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 'rooted' option.
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'.
38 o The DESCRIPTION file has been updated.
40 o The option 'original.data' of write.nexus() has been removed.
44 CHANGES IN APE VERSION 3.0-1
49 o dist.dna() has two new models: "indel" and "indelblock".
51 o bind.tree() now accepts 'position' > 0 when the trees have no
52 banch length permitting to create a node in 'x' when grafting
53 'y' (see ?bind.tree for details).
58 o cophyloplot( , rotate = TRUE) made R hanged after a few clicks.
59 Also the tree is no more plotted twice.
61 o read.GenBank() has been updated to work with EFetch 2.0.
63 o unroot() on trees in "pruningwise" order did not respect this
68 CHANGES IN APE VERSION 3.0
73 o The three functions dyule, dbd, and dbdTime calculate the
74 density probability (i.e., the distribution of the number of
75 species) for the Yule, the constant and the time-dependent
76 birth-beath models, respectively. These probabilities can be
77 conditional on no extinction and/or on a log-scale.
79 o plot.phylo() has a new option 'rotate.tree' to rotate unrooted,
80 fan, or radial trees around the center of the plot.
82 o boot.phylo() and prop.clades() have a new option rooted =
83 FALSE. Note that the behaviour of prop.part() is unchanged.
85 o edgelabels() has a new option 'date' to place labels on edges of
86 chronograms using the time scale (suggestion by Rob Lanfear).
91 o In chronopl(), the code setting the initial dates failed in
92 complicated settings (several dates known within intervals).
93 This has been generally improved and should result in faster
94 and more efficient convergence even in simple settings.
96 o mantel.test() sometimes returned P-values > 1 with the default
99 o extract.clade() sometimes shuffled some tip labels (thanks to
100 Ludovic Mallet and Mahendra Mariadassou for the fix).
102 o clustal() should now find by default the executable under Windows.
107 o The code of yule() has been simplified and is now much faster for
110 o The code of mantel.test() has been adjusted to be consistent
111 with common permutation tests.
113 o The C code of base.freq() has been improved and is now nearly 8
116 o The option 'original.data' of write.nexus() is now deprecated and
117 will be removed in a future release.
119 o The code of is.ultrametric() has been improved and is now 3 times
122 o The code of vcv.phylo() has been improved and is now 10 or 30
123 times faster for 100 or 1000 tips, respectively. Consequently,
124 fitting models with PGLS will be faster overall.
128 CHANGES IN APE VERSION 2.8
133 o Twelve new functions have been written by Andrei-Alin Popescu:
134 additive, ultrametric, is.compatible, arecompatible, mvr, mvrs,
135 njs, bionjs, SDM, treePop, triangMtd, triangMtd*.
137 o A new class "bitsplits" has been created by Andrei-Alin Popescu
138 to code splits (aka, bipartition).
140 o There is a new generic function as.bitsplits with a method to
141 convert from the class "prop.part" to the class "bitsplits".
143 o The new function ltt.coplot plots on the same scales a tree and
144 the derived LTT plot.
146 o ltt.plot() has two new options: backward and tol. It can now
147 handle non-ultrametic trees and its internal coding has been
148 improved. The coordinates of the plot can now be computed with
149 the new function ltt.plot.coords.
154 o prop.part() crashed if some trees had some multichotomies.
158 CHANGES IN APE VERSION 2.7-3
163 o The new function compute.brtime computes and sets branching times.
165 o mantel.test() has a new argument 'alternative' which is
166 "two-sided" by default. Previously, this test was one-tailed
167 with no possibility to change.
169 o ace() can now do REML estimation with continuous characters,
170 giving better estimates of the variance of the Brownian motion
176 o Branch lengths were wrongly updated with bind.tree(, where = <tip>,
177 position = 0). (Thanks to Liam Revell for digging this bug out.)
179 o Simulation of OU process with rTraitCont() did not work correctly.
180 This now uses formula from Gillespie (1996) reduced to a BM
181 process when alpha = 0 to avoid division by zero. The option
182 'linear' has been removed.
184 o Cross-validation in chronopl() did not work when 'age.max' was
187 o consensus(, p = 0.5) could return an incorrect tree if some
188 incompatible splits occur in 50% of the trees (especially with
189 small number of trees).
191 o c() with "multiPhylo" did not work correctly (thanks to Klaus
192 Schliep for the fix).
194 o root() failed in some cases with an outgroup made of several tips.
195 The help page has been clarified a bit.
199 CHANGES IN APE VERSION 2.7-2
204 o There is a new class "evonet" to code evolutionary networks, with
205 a constructor function evonet(), a print() and a plot() methods,
206 and four conversion methods to the classes "phylo", "networx",
207 "network", and "igraph".
209 o The new function rTraitMult does multivariate traits simulation
210 with user-defined models.
212 o plot.phylo() has a new option 'plot = TRUE'. If FALSE, the tree
213 is not plotted but the graphical device is set and the
214 coordinates are saved as usual.
216 o diversity.contrast.test() gains a fourth version of the test with
217 method = "logratio"; the literature citations have been clarified.
219 o add.scale.bar() has two new options, 'lwd' and 'lcol', to modify
220 the aspect of the bar.
222 o boot.phylo() now displays a progress bar by default (can be off
225 o There is a new predict() method for compar.gee().
230 o bionj() made R crash if distances were too large. It now returns
231 an error if at least one distance is greater than 100.
233 o drop.tip() returned a wrong tree if 'tip' was of zero length.
235 o read.nexus.data() failed with URLs.
237 o boot.phylo() returned overestimated support values in the
238 presence of identical or nearly identical sequences.
243 o The data bird.families, bird.orders, cynipids, and woodmouse are
244 now provided as .rda files.
248 CHANGES IN APE VERSION 2.7-1
253 o The new function trex does tree exploration with multiple
256 o The new function kronoviz plots several rooted (dated) trees on
259 o identify.phylo() has a new option 'quiet' (FALSE by default).
264 o A bug was introduced in read.nexus() in ape 2.7.
266 o image.DNAbin() did not colour correctly the bases if there were
269 o .compressTipLabel() failed with a list with a single tree.
271 o identify.phylo() returned a wrong answer when the x- and y-scales
274 o write.nexus() failed with lists of trees with compressed labels.
279 o identify.phylo() now returns NULL if the user right- (instead of
280 left-) clicks (an error was returned previously).
282 o read.nexus() should be robust to commands inserted in the TREES
287 CHANGES IN APE VERSION 2.7
292 o There is a new image() method for "DNAbin" objects: it plots DNA
293 alignments in a flexible and efficient way.
295 o Two new functions as.network.phylo and as.igraph.phylo convert
296 trees of class "phylo" into these respective network classes
297 defined in the packages of the same names.
299 o The three new functions clustal, muscle, and tcoffee perform
300 nucleotide sequence alignment by calling the external programs
303 o Four new functions, diversity.contrast.test, mcconwaysims.test,
304 richness.yule.test, and slowinskiguyer.test, implement various
305 tests of diversification shifts using sister-clade comparisons.
307 o base.freq() gains an option 'all' to count all the possible bases
308 including the ambiguous ones (defaults to FALSE).
310 o read.nexus() now writes tree names in the NEXUS file if given a
311 list of trees with names.
316 o prop.part() failed in some situations with unrooted trees.
318 o read.nexus() shuffled node labels when a TRANSLATE block was
321 o varCompPhylip() did not work if 'exec' was specified.
323 o bind.tree() shuffled node labels when position > 0 and 'where'
329 o BaseProportion in src/dist_dna.c has been modified.
331 o A number of functions in src/tree_build.c have been modified.
333 o The matching representation has now only two columns as the third
334 column was redundant.
338 CHANGES IN APE VERSION 2.6-3
343 o rTraitCont() and rTraitDisc() gains a '...' argument used with
344 user-defined models (suggestion by Gene Hunt).
349 o as.hclust.phylo() now returns an error with unrooted trees.
351 o as.hclust.phylo() failed with trees with node labels (thanks to
352 Jinlong Zhang for pointing this bug out).
354 o read.dna(, "fasta") failed if sequences were not all of the same
357 o plot.phylo() did not recycle values of 'font', 'cex' and
358 'tip.color' correctly when type = "fan" or "radial".
