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.
22 CHANGES IN APE VERSION 3.0-1
27 o dist.dna() has two new models: "indel" and "indelblock".
29 o bind.tree() now accepts 'position' > 0 when the trees have no
30 banch length permitting to create a node in 'x' when grafting
31 'y' (see ?bind.tree for details).
36 o cophyloplot( , rotate = TRUE) made R hanged after a few clicks.
37 Also the tree is no more plotted twice.
39 o read.GenBank() has been updated to work with EFetch 2.0.
41 o unroot() on trees in "pruningwise" order did not respect this
46 CHANGES IN APE VERSION 3.0
51 o The three functions dyule, dbd, and dbdTime calculate the
52 density probability (i.e., the distribution of the number of
53 species) for the Yule, the constant and the time-dependent
54 birth-beath models, respectively. These probabilities can be
55 conditional on no extinction and/or on a log-scale.
57 o plot.phylo() has a new option 'rotate.tree' to rotate unrooted,
58 fan, or radial trees around the center of the plot.
60 o boot.phylo() and prop.clades() have a new option rooted =
61 FALSE. Note that the behaviour of prop.part() is unchanged.
63 o edgelabels() has a new option 'date' to place labels on edges of
64 chronograms using the time scale (suggestion by Rob Lanfear).
69 o In chronopl(), the code setting the initial dates failed in
70 complicated settings (several dates known within intervals).
71 This has been generally improved and should result in faster
72 and more efficient convergence even in simple settings.
74 o mantel.test() sometimes returned P-values > 1 with the default
77 o extract.clade() sometimes shuffled some tip labels (thanks to
78 Ludovic Mallet and Mahendra Mariadassou for the fix).
80 o clustal() should now find by default the executable under Windows.
85 o The code of yule() has been simplified and is now much faster for
88 o The code of mantel.test() has been adjusted to be consistent
89 with common permutation tests.
91 o The C code of base.freq() has been improved and is now nearly 8
94 o The option 'original.data' of write.nexus() is now deprecated and
95 will be removed in a future release.
97 o The code of is.ultrametric() has been improved and is now 3 times
100 o The code of vcv.phylo() has been improved and is now 10 or 30
101 times faster for 100 or 1000 tips, respectively. Consequently,
102 fitting models with PGLS will be faster overall.
106 CHANGES IN APE VERSION 2.8
111 o Twelve new functions have been written by Andrei-Alin Popescu:
112 additive, ultrametric, is.compatible, arecompatible, mvr, mvrs,
113 njs, bionjs, SDM, treePop, triangMtd, triangMtd*.
115 o A new class "bitsplits" has been created by Andrei-Alin Popescu
116 to code splits (aka, bipartition).
118 o There is a new generic function as.bitsplits with a method to
119 convert from the class "prop.part" to the class "bitsplits".
121 o The new function ltt.coplot plots on the same scales a tree and
122 the derived LTT plot.
124 o ltt.plot() has two new options: backward and tol. It can now
125 handle non-ultrametic trees and its internal coding has been
126 improved. The coordinates of the plot can now be computed with
127 the new function ltt.plot.coords.
132 o prop.part() crashed if some trees had some multichotomies.
136 CHANGES IN APE VERSION 2.7-3
141 o The new function compute.brtime computes and sets branching times.
143 o mantel.test() has a new argument 'alternative' which is
144 "two-sided" by default. Previously, this test was one-tailed
145 with no possibility to change.
147 o ace() can now do REML estimation with continuous characters,
148 giving better estimates of the variance of the Brownian motion
154 o Branch lengths were wrongly updated with bind.tree(, where = <tip>,
155 position = 0). (Thanks to Liam Revell for digging this bug out.)
157 o Simulation of OU process with rTraitCont() did not work correctly.
158 This now uses formula from Gillespie (1996) reduced to a BM
159 process when alpha = 0 to avoid division by zero. The option
160 'linear' has been removed.
162 o Cross-validation in chronopl() did not work when 'age.max' was
165 o consensus(, p = 0.5) could return an incorrect tree if some
166 incompatible splits occur in 50% of the trees (especially with
167 small number of trees).
169 o c() with "multiPhylo" did not work correctly (thanks to Klaus
170 Schliep for the fix).
172 o root() failed in some cases with an outgroup made of several tips.
173 The help page has been clarified a bit.
177 CHANGES IN APE VERSION 2.7-2
182 o There is a new class "evonet" to code evolutionary networks, with
183 a constructor function evonet(), a print() and a plot() methods,
184 and four conversion methods to the classes "phylo", "networx",
185 "network", and "igraph".
187 o The new function rTraitMult does multivariate traits simulation
188 with user-defined models.
190 o plot.phylo() has a new option 'plot = TRUE'. If FALSE, the tree
191 is not plotted but the graphical device is set and the
192 coordinates are saved as usual.
194 o diversity.contrast.test() gains a fourth version of the test with
195 method = "logratio"; the literature citations have been clarified.
197 o add.scale.bar() has two new options, 'lwd' and 'lcol', to modify
198 the aspect of the bar.
200 o boot.phylo() now displays a progress bar by default (can be off
203 o There is a new predict() method for compar.gee().
208 o bionj() made R crash if distances were too large. It now returns
209 an error if at least one distance is greater than 100.
211 o drop.tip() returned a wrong tree if 'tip' was of zero length.
213 o read.nexus.data() failed with URLs.
215 o boot.phylo() returned overestimated support values in the
216 presence of identical or nearly identical sequences.
221 o The data bird.families, bird.orders, cynipids, and woodmouse are
222 now provided as .rda files.
226 CHANGES IN APE VERSION 2.7-1
231 o The new function trex does tree exploration with multiple
234 o The new function kronoviz plots several rooted (dated) trees on
237 o identify.phylo() has a new option 'quiet' (FALSE by default).
242 o A bug was introduced in read.nexus() in ape 2.7.
244 o image.DNAbin() did not colour correctly the bases if there were
247 o .compressTipLabel() failed with a list with a single tree.
249 o identify.phylo() returned a wrong answer when the x- and y-scales
252 o write.nexus() failed with lists of trees with compressed labels.
257 o identify.phylo() now returns NULL if the user right- (instead of
258 left-) clicks (an error was returned previously).
260 o read.nexus() should be robust to commands inserted in the TREES
265 CHANGES IN APE VERSION 2.7
270 o There is a new image() method for "DNAbin" objects: it plots DNA
271 alignments in a flexible and efficient way.
273 o Two new functions as.network.phylo and as.igraph.phylo convert
274 trees of class "phylo" into these respective network classes
275 defined in the packages of the same names.
277 o The three new functions clustal, muscle, and tcoffee perform
278 nucleotide sequence alignment by calling the external programs
281 o Four new functions, diversity.contrast.test, mcconwaysims.test,
282 richness.yule.test, and slowinskiguyer.test, implement various
283 tests of diversification shifts using sister-clade comparisons.
285 o base.freq() gains an option 'all' to count all the possible bases
286 including the ambiguous ones (defaults to FALSE).
288 o read.nexus() now writes tree names in the NEXUS file if given a
289 list of trees with names.
294 o prop.part() failed in some situations with unrooted trees.
296 o read.nexus() shuffled node labels when a TRANSLATE block was
299 o varCompPhylip() did not work if 'exec' was specified.
301 o bind.tree() shuffled node labels when position > 0 and 'where'
307 o BaseProportion in src/dist_dna.c has been modified.
309 o A number of functions in src/tree_build.c have been modified.
311 o The matching representation has now only two columns as the third
312 column was redundant.
316 CHANGES IN APE VERSION 2.6-3
321 o rTraitCont() and rTraitDisc() gains a '...' argument used with
322 user-defined models (suggestion by Gene Hunt).
327 o as.hclust.phylo() now returns an error with unrooted trees.
329 o as.hclust.phylo() failed with trees with node labels (thanks to
330 Jinlong Zhang for pointing this bug out).
332 o read.dna(, "fasta") failed if sequences were not all of the same
335 o plot.phylo() did not recycle values of 'font', 'cex' and
336 'tip.color' correctly when type = "fan" or "radial".
338 o plot.phylo() ignored 'label.offset' when type = "radial", "fan", or
339 "unrooted" with lab4ut = "axial" (the placement of tip labels still
340 needs to be improved with lab4ut = "horizontal").
