1 CHANGES IN APE VERSION 2.7-3
6 o Branch lengths were wrongly updated with bind.tree(, where = <tip>,
7 position = 0). (Thanks to Liam Revell for digging this bug out.)
11 CHANGES IN APE VERSION 2.7-2
16 o There is a new class "evonet" to code evolutionary networks, with
17 a constructor function evonet(), a print() and a plot() methods,
18 and four conversion methods to the classes "phylo", "networx",
19 "network", and "igraph".
21 o The new function rTraitMult does multivariate traits simulation
22 with user-defined models.
24 o plot.phylo() has a new option 'plot = TRUE'. If FALSE, the tree
25 is not plotted but the graphical device is set and the
26 coordinates are saved as usual.
28 o diversity.contrast.test() gains a fourth version of the test with
29 method = "logratio"; the literature citations have been clarified.
31 o add.scale.bar() has two new options, 'lwd' and 'lcol', to modify
32 the aspect of the bar.
34 o boot.phylo() now displays a progress bar by default (can be off
37 o There is a new predict() method for compar.gee().
42 o bionj() made R crash if distances were too large. It now returns
43 an error if at least one distance is greater than 100.
45 o drop.tip() returned a wrong tree if 'tip' was of zero length.
47 o read.nexus.data() failed with URLs.
49 o boot.phylo() returned overestimated support values in the
50 presence of identical or nearly identical sequences.
55 o The data bird.families, bird.orders, cynipids, and woodmouse are
56 now provided as .rda files.
60 CHANGES IN APE VERSION 2.7-1
65 o The new function trex does tree exploration with multiple
68 o The new function kronoviz plots several rooted (dated) trees on
71 o identify.phylo() has a new option 'quiet' (FALSE by default).
76 o A bug was introduced in read.nexus() in ape 2.7.
78 o image.DNAbin() did not colour correctly the bases if there were
81 o .compressTipLabel() failed with a list with a single tree.
83 o identify.phylo() returned a wrong answer when the x- and y-scales
86 o write.nexus() failed with lists of trees with compressed labels.
91 o identify.phylo() now returns NULL if the user right-(instead of
92 left-)clicks (an error was returned previously).
94 o read.nexus() should be robust to commands inserted in the TREES
99 CHANGES IN APE VERSION 2.7
104 o There is a new image() method for "DNAbin" objects: it plots DNA
105 alignments in a flexible and efficient way.
107 o Two new functions as.network.phylo and as.igraph.phylo convert
108 trees of class "phylo" into these respective network classes
109 defined in the packages of the same names.
111 o The three new functions clustal, muscle, and tcoffee perform
112 nucleotide sequence alignment by calling the external programs
115 o Four new functions, diversity.contrast.test, mcconwaysims.test,
116 richness.yule.test, and slowinskiguyer.test, implement various
117 tests of diversification shifts using sister-clade comparisons.
119 o base.freq() gains an option 'all' to count all the possible bases
120 including the ambiguous ones (defaults to FALSE).
122 o read.nexus() now writes tree names in the NEXUS file if given a
123 list of trees with names.
128 o prop.part() failed in some situations with unrooted trees.
130 o read.nexus() shuffled node labels when a TRANSLATE block was
133 o varCompPhylip() did not work if 'exec' was specified.
135 o bind.tree() shuffled node labels when position > 0 and 'where'
141 o BaseProportion in src/dist_dna.c has been modified.
143 o A number of functions in src/tree_build.c have been modified.
145 o The matching representation has now only two columns as the third
146 column was redundant.
150 CHANGES IN APE VERSION 2.6-3
155 o rTraitCont() and rTraitDisc() gains a '...' argument used with
156 user-defined models (suggestion by Gene Hunt).
161 o as.hclust.phylo() now returns an error with unrooted trees.
163 o as.hclust.phylo() failed with trees with node labels (thanks to
164 Jinlong Zhang for pointing this bug out).
166 o read.dna(, "fasta") failed if sequences were not all of the same
169 o plot.phylo() did not recycle values of 'font', 'cex' and
170 'tip.color' correctly when type = "fan" or "radial".
172 o plot.phylo() ignored 'label.offset' when type = "radial", "fan", or
173 "unrooted" with lab4ut = "axial" (the placement of tip labels still
174 needs to be improved with lab4ut = "horizontal").
