1 CHANGES IN APE VERSION 2.6-3
6 o rTraitCont() and rTraitDisc() gains a '...' argument used with
7 user-defined models (suggestion by Gene Hunt).
12 o as.hclust.phylo() now returns an error with unrooted trees.
14 o as.hclust.phylo() failed with trees with node labels (thanks to
15 Jinlong Zhang for pointing this bug out).
17 o read.dna(, "fasta") failed if sequences were not all of the same
23 o In drop.fossil() the default tol = 0 has been raised to 1e-8.
27 CHANGES IN APE VERSION 2.6-2
32 o Two new functions, pic.ortho and varCompPhylip, implements the
33 orthonormal contrasts of Felsenstein (2008, Am Nat, 171:713). The
34 second function requires Phylip to be installed on the computer.
36 o bd.ext() has a new option conditional = TRUE to use probabilities
37 conditioned on no extinction for the taxonomic data.
42 o write.tree() failed to output correctly tree names.
44 o dist.nodes() returned duplicated column(s) with unrooted and/or
47 o mcmc.popsize() terminated unexpectedly if the progress bar was
50 o prop.part(x) made R frozen if 'x' is of class "multiPhylo".
52 o Compilation under Mandriva failed (thanks to Jos Käfer for the fix).
54 o drop.tip() shuffled tip labels with subtree = TRUE or trim.internal
57 o Objects returned by as.hclust.phylo() failed when analysed with
58 cutree() or rect.hclust().
60 o write.tree() did not output correctly node labels (thanks to Naim
61 Matasci and Jeremy Beaulieu for the fix).
63 o ace(type = "discrete") has been improved thanks to Naim Marasci and
68 CHANGES IN APE VERSION 2.6-1
73 o The new function speciesTree calculates the species tree from a set
74 of gene trees. Several methods are available including maximum tree
75 and shallowest divergence tree.
80 o A bug introduced in write.tree() with ape 2.6 has been fixed.
82 o as.list.DNAbin() did not work correctly with vectors.
84 o as.hclust.phylo() failed with trees with node labels (thanks to
85 Filipe Vieira for the fix).
89 CHANGES IN APE VERSION 2.6
94 o The new functions rlineage and rbdtree simulate phylogenies under
95 any user-defined time-dependent speciation-extinction model. They
96 use continuous time algorithms.
98 o The new function drop.fossil removes the extinct species from a
101 o The new function bd.time fits a user-defined time-dependent
102 birth-death model. It is a generalization of yule.time() taking
103 extinction into account.
105 o The new function MPR does most parsimonious reconstruction of
108 o The new function Ftab computes the contingency table of base
109 frequencies from a pair of sequences.
111 o There is now an 'as.list' method for the class "DNAbin".
113 o dist.dna() can compute the number of transitions or transversions
114 with the option model = "Ts" or model = "Tv", respectively.
116 o [node|tip|edge]labels() gain three options with default values to
117 control the aspect of thermometers: horiz = TRUE, width = NULL,
120 o compar.gee() has been improved with the new option 'corStruct' as an
121 alternative to 'phy' to specify the correlation structure, and
122 calculation of the QIC (Pan 2001, Biometrics). The display of the
123 results has also been improved.
125 o read.GenBank() has a new option 'gene.names' to return the name of
126 the gene (FALSE by default).
131 o extract.clade() sometimes shuffled the tip labels.
133 o plot.phylo(type = "unrooted") did not force asp = 1 (thanks to Klaus
136 o dist.dna(model = "logdet") used to divide distances by 4. The
137 documentation has been clarified on the formulae used.
142 o rTraitCont(model = "OU") has an option 'linear = TRUE' to possibly
143 change the parameterisation (see ?rTraitCont for details).
145 o pic() now returns a vector with the node labels of the tree (if
148 o write.tree() and read.tree() have been substantially improved thanks
149 to contributions by Klaus Schliep.
153 CHANGES IN APE VERSION 2.5-3
158 o The new function mixedFontLabel helps to make labels with bits of
159 text to be plotted in different fonts.
161 o There are now replacement operators for [, [[, and $ for the class
162 "multiPhylo" (i.e., TREES[11:20] <- rmtree(10, 100)). They possibly
163 check that the tip labels are the same in all trees.
165 o Objects of class "multiPhylo" can be built with c(): there are
166 methods for the classes "phylo" and "multiPhylo".
168 o The internal functions .compressTipLabel and .uncompressTipLabel are
174 o bind.tree(x, y, where, position = 0) did not work correctly if 'y'
175 was a single-edge tree and 'where' was a tip.
177 o rTraitCont() did not use the square-root of branch lengths when
178 simulating a Brownian motion model.
182 CHANGES IN APE VERSION 2.5-2
187 o There is now a print method for results from ace().
189 o There is a labels() method for objects of class "DNAbin".
191 o read.dna() has a new option 'as.matrix' to possibly force sequences
192 in a FASTA file to be stored in a matrix (see ?read.dna for details).
197 o as.phylo.hclust() used to multiply edge lengths by 2.
199 o A minor bug was fixed in rTraitDisc().
201 o ace() sometimes failed (parameter value was NaN and the optimisation
207 o evolve.phylo() and plot.ancestral() have been removed.
209 o chronogram(), ratogram(), and NPRS.criterion() have been removed.
214 o nj() has been improved and is now about 30% faster.
216 o The default option 'drop' of [.DNAbin has been changed to FALSE to
217 avoid dropping rownames when selecting a single sequence.
219 o print.DNAbin() has been changed to summary.DNAbin() which has been
224 CHANGES IN APE VERSION 2.5-1
229 o The new function stree generates trees with regular shapes.
231 o It is now possible to bind two trees with x + y (see ?bind.tree for
234 o drop.tip(), extract.clade(), root(), and bind.tree() now have an
235 'interactive' option to make the operation on a plotted tree.
237 o cophyloplot() gains two new arguments 'lwd' and 'lty' for the
238 association links; they are recycled like 'col' (which wasn't before).
243 o rTraitDisc() did not use its 'freq' argument correctly (it was
244 multiplied with the rate matrix column-wise instead of row-wise).
246 o [node|tip|edge]labels(thermo = ) used to draw empty thermometers
247 with NA values. Nothing is drawn now like with 'text' or 'pch'.
248 The same bug occurred with the 'pie' option.
250 o A bug was fixed in compar.ou() and the help page was clarified.
252 o bind.tree() has been rewritten fixing several bugs and making it
255 o plot.phylo(type = "p") sometimes failed to colour correctly the
256 vertical lines representing the nodes.
258 o plot.phylo(direction = "l", x.lim = 30) failed to plot the branches
259 in the correct direction though the tip labels were displayed
265 o The c, cbind, and rbind methods for "DNAbin" objetcs now check that
266 the sequences are correctly stored (in a list for c, in a matrix
267 for the two other functions).
271 CHANGES IN APE VERSION 2.5
276 o The new function parafit by Pierre Legendre tests for the
277 coevolution between hosts and parasites. It has a companion
278 function, pcoa, that does principal coordinate decomposition.
279 The latter has a biplot method.
281 o The new function lmorigin by Pierre Legendre performs multiple
282 regression through the origin with testing by permutation.
