" have been replaced
296 by inherits(phy, "phylo").
298 o rcoal() is now faster.
303 o klastorin() has been removed.
307 CHANGES IN APE VERSION 2.3
312 o The new functions CADM.global and CADM.post, contributed by
313 Pierre Legendre, test the congruence among several distance
316 o The new function yule.time fits a user-defined time-dependent
317 Yule model by maximum likelihood.
319 o The new function makeNodeLabel creates and/or modifies node
320 labels in a flexible way.
322 o read.tree() and write.tree() have been modified so that they can
323 handle individual tree names.
325 o plot.phylo() has a new argument 'edge.lty' that specifies the
326 types of lines used for the edges (plain, dotted, dashed, ...)
328 o phymltest() has been updated to work with PhyML 3.0.1.
333 o drop.tip() shuffled tip labels in some cases.
335 o drop.tip() did not handle node.label correctly.
337 o is.ultrametric() now checks the ordering of the edge matrix.
339 o ace() sometimes returned negative values of likelihoods of
340 ancestral states (thanks to Dan Rabosky for solving this long
346 o The data set xenarthra has been removed.
350 CHANGES IN APE VERSION 2.2-4
354 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
355 now fixed. (Thanks to Peter Wragg for the fix!)
357 o A warning message occurred for no reason with ace(method="GLS").
362 o There is now a general help page displayed with '?ape'.
366 CHANGES IN APE VERSION 2.2-3
371 o The new function extract.clade extracts a clade from a tree by
372 specifying a node number or label.
374 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
375 operations of the same names.
377 o dist.dna() can now return the number of site differences by
378 specifying model="N".
383 o chronopl() did not work with CV = TRUE.
385 o read.nexus() did not work correctly in some situations (trees on
386 multiple lines with different numbers of lines and/or with
387 comments inserted within the trees).
389 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
390 the number of lineages with non-binary trees.
395 o ape has now a namespace.
397 o drop.tip() has been improved: it should be much faster and work
398 better in some cases (e.g., see the example in ?zoom).
402 CHANGES IN APE VERSION 2.2-2
407 o dist.gene() has been substantially improved and gains an option
410 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
416 o prop.part() failed with a single tree with the default option
417 'check.labels = TRUE'.
419 o summary.DNAbin() failed to display correctly the summary of
420 sequence lengths with lists of sequences of 10,000 bases or more
421 (because summary.default uses 4 significant digits by default).
423 o read.nexus() failed to read a file with a single tree with line
424 breaks in the Newick string.
426 o del.gaps() returned a list of empty sequences when there were no
432 o phymltest() has been updated for PhyML 3.0 and gains an option
433 'append', whereas the option 'path2exec' has been removed.
435 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
436 which is returned unchanged (instead of an error).
438 o The data sets bird.orders and bird.families are now stored as
439 Newick strings; i.e., the command data(bird.orders) calls
444 CHANGES IN APE VERSION 2.2-1
449 o The new function makeLabel() helps to modify labels of trees,
450 lists of trees, or DNA sequences, with several utilities to
451 truncate and/or make them unique, substituting some
452 characters, and so on.
454 o The new function del.gaps() removes insertion gaps ("-") in a
455 set of DNA sequences.
457 o read.dna() can now read Clustal files (*.aln).
462 o root() failed with 'resolve.root = TRUE' when the root was
463 already the specified root.
465 o Several bugs were fixed in mlphylo().
467 o collapsed.singles() did not propagate the 'Nnode' and
468 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
470 o read.nexus() failed to remove correctly the comments within
473 o read.nexus() failed to read a file with a single tree and no
474 translation of tip labels.
476 o read.nexus() failed to place correctly tip labels when reading
477 a single tree with no edge lengths.
479 o A bug was fixed in sh.test().
484 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
487 o The option 'check.labels' of consensus() and prop.part() is now
490 o write.dna() now does not truncate names to 10 characters with
495 CHANGES IN APE VERSION 2.2
500 o Four new functions have been written by Damien de Vienne for the
501 graphical exploration of large trees (cophyloplot, subtrees,
502 subtreeplot), and to return the graphical coordinates of tree
505 o The new functions corPagel and corBlomberg implement the Pagel's
506 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
508 o chronopl() has been improved and gains several options: see its
509 help page for details.
511 o boot.phylo() has now an option 'trees' to possibly return the
512 bootstraped trees (the default is FALSE).
514 o prop.part() has been improved and should now be faster in all
520 o read.dna() failed if "?" occurred in the first 10 sites of the
523 o The x/y aspect of the plot is now respected when plotting a
524 circular tree (type = "r" or "f").
526 o Drawing the tip labels sometimes failed when plotting circular
529 o zoom() failed when tip labels were used instead of their numbers
530 (thanks to Yan Wong for the fix).
532 o drop.tip() failed with some trees (fixed by Yan Wong).
534 o seg.sites() failed with a list.
536 o consensus() failed in some cases. The function has been improved
537 as well and is faster.
541 CHANGES IN APE VERSION 2.1-3
546 o A bug in read.nexus() made the Windows R-GUI crash.
548 o An error was fixed in the computation of ancestral character
549 states by generalized least squares in ace().
551 o di2multi() did not modify node labels correctly.
553 o multi2di() failed if the tree had its attribute "order" set to
558 CHANGES IN APE VERSION 2.1-2
563 o There three new methods for the "multiPhylo" class: str, $,
566 o root() gains the options 'node' and 'resolve.root'
567 (FALSE by default) as well as its code being improved.
569 o mltt.plot() has now an option 'log' used in the same way
570 than in plot.default().