345 o In drop.fossil() the default tol = 0 has been raised to 1e-8.
347 o The help command ?phylo now points to the man page of read.tree()
348 where this class is described. Similarly, ?matching points to the
349 man page of as.matching().
353 CHANGES IN APE VERSION 2.6-2
358 o Two new functions, pic.ortho and varCompPhylip, implements the
359 orthonormal contrasts of Felsenstein (2008, Am Nat, 171:713). The
360 second function requires Phylip to be installed on the computer.
362 o bd.ext() has a new option conditional = TRUE to use probabilities
363 conditioned on no extinction for the taxonomic data.
368 o write.tree() failed to output correctly tree names.
370 o dist.nodes() returned duplicated column(s) with unrooted and/or
371 multichotomous trees.
373 o mcmc.popsize() terminated unexpectedly if the progress bar was
376 o prop.part(x) made R frozen if 'x' is of class "multiPhylo".
378 o Compilation under Mandriva failed (thanks to Jos Käfer for the fix).
380 o drop.tip() shuffled tip labels with subtree = TRUE or trim.internal
383 o Objects returned by as.hclust.phylo() failed when analysed with
384 cutree() or rect.hclust().
386 o write.tree() did not output correctly node labels (thanks to Naim
387 Matasci and Jeremy Beaulieu for the fix).
389 o ace(type = "discrete") has been improved thanks to Naim Marasci and
394 CHANGES IN APE VERSION 2.6-1
399 o The new function speciesTree calculates the species tree from a set
400 of gene trees. Several methods are available including maximum tree
401 and shallowest divergence tree.
406 o A bug introduced in write.tree() with ape 2.6 has been fixed.
408 o as.list.DNAbin() did not work correctly with vectors.
410 o as.hclust.phylo() failed with trees with node labels (thanks to
411 Filipe Vieira for the fix).
415 CHANGES IN APE VERSION 2.6
420 o The new functions rlineage and rbdtree simulate phylogenies under
421 any user-defined time-dependent speciation-extinction model. They
422 use continuous time algorithms.
424 o The new function drop.fossil removes the extinct species from a
427 o The new function bd.time fits a user-defined time-dependent
428 birth-death model. It is a generalization of yule.time() taking
429 extinction into account.
431 o The new function MPR does most parsimonious reconstruction of
434 o The new function Ftab computes the contingency table of base
435 frequencies from a pair of sequences.
437 o There is now an 'as.list' method for the class "DNAbin".
439 o dist.dna() can compute the number of transitions or transversions
440 with the option model = "Ts" or model = "Tv", respectively.
442 o [node|tip|edge]labels() gain three options with default values to
443 control the aspect of thermometers: horiz = TRUE, width = NULL,
446 o compar.gee() has been improved with the new option 'corStruct' as an
447 alternative to 'phy' to specify the correlation structure, and
448 calculation of the QIC (Pan 2001, Biometrics). The display of the
449 results has also been improved.
451 o read.GenBank() has a new option 'gene.names' to return the name of
452 the gene (FALSE by default).
457 o extract.clade() sometimes shuffled the tip labels.
459 o plot.phylo(type = "unrooted") did not force asp = 1 (thanks to Klaus
462 o dist.dna(model = "logdet") used to divide distances by 4. The
463 documentation has been clarified on the formulae used.
468 o rTraitCont(model = "OU") has an option 'linear = TRUE' to possibly
469 change the parameterisation (see ?rTraitCont for details).
471 o pic() now returns a vector with the node labels of the tree (if
474 o write.tree() and read.tree() have been substantially improved thanks
475 to contributions by Klaus Schliep.
479 CHANGES IN APE VERSION 2.5-3
484 o The new function mixedFontLabel helps to make labels with bits of
485 text to be plotted in different fonts.
487 o There are now replacement operators for [, [[, and $ for the class
488 "multiPhylo" (i.e., TREES[11:20] <- rmtree(10, 100)). They possibly
489 check that the tip labels are the same in all trees.
491 o Objects of class "multiPhylo" can be built with c(): there are
492 methods for the classes "phylo" and "multiPhylo".
494 o The internal functions .compressTipLabel and .uncompressTipLabel are
500 o bind.tree(x, y, where, position = 0) did not work correctly if 'y'
501 was a single-edge tree and 'where' was a tip.
503 o rTraitCont() did not use the square-root of branch lengths when
504 simulating a Brownian motion model.
508 CHANGES IN APE VERSION 2.5-2
513 o There is now a print method for results from ace().
515 o There is a labels() method for objects of class "DNAbin".
517 o read.dna() has a new option 'as.matrix' to possibly force sequences
518 in a FASTA file to be stored in a matrix (see ?read.dna for details).
523 o as.phylo.hclust() used to multiply edge lengths by 2.
525 o A minor bug was fixed in rTraitDisc().
527 o ace() sometimes failed (parameter value was NaN and the optimisation
533 o evolve.phylo() and plot.ancestral() have been removed.
535 o chronogram(), ratogram(), and NPRS.criterion() have been removed.
540 o nj() has been improved and is now about 30% faster.
542 o The default option 'drop' of [.DNAbin has been changed to FALSE to
543 avoid dropping rownames when selecting a single sequence.
545 o print.DNAbin() has been changed to summary.DNAbin() which has been
550 CHANGES IN APE VERSION 2.5-1
555 o The new function stree generates trees with regular shapes.
557 o It is now possible to bind two trees with x + y (see ?bind.tree for
560 o drop.tip(), extract.clade(), root(), and bind.tree() now have an
561 'interactive' option to make the operation on a plotted tree.
563 o cophyloplot() gains two new arguments 'lwd' and 'lty' for the
564 association links; they are recycled like 'col' (which wasn't before).
569 o rTraitDisc() did not use its 'freq' argument correctly (it was
570 multiplied with the rate matrix column-wise instead of row-wise).
572 o [node|tip|edge]labels(thermo = ) used to draw empty thermometers
573 with NA values. Nothing is drawn now like with 'text' or 'pch'.
574 The same bug occurred with the 'pie' option.
576 o A bug was fixed in compar.ou() and the help page was clarified.
578 o bind.tree() has been rewritten fixing several bugs and making it
581 o plot.phylo(type = "p") sometimes failed to colour correctly the
582 vertical lines representing the nodes.
584 o plot.phylo(direction = "l", x.lim = 30) failed to plot the branches
585 in the correct direction though the tip labels were displayed
591 o The c, cbind, and rbind methods for "DNAbin" objetcs now check that
592 the sequences are correctly stored (in a list for c, in a matrix
593 for the two other functions).
597 CHANGES IN APE VERSION 2.5
602 o The new function parafit by Pierre Legendre tests for the
603 coevolution between hosts and parasites. It has a companion
604 function, pcoa, that does principal coordinate decomposition.
605 The latter has a biplot method.
607 o The new function lmorigin by Pierre Legendre performs multiple
608 regression through the origin with testing by permutation.
610 o The new functions rTraitCont and rTraitDisc simulate continuous and
611 discrete traits under a wide range of evolutionary models.
613 o The new function delta.plot does a delta plot following Holland et
614 al. (2002, Mol. Biol. Evol. 12:2051).
616 o The new function edges draws additional branches between any nodes
617 and/or tips on a plotted tree.
619 o The new function fancyarrows enhances arrows from graphics with
620 triangle and harpoon heads; it can be called from edges().
622 o add.scale.bar() has a new option 'ask' to draw interactively.
624 o The branch length score replaces the geodesic distance in dist.topo.
626 o Three new data sets are included: the gopher-lice data (gopher.D),
627 SO2 air pollution in 41 US cities (lmorigin.ex1, from Sokal &
628 Rohlf 1995), and some host-parasite specificity data
629 (lmorigin.ex2, from Legendre & Desdevises 2009).
634 o add.scale.bar() drew the bar outside the plotting region with the
635 default options with unrooted or radial trees.
637 o dist.topo() made R stuck when the trees had different sizes (thanks
638 to Otto Cordero for the fix).
643 o The geodesic distance has been replaced by the branch length score
648 CHANGES IN APE VERSION 2.4-1
653 o rtree() and rcoal() now accept a numeric vector for the 'br'
656 o vcv() is a new generic function with methods for the classes "phylo"
657 and "corPhyl" so that it is possible to calculate the var-cov matrix
658 for "transformation models". vcv.phylo() can still be used for trees
659 of class "phylo"; its argument 'cor' has been renamed 'corr'.