284 o The new functions rTraitCont and rTraitDisc simulate continuous and
285 discrete traits under a wide range of evolutionary models.
287 o The new function delta.plot does a delta plot following Holland et
288 al. (2002, Mol. Biol. Evol. 12:2051).
290 o The new function edges draws additional branches between any nodes
291 and/or tips on a plotted tree.
293 o The new function fancyarrows enhances arrows from graphics with
294 triangle and harpoon heads; it can be called from edges().
296 o add.scale.bar() has a new option 'ask' to draw interactively.
298 o The branch length score replaces the geodesic distance in dist.topo.
300 o Three new data sets are included: the gopher-lice data (gopher.D),
301 SO2 air pollution in 41 US cities (lmorigin.ex1, from Sokal &
302 Rohlf 1995), and some host-parasite specificity data
303 (lmorigin.ex2, from Legendre & Desdevises 2009).
308 o add.scale.bar() drew the bar outside the plotting region with the
309 default options with unrooted or radial trees.
311 o dist.topo() made R stuck when the trees had different sizes (thanks
312 to Otto Cordero for the fix).
317 o The geodesic distance has been replaced by the branch length score
322 CHANGES IN APE VERSION 2.4-1
327 o rtree() and rcoal() now accept a numeric vector for the 'br'
330 o vcv() is a new generic function with methods for the classes "phylo"
331 and "corPhyl" so that it is possible to calculate the var-cov matrix
332 for "transformation models". vcv.phylo() can still be used for trees
333 of class "phylo"; its argument 'cor' has been renamed 'corr'.
338 o bind.tree() failed when 'y' had no root edge.
340 o read.nexus() shuffled tip labels when the trees have no branch
341 lengths and there is a TRANSLATE block.
343 o read.nexus() does not try to translate node labels if there is a
344 translation table in the NEXUS file. See ?read.nexus for a
345 clarification on this behaviour.
347 o plot.multiPhylo() crashed R when plotting a list of trees with
348 compressed tip labels.
350 o write.nexus() did not translate the taxa names when asked for.
352 o plot.phylo(type = "fan") did not rotate the tip labels correctly
353 when the tree has branch lengths.
355 o ace(type = "continuous", method = "ML") now avoids sigma² being
356 negative (which resulted in an error).
358 o nj() crashed with NA/NaN in the distance matrix: an error in now
363 CHANGES IN APE VERSION 2.4
368 o base.freq() has a new option 'freq' to return the counts; the
369 default is still to return the proportions.
374 o seg.sites() did not handle ambiguous nucleotides correctly: they
377 o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
378 the tree: the argument is now ignored.
380 o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
386 o Trying to plot a tree with a single tip now returns NULL with a
387 warning (it returned an error previously).
389 o The way lines representing nodes are coloured in phylograms has
390 been modified (as well as their widths and types) following some
391 users' request; this is only for dichotomous nodes.
393 o The argument 'adj' in [node][tip][edge]labels() now works when
394 using 'pie' or 'thermo'.
396 o A more informative message error is now returned by dist.dna() when
397 'model' is badly specified (partial matching of this argument is
400 o Deprecated functions are now listed in a help page: see
401 help("ape-defunct") with the quotes.
406 o The functions heterozygosity, nuc.div, theta.h, theta.k and
407 theta.s have been moved from ape to pegas.
409 o The functions mlphylo, DNAmodel and sh.test have been removed.
413 CHANGES IN APE VERSION 2.3-3
418 o add.scale.bar() always drew a horizontal bar.
420 o zoom() shuffled tips with unrooted trees.
422 o write.nexus() failed to write correctly trees with a "TipLabel"
425 o rcoal() failed to compute branch lengths with very large n.
427 o A small bug was fixed in compar.cheverud() (thanks to Michael
430 o seg.sites() failed when passing a vector.
432 o drop.tip() sometimes shuffled tip labels.
434 o root() shuffled node labels with 'resolve.root = TRUE'.
438 CHANGES IN APE VERSION 2.3-2
443 o all.equal.phylo() did not compare unrooted trees correctly.
445 o dist.topo(... method = "PH85") did not treat unrooted trees
446 correctly (thanks to Tim Wallstrom for the fix).
448 o root() sometimes failed to test for the monophyly of the
451 o extract.clade() sometimes included too many edges.
453 o vcv.phylo() did not work correctly when the tree is in
456 o nj() did not handle correctly distance matrices with many 0's.
457 The code has also been significantly improved: 7, 70, 160 times
458 faster with n = 100, 500, 1000, respectively.
462 CHANGES IN APE VERSION 2.3-1
467 o The new function is.monophyletic tests the monophyly of a group.
469 o There is now a c() method for lists of class "DNAbin".
471 o yule.cov() now fits the null model, and its help page has been
472 corrected with respect to this change.
474 o drop.tip() has a new option 'rooted' to force (or not) a tree
475 to be treated as (un)rooted.
480 o dist.gene() failed on most occasions with the default
481 pairwise.deletion = FALSE.
483 o read.tree() failed to read correctly the tree name(s).
485 o boot.phylo() now treats correctly data frames.
487 o del.gaps() did not copy the rownames of a matrix.
489 o A small bug was fixed in CDAM.global().
491 o ace() failed with large data sets. Thanks to Rich FitzJohn for
492 the fix. With other improvements, this function is now about 6
495 o write.tree() failed with objects of class "multiPhylo".
497 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
502 o [.multiPhylo and [.DNAbin now respect the original class.
504 o Instances of the form class(phy) == "phylo" have been replaced
505 by inherits(phy, "phylo").
507 o rcoal() is now faster.
512 o klastorin() has been removed.
516 CHANGES IN APE VERSION 2.3
521 o The new functions CADM.global and CADM.post, contributed by
522 Pierre Legendre, test the congruence among several distance
525 o The new function yule.time fits a user-defined time-dependent
526 Yule model by maximum likelihood.
528 o The new function makeNodeLabel creates and/or modifies node
529 labels in a flexible way.
531 o read.tree() and write.tree() have been modified so that they can
532 handle individual tree names.
534 o plot.phylo() has a new argument 'edge.lty' that specifies the
535 types of lines used for the edges (plain, dotted, dashed, ...)
537 o phymltest() has been updated to work with PhyML 3.0.1.
542 o drop.tip() shuffled tip labels in some cases.
544 o drop.tip() did not handle node.label correctly.
546 o is.ultrametric() now checks the ordering of the edge matrix.
548 o ace() sometimes returned negative values of likelihoods of
549 ancestral states (thanks to Dan Rabosky for solving this long
555 o The data set xenarthra has been removed.
559 CHANGES IN APE VERSION 2.2-4
563 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
564 now fixed. (Thanks to Peter Wragg for the fix!)
566 o A warning message occurred for no reason with ace(method="GLS").
571 o There is now a general help page displayed with '?ape'.
575 CHANGES IN APE VERSION 2.2-3
580 o The new function extract.clade extracts a clade from a tree by
581 specifying a node number or label.
583 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
584 operations of the same names.
586 o dist.dna() can now return the number of site differences by
587 specifying model="N".
592 o chronopl() did not work with CV = TRUE.
594 o read.nexus() did not work correctly in some situations (trees on
595 multiple lines with different numbers of lines and/or with
596 comments inserted within the trees).