575 o mltt.plot() failed to display the legend with an unnamed
578 o nodelabels() with pies now correcly uses the argument
579 'cex' to draw symbols of different sizes (which has
580 worked already for thermometers).
582 o read.nexus() generally failed to read very big files.
587 o The argument 'family' of compar.gee() can now be a function
588 as well as a character string.
590 o read.tree() and read.nexus() now return an unnamed list if
593 o read.nexus() now returns a modified object of class "multiPhylo"
594 when there is a TRANSLATE block in the NEXUS file: the individual
595 trees have no 'tip.label' vector, but the list has a 'TipLabel'
596 attribute. The new methods '$' and '[[' set these elements
597 correctly when extracting trees.
601 CHANGES IN APE VERSION 2.1-1
606 o The new function rmtree generates lists of random trees.
608 o rcoal() now generates a genuine coalescent tree by default
609 (thanks to Vladimir Minin for the code).
614 o nuc.div() returned an incorrect value with the default
615 pairwise.deletion = FALSE.
620 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
621 have been improved so that they are stabler and faster.
623 o R packages used by ape are now loaded silently; lattice and gee
624 are loaded only when needed.
628 CHANGES IN APE VERSION 2.1
633 o The new function identify.phylo identifies clades on a plotted
634 tree using the mouse.
636 o It is now possible to subset a list of trees (object of class
637 "multiPhylo") with "[" while keeping its class correct.
639 o The new function as.DNAbin.alignment converts DNA sequences
640 stored in the "alignment" format of the package seqinr into
641 an object of class "DNAbin".
643 o The new function weight.taxo2 helps to build similarity matrices
644 given two taxonomic levels (usually called by other functions).
646 o write.tree() can now take a list of trees (class "multiPhylo")
647 as its main argument.
649 o plot.correlogram() and plot.correlogramList() have been
650 improved, and gain several options (see the help page for
651 details). A legend is now plotted by default.
656 o dist.dna() returned some incorrect values with `model = "JC69"'
657 and `pairwise.deletion = TRUE'. This affected only the
658 distances involving sequences with missing values. (Thanks
659 to Bruno Toupance for digging this bug out.)
661 o write.tree() failed with some trees: this is fixed by removing
662 the `multi.line' option (trees are now always printed on a
665 o read.nexus() did not correctly detect trees with multiple root
666 edges (see OTHER CHANGES).
671 o The code of mlphylo() has been almost entirely rewritten, and
672 should be much stabler. The options have been also greatly
673 simplified (see ?mlphylo and ?DNAmodel for details).
675 o The internal function nTips has been renamed klastorin_nTips.
677 o The code of is.ultrametric() contained redundancies and has
680 o The code of Moran.I() and of correlogram.formula() have been
683 o read.tree() and read.nexus() now return an error when trying to
684 read a tree with multiple root edges (see BUG FIXES). The
685 correction applied in previous version did not work in all
688 o The class c("multi.tree", "phylo") has been renamed
694 o There is now a vignette in ape: see vignette("MoranI", "ape").
699 o as.matching() and as.phylo.matching() do not support branch
702 o correlogram.phylo() and discrete.dist() have been removed.
706 CHANGES IN APE VERSION 2.0-2
711 o The new function matexpo computes the exponential of a square
714 o The new function unique.multi.tree removes duplicate trees from
717 o yule() has a new option `use.root.edge = FALSE' that specifies
718 to ignore, by default, the root edge of the tree if it exists.
723 o which.edge() failed when the index of a single terminal edge was
726 o In diversi.time(), the values returned for model C were
729 o A bug was fixed in yule() that affected the calculation of the
730 likelihood in the presence of ties in the branching times.
732 o There was a bug in the C function mat_expo4x4 affecting the
733 calculations of the transition probabilities for models HKY and
736 o A small bug was fixed in as.matrix.DNAbin (thanks to James
739 o rtree() did not `shuffle' the tip labels by default, so only a
740 limited number of labelled topologies could be generated.
744 CHANGES IN APE VERSION 2.0-1
749 o The three new functions bionj, fastme.ols, and fastme.bal
750 perform phylogeny estimation by the BIONJ and fastME methods in
751 OLS and balanced versions. This is a port to R of previous
752 previous programs done by Vincent Lefort.
754 o The new function chronoMPL performs molecular dating with the
755 mean path lengths method of Britton et al. (2002, Mol. Phyl.
758 o The new function rotate, contributed by Christoph Heibl, swaps
759 two clades connected to the same node. It works also with
760 multichotomous nodes.
762 o The new `method' as.matrix.DNAbin() may be used to convert
763 easily DNA sequences stored in a list into a matrix while
764 keeping the names and the class.
769 o chronopl() failed when some branch lengths were equal to zero:
770 an error message is now returned.
772 o di2multi() failed when there was a series of consecutive edges
777 CHANGES IN APE VERSION 1.10-2
782 o plot.phylo() can now plot circular trees: the option is type =
783 "fan" or type = "f" (to avoid the ambiguity with type = "c").
785 o prop.part() has a new option `check.labels = FALSE' which allows
786 to considerably speed-up the calculations of bipartitions. As a
787 consequence, calculations of bootstrap values with boot.phylo()
788 should be much faster.
793 o read.GenBank() did not return correctly the list of species as
794 from ape 1.10: this is fixed in this version
796 o Applying as.phylo() on a tree of class "phylo" failed: the
797 object is now returned unchanged.
801 CHANGES IN APE VERSION 1.10-1
806 o The three new functions Ntip, Nnode, and Nedge return, for a
807 given tree, the number of tips, nodes, or edges, respectively.
812 o read.nexus() did not set correctly the class of the returned
813 object when reading multiple trees.
