1 CHANGES IN APE VERSION 3.0-2
6 o The new function alex (alignment explorator) zooms in a DNA
7 alignment and opens the result in a new window.
12 o compute.brtime() did not completely randomized the order of the
15 o write.nexus() did not work correctly with rooted trees (thanks
16 to Matt Johnson for the fix).
18 o mltt.plot(, backward = FALSE) did not set the x-axis correctly.
20 o A bug was introduced in prop.clades() with ape 3.0.
22 o mantel.test() printed a useless warning message.
24 o plot.phylo(, direction = "downward") ignored 'y.lim'.
26 o is.monophyletic() did not work correctly if 'tips' was not stored
31 CHANGES IN APE VERSION 3.0-1
36 o dist.dna() has two new models: "indel" and "indelblock".
38 o bind.tree() now accepts 'position' > 0 when the trees have no
39 banch length permitting to create a node in 'x' when grafting
40 'y' (see ?bind.tree for details).
45 o cophyloplot( , rotate = TRUE) made R hanged after a few clicks.
46 Also the tree is no more plotted twice.
48 o read.GenBank() has been updated to work with EFetch 2.0.
50 o unroot() on trees in "pruningwise" order did not respect this
55 CHANGES IN APE VERSION 3.0
60 o The three functions dyule, dbd, and dbdTime calculate the
61 density probability (i.e., the distribution of the number of
62 species) for the Yule, the constant and the time-dependent
63 birth-beath models, respectively. These probabilities can be
64 conditional on no extinction and/or on a log-scale.
66 o plot.phylo() has a new option 'rotate.tree' to rotate unrooted,
67 fan, or radial trees around the center of the plot.
69 o boot.phylo() and prop.clades() have a new option rooted =
70 FALSE. Note that the behaviour of prop.part() is unchanged.
72 o edgelabels() has a new option 'date' to place labels on edges of
73 chronograms using the time scale (suggestion by Rob Lanfear).
78 o In chronopl(), the code setting the initial dates failed in
79 complicated settings (several dates known within intervals).
80 This has been generally improved and should result in faster
81 and more efficient convergence even in simple settings.
83 o mantel.test() sometimes returned P-values > 1 with the default
86 o extract.clade() sometimes shuffled some tip labels (thanks to
87 Ludovic Mallet and Mahendra Mariadassou for the fix).
89 o clustal() should now find by default the executable under Windows.
94 o The code of yule() has been simplified and is now much faster for
97 o The code of mantel.test() has been adjusted to be consistent
98 with common permutation tests.
100 o The C code of base.freq() has been improved and is now nearly 8
103 o The option 'original.data' of write.nexus() is now deprecated and
104 will be removed in a future release.
106 o The code of is.ultrametric() has been improved and is now 3 times
109 o The code of vcv.phylo() has been improved and is now 10 or 30
110 times faster for 100 or 1000 tips, respectively. Consequently,
111 fitting models with PGLS will be faster overall.
115 CHANGES IN APE VERSION 2.8
120 o Twelve new functions have been written by Andrei-Alin Popescu:
121 additive, ultrametric, is.compatible, arecompatible, mvr, mvrs,
122 njs, bionjs, SDM, treePop, triangMtd, triangMtd*.
124 o A new class "bitsplits" has been created by Andrei-Alin Popescu
125 to code splits (aka, bipartition).
127 o There is a new generic function as.bitsplits with a method to
128 convert from the class "prop.part" to the class "bitsplits".
130 o The new function ltt.coplot plots on the same scales a tree and
131 the derived LTT plot.
133 o ltt.plot() has two new options: backward and tol. It can now
134 handle non-ultrametic trees and its internal coding has been
135 improved. The coordinates of the plot can now be computed with
136 the new function ltt.plot.coords.
141 o prop.part() crashed if some trees had some multichotomies.
145 CHANGES IN APE VERSION 2.7-3
150 o The new function compute.brtime computes and sets branching times.
152 o mantel.test() has a new argument 'alternative' which is
153 "two-sided" by default. Previously, this test was one-tailed
154 with no possibility to change.
156 o ace() can now do REML estimation with continuous characters,
157 giving better estimates of the variance of the Brownian motion
163 o Branch lengths were wrongly updated with bind.tree(, where = <tip>,
164 position = 0). (Thanks to Liam Revell for digging this bug out.)
166 o Simulation of OU process with rTraitCont() did not work correctly.
167 This now uses formula from Gillespie (1996) reduced to a BM
168 process when alpha = 0 to avoid division by zero. The option
169 'linear' has been removed.
171 o Cross-validation in chronopl() did not work when 'age.max' was
174 o consensus(, p = 0.5) could return an incorrect tree if some
175 incompatible splits occur in 50% of the trees (especially with
176 small number of trees).
178 o c() with "multiPhylo" did not work correctly (thanks to Klaus
179 Schliep for the fix).
181 o root() failed in some cases with an outgroup made of several tips.
182 The help page has been clarified a bit.
186 CHANGES IN APE VERSION 2.7-2
191 o There is a new class "evonet" to code evolutionary networks, with
192 a constructor function evonet(), a print() and a plot() methods,
193 and four conversion methods to the classes "phylo", "networx",
194 "network", and "igraph".
196 o The new function rTraitMult does multivariate traits simulation
197 with user-defined models.
199 o plot.phylo() has a new option 'plot = TRUE'. If FALSE, the tree
200 is not plotted but the graphical device is set and the
201 coordinates are saved as usual.
203 o diversity.contrast.test() gains a fourth version of the test with
204 method = "logratio"; the literature citations have been clarified.
206 o add.scale.bar() has two new options, 'lwd' and 'lcol', to modify
207 the aspect of the bar.
209 o boot.phylo() now displays a progress bar by default (can be off
212 o There is a new predict() method for compar.gee().
217 o bionj() made R crash if distances were too large. It now returns
218 an error if at least one distance is greater than 100.
220 o drop.tip() returned a wrong tree if 'tip' was of zero length.
222 o read.nexus.data() failed with URLs.
224 o boot.phylo() returned overestimated support values in the
225 presence of identical or nearly identical sequences.
230 o The data bird.families, bird.orders, cynipids, and woodmouse are
231 now provided as .rda files.
235 CHANGES IN APE VERSION 2.7-1
240 o The new function trex does tree exploration with multiple
243 o The new function kronoviz plots several rooted (dated) trees on
246 o identify.phylo() has a new option 'quiet' (FALSE by default).
251 o A bug was introduced in read.nexus() in ape 2.7.
253 o image.DNAbin() did not colour correctly the bases if there were
256 o .compressTipLabel() failed with a list with a single tree.
258 o identify.phylo() returned a wrong answer when the x- and y-scales
261 o write.nexus() failed with lists of trees with compressed labels.
266 o identify.phylo() now returns NULL if the user right- (instead of
267 left-) clicks (an error was returned previously).
269 o read.nexus() should be robust to commands inserted in the TREES
274 CHANGES IN APE VERSION 2.7
279 o There is a new image() method for "DNAbin" objects: it plots DNA
280 alignments in a flexible and efficient way.
282 o Two new functions as.network.phylo and as.igraph.phylo convert
283 trees of class "phylo" into these respective network classes
284 defined in the packages of the same names.
286 o The three new functions clustal, muscle, and tcoffee perform
287 nucleotide sequence alignment by calling the external programs
290 o Four new functions, diversity.contrast.test, mcconwaysims.test,
291 richness.yule.test, and slowinskiguyer.test, implement various
292 tests of diversification shifts using sister-clade comparisons.
294 o base.freq() gains an option 'all' to count all the possible bases
295 including the ambiguous ones (defaults to FALSE).
297 o read.nexus() now writes tree names in the NEXUS file if given a
298 list of trees with names.
303 o prop.part() failed in some situations with unrooted trees.
305 o read.nexus() shuffled node labels when a TRANSLATE block was
308 o varCompPhylip() did not work if 'exec' was specified.
310 o bind.tree() shuffled node labels when position > 0 and 'where'
316 o BaseProportion in src/dist_dna.c has been modified.
318 o A number of functions in src/tree_build.c have been modified.
320 o The matching representation has now only two columns as the third
321 column was redundant.
325 CHANGES IN APE VERSION 2.6-3
330 o rTraitCont() and rTraitDisc() gains a '...' argument used with
331 user-defined models (suggestion by Gene Hunt).