598 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
599 the number of lineages with non-binary trees.
604 o ape has now a namespace.
606 o drop.tip() has been improved: it should be much faster and work
607 better in some cases (e.g., see the example in ?zoom).
611 CHANGES IN APE VERSION 2.2-2
616 o dist.gene() has been substantially improved and gains an option
619 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
625 o prop.part() failed with a single tree with the default option
626 'check.labels = TRUE'.
628 o summary.DNAbin() failed to display correctly the summary of
629 sequence lengths with lists of sequences of 10,000 bases or more
630 (because summary.default uses 4 significant digits by default).
632 o read.nexus() failed to read a file with a single tree with line
633 breaks in the Newick string.
635 o del.gaps() returned a list of empty sequences when there were no
641 o phymltest() has been updated for PhyML 3.0 and gains an option
642 'append', whereas the option 'path2exec' has been removed.
644 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
645 which is returned unchanged (instead of an error).
647 o The data sets bird.orders and bird.families are now stored as
648 Newick strings; i.e., the command data(bird.orders) calls
653 CHANGES IN APE VERSION 2.2-1
658 o The new function makeLabel() helps to modify labels of trees,
659 lists of trees, or DNA sequences, with several utilities to
660 truncate and/or make them unique, substituting some
661 characters, and so on.
663 o The new function del.gaps() removes insertion gaps ("-") in a
664 set of DNA sequences.
666 o read.dna() can now read Clustal files (*.aln).
671 o root() failed with 'resolve.root = TRUE' when the root was
672 already the specified root.
674 o Several bugs were fixed in mlphylo().
676 o collapsed.singles() did not propagate the 'Nnode' and
677 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
679 o read.nexus() failed to remove correctly the comments within
682 o read.nexus() failed to read a file with a single tree and no
683 translation of tip labels.
685 o read.nexus() failed to place correctly tip labels when reading
686 a single tree with no edge lengths.
688 o A bug was fixed in sh.test().
693 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
696 o The option 'check.labels' of consensus() and prop.part() is now
699 o write.dna() now does not truncate names to 10 characters with
704 CHANGES IN APE VERSION 2.2
709 o Four new functions have been written by Damien de Vienne for the
710 graphical exploration of large trees (cophyloplot, subtrees,
711 subtreeplot), and to return the graphical coordinates of tree
714 o The new functions corPagel and corBlomberg implement the Pagel's
715 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
717 o chronopl() has been improved and gains several options: see its
718 help page for details.
720 o boot.phylo() has now an option 'trees' to possibly return the
721 bootstraped trees (the default is FALSE).
723 o prop.part() has been improved and should now be faster in all
729 o read.dna() failed if "?" occurred in the first 10 sites of the
732 o The x/y aspect of the plot is now respected when plotting a
733 circular tree (type = "r" or "f").
735 o Drawing the tip labels sometimes failed when plotting circular
738 o zoom() failed when tip labels were used instead of their numbers
739 (thanks to Yan Wong for the fix).
741 o drop.tip() failed with some trees (fixed by Yan Wong).
743 o seg.sites() failed with a list.
745 o consensus() failed in some cases. The function has been improved
746 as well and is faster.
750 CHANGES IN APE VERSION 2.1-3
755 o A bug in read.nexus() made the Windows R-GUI crash.
757 o An error was fixed in the computation of ancestral character
758 states by generalized least squares in ace().
760 o di2multi() did not modify node labels correctly.
762 o multi2di() failed if the tree had its attribute "order" set to
767 CHANGES IN APE VERSION 2.1-2
772 o There three new methods for the "multiPhylo" class: str, $,
775 o root() gains the options 'node' and 'resolve.root'
776 (FALSE by default) as well as its code being improved.
778 o mltt.plot() has now an option 'log' used in the same way
779 than in plot.default().
784 o mltt.plot() failed to display the legend with an unnamed
787 o nodelabels() with pies now correcly uses the argument
788 'cex' to draw symbols of different sizes (which has
789 worked already for thermometers).
791 o read.nexus() generally failed to read very big files.
796 o The argument 'family' of compar.gee() can now be a function
797 as well as a character string.
799 o read.tree() and read.nexus() now return an unnamed list if
802 o read.nexus() now returns a modified object of class "multiPhylo"
803 when there is a TRANSLATE block in the NEXUS file: the individual
804 trees have no 'tip.label' vector, but the list has a 'TipLabel'
805 attribute. The new methods '$' and '[[' set these elements
806 correctly when extracting trees.
810 CHANGES IN APE VERSION 2.1-1
815 o The new function rmtree generates lists of random trees.
817 o rcoal() now generates a genuine coalescent tree by default
818 (thanks to Vladimir Minin for the code).
823 o nuc.div() returned an incorrect value with the default
824 pairwise.deletion = FALSE.
829 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
830 have been improved so that they are stabler and faster.
832 o R packages used by ape are now loaded silently; lattice and gee
833 are loaded only when needed.
837 CHANGES IN APE VERSION 2.1
842 o The new function identify.phylo identifies clades on a plotted
843 tree using the mouse.
845 o It is now possible to subset a list of trees (object of class
846 "multiPhylo") with "[" while keeping its class correct.
848 o The new function as.DNAbin.alignment converts DNA sequences
849 stored in the "alignment" format of the package seqinr into
850 an object of class "DNAbin".
852 o The new function weight.taxo2 helps to build similarity matrices
853 given two taxonomic levels (usually called by other functions).
855 o write.tree() can now take a list of trees (class "multiPhylo")
856 as its main argument.
858 o plot.correlogram() and plot.correlogramList() have been
859 improved, and gain several options (see the help page for
860 details). A legend is now plotted by default.
865 o dist.dna() returned some incorrect values with `model = "JC69"'
866 and `pairwise.deletion = TRUE'. This affected only the
867 distances involving sequences with missing values. (Thanks
868 to Bruno Toupance for digging this bug out.)
870 o write.tree() failed with some trees: this is fixed by removing
871 the `multi.line' option (trees are now always printed on a
874 o read.nexus() did not correctly detect trees with multiple root
875 edges (see OTHER CHANGES).
880 o The code of mlphylo() has been almost entirely rewritten, and
881 should be much stabler. The options have been also greatly
882 simplified (see ?mlphylo and ?DNAmodel for details).
884 o The internal function nTips has been renamed klastorin_nTips.
886 o The code of is.ultrametric() contained redundancies and has
889 o The code of Moran.I() and of correlogram.formula() have been
892 o read.tree() and read.nexus() now return an error when trying to
893 read a tree with multiple root edges (see BUG FIXES). The
894 correction applied in previous version did not work in all
897 o The class c("multi.tree", "phylo") has been renamed
903 o There is now a vignette in ape: see vignette("MoranI", "ape").
908 o as.matching() and as.phylo.matching() do not support branch
911 o correlogram.phylo() and discrete.dist() have been removed.
915 CHANGES IN APE VERSION 2.0-2
920 o The new function matexpo computes the exponential of a square
923 o The new function unique.multi.tree removes duplicate trees from
926 o yule() has a new option `use.root.edge = FALSE' that specifies
927 to ignore, by default, the root edge of the tree if it exists.
