1 CHANGES IN APE VERSION 2.6-2
6 o Two new functions, pic.ortho and varCompPhylip, implements the
7 orthonormal contrasts of Felsenstein (2008, Am Nat, 171:713). The
8 second function requires Phylip to be installed on the computer.
10 o bd.ext() has a new option conditional = TRUE to use probabilities
11 conditioned on no extinction for the taxonomic data.
16 o write.tree() failed to output correctly tree names.
18 o dist.nodes() returned duplicated column(s) with unrooted and/or
21 o mcmc.popsize() terminated unexpectedly if the progress bar was
24 o prop.part(x) made R frozen if 'x' is of class "multiPhylo".
26 o Compilation under Mandriva failed (thanks to Jos Käfer for the fix).
28 o drop.tip() shuffled tip labels with subtree = TRUE or trim.internal
31 o Objects returned by as.hclust.phylo() failed when analysed with
32 cutree() or rect.hclust().
34 o write.tree() did not output correctly node labels (thanks to Naim
39 CHANGES IN APE VERSION 2.6-1
44 o The new function speciesTree calculates the species tree from a set
45 of gene trees. Several methods are available including maximum tree
46 and shallowest divergence tree.
51 o A bug introduced in write.tree() with ape 2.6 has been fixed.
53 o as.list.DNAbin() did not work correctly with vectors.
55 o as.hclust.phylo() failed with trees with node labels (thanks to
56 Filipe Vieira for the fix).
60 CHANGES IN APE VERSION 2.6
65 o The new functions rlineage and rbdtree simulate phylogenies under
66 any user-defined time-dependent speciation-extinction model. They
67 use continuous time algorithms.
69 o The new function drop.fossil removes the extinct species from a
72 o The new function bd.time fits a user-defined time-dependent
73 birth-death model. It is a generalization of yule.time() taking
74 extinction into account.
76 o The new function MPR does most parsimonious reconstruction of
79 o The new function Ftab computes the contingency table of base
80 frequencies from a pair of sequences.
82 o There is now an 'as.list' method for the class "DNAbin".
84 o dist.dna() can compute the number of transitions or transversions
85 with the option model = "Ts" or model = "Tv", respectively.
87 o [node|tip|edge]labels() gain three options with default values to
88 control the aspect of thermometers: horiz = TRUE, width = NULL,
91 o compar.gee() has been improved with the new option 'corStruct' as an
92 alternative to 'phy' to specify the correlation structure, and
93 calculation of the QIC (Pan 2001, Biometrics). The display of the
94 results has also been improved.
96 o read.GenBank() has a new option 'gene.names' to return the name of
97 the gene (FALSE by default).
102 o extract.clade() sometimes shuffled the tip labels.
104 o plot.phylo(type = "unrooted") did not force asp = 1 (thanks to Klaus
107 o dist.dna(model = "logdet") used to divide distances by 4. The
108 documentation has been clarified on the formulae used.
113 o rTraitCont(model = "OU") has an option 'linear = TRUE' to possibly
114 change the parameterisation (see ?rTraitCont for details).
116 o pic() now returns a vector with the node labels of the tree (if
119 o write.tree() and read.tree() have been substantially improved thanks
120 to contributions by Klaus Schliep.
124 CHANGES IN APE VERSION 2.5-3
129 o The new function mixedFontLabel helps to make labels with bits of
130 text to be plotted in different fonts.
132 o There are now replacement operators for [, [[, and $ for the class
133 "multiPhylo" (i.e., TREES[11:20] <- rmtree(10, 100)). They possibly
134 check that the tip labels are the same in all trees.
136 o Objects of class "multiPhylo" can be built with c(): there are
137 methods for the classes "phylo" and "multiPhylo".
139 o The internal functions .compressTipLabel and .uncompressTipLabel are
145 o bind.tree(x, y, where, position = 0) did not work correctly if 'y'
146 was a single-edge tree and 'where' was a tip.
148 o rTraitCont() did not use the square-root of branch lengths when
149 simulating a Brownian motion model.
153 CHANGES IN APE VERSION 2.5-2
158 o There is now a print method for results from ace().
160 o There is a labels() method for objects of class "DNAbin".
162 o read.dna() has a new option 'as.matrix' to possibly force sequences
163 in a FASTA file to be stored in a matrix (see ?read.dna for details).
168 o as.phylo.hclust() used to multiply edge lengths by 2.
170 o A minor bug was fixed in rTraitDisc().
172 o ace() sometimes failed (parameter value was NaN and the optimisation
178 o evolve.phylo() and plot.ancestral() have been removed.
180 o chronogram(), ratogram(), and NPRS.criterion() have been removed.
185 o nj() has been improved and is now about 30% faster.
187 o The default option 'drop' of [.DNAbin has been changed to FALSE to
188 avoid dropping rownames when selecting a single sequence.
190 o print.DNAbin() has been changed to summary.DNAbin() which has been
195 CHANGES IN APE VERSION 2.5-1
200 o The new function stree generates trees with regular shapes.
202 o It is now possible to bind two trees with x + y (see ?bind.tree for
205 o drop.tip(), extract.clade(), root(), and bind.tree() now have an
206 'interactive' option to make the operation on a plotted tree.
208 o cophyloplot() gains two new arguments 'lwd' and 'lty' for the
209 association links; they are recycled like 'col' (which wasn't before).
214 o rTraitDisc() did not use its 'freq' argument correctly (it was
215 multiplied with the rate matrix column-wise instead of row-wise).
217 o [node|tip|edge]labels(thermo = ) used to draw empty thermometers
218 with NA values. Nothing is drawn now like with 'text' or 'pch'.
219 The same bug occurred with the 'pie' option.
221 o A bug was fixed in compar.ou() and the help page was clarified.
223 o bind.tree() has been rewritten fixing several bugs and making it
226 o plot.phylo(type = "p") sometimes failed to colour correctly the
227 vertical lines representing the nodes.
229 o plot.phylo(direction = "l", x.lim = 30) failed to plot the branches
230 in the correct direction though the tip labels were displayed
236 o The c, cbind, and rbind methods for "DNAbin" objetcs now check that
237 the sequences are correctly stored (in a list for c, in a matrix
238 for the two other functions).
242 CHANGES IN APE VERSION 2.5
247 o The new function parafit by Pierre Legendre tests for the
248 coevolution between hosts and parasites. It has a companion
249 function, pcoa, that does principal coordinate decomposition.
250 The latter has a biplot method.
252 o The new function lmorigin by Pierre Legendre performs multiple
253 regression through the origin with testing by permutation.
255 o The new functions rTraitCont and rTraitDisc simulate continuous and
256 discrete traits under a wide range of evolutionary models.
258 o The new function delta.plot does a delta plot following Holland et
259 al. (2002, Mol. Biol. Evol. 12:2051).
261 o The new function edges draws additional branches between any nodes
262 and/or tips on a plotted tree.
264 o The new function fancyarrows enhances arrows from graphics with
265 triangle and harpoon heads; it can be called from edges().
267 o add.scale.bar() has a new option 'ask' to draw interactively.
269 o The branch length score replaces the geodesic distance in dist.topo.
