1 CHANGES IN APE VERSION 2.6-4
6 o base.freq() gains an option 'all' to count all the possible bases
7 including the ambiguous ones (defaults to FALSE).
9 o read.nexus() now writes tree names in the NEXUS file if given a list
15 o prop.part() failed in some situations with unrooted trees.
17 o read.nexus() shuffled node labels when a TRANSLATE block was
23 o BaseProportion in src/dist_dna.c has been modified.
25 o A number of functions in src/tree_build.c have been modified.
27 o The matching representation has now only two columns as the third
28 column was repetitive.
32 CHANGES IN APE VERSION 2.6-3
37 o rTraitCont() and rTraitDisc() gains a '...' argument used with
38 user-defined models (suggestion by Gene Hunt).
43 o as.hclust.phylo() now returns an error with unrooted trees.
45 o as.hclust.phylo() failed with trees with node labels (thanks to
46 Jinlong Zhang for pointing this bug out).
48 o read.dna(, "fasta") failed if sequences were not all of the same
51 o plot.phylo() did not recycle values of 'font', 'cex' and
52 'tip.color' correctly when type = "fan" or "radial".
54 o plot.phylo() ignored 'label.offset' when type = "radial", "fan", or
55 "unrooted" with lab4ut = "axial" (the placement of tip labels still
56 needs to be improved with lab4ut = "horizontal").
61 o In drop.fossil() the default tol = 0 has been raised to 1e-8.
63 o The help command ?phylo now points to the man page of read.tree()
64 where this class is described. Similarly, ?matching points to the
65 man page of as.matching().
69 CHANGES IN APE VERSION 2.6-2
74 o Two new functions, pic.ortho and varCompPhylip, implements the
75 orthonormal contrasts of Felsenstein (2008, Am Nat, 171:713). The
76 second function requires Phylip to be installed on the computer.
78 o bd.ext() has a new option conditional = TRUE to use probabilities
79 conditioned on no extinction for the taxonomic data.
84 o write.tree() failed to output correctly tree names.
86 o dist.nodes() returned duplicated column(s) with unrooted and/or
89 o mcmc.popsize() terminated unexpectedly if the progress bar was
92 o prop.part(x) made R frozen if 'x' is of class "multiPhylo".
94 o Compilation under Mandriva failed (thanks to Jos Käfer for the fix).
96 o drop.tip() shuffled tip labels with subtree = TRUE or trim.internal
99 o Objects returned by as.hclust.phylo() failed when analysed with
100 cutree() or rect.hclust().
102 o write.tree() did not output correctly node labels (thanks to Naim
103 Matasci and Jeremy Beaulieu for the fix).
105 o ace(type = "discrete") has been improved thanks to Naim Marasci and
110 CHANGES IN APE VERSION 2.6-1
115 o The new function speciesTree calculates the species tree from a set
116 of gene trees. Several methods are available including maximum tree
117 and shallowest divergence tree.
122 o A bug introduced in write.tree() with ape 2.6 has been fixed.
124 o as.list.DNAbin() did not work correctly with vectors.
126 o as.hclust.phylo() failed with trees with node labels (thanks to
127 Filipe Vieira for the fix).
131 CHANGES IN APE VERSION 2.6
136 o The new functions rlineage and rbdtree simulate phylogenies under
137 any user-defined time-dependent speciation-extinction model. They
138 use continuous time algorithms.
140 o The new function drop.fossil removes the extinct species from a
143 o The new function bd.time fits a user-defined time-dependent
144 birth-death model. It is a generalization of yule.time() taking
145 extinction into account.
147 o The new function MPR does most parsimonious reconstruction of
150 o The new function Ftab computes the contingency table of base
151 frequencies from a pair of sequences.
153 o There is now an 'as.list' method for the class "DNAbin".
155 o dist.dna() can compute the number of transitions or transversions
156 with the option model = "Ts" or model = "Tv", respectively.
158 o [node|tip|edge]labels() gain three options with default values to
159 control the aspect of thermometers: horiz = TRUE, width = NULL,
162 o compar.gee() has been improved with the new option 'corStruct' as an
163 alternative to 'phy' to specify the correlation structure, and
164 calculation of the QIC (Pan 2001, Biometrics). The display of the
165 results has also been improved.
167 o read.GenBank() has a new option 'gene.names' to return the name of
168 the gene (FALSE by default).
173 o extract.clade() sometimes shuffled the tip labels.
175 o plot.phylo(type = "unrooted") did not force asp = 1 (thanks to Klaus
178 o dist.dna(model = "logdet") used to divide distances by 4. The
179 documentation has been clarified on the formulae used.
184 o rTraitCont(model = "OU") has an option 'linear = TRUE' to possibly
185 change the parameterisation (see ?rTraitCont for details).
187 o pic() now returns a vector with the node labels of the tree (if
190 o write.tree() and read.tree() have been substantially improved thanks
191 to contributions by Klaus Schliep.
195 CHANGES IN APE VERSION 2.5-3
200 o The new function mixedFontLabel helps to make labels with bits of
201 text to be plotted in different fonts.
203 o There are now replacement operators for [, [[, and $ for the class
204 "multiPhylo" (i.e., TREES[11:20] <- rmtree(10, 100)). They possibly
205 check that the tip labels are the same in all trees.
207 o Objects of class "multiPhylo" can be built with c(): there are
208 methods for the classes "phylo" and "multiPhylo".
210 o The internal functions .compressTipLabel and .uncompressTipLabel are
216 o bind.tree(x, y, where, position = 0) did not work correctly if 'y'
217 was a single-edge tree and 'where' was a tip.
219 o rTraitCont() did not use the square-root of branch lengths when
220 simulating a Brownian motion model.
224 CHANGES IN APE VERSION 2.5-2
229 o There is now a print method for results from ace().
231 o There is a labels() method for objects of class "DNAbin".
233 o read.dna() has a new option 'as.matrix' to possibly force sequences
234 in a FASTA file to be stored in a matrix (see ?read.dna for details).
239 o as.phylo.hclust() used to multiply edge lengths by 2.
241 o A minor bug was fixed in rTraitDisc().
243 o ace() sometimes failed (parameter value was NaN and the optimisation
249 o evolve.phylo() and plot.ancestral() have been removed.
251 o chronogram(), ratogram(), and NPRS.criterion() have been removed.
256 o nj() has been improved and is now about 30% faster.
258 o The default option 'drop' of [.DNAbin has been changed to FALSE to
259 avoid dropping rownames when selecting a single sequence.
261 o print.DNAbin() has been changed to summary.DNAbin() which has been
266 CHANGES IN APE VERSION 2.5-1
271 o The new function stree generates trees with regular shapes.
273 o It is now possible to bind two trees with x + y (see ?bind.tree for
276 o drop.tip(), extract.clade(), root(), and bind.tree() now have an
277 'interactive' option to make the operation on a plotted tree.
279 o cophyloplot() gains two new arguments 'lwd' and 'lty' for the
280 association links; they are recycled like 'col' (which wasn't before).
285 o rTraitDisc() did not use its 'freq' argument correctly (it was
286 multiplied with the rate matrix column-wise instead of row-wise).
288 o [node|tip|edge]labels(thermo = ) used to draw empty thermometers
289 with NA values. Nothing is drawn now like with 'text' or 'pch'.
290 The same bug occurred with the 'pie' option.
292 o A bug was fixed in compar.ou() and the help page was clarified.
