1 CHANGES IN APE VERSION 3.0-2
6 o birthdeath() now catches errors and warnings much better so that
7 a result is returned in most cases.
11 CHANGES IN APE VERSION 3.0-2
16 o The new function alex (alignment explorator) zooms in a DNA
17 alignment and opens the result in a new window.
22 o compute.brtime() did not completely randomized the order of the
25 o write.nexus() did not work correctly with rooted trees (thanks
26 to Matt Johnson for the fix).
28 o mltt.plot(, backward = FALSE) did not set the x-axis correctly.
30 o A bug was introduced in prop.clades() with ape 3.0. The help page
31 has been clarified relative to the use of the option 'rooted'.
33 o mantel.test() printed a useless warning message.
35 o plot.phylo(, direction = "downward") ignored 'y.lim'.
37 o is.monophyletic() did not work correctly if 'tips' was not stored
40 o prop.part() could make R crash if the first tree had many
43 o njs(), bionjs(), and mvrs() now return an error if 'fs < 1'.
45 o SDM() did not work correctly. The code has also been generally
51 o The DESCRIPTION file has been updated.
53 o The option 'original.data' of write.nexus() has been removed.
55 o The files bionjs.c, mvr.c, mvrs.c, njs.c, triangMtd.c, and
56 triangMtds.c have been improved which should fix some bugs in
57 the corresponding functions.
59 o dist.gene() now coerces input data frame as matrix resulting in
60 much faster calculations (thanks to a suggestion by Markus
65 CHANGES IN APE VERSION 3.0-1
70 o dist.dna() has two new models: "indel" and "indelblock".
72 o bind.tree() now accepts 'position' > 0 when the trees have no
73 banch length permitting to create a node in 'x' when grafting
74 'y' (see ?bind.tree for details).
79 o cophyloplot( , rotate = TRUE) made R hanged after a few clicks.
80 Also the tree is no more plotted twice.
82 o read.GenBank() has been updated to work with EFetch 2.0.
84 o unroot() on trees in "pruningwise" order did not respect this
89 CHANGES IN APE VERSION 3.0
94 o The three functions dyule, dbd, and dbdTime calculate the
95 density probability (i.e., the distribution of the number of
96 species) for the Yule, the constant and the time-dependent
97 birth-beath models, respectively. These probabilities can be
98 conditional on no extinction and/or on a log-scale.
100 o plot.phylo() has a new option 'rotate.tree' to rotate unrooted,
101 fan, or radial trees around the center of the plot.
103 o boot.phylo() and prop.clades() have a new option rooted =
104 FALSE. Note that the behaviour of prop.part() is unchanged.
106 o edgelabels() has a new option 'date' to place labels on edges of
107 chronograms using the time scale (suggestion by Rob Lanfear).
112 o In chronopl(), the code setting the initial dates failed in
113 complicated settings (several dates known within intervals).
114 This has been generally improved and should result in faster
115 and more efficient convergence even in simple settings.
117 o mantel.test() sometimes returned P-values > 1 with the default
120 o extract.clade() sometimes shuffled some tip labels (thanks to
121 Ludovic Mallet and Mahendra Mariadassou for the fix).
123 o clustal() should now find by default the executable under Windows.
128 o The code of yule() has been simplified and is now much faster for
131 o The code of mantel.test() has been adjusted to be consistent
132 with common permutation tests.
134 o The C code of base.freq() has been improved and is now nearly 8
137 o The option 'original.data' of write.nexus() is now deprecated and
138 will be removed in a future release.
140 o The code of is.ultrametric() has been improved and is now 3 times
143 o The code of vcv.phylo() has been improved and is now 10 or 30
144 times faster for 100 or 1000 tips, respectively. Consequently,
145 fitting models with PGLS will be faster overall.
149 CHANGES IN APE VERSION 2.8
154 o Twelve new functions have been written by Andrei-Alin Popescu:
155 additive, ultrametric, is.compatible, arecompatible, mvr, mvrs,
156 njs, bionjs, SDM, treePop, triangMtd, triangMtd*.
158 o A new class "bitsplits" has been created by Andrei-Alin Popescu
159 to code splits (aka, bipartition).
161 o There is a new generic function as.bitsplits with a method to
162 convert from the class "prop.part" to the class "bitsplits".
164 o The new function ltt.coplot plots on the same scales a tree and
165 the derived LTT plot.
167 o ltt.plot() has two new options: backward and tol. It can now
168 handle non-ultrametic trees and its internal coding has been
169 improved. The coordinates of the plot can now be computed with
170 the new function ltt.plot.coords.
175 o prop.part() crashed if some trees had some multichotomies.
179 CHANGES IN APE VERSION 2.7-3
184 o The new function compute.brtime computes and sets branching times.
186 o mantel.test() has a new argument 'alternative' which is
187 "two-sided" by default. Previously, this test was one-tailed
188 with no possibility to change.
190 o ace() can now do REML estimation with continuous characters,
191 giving better estimates of the variance of the Brownian motion
197 o Branch lengths were wrongly updated with bind.tree(, where = <tip>,
198 position = 0). (Thanks to Liam Revell for digging this bug out.)
200 o Simulation of OU process with rTraitCont() did not work correctly.
201 This now uses formula from Gillespie (1996) reduced to a BM
202 process when alpha = 0 to avoid division by zero. The option
203 'linear' has been removed.
205 o Cross-validation in chronopl() did not work when 'age.max' was
208 o consensus(, p = 0.5) could return an incorrect tree if some
209 incompatible splits occur in 50% of the trees (especially with
210 small number of trees).
212 o c() with "multiPhylo" did not work correctly (thanks to Klaus
213 Schliep for the fix).
215 o root() failed in some cases with an outgroup made of several tips.
216 The help page has been clarified a bit.
220 CHANGES IN APE VERSION 2.7-2
225 o There is a new class "evonet" to code evolutionary networks, with
226 a constructor function evonet(), a print() and a plot() methods,
227 and four conversion methods to the classes "phylo", "networx",
228 "network", and "igraph".
230 o The new function rTraitMult does multivariate traits simulation
231 with user-defined models.
233 o plot.phylo() has a new option 'plot = TRUE'. If FALSE, the tree
234 is not plotted but the graphical device is set and the
235 coordinates are saved as usual.
237 o diversity.contrast.test() gains a fourth version of the test with
238 method = "logratio"; the literature citations have been clarified.
240 o add.scale.bar() has two new options, 'lwd' and 'lcol', to modify
241 the aspect of the bar.
243 o boot.phylo() now displays a progress bar by default (can be off
246 o There is a new predict() method for compar.gee().
251 o bionj() made R crash if distances were too large. It now returns
252 an error if at least one distance is greater than 100.
254 o drop.tip() returned a wrong tree if 'tip' was of zero length.
256 o read.nexus.data() failed with URLs.
258 o boot.phylo() returned overestimated support values in the
259 presence of identical or nearly identical sequences.
264 o The data bird.families, bird.orders, cynipids, and woodmouse are
265 now provided as .rda files.
269 CHANGES IN APE VERSION 2.7-1
274 o The new function trex does tree exploration with multiple
277 o The new function kronoviz plots several rooted (dated) trees on
280 o identify.phylo() has a new option 'quiet' (FALSE by default).
285 o A bug was introduced in read.nexus() in ape 2.7.
287 o image.DNAbin() did not colour correctly the bases if there were
290 o .compressTipLabel() failed with a list with a single tree.
292 o identify.phylo() returned a wrong answer when the x- and y-scales
295 o write.nexus() failed with lists of trees with compressed labels.
300 o identify.phylo() now returns NULL if the user right- (instead of
301 left-) clicks (an error was returned previously).
303 o read.nexus() should be robust to commands inserted in the TREES
308 CHANGES IN APE VERSION 2.7
313 o There is a new image() method for "DNAbin" objects: it plots DNA
314 alignments in a flexible and efficient way.
316 o Two new functions as.network.phylo and as.igraph.phylo convert
317 trees of class "phylo" into these respective network classes
318 defined in the packages of the same names.
320 o The three new functions clustal, muscle, and tcoffee perform
321 nucleotide sequence alignment by calling the external programs
324 o Four new functions, diversity.contrast.test, mcconwaysims.test,
325 richness.yule.test, and slowinskiguyer.test, implement various
326 tests of diversification shifts using sister-clade comparisons.
328 o base.freq() gains an option 'all' to count all the possible bases
329 including the ambiguous ones (defaults to FALSE).