271 o Three new data sets are included: the gopher-lice data (gopher.D),
272 SO2 air pollution in 41 US cities (lmorigin.ex1, from Sokal &
273 Rohlf 1995), and some host-parasite specificity data
274 (lmorigin.ex2, from Legendre & Desdevises 2009).
279 o add.scale.bar() drew the bar outside the plotting region with the
280 default options with unrooted or radial trees.
282 o dist.topo() made R stuck when the trees had different sizes (thanks
283 to Otto Cordero for the fix).
288 o The geodesic distance has been replaced by the branch length score
293 CHANGES IN APE VERSION 2.4-1
298 o rtree() and rcoal() now accept a numeric vector for the 'br'
301 o vcv() is a new generic function with methods for the classes "phylo"
302 and "corPhyl" so that it is possible to calculate the var-cov matrix
303 for "transformation models". vcv.phylo() can still be used for trees
304 of class "phylo"; its argument 'cor' has been renamed 'corr'.
309 o bind.tree() failed when 'y' had no root edge.
311 o read.nexus() shuffled tip labels when the trees have no branch
312 lengths and there is a TRANSLATE block.
314 o read.nexus() does not try to translate node labels if there is a
315 translation table in the NEXUS file. See ?read.nexus for a
316 clarification on this behaviour.
318 o plot.multiPhylo() crashed R when plotting a list of trees with
319 compressed tip labels.
321 o write.nexus() did not translate the taxa names when asked for.
323 o plot.phylo(type = "fan") did not rotate the tip labels correctly
324 when the tree has branch lengths.
326 o ace(type = "continuous", method = "ML") now avoids sigma² being
327 negative (which resulted in an error).
329 o nj() crashed with NA/NaN in the distance matrix: an error in now
334 CHANGES IN APE VERSION 2.4
339 o base.freq() has a new option 'freq' to return the counts; the
340 default is still to return the proportions.
345 o seg.sites() did not handle ambiguous nucleotides correctly: they
348 o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
349 the tree: the argument is now ignored.
351 o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
357 o Trying to plot a tree with a single tip now returns NULL with a
358 warning (it returned an error previously).
360 o The way lines representing nodes are coloured in phylograms has
361 been modified (as well as their widths and types) following some
362 users' request; this is only for dichotomous nodes.
364 o The argument 'adj' in [node][tip][edge]labels() now works when
365 using 'pie' or 'thermo'.
367 o A more informative message error is now returned by dist.dna() when
368 'model' is badly specified (partial matching of this argument is
371 o Deprecated functions are now listed in a help page: see
372 help("ape-defunct") with the quotes.
377 o The functions heterozygosity, nuc.div, theta.h, theta.k and
378 theta.s have been moved from ape to pegas.
380 o The functions mlphylo, DNAmodel and sh.test have been removed.
384 CHANGES IN APE VERSION 2.3-3
389 o add.scale.bar() always drew a horizontal bar.
391 o zoom() shuffled tips with unrooted trees.
393 o write.nexus() failed to write correctly trees with a "TipLabel"
396 o rcoal() failed to compute branch lengths with very large n.
398 o A small bug was fixed in compar.cheverud() (thanks to Michael
401 o seg.sites() failed when passing a vector.
403 o drop.tip() sometimes shuffled tip labels.
405 o root() shuffled node labels with 'resolve.root = TRUE'.
409 CHANGES IN APE VERSION 2.3-2
414 o all.equal.phylo() did not compare unrooted trees correctly.
416 o dist.topo(... method = "PH85") did not treat unrooted trees
417 correctly (thanks to Tim Wallstrom for the fix).
419 o root() sometimes failed to test for the monophyly of the
422 o extract.clade() sometimes included too many edges.
424 o vcv.phylo() did not work correctly when the tree is in
427 o nj() did not handle correctly distance matrices with many 0's.
428 The code has also been significantly improved: 7, 70, 160 times
429 faster with n = 100, 500, 1000, respectively.
433 CHANGES IN APE VERSION 2.3-1
438 o The new function is.monophyletic tests the monophyly of a group.
440 o There is now a c() method for lists of class "DNAbin".
442 o yule.cov() now fits the null model, and its help page has been
443 corrected with respect to this change.
445 o drop.tip() has a new option 'rooted' to force (or not) a tree
446 to be treated as (un)rooted.
451 o dist.gene() failed on most occasions with the default
452 pairwise.deletion = FALSE.
454 o read.tree() failed to read correctly the tree name(s).
456 o boot.phylo() now treats correctly data frames.
458 o del.gaps() did not copy the rownames of a matrix.
460 o A small bug was fixed in CDAM.global().
462 o ace() failed with large data sets. Thanks to Rich FitzJohn for
463 the fix. With other improvements, this function is now about 6
466 o write.tree() failed with objects of class "multiPhylo".
468 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
473 o [.multiPhylo and [.DNAbin now respect the original class.
475 o Instances of the form class(phy) == "phylo" have been replaced
476 by inherits(phy, "phylo").
478 o rcoal() is now faster.
483 o klastorin() has been removed.
487 CHANGES IN APE VERSION 2.3
492 o The new functions CADM.global and CADM.post, contributed by
493 Pierre Legendre, test the congruence among several distance
496 o The new function yule.time fits a user-defined time-dependent
497 Yule model by maximum likelihood.
499 o The new function makeNodeLabel creates and/or modifies node
500 labels in a flexible way.
502 o read.tree() and write.tree() have been modified so that they can
503 handle individual tree names.
505 o plot.phylo() has a new argument 'edge.lty' that specifies the
506 types of lines used for the edges (plain, dotted, dashed, ...)
508 o phymltest() has been updated to work with PhyML 3.0.1.
513 o drop.tip() shuffled tip labels in some cases.
515 o drop.tip() did not handle node.label correctly.
517 o is.ultrametric() now checks the ordering of the edge matrix.
519 o ace() sometimes returned negative values of likelihoods of
520 ancestral states (thanks to Dan Rabosky for solving this long
526 o The data set xenarthra has been removed.
530 CHANGES IN APE VERSION 2.2-4
534 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
535 now fixed. (Thanks to Peter Wragg for the fix!)
537 o A warning message occurred for no reason with ace(method="GLS").
542 o There is now a general help page displayed with '?ape'.
546 CHANGES IN APE VERSION 2.2-3
551 o The new function extract.clade extracts a clade from a tree by
552 specifying a node number or label.
554 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
555 operations of the same names.
557 o dist.dna() can now return the number of site differences by
558 specifying model="N".
563 o chronopl() did not work with CV = TRUE.
565 o read.nexus() did not work correctly in some situations (trees on
566 multiple lines with different numbers of lines and/or with
567 comments inserted within the trees).
569 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
570 the number of lineages with non-binary trees.
575 o ape has now a namespace.
577 o drop.tip() has been improved: it should be much faster and work
578 better in some cases (e.g., see the example in ?zoom).
582 CHANGES IN APE VERSION 2.2-2
587 o dist.gene() has been substantially improved and gains an option
590 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
596 o prop.part() failed with a single tree with the default option
597 'check.labels = TRUE'.