664 o bind.tree() failed when 'y' had no root edge.
666 o read.nexus() shuffled tip labels when the trees have no branch
667 lengths and there is a TRANSLATE block.
669 o read.nexus() does not try to translate node labels if there is a
670 translation table in the NEXUS file. See ?read.nexus for a
671 clarification on this behaviour.
673 o plot.multiPhylo() crashed R when plotting a list of trees with
674 compressed tip labels.
676 o write.nexus() did not translate the taxa names when asked for.
678 o plot.phylo(type = "fan") did not rotate the tip labels correctly
679 when the tree has branch lengths.
681 o ace(type = "continuous", method = "ML") now avoids sigma² being
682 negative (which resulted in an error).
684 o nj() crashed with NA/NaN in the distance matrix: an error in now
689 CHANGES IN APE VERSION 2.4
694 o base.freq() has a new option 'freq' to return the counts; the
695 default is still to return the proportions.
700 o seg.sites() did not handle ambiguous nucleotides correctly: they
703 o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
704 the tree: the argument is now ignored.
706 o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
712 o Trying to plot a tree with a single tip now returns NULL with a
713 warning (it returned an error previously).
715 o The way lines representing nodes are coloured in phylograms has
716 been modified (as well as their widths and types) following some
717 users' request; this is only for dichotomous nodes.
719 o The argument 'adj' in [node][tip][edge]labels() now works when
720 using 'pie' or 'thermo'.
722 o A more informative message error is now returned by dist.dna() when
723 'model' is badly specified (partial matching of this argument is
726 o Deprecated functions are now listed in a help page: see
727 help("ape-defunct") with the quotes.
732 o The functions heterozygosity, nuc.div, theta.h, theta.k and
733 theta.s have been moved from ape to pegas.
735 o The functions mlphylo, DNAmodel and sh.test have been removed.
739 CHANGES IN APE VERSION 2.3-3
744 o add.scale.bar() always drew a horizontal bar.
746 o zoom() shuffled tips with unrooted trees.
748 o write.nexus() failed to write correctly trees with a "TipLabel"
751 o rcoal() failed to compute branch lengths with very large n.
753 o A small bug was fixed in compar.cheverud() (thanks to Michael
756 o seg.sites() failed when passing a vector.
758 o drop.tip() sometimes shuffled tip labels.
760 o root() shuffled node labels with 'resolve.root = TRUE'.
764 CHANGES IN APE VERSION 2.3-2
769 o all.equal.phylo() did not compare unrooted trees correctly.
771 o dist.topo(... method = "PH85") did not treat unrooted trees
772 correctly (thanks to Tim Wallstrom for the fix).
774 o root() sometimes failed to test for the monophyly of the
777 o extract.clade() sometimes included too many edges.
779 o vcv.phylo() did not work correctly when the tree is in
782 o nj() did not handle correctly distance matrices with many 0's.
783 The code has also been significantly improved: 7, 70, 160 times
784 faster with n = 100, 500, 1000, respectively.
788 CHANGES IN APE VERSION 2.3-1
793 o The new function is.monophyletic tests the monophyly of a group.
795 o There is now a c() method for lists of class "DNAbin".
797 o yule.cov() now fits the null model, and its help page has been
798 corrected with respect to this change.
800 o drop.tip() has a new option 'rooted' to force (or not) a tree
801 to be treated as (un)rooted.
806 o dist.gene() failed on most occasions with the default
807 pairwise.deletion = FALSE.
809 o read.tree() failed to read correctly the tree name(s).
811 o boot.phylo() now treats correctly data frames.
813 o del.gaps() did not copy the rownames of a matrix.
815 o A small bug was fixed in CDAM.global().
817 o ace() failed with large data sets. Thanks to Rich FitzJohn for
818 the fix. With other improvements, this function is now about 6
821 o write.tree() failed with objects of class "multiPhylo".
823 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
828 o [.multiPhylo and [.DNAbin now respect the original class.
830 o Instances of the form class(phy) == "phylo" have been replaced
831 by inherits(phy, "phylo").
833 o rcoal() is now faster.
838 o klastorin() has been removed.
842 CHANGES IN APE VERSION 2.3
847 o The new functions CADM.global and CADM.post, contributed by
848 Pierre Legendre, test the congruence among several distance
851 o The new function yule.time fits a user-defined time-dependent
852 Yule model by maximum likelihood.
854 o The new function makeNodeLabel creates and/or modifies node
855 labels in a flexible way.
857 o read.tree() and write.tree() have been modified so that they can
858 handle individual tree names.
860 o plot.phylo() has a new argument 'edge.lty' that specifies the
861 types of lines used for the edges (plain, dotted, dashed, ...)
863 o phymltest() has been updated to work with PhyML 3.0.1.
868 o drop.tip() shuffled tip labels in some cases.
870 o drop.tip() did not handle node.label correctly.
872 o is.ultrametric() now checks the ordering of the edge matrix.
874 o ace() sometimes returned negative values of likelihoods of
875 ancestral states (thanks to Dan Rabosky for solving this long
881 o The data set xenarthra has been removed.
885 CHANGES IN APE VERSION 2.2-4
889 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
890 now fixed. (Thanks to Peter Wragg for the fix!)
892 o A warning message occurred for no reason with ace(method="GLS").
897 o There is now a general help page displayed with '?ape'.
901 CHANGES IN APE VERSION 2.2-3
906 o The new function extract.clade extracts a clade from a tree by
907 specifying a node number or label.
909 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
910 operations of the same names.
912 o dist.dna() can now return the number of site differences by
913 specifying model="N".
918 o chronopl() did not work with CV = TRUE.
920 o read.nexus() did not work correctly in some situations (trees on
921 multiple lines with different numbers of lines and/or with
922 comments inserted within the trees).
924 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
925 the number of lineages with non-binary trees.
930 o ape has now a namespace.
932 o drop.tip() has been improved: it should be much faster and work
933 better in some cases (e.g., see the example in ?zoom).
937 CHANGES IN APE VERSION 2.2-2
942 o dist.gene() has been substantially improved and gains an option
945 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
951 o prop.part() failed with a single tree with the default option
952 'check.labels = TRUE'.
954 o summary.DNAbin() failed to display correctly the summary of
955 sequence lengths with lists of sequences of 10,000 bases or more
956 (because summary.default uses 4 significant digits by default).
958 o read.nexus() failed to read a file with a single tree with line
959 breaks in the Newick string.
961 o del.gaps() returned a list of empty sequences when there were no
967 o phymltest() has been updated for PhyML 3.0 and gains an option
968 'append', whereas the option 'path2exec' has been removed.
970 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
971 which is returned unchanged (instead of an error).
973 o The data sets bird.orders and bird.families are now stored as
974 Newick strings; i.e., the command data(bird.orders) calls
979 CHANGES IN APE VERSION 2.2-1
984 o The new function makeLabel() helps to modify labels of trees,
985 lists of trees, or DNA sequences, with several utilities to
986 truncate and/or make them unique, substituting some
987 characters, and so on.
989 o The new function del.gaps() removes insertion gaps ("-") in a
990 set of DNA sequences.
992 o read.dna() can now read Clustal files (*.aln).
997 o root() failed with 'resolve.root = TRUE' when the root was
998 already the specified root.
1000 o Several bugs were fixed in mlphylo().
1002 o collapsed.singles() did not propagate the 'Nnode' and
1003 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
1005 o read.nexus() failed to remove correctly the comments within
1008 o read.nexus() failed to read a file with a single tree and no
1009 translation of tip labels.
1011 o read.nexus() failed to place correctly tip labels when reading
1012 a single tree with no edge lengths.
1014 o A bug was fixed in sh.test().
1019 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
1022 o The option 'check.labels' of consensus() and prop.part() is now
1025 o write.dna() now does not truncate names to 10 characters with
1030 CHANGES IN APE VERSION 2.2
1035 o Four new functions have been written by Damien de Vienne for the
1036 graphical exploration of large trees (cophyloplot, subtrees,
1037 subtreeplot), and to return the graphical coordinates of tree
1040 o The new functions corPagel and corBlomberg implement the Pagel's
1041 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
1043 o chronopl() has been improved and gains several options: see its
1044 help page for details.