331 o read.nexus() now writes tree names in the NEXUS file if given a
332 list of trees with names.
337 o prop.part() failed in some situations with unrooted trees.
339 o read.nexus() shuffled node labels when a TRANSLATE block was
342 o varCompPhylip() did not work if 'exec' was specified.
344 o bind.tree() shuffled node labels when position > 0 and 'where'
350 o BaseProportion in src/dist_dna.c has been modified.
352 o A number of functions in src/tree_build.c have been modified.
354 o The matching representation has now only two columns as the third
355 column was redundant.
359 CHANGES IN APE VERSION 2.6-3
364 o rTraitCont() and rTraitDisc() gains a '...' argument used with
365 user-defined models (suggestion by Gene Hunt).
370 o as.hclust.phylo() now returns an error with unrooted trees.
372 o as.hclust.phylo() failed with trees with node labels (thanks to
373 Jinlong Zhang for pointing this bug out).
375 o read.dna(, "fasta") failed if sequences were not all of the same
378 o plot.phylo() did not recycle values of 'font', 'cex' and
379 'tip.color' correctly when type = "fan" or "radial".
381 o plot.phylo() ignored 'label.offset' when type = "radial", "fan", or
382 "unrooted" with lab4ut = "axial" (the placement of tip labels still
383 needs to be improved with lab4ut = "horizontal").
388 o In drop.fossil() the default tol = 0 has been raised to 1e-8.
390 o The help command ?phylo now points to the man page of read.tree()
391 where this class is described. Similarly, ?matching points to the
392 man page of as.matching().
396 CHANGES IN APE VERSION 2.6-2
401 o Two new functions, pic.ortho and varCompPhylip, implements the
402 orthonormal contrasts of Felsenstein (2008, Am Nat, 171:713). The
403 second function requires Phylip to be installed on the computer.
405 o bd.ext() has a new option conditional = TRUE to use probabilities
406 conditioned on no extinction for the taxonomic data.
411 o write.tree() failed to output correctly tree names.
413 o dist.nodes() returned duplicated column(s) with unrooted and/or
414 multichotomous trees.
416 o mcmc.popsize() terminated unexpectedly if the progress bar was
419 o prop.part(x) made R frozen if 'x' is of class "multiPhylo".
421 o Compilation under Mandriva failed (thanks to Jos Käfer for the fix).
423 o drop.tip() shuffled tip labels with subtree = TRUE or trim.internal
426 o Objects returned by as.hclust.phylo() failed when analysed with
427 cutree() or rect.hclust().
429 o write.tree() did not output correctly node labels (thanks to Naim
430 Matasci and Jeremy Beaulieu for the fix).
432 o ace(type = "discrete") has been improved thanks to Naim Marasci and
437 CHANGES IN APE VERSION 2.6-1
442 o The new function speciesTree calculates the species tree from a set
443 of gene trees. Several methods are available including maximum tree
444 and shallowest divergence tree.
449 o A bug introduced in write.tree() with ape 2.6 has been fixed.
451 o as.list.DNAbin() did not work correctly with vectors.
453 o as.hclust.phylo() failed with trees with node labels (thanks to
454 Filipe Vieira for the fix).
458 CHANGES IN APE VERSION 2.6
463 o The new functions rlineage and rbdtree simulate phylogenies under
464 any user-defined time-dependent speciation-extinction model. They
465 use continuous time algorithms.
467 o The new function drop.fossil removes the extinct species from a
470 o The new function bd.time fits a user-defined time-dependent
471 birth-death model. It is a generalization of yule.time() taking
472 extinction into account.
474 o The new function MPR does most parsimonious reconstruction of
477 o The new function Ftab computes the contingency table of base
478 frequencies from a pair of sequences.
480 o There is now an 'as.list' method for the class "DNAbin".
482 o dist.dna() can compute the number of transitions or transversions
483 with the option model = "Ts" or model = "Tv", respectively.
485 o [node|tip|edge]labels() gain three options with default values to
486 control the aspect of thermometers: horiz = TRUE, width = NULL,
489 o compar.gee() has been improved with the new option 'corStruct' as an
490 alternative to 'phy' to specify the correlation structure, and
491 calculation of the QIC (Pan 2001, Biometrics). The display of the
492 results has also been improved.
494 o read.GenBank() has a new option 'gene.names' to return the name of
495 the gene (FALSE by default).
500 o extract.clade() sometimes shuffled the tip labels.
502 o plot.phylo(type = "unrooted") did not force asp = 1 (thanks to Klaus
505 o dist.dna(model = "logdet") used to divide distances by 4. The
506 documentation has been clarified on the formulae used.
511 o rTraitCont(model = "OU") has an option 'linear = TRUE' to possibly
512 change the parameterisation (see ?rTraitCont for details).
514 o pic() now returns a vector with the node labels of the tree (if
517 o write.tree() and read.tree() have been substantially improved thanks
518 to contributions by Klaus Schliep.
522 CHANGES IN APE VERSION 2.5-3
527 o The new function mixedFontLabel helps to make labels with bits of
528 text to be plotted in different fonts.
530 o There are now replacement operators for [, [[, and $ for the class
531 "multiPhylo" (i.e., TREES[11:20] <- rmtree(10, 100)). They possibly
532 check that the tip labels are the same in all trees.
534 o Objects of class "multiPhylo" can be built with c(): there are
535 methods for the classes "phylo" and "multiPhylo".
537 o The internal functions .compressTipLabel and .uncompressTipLabel are
543 o bind.tree(x, y, where, position = 0) did not work correctly if 'y'
544 was a single-edge tree and 'where' was a tip.
546 o rTraitCont() did not use the square-root of branch lengths when
547 simulating a Brownian motion model.
551 CHANGES IN APE VERSION 2.5-2
556 o There is now a print method for results from ace().
558 o There is a labels() method for objects of class "DNAbin".
560 o read.dna() has a new option 'as.matrix' to possibly force sequences
561 in a FASTA file to be stored in a matrix (see ?read.dna for details).
566 o as.phylo.hclust() used to multiply edge lengths by 2.
568 o A minor bug was fixed in rTraitDisc().
570 o ace() sometimes failed (parameter value was NaN and the optimisation
576 o evolve.phylo() and plot.ancestral() have been removed.
578 o chronogram(), ratogram(), and NPRS.criterion() have been removed.
583 o nj() has been improved and is now about 30% faster.
585 o The default option 'drop' of [.DNAbin has been changed to FALSE to
586 avoid dropping rownames when selecting a single sequence.
588 o print.DNAbin() has been changed to summary.DNAbin() which has been
593 CHANGES IN APE VERSION 2.5-1
598 o The new function stree generates trees with regular shapes.
600 o It is now possible to bind two trees with x + y (see ?bind.tree for
603 o drop.tip(), extract.clade(), root(), and bind.tree() now have an
604 'interactive' option to make the operation on a plotted tree.
606 o cophyloplot() gains two new arguments 'lwd' and 'lty' for the
607 association links; they are recycled like 'col' (which wasn't before).
612 o rTraitDisc() did not use its 'freq' argument correctly (it was
613 multiplied with the rate matrix column-wise instead of row-wise).
615 o [node|tip|edge]labels(thermo = ) used to draw empty thermometers
616 with NA values. Nothing is drawn now like with 'text' or 'pch'.
617 The same bug occurred with the 'pie' option.
619 o A bug was fixed in compar.ou() and the help page was clarified.
621 o bind.tree() has been rewritten fixing several bugs and making it
624 o plot.phylo(type = "p") sometimes failed to colour correctly the
625 vertical lines representing the nodes.
627 o plot.phylo(direction = "l", x.lim = 30) failed to plot the branches
628 in the correct direction though the tip labels were displayed
634 o The c, cbind, and rbind methods for "DNAbin" objetcs now check that
635 the sequences are correctly stored (in a list for c, in a matrix
636 for the two other functions).
640 CHANGES IN APE VERSION 2.5
645 o The new function parafit by Pierre Legendre tests for the
646 coevolution between hosts and parasites. It has a companion
647 function, pcoa, that does principal coordinate decomposition.
648 The latter has a biplot method.
650 o The new function lmorigin by Pierre Legendre performs multiple
651 regression through the origin with testing by permutation.
653 o The new functions rTraitCont and rTraitDisc simulate continuous and
654 discrete traits under a wide range of evolutionary models.
656 o The new function delta.plot does a delta plot following Holland et
657 al. (2002, Mol. Biol. Evol. 12:2051).
