1 CHANGES IN APE VERSION 3.0-2
6 o The new function alex (alignment explorator) zooms in a DNA
7 alignment and opens the result in a new window.
12 o compute.brtime() did not completely randomized the order of the
15 o write.nexus() did not work correctly with rooted trees (thanks
16 to Matt Johnson for the fix).
18 o mltt.plot(, backward = FALSE) did not set the x-axis correctly.
20 o A bug was introduced in prop.clades() with ape 3.0. The help page
21 has been clarified relative to the use of the option 'rooted'.
23 o mantel.test() printed a useless warning message.
25 o plot.phylo(, direction = "downward") ignored 'y.lim'.
27 o is.monophyletic() did not work correctly if 'tips' was not stored
30 o prop.part() could make R crash if the first tree had many
33 o njs(), bionjs(), and mvrs() now return an error if 'fs < 1'.
35 o SDM() did not work correctly. The code has also been generally
41 o The DESCRIPTION file has been updated.
43 o The option 'original.data' of write.nexus() has been removed.
45 o The files bionjs.c, mvr.c, mvrs.c, njs.c, triangMtd.c, and
46 triangMtds.c have been improved which should fix some bugs in
47 the corresponding functions.
49 o dist.gene() now coerces input data frame as matrix resulting in
50 much faster calculations (thanks to a suggestion by Markus
55 CHANGES IN APE VERSION 3.0-1
60 o dist.dna() has two new models: "indel" and "indelblock".
62 o bind.tree() now accepts 'position' > 0 when the trees have no
63 banch length permitting to create a node in 'x' when grafting
64 'y' (see ?bind.tree for details).
69 o cophyloplot( , rotate = TRUE) made R hanged after a few clicks.
70 Also the tree is no more plotted twice.
72 o read.GenBank() has been updated to work with EFetch 2.0.
74 o unroot() on trees in "pruningwise" order did not respect this
79 CHANGES IN APE VERSION 3.0
84 o The three functions dyule, dbd, and dbdTime calculate the
85 density probability (i.e., the distribution of the number of
86 species) for the Yule, the constant and the time-dependent
87 birth-beath models, respectively. These probabilities can be
88 conditional on no extinction and/or on a log-scale.
90 o plot.phylo() has a new option 'rotate.tree' to rotate unrooted,
91 fan, or radial trees around the center of the plot.
93 o boot.phylo() and prop.clades() have a new option rooted =
94 FALSE. Note that the behaviour of prop.part() is unchanged.
96 o edgelabels() has a new option 'date' to place labels on edges of
97 chronograms using the time scale (suggestion by Rob Lanfear).
102 o In chronopl(), the code setting the initial dates failed in
103 complicated settings (several dates known within intervals).
104 This has been generally improved and should result in faster
105 and more efficient convergence even in simple settings.
107 o mantel.test() sometimes returned P-values > 1 with the default
110 o extract.clade() sometimes shuffled some tip labels (thanks to
111 Ludovic Mallet and Mahendra Mariadassou for the fix).
113 o clustal() should now find by default the executable under Windows.
118 o The code of yule() has been simplified and is now much faster for
121 o The code of mantel.test() has been adjusted to be consistent
122 with common permutation tests.
124 o The C code of base.freq() has been improved and is now nearly 8
127 o The option 'original.data' of write.nexus() is now deprecated and
128 will be removed in a future release.
130 o The code of is.ultrametric() has been improved and is now 3 times
133 o The code of vcv.phylo() has been improved and is now 10 or 30
134 times faster for 100 or 1000 tips, respectively. Consequently,
135 fitting models with PGLS will be faster overall.
139 CHANGES IN APE VERSION 2.8
144 o Twelve new functions have been written by Andrei-Alin Popescu:
145 additive, ultrametric, is.compatible, arecompatible, mvr, mvrs,
146 njs, bionjs, SDM, treePop, triangMtd, triangMtd*.
148 o A new class "bitsplits" has been created by Andrei-Alin Popescu
149 to code splits (aka, bipartition).
151 o There is a new generic function as.bitsplits with a method to
152 convert from the class "prop.part" to the class "bitsplits".
154 o The new function ltt.coplot plots on the same scales a tree and
155 the derived LTT plot.
157 o ltt.plot() has two new options: backward and tol. It can now
158 handle non-ultrametic trees and its internal coding has been
159 improved. The coordinates of the plot can now be computed with
160 the new function ltt.plot.coords.
165 o prop.part() crashed if some trees had some multichotomies.
169 CHANGES IN APE VERSION 2.7-3
174 o The new function compute.brtime computes and sets branching times.
176 o mantel.test() has a new argument 'alternative' which is
177 "two-sided" by default. Previously, this test was one-tailed
178 with no possibility to change.
180 o ace() can now do REML estimation with continuous characters,
181 giving better estimates of the variance of the Brownian motion
187 o Branch lengths were wrongly updated with bind.tree(, where = <tip>,
188 position = 0). (Thanks to Liam Revell for digging this bug out.)
190 o Simulation of OU process with rTraitCont() did not work correctly.
191 This now uses formula from Gillespie (1996) reduced to a BM
192 process when alpha = 0 to avoid division by zero. The option
193 'linear' has been removed.
195 o Cross-validation in chronopl() did not work when 'age.max' was
198 o consensus(, p = 0.5) could return an incorrect tree if some
199 incompatible splits occur in 50% of the trees (especially with
200 small number of trees).
202 o c() with "multiPhylo" did not work correctly (thanks to Klaus
203 Schliep for the fix).
205 o root() failed in some cases with an outgroup made of several tips.
206 The help page has been clarified a bit.
210 CHANGES IN APE VERSION 2.7-2
215 o There is a new class "evonet" to code evolutionary networks, with
216 a constructor function evonet(), a print() and a plot() methods,
217 and four conversion methods to the classes "phylo", "networx",
218 "network", and "igraph".
220 o The new function rTraitMult does multivariate traits simulation
221 with user-defined models.
223 o plot.phylo() has a new option 'plot = TRUE'. If FALSE, the tree
224 is not plotted but the graphical device is set and the
225 coordinates are saved as usual.
227 o diversity.contrast.test() gains a fourth version of the test with
228 method = "logratio"; the literature citations have been clarified.
230 o add.scale.bar() has two new options, 'lwd' and 'lcol', to modify
231 the aspect of the bar.
233 o boot.phylo() now displays a progress bar by default (can be off
236 o There is a new predict() method for compar.gee().
241 o bionj() made R crash if distances were too large. It now returns
242 an error if at least one distance is greater than 100.
244 o drop.tip() returned a wrong tree if 'tip' was of zero length.
246 o read.nexus.data() failed with URLs.
248 o boot.phylo() returned overestimated support values in the
249 presence of identical or nearly identical sequences.
254 o The data bird.families, bird.orders, cynipids, and woodmouse are
255 now provided as .rda files.
259 CHANGES IN APE VERSION 2.7-1
264 o The new function trex does tree exploration with multiple
267 o The new function kronoviz plots several rooted (dated) trees on
270 o identify.phylo() has a new option 'quiet' (FALSE by default).
275 o A bug was introduced in read.nexus() in ape 2.7.
277 o image.DNAbin() did not colour correctly the bases if there were
280 o .compressTipLabel() failed with a list with a single tree.
282 o identify.phylo() returned a wrong answer when the x- and y-scales
285 o write.nexus() failed with lists of trees with compressed labels.
290 o identify.phylo() now returns NULL if the user right- (instead of
291 left-) clicks (an error was returned previously).
293 o read.nexus() should be robust to commands inserted in the TREES
298 CHANGES IN APE VERSION 2.7
303 o There is a new image() method for "DNAbin" objects: it plots DNA
304 alignments in a flexible and efficient way.
306 o Two new functions as.network.phylo and as.igraph.phylo convert
307 trees of class "phylo" into these respective network classes
308 defined in the packages of the same names.
310 o The three new functions clustal, muscle, and tcoffee perform
311 nucleotide sequence alignment by calling the external programs
314 o Four new functions, diversity.contrast.test, mcconwaysims.test,
315 richness.yule.test, and slowinskiguyer.test, implement various
316 tests of diversification shifts using sister-clade comparisons.
318 o base.freq() gains an option 'all' to count all the possible bases
319 including the ambiguous ones (defaults to FALSE).
321 o read.nexus() now writes tree names in the NEXUS file if given a
322 list of trees with names.
327 o prop.part() failed in some situations with unrooted trees.