815 o mllt.plot() failed with objects of class c("multi.tree",
818 o unroot() did not work correctly in most cases.
820 o reorder.phylo() made R freeze in some occasions.
822 o Plotting a tree in pruningwise order failed.
824 o When plotting an unrooted tree, the tip labels where not all
825 correctly positioned if the option `cex' was used.
829 CHANGES IN APE VERSION 1.10
834 o Five new `method' functions have been introduced to manipulate
835 DNA sequences in binary format (see below).
837 o Three new functions have been introduced to convert between the
838 new binary and the character formats.
840 o The new function as.alignment converts DNA sequences stored as
841 single characters into the class "alignment" used by the package
844 o read.dna() and read.GenBank() have a new argument `as.character'
845 controlling whether the sequences are returned in binary format
851 o root() failed when the tree had node labels: this is fixed.
853 o plot.phylo() did not correctly set the limits on the y-axis with
854 the default setting: this is fixed.
856 o dist.dna() returned a wrong result for the LogDet, paralinear,
857 and BH87 models with `pairwise.deletion = TRUE'.
862 o DNA sequences are now internally stored in a binary format. See
863 the document "A Bit-Level Coding Scheme for Nucleotides" for the
864 details. Most functions analyzing DNA functions have been
865 modified accordingly and are now much faster (dist.dna is now
866 ca. 60 times faster).
870 CHANGES IN APE VERSION 1.9-4
875 o A bug was fixed in edgelabels().
877 o as.phylo.hclust() did not work correctly when the object of
878 class "hclust" has its labels set to NULL: the returned tree has
879 now its tip labels set to "1", "2", ...
881 o consensus could fail if some tip labels are a subset of others
882 (e.g., "a" and "a_1"): this is now fixed.
884 o mlphylo() failed in most cases if some branch lengths of the
885 initial tree were greater than one: an error message is now
888 o mlphylo() failed in most cases when estimating the proportion of
889 invariants: this is fixed.
893 CHANGES IN APE VERSION 1.9-3
898 o The new function edgelabels adds labels on the edge of the tree
899 in the same way than nodelabels or tiplabels.
904 o multi2di() did not handle correctly branch lengths with the
905 default option `random = TRUE': this is now fixed.
907 o A bug was fixed in nuc.div() when using pairwise deletions.
909 o A bug occurred in the analysis of bipartitions with large
910 numbers of large trees, with consequences on prop.part,
911 prop.clades, and boot.phylo.
913 o The calculation of the Billera-Holmes-Vogtmann distance in
914 dist.topo was wrong: this has been fixed.
918 CHANGES IN APE VERSION 1.9-2
923 o The new function ladderize reorganizes the internal structure of
924 a tree to plot them left- or right-ladderized.
926 o The new function dist.nodes computes the patristic distances
927 between all nodes, internal and terminal, of a tree. It replaces
928 the option `full = TRUE' of cophenetic.phylo (see below).
933 o A bug was fixed in old2new.phylo().
935 o Some bugs were fixed in chronopl().
937 o The edge colours were not correctly displayed by plot.phylo
938 (thank you to Li-San Wang for the fix).
940 o cophenetic.phylo() failed with multichotomous trees: this is
946 o read.dna() now returns the sequences in a matrix if they are
947 aligned (interleaved or sequential format). Sequences in FASTA
948 format are still returned in a list.
950 o The option `full' of cophenetic.phylo() has been removed because
951 it could not be used from the generic.
956 o rotate() has been removed; this function did not work correctly
961 CHANGES IN APE VERSION 1.9-1
966 o Trees with a single tip were not read correctly in R as the
967 element `Nnode' was not set: this is fixed.
969 o unroot() did not set correctly the number of nodes of the
970 unrooted tree in most cases.
972 o read.GenBank() failed when fetching very long sequences,
973 particularly of the BX-series.
975 o A bug was introduced in read.tree() with ape 1.9: it has been
980 CHANGES IN APE VERSION 1.9
985 o There are two new print `methods' for trees of class "phylo" and
986 lists of trees of class "multi.tree", so that they are now
987 displayed in a compact and informative way.
989 o There are two new functions, old2new.phylo and new2old.phylo,
990 for converting between the old and new coding of the class
993 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
994 LogDet ("logdet"), and paralinear ("paralin").
996 o compute.brlen() has been extended: several methods are now
997 available to compute branch lengths.
999 o write.dna() can now handle matrices as well as lists.
1004 o cophenetic.phylo() sometimes returned a wrong result with
1005 multichotomous trees: this is fixed.
1007 o rotate() failed when a single tip was specified: the tree is now
1010 o ace() did not return the correct index matrix with custom
1011 models: this is fixed.
1013 o multi2di() did not work correctly when resolving multichotomies
1014 randomly: the topology was always the same, only the arrangement
1015 of clades was randomized: this is fixed. This function now
1016 accepts trees with no branch lengths.
1018 o The output of diversi.gof() was blurred by useless prints when a
1019 user distribution was specified. This has been corrected, and
1020 the help page of this function has been expanded.
1025 o The internal structure of the class "phylo" has been changed:
1026 see the document "Definition of Formats for Coding Phylogenetic
1027 Trees in R" for the details. In addition, the code of most
1028 functions has been improved.
1030 o Several functions have been improved by replacing some R codes
1031 by C codes: pic, plot.phylo, and reorder.phylo.
1033 o There is now a citation information: see citation("ape") in R.
1035 o write.tree() now does not add extra 0's to branch lengths so
1036 that 1.23 is printed "1.23" by default, not "1.2300000000".