599 o summary.DNAbin() failed to display correctly the summary of
600 sequence lengths with lists of sequences of 10,000 bases or more
601 (because summary.default uses 4 significant digits by default).
603 o read.nexus() failed to read a file with a single tree with line
604 breaks in the Newick string.
606 o del.gaps() returned a list of empty sequences when there were no
612 o phymltest() has been updated for PhyML 3.0 and gains an option
613 'append', whereas the option 'path2exec' has been removed.
615 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
616 which is returned unchanged (instead of an error).
618 o The data sets bird.orders and bird.families are now stored as
619 Newick strings; i.e., the command data(bird.orders) calls
624 CHANGES IN APE VERSION 2.2-1
629 o The new function makeLabel() helps to modify labels of trees,
630 lists of trees, or DNA sequences, with several utilities to
631 truncate and/or make them unique, substituting some
632 characters, and so on.
634 o The new function del.gaps() removes insertion gaps ("-") in a
635 set of DNA sequences.
637 o read.dna() can now read Clustal files (*.aln).
642 o root() failed with 'resolve.root = TRUE' when the root was
643 already the specified root.
645 o Several bugs were fixed in mlphylo().
647 o collapsed.singles() did not propagate the 'Nnode' and
648 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
650 o read.nexus() failed to remove correctly the comments within
653 o read.nexus() failed to read a file with a single tree and no
654 translation of tip labels.
656 o read.nexus() failed to place correctly tip labels when reading
657 a single tree with no edge lengths.
659 o A bug was fixed in sh.test().
664 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
667 o The option 'check.labels' of consensus() and prop.part() is now
670 o write.dna() now does not truncate names to 10 characters with
675 CHANGES IN APE VERSION 2.2
680 o Four new functions have been written by Damien de Vienne for the
681 graphical exploration of large trees (cophyloplot, subtrees,
682 subtreeplot), and to return the graphical coordinates of tree
685 o The new functions corPagel and corBlomberg implement the Pagel's
686 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
688 o chronopl() has been improved and gains several options: see its
689 help page for details.
691 o boot.phylo() has now an option 'trees' to possibly return the
692 bootstraped trees (the default is FALSE).
694 o prop.part() has been improved and should now be faster in all
700 o read.dna() failed if "?" occurred in the first 10 sites of the
703 o The x/y aspect of the plot is now respected when plotting a
704 circular tree (type = "r" or "f").
706 o Drawing the tip labels sometimes failed when plotting circular
709 o zoom() failed when tip labels were used instead of their numbers
710 (thanks to Yan Wong for the fix).
712 o drop.tip() failed with some trees (fixed by Yan Wong).
714 o seg.sites() failed with a list.
716 o consensus() failed in some cases. The function has been improved
717 as well and is faster.
721 CHANGES IN APE VERSION 2.1-3
726 o A bug in read.nexus() made the Windows R-GUI crash.
728 o An error was fixed in the computation of ancestral character
729 states by generalized least squares in ace().
731 o di2multi() did not modify node labels correctly.
733 o multi2di() failed if the tree had its attribute "order" set to
738 CHANGES IN APE VERSION 2.1-2
743 o There three new methods for the "multiPhylo" class: str, $,
746 o root() gains the options 'node' and 'resolve.root'
747 (FALSE by default) as well as its code being improved.
749 o mltt.plot() has now an option 'log' used in the same way
750 than in plot.default().
755 o mltt.plot() failed to display the legend with an unnamed
758 o nodelabels() with pies now correcly uses the argument
759 'cex' to draw symbols of different sizes (which has
760 worked already for thermometers).
762 o read.nexus() generally failed to read very big files.
767 o The argument 'family' of compar.gee() can now be a function
768 as well as a character string.
770 o read.tree() and read.nexus() now return an unnamed list if
773 o read.nexus() now returns a modified object of class "multiPhylo"
774 when there is a TRANSLATE block in the NEXUS file: the individual
775 trees have no 'tip.label' vector, but the list has a 'TipLabel'
776 attribute. The new methods '$' and '[[' set these elements
777 correctly when extracting trees.
781 CHANGES IN APE VERSION 2.1-1
786 o The new function rmtree generates lists of random trees.
788 o rcoal() now generates a genuine coalescent tree by default
789 (thanks to Vladimir Minin for the code).
794 o nuc.div() returned an incorrect value with the default
795 pairwise.deletion = FALSE.
800 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
801 have been improved so that they are stabler and faster.
803 o R packages used by ape are now loaded silently; lattice and gee
804 are loaded only when needed.
808 CHANGES IN APE VERSION 2.1
813 o The new function identify.phylo identifies clades on a plotted
814 tree using the mouse.
816 o It is now possible to subset a list of trees (object of class
817 "multiPhylo") with "[" while keeping its class correct.
819 o The new function as.DNAbin.alignment converts DNA sequences
820 stored in the "alignment" format of the package seqinr into
821 an object of class "DNAbin".
823 o The new function weight.taxo2 helps to build similarity matrices
824 given two taxonomic levels (usually called by other functions).
826 o write.tree() can now take a list of trees (class "multiPhylo")
827 as its main argument.
829 o plot.correlogram() and plot.correlogramList() have been
830 improved, and gain several options (see the help page for
831 details). A legend is now plotted by default.
836 o dist.dna() returned some incorrect values with `model = "JC69"'
837 and `pairwise.deletion = TRUE'. This affected only the
838 distances involving sequences with missing values. (Thanks
839 to Bruno Toupance for digging this bug out.)
841 o write.tree() failed with some trees: this is fixed by removing
842 the `multi.line' option (trees are now always printed on a
845 o read.nexus() did not correctly detect trees with multiple root
846 edges (see OTHER CHANGES).
851 o The code of mlphylo() has been almost entirely rewritten, and
852 should be much stabler. The options have been also greatly
853 simplified (see ?mlphylo and ?DNAmodel for details).
855 o The internal function nTips has been renamed klastorin_nTips.
857 o The code of is.ultrametric() contained redundancies and has
860 o The code of Moran.I() and of correlogram.formula() have been
863 o read.tree() and read.nexus() now return an error when trying to
864 read a tree with multiple root edges (see BUG FIXES). The
865 correction applied in previous version did not work in all
868 o The class c("multi.tree", "phylo") has been renamed
874 o There is now a vignette in ape: see vignette("MoranI", "ape").
879 o as.matching() and as.phylo.matching() do not support branch
882 o correlogram.phylo() and discrete.dist() have been removed.
886 CHANGES IN APE VERSION 2.0-2
891 o The new function matexpo computes the exponential of a square
894 o The new function unique.multi.tree removes duplicate trees from
897 o yule() has a new option `use.root.edge = FALSE' that specifies
898 to ignore, by default, the root edge of the tree if it exists.
903 o which.edge() failed when the index of a single terminal edge was
906 o In diversi.time(), the values returned for model C were
909 o A bug was fixed in yule() that affected the calculation of the
910 likelihood in the presence of ties in the branching times.
912 o There was a bug in the C function mat_expo4x4 affecting the
913 calculations of the transition probabilities for models HKY and
916 o A small bug was fixed in as.matrix.DNAbin (thanks to James
919 o rtree() did not `shuffle' the tip labels by default, so only a
920 limited number of labelled topologies could be generated.