360 o plot.phylo() ignored 'label.offset' when type = "radial", "fan", or
361 "unrooted" with lab4ut = "axial" (the placement of tip labels still
362 needs to be improved with lab4ut = "horizontal").
367 o In drop.fossil() the default tol = 0 has been raised to 1e-8.
369 o The help command ?phylo now points to the man page of read.tree()
370 where this class is described. Similarly, ?matching points to the
371 man page of as.matching().
375 CHANGES IN APE VERSION 2.6-2
380 o Two new functions, pic.ortho and varCompPhylip, implements the
381 orthonormal contrasts of Felsenstein (2008, Am Nat, 171:713). The
382 second function requires Phylip to be installed on the computer.
384 o bd.ext() has a new option conditional = TRUE to use probabilities
385 conditioned on no extinction for the taxonomic data.
390 o write.tree() failed to output correctly tree names.
392 o dist.nodes() returned duplicated column(s) with unrooted and/or
393 multichotomous trees.
395 o mcmc.popsize() terminated unexpectedly if the progress bar was
398 o prop.part(x) made R frozen if 'x' is of class "multiPhylo".
400 o Compilation under Mandriva failed (thanks to Jos Käfer for the fix).
402 o drop.tip() shuffled tip labels with subtree = TRUE or trim.internal
405 o Objects returned by as.hclust.phylo() failed when analysed with
406 cutree() or rect.hclust().
408 o write.tree() did not output correctly node labels (thanks to Naim
409 Matasci and Jeremy Beaulieu for the fix).
411 o ace(type = "discrete") has been improved thanks to Naim Marasci and
416 CHANGES IN APE VERSION 2.6-1
421 o The new function speciesTree calculates the species tree from a set
422 of gene trees. Several methods are available including maximum tree
423 and shallowest divergence tree.
428 o A bug introduced in write.tree() with ape 2.6 has been fixed.
430 o as.list.DNAbin() did not work correctly with vectors.
432 o as.hclust.phylo() failed with trees with node labels (thanks to
433 Filipe Vieira for the fix).
437 CHANGES IN APE VERSION 2.6
442 o The new functions rlineage and rbdtree simulate phylogenies under
443 any user-defined time-dependent speciation-extinction model. They
444 use continuous time algorithms.
446 o The new function drop.fossil removes the extinct species from a
449 o The new function bd.time fits a user-defined time-dependent
450 birth-death model. It is a generalization of yule.time() taking
451 extinction into account.
453 o The new function MPR does most parsimonious reconstruction of
456 o The new function Ftab computes the contingency table of base
457 frequencies from a pair of sequences.
459 o There is now an 'as.list' method for the class "DNAbin".
461 o dist.dna() can compute the number of transitions or transversions
462 with the option model = "Ts" or model = "Tv", respectively.
464 o [node|tip|edge]labels() gain three options with default values to
465 control the aspect of thermometers: horiz = TRUE, width = NULL,
468 o compar.gee() has been improved with the new option 'corStruct' as an
469 alternative to 'phy' to specify the correlation structure, and
470 calculation of the QIC (Pan 2001, Biometrics). The display of the
471 results has also been improved.
473 o read.GenBank() has a new option 'gene.names' to return the name of
474 the gene (FALSE by default).
479 o extract.clade() sometimes shuffled the tip labels.
481 o plot.phylo(type = "unrooted") did not force asp = 1 (thanks to Klaus
484 o dist.dna(model = "logdet") used to divide distances by 4. The
485 documentation has been clarified on the formulae used.
490 o rTraitCont(model = "OU") has an option 'linear = TRUE' to possibly
491 change the parameterisation (see ?rTraitCont for details).
493 o pic() now returns a vector with the node labels of the tree (if
496 o write.tree() and read.tree() have been substantially improved thanks
497 to contributions by Klaus Schliep.
501 CHANGES IN APE VERSION 2.5-3
506 o The new function mixedFontLabel helps to make labels with bits of
507 text to be plotted in different fonts.
509 o There are now replacement operators for [, [[, and $ for the class
510 "multiPhylo" (i.e., TREES[11:20] <- rmtree(10, 100)). They possibly
511 check that the tip labels are the same in all trees.
513 o Objects of class "multiPhylo" can be built with c(): there are
514 methods for the classes "phylo" and "multiPhylo".
516 o The internal functions .compressTipLabel and .uncompressTipLabel are
522 o bind.tree(x, y, where, position = 0) did not work correctly if 'y'
523 was a single-edge tree and 'where' was a tip.
525 o rTraitCont() did not use the square-root of branch lengths when
526 simulating a Brownian motion model.
530 CHANGES IN APE VERSION 2.5-2
535 o There is now a print method for results from ace().
537 o There is a labels() method for objects of class "DNAbin".
539 o read.dna() has a new option 'as.matrix' to possibly force sequences
540 in a FASTA file to be stored in a matrix (see ?read.dna for details).
545 o as.phylo.hclust() used to multiply edge lengths by 2.
547 o A minor bug was fixed in rTraitDisc().
549 o ace() sometimes failed (parameter value was NaN and the optimisation
555 o evolve.phylo() and plot.ancestral() have been removed.
557 o chronogram(), ratogram(), and NPRS.criterion() have been removed.
562 o nj() has been improved and is now about 30% faster.
564 o The default option 'drop' of [.DNAbin has been changed to FALSE to
565 avoid dropping rownames when selecting a single sequence.
567 o print.DNAbin() has been changed to summary.DNAbin() which has been
572 CHANGES IN APE VERSION 2.5-1
577 o The new function stree generates trees with regular shapes.
579 o It is now possible to bind two trees with x + y (see ?bind.tree for
582 o drop.tip(), extract.clade(), root(), and bind.tree() now have an
583 'interactive' option to make the operation on a plotted tree.
585 o cophyloplot() gains two new arguments 'lwd' and 'lty' for the
586 association links; they are recycled like 'col' (which wasn't before).
591 o rTraitDisc() did not use its 'freq' argument correctly (it was
592 multiplied with the rate matrix column-wise instead of row-wise).
594 o [node|tip|edge]labels(thermo = ) used to draw empty thermometers
595 with NA values. Nothing is drawn now like with 'text' or 'pch'.
596 The same bug occurred with the 'pie' option.
598 o A bug was fixed in compar.ou() and the help page was clarified.
600 o bind.tree() has been rewritten fixing several bugs and making it
603 o plot.phylo(type = "p") sometimes failed to colour correctly the
604 vertical lines representing the nodes.
606 o plot.phylo(direction = "l", x.lim = 30) failed to plot the branches
607 in the correct direction though the tip labels were displayed
613 o The c, cbind, and rbind methods for "DNAbin" objetcs now check that
614 the sequences are correctly stored (in a list for c, in a matrix
615 for the two other functions).
619 CHANGES IN APE VERSION 2.5
624 o The new function parafit by Pierre Legendre tests for the
625 coevolution between hosts and parasites. It has a companion
626 function, pcoa, that does principal coordinate decomposition.
627 The latter has a biplot method.
629 o The new function lmorigin by Pierre Legendre performs multiple
630 regression through the origin with testing by permutation.
632 o The new functions rTraitCont and rTraitDisc simulate continuous and
633 discrete traits under a wide range of evolutionary models.
635 o The new function delta.plot does a delta plot following Holland et
636 al. (2002, Mol. Biol. Evol. 12:2051).
638 o The new function edges draws additional branches between any nodes
639 and/or tips on a plotted tree.
641 o The new function fancyarrows enhances arrows from graphics with
642 triangle and harpoon heads; it can be called from edges().
644 o add.scale.bar() has a new option 'ask' to draw interactively.
646 o The branch length score replaces the geodesic distance in dist.topo.
648 o Three new data sets are included: the gopher-lice data (gopher.D),
649 SO2 air pollution in 41 US cities (lmorigin.ex1, from Sokal &
650 Rohlf 1995), and some host-parasite specificity data
651 (lmorigin.ex2, from Legendre & Desdevises 2009).
656 o add.scale.bar() drew the bar outside the plotting region with the
657 default options with unrooted or radial trees.
659 o dist.topo() made R stuck when the trees had different sizes (thanks
660 to Otto Cordero for the fix).