1038 o The syntax of bind.tree() has been simplified. This function now
1039 accepts trees with no branch lengths, and handles correctly node
1042 o The option `as.numeric' of mrca() has been removed.
1044 o The unused options `format' and `rooted' of read.tree() have
1047 o The unused option `format' of write.tree() has been removed.
1049 o The use of node.depth() has been simplified.
1053 CHANGES IN APE VERSION 1.8-5
1058 o Two new functions read.nexus.data() and write.nexus.data(),
1059 contributed by Johan Nylander, allow to read and write molecular
1060 sequences in NEXUS files.
1062 o The new function reorder.phylo() reorders the internal structure
1063 of a tree of class "phylo". It is used as the generic, e.g.,
1066 o read.tree() and read.nexus() can now read trees with a single
1069 o The new data set `cynipids' supplies a set of protein sequences
1075 o The code of all.equal.phylo() has been completely rewritten
1076 (thanks to Benoît Durand) which fixes several bugs.
1078 o read.tree() and read.nexus() now checks the labels of the tree
1079 to remove or substitute any characters that are illegal in the
1080 Newick format (parentheses, etc.)
1082 o A negative P-value could be returned by mantel.test(): this is
1087 CHANGES IN APE VERSION 1.8-4
1092 o The new function sh.test() computes the Shimodaira-
1095 o The new function collapse.singles() removes the nodes with a
1096 single descendant from a tree.
1098 o plot.phylo() has a new argument `tip.color' to specify the
1099 colours of the tips.
1101 o mlphylo() has now an option `quiet' to control the display of
1102 the progress of the analysis (the default is FALSE).
1107 o read.dna() did not read correctly sequences in sequential format
1108 with leading alignment gaps "-": this is fixed.
1110 o ace() returned a list with no class so that the generic
1111 functions (anova, logLik, ...) could not be used directly. This
1112 is fixed as ace() now returns an object of class "ace".
1114 o anova.ace() had a small bug when computing the number of degrees
1115 of freedom: this is fixed.
1117 o mlphylo() did not work when the sequences were in a matrix or
1118 a data frame: this is fixed.
1120 o rtree() did not work correctly when trying to simulate an
1121 unrooted tree with two tips: an error message is now issued.
1126 o The algorithm of rtree() has been changed: it is now about 40,
1127 100, and 130 times faster for 10, 100, and 1000 tips,
1132 CHANGES IN APE VERSION 1.8-3
1137 o There are four new `method' functions to be used with the
1138 results of ace(): logLik(), deviance(), AIC(), and anova().
1140 o The plot method of phymltest has two new arguments: `main' to
1141 change the title, and `col' to control the colour of the
1142 segments showing the AIC values.
1144 o ace() has a new argument `ip' that gives the initial values used
1145 in the ML estimation with discrete characters (see the examples
1146 in ?ace). This function now returns a matrix giving the indices
1147 of the estimated rates when analysing discrete characters.
1149 o nodelabels() and tiplabels() have a new argument `pie' to
1150 represent proportions, with any number of categories, as
1151 piecharts. The use of the option `thermo' has been improved:
1152 there is now no limitation on the number of categories.
1157 o mlphylo() did not work with more than two partitions: this is
1160 o root() failed if the proposed outgroup was already an outgroup
1161 in the tree: this is fixed.
1163 o The `col' argument in nodelabels() and tiplabels() was not
1164 correctly passed when `text' was used: this is fixed.
1166 o Two bugs were fixed in mlphylo(): parameters were not always
1167 correctly output, and the estimation failed in some cases.
1169 o plot.phylo() was stuck when given a tree with a single tip: this
1170 is fixed and a message error is now returned.
1172 o An error was corrected in the help page of gammaStat regarding
1173 the calculation of P-values.
1175 o Using gls() could crash R when the number of species in the tree
1176 and in the variables were different: this is fixed.
1180 CHANGES IN APE VERSION 1.8-2
1185 o The new function mlphylo() fits a phylogenetic tree by maximum
1186 likelihood from DNA sequences. Its companion function DNAmodel()
1187 is used to define the substitution model which may include
1188 partitioning. There are methods for logLik(), deviance(), and
1189 AIC(), and the summary() method has been extended to display in
1190 a friendly way the results of this model fitting. Currently, the
1191 functionality is limited to estimating the substitution and
1192 associated parameters and computing the likelihood.
1194 o The new function drop1.compar.gee (used as, e.g., drop1(m))
1195 tests for single effects in GEE-based comparative method. A
1196 warning message is printed if there is not enough degrees of
1202 o An error message was sometimes issued by plot.multi.tree(),
1203 though with no consequence.
1207 CHANGES IN APE VERSION 1.8-1
1212 o There is a new plot method for lists of trees (objects of class
1213 "multi.tree"): it calls plot.phylo() internally and is
1214 documented on the same help page.
1219 o A bug was fixed in the C code that analyzes bipartitions: this
1220 has impact on several functions like prop.part, prop.clades,
1221 boot.phylo, or consensus.
1223 o root() did not work correctly when the specified outgroup had
1224 more than one element: this is fixed.
1226 o dist.dna() sometimes returned a warning inappropriately: this
1229 o If the distance object given to nj() had no rownames, nj()
1230 returned a tree with no tip labels: it now returns tips labelled
1231 "1", "2", ..., corresponding to the row numbers.
1236 o nj() has been slightly changed so that tips with a zero distance
1237 are first aggregated with zero-lengthed branches; the usual NJ
1238 procedure is then performed on a distance matrix without 0's.