924 CHANGES IN APE VERSION 2.0-1
929 o The three new functions bionj, fastme.ols, and fastme.bal
930 perform phylogeny estimation by the BIONJ and fastME methods in
931 OLS and balanced versions. This is a port to R of previous
932 previous programs done by Vincent Lefort.
934 o The new function chronoMPL performs molecular dating with the
935 mean path lengths method of Britton et al. (2002, Mol. Phyl.
938 o The new function rotate, contributed by Christoph Heibl, swaps
939 two clades connected to the same node. It works also with
940 multichotomous nodes.
942 o The new `method' as.matrix.DNAbin() may be used to convert
943 easily DNA sequences stored in a list into a matrix while
944 keeping the names and the class.
949 o chronopl() failed when some branch lengths were equal to zero:
950 an error message is now returned.
952 o di2multi() failed when there was a series of consecutive edges
957 CHANGES IN APE VERSION 1.10-2
962 o plot.phylo() can now plot circular trees: the option is type =
963 "fan" or type = "f" (to avoid the ambiguity with type = "c").
965 o prop.part() has a new option `check.labels = FALSE' which allows
966 to considerably speed-up the calculations of bipartitions. As a
967 consequence, calculations of bootstrap values with boot.phylo()
968 should be much faster.
973 o read.GenBank() did not return correctly the list of species as
974 from ape 1.10: this is fixed in this version
976 o Applying as.phylo() on a tree of class "phylo" failed: the
977 object is now returned unchanged.
981 CHANGES IN APE VERSION 1.10-1
986 o The three new functions Ntip, Nnode, and Nedge return, for a
987 given tree, the number of tips, nodes, or edges, respectively.
992 o read.nexus() did not set correctly the class of the returned
993 object when reading multiple trees.
995 o mllt.plot() failed with objects of class c("multi.tree",
998 o unroot() did not work correctly in most cases.
1000 o reorder.phylo() made R freeze in some occasions.
1002 o Plotting a tree in pruningwise order failed.
1004 o When plotting an unrooted tree, the tip labels where not all
1005 correctly positioned if the option `cex' was used.
1009 CHANGES IN APE VERSION 1.10
1014 o Five new `method' functions have been introduced to manipulate
1015 DNA sequences in binary format (see below).
1017 o Three new functions have been introduced to convert between the
1018 new binary and the character formats.
1020 o The new function as.alignment converts DNA sequences stored as
1021 single characters into the class "alignment" used by the package
1024 o read.dna() and read.GenBank() have a new argument `as.character'
1025 controlling whether the sequences are returned in binary format
1031 o root() failed when the tree had node labels: this is fixed.
1033 o plot.phylo() did not correctly set the limits on the y-axis with
1034 the default setting: this is fixed.
1036 o dist.dna() returned a wrong result for the LogDet, paralinear,
1037 and BH87 models with `pairwise.deletion = TRUE'.
1042 o DNA sequences are now internally stored in a binary format. See
1043 the document "A Bit-Level Coding Scheme for Nucleotides" for the
1044 details. Most functions analyzing DNA functions have been
1045 modified accordingly and are now much faster (dist.dna is now
1046 ca. 60 times faster).
1050 CHANGES IN APE VERSION 1.9-4
1055 o A bug was fixed in edgelabels().
1057 o as.phylo.hclust() did not work correctly when the object of
1058 class "hclust" has its labels set to NULL: the returned tree has
1059 now its tip labels set to "1", "2", ...
1061 o consensus could fail if some tip labels are a subset of others
1062 (e.g., "a" and "a_1"): this is now fixed.
1064 o mlphylo() failed in most cases if some branch lengths of the
1065 initial tree were greater than one: an error message is now
1068 o mlphylo() failed in most cases when estimating the proportion of
1069 invariants: this is fixed.
1073 CHANGES IN APE VERSION 1.9-3
1078 o The new function edgelabels adds labels on the edge of the tree
1079 in the same way than nodelabels or tiplabels.
1084 o multi2di() did not handle correctly branch lengths with the
1085 default option `random = TRUE': this is now fixed.
1087 o A bug was fixed in nuc.div() when using pairwise deletions.
1089 o A bug occurred in the analysis of bipartitions with large
1090 numbers of large trees, with consequences on prop.part,
1091 prop.clades, and boot.phylo.
1093 o The calculation of the Billera-Holmes-Vogtmann distance in
1094 dist.topo was wrong: this has been fixed.
1098 CHANGES IN APE VERSION 1.9-2
1103 o The new function ladderize reorganizes the internal structure of
1104 a tree to plot them left- or right-ladderized.
1106 o The new function dist.nodes computes the patristic distances
1107 between all nodes, internal and terminal, of a tree. It replaces
1108 the option `full = TRUE' of cophenetic.phylo (see below).
1113 o A bug was fixed in old2new.phylo().
1115 o Some bugs were fixed in chronopl().
1117 o The edge colours were not correctly displayed by plot.phylo
1118 (thank you to Li-San Wang for the fix).
1120 o cophenetic.phylo() failed with multichotomous trees: this is
1126 o read.dna() now returns the sequences in a matrix if they are
1127 aligned (interleaved or sequential format). Sequences in FASTA
1128 format are still returned in a list.
1130 o The option `full' of cophenetic.phylo() has been removed because
1131 it could not be used from the generic.
1134 DEPRECATED & DEFUNCT
1136 o rotate() has been removed; this function did not work correctly
1141 CHANGES IN APE VERSION 1.9-1
1146 o Trees with a single tip were not read correctly in R as the
1147 element `Nnode' was not set: this is fixed.
1149 o unroot() did not set correctly the number of nodes of the
1150 unrooted tree in most cases.
1152 o read.GenBank() failed when fetching very long sequences,
1153 particularly of the BX-series.
1155 o A bug was introduced in read.tree() with ape 1.9: it has been
1160 CHANGES IN APE VERSION 1.9
1165 o There are two new print `methods' for trees of class "phylo" and
1166 lists of trees of class "multi.tree", so that they are now
1167 displayed in a compact and informative way.
1169 o There are two new functions, old2new.phylo and new2old.phylo,
1170 for converting between the old and new coding of the class
1173 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
1174 LogDet ("logdet"), and paralinear ("paralin").
1176 o compute.brlen() has been extended: several methods are now
1177 available to compute branch lengths.
1179 o write.dna() can now handle matrices as well as lists.
1184 o cophenetic.phylo() sometimes returned a wrong result with
1185 multichotomous trees: this is fixed.
1187 o rotate() failed when a single tip was specified: the tree is now
1190 o ace() did not return the correct index matrix with custom
1191 models: this is fixed.
1193 o multi2di() did not work correctly when resolving multichotomies
1194 randomly: the topology was always the same, only the arrangement
1195 of clades was randomized: this is fixed. This function now
1196 accepts trees with no branch lengths.
1198 o The output of diversi.gof() was blurred by useless prints when a
1199 user distribution was specified. This has been corrected, and
1200 the help page of this function has been expanded.