659 o The new function edges draws additional branches between any nodes
660 and/or tips on a plotted tree.
662 o The new function fancyarrows enhances arrows from graphics with
663 triangle and harpoon heads; it can be called from edges().
665 o add.scale.bar() has a new option 'ask' to draw interactively.
667 o The branch length score replaces the geodesic distance in dist.topo.
669 o Three new data sets are included: the gopher-lice data (gopher.D),
670 SO2 air pollution in 41 US cities (lmorigin.ex1, from Sokal &
671 Rohlf 1995), and some host-parasite specificity data
672 (lmorigin.ex2, from Legendre & Desdevises 2009).
677 o add.scale.bar() drew the bar outside the plotting region with the
678 default options with unrooted or radial trees.
680 o dist.topo() made R stuck when the trees had different sizes (thanks
681 to Otto Cordero for the fix).
686 o The geodesic distance has been replaced by the branch length score
691 CHANGES IN APE VERSION 2.4-1
696 o rtree() and rcoal() now accept a numeric vector for the 'br'
699 o vcv() is a new generic function with methods for the classes "phylo"
700 and "corPhyl" so that it is possible to calculate the var-cov matrix
701 for "transformation models". vcv.phylo() can still be used for trees
702 of class "phylo"; its argument 'cor' has been renamed 'corr'.
707 o bind.tree() failed when 'y' had no root edge.
709 o read.nexus() shuffled tip labels when the trees have no branch
710 lengths and there is a TRANSLATE block.
712 o read.nexus() does not try to translate node labels if there is a
713 translation table in the NEXUS file. See ?read.nexus for a
714 clarification on this behaviour.
716 o plot.multiPhylo() crashed R when plotting a list of trees with
717 compressed tip labels.
719 o write.nexus() did not translate the taxa names when asked for.
721 o plot.phylo(type = "fan") did not rotate the tip labels correctly
722 when the tree has branch lengths.
724 o ace(type = "continuous", method = "ML") now avoids sigma² being
725 negative (which resulted in an error).
727 o nj() crashed with NA/NaN in the distance matrix: an error in now
732 CHANGES IN APE VERSION 2.4
737 o base.freq() has a new option 'freq' to return the counts; the
738 default is still to return the proportions.
743 o seg.sites() did not handle ambiguous nucleotides correctly: they
746 o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
747 the tree: the argument is now ignored.
749 o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
755 o Trying to plot a tree with a single tip now returns NULL with a
756 warning (it returned an error previously).
758 o The way lines representing nodes are coloured in phylograms has
759 been modified (as well as their widths and types) following some
760 users' request; this is only for dichotomous nodes.
762 o The argument 'adj' in [node][tip][edge]labels() now works when
763 using 'pie' or 'thermo'.
765 o A more informative message error is now returned by dist.dna() when
766 'model' is badly specified (partial matching of this argument is
769 o Deprecated functions are now listed in a help page: see
770 help("ape-defunct") with the quotes.
775 o The functions heterozygosity, nuc.div, theta.h, theta.k and
776 theta.s have been moved from ape to pegas.
778 o The functions mlphylo, DNAmodel and sh.test have been removed.
782 CHANGES IN APE VERSION 2.3-3
787 o add.scale.bar() always drew a horizontal bar.
789 o zoom() shuffled tips with unrooted trees.
791 o write.nexus() failed to write correctly trees with a "TipLabel"
794 o rcoal() failed to compute branch lengths with very large n.
796 o A small bug was fixed in compar.cheverud() (thanks to Michael
799 o seg.sites() failed when passing a vector.
801 o drop.tip() sometimes shuffled tip labels.
803 o root() shuffled node labels with 'resolve.root = TRUE'.
807 CHANGES IN APE VERSION 2.3-2
812 o all.equal.phylo() did not compare unrooted trees correctly.
814 o dist.topo(... method = "PH85") did not treat unrooted trees
815 correctly (thanks to Tim Wallstrom for the fix).
817 o root() sometimes failed to test for the monophyly of the
820 o extract.clade() sometimes included too many edges.
822 o vcv.phylo() did not work correctly when the tree is in
825 o nj() did not handle correctly distance matrices with many 0's.
826 The code has also been significantly improved: 7, 70, 160 times
827 faster with n = 100, 500, 1000, respectively.
831 CHANGES IN APE VERSION 2.3-1
836 o The new function is.monophyletic tests the monophyly of a group.
838 o There is now a c() method for lists of class "DNAbin".
840 o yule.cov() now fits the null model, and its help page has been
841 corrected with respect to this change.
843 o drop.tip() has a new option 'rooted' to force (or not) a tree
844 to be treated as (un)rooted.
849 o dist.gene() failed on most occasions with the default
850 pairwise.deletion = FALSE.
852 o read.tree() failed to read correctly the tree name(s).
854 o boot.phylo() now treats correctly data frames.
856 o del.gaps() did not copy the rownames of a matrix.
858 o A small bug was fixed in CDAM.global().
860 o ace() failed with large data sets. Thanks to Rich FitzJohn for
861 the fix. With other improvements, this function is now about 6
864 o write.tree() failed with objects of class "multiPhylo".
866 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
871 o [.multiPhylo and [.DNAbin now respect the original class.
873 o Instances of the form class(phy) == "phylo" have been replaced
874 by inherits(phy, "phylo").
876 o rcoal() is now faster.
881 o klastorin() has been removed.
885 CHANGES IN APE VERSION 2.3
890 o The new functions CADM.global and CADM.post, contributed by
891 Pierre Legendre, test the congruence among several distance
894 o The new function yule.time fits a user-defined time-dependent
895 Yule model by maximum likelihood.
897 o The new function makeNodeLabel creates and/or modifies node
898 labels in a flexible way.
900 o read.tree() and write.tree() have been modified so that they can
901 handle individual tree names.
903 o plot.phylo() has a new argument 'edge.lty' that specifies the
904 types of lines used for the edges (plain, dotted, dashed, ...)
906 o phymltest() has been updated to work with PhyML 3.0.1.
911 o drop.tip() shuffled tip labels in some cases.
913 o drop.tip() did not handle node.label correctly.
915 o is.ultrametric() now checks the ordering of the edge matrix.
917 o ace() sometimes returned negative values of likelihoods of
918 ancestral states (thanks to Dan Rabosky for solving this long
924 o The data set xenarthra has been removed.
928 CHANGES IN APE VERSION 2.2-4
932 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
933 now fixed. (Thanks to Peter Wragg for the fix!)
935 o A warning message occurred for no reason with ace(method="GLS").
940 o There is now a general help page displayed with '?ape'.
944 CHANGES IN APE VERSION 2.2-3
949 o The new function extract.clade extracts a clade from a tree by
950 specifying a node number or label.
952 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
953 operations of the same names.
955 o dist.dna() can now return the number of site differences by
956 specifying model="N".
961 o chronopl() did not work with CV = TRUE.
963 o read.nexus() did not work correctly in some situations (trees on
964 multiple lines with different numbers of lines and/or with
965 comments inserted within the trees).
967 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
968 the number of lineages with non-binary trees.
973 o ape has now a namespace.
975 o drop.tip() has been improved: it should be much faster and work
976 better in some cases (e.g., see the example in ?zoom).
980 CHANGES IN APE VERSION 2.2-2
985 o dist.gene() has been substantially improved and gains an option
988 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
994 o prop.part() failed with a single tree with the default option
995 'check.labels = TRUE'.
997 o summary.DNAbin() failed to display correctly the summary of
998 sequence lengths with lists of sequences of 10,000 bases or more
999 (because summary.default uses 4 significant digits by default).
1001 o read.nexus() failed to read a file with a single tree with line
1002 breaks in the Newick string.
1004 o del.gaps() returned a list of empty sequences when there were no
1010 o phymltest() has been updated for PhyML 3.0 and gains an option
1011 'append', whereas the option 'path2exec' has been removed.
1013 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
1014 which is returned unchanged (instead of an error).
1016 o The data sets bird.orders and bird.families are now stored as
1017 Newick strings; i.e., the command data(bird.orders) calls
1022 CHANGES IN APE VERSION 2.2-1
1027 o The new function makeLabel() helps to modify labels of trees,
1028 lists of trees, or DNA sequences, with several utilities to
1029 truncate and/or make them unique, substituting some
1030 characters, and so on.
1032 o The new function del.gaps() removes insertion gaps ("-") in a
1033 set of DNA sequences.
1035 o read.dna() can now read Clustal files (*.aln).