336 o as.hclust.phylo() now returns an error with unrooted trees.
338 o as.hclust.phylo() failed with trees with node labels (thanks to
339 Jinlong Zhang for pointing this bug out).
341 o read.dna(, "fasta") failed if sequences were not all of the same
344 o plot.phylo() did not recycle values of 'font', 'cex' and
345 'tip.color' correctly when type = "fan" or "radial".
347 o plot.phylo() ignored 'label.offset' when type = "radial", "fan", or
348 "unrooted" with lab4ut = "axial" (the placement of tip labels still
349 needs to be improved with lab4ut = "horizontal").
354 o In drop.fossil() the default tol = 0 has been raised to 1e-8.
356 o The help command ?phylo now points to the man page of read.tree()
357 where this class is described. Similarly, ?matching points to the
358 man page of as.matching().
362 CHANGES IN APE VERSION 2.6-2
367 o Two new functions, pic.ortho and varCompPhylip, implements the
368 orthonormal contrasts of Felsenstein (2008, Am Nat, 171:713). The
369 second function requires Phylip to be installed on the computer.
371 o bd.ext() has a new option conditional = TRUE to use probabilities
372 conditioned on no extinction for the taxonomic data.
377 o write.tree() failed to output correctly tree names.
379 o dist.nodes() returned duplicated column(s) with unrooted and/or
380 multichotomous trees.
382 o mcmc.popsize() terminated unexpectedly if the progress bar was
385 o prop.part(x) made R frozen if 'x' is of class "multiPhylo".
387 o Compilation under Mandriva failed (thanks to Jos Käfer for the fix).
389 o drop.tip() shuffled tip labels with subtree = TRUE or trim.internal
392 o Objects returned by as.hclust.phylo() failed when analysed with
393 cutree() or rect.hclust().
395 o write.tree() did not output correctly node labels (thanks to Naim
396 Matasci and Jeremy Beaulieu for the fix).
398 o ace(type = "discrete") has been improved thanks to Naim Marasci and
403 CHANGES IN APE VERSION 2.6-1
408 o The new function speciesTree calculates the species tree from a set
409 of gene trees. Several methods are available including maximum tree
410 and shallowest divergence tree.
415 o A bug introduced in write.tree() with ape 2.6 has been fixed.
417 o as.list.DNAbin() did not work correctly with vectors.
419 o as.hclust.phylo() failed with trees with node labels (thanks to
420 Filipe Vieira for the fix).
424 CHANGES IN APE VERSION 2.6
429 o The new functions rlineage and rbdtree simulate phylogenies under
430 any user-defined time-dependent speciation-extinction model. They
431 use continuous time algorithms.
433 o The new function drop.fossil removes the extinct species from a
436 o The new function bd.time fits a user-defined time-dependent
437 birth-death model. It is a generalization of yule.time() taking
438 extinction into account.
440 o The new function MPR does most parsimonious reconstruction of
443 o The new function Ftab computes the contingency table of base
444 frequencies from a pair of sequences.
446 o There is now an 'as.list' method for the class "DNAbin".
448 o dist.dna() can compute the number of transitions or transversions
449 with the option model = "Ts" or model = "Tv", respectively.
451 o [node|tip|edge]labels() gain three options with default values to
452 control the aspect of thermometers: horiz = TRUE, width = NULL,
455 o compar.gee() has been improved with the new option 'corStruct' as an
456 alternative to 'phy' to specify the correlation structure, and
457 calculation of the QIC (Pan 2001, Biometrics). The display of the
458 results has also been improved.
460 o read.GenBank() has a new option 'gene.names' to return the name of
461 the gene (FALSE by default).
466 o extract.clade() sometimes shuffled the tip labels.
468 o plot.phylo(type = "unrooted") did not force asp = 1 (thanks to Klaus
471 o dist.dna(model = "logdet") used to divide distances by 4. The
472 documentation has been clarified on the formulae used.
477 o rTraitCont(model = "OU") has an option 'linear = TRUE' to possibly
478 change the parameterisation (see ?rTraitCont for details).
480 o pic() now returns a vector with the node labels of the tree (if
483 o write.tree() and read.tree() have been substantially improved thanks
484 to contributions by Klaus Schliep.
488 CHANGES IN APE VERSION 2.5-3
493 o The new function mixedFontLabel helps to make labels with bits of
494 text to be plotted in different fonts.
496 o There are now replacement operators for [, [[, and $ for the class
497 "multiPhylo" (i.e., TREES[11:20] <- rmtree(10, 100)). They possibly
498 check that the tip labels are the same in all trees.
500 o Objects of class "multiPhylo" can be built with c(): there are
501 methods for the classes "phylo" and "multiPhylo".
503 o The internal functions .compressTipLabel and .uncompressTipLabel are
509 o bind.tree(x, y, where, position = 0) did not work correctly if 'y'
510 was a single-edge tree and 'where' was a tip.
512 o rTraitCont() did not use the square-root of branch lengths when
513 simulating a Brownian motion model.
517 CHANGES IN APE VERSION 2.5-2
522 o There is now a print method for results from ace().
524 o There is a labels() method for objects of class "DNAbin".
526 o read.dna() has a new option 'as.matrix' to possibly force sequences
527 in a FASTA file to be stored in a matrix (see ?read.dna for details).
532 o as.phylo.hclust() used to multiply edge lengths by 2.
534 o A minor bug was fixed in rTraitDisc().
536 o ace() sometimes failed (parameter value was NaN and the optimisation
542 o evolve.phylo() and plot.ancestral() have been removed.
544 o chronogram(), ratogram(), and NPRS.criterion() have been removed.
549 o nj() has been improved and is now about 30% faster.
551 o The default option 'drop' of [.DNAbin has been changed to FALSE to
552 avoid dropping rownames when selecting a single sequence.
554 o print.DNAbin() has been changed to summary.DNAbin() which has been
559 CHANGES IN APE VERSION 2.5-1
564 o The new function stree generates trees with regular shapes.
566 o It is now possible to bind two trees with x + y (see ?bind.tree for
569 o drop.tip(), extract.clade(), root(), and bind.tree() now have an
570 'interactive' option to make the operation on a plotted tree.
572 o cophyloplot() gains two new arguments 'lwd' and 'lty' for the
573 association links; they are recycled like 'col' (which wasn't before).
578 o rTraitDisc() did not use its 'freq' argument correctly (it was
579 multiplied with the rate matrix column-wise instead of row-wise).
581 o [node|tip|edge]labels(thermo = ) used to draw empty thermometers
582 with NA values. Nothing is drawn now like with 'text' or 'pch'.
583 The same bug occurred with the 'pie' option.
585 o A bug was fixed in compar.ou() and the help page was clarified.
587 o bind.tree() has been rewritten fixing several bugs and making it
590 o plot.phylo(type = "p") sometimes failed to colour correctly the
591 vertical lines representing the nodes.
593 o plot.phylo(direction = "l", x.lim = 30) failed to plot the branches
594 in the correct direction though the tip labels were displayed
600 o The c, cbind, and rbind methods for "DNAbin" objetcs now check that
601 the sequences are correctly stored (in a list for c, in a matrix
602 for the two other functions).
606 CHANGES IN APE VERSION 2.5
611 o The new function parafit by Pierre Legendre tests for the
612 coevolution between hosts and parasites. It has a companion
613 function, pcoa, that does principal coordinate decomposition.
614 The latter has a biplot method.
616 o The new function lmorigin by Pierre Legendre performs multiple
617 regression through the origin with testing by permutation.
619 o The new functions rTraitCont and rTraitDisc simulate continuous and
620 discrete traits under a wide range of evolutionary models.
622 o The new function delta.plot does a delta plot following Holland et
623 al. (2002, Mol. Biol. Evol. 12:2051).
625 o The new function edges draws additional branches between any nodes
626 and/or tips on a plotted tree.
628 o The new function fancyarrows enhances arrows from graphics with
629 triangle and harpoon heads; it can be called from edges().
631 o add.scale.bar() has a new option 'ask' to draw interactively.
633 o The branch length score replaces the geodesic distance in dist.topo.
635 o Three new data sets are included: the gopher-lice data (gopher.D),
636 SO2 air pollution in 41 US cities (lmorigin.ex1, from Sokal &
637 Rohlf 1995), and some host-parasite specificity data
638 (lmorigin.ex2, from Legendre & Desdevises 2009).