1046 o boot.phylo() has now an option 'trees' to possibly return the
1047 bootstraped trees (the default is FALSE).
1049 o prop.part() has been improved and should now be faster in all
1055 o read.dna() failed if "?" occurred in the first 10 sites of the
1058 o The x/y aspect of the plot is now respected when plotting a
1059 circular tree (type = "r" or "f").
1061 o Drawing the tip labels sometimes failed when plotting circular
1064 o zoom() failed when tip labels were used instead of their numbers
1065 (thanks to Yan Wong for the fix).
1067 o drop.tip() failed with some trees (fixed by Yan Wong).
1069 o seg.sites() failed with a list.
1071 o consensus() failed in some cases. The function has been improved
1072 as well and is faster.
1076 CHANGES IN APE VERSION 2.1-3
1081 o A bug in read.nexus() made the Windows R-GUI crash.
1083 o An error was fixed in the computation of ancestral character
1084 states by generalized least squares in ace().
1086 o di2multi() did not modify node labels correctly.
1088 o multi2di() failed if the tree had its attribute "order" set to
1093 CHANGES IN APE VERSION 2.1-2
1098 o There three new methods for the "multiPhylo" class: str, $,
1101 o root() gains the options 'node' and 'resolve.root'
1102 (FALSE by default) as well as its code being improved.
1104 o mltt.plot() has now an option 'log' used in the same way
1105 than in plot.default().
1110 o mltt.plot() failed to display the legend with an unnamed
1113 o nodelabels() with pies now correcly uses the argument
1114 'cex' to draw symbols of different sizes (which has
1115 worked already for thermometers).
1117 o read.nexus() generally failed to read very big files.
1122 o The argument 'family' of compar.gee() can now be a function
1123 as well as a character string.
1125 o read.tree() and read.nexus() now return an unnamed list if
1126 'tree.names = NULL'.
1128 o read.nexus() now returns a modified object of class "multiPhylo"
1129 when there is a TRANSLATE block in the NEXUS file: the individual
1130 trees have no 'tip.label' vector, but the list has a 'TipLabel'
1131 attribute. The new methods '$' and '[[' set these elements
1132 correctly when extracting trees.
1136 CHANGES IN APE VERSION 2.1-1
1141 o The new function rmtree generates lists of random trees.
1143 o rcoal() now generates a genuine coalescent tree by default
1144 (thanks to Vladimir Minin for the code).
1149 o nuc.div() returned an incorrect value with the default
1150 pairwise.deletion = FALSE.
1155 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
1156 have been improved so that they are stabler and faster.
1158 o R packages used by ape are now loaded silently; lattice and gee
1159 are loaded only when needed.
1163 CHANGES IN APE VERSION 2.1
1168 o The new function identify.phylo identifies clades on a plotted
1169 tree using the mouse.
1171 o It is now possible to subset a list of trees (object of class
1172 "multiPhylo") with "[" while keeping its class correct.
1174 o The new function as.DNAbin.alignment converts DNA sequences
1175 stored in the "alignment" format of the package seqinr into
1176 an object of class "DNAbin".
1178 o The new function weight.taxo2 helps to build similarity matrices
1179 given two taxonomic levels (usually called by other functions).
1181 o write.tree() can now take a list of trees (class "multiPhylo")
1182 as its main argument.
1184 o plot.correlogram() and plot.correlogramList() have been
1185 improved, and gain several options (see the help page for
1186 details). A legend is now plotted by default.
1191 o dist.dna() returned some incorrect values with `model = "JC69"'
1192 and `pairwise.deletion = TRUE'. This affected only the
1193 distances involving sequences with missing values. (Thanks
1194 to Bruno Toupance for digging this bug out.)
1196 o write.tree() failed with some trees: this is fixed by removing
1197 the `multi.line' option (trees are now always printed on a
1200 o read.nexus() did not correctly detect trees with multiple root
1201 edges (see OTHER CHANGES).
1206 o The code of mlphylo() has been almost entirely rewritten, and
1207 should be much stabler. The options have been also greatly
1208 simplified (see ?mlphylo and ?DNAmodel for details).
1210 o The internal function nTips has been renamed klastorin_nTips.
1212 o The code of is.ultrametric() contained redundancies and has
1215 o The code of Moran.I() and of correlogram.formula() have been
1218 o read.tree() and read.nexus() now return an error when trying to
1219 read a tree with multiple root edges (see BUG FIXES). The
1220 correction applied in previous version did not work in all
1223 o The class c("multi.tree", "phylo") has been renamed
1229 o There is now a vignette in ape: see vignette("MoranI", "ape").
1232 DEPRECATED & DEFUNCT
1234 o as.matching() and as.phylo.matching() do not support branch
1237 o correlogram.phylo() and discrete.dist() have been removed.
1241 CHANGES IN APE VERSION 2.0-2
1246 o The new function matexpo computes the exponential of a square
1249 o The new function unique.multi.tree removes duplicate trees from
1252 o yule() has a new option `use.root.edge = FALSE' that specifies
1253 to ignore, by default, the root edge of the tree if it exists.
1258 o which.edge() failed when the index of a single terminal edge was
1261 o In diversi.time(), the values returned for model C were
1264 o A bug was fixed in yule() that affected the calculation of the
1265 likelihood in the presence of ties in the branching times.
1267 o There was a bug in the C function mat_expo4x4 affecting the
1268 calculations of the transition probabilities for models HKY and
1271 o A small bug was fixed in as.matrix.DNAbin (thanks to James
1274 o rtree() did not `shuffle' the tip labels by default, so only a
1275 limited number of labelled topologies could be generated.
1279 CHANGES IN APE VERSION 2.0-1
1284 o The three new functions bionj, fastme.ols, and fastme.bal
1285 perform phylogeny estimation by the BIONJ and fastME methods in
1286 OLS and balanced versions. This is a port to R of previous
1287 previous programs done by Vincent Lefort.
1289 o The new function chronoMPL performs molecular dating with the
1290 mean path lengths method of Britton et al. (2002, Mol. Phyl.
1293 o The new function rotate, contributed by Christoph Heibl, swaps
1294 two clades connected to the same node. It works also with
1295 multichotomous nodes.
1297 o The new `method' as.matrix.DNAbin() may be used to convert
1298 easily DNA sequences stored in a list into a matrix while
1299 keeping the names and the class.
1304 o chronopl() failed when some branch lengths were equal to zero:
1305 an error message is now returned.
1307 o di2multi() failed when there was a series of consecutive edges
1312 CHANGES IN APE VERSION 1.10-2
1317 o plot.phylo() can now plot circular trees: the option is type =
1318 "fan" or type = "f" (to avoid the ambiguity with type = "c").
1320 o prop.part() has a new option `check.labels = FALSE' which allows
1321 to considerably speed-up the calculations of bipartitions. As a
1322 consequence, calculations of bootstrap values with boot.phylo()
1323 should be much faster.
1328 o read.GenBank() did not return correctly the list of species as
1329 from ape 1.10: this is fixed in this version
1331 o Applying as.phylo() on a tree of class "phylo" failed: the
1332 object is now returned unchanged.
1336 CHANGES IN APE VERSION 1.10-1
1341 o The three new functions Ntip, Nnode, and Nedge return, for a
1342 given tree, the number of tips, nodes, or edges, respectively.
1347 o read.nexus() did not set correctly the class of the returned
1348 object when reading multiple trees.
1350 o mllt.plot() failed with objects of class c("multi.tree",
1353 o unroot() did not work correctly in most cases.
1355 o reorder.phylo() made R freeze in some occasions.
1357 o Plotting a tree in pruningwise order failed.
1359 o When plotting an unrooted tree, the tip labels where not all
1360 correctly positioned if the option `cex' was used.
1364 CHANGES IN APE VERSION 1.10
1369 o Five new `method' functions have been introduced to manipulate
1370 DNA sequences in binary format (see below).
1372 o Three new functions have been introduced to convert between the
1373 new binary and the character formats.
1375 o The new function as.alignment converts DNA sequences stored as
1376 single characters into the class "alignment" used by the package
1379 o read.dna() and read.GenBank() have a new argument `as.character'
1380 controlling whether the sequences are returned in binary format
1386 o root() failed when the tree had node labels: this is fixed.