932 o which.edge() failed when the index of a single terminal edge was
935 o In diversi.time(), the values returned for model C were
938 o A bug was fixed in yule() that affected the calculation of the
939 likelihood in the presence of ties in the branching times.
941 o There was a bug in the C function mat_expo4x4 affecting the
942 calculations of the transition probabilities for models HKY and
945 o A small bug was fixed in as.matrix.DNAbin (thanks to James
948 o rtree() did not `shuffle' the tip labels by default, so only a
949 limited number of labelled topologies could be generated.
953 CHANGES IN APE VERSION 2.0-1
958 o The three new functions bionj, fastme.ols, and fastme.bal
959 perform phylogeny estimation by the BIONJ and fastME methods in
960 OLS and balanced versions. This is a port to R of previous
961 previous programs done by Vincent Lefort.
963 o The new function chronoMPL performs molecular dating with the
964 mean path lengths method of Britton et al. (2002, Mol. Phyl.
967 o The new function rotate, contributed by Christoph Heibl, swaps
968 two clades connected to the same node. It works also with
969 multichotomous nodes.
971 o The new `method' as.matrix.DNAbin() may be used to convert
972 easily DNA sequences stored in a list into a matrix while
973 keeping the names and the class.
978 o chronopl() failed when some branch lengths were equal to zero:
979 an error message is now returned.
981 o di2multi() failed when there was a series of consecutive edges
986 CHANGES IN APE VERSION 1.10-2
991 o plot.phylo() can now plot circular trees: the option is type =
992 "fan" or type = "f" (to avoid the ambiguity with type = "c").
994 o prop.part() has a new option `check.labels = FALSE' which allows
995 to considerably speed-up the calculations of bipartitions. As a
996 consequence, calculations of bootstrap values with boot.phylo()
997 should be much faster.
1002 o read.GenBank() did not return correctly the list of species as
1003 from ape 1.10: this is fixed in this version
1005 o Applying as.phylo() on a tree of class "phylo" failed: the
1006 object is now returned unchanged.
1010 CHANGES IN APE VERSION 1.10-1
1015 o The three new functions Ntip, Nnode, and Nedge return, for a
1016 given tree, the number of tips, nodes, or edges, respectively.
1021 o read.nexus() did not set correctly the class of the returned
1022 object when reading multiple trees.
1024 o mllt.plot() failed with objects of class c("multi.tree",
1027 o unroot() did not work correctly in most cases.
1029 o reorder.phylo() made R freeze in some occasions.
1031 o Plotting a tree in pruningwise order failed.
1033 o When plotting an unrooted tree, the tip labels where not all
1034 correctly positioned if the option `cex' was used.
1038 CHANGES IN APE VERSION 1.10
1043 o Five new `method' functions have been introduced to manipulate
1044 DNA sequences in binary format (see below).
1046 o Three new functions have been introduced to convert between the
1047 new binary and the character formats.
1049 o The new function as.alignment converts DNA sequences stored as
1050 single characters into the class "alignment" used by the package
1053 o read.dna() and read.GenBank() have a new argument `as.character'
1054 controlling whether the sequences are returned in binary format
1060 o root() failed when the tree had node labels: this is fixed.
1062 o plot.phylo() did not correctly set the limits on the y-axis with
1063 the default setting: this is fixed.
1065 o dist.dna() returned a wrong result for the LogDet, paralinear,
1066 and BH87 models with `pairwise.deletion = TRUE'.
1071 o DNA sequences are now internally stored in a binary format. See
1072 the document "A Bit-Level Coding Scheme for Nucleotides" for the
1073 details. Most functions analyzing DNA functions have been
1074 modified accordingly and are now much faster (dist.dna is now
1075 ca. 60 times faster).
1079 CHANGES IN APE VERSION 1.9-4
1084 o A bug was fixed in edgelabels().
1086 o as.phylo.hclust() did not work correctly when the object of
1087 class "hclust" has its labels set to NULL: the returned tree has
1088 now its tip labels set to "1", "2", ...
1090 o consensus could fail if some tip labels are a subset of others
1091 (e.g., "a" and "a_1"): this is now fixed.
1093 o mlphylo() failed in most cases if some branch lengths of the
1094 initial tree were greater than one: an error message is now
1097 o mlphylo() failed in most cases when estimating the proportion of
1098 invariants: this is fixed.
1102 CHANGES IN APE VERSION 1.9-3
1107 o The new function edgelabels adds labels on the edge of the tree
1108 in the same way than nodelabels or tiplabels.
1113 o multi2di() did not handle correctly branch lengths with the
1114 default option `random = TRUE': this is now fixed.
1116 o A bug was fixed in nuc.div() when using pairwise deletions.
1118 o A bug occurred in the analysis of bipartitions with large
1119 numbers of large trees, with consequences on prop.part,
1120 prop.clades, and boot.phylo.
1122 o The calculation of the Billera-Holmes-Vogtmann distance in
1123 dist.topo was wrong: this has been fixed.
1127 CHANGES IN APE VERSION 1.9-2
1132 o The new function ladderize reorganizes the internal structure of
1133 a tree to plot them left- or right-ladderized.
1135 o The new function dist.nodes computes the patristic distances
1136 between all nodes, internal and terminal, of a tree. It replaces
1137 the option `full = TRUE' of cophenetic.phylo (see below).
1142 o A bug was fixed in old2new.phylo().
1144 o Some bugs were fixed in chronopl().
1146 o The edge colours were not correctly displayed by plot.phylo
1147 (thank you to Li-San Wang for the fix).
1149 o cophenetic.phylo() failed with multichotomous trees: this is
1155 o read.dna() now returns the sequences in a matrix if they are
1156 aligned (interleaved or sequential format). Sequences in FASTA
1157 format are still returned in a list.
1159 o The option `full' of cophenetic.phylo() has been removed because
1160 it could not be used from the generic.
1163 DEPRECATED & DEFUNCT
1165 o rotate() has been removed; this function did not work correctly
1170 CHANGES IN APE VERSION 1.9-1
1175 o Trees with a single tip were not read correctly in R as the
1176 element `Nnode' was not set: this is fixed.
1178 o unroot() did not set correctly the number of nodes of the
1179 unrooted tree in most cases.
1181 o read.GenBank() failed when fetching very long sequences,
1182 particularly of the BX-series.
1184 o A bug was introduced in read.tree() with ape 1.9: it has been
1189 CHANGES IN APE VERSION 1.9
1194 o There are two new print `methods' for trees of class "phylo" and
1195 lists of trees of class "multi.tree", so that they are now
1196 displayed in a compact and informative way.
1198 o There are two new functions, old2new.phylo and new2old.phylo,
1199 for converting between the old and new coding of the class
1202 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
1203 LogDet ("logdet"), and paralinear ("paralin").
1205 o compute.brlen() has been extended: several methods are now
1206 available to compute branch lengths.
1208 o write.dna() can now handle matrices as well as lists.
1213 o cophenetic.phylo() sometimes returned a wrong result with
1214 multichotomous trees: this is fixed.
1216 o rotate() failed when a single tip was specified: the tree is now
1219 o ace() did not return the correct index matrix with custom
1220 models: this is fixed.