643 o add.scale.bar() drew the bar outside the plotting region with the
644 default options with unrooted or radial trees.
646 o dist.topo() made R stuck when the trees had different sizes (thanks
647 to Otto Cordero for the fix).
652 o The geodesic distance has been replaced by the branch length score
657 CHANGES IN APE VERSION 2.4-1
662 o rtree() and rcoal() now accept a numeric vector for the 'br'
665 o vcv() is a new generic function with methods for the classes "phylo"
666 and "corPhyl" so that it is possible to calculate the var-cov matrix
667 for "transformation models". vcv.phylo() can still be used for trees
668 of class "phylo"; its argument 'cor' has been renamed 'corr'.
673 o bind.tree() failed when 'y' had no root edge.
675 o read.nexus() shuffled tip labels when the trees have no branch
676 lengths and there is a TRANSLATE block.
678 o read.nexus() does not try to translate node labels if there is a
679 translation table in the NEXUS file. See ?read.nexus for a
680 clarification on this behaviour.
682 o plot.multiPhylo() crashed R when plotting a list of trees with
683 compressed tip labels.
685 o write.nexus() did not translate the taxa names when asked for.
687 o plot.phylo(type = "fan") did not rotate the tip labels correctly
688 when the tree has branch lengths.
690 o ace(type = "continuous", method = "ML") now avoids sigma² being
691 negative (which resulted in an error).
693 o nj() crashed with NA/NaN in the distance matrix: an error in now
698 CHANGES IN APE VERSION 2.4
703 o base.freq() has a new option 'freq' to return the counts; the
704 default is still to return the proportions.
709 o seg.sites() did not handle ambiguous nucleotides correctly: they
712 o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
713 the tree: the argument is now ignored.
715 o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
721 o Trying to plot a tree with a single tip now returns NULL with a
722 warning (it returned an error previously).
724 o The way lines representing nodes are coloured in phylograms has
725 been modified (as well as their widths and types) following some
726 users' request; this is only for dichotomous nodes.
728 o The argument 'adj' in [node][tip][edge]labels() now works when
729 using 'pie' or 'thermo'.
731 o A more informative message error is now returned by dist.dna() when
732 'model' is badly specified (partial matching of this argument is
735 o Deprecated functions are now listed in a help page: see
736 help("ape-defunct") with the quotes.
741 o The functions heterozygosity, nuc.div, theta.h, theta.k and
742 theta.s have been moved from ape to pegas.
744 o The functions mlphylo, DNAmodel and sh.test have been removed.
748 CHANGES IN APE VERSION 2.3-3
753 o add.scale.bar() always drew a horizontal bar.
755 o zoom() shuffled tips with unrooted trees.
757 o write.nexus() failed to write correctly trees with a "TipLabel"
760 o rcoal() failed to compute branch lengths with very large n.
762 o A small bug was fixed in compar.cheverud() (thanks to Michael
765 o seg.sites() failed when passing a vector.
767 o drop.tip() sometimes shuffled tip labels.
769 o root() shuffled node labels with 'resolve.root = TRUE'.
773 CHANGES IN APE VERSION 2.3-2
778 o all.equal.phylo() did not compare unrooted trees correctly.
780 o dist.topo(... method = "PH85") did not treat unrooted trees
781 correctly (thanks to Tim Wallstrom for the fix).
783 o root() sometimes failed to test for the monophyly of the
786 o extract.clade() sometimes included too many edges.
788 o vcv.phylo() did not work correctly when the tree is in
791 o nj() did not handle correctly distance matrices with many 0's.
792 The code has also been significantly improved: 7, 70, 160 times
793 faster with n = 100, 500, 1000, respectively.
797 CHANGES IN APE VERSION 2.3-1
802 o The new function is.monophyletic tests the monophyly of a group.
804 o There is now a c() method for lists of class "DNAbin".
806 o yule.cov() now fits the null model, and its help page has been
807 corrected with respect to this change.
809 o drop.tip() has a new option 'rooted' to force (or not) a tree
810 to be treated as (un)rooted.
815 o dist.gene() failed on most occasions with the default
816 pairwise.deletion = FALSE.
818 o read.tree() failed to read correctly the tree name(s).
820 o boot.phylo() now treats correctly data frames.
822 o del.gaps() did not copy the rownames of a matrix.
824 o A small bug was fixed in CDAM.global().
826 o ace() failed with large data sets. Thanks to Rich FitzJohn for
827 the fix. With other improvements, this function is now about 6
830 o write.tree() failed with objects of class "multiPhylo".
832 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
837 o [.multiPhylo and [.DNAbin now respect the original class.
839 o Instances of the form class(phy) == "phylo" have been replaced
840 by inherits(phy, "phylo").
842 o rcoal() is now faster.
847 o klastorin() has been removed.
851 CHANGES IN APE VERSION 2.3
856 o The new functions CADM.global and CADM.post, contributed by
857 Pierre Legendre, test the congruence among several distance
860 o The new function yule.time fits a user-defined time-dependent
861 Yule model by maximum likelihood.
863 o The new function makeNodeLabel creates and/or modifies node
864 labels in a flexible way.
866 o read.tree() and write.tree() have been modified so that they can
867 handle individual tree names.
869 o plot.phylo() has a new argument 'edge.lty' that specifies the
870 types of lines used for the edges (plain, dotted, dashed, ...)
872 o phymltest() has been updated to work with PhyML 3.0.1.
877 o drop.tip() shuffled tip labels in some cases.
879 o drop.tip() did not handle node.label correctly.
881 o is.ultrametric() now checks the ordering of the edge matrix.
883 o ace() sometimes returned negative values of likelihoods of
884 ancestral states (thanks to Dan Rabosky for solving this long
890 o The data set xenarthra has been removed.
894 CHANGES IN APE VERSION 2.2-4
898 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
899 now fixed. (Thanks to Peter Wragg for the fix!)
901 o A warning message occurred for no reason with ace(method="GLS").
906 o There is now a general help page displayed with '?ape'.
910 CHANGES IN APE VERSION 2.2-3
915 o The new function extract.clade extracts a clade from a tree by
916 specifying a node number or label.
918 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
919 operations of the same names.
921 o dist.dna() can now return the number of site differences by
922 specifying model="N".
927 o chronopl() did not work with CV = TRUE.
929 o read.nexus() did not work correctly in some situations (trees on
930 multiple lines with different numbers of lines and/or with
931 comments inserted within the trees).
933 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
934 the number of lineages with non-binary trees.
939 o ape has now a namespace.
941 o drop.tip() has been improved: it should be much faster and work
942 better in some cases (e.g., see the example in ?zoom).
946 CHANGES IN APE VERSION 2.2-2
951 o dist.gene() has been substantially improved and gains an option
954 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
960 o prop.part() failed with a single tree with the default option
961 'check.labels = TRUE'.
963 o summary.DNAbin() failed to display correctly the summary of
964 sequence lengths with lists of sequences of 10,000 bases or more
965 (because summary.default uses 4 significant digits by default).
967 o read.nexus() failed to read a file with a single tree with line
968 breaks in the Newick string.
970 o del.gaps() returned a list of empty sequences when there were no
976 o phymltest() has been updated for PhyML 3.0 and gains an option
977 'append', whereas the option 'path2exec' has been removed.
979 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
980 which is returned unchanged (instead of an error).
982 o The data sets bird.orders and bird.families are now stored as
983 Newick strings; i.e., the command data(bird.orders) calls
988 CHANGES IN APE VERSION 2.2-1
993 o The new function makeLabel() helps to modify labels of trees,
994 lists of trees, or DNA sequences, with several utilities to
995 truncate and/or make them unique, substituting some
996 characters, and so on.
998 o The new function del.gaps() removes insertion gaps ("-") in a
999 set of DNA sequences.
1001 o read.dna() can now read Clustal files (*.aln).
1006 o root() failed with 'resolve.root = TRUE' when the root was
1007 already the specified root.
1009 o Several bugs were fixed in mlphylo().
1011 o collapsed.singles() did not propagate the 'Nnode' and
1012 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
1014 o read.nexus() failed to remove correctly the comments within
1017 o read.nexus() failed to read a file with a single tree and no
1018 translation of tip labels.
1020 o read.nexus() failed to place correctly tip labels when reading
1021 a single tree with no edge lengths.
1023 o A bug was fixed in sh.test().
