1 CHANGES IN APE VERSION 2.8-1
6 o mantel.test() could return P-values > 1 with the default
9 o extract.clade() sometimes shuffled some tip labels (thanks to
10 Ludovic Mallet and Mahendra Mariadassou for the fix).
15 o The code of yule() has been simplified and is now much faster for
18 o The code of mantel.test() has been adjusted to be consistent
19 with common permutation tests.
23 CHANGES IN APE VERSION 2.8
28 o Twelve new functions have been written by Andrei-Alin Popescu:
29 additive, ultrametric, is.compatible, arecompatible, mvr, mvrs,
30 njs, bionjs, SDM, treePop, triangMtd, triangMtd*.
32 o A new class "bitsplits" has been created by Andrei-Alin Popescu
33 to code splits (aka, bipartition).
35 o There is a new generic function as.bitsplits with a method to
36 convert from the class "prop.part" to the class "bitsplits".
38 o The new function ltt.coplot plots on the same scales a tree and
41 o ltt.plot() has two new options: backward and tol. It can now
42 handle non-ultrametic trees and its internal coding has been
43 improved. The coordinates of the plot can now be computed with
44 the new function ltt.plot.coords.
49 o prop.part() crashed if some trees had some multichotomies.
53 CHANGES IN APE VERSION 2.7-3
58 o The new function compute.brtime computes and sets branching times.
60 o mantel.test() has a new argument 'alternative' which is
61 "two-sided" by default. Previously, this test was one-tailed
62 with no possibility to change.
64 o ace() can now do REML estimation with continuous characters,
65 giving better estimates of the variance of the Brownian motion
71 o Branch lengths were wrongly updated with bind.tree(, where = <tip>,
72 position = 0). (Thanks to Liam Revell for digging this bug out.)
74 o Simulation of OU process with rTraitCont() did not work correctly.
75 This now uses formula from Gillespie (1996) reduced to a BM
76 process when alpha = 0 to avoid division by zero. The option
77 'linear' has been removed.
79 o Cross-validation in chronopl() did not work when 'age.max' was
82 o consensus(, p = 0.5) could return an incorrect tree if some
83 incompatible splits occur in 50% of the trees (especially with
84 small number of trees).
86 o c() with "multiPhylo" did not work correctly (thanks to Klaus
89 o root() failed in some cases with an outgroup made of several tips.
90 The help page has been clarified a bit.
94 CHANGES IN APE VERSION 2.7-2
99 o There is a new class "evonet" to code evolutionary networks, with
100 a constructor function evonet(), a print() and a plot() methods,
101 and four conversion methods to the classes "phylo", "networx",
102 "network", and "igraph".
104 o The new function rTraitMult does multivariate traits simulation
105 with user-defined models.
107 o plot.phylo() has a new option 'plot = TRUE'. If FALSE, the tree
108 is not plotted but the graphical device is set and the
109 coordinates are saved as usual.
111 o diversity.contrast.test() gains a fourth version of the test with
112 method = "logratio"; the literature citations have been clarified.
114 o add.scale.bar() has two new options, 'lwd' and 'lcol', to modify
115 the aspect of the bar.
117 o boot.phylo() now displays a progress bar by default (can be off
120 o There is a new predict() method for compar.gee().
125 o bionj() made R crash if distances were too large. It now returns
126 an error if at least one distance is greater than 100.
128 o drop.tip() returned a wrong tree if 'tip' was of zero length.
130 o read.nexus.data() failed with URLs.
132 o boot.phylo() returned overestimated support values in the
133 presence of identical or nearly identical sequences.
138 o The data bird.families, bird.orders, cynipids, and woodmouse are
139 now provided as .rda files.
143 CHANGES IN APE VERSION 2.7-1
148 o The new function trex does tree exploration with multiple
151 o The new function kronoviz plots several rooted (dated) trees on
154 o identify.phylo() has a new option 'quiet' (FALSE by default).
159 o A bug was introduced in read.nexus() in ape 2.7.
161 o image.DNAbin() did not colour correctly the bases if there were
164 o .compressTipLabel() failed with a list with a single tree.
166 o identify.phylo() returned a wrong answer when the x- and y-scales
169 o write.nexus() failed with lists of trees with compressed labels.
174 o identify.phylo() now returns NULL if the user right-(instead of
175 left-)clicks (an error was returned previously).
177 o read.nexus() should be robust to commands inserted in the TREES
182 CHANGES IN APE VERSION 2.7
187 o There is a new image() method for "DNAbin" objects: it plots DNA
188 alignments in a flexible and efficient way.
190 o Two new functions as.network.phylo and as.igraph.phylo convert
191 trees of class "phylo" into these respective network classes
192 defined in the packages of the same names.
194 o The three new functions clustal, muscle, and tcoffee perform
195 nucleotide sequence alignment by calling the external programs
198 o Four new functions, diversity.contrast.test, mcconwaysims.test,
199 richness.yule.test, and slowinskiguyer.test, implement various
200 tests of diversification shifts using sister-clade comparisons.
202 o base.freq() gains an option 'all' to count all the possible bases
203 including the ambiguous ones (defaults to FALSE).
205 o read.nexus() now writes tree names in the NEXUS file if given a
206 list of trees with names.
211 o prop.part() failed in some situations with unrooted trees.
213 o read.nexus() shuffled node labels when a TRANSLATE block was
216 o varCompPhylip() did not work if 'exec' was specified.
218 o bind.tree() shuffled node labels when position > 0 and 'where'
224 o BaseProportion in src/dist_dna.c has been modified.
226 o A number of functions in src/tree_build.c have been modified.
228 o The matching representation has now only two columns as the third
229 column was redundant.
233 CHANGES IN APE VERSION 2.6-3
238 o rTraitCont() and rTraitDisc() gains a '...' argument used with
239 user-defined models (suggestion by Gene Hunt).
244 o as.hclust.phylo() now returns an error with unrooted trees.
246 o as.hclust.phylo() failed with trees with node labels (thanks to
247 Jinlong Zhang for pointing this bug out).
249 o read.dna(, "fasta") failed if sequences were not all of the same
252 o plot.phylo() did not recycle values of 'font', 'cex' and
253 'tip.color' correctly when type = "fan" or "radial".
255 o plot.phylo() ignored 'label.offset' when type = "radial", "fan", or
256 "unrooted" with lab4ut = "axial" (the placement of tip labels still
257 needs to be improved with lab4ut = "horizontal").
262 o In drop.fossil() the default tol = 0 has been raised to 1e-8.
264 o The help command ?phylo now points to the man page of read.tree()
265 where this class is described. Similarly, ?matching points to the
266 man page of as.matching().
270 CHANGES IN APE VERSION 2.6-2
275 o Two new functions, pic.ortho and varCompPhylip, implements the
276 orthonormal contrasts of Felsenstein (2008, Am Nat, 171:713). The
277 second function requires Phylip to be installed on the computer.
279 o bd.ext() has a new option conditional = TRUE to use probabilities
280 conditioned on no extinction for the taxonomic data.
285 o write.tree() failed to output correctly tree names.
287 o dist.nodes() returned duplicated column(s) with unrooted and/or
288 multichotomous trees.
290 o mcmc.popsize() terminated unexpectedly if the progress bar was
293 o prop.part(x) made R frozen if 'x' is of class "multiPhylo".
295 o Compilation under Mandriva failed (thanks to Jos Käfer for the fix).
297 o drop.tip() shuffled tip labels with subtree = TRUE or trim.internal
300 o Objects returned by as.hclust.phylo() failed when analysed with
301 cutree() or rect.hclust().
303 o write.tree() did not output correctly node labels (thanks to Naim
304 Matasci and Jeremy Beaulieu for the fix).
306 o ace(type = "discrete") has been improved thanks to Naim Marasci and
311 CHANGES IN APE VERSION 2.6-1
316 o The new function speciesTree calculates the species tree from a set
317 of gene trees. Several methods are available including maximum tree
318 and shallowest divergence tree.
323 o A bug introduced in write.tree() with ape 2.6 has been fixed.