329 o read.nexus() shuffled node labels when a TRANSLATE block was
332 o varCompPhylip() did not work if 'exec' was specified.
334 o bind.tree() shuffled node labels when position > 0 and 'where'
340 o BaseProportion in src/dist_dna.c has been modified.
342 o A number of functions in src/tree_build.c have been modified.
344 o The matching representation has now only two columns as the third
345 column was redundant.
349 CHANGES IN APE VERSION 2.6-3
354 o rTraitCont() and rTraitDisc() gains a '...' argument used with
355 user-defined models (suggestion by Gene Hunt).
360 o as.hclust.phylo() now returns an error with unrooted trees.
362 o as.hclust.phylo() failed with trees with node labels (thanks to
363 Jinlong Zhang for pointing this bug out).
365 o read.dna(, "fasta") failed if sequences were not all of the same
368 o plot.phylo() did not recycle values of 'font', 'cex' and
369 'tip.color' correctly when type = "fan" or "radial".
371 o plot.phylo() ignored 'label.offset' when type = "radial", "fan", or
372 "unrooted" with lab4ut = "axial" (the placement of tip labels still
373 needs to be improved with lab4ut = "horizontal").
378 o In drop.fossil() the default tol = 0 has been raised to 1e-8.
380 o The help command ?phylo now points to the man page of read.tree()
381 where this class is described. Similarly, ?matching points to the
382 man page of as.matching().
386 CHANGES IN APE VERSION 2.6-2
391 o Two new functions, pic.ortho and varCompPhylip, implements the
392 orthonormal contrasts of Felsenstein (2008, Am Nat, 171:713). The
393 second function requires Phylip to be installed on the computer.
395 o bd.ext() has a new option conditional = TRUE to use probabilities
396 conditioned on no extinction for the taxonomic data.
401 o write.tree() failed to output correctly tree names.
403 o dist.nodes() returned duplicated column(s) with unrooted and/or
404 multichotomous trees.
406 o mcmc.popsize() terminated unexpectedly if the progress bar was
409 o prop.part(x) made R frozen if 'x' is of class "multiPhylo".
411 o Compilation under Mandriva failed (thanks to Jos Käfer for the fix).
413 o drop.tip() shuffled tip labels with subtree = TRUE or trim.internal
416 o Objects returned by as.hclust.phylo() failed when analysed with
417 cutree() or rect.hclust().
419 o write.tree() did not output correctly node labels (thanks to Naim
420 Matasci and Jeremy Beaulieu for the fix).
422 o ace(type = "discrete") has been improved thanks to Naim Marasci and
427 CHANGES IN APE VERSION 2.6-1
432 o The new function speciesTree calculates the species tree from a set
433 of gene trees. Several methods are available including maximum tree
434 and shallowest divergence tree.
439 o A bug introduced in write.tree() with ape 2.6 has been fixed.
441 o as.list.DNAbin() did not work correctly with vectors.
443 o as.hclust.phylo() failed with trees with node labels (thanks to
444 Filipe Vieira for the fix).
448 CHANGES IN APE VERSION 2.6
453 o The new functions rlineage and rbdtree simulate phylogenies under
454 any user-defined time-dependent speciation-extinction model. They
455 use continuous time algorithms.
457 o The new function drop.fossil removes the extinct species from a
460 o The new function bd.time fits a user-defined time-dependent
461 birth-death model. It is a generalization of yule.time() taking
462 extinction into account.
464 o The new function MPR does most parsimonious reconstruction of
467 o The new function Ftab computes the contingency table of base
468 frequencies from a pair of sequences.
470 o There is now an 'as.list' method for the class "DNAbin".
472 o dist.dna() can compute the number of transitions or transversions
473 with the option model = "Ts" or model = "Tv", respectively.
475 o [node|tip|edge]labels() gain three options with default values to
476 control the aspect of thermometers: horiz = TRUE, width = NULL,
479 o compar.gee() has been improved with the new option 'corStruct' as an
480 alternative to 'phy' to specify the correlation structure, and
481 calculation of the QIC (Pan 2001, Biometrics). The display of the
482 results has also been improved.
484 o read.GenBank() has a new option 'gene.names' to return the name of
485 the gene (FALSE by default).
490 o extract.clade() sometimes shuffled the tip labels.
492 o plot.phylo(type = "unrooted") did not force asp = 1 (thanks to Klaus
495 o dist.dna(model = "logdet") used to divide distances by 4. The
496 documentation has been clarified on the formulae used.
501 o rTraitCont(model = "OU") has an option 'linear = TRUE' to possibly
502 change the parameterisation (see ?rTraitCont for details).
504 o pic() now returns a vector with the node labels of the tree (if
507 o write.tree() and read.tree() have been substantially improved thanks
508 to contributions by Klaus Schliep.
512 CHANGES IN APE VERSION 2.5-3
517 o The new function mixedFontLabel helps to make labels with bits of
518 text to be plotted in different fonts.
520 o There are now replacement operators for [, [[, and $ for the class
521 "multiPhylo" (i.e., TREES[11:20] <- rmtree(10, 100)). They possibly
522 check that the tip labels are the same in all trees.
524 o Objects of class "multiPhylo" can be built with c(): there are
525 methods for the classes "phylo" and "multiPhylo".
527 o The internal functions .compressTipLabel and .uncompressTipLabel are
533 o bind.tree(x, y, where, position = 0) did not work correctly if 'y'
534 was a single-edge tree and 'where' was a tip.
536 o rTraitCont() did not use the square-root of branch lengths when
537 simulating a Brownian motion model.
541 CHANGES IN APE VERSION 2.5-2
546 o There is now a print method for results from ace().
548 o There is a labels() method for objects of class "DNAbin".
550 o read.dna() has a new option 'as.matrix' to possibly force sequences
551 in a FASTA file to be stored in a matrix (see ?read.dna for details).
556 o as.phylo.hclust() used to multiply edge lengths by 2.
558 o A minor bug was fixed in rTraitDisc().
560 o ace() sometimes failed (parameter value was NaN and the optimisation
566 o evolve.phylo() and plot.ancestral() have been removed.
568 o chronogram(), ratogram(), and NPRS.criterion() have been removed.
573 o nj() has been improved and is now about 30% faster.
575 o The default option 'drop' of [.DNAbin has been changed to FALSE to
576 avoid dropping rownames when selecting a single sequence.
578 o print.DNAbin() has been changed to summary.DNAbin() which has been
583 CHANGES IN APE VERSION 2.5-1
588 o The new function stree generates trees with regular shapes.
590 o It is now possible to bind two trees with x + y (see ?bind.tree for
593 o drop.tip(), extract.clade(), root(), and bind.tree() now have an
594 'interactive' option to make the operation on a plotted tree.
596 o cophyloplot() gains two new arguments 'lwd' and 'lty' for the
597 association links; they are recycled like 'col' (which wasn't before).
602 o rTraitDisc() did not use its 'freq' argument correctly (it was
603 multiplied with the rate matrix column-wise instead of row-wise).
605 o [node|tip|edge]labels(thermo = ) used to draw empty thermometers
606 with NA values. Nothing is drawn now like with 'text' or 'pch'.
607 The same bug occurred with the 'pie' option.
609 o A bug was fixed in compar.ou() and the help page was clarified.
611 o bind.tree() has been rewritten fixing several bugs and making it
614 o plot.phylo(type = "p") sometimes failed to colour correctly the
615 vertical lines representing the nodes.
617 o plot.phylo(direction = "l", x.lim = 30) failed to plot the branches
618 in the correct direction though the tip labels were displayed
624 o The c, cbind, and rbind methods for "DNAbin" objetcs now check that
625 the sequences are correctly stored (in a list for c, in a matrix
626 for the two other functions).
630 CHANGES IN APE VERSION 2.5
635 o The new function parafit by Pierre Legendre tests for the
636 coevolution between hosts and parasites. It has a companion
637 function, pcoa, that does principal coordinate decomposition.
638 The latter has a biplot method.
640 o The new function lmorigin by Pierre Legendre performs multiple
641 regression through the origin with testing by permutation.
643 o The new functions rTraitCont and rTraitDisc simulate continuous and
644 discrete traits under a wide range of evolutionary models.
646 o The new function delta.plot does a delta plot following Holland et
647 al. (2002, Mol. Biol. Evol. 12:2051).
649 o The new function edges draws additional branches between any nodes
650 and/or tips on a plotted tree.