1040 o root() failed with 'resolve.root = TRUE' when the root was
1041 already the specified root.
1043 o Several bugs were fixed in mlphylo().
1045 o collapsed.singles() did not propagate the 'Nnode' and
1046 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
1048 o read.nexus() failed to remove correctly the comments within
1051 o read.nexus() failed to read a file with a single tree and no
1052 translation of tip labels.
1054 o read.nexus() failed to place correctly tip labels when reading
1055 a single tree with no edge lengths.
1057 o A bug was fixed in sh.test().
1062 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
1065 o The option 'check.labels' of consensus() and prop.part() is now
1068 o write.dna() now does not truncate names to 10 characters with
1073 CHANGES IN APE VERSION 2.2
1078 o Four new functions have been written by Damien de Vienne for the
1079 graphical exploration of large trees (cophyloplot, subtrees,
1080 subtreeplot), and to return the graphical coordinates of tree
1083 o The new functions corPagel and corBlomberg implement the Pagel's
1084 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
1086 o chronopl() has been improved and gains several options: see its
1087 help page for details.
1089 o boot.phylo() has now an option 'trees' to possibly return the
1090 bootstraped trees (the default is FALSE).
1092 o prop.part() has been improved and should now be faster in all
1098 o read.dna() failed if "?" occurred in the first 10 sites of the
1101 o The x/y aspect of the plot is now respected when plotting a
1102 circular tree (type = "r" or "f").
1104 o Drawing the tip labels sometimes failed when plotting circular
1107 o zoom() failed when tip labels were used instead of their numbers
1108 (thanks to Yan Wong for the fix).
1110 o drop.tip() failed with some trees (fixed by Yan Wong).
1112 o seg.sites() failed with a list.
1114 o consensus() failed in some cases. The function has been improved
1115 as well and is faster.
1119 CHANGES IN APE VERSION 2.1-3
1124 o A bug in read.nexus() made the Windows R-GUI crash.
1126 o An error was fixed in the computation of ancestral character
1127 states by generalized least squares in ace().
1129 o di2multi() did not modify node labels correctly.
1131 o multi2di() failed if the tree had its attribute "order" set to
1136 CHANGES IN APE VERSION 2.1-2
1141 o There three new methods for the "multiPhylo" class: str, $,
1144 o root() gains the options 'node' and 'resolve.root'
1145 (FALSE by default) as well as its code being improved.
1147 o mltt.plot() has now an option 'log' used in the same way
1148 than in plot.default().
1153 o mltt.plot() failed to display the legend with an unnamed
1156 o nodelabels() with pies now correcly uses the argument
1157 'cex' to draw symbols of different sizes (which has
1158 worked already for thermometers).
1160 o read.nexus() generally failed to read very big files.
1165 o The argument 'family' of compar.gee() can now be a function
1166 as well as a character string.
1168 o read.tree() and read.nexus() now return an unnamed list if
1169 'tree.names = NULL'.
1171 o read.nexus() now returns a modified object of class "multiPhylo"
1172 when there is a TRANSLATE block in the NEXUS file: the individual
1173 trees have no 'tip.label' vector, but the list has a 'TipLabel'
1174 attribute. The new methods '$' and '[[' set these elements
1175 correctly when extracting trees.
1179 CHANGES IN APE VERSION 2.1-1
1184 o The new function rmtree generates lists of random trees.
1186 o rcoal() now generates a genuine coalescent tree by default
1187 (thanks to Vladimir Minin for the code).
1192 o nuc.div() returned an incorrect value with the default
1193 pairwise.deletion = FALSE.
1198 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
1199 have been improved so that they are stabler and faster.
1201 o R packages used by ape are now loaded silently; lattice and gee
1202 are loaded only when needed.
1206 CHANGES IN APE VERSION 2.1
1211 o The new function identify.phylo identifies clades on a plotted
1212 tree using the mouse.
1214 o It is now possible to subset a list of trees (object of class
1215 "multiPhylo") with "[" while keeping its class correct.
1217 o The new function as.DNAbin.alignment converts DNA sequences
1218 stored in the "alignment" format of the package seqinr into
1219 an object of class "DNAbin".
1221 o The new function weight.taxo2 helps to build similarity matrices
1222 given two taxonomic levels (usually called by other functions).
1224 o write.tree() can now take a list of trees (class "multiPhylo")
1225 as its main argument.
1227 o plot.correlogram() and plot.correlogramList() have been
1228 improved, and gain several options (see the help page for
1229 details). A legend is now plotted by default.
1234 o dist.dna() returned some incorrect values with `model = "JC69"'
1235 and `pairwise.deletion = TRUE'. This affected only the
1236 distances involving sequences with missing values. (Thanks
1237 to Bruno Toupance for digging this bug out.)
1239 o write.tree() failed with some trees: this is fixed by removing
1240 the `multi.line' option (trees are now always printed on a
1243 o read.nexus() did not correctly detect trees with multiple root
1244 edges (see OTHER CHANGES).
1249 o The code of mlphylo() has been almost entirely rewritten, and
1250 should be much stabler. The options have been also greatly
1251 simplified (see ?mlphylo and ?DNAmodel for details).
1253 o The internal function nTips has been renamed klastorin_nTips.
1255 o The code of is.ultrametric() contained redundancies and has
1258 o The code of Moran.I() and of correlogram.formula() have been
1261 o read.tree() and read.nexus() now return an error when trying to
1262 read a tree with multiple root edges (see BUG FIXES). The
1263 correction applied in previous version did not work in all
1266 o The class c("multi.tree", "phylo") has been renamed
1272 o There is now a vignette in ape: see vignette("MoranI", "ape").
1275 DEPRECATED & DEFUNCT
1277 o as.matching() and as.phylo.matching() do not support branch
1280 o correlogram.phylo() and discrete.dist() have been removed.
1284 CHANGES IN APE VERSION 2.0-2
1289 o The new function matexpo computes the exponential of a square
1292 o The new function unique.multi.tree removes duplicate trees from
1295 o yule() has a new option `use.root.edge = FALSE' that specifies
1296 to ignore, by default, the root edge of the tree if it exists.
1301 o which.edge() failed when the index of a single terminal edge was
1304 o In diversi.time(), the values returned for model C were
1307 o A bug was fixed in yule() that affected the calculation of the
1308 likelihood in the presence of ties in the branching times.
1310 o There was a bug in the C function mat_expo4x4 affecting the
1311 calculations of the transition probabilities for models HKY and
1314 o A small bug was fixed in as.matrix.DNAbin (thanks to James
1317 o rtree() did not `shuffle' the tip labels by default, so only a
1318 limited number of labelled topologies could be generated.
1322 CHANGES IN APE VERSION 2.0-1
1327 o The three new functions bionj, fastme.ols, and fastme.bal
1328 perform phylogeny estimation by the BIONJ and fastME methods in
1329 OLS and balanced versions. This is a port to R of previous
1330 previous programs done by Vincent Lefort.
1332 o The new function chronoMPL performs molecular dating with the
1333 mean path lengths method of Britton et al. (2002, Mol. Phyl.
1336 o The new function rotate, contributed by Christoph Heibl, swaps
1337 two clades connected to the same node. It works also with
1338 multichotomous nodes.
1340 o The new `method' as.matrix.DNAbin() may be used to convert
1341 easily DNA sequences stored in a list into a matrix while
1342 keeping the names and the class.
1347 o chronopl() failed when some branch lengths were equal to zero:
1348 an error message is now returned.
1350 o di2multi() failed when there was a series of consecutive edges
1355 CHANGES IN APE VERSION 1.10-2
1360 o plot.phylo() can now plot circular trees: the option is type =
1361 "fan" or type = "f" (to avoid the ambiguity with type = "c").
1363 o prop.part() has a new option `check.labels = FALSE' which allows
1364 to considerably speed-up the calculations of bipartitions. As a
1365 consequence, calculations of bootstrap values with boot.phylo()
1366 should be much faster.
1371 o read.GenBank() did not return correctly the list of species as
1372 from ape 1.10: this is fixed in this version
1374 o Applying as.phylo() on a tree of class "phylo" failed: the
1375 object is now returned unchanged.
1379 CHANGES IN APE VERSION 1.10-1
1384 o The three new functions Ntip, Nnode, and Nedge return, for a
1385 given tree, the number of tips, nodes, or edges, respectively.
1390 o read.nexus() did not set correctly the class of the returned
1391 object when reading multiple trees.