179 o In drop.fossil() the default tol = 0 has been raised to 1e-8.
181 o The help command ?phylo now points to the man page of read.tree()
182 where this class is described. Similarly, ?matching points to the
183 man page of as.matching().
187 CHANGES IN APE VERSION 2.6-2
192 o Two new functions, pic.ortho and varCompPhylip, implements the
193 orthonormal contrasts of Felsenstein (2008, Am Nat, 171:713). The
194 second function requires Phylip to be installed on the computer.
196 o bd.ext() has a new option conditional = TRUE to use probabilities
197 conditioned on no extinction for the taxonomic data.
202 o write.tree() failed to output correctly tree names.
204 o dist.nodes() returned duplicated column(s) with unrooted and/or
205 multichotomous trees.
207 o mcmc.popsize() terminated unexpectedly if the progress bar was
210 o prop.part(x) made R frozen if 'x' is of class "multiPhylo".
212 o Compilation under Mandriva failed (thanks to Jos Käfer for the fix).
214 o drop.tip() shuffled tip labels with subtree = TRUE or trim.internal
217 o Objects returned by as.hclust.phylo() failed when analysed with
218 cutree() or rect.hclust().
220 o write.tree() did not output correctly node labels (thanks to Naim
221 Matasci and Jeremy Beaulieu for the fix).
223 o ace(type = "discrete") has been improved thanks to Naim Marasci and
228 CHANGES IN APE VERSION 2.6-1
233 o The new function speciesTree calculates the species tree from a set
234 of gene trees. Several methods are available including maximum tree
235 and shallowest divergence tree.
240 o A bug introduced in write.tree() with ape 2.6 has been fixed.
242 o as.list.DNAbin() did not work correctly with vectors.
244 o as.hclust.phylo() failed with trees with node labels (thanks to
245 Filipe Vieira for the fix).
249 CHANGES IN APE VERSION 2.6
254 o The new functions rlineage and rbdtree simulate phylogenies under
255 any user-defined time-dependent speciation-extinction model. They
256 use continuous time algorithms.
258 o The new function drop.fossil removes the extinct species from a
261 o The new function bd.time fits a user-defined time-dependent
262 birth-death model. It is a generalization of yule.time() taking
263 extinction into account.
265 o The new function MPR does most parsimonious reconstruction of
268 o The new function Ftab computes the contingency table of base
269 frequencies from a pair of sequences.
271 o There is now an 'as.list' method for the class "DNAbin".
273 o dist.dna() can compute the number of transitions or transversions
274 with the option model = "Ts" or model = "Tv", respectively.
276 o [node|tip|edge]labels() gain three options with default values to
277 control the aspect of thermometers: horiz = TRUE, width = NULL,
280 o compar.gee() has been improved with the new option 'corStruct' as an
281 alternative to 'phy' to specify the correlation structure, and
282 calculation of the QIC (Pan 2001, Biometrics). The display of the
283 results has also been improved.
285 o read.GenBank() has a new option 'gene.names' to return the name of
286 the gene (FALSE by default).
291 o extract.clade() sometimes shuffled the tip labels.
293 o plot.phylo(type = "unrooted") did not force asp = 1 (thanks to Klaus
296 o dist.dna(model = "logdet") used to divide distances by 4. The
297 documentation has been clarified on the formulae used.
302 o rTraitCont(model = "OU") has an option 'linear = TRUE' to possibly
303 change the parameterisation (see ?rTraitCont for details).
305 o pic() now returns a vector with the node labels of the tree (if
308 o write.tree() and read.tree() have been substantially improved thanks
309 to contributions by Klaus Schliep.
313 CHANGES IN APE VERSION 2.5-3
318 o The new function mixedFontLabel helps to make labels with bits of
319 text to be plotted in different fonts.
321 o There are now replacement operators for [, [[, and $ for the class
322 "multiPhylo" (i.e., TREES[11:20] <- rmtree(10, 100)). They possibly
323 check that the tip labels are the same in all trees.
325 o Objects of class "multiPhylo" can be built with c(): there are
326 methods for the classes "phylo" and "multiPhylo".
328 o The internal functions .compressTipLabel and .uncompressTipLabel are
334 o bind.tree(x, y, where, position = 0) did not work correctly if 'y'
335 was a single-edge tree and 'where' was a tip.
337 o rTraitCont() did not use the square-root of branch lengths when
338 simulating a Brownian motion model.