1242 CHANGES IN APE VERSION 1.8
1247 o The new function chronopl() estimates dates using the penalized
1248 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1250 o The new function consensus() calculates the consensus tree of a
1253 o The new function evolve.phylo() simulates the evolution of
1254 continuous characters along a phylogeny under a Brownian model.
1256 o The new plot method for objects of class "ancestral" displays a
1257 tree together with ancestral values, as returned by the above
1260 o The new function as.phylo.formula() returns a phylogeny from a
1261 set of nested taxonomic variables given as a formula.
1263 o The new function read.caic() reads trees in CAIC format.
1265 o The new function tiplabels() allows to add labels to the tips
1266 of a tree using text or plotting symbols in a flexible way.
1268 o The new function unroot() unroots a phylogeny.
1270 o multi2di() has a new option, `random', which specifies whether
1271 to resolve the multichotomies randomly (the default) or not.
1273 o prop.part() now returns an object of class "prop.part" for which
1274 there are print (to display a partition in a more friendly way)
1275 and summary (to extract the numbers) methods.
1277 o plot.phylo() has a new option, `show.tip.label', specifying
1278 whether to print the labels of the tips. The default is TRUE.
1280 o The code of nj() has been replaced by a faster C code: it is now
1281 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1284 o write.nexus() now writes whether a tree is rooted or not.
1289 o Two bugs have been fixed in root(): unrooted trees are now
1290 handled corretly, and node labels are now output normally.
1292 o A bug was fixed in phymltest(): the executable couldn't be found
1295 o Three bug have been fixed in ace(): computing the likelihood of
1296 ancestral states of discrete characters failed, custom models
1297 did not work, and the function failed with a null gradient (a
1298 warning message is now returned; this latter bug was also
1299 present in yule.cov() as well and is now fixed).
1301 o pic() hanged out when missing data were present: a message error
1304 o A small bug was fixed in dist.dna() where the gamma correction
1305 was not always correctly dispatched.
1307 o plot.phylo() plotted correctly the root edge only when the tree
1308 was plotted rightwards: this works now for all directions.
1313 o dist.taxo() has been renamed as weight.taxo().
1315 o dist.phylo() has been replaced by the method cophenetic.phylo().
1317 o Various error and warning messages have been improved.
1321 CHANGES IN APE VERSION 1.7
1324 o The new function ace() estimates ancestral character states for
1325 continuous characters (with ML, GLS, and contrasts methods), and
1326 discrete characters (with ML only) for any number of states.
1328 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1329 of directional evolution for continuous characters. The user
1330 specifies the node(s) of the tree where the character optimum
1333 o The new function is.rooted() tests whether a tree (of class
1336 o The new function rcoal() generates random ultrametric trees with
1337 the possibility to specify the function that generates the
1338 inter-nodes distances.
1340 o The new function mrca() gives for all pairs of tips in a tree
1341 (and optionally nodes too) the most recent common ancestor.
1343 o nodelabels() has a new option `thermo' to plot proportions (up
1344 to three classes) on the nodes of a tree.
1346 o rtree() has been improved: it can now generate rooted or
1347 unrooted trees, and the mathematical function that generates the
1348 branch lengths may be specified by the user. The tip labels may
1349 be given directly in the call to rtree. The limit cases (n = 2,
1350 3) are now handled correctly.
1352 o dist.topo() has a new argument `method' with two choices: "PH85"
1353 for Penny and Henny's method (already available before and now
1354 the default), and "BHV01" for the geometric distance by Billera
1355 et al. (2001, Adv. Appl. Math. 27:733).
1357 o write.tree() has a new option, `digits', which specifies the
1358 number of digits to be printed in the Newick tree. By default
1359 digits = 10. The numbers are now always printed in decimal form
1360 (i.e., 1.0e-1 is now avoided).
1362 o dist.dna() can now compute the raw distances between pairs of
1363 DNA sequences by specifying model = "raw".
1365 o dist.phylo() has a new option `full' to possibly compute the
1366 distances among all tips and nodes of the tree. The default if
1372 o Several bugs were fixed in all.equal.phylo().
1374 o dist.dna() did not handle correctly gaps ("-") in alignments:
1375 they are now considered as missing data.
1377 o rotate() did not work if the tips were not ordered: this is
1380 o mantel.test() returned NA in some special cases: this is fixed
1381 and the function has been improved and is now faster.
1383 o A bug was fixed in diversi.gof() where the calculation of A² was
1386 o cherry() did not work correctly under some OSs (mainly Linux):
1389 o is.binary.tree() has been modified so that it works with both
1390 rooted and unrooted trees.
1392 o The documentation of theta.s() was not correct: this has been
1395 o plot.mst() did not work correctly: this is fixed.
1399 CHANGES IN APE VERSION 1.6
1404 o The new function dist.topo() computes the topological distances
1407 o The new function boot.phylo() performs a bootstrap analysis on
1408 phylogeny estimation.
1410 o The new functions prop.part() and prop.clades() analyse
1411 bipartitions from a series of trees.
1416 o read.GenBank() now uses the EFetch utility of NCBI instead of
1417 the usual Web interface: it is now much faster (e.g., 12 times
1418 faster to retrieve 8 sequences, 37 times for 60 sequences).
1423 o Several bugs were fixed in read.dna().
1425 o Several bugs were fixed in diversi.time().
1427 o is.binary.tree() did not work correctly if the tree has no edge
1428 lengths: this is fixed.
1430 o drop.tip() did not correctly propagated the `node.label' of a
1431 tree: this is fixed.
1435 CHANGES IN APE VERSION 1.5
1440 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1441 convert objects between the classes "phylo" and "matching". The
1442 latter implements the representation of binary trees introduced by
1443 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1444 as.matching() has been introduced as well.