1205 o The internal structure of the class "phylo" has been changed:
1206 see the document "Definition of Formats for Coding Phylogenetic
1207 Trees in R" for the details. In addition, the code of most
1208 functions has been improved.
1210 o Several functions have been improved by replacing some R codes
1211 by C codes: pic, plot.phylo, and reorder.phylo.
1213 o There is now a citation information: see citation("ape") in R.
1215 o write.tree() now does not add extra 0's to branch lengths so
1216 that 1.23 is printed "1.23" by default, not "1.2300000000".
1218 o The syntax of bind.tree() has been simplified. This function now
1219 accepts trees with no branch lengths, and handles correctly node
1222 o The option `as.numeric' of mrca() has been removed.
1224 o The unused options `format' and `rooted' of read.tree() have
1227 o The unused option `format' of write.tree() has been removed.
1229 o The use of node.depth() has been simplified.
1233 CHANGES IN APE VERSION 1.8-5
1238 o Two new functions read.nexus.data() and write.nexus.data(),
1239 contributed by Johan Nylander, allow to read and write molecular
1240 sequences in NEXUS files.
1242 o The new function reorder.phylo() reorders the internal structure
1243 of a tree of class "phylo". It is used as the generic, e.g.,
1246 o read.tree() and read.nexus() can now read trees with a single
1249 o The new data set `cynipids' supplies a set of protein sequences
1255 o The code of all.equal.phylo() has been completely rewritten
1256 (thanks to Benoît Durand) which fixes several bugs.
1258 o read.tree() and read.nexus() now checks the labels of the tree
1259 to remove or substitute any characters that are illegal in the
1260 Newick format (parentheses, etc.)
1262 o A negative P-value could be returned by mantel.test(): this is
1267 CHANGES IN APE VERSION 1.8-4
1272 o The new function sh.test() computes the Shimodaira-
1275 o The new function collapse.singles() removes the nodes with a
1276 single descendant from a tree.
1278 o plot.phylo() has a new argument `tip.color' to specify the
1279 colours of the tips.
1281 o mlphylo() has now an option `quiet' to control the display of
1282 the progress of the analysis (the default is FALSE).
1287 o read.dna() did not read correctly sequences in sequential format
1288 with leading alignment gaps "-": this is fixed.
1290 o ace() returned a list with no class so that the generic
1291 functions (anova, logLik, ...) could not be used directly. This
1292 is fixed as ace() now returns an object of class "ace".
1294 o anova.ace() had a small bug when computing the number of degrees
1295 of freedom: this is fixed.
1297 o mlphylo() did not work when the sequences were in a matrix or
1298 a data frame: this is fixed.
1300 o rtree() did not work correctly when trying to simulate an
1301 unrooted tree with two tips: an error message is now issued.
1306 o The algorithm of rtree() has been changed: it is now about 40,
1307 100, and 130 times faster for 10, 100, and 1000 tips,
1312 CHANGES IN APE VERSION 1.8-3
1317 o There are four new `method' functions to be used with the
1318 results of ace(): logLik(), deviance(), AIC(), and anova().
1320 o The plot method of phymltest has two new arguments: `main' to
1321 change the title, and `col' to control the colour of the
1322 segments showing the AIC values.
1324 o ace() has a new argument `ip' that gives the initial values used
1325 in the ML estimation with discrete characters (see the examples
1326 in ?ace). This function now returns a matrix giving the indices
1327 of the estimated rates when analysing discrete characters.
1329 o nodelabels() and tiplabels() have a new argument `pie' to
1330 represent proportions, with any number of categories, as
1331 piecharts. The use of the option `thermo' has been improved:
1332 there is now no limitation on the number of categories.
1337 o mlphylo() did not work with more than two partitions: this is
1340 o root() failed if the proposed outgroup was already an outgroup
1341 in the tree: this is fixed.
1343 o The `col' argument in nodelabels() and tiplabels() was not
1344 correctly passed when `text' was used: this is fixed.
1346 o Two bugs were fixed in mlphylo(): parameters were not always
1347 correctly output, and the estimation failed in some cases.
1349 o plot.phylo() was stuck when given a tree with a single tip: this
1350 is fixed and a message error is now returned.
1352 o An error was corrected in the help page of gammaStat regarding
1353 the calculation of P-values.
1355 o Using gls() could crash R when the number of species in the tree
1356 and in the variables were different: this is fixed.
1360 CHANGES IN APE VERSION 1.8-2
1365 o The new function mlphylo() fits a phylogenetic tree by maximum
1366 likelihood from DNA sequences. Its companion function DNAmodel()
1367 is used to define the substitution model which may include
1368 partitioning. There are methods for logLik(), deviance(), and
1369 AIC(), and the summary() method has been extended to display in
1370 a friendly way the results of this model fitting. Currently, the
1371 functionality is limited to estimating the substitution and
1372 associated parameters and computing the likelihood.
1374 o The new function drop1.compar.gee (used as, e.g., drop1(m))
1375 tests for single effects in GEE-based comparative method. A
1376 warning message is printed if there is not enough degrees of
1382 o An error message was sometimes issued by plot.multi.tree(),
1383 though with no consequence.
1387 CHANGES IN APE VERSION 1.8-1
1392 o There is a new plot method for lists of trees (objects of class
1393 "multi.tree"): it calls plot.phylo() internally and is
1394 documented on the same help page.
1399 o A bug was fixed in the C code that analyzes bipartitions: this
1400 has impact on several functions like prop.part, prop.clades,
1401 boot.phylo, or consensus.
1403 o root() did not work correctly when the specified outgroup had
1404 more than one element: this is fixed.
1406 o dist.dna() sometimes returned a warning inappropriately: this
1409 o If the distance object given to nj() had no rownames, nj()
1410 returned a tree with no tip labels: it now returns tips labelled
1411 "1", "2", ..., corresponding to the row numbers.
1416 o nj() has been slightly changed so that tips with a zero distance
1417 are first aggregated with zero-lengthed branches; the usual NJ
1418 procedure is then performed on a distance matrix without 0's.
1422 CHANGES IN APE VERSION 1.8
1427 o The new function chronopl() estimates dates using the penalized
1428 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1430 o The new function consensus() calculates the consensus tree of a
1433 o The new function evolve.phylo() simulates the evolution of
1434 continuous characters along a phylogeny under a Brownian model.
1436 o The new plot method for objects of class "ancestral" displays a
1437 tree together with ancestral values, as returned by the above
1440 o The new function as.phylo.formula() returns a phylogeny from a
1441 set of nested taxonomic variables given as a formula.
1443 o The new function read.caic() reads trees in CAIC format.
1445 o The new function tiplabels() allows to add labels to the tips
1446 of a tree using text or plotting symbols in a flexible way.
1448 o The new function unroot() unroots a phylogeny.
1450 o multi2di() has a new option, `random', which specifies whether
1451 to resolve the multichotomies randomly (the default) or not.
1453 o prop.part() now returns an object of class "prop.part" for which
1454 there are print (to display a partition in a more friendly way)
1455 and summary (to extract the numbers) methods.
1457 o plot.phylo() has a new option, `show.tip.label', specifying
1458 whether to print the labels of the tips. The default is TRUE.