342 CHANGES IN APE VERSION 2.5-2
347 o There is now a print method for results from ace().
349 o There is a labels() method for objects of class "DNAbin".
351 o read.dna() has a new option 'as.matrix' to possibly force sequences
352 in a FASTA file to be stored in a matrix (see ?read.dna for details).
357 o as.phylo.hclust() used to multiply edge lengths by 2.
359 o A minor bug was fixed in rTraitDisc().
361 o ace() sometimes failed (parameter value was NaN and the optimisation
367 o evolve.phylo() and plot.ancestral() have been removed.
369 o chronogram(), ratogram(), and NPRS.criterion() have been removed.
374 o nj() has been improved and is now about 30% faster.
376 o The default option 'drop' of [.DNAbin has been changed to FALSE to
377 avoid dropping rownames when selecting a single sequence.
379 o print.DNAbin() has been changed to summary.DNAbin() which has been
384 CHANGES IN APE VERSION 2.5-1
389 o The new function stree generates trees with regular shapes.
391 o It is now possible to bind two trees with x + y (see ?bind.tree for
394 o drop.tip(), extract.clade(), root(), and bind.tree() now have an
395 'interactive' option to make the operation on a plotted tree.
397 o cophyloplot() gains two new arguments 'lwd' and 'lty' for the
398 association links; they are recycled like 'col' (which wasn't before).
403 o rTraitDisc() did not use its 'freq' argument correctly (it was
404 multiplied with the rate matrix column-wise instead of row-wise).
406 o [node|tip|edge]labels(thermo = ) used to draw empty thermometers
407 with NA values. Nothing is drawn now like with 'text' or 'pch'.
408 The same bug occurred with the 'pie' option.
410 o A bug was fixed in compar.ou() and the help page was clarified.
412 o bind.tree() has been rewritten fixing several bugs and making it
415 o plot.phylo(type = "p") sometimes failed to colour correctly the
416 vertical lines representing the nodes.
418 o plot.phylo(direction = "l", x.lim = 30) failed to plot the branches
419 in the correct direction though the tip labels were displayed
425 o The c, cbind, and rbind methods for "DNAbin" objetcs now check that
426 the sequences are correctly stored (in a list for c, in a matrix
427 for the two other functions).
431 CHANGES IN APE VERSION 2.5
436 o The new function parafit by Pierre Legendre tests for the
437 coevolution between hosts and parasites. It has a companion
438 function, pcoa, that does principal coordinate decomposition.
439 The latter has a biplot method.
441 o The new function lmorigin by Pierre Legendre performs multiple
442 regression through the origin with testing by permutation.
444 o The new functions rTraitCont and rTraitDisc simulate continuous and
445 discrete traits under a wide range of evolutionary models.
447 o The new function delta.plot does a delta plot following Holland et
448 al. (2002, Mol. Biol. Evol. 12:2051).
450 o The new function edges draws additional branches between any nodes
451 and/or tips on a plotted tree.
453 o The new function fancyarrows enhances arrows from graphics with
454 triangle and harpoon heads; it can be called from edges().
456 o add.scale.bar() has a new option 'ask' to draw interactively.
458 o The branch length score replaces the geodesic distance in dist.topo.
460 o Three new data sets are included: the gopher-lice data (gopher.D),
461 SO2 air pollution in 41 US cities (lmorigin.ex1, from Sokal &
462 Rohlf 1995), and some host-parasite specificity data
463 (lmorigin.ex2, from Legendre & Desdevises 2009).
468 o add.scale.bar() drew the bar outside the plotting region with the
469 default options with unrooted or radial trees.
471 o dist.topo() made R stuck when the trees had different sizes (thanks
472 to Otto Cordero for the fix).
477 o The geodesic distance has been replaced by the branch length score
482 CHANGES IN APE VERSION 2.4-1
487 o rtree() and rcoal() now accept a numeric vector for the 'br'
490 o vcv() is a new generic function with methods for the classes "phylo"
491 and "corPhyl" so that it is possible to calculate the var-cov matrix
492 for "transformation models". vcv.phylo() can still be used for trees
493 of class "phylo"; its argument 'cor' has been renamed 'corr'.
498 o bind.tree() failed when 'y' had no root edge.
500 o read.nexus() shuffled tip labels when the trees have no branch
501 lengths and there is a TRANSLATE block.