665 o The geodesic distance has been replaced by the branch length score
670 CHANGES IN APE VERSION 2.4-1
675 o rtree() and rcoal() now accept a numeric vector for the 'br'
678 o vcv() is a new generic function with methods for the classes "phylo"
679 and "corPhyl" so that it is possible to calculate the var-cov matrix
680 for "transformation models". vcv.phylo() can still be used for trees
681 of class "phylo"; its argument 'cor' has been renamed 'corr'.
686 o bind.tree() failed when 'y' had no root edge.
688 o read.nexus() shuffled tip labels when the trees have no branch
689 lengths and there is a TRANSLATE block.
691 o read.nexus() does not try to translate node labels if there is a
692 translation table in the NEXUS file. See ?read.nexus for a
693 clarification on this behaviour.
695 o plot.multiPhylo() crashed R when plotting a list of trees with
696 compressed tip labels.
698 o write.nexus() did not translate the taxa names when asked for.
700 o plot.phylo(type = "fan") did not rotate the tip labels correctly
701 when the tree has branch lengths.
703 o ace(type = "continuous", method = "ML") now avoids sigma² being
704 negative (which resulted in an error).
706 o nj() crashed with NA/NaN in the distance matrix: an error in now
711 CHANGES IN APE VERSION 2.4
716 o base.freq() has a new option 'freq' to return the counts; the
717 default is still to return the proportions.
722 o seg.sites() did not handle ambiguous nucleotides correctly: they
725 o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
726 the tree: the argument is now ignored.
728 o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
734 o Trying to plot a tree with a single tip now returns NULL with a
735 warning (it returned an error previously).
737 o The way lines representing nodes are coloured in phylograms has
738 been modified (as well as their widths and types) following some
739 users' request; this is only for dichotomous nodes.
741 o The argument 'adj' in [node][tip][edge]labels() now works when
742 using 'pie' or 'thermo'.
744 o A more informative message error is now returned by dist.dna() when
745 'model' is badly specified (partial matching of this argument is
748 o Deprecated functions are now listed in a help page: see
749 help("ape-defunct") with the quotes.
754 o The functions heterozygosity, nuc.div, theta.h, theta.k and
755 theta.s have been moved from ape to pegas.
757 o The functions mlphylo, DNAmodel and sh.test have been removed.
761 CHANGES IN APE VERSION 2.3-3
766 o add.scale.bar() always drew a horizontal bar.
768 o zoom() shuffled tips with unrooted trees.
770 o write.nexus() failed to write correctly trees with a "TipLabel"
773 o rcoal() failed to compute branch lengths with very large n.
775 o A small bug was fixed in compar.cheverud() (thanks to Michael
778 o seg.sites() failed when passing a vector.
780 o drop.tip() sometimes shuffled tip labels.
782 o root() shuffled node labels with 'resolve.root = TRUE'.
786 CHANGES IN APE VERSION 2.3-2
791 o all.equal.phylo() did not compare unrooted trees correctly.
793 o dist.topo(... method = "PH85") did not treat unrooted trees
794 correctly (thanks to Tim Wallstrom for the fix).
796 o root() sometimes failed to test for the monophyly of the
799 o extract.clade() sometimes included too many edges.
801 o vcv.phylo() did not work correctly when the tree is in
804 o nj() did not handle correctly distance matrices with many 0's.
805 The code has also been significantly improved: 7, 70, 160 times
806 faster with n = 100, 500, 1000, respectively.
810 CHANGES IN APE VERSION 2.3-1
815 o The new function is.monophyletic tests the monophyly of a group.
817 o There is now a c() method for lists of class "DNAbin".
819 o yule.cov() now fits the null model, and its help page has been
820 corrected with respect to this change.
822 o drop.tip() has a new option 'rooted' to force (or not) a tree
823 to be treated as (un)rooted.
828 o dist.gene() failed on most occasions with the default
829 pairwise.deletion = FALSE.
831 o read.tree() failed to read correctly the tree name(s).
833 o boot.phylo() now treats correctly data frames.
835 o del.gaps() did not copy the rownames of a matrix.
837 o A small bug was fixed in CDAM.global().
839 o ace() failed with large data sets. Thanks to Rich FitzJohn for
840 the fix. With other improvements, this function is now about 6
843 o write.tree() failed with objects of class "multiPhylo".
845 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
850 o [.multiPhylo and [.DNAbin now respect the original class.
852 o Instances of the form class(phy) == "phylo" have been replaced
853 by inherits(phy, "phylo").
855 o rcoal() is now faster.
860 o klastorin() has been removed.
864 CHANGES IN APE VERSION 2.3
869 o The new functions CADM.global and CADM.post, contributed by
870 Pierre Legendre, test the congruence among several distance
873 o The new function yule.time fits a user-defined time-dependent
874 Yule model by maximum likelihood.
876 o The new function makeNodeLabel creates and/or modifies node
877 labels in a flexible way.
879 o read.tree() and write.tree() have been modified so that they can
880 handle individual tree names.
882 o plot.phylo() has a new argument 'edge.lty' that specifies the
883 types of lines used for the edges (plain, dotted, dashed, ...)
885 o phymltest() has been updated to work with PhyML 3.0.1.
890 o drop.tip() shuffled tip labels in some cases.
892 o drop.tip() did not handle node.label correctly.
894 o is.ultrametric() now checks the ordering of the edge matrix.
896 o ace() sometimes returned negative values of likelihoods of
897 ancestral states (thanks to Dan Rabosky for solving this long
903 o The data set xenarthra has been removed.
907 CHANGES IN APE VERSION 2.2-4
911 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
912 now fixed. (Thanks to Peter Wragg for the fix!)
914 o A warning message occurred for no reason with ace(method="GLS").
919 o There is now a general help page displayed with '?ape'.
923 CHANGES IN APE VERSION 2.2-3
928 o The new function extract.clade extracts a clade from a tree by
929 specifying a node number or label.
931 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
932 operations of the same names.
934 o dist.dna() can now return the number of site differences by
935 specifying model="N".
940 o chronopl() did not work with CV = TRUE.
942 o read.nexus() did not work correctly in some situations (trees on
943 multiple lines with different numbers of lines and/or with
944 comments inserted within the trees).
946 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
947 the number of lineages with non-binary trees.
952 o ape has now a namespace.
954 o drop.tip() has been improved: it should be much faster and work
955 better in some cases (e.g., see the example in ?zoom).
959 CHANGES IN APE VERSION 2.2-2
964 o dist.gene() has been substantially improved and gains an option
967 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
973 o prop.part() failed with a single tree with the default option
974 'check.labels = TRUE'.
976 o summary.DNAbin() failed to display correctly the summary of
977 sequence lengths with lists of sequences of 10,000 bases or more
978 (because summary.default uses 4 significant digits by default).
980 o read.nexus() failed to read a file with a single tree with line
981 breaks in the Newick string.
983 o del.gaps() returned a list of empty sequences when there were no
989 o phymltest() has been updated for PhyML 3.0 and gains an option
990 'append', whereas the option 'path2exec' has been removed.
992 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
993 which is returned unchanged (instead of an error).
995 o The data sets bird.orders and bird.families are now stored as
996 Newick strings; i.e., the command data(bird.orders) calls
1001 CHANGES IN APE VERSION 2.2-1
1006 o The new function makeLabel() helps to modify labels of trees,
1007 lists of trees, or DNA sequences, with several utilities to
1008 truncate and/or make them unique, substituting some
1009 characters, and so on.
1011 o The new function del.gaps() removes insertion gaps ("-") in a
1012 set of DNA sequences.
1014 o read.dna() can now read Clustal files (*.aln).
1019 o root() failed with 'resolve.root = TRUE' when the root was
1020 already the specified root.
1022 o Several bugs were fixed in mlphylo().
1024 o collapsed.singles() did not propagate the 'Nnode' and
1025 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
1027 o read.nexus() failed to remove correctly the comments within
1030 o read.nexus() failed to read a file with a single tree and no
1031 translation of tip labels.
1033 o read.nexus() failed to place correctly tip labels when reading
1034 a single tree with no edge lengths.
1036 o A bug was fixed in sh.test().
1041 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
1044 o The option 'check.labels' of consensus() and prop.part() is now
1047 o write.dna() now does not truncate names to 10 characters with
1052 CHANGES IN APE VERSION 2.2
1057 o Four new functions have been written by Damien de Vienne for the
1058 graphical exploration of large trees (cophyloplot, subtrees,
1059 subtreeplot), and to return the graphical coordinates of tree
1062 o The new functions corPagel and corBlomberg implement the Pagel's
1063 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
1065 o chronopl() has been improved and gains several options: see its
1066 help page for details.