294 o bind.tree() has been rewritten fixing several bugs and making it
297 o plot.phylo(type = "p") sometimes failed to colour correctly the
298 vertical lines representing the nodes.
300 o plot.phylo(direction = "l", x.lim = 30) failed to plot the branches
301 in the correct direction though the tip labels were displayed
307 o The c, cbind, and rbind methods for "DNAbin" objetcs now check that
308 the sequences are correctly stored (in a list for c, in a matrix
309 for the two other functions).
313 CHANGES IN APE VERSION 2.5
318 o The new function parafit by Pierre Legendre tests for the
319 coevolution between hosts and parasites. It has a companion
320 function, pcoa, that does principal coordinate decomposition.
321 The latter has a biplot method.
323 o The new function lmorigin by Pierre Legendre performs multiple
324 regression through the origin with testing by permutation.
326 o The new functions rTraitCont and rTraitDisc simulate continuous and
327 discrete traits under a wide range of evolutionary models.
329 o The new function delta.plot does a delta plot following Holland et
330 al. (2002, Mol. Biol. Evol. 12:2051).
332 o The new function edges draws additional branches between any nodes
333 and/or tips on a plotted tree.
335 o The new function fancyarrows enhances arrows from graphics with
336 triangle and harpoon heads; it can be called from edges().
338 o add.scale.bar() has a new option 'ask' to draw interactively.
340 o The branch length score replaces the geodesic distance in dist.topo.
342 o Three new data sets are included: the gopher-lice data (gopher.D),
343 SO2 air pollution in 41 US cities (lmorigin.ex1, from Sokal &
344 Rohlf 1995), and some host-parasite specificity data
345 (lmorigin.ex2, from Legendre & Desdevises 2009).
350 o add.scale.bar() drew the bar outside the plotting region with the
351 default options with unrooted or radial trees.
353 o dist.topo() made R stuck when the trees had different sizes (thanks
354 to Otto Cordero for the fix).
359 o The geodesic distance has been replaced by the branch length score
364 CHANGES IN APE VERSION 2.4-1
369 o rtree() and rcoal() now accept a numeric vector for the 'br'
372 o vcv() is a new generic function with methods for the classes "phylo"
373 and "corPhyl" so that it is possible to calculate the var-cov matrix
374 for "transformation models". vcv.phylo() can still be used for trees
375 of class "phylo"; its argument 'cor' has been renamed 'corr'.
380 o bind.tree() failed when 'y' had no root edge.
382 o read.nexus() shuffled tip labels when the trees have no branch
383 lengths and there is a TRANSLATE block.
385 o read.nexus() does not try to translate node labels if there is a
386 translation table in the NEXUS file. See ?read.nexus for a
387 clarification on this behaviour.
389 o plot.multiPhylo() crashed R when plotting a list of trees with
390 compressed tip labels.
392 o write.nexus() did not translate the taxa names when asked for.
394 o plot.phylo(type = "fan") did not rotate the tip labels correctly
395 when the tree has branch lengths.
397 o ace(type = "continuous", method = "ML") now avoids sigma² being
398 negative (which resulted in an error).
400 o nj() crashed with NA/NaN in the distance matrix: an error in now
405 CHANGES IN APE VERSION 2.4
410 o base.freq() has a new option 'freq' to return the counts; the
411 default is still to return the proportions.
416 o seg.sites() did not handle ambiguous nucleotides correctly: they
419 o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
420 the tree: the argument is now ignored.
422 o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
428 o Trying to plot a tree with a single tip now returns NULL with a
429 warning (it returned an error previously).
431 o The way lines representing nodes are coloured in phylograms has
432 been modified (as well as their widths and types) following some
433 users' request; this is only for dichotomous nodes.
435 o The argument 'adj' in [node][tip][edge]labels() now works when
436 using 'pie' or 'thermo'.
438 o A more informative message error is now returned by dist.dna() when
439 'model' is badly specified (partial matching of this argument is
442 o Deprecated functions are now listed in a help page: see
443 help("ape-defunct") with the quotes.
448 o The functions heterozygosity, nuc.div, theta.h, theta.k and
449 theta.s have been moved from ape to pegas.
451 o The functions mlphylo, DNAmodel and sh.test have been removed.
455 CHANGES IN APE VERSION 2.3-3
460 o add.scale.bar() always drew a horizontal bar.
462 o zoom() shuffled tips with unrooted trees.
464 o write.nexus() failed to write correctly trees with a "TipLabel"
467 o rcoal() failed to compute branch lengths with very large n.
469 o A small bug was fixed in compar.cheverud() (thanks to Michael
472 o seg.sites() failed when passing a vector.
474 o drop.tip() sometimes shuffled tip labels.
476 o root() shuffled node labels with 'resolve.root = TRUE'.
480 CHANGES IN APE VERSION 2.3-2
485 o all.equal.phylo() did not compare unrooted trees correctly.
487 o dist.topo(... method = "PH85") did not treat unrooted trees
488 correctly (thanks to Tim Wallstrom for the fix).
490 o root() sometimes failed to test for the monophyly of the
493 o extract.clade() sometimes included too many edges.
495 o vcv.phylo() did not work correctly when the tree is in
498 o nj() did not handle correctly distance matrices with many 0's.
499 The code has also been significantly improved: 7, 70, 160 times
500 faster with n = 100, 500, 1000, respectively.
504 CHANGES IN APE VERSION 2.3-1
509 o The new function is.monophyletic tests the monophyly of a group.
511 o There is now a c() method for lists of class "DNAbin".
513 o yule.cov() now fits the null model, and its help page has been
514 corrected with respect to this change.
516 o drop.tip() has a new option 'rooted' to force (or not) a tree
517 to be treated as (un)rooted.
522 o dist.gene() failed on most occasions with the default
523 pairwise.deletion = FALSE.
525 o read.tree() failed to read correctly the tree name(s).
527 o boot.phylo() now treats correctly data frames.
529 o del.gaps() did not copy the rownames of a matrix.
531 o A small bug was fixed in CDAM.global().
533 o ace() failed with large data sets. Thanks to Rich FitzJohn for
534 the fix. With other improvements, this function is now about 6
537 o write.tree() failed with objects of class "multiPhylo".
539 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
544 o [.multiPhylo and [.DNAbin now respect the original class.
546 o Instances of the form class(phy) == "phylo" have been replaced
547 by inherits(phy, "phylo").
549 o rcoal() is now faster.
554 o klastorin() has been removed.
558 CHANGES IN APE VERSION 2.3
563 o The new functions CADM.global and CADM.post, contributed by
564 Pierre Legendre, test the congruence among several distance
567 o The new function yule.time fits a user-defined time-dependent
568 Yule model by maximum likelihood.
570 o The new function makeNodeLabel creates and/or modifies node
571 labels in a flexible way.
573 o read.tree() and write.tree() have been modified so that they can
574 handle individual tree names.
576 o plot.phylo() has a new argument 'edge.lty' that specifies the
577 types of lines used for the edges (plain, dotted, dashed, ...)
579 o phymltest() has been updated to work with PhyML 3.0.1.
584 o drop.tip() shuffled tip labels in some cases.
586 o drop.tip() did not handle node.label correctly.
588 o is.ultrametric() now checks the ordering of the edge matrix.