325 o as.list.DNAbin() did not work correctly with vectors.
327 o as.hclust.phylo() failed with trees with node labels (thanks to
328 Filipe Vieira for the fix).
332 CHANGES IN APE VERSION 2.6
337 o The new functions rlineage and rbdtree simulate phylogenies under
338 any user-defined time-dependent speciation-extinction model. They
339 use continuous time algorithms.
341 o The new function drop.fossil removes the extinct species from a
344 o The new function bd.time fits a user-defined time-dependent
345 birth-death model. It is a generalization of yule.time() taking
346 extinction into account.
348 o The new function MPR does most parsimonious reconstruction of
351 o The new function Ftab computes the contingency table of base
352 frequencies from a pair of sequences.
354 o There is now an 'as.list' method for the class "DNAbin".
356 o dist.dna() can compute the number of transitions or transversions
357 with the option model = "Ts" or model = "Tv", respectively.
359 o [node|tip|edge]labels() gain three options with default values to
360 control the aspect of thermometers: horiz = TRUE, width = NULL,
363 o compar.gee() has been improved with the new option 'corStruct' as an
364 alternative to 'phy' to specify the correlation structure, and
365 calculation of the QIC (Pan 2001, Biometrics). The display of the
366 results has also been improved.
368 o read.GenBank() has a new option 'gene.names' to return the name of
369 the gene (FALSE by default).
374 o extract.clade() sometimes shuffled the tip labels.
376 o plot.phylo(type = "unrooted") did not force asp = 1 (thanks to Klaus
379 o dist.dna(model = "logdet") used to divide distances by 4. The
380 documentation has been clarified on the formulae used.
385 o rTraitCont(model = "OU") has an option 'linear = TRUE' to possibly
386 change the parameterisation (see ?rTraitCont for details).
388 o pic() now returns a vector with the node labels of the tree (if
391 o write.tree() and read.tree() have been substantially improved thanks
392 to contributions by Klaus Schliep.
396 CHANGES IN APE VERSION 2.5-3
401 o The new function mixedFontLabel helps to make labels with bits of
402 text to be plotted in different fonts.
404 o There are now replacement operators for [, [[, and $ for the class
405 "multiPhylo" (i.e., TREES[11:20] <- rmtree(10, 100)). They possibly
406 check that the tip labels are the same in all trees.
408 o Objects of class "multiPhylo" can be built with c(): there are
409 methods for the classes "phylo" and "multiPhylo".
411 o The internal functions .compressTipLabel and .uncompressTipLabel are
417 o bind.tree(x, y, where, position = 0) did not work correctly if 'y'
418 was a single-edge tree and 'where' was a tip.
420 o rTraitCont() did not use the square-root of branch lengths when
421 simulating a Brownian motion model.
425 CHANGES IN APE VERSION 2.5-2
430 o There is now a print method for results from ace().
432 o There is a labels() method for objects of class "DNAbin".
434 o read.dna() has a new option 'as.matrix' to possibly force sequences
435 in a FASTA file to be stored in a matrix (see ?read.dna for details).
440 o as.phylo.hclust() used to multiply edge lengths by 2.
442 o A minor bug was fixed in rTraitDisc().
444 o ace() sometimes failed (parameter value was NaN and the optimisation
450 o evolve.phylo() and plot.ancestral() have been removed.
452 o chronogram(), ratogram(), and NPRS.criterion() have been removed.
457 o nj() has been improved and is now about 30% faster.
459 o The default option 'drop' of [.DNAbin has been changed to FALSE to
460 avoid dropping rownames when selecting a single sequence.
462 o print.DNAbin() has been changed to summary.DNAbin() which has been
467 CHANGES IN APE VERSION 2.5-1
472 o The new function stree generates trees with regular shapes.
474 o It is now possible to bind two trees with x + y (see ?bind.tree for
477 o drop.tip(), extract.clade(), root(), and bind.tree() now have an
478 'interactive' option to make the operation on a plotted tree.
480 o cophyloplot() gains two new arguments 'lwd' and 'lty' for the
481 association links; they are recycled like 'col' (which wasn't before).
486 o rTraitDisc() did not use its 'freq' argument correctly (it was
487 multiplied with the rate matrix column-wise instead of row-wise).
489 o [node|tip|edge]labels(thermo = ) used to draw empty thermometers
490 with NA values. Nothing is drawn now like with 'text' or 'pch'.
491 The same bug occurred with the 'pie' option.
493 o A bug was fixed in compar.ou() and the help page was clarified.
495 o bind.tree() has been rewritten fixing several bugs and making it
498 o plot.phylo(type = "p") sometimes failed to colour correctly the
499 vertical lines representing the nodes.
501 o plot.phylo(direction = "l", x.lim = 30) failed to plot the branches
502 in the correct direction though the tip labels were displayed
508 o The c, cbind, and rbind methods for "DNAbin" objetcs now check that
509 the sequences are correctly stored (in a list for c, in a matrix
510 for the two other functions).
514 CHANGES IN APE VERSION 2.5
519 o The new function parafit by Pierre Legendre tests for the
520 coevolution between hosts and parasites. It has a companion
521 function, pcoa, that does principal coordinate decomposition.
522 The latter has a biplot method.
524 o The new function lmorigin by Pierre Legendre performs multiple
525 regression through the origin with testing by permutation.
527 o The new functions rTraitCont and rTraitDisc simulate continuous and
528 discrete traits under a wide range of evolutionary models.
530 o The new function delta.plot does a delta plot following Holland et
531 al. (2002, Mol. Biol. Evol. 12:2051).
533 o The new function edges draws additional branches between any nodes
534 and/or tips on a plotted tree.
536 o The new function fancyarrows enhances arrows from graphics with
537 triangle and harpoon heads; it can be called from edges().
539 o add.scale.bar() has a new option 'ask' to draw interactively.
541 o The branch length score replaces the geodesic distance in dist.topo.
543 o Three new data sets are included: the gopher-lice data (gopher.D),
544 SO2 air pollution in 41 US cities (lmorigin.ex1, from Sokal &
545 Rohlf 1995), and some host-parasite specificity data
546 (lmorigin.ex2, from Legendre & Desdevises 2009).
551 o add.scale.bar() drew the bar outside the plotting region with the
552 default options with unrooted or radial trees.
554 o dist.topo() made R stuck when the trees had different sizes (thanks
555 to Otto Cordero for the fix).
560 o The geodesic distance has been replaced by the branch length score
565 CHANGES IN APE VERSION 2.4-1
570 o rtree() and rcoal() now accept a numeric vector for the 'br'
573 o vcv() is a new generic function with methods for the classes "phylo"
574 and "corPhyl" so that it is possible to calculate the var-cov matrix
575 for "transformation models". vcv.phylo() can still be used for trees
576 of class "phylo"; its argument 'cor' has been renamed 'corr'.
581 o bind.tree() failed when 'y' had no root edge.
583 o read.nexus() shuffled tip labels when the trees have no branch
584 lengths and there is a TRANSLATE block.
586 o read.nexus() does not try to translate node labels if there is a
587 translation table in the NEXUS file. See ?read.nexus for a
588 clarification on this behaviour.
590 o plot.multiPhylo() crashed R when plotting a list of trees with
591 compressed tip labels.
593 o write.nexus() did not translate the taxa names when asked for.
595 o plot.phylo(type = "fan") did not rotate the tip labels correctly
596 when the tree has branch lengths.
598 o ace(type = "continuous", method = "ML") now avoids sigma² being
599 negative (which resulted in an error).
601 o nj() crashed with NA/NaN in the distance matrix: an error in now
606 CHANGES IN APE VERSION 2.4
611 o base.freq() has a new option 'freq' to return the counts; the
612 default is still to return the proportions.
617 o seg.sites() did not handle ambiguous nucleotides correctly: they
620 o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
621 the tree: the argument is now ignored.
623 o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
629 o Trying to plot a tree with a single tip now returns NULL with a
630 warning (it returned an error previously).