503 o read.nexus() does not try to translate node labels if there is a
504 translation table in the NEXUS file. See ?read.nexus for a
505 clarification on this behaviour.
507 o plot.multiPhylo() crashed R when plotting a list of trees with
508 compressed tip labels.
510 o write.nexus() did not translate the taxa names when asked for.
512 o plot.phylo(type = "fan") did not rotate the tip labels correctly
513 when the tree has branch lengths.
515 o ace(type = "continuous", method = "ML") now avoids sigma² being
516 negative (which resulted in an error).
518 o nj() crashed with NA/NaN in the distance matrix: an error in now
523 CHANGES IN APE VERSION 2.4
528 o base.freq() has a new option 'freq' to return the counts; the
529 default is still to return the proportions.
534 o seg.sites() did not handle ambiguous nucleotides correctly: they
537 o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
538 the tree: the argument is now ignored.
540 o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
546 o Trying to plot a tree with a single tip now returns NULL with a
547 warning (it returned an error previously).
549 o The way lines representing nodes are coloured in phylograms has
550 been modified (as well as their widths and types) following some
551 users' request; this is only for dichotomous nodes.
553 o The argument 'adj' in [node][tip][edge]labels() now works when
554 using 'pie' or 'thermo'.
556 o A more informative message error is now returned by dist.dna() when
557 'model' is badly specified (partial matching of this argument is
560 o Deprecated functions are now listed in a help page: see
561 help("ape-defunct") with the quotes.
566 o The functions heterozygosity, nuc.div, theta.h, theta.k and
567 theta.s have been moved from ape to pegas.
569 o The functions mlphylo, DNAmodel and sh.test have been removed.
573 CHANGES IN APE VERSION 2.3-3
578 o add.scale.bar() always drew a horizontal bar.
580 o zoom() shuffled tips with unrooted trees.
582 o write.nexus() failed to write correctly trees with a "TipLabel"
585 o rcoal() failed to compute branch lengths with very large n.
587 o A small bug was fixed in compar.cheverud() (thanks to Michael
590 o seg.sites() failed when passing a vector.
592 o drop.tip() sometimes shuffled tip labels.
594 o root() shuffled node labels with 'resolve.root = TRUE'.
598 CHANGES IN APE VERSION 2.3-2
603 o all.equal.phylo() did not compare unrooted trees correctly.
605 o dist.topo(... method = "PH85") did not treat unrooted trees
606 correctly (thanks to Tim Wallstrom for the fix).
608 o root() sometimes failed to test for the monophyly of the
611 o extract.clade() sometimes included too many edges.
613 o vcv.phylo() did not work correctly when the tree is in
616 o nj() did not handle correctly distance matrices with many 0's.
617 The code has also been significantly improved: 7, 70, 160 times
618 faster with n = 100, 500, 1000, respectively.
622 CHANGES IN APE VERSION 2.3-1
627 o The new function is.monophyletic tests the monophyly of a group.
629 o There is now a c() method for lists of class "DNAbin".
631 o yule.cov() now fits the null model, and its help page has been
632 corrected with respect to this change.
634 o drop.tip() has a new option 'rooted' to force (or not) a tree
635 to be treated as (un)rooted.
640 o dist.gene() failed on most occasions with the default
641 pairwise.deletion = FALSE.
643 o read.tree() failed to read correctly the tree name(s).
645 o boot.phylo() now treats correctly data frames.
647 o del.gaps() did not copy the rownames of a matrix.
649 o A small bug was fixed in CDAM.global().
651 o ace() failed with large data sets. Thanks to Rich FitzJohn for
652 the fix. With other improvements, this function is now about 6
655 o write.tree() failed with objects of class "multiPhylo".
657 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
662 o [.multiPhylo and [.DNAbin now respect the original class.
664 o Instances of the form class(phy) == "phylo" have been replaced
665 by inherits(phy, "phylo").
667 o rcoal() is now faster.
672 o klastorin() has been removed.
676 CHANGES IN APE VERSION 2.3
681 o The new functions CADM.global and CADM.post, contributed by
682 Pierre Legendre, test the congruence among several distance
685 o The new function yule.time fits a user-defined time-dependent
686 Yule model by maximum likelihood.
688 o The new function makeNodeLabel creates and/or modifies node
689 labels in a flexible way.
691 o read.tree() and write.tree() have been modified so that they can
692 handle individual tree names.