1222 o multi2di() did not work correctly when resolving multichotomies
1223 randomly: the topology was always the same, only the arrangement
1224 of clades was randomized: this is fixed. This function now
1225 accepts trees with no branch lengths.
1227 o The output of diversi.gof() was blurred by useless prints when a
1228 user distribution was specified. This has been corrected, and
1229 the help page of this function has been expanded.
1234 o The internal structure of the class "phylo" has been changed:
1235 see the document "Definition of Formats for Coding Phylogenetic
1236 Trees in R" for the details. In addition, the code of most
1237 functions has been improved.
1239 o Several functions have been improved by replacing some R codes
1240 by C codes: pic, plot.phylo, and reorder.phylo.
1242 o There is now a citation information: see citation("ape") in R.
1244 o write.tree() now does not add extra 0's to branch lengths so
1245 that 1.23 is printed "1.23" by default, not "1.2300000000".
1247 o The syntax of bind.tree() has been simplified. This function now
1248 accepts trees with no branch lengths, and handles correctly node
1251 o The option `as.numeric' of mrca() has been removed.
1253 o The unused options `format' and `rooted' of read.tree() have
1256 o The unused option `format' of write.tree() has been removed.
1258 o The use of node.depth() has been simplified.
1262 CHANGES IN APE VERSION 1.8-5
1267 o Two new functions read.nexus.data() and write.nexus.data(),
1268 contributed by Johan Nylander, allow to read and write molecular
1269 sequences in NEXUS files.
1271 o The new function reorder.phylo() reorders the internal structure
1272 of a tree of class "phylo". It is used as the generic, e.g.,
1275 o read.tree() and read.nexus() can now read trees with a single
1278 o The new data set `cynipids' supplies a set of protein sequences
1284 o The code of all.equal.phylo() has been completely rewritten
1285 (thanks to Benoît Durand) which fixes several bugs.
1287 o read.tree() and read.nexus() now checks the labels of the tree
1288 to remove or substitute any characters that are illegal in the
1289 Newick format (parentheses, etc.)
1291 o A negative P-value could be returned by mantel.test(): this is
1296 CHANGES IN APE VERSION 1.8-4
1301 o The new function sh.test() computes the Shimodaira-
1304 o The new function collapse.singles() removes the nodes with a
1305 single descendant from a tree.
1307 o plot.phylo() has a new argument `tip.color' to specify the
1308 colours of the tips.
1310 o mlphylo() has now an option `quiet' to control the display of
1311 the progress of the analysis (the default is FALSE).
1316 o read.dna() did not read correctly sequences in sequential format
1317 with leading alignment gaps "-": this is fixed.
1319 o ace() returned a list with no class so that the generic
1320 functions (anova, logLik, ...) could not be used directly. This
1321 is fixed as ace() now returns an object of class "ace".
1323 o anova.ace() had a small bug when computing the number of degrees
1324 of freedom: this is fixed.
1326 o mlphylo() did not work when the sequences were in a matrix or
1327 a data frame: this is fixed.
1329 o rtree() did not work correctly when trying to simulate an
1330 unrooted tree with two tips: an error message is now issued.
1335 o The algorithm of rtree() has been changed: it is now about 40,
1336 100, and 130 times faster for 10, 100, and 1000 tips,
1341 CHANGES IN APE VERSION 1.8-3
1346 o There are four new `method' functions to be used with the
1347 results of ace(): logLik(), deviance(), AIC(), and anova().
1349 o The plot method of phymltest has two new arguments: `main' to
1350 change the title, and `col' to control the colour of the
1351 segments showing the AIC values.
1353 o ace() has a new argument `ip' that gives the initial values used
1354 in the ML estimation with discrete characters (see the examples
1355 in ?ace). This function now returns a matrix giving the indices
1356 of the estimated rates when analysing discrete characters.
1358 o nodelabels() and tiplabels() have a new argument `pie' to
1359 represent proportions, with any number of categories, as
1360 piecharts. The use of the option `thermo' has been improved:
1361 there is now no limitation on the number of categories.
1366 o mlphylo() did not work with more than two partitions: this is
1369 o root() failed if the proposed outgroup was already an outgroup
1370 in the tree: this is fixed.
1372 o The `col' argument in nodelabels() and tiplabels() was not
1373 correctly passed when `text' was used: this is fixed.
1375 o Two bugs were fixed in mlphylo(): parameters were not always
1376 correctly output, and the estimation failed in some cases.
1378 o plot.phylo() was stuck when given a tree with a single tip: this
1379 is fixed and a message error is now returned.
1381 o An error was corrected in the help page of gammaStat regarding
1382 the calculation of P-values.
1384 o Using gls() could crash R when the number of species in the tree
1385 and in the variables were different: this is fixed.
1389 CHANGES IN APE VERSION 1.8-2
1394 o The new function mlphylo() fits a phylogenetic tree by maximum
1395 likelihood from DNA sequences. Its companion function DNAmodel()
1396 is used to define the substitution model which may include
1397 partitioning. There are methods for logLik(), deviance(), and
1398 AIC(), and the summary() method has been extended to display in
1399 a friendly way the results of this model fitting. Currently, the
1400 functionality is limited to estimating the substitution and
1401 associated parameters and computing the likelihood.
1403 o The new function drop1.compar.gee (used as, e.g., drop1(m))
1404 tests for single effects in GEE-based comparative method. A
1405 warning message is printed if there is not enough degrees of
1411 o An error message was sometimes issued by plot.multi.tree(),
1412 though with no consequence.
1416 CHANGES IN APE VERSION 1.8-1
1421 o There is a new plot method for lists of trees (objects of class
1422 "multi.tree"): it calls plot.phylo() internally and is
1423 documented on the same help page.
1428 o A bug was fixed in the C code that analyzes bipartitions: this
1429 has impact on several functions like prop.part, prop.clades,
1430 boot.phylo, or consensus.
1432 o root() did not work correctly when the specified outgroup had
1433 more than one element: this is fixed.
1435 o dist.dna() sometimes returned a warning inappropriately: this
1438 o If the distance object given to nj() had no rownames, nj()
1439 returned a tree with no tip labels: it now returns tips labelled
1440 "1", "2", ..., corresponding to the row numbers.
1445 o nj() has been slightly changed so that tips with a zero distance
1446 are first aggregated with zero-lengthed branches; the usual NJ
1447 procedure is then performed on a distance matrix without 0's.
1451 CHANGES IN APE VERSION 1.8
1456 o The new function chronopl() estimates dates using the penalized
1457 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1459 o The new function consensus() calculates the consensus tree of a
1462 o The new function evolve.phylo() simulates the evolution of
1463 continuous characters along a phylogeny under a Brownian model.
1465 o The new plot method for objects of class "ancestral" displays a
1466 tree together with ancestral values, as returned by the above
1469 o The new function as.phylo.formula() returns a phylogeny from a
1470 set of nested taxonomic variables given as a formula.
1472 o The new function read.caic() reads trees in CAIC format.
1474 o The new function tiplabels() allows to add labels to the tips
1475 of a tree using text or plotting symbols in a flexible way.
1477 o The new function unroot() unroots a phylogeny.
1479 o multi2di() has a new option, `random', which specifies whether
1480 to resolve the multichotomies randomly (the default) or not.