632 o The way lines representing nodes are coloured in phylograms has
633 been modified (as well as their widths and types) following some
634 users' request; this is only for dichotomous nodes.
636 o The argument 'adj' in [node][tip][edge]labels() now works when
637 using 'pie' or 'thermo'.
639 o A more informative message error is now returned by dist.dna() when
640 'model' is badly specified (partial matching of this argument is
643 o Deprecated functions are now listed in a help page: see
644 help("ape-defunct") with the quotes.
649 o The functions heterozygosity, nuc.div, theta.h, theta.k and
650 theta.s have been moved from ape to pegas.
652 o The functions mlphylo, DNAmodel and sh.test have been removed.
656 CHANGES IN APE VERSION 2.3-3
661 o add.scale.bar() always drew a horizontal bar.
663 o zoom() shuffled tips with unrooted trees.
665 o write.nexus() failed to write correctly trees with a "TipLabel"
668 o rcoal() failed to compute branch lengths with very large n.
670 o A small bug was fixed in compar.cheverud() (thanks to Michael
673 o seg.sites() failed when passing a vector.
675 o drop.tip() sometimes shuffled tip labels.
677 o root() shuffled node labels with 'resolve.root = TRUE'.
681 CHANGES IN APE VERSION 2.3-2
686 o all.equal.phylo() did not compare unrooted trees correctly.
688 o dist.topo(... method = "PH85") did not treat unrooted trees
689 correctly (thanks to Tim Wallstrom for the fix).
691 o root() sometimes failed to test for the monophyly of the
694 o extract.clade() sometimes included too many edges.
696 o vcv.phylo() did not work correctly when the tree is in
699 o nj() did not handle correctly distance matrices with many 0's.
700 The code has also been significantly improved: 7, 70, 160 times
701 faster with n = 100, 500, 1000, respectively.
705 CHANGES IN APE VERSION 2.3-1
710 o The new function is.monophyletic tests the monophyly of a group.
712 o There is now a c() method for lists of class "DNAbin".
714 o yule.cov() now fits the null model, and its help page has been
715 corrected with respect to this change.
717 o drop.tip() has a new option 'rooted' to force (or not) a tree
718 to be treated as (un)rooted.
723 o dist.gene() failed on most occasions with the default
724 pairwise.deletion = FALSE.
726 o read.tree() failed to read correctly the tree name(s).
728 o boot.phylo() now treats correctly data frames.
730 o del.gaps() did not copy the rownames of a matrix.
732 o A small bug was fixed in CDAM.global().
734 o ace() failed with large data sets. Thanks to Rich FitzJohn for
735 the fix. With other improvements, this function is now about 6
738 o write.tree() failed with objects of class "multiPhylo".
740 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
745 o [.multiPhylo and [.DNAbin now respect the original class.
747 o Instances of the form class(phy) == "phylo" have been replaced
748 by inherits(phy, "phylo").
750 o rcoal() is now faster.
755 o klastorin() has been removed.
759 CHANGES IN APE VERSION 2.3
764 o The new functions CADM.global and CADM.post, contributed by
765 Pierre Legendre, test the congruence among several distance
768 o The new function yule.time fits a user-defined time-dependent
769 Yule model by maximum likelihood.
771 o The new function makeNodeLabel creates and/or modifies node
772 labels in a flexible way.
774 o read.tree() and write.tree() have been modified so that they can
775 handle individual tree names.
777 o plot.phylo() has a new argument 'edge.lty' that specifies the
778 types of lines used for the edges (plain, dotted, dashed, ...)
780 o phymltest() has been updated to work with PhyML 3.0.1.
785 o drop.tip() shuffled tip labels in some cases.
787 o drop.tip() did not handle node.label correctly.
789 o is.ultrametric() now checks the ordering of the edge matrix.
791 o ace() sometimes returned negative values of likelihoods of
792 ancestral states (thanks to Dan Rabosky for solving this long
798 o The data set xenarthra has been removed.
802 CHANGES IN APE VERSION 2.2-4
806 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
807 now fixed. (Thanks to Peter Wragg for the fix!)
809 o A warning message occurred for no reason with ace(method="GLS").
814 o There is now a general help page displayed with '?ape'.
818 CHANGES IN APE VERSION 2.2-3
823 o The new function extract.clade extracts a clade from a tree by
824 specifying a node number or label.
826 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
827 operations of the same names.
829 o dist.dna() can now return the number of site differences by
830 specifying model="N".
835 o chronopl() did not work with CV = TRUE.
837 o read.nexus() did not work correctly in some situations (trees on
838 multiple lines with different numbers of lines and/or with
839 comments inserted within the trees).
841 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
842 the number of lineages with non-binary trees.
847 o ape has now a namespace.
849 o drop.tip() has been improved: it should be much faster and work
850 better in some cases (e.g., see the example in ?zoom).
854 CHANGES IN APE VERSION 2.2-2
859 o dist.gene() has been substantially improved and gains an option
862 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
868 o prop.part() failed with a single tree with the default option
869 'check.labels = TRUE'.
871 o summary.DNAbin() failed to display correctly the summary of
872 sequence lengths with lists of sequences of 10,000 bases or more
873 (because summary.default uses 4 significant digits by default).
875 o read.nexus() failed to read a file with a single tree with line
876 breaks in the Newick string.
878 o del.gaps() returned a list of empty sequences when there were no
884 o phymltest() has been updated for PhyML 3.0 and gains an option
885 'append', whereas the option 'path2exec' has been removed.
887 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
888 which is returned unchanged (instead of an error).
890 o The data sets bird.orders and bird.families are now stored as
891 Newick strings; i.e., the command data(bird.orders) calls
896 CHANGES IN APE VERSION 2.2-1
901 o The new function makeLabel() helps to modify labels of trees,
902 lists of trees, or DNA sequences, with several utilities to
903 truncate and/or make them unique, substituting some
904 characters, and so on.
906 o The new function del.gaps() removes insertion gaps ("-") in a
907 set of DNA sequences.
909 o read.dna() can now read Clustal files (*.aln).
914 o root() failed with 'resolve.root = TRUE' when the root was
915 already the specified root.
917 o Several bugs were fixed in mlphylo().
919 o collapsed.singles() did not propagate the 'Nnode' and
920 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
922 o read.nexus() failed to remove correctly the comments within
925 o read.nexus() failed to read a file with a single tree and no
926 translation of tip labels.
928 o read.nexus() failed to place correctly tip labels when reading
929 a single tree with no edge lengths.
931 o A bug was fixed in sh.test().
936 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
939 o The option 'check.labels' of consensus() and prop.part() is now
942 o write.dna() now does not truncate names to 10 characters with
947 CHANGES IN APE VERSION 2.2
952 o Four new functions have been written by Damien de Vienne for the
953 graphical exploration of large trees (cophyloplot, subtrees,
954 subtreeplot), and to return the graphical coordinates of tree
957 o The new functions corPagel and corBlomberg implement the Pagel's
958 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
960 o chronopl() has been improved and gains several options: see its
961 help page for details.
963 o boot.phylo() has now an option 'trees' to possibly return the
964 bootstraped trees (the default is FALSE).
966 o prop.part() has been improved and should now be faster in all
972 o read.dna() failed if "?" occurred in the first 10 sites of the
975 o The x/y aspect of the plot is now respected when plotting a
976 circular tree (type = "r" or "f").
978 o Drawing the tip labels sometimes failed when plotting circular
981 o zoom() failed when tip labels were used instead of their numbers
982 (thanks to Yan Wong for the fix).
984 o drop.tip() failed with some trees (fixed by Yan Wong).
986 o seg.sites() failed with a list.
988 o consensus() failed in some cases. The function has been improved
989 as well and is faster.
993 CHANGES IN APE VERSION 2.1-3
998 o A bug in read.nexus() made the Windows R-GUI crash.
1000 o An error was fixed in the computation of ancestral character
1001 states by generalized least squares in ace().
1003 o di2multi() did not modify node labels correctly.