694 o plot.phylo() has a new argument 'edge.lty' that specifies the
695 types of lines used for the edges (plain, dotted, dashed, ...)
697 o phymltest() has been updated to work with PhyML 3.0.1.
702 o drop.tip() shuffled tip labels in some cases.
704 o drop.tip() did not handle node.label correctly.
706 o is.ultrametric() now checks the ordering of the edge matrix.
708 o ace() sometimes returned negative values of likelihoods of
709 ancestral states (thanks to Dan Rabosky for solving this long
715 o The data set xenarthra has been removed.
719 CHANGES IN APE VERSION 2.2-4
723 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
724 now fixed. (Thanks to Peter Wragg for the fix!)
726 o A warning message occurred for no reason with ace(method="GLS").
731 o There is now a general help page displayed with '?ape'.
735 CHANGES IN APE VERSION 2.2-3
740 o The new function extract.clade extracts a clade from a tree by
741 specifying a node number or label.
743 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
744 operations of the same names.
746 o dist.dna() can now return the number of site differences by
747 specifying model="N".
752 o chronopl() did not work with CV = TRUE.
754 o read.nexus() did not work correctly in some situations (trees on
755 multiple lines with different numbers of lines and/or with
756 comments inserted within the trees).
758 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
759 the number of lineages with non-binary trees.
764 o ape has now a namespace.
766 o drop.tip() has been improved: it should be much faster and work
767 better in some cases (e.g., see the example in ?zoom).
771 CHANGES IN APE VERSION 2.2-2
776 o dist.gene() has been substantially improved and gains an option
779 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
785 o prop.part() failed with a single tree with the default option
786 'check.labels = TRUE'.
788 o summary.DNAbin() failed to display correctly the summary of
789 sequence lengths with lists of sequences of 10,000 bases or more
790 (because summary.default uses 4 significant digits by default).
792 o read.nexus() failed to read a file with a single tree with line
793 breaks in the Newick string.
795 o del.gaps() returned a list of empty sequences when there were no
801 o phymltest() has been updated for PhyML 3.0 and gains an option
802 'append', whereas the option 'path2exec' has been removed.
804 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
805 which is returned unchanged (instead of an error).
807 o The data sets bird.orders and bird.families are now stored as
808 Newick strings; i.e., the command data(bird.orders) calls
813 CHANGES IN APE VERSION 2.2-1
818 o The new function makeLabel() helps to modify labels of trees,
819 lists of trees, or DNA sequences, with several utilities to
820 truncate and/or make them unique, substituting some
821 characters, and so on.
823 o The new function del.gaps() removes insertion gaps ("-") in a
824 set of DNA sequences.
826 o read.dna() can now read Clustal files (*.aln).
831 o root() failed with 'resolve.root = TRUE' when the root was
832 already the specified root.
834 o Several bugs were fixed in mlphylo().
836 o collapsed.singles() did not propagate the 'Nnode' and
837 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
839 o read.nexus() failed to remove correctly the comments within
842 o read.nexus() failed to read a file with a single tree and no
843 translation of tip labels.
845 o read.nexus() failed to place correctly tip labels when reading
846 a single tree with no edge lengths.
848 o A bug was fixed in sh.test().
853 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
856 o The option 'check.labels' of consensus() and prop.part() is now
859 o write.dna() now does not truncate names to 10 characters with
864 CHANGES IN APE VERSION 2.2
869 o Four new functions have been written by Damien de Vienne for the
870 graphical exploration of large trees (cophyloplot, subtrees,
871 subtreeplot), and to return the graphical coordinates of tree
874 o The new functions corPagel and corBlomberg implement the Pagel's
875 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
877 o chronopl() has been improved and gains several options: see its
878 help page for details.
880 o boot.phylo() has now an option 'trees' to possibly return the
881 bootstraped trees (the default is FALSE).
883 o prop.part() has been improved and should now be faster in all
889 o read.dna() failed if "?" occurred in the first 10 sites of the
892 o The x/y aspect of the plot is now respected when plotting a
893 circular tree (type = "r" or "f").
895 o Drawing the tip labels sometimes failed when plotting circular
898 o zoom() failed when tip labels were used instead of their numbers
899 (thanks to Yan Wong for the fix).
901 o drop.tip() failed with some trees (fixed by Yan Wong).
903 o seg.sites() failed with a list.