1393 o mllt.plot() failed with objects of class c("multi.tree",
1396 o unroot() did not work correctly in most cases.
1398 o reorder.phylo() made R freeze in some occasions.
1400 o Plotting a tree in pruningwise order failed.
1402 o When plotting an unrooted tree, the tip labels where not all
1403 correctly positioned if the option `cex' was used.
1407 CHANGES IN APE VERSION 1.10
1412 o Five new `method' functions have been introduced to manipulate
1413 DNA sequences in binary format (see below).
1415 o Three new functions have been introduced to convert between the
1416 new binary and the character formats.
1418 o The new function as.alignment converts DNA sequences stored as
1419 single characters into the class "alignment" used by the package
1422 o read.dna() and read.GenBank() have a new argument `as.character'
1423 controlling whether the sequences are returned in binary format
1429 o root() failed when the tree had node labels: this is fixed.
1431 o plot.phylo() did not correctly set the limits on the y-axis with
1432 the default setting: this is fixed.
1434 o dist.dna() returned a wrong result for the LogDet, paralinear,
1435 and BH87 models with `pairwise.deletion = TRUE'.
1440 o DNA sequences are now internally stored in a binary format. See
1441 the document "A Bit-Level Coding Scheme for Nucleotides" for the
1442 details. Most functions analyzing DNA functions have been
1443 modified accordingly and are now much faster (dist.dna is now
1444 ca. 60 times faster).
1448 CHANGES IN APE VERSION 1.9-4
1453 o A bug was fixed in edgelabels().
1455 o as.phylo.hclust() did not work correctly when the object of
1456 class "hclust" has its labels set to NULL: the returned tree has
1457 now its tip labels set to "1", "2", ...
1459 o consensus could fail if some tip labels are a subset of others
1460 (e.g., "a" and "a_1"): this is now fixed.
1462 o mlphylo() failed in most cases if some branch lengths of the
1463 initial tree were greater than one: an error message is now
1466 o mlphylo() failed in most cases when estimating the proportion of
1467 invariants: this is fixed.
1471 CHANGES IN APE VERSION 1.9-3
1476 o The new function edgelabels adds labels on the edge of the tree
1477 in the same way than nodelabels or tiplabels.
1482 o multi2di() did not handle correctly branch lengths with the
1483 default option `random = TRUE': this is now fixed.
1485 o A bug was fixed in nuc.div() when using pairwise deletions.
1487 o A bug occurred in the analysis of bipartitions with large
1488 numbers of large trees, with consequences on prop.part,
1489 prop.clades, and boot.phylo.
1491 o The calculation of the Billera-Holmes-Vogtmann distance in
1492 dist.topo was wrong: this has been fixed.
1496 CHANGES IN APE VERSION 1.9-2
1501 o The new function ladderize reorganizes the internal structure of
1502 a tree to plot them left- or right-ladderized.
1504 o The new function dist.nodes computes the patristic distances
1505 between all nodes, internal and terminal, of a tree. It replaces
1506 the option `full = TRUE' of cophenetic.phylo (see below).
1511 o A bug was fixed in old2new.phylo().
1513 o Some bugs were fixed in chronopl().
1515 o The edge colours were not correctly displayed by plot.phylo
1516 (thank you to Li-San Wang for the fix).
1518 o cophenetic.phylo() failed with multichotomous trees: this is
1524 o read.dna() now returns the sequences in a matrix if they are
1525 aligned (interleaved or sequential format). Sequences in FASTA
1526 format are still returned in a list.
1528 o The option `full' of cophenetic.phylo() has been removed because
1529 it could not be used from the generic.
1532 DEPRECATED & DEFUNCT
1534 o rotate() has been removed; this function did not work correctly
1539 CHANGES IN APE VERSION 1.9-1
1544 o Trees with a single tip were not read correctly in R as the
1545 element `Nnode' was not set: this is fixed.
1547 o unroot() did not set correctly the number of nodes of the
1548 unrooted tree in most cases.
1550 o read.GenBank() failed when fetching very long sequences,
1551 particularly of the BX-series.
1553 o A bug was introduced in read.tree() with ape 1.9: it has been
1558 CHANGES IN APE VERSION 1.9
1563 o There are two new print `methods' for trees of class "phylo" and
1564 lists of trees of class "multi.tree", so that they are now
1565 displayed in a compact and informative way.
1567 o There are two new functions, old2new.phylo and new2old.phylo,
1568 for converting between the old and new coding of the class
1571 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
1572 LogDet ("logdet"), and paralinear ("paralin").
1574 o compute.brlen() has been extended: several methods are now
1575 available to compute branch lengths.
1577 o write.dna() can now handle matrices as well as lists.
1582 o cophenetic.phylo() sometimes returned a wrong result with
1583 multichotomous trees: this is fixed.
1585 o rotate() failed when a single tip was specified: the tree is now
1588 o ace() did not return the correct index matrix with custom
1589 models: this is fixed.
1591 o multi2di() did not work correctly when resolving multichotomies
1592 randomly: the topology was always the same, only the arrangement
1593 of clades was randomized: this is fixed. This function now
1594 accepts trees with no branch lengths.
1596 o The output of diversi.gof() was blurred by useless prints when a
1597 user distribution was specified. This has been corrected, and
1598 the help page of this function has been expanded.
1603 o The internal structure of the class "phylo" has been changed:
1604 see the document "Definition of Formats for Coding Phylogenetic
1605 Trees in R" for the details. In addition, the code of most
1606 functions has been improved.
1608 o Several functions have been improved by replacing some R codes
1609 by C codes: pic, plot.phylo, and reorder.phylo.
1611 o There is now a citation information: see citation("ape") in R.
1613 o write.tree() now does not add extra 0's to branch lengths so
1614 that 1.23 is printed "1.23" by default, not "1.2300000000".
1616 o The syntax of bind.tree() has been simplified. This function now
1617 accepts trees with no branch lengths, and handles correctly node
1620 o The option `as.numeric' of mrca() has been removed.
1622 o The unused options `format' and `rooted' of read.tree() have
1625 o The unused option `format' of write.tree() has been removed.
1627 o The use of node.depth() has been simplified.
1631 CHANGES IN APE VERSION 1.8-5
1636 o Two new functions read.nexus.data() and write.nexus.data(),
1637 contributed by Johan Nylander, allow to read and write molecular
1638 sequences in NEXUS files.
1640 o The new function reorder.phylo() reorders the internal structure
1641 of a tree of class "phylo". It is used as the generic, e.g.,
1644 o read.tree() and read.nexus() can now read trees with a single
1647 o The new data set `cynipids' supplies a set of protein sequences
1653 o The code of all.equal.phylo() has been completely rewritten
1654 (thanks to Benoît Durand) which fixes several bugs.
1656 o read.tree() and read.nexus() now checks the labels of the tree
1657 to remove or substitute any characters that are illegal in the
1658 Newick format (parentheses, etc.)
1660 o A negative P-value could be returned by mantel.test(): this is
1665 CHANGES IN APE VERSION 1.8-4
1670 o The new function sh.test() computes the Shimodaira-
1673 o The new function collapse.singles() removes the nodes with a
1674 single descendant from a tree.
1676 o plot.phylo() has a new argument `tip.color' to specify the
1677 colours of the tips.
1679 o mlphylo() has now an option `quiet' to control the display of
1680 the progress of the analysis (the default is FALSE).
1685 o read.dna() did not read correctly sequences in sequential format
1686 with leading alignment gaps "-": this is fixed.
1688 o ace() returned a list with no class so that the generic
1689 functions (anova, logLik, ...) could not be used directly. This
1690 is fixed as ace() now returns an object of class "ace".
1692 o anova.ace() had a small bug when computing the number of degrees
1693 of freedom: this is fixed.
1695 o mlphylo() did not work when the sequences were in a matrix or
1696 a data frame: this is fixed.
1698 o rtree() did not work correctly when trying to simulate an
1699 unrooted tree with two tips: an error message is now issued.
1704 o The algorithm of rtree() has been changed: it is now about 40,
1705 100, and 130 times faster for 10, 100, and 1000 tips,
1710 CHANGES IN APE VERSION 1.8-3
1715 o There are four new `method' functions to be used with the
1716 results of ace(): logLik(), deviance(), AIC(), and anova().
1718 o The plot method of phymltest has two new arguments: `main' to
1719 change the title, and `col' to control the colour of the
1720 segments showing the AIC values.