652 o The new function fancyarrows enhances arrows from graphics with
653 triangle and harpoon heads; it can be called from edges().
655 o add.scale.bar() has a new option 'ask' to draw interactively.
657 o The branch length score replaces the geodesic distance in dist.topo.
659 o Three new data sets are included: the gopher-lice data (gopher.D),
660 SO2 air pollution in 41 US cities (lmorigin.ex1, from Sokal &
661 Rohlf 1995), and some host-parasite specificity data
662 (lmorigin.ex2, from Legendre & Desdevises 2009).
667 o add.scale.bar() drew the bar outside the plotting region with the
668 default options with unrooted or radial trees.
670 o dist.topo() made R stuck when the trees had different sizes (thanks
671 to Otto Cordero for the fix).
676 o The geodesic distance has been replaced by the branch length score
681 CHANGES IN APE VERSION 2.4-1
686 o rtree() and rcoal() now accept a numeric vector for the 'br'
689 o vcv() is a new generic function with methods for the classes "phylo"
690 and "corPhyl" so that it is possible to calculate the var-cov matrix
691 for "transformation models". vcv.phylo() can still be used for trees
692 of class "phylo"; its argument 'cor' has been renamed 'corr'.
697 o bind.tree() failed when 'y' had no root edge.
699 o read.nexus() shuffled tip labels when the trees have no branch
700 lengths and there is a TRANSLATE block.
702 o read.nexus() does not try to translate node labels if there is a
703 translation table in the NEXUS file. See ?read.nexus for a
704 clarification on this behaviour.
706 o plot.multiPhylo() crashed R when plotting a list of trees with
707 compressed tip labels.
709 o write.nexus() did not translate the taxa names when asked for.
711 o plot.phylo(type = "fan") did not rotate the tip labels correctly
712 when the tree has branch lengths.
714 o ace(type = "continuous", method = "ML") now avoids sigma² being
715 negative (which resulted in an error).
717 o nj() crashed with NA/NaN in the distance matrix: an error in now
722 CHANGES IN APE VERSION 2.4
727 o base.freq() has a new option 'freq' to return the counts; the
728 default is still to return the proportions.
733 o seg.sites() did not handle ambiguous nucleotides correctly: they
736 o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
737 the tree: the argument is now ignored.
739 o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
745 o Trying to plot a tree with a single tip now returns NULL with a
746 warning (it returned an error previously).
748 o The way lines representing nodes are coloured in phylograms has
749 been modified (as well as their widths and types) following some
750 users' request; this is only for dichotomous nodes.
752 o The argument 'adj' in [node][tip][edge]labels() now works when
753 using 'pie' or 'thermo'.
755 o A more informative message error is now returned by dist.dna() when
756 'model' is badly specified (partial matching of this argument is
759 o Deprecated functions are now listed in a help page: see
760 help("ape-defunct") with the quotes.
765 o The functions heterozygosity, nuc.div, theta.h, theta.k and
766 theta.s have been moved from ape to pegas.
768 o The functions mlphylo, DNAmodel and sh.test have been removed.
772 CHANGES IN APE VERSION 2.3-3
777 o add.scale.bar() always drew a horizontal bar.
779 o zoom() shuffled tips with unrooted trees.
781 o write.nexus() failed to write correctly trees with a "TipLabel"
784 o rcoal() failed to compute branch lengths with very large n.
786 o A small bug was fixed in compar.cheverud() (thanks to Michael
789 o seg.sites() failed when passing a vector.
791 o drop.tip() sometimes shuffled tip labels.
793 o root() shuffled node labels with 'resolve.root = TRUE'.
797 CHANGES IN APE VERSION 2.3-2
802 o all.equal.phylo() did not compare unrooted trees correctly.
804 o dist.topo(... method = "PH85") did not treat unrooted trees
805 correctly (thanks to Tim Wallstrom for the fix).
807 o root() sometimes failed to test for the monophyly of the
810 o extract.clade() sometimes included too many edges.
812 o vcv.phylo() did not work correctly when the tree is in
815 o nj() did not handle correctly distance matrices with many 0's.
816 The code has also been significantly improved: 7, 70, 160 times
817 faster with n = 100, 500, 1000, respectively.
821 CHANGES IN APE VERSION 2.3-1
826 o The new function is.monophyletic tests the monophyly of a group.
828 o There is now a c() method for lists of class "DNAbin".
830 o yule.cov() now fits the null model, and its help page has been
831 corrected with respect to this change.
833 o drop.tip() has a new option 'rooted' to force (or not) a tree
834 to be treated as (un)rooted.
839 o dist.gene() failed on most occasions with the default
840 pairwise.deletion = FALSE.
842 o read.tree() failed to read correctly the tree name(s).
844 o boot.phylo() now treats correctly data frames.
846 o del.gaps() did not copy the rownames of a matrix.
848 o A small bug was fixed in CDAM.global().
850 o ace() failed with large data sets. Thanks to Rich FitzJohn for
851 the fix. With other improvements, this function is now about 6
854 o write.tree() failed with objects of class "multiPhylo".
856 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
861 o [.multiPhylo and [.DNAbin now respect the original class.
863 o Instances of the form class(phy) == "phylo" have been replaced
864 by inherits(phy, "phylo").
866 o rcoal() is now faster.
871 o klastorin() has been removed.
875 CHANGES IN APE VERSION 2.3
880 o The new functions CADM.global and CADM.post, contributed by
881 Pierre Legendre, test the congruence among several distance
884 o The new function yule.time fits a user-defined time-dependent
885 Yule model by maximum likelihood.
887 o The new function makeNodeLabel creates and/or modifies node
888 labels in a flexible way.
890 o read.tree() and write.tree() have been modified so that they can
891 handle individual tree names.
893 o plot.phylo() has a new argument 'edge.lty' that specifies the
894 types of lines used for the edges (plain, dotted, dashed, ...)
896 o phymltest() has been updated to work with PhyML 3.0.1.
901 o drop.tip() shuffled tip labels in some cases.
903 o drop.tip() did not handle node.label correctly.
905 o is.ultrametric() now checks the ordering of the edge matrix.
907 o ace() sometimes returned negative values of likelihoods of
908 ancestral states (thanks to Dan Rabosky for solving this long
914 o The data set xenarthra has been removed.
918 CHANGES IN APE VERSION 2.2-4
922 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
923 now fixed. (Thanks to Peter Wragg for the fix!)
925 o A warning message occurred for no reason with ace(method="GLS").
930 o There is now a general help page displayed with '?ape'.
934 CHANGES IN APE VERSION 2.2-3
939 o The new function extract.clade extracts a clade from a tree by
940 specifying a node number or label.
942 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
943 operations of the same names.
945 o dist.dna() can now return the number of site differences by
946 specifying model="N".
951 o chronopl() did not work with CV = TRUE.
953 o read.nexus() did not work correctly in some situations (trees on
954 multiple lines with different numbers of lines and/or with
955 comments inserted within the trees).
957 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
958 the number of lineages with non-binary trees.
963 o ape has now a namespace.
965 o drop.tip() has been improved: it should be much faster and work
966 better in some cases (e.g., see the example in ?zoom).
970 CHANGES IN APE VERSION 2.2-2
975 o dist.gene() has been substantially improved and gains an option
978 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
984 o prop.part() failed with a single tree with the default option
985 'check.labels = TRUE'.
987 o summary.DNAbin() failed to display correctly the summary of
988 sequence lengths with lists of sequences of 10,000 bases or more
989 (because summary.default uses 4 significant digits by default).
991 o read.nexus() failed to read a file with a single tree with line
992 breaks in the Newick string.
994 o del.gaps() returned a list of empty sequences when there were no
1000 o phymltest() has been updated for PhyML 3.0 and gains an option
1001 'append', whereas the option 'path2exec' has been removed.
1003 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
1004 which is returned unchanged (instead of an error).
1006 o The data sets bird.orders and bird.families are now stored as
1007 Newick strings; i.e., the command data(bird.orders) calls
1012 CHANGES IN APE VERSION 2.2-1
1017 o The new function makeLabel() helps to modify labels of trees,
1018 lists of trees, or DNA sequences, with several utilities to
1019 truncate and/or make them unique, substituting some
1020 characters, and so on.
1022 o The new function del.gaps() removes insertion gaps ("-") in a
1023 set of DNA sequences.
1025 o read.dna() can now read Clustal files (*.aln).
1030 o root() failed with 'resolve.root = TRUE' when the root was
1031 already the specified root.