1482 o prop.part() now returns an object of class "prop.part" for which
1483 there are print (to display a partition in a more friendly way)
1484 and summary (to extract the numbers) methods.
1486 o plot.phylo() has a new option, `show.tip.label', specifying
1487 whether to print the labels of the tips. The default is TRUE.
1489 o The code of nj() has been replaced by a faster C code: it is now
1490 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1493 o write.nexus() now writes whether a tree is rooted or not.
1498 o Two bugs have been fixed in root(): unrooted trees are now
1499 handled corretly, and node labels are now output normally.
1501 o A bug was fixed in phymltest(): the executable couldn't be found
1504 o Three bug have been fixed in ace(): computing the likelihood of
1505 ancestral states of discrete characters failed, custom models
1506 did not work, and the function failed with a null gradient (a
1507 warning message is now returned; this latter bug was also
1508 present in yule.cov() as well and is now fixed).
1510 o pic() hanged out when missing data were present: a message error
1513 o A small bug was fixed in dist.dna() where the gamma correction
1514 was not always correctly dispatched.
1516 o plot.phylo() plotted correctly the root edge only when the tree
1517 was plotted rightwards: this works now for all directions.
1522 o dist.taxo() has been renamed as weight.taxo().
1524 o dist.phylo() has been replaced by the method cophenetic.phylo().
1526 o Various error and warning messages have been improved.
1530 CHANGES IN APE VERSION 1.7
1533 o The new function ace() estimates ancestral character states for
1534 continuous characters (with ML, GLS, and contrasts methods), and
1535 discrete characters (with ML only) for any number of states.
1537 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1538 of directional evolution for continuous characters. The user
1539 specifies the node(s) of the tree where the character optimum
1542 o The new function is.rooted() tests whether a tree (of class
1545 o The new function rcoal() generates random ultrametric trees with
1546 the possibility to specify the function that generates the
1547 inter-nodes distances.
1549 o The new function mrca() gives for all pairs of tips in a tree
1550 (and optionally nodes too) the most recent common ancestor.
1552 o nodelabels() has a new option `thermo' to plot proportions (up
1553 to three classes) on the nodes of a tree.
1555 o rtree() has been improved: it can now generate rooted or
1556 unrooted trees, and the mathematical function that generates the
1557 branch lengths may be specified by the user. The tip labels may
1558 be given directly in the call to rtree. The limit cases (n = 2,
1559 3) are now handled correctly.
1561 o dist.topo() has a new argument `method' with two choices: "PH85"
1562 for Penny and Henny's method (already available before and now
1563 the default), and "BHV01" for the geometric distance by Billera
1564 et al. (2001, Adv. Appl. Math. 27:733).
1566 o write.tree() has a new option, `digits', which specifies the
1567 number of digits to be printed in the Newick tree. By default
1568 digits = 10. The numbers are now always printed in decimal form
1569 (i.e., 1.0e-1 is now avoided).
1571 o dist.dna() can now compute the raw distances between pairs of
1572 DNA sequences by specifying model = "raw".
1574 o dist.phylo() has a new option `full' to possibly compute the
1575 distances among all tips and nodes of the tree. The default if
1581 o Several bugs were fixed in all.equal.phylo().
1583 o dist.dna() did not handle correctly gaps ("-") in alignments:
1584 they are now considered as missing data.
1586 o rotate() did not work if the tips were not ordered: this is
1589 o mantel.test() returned NA in some special cases: this is fixed
1590 and the function has been improved and is now faster.
1592 o A bug was fixed in diversi.gof() where the calculation of A² was
1595 o cherry() did not work correctly under some OSs (mainly Linux):
1598 o is.binary.tree() has been modified so that it works with both
1599 rooted and unrooted trees.
1601 o The documentation of theta.s() was not correct: this has been
1604 o plot.mst() did not work correctly: this is fixed.
1608 CHANGES IN APE VERSION 1.6
1613 o The new function dist.topo() computes the topological distances
1616 o The new function boot.phylo() performs a bootstrap analysis on
1617 phylogeny estimation.
1619 o The new functions prop.part() and prop.clades() analyse
1620 bipartitions from a series of trees.
1625 o read.GenBank() now uses the EFetch utility of NCBI instead of
1626 the usual Web interface: it is now much faster (e.g., 12 times
1627 faster to retrieve 8 sequences, 37 times for 60 sequences).
1632 o Several bugs were fixed in read.dna().
1634 o Several bugs were fixed in diversi.time().
1636 o is.binary.tree() did not work correctly if the tree has no edge
1637 lengths: this is fixed.
1639 o drop.tip() did not correctly propagated the `node.label' of a
1640 tree: this is fixed.
1644 CHANGES IN APE VERSION 1.5
1649 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1650 convert objects between the classes "phylo" and "matching". The
1651 latter implements the representation of binary trees introduced by
1652 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1653 as.matching() has been introduced as well.
1655 o Two new functions, multi2di() and di2multi(), allow to resolve
1656 and collapse multichotomies with branches of length zero.
1658 o The new function nuc.div() computes the nucleotide diversity
1659 from a sample a DNA sequences.
1661 o dist.dna() has been completely rewritten with a much faster
1662 (particularly for large data sets) C code. Eight models are
1663 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1664 option `method' has been renamed `model'). Computation of variance
1665 is available for all models. A gamma-correction is possible for
1666 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1667 to remove sites with missing data on a pairwise basis. The option
1668 `GCcontent' has been removed.
1670 o read.GenBank() has a new option (species.names) which specifies
1671 whether to return the species names of the organisms in addition
1672 to the accession numbers of the sequences (this is the default
1675 o write.nexus() can now write several trees in the same NEXUS file.
1677 o drop.tip() has a new option `root.edge' that allows to specify the
1678 new root edge if internal branches are trimmed.
1683 o as.phylo.hclust() failed if some labels had parentheses: this
1686 o Several bugs were fixed in all.equal.phylo(). This function now
1687 returns the logical TRUE if the trees are identical but with
1688 different representations (a report was printed previously).
1690 o read.GenBank() did not correctly handle ambiguous base codes:
1696 o birthdeath() now returns an object of class "birthdeath" for
1697 which there is a print method.
1701 CHANGES IN APE VERSION 1.4
1706 o The new function nj() performs phylogeny estimation with the
1707 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1710 o The new function which.edge() identifies the edges of a tree
1711 that belong to a group specified as a set of tips.
1713 o The new function as.phylo.phylog() converts an object of class
1714 "phylog" (from the package ade4) into an object of class
1717 o The new function axisPhylo() draws axes on the side of a
1720 o The new function howmanytrees() calculates the number of trees
1721 in different cases and giving a number of tips.
1723 o write.tree() has a new option `multi.line' (TRUE by default) to
1724 write a Newick tree on several lines rather than on a single
1727 o The functionalities of zoom() have been extended. Several
1728 subtrees can be visualized at the same time, and they are marked
1729 on the main tree with colors. The context of the subtrees can be
1730 marked with the option `subtree' (see below).
1732 o drop.tip() has a new option `subtree' (FALSE by default) which
1733 specifies whether to output in the tree how many tips have been
1736 o The arguments of add.scale.bar() have been redefined and have
1737 now default values (see ?add.scale.bar for details). This
1738 function now works even if the plotted tree has no edge length.