1460 o The code of nj() has been replaced by a faster C code: it is now
1461 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1464 o write.nexus() now writes whether a tree is rooted or not.
1469 o Two bugs have been fixed in root(): unrooted trees are now
1470 handled corretly, and node labels are now output normally.
1472 o A bug was fixed in phymltest(): the executable couldn't be found
1475 o Three bug have been fixed in ace(): computing the likelihood of
1476 ancestral states of discrete characters failed, custom models
1477 did not work, and the function failed with a null gradient (a
1478 warning message is now returned; this latter bug was also
1479 present in yule.cov() as well and is now fixed).
1481 o pic() hanged out when missing data were present: a message error
1484 o A small bug was fixed in dist.dna() where the gamma correction
1485 was not always correctly dispatched.
1487 o plot.phylo() plotted correctly the root edge only when the tree
1488 was plotted rightwards: this works now for all directions.
1493 o dist.taxo() has been renamed as weight.taxo().
1495 o dist.phylo() has been replaced by the method cophenetic.phylo().
1497 o Various error and warning messages have been improved.
1501 CHANGES IN APE VERSION 1.7
1504 o The new function ace() estimates ancestral character states for
1505 continuous characters (with ML, GLS, and contrasts methods), and
1506 discrete characters (with ML only) for any number of states.
1508 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1509 of directional evolution for continuous characters. The user
1510 specifies the node(s) of the tree where the character optimum
1513 o The new function is.rooted() tests whether a tree (of class
1516 o The new function rcoal() generates random ultrametric trees with
1517 the possibility to specify the function that generates the
1518 inter-nodes distances.
1520 o The new function mrca() gives for all pairs of tips in a tree
1521 (and optionally nodes too) the most recent common ancestor.
1523 o nodelabels() has a new option `thermo' to plot proportions (up
1524 to three classes) on the nodes of a tree.
1526 o rtree() has been improved: it can now generate rooted or
1527 unrooted trees, and the mathematical function that generates the
1528 branch lengths may be specified by the user. The tip labels may
1529 be given directly in the call to rtree. The limit cases (n = 2,
1530 3) are now handled correctly.
1532 o dist.topo() has a new argument `method' with two choices: "PH85"
1533 for Penny and Henny's method (already available before and now
1534 the default), and "BHV01" for the geometric distance by Billera
1535 et al. (2001, Adv. Appl. Math. 27:733).
1537 o write.tree() has a new option, `digits', which specifies the
1538 number of digits to be printed in the Newick tree. By default
1539 digits = 10. The numbers are now always printed in decimal form
1540 (i.e., 1.0e-1 is now avoided).
1542 o dist.dna() can now compute the raw distances between pairs of
1543 DNA sequences by specifying model = "raw".
1545 o dist.phylo() has a new option `full' to possibly compute the
1546 distances among all tips and nodes of the tree. The default if
1552 o Several bugs were fixed in all.equal.phylo().
1554 o dist.dna() did not handle correctly gaps ("-") in alignments:
1555 they are now considered as missing data.
1557 o rotate() did not work if the tips were not ordered: this is
1560 o mantel.test() returned NA in some special cases: this is fixed
1561 and the function has been improved and is now faster.
1563 o A bug was fixed in diversi.gof() where the calculation of A² was
1566 o cherry() did not work correctly under some OSs (mainly Linux):
1569 o is.binary.tree() has been modified so that it works with both
1570 rooted and unrooted trees.
1572 o The documentation of theta.s() was not correct: this has been
1575 o plot.mst() did not work correctly: this is fixed.
1579 CHANGES IN APE VERSION 1.6
1584 o The new function dist.topo() computes the topological distances
1587 o The new function boot.phylo() performs a bootstrap analysis on
1588 phylogeny estimation.
1590 o The new functions prop.part() and prop.clades() analyse
1591 bipartitions from a series of trees.
1596 o read.GenBank() now uses the EFetch utility of NCBI instead of
1597 the usual Web interface: it is now much faster (e.g., 12 times
1598 faster to retrieve 8 sequences, 37 times for 60 sequences).
1603 o Several bugs were fixed in read.dna().
1605 o Several bugs were fixed in diversi.time().
1607 o is.binary.tree() did not work correctly if the tree has no edge
1608 lengths: this is fixed.
1610 o drop.tip() did not correctly propagated the `node.label' of a
1611 tree: this is fixed.
1615 CHANGES IN APE VERSION 1.5
1620 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1621 convert objects between the classes "phylo" and "matching". The
1622 latter implements the representation of binary trees introduced by
1623 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1624 as.matching() has been introduced as well.
1626 o Two new functions, multi2di() and di2multi(), allow to resolve
1627 and collapse multichotomies with branches of length zero.
1629 o The new function nuc.div() computes the nucleotide diversity
1630 from a sample a DNA sequences.
1632 o dist.dna() has been completely rewritten with a much faster
1633 (particularly for large data sets) C code. Eight models are
1634 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1635 option `method' has been renamed `model'). Computation of variance
1636 is available for all models. A gamma-correction is possible for
1637 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1638 to remove sites with missing data on a pairwise basis. The option
1639 `GCcontent' has been removed.
1641 o read.GenBank() has a new option (species.names) which specifies
1642 whether to return the species names of the organisms in addition
1643 to the accession numbers of the sequences (this is the default
1646 o write.nexus() can now write several trees in the same NEXUS file.
1648 o drop.tip() has a new option `root.edge' that allows to specify the
1649 new root edge if internal branches are trimmed.
1654 o as.phylo.hclust() failed if some labels had parentheses: this
1657 o Several bugs were fixed in all.equal.phylo(). This function now
1658 returns the logical TRUE if the trees are identical but with
1659 different representations (a report was printed previously).
1661 o read.GenBank() did not correctly handle ambiguous base codes:
1667 o birthdeath() now returns an object of class "birthdeath" for
1668 which there is a print method.
1672 CHANGES IN APE VERSION 1.4
1677 o The new function nj() performs phylogeny estimation with the
1678 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1681 o The new function which.edge() identifies the edges of a tree
1682 that belong to a group specified as a set of tips.
1684 o The new function as.phylo.phylog() converts an object of class
1685 "phylog" (from the package ade4) into an object of class
1688 o The new function axisPhylo() draws axes on the side of a
1691 o The new function howmanytrees() calculates the number of trees
1692 in different cases and giving a number of tips.
1694 o write.tree() has a new option `multi.line' (TRUE by default) to
1695 write a Newick tree on several lines rather than on a single
1698 o The functionalities of zoom() have been extended. Several
1699 subtrees can be visualized at the same time, and they are marked
1700 on the main tree with colors. The context of the subtrees can be
1701 marked with the option `subtree' (see below).
1703 o drop.tip() has a new option `subtree' (FALSE by default) which
1704 specifies whether to output in the tree how many tips have been
1707 o The arguments of add.scale.bar() have been redefined and have
1708 now default values (see ?add.scale.bar for details). This
1709 function now works even if the plotted tree has no edge length.
1711 o plot.phylo() can now plot radial trees, but this does not take
1712 edge lengths into account.