1068 o boot.phylo() has now an option 'trees' to possibly return the
1069 bootstraped trees (the default is FALSE).
1071 o prop.part() has been improved and should now be faster in all
1077 o read.dna() failed if "?" occurred in the first 10 sites of the
1080 o The x/y aspect of the plot is now respected when plotting a
1081 circular tree (type = "r" or "f").
1083 o Drawing the tip labels sometimes failed when plotting circular
1086 o zoom() failed when tip labels were used instead of their numbers
1087 (thanks to Yan Wong for the fix).
1089 o drop.tip() failed with some trees (fixed by Yan Wong).
1091 o seg.sites() failed with a list.
1093 o consensus() failed in some cases. The function has been improved
1094 as well and is faster.
1098 CHANGES IN APE VERSION 2.1-3
1103 o A bug in read.nexus() made the Windows R-GUI crash.
1105 o An error was fixed in the computation of ancestral character
1106 states by generalized least squares in ace().
1108 o di2multi() did not modify node labels correctly.
1110 o multi2di() failed if the tree had its attribute "order" set to
1115 CHANGES IN APE VERSION 2.1-2
1120 o There three new methods for the "multiPhylo" class: str, $,
1123 o root() gains the options 'node' and 'resolve.root'
1124 (FALSE by default) as well as its code being improved.
1126 o mltt.plot() has now an option 'log' used in the same way
1127 than in plot.default().
1132 o mltt.plot() failed to display the legend with an unnamed
1135 o nodelabels() with pies now correcly uses the argument
1136 'cex' to draw symbols of different sizes (which has
1137 worked already for thermometers).
1139 o read.nexus() generally failed to read very big files.
1144 o The argument 'family' of compar.gee() can now be a function
1145 as well as a character string.
1147 o read.tree() and read.nexus() now return an unnamed list if
1148 'tree.names = NULL'.
1150 o read.nexus() now returns a modified object of class "multiPhylo"
1151 when there is a TRANSLATE block in the NEXUS file: the individual
1152 trees have no 'tip.label' vector, but the list has a 'TipLabel'
1153 attribute. The new methods '$' and '[[' set these elements
1154 correctly when extracting trees.
1158 CHANGES IN APE VERSION 2.1-1
1163 o The new function rmtree generates lists of random trees.
1165 o rcoal() now generates a genuine coalescent tree by default
1166 (thanks to Vladimir Minin for the code).
1171 o nuc.div() returned an incorrect value with the default
1172 pairwise.deletion = FALSE.
1177 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
1178 have been improved so that they are stabler and faster.
1180 o R packages used by ape are now loaded silently; lattice and gee
1181 are loaded only when needed.
1185 CHANGES IN APE VERSION 2.1
1190 o The new function identify.phylo identifies clades on a plotted
1191 tree using the mouse.
1193 o It is now possible to subset a list of trees (object of class
1194 "multiPhylo") with "[" while keeping its class correct.
1196 o The new function as.DNAbin.alignment converts DNA sequences
1197 stored in the "alignment" format of the package seqinr into
1198 an object of class "DNAbin".
1200 o The new function weight.taxo2 helps to build similarity matrices
1201 given two taxonomic levels (usually called by other functions).
1203 o write.tree() can now take a list of trees (class "multiPhylo")
1204 as its main argument.
1206 o plot.correlogram() and plot.correlogramList() have been
1207 improved, and gain several options (see the help page for
1208 details). A legend is now plotted by default.
1213 o dist.dna() returned some incorrect values with `model = "JC69"'
1214 and `pairwise.deletion = TRUE'. This affected only the
1215 distances involving sequences with missing values. (Thanks
1216 to Bruno Toupance for digging this bug out.)
1218 o write.tree() failed with some trees: this is fixed by removing
1219 the `multi.line' option (trees are now always printed on a
1222 o read.nexus() did not correctly detect trees with multiple root
1223 edges (see OTHER CHANGES).
1228 o The code of mlphylo() has been almost entirely rewritten, and
1229 should be much stabler. The options have been also greatly
1230 simplified (see ?mlphylo and ?DNAmodel for details).
1232 o The internal function nTips has been renamed klastorin_nTips.
1234 o The code of is.ultrametric() contained redundancies and has
1237 o The code of Moran.I() and of correlogram.formula() have been
1240 o read.tree() and read.nexus() now return an error when trying to
1241 read a tree with multiple root edges (see BUG FIXES). The
1242 correction applied in previous version did not work in all
1245 o The class c("multi.tree", "phylo") has been renamed
1251 o There is now a vignette in ape: see vignette("MoranI", "ape").
1254 DEPRECATED & DEFUNCT
1256 o as.matching() and as.phylo.matching() do not support branch
1259 o correlogram.phylo() and discrete.dist() have been removed.
1263 CHANGES IN APE VERSION 2.0-2
1268 o The new function matexpo computes the exponential of a square
1271 o The new function unique.multi.tree removes duplicate trees from
1274 o yule() has a new option `use.root.edge = FALSE' that specifies
1275 to ignore, by default, the root edge of the tree if it exists.
1280 o which.edge() failed when the index of a single terminal edge was
1283 o In diversi.time(), the values returned for model C were
1286 o A bug was fixed in yule() that affected the calculation of the
1287 likelihood in the presence of ties in the branching times.
1289 o There was a bug in the C function mat_expo4x4 affecting the
1290 calculations of the transition probabilities for models HKY and
1293 o A small bug was fixed in as.matrix.DNAbin (thanks to James
1296 o rtree() did not `shuffle' the tip labels by default, so only a
1297 limited number of labelled topologies could be generated.
1301 CHANGES IN APE VERSION 2.0-1
1306 o The three new functions bionj, fastme.ols, and fastme.bal
1307 perform phylogeny estimation by the BIONJ and fastME methods in
1308 OLS and balanced versions. This is a port to R of previous
1309 previous programs done by Vincent Lefort.
1311 o The new function chronoMPL performs molecular dating with the
1312 mean path lengths method of Britton et al. (2002, Mol. Phyl.
1315 o The new function rotate, contributed by Christoph Heibl, swaps
1316 two clades connected to the same node. It works also with
1317 multichotomous nodes.
1319 o The new `method' as.matrix.DNAbin() may be used to convert
1320 easily DNA sequences stored in a list into a matrix while
1321 keeping the names and the class.
1326 o chronopl() failed when some branch lengths were equal to zero:
1327 an error message is now returned.
1329 o di2multi() failed when there was a series of consecutive edges
1334 CHANGES IN APE VERSION 1.10-2
1339 o plot.phylo() can now plot circular trees: the option is type =
1340 "fan" or type = "f" (to avoid the ambiguity with type = "c").
1342 o prop.part() has a new option `check.labels = FALSE' which allows
1343 to considerably speed-up the calculations of bipartitions. As a
1344 consequence, calculations of bootstrap values with boot.phylo()
1345 should be much faster.
1350 o read.GenBank() did not return correctly the list of species as
1351 from ape 1.10: this is fixed in this version
1353 o Applying as.phylo() on a tree of class "phylo" failed: the
1354 object is now returned unchanged.
1358 CHANGES IN APE VERSION 1.10-1
1363 o The three new functions Ntip, Nnode, and Nedge return, for a
1364 given tree, the number of tips, nodes, or edges, respectively.
1369 o read.nexus() did not set correctly the class of the returned
1370 object when reading multiple trees.
1372 o mllt.plot() failed with objects of class c("multi.tree",
1375 o unroot() did not work correctly in most cases.
1377 o reorder.phylo() made R freeze in some occasions.
1379 o Plotting a tree in pruningwise order failed.
1381 o When plotting an unrooted tree, the tip labels where not all
1382 correctly positioned if the option `cex' was used.
1386 CHANGES IN APE VERSION 1.10
1391 o Five new `method' functions have been introduced to manipulate
1392 DNA sequences in binary format (see below).
1394 o Three new functions have been introduced to convert between the
1395 new binary and the character formats.