1005 o multi2di() failed if the tree had its attribute "order" set to
1010 CHANGES IN APE VERSION 2.1-2
1015 o There three new methods for the "multiPhylo" class: str, $,
1018 o root() gains the options 'node' and 'resolve.root'
1019 (FALSE by default) as well as its code being improved.
1021 o mltt.plot() has now an option 'log' used in the same way
1022 than in plot.default().
1027 o mltt.plot() failed to display the legend with an unnamed
1030 o nodelabels() with pies now correcly uses the argument
1031 'cex' to draw symbols of different sizes (which has
1032 worked already for thermometers).
1034 o read.nexus() generally failed to read very big files.
1039 o The argument 'family' of compar.gee() can now be a function
1040 as well as a character string.
1042 o read.tree() and read.nexus() now return an unnamed list if
1043 'tree.names = NULL'.
1045 o read.nexus() now returns a modified object of class "multiPhylo"
1046 when there is a TRANSLATE block in the NEXUS file: the individual
1047 trees have no 'tip.label' vector, but the list has a 'TipLabel'
1048 attribute. The new methods '$' and '[[' set these elements
1049 correctly when extracting trees.
1053 CHANGES IN APE VERSION 2.1-1
1058 o The new function rmtree generates lists of random trees.
1060 o rcoal() now generates a genuine coalescent tree by default
1061 (thanks to Vladimir Minin for the code).
1066 o nuc.div() returned an incorrect value with the default
1067 pairwise.deletion = FALSE.
1072 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
1073 have been improved so that they are stabler and faster.
1075 o R packages used by ape are now loaded silently; lattice and gee
1076 are loaded only when needed.
1080 CHANGES IN APE VERSION 2.1
1085 o The new function identify.phylo identifies clades on a plotted
1086 tree using the mouse.
1088 o It is now possible to subset a list of trees (object of class
1089 "multiPhylo") with "[" while keeping its class correct.
1091 o The new function as.DNAbin.alignment converts DNA sequences
1092 stored in the "alignment" format of the package seqinr into
1093 an object of class "DNAbin".
1095 o The new function weight.taxo2 helps to build similarity matrices
1096 given two taxonomic levels (usually called by other functions).
1098 o write.tree() can now take a list of trees (class "multiPhylo")
1099 as its main argument.
1101 o plot.correlogram() and plot.correlogramList() have been
1102 improved, and gain several options (see the help page for
1103 details). A legend is now plotted by default.
1108 o dist.dna() returned some incorrect values with `model = "JC69"'
1109 and `pairwise.deletion = TRUE'. This affected only the
1110 distances involving sequences with missing values. (Thanks
1111 to Bruno Toupance for digging this bug out.)
1113 o write.tree() failed with some trees: this is fixed by removing
1114 the `multi.line' option (trees are now always printed on a
1117 o read.nexus() did not correctly detect trees with multiple root
1118 edges (see OTHER CHANGES).
1123 o The code of mlphylo() has been almost entirely rewritten, and
1124 should be much stabler. The options have been also greatly
1125 simplified (see ?mlphylo and ?DNAmodel for details).
1127 o The internal function nTips has been renamed klastorin_nTips.
1129 o The code of is.ultrametric() contained redundancies and has
1132 o The code of Moran.I() and of correlogram.formula() have been
1135 o read.tree() and read.nexus() now return an error when trying to
1136 read a tree with multiple root edges (see BUG FIXES). The
1137 correction applied in previous version did not work in all
1140 o The class c("multi.tree", "phylo") has been renamed
1146 o There is now a vignette in ape: see vignette("MoranI", "ape").
1149 DEPRECATED & DEFUNCT
1151 o as.matching() and as.phylo.matching() do not support branch
1154 o correlogram.phylo() and discrete.dist() have been removed.
1158 CHANGES IN APE VERSION 2.0-2
1163 o The new function matexpo computes the exponential of a square
1166 o The new function unique.multi.tree removes duplicate trees from
1169 o yule() has a new option `use.root.edge = FALSE' that specifies
1170 to ignore, by default, the root edge of the tree if it exists.
1175 o which.edge() failed when the index of a single terminal edge was
1178 o In diversi.time(), the values returned for model C were
1181 o A bug was fixed in yule() that affected the calculation of the
1182 likelihood in the presence of ties in the branching times.
1184 o There was a bug in the C function mat_expo4x4 affecting the
1185 calculations of the transition probabilities for models HKY and
1188 o A small bug was fixed in as.matrix.DNAbin (thanks to James
1191 o rtree() did not `shuffle' the tip labels by default, so only a
1192 limited number of labelled topologies could be generated.
1196 CHANGES IN APE VERSION 2.0-1
1201 o The three new functions bionj, fastme.ols, and fastme.bal
1202 perform phylogeny estimation by the BIONJ and fastME methods in
1203 OLS and balanced versions. This is a port to R of previous
1204 previous programs done by Vincent Lefort.
1206 o The new function chronoMPL performs molecular dating with the
1207 mean path lengths method of Britton et al. (2002, Mol. Phyl.
1210 o The new function rotate, contributed by Christoph Heibl, swaps
1211 two clades connected to the same node. It works also with
1212 multichotomous nodes.
1214 o The new `method' as.matrix.DNAbin() may be used to convert
1215 easily DNA sequences stored in a list into a matrix while
1216 keeping the names and the class.
1221 o chronopl() failed when some branch lengths were equal to zero:
1222 an error message is now returned.
1224 o di2multi() failed when there was a series of consecutive edges
1229 CHANGES IN APE VERSION 1.10-2
1234 o plot.phylo() can now plot circular trees: the option is type =
1235 "fan" or type = "f" (to avoid the ambiguity with type = "c").
1237 o prop.part() has a new option `check.labels = FALSE' which allows
1238 to considerably speed-up the calculations of bipartitions. As a
1239 consequence, calculations of bootstrap values with boot.phylo()
1240 should be much faster.
1245 o read.GenBank() did not return correctly the list of species as
1246 from ape 1.10: this is fixed in this version
1248 o Applying as.phylo() on a tree of class "phylo" failed: the
1249 object is now returned unchanged.
1253 CHANGES IN APE VERSION 1.10-1
1258 o The three new functions Ntip, Nnode, and Nedge return, for a
1259 given tree, the number of tips, nodes, or edges, respectively.
1264 o read.nexus() did not set correctly the class of the returned
1265 object when reading multiple trees.
1267 o mllt.plot() failed with objects of class c("multi.tree",
1270 o unroot() did not work correctly in most cases.
1272 o reorder.phylo() made R freeze in some occasions.
1274 o Plotting a tree in pruningwise order failed.
1276 o When plotting an unrooted tree, the tip labels where not all
1277 correctly positioned if the option `cex' was used.
1281 CHANGES IN APE VERSION 1.10
1286 o Five new `method' functions have been introduced to manipulate
1287 DNA sequences in binary format (see below).
1289 o Three new functions have been introduced to convert between the
1290 new binary and the character formats.
1292 o The new function as.alignment converts DNA sequences stored as
1293 single characters into the class "alignment" used by the package
1296 o read.dna() and read.GenBank() have a new argument `as.character'
1297 controlling whether the sequences are returned in binary format
1303 o root() failed when the tree had node labels: this is fixed.
1305 o plot.phylo() did not correctly set the limits on the y-axis with
1306 the default setting: this is fixed.
1308 o dist.dna() returned a wrong result for the LogDet, paralinear,
1309 and BH87 models with `pairwise.deletion = TRUE'.
1314 o DNA sequences are now internally stored in a binary format. See
1315 the document "A Bit-Level Coding Scheme for Nucleotides" for the
1316 details. Most functions analyzing DNA functions have been
1317 modified accordingly and are now much faster (dist.dna is now
1318 ca. 60 times faster).
1322 CHANGES IN APE VERSION 1.9-4
1327 o A bug was fixed in edgelabels().
1329 o as.phylo.hclust() did not work correctly when the object of
1330 class "hclust" has its labels set to NULL: the returned tree has
1331 now its tip labels set to "1", "2", ...
1333 o consensus could fail if some tip labels are a subset of others
1334 (e.g., "a" and "a_1"): this is now fixed.