1033 o Several bugs were fixed in mlphylo().
1035 o collapsed.singles() did not propagate the 'Nnode' and
1036 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
1038 o read.nexus() failed to remove correctly the comments within
1041 o read.nexus() failed to read a file with a single tree and no
1042 translation of tip labels.
1044 o read.nexus() failed to place correctly tip labels when reading
1045 a single tree with no edge lengths.
1047 o A bug was fixed in sh.test().
1052 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
1055 o The option 'check.labels' of consensus() and prop.part() is now
1058 o write.dna() now does not truncate names to 10 characters with
1063 CHANGES IN APE VERSION 2.2
1068 o Four new functions have been written by Damien de Vienne for the
1069 graphical exploration of large trees (cophyloplot, subtrees,
1070 subtreeplot), and to return the graphical coordinates of tree
1073 o The new functions corPagel and corBlomberg implement the Pagel's
1074 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
1076 o chronopl() has been improved and gains several options: see its
1077 help page for details.
1079 o boot.phylo() has now an option 'trees' to possibly return the
1080 bootstraped trees (the default is FALSE).
1082 o prop.part() has been improved and should now be faster in all
1088 o read.dna() failed if "?" occurred in the first 10 sites of the
1091 o The x/y aspect of the plot is now respected when plotting a
1092 circular tree (type = "r" or "f").
1094 o Drawing the tip labels sometimes failed when plotting circular
1097 o zoom() failed when tip labels were used instead of their numbers
1098 (thanks to Yan Wong for the fix).
1100 o drop.tip() failed with some trees (fixed by Yan Wong).
1102 o seg.sites() failed with a list.
1104 o consensus() failed in some cases. The function has been improved
1105 as well and is faster.
1109 CHANGES IN APE VERSION 2.1-3
1114 o A bug in read.nexus() made the Windows R-GUI crash.
1116 o An error was fixed in the computation of ancestral character
1117 states by generalized least squares in ace().
1119 o di2multi() did not modify node labels correctly.
1121 o multi2di() failed if the tree had its attribute "order" set to
1126 CHANGES IN APE VERSION 2.1-2
1131 o There three new methods for the "multiPhylo" class: str, $,
1134 o root() gains the options 'node' and 'resolve.root'
1135 (FALSE by default) as well as its code being improved.
1137 o mltt.plot() has now an option 'log' used in the same way
1138 than in plot.default().
1143 o mltt.plot() failed to display the legend with an unnamed
1146 o nodelabels() with pies now correcly uses the argument
1147 'cex' to draw symbols of different sizes (which has
1148 worked already for thermometers).
1150 o read.nexus() generally failed to read very big files.
1155 o The argument 'family' of compar.gee() can now be a function
1156 as well as a character string.
1158 o read.tree() and read.nexus() now return an unnamed list if
1159 'tree.names = NULL'.
1161 o read.nexus() now returns a modified object of class "multiPhylo"
1162 when there is a TRANSLATE block in the NEXUS file: the individual
1163 trees have no 'tip.label' vector, but the list has a 'TipLabel'
1164 attribute. The new methods '$' and '[[' set these elements
1165 correctly when extracting trees.
1169 CHANGES IN APE VERSION 2.1-1
1174 o The new function rmtree generates lists of random trees.
1176 o rcoal() now generates a genuine coalescent tree by default
1177 (thanks to Vladimir Minin for the code).
1182 o nuc.div() returned an incorrect value with the default
1183 pairwise.deletion = FALSE.
1188 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
1189 have been improved so that they are stabler and faster.
1191 o R packages used by ape are now loaded silently; lattice and gee
1192 are loaded only when needed.
1196 CHANGES IN APE VERSION 2.1
1201 o The new function identify.phylo identifies clades on a plotted
1202 tree using the mouse.
1204 o It is now possible to subset a list of trees (object of class
1205 "multiPhylo") with "[" while keeping its class correct.
1207 o The new function as.DNAbin.alignment converts DNA sequences
1208 stored in the "alignment" format of the package seqinr into
1209 an object of class "DNAbin".
1211 o The new function weight.taxo2 helps to build similarity matrices
1212 given two taxonomic levels (usually called by other functions).
1214 o write.tree() can now take a list of trees (class "multiPhylo")
1215 as its main argument.
1217 o plot.correlogram() and plot.correlogramList() have been
1218 improved, and gain several options (see the help page for
1219 details). A legend is now plotted by default.
1224 o dist.dna() returned some incorrect values with `model = "JC69"'
1225 and `pairwise.deletion = TRUE'. This affected only the
1226 distances involving sequences with missing values. (Thanks
1227 to Bruno Toupance for digging this bug out.)
1229 o write.tree() failed with some trees: this is fixed by removing
1230 the `multi.line' option (trees are now always printed on a
1233 o read.nexus() did not correctly detect trees with multiple root
1234 edges (see OTHER CHANGES).
1239 o The code of mlphylo() has been almost entirely rewritten, and
1240 should be much stabler. The options have been also greatly
1241 simplified (see ?mlphylo and ?DNAmodel for details).
1243 o The internal function nTips has been renamed klastorin_nTips.
1245 o The code of is.ultrametric() contained redundancies and has
1248 o The code of Moran.I() and of correlogram.formula() have been
1251 o read.tree() and read.nexus() now return an error when trying to
1252 read a tree with multiple root edges (see BUG FIXES). The
1253 correction applied in previous version did not work in all
1256 o The class c("multi.tree", "phylo") has been renamed
1262 o There is now a vignette in ape: see vignette("MoranI", "ape").
1265 DEPRECATED & DEFUNCT
1267 o as.matching() and as.phylo.matching() do not support branch
1270 o correlogram.phylo() and discrete.dist() have been removed.
1274 CHANGES IN APE VERSION 2.0-2
1279 o The new function matexpo computes the exponential of a square
1282 o The new function unique.multi.tree removes duplicate trees from
1285 o yule() has a new option `use.root.edge = FALSE' that specifies
1286 to ignore, by default, the root edge of the tree if it exists.
1291 o which.edge() failed when the index of a single terminal edge was
1294 o In diversi.time(), the values returned for model C were
1297 o A bug was fixed in yule() that affected the calculation of the
1298 likelihood in the presence of ties in the branching times.
1300 o There was a bug in the C function mat_expo4x4 affecting the
1301 calculations of the transition probabilities for models HKY and
1304 o A small bug was fixed in as.matrix.DNAbin (thanks to James
1307 o rtree() did not `shuffle' the tip labels by default, so only a
1308 limited number of labelled topologies could be generated.
1312 CHANGES IN APE VERSION 2.0-1
1317 o The three new functions bionj, fastme.ols, and fastme.bal
1318 perform phylogeny estimation by the BIONJ and fastME methods in
1319 OLS and balanced versions. This is a port to R of previous
1320 previous programs done by Vincent Lefort.
1322 o The new function chronoMPL performs molecular dating with the
1323 mean path lengths method of Britton et al. (2002, Mol. Phyl.
1326 o The new function rotate, contributed by Christoph Heibl, swaps
1327 two clades connected to the same node. It works also with
1328 multichotomous nodes.
1330 o The new `method' as.matrix.DNAbin() may be used to convert
1331 easily DNA sequences stored in a list into a matrix while
1332 keeping the names and the class.
1337 o chronopl() failed when some branch lengths were equal to zero:
1338 an error message is now returned.
1340 o di2multi() failed when there was a series of consecutive edges
1345 CHANGES IN APE VERSION 1.10-2
1350 o plot.phylo() can now plot circular trees: the option is type =
1351 "fan" or type = "f" (to avoid the ambiguity with type = "c").
1353 o prop.part() has a new option `check.labels = FALSE' which allows
1354 to considerably speed-up the calculations of bipartitions. As a
1355 consequence, calculations of bootstrap values with boot.phylo()
1356 should be much faster.
1361 o read.GenBank() did not return correctly the list of species as
1362 from ape 1.10: this is fixed in this version
1364 o Applying as.phylo() on a tree of class "phylo" failed: the
1365 object is now returned unchanged.
1369 CHANGES IN APE VERSION 1.10-1
1374 o The three new functions Ntip, Nnode, and Nedge return, for a
1375 given tree, the number of tips, nodes, or edges, respectively.
1380 o read.nexus() did not set correctly the class of the returned
1381 object when reading multiple trees.
1383 o mllt.plot() failed with objects of class c("multi.tree",
1386 o unroot() did not work correctly in most cases.