1714 o In plot.phylo() with `type = "phylogram"', if the values of
1715 `edge.color' and `edge.width' are identical for sister-branches,
1716 they are propagated to the vertical line that link them.
1721 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1722 crashing. This is fixed.
1724 o In plot.phylo(), the options `edge.color' and `edge.width' are
1725 now properly recycled; their default values are now "black" and
1728 o A bug has been fixed in write.nexus().
1733 o The function node.depth.edgelength() has been removed and
1734 replaced by a C code.
1738 CHANGES IN APE VERSION 1.3-1
1743 o The new function nodelabels() allows to add labels to the nodes
1744 of a tree using text or plotting symbols in a flexible way.
1746 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1747 numeric values specifying the lower and upper limits on the x-
1748 and y-axes. This allows to leave some space on any side of the
1749 tree. If a single value is given, this is taken as the upper
1754 CHANGES IN APE VERSION 1.3
1759 o The new function phymltest() calls the software PHYML and fits
1760 28 models of DNA sequence evolution. There are a print method to
1761 display likelihood and AIC values, a summary method to compute
1762 the hierarchical likelihood ratio tests, and a plot method to
1763 display graphically the AIC values of each model.
1765 o The new function yule.cov() fits the Yule model with covariates,
1766 a model where the speciation rate is affected by several species
1767 traits through a generalized linear model. The parameters are
1768 estimated by maximum likelihood.
1770 o Three new functions, corBrownian(), corGrafen(), and
1771 corMartins(), compute the expected correlation structures among
1772 species given a phylogeny under different models of evolution.
1773 These can be used for GLS comparative phylogenetic methods (see
1774 the examples). There are coef() and corMatrix() methods and an
1775 Initialize.corPhyl() function associated.
1777 o The new function compar.cheverud() implements Cheverud et al.'s
1778 (1985; Evolution 39:1335) phylogenetic comparative method.
1780 o The new function varcomp() estimates variance components; it has
1783 o Two new functions, panel.superpose.correlogram() and
1784 plot.correlogramList(), allow to plot several phylogenetic
1787 o The new function node.leafnumber() computes the number of leaves
1788 of a subtree defined by a particular node.
1790 o The new function node.sons() gets all tags of son nodes from a
1793 o The new function compute.brlen() computes the branch lengths of
1794 a tree according to a specified method.
1796 o plot.phylo() has three new options: "cex" controls the size of
1797 the (tip and node) labels (thus it is no more needed to change
1798 the global graphical parameter), "direction" which allows to
1799 plot the tree rightwards, leftwards, upwards, or downwards, and
1800 "y.lim" which sets the upper limit on the y-axis.
1805 o Some functions which try to match tip labels and names of
1806 additional data (e.g. vector) are likely to fail if there are
1807 typing or syntax errors. If both series of names do not perfectly
1808 match, they are ignored and a warning message is now issued.
1809 These functions are bd.ext, compar.gee, pic. Their help pages
1810 have been clarified on this point.
1814 CHANGES IN APE VERSION 1.2-7
1819 o The new function root() reroots a phylogenetic tree with respect
1820 to a specified outgroup.
1822 o The new function rotate() rotates an internal branch of a tree.
1824 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1825 trees) controls the display of the tip labels in unrooted trees.
1826 This display has been greatly improved: the tip labels are now not
1827 expected to overlap with the tree (particularly if lab4ut =
1828 "axial"). In all cases, combining appropriate values of "lab4ut"
1829 and the font size (via "par(cex = )") should result in readable
1830 unrooted trees. See ?plot.phylo for some examples.
1832 o In drop.tip(), the argument `tip' can now be numeric or character.
1837 o drop.tip() did not work correctly with trees with no branch
1838 lengths: this is fixed.
1840 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1841 plotted with some line crossings: this is now fixed.
1845 CHANGES IN APE VERSION 1.2-6
1850 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1851 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1852 to implement comparative methods with an autocorrelation approach.
1854 o A new data set describing some life history traits of Carnivores
1860 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1865 o When plotting a tree with plot.phylo(), the new default of the
1866 option `label.offset' is now 0, so the labels are always visible.
1870 CHANGES IN APE VERSION 1.2-5
1875 o The new function bd.ext() fits a birth-death model with combined
1876 phylogenetic and taxonomic data, and estimates the corresponding
1877 speciation and extinction rates.
1882 o The package gee is no more required by ape but only suggested
1883 since only the function compar.gee() calls gee.
1887 CHANGES IN APE VERSION 1.2-4
1892 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1893 and lines.popsize) implementing a new approach for inferring the
1894 demographic history from genealogies using a reversible jump
1895 MCMC have been introduced.
1897 o The unit of time in the skyline plot and in the new plots can
1898 now be chosen to be actual years, rather than substitutions.
1902 CHANGES IN APE VERSION 1.2-3
1907 o The new function rtree() generates a random binary tree with or
1908 without branch lengths.
1910 o Two new functions for drawing lineages-through-time (LTT) plots
1911 are provided: ltt.lines() adds a LTT curve to an existing plot,
1912 and mltt.plot() does a multiple LTT plot giving several trees as
1913 arguments (see `?ltt.plot' for details).
1918 o Some taxon names made R crashing when calling as.phylo.hclust():
1921 o dist.dna() returned an error with two identical DNA sequences
1922 (only using the Jukes-Cantor method returned 0): this is fixed.
1927 o The function dist.phylo() has been re-written using a different
1928 algorithm: it is now about four times faster.
1930 o The code of branching.times() has been improved: it is now about
1935 CHANGES IN APE VERSION 1.2-2
1940 o The new function seg.sites() finds the segregating sites in a
1941 sample of DNA sequences.
1946 o A bug introduced in read.tree() and in read.nexus() with version
1949 o A few errors were corrected and a few examples were added in the
1954 CHANGES IN APE VERSION 1.2-1
1959 o plot.phylo() can now draw the edge of the root of a tree if it
1960 has one (see the new option `root.edge', its default is FALSE).
1965 o A bug was fixed in read.nexus(): files with semicolons inside
1966 comment blocks were not read correctly.
1968 o The behaviour of read.tree() and read.nexus() was corrected so
1969 that tree files with badly represented root edges (e.g., with
1970 an extra pair of parentheses, see the help pages for details)
1971 are now correctly represented in the object of class "phylo";
1972 a warning message is now issued.
1976 CHANGES IN APE VERSION 1.2
1981 o plot.phylo() has been completely re-written and offers several
1982 new functionalities. Three types of trees can now be drawn:
1983 phylogram (as previously), cladogram, and unrooted tree; in
1984 all three types the branch lengths can be drawn using the edge
1985 lengths of the phylogeny or not (e.g., if the latter is absent).
1986 The vertical position of the nodes can be adjusted with two
1987 choices (see option `node.pos'). The code has been re-structured,
1988 and two new functions (potentially useful for developpers) are
1989 documented separately: node.depth.edgelength() and node.depth();
1990 see the respective help pages for details.
1992 o The new function zoom() allows to explore very large trees by
1993 focusing on a small portion of it.
1995 o The new function yule() fits by maximum likelihood the Yule model
1996 (birth-only process) to a phylogenetic tree.