1336 o mlphylo() failed in most cases if some branch lengths of the
1337 initial tree were greater than one: an error message is now
1340 o mlphylo() failed in most cases when estimating the proportion of
1341 invariants: this is fixed.
1345 CHANGES IN APE VERSION 1.9-3
1350 o The new function edgelabels adds labels on the edge of the tree
1351 in the same way than nodelabels or tiplabels.
1356 o multi2di() did not handle correctly branch lengths with the
1357 default option `random = TRUE': this is now fixed.
1359 o A bug was fixed in nuc.div() when using pairwise deletions.
1361 o A bug occurred in the analysis of bipartitions with large
1362 numbers of large trees, with consequences on prop.part,
1363 prop.clades, and boot.phylo.
1365 o The calculation of the Billera-Holmes-Vogtmann distance in
1366 dist.topo was wrong: this has been fixed.
1370 CHANGES IN APE VERSION 1.9-2
1375 o The new function ladderize reorganizes the internal structure of
1376 a tree to plot them left- or right-ladderized.
1378 o The new function dist.nodes computes the patristic distances
1379 between all nodes, internal and terminal, of a tree. It replaces
1380 the option `full = TRUE' of cophenetic.phylo (see below).
1385 o A bug was fixed in old2new.phylo().
1387 o Some bugs were fixed in chronopl().
1389 o The edge colours were not correctly displayed by plot.phylo
1390 (thank you to Li-San Wang for the fix).
1392 o cophenetic.phylo() failed with multichotomous trees: this is
1398 o read.dna() now returns the sequences in a matrix if they are
1399 aligned (interleaved or sequential format). Sequences in FASTA
1400 format are still returned in a list.
1402 o The option `full' of cophenetic.phylo() has been removed because
1403 it could not be used from the generic.
1406 DEPRECATED & DEFUNCT
1408 o rotate() has been removed; this function did not work correctly
1413 CHANGES IN APE VERSION 1.9-1
1418 o Trees with a single tip were not read correctly in R as the
1419 element `Nnode' was not set: this is fixed.
1421 o unroot() did not set correctly the number of nodes of the
1422 unrooted tree in most cases.
1424 o read.GenBank() failed when fetching very long sequences,
1425 particularly of the BX-series.
1427 o A bug was introduced in read.tree() with ape 1.9: it has been
1432 CHANGES IN APE VERSION 1.9
1437 o There are two new print `methods' for trees of class "phylo" and
1438 lists of trees of class "multi.tree", so that they are now
1439 displayed in a compact and informative way.
1441 o There are two new functions, old2new.phylo and new2old.phylo,
1442 for converting between the old and new coding of the class
1445 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
1446 LogDet ("logdet"), and paralinear ("paralin").
1448 o compute.brlen() has been extended: several methods are now
1449 available to compute branch lengths.
1451 o write.dna() can now handle matrices as well as lists.
1456 o cophenetic.phylo() sometimes returned a wrong result with
1457 multichotomous trees: this is fixed.
1459 o rotate() failed when a single tip was specified: the tree is now
1462 o ace() did not return the correct index matrix with custom
1463 models: this is fixed.
1465 o multi2di() did not work correctly when resolving multichotomies
1466 randomly: the topology was always the same, only the arrangement
1467 of clades was randomized: this is fixed. This function now
1468 accepts trees with no branch lengths.
1470 o The output of diversi.gof() was blurred by useless prints when a
1471 user distribution was specified. This has been corrected, and
1472 the help page of this function has been expanded.
1477 o The internal structure of the class "phylo" has been changed:
1478 see the document "Definition of Formats for Coding Phylogenetic
1479 Trees in R" for the details. In addition, the code of most
1480 functions has been improved.
1482 o Several functions have been improved by replacing some R codes
1483 by C codes: pic, plot.phylo, and reorder.phylo.
1485 o There is now a citation information: see citation("ape") in R.
1487 o write.tree() now does not add extra 0's to branch lengths so
1488 that 1.23 is printed "1.23" by default, not "1.2300000000".
1490 o The syntax of bind.tree() has been simplified. This function now
1491 accepts trees with no branch lengths, and handles correctly node
1494 o The option `as.numeric' of mrca() has been removed.
1496 o The unused options `format' and `rooted' of read.tree() have
1499 o The unused option `format' of write.tree() has been removed.
1501 o The use of node.depth() has been simplified.
1505 CHANGES IN APE VERSION 1.8-5
1510 o Two new functions read.nexus.data() and write.nexus.data(),
1511 contributed by Johan Nylander, allow to read and write molecular
1512 sequences in NEXUS files.
1514 o The new function reorder.phylo() reorders the internal structure
1515 of a tree of class "phylo". It is used as the generic, e.g.,
1518 o read.tree() and read.nexus() can now read trees with a single
1521 o The new data set `cynipids' supplies a set of protein sequences
1527 o The code of all.equal.phylo() has been completely rewritten
1528 (thanks to Benoît Durand) which fixes several bugs.
1530 o read.tree() and read.nexus() now checks the labels of the tree
1531 to remove or substitute any characters that are illegal in the
1532 Newick format (parentheses, etc.)
1534 o A negative P-value could be returned by mantel.test(): this is
1539 CHANGES IN APE VERSION 1.8-4
1544 o The new function sh.test() computes the Shimodaira-
1547 o The new function collapse.singles() removes the nodes with a
1548 single descendant from a tree.
1550 o plot.phylo() has a new argument `tip.color' to specify the
1551 colours of the tips.
1553 o mlphylo() has now an option `quiet' to control the display of
1554 the progress of the analysis (the default is FALSE).
1559 o read.dna() did not read correctly sequences in sequential format
1560 with leading alignment gaps "-": this is fixed.
1562 o ace() returned a list with no class so that the generic
1563 functions (anova, logLik, ...) could not be used directly. This
1564 is fixed as ace() now returns an object of class "ace".
1566 o anova.ace() had a small bug when computing the number of degrees
1567 of freedom: this is fixed.
1569 o mlphylo() did not work when the sequences were in a matrix or
1570 a data frame: this is fixed.
1572 o rtree() did not work correctly when trying to simulate an
1573 unrooted tree with two tips: an error message is now issued.
1578 o The algorithm of rtree() has been changed: it is now about 40,
1579 100, and 130 times faster for 10, 100, and 1000 tips,
1584 CHANGES IN APE VERSION 1.8-3
1589 o There are four new `method' functions to be used with the
1590 results of ace(): logLik(), deviance(), AIC(), and anova().
1592 o The plot method of phymltest has two new arguments: `main' to
1593 change the title, and `col' to control the colour of the
1594 segments showing the AIC values.
1596 o ace() has a new argument `ip' that gives the initial values used
1597 in the ML estimation with discrete characters (see the examples
1598 in ?ace). This function now returns a matrix giving the indices
1599 of the estimated rates when analysing discrete characters.
1601 o nodelabels() and tiplabels() have a new argument `pie' to
1602 represent proportions, with any number of categories, as
1603 piecharts. The use of the option `thermo' has been improved:
1604 there is now no limitation on the number of categories.
1609 o mlphylo() did not work with more than two partitions: this is
1612 o root() failed if the proposed outgroup was already an outgroup
1613 in the tree: this is fixed.
1615 o The `col' argument in nodelabels() and tiplabels() was not
1616 correctly passed when `text' was used: this is fixed.
1618 o Two bugs were fixed in mlphylo(): parameters were not always
1619 correctly output, and the estimation failed in some cases.
1621 o plot.phylo() was stuck when given a tree with a single tip: this
1622 is fixed and a message error is now returned.
1624 o An error was corrected in the help page of gammaStat regarding
1625 the calculation of P-values.
1627 o Using gls() could crash R when the number of species in the tree
1628 and in the variables were different: this is fixed.