1388 o reorder.phylo() made R freeze in some occasions.
1390 o Plotting a tree in pruningwise order failed.
1392 o When plotting an unrooted tree, the tip labels where not all
1393 correctly positioned if the option `cex' was used.
1397 CHANGES IN APE VERSION 1.10
1402 o Five new `method' functions have been introduced to manipulate
1403 DNA sequences in binary format (see below).
1405 o Three new functions have been introduced to convert between the
1406 new binary and the character formats.
1408 o The new function as.alignment converts DNA sequences stored as
1409 single characters into the class "alignment" used by the package
1412 o read.dna() and read.GenBank() have a new argument `as.character'
1413 controlling whether the sequences are returned in binary format
1419 o root() failed when the tree had node labels: this is fixed.
1421 o plot.phylo() did not correctly set the limits on the y-axis with
1422 the default setting: this is fixed.
1424 o dist.dna() returned a wrong result for the LogDet, paralinear,
1425 and BH87 models with `pairwise.deletion = TRUE'.
1430 o DNA sequences are now internally stored in a binary format. See
1431 the document "A Bit-Level Coding Scheme for Nucleotides" for the
1432 details. Most functions analyzing DNA functions have been
1433 modified accordingly and are now much faster (dist.dna is now
1434 ca. 60 times faster).
1438 CHANGES IN APE VERSION 1.9-4
1443 o A bug was fixed in edgelabels().
1445 o as.phylo.hclust() did not work correctly when the object of
1446 class "hclust" has its labels set to NULL: the returned tree has
1447 now its tip labels set to "1", "2", ...
1449 o consensus could fail if some tip labels are a subset of others
1450 (e.g., "a" and "a_1"): this is now fixed.
1452 o mlphylo() failed in most cases if some branch lengths of the
1453 initial tree were greater than one: an error message is now
1456 o mlphylo() failed in most cases when estimating the proportion of
1457 invariants: this is fixed.
1461 CHANGES IN APE VERSION 1.9-3
1466 o The new function edgelabels adds labels on the edge of the tree
1467 in the same way than nodelabels or tiplabels.
1472 o multi2di() did not handle correctly branch lengths with the
1473 default option `random = TRUE': this is now fixed.
1475 o A bug was fixed in nuc.div() when using pairwise deletions.
1477 o A bug occurred in the analysis of bipartitions with large
1478 numbers of large trees, with consequences on prop.part,
1479 prop.clades, and boot.phylo.
1481 o The calculation of the Billera-Holmes-Vogtmann distance in
1482 dist.topo was wrong: this has been fixed.
1486 CHANGES IN APE VERSION 1.9-2
1491 o The new function ladderize reorganizes the internal structure of
1492 a tree to plot them left- or right-ladderized.
1494 o The new function dist.nodes computes the patristic distances
1495 between all nodes, internal and terminal, of a tree. It replaces
1496 the option `full = TRUE' of cophenetic.phylo (see below).
1501 o A bug was fixed in old2new.phylo().
1503 o Some bugs were fixed in chronopl().
1505 o The edge colours were not correctly displayed by plot.phylo
1506 (thank you to Li-San Wang for the fix).
1508 o cophenetic.phylo() failed with multichotomous trees: this is
1514 o read.dna() now returns the sequences in a matrix if they are
1515 aligned (interleaved or sequential format). Sequences in FASTA
1516 format are still returned in a list.
1518 o The option `full' of cophenetic.phylo() has been removed because
1519 it could not be used from the generic.
1522 DEPRECATED & DEFUNCT
1524 o rotate() has been removed; this function did not work correctly
1529 CHANGES IN APE VERSION 1.9-1
1534 o Trees with a single tip were not read correctly in R as the
1535 element `Nnode' was not set: this is fixed.
1537 o unroot() did not set correctly the number of nodes of the
1538 unrooted tree in most cases.
1540 o read.GenBank() failed when fetching very long sequences,
1541 particularly of the BX-series.
1543 o A bug was introduced in read.tree() with ape 1.9: it has been
1548 CHANGES IN APE VERSION 1.9
1553 o There are two new print `methods' for trees of class "phylo" and
1554 lists of trees of class "multi.tree", so that they are now
1555 displayed in a compact and informative way.
1557 o There are two new functions, old2new.phylo and new2old.phylo,
1558 for converting between the old and new coding of the class
1561 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
1562 LogDet ("logdet"), and paralinear ("paralin").
1564 o compute.brlen() has been extended: several methods are now
1565 available to compute branch lengths.
1567 o write.dna() can now handle matrices as well as lists.
1572 o cophenetic.phylo() sometimes returned a wrong result with
1573 multichotomous trees: this is fixed.
1575 o rotate() failed when a single tip was specified: the tree is now
1578 o ace() did not return the correct index matrix with custom
1579 models: this is fixed.
1581 o multi2di() did not work correctly when resolving multichotomies
1582 randomly: the topology was always the same, only the arrangement
1583 of clades was randomized: this is fixed. This function now
1584 accepts trees with no branch lengths.
1586 o The output of diversi.gof() was blurred by useless prints when a
1587 user distribution was specified. This has been corrected, and
1588 the help page of this function has been expanded.
1593 o The internal structure of the class "phylo" has been changed:
1594 see the document "Definition of Formats for Coding Phylogenetic
1595 Trees in R" for the details. In addition, the code of most
1596 functions has been improved.
1598 o Several functions have been improved by replacing some R codes
1599 by C codes: pic, plot.phylo, and reorder.phylo.
1601 o There is now a citation information: see citation("ape") in R.
1603 o write.tree() now does not add extra 0's to branch lengths so
1604 that 1.23 is printed "1.23" by default, not "1.2300000000".
1606 o The syntax of bind.tree() has been simplified. This function now
1607 accepts trees with no branch lengths, and handles correctly node
1610 o The option `as.numeric' of mrca() has been removed.
1612 o The unused options `format' and `rooted' of read.tree() have
1615 o The unused option `format' of write.tree() has been removed.
1617 o The use of node.depth() has been simplified.
1621 CHANGES IN APE VERSION 1.8-5
1626 o Two new functions read.nexus.data() and write.nexus.data(),
1627 contributed by Johan Nylander, allow to read and write molecular
1628 sequences in NEXUS files.
1630 o The new function reorder.phylo() reorders the internal structure
1631 of a tree of class "phylo". It is used as the generic, e.g.,
1634 o read.tree() and read.nexus() can now read trees with a single
1637 o The new data set `cynipids' supplies a set of protein sequences
1643 o The code of all.equal.phylo() has been completely rewritten
1644 (thanks to Benoît Durand) which fixes several bugs.
1646 o read.tree() and read.nexus() now checks the labels of the tree
1647 to remove or substitute any characters that are illegal in the
1648 Newick format (parentheses, etc.)
1650 o A negative P-value could be returned by mantel.test(): this is
1655 CHANGES IN APE VERSION 1.8-4
1660 o The new function sh.test() computes the Shimodaira-
1663 o The new function collapse.singles() removes the nodes with a
1664 single descendant from a tree.
1666 o plot.phylo() has a new argument `tip.color' to specify the
1667 colours of the tips.
1669 o mlphylo() has now an option `quiet' to control the display of
1670 the progress of the analysis (the default is FALSE).
1675 o read.dna() did not read correctly sequences in sequential format
1676 with leading alignment gaps "-": this is fixed.
1678 o ace() returned a list with no class so that the generic
1679 functions (anova, logLik, ...) could not be used directly. This
1680 is fixed as ace() now returns an object of class "ace".
1682 o anova.ace() had a small bug when computing the number of degrees
1683 of freedom: this is fixed.
1685 o mlphylo() did not work when the sequences were in a matrix or
1686 a data frame: this is fixed.
1688 o rtree() did not work correctly when trying to simulate an
1689 unrooted tree with two tips: an error message is now issued.
1694 o The algorithm of rtree() has been changed: it is now about 40,
1695 100, and 130 times faster for 10, 100, and 1000 tips,
1700 CHANGES IN APE VERSION 1.8-3
1705 o There are four new `method' functions to be used with the
1706 results of ace(): logLik(), deviance(), AIC(), and anova().
1708 o The plot method of phymltest has two new arguments: `main' to
1709 change the title, and `col' to control the colour of the
1710 segments showing the AIC values.
1712 o ace() has a new argument `ip' that gives the initial values used
1713 in the ML estimation with discrete characters (see the examples
1714 in ?ace). This function now returns a matrix giving the indices
1715 of the estimated rates when analysing discrete characters.