1397 o The new function as.alignment converts DNA sequences stored as
1398 single characters into the class "alignment" used by the package
1401 o read.dna() and read.GenBank() have a new argument `as.character'
1402 controlling whether the sequences are returned in binary format
1408 o root() failed when the tree had node labels: this is fixed.
1410 o plot.phylo() did not correctly set the limits on the y-axis with
1411 the default setting: this is fixed.
1413 o dist.dna() returned a wrong result for the LogDet, paralinear,
1414 and BH87 models with `pairwise.deletion = TRUE'.
1419 o DNA sequences are now internally stored in a binary format. See
1420 the document "A Bit-Level Coding Scheme for Nucleotides" for the
1421 details. Most functions analyzing DNA functions have been
1422 modified accordingly and are now much faster (dist.dna is now
1423 ca. 60 times faster).
1427 CHANGES IN APE VERSION 1.9-4
1432 o A bug was fixed in edgelabels().
1434 o as.phylo.hclust() did not work correctly when the object of
1435 class "hclust" has its labels set to NULL: the returned tree has
1436 now its tip labels set to "1", "2", ...
1438 o consensus could fail if some tip labels are a subset of others
1439 (e.g., "a" and "a_1"): this is now fixed.
1441 o mlphylo() failed in most cases if some branch lengths of the
1442 initial tree were greater than one: an error message is now
1445 o mlphylo() failed in most cases when estimating the proportion of
1446 invariants: this is fixed.
1450 CHANGES IN APE VERSION 1.9-3
1455 o The new function edgelabels adds labels on the edge of the tree
1456 in the same way than nodelabels or tiplabels.
1461 o multi2di() did not handle correctly branch lengths with the
1462 default option `random = TRUE': this is now fixed.
1464 o A bug was fixed in nuc.div() when using pairwise deletions.
1466 o A bug occurred in the analysis of bipartitions with large
1467 numbers of large trees, with consequences on prop.part,
1468 prop.clades, and boot.phylo.
1470 o The calculation of the Billera-Holmes-Vogtmann distance in
1471 dist.topo was wrong: this has been fixed.
1475 CHANGES IN APE VERSION 1.9-2
1480 o The new function ladderize reorganizes the internal structure of
1481 a tree to plot them left- or right-ladderized.
1483 o The new function dist.nodes computes the patristic distances
1484 between all nodes, internal and terminal, of a tree. It replaces
1485 the option `full = TRUE' of cophenetic.phylo (see below).
1490 o A bug was fixed in old2new.phylo().
1492 o Some bugs were fixed in chronopl().
1494 o The edge colours were not correctly displayed by plot.phylo
1495 (thank you to Li-San Wang for the fix).
1497 o cophenetic.phylo() failed with multichotomous trees: this is
1503 o read.dna() now returns the sequences in a matrix if they are
1504 aligned (interleaved or sequential format). Sequences in FASTA
1505 format are still returned in a list.
1507 o The option `full' of cophenetic.phylo() has been removed because
1508 it could not be used from the generic.
1511 DEPRECATED & DEFUNCT
1513 o rotate() has been removed; this function did not work correctly
1518 CHANGES IN APE VERSION 1.9-1
1523 o Trees with a single tip were not read correctly in R as the
1524 element `Nnode' was not set: this is fixed.
1526 o unroot() did not set correctly the number of nodes of the
1527 unrooted tree in most cases.
1529 o read.GenBank() failed when fetching very long sequences,
1530 particularly of the BX-series.
1532 o A bug was introduced in read.tree() with ape 1.9: it has been
1537 CHANGES IN APE VERSION 1.9
1542 o There are two new print `methods' for trees of class "phylo" and
1543 lists of trees of class "multi.tree", so that they are now
1544 displayed in a compact and informative way.
1546 o There are two new functions, old2new.phylo and new2old.phylo,
1547 for converting between the old and new coding of the class
1550 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
1551 LogDet ("logdet"), and paralinear ("paralin").
1553 o compute.brlen() has been extended: several methods are now
1554 available to compute branch lengths.
1556 o write.dna() can now handle matrices as well as lists.
1561 o cophenetic.phylo() sometimes returned a wrong result with
1562 multichotomous trees: this is fixed.
1564 o rotate() failed when a single tip was specified: the tree is now
1567 o ace() did not return the correct index matrix with custom
1568 models: this is fixed.
1570 o multi2di() did not work correctly when resolving multichotomies
1571 randomly: the topology was always the same, only the arrangement
1572 of clades was randomized: this is fixed. This function now
1573 accepts trees with no branch lengths.
1575 o The output of diversi.gof() was blurred by useless prints when a
1576 user distribution was specified. This has been corrected, and
1577 the help page of this function has been expanded.
1582 o The internal structure of the class "phylo" has been changed:
1583 see the document "Definition of Formats for Coding Phylogenetic
1584 Trees in R" for the details. In addition, the code of most
1585 functions has been improved.
1587 o Several functions have been improved by replacing some R codes
1588 by C codes: pic, plot.phylo, and reorder.phylo.
1590 o There is now a citation information: see citation("ape") in R.
1592 o write.tree() now does not add extra 0's to branch lengths so
1593 that 1.23 is printed "1.23" by default, not "1.2300000000".
1595 o The syntax of bind.tree() has been simplified. This function now
1596 accepts trees with no branch lengths, and handles correctly node
1599 o The option `as.numeric' of mrca() has been removed.
1601 o The unused options `format' and `rooted' of read.tree() have
1604 o The unused option `format' of write.tree() has been removed.
1606 o The use of node.depth() has been simplified.
1610 CHANGES IN APE VERSION 1.8-5
1615 o Two new functions read.nexus.data() and write.nexus.data(),
1616 contributed by Johan Nylander, allow to read and write molecular
1617 sequences in NEXUS files.
1619 o The new function reorder.phylo() reorders the internal structure
1620 of a tree of class "phylo". It is used as the generic, e.g.,
1623 o read.tree() and read.nexus() can now read trees with a single
1626 o The new data set `cynipids' supplies a set of protein sequences
1632 o The code of all.equal.phylo() has been completely rewritten
1633 (thanks to Benoît Durand) which fixes several bugs.
1635 o read.tree() and read.nexus() now checks the labels of the tree
1636 to remove or substitute any characters that are illegal in the
1637 Newick format (parentheses, etc.)
1639 o A negative P-value could be returned by mantel.test(): this is
1644 CHANGES IN APE VERSION 1.8-4
1649 o The new function sh.test() computes the Shimodaira-
1652 o The new function collapse.singles() removes the nodes with a
1653 single descendant from a tree.
1655 o plot.phylo() has a new argument `tip.color' to specify the
1656 colours of the tips.
1658 o mlphylo() has now an option `quiet' to control the display of
1659 the progress of the analysis (the default is FALSE).
1664 o read.dna() did not read correctly sequences in sequential format
1665 with leading alignment gaps "-": this is fixed.
1667 o ace() returned a list with no class so that the generic
1668 functions (anova, logLik, ...) could not be used directly. This
1669 is fixed as ace() now returns an object of class "ace".
1671 o anova.ace() had a small bug when computing the number of degrees
1672 of freedom: this is fixed.
1674 o mlphylo() did not work when the sequences were in a matrix or
1675 a data frame: this is fixed.
1677 o rtree() did not work correctly when trying to simulate an
1678 unrooted tree with two tips: an error message is now issued.
1683 o The algorithm of rtree() has been changed: it is now about 40,
1684 100, and 130 times faster for 10, 100, and 1000 tips,
1689 CHANGES IN APE VERSION 1.8-3
1694 o There are four new `method' functions to be used with the
1695 results of ace(): logLik(), deviance(), AIC(), and anova().
1697 o The plot method of phymltest has two new arguments: `main' to
1698 change the title, and `col' to control the colour of the
1699 segments showing the AIC values.
1701 o ace() has a new argument `ip' that gives the initial values used
1702 in the ML estimation with discrete characters (see the examples
1703 in ?ace). This function now returns a matrix giving the indices
1704 of the estimated rates when analysing discrete characters.
1706 o nodelabels() and tiplabels() have a new argument `pie' to
1707 represent proportions, with any number of categories, as
1708 piecharts. The use of the option `thermo' has been improved:
1709 there is now no limitation on the number of categories.
1714 o mlphylo() did not work with more than two partitions: this is
1717 o root() failed if the proposed outgroup was already an outgroup
1718 in the tree: this is fixed.