905 o consensus() failed in some cases. The function has been improved
906 as well and is faster.
910 CHANGES IN APE VERSION 2.1-3
915 o A bug in read.nexus() made the Windows R-GUI crash.
917 o An error was fixed in the computation of ancestral character
918 states by generalized least squares in ace().
920 o di2multi() did not modify node labels correctly.
922 o multi2di() failed if the tree had its attribute "order" set to
927 CHANGES IN APE VERSION 2.1-2
932 o There three new methods for the "multiPhylo" class: str, $,
935 o root() gains the options 'node' and 'resolve.root'
936 (FALSE by default) as well as its code being improved.
938 o mltt.plot() has now an option 'log' used in the same way
939 than in plot.default().
944 o mltt.plot() failed to display the legend with an unnamed
947 o nodelabels() with pies now correcly uses the argument
948 'cex' to draw symbols of different sizes (which has
949 worked already for thermometers).
951 o read.nexus() generally failed to read very big files.
956 o The argument 'family' of compar.gee() can now be a function
957 as well as a character string.
959 o read.tree() and read.nexus() now return an unnamed list if
962 o read.nexus() now returns a modified object of class "multiPhylo"
963 when there is a TRANSLATE block in the NEXUS file: the individual
964 trees have no 'tip.label' vector, but the list has a 'TipLabel'
965 attribute. The new methods '$' and '[[' set these elements
966 correctly when extracting trees.
970 CHANGES IN APE VERSION 2.1-1
975 o The new function rmtree generates lists of random trees.
977 o rcoal() now generates a genuine coalescent tree by default
978 (thanks to Vladimir Minin for the code).
983 o nuc.div() returned an incorrect value with the default
984 pairwise.deletion = FALSE.
989 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
990 have been improved so that they are stabler and faster.
992 o R packages used by ape are now loaded silently; lattice and gee
993 are loaded only when needed.
997 CHANGES IN APE VERSION 2.1
1002 o The new function identify.phylo identifies clades on a plotted
1003 tree using the mouse.
1005 o It is now possible to subset a list of trees (object of class
1006 "multiPhylo") with "[" while keeping its class correct.
1008 o The new function as.DNAbin.alignment converts DNA sequences
1009 stored in the "alignment" format of the package seqinr into
1010 an object of class "DNAbin".
1012 o The new function weight.taxo2 helps to build similarity matrices
1013 given two taxonomic levels (usually called by other functions).
1015 o write.tree() can now take a list of trees (class "multiPhylo")
1016 as its main argument.
1018 o plot.correlogram() and plot.correlogramList() have been
1019 improved, and gain several options (see the help page for
1020 details). A legend is now plotted by default.
1025 o dist.dna() returned some incorrect values with `model = "JC69"'
1026 and `pairwise.deletion = TRUE'. This affected only the
1027 distances involving sequences with missing values. (Thanks
1028 to Bruno Toupance for digging this bug out.)
1030 o write.tree() failed with some trees: this is fixed by removing
1031 the `multi.line' option (trees are now always printed on a
1034 o read.nexus() did not correctly detect trees with multiple root
1035 edges (see OTHER CHANGES).
1040 o The code of mlphylo() has been almost entirely rewritten, and
1041 should be much stabler. The options have been also greatly
1042 simplified (see ?mlphylo and ?DNAmodel for details).
1044 o The internal function nTips has been renamed klastorin_nTips.
1046 o The code of is.ultrametric() contained redundancies and has
1049 o The code of Moran.I() and of correlogram.formula() have been
1052 o read.tree() and read.nexus() now return an error when trying to
1053 read a tree with multiple root edges (see BUG FIXES). The
1054 correction applied in previous version did not work in all
1057 o The class c("multi.tree", "phylo") has been renamed
1063 o There is now a vignette in ape: see vignette("MoranI", "ape").
1066 DEPRECATED & DEFUNCT
1068 o as.matching() and as.phylo.matching() do not support branch
1071 o correlogram.phylo() and discrete.dist() have been removed.
1075 CHANGES IN APE VERSION 2.0-2
1080 o The new function matexpo computes the exponential of a square
1083 o The new function unique.multi.tree removes duplicate trees from
1086 o yule() has a new option `use.root.edge = FALSE' that specifies
1087 to ignore, by default, the root edge of the tree if it exists.