1446 o Two new functions, multi2di() and di2multi(), allow to resolve
1447 and collapse multichotomies with branches of length zero.
1449 o The new function nuc.div() computes the nucleotide diversity
1450 from a sample a DNA sequences.
1452 o dist.dna() has been completely rewritten with a much faster
1453 (particularly for large data sets) C code. Eight models are
1454 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1455 option `method' has been renamed `model'). Computation of variance
1456 is available for all models. A gamma-correction is possible for
1457 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1458 to remove sites with missing data on a pairwise basis. The option
1459 `GCcontent' has been removed.
1461 o read.GenBank() has a new option (species.names) which specifies
1462 whether to return the species names of the organisms in addition
1463 to the accession numbers of the sequences (this is the default
1466 o write.nexus() can now write several trees in the same NEXUS file.
1468 o drop.tip() has a new option `root.edge' that allows to specify the
1469 new root edge if internal branches are trimmed.
1474 o as.phylo.hclust() failed if some labels had parentheses: this
1477 o Several bugs were fixed in all.equal.phylo(). This function now
1478 returns the logical TRUE if the trees are identical but with
1479 different representations (a report was printed previously).
1481 o read.GenBank() did not correctly handle ambiguous base codes:
1487 o birthdeath() now returns an object of class "birthdeath" for
1488 which there is a print method.
1492 CHANGES IN APE VERSION 1.4
1497 o The new function nj() performs phylogeny estimation with the
1498 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1501 o The new function which.edge() identifies the edges of a tree
1502 that belong to a group specified as a set of tips.
1504 o The new function as.phylo.phylog() converts an object of class
1505 "phylog" (from the package ade4) into an object of class
1508 o The new function axisPhylo() draws axes on the side of a
1511 o The new function howmanytrees() calculates the number of trees
1512 in different cases and giving a number of tips.
1514 o write.tree() has a new option `multi.line' (TRUE by default) to
1515 write a Newick tree on several lines rather than on a single
1518 o The functionalities of zoom() have been extended. Several
1519 subtrees can be visualized at the same time, and they are marked
1520 on the main tree with colors. The context of the subtrees can be
1521 marked with the option `subtree' (see below).
1523 o drop.tip() has a new option `subtree' (FALSE by default) which
1524 specifies whether to output in the tree how many tips have been
1527 o The arguments of add.scale.bar() have been redefined and have
1528 now default values (see ?add.scale.bar for details). This
1529 function now works even if the plotted tree has no edge length.
1531 o plot.phylo() can now plot radial trees, but this does not take
1532 edge lengths into account.
1534 o In plot.phylo() with `type = "phylogram"', if the values of
1535 `edge.color' and `edge.width' are identical for sister-branches,
1536 they are propagated to the vertical line that link them.
1541 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1542 crashing. This is fixed.
1544 o In plot.phylo(), the options `edge.color' and `edge.width' are
1545 now properly recycled; their default values are now "black" and
1548 o A bug has been fixed in write.nexus().
1553 o The function node.depth.edgelength() has been removed and
1554 replaced by a C code.
1558 CHANGES IN APE VERSION 1.3-1
1563 o The new function nodelabels() allows to add labels to the nodes
1564 of a tree using text or plotting symbols in a flexible way.
1566 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1567 numeric values specifying the lower and upper limits on the x-
1568 and y-axes. This allows to leave some space on any side of the
1569 tree. If a single value is given, this is taken as the upper
1574 CHANGES IN APE VERSION 1.3
1579 o The new function phymltest() calls the software PHYML and fits
1580 28 models of DNA sequence evolution. There are a print method to
1581 display likelihood and AIC values, a summary method to compute
1582 the hierarchical likelihood ratio tests, and a plot method to
1583 display graphically the AIC values of each model.
1585 o The new function yule.cov() fits the Yule model with covariates,
1586 a model where the speciation rate is affected by several species
1587 traits through a generalized linear model. The parameters are
1588 estimated by maximum likelihood.
1590 o Three new functions, corBrownian(), corGrafen(), and
1591 corMartins(), compute the expected correlation structures among
1592 species given a phylogeny under different models of evolution.
1593 These can be used for GLS comparative phylogenetic methods (see
1594 the examples). There are coef() and corMatrix() methods and an
1595 Initialize.corPhyl() function associated.
1597 o The new function compar.cheverud() implements Cheverud et al.'s
1598 (1985; Evolution 39:1335) phylogenetic comparative method.
1600 o The new function varcomp() estimates variance components; it has
1603 o Two new functions, panel.superpose.correlogram() and
1604 plot.correlogramList(), allow to plot several phylogenetic
1607 o The new function node.leafnumber() computes the number of leaves
1608 of a subtree defined by a particular node.
1610 o The new function node.sons() gets all tags of son nodes from a
1613 o The new function compute.brlen() computes the branch lengths of
1614 a tree according to a specified method.
1616 o plot.phylo() has three new options: "cex" controls the size of
1617 the (tip and node) labels (thus it is no more needed to change
1618 the global graphical parameter), "direction" which allows to
1619 plot the tree rightwards, leftwards, upwards, or downwards, and
1620 "y.lim" which sets the upper limit on the y-axis.
1625 o Some functions which try to match tip labels and names of
1626 additional data (e.g. vector) are likely to fail if there are
1627 typing or syntax errors. If both series of names do not perfectly
1628 match, they are ignored and a warning message is now issued.
1629 These functions are bd.ext, compar.gee, pic. Their help pages
1630 have been clarified on this point.
1634 CHANGES IN APE VERSION 1.2-7
1639 o The new function root() reroots a phylogenetic tree with respect
1640 to a specified outgroup.