1028 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
1031 o The option 'check.labels' of consensus() and prop.part() is now
1034 o write.dna() now does not truncate names to 10 characters with
1039 CHANGES IN APE VERSION 2.2
1044 o Four new functions have been written by Damien de Vienne for the
1045 graphical exploration of large trees (cophyloplot, subtrees,
1046 subtreeplot), and to return the graphical coordinates of tree
1049 o The new functions corPagel and corBlomberg implement the Pagel's
1050 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
1052 o chronopl() has been improved and gains several options: see its
1053 help page for details.
1055 o boot.phylo() has now an option 'trees' to possibly return the
1056 bootstraped trees (the default is FALSE).
1058 o prop.part() has been improved and should now be faster in all
1064 o read.dna() failed if "?" occurred in the first 10 sites of the
1067 o The x/y aspect of the plot is now respected when plotting a
1068 circular tree (type = "r" or "f").
1070 o Drawing the tip labels sometimes failed when plotting circular
1073 o zoom() failed when tip labels were used instead of their numbers
1074 (thanks to Yan Wong for the fix).
1076 o drop.tip() failed with some trees (fixed by Yan Wong).
1078 o seg.sites() failed with a list.
1080 o consensus() failed in some cases. The function has been improved
1081 as well and is faster.
1085 CHANGES IN APE VERSION 2.1-3
1090 o A bug in read.nexus() made the Windows R-GUI crash.
1092 o An error was fixed in the computation of ancestral character
1093 states by generalized least squares in ace().
1095 o di2multi() did not modify node labels correctly.
1097 o multi2di() failed if the tree had its attribute "order" set to
1102 CHANGES IN APE VERSION 2.1-2
1107 o There three new methods for the "multiPhylo" class: str, $,
1110 o root() gains the options 'node' and 'resolve.root'
1111 (FALSE by default) as well as its code being improved.
1113 o mltt.plot() has now an option 'log' used in the same way
1114 than in plot.default().
1119 o mltt.plot() failed to display the legend with an unnamed
1122 o nodelabels() with pies now correcly uses the argument
1123 'cex' to draw symbols of different sizes (which has
1124 worked already for thermometers).
1126 o read.nexus() generally failed to read very big files.
1131 o The argument 'family' of compar.gee() can now be a function
1132 as well as a character string.
1134 o read.tree() and read.nexus() now return an unnamed list if
1135 'tree.names = NULL'.
1137 o read.nexus() now returns a modified object of class "multiPhylo"
1138 when there is a TRANSLATE block in the NEXUS file: the individual
1139 trees have no 'tip.label' vector, but the list has a 'TipLabel'
1140 attribute. The new methods '$' and '[[' set these elements
1141 correctly when extracting trees.
1145 CHANGES IN APE VERSION 2.1-1
1150 o The new function rmtree generates lists of random trees.
1152 o rcoal() now generates a genuine coalescent tree by default
1153 (thanks to Vladimir Minin for the code).
1158 o nuc.div() returned an incorrect value with the default
1159 pairwise.deletion = FALSE.
1164 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
1165 have been improved so that they are stabler and faster.
1167 o R packages used by ape are now loaded silently; lattice and gee
1168 are loaded only when needed.
1172 CHANGES IN APE VERSION 2.1
1177 o The new function identify.phylo identifies clades on a plotted
1178 tree using the mouse.
1180 o It is now possible to subset a list of trees (object of class
1181 "multiPhylo") with "[" while keeping its class correct.
1183 o The new function as.DNAbin.alignment converts DNA sequences
1184 stored in the "alignment" format of the package seqinr into
1185 an object of class "DNAbin".
1187 o The new function weight.taxo2 helps to build similarity matrices
1188 given two taxonomic levels (usually called by other functions).
1190 o write.tree() can now take a list of trees (class "multiPhylo")
1191 as its main argument.
1193 o plot.correlogram() and plot.correlogramList() have been
1194 improved, and gain several options (see the help page for
1195 details). A legend is now plotted by default.
1200 o dist.dna() returned some incorrect values with `model = "JC69"'
1201 and `pairwise.deletion = TRUE'. This affected only the
1202 distances involving sequences with missing values. (Thanks
1203 to Bruno Toupance for digging this bug out.)
1205 o write.tree() failed with some trees: this is fixed by removing
1206 the `multi.line' option (trees are now always printed on a
1209 o read.nexus() did not correctly detect trees with multiple root
1210 edges (see OTHER CHANGES).
1215 o The code of mlphylo() has been almost entirely rewritten, and
1216 should be much stabler. The options have been also greatly
1217 simplified (see ?mlphylo and ?DNAmodel for details).
1219 o The internal function nTips has been renamed klastorin_nTips.
1221 o The code of is.ultrametric() contained redundancies and has
1224 o The code of Moran.I() and of correlogram.formula() have been
1227 o read.tree() and read.nexus() now return an error when trying to
1228 read a tree with multiple root edges (see BUG FIXES). The
1229 correction applied in previous version did not work in all
1232 o The class c("multi.tree", "phylo") has been renamed
1238 o There is now a vignette in ape: see vignette("MoranI", "ape").
1241 DEPRECATED & DEFUNCT
1243 o as.matching() and as.phylo.matching() do not support branch
1246 o correlogram.phylo() and discrete.dist() have been removed.
1250 CHANGES IN APE VERSION 2.0-2
1255 o The new function matexpo computes the exponential of a square
1258 o The new function unique.multi.tree removes duplicate trees from
1261 o yule() has a new option `use.root.edge = FALSE' that specifies
1262 to ignore, by default, the root edge of the tree if it exists.
1267 o which.edge() failed when the index of a single terminal edge was
1270 o In diversi.time(), the values returned for model C were
1273 o A bug was fixed in yule() that affected the calculation of the
1274 likelihood in the presence of ties in the branching times.
1276 o There was a bug in the C function mat_expo4x4 affecting the
1277 calculations of the transition probabilities for models HKY and
1280 o A small bug was fixed in as.matrix.DNAbin (thanks to James
1283 o rtree() did not `shuffle' the tip labels by default, so only a
1284 limited number of labelled topologies could be generated.
1288 CHANGES IN APE VERSION 2.0-1
1293 o The three new functions bionj, fastme.ols, and fastme.bal
1294 perform phylogeny estimation by the BIONJ and fastME methods in
1295 OLS and balanced versions. This is a port to R of previous
1296 previous programs done by Vincent Lefort.
1298 o The new function chronoMPL performs molecular dating with the
1299 mean path lengths method of Britton et al. (2002, Mol. Phyl.
1302 o The new function rotate, contributed by Christoph Heibl, swaps
1303 two clades connected to the same node. It works also with
1304 multichotomous nodes.
1306 o The new `method' as.matrix.DNAbin() may be used to convert
1307 easily DNA sequences stored in a list into a matrix while
1308 keeping the names and the class.
1313 o chronopl() failed when some branch lengths were equal to zero:
1314 an error message is now returned.
1316 o di2multi() failed when there was a series of consecutive edges
1321 CHANGES IN APE VERSION 1.10-2
1326 o plot.phylo() can now plot circular trees: the option is type =
1327 "fan" or type = "f" (to avoid the ambiguity with type = "c").
1329 o prop.part() has a new option `check.labels = FALSE' which allows
1330 to considerably speed-up the calculations of bipartitions. As a
1331 consequence, calculations of bootstrap values with boot.phylo()
1332 should be much faster.
1337 o read.GenBank() did not return correctly the list of species as
1338 from ape 1.10: this is fixed in this version
1340 o Applying as.phylo() on a tree of class "phylo" failed: the
1341 object is now returned unchanged.
1345 CHANGES IN APE VERSION 1.10-1
1350 o The three new functions Ntip, Nnode, and Nedge return, for a
1351 given tree, the number of tips, nodes, or edges, respectively.
1356 o read.nexus() did not set correctly the class of the returned
1357 object when reading multiple trees.
1359 o mllt.plot() failed with objects of class c("multi.tree",
1362 o unroot() did not work correctly in most cases.
1364 o reorder.phylo() made R freeze in some occasions.
1366 o Plotting a tree in pruningwise order failed.
1368 o When plotting an unrooted tree, the tip labels where not all
1369 correctly positioned if the option `cex' was used.