590 o ace() sometimes returned negative values of likelihoods of
591 ancestral states (thanks to Dan Rabosky for solving this long
597 o The data set xenarthra has been removed.
601 CHANGES IN APE VERSION 2.2-4
605 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
606 now fixed. (Thanks to Peter Wragg for the fix!)
608 o A warning message occurred for no reason with ace(method="GLS").
613 o There is now a general help page displayed with '?ape'.
617 CHANGES IN APE VERSION 2.2-3
622 o The new function extract.clade extracts a clade from a tree by
623 specifying a node number or label.
625 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
626 operations of the same names.
628 o dist.dna() can now return the number of site differences by
629 specifying model="N".
634 o chronopl() did not work with CV = TRUE.
636 o read.nexus() did not work correctly in some situations (trees on
637 multiple lines with different numbers of lines and/or with
638 comments inserted within the trees).
640 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
641 the number of lineages with non-binary trees.
646 o ape has now a namespace.
648 o drop.tip() has been improved: it should be much faster and work
649 better in some cases (e.g., see the example in ?zoom).
653 CHANGES IN APE VERSION 2.2-2
658 o dist.gene() has been substantially improved and gains an option
661 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
667 o prop.part() failed with a single tree with the default option
668 'check.labels = TRUE'.
670 o summary.DNAbin() failed to display correctly the summary of
671 sequence lengths with lists of sequences of 10,000 bases or more
672 (because summary.default uses 4 significant digits by default).
674 o read.nexus() failed to read a file with a single tree with line
675 breaks in the Newick string.
677 o del.gaps() returned a list of empty sequences when there were no
683 o phymltest() has been updated for PhyML 3.0 and gains an option
684 'append', whereas the option 'path2exec' has been removed.
686 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
687 which is returned unchanged (instead of an error).
689 o The data sets bird.orders and bird.families are now stored as
690 Newick strings; i.e., the command data(bird.orders) calls
695 CHANGES IN APE VERSION 2.2-1
700 o The new function makeLabel() helps to modify labels of trees,
701 lists of trees, or DNA sequences, with several utilities to
702 truncate and/or make them unique, substituting some
703 characters, and so on.
705 o The new function del.gaps() removes insertion gaps ("-") in a
706 set of DNA sequences.
708 o read.dna() can now read Clustal files (*.aln).
713 o root() failed with 'resolve.root = TRUE' when the root was
714 already the specified root.
716 o Several bugs were fixed in mlphylo().
718 o collapsed.singles() did not propagate the 'Nnode' and
719 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
721 o read.nexus() failed to remove correctly the comments within
724 o read.nexus() failed to read a file with a single tree and no
725 translation of tip labels.
727 o read.nexus() failed to place correctly tip labels when reading
728 a single tree with no edge lengths.
730 o A bug was fixed in sh.test().
735 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
738 o The option 'check.labels' of consensus() and prop.part() is now
741 o write.dna() now does not truncate names to 10 characters with
746 CHANGES IN APE VERSION 2.2
751 o Four new functions have been written by Damien de Vienne for the
752 graphical exploration of large trees (cophyloplot, subtrees,
753 subtreeplot), and to return the graphical coordinates of tree
756 o The new functions corPagel and corBlomberg implement the Pagel's
757 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
759 o chronopl() has been improved and gains several options: see its
760 help page for details.
762 o boot.phylo() has now an option 'trees' to possibly return the
763 bootstraped trees (the default is FALSE).
765 o prop.part() has been improved and should now be faster in all
771 o read.dna() failed if "?" occurred in the first 10 sites of the
774 o The x/y aspect of the plot is now respected when plotting a
775 circular tree (type = "r" or "f").
777 o Drawing the tip labels sometimes failed when plotting circular
780 o zoom() failed when tip labels were used instead of their numbers
781 (thanks to Yan Wong for the fix).
783 o drop.tip() failed with some trees (fixed by Yan Wong).
785 o seg.sites() failed with a list.
787 o consensus() failed in some cases. The function has been improved
788 as well and is faster.
792 CHANGES IN APE VERSION 2.1-3
797 o A bug in read.nexus() made the Windows R-GUI crash.
799 o An error was fixed in the computation of ancestral character
800 states by generalized least squares in ace().
802 o di2multi() did not modify node labels correctly.
804 o multi2di() failed if the tree had its attribute "order" set to
809 CHANGES IN APE VERSION 2.1-2
814 o There three new methods for the "multiPhylo" class: str, $,
817 o root() gains the options 'node' and 'resolve.root'
818 (FALSE by default) as well as its code being improved.
820 o mltt.plot() has now an option 'log' used in the same way
821 than in plot.default().
826 o mltt.plot() failed to display the legend with an unnamed
829 o nodelabels() with pies now correcly uses the argument
830 'cex' to draw symbols of different sizes (which has
831 worked already for thermometers).
833 o read.nexus() generally failed to read very big files.
838 o The argument 'family' of compar.gee() can now be a function
839 as well as a character string.
841 o read.tree() and read.nexus() now return an unnamed list if
844 o read.nexus() now returns a modified object of class "multiPhylo"
845 when there is a TRANSLATE block in the NEXUS file: the individual
846 trees have no 'tip.label' vector, but the list has a 'TipLabel'
847 attribute. The new methods '$' and '[[' set these elements
848 correctly when extracting trees.
852 CHANGES IN APE VERSION 2.1-1
857 o The new function rmtree generates lists of random trees.
859 o rcoal() now generates a genuine coalescent tree by default
860 (thanks to Vladimir Minin for the code).
865 o nuc.div() returned an incorrect value with the default
866 pairwise.deletion = FALSE.
871 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
872 have been improved so that they are stabler and faster.
874 o R packages used by ape are now loaded silently; lattice and gee
875 are loaded only when needed.
879 CHANGES IN APE VERSION 2.1
884 o The new function identify.phylo identifies clades on a plotted
885 tree using the mouse.
887 o It is now possible to subset a list of trees (object of class
888 "multiPhylo") with "[" while keeping its class correct.
890 o The new function as.DNAbin.alignment converts DNA sequences
891 stored in the "alignment" format of the package seqinr into
892 an object of class "DNAbin".
894 o The new function weight.taxo2 helps to build similarity matrices
895 given two taxonomic levels (usually called by other functions).
897 o write.tree() can now take a list of trees (class "multiPhylo")
898 as its main argument.
900 o plot.correlogram() and plot.correlogramList() have been
901 improved, and gain several options (see the help page for
902 details). A legend is now plotted by default.
907 o dist.dna() returned some incorrect values with `model = "JC69"'
908 and `pairwise.deletion = TRUE'. This affected only the
909 distances involving sequences with missing values. (Thanks
910 to Bruno Toupance for digging this bug out.)
912 o write.tree() failed with some trees: this is fixed by removing
913 the `multi.line' option (trees are now always printed on a
916 o read.nexus() did not correctly detect trees with multiple root
917 edges (see OTHER CHANGES).
922 o The code of mlphylo() has been almost entirely rewritten, and
923 should be much stabler. The options have been also greatly
924 simplified (see ?mlphylo and ?DNAmodel for details).
926 o The internal function nTips has been renamed klastorin_nTips.
928 o The code of is.ultrametric() contained redundancies and has
931 o The code of Moran.I() and of correlogram.formula() have been
934 o read.tree() and read.nexus() now return an error when trying to
935 read a tree with multiple root edges (see BUG FIXES). The
936 correction applied in previous version did not work in all
939 o The class c("multi.tree", "phylo") has been renamed
945 o There is now a vignette in ape: see vignette("MoranI", "ape").