1722 o ace() has a new argument `ip' that gives the initial values used
1723 in the ML estimation with discrete characters (see the examples
1724 in ?ace). This function now returns a matrix giving the indices
1725 of the estimated rates when analysing discrete characters.
1727 o nodelabels() and tiplabels() have a new argument `pie' to
1728 represent proportions, with any number of categories, as
1729 piecharts. The use of the option `thermo' has been improved:
1730 there is now no limitation on the number of categories.
1735 o mlphylo() did not work with more than two partitions: this is
1738 o root() failed if the proposed outgroup was already an outgroup
1739 in the tree: this is fixed.
1741 o The `col' argument in nodelabels() and tiplabels() was not
1742 correctly passed when `text' was used: this is fixed.
1744 o Two bugs were fixed in mlphylo(): parameters were not always
1745 correctly output, and the estimation failed in some cases.
1747 o plot.phylo() was stuck when given a tree with a single tip: this
1748 is fixed and a message error is now returned.
1750 o An error was corrected in the help page of gammaStat regarding
1751 the calculation of P-values.
1753 o Using gls() could crash R when the number of species in the tree
1754 and in the variables were different: this is fixed.
1758 CHANGES IN APE VERSION 1.8-2
1763 o The new function mlphylo() fits a phylogenetic tree by maximum
1764 likelihood from DNA sequences. Its companion function DNAmodel()
1765 is used to define the substitution model which may include
1766 partitioning. There are methods for logLik(), deviance(), and
1767 AIC(), and the summary() method has been extended to display in
1768 a friendly way the results of this model fitting. Currently, the
1769 functionality is limited to estimating the substitution and
1770 associated parameters and computing the likelihood.
1772 o The new function drop1.compar.gee (used as, e.g., drop1(m))
1773 tests for single effects in GEE-based comparative method. A
1774 warning message is printed if there is not enough degrees of
1780 o An error message was sometimes issued by plot.multi.tree(),
1781 though with no consequence.
1785 CHANGES IN APE VERSION 1.8-1
1790 o There is a new plot method for lists of trees (objects of class
1791 "multi.tree"): it calls plot.phylo() internally and is
1792 documented on the same help page.
1797 o A bug was fixed in the C code that analyzes bipartitions: this
1798 has impact on several functions like prop.part, prop.clades,
1799 boot.phylo, or consensus.
1801 o root() did not work correctly when the specified outgroup had
1802 more than one element: this is fixed.
1804 o dist.dna() sometimes returned a warning inappropriately: this
1807 o If the distance object given to nj() had no rownames, nj()
1808 returned a tree with no tip labels: it now returns tips labelled
1809 "1", "2", ..., corresponding to the row numbers.
1814 o nj() has been slightly changed so that tips with a zero distance
1815 are first aggregated with zero-lengthed branches; the usual NJ
1816 procedure is then performed on a distance matrix without 0's.
1820 CHANGES IN APE VERSION 1.8
1825 o The new function chronopl() estimates dates using the penalized
1826 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1828 o The new function consensus() calculates the consensus tree of a
1831 o The new function evolve.phylo() simulates the evolution of
1832 continuous characters along a phylogeny under a Brownian model.
1834 o The new plot method for objects of class "ancestral" displays a
1835 tree together with ancestral values, as returned by the above
1838 o The new function as.phylo.formula() returns a phylogeny from a
1839 set of nested taxonomic variables given as a formula.
1841 o The new function read.caic() reads trees in CAIC format.
1843 o The new function tiplabels() allows to add labels to the tips
1844 of a tree using text or plotting symbols in a flexible way.
1846 o The new function unroot() unroots a phylogeny.
1848 o multi2di() has a new option, `random', which specifies whether
1849 to resolve the multichotomies randomly (the default) or not.
1851 o prop.part() now returns an object of class "prop.part" for which
1852 there are print (to display a partition in a more friendly way)
1853 and summary (to extract the numbers) methods.
1855 o plot.phylo() has a new option, `show.tip.label', specifying
1856 whether to print the labels of the tips. The default is TRUE.
1858 o The code of nj() has been replaced by a faster C code: it is now
1859 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1862 o write.nexus() now writes whether a tree is rooted or not.
1867 o Two bugs have been fixed in root(): unrooted trees are now
1868 handled corretly, and node labels are now output normally.
1870 o A bug was fixed in phymltest(): the executable couldn't be found
1873 o Three bug have been fixed in ace(): computing the likelihood of
1874 ancestral states of discrete characters failed, custom models
1875 did not work, and the function failed with a null gradient (a
1876 warning message is now returned; this latter bug was also
1877 present in yule.cov() as well and is now fixed).
1879 o pic() hanged out when missing data were present: a message error
1882 o A small bug was fixed in dist.dna() where the gamma correction
1883 was not always correctly dispatched.
1885 o plot.phylo() plotted correctly the root edge only when the tree
1886 was plotted rightwards: this works now for all directions.
1891 o dist.taxo() has been renamed as weight.taxo().
1893 o dist.phylo() has been replaced by the method cophenetic.phylo().
1895 o Various error and warning messages have been improved.
1899 CHANGES IN APE VERSION 1.7
1902 o The new function ace() estimates ancestral character states for
1903 continuous characters (with ML, GLS, and contrasts methods), and
1904 discrete characters (with ML only) for any number of states.
1906 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1907 of directional evolution for continuous characters. The user
1908 specifies the node(s) of the tree where the character optimum
1911 o The new function is.rooted() tests whether a tree (of class
1914 o The new function rcoal() generates random ultrametric trees with
1915 the possibility to specify the function that generates the
1916 inter-nodes distances.
1918 o The new function mrca() gives for all pairs of tips in a tree
1919 (and optionally nodes too) the most recent common ancestor.
1921 o nodelabels() has a new option `thermo' to plot proportions (up
1922 to three classes) on the nodes of a tree.
1924 o rtree() has been improved: it can now generate rooted or
1925 unrooted trees, and the mathematical function that generates the
1926 branch lengths may be specified by the user. The tip labels may
1927 be given directly in the call to rtree. The limit cases (n = 2,
1928 3) are now handled correctly.
1930 o dist.topo() has a new argument `method' with two choices: "PH85"
1931 for Penny and Henny's method (already available before and now
1932 the default), and "BHV01" for the geometric distance by Billera
1933 et al. (2001, Adv. Appl. Math. 27:733).
1935 o write.tree() has a new option, `digits', which specifies the
1936 number of digits to be printed in the Newick tree. By default
1937 digits = 10. The numbers are now always printed in decimal form
1938 (i.e., 1.0e-1 is now avoided).
1940 o dist.dna() can now compute the raw distances between pairs of
1941 DNA sequences by specifying model = "raw".
1943 o dist.phylo() has a new option `full' to possibly compute the
1944 distances among all tips and nodes of the tree. The default if
1950 o Several bugs were fixed in all.equal.phylo().
1952 o dist.dna() did not handle correctly gaps ("-") in alignments:
1953 they are now considered as missing data.
1955 o rotate() did not work if the tips were not ordered: this is
1958 o mantel.test() returned NA in some special cases: this is fixed
1959 and the function has been improved and is now faster.
1961 o A bug was fixed in diversi.gof() where the calculation of A² was
1964 o cherry() did not work correctly under some OSs (mainly Linux):
1967 o is.binary.tree() has been modified so that it works with both
1968 rooted and unrooted trees.
1970 o The documentation of theta.s() was not correct: this has been
1973 o plot.mst() did not work correctly: this is fixed.
1977 CHANGES IN APE VERSION 1.6
1982 o The new function dist.topo() computes the topological distances
1985 o The new function boot.phylo() performs a bootstrap analysis on
1986 phylogeny estimation.
1988 o The new functions prop.part() and prop.clades() analyse
1989 bipartitions from a series of trees.
1994 o read.GenBank() now uses the EFetch utility of NCBI instead of
1995 the usual Web interface: it is now much faster (e.g., 12 times
1996 faster to retrieve 8 sequences, 37 times for 60 sequences).
2001 o Several bugs were fixed in read.dna().
2003 o Several bugs were fixed in diversi.time().
2005 o is.binary.tree() did not work correctly if the tree has no edge
2006 lengths: this is fixed.
2008 o drop.tip() did not correctly propagated the `node.label' of a
2009 tree: this is fixed.
2013 CHANGES IN APE VERSION 1.5
2018 o Two new functions, as.matching.phylo() and as.phylo.matching(),
2019 convert objects between the classes "phylo" and "matching". The
2020 latter implements the representation of binary trees introduced by
2021 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
2022 as.matching() has been introduced as well.