1373 CHANGES IN APE VERSION 1.10
1378 o Five new `method' functions have been introduced to manipulate
1379 DNA sequences in binary format (see below).
1381 o Three new functions have been introduced to convert between the
1382 new binary and the character formats.
1384 o The new function as.alignment converts DNA sequences stored as
1385 single characters into the class "alignment" used by the package
1388 o read.dna() and read.GenBank() have a new argument `as.character'
1389 controlling whether the sequences are returned in binary format
1395 o root() failed when the tree had node labels: this is fixed.
1397 o plot.phylo() did not correctly set the limits on the y-axis with
1398 the default setting: this is fixed.
1400 o dist.dna() returned a wrong result for the LogDet, paralinear,
1401 and BH87 models with `pairwise.deletion = TRUE'.
1406 o DNA sequences are now internally stored in a binary format. See
1407 the document "A Bit-Level Coding Scheme for Nucleotides" for the
1408 details. Most functions analyzing DNA functions have been
1409 modified accordingly and are now much faster (dist.dna is now
1410 ca. 60 times faster).
1414 CHANGES IN APE VERSION 1.9-4
1419 o A bug was fixed in edgelabels().
1421 o as.phylo.hclust() did not work correctly when the object of
1422 class "hclust" has its labels set to NULL: the returned tree has
1423 now its tip labels set to "1", "2", ...
1425 o consensus could fail if some tip labels are a subset of others
1426 (e.g., "a" and "a_1"): this is now fixed.
1428 o mlphylo() failed in most cases if some branch lengths of the
1429 initial tree were greater than one: an error message is now
1432 o mlphylo() failed in most cases when estimating the proportion of
1433 invariants: this is fixed.
1437 CHANGES IN APE VERSION 1.9-3
1442 o The new function edgelabels adds labels on the edge of the tree
1443 in the same way than nodelabels or tiplabels.
1448 o multi2di() did not handle correctly branch lengths with the
1449 default option `random = TRUE': this is now fixed.
1451 o A bug was fixed in nuc.div() when using pairwise deletions.
1453 o A bug occurred in the analysis of bipartitions with large
1454 numbers of large trees, with consequences on prop.part,
1455 prop.clades, and boot.phylo.
1457 o The calculation of the Billera-Holmes-Vogtmann distance in
1458 dist.topo was wrong: this has been fixed.
1462 CHANGES IN APE VERSION 1.9-2
1467 o The new function ladderize reorganizes the internal structure of
1468 a tree to plot them left- or right-ladderized.
1470 o The new function dist.nodes computes the patristic distances
1471 between all nodes, internal and terminal, of a tree. It replaces
1472 the option `full = TRUE' of cophenetic.phylo (see below).
1477 o A bug was fixed in old2new.phylo().
1479 o Some bugs were fixed in chronopl().
1481 o The edge colours were not correctly displayed by plot.phylo
1482 (thank you to Li-San Wang for the fix).
1484 o cophenetic.phylo() failed with multichotomous trees: this is
1490 o read.dna() now returns the sequences in a matrix if they are
1491 aligned (interleaved or sequential format). Sequences in FASTA
1492 format are still returned in a list.
1494 o The option `full' of cophenetic.phylo() has been removed because
1495 it could not be used from the generic.
1498 DEPRECATED & DEFUNCT
1500 o rotate() has been removed; this function did not work correctly
1505 CHANGES IN APE VERSION 1.9-1
1510 o Trees with a single tip were not read correctly in R as the
1511 element `Nnode' was not set: this is fixed.
1513 o unroot() did not set correctly the number of nodes of the
1514 unrooted tree in most cases.
1516 o read.GenBank() failed when fetching very long sequences,
1517 particularly of the BX-series.
1519 o A bug was introduced in read.tree() with ape 1.9: it has been
1524 CHANGES IN APE VERSION 1.9
1529 o There are two new print `methods' for trees of class "phylo" and
1530 lists of trees of class "multi.tree", so that they are now
1531 displayed in a compact and informative way.
1533 o There are two new functions, old2new.phylo and new2old.phylo,
1534 for converting between the old and new coding of the class
1537 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
1538 LogDet ("logdet"), and paralinear ("paralin").
1540 o compute.brlen() has been extended: several methods are now
1541 available to compute branch lengths.
1543 o write.dna() can now handle matrices as well as lists.
1548 o cophenetic.phylo() sometimes returned a wrong result with
1549 multichotomous trees: this is fixed.
1551 o rotate() failed when a single tip was specified: the tree is now
1554 o ace() did not return the correct index matrix with custom
1555 models: this is fixed.
1557 o multi2di() did not work correctly when resolving multichotomies
1558 randomly: the topology was always the same, only the arrangement
1559 of clades was randomized: this is fixed. This function now
1560 accepts trees with no branch lengths.
1562 o The output of diversi.gof() was blurred by useless prints when a
1563 user distribution was specified. This has been corrected, and
1564 the help page of this function has been expanded.
1569 o The internal structure of the class "phylo" has been changed:
1570 see the document "Definition of Formats for Coding Phylogenetic
1571 Trees in R" for the details. In addition, the code of most
1572 functions has been improved.
1574 o Several functions have been improved by replacing some R codes
1575 by C codes: pic, plot.phylo, and reorder.phylo.
1577 o There is now a citation information: see citation("ape") in R.
1579 o write.tree() now does not add extra 0's to branch lengths so
1580 that 1.23 is printed "1.23" by default, not "1.2300000000".
1582 o The syntax of bind.tree() has been simplified. This function now
1583 accepts trees with no branch lengths, and handles correctly node
1586 o The option `as.numeric' of mrca() has been removed.
1588 o The unused options `format' and `rooted' of read.tree() have
1591 o The unused option `format' of write.tree() has been removed.
1593 o The use of node.depth() has been simplified.
1597 CHANGES IN APE VERSION 1.8-5
1602 o Two new functions read.nexus.data() and write.nexus.data(),
1603 contributed by Johan Nylander, allow to read and write molecular
1604 sequences in NEXUS files.
1606 o The new function reorder.phylo() reorders the internal structure
1607 of a tree of class "phylo". It is used as the generic, e.g.,
1610 o read.tree() and read.nexus() can now read trees with a single
1613 o The new data set `cynipids' supplies a set of protein sequences
1619 o The code of all.equal.phylo() has been completely rewritten
1620 (thanks to Benoît Durand) which fixes several bugs.
1622 o read.tree() and read.nexus() now checks the labels of the tree
1623 to remove or substitute any characters that are illegal in the
1624 Newick format (parentheses, etc.)
1626 o A negative P-value could be returned by mantel.test(): this is
1631 CHANGES IN APE VERSION 1.8-4
1636 o The new function sh.test() computes the Shimodaira-
1639 o The new function collapse.singles() removes the nodes with a
1640 single descendant from a tree.
1642 o plot.phylo() has a new argument `tip.color' to specify the
1643 colours of the tips.
1645 o mlphylo() has now an option `quiet' to control the display of
1646 the progress of the analysis (the default is FALSE).
1651 o read.dna() did not read correctly sequences in sequential format
1652 with leading alignment gaps "-": this is fixed.
1654 o ace() returned a list with no class so that the generic
1655 functions (anova, logLik, ...) could not be used directly. This
1656 is fixed as ace() now returns an object of class "ace".
1658 o anova.ace() had a small bug when computing the number of degrees
1659 of freedom: this is fixed.
1661 o mlphylo() did not work when the sequences were in a matrix or
1662 a data frame: this is fixed.
1664 o rtree() did not work correctly when trying to simulate an
1665 unrooted tree with two tips: an error message is now issued.
1670 o The algorithm of rtree() has been changed: it is now about 40,
1671 100, and 130 times faster for 10, 100, and 1000 tips,
1676 CHANGES IN APE VERSION 1.8-3
1681 o There are four new `method' functions to be used with the
1682 results of ace(): logLik(), deviance(), AIC(), and anova().
1684 o The plot method of phymltest has two new arguments: `main' to
1685 change the title, and `col' to control the colour of the
1686 segments showing the AIC values.
1688 o ace() has a new argument `ip' that gives the initial values used
1689 in the ML estimation with discrete characters (see the examples
1690 in ?ace). This function now returns a matrix giving the indices
1691 of the estimated rates when analysing discrete characters.
1693 o nodelabels() and tiplabels() have a new argument `pie' to
1694 represent proportions, with any number of categories, as
1695 piecharts. The use of the option `thermo' has been improved:
1696 there is now no limitation on the number of categories.