1632 CHANGES IN APE VERSION 1.8-2
1637 o The new function mlphylo() fits a phylogenetic tree by maximum
1638 likelihood from DNA sequences. Its companion function DNAmodel()
1639 is used to define the substitution model which may include
1640 partitioning. There are methods for logLik(), deviance(), and
1641 AIC(), and the summary() method has been extended to display in
1642 a friendly way the results of this model fitting. Currently, the
1643 functionality is limited to estimating the substitution and
1644 associated parameters and computing the likelihood.
1646 o The new function drop1.compar.gee (used as, e.g., drop1(m))
1647 tests for single effects in GEE-based comparative method. A
1648 warning message is printed if there is not enough degrees of
1654 o An error message was sometimes issued by plot.multi.tree(),
1655 though with no consequence.
1659 CHANGES IN APE VERSION 1.8-1
1664 o There is a new plot method for lists of trees (objects of class
1665 "multi.tree"): it calls plot.phylo() internally and is
1666 documented on the same help page.
1671 o A bug was fixed in the C code that analyzes bipartitions: this
1672 has impact on several functions like prop.part, prop.clades,
1673 boot.phylo, or consensus.
1675 o root() did not work correctly when the specified outgroup had
1676 more than one element: this is fixed.
1678 o dist.dna() sometimes returned a warning inappropriately: this
1681 o If the distance object given to nj() had no rownames, nj()
1682 returned a tree with no tip labels: it now returns tips labelled
1683 "1", "2", ..., corresponding to the row numbers.
1688 o nj() has been slightly changed so that tips with a zero distance
1689 are first aggregated with zero-lengthed branches; the usual NJ
1690 procedure is then performed on a distance matrix without 0's.
1694 CHANGES IN APE VERSION 1.8
1699 o The new function chronopl() estimates dates using the penalized
1700 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1702 o The new function consensus() calculates the consensus tree of a
1705 o The new function evolve.phylo() simulates the evolution of
1706 continuous characters along a phylogeny under a Brownian model.
1708 o The new plot method for objects of class "ancestral" displays a
1709 tree together with ancestral values, as returned by the above
1712 o The new function as.phylo.formula() returns a phylogeny from a
1713 set of nested taxonomic variables given as a formula.
1715 o The new function read.caic() reads trees in CAIC format.
1717 o The new function tiplabels() allows to add labels to the tips
1718 of a tree using text or plotting symbols in a flexible way.
1720 o The new function unroot() unroots a phylogeny.
1722 o multi2di() has a new option, `random', which specifies whether
1723 to resolve the multichotomies randomly (the default) or not.
1725 o prop.part() now returns an object of class "prop.part" for which
1726 there are print (to display a partition in a more friendly way)
1727 and summary (to extract the numbers) methods.
1729 o plot.phylo() has a new option, `show.tip.label', specifying
1730 whether to print the labels of the tips. The default is TRUE.
1732 o The code of nj() has been replaced by a faster C code: it is now
1733 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1736 o write.nexus() now writes whether a tree is rooted or not.
1741 o Two bugs have been fixed in root(): unrooted trees are now
1742 handled corretly, and node labels are now output normally.
1744 o A bug was fixed in phymltest(): the executable couldn't be found
1747 o Three bug have been fixed in ace(): computing the likelihood of
1748 ancestral states of discrete characters failed, custom models
1749 did not work, and the function failed with a null gradient (a
1750 warning message is now returned; this latter bug was also
1751 present in yule.cov() as well and is now fixed).
1753 o pic() hanged out when missing data were present: a message error
1756 o A small bug was fixed in dist.dna() where the gamma correction
1757 was not always correctly dispatched.
1759 o plot.phylo() plotted correctly the root edge only when the tree
1760 was plotted rightwards: this works now for all directions.
1765 o dist.taxo() has been renamed as weight.taxo().
1767 o dist.phylo() has been replaced by the method cophenetic.phylo().
1769 o Various error and warning messages have been improved.
1773 CHANGES IN APE VERSION 1.7
1776 o The new function ace() estimates ancestral character states for
1777 continuous characters (with ML, GLS, and contrasts methods), and
1778 discrete characters (with ML only) for any number of states.
1780 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1781 of directional evolution for continuous characters. The user
1782 specifies the node(s) of the tree where the character optimum
1785 o The new function is.rooted() tests whether a tree (of class
1788 o The new function rcoal() generates random ultrametric trees with
1789 the possibility to specify the function that generates the
1790 inter-nodes distances.
1792 o The new function mrca() gives for all pairs of tips in a tree
1793 (and optionally nodes too) the most recent common ancestor.
1795 o nodelabels() has a new option `thermo' to plot proportions (up
1796 to three classes) on the nodes of a tree.
1798 o rtree() has been improved: it can now generate rooted or
1799 unrooted trees, and the mathematical function that generates the
1800 branch lengths may be specified by the user. The tip labels may
1801 be given directly in the call to rtree. The limit cases (n = 2,
1802 3) are now handled correctly.
1804 o dist.topo() has a new argument `method' with two choices: "PH85"
1805 for Penny and Henny's method (already available before and now
1806 the default), and "BHV01" for the geometric distance by Billera
1807 et al. (2001, Adv. Appl. Math. 27:733).
1809 o write.tree() has a new option, `digits', which specifies the
1810 number of digits to be printed in the Newick tree. By default
1811 digits = 10. The numbers are now always printed in decimal form
1812 (i.e., 1.0e-1 is now avoided).
1814 o dist.dna() can now compute the raw distances between pairs of
1815 DNA sequences by specifying model = "raw".
1817 o dist.phylo() has a new option `full' to possibly compute the
1818 distances among all tips and nodes of the tree. The default if
1824 o Several bugs were fixed in all.equal.phylo().
1826 o dist.dna() did not handle correctly gaps ("-") in alignments:
1827 they are now considered as missing data.
1829 o rotate() did not work if the tips were not ordered: this is
1832 o mantel.test() returned NA in some special cases: this is fixed
1833 and the function has been improved and is now faster.
1835 o A bug was fixed in diversi.gof() where the calculation of A² was
1838 o cherry() did not work correctly under some OSs (mainly Linux):
1841 o is.binary.tree() has been modified so that it works with both
1842 rooted and unrooted trees.
1844 o The documentation of theta.s() was not correct: this has been
1847 o plot.mst() did not work correctly: this is fixed.
1851 CHANGES IN APE VERSION 1.6
1856 o The new function dist.topo() computes the topological distances
1859 o The new function boot.phylo() performs a bootstrap analysis on
1860 phylogeny estimation.
1862 o The new functions prop.part() and prop.clades() analyse
1863 bipartitions from a series of trees.
1868 o read.GenBank() now uses the EFetch utility of NCBI instead of
1869 the usual Web interface: it is now much faster (e.g., 12 times
1870 faster to retrieve 8 sequences, 37 times for 60 sequences).
1875 o Several bugs were fixed in read.dna().
1877 o Several bugs were fixed in diversi.time().
1879 o is.binary.tree() did not work correctly if the tree has no edge
1880 lengths: this is fixed.
1882 o drop.tip() did not correctly propagated the `node.label' of a
1883 tree: this is fixed.
1887 CHANGES IN APE VERSION 1.5
1892 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1893 convert objects between the classes "phylo" and "matching". The
1894 latter implements the representation of binary trees introduced by
1895 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1896 as.matching() has been introduced as well.
1898 o Two new functions, multi2di() and di2multi(), allow to resolve
1899 and collapse multichotomies with branches of length zero.
1901 o The new function nuc.div() computes the nucleotide diversity
1902 from a sample a DNA sequences.
1904 o dist.dna() has been completely rewritten with a much faster
1905 (particularly for large data sets) C code. Eight models are
1906 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1907 option `method' has been renamed `model'). Computation of variance
1908 is available for all models. A gamma-correction is possible for
1909 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1910 to remove sites with missing data on a pairwise basis. The option
1911 `GCcontent' has been removed.
1913 o read.GenBank() has a new option (species.names) which specifies
1914 whether to return the species names of the organisms in addition
1915 to the accession numbers of the sequences (this is the default
1918 o write.nexus() can now write several trees in the same NEXUS file.
1920 o drop.tip() has a new option `root.edge' that allows to specify the
1921 new root edge if internal branches are trimmed.