1717 o nodelabels() and tiplabels() have a new argument `pie' to
1718 represent proportions, with any number of categories, as
1719 piecharts. The use of the option `thermo' has been improved:
1720 there is now no limitation on the number of categories.
1725 o mlphylo() did not work with more than two partitions: this is
1728 o root() failed if the proposed outgroup was already an outgroup
1729 in the tree: this is fixed.
1731 o The `col' argument in nodelabels() and tiplabels() was not
1732 correctly passed when `text' was used: this is fixed.
1734 o Two bugs were fixed in mlphylo(): parameters were not always
1735 correctly output, and the estimation failed in some cases.
1737 o plot.phylo() was stuck when given a tree with a single tip: this
1738 is fixed and a message error is now returned.
1740 o An error was corrected in the help page of gammaStat regarding
1741 the calculation of P-values.
1743 o Using gls() could crash R when the number of species in the tree
1744 and in the variables were different: this is fixed.
1748 CHANGES IN APE VERSION 1.8-2
1753 o The new function mlphylo() fits a phylogenetic tree by maximum
1754 likelihood from DNA sequences. Its companion function DNAmodel()
1755 is used to define the substitution model which may include
1756 partitioning. There are methods for logLik(), deviance(), and
1757 AIC(), and the summary() method has been extended to display in
1758 a friendly way the results of this model fitting. Currently, the
1759 functionality is limited to estimating the substitution and
1760 associated parameters and computing the likelihood.
1762 o The new function drop1.compar.gee (used as, e.g., drop1(m))
1763 tests for single effects in GEE-based comparative method. A
1764 warning message is printed if there is not enough degrees of
1770 o An error message was sometimes issued by plot.multi.tree(),
1771 though with no consequence.
1775 CHANGES IN APE VERSION 1.8-1
1780 o There is a new plot method for lists of trees (objects of class
1781 "multi.tree"): it calls plot.phylo() internally and is
1782 documented on the same help page.
1787 o A bug was fixed in the C code that analyzes bipartitions: this
1788 has impact on several functions like prop.part, prop.clades,
1789 boot.phylo, or consensus.
1791 o root() did not work correctly when the specified outgroup had
1792 more than one element: this is fixed.
1794 o dist.dna() sometimes returned a warning inappropriately: this
1797 o If the distance object given to nj() had no rownames, nj()
1798 returned a tree with no tip labels: it now returns tips labelled
1799 "1", "2", ..., corresponding to the row numbers.
1804 o nj() has been slightly changed so that tips with a zero distance
1805 are first aggregated with zero-lengthed branches; the usual NJ
1806 procedure is then performed on a distance matrix without 0's.
1810 CHANGES IN APE VERSION 1.8
1815 o The new function chronopl() estimates dates using the penalized
1816 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1818 o The new function consensus() calculates the consensus tree of a
1821 o The new function evolve.phylo() simulates the evolution of
1822 continuous characters along a phylogeny under a Brownian model.
1824 o The new plot method for objects of class "ancestral" displays a
1825 tree together with ancestral values, as returned by the above
1828 o The new function as.phylo.formula() returns a phylogeny from a
1829 set of nested taxonomic variables given as a formula.
1831 o The new function read.caic() reads trees in CAIC format.
1833 o The new function tiplabels() allows to add labels to the tips
1834 of a tree using text or plotting symbols in a flexible way.
1836 o The new function unroot() unroots a phylogeny.
1838 o multi2di() has a new option, `random', which specifies whether
1839 to resolve the multichotomies randomly (the default) or not.
1841 o prop.part() now returns an object of class "prop.part" for which
1842 there are print (to display a partition in a more friendly way)
1843 and summary (to extract the numbers) methods.
1845 o plot.phylo() has a new option, `show.tip.label', specifying
1846 whether to print the labels of the tips. The default is TRUE.
1848 o The code of nj() has been replaced by a faster C code: it is now
1849 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1852 o write.nexus() now writes whether a tree is rooted or not.
1857 o Two bugs have been fixed in root(): unrooted trees are now
1858 handled corretly, and node labels are now output normally.
1860 o A bug was fixed in phymltest(): the executable couldn't be found
1863 o Three bug have been fixed in ace(): computing the likelihood of
1864 ancestral states of discrete characters failed, custom models
1865 did not work, and the function failed with a null gradient (a
1866 warning message is now returned; this latter bug was also
1867 present in yule.cov() as well and is now fixed).
1869 o pic() hanged out when missing data were present: a message error
1872 o A small bug was fixed in dist.dna() where the gamma correction
1873 was not always correctly dispatched.
1875 o plot.phylo() plotted correctly the root edge only when the tree
1876 was plotted rightwards: this works now for all directions.
1881 o dist.taxo() has been renamed as weight.taxo().
1883 o dist.phylo() has been replaced by the method cophenetic.phylo().
1885 o Various error and warning messages have been improved.
1889 CHANGES IN APE VERSION 1.7
1892 o The new function ace() estimates ancestral character states for
1893 continuous characters (with ML, GLS, and contrasts methods), and
1894 discrete characters (with ML only) for any number of states.
1896 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1897 of directional evolution for continuous characters. The user
1898 specifies the node(s) of the tree where the character optimum
1901 o The new function is.rooted() tests whether a tree (of class
1904 o The new function rcoal() generates random ultrametric trees with
1905 the possibility to specify the function that generates the
1906 inter-nodes distances.
1908 o The new function mrca() gives for all pairs of tips in a tree
1909 (and optionally nodes too) the most recent common ancestor.
1911 o nodelabels() has a new option `thermo' to plot proportions (up
1912 to three classes) on the nodes of a tree.
1914 o rtree() has been improved: it can now generate rooted or
1915 unrooted trees, and the mathematical function that generates the
1916 branch lengths may be specified by the user. The tip labels may
1917 be given directly in the call to rtree. The limit cases (n = 2,
1918 3) are now handled correctly.
1920 o dist.topo() has a new argument `method' with two choices: "PH85"
1921 for Penny and Henny's method (already available before and now
1922 the default), and "BHV01" for the geometric distance by Billera
1923 et al. (2001, Adv. Appl. Math. 27:733).
1925 o write.tree() has a new option, `digits', which specifies the
1926 number of digits to be printed in the Newick tree. By default
1927 digits = 10. The numbers are now always printed in decimal form
1928 (i.e., 1.0e-1 is now avoided).
1930 o dist.dna() can now compute the raw distances between pairs of
1931 DNA sequences by specifying model = "raw".
1933 o dist.phylo() has a new option `full' to possibly compute the
1934 distances among all tips and nodes of the tree. The default if
1940 o Several bugs were fixed in all.equal.phylo().
1942 o dist.dna() did not handle correctly gaps ("-") in alignments:
1943 they are now considered as missing data.
1945 o rotate() did not work if the tips were not ordered: this is
1948 o mantel.test() returned NA in some special cases: this is fixed
1949 and the function has been improved and is now faster.
1951 o A bug was fixed in diversi.gof() where the calculation of A² was
1954 o cherry() did not work correctly under some OSs (mainly Linux):
1957 o is.binary.tree() has been modified so that it works with both
1958 rooted and unrooted trees.
1960 o The documentation of theta.s() was not correct: this has been
1963 o plot.mst() did not work correctly: this is fixed.
1967 CHANGES IN APE VERSION 1.6
1972 o The new function dist.topo() computes the topological distances
1975 o The new function boot.phylo() performs a bootstrap analysis on
1976 phylogeny estimation.
1978 o The new functions prop.part() and prop.clades() analyse
1979 bipartitions from a series of trees.
1984 o read.GenBank() now uses the EFetch utility of NCBI instead of
1985 the usual Web interface: it is now much faster (e.g., 12 times
1986 faster to retrieve 8 sequences, 37 times for 60 sequences).
1991 o Several bugs were fixed in read.dna().
1993 o Several bugs were fixed in diversi.time().
1995 o is.binary.tree() did not work correctly if the tree has no edge
1996 lengths: this is fixed.
1998 o drop.tip() did not correctly propagated the `node.label' of a
1999 tree: this is fixed.
2003 CHANGES IN APE VERSION 1.5
2008 o Two new functions, as.matching.phylo() and as.phylo.matching(),
2009 convert objects between the classes "phylo" and "matching". The
2010 latter implements the representation of binary trees introduced by
2011 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
2012 as.matching() has been introduced as well.