1720 o The `col' argument in nodelabels() and tiplabels() was not
1721 correctly passed when `text' was used: this is fixed.
1723 o Two bugs were fixed in mlphylo(): parameters were not always
1724 correctly output, and the estimation failed in some cases.
1726 o plot.phylo() was stuck when given a tree with a single tip: this
1727 is fixed and a message error is now returned.
1729 o An error was corrected in the help page of gammaStat regarding
1730 the calculation of P-values.
1732 o Using gls() could crash R when the number of species in the tree
1733 and in the variables were different: this is fixed.
1737 CHANGES IN APE VERSION 1.8-2
1742 o The new function mlphylo() fits a phylogenetic tree by maximum
1743 likelihood from DNA sequences. Its companion function DNAmodel()
1744 is used to define the substitution model which may include
1745 partitioning. There are methods for logLik(), deviance(), and
1746 AIC(), and the summary() method has been extended to display in
1747 a friendly way the results of this model fitting. Currently, the
1748 functionality is limited to estimating the substitution and
1749 associated parameters and computing the likelihood.
1751 o The new function drop1.compar.gee (used as, e.g., drop1(m))
1752 tests for single effects in GEE-based comparative method. A
1753 warning message is printed if there is not enough degrees of
1759 o An error message was sometimes issued by plot.multi.tree(),
1760 though with no consequence.
1764 CHANGES IN APE VERSION 1.8-1
1769 o There is a new plot method for lists of trees (objects of class
1770 "multi.tree"): it calls plot.phylo() internally and is
1771 documented on the same help page.
1776 o A bug was fixed in the C code that analyzes bipartitions: this
1777 has impact on several functions like prop.part, prop.clades,
1778 boot.phylo, or consensus.
1780 o root() did not work correctly when the specified outgroup had
1781 more than one element: this is fixed.
1783 o dist.dna() sometimes returned a warning inappropriately: this
1786 o If the distance object given to nj() had no rownames, nj()
1787 returned a tree with no tip labels: it now returns tips labelled
1788 "1", "2", ..., corresponding to the row numbers.
1793 o nj() has been slightly changed so that tips with a zero distance
1794 are first aggregated with zero-lengthed branches; the usual NJ
1795 procedure is then performed on a distance matrix without 0's.
1799 CHANGES IN APE VERSION 1.8
1804 o The new function chronopl() estimates dates using the penalized
1805 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1807 o The new function consensus() calculates the consensus tree of a
1810 o The new function evolve.phylo() simulates the evolution of
1811 continuous characters along a phylogeny under a Brownian model.
1813 o The new plot method for objects of class "ancestral" displays a
1814 tree together with ancestral values, as returned by the above
1817 o The new function as.phylo.formula() returns a phylogeny from a
1818 set of nested taxonomic variables given as a formula.
1820 o The new function read.caic() reads trees in CAIC format.
1822 o The new function tiplabels() allows to add labels to the tips
1823 of a tree using text or plotting symbols in a flexible way.
1825 o The new function unroot() unroots a phylogeny.
1827 o multi2di() has a new option, `random', which specifies whether
1828 to resolve the multichotomies randomly (the default) or not.
1830 o prop.part() now returns an object of class "prop.part" for which
1831 there are print (to display a partition in a more friendly way)
1832 and summary (to extract the numbers) methods.
1834 o plot.phylo() has a new option, `show.tip.label', specifying
1835 whether to print the labels of the tips. The default is TRUE.
1837 o The code of nj() has been replaced by a faster C code: it is now
1838 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1841 o write.nexus() now writes whether a tree is rooted or not.
1846 o Two bugs have been fixed in root(): unrooted trees are now
1847 handled corretly, and node labels are now output normally.
1849 o A bug was fixed in phymltest(): the executable couldn't be found
1852 o Three bug have been fixed in ace(): computing the likelihood of
1853 ancestral states of discrete characters failed, custom models
1854 did not work, and the function failed with a null gradient (a
1855 warning message is now returned; this latter bug was also
1856 present in yule.cov() as well and is now fixed).
1858 o pic() hanged out when missing data were present: a message error
1861 o A small bug was fixed in dist.dna() where the gamma correction
1862 was not always correctly dispatched.
1864 o plot.phylo() plotted correctly the root edge only when the tree
1865 was plotted rightwards: this works now for all directions.
1870 o dist.taxo() has been renamed as weight.taxo().
1872 o dist.phylo() has been replaced by the method cophenetic.phylo().
1874 o Various error and warning messages have been improved.
1878 CHANGES IN APE VERSION 1.7
1881 o The new function ace() estimates ancestral character states for
1882 continuous characters (with ML, GLS, and contrasts methods), and
1883 discrete characters (with ML only) for any number of states.
1885 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1886 of directional evolution for continuous characters. The user
1887 specifies the node(s) of the tree where the character optimum
1890 o The new function is.rooted() tests whether a tree (of class
1893 o The new function rcoal() generates random ultrametric trees with
1894 the possibility to specify the function that generates the
1895 inter-nodes distances.
1897 o The new function mrca() gives for all pairs of tips in a tree
1898 (and optionally nodes too) the most recent common ancestor.
1900 o nodelabels() has a new option `thermo' to plot proportions (up
1901 to three classes) on the nodes of a tree.
1903 o rtree() has been improved: it can now generate rooted or
1904 unrooted trees, and the mathematical function that generates the
1905 branch lengths may be specified by the user. The tip labels may
1906 be given directly in the call to rtree. The limit cases (n = 2,
1907 3) are now handled correctly.
1909 o dist.topo() has a new argument `method' with two choices: "PH85"
1910 for Penny and Henny's method (already available before and now
1911 the default), and "BHV01" for the geometric distance by Billera
1912 et al. (2001, Adv. Appl. Math. 27:733).
1914 o write.tree() has a new option, `digits', which specifies the
1915 number of digits to be printed in the Newick tree. By default
1916 digits = 10. The numbers are now always printed in decimal form
1917 (i.e., 1.0e-1 is now avoided).
1919 o dist.dna() can now compute the raw distances between pairs of
1920 DNA sequences by specifying model = "raw".
1922 o dist.phylo() has a new option `full' to possibly compute the
1923 distances among all tips and nodes of the tree. The default if
1929 o Several bugs were fixed in all.equal.phylo().
1931 o dist.dna() did not handle correctly gaps ("-") in alignments:
1932 they are now considered as missing data.
1934 o rotate() did not work if the tips were not ordered: this is
1937 o mantel.test() returned NA in some special cases: this is fixed
1938 and the function has been improved and is now faster.
1940 o A bug was fixed in diversi.gof() where the calculation of A² was
1943 o cherry() did not work correctly under some OSs (mainly Linux):
1946 o is.binary.tree() has been modified so that it works with both
1947 rooted and unrooted trees.
1949 o The documentation of theta.s() was not correct: this has been
1952 o plot.mst() did not work correctly: this is fixed.
1956 CHANGES IN APE VERSION 1.6
1961 o The new function dist.topo() computes the topological distances
1964 o The new function boot.phylo() performs a bootstrap analysis on
1965 phylogeny estimation.
1967 o The new functions prop.part() and prop.clades() analyse
1968 bipartitions from a series of trees.
1973 o read.GenBank() now uses the EFetch utility of NCBI instead of
1974 the usual Web interface: it is now much faster (e.g., 12 times
1975 faster to retrieve 8 sequences, 37 times for 60 sequences).
1980 o Several bugs were fixed in read.dna().
1982 o Several bugs were fixed in diversi.time().
1984 o is.binary.tree() did not work correctly if the tree has no edge
1985 lengths: this is fixed.
1987 o drop.tip() did not correctly propagated the `node.label' of a
1988 tree: this is fixed.
1992 CHANGES IN APE VERSION 1.5
1997 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1998 convert objects between the classes "phylo" and "matching". The
1999 latter implements the representation of binary trees introduced by
2000 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
2001 as.matching() has been introduced as well.
2003 o Two new functions, multi2di() and di2multi(), allow to resolve
2004 and collapse multichotomies with branches of length zero.
2006 o The new function nuc.div() computes the nucleotide diversity
2007 from a sample a DNA sequences.