1926 o as.phylo.hclust() failed if some labels had parentheses: this
1929 o Several bugs were fixed in all.equal.phylo(). This function now
1930 returns the logical TRUE if the trees are identical but with
1931 different representations (a report was printed previously).
1933 o read.GenBank() did not correctly handle ambiguous base codes:
1939 o birthdeath() now returns an object of class "birthdeath" for
1940 which there is a print method.
1944 CHANGES IN APE VERSION 1.4
1949 o The new function nj() performs phylogeny estimation with the
1950 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1953 o The new function which.edge() identifies the edges of a tree
1954 that belong to a group specified as a set of tips.
1956 o The new function as.phylo.phylog() converts an object of class
1957 "phylog" (from the package ade4) into an object of class
1960 o The new function axisPhylo() draws axes on the side of a
1963 o The new function howmanytrees() calculates the number of trees
1964 in different cases and giving a number of tips.
1966 o write.tree() has a new option `multi.line' (TRUE by default) to
1967 write a Newick tree on several lines rather than on a single
1970 o The functionalities of zoom() have been extended. Several
1971 subtrees can be visualized at the same time, and they are marked
1972 on the main tree with colors. The context of the subtrees can be
1973 marked with the option `subtree' (see below).
1975 o drop.tip() has a new option `subtree' (FALSE by default) which
1976 specifies whether to output in the tree how many tips have been
1979 o The arguments of add.scale.bar() have been redefined and have
1980 now default values (see ?add.scale.bar for details). This
1981 function now works even if the plotted tree has no edge length.
1983 o plot.phylo() can now plot radial trees, but this does not take
1984 edge lengths into account.
1986 o In plot.phylo() with `type = "phylogram"', if the values of
1987 `edge.color' and `edge.width' are identical for sister-branches,
1988 they are propagated to the vertical line that link them.
1993 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1994 crashing. This is fixed.
1996 o In plot.phylo(), the options `edge.color' and `edge.width' are
1997 now properly recycled; their default values are now "black" and
2000 o A bug has been fixed in write.nexus().
2005 o The function node.depth.edgelength() has been removed and
2006 replaced by a C code.
2010 CHANGES IN APE VERSION 1.3-1
2015 o The new function nodelabels() allows to add labels to the nodes
2016 of a tree using text or plotting symbols in a flexible way.
2018 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
2019 numeric values specifying the lower and upper limits on the x-
2020 and y-axes. This allows to leave some space on any side of the
2021 tree. If a single value is given, this is taken as the upper
2026 CHANGES IN APE VERSION 1.3
2031 o The new function phymltest() calls the software PHYML and fits
2032 28 models of DNA sequence evolution. There are a print method to
2033 display likelihood and AIC values, a summary method to compute
2034 the hierarchical likelihood ratio tests, and a plot method to
2035 display graphically the AIC values of each model.
2037 o The new function yule.cov() fits the Yule model with covariates,
2038 a model where the speciation rate is affected by several species
2039 traits through a generalized linear model. The parameters are
2040 estimated by maximum likelihood.
2042 o Three new functions, corBrownian(), corGrafen(), and
2043 corMartins(), compute the expected correlation structures among
2044 species given a phylogeny under different models of evolution.
2045 These can be used for GLS comparative phylogenetic methods (see
2046 the examples). There are coef() and corMatrix() methods and an
2047 Initialize.corPhyl() function associated.
2049 o The new function compar.cheverud() implements Cheverud et al.'s
2050 (1985; Evolution 39:1335) phylogenetic comparative method.
2052 o The new function varcomp() estimates variance components; it has
2055 o Two new functions, panel.superpose.correlogram() and
2056 plot.correlogramList(), allow to plot several phylogenetic
2059 o The new function node.leafnumber() computes the number of leaves
2060 of a subtree defined by a particular node.
2062 o The new function node.sons() gets all tags of son nodes from a
2065 o The new function compute.brlen() computes the branch lengths of
2066 a tree according to a specified method.
2068 o plot.phylo() has three new options: "cex" controls the size of
2069 the (tip and node) labels (thus it is no more needed to change
2070 the global graphical parameter), "direction" which allows to
2071 plot the tree rightwards, leftwards, upwards, or downwards, and
2072 "y.lim" which sets the upper limit on the y-axis.
2077 o Some functions which try to match tip labels and names of
2078 additional data (e.g. vector) are likely to fail if there are
2079 typing or syntax errors. If both series of names do not perfectly
2080 match, they are ignored and a warning message is now issued.
2081 These functions are bd.ext, compar.gee, pic. Their help pages
2082 have been clarified on this point.
2086 CHANGES IN APE VERSION 1.2-7
2091 o The new function root() reroots a phylogenetic tree with respect
2092 to a specified outgroup.
2094 o The new function rotate() rotates an internal branch of a tree.
2096 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
2097 trees) controls the display of the tip labels in unrooted trees.
2098 This display has been greatly improved: the tip labels are now not
2099 expected to overlap with the tree (particularly if lab4ut =
2100 "axial"). In all cases, combining appropriate values of "lab4ut"
2101 and the font size (via "par(cex = )") should result in readable
2102 unrooted trees. See ?plot.phylo for some examples.
2104 o In drop.tip(), the argument `tip' can now be numeric or character.
2109 o drop.tip() did not work correctly with trees with no branch
2110 lengths: this is fixed.
2112 o A bug in plot.phylo(..., type = "unrooted") made some trees being
2113 plotted with some line crossings: this is now fixed.
2117 CHANGES IN APE VERSION 1.2-6
2122 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
2123 correlogram.phylo, dist.taxo, plot.correlogram) have been added
2124 to implement comparative methods with an autocorrelation approach.
2126 o A new data set describing some life history traits of Carnivores
2132 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
2137 o When plotting a tree with plot.phylo(), the new default of the
2138 option `label.offset' is now 0, so the labels are always visible.
2142 CHANGES IN APE VERSION 1.2-5
2147 o The new function bd.ext() fits a birth-death model with combined
2148 phylogenetic and taxonomic data, and estimates the corresponding
2149 speciation and extinction rates.
2154 o The package gee is no more required by ape but only suggested
2155 since only the function compar.gee() calls gee.
2159 CHANGES IN APE VERSION 1.2-4
2164 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
2165 and lines.popsize) implementing a new approach for inferring the
2166 demographic history from genealogies using a reversible jump
2167 MCMC have been introduced.
2169 o The unit of time in the skyline plot and in the new plots can
2170 now be chosen to be actual years, rather than substitutions.
2174 CHANGES IN APE VERSION 1.2-3
2179 o The new function rtree() generates a random binary tree with or
2180 without branch lengths.
2182 o Two new functions for drawing lineages-through-time (LTT) plots
2183 are provided: ltt.lines() adds a LTT curve to an existing plot,
2184 and mltt.plot() does a multiple LTT plot giving several trees as
2185 arguments (see `?ltt.plot' for details).
2190 o Some taxon names made R crashing when calling as.phylo.hclust():
2193 o dist.dna() returned an error with two identical DNA sequences
2194 (only using the Jukes-Cantor method returned 0): this is fixed.
2199 o The function dist.phylo() has been re-written using a different
2200 algorithm: it is now about four times faster.
2202 o The code of branching.times() has been improved: it is now about
2207 CHANGES IN APE VERSION 1.2-2
2212 o The new function seg.sites() finds the segregating sites in a
2213 sample of DNA sequences.
2218 o A bug introduced in read.tree() and in read.nexus() with version
2221 o A few errors were corrected and a few examples were added in the
2226 CHANGES IN APE VERSION 1.2-1
2231 o plot.phylo() can now draw the edge of the root of a tree if it
2232 has one (see the new option `root.edge', its default is FALSE).
2237 o A bug was fixed in read.nexus(): files with semicolons inside
2238 comment blocks were not read correctly.
2240 o The behaviour of read.tree() and read.nexus() was corrected so
2241 that tree files with badly represented root edges (e.g., with
2242 an extra pair of parentheses, see the help pages for details)
2243 are now correctly represented in the object of class "phylo";
2244 a warning message is now issued.