1388 o plot.phylo() did not correctly set the limits on the y-axis with
1389 the default setting: this is fixed.
1391 o dist.dna() returned a wrong result for the LogDet, paralinear,
1392 and BH87 models with `pairwise.deletion = TRUE'.
1397 o DNA sequences are now internally stored in a binary format. See
1398 the document "A Bit-Level Coding Scheme for Nucleotides" for the
1399 details. Most functions analyzing DNA functions have been
1400 modified accordingly and are now much faster (dist.dna is now
1401 ca. 60 times faster).
1405 CHANGES IN APE VERSION 1.9-4
1410 o A bug was fixed in edgelabels().
1412 o as.phylo.hclust() did not work correctly when the object of
1413 class "hclust" has its labels set to NULL: the returned tree has
1414 now its tip labels set to "1", "2", ...
1416 o consensus could fail if some tip labels are a subset of others
1417 (e.g., "a" and "a_1"): this is now fixed.
1419 o mlphylo() failed in most cases if some branch lengths of the
1420 initial tree were greater than one: an error message is now
1423 o mlphylo() failed in most cases when estimating the proportion of
1424 invariants: this is fixed.
1428 CHANGES IN APE VERSION 1.9-3
1433 o The new function edgelabels adds labels on the edge of the tree
1434 in the same way than nodelabels or tiplabels.
1439 o multi2di() did not handle correctly branch lengths with the
1440 default option `random = TRUE': this is now fixed.
1442 o A bug was fixed in nuc.div() when using pairwise deletions.
1444 o A bug occurred in the analysis of bipartitions with large
1445 numbers of large trees, with consequences on prop.part,
1446 prop.clades, and boot.phylo.
1448 o The calculation of the Billera-Holmes-Vogtmann distance in
1449 dist.topo was wrong: this has been fixed.
1453 CHANGES IN APE VERSION 1.9-2
1458 o The new function ladderize reorganizes the internal structure of
1459 a tree to plot them left- or right-ladderized.
1461 o The new function dist.nodes computes the patristic distances
1462 between all nodes, internal and terminal, of a tree. It replaces
1463 the option `full = TRUE' of cophenetic.phylo (see below).
1468 o A bug was fixed in old2new.phylo().
1470 o Some bugs were fixed in chronopl().
1472 o The edge colours were not correctly displayed by plot.phylo
1473 (thank you to Li-San Wang for the fix).
1475 o cophenetic.phylo() failed with multichotomous trees: this is
1481 o read.dna() now returns the sequences in a matrix if they are
1482 aligned (interleaved or sequential format). Sequences in FASTA
1483 format are still returned in a list.
1485 o The option `full' of cophenetic.phylo() has been removed because
1486 it could not be used from the generic.
1489 DEPRECATED & DEFUNCT
1491 o rotate() has been removed; this function did not work correctly
1496 CHANGES IN APE VERSION 1.9-1
1501 o Trees with a single tip were not read correctly in R as the
1502 element `Nnode' was not set: this is fixed.
1504 o unroot() did not set correctly the number of nodes of the
1505 unrooted tree in most cases.
1507 o read.GenBank() failed when fetching very long sequences,
1508 particularly of the BX-series.
1510 o A bug was introduced in read.tree() with ape 1.9: it has been
1515 CHANGES IN APE VERSION 1.9
1520 o There are two new print `methods' for trees of class "phylo" and
1521 lists of trees of class "multi.tree", so that they are now
1522 displayed in a compact and informative way.
1524 o There are two new functions, old2new.phylo and new2old.phylo,
1525 for converting between the old and new coding of the class
1528 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
1529 LogDet ("logdet"), and paralinear ("paralin").
1531 o compute.brlen() has been extended: several methods are now
1532 available to compute branch lengths.
1534 o write.dna() can now handle matrices as well as lists.
1539 o cophenetic.phylo() sometimes returned a wrong result with
1540 multichotomous trees: this is fixed.
1542 o rotate() failed when a single tip was specified: the tree is now
1545 o ace() did not return the correct index matrix with custom
1546 models: this is fixed.
1548 o multi2di() did not work correctly when resolving multichotomies
1549 randomly: the topology was always the same, only the arrangement
1550 of clades was randomized: this is fixed. This function now
1551 accepts trees with no branch lengths.
1553 o The output of diversi.gof() was blurred by useless prints when a
1554 user distribution was specified. This has been corrected, and
1555 the help page of this function has been expanded.
1560 o The internal structure of the class "phylo" has been changed:
1561 see the document "Definition of Formats for Coding Phylogenetic
1562 Trees in R" for the details. In addition, the code of most
1563 functions has been improved.
1565 o Several functions have been improved by replacing some R codes
1566 by C codes: pic, plot.phylo, and reorder.phylo.
1568 o There is now a citation information: see citation("ape") in R.
1570 o write.tree() now does not add extra 0's to branch lengths so
1571 that 1.23 is printed "1.23" by default, not "1.2300000000".
1573 o The syntax of bind.tree() has been simplified. This function now
1574 accepts trees with no branch lengths, and handles correctly node
1577 o The option `as.numeric' of mrca() has been removed.
1579 o The unused options `format' and `rooted' of read.tree() have
1582 o The unused option `format' of write.tree() has been removed.
1584 o The use of node.depth() has been simplified.
1588 CHANGES IN APE VERSION 1.8-5
1593 o Two new functions read.nexus.data() and write.nexus.data(),
1594 contributed by Johan Nylander, allow to read and write molecular
1595 sequences in NEXUS files.
1597 o The new function reorder.phylo() reorders the internal structure
1598 of a tree of class "phylo". It is used as the generic, e.g.,
1601 o read.tree() and read.nexus() can now read trees with a single
1604 o The new data set `cynipids' supplies a set of protein sequences
1610 o The code of all.equal.phylo() has been completely rewritten
1611 (thanks to Benoît Durand) which fixes several bugs.
1613 o read.tree() and read.nexus() now checks the labels of the tree
1614 to remove or substitute any characters that are illegal in the
1615 Newick format (parentheses, etc.)
1617 o A negative P-value could be returned by mantel.test(): this is
1622 CHANGES IN APE VERSION 1.8-4
1627 o The new function sh.test() computes the Shimodaira-
1630 o The new function collapse.singles() removes the nodes with a
1631 single descendant from a tree.
1633 o plot.phylo() has a new argument `tip.color' to specify the
1634 colours of the tips.
1636 o mlphylo() has now an option `quiet' to control the display of
1637 the progress of the analysis (the default is FALSE).
1642 o read.dna() did not read correctly sequences in sequential format
1643 with leading alignment gaps "-": this is fixed.
1645 o ace() returned a list with no class so that the generic
1646 functions (anova, logLik, ...) could not be used directly. This
1647 is fixed as ace() now returns an object of class "ace".
1649 o anova.ace() had a small bug when computing the number of degrees
1650 of freedom: this is fixed.
1652 o mlphylo() did not work when the sequences were in a matrix or
1653 a data frame: this is fixed.
1655 o rtree() did not work correctly when trying to simulate an
1656 unrooted tree with two tips: an error message is now issued.
1661 o The algorithm of rtree() has been changed: it is now about 40,
1662 100, and 130 times faster for 10, 100, and 1000 tips,
1667 CHANGES IN APE VERSION 1.8-3
1672 o There are four new `method' functions to be used with the
1673 results of ace(): logLik(), deviance(), AIC(), and anova().
1675 o The plot method of phymltest has two new arguments: `main' to
1676 change the title, and `col' to control the colour of the
1677 segments showing the AIC values.
1679 o ace() has a new argument `ip' that gives the initial values used
1680 in the ML estimation with discrete characters (see the examples
1681 in ?ace). This function now returns a matrix giving the indices
1682 of the estimated rates when analysing discrete characters.
1684 o nodelabels() and tiplabels() have a new argument `pie' to
1685 represent proportions, with any number of categories, as
1686 piecharts. The use of the option `thermo' has been improved:
1687 there is now no limitation on the number of categories.
1692 o mlphylo() did not work with more than two partitions: this is
1695 o root() failed if the proposed outgroup was already an outgroup
1696 in the tree: this is fixed.