1642 o The new function rotate() rotates an internal branch of a tree.
1644 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1645 trees) controls the display of the tip labels in unrooted trees.
1646 This display has been greatly improved: the tip labels are now not
1647 expected to overlap with the tree (particularly if lab4ut =
1648 "axial"). In all cases, combining appropriate values of "lab4ut"
1649 and the font size (via "par(cex = )") should result in readable
1650 unrooted trees. See ?plot.phylo for some examples.
1652 o In drop.tip(), the argument `tip' can now be numeric or character.
1657 o drop.tip() did not work correctly with trees with no branch
1658 lengths: this is fixed.
1660 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1661 plotted with some line crossings: this is now fixed.
1665 CHANGES IN APE VERSION 1.2-6
1670 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1671 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1672 to implement comparative methods with an autocorrelation approach.
1674 o A new data set describing some life history traits of Carnivores
1680 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1685 o When plotting a tree with plot.phylo(), the new default of the
1686 option `label.offset' is now 0, so the labels are always visible.
1690 CHANGES IN APE VERSION 1.2-5
1695 o The new function bd.ext() fits a birth-death model with combined
1696 phylogenetic and taxonomic data, and estimates the corresponding
1697 speciation and extinction rates.
1702 o The package gee is no more required by ape but only suggested
1703 since only the function compar.gee() calls gee.
1707 CHANGES IN APE VERSION 1.2-4
1712 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1713 and lines.popsize) implementing a new approach for inferring the
1714 demographic history from genealogies using a reversible jump
1715 MCMC have been introduced.
1717 o The unit of time in the skyline plot and in the new plots can
1718 now be chosen to be actual years, rather than substitutions.
1722 CHANGES IN APE VERSION 1.2-3
1727 o The new function rtree() generates a random binary tree with or
1728 without branch lengths.
1730 o Two new functions for drawing lineages-through-time (LTT) plots
1731 are provided: ltt.lines() adds a LTT curve to an existing plot,
1732 and mltt.plot() does a multiple LTT plot giving several trees as
1733 arguments (see `?ltt.plot' for details).
1738 o Some taxon names made R crashing when calling as.phylo.hclust():
1741 o dist.dna() returned an error with two identical DNA sequences
1742 (only using the Jukes-Cantor method returned 0): this is fixed.
1747 o The function dist.phylo() has been re-written using a different
1748 algorithm: it is now about four times faster.
1750 o The code of branching.times() has been improved: it is now about
1755 CHANGES IN APE VERSION 1.2-2
1760 o The new function seg.sites() finds the segregating sites in a
1761 sample of DNA sequences.
1766 o A bug introduced in read.tree() and in read.nexus() with version
1769 o A few errors were corrected and a few examples were added in the
1774 CHANGES IN APE VERSION 1.2-1
1779 o plot.phylo() can now draw the edge of the root of a tree if it
1780 has one (see the new option `root.edge', its default is FALSE).
1785 o A bug was fixed in read.nexus(): files with semicolons inside
1786 comment blocks were not read correctly.
1788 o The behaviour of read.tree() and read.nexus() was corrected so
1789 that tree files with badly represented root edges (e.g., with
1790 an extra pair of parentheses, see the help pages for details)
1791 are now correctly represented in the object of class "phylo";
1792 a warning message is now issued.
1796 CHANGES IN APE VERSION 1.2
1801 o plot.phylo() has been completely re-written and offers several
1802 new functionalities. Three types of trees can now be drawn:
1803 phylogram (as previously), cladogram, and unrooted tree; in
1804 all three types the branch lengths can be drawn using the edge
1805 lengths of the phylogeny or not (e.g., if the latter is absent).
1806 The vertical position of the nodes can be adjusted with two
1807 choices (see option `node.pos'). The code has been re-structured,
1808 and two new functions (potentially useful for developpers) are
1809 documented separately: node.depth.edgelength() and node.depth();
1810 see the respective help pages for details.
1812 o The new function zoom() allows to explore very large trees by
1813 focusing on a small portion of it.
1815 o The new function yule() fits by maximum likelihood the Yule model
1816 (birth-only process) to a phylogenetic tree.
1818 o Support for writing DNA sequences in FASTA format has been
1819 introduced in write.dna() (support for reading sequences in
1820 this format was introduced in read.dna() in version 1.1-2).
1821 The function has been completely re-written, fixing some bugs
1822 (see below); the default behaviour is no more to display the
1823 sequences on the standard output. Several options have been
1824 introduced to control the sequence printing in a flexible
1825 way. The help page has been extended.
1827 o A new data set is included: a supertree of bats in NEXUS format.
1832 o In theta.s(), the default of the option `variance' has
1833 been changed to `FALSE' (as was indicated in the help page).
1835 o Several bugs were fixed in the code of all.equal.phylo().
1837 o Several bugs were fixed in write.dna(), particularly this
1838 function did not work with `format = "interleaved"'.
1840 o Various errors were corrected in the help pages.
1845 o The argument names of as.hclust.phylo() have been changed
1846 from "(phy)" to "(x, ...)" to conform to the definition of
1847 the corresponding generic function.
1849 o gamma.stat() has been renamed gammaStat() to avoid confusion
1850 since gamma() is a generic function.
1854 CHANGES IN APE VERSION 1.1-3
1859 o base.freq() previously did not return a value of 0 for
1860 bases absent in the data (e.g., a vector of length 3 was
1861 returned if one base was absent). This is now fixed (a
1862 vector of length 4 is always returned).