2009 o dist.dna() has been completely rewritten with a much faster
2010 (particularly for large data sets) C code. Eight models are
2011 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
2012 option `method' has been renamed `model'). Computation of variance
2013 is available for all models. A gamma-correction is possible for
2014 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
2015 to remove sites with missing data on a pairwise basis. The option
2016 `GCcontent' has been removed.
2018 o read.GenBank() has a new option (species.names) which specifies
2019 whether to return the species names of the organisms in addition
2020 to the accession numbers of the sequences (this is the default
2023 o write.nexus() can now write several trees in the same NEXUS file.
2025 o drop.tip() has a new option `root.edge' that allows to specify the
2026 new root edge if internal branches are trimmed.
2031 o as.phylo.hclust() failed if some labels had parentheses: this
2034 o Several bugs were fixed in all.equal.phylo(). This function now
2035 returns the logical TRUE if the trees are identical but with
2036 different representations (a report was printed previously).
2038 o read.GenBank() did not correctly handle ambiguous base codes:
2044 o birthdeath() now returns an object of class "birthdeath" for
2045 which there is a print method.
2049 CHANGES IN APE VERSION 1.4
2054 o The new function nj() performs phylogeny estimation with the
2055 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
2058 o The new function which.edge() identifies the edges of a tree
2059 that belong to a group specified as a set of tips.
2061 o The new function as.phylo.phylog() converts an object of class
2062 "phylog" (from the package ade4) into an object of class
2065 o The new function axisPhylo() draws axes on the side of a
2068 o The new function howmanytrees() calculates the number of trees
2069 in different cases and giving a number of tips.
2071 o write.tree() has a new option `multi.line' (TRUE by default) to
2072 write a Newick tree on several lines rather than on a single
2075 o The functionalities of zoom() have been extended. Several
2076 subtrees can be visualized at the same time, and they are marked
2077 on the main tree with colors. The context of the subtrees can be
2078 marked with the option `subtree' (see below).
2080 o drop.tip() has a new option `subtree' (FALSE by default) which
2081 specifies whether to output in the tree how many tips have been
2084 o The arguments of add.scale.bar() have been redefined and have
2085 now default values (see ?add.scale.bar for details). This
2086 function now works even if the plotted tree has no edge length.
2088 o plot.phylo() can now plot radial trees, but this does not take
2089 edge lengths into account.
2091 o In plot.phylo() with `type = "phylogram"', if the values of
2092 `edge.color' and `edge.width' are identical for sister-branches,
2093 they are propagated to the vertical line that link them.
2098 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
2099 crashing. This is fixed.
2101 o In plot.phylo(), the options `edge.color' and `edge.width' are
2102 now properly recycled; their default values are now "black" and
2105 o A bug has been fixed in write.nexus().
2110 o The function node.depth.edgelength() has been removed and
2111 replaced by a C code.
2115 CHANGES IN APE VERSION 1.3-1
2120 o The new function nodelabels() allows to add labels to the nodes
2121 of a tree using text or plotting symbols in a flexible way.
2123 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
2124 numeric values specifying the lower and upper limits on the x-
2125 and y-axes. This allows to leave some space on any side of the
2126 tree. If a single value is given, this is taken as the upper
2131 CHANGES IN APE VERSION 1.3
2136 o The new function phymltest() calls the software PHYML and fits
2137 28 models of DNA sequence evolution. There are a print method to
2138 display likelihood and AIC values, a summary method to compute
2139 the hierarchical likelihood ratio tests, and a plot method to
2140 display graphically the AIC values of each model.
2142 o The new function yule.cov() fits the Yule model with covariates,
2143 a model where the speciation rate is affected by several species
2144 traits through a generalized linear model. The parameters are
2145 estimated by maximum likelihood.
2147 o Three new functions, corBrownian(), corGrafen(), and
2148 corMartins(), compute the expected correlation structures among
2149 species given a phylogeny under different models of evolution.
2150 These can be used for GLS comparative phylogenetic methods (see
2151 the examples). There are coef() and corMatrix() methods and an
2152 Initialize.corPhyl() function associated.
2154 o The new function compar.cheverud() implements Cheverud et al.'s
2155 (1985; Evolution 39:1335) phylogenetic comparative method.
2157 o The new function varcomp() estimates variance components; it has
2160 o Two new functions, panel.superpose.correlogram() and
2161 plot.correlogramList(), allow to plot several phylogenetic
2164 o The new function node.leafnumber() computes the number of leaves
2165 of a subtree defined by a particular node.
2167 o The new function node.sons() gets all tags of son nodes from a
2170 o The new function compute.brlen() computes the branch lengths of
2171 a tree according to a specified method.
2173 o plot.phylo() has three new options: "cex" controls the size of
2174 the (tip and node) labels (thus it is no more needed to change
2175 the global graphical parameter), "direction" which allows to
2176 plot the tree rightwards, leftwards, upwards, or downwards, and
2177 "y.lim" which sets the upper limit on the y-axis.
2182 o Some functions which try to match tip labels and names of
2183 additional data (e.g. vector) are likely to fail if there are
2184 typing or syntax errors. If both series of names do not perfectly
2185 match, they are ignored and a warning message is now issued.
2186 These functions are bd.ext, compar.gee, pic. Their help pages
2187 have been clarified on this point.
2191 CHANGES IN APE VERSION 1.2-7
2196 o The new function root() reroots a phylogenetic tree with respect
2197 to a specified outgroup.
2199 o The new function rotate() rotates an internal branch of a tree.
2201 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
2202 trees) controls the display of the tip labels in unrooted trees.
2203 This display has been greatly improved: the tip labels are now not
2204 expected to overlap with the tree (particularly if lab4ut =
2205 "axial"). In all cases, combining appropriate values of "lab4ut"
2206 and the font size (via "par(cex = )") should result in readable
2207 unrooted trees. See ?plot.phylo for some examples.
2209 o In drop.tip(), the argument `tip' can now be numeric or character.
2214 o drop.tip() did not work correctly with trees with no branch
2215 lengths: this is fixed.
2217 o A bug in plot.phylo(..., type = "unrooted") made some trees being
2218 plotted with some line crossings: this is now fixed.
2222 CHANGES IN APE VERSION 1.2-6
2227 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
2228 correlogram.phylo, dist.taxo, plot.correlogram) have been added
2229 to implement comparative methods with an autocorrelation approach.
2231 o A new data set describing some life history traits of Carnivores
2237 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
2242 o When plotting a tree with plot.phylo(), the new default of the
2243 option `label.offset' is now 0, so the labels are always visible.
2247 CHANGES IN APE VERSION 1.2-5
2252 o The new function bd.ext() fits a birth-death model with combined
2253 phylogenetic and taxonomic data, and estimates the corresponding
2254 speciation and extinction rates.
2259 o The package gee is no more required by ape but only suggested
2260 since only the function compar.gee() calls gee.
2264 CHANGES IN APE VERSION 1.2-4
2269 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
2270 and lines.popsize) implementing a new approach for inferring the
2271 demographic history from genealogies using a reversible jump
2272 MCMC have been introduced.
2274 o The unit of time in the skyline plot and in the new plots can
2275 now be chosen to be actual years, rather than substitutions.
2279 CHANGES IN APE VERSION 1.2-3
2284 o The new function rtree() generates a random binary tree with or
2285 without branch lengths.
2287 o Two new functions for drawing lineages-through-time (LTT) plots
2288 are provided: ltt.lines() adds a LTT curve to an existing plot,
2289 and mltt.plot() does a multiple LTT plot giving several trees as
2290 arguments (see `?ltt.plot' for details).
2295 o Some taxon names made R crashing when calling as.phylo.hclust():
2298 o dist.dna() returned an error with two identical DNA sequences
2299 (only using the Jukes-Cantor method returned 0): this is fixed.
2304 o The function dist.phylo() has been re-written using a different
2305 algorithm: it is now about four times faster.
2307 o The code of branching.times() has been improved: it is now about
2312 CHANGES IN APE VERSION 1.2-2
2317 o The new function seg.sites() finds the segregating sites in a
2318 sample of DNA sequences.
2323 o A bug introduced in read.tree() and in read.nexus() with version
2326 o A few errors were corrected and a few examples were added in the
2331 CHANGES IN APE VERSION 1.2-1
2336 o plot.phylo() can now draw the edge of the root of a tree if it
2337 has one (see the new option `root.edge', its default is FALSE).