1701 o mlphylo() did not work with more than two partitions: this is
1704 o root() failed if the proposed outgroup was already an outgroup
1705 in the tree: this is fixed.
1707 o The `col' argument in nodelabels() and tiplabels() was not
1708 correctly passed when `text' was used: this is fixed.
1710 o Two bugs were fixed in mlphylo(): parameters were not always
1711 correctly output, and the estimation failed in some cases.
1713 o plot.phylo() was stuck when given a tree with a single tip: this
1714 is fixed and a message error is now returned.
1716 o An error was corrected in the help page of gammaStat regarding
1717 the calculation of P-values.
1719 o Using gls() could crash R when the number of species in the tree
1720 and in the variables were different: this is fixed.
1724 CHANGES IN APE VERSION 1.8-2
1729 o The new function mlphylo() fits a phylogenetic tree by maximum
1730 likelihood from DNA sequences. Its companion function DNAmodel()
1731 is used to define the substitution model which may include
1732 partitioning. There are methods for logLik(), deviance(), and
1733 AIC(), and the summary() method has been extended to display in
1734 a friendly way the results of this model fitting. Currently, the
1735 functionality is limited to estimating the substitution and
1736 associated parameters and computing the likelihood.
1738 o The new function drop1.compar.gee (used as, e.g., drop1(m))
1739 tests for single effects in GEE-based comparative method. A
1740 warning message is printed if there is not enough degrees of
1746 o An error message was sometimes issued by plot.multi.tree(),
1747 though with no consequence.
1751 CHANGES IN APE VERSION 1.8-1
1756 o There is a new plot method for lists of trees (objects of class
1757 "multi.tree"): it calls plot.phylo() internally and is
1758 documented on the same help page.
1763 o A bug was fixed in the C code that analyzes bipartitions: this
1764 has impact on several functions like prop.part, prop.clades,
1765 boot.phylo, or consensus.
1767 o root() did not work correctly when the specified outgroup had
1768 more than one element: this is fixed.
1770 o dist.dna() sometimes returned a warning inappropriately: this
1773 o If the distance object given to nj() had no rownames, nj()
1774 returned a tree with no tip labels: it now returns tips labelled
1775 "1", "2", ..., corresponding to the row numbers.
1780 o nj() has been slightly changed so that tips with a zero distance
1781 are first aggregated with zero-lengthed branches; the usual NJ
1782 procedure is then performed on a distance matrix without 0's.
1786 CHANGES IN APE VERSION 1.8
1791 o The new function chronopl() estimates dates using the penalized
1792 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1794 o The new function consensus() calculates the consensus tree of a
1797 o The new function evolve.phylo() simulates the evolution of
1798 continuous characters along a phylogeny under a Brownian model.
1800 o The new plot method for objects of class "ancestral" displays a
1801 tree together with ancestral values, as returned by the above
1804 o The new function as.phylo.formula() returns a phylogeny from a
1805 set of nested taxonomic variables given as a formula.
1807 o The new function read.caic() reads trees in CAIC format.
1809 o The new function tiplabels() allows to add labels to the tips
1810 of a tree using text or plotting symbols in a flexible way.
1812 o The new function unroot() unroots a phylogeny.
1814 o multi2di() has a new option, `random', which specifies whether
1815 to resolve the multichotomies randomly (the default) or not.
1817 o prop.part() now returns an object of class "prop.part" for which
1818 there are print (to display a partition in a more friendly way)
1819 and summary (to extract the numbers) methods.
1821 o plot.phylo() has a new option, `show.tip.label', specifying
1822 whether to print the labels of the tips. The default is TRUE.
1824 o The code of nj() has been replaced by a faster C code: it is now
1825 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1828 o write.nexus() now writes whether a tree is rooted or not.
1833 o Two bugs have been fixed in root(): unrooted trees are now
1834 handled corretly, and node labels are now output normally.
1836 o A bug was fixed in phymltest(): the executable couldn't be found
1839 o Three bug have been fixed in ace(): computing the likelihood of
1840 ancestral states of discrete characters failed, custom models
1841 did not work, and the function failed with a null gradient (a
1842 warning message is now returned; this latter bug was also
1843 present in yule.cov() as well and is now fixed).
1845 o pic() hanged out when missing data were present: a message error
1848 o A small bug was fixed in dist.dna() where the gamma correction
1849 was not always correctly dispatched.
1851 o plot.phylo() plotted correctly the root edge only when the tree
1852 was plotted rightwards: this works now for all directions.
1857 o dist.taxo() has been renamed as weight.taxo().
1859 o dist.phylo() has been replaced by the method cophenetic.phylo().
1861 o Various error and warning messages have been improved.
1865 CHANGES IN APE VERSION 1.7
1868 o The new function ace() estimates ancestral character states for
1869 continuous characters (with ML, GLS, and contrasts methods), and
1870 discrete characters (with ML only) for any number of states.
1872 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1873 of directional evolution for continuous characters. The user
1874 specifies the node(s) of the tree where the character optimum
1877 o The new function is.rooted() tests whether a tree (of class
1880 o The new function rcoal() generates random ultrametric trees with
1881 the possibility to specify the function that generates the
1882 inter-nodes distances.
1884 o The new function mrca() gives for all pairs of tips in a tree
1885 (and optionally nodes too) the most recent common ancestor.
1887 o nodelabels() has a new option `thermo' to plot proportions (up
1888 to three classes) on the nodes of a tree.
1890 o rtree() has been improved: it can now generate rooted or
1891 unrooted trees, and the mathematical function that generates the
1892 branch lengths may be specified by the user. The tip labels may
1893 be given directly in the call to rtree. The limit cases (n = 2,
1894 3) are now handled correctly.
1896 o dist.topo() has a new argument `method' with two choices: "PH85"
1897 for Penny and Henny's method (already available before and now
1898 the default), and "BHV01" for the geometric distance by Billera
1899 et al. (2001, Adv. Appl. Math. 27:733).
1901 o write.tree() has a new option, `digits', which specifies the
1902 number of digits to be printed in the Newick tree. By default
1903 digits = 10. The numbers are now always printed in decimal form
1904 (i.e., 1.0e-1 is now avoided).
1906 o dist.dna() can now compute the raw distances between pairs of
1907 DNA sequences by specifying model = "raw".
1909 o dist.phylo() has a new option `full' to possibly compute the
1910 distances among all tips and nodes of the tree. The default if
1916 o Several bugs were fixed in all.equal.phylo().
1918 o dist.dna() did not handle correctly gaps ("-") in alignments:
1919 they are now considered as missing data.
1921 o rotate() did not work if the tips were not ordered: this is
1924 o mantel.test() returned NA in some special cases: this is fixed
1925 and the function has been improved and is now faster.
1927 o A bug was fixed in diversi.gof() where the calculation of A² was
1930 o cherry() did not work correctly under some OSs (mainly Linux):
1933 o is.binary.tree() has been modified so that it works with both
1934 rooted and unrooted trees.
1936 o The documentation of theta.s() was not correct: this has been
1939 o plot.mst() did not work correctly: this is fixed.
1943 CHANGES IN APE VERSION 1.6
1948 o The new function dist.topo() computes the topological distances
1951 o The new function boot.phylo() performs a bootstrap analysis on
1952 phylogeny estimation.
1954 o The new functions prop.part() and prop.clades() analyse
1955 bipartitions from a series of trees.
1960 o read.GenBank() now uses the EFetch utility of NCBI instead of
1961 the usual Web interface: it is now much faster (e.g., 12 times
1962 faster to retrieve 8 sequences, 37 times for 60 sequences).
1967 o Several bugs were fixed in read.dna().
1969 o Several bugs were fixed in diversi.time().
1971 o is.binary.tree() did not work correctly if the tree has no edge
1972 lengths: this is fixed.
1974 o drop.tip() did not correctly propagated the `node.label' of a
1975 tree: this is fixed.
1979 CHANGES IN APE VERSION 1.5
1984 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1985 convert objects between the classes "phylo" and "matching". The
1986 latter implements the representation of binary trees introduced by
1987 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1988 as.matching() has been introduced as well.
1990 o Two new functions, multi2di() and di2multi(), allow to resolve
1991 and collapse multichotomies with branches of length zero.
1993 o The new function nuc.div() computes the nucleotide diversity
1994 from a sample a DNA sequences.