1998 o Support for writing DNA sequences in FASTA format has been
1999 introduced in write.dna() (support for reading sequences in
2000 this format was introduced in read.dna() in version 1.1-2).
2001 The function has been completely re-written, fixing some bugs
2002 (see below); the default behaviour is no more to display the
2003 sequences on the standard output. Several options have been
2004 introduced to control the sequence printing in a flexible
2005 way. The help page has been extended.
2007 o A new data set is included: a supertree of bats in NEXUS format.
2012 o In theta.s(), the default of the option `variance' has
2013 been changed to `FALSE' (as was indicated in the help page).
2015 o Several bugs were fixed in the code of all.equal.phylo().
2017 o Several bugs were fixed in write.dna(), particularly this
2018 function did not work with `format = "interleaved"'.
2020 o Various errors were corrected in the help pages.
2025 o The argument names of as.hclust.phylo() have been changed
2026 from "(phy)" to "(x, ...)" to conform to the definition of
2027 the corresponding generic function.
2029 o gamma.stat() has been renamed gammaStat() to avoid confusion
2030 since gamma() is a generic function.
2034 CHANGES IN APE VERSION 1.1-3
2039 o base.freq() previously did not return a value of 0 for
2040 bases absent in the data (e.g., a vector of length 3 was
2041 returned if one base was absent). This is now fixed (a
2042 vector of length 4 is always returned).
2044 o Several bugs were fixed in read.nexus(), including that this
2045 function did not work in this absence of a "TRANSLATE"
2046 command in the NEXUS file, and that the commands were
2051 CHANGES IN APE VERSION 1.1-2
2056 o The Tamura and Nei (1993) model of DNA distance is now implemented
2057 in dist.dna(): five models are now available in this function.
2059 o A new data set is included: a set of 15 sequences of the
2060 cytochrome b mitochondrial gene of the woodmouse (Apodemus
2066 o A bug in read.nexus() was fixed.
2068 o read.dna() previously did not work correctly in most cases.
2069 The function has been completely re-written and its help page
2070 has been considerably extended (see ?read.dna for details).
2071 Underscores (_) in taxon names are no more replaced with
2072 spaces (this behaviour was undocumented).
2074 o A bug was fixed in write.dna().
2078 CHANGES IN APE VERSION 1.1-1
2083 o A bug in read.tree() introduced in APE 1.1 was fixed.
2085 o A bug in compar.gee() resulted in an error when trying to fit
2086 a model with `family = "binomial"'. This is now fixed.
2090 CHANGES IN APE VERSION 1.1
2095 o The Klastorin (1982) method as suggested by Misawa and Tajima
2096 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
2097 on the basis of phylogenetic trees has been implemented (see
2098 the function klastorin()).
2100 o Functions have been added to convert APE's "phylo" objects in
2101 "hclust" cluster objects and vice versa (see the help page of
2102 as.phylo for details).
2104 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
2105 are introduced for the estimation of absolute evolutionary rates
2106 (ratogram) and dated clock-like trees (chronogram) from
2107 phylogenetic trees using the non-parametric rate smoothing approach
2108 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
2110 o A summary method is now provided printing a summary information on a
2111 phylogenetic tree with, for instance, `summary(tree)'.
2113 o The behaviour of read.tree() was changed so that all spaces and
2114 tabulations in tree files are now ignored. Consequently, spaces in tip
2115 labels are no more allowed. Another side effect is that read.nexus()
2116 now does not replace the underscores (_) in tip labels with spaces
2117 (this behaviour was undocumented).
2119 o The function plot.phylo() has a new option (`underscore') which
2120 specifies whether the underscores in tip labels should be written on
2121 the plot as such or replaced with spaces (the default).
2123 o The function birthdeath() now computes 95% confidence intervals of
2124 the estimated parameters using profile likelihood.
2126 o Three new data sets are included: a gene tree estimated from 36
2127 landplant rbcL sequences, a gene tree estimated from 32 opsin
2128 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
2133 o A bug was fixed in dist.gene() where nothing was returned.
2135 o A bug in plot.mst() was fixed.
2137 o A bug in vcv.phylo() resulted in false correlations when the
2138 option `cor = TRUE' was used (now fixed).
2142 CHANGES IN APE VERSION 1.0
2147 o Two new functions, read.dna() and write.dna(), read/write in a file
2148 DNA sequences in interleaved or in sequential format.
2150 o Two new functions, read.nexus() and write.nexus(), read/write trees
2153 o The new function bind.tree() allows to bind two trees together,
2154 possibly handling root edges to give internal branches.
2156 o The new function drop.tip() removes the tips in a phylogenetic tree,
2157 and trims (or not) the corresponding internal branches.
2159 o The new function is.ultrametric() tests if a tree is ultrametric.
2161 o The function plot.phylo() has more functionalities such as drawing the
2162 branches with different colours and/or different widths, showing the
2163 node labels, controling the position and font of the labels, rotating
2164 the labels, and controling the space around the plot.
2166 o The function read.tree() can now read trees with no branch length,
2167 such as "(a,b),c);". Consequently, the element `edge.length' in
2168 objects of class "phylo" is now optional.
2170 o The function write.tree() has a new default behaviour: if the default
2171 for the option `file' is used (i.e. file = ""), then a variable of
2172 mode character containing the tree in Newick format is returned which
2173 can thus be assigned (e.g., tree <- write.tree(phy)).
2175 o The function read.tree() has a new argument `text' which allows
2176 to read the tree in a variable of mode character.
2178 o A new data set is included: the phylogenetic relationships among
2179 the orders of birds from Sibley and Ahlquist (1990).
2183 CHANGES IN APE VERSION 0.2-1
2188 o Several bugs were fixed in the help pages.
2192 CHANGES IN APE VERSION 0.2
2197 o The function write.tree() writes phylogenetic trees (objects of class
2198 "phylo") in an ASCII file using the Newick parenthetic format.
2200 o The function birthdeath() fits a birth-death model to branching times
2201 by maximum likelihood, and estimates the corresponding speciation and
2204 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
2207 o The function is.binary.tree() tests whether a phylogeny is binary.
2209 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
2210 as well as some methods are introduced.
2212 o Several functions, including some generics and methods, for computing
2213 skyline plot estimates (classic and generalized) of effective
2214 population size through time are introduced and replace the function
2215 skyline.plot() in version 0.1.
2217 o Two data sets are now included: the phylogenetic relationships among
2218 the families of birds from Sibley and Ahlquist (1990), and an
2219 estimated clock-like phylogeny of HIV sequences sampled in the
2220 Democratic Republic of Congo.
2223 DEPRECATED & DEFUNCT
2225 o The function skyline.plot() in ape 0.1 has been deprecated and
2226 replaced by more elaborate functions (see above).
2231 o Two important bugs were fixed in plot.phylo(): phylogenies with
2232 multichotomies not at the root or not with only terminal branches,
2233 and phylogenies with a single node (i.e. only terminal branches)
2234 did not plot. These trees should be plotted correctly now.
2236 o Several bugs were fixed in diversi.time() in the computation of
2239 o Various errors were corrected in the help pages.
projects / ape.git / blob