950 o as.matching() and as.phylo.matching() do not support branch
953 o correlogram.phylo() and discrete.dist() have been removed.
957 CHANGES IN APE VERSION 2.0-2
962 o The new function matexpo computes the exponential of a square
965 o The new function unique.multi.tree removes duplicate trees from
968 o yule() has a new option `use.root.edge = FALSE' that specifies
969 to ignore, by default, the root edge of the tree if it exists.
974 o which.edge() failed when the index of a single terminal edge was
977 o In diversi.time(), the values returned for model C were
980 o A bug was fixed in yule() that affected the calculation of the
981 likelihood in the presence of ties in the branching times.
983 o There was a bug in the C function mat_expo4x4 affecting the
984 calculations of the transition probabilities for models HKY and
987 o A small bug was fixed in as.matrix.DNAbin (thanks to James
990 o rtree() did not `shuffle' the tip labels by default, so only a
991 limited number of labelled topologies could be generated.
995 CHANGES IN APE VERSION 2.0-1
1000 o The three new functions bionj, fastme.ols, and fastme.bal
1001 perform phylogeny estimation by the BIONJ and fastME methods in
1002 OLS and balanced versions. This is a port to R of previous
1003 previous programs done by Vincent Lefort.
1005 o The new function chronoMPL performs molecular dating with the
1006 mean path lengths method of Britton et al. (2002, Mol. Phyl.
1009 o The new function rotate, contributed by Christoph Heibl, swaps
1010 two clades connected to the same node. It works also with
1011 multichotomous nodes.
1013 o The new `method' as.matrix.DNAbin() may be used to convert
1014 easily DNA sequences stored in a list into a matrix while
1015 keeping the names and the class.
1020 o chronopl() failed when some branch lengths were equal to zero:
1021 an error message is now returned.
1023 o di2multi() failed when there was a series of consecutive edges
1028 CHANGES IN APE VERSION 1.10-2
1033 o plot.phylo() can now plot circular trees: the option is type =
1034 "fan" or type = "f" (to avoid the ambiguity with type = "c").
1036 o prop.part() has a new option `check.labels = FALSE' which allows
1037 to considerably speed-up the calculations of bipartitions. As a
1038 consequence, calculations of bootstrap values with boot.phylo()
1039 should be much faster.
1044 o read.GenBank() did not return correctly the list of species as
1045 from ape 1.10: this is fixed in this version
1047 o Applying as.phylo() on a tree of class "phylo" failed: the
1048 object is now returned unchanged.
1052 CHANGES IN APE VERSION 1.10-1
1057 o The three new functions Ntip, Nnode, and Nedge return, for a
1058 given tree, the number of tips, nodes, or edges, respectively.
1063 o read.nexus() did not set correctly the class of the returned
1064 object when reading multiple trees.
1066 o mllt.plot() failed with objects of class c("multi.tree",
1069 o unroot() did not work correctly in most cases.
1071 o reorder.phylo() made R freeze in some occasions.
1073 o Plotting a tree in pruningwise order failed.
1075 o When plotting an unrooted tree, the tip labels where not all
1076 correctly positioned if the option `cex' was used.
1080 CHANGES IN APE VERSION 1.10
1085 o Five new `method' functions have been introduced to manipulate
1086 DNA sequences in binary format (see below).
1088 o Three new functions have been introduced to convert between the
1089 new binary and the character formats.
1091 o The new function as.alignment converts DNA sequences stored as
1092 single characters into the class "alignment" used by the package
1095 o read.dna() and read.GenBank() have a new argument `as.character'
1096 controlling whether the sequences are returned in binary format
1102 o root() failed when the tree had node labels: this is fixed.
1104 o plot.phylo() did not correctly set the limits on the y-axis with
1105 the default setting: this is fixed.
1107 o dist.dna() returned a wrong result for the LogDet, paralinear,
1108 and BH87 models with `pairwise.deletion = TRUE'.
1113 o DNA sequences are now internally stored in a binary format. See
1114 the document "A Bit-Level Coding Scheme for Nucleotides" for the
1115 details. Most functions analyzing DNA functions have been
1116 modified accordingly and are now much faster (dist.dna is now
1117 ca. 60 times faster).
1121 CHANGES IN APE VERSION 1.9-4
1126 o A bug was fixed in edgelabels().
1128 o as.phylo.hclust() did not work correctly when the object of
1129 class "hclust" has its labels set to NULL: the returned tree has
1130 now its tip labels set to "1", "2", ...
1132 o consensus could fail if some tip labels are a subset of others
1133 (e.g., "a" and "a_1"): this is now fixed.
1135 o mlphylo() failed in most cases if some branch lengths of the
1136 initial tree were greater than one: an error message is now
1139 o mlphylo() failed in most cases when estimating the proportion of
1140 invariants: this is fixed.
1144 CHANGES IN APE VERSION 1.9-3
1149 o The new function edgelabels adds labels on the edge of the tree
1150 in the same way than nodelabels or tiplabels.
1155 o multi2di() did not handle correctly branch lengths with the
1156 default option `random = TRUE': this is now fixed.
1158 o A bug was fixed in nuc.div() when using pairwise deletions.
1160 o A bug occurred in the analysis of bipartitions with large
1161 numbers of large trees, with consequences on prop.part,
1162 prop.clades, and boot.phylo.
1164 o The calculation of the Billera-Holmes-Vogtmann distance in
1165 dist.topo was wrong: this has been fixed.
1169 CHANGES IN APE VERSION 1.9-2
1174 o The new function ladderize reorganizes the internal structure of
1175 a tree to plot them left- or right-ladderized.
1177 o The new function dist.nodes computes the patristic distances
1178 between all nodes, internal and terminal, of a tree. It replaces
1179 the option `full = TRUE' of cophenetic.phylo (see below).
1184 o A bug was fixed in old2new.phylo().
1186 o Some bugs were fixed in chronopl().
1188 o The edge colours were not correctly displayed by plot.phylo
1189 (thank you to Li-San Wang for the fix).
1191 o cophenetic.phylo() failed with multichotomous trees: this is
1197 o read.dna() now returns the sequences in a matrix if they are
1198 aligned (interleaved or sequential format). Sequences in FASTA
1199 format are still returned in a list.
1201 o The option `full' of cophenetic.phylo() has been removed because
1202 it could not be used from the generic.
1205 DEPRECATED & DEFUNCT
1207 o rotate() has been removed; this function did not work correctly
1212 CHANGES IN APE VERSION 1.9-1
1217 o Trees with a single tip were not read correctly in R as the
1218 element `Nnode' was not set: this is fixed.
1220 o unroot() did not set correctly the number of nodes of the
1221 unrooted tree in most cases.
1223 o read.GenBank() failed when fetching very long sequences,
1224 particularly of the BX-series.
1226 o A bug was introduced in read.tree() with ape 1.9: it has been
1231 CHANGES IN APE VERSION 1.9
1236 o There are two new print `methods' for trees of class "phylo" and
1237 lists of trees of class "multi.tree", so that they are now
1238 displayed in a compact and informative way.