2248 CHANGES IN APE VERSION 1.2
2253 o plot.phylo() has been completely re-written and offers several
2254 new functionalities. Three types of trees can now be drawn:
2255 phylogram (as previously), cladogram, and unrooted tree; in
2256 all three types the branch lengths can be drawn using the edge
2257 lengths of the phylogeny or not (e.g., if the latter is absent).
2258 The vertical position of the nodes can be adjusted with two
2259 choices (see option `node.pos'). The code has been re-structured,
2260 and two new functions (potentially useful for developpers) are
2261 documented separately: node.depth.edgelength() and node.depth();
2262 see the respective help pages for details.
2264 o The new function zoom() allows to explore very large trees by
2265 focusing on a small portion of it.
2267 o The new function yule() fits by maximum likelihood the Yule model
2268 (birth-only process) to a phylogenetic tree.
2270 o Support for writing DNA sequences in FASTA format has been
2271 introduced in write.dna() (support for reading sequences in
2272 this format was introduced in read.dna() in version 1.1-2).
2273 The function has been completely re-written, fixing some bugs
2274 (see below); the default behaviour is no more to display the
2275 sequences on the standard output. Several options have been
2276 introduced to control the sequence printing in a flexible
2277 way. The help page has been extended.
2279 o A new data set is included: a supertree of bats in NEXUS format.
2284 o In theta.s(), the default of the option `variance' has
2285 been changed to `FALSE' (as was indicated in the help page).
2287 o Several bugs were fixed in the code of all.equal.phylo().
2289 o Several bugs were fixed in write.dna(), particularly this
2290 function did not work with `format = "interleaved"'.
2292 o Various errors were corrected in the help pages.
2297 o The argument names of as.hclust.phylo() have been changed
2298 from "(phy)" to "(x, ...)" to conform to the definition of
2299 the corresponding generic function.
2301 o gamma.stat() has been renamed gammaStat() to avoid confusion
2302 since gamma() is a generic function.
2306 CHANGES IN APE VERSION 1.1-3
2311 o base.freq() previously did not return a value of 0 for
2312 bases absent in the data (e.g., a vector of length 3 was
2313 returned if one base was absent). This is now fixed (a
2314 vector of length 4 is always returned).
2316 o Several bugs were fixed in read.nexus(), including that this
2317 function did not work in this absence of a "TRANSLATE"
2318 command in the NEXUS file, and that the commands were
2323 CHANGES IN APE VERSION 1.1-2
2328 o The Tamura and Nei (1993) model of DNA distance is now implemented
2329 in dist.dna(): five models are now available in this function.
2331 o A new data set is included: a set of 15 sequences of the
2332 cytochrome b mitochondrial gene of the woodmouse (Apodemus
2338 o A bug in read.nexus() was fixed.
2340 o read.dna() previously did not work correctly in most cases.
2341 The function has been completely re-written and its help page
2342 has been considerably extended (see ?read.dna for details).
2343 Underscores (_) in taxon names are no more replaced with
2344 spaces (this behaviour was undocumented).
2346 o A bug was fixed in write.dna().
2350 CHANGES IN APE VERSION 1.1-1
2355 o A bug in read.tree() introduced in APE 1.1 was fixed.
2357 o A bug in compar.gee() resulted in an error when trying to fit
2358 a model with `family = "binomial"'. This is now fixed.
2362 CHANGES IN APE VERSION 1.1
2367 o The Klastorin (1982) method as suggested by Misawa and Tajima
2368 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
2369 on the basis of phylogenetic trees has been implemented (see
2370 the function klastorin()).
2372 o Functions have been added to convert APE's "phylo" objects in
2373 "hclust" cluster objects and vice versa (see the help page of
2374 as.phylo for details).
2376 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
2377 are introduced for the estimation of absolute evolutionary rates
2378 (ratogram) and dated clock-like trees (chronogram) from
2379 phylogenetic trees using the non-parametric rate smoothing approach
2380 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
2382 o A summary method is now provided printing a summary information on a
2383 phylogenetic tree with, for instance, `summary(tree)'.
2385 o The behaviour of read.tree() was changed so that all spaces and
2386 tabulations in tree files are now ignored. Consequently, spaces in tip
2387 labels are no more allowed. Another side effect is that read.nexus()
2388 now does not replace the underscores (_) in tip labels with spaces
2389 (this behaviour was undocumented).
2391 o The function plot.phylo() has a new option (`underscore') which
2392 specifies whether the underscores in tip labels should be written on
2393 the plot as such or replaced with spaces (the default).
2395 o The function birthdeath() now computes 95% confidence intervals of
2396 the estimated parameters using profile likelihood.
2398 o Three new data sets are included: a gene tree estimated from 36
2399 landplant rbcL sequences, a gene tree estimated from 32 opsin
2400 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
2405 o A bug was fixed in dist.gene() where nothing was returned.
2407 o A bug in plot.mst() was fixed.
2409 o A bug in vcv.phylo() resulted in false correlations when the
2410 option `cor = TRUE' was used (now fixed).
2414 CHANGES IN APE VERSION 1.0
2419 o Two new functions, read.dna() and write.dna(), read/write in a file
2420 DNA sequences in interleaved or in sequential format.
2422 o Two new functions, read.nexus() and write.nexus(), read/write trees
2425 o The new function bind.tree() allows to bind two trees together,
2426 possibly handling root edges to give internal branches.
2428 o The new function drop.tip() removes the tips in a phylogenetic tree,
2429 and trims (or not) the corresponding internal branches.
2431 o The new function is.ultrametric() tests if a tree is ultrametric.
2433 o The function plot.phylo() has more functionalities such as drawing the
2434 branches with different colours and/or different widths, showing the
2435 node labels, controling the position and font of the labels, rotating
2436 the labels, and controling the space around the plot.
2438 o The function read.tree() can now read trees with no branch length,
2439 such as "(a,b),c);". Consequently, the element `edge.length' in
2440 objects of class "phylo" is now optional.
2442 o The function write.tree() has a new default behaviour: if the default
2443 for the option `file' is used (i.e. file = ""), then a variable of
2444 mode character containing the tree in Newick format is returned which
2445 can thus be assigned (e.g., tree <- write.tree(phy)).
2447 o The function read.tree() has a new argument `text' which allows
2448 to read the tree in a variable of mode character.
2450 o A new data set is included: the phylogenetic relationships among
2451 the orders of birds from Sibley and Ahlquist (1990).
2455 CHANGES IN APE VERSION 0.2-1
2460 o Several bugs were fixed in the help pages.
2464 CHANGES IN APE VERSION 0.2
2469 o The function write.tree() writes phylogenetic trees (objects of class
2470 "phylo") in an ASCII file using the Newick parenthetic format.
2472 o The function birthdeath() fits a birth-death model to branching times
2473 by maximum likelihood, and estimates the corresponding speciation and
2476 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
2479 o The function is.binary.tree() tests whether a phylogeny is binary.
2481 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
2482 as well as some methods are introduced.
2484 o Several functions, including some generics and methods, for computing
2485 skyline plot estimates (classic and generalized) of effective
2486 population size through time are introduced and replace the function
2487 skyline.plot() in version 0.1.
2489 o Two data sets are now included: the phylogenetic relationships among
2490 the families of birds from Sibley and Ahlquist (1990), and an
2491 estimated clock-like phylogeny of HIV sequences sampled in the
2492 Democratic Republic of Congo.
2495 DEPRECATED & DEFUNCT
2497 o The function skyline.plot() in ape 0.1 has been deprecated and
2498 replaced by more elaborate functions (see above).
2503 o Two important bugs were fixed in plot.phylo(): phylogenies with
2504 multichotomies not at the root or not with only terminal branches,
2505 and phylogenies with a single node (i.e. only terminal branches)
2506 did not plot. These trees should be plotted correctly now.
2508 o Several bugs were fixed in diversi.time() in the computation of
2511 o Various errors were corrected in the help pages.