1698 o The `col' argument in nodelabels() and tiplabels() was not
1699 correctly passed when `text' was used: this is fixed.
1701 o Two bugs were fixed in mlphylo(): parameters were not always
1702 correctly output, and the estimation failed in some cases.
1704 o plot.phylo() was stuck when given a tree with a single tip: this
1705 is fixed and a message error is now returned.
1707 o An error was corrected in the help page of gammaStat regarding
1708 the calculation of P-values.
1710 o Using gls() could crash R when the number of species in the tree
1711 and in the variables were different: this is fixed.
1715 CHANGES IN APE VERSION 1.8-2
1720 o The new function mlphylo() fits a phylogenetic tree by maximum
1721 likelihood from DNA sequences. Its companion function DNAmodel()
1722 is used to define the substitution model which may include
1723 partitioning. There are methods for logLik(), deviance(), and
1724 AIC(), and the summary() method has been extended to display in
1725 a friendly way the results of this model fitting. Currently, the
1726 functionality is limited to estimating the substitution and
1727 associated parameters and computing the likelihood.
1729 o The new function drop1.compar.gee (used as, e.g., drop1(m))
1730 tests for single effects in GEE-based comparative method. A
1731 warning message is printed if there is not enough degrees of
1737 o An error message was sometimes issued by plot.multi.tree(),
1738 though with no consequence.
1742 CHANGES IN APE VERSION 1.8-1
1747 o There is a new plot method for lists of trees (objects of class
1748 "multi.tree"): it calls plot.phylo() internally and is
1749 documented on the same help page.
1754 o A bug was fixed in the C code that analyzes bipartitions: this
1755 has impact on several functions like prop.part, prop.clades,
1756 boot.phylo, or consensus.
1758 o root() did not work correctly when the specified outgroup had
1759 more than one element: this is fixed.
1761 o dist.dna() sometimes returned a warning inappropriately: this
1764 o If the distance object given to nj() had no rownames, nj()
1765 returned a tree with no tip labels: it now returns tips labelled
1766 "1", "2", ..., corresponding to the row numbers.
1771 o nj() has been slightly changed so that tips with a zero distance
1772 are first aggregated with zero-lengthed branches; the usual NJ
1773 procedure is then performed on a distance matrix without 0's.
1777 CHANGES IN APE VERSION 1.8
1782 o The new function chronopl() estimates dates using the penalized
1783 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1785 o The new function consensus() calculates the consensus tree of a
1788 o The new function evolve.phylo() simulates the evolution of
1789 continuous characters along a phylogeny under a Brownian model.
1791 o The new plot method for objects of class "ancestral" displays a
1792 tree together with ancestral values, as returned by the above
1795 o The new function as.phylo.formula() returns a phylogeny from a
1796 set of nested taxonomic variables given as a formula.
1798 o The new function read.caic() reads trees in CAIC format.
1800 o The new function tiplabels() allows to add labels to the tips
1801 of a tree using text or plotting symbols in a flexible way.
1803 o The new function unroot() unroots a phylogeny.
1805 o multi2di() has a new option, `random', which specifies whether
1806 to resolve the multichotomies randomly (the default) or not.
1808 o prop.part() now returns an object of class "prop.part" for which
1809 there are print (to display a partition in a more friendly way)
1810 and summary (to extract the numbers) methods.
1812 o plot.phylo() has a new option, `show.tip.label', specifying
1813 whether to print the labels of the tips. The default is TRUE.
1815 o The code of nj() has been replaced by a faster C code: it is now
1816 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1819 o write.nexus() now writes whether a tree is rooted or not.
1824 o Two bugs have been fixed in root(): unrooted trees are now
1825 handled corretly, and node labels are now output normally.
1827 o A bug was fixed in phymltest(): the executable couldn't be found
1830 o Three bug have been fixed in ace(): computing the likelihood of
1831 ancestral states of discrete characters failed, custom models
1832 did not work, and the function failed with a null gradient (a
1833 warning message is now returned; this latter bug was also
1834 present in yule.cov() as well and is now fixed).
1836 o pic() hanged out when missing data were present: a message error
1839 o A small bug was fixed in dist.dna() where the gamma correction
1840 was not always correctly dispatched.
1842 o plot.phylo() plotted correctly the root edge only when the tree
1843 was plotted rightwards: this works now for all directions.
1848 o dist.taxo() has been renamed as weight.taxo().
1850 o dist.phylo() has been replaced by the method cophenetic.phylo().
1852 o Various error and warning messages have been improved.
1856 CHANGES IN APE VERSION 1.7
1859 o The new function ace() estimates ancestral character states for
1860 continuous characters (with ML, GLS, and contrasts methods), and
1861 discrete characters (with ML only) for any number of states.
1863 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1864 of directional evolution for continuous characters. The user
1865 specifies the node(s) of the tree where the character optimum
1868 o The new function is.rooted() tests whether a tree (of class
1871 o The new function rcoal() generates random ultrametric trees with
1872 the possibility to specify the function that generates the
1873 inter-nodes distances.
1875 o The new function mrca() gives for all pairs of tips in a tree
1876 (and optionally nodes too) the most recent common ancestor.
1878 o nodelabels() has a new option `thermo' to plot proportions (up
1879 to three classes) on the nodes of a tree.
1881 o rtree() has been improved: it can now generate rooted or
1882 unrooted trees, and the mathematical function that generates the
1883 branch lengths may be specified by the user. The tip labels may
1884 be given directly in the call to rtree. The limit cases (n = 2,
1885 3) are now handled correctly.
1887 o dist.topo() has a new argument `method' with two choices: "PH85"
1888 for Penny and Henny's method (already available before and now
1889 the default), and "BHV01" for the geometric distance by Billera
1890 et al. (2001, Adv. Appl. Math. 27:733).
1892 o write.tree() has a new option, `digits', which specifies the
1893 number of digits to be printed in the Newick tree. By default
1894 digits = 10. The numbers are now always printed in decimal form
1895 (i.e., 1.0e-1 is now avoided).
1897 o dist.dna() can now compute the raw distances between pairs of
1898 DNA sequences by specifying model = "raw".
1900 o dist.phylo() has a new option `full' to possibly compute the
1901 distances among all tips and nodes of the tree. The default if
1907 o Several bugs were fixed in all.equal.phylo().
1909 o dist.dna() did not handle correctly gaps ("-") in alignments:
1910 they are now considered as missing data.
1912 o rotate() did not work if the tips were not ordered: this is
1915 o mantel.test() returned NA in some special cases: this is fixed
1916 and the function has been improved and is now faster.
1918 o A bug was fixed in diversi.gof() where the calculation of A² was
1921 o cherry() did not work correctly under some OSs (mainly Linux):
1924 o is.binary.tree() has been modified so that it works with both
1925 rooted and unrooted trees.
1927 o The documentation of theta.s() was not correct: this has been
1930 o plot.mst() did not work correctly: this is fixed.
1934 CHANGES IN APE VERSION 1.6
1939 o The new function dist.topo() computes the topological distances
1942 o The new function boot.phylo() performs a bootstrap analysis on
1943 phylogeny estimation.
1945 o The new functions prop.part() and prop.clades() analyse
1946 bipartitions from a series of trees.
1951 o read.GenBank() now uses the EFetch utility of NCBI instead of
1952 the usual Web interface: it is now much faster (e.g., 12 times
1953 faster to retrieve 8 sequences, 37 times for 60 sequences).
1958 o Several bugs were fixed in read.dna().
1960 o Several bugs were fixed in diversi.time().
1962 o is.binary.tree() did not work correctly if the tree has no edge
1963 lengths: this is fixed.
1965 o drop.tip() did not correctly propagated the `node.label' of a
1966 tree: this is fixed.
1970 CHANGES IN APE VERSION 1.5
1975 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1976 convert objects between the classes "phylo" and "matching". The
1977 latter implements the representation of binary trees introduced by
1978 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1979 as.matching() has been introduced as well.
1981 o Two new functions, multi2di() and di2multi(), allow to resolve
1982 and collapse multichotomies with branches of length zero.
1984 o The new function nuc.div() computes the nucleotide diversity
1985 from a sample a DNA sequences.