1240 o There are two new functions, old2new.phylo and new2old.phylo,
1241 for converting between the old and new coding of the class
1244 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
1245 LogDet ("logdet"), and paralinear ("paralin").
1247 o compute.brlen() has been extended: several methods are now
1248 available to compute branch lengths.
1250 o write.dna() can now handle matrices as well as lists.
1255 o cophenetic.phylo() sometimes returned a wrong result with
1256 multichotomous trees: this is fixed.
1258 o rotate() failed when a single tip was specified: the tree is now
1261 o ace() did not return the correct index matrix with custom
1262 models: this is fixed.
1264 o multi2di() did not work correctly when resolving multichotomies
1265 randomly: the topology was always the same, only the arrangement
1266 of clades was randomized: this is fixed. This function now
1267 accepts trees with no branch lengths.
1269 o The output of diversi.gof() was blurred by useless prints when a
1270 user distribution was specified. This has been corrected, and
1271 the help page of this function has been expanded.
1276 o The internal structure of the class "phylo" has been changed:
1277 see the document "Definition of Formats for Coding Phylogenetic
1278 Trees in R" for the details. In addition, the code of most
1279 functions has been improved.
1281 o Several functions have been improved by replacing some R codes
1282 by C codes: pic, plot.phylo, and reorder.phylo.
1284 o There is now a citation information: see citation("ape") in R.
1286 o write.tree() now does not add extra 0's to branch lengths so
1287 that 1.23 is printed "1.23" by default, not "1.2300000000".
1289 o The syntax of bind.tree() has been simplified. This function now
1290 accepts trees with no branch lengths, and handles correctly node
1293 o The option `as.numeric' of mrca() has been removed.
1295 o The unused options `format' and `rooted' of read.tree() have
1298 o The unused option `format' of write.tree() has been removed.
1300 o The use of node.depth() has been simplified.
1304 CHANGES IN APE VERSION 1.8-5
1309 o Two new functions read.nexus.data() and write.nexus.data(),
1310 contributed by Johan Nylander, allow to read and write molecular
1311 sequences in NEXUS files.
1313 o The new function reorder.phylo() reorders the internal structure
1314 of a tree of class "phylo". It is used as the generic, e.g.,
1317 o read.tree() and read.nexus() can now read trees with a single
1320 o The new data set `cynipids' supplies a set of protein sequences
1326 o The code of all.equal.phylo() has been completely rewritten
1327 (thanks to Benoît Durand) which fixes several bugs.
1329 o read.tree() and read.nexus() now checks the labels of the tree
1330 to remove or substitute any characters that are illegal in the
1331 Newick format (parentheses, etc.)
1333 o A negative P-value could be returned by mantel.test(): this is
1338 CHANGES IN APE VERSION 1.8-4
1343 o The new function sh.test() computes the Shimodaira-
1346 o The new function collapse.singles() removes the nodes with a
1347 single descendant from a tree.
1349 o plot.phylo() has a new argument `tip.color' to specify the
1350 colours of the tips.
1352 o mlphylo() has now an option `quiet' to control the display of
1353 the progress of the analysis (the default is FALSE).
1358 o read.dna() did not read correctly sequences in sequential format
1359 with leading alignment gaps "-": this is fixed.
1361 o ace() returned a list with no class so that the generic
1362 functions (anova, logLik, ...) could not be used directly. This
1363 is fixed as ace() now returns an object of class "ace".
1365 o anova.ace() had a small bug when computing the number of degrees
1366 of freedom: this is fixed.
1368 o mlphylo() did not work when the sequences were in a matrix or
1369 a data frame: this is fixed.
1371 o rtree() did not work correctly when trying to simulate an
1372 unrooted tree with two tips: an error message is now issued.
1377 o The algorithm of rtree() has been changed: it is now about 40,
1378 100, and 130 times faster for 10, 100, and 1000 tips,
1383 CHANGES IN APE VERSION 1.8-3
1388 o There are four new `method' functions to be used with the
1389 results of ace(): logLik(), deviance(), AIC(), and anova().
1391 o The plot method of phymltest has two new arguments: `main' to
1392 change the title, and `col' to control the colour of the
1393 segments showing the AIC values.
1395 o ace() has a new argument `ip' that gives the initial values used
1396 in the ML estimation with discrete characters (see the examples
1397 in ?ace). This function now returns a matrix giving the indices
1398 of the estimated rates when analysing discrete characters.
1400 o nodelabels() and tiplabels() have a new argument `pie' to
1401 represent proportions, with any number of categories, as
1402 piecharts. The use of the option `thermo' has been improved:
1403 there is now no limitation on the number of categories.
1408 o mlphylo() did not work with more than two partitions: this is
1411 o root() failed if the proposed outgroup was already an outgroup
1412 in the tree: this is fixed.
1414 o The `col' argument in nodelabels() and tiplabels() was not
1415 correctly passed when `text' was used: this is fixed.
1417 o Two bugs were fixed in mlphylo(): parameters were not always
1418 correctly output, and the estimation failed in some cases.
1420 o plot.phylo() was stuck when given a tree with a single tip: this
1421 is fixed and a message error is now returned.
1423 o An error was corrected in the help page of gammaStat regarding
1424 the calculation of P-values.
1426 o Using gls() could crash R when the number of species in the tree
1427 and in the variables were different: this is fixed.
1431 CHANGES IN APE VERSION 1.8-2
1436 o The new function mlphylo() fits a phylogenetic tree by maximum
1437 likelihood from DNA sequences. Its companion function DNAmodel()
1438 is used to define the substitution model which may include
1439 partitioning. There are methods for logLik(), deviance(), and
1440 AIC(), and the summary() method has been extended to display in
1441 a friendly way the results of this model fitting. Currently, the
1442 functionality is limited to estimating the substitution and
1443 associated parameters and computing the likelihood.
1445 o The new function drop1.compar.gee (used as, e.g., drop1(m))
1446 tests for single effects in GEE-based comparative method. A
1447 warning message is printed if there is not enough degrees of
1453 o An error message was sometimes issued by plot.multi.tree(),
1454 though with no consequence.
1458 CHANGES IN APE VERSION 1.8-1
1463 o There is a new plot method for lists of trees (objects of class
1464 "multi.tree"): it calls plot.phylo() internally and is
1465 documented on the same help page.
1470 o A bug was fixed in the C code that analyzes bipartitions: this
1471 has impact on several functions like prop.part, prop.clades,
1472 boot.phylo, or consensus.
1474 o root() did not work correctly when the specified outgroup had
1475 more than one element: this is fixed.
1477 o dist.dna() sometimes returned a warning inappropriately: this
1480 o If the distance object given to nj() had no rownames, nj()
1481 returned a tree with no tip labels: it now returns tips labelled
1482 "1", "2", ..., corresponding to the row numbers.
1487 o nj() has been slightly changed so that tips with a zero distance
1488 are first aggregated with zero-lengthed branches; the usual NJ
1489 procedure is then performed on a distance matrix without 0's.
1493 CHANGES IN APE VERSION 1.8
1498 o The new function chronopl() estimates dates using the penalized
1499 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1501 o The new function consensus() calculates the consensus tree of a
1504 o The new function evolve.phylo() simulates the evolution of
1505 continuous characters along a phylogeny under a Brownian model.
1507 o The new plot method for objects of class "ancestral" displays a
1508 tree together with ancestral values, as returned by the above
1511 o The new function as.phylo.formula() returns a phylogeny from a
1512 set of nested taxonomic variables given as a formula.