1740 o plot.phylo() can now plot radial trees, but this does not take
1741 edge lengths into account.
1743 o In plot.phylo() with `type = "phylogram"', if the values of
1744 `edge.color' and `edge.width' are identical for sister-branches,
1745 they are propagated to the vertical line that link them.
1750 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1751 crashing. This is fixed.
1753 o In plot.phylo(), the options `edge.color' and `edge.width' are
1754 now properly recycled; their default values are now "black" and
1757 o A bug has been fixed in write.nexus().
1762 o The function node.depth.edgelength() has been removed and
1763 replaced by a C code.
1767 CHANGES IN APE VERSION 1.3-1
1772 o The new function nodelabels() allows to add labels to the nodes
1773 of a tree using text or plotting symbols in a flexible way.
1775 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1776 numeric values specifying the lower and upper limits on the x-
1777 and y-axes. This allows to leave some space on any side of the
1778 tree. If a single value is given, this is taken as the upper
1783 CHANGES IN APE VERSION 1.3
1788 o The new function phymltest() calls the software PHYML and fits
1789 28 models of DNA sequence evolution. There are a print method to
1790 display likelihood and AIC values, a summary method to compute
1791 the hierarchical likelihood ratio tests, and a plot method to
1792 display graphically the AIC values of each model.
1794 o The new function yule.cov() fits the Yule model with covariates,
1795 a model where the speciation rate is affected by several species
1796 traits through a generalized linear model. The parameters are
1797 estimated by maximum likelihood.
1799 o Three new functions, corBrownian(), corGrafen(), and
1800 corMartins(), compute the expected correlation structures among
1801 species given a phylogeny under different models of evolution.
1802 These can be used for GLS comparative phylogenetic methods (see
1803 the examples). There are coef() and corMatrix() methods and an
1804 Initialize.corPhyl() function associated.
1806 o The new function compar.cheverud() implements Cheverud et al.'s
1807 (1985; Evolution 39:1335) phylogenetic comparative method.
1809 o The new function varcomp() estimates variance components; it has
1812 o Two new functions, panel.superpose.correlogram() and
1813 plot.correlogramList(), allow to plot several phylogenetic
1816 o The new function node.leafnumber() computes the number of leaves
1817 of a subtree defined by a particular node.
1819 o The new function node.sons() gets all tags of son nodes from a
1822 o The new function compute.brlen() computes the branch lengths of
1823 a tree according to a specified method.
1825 o plot.phylo() has three new options: "cex" controls the size of
1826 the (tip and node) labels (thus it is no more needed to change
1827 the global graphical parameter), "direction" which allows to
1828 plot the tree rightwards, leftwards, upwards, or downwards, and
1829 "y.lim" which sets the upper limit on the y-axis.
1834 o Some functions which try to match tip labels and names of
1835 additional data (e.g. vector) are likely to fail if there are
1836 typing or syntax errors. If both series of names do not perfectly
1837 match, they are ignored and a warning message is now issued.
1838 These functions are bd.ext, compar.gee, pic. Their help pages
1839 have been clarified on this point.
1843 CHANGES IN APE VERSION 1.2-7
1848 o The new function root() reroots a phylogenetic tree with respect
1849 to a specified outgroup.
1851 o The new function rotate() rotates an internal branch of a tree.
1853 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1854 trees) controls the display of the tip labels in unrooted trees.
1855 This display has been greatly improved: the tip labels are now not
1856 expected to overlap with the tree (particularly if lab4ut =
1857 "axial"). In all cases, combining appropriate values of "lab4ut"
1858 and the font size (via "par(cex = )") should result in readable
1859 unrooted trees. See ?plot.phylo for some examples.
1861 o In drop.tip(), the argument `tip' can now be numeric or character.
1866 o drop.tip() did not work correctly with trees with no branch
1867 lengths: this is fixed.
1869 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1870 plotted with some line crossings: this is now fixed.
1874 CHANGES IN APE VERSION 1.2-6
1879 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1880 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1881 to implement comparative methods with an autocorrelation approach.
1883 o A new data set describing some life history traits of Carnivores
1889 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1894 o When plotting a tree with plot.phylo(), the new default of the
1895 option `label.offset' is now 0, so the labels are always visible.
1899 CHANGES IN APE VERSION 1.2-5
1904 o The new function bd.ext() fits a birth-death model with combined
1905 phylogenetic and taxonomic data, and estimates the corresponding
1906 speciation and extinction rates.
1911 o The package gee is no more required by ape but only suggested
1912 since only the function compar.gee() calls gee.
1916 CHANGES IN APE VERSION 1.2-4
1921 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1922 and lines.popsize) implementing a new approach for inferring the
1923 demographic history from genealogies using a reversible jump
1924 MCMC have been introduced.
1926 o The unit of time in the skyline plot and in the new plots can
1927 now be chosen to be actual years, rather than substitutions.
1931 CHANGES IN APE VERSION 1.2-3
1936 o The new function rtree() generates a random binary tree with or
1937 without branch lengths.
1939 o Two new functions for drawing lineages-through-time (LTT) plots
1940 are provided: ltt.lines() adds a LTT curve to an existing plot,
1941 and mltt.plot() does a multiple LTT plot giving several trees as
1942 arguments (see `?ltt.plot' for details).
1947 o Some taxon names made R crashing when calling as.phylo.hclust():
1950 o dist.dna() returned an error with two identical DNA sequences
1951 (only using the Jukes-Cantor method returned 0): this is fixed.
1956 o The function dist.phylo() has been re-written using a different
1957 algorithm: it is now about four times faster.
1959 o The code of branching.times() has been improved: it is now about
1964 CHANGES IN APE VERSION 1.2-2
1969 o The new function seg.sites() finds the segregating sites in a
1970 sample of DNA sequences.
1975 o A bug introduced in read.tree() and in read.nexus() with version
1978 o A few errors were corrected and a few examples were added in the
1983 CHANGES IN APE VERSION 1.2-1
1988 o plot.phylo() can now draw the edge of the root of a tree if it
1989 has one (see the new option `root.edge', its default is FALSE).
1994 o A bug was fixed in read.nexus(): files with semicolons inside
1995 comment blocks were not read correctly.
1997 o The behaviour of read.tree() and read.nexus() was corrected so
1998 that tree files with badly represented root edges (e.g., with
1999 an extra pair of parentheses, see the help pages for details)
2000 are now correctly represented in the object of class "phylo";
2001 a warning message is now issued.
2005 CHANGES IN APE VERSION 1.2
2010 o plot.phylo() has been completely re-written and offers several
2011 new functionalities. Three types of trees can now be drawn:
2012 phylogram (as previously), cladogram, and unrooted tree; in
2013 all three types the branch lengths can be drawn using the edge
2014 lengths of the phylogeny or not (e.g., if the latter is absent).
2015 The vertical position of the nodes can be adjusted with two
2016 choices (see option `node.pos'). The code has been re-structured,
2017 and two new functions (potentially useful for developpers) are
2018 documented separately: node.depth.edgelength() and node.depth();
2019 see the respective help pages for details.
2021 o The new function zoom() allows to explore very large trees by
2022 focusing on a small portion of it.