1996 o dist.dna() has been completely rewritten with a much faster
1997 (particularly for large data sets) C code. Eight models are
1998 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1999 option `method' has been renamed `model'). Computation of variance
2000 is available for all models. A gamma-correction is possible for
2001 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
2002 to remove sites with missing data on a pairwise basis. The option
2003 `GCcontent' has been removed.
2005 o read.GenBank() has a new option (species.names) which specifies
2006 whether to return the species names of the organisms in addition
2007 to the accession numbers of the sequences (this is the default
2010 o write.nexus() can now write several trees in the same NEXUS file.
2012 o drop.tip() has a new option `root.edge' that allows to specify the
2013 new root edge if internal branches are trimmed.
2018 o as.phylo.hclust() failed if some labels had parentheses: this
2021 o Several bugs were fixed in all.equal.phylo(). This function now
2022 returns the logical TRUE if the trees are identical but with
2023 different representations (a report was printed previously).
2025 o read.GenBank() did not correctly handle ambiguous base codes:
2031 o birthdeath() now returns an object of class "birthdeath" for
2032 which there is a print method.
2036 CHANGES IN APE VERSION 1.4
2041 o The new function nj() performs phylogeny estimation with the
2042 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
2045 o The new function which.edge() identifies the edges of a tree
2046 that belong to a group specified as a set of tips.
2048 o The new function as.phylo.phylog() converts an object of class
2049 "phylog" (from the package ade4) into an object of class
2052 o The new function axisPhylo() draws axes on the side of a
2055 o The new function howmanytrees() calculates the number of trees
2056 in different cases and giving a number of tips.
2058 o write.tree() has a new option `multi.line' (TRUE by default) to
2059 write a Newick tree on several lines rather than on a single
2062 o The functionalities of zoom() have been extended. Several
2063 subtrees can be visualized at the same time, and they are marked
2064 on the main tree with colors. The context of the subtrees can be
2065 marked with the option `subtree' (see below).
2067 o drop.tip() has a new option `subtree' (FALSE by default) which
2068 specifies whether to output in the tree how many tips have been
2071 o The arguments of add.scale.bar() have been redefined and have
2072 now default values (see ?add.scale.bar for details). This
2073 function now works even if the plotted tree has no edge length.
2075 o plot.phylo() can now plot radial trees, but this does not take
2076 edge lengths into account.
2078 o In plot.phylo() with `type = "phylogram"', if the values of
2079 `edge.color' and `edge.width' are identical for sister-branches,
2080 they are propagated to the vertical line that link them.
2085 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
2086 crashing. This is fixed.
2088 o In plot.phylo(), the options `edge.color' and `edge.width' are
2089 now properly recycled; their default values are now "black" and
2092 o A bug has been fixed in write.nexus().
2097 o The function node.depth.edgelength() has been removed and
2098 replaced by a C code.
2102 CHANGES IN APE VERSION 1.3-1
2107 o The new function nodelabels() allows to add labels to the nodes
2108 of a tree using text or plotting symbols in a flexible way.
2110 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
2111 numeric values specifying the lower and upper limits on the x-
2112 and y-axes. This allows to leave some space on any side of the
2113 tree. If a single value is given, this is taken as the upper
2118 CHANGES IN APE VERSION 1.3
2123 o The new function phymltest() calls the software PHYML and fits
2124 28 models of DNA sequence evolution. There are a print method to
2125 display likelihood and AIC values, a summary method to compute
2126 the hierarchical likelihood ratio tests, and a plot method to
2127 display graphically the AIC values of each model.
2129 o The new function yule.cov() fits the Yule model with covariates,
2130 a model where the speciation rate is affected by several species
2131 traits through a generalized linear model. The parameters are
2132 estimated by maximum likelihood.
2134 o Three new functions, corBrownian(), corGrafen(), and
2135 corMartins(), compute the expected correlation structures among
2136 species given a phylogeny under different models of evolution.
2137 These can be used for GLS comparative phylogenetic methods (see
2138 the examples). There are coef() and corMatrix() methods and an
2139 Initialize.corPhyl() function associated.
2141 o The new function compar.cheverud() implements Cheverud et al.'s
2142 (1985; Evolution 39:1335) phylogenetic comparative method.
2144 o The new function varcomp() estimates variance components; it has
2147 o Two new functions, panel.superpose.correlogram() and
2148 plot.correlogramList(), allow to plot several phylogenetic
2151 o The new function node.leafnumber() computes the number of leaves
2152 of a subtree defined by a particular node.
2154 o The new function node.sons() gets all tags of son nodes from a
2157 o The new function compute.brlen() computes the branch lengths of
2158 a tree according to a specified method.
2160 o plot.phylo() has three new options: "cex" controls the size of
2161 the (tip and node) labels (thus it is no more needed to change
2162 the global graphical parameter), "direction" which allows to
2163 plot the tree rightwards, leftwards, upwards, or downwards, and
2164 "y.lim" which sets the upper limit on the y-axis.
2169 o Some functions which try to match tip labels and names of
2170 additional data (e.g. vector) are likely to fail if there are
2171 typing or syntax errors. If both series of names do not perfectly
2172 match, they are ignored and a warning message is now issued.
2173 These functions are bd.ext, compar.gee, pic. Their help pages
2174 have been clarified on this point.
2178 CHANGES IN APE VERSION 1.2-7
2183 o The new function root() reroots a phylogenetic tree with respect
2184 to a specified outgroup.
2186 o The new function rotate() rotates an internal branch of a tree.
2188 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
2189 trees) controls the display of the tip labels in unrooted trees.
2190 This display has been greatly improved: the tip labels are now not
2191 expected to overlap with the tree (particularly if lab4ut =
2192 "axial"). In all cases, combining appropriate values of "lab4ut"
2193 and the font size (via "par(cex = )") should result in readable
2194 unrooted trees. See ?plot.phylo for some examples.
2196 o In drop.tip(), the argument `tip' can now be numeric or character.
2201 o drop.tip() did not work correctly with trees with no branch
2202 lengths: this is fixed.
2204 o A bug in plot.phylo(..., type = "unrooted") made some trees being
2205 plotted with some line crossings: this is now fixed.
2209 CHANGES IN APE VERSION 1.2-6
2214 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
2215 correlogram.phylo, dist.taxo, plot.correlogram) have been added
2216 to implement comparative methods with an autocorrelation approach.
2218 o A new data set describing some life history traits of Carnivores
2224 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
2229 o When plotting a tree with plot.phylo(), the new default of the
2230 option `label.offset' is now 0, so the labels are always visible.
2234 CHANGES IN APE VERSION 1.2-5
2239 o The new function bd.ext() fits a birth-death model with combined
2240 phylogenetic and taxonomic data, and estimates the corresponding
2241 speciation and extinction rates.
2246 o The package gee is no more required by ape but only suggested
2247 since only the function compar.gee() calls gee.
2251 CHANGES IN APE VERSION 1.2-4
2256 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
2257 and lines.popsize) implementing a new approach for inferring the
2258 demographic history from genealogies using a reversible jump
2259 MCMC have been introduced.
2261 o The unit of time in the skyline plot and in the new plots can
2262 now be chosen to be actual years, rather than substitutions.
2266 CHANGES IN APE VERSION 1.2-3
2271 o The new function rtree() generates a random binary tree with or
2272 without branch lengths.
2274 o Two new functions for drawing lineages-through-time (LTT) plots
2275 are provided: ltt.lines() adds a LTT curve to an existing plot,
2276 and mltt.plot() does a multiple LTT plot giving several trees as
2277 arguments (see `?ltt.plot' for details).
2282 o Some taxon names made R crashing when calling as.phylo.hclust():
2285 o dist.dna() returned an error with two identical DNA sequences
2286 (only using the Jukes-Cantor method returned 0): this is fixed.
2291 o The function dist.phylo() has been re-written using a different
2292 algorithm: it is now about four times faster.
2294 o The code of branching.times() has been improved: it is now about
2299 CHANGES IN APE VERSION 1.2-2
2304 o The new function seg.sites() finds the segregating sites in a
2305 sample of DNA sequences.
2310 o A bug introduced in read.tree() and in read.nexus() with version
2313 o A few errors were corrected and a few examples were added in the
2318 CHANGES IN APE VERSION 1.2-1
2323 o plot.phylo() can now draw the edge of the root of a tree if it
2324 has one (see the new option `root.edge', its default is FALSE).