1514 o The new function read.caic() reads trees in CAIC format.
1516 o The new function tiplabels() allows to add labels to the tips
1517 of a tree using text or plotting symbols in a flexible way.
1519 o The new function unroot() unroots a phylogeny.
1521 o multi2di() has a new option, `random', which specifies whether
1522 to resolve the multichotomies randomly (the default) or not.
1524 o prop.part() now returns an object of class "prop.part" for which
1525 there are print (to display a partition in a more friendly way)
1526 and summary (to extract the numbers) methods.
1528 o plot.phylo() has a new option, `show.tip.label', specifying
1529 whether to print the labels of the tips. The default is TRUE.
1531 o The code of nj() has been replaced by a faster C code: it is now
1532 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1535 o write.nexus() now writes whether a tree is rooted or not.
1540 o Two bugs have been fixed in root(): unrooted trees are now
1541 handled corretly, and node labels are now output normally.
1543 o A bug was fixed in phymltest(): the executable couldn't be found
1546 o Three bug have been fixed in ace(): computing the likelihood of
1547 ancestral states of discrete characters failed, custom models
1548 did not work, and the function failed with a null gradient (a
1549 warning message is now returned; this latter bug was also
1550 present in yule.cov() as well and is now fixed).
1552 o pic() hanged out when missing data were present: a message error
1555 o A small bug was fixed in dist.dna() where the gamma correction
1556 was not always correctly dispatched.
1558 o plot.phylo() plotted correctly the root edge only when the tree
1559 was plotted rightwards: this works now for all directions.
1564 o dist.taxo() has been renamed as weight.taxo().
1566 o dist.phylo() has been replaced by the method cophenetic.phylo().
1568 o Various error and warning messages have been improved.
1572 CHANGES IN APE VERSION 1.7
1575 o The new function ace() estimates ancestral character states for
1576 continuous characters (with ML, GLS, and contrasts methods), and
1577 discrete characters (with ML only) for any number of states.
1579 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1580 of directional evolution for continuous characters. The user
1581 specifies the node(s) of the tree where the character optimum
1584 o The new function is.rooted() tests whether a tree (of class
1587 o The new function rcoal() generates random ultrametric trees with
1588 the possibility to specify the function that generates the
1589 inter-nodes distances.
1591 o The new function mrca() gives for all pairs of tips in a tree
1592 (and optionally nodes too) the most recent common ancestor.
1594 o nodelabels() has a new option `thermo' to plot proportions (up
1595 to three classes) on the nodes of a tree.
1597 o rtree() has been improved: it can now generate rooted or
1598 unrooted trees, and the mathematical function that generates the
1599 branch lengths may be specified by the user. The tip labels may
1600 be given directly in the call to rtree. The limit cases (n = 2,
1601 3) are now handled correctly.
1603 o dist.topo() has a new argument `method' with two choices: "PH85"
1604 for Penny and Henny's method (already available before and now
1605 the default), and "BHV01" for the geometric distance by Billera
1606 et al. (2001, Adv. Appl. Math. 27:733).
1608 o write.tree() has a new option, `digits', which specifies the
1609 number of digits to be printed in the Newick tree. By default
1610 digits = 10. The numbers are now always printed in decimal form
1611 (i.e., 1.0e-1 is now avoided).
1613 o dist.dna() can now compute the raw distances between pairs of
1614 DNA sequences by specifying model = "raw".
1616 o dist.phylo() has a new option `full' to possibly compute the
1617 distances among all tips and nodes of the tree. The default if
1623 o Several bugs were fixed in all.equal.phylo().
1625 o dist.dna() did not handle correctly gaps ("-") in alignments:
1626 they are now considered as missing data.
1628 o rotate() did not work if the tips were not ordered: this is
1631 o mantel.test() returned NA in some special cases: this is fixed
1632 and the function has been improved and is now faster.
1634 o A bug was fixed in diversi.gof() where the calculation of A² was
1637 o cherry() did not work correctly under some OSs (mainly Linux):
1640 o is.binary.tree() has been modified so that it works with both
1641 rooted and unrooted trees.
1643 o The documentation of theta.s() was not correct: this has been
1646 o plot.mst() did not work correctly: this is fixed.
1650 CHANGES IN APE VERSION 1.6
1655 o The new function dist.topo() computes the topological distances
1658 o The new function boot.phylo() performs a bootstrap analysis on
1659 phylogeny estimation.
1661 o The new functions prop.part() and prop.clades() analyse
1662 bipartitions from a series of trees.
1667 o read.GenBank() now uses the EFetch utility of NCBI instead of
1668 the usual Web interface: it is now much faster (e.g., 12 times
1669 faster to retrieve 8 sequences, 37 times for 60 sequences).
1674 o Several bugs were fixed in read.dna().
1676 o Several bugs were fixed in diversi.time().
1678 o is.binary.tree() did not work correctly if the tree has no edge
1679 lengths: this is fixed.
1681 o drop.tip() did not correctly propagated the `node.label' of a
1682 tree: this is fixed.
1686 CHANGES IN APE VERSION 1.5
1691 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1692 convert objects between the classes "phylo" and "matching". The
1693 latter implements the representation of binary trees introduced by
1694 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1695 as.matching() has been introduced as well.
1697 o Two new functions, multi2di() and di2multi(), allow to resolve
1698 and collapse multichotomies with branches of length zero.
1700 o The new function nuc.div() computes the nucleotide diversity
1701 from a sample a DNA sequences.
1703 o dist.dna() has been completely rewritten with a much faster
1704 (particularly for large data sets) C code. Eight models are
1705 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1706 option `method' has been renamed `model'). Computation of variance
1707 is available for all models. A gamma-correction is possible for
1708 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1709 to remove sites with missing data on a pairwise basis. The option
1710 `GCcontent' has been removed.
1712 o read.GenBank() has a new option (species.names) which specifies
1713 whether to return the species names of the organisms in addition
1714 to the accession numbers of the sequences (this is the default
1717 o write.nexus() can now write several trees in the same NEXUS file.
1719 o drop.tip() has a new option `root.edge' that allows to specify the
1720 new root edge if internal branches are trimmed.
1725 o as.phylo.hclust() failed if some labels had parentheses: this
1728 o Several bugs were fixed in all.equal.phylo(). This function now
1729 returns the logical TRUE if the trees are identical but with
1730 different representations (a report was printed previously).
1732 o read.GenBank() did not correctly handle ambiguous base codes:
1738 o birthdeath() now returns an object of class "birthdeath" for
1739 which there is a print method.
1743 CHANGES IN APE VERSION 1.4
1748 o The new function nj() performs phylogeny estimation with the
1749 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1752 o The new function which.edge() identifies the edges of a tree
1753 that belong to a group specified as a set of tips.
1755 o The new function as.phylo.phylog() converts an object of class
1756 "phylog" (from the package ade4) into an object of class
1759 o The new function axisPhylo() draws axes on the side of a
1762 o The new function howmanytrees() calculates the number of trees
1763 in different cases and giving a number of tips.
1765 o write.tree() has a new option `multi.line' (TRUE by default) to
1766 write a Newick tree on several lines rather than on a single
1769 o The functionalities of zoom() have been extended. Several
1770 subtrees can be visualized at the same time, and they are marked
1771 on the main tree with colors. The context of the subtrees can be
1772 marked with the option `subtree' (see below).