2014 o Two new functions, multi2di() and di2multi(), allow to resolve
2015 and collapse multichotomies with branches of length zero.
2017 o The new function nuc.div() computes the nucleotide diversity
2018 from a sample a DNA sequences.
2020 o dist.dna() has been completely rewritten with a much faster
2021 (particularly for large data sets) C code. Eight models are
2022 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
2023 option `method' has been renamed `model'). Computation of variance
2024 is available for all models. A gamma-correction is possible for
2025 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
2026 to remove sites with missing data on a pairwise basis. The option
2027 `GCcontent' has been removed.
2029 o read.GenBank() has a new option (species.names) which specifies
2030 whether to return the species names of the organisms in addition
2031 to the accession numbers of the sequences (this is the default
2034 o write.nexus() can now write several trees in the same NEXUS file.
2036 o drop.tip() has a new option `root.edge' that allows to specify the
2037 new root edge if internal branches are trimmed.
2042 o as.phylo.hclust() failed if some labels had parentheses: this
2045 o Several bugs were fixed in all.equal.phylo(). This function now
2046 returns the logical TRUE if the trees are identical but with
2047 different representations (a report was printed previously).
2049 o read.GenBank() did not correctly handle ambiguous base codes:
2055 o birthdeath() now returns an object of class "birthdeath" for
2056 which there is a print method.
2060 CHANGES IN APE VERSION 1.4
2065 o The new function nj() performs phylogeny estimation with the
2066 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
2069 o The new function which.edge() identifies the edges of a tree
2070 that belong to a group specified as a set of tips.
2072 o The new function as.phylo.phylog() converts an object of class
2073 "phylog" (from the package ade4) into an object of class
2076 o The new function axisPhylo() draws axes on the side of a
2079 o The new function howmanytrees() calculates the number of trees
2080 in different cases and giving a number of tips.
2082 o write.tree() has a new option `multi.line' (TRUE by default) to
2083 write a Newick tree on several lines rather than on a single
2086 o The functionalities of zoom() have been extended. Several
2087 subtrees can be visualized at the same time, and they are marked
2088 on the main tree with colors. The context of the subtrees can be
2089 marked with the option `subtree' (see below).
2091 o drop.tip() has a new option `subtree' (FALSE by default) which
2092 specifies whether to output in the tree how many tips have been
2095 o The arguments of add.scale.bar() have been redefined and have
2096 now default values (see ?add.scale.bar for details). This
2097 function now works even if the plotted tree has no edge length.
2099 o plot.phylo() can now plot radial trees, but this does not take
2100 edge lengths into account.
2102 o In plot.phylo() with `type = "phylogram"', if the values of
2103 `edge.color' and `edge.width' are identical for sister-branches,
2104 they are propagated to the vertical line that link them.
2109 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
2110 crashing. This is fixed.
2112 o In plot.phylo(), the options `edge.color' and `edge.width' are
2113 now properly recycled; their default values are now "black" and
2116 o A bug has been fixed in write.nexus().
2121 o The function node.depth.edgelength() has been removed and
2122 replaced by a C code.
2126 CHANGES IN APE VERSION 1.3-1
2131 o The new function nodelabels() allows to add labels to the nodes
2132 of a tree using text or plotting symbols in a flexible way.
2134 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
2135 numeric values specifying the lower and upper limits on the x-
2136 and y-axes. This allows to leave some space on any side of the
2137 tree. If a single value is given, this is taken as the upper
2142 CHANGES IN APE VERSION 1.3
2147 o The new function phymltest() calls the software PHYML and fits
2148 28 models of DNA sequence evolution. There are a print method to
2149 display likelihood and AIC values, a summary method to compute
2150 the hierarchical likelihood ratio tests, and a plot method to
2151 display graphically the AIC values of each model.
2153 o The new function yule.cov() fits the Yule model with covariates,
2154 a model where the speciation rate is affected by several species
2155 traits through a generalized linear model. The parameters are
2156 estimated by maximum likelihood.
2158 o Three new functions, corBrownian(), corGrafen(), and
2159 corMartins(), compute the expected correlation structures among
2160 species given a phylogeny under different models of evolution.
2161 These can be used for GLS comparative phylogenetic methods (see
2162 the examples). There are coef() and corMatrix() methods and an
2163 Initialize.corPhyl() function associated.
2165 o The new function compar.cheverud() implements Cheverud et al.'s
2166 (1985; Evolution 39:1335) phylogenetic comparative method.
2168 o The new function varcomp() estimates variance components; it has
2171 o Two new functions, panel.superpose.correlogram() and
2172 plot.correlogramList(), allow to plot several phylogenetic
2175 o The new function node.leafnumber() computes the number of leaves
2176 of a subtree defined by a particular node.
2178 o The new function node.sons() gets all tags of son nodes from a
2181 o The new function compute.brlen() computes the branch lengths of
2182 a tree according to a specified method.
2184 o plot.phylo() has three new options: "cex" controls the size of
2185 the (tip and node) labels (thus it is no more needed to change
2186 the global graphical parameter), "direction" which allows to
2187 plot the tree rightwards, leftwards, upwards, or downwards, and
2188 "y.lim" which sets the upper limit on the y-axis.
2193 o Some functions which try to match tip labels and names of
2194 additional data (e.g. vector) are likely to fail if there are
2195 typing or syntax errors. If both series of names do not perfectly
2196 match, they are ignored and a warning message is now issued.
2197 These functions are bd.ext, compar.gee, pic. Their help pages
2198 have been clarified on this point.
2202 CHANGES IN APE VERSION 1.2-7
2207 o The new function root() reroots a phylogenetic tree with respect
2208 to a specified outgroup.
2210 o The new function rotate() rotates an internal branch of a tree.
2212 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
2213 trees) controls the display of the tip labels in unrooted trees.
2214 This display has been greatly improved: the tip labels are now not
2215 expected to overlap with the tree (particularly if lab4ut =
2216 "axial"). In all cases, combining appropriate values of "lab4ut"
2217 and the font size (via "par(cex = )") should result in readable
2218 unrooted trees. See ?plot.phylo for some examples.
2220 o In drop.tip(), the argument `tip' can now be numeric or character.
2225 o drop.tip() did not work correctly with trees with no branch
2226 lengths: this is fixed.
2228 o A bug in plot.phylo(..., type = "unrooted") made some trees being
2229 plotted with some line crossings: this is now fixed.
2233 CHANGES IN APE VERSION 1.2-6
2238 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
2239 correlogram.phylo, dist.taxo, plot.correlogram) have been added
2240 to implement comparative methods with an autocorrelation approach.
2242 o A new data set describing some life history traits of Carnivores
2248 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
2253 o When plotting a tree with plot.phylo(), the new default of the
2254 option `label.offset' is now 0, so the labels are always visible.
2258 CHANGES IN APE VERSION 1.2-5
2263 o The new function bd.ext() fits a birth-death model with combined
2264 phylogenetic and taxonomic data, and estimates the corresponding
2265 speciation and extinction rates.
2270 o The package gee is no more required by ape but only suggested
2271 since only the function compar.gee() calls gee.
2275 CHANGES IN APE VERSION 1.2-4
2280 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
2281 and lines.popsize) implementing a new approach for inferring the
2282 demographic history from genealogies using a reversible jump
2283 MCMC have been introduced.
2285 o The unit of time in the skyline plot and in the new plots can
2286 now be chosen to be actual years, rather than substitutions.
2290 CHANGES IN APE VERSION 1.2-3
2295 o The new function rtree() generates a random binary tree with or
2296 without branch lengths.
2298 o Two new functions for drawing lineages-through-time (LTT) plots
2299 are provided: ltt.lines() adds a LTT curve to an existing plot,
2300 and mltt.plot() does a multiple LTT plot giving several trees as
2301 arguments (see `?ltt.plot' for details).
2306 o Some taxon names made R crashing when calling as.phylo.hclust():
2309 o dist.dna() returned an error with two identical DNA sequences
2310 (only using the Jukes-Cantor method returned 0): this is fixed.
2315 o The function dist.phylo() has been re-written using a different
2316 algorithm: it is now about four times faster.
2318 o The code of branching.times() has been improved: it is now about
2323 CHANGES IN APE VERSION 1.2-2
2328 o The new function seg.sites() finds the segregating sites in a
2329 sample of DNA sequences.
2334 o A bug introduced in read.tree() and in read.nexus() with version
2337 o A few errors were corrected and a few examples were added in the
2342 CHANGES IN APE VERSION 1.2-1
2347 o plot.phylo() can now draw the edge of the root of a tree if it
2348 has one (see the new option `root.edge', its default is FALSE).