1864 o Several bugs were fixed in read.nexus(), including that this
1865 function did not work in this absence of a "TRANSLATE"
1866 command in the NEXUS file, and that the commands were
1871 CHANGES IN APE VERSION 1.1-2
1876 o The Tamura and Nei (1993) model of DNA distance is now implemented
1877 in dist.dna(): five models are now available in this function.
1879 o A new data set is included: a set of 15 sequences of the
1880 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1886 o A bug in read.nexus() was fixed.
1888 o read.dna() previously did not work correctly in most cases.
1889 The function has been completely re-written and its help page
1890 has been considerably extended (see ?read.dna for details).
1891 Underscores (_) in taxon names are no more replaced with
1892 spaces (this behaviour was undocumented).
1894 o A bug was fixed in write.dna().
1898 CHANGES IN APE VERSION 1.1-1
1903 o A bug in read.tree() introduced in APE 1.1 was fixed.
1905 o A bug in compar.gee() resulted in an error when trying to fit
1906 a model with `family = "binomial"'. This is now fixed.
1910 CHANGES IN APE VERSION 1.1
1915 o The Klastorin (1982) method as suggested by Misawa and Tajima
1916 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1917 on the basis of phylogenetic trees has been implemented (see
1918 the function klastorin()).
1920 o Functions have been added to convert APE's "phylo" objects in
1921 "hclust" cluster objects and vice versa (see the help page of
1922 as.phylo for details).
1924 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1925 are introduced for the estimation of absolute evolutionary rates
1926 (ratogram) and dated clock-like trees (chronogram) from
1927 phylogenetic trees using the non-parametric rate smoothing approach
1928 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1930 o A summary method is now provided printing a summary information on a
1931 phylogenetic tree with, for instance, `summary(tree)'.
1933 o The behaviour of read.tree() was changed so that all spaces and
1934 tabulations in tree files are now ignored. Consequently, spaces in tip
1935 labels are no more allowed. Another side effect is that read.nexus()
1936 now does not replace the underscores (_) in tip labels with spaces
1937 (this behaviour was undocumented).
1939 o The function plot.phylo() has a new option (`underscore') which
1940 specifies whether the underscores in tip labels should be written on
1941 the plot as such or replaced with spaces (the default).
1943 o The function birthdeath() now computes 95% confidence intervals of
1944 the estimated parameters using profile likelihood.
1946 o Three new data sets are included: a gene tree estimated from 36
1947 landplant rbcL sequences, a gene tree estimated from 32 opsin
1948 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1953 o A bug was fixed in dist.gene() where nothing was returned.
1955 o A bug in plot.mst() was fixed.
1957 o A bug in vcv.phylo() resulted in false correlations when the
1958 option `cor = TRUE' was used (now fixed).
1962 CHANGES IN APE VERSION 1.0
1967 o Two new functions, read.dna() and write.dna(), read/write in a file
1968 DNA sequences in interleaved or in sequential format.
1970 o Two new functions, read.nexus() and write.nexus(), read/write trees
1973 o The new function bind.tree() allows to bind two trees together,
1974 possibly handling root edges to give internal branches.
1976 o The new function drop.tip() removes the tips in a phylogenetic tree,
1977 and trims (or not) the corresponding internal branches.
1979 o The new function is.ultrametric() tests if a tree is ultrametric.
1981 o The function plot.phylo() has more functionalities such as drawing the
1982 branches with different colours and/or different widths, showing the
1983 node labels, controling the position and font of the labels, rotating
1984 the labels, and controling the space around the plot.
1986 o The function read.tree() can now read trees with no branch length,
1987 such as "(a,b),c);". Consequently, the element `edge.length' in
1988 objects of class "phylo" is now optional.
1990 o The function write.tree() has a new default behaviour: if the default
1991 for the option `file' is used (i.e. file = ""), then a variable of
1992 mode character containing the tree in Newick format is returned which
1993 can thus be assigned (e.g., tree <- write.tree(phy)).
1995 o The function read.tree() has a new argument `text' which allows
1996 to read the tree in a variable of mode character.
1998 o A new data set is included: the phylogenetic relationships among
1999 the orders of birds from Sibley and Ahlquist (1990).
2003 CHANGES IN APE VERSION 0.2-1
2008 o Several bugs were fixed in the help pages.
2012 CHANGES IN APE VERSION 0.2
2017 o The function write.tree() writes phylogenetic trees (objects of class
2018 "phylo") in an ASCII file using the Newick parenthetic format.
2020 o The function birthdeath() fits a birth-death model to branching times
2021 by maximum likelihood, and estimates the corresponding speciation and
2024 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
2027 o The function is.binary.tree() tests whether a phylogeny is binary.
2029 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
2030 as well as some methods are introduced.
2032 o Several functions, including some generics and methods, for computing
2033 skyline plot estimates (classic and generalized) of effective
2034 population size through time are introduced and replace the function
2035 skyline.plot() in version 0.1.
2037 o Two data sets are now included: the phylogenetic relationships among
2038 the families of birds from Sibley and Ahlquist (1990), and an
2039 estimated clock-like phylogeny of HIV sequences sampled in the
2040 Democratic Republic of Congo.
2043 DEPRECATED & DEFUNCT
2045 o The function skyline.plot() in ape 0.1 has been deprecated and
2046 replaced by more elaborate functions (see above).
2051 o Two important bugs were fixed in plot.phylo(): phylogenies with
2052 multichotomies not at the root or not with only terminal branches,
2053 and phylogenies with a single node (i.e. only terminal branches)
2054 did not plot. These trees should be plotted correctly now.
2056 o Several bugs were fixed in diversi.time() in the computation of
2059 o Various errors were corrected in the help pages.
projects / ape.git / blob