1092 o which.edge() failed when the index of a single terminal edge was
1095 o In diversi.time(), the values returned for model C were
1098 o A bug was fixed in yule() that affected the calculation of the
1099 likelihood in the presence of ties in the branching times.
1101 o There was a bug in the C function mat_expo4x4 affecting the
1102 calculations of the transition probabilities for models HKY and
1105 o A small bug was fixed in as.matrix.DNAbin (thanks to James
1108 o rtree() did not `shuffle' the tip labels by default, so only a
1109 limited number of labelled topologies could be generated.
1113 CHANGES IN APE VERSION 2.0-1
1118 o The three new functions bionj, fastme.ols, and fastme.bal
1119 perform phylogeny estimation by the BIONJ and fastME methods in
1120 OLS and balanced versions. This is a port to R of previous
1121 previous programs done by Vincent Lefort.
1123 o The new function chronoMPL performs molecular dating with the
1124 mean path lengths method of Britton et al. (2002, Mol. Phyl.
1127 o The new function rotate, contributed by Christoph Heibl, swaps
1128 two clades connected to the same node. It works also with
1129 multichotomous nodes.
1131 o The new `method' as.matrix.DNAbin() may be used to convert
1132 easily DNA sequences stored in a list into a matrix while
1133 keeping the names and the class.
1138 o chronopl() failed when some branch lengths were equal to zero:
1139 an error message is now returned.
1141 o di2multi() failed when there was a series of consecutive edges
1146 CHANGES IN APE VERSION 1.10-2
1151 o plot.phylo() can now plot circular trees: the option is type =
1152 "fan" or type = "f" (to avoid the ambiguity with type = "c").
1154 o prop.part() has a new option `check.labels = FALSE' which allows
1155 to considerably speed-up the calculations of bipartitions. As a
1156 consequence, calculations of bootstrap values with boot.phylo()
1157 should be much faster.
1162 o read.GenBank() did not return correctly the list of species as
1163 from ape 1.10: this is fixed in this version
1165 o Applying as.phylo() on a tree of class "phylo" failed: the
1166 object is now returned unchanged.
1170 CHANGES IN APE VERSION 1.10-1
1175 o The three new functions Ntip, Nnode, and Nedge return, for a
1176 given tree, the number of tips, nodes, or edges, respectively.
1181 o read.nexus() did not set correctly the class of the returned
1182 object when reading multiple trees.
1184 o mllt.plot() failed with objects of class c("multi.tree",
1187 o unroot() did not work correctly in most cases.
1189 o reorder.phylo() made R freeze in some occasions.
1191 o Plotting a tree in pruningwise order failed.
1193 o When plotting an unrooted tree, the tip labels where not all
1194 correctly positioned if the option `cex' was used.
1198 CHANGES IN APE VERSION 1.10
1203 o Five new `method' functions have been introduced to manipulate
1204 DNA sequences in binary format (see below).
1206 o Three new functions have been introduced to convert between the
1207 new binary and the character formats.
1209 o The new function as.alignment converts DNA sequences stored as
1210 single characters into the class "alignment" used by the package
1213 o read.dna() and read.GenBank() have a new argument `as.character'
1214 controlling whether the sequences are returned in binary format
1220 o root() failed when the tree had node labels: this is fixed.
1222 o plot.phylo() did not correctly set the limits on the y-axis with
1223 the default setting: this is fixed.
1225 o dist.dna() returned a wrong result for the LogDet, paralinear,
1226 and BH87 models with `pairwise.deletion = TRUE'.
1231 o DNA sequences are now internally stored in a binary format. See
1232 the document "A Bit-Level Coding Scheme for Nucleotides" for the
1233 details. Most functions analyzing DNA functions have been
1234 modified accordingly and are now much faster (dist.dna is now
1235 ca. 60 times faster).
1239 CHANGES IN APE VERSION 1.9-4
1244 o A bug was fixed in edgelabels().
1246 o as.phylo.hclust() did not work correctly when the object of
1247 class "hclust" has its labels set to NULL: the returned tree has
1248 now its tip labels set to "1", "2", ...
1250 o consensus could fail if some tip labels are a subset of others
1251 (e.g., "a" and "a_1"): this is now fixed.
1253 o mlphylo() failed in most cases if some branch lengths of the
1254 initial tree were greater than one: an error message is now
1257 o mlphylo() failed in most cases when estimating the proportion of
1258 invariants: this is fixed.