2024 o Two new functions, multi2di() and di2multi(), allow to resolve
2025 and collapse multichotomies with branches of length zero.
2027 o The new function nuc.div() computes the nucleotide diversity
2028 from a sample a DNA sequences.
2030 o dist.dna() has been completely rewritten with a much faster
2031 (particularly for large data sets) C code. Eight models are
2032 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
2033 option `method' has been renamed `model'). Computation of variance
2034 is available for all models. A gamma-correction is possible for
2035 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
2036 to remove sites with missing data on a pairwise basis. The option
2037 `GCcontent' has been removed.
2039 o read.GenBank() has a new option (species.names) which specifies
2040 whether to return the species names of the organisms in addition
2041 to the accession numbers of the sequences (this is the default
2044 o write.nexus() can now write several trees in the same NEXUS file.
2046 o drop.tip() has a new option `root.edge' that allows to specify the
2047 new root edge if internal branches are trimmed.
2052 o as.phylo.hclust() failed if some labels had parentheses: this
2055 o Several bugs were fixed in all.equal.phylo(). This function now
2056 returns the logical TRUE if the trees are identical but with
2057 different representations (a report was printed previously).
2059 o read.GenBank() did not correctly handle ambiguous base codes:
2065 o birthdeath() now returns an object of class "birthdeath" for
2066 which there is a print method.
2070 CHANGES IN APE VERSION 1.4
2075 o The new function nj() performs phylogeny estimation with the
2076 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
2079 o The new function which.edge() identifies the edges of a tree
2080 that belong to a group specified as a set of tips.
2082 o The new function as.phylo.phylog() converts an object of class
2083 "phylog" (from the package ade4) into an object of class
2086 o The new function axisPhylo() draws axes on the side of a
2089 o The new function howmanytrees() calculates the number of trees
2090 in different cases and giving a number of tips.
2092 o write.tree() has a new option `multi.line' (TRUE by default) to
2093 write a Newick tree on several lines rather than on a single
2096 o The functionalities of zoom() have been extended. Several
2097 subtrees can be visualized at the same time, and they are marked
2098 on the main tree with colors. The context of the subtrees can be
2099 marked with the option `subtree' (see below).
2101 o drop.tip() has a new option `subtree' (FALSE by default) which
2102 specifies whether to output in the tree how many tips have been
2105 o The arguments of add.scale.bar() have been redefined and have
2106 now default values (see ?add.scale.bar for details). This
2107 function now works even if the plotted tree has no edge length.
2109 o plot.phylo() can now plot radial trees, but this does not take
2110 edge lengths into account.
2112 o In plot.phylo() with `type = "phylogram"', if the values of
2113 `edge.color' and `edge.width' are identical for sister-branches,
2114 they are propagated to the vertical line that link them.
2119 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
2120 crashing. This is fixed.
2122 o In plot.phylo(), the options `edge.color' and `edge.width' are
2123 now properly recycled; their default values are now "black" and
2126 o A bug has been fixed in write.nexus().
2131 o The function node.depth.edgelength() has been removed and
2132 replaced by a C code.
2136 CHANGES IN APE VERSION 1.3-1
2141 o The new function nodelabels() allows to add labels to the nodes
2142 of a tree using text or plotting symbols in a flexible way.
2144 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
2145 numeric values specifying the lower and upper limits on the x-
2146 and y-axes. This allows to leave some space on any side of the
2147 tree. If a single value is given, this is taken as the upper
2152 CHANGES IN APE VERSION 1.3
2157 o The new function phymltest() calls the software PHYML and fits
2158 28 models of DNA sequence evolution. There are a print method to
2159 display likelihood and AIC values, a summary method to compute
2160 the hierarchical likelihood ratio tests, and a plot method to
2161 display graphically the AIC values of each model.
2163 o The new function yule.cov() fits the Yule model with covariates,
2164 a model where the speciation rate is affected by several species
2165 traits through a generalized linear model. The parameters are
2166 estimated by maximum likelihood.
2168 o Three new functions, corBrownian(), corGrafen(), and
2169 corMartins(), compute the expected correlation structures among
2170 species given a phylogeny under different models of evolution.
2171 These can be used for GLS comparative phylogenetic methods (see
2172 the examples). There are coef() and corMatrix() methods and an
2173 Initialize.corPhyl() function associated.
2175 o The new function compar.cheverud() implements Cheverud et al.'s
2176 (1985; Evolution 39:1335) phylogenetic comparative method.
2178 o The new function varcomp() estimates variance components; it has
2181 o Two new functions, panel.superpose.correlogram() and
2182 plot.correlogramList(), allow to plot several phylogenetic
2185 o The new function node.leafnumber() computes the number of leaves
2186 of a subtree defined by a particular node.
2188 o The new function node.sons() gets all tags of son nodes from a
2191 o The new function compute.brlen() computes the branch lengths of
2192 a tree according to a specified method.
2194 o plot.phylo() has three new options: "cex" controls the size of
2195 the (tip and node) labels (thus it is no more needed to change
2196 the global graphical parameter), "direction" which allows to
2197 plot the tree rightwards, leftwards, upwards, or downwards, and
2198 "y.lim" which sets the upper limit on the y-axis.
2203 o Some functions which try to match tip labels and names of
2204 additional data (e.g. vector) are likely to fail if there are
2205 typing or syntax errors. If both series of names do not perfectly
2206 match, they are ignored and a warning message is now issued.
2207 These functions are bd.ext, compar.gee, pic. Their help pages
2208 have been clarified on this point.
2212 CHANGES IN APE VERSION 1.2-7
2217 o The new function root() reroots a phylogenetic tree with respect
2218 to a specified outgroup.
2220 o The new function rotate() rotates an internal branch of a tree.
2222 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
2223 trees) controls the display of the tip labels in unrooted trees.
2224 This display has been greatly improved: the tip labels are now not
2225 expected to overlap with the tree (particularly if lab4ut =
2226 "axial"). In all cases, combining appropriate values of "lab4ut"
2227 and the font size (via "par(cex = )") should result in readable
2228 unrooted trees. See ?plot.phylo for some examples.
2230 o In drop.tip(), the argument `tip' can now be numeric or character.
2235 o drop.tip() did not work correctly with trees with no branch
2236 lengths: this is fixed.
2238 o A bug in plot.phylo(..., type = "unrooted") made some trees being
2239 plotted with some line crossings: this is now fixed.
2243 CHANGES IN APE VERSION 1.2-6
2248 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
2249 correlogram.phylo, dist.taxo, plot.correlogram) have been added
2250 to implement comparative methods with an autocorrelation approach.
2252 o A new data set describing some life history traits of Carnivores
2258 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
2263 o When plotting a tree with plot.phylo(), the new default of the
2264 option `label.offset' is now 0, so the labels are always visible.
2268 CHANGES IN APE VERSION 1.2-5
2273 o The new function bd.ext() fits a birth-death model with combined
2274 phylogenetic and taxonomic data, and estimates the corresponding
2275 speciation and extinction rates.
2280 o The package gee is no more required by ape but only suggested
2281 since only the function compar.gee() calls gee.
2285 CHANGES IN APE VERSION 1.2-4
2290 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
2291 and lines.popsize) implementing a new approach for inferring the
2292 demographic history from genealogies using a reversible jump
2293 MCMC have been introduced.
2295 o The unit of time in the skyline plot and in the new plots can
2296 now be chosen to be actual years, rather than substitutions.
2300 CHANGES IN APE VERSION 1.2-3
2305 o The new function rtree() generates a random binary tree with or
2306 without branch lengths.
2308 o Two new functions for drawing lineages-through-time (LTT) plots
2309 are provided: ltt.lines() adds a LTT curve to an existing plot,
2310 and mltt.plot() does a multiple LTT plot giving several trees as
2311 arguments (see `?ltt.plot' for details).
2316 o Some taxon names made R crashing when calling as.phylo.hclust():
2319 o dist.dna() returned an error with two identical DNA sequences
2320 (only using the Jukes-Cantor method returned 0): this is fixed.
2325 o The function dist.phylo() has been re-written using a different
2326 algorithm: it is now about four times faster.
2328 o The code of branching.times() has been improved: it is now about
2333 CHANGES IN APE VERSION 1.2-2
2338 o The new function seg.sites() finds the segregating sites in a
2339 sample of DNA sequences.