1774 o drop.tip() has a new option `subtree' (FALSE by default) which
1775 specifies whether to output in the tree how many tips have been
1778 o The arguments of add.scale.bar() have been redefined and have
1779 now default values (see ?add.scale.bar for details). This
1780 function now works even if the plotted tree has no edge length.
1782 o plot.phylo() can now plot radial trees, but this does not take
1783 edge lengths into account.
1785 o In plot.phylo() with `type = "phylogram"', if the values of
1786 `edge.color' and `edge.width' are identical for sister-branches,
1787 they are propagated to the vertical line that link them.
1792 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1793 crashing. This is fixed.
1795 o In plot.phylo(), the options `edge.color' and `edge.width' are
1796 now properly recycled; their default values are now "black" and
1799 o A bug has been fixed in write.nexus().
1804 o The function node.depth.edgelength() has been removed and
1805 replaced by a C code.
1809 CHANGES IN APE VERSION 1.3-1
1814 o The new function nodelabels() allows to add labels to the nodes
1815 of a tree using text or plotting symbols in a flexible way.
1817 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1818 numeric values specifying the lower and upper limits on the x-
1819 and y-axes. This allows to leave some space on any side of the
1820 tree. If a single value is given, this is taken as the upper
1825 CHANGES IN APE VERSION 1.3
1830 o The new function phymltest() calls the software PHYML and fits
1831 28 models of DNA sequence evolution. There are a print method to
1832 display likelihood and AIC values, a summary method to compute
1833 the hierarchical likelihood ratio tests, and a plot method to
1834 display graphically the AIC values of each model.
1836 o The new function yule.cov() fits the Yule model with covariates,
1837 a model where the speciation rate is affected by several species
1838 traits through a generalized linear model. The parameters are
1839 estimated by maximum likelihood.
1841 o Three new functions, corBrownian(), corGrafen(), and
1842 corMartins(), compute the expected correlation structures among
1843 species given a phylogeny under different models of evolution.
1844 These can be used for GLS comparative phylogenetic methods (see
1845 the examples). There are coef() and corMatrix() methods and an
1846 Initialize.corPhyl() function associated.
1848 o The new function compar.cheverud() implements Cheverud et al.'s
1849 (1985; Evolution 39:1335) phylogenetic comparative method.
1851 o The new function varcomp() estimates variance components; it has
1854 o Two new functions, panel.superpose.correlogram() and
1855 plot.correlogramList(), allow to plot several phylogenetic
1858 o The new function node.leafnumber() computes the number of leaves
1859 of a subtree defined by a particular node.
1861 o The new function node.sons() gets all tags of son nodes from a
1864 o The new function compute.brlen() computes the branch lengths of
1865 a tree according to a specified method.
1867 o plot.phylo() has three new options: "cex" controls the size of
1868 the (tip and node) labels (thus it is no more needed to change
1869 the global graphical parameter), "direction" which allows to
1870 plot the tree rightwards, leftwards, upwards, or downwards, and
1871 "y.lim" which sets the upper limit on the y-axis.
1876 o Some functions which try to match tip labels and names of
1877 additional data (e.g. vector) are likely to fail if there are
1878 typing or syntax errors. If both series of names do not perfectly
1879 match, they are ignored and a warning message is now issued.
1880 These functions are bd.ext, compar.gee, pic. Their help pages
1881 have been clarified on this point.
1885 CHANGES IN APE VERSION 1.2-7
1890 o The new function root() reroots a phylogenetic tree with respect
1891 to a specified outgroup.
1893 o The new function rotate() rotates an internal branch of a tree.
1895 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1896 trees) controls the display of the tip labels in unrooted trees.
1897 This display has been greatly improved: the tip labels are now not
1898 expected to overlap with the tree (particularly if lab4ut =
1899 "axial"). In all cases, combining appropriate values of "lab4ut"
1900 and the font size (via "par(cex = )") should result in readable
1901 unrooted trees. See ?plot.phylo for some examples.
1903 o In drop.tip(), the argument `tip' can now be numeric or character.
1908 o drop.tip() did not work correctly with trees with no branch
1909 lengths: this is fixed.
1911 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1912 plotted with some line crossings: this is now fixed.
1916 CHANGES IN APE VERSION 1.2-6
1921 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1922 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1923 to implement comparative methods with an autocorrelation approach.
1925 o A new data set describing some life history traits of Carnivores
1931 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1936 o When plotting a tree with plot.phylo(), the new default of the
1937 option `label.offset' is now 0, so the labels are always visible.
1941 CHANGES IN APE VERSION 1.2-5
1946 o The new function bd.ext() fits a birth-death model with combined
1947 phylogenetic and taxonomic data, and estimates the corresponding
1948 speciation and extinction rates.
1953 o The package gee is no more required by ape but only suggested
1954 since only the function compar.gee() calls gee.
1958 CHANGES IN APE VERSION 1.2-4
1963 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1964 and lines.popsize) implementing a new approach for inferring the
1965 demographic history from genealogies using a reversible jump
1966 MCMC have been introduced.
1968 o The unit of time in the skyline plot and in the new plots can
1969 now be chosen to be actual years, rather than substitutions.
1973 CHANGES IN APE VERSION 1.2-3
1978 o The new function rtree() generates a random binary tree with or
1979 without branch lengths.
1981 o Two new functions for drawing lineages-through-time (LTT) plots
1982 are provided: ltt.lines() adds a LTT curve to an existing plot,
1983 and mltt.plot() does a multiple LTT plot giving several trees as
1984 arguments (see `?ltt.plot' for details).
1989 o Some taxon names made R crashing when calling as.phylo.hclust():
1992 o dist.dna() returned an error with two identical DNA sequences
1993 (only using the Jukes-Cantor method returned 0): this is fixed.
1998 o The function dist.phylo() has been re-written using a different
1999 algorithm: it is now about four times faster.
2001 o The code of branching.times() has been improved: it is now about
2006 CHANGES IN APE VERSION 1.2-2
2011 o The new function seg.sites() finds the segregating sites in a
2012 sample of DNA sequences.
2017 o A bug introduced in read.tree() and in read.nexus() with version
2020 o A few errors were corrected and a few examples were added in the
2025 CHANGES IN APE VERSION 1.2-1
2030 o plot.phylo() can now draw the edge of the root of a tree if it
2031 has one (see the new option `root.edge', its default is FALSE).
2036 o A bug was fixed in read.nexus(): files with semicolons inside
2037 comment blocks were not read correctly.
2039 o The behaviour of read.tree() and read.nexus() was corrected so
2040 that tree files with badly represented root edges (e.g., with
2041 an extra pair of parentheses, see the help pages for details)
2042 are now correctly represented in the object of class "phylo";
2043 a warning message is now issued.
2047 CHANGES IN APE VERSION 1.2
2052 o plot.phylo() has been completely re-written and offers several
2053 new functionalities. Three types of trees can now be drawn:
2054 phylogram (as previously), cladogram, and unrooted tree; in
2055 all three types the branch lengths can be drawn using the edge
2056 lengths of the phylogeny or not (e.g., if the latter is absent).
2057 The vertical position of the nodes can be adjusted with two
2058 choices (see option `node.pos'). The code has been re-structured,
2059 and two new functions (potentially useful for developpers) are
2060 documented separately: node.depth.edgelength() and node.depth();
2061 see the respective help pages for details.