2024 o The new function yule() fits by maximum likelihood the Yule model
2025 (birth-only process) to a phylogenetic tree.
2027 o Support for writing DNA sequences in FASTA format has been
2028 introduced in write.dna() (support for reading sequences in
2029 this format was introduced in read.dna() in version 1.1-2).
2030 The function has been completely re-written, fixing some bugs
2031 (see below); the default behaviour is no more to display the
2032 sequences on the standard output. Several options have been
2033 introduced to control the sequence printing in a flexible
2034 way. The help page has been extended.
2036 o A new data set is included: a supertree of bats in NEXUS format.
2041 o In theta.s(), the default of the option `variance' has
2042 been changed to `FALSE' (as was indicated in the help page).
2044 o Several bugs were fixed in the code of all.equal.phylo().
2046 o Several bugs were fixed in write.dna(), particularly this
2047 function did not work with `format = "interleaved"'.
2049 o Various errors were corrected in the help pages.
2054 o The argument names of as.hclust.phylo() have been changed
2055 from "(phy)" to "(x, ...)" to conform to the definition of
2056 the corresponding generic function.
2058 o gamma.stat() has been renamed gammaStat() to avoid confusion
2059 since gamma() is a generic function.
2063 CHANGES IN APE VERSION 1.1-3
2068 o base.freq() previously did not return a value of 0 for
2069 bases absent in the data (e.g., a vector of length 3 was
2070 returned if one base was absent). This is now fixed (a
2071 vector of length 4 is always returned).
2073 o Several bugs were fixed in read.nexus(), including that this
2074 function did not work in this absence of a "TRANSLATE"
2075 command in the NEXUS file, and that the commands were
2080 CHANGES IN APE VERSION 1.1-2
2085 o The Tamura and Nei (1993) model of DNA distance is now implemented
2086 in dist.dna(): five models are now available in this function.
2088 o A new data set is included: a set of 15 sequences of the
2089 cytochrome b mitochondrial gene of the woodmouse (Apodemus
2095 o A bug in read.nexus() was fixed.
2097 o read.dna() previously did not work correctly in most cases.
2098 The function has been completely re-written and its help page
2099 has been considerably extended (see ?read.dna for details).
2100 Underscores (_) in taxon names are no more replaced with
2101 spaces (this behaviour was undocumented).
2103 o A bug was fixed in write.dna().
2107 CHANGES IN APE VERSION 1.1-1
2112 o A bug in read.tree() introduced in APE 1.1 was fixed.
2114 o A bug in compar.gee() resulted in an error when trying to fit
2115 a model with `family = "binomial"'. This is now fixed.
2119 CHANGES IN APE VERSION 1.1
2124 o The Klastorin (1982) method as suggested by Misawa and Tajima
2125 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
2126 on the basis of phylogenetic trees has been implemented (see
2127 the function klastorin()).
2129 o Functions have been added to convert APE's "phylo" objects in
2130 "hclust" cluster objects and vice versa (see the help page of
2131 as.phylo for details).
2133 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
2134 are introduced for the estimation of absolute evolutionary rates
2135 (ratogram) and dated clock-like trees (chronogram) from
2136 phylogenetic trees using the non-parametric rate smoothing approach
2137 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
2139 o A summary method is now provided printing a summary information on a
2140 phylogenetic tree with, for instance, `summary(tree)'.
2142 o The behaviour of read.tree() was changed so that all spaces and
2143 tabulations in tree files are now ignored. Consequently, spaces in tip
2144 labels are no more allowed. Another side effect is that read.nexus()
2145 now does not replace the underscores (_) in tip labels with spaces
2146 (this behaviour was undocumented).
2148 o The function plot.phylo() has a new option (`underscore') which
2149 specifies whether the underscores in tip labels should be written on
2150 the plot as such or replaced with spaces (the default).
2152 o The function birthdeath() now computes 95% confidence intervals of
2153 the estimated parameters using profile likelihood.
2155 o Three new data sets are included: a gene tree estimated from 36
2156 landplant rbcL sequences, a gene tree estimated from 32 opsin
2157 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
2162 o A bug was fixed in dist.gene() where nothing was returned.
2164 o A bug in plot.mst() was fixed.
2166 o A bug in vcv.phylo() resulted in false correlations when the
2167 option `cor = TRUE' was used (now fixed).
2171 CHANGES IN APE VERSION 1.0
2176 o Two new functions, read.dna() and write.dna(), read/write in a file
2177 DNA sequences in interleaved or in sequential format.
2179 o Two new functions, read.nexus() and write.nexus(), read/write trees
2182 o The new function bind.tree() allows to bind two trees together,
2183 possibly handling root edges to give internal branches.
2185 o The new function drop.tip() removes the tips in a phylogenetic tree,
2186 and trims (or not) the corresponding internal branches.
2188 o The new function is.ultrametric() tests if a tree is ultrametric.
2190 o The function plot.phylo() has more functionalities such as drawing the
2191 branches with different colours and/or different widths, showing the
2192 node labels, controling the position and font of the labels, rotating
2193 the labels, and controling the space around the plot.
2195 o The function read.tree() can now read trees with no branch length,
2196 such as "(a,b),c);". Consequently, the element `edge.length' in
2197 objects of class "phylo" is now optional.
2199 o The function write.tree() has a new default behaviour: if the default
2200 for the option `file' is used (i.e. file = ""), then a variable of
2201 mode character containing the tree in Newick format is returned which
2202 can thus be assigned (e.g., tree <- write.tree(phy)).
2204 o The function read.tree() has a new argument `text' which allows
2205 to read the tree in a variable of mode character.
2207 o A new data set is included: the phylogenetic relationships among
2208 the orders of birds from Sibley and Ahlquist (1990).
2212 CHANGES IN APE VERSION 0.2-1
2217 o Several bugs were fixed in the help pages.
2221 CHANGES IN APE VERSION 0.2
2226 o The function write.tree() writes phylogenetic trees (objects of class
2227 "phylo") in an ASCII file using the Newick parenthetic format.
2229 o The function birthdeath() fits a birth-death model to branching times
2230 by maximum likelihood, and estimates the corresponding speciation and
2233 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
2236 o The function is.binary.tree() tests whether a phylogeny is binary.
2238 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
2239 as well as some methods are introduced.
2241 o Several functions, including some generics and methods, for computing
2242 skyline plot estimates (classic and generalized) of effective
2243 population size through time are introduced and replace the function
2244 skyline.plot() in version 0.1.
2246 o Two data sets are now included: the phylogenetic relationships among
2247 the families of birds from Sibley and Ahlquist (1990), and an
2248 estimated clock-like phylogeny of HIV sequences sampled in the
2249 Democratic Republic of Congo.
2252 DEPRECATED & DEFUNCT
2254 o The function skyline.plot() in ape 0.1 has been deprecated and
2255 replaced by more elaborate functions (see above).
2260 o Two important bugs were fixed in plot.phylo(): phylogenies with
2261 multichotomies not at the root or not with only terminal branches,
2262 and phylogenies with a single node (i.e. only terminal branches)
2263 did not plot. These trees should be plotted correctly now.
2265 o Several bugs were fixed in diversi.time() in the computation of
2268 o Various errors were corrected in the help pages.
projects / ape.git / blob