2342 o A bug was fixed in read.nexus(): files with semicolons inside
2343 comment blocks were not read correctly.
2345 o The behaviour of read.tree() and read.nexus() was corrected so
2346 that tree files with badly represented root edges (e.g., with
2347 an extra pair of parentheses, see the help pages for details)
2348 are now correctly represented in the object of class "phylo";
2349 a warning message is now issued.
2353 CHANGES IN APE VERSION 1.2
2358 o plot.phylo() has been completely re-written and offers several
2359 new functionalities. Three types of trees can now be drawn:
2360 phylogram (as previously), cladogram, and unrooted tree; in
2361 all three types the branch lengths can be drawn using the edge
2362 lengths of the phylogeny or not (e.g., if the latter is absent).
2363 The vertical position of the nodes can be adjusted with two
2364 choices (see option `node.pos'). The code has been re-structured,
2365 and two new functions (potentially useful for developpers) are
2366 documented separately: node.depth.edgelength() and node.depth();
2367 see the respective help pages for details.
2369 o The new function zoom() allows to explore very large trees by
2370 focusing on a small portion of it.
2372 o The new function yule() fits by maximum likelihood the Yule model
2373 (birth-only process) to a phylogenetic tree.
2375 o Support for writing DNA sequences in FASTA format has been
2376 introduced in write.dna() (support for reading sequences in
2377 this format was introduced in read.dna() in version 1.1-2).
2378 The function has been completely re-written, fixing some bugs
2379 (see below); the default behaviour is no more to display the
2380 sequences on the standard output. Several options have been
2381 introduced to control the sequence printing in a flexible
2382 way. The help page has been extended.
2384 o A new data set is included: a supertree of bats in NEXUS format.
2389 o In theta.s(), the default of the option `variance' has
2390 been changed to `FALSE' (as was indicated in the help page).
2392 o Several bugs were fixed in the code of all.equal.phylo().
2394 o Several bugs were fixed in write.dna(), particularly this
2395 function did not work with `format = "interleaved"'.
2397 o Various errors were corrected in the help pages.
2402 o The argument names of as.hclust.phylo() have been changed
2403 from "(phy)" to "(x, ...)" to conform to the definition of
2404 the corresponding generic function.
2406 o gamma.stat() has been renamed gammaStat() to avoid confusion
2407 since gamma() is a generic function.
2411 CHANGES IN APE VERSION 1.1-3
2416 o base.freq() previously did not return a value of 0 for
2417 bases absent in the data (e.g., a vector of length 3 was
2418 returned if one base was absent). This is now fixed (a
2419 vector of length 4 is always returned).
2421 o Several bugs were fixed in read.nexus(), including that this
2422 function did not work in this absence of a "TRANSLATE"
2423 command in the NEXUS file, and that the commands were
2428 CHANGES IN APE VERSION 1.1-2
2433 o The Tamura and Nei (1993) model of DNA distance is now implemented
2434 in dist.dna(): five models are now available in this function.
2436 o A new data set is included: a set of 15 sequences of the
2437 cytochrome b mitochondrial gene of the woodmouse (Apodemus
2443 o A bug in read.nexus() was fixed.
2445 o read.dna() previously did not work correctly in most cases.
2446 The function has been completely re-written and its help page
2447 has been considerably extended (see ?read.dna for details).
2448 Underscores (_) in taxon names are no more replaced with
2449 spaces (this behaviour was undocumented).
2451 o A bug was fixed in write.dna().
2455 CHANGES IN APE VERSION 1.1-1
2460 o A bug in read.tree() introduced in APE 1.1 was fixed.
2462 o A bug in compar.gee() resulted in an error when trying to fit
2463 a model with `family = "binomial"'. This is now fixed.
2467 CHANGES IN APE VERSION 1.1
2472 o The Klastorin (1982) method as suggested by Misawa and Tajima
2473 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
2474 on the basis of phylogenetic trees has been implemented (see
2475 the function klastorin()).
2477 o Functions have been added to convert APE's "phylo" objects in
2478 "hclust" cluster objects and vice versa (see the help page of
2479 as.phylo for details).
2481 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
2482 are introduced for the estimation of absolute evolutionary rates
2483 (ratogram) and dated clock-like trees (chronogram) from
2484 phylogenetic trees using the non-parametric rate smoothing approach
2485 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
2487 o A summary method is now provided printing a summary information on a
2488 phylogenetic tree with, for instance, `summary(tree)'.
2490 o The behaviour of read.tree() was changed so that all spaces and
2491 tabulations in tree files are now ignored. Consequently, spaces in tip
2492 labels are no more allowed. Another side effect is that read.nexus()
2493 now does not replace the underscores (_) in tip labels with spaces
2494 (this behaviour was undocumented).
2496 o The function plot.phylo() has a new option (`underscore') which
2497 specifies whether the underscores in tip labels should be written on
2498 the plot as such or replaced with spaces (the default).
2500 o The function birthdeath() now computes 95% confidence intervals of
2501 the estimated parameters using profile likelihood.
2503 o Three new data sets are included: a gene tree estimated from 36
2504 landplant rbcL sequences, a gene tree estimated from 32 opsin
2505 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
2510 o A bug was fixed in dist.gene() where nothing was returned.
2512 o A bug in plot.mst() was fixed.
2514 o A bug in vcv.phylo() resulted in false correlations when the
2515 option `cor = TRUE' was used (now fixed).
2519 CHANGES IN APE VERSION 1.0
2524 o Two new functions, read.dna() and write.dna(), read/write in a file
2525 DNA sequences in interleaved or in sequential format.
2527 o Two new functions, read.nexus() and write.nexus(), read/write trees
2530 o The new function bind.tree() allows to bind two trees together,
2531 possibly handling root edges to give internal branches.
2533 o The new function drop.tip() removes the tips in a phylogenetic tree,
2534 and trims (or not) the corresponding internal branches.
2536 o The new function is.ultrametric() tests if a tree is ultrametric.
2538 o The function plot.phylo() has more functionalities such as drawing the
2539 branches with different colours and/or different widths, showing the
2540 node labels, controling the position and font of the labels, rotating
2541 the labels, and controling the space around the plot.
2543 o The function read.tree() can now read trees with no branch length,
2544 such as "(a,b),c);". Consequently, the element `edge.length' in
2545 objects of class "phylo" is now optional.
2547 o The function write.tree() has a new default behaviour: if the default
2548 for the option `file' is used (i.e. file = ""), then a variable of
2549 mode character containing the tree in Newick format is returned which
2550 can thus be assigned (e.g., tree <- write.tree(phy)).
2552 o The function read.tree() has a new argument `text' which allows
2553 to read the tree in a variable of mode character.
2555 o A new data set is included: the phylogenetic relationships among
2556 the orders of birds from Sibley and Ahlquist (1990).
2560 CHANGES IN APE VERSION 0.2-1
2565 o Several bugs were fixed in the help pages.
2569 CHANGES IN APE VERSION 0.2
2574 o The function write.tree() writes phylogenetic trees (objects of class
2575 "phylo") in an ASCII file using the Newick parenthetic format.
2577 o The function birthdeath() fits a birth-death model to branching times
2578 by maximum likelihood, and estimates the corresponding speciation and
2581 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
2584 o The function is.binary.tree() tests whether a phylogeny is binary.
2586 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
2587 as well as some methods are introduced.
2589 o Several functions, including some generics and methods, for computing
2590 skyline plot estimates (classic and generalized) of effective
2591 population size through time are introduced and replace the function
2592 skyline.plot() in version 0.1.
2594 o Two data sets are now included: the phylogenetic relationships among
2595 the families of birds from Sibley and Ahlquist (1990), and an
2596 estimated clock-like phylogeny of HIV sequences sampled in the
2597 Democratic Republic of Congo.
2600 DEPRECATED & DEFUNCT
2602 o The function skyline.plot() in ape 0.1 has been deprecated and
2603 replaced by more elaborate functions (see above).
2608 o Two important bugs were fixed in plot.phylo(): phylogenies with
2609 multichotomies not at the root or not with only terminal branches,
2610 and phylogenies with a single node (i.e. only terminal branches)
2611 did not plot. These trees should be plotted correctly now.
2613 o Several bugs were fixed in diversi.time() in the computation of
2616 o Various errors were corrected in the help pages.
projects / ape.git / blob