2063 o The new function zoom() allows to explore very large trees by
2064 focusing on a small portion of it.
2066 o The new function yule() fits by maximum likelihood the Yule model
2067 (birth-only process) to a phylogenetic tree.
2069 o Support for writing DNA sequences in FASTA format has been
2070 introduced in write.dna() (support for reading sequences in
2071 this format was introduced in read.dna() in version 1.1-2).
2072 The function has been completely re-written, fixing some bugs
2073 (see below); the default behaviour is no more to display the
2074 sequences on the standard output. Several options have been
2075 introduced to control the sequence printing in a flexible
2076 way. The help page has been extended.
2078 o A new data set is included: a supertree of bats in NEXUS format.
2083 o In theta.s(), the default of the option `variance' has
2084 been changed to `FALSE' (as was indicated in the help page).
2086 o Several bugs were fixed in the code of all.equal.phylo().
2088 o Several bugs were fixed in write.dna(), particularly this
2089 function did not work with `format = "interleaved"'.
2091 o Various errors were corrected in the help pages.
2096 o The argument names of as.hclust.phylo() have been changed
2097 from "(phy)" to "(x, ...)" to conform to the definition of
2098 the corresponding generic function.
2100 o gamma.stat() has been renamed gammaStat() to avoid confusion
2101 since gamma() is a generic function.
2105 CHANGES IN APE VERSION 1.1-3
2110 o base.freq() previously did not return a value of 0 for
2111 bases absent in the data (e.g., a vector of length 3 was
2112 returned if one base was absent). This is now fixed (a
2113 vector of length 4 is always returned).
2115 o Several bugs were fixed in read.nexus(), including that this
2116 function did not work in this absence of a "TRANSLATE"
2117 command in the NEXUS file, and that the commands were
2122 CHANGES IN APE VERSION 1.1-2
2127 o The Tamura and Nei (1993) model of DNA distance is now implemented
2128 in dist.dna(): five models are now available in this function.
2130 o A new data set is included: a set of 15 sequences of the
2131 cytochrome b mitochondrial gene of the woodmouse (Apodemus
2137 o A bug in read.nexus() was fixed.
2139 o read.dna() previously did not work correctly in most cases.
2140 The function has been completely re-written and its help page
2141 has been considerably extended (see ?read.dna for details).
2142 Underscores (_) in taxon names are no more replaced with
2143 spaces (this behaviour was undocumented).
2145 o A bug was fixed in write.dna().
2149 CHANGES IN APE VERSION 1.1-1
2154 o A bug in read.tree() introduced in APE 1.1 was fixed.
2156 o A bug in compar.gee() resulted in an error when trying to fit
2157 a model with `family = "binomial"'. This is now fixed.
2161 CHANGES IN APE VERSION 1.1
2166 o The Klastorin (1982) method as suggested by Misawa and Tajima
2167 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
2168 on the basis of phylogenetic trees has been implemented (see
2169 the function klastorin()).
2171 o Functions have been added to convert APE's "phylo" objects in
2172 "hclust" cluster objects and vice versa (see the help page of
2173 as.phylo for details).
2175 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
2176 are introduced for the estimation of absolute evolutionary rates
2177 (ratogram) and dated clock-like trees (chronogram) from
2178 phylogenetic trees using the non-parametric rate smoothing approach
2179 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
2181 o A summary method is now provided printing a summary information on a
2182 phylogenetic tree with, for instance, `summary(tree)'.
2184 o The behaviour of read.tree() was changed so that all spaces and
2185 tabulations in tree files are now ignored. Consequently, spaces in tip
2186 labels are no more allowed. Another side effect is that read.nexus()
2187 now does not replace the underscores (_) in tip labels with spaces
2188 (this behaviour was undocumented).
2190 o The function plot.phylo() has a new option (`underscore') which
2191 specifies whether the underscores in tip labels should be written on
2192 the plot as such or replaced with spaces (the default).
2194 o The function birthdeath() now computes 95% confidence intervals of
2195 the estimated parameters using profile likelihood.
2197 o Three new data sets are included: a gene tree estimated from 36
2198 landplant rbcL sequences, a gene tree estimated from 32 opsin
2199 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
2204 o A bug was fixed in dist.gene() where nothing was returned.
2206 o A bug in plot.mst() was fixed.
2208 o A bug in vcv.phylo() resulted in false correlations when the
2209 option `cor = TRUE' was used (now fixed).
2213 CHANGES IN APE VERSION 1.0
2218 o Two new functions, read.dna() and write.dna(), read/write in a file
2219 DNA sequences in interleaved or in sequential format.
2221 o Two new functions, read.nexus() and write.nexus(), read/write trees
2224 o The new function bind.tree() allows to bind two trees together,
2225 possibly handling root edges to give internal branches.
2227 o The new function drop.tip() removes the tips in a phylogenetic tree,
2228 and trims (or not) the corresponding internal branches.
2230 o The new function is.ultrametric() tests if a tree is ultrametric.
2232 o The function plot.phylo() has more functionalities such as drawing the
2233 branches with different colours and/or different widths, showing the
2234 node labels, controling the position and font of the labels, rotating
2235 the labels, and controling the space around the plot.
2237 o The function read.tree() can now read trees with no branch length,
2238 such as "(a,b),c);". Consequently, the element `edge.length' in
2239 objects of class "phylo" is now optional.
2241 o The function write.tree() has a new default behaviour: if the default
2242 for the option `file' is used (i.e. file = ""), then a variable of
2243 mode character containing the tree in Newick format is returned which
2244 can thus be assigned (e.g., tree <- write.tree(phy)).
2246 o The function read.tree() has a new argument `text' which allows
2247 to read the tree in a variable of mode character.
2249 o A new data set is included: the phylogenetic relationships among
2250 the orders of birds from Sibley and Ahlquist (1990).
2254 CHANGES IN APE VERSION 0.2-1
2259 o Several bugs were fixed in the help pages.
2263 CHANGES IN APE VERSION 0.2
2268 o The function write.tree() writes phylogenetic trees (objects of class
2269 "phylo") in an ASCII file using the Newick parenthetic format.
2271 o The function birthdeath() fits a birth-death model to branching times
2272 by maximum likelihood, and estimates the corresponding speciation and
2275 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
2278 o The function is.binary.tree() tests whether a phylogeny is binary.
2280 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
2281 as well as some methods are introduced.
2283 o Several functions, including some generics and methods, for computing
2284 skyline plot estimates (classic and generalized) of effective
2285 population size through time are introduced and replace the function
2286 skyline.plot() in version 0.1.
2288 o Two data sets are now included: the phylogenetic relationships among
2289 the families of birds from Sibley and Ahlquist (1990), and an
2290 estimated clock-like phylogeny of HIV sequences sampled in the
2291 Democratic Republic of Congo.
2294 DEPRECATED & DEFUNCT
2296 o The function skyline.plot() in ape 0.1 has been deprecated and
2297 replaced by more elaborate functions (see above).
2302 o Two important bugs were fixed in plot.phylo(): phylogenies with
2303 multichotomies not at the root or not with only terminal branches,
2304 and phylogenies with a single node (i.e. only terminal branches)
2305 did not plot. These trees should be plotted correctly now.
2307 o Several bugs were fixed in diversi.time() in the computation of
2310 o Various errors were corrected in the help pages.