2344 o A bug introduced in read.tree() and in read.nexus() with version
2347 o A few errors were corrected and a few examples were added in the
2352 CHANGES IN APE VERSION 1.2-1
2357 o plot.phylo() can now draw the edge of the root of a tree if it
2358 has one (see the new option `root.edge', its default is FALSE).
2363 o A bug was fixed in read.nexus(): files with semicolons inside
2364 comment blocks were not read correctly.
2366 o The behaviour of read.tree() and read.nexus() was corrected so
2367 that tree files with badly represented root edges (e.g., with
2368 an extra pair of parentheses, see the help pages for details)
2369 are now correctly represented in the object of class "phylo";
2370 a warning message is now issued.
2374 CHANGES IN APE VERSION 1.2
2379 o plot.phylo() has been completely re-written and offers several
2380 new functionalities. Three types of trees can now be drawn:
2381 phylogram (as previously), cladogram, and unrooted tree; in
2382 all three types the branch lengths can be drawn using the edge
2383 lengths of the phylogeny or not (e.g., if the latter is absent).
2384 The vertical position of the nodes can be adjusted with two
2385 choices (see option `node.pos'). The code has been re-structured,
2386 and two new functions (potentially useful for developpers) are
2387 documented separately: node.depth.edgelength() and node.depth();
2388 see the respective help pages for details.
2390 o The new function zoom() allows to explore very large trees by
2391 focusing on a small portion of it.
2393 o The new function yule() fits by maximum likelihood the Yule model
2394 (birth-only process) to a phylogenetic tree.
2396 o Support for writing DNA sequences in FASTA format has been
2397 introduced in write.dna() (support for reading sequences in
2398 this format was introduced in read.dna() in version 1.1-2).
2399 The function has been completely re-written, fixing some bugs
2400 (see below); the default behaviour is no more to display the
2401 sequences on the standard output. Several options have been
2402 introduced to control the sequence printing in a flexible
2403 way. The help page has been extended.
2405 o A new data set is included: a supertree of bats in NEXUS format.
2410 o In theta.s(), the default of the option `variance' has
2411 been changed to `FALSE' (as was indicated in the help page).
2413 o Several bugs were fixed in the code of all.equal.phylo().
2415 o Several bugs were fixed in write.dna(), particularly this
2416 function did not work with `format = "interleaved"'.
2418 o Various errors were corrected in the help pages.
2423 o The argument names of as.hclust.phylo() have been changed
2424 from "(phy)" to "(x, ...)" to conform to the definition of
2425 the corresponding generic function.
2427 o gamma.stat() has been renamed gammaStat() to avoid confusion
2428 since gamma() is a generic function.
2432 CHANGES IN APE VERSION 1.1-3
2437 o base.freq() previously did not return a value of 0 for
2438 bases absent in the data (e.g., a vector of length 3 was
2439 returned if one base was absent). This is now fixed (a
2440 vector of length 4 is always returned).
2442 o Several bugs were fixed in read.nexus(), including that this
2443 function did not work in this absence of a "TRANSLATE"
2444 command in the NEXUS file, and that the commands were
2449 CHANGES IN APE VERSION 1.1-2
2454 o The Tamura and Nei (1993) model of DNA distance is now implemented
2455 in dist.dna(): five models are now available in this function.
2457 o A new data set is included: a set of 15 sequences of the
2458 cytochrome b mitochondrial gene of the woodmouse (Apodemus
2464 o A bug in read.nexus() was fixed.
2466 o read.dna() previously did not work correctly in most cases.
2467 The function has been completely re-written and its help page
2468 has been considerably extended (see ?read.dna for details).
2469 Underscores (_) in taxon names are no more replaced with
2470 spaces (this behaviour was undocumented).
2472 o A bug was fixed in write.dna().
2476 CHANGES IN APE VERSION 1.1-1
2481 o A bug in read.tree() introduced in APE 1.1 was fixed.
2483 o A bug in compar.gee() resulted in an error when trying to fit
2484 a model with `family = "binomial"'. This is now fixed.
2488 CHANGES IN APE VERSION 1.1
2493 o The Klastorin (1982) method as suggested by Misawa and Tajima
2494 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
2495 on the basis of phylogenetic trees has been implemented (see
2496 the function klastorin()).
2498 o Functions have been added to convert APE's "phylo" objects in
2499 "hclust" cluster objects and vice versa (see the help page of
2500 as.phylo for details).
2502 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
2503 are introduced for the estimation of absolute evolutionary rates
2504 (ratogram) and dated clock-like trees (chronogram) from
2505 phylogenetic trees using the non-parametric rate smoothing approach
2506 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
2508 o A summary method is now provided printing a summary information on a
2509 phylogenetic tree with, for instance, `summary(tree)'.
2511 o The behaviour of read.tree() was changed so that all spaces and
2512 tabulations in tree files are now ignored. Consequently, spaces in tip
2513 labels are no more allowed. Another side effect is that read.nexus()
2514 now does not replace the underscores (_) in tip labels with spaces
2515 (this behaviour was undocumented).
2517 o The function plot.phylo() has a new option (`underscore') which
2518 specifies whether the underscores in tip labels should be written on
2519 the plot as such or replaced with spaces (the default).
2521 o The function birthdeath() now computes 95% confidence intervals of
2522 the estimated parameters using profile likelihood.
2524 o Three new data sets are included: a gene tree estimated from 36
2525 landplant rbcL sequences, a gene tree estimated from 32 opsin
2526 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
2531 o A bug was fixed in dist.gene() where nothing was returned.
2533 o A bug in plot.mst() was fixed.
2535 o A bug in vcv.phylo() resulted in false correlations when the
2536 option `cor = TRUE' was used (now fixed).
2540 CHANGES IN APE VERSION 1.0
2545 o Two new functions, read.dna() and write.dna(), read/write in a file
2546 DNA sequences in interleaved or in sequential format.
2548 o Two new functions, read.nexus() and write.nexus(), read/write trees
2551 o The new function bind.tree() allows to bind two trees together,
2552 possibly handling root edges to give internal branches.
2554 o The new function drop.tip() removes the tips in a phylogenetic tree,
2555 and trims (or not) the corresponding internal branches.
2557 o The new function is.ultrametric() tests if a tree is ultrametric.
2559 o The function plot.phylo() has more functionalities such as drawing the
2560 branches with different colours and/or different widths, showing the
2561 node labels, controling the position and font of the labels, rotating
2562 the labels, and controling the space around the plot.
2564 o The function read.tree() can now read trees with no branch length,
2565 such as "(a,b),c);". Consequently, the element `edge.length' in
2566 objects of class "phylo" is now optional.
2568 o The function write.tree() has a new default behaviour: if the default
2569 for the option `file' is used (i.e. file = ""), then a variable of
2570 mode character containing the tree in Newick format is returned which
2571 can thus be assigned (e.g., tree <- write.tree(phy)).
2573 o The function read.tree() has a new argument `text' which allows
2574 to read the tree in a variable of mode character.
2576 o A new data set is included: the phylogenetic relationships among
2577 the orders of birds from Sibley and Ahlquist (1990).
2581 CHANGES IN APE VERSION 0.2-1
2586 o Several bugs were fixed in the help pages.
2590 CHANGES IN APE VERSION 0.2
2595 o The function write.tree() writes phylogenetic trees (objects of class
2596 "phylo") in an ASCII file using the Newick parenthetic format.
2598 o The function birthdeath() fits a birth-death model to branching times
2599 by maximum likelihood, and estimates the corresponding speciation and
2602 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
2605 o The function is.binary.tree() tests whether a phylogeny is binary.
2607 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
2608 as well as some methods are introduced.
2610 o Several functions, including some generics and methods, for computing
2611 skyline plot estimates (classic and generalized) of effective
2612 population size through time are introduced and replace the function
2613 skyline.plot() in version 0.1.
2615 o Two data sets are now included: the phylogenetic relationships among
2616 the families of birds from Sibley and Ahlquist (1990), and an
2617 estimated clock-like phylogeny of HIV sequences sampled in the
2618 Democratic Republic of Congo.
2621 DEPRECATED & DEFUNCT
2623 o The function skyline.plot() in ape 0.1 has been deprecated and
2624 replaced by more elaborate functions (see above).
2629 o Two important bugs were fixed in plot.phylo(): phylogenies with
2630 multichotomies not at the root or not with only terminal branches,
2631 and phylogenies with a single node (i.e. only terminal branches)
2632 did not plot. These trees should be plotted correctly now.
2634 o Several bugs were fixed in diversi.time() in the computation of
2637 o Various errors were corrected in the help pages.