2353 o A bug was fixed in read.nexus(): files with semicolons inside
2354 comment blocks were not read correctly.
2356 o The behaviour of read.tree() and read.nexus() was corrected so
2357 that tree files with badly represented root edges (e.g., with
2358 an extra pair of parentheses, see the help pages for details)
2359 are now correctly represented in the object of class "phylo";
2360 a warning message is now issued.
2364 CHANGES IN APE VERSION 1.2
2369 o plot.phylo() has been completely re-written and offers several
2370 new functionalities. Three types of trees can now be drawn:
2371 phylogram (as previously), cladogram, and unrooted tree; in
2372 all three types the branch lengths can be drawn using the edge
2373 lengths of the phylogeny or not (e.g., if the latter is absent).
2374 The vertical position of the nodes can be adjusted with two
2375 choices (see option `node.pos'). The code has been re-structured,
2376 and two new functions (potentially useful for developpers) are
2377 documented separately: node.depth.edgelength() and node.depth();
2378 see the respective help pages for details.
2380 o The new function zoom() allows to explore very large trees by
2381 focusing on a small portion of it.
2383 o The new function yule() fits by maximum likelihood the Yule model
2384 (birth-only process) to a phylogenetic tree.
2386 o Support for writing DNA sequences in FASTA format has been
2387 introduced in write.dna() (support for reading sequences in
2388 this format was introduced in read.dna() in version 1.1-2).
2389 The function has been completely re-written, fixing some bugs
2390 (see below); the default behaviour is no more to display the
2391 sequences on the standard output. Several options have been
2392 introduced to control the sequence printing in a flexible
2393 way. The help page has been extended.
2395 o A new data set is included: a supertree of bats in NEXUS format.
2400 o In theta.s(), the default of the option `variance' has
2401 been changed to `FALSE' (as was indicated in the help page).
2403 o Several bugs were fixed in the code of all.equal.phylo().
2405 o Several bugs were fixed in write.dna(), particularly this
2406 function did not work with `format = "interleaved"'.
2408 o Various errors were corrected in the help pages.
2413 o The argument names of as.hclust.phylo() have been changed
2414 from "(phy)" to "(x, ...)" to conform to the definition of
2415 the corresponding generic function.
2417 o gamma.stat() has been renamed gammaStat() to avoid confusion
2418 since gamma() is a generic function.
2422 CHANGES IN APE VERSION 1.1-3
2427 o base.freq() previously did not return a value of 0 for
2428 bases absent in the data (e.g., a vector of length 3 was
2429 returned if one base was absent). This is now fixed (a
2430 vector of length 4 is always returned).
2432 o Several bugs were fixed in read.nexus(), including that this
2433 function did not work in this absence of a "TRANSLATE"
2434 command in the NEXUS file, and that the commands were
2439 CHANGES IN APE VERSION 1.1-2
2444 o The Tamura and Nei (1993) model of DNA distance is now implemented
2445 in dist.dna(): five models are now available in this function.
2447 o A new data set is included: a set of 15 sequences of the
2448 cytochrome b mitochondrial gene of the woodmouse (Apodemus
2454 o A bug in read.nexus() was fixed.
2456 o read.dna() previously did not work correctly in most cases.
2457 The function has been completely re-written and its help page
2458 has been considerably extended (see ?read.dna for details).
2459 Underscores (_) in taxon names are no more replaced with
2460 spaces (this behaviour was undocumented).
2462 o A bug was fixed in write.dna().
2466 CHANGES IN APE VERSION 1.1-1
2471 o A bug in read.tree() introduced in APE 1.1 was fixed.
2473 o A bug in compar.gee() resulted in an error when trying to fit
2474 a model with `family = "binomial"'. This is now fixed.
2478 CHANGES IN APE VERSION 1.1
2483 o The Klastorin (1982) method as suggested by Misawa and Tajima
2484 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
2485 on the basis of phylogenetic trees has been implemented (see
2486 the function klastorin()).
2488 o Functions have been added to convert APE's "phylo" objects in
2489 "hclust" cluster objects and vice versa (see the help page of
2490 as.phylo for details).
2492 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
2493 are introduced for the estimation of absolute evolutionary rates
2494 (ratogram) and dated clock-like trees (chronogram) from
2495 phylogenetic trees using the non-parametric rate smoothing approach
2496 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
2498 o A summary method is now provided printing a summary information on a
2499 phylogenetic tree with, for instance, `summary(tree)'.
2501 o The behaviour of read.tree() was changed so that all spaces and
2502 tabulations in tree files are now ignored. Consequently, spaces in tip
2503 labels are no more allowed. Another side effect is that read.nexus()
2504 now does not replace the underscores (_) in tip labels with spaces
2505 (this behaviour was undocumented).
2507 o The function plot.phylo() has a new option (`underscore') which
2508 specifies whether the underscores in tip labels should be written on
2509 the plot as such or replaced with spaces (the default).
2511 o The function birthdeath() now computes 95% confidence intervals of
2512 the estimated parameters using profile likelihood.
2514 o Three new data sets are included: a gene tree estimated from 36
2515 landplant rbcL sequences, a gene tree estimated from 32 opsin
2516 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
2521 o A bug was fixed in dist.gene() where nothing was returned.
2523 o A bug in plot.mst() was fixed.
2525 o A bug in vcv.phylo() resulted in false correlations when the
2526 option `cor = TRUE' was used (now fixed).
2530 CHANGES IN APE VERSION 1.0
2535 o Two new functions, read.dna() and write.dna(), read/write in a file
2536 DNA sequences in interleaved or in sequential format.
2538 o Two new functions, read.nexus() and write.nexus(), read/write trees
2541 o The new function bind.tree() allows to bind two trees together,
2542 possibly handling root edges to give internal branches.
2544 o The new function drop.tip() removes the tips in a phylogenetic tree,
2545 and trims (or not) the corresponding internal branches.
2547 o The new function is.ultrametric() tests if a tree is ultrametric.
2549 o The function plot.phylo() has more functionalities such as drawing the
2550 branches with different colours and/or different widths, showing the
2551 node labels, controling the position and font of the labels, rotating
2552 the labels, and controling the space around the plot.
2554 o The function read.tree() can now read trees with no branch length,
2555 such as "(a,b),c);". Consequently, the element `edge.length' in
2556 objects of class "phylo" is now optional.
2558 o The function write.tree() has a new default behaviour: if the default
2559 for the option `file' is used (i.e. file = ""), then a variable of
2560 mode character containing the tree in Newick format is returned which
2561 can thus be assigned (e.g., tree <- write.tree(phy)).
2563 o The function read.tree() has a new argument `text' which allows
2564 to read the tree in a variable of mode character.
2566 o A new data set is included: the phylogenetic relationships among
2567 the orders of birds from Sibley and Ahlquist (1990).
2571 CHANGES IN APE VERSION 0.2-1
2576 o Several bugs were fixed in the help pages.
2580 CHANGES IN APE VERSION 0.2
2585 o The function write.tree() writes phylogenetic trees (objects of class
2586 "phylo") in an ASCII file using the Newick parenthetic format.
2588 o The function birthdeath() fits a birth-death model to branching times
2589 by maximum likelihood, and estimates the corresponding speciation and
2592 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
2595 o The function is.binary.tree() tests whether a phylogeny is binary.
2597 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
2598 as well as some methods are introduced.
2600 o Several functions, including some generics and methods, for computing
2601 skyline plot estimates (classic and generalized) of effective
2602 population size through time are introduced and replace the function
2603 skyline.plot() in version 0.1.
2605 o Two data sets are now included: the phylogenetic relationships among
2606 the families of birds from Sibley and Ahlquist (1990), and an
2607 estimated clock-like phylogeny of HIV sequences sampled in the
2608 Democratic Republic of Congo.
2611 DEPRECATED & DEFUNCT
2613 o The function skyline.plot() in ape 0.1 has been deprecated and
2614 replaced by more elaborate functions (see above).
2619 o Two important bugs were fixed in plot.phylo(): phylogenies with
2620 multichotomies not at the root or not with only terminal branches,
2621 and phylogenies with a single node (i.e. only terminal branches)
2622 did not plot. These trees should be plotted correctly now.
2624 o Several bugs were fixed in diversi.time() in the computation of
2627 o Various errors were corrected in the help pages.
projects / ape.git / blob