1987 o dist.dna() has been completely rewritten with a much faster
1988 (particularly for large data sets) C code. Eight models are
1989 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1990 option `method' has been renamed `model'). Computation of variance
1991 is available for all models. A gamma-correction is possible for
1992 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1993 to remove sites with missing data on a pairwise basis. The option
1994 `GCcontent' has been removed.
1996 o read.GenBank() has a new option (species.names) which specifies
1997 whether to return the species names of the organisms in addition
1998 to the accession numbers of the sequences (this is the default
2001 o write.nexus() can now write several trees in the same NEXUS file.
2003 o drop.tip() has a new option `root.edge' that allows to specify the
2004 new root edge if internal branches are trimmed.
2009 o as.phylo.hclust() failed if some labels had parentheses: this
2012 o Several bugs were fixed in all.equal.phylo(). This function now
2013 returns the logical TRUE if the trees are identical but with
2014 different representations (a report was printed previously).
2016 o read.GenBank() did not correctly handle ambiguous base codes:
2022 o birthdeath() now returns an object of class "birthdeath" for
2023 which there is a print method.
2027 CHANGES IN APE VERSION 1.4
2032 o The new function nj() performs phylogeny estimation with the
2033 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
2036 o The new function which.edge() identifies the edges of a tree
2037 that belong to a group specified as a set of tips.
2039 o The new function as.phylo.phylog() converts an object of class
2040 "phylog" (from the package ade4) into an object of class
2043 o The new function axisPhylo() draws axes on the side of a
2046 o The new function howmanytrees() calculates the number of trees
2047 in different cases and giving a number of tips.
2049 o write.tree() has a new option `multi.line' (TRUE by default) to
2050 write a Newick tree on several lines rather than on a single
2053 o The functionalities of zoom() have been extended. Several
2054 subtrees can be visualized at the same time, and they are marked
2055 on the main tree with colors. The context of the subtrees can be
2056 marked with the option `subtree' (see below).
2058 o drop.tip() has a new option `subtree' (FALSE by default) which
2059 specifies whether to output in the tree how many tips have been
2062 o The arguments of add.scale.bar() have been redefined and have
2063 now default values (see ?add.scale.bar for details). This
2064 function now works even if the plotted tree has no edge length.
2066 o plot.phylo() can now plot radial trees, but this does not take
2067 edge lengths into account.
2069 o In plot.phylo() with `type = "phylogram"', if the values of
2070 `edge.color' and `edge.width' are identical for sister-branches,
2071 they are propagated to the vertical line that link them.
2076 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
2077 crashing. This is fixed.
2079 o In plot.phylo(), the options `edge.color' and `edge.width' are
2080 now properly recycled; their default values are now "black" and
2083 o A bug has been fixed in write.nexus().
2088 o The function node.depth.edgelength() has been removed and
2089 replaced by a C code.
2093 CHANGES IN APE VERSION 1.3-1
2098 o The new function nodelabels() allows to add labels to the nodes
2099 of a tree using text or plotting symbols in a flexible way.
2101 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
2102 numeric values specifying the lower and upper limits on the x-
2103 and y-axes. This allows to leave some space on any side of the
2104 tree. If a single value is given, this is taken as the upper
2109 CHANGES IN APE VERSION 1.3
2114 o The new function phymltest() calls the software PHYML and fits
2115 28 models of DNA sequence evolution. There are a print method to
2116 display likelihood and AIC values, a summary method to compute
2117 the hierarchical likelihood ratio tests, and a plot method to
2118 display graphically the AIC values of each model.
2120 o The new function yule.cov() fits the Yule model with covariates,
2121 a model where the speciation rate is affected by several species
2122 traits through a generalized linear model. The parameters are
2123 estimated by maximum likelihood.
2125 o Three new functions, corBrownian(), corGrafen(), and
2126 corMartins(), compute the expected correlation structures among
2127 species given a phylogeny under different models of evolution.
2128 These can be used for GLS comparative phylogenetic methods (see
2129 the examples). There are coef() and corMatrix() methods and an
2130 Initialize.corPhyl() function associated.
2132 o The new function compar.cheverud() implements Cheverud et al.'s
2133 (1985; Evolution 39:1335) phylogenetic comparative method.
2135 o The new function varcomp() estimates variance components; it has
2138 o Two new functions, panel.superpose.correlogram() and
2139 plot.correlogramList(), allow to plot several phylogenetic
2142 o The new function node.leafnumber() computes the number of leaves
2143 of a subtree defined by a particular node.
2145 o The new function node.sons() gets all tags of son nodes from a
2148 o The new function compute.brlen() computes the branch lengths of
2149 a tree according to a specified method.
2151 o plot.phylo() has three new options: "cex" controls the size of
2152 the (tip and node) labels (thus it is no more needed to change
2153 the global graphical parameter), "direction" which allows to
2154 plot the tree rightwards, leftwards, upwards, or downwards, and
2155 "y.lim" which sets the upper limit on the y-axis.
2160 o Some functions which try to match tip labels and names of
2161 additional data (e.g. vector) are likely to fail if there are
2162 typing or syntax errors. If both series of names do not perfectly
2163 match, they are ignored and a warning message is now issued.
2164 These functions are bd.ext, compar.gee, pic. Their help pages
2165 have been clarified on this point.
2169 CHANGES IN APE VERSION 1.2-7
2174 o The new function root() reroots a phylogenetic tree with respect
2175 to a specified outgroup.
2177 o The new function rotate() rotates an internal branch of a tree.
2179 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
2180 trees) controls the display of the tip labels in unrooted trees.
2181 This display has been greatly improved: the tip labels are now not
2182 expected to overlap with the tree (particularly if lab4ut =
2183 "axial"). In all cases, combining appropriate values of "lab4ut"
2184 and the font size (via "par(cex = )") should result in readable
2185 unrooted trees. See ?plot.phylo for some examples.
2187 o In drop.tip(), the argument `tip' can now be numeric or character.
2192 o drop.tip() did not work correctly with trees with no branch
2193 lengths: this is fixed.
2195 o A bug in plot.phylo(..., type = "unrooted") made some trees being
2196 plotted with some line crossings: this is now fixed.
2200 CHANGES IN APE VERSION 1.2-6
2205 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
2206 correlogram.phylo, dist.taxo, plot.correlogram) have been added
2207 to implement comparative methods with an autocorrelation approach.
2209 o A new data set describing some life history traits of Carnivores
2215 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
2220 o When plotting a tree with plot.phylo(), the new default of the
2221 option `label.offset' is now 0, so the labels are always visible.
2225 CHANGES IN APE VERSION 1.2-5
2230 o The new function bd.ext() fits a birth-death model with combined
2231 phylogenetic and taxonomic data, and estimates the corresponding
2232 speciation and extinction rates.
2237 o The package gee is no more required by ape but only suggested
2238 since only the function compar.gee() calls gee.
2242 CHANGES IN APE VERSION 1.2-4
2247 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
2248 and lines.popsize) implementing a new approach for inferring the
2249 demographic history from genealogies using a reversible jump
2250 MCMC have been introduced.
2252 o The unit of time in the skyline plot and in the new plots can
2253 now be chosen to be actual years, rather than substitutions.
2257 CHANGES IN APE VERSION 1.2-3
2262 o The new function rtree() generates a random binary tree with or
2263 without branch lengths.
2265 o Two new functions for drawing lineages-through-time (LTT) plots
2266 are provided: ltt.lines() adds a LTT curve to an existing plot,
2267 and mltt.plot() does a multiple LTT plot giving several trees as
2268 arguments (see `?ltt.plot' for details).
2273 o Some taxon names made R crashing when calling as.phylo.hclust():
2276 o dist.dna() returned an error with two identical DNA sequences
2277 (only using the Jukes-Cantor method returned 0): this is fixed.
2282 o The function dist.phylo() has been re-written using a different
2283 algorithm: it is now about four times faster.
2285 o The code of branching.times() has been improved: it is now about
2290 CHANGES IN APE VERSION 1.2-2
2295 o The new function seg.sites() finds the segregating sites in a
2296 sample of DNA sequences.
2301 o A bug introduced in read.tree() and in read.nexus() with version
2304 o A few errors were corrected and a few examples were added in the
2309 CHANGES IN APE VERSION 1.2-1
2314 o plot.phylo() can now draw the edge of the root of a tree if it
2315 has one (see the new option `root.edge', its default is FALSE).