2329 o A bug was fixed in read.nexus(): files with semicolons inside
2330 comment blocks were not read correctly.
2332 o The behaviour of read.tree() and read.nexus() was corrected so
2333 that tree files with badly represented root edges (e.g., with
2334 an extra pair of parentheses, see the help pages for details)
2335 are now correctly represented in the object of class "phylo";
2336 a warning message is now issued.
2340 CHANGES IN APE VERSION 1.2
2345 o plot.phylo() has been completely re-written and offers several
2346 new functionalities. Three types of trees can now be drawn:
2347 phylogram (as previously), cladogram, and unrooted tree; in
2348 all three types the branch lengths can be drawn using the edge
2349 lengths of the phylogeny or not (e.g., if the latter is absent).
2350 The vertical position of the nodes can be adjusted with two
2351 choices (see option `node.pos'). The code has been re-structured,
2352 and two new functions (potentially useful for developpers) are
2353 documented separately: node.depth.edgelength() and node.depth();
2354 see the respective help pages for details.
2356 o The new function zoom() allows to explore very large trees by
2357 focusing on a small portion of it.
2359 o The new function yule() fits by maximum likelihood the Yule model
2360 (birth-only process) to a phylogenetic tree.
2362 o Support for writing DNA sequences in FASTA format has been
2363 introduced in write.dna() (support for reading sequences in
2364 this format was introduced in read.dna() in version 1.1-2).
2365 The function has been completely re-written, fixing some bugs
2366 (see below); the default behaviour is no more to display the
2367 sequences on the standard output. Several options have been
2368 introduced to control the sequence printing in a flexible
2369 way. The help page has been extended.
2371 o A new data set is included: a supertree of bats in NEXUS format.
2376 o In theta.s(), the default of the option `variance' has
2377 been changed to `FALSE' (as was indicated in the help page).
2379 o Several bugs were fixed in the code of all.equal.phylo().
2381 o Several bugs were fixed in write.dna(), particularly this
2382 function did not work with `format = "interleaved"'.
2384 o Various errors were corrected in the help pages.
2389 o The argument names of as.hclust.phylo() have been changed
2390 from "(phy)" to "(x, ...)" to conform to the definition of
2391 the corresponding generic function.
2393 o gamma.stat() has been renamed gammaStat() to avoid confusion
2394 since gamma() is a generic function.
2398 CHANGES IN APE VERSION 1.1-3
2403 o base.freq() previously did not return a value of 0 for
2404 bases absent in the data (e.g., a vector of length 3 was
2405 returned if one base was absent). This is now fixed (a
2406 vector of length 4 is always returned).
2408 o Several bugs were fixed in read.nexus(), including that this
2409 function did not work in this absence of a "TRANSLATE"
2410 command in the NEXUS file, and that the commands were
2415 CHANGES IN APE VERSION 1.1-2
2420 o The Tamura and Nei (1993) model of DNA distance is now implemented
2421 in dist.dna(): five models are now available in this function.
2423 o A new data set is included: a set of 15 sequences of the
2424 cytochrome b mitochondrial gene of the woodmouse (Apodemus
2430 o A bug in read.nexus() was fixed.
2432 o read.dna() previously did not work correctly in most cases.
2433 The function has been completely re-written and its help page
2434 has been considerably extended (see ?read.dna for details).
2435 Underscores (_) in taxon names are no more replaced with
2436 spaces (this behaviour was undocumented).
2438 o A bug was fixed in write.dna().
2442 CHANGES IN APE VERSION 1.1-1
2447 o A bug in read.tree() introduced in APE 1.1 was fixed.
2449 o A bug in compar.gee() resulted in an error when trying to fit
2450 a model with `family = "binomial"'. This is now fixed.
2454 CHANGES IN APE VERSION 1.1
2459 o The Klastorin (1982) method as suggested by Misawa and Tajima
2460 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
2461 on the basis of phylogenetic trees has been implemented (see
2462 the function klastorin()).
2464 o Functions have been added to convert APE's "phylo" objects in
2465 "hclust" cluster objects and vice versa (see the help page of
2466 as.phylo for details).
2468 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
2469 are introduced for the estimation of absolute evolutionary rates
2470 (ratogram) and dated clock-like trees (chronogram) from
2471 phylogenetic trees using the non-parametric rate smoothing approach
2472 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
2474 o A summary method is now provided printing a summary information on a
2475 phylogenetic tree with, for instance, `summary(tree)'.
2477 o The behaviour of read.tree() was changed so that all spaces and
2478 tabulations in tree files are now ignored. Consequently, spaces in tip
2479 labels are no more allowed. Another side effect is that read.nexus()
2480 now does not replace the underscores (_) in tip labels with spaces
2481 (this behaviour was undocumented).
2483 o The function plot.phylo() has a new option (`underscore') which
2484 specifies whether the underscores in tip labels should be written on
2485 the plot as such or replaced with spaces (the default).
2487 o The function birthdeath() now computes 95% confidence intervals of
2488 the estimated parameters using profile likelihood.
2490 o Three new data sets are included: a gene tree estimated from 36
2491 landplant rbcL sequences, a gene tree estimated from 32 opsin
2492 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
2497 o A bug was fixed in dist.gene() where nothing was returned.
2499 o A bug in plot.mst() was fixed.
2501 o A bug in vcv.phylo() resulted in false correlations when the
2502 option `cor = TRUE' was used (now fixed).
2506 CHANGES IN APE VERSION 1.0
2511 o Two new functions, read.dna() and write.dna(), read/write in a file
2512 DNA sequences in interleaved or in sequential format.
2514 o Two new functions, read.nexus() and write.nexus(), read/write trees
2517 o The new function bind.tree() allows to bind two trees together,
2518 possibly handling root edges to give internal branches.
2520 o The new function drop.tip() removes the tips in a phylogenetic tree,
2521 and trims (or not) the corresponding internal branches.
2523 o The new function is.ultrametric() tests if a tree is ultrametric.
2525 o The function plot.phylo() has more functionalities such as drawing the
2526 branches with different colours and/or different widths, showing the
2527 node labels, controling the position and font of the labels, rotating
2528 the labels, and controling the space around the plot.
2530 o The function read.tree() can now read trees with no branch length,
2531 such as "(a,b),c);". Consequently, the element `edge.length' in
2532 objects of class "phylo" is now optional.
2534 o The function write.tree() has a new default behaviour: if the default
2535 for the option `file' is used (i.e. file = ""), then a variable of
2536 mode character containing the tree in Newick format is returned which
2537 can thus be assigned (e.g., tree <- write.tree(phy)).
2539 o The function read.tree() has a new argument `text' which allows
2540 to read the tree in a variable of mode character.
2542 o A new data set is included: the phylogenetic relationships among
2543 the orders of birds from Sibley and Ahlquist (1990).
2547 CHANGES IN APE VERSION 0.2-1
2552 o Several bugs were fixed in the help pages.
2556 CHANGES IN APE VERSION 0.2
2561 o The function write.tree() writes phylogenetic trees (objects of class
2562 "phylo") in an ASCII file using the Newick parenthetic format.
2564 o The function birthdeath() fits a birth-death model to branching times
2565 by maximum likelihood, and estimates the corresponding speciation and
2568 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
2571 o The function is.binary.tree() tests whether a phylogeny is binary.
2573 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
2574 as well as some methods are introduced.
2576 o Several functions, including some generics and methods, for computing
2577 skyline plot estimates (classic and generalized) of effective
2578 population size through time are introduced and replace the function
2579 skyline.plot() in version 0.1.
2581 o Two data sets are now included: the phylogenetic relationships among
2582 the families of birds from Sibley and Ahlquist (1990), and an
2583 estimated clock-like phylogeny of HIV sequences sampled in the
2584 Democratic Republic of Congo.
2587 DEPRECATED & DEFUNCT
2589 o The function skyline.plot() in ape 0.1 has been deprecated and
2590 replaced by more elaborate functions (see above).
2595 o Two important bugs were fixed in plot.phylo(): phylogenies with
2596 multichotomies not at the root or not with only terminal branches,
2597 and phylogenies with a single node (i.e. only terminal branches)
2598 did not plot. These trees should be plotted correctly now.
2600 o Several bugs were fixed in diversi.time() in the computation of
2603 o Various errors were corrected in the help pages.
projects / ape.git / blob