2320 o A bug was fixed in read.nexus(): files with semicolons inside
2321 comment blocks were not read correctly.
2323 o The behaviour of read.tree() and read.nexus() was corrected so
2324 that tree files with badly represented root edges (e.g., with
2325 an extra pair of parentheses, see the help pages for details)
2326 are now correctly represented in the object of class "phylo";
2327 a warning message is now issued.
2331 CHANGES IN APE VERSION 1.2
2336 o plot.phylo() has been completely re-written and offers several
2337 new functionalities. Three types of trees can now be drawn:
2338 phylogram (as previously), cladogram, and unrooted tree; in
2339 all three types the branch lengths can be drawn using the edge
2340 lengths of the phylogeny or not (e.g., if the latter is absent).
2341 The vertical position of the nodes can be adjusted with two
2342 choices (see option `node.pos'). The code has been re-structured,
2343 and two new functions (potentially useful for developpers) are
2344 documented separately: node.depth.edgelength() and node.depth();
2345 see the respective help pages for details.
2347 o The new function zoom() allows to explore very large trees by
2348 focusing on a small portion of it.
2350 o The new function yule() fits by maximum likelihood the Yule model
2351 (birth-only process) to a phylogenetic tree.
2353 o Support for writing DNA sequences in FASTA format has been
2354 introduced in write.dna() (support for reading sequences in
2355 this format was introduced in read.dna() in version 1.1-2).
2356 The function has been completely re-written, fixing some bugs
2357 (see below); the default behaviour is no more to display the
2358 sequences on the standard output. Several options have been
2359 introduced to control the sequence printing in a flexible
2360 way. The help page has been extended.
2362 o A new data set is included: a supertree of bats in NEXUS format.
2367 o In theta.s(), the default of the option `variance' has
2368 been changed to `FALSE' (as was indicated in the help page).
2370 o Several bugs were fixed in the code of all.equal.phylo().
2372 o Several bugs were fixed in write.dna(), particularly this
2373 function did not work with `format = "interleaved"'.
2375 o Various errors were corrected in the help pages.
2380 o The argument names of as.hclust.phylo() have been changed
2381 from "(phy)" to "(x, ...)" to conform to the definition of
2382 the corresponding generic function.
2384 o gamma.stat() has been renamed gammaStat() to avoid confusion
2385 since gamma() is a generic function.
2389 CHANGES IN APE VERSION 1.1-3
2394 o base.freq() previously did not return a value of 0 for
2395 bases absent in the data (e.g., a vector of length 3 was
2396 returned if one base was absent). This is now fixed (a
2397 vector of length 4 is always returned).
2399 o Several bugs were fixed in read.nexus(), including that this
2400 function did not work in this absence of a "TRANSLATE"
2401 command in the NEXUS file, and that the commands were
2406 CHANGES IN APE VERSION 1.1-2
2411 o The Tamura and Nei (1993) model of DNA distance is now implemented
2412 in dist.dna(): five models are now available in this function.
2414 o A new data set is included: a set of 15 sequences of the
2415 cytochrome b mitochondrial gene of the woodmouse (Apodemus
2421 o A bug in read.nexus() was fixed.
2423 o read.dna() previously did not work correctly in most cases.
2424 The function has been completely re-written and its help page
2425 has been considerably extended (see ?read.dna for details).
2426 Underscores (_) in taxon names are no more replaced with
2427 spaces (this behaviour was undocumented).
2429 o A bug was fixed in write.dna().
2433 CHANGES IN APE VERSION 1.1-1
2438 o A bug in read.tree() introduced in APE 1.1 was fixed.
2440 o A bug in compar.gee() resulted in an error when trying to fit
2441 a model with `family = "binomial"'. This is now fixed.
2445 CHANGES IN APE VERSION 1.1
2450 o The Klastorin (1982) method as suggested by Misawa and Tajima
2451 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
2452 on the basis of phylogenetic trees has been implemented (see
2453 the function klastorin()).
2455 o Functions have been added to convert APE's "phylo" objects in
2456 "hclust" cluster objects and vice versa (see the help page of
2457 as.phylo for details).
2459 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
2460 are introduced for the estimation of absolute evolutionary rates
2461 (ratogram) and dated clock-like trees (chronogram) from
2462 phylogenetic trees using the non-parametric rate smoothing approach
2463 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
2465 o A summary method is now provided printing a summary information on a
2466 phylogenetic tree with, for instance, `summary(tree)'.
2468 o The behaviour of read.tree() was changed so that all spaces and
2469 tabulations in tree files are now ignored. Consequently, spaces in tip
2470 labels are no more allowed. Another side effect is that read.nexus()
2471 now does not replace the underscores (_) in tip labels with spaces
2472 (this behaviour was undocumented).
2474 o The function plot.phylo() has a new option (`underscore') which
2475 specifies whether the underscores in tip labels should be written on
2476 the plot as such or replaced with spaces (the default).
2478 o The function birthdeath() now computes 95% confidence intervals of
2479 the estimated parameters using profile likelihood.
2481 o Three new data sets are included: a gene tree estimated from 36
2482 landplant rbcL sequences, a gene tree estimated from 32 opsin
2483 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
2488 o A bug was fixed in dist.gene() where nothing was returned.
2490 o A bug in plot.mst() was fixed.
2492 o A bug in vcv.phylo() resulted in false correlations when the
2493 option `cor = TRUE' was used (now fixed).
2497 CHANGES IN APE VERSION 1.0
2502 o Two new functions, read.dna() and write.dna(), read/write in a file
2503 DNA sequences in interleaved or in sequential format.
2505 o Two new functions, read.nexus() and write.nexus(), read/write trees
2508 o The new function bind.tree() allows to bind two trees together,
2509 possibly handling root edges to give internal branches.
2511 o The new function drop.tip() removes the tips in a phylogenetic tree,
2512 and trims (or not) the corresponding internal branches.
2514 o The new function is.ultrametric() tests if a tree is ultrametric.
2516 o The function plot.phylo() has more functionalities such as drawing the
2517 branches with different colours and/or different widths, showing the
2518 node labels, controling the position and font of the labels, rotating
2519 the labels, and controling the space around the plot.
2521 o The function read.tree() can now read trees with no branch length,
2522 such as "(a,b),c);". Consequently, the element `edge.length' in
2523 objects of class "phylo" is now optional.
2525 o The function write.tree() has a new default behaviour: if the default
2526 for the option `file' is used (i.e. file = ""), then a variable of
2527 mode character containing the tree in Newick format is returned which
2528 can thus be assigned (e.g., tree <- write.tree(phy)).
2530 o The function read.tree() has a new argument `text' which allows
2531 to read the tree in a variable of mode character.
2533 o A new data set is included: the phylogenetic relationships among
2534 the orders of birds from Sibley and Ahlquist (1990).
2538 CHANGES IN APE VERSION 0.2-1
2543 o Several bugs were fixed in the help pages.
2547 CHANGES IN APE VERSION 0.2
2552 o The function write.tree() writes phylogenetic trees (objects of class
2553 "phylo") in an ASCII file using the Newick parenthetic format.
2555 o The function birthdeath() fits a birth-death model to branching times
2556 by maximum likelihood, and estimates the corresponding speciation and
2559 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
2562 o The function is.binary.tree() tests whether a phylogeny is binary.
2564 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
2565 as well as some methods are introduced.
2567 o Several functions, including some generics and methods, for computing
2568 skyline plot estimates (classic and generalized) of effective
2569 population size through time are introduced and replace the function
2570 skyline.plot() in version 0.1.
2572 o Two data sets are now included: the phylogenetic relationships among
2573 the families of birds from Sibley and Ahlquist (1990), and an
2574 estimated clock-like phylogeny of HIV sequences sampled in the
2575 Democratic Republic of Congo.
2578 DEPRECATED & DEFUNCT
2580 o The function skyline.plot() in ape 0.1 has been deprecated and
2581 replaced by more elaborate functions (see above).
2586 o Two important bugs were fixed in plot.phylo(): phylogenies with
2587 multichotomies not at the root or not with only terminal branches,
2588 and phylogenies with a single node (i.e. only terminal branches)
2589 did not plot. These trees should be plotted correctly now.
2591 o Several bugs were fixed in diversi.time() in the computation of
2594 o Various errors were corrected in the help pages.