1262 CHANGES IN APE VERSION 1.9-3
1267 o The new function edgelabels adds labels on the edge of the tree
1268 in the same way than nodelabels or tiplabels.
1273 o multi2di() did not handle correctly branch lengths with the
1274 default option `random = TRUE': this is now fixed.
1276 o A bug was fixed in nuc.div() when using pairwise deletions.
1278 o A bug occurred in the analysis of bipartitions with large
1279 numbers of large trees, with consequences on prop.part,
1280 prop.clades, and boot.phylo.
1282 o The calculation of the Billera-Holmes-Vogtmann distance in
1283 dist.topo was wrong: this has been fixed.
1287 CHANGES IN APE VERSION 1.9-2
1292 o The new function ladderize reorganizes the internal structure of
1293 a tree to plot them left- or right-ladderized.
1295 o The new function dist.nodes computes the patristic distances
1296 between all nodes, internal and terminal, of a tree. It replaces
1297 the option `full = TRUE' of cophenetic.phylo (see below).
1302 o A bug was fixed in old2new.phylo().
1304 o Some bugs were fixed in chronopl().
1306 o The edge colours were not correctly displayed by plot.phylo
1307 (thank you to Li-San Wang for the fix).
1309 o cophenetic.phylo() failed with multichotomous trees: this is
1315 o read.dna() now returns the sequences in a matrix if they are
1316 aligned (interleaved or sequential format). Sequences in FASTA
1317 format are still returned in a list.
1319 o The option `full' of cophenetic.phylo() has been removed because
1320 it could not be used from the generic.
1323 DEPRECATED & DEFUNCT
1325 o rotate() has been removed; this function did not work correctly
1330 CHANGES IN APE VERSION 1.9-1
1335 o Trees with a single tip were not read correctly in R as the
1336 element `Nnode' was not set: this is fixed.
1338 o unroot() did not set correctly the number of nodes of the
1339 unrooted tree in most cases.
1341 o read.GenBank() failed when fetching very long sequences,
1342 particularly of the BX-series.
1344 o A bug was introduced in read.tree() with ape 1.9: it has been
1349 CHANGES IN APE VERSION 1.9
1354 o There are two new print `methods' for trees of class "phylo" and
1355 lists of trees of class "multi.tree", so that they are now
1356 displayed in a compact and informative way.
1358 o There are two new functions, old2new.phylo and new2old.phylo,
1359 for converting between the old and new coding of the class
1362 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
1363 LogDet ("logdet"), and paralinear ("paralin").
1365 o compute.brlen() has been extended: several methods are now
1366 available to compute branch lengths.
1368 o write.dna() can now handle matrices as well as lists.
1373 o cophenetic.phylo() sometimes returned a wrong result with
1374 multichotomous trees: this is fixed.
1376 o rotate() failed when a single tip was specified: the tree is now
1379 o ace() did not return the correct index matrix with custom
1380 models: this is fixed.
1382 o multi2di() did not work correctly when resolving multichotomies
1383 randomly: the topology was always the same, only the arrangement
1384 of clades was randomized: this is fixed. This function now
1385 accepts trees with no branch lengths.
1387 o The output of diversi.gof() was blurred by useless prints when a
1388 user distribution was specified. This has been corrected, and
1389 the help page of this function has been expanded.
1394 o The internal structure of the class "phylo" has been changed:
1395 see the document "Definition of Formats for Coding Phylogenetic
1396 Trees in R" for the details. In addition, the code of most
1397 functions has been improved.
1399 o Several functions have been improved by replacing some R codes
1400 by C codes: pic, plot.phylo, and reorder.phylo.
1402 o There is now a citation information: see citation("ape") in R.
1404 o write.tree() now does not add extra 0's to branch lengths so
1405 that 1.23 is printed "1.23" by default, not "1.2300000000".
1407 o The syntax of bind.tree() has been simplified. This function now
1408 accepts trees with no branch lengths, and handles correctly node
1411 o The option `as.numeric' of mrca() has been removed.
1413 o The unused options `format' and `rooted' of read.tree() have
1416 o The unused option `format' of write.tree() has been removed.
1418 o The use of node.depth() has been simplified.
1422 CHANGES IN APE VERSION 1.8-5
1427 o Two new functions read.nexus.data() and write.nexus.data(),
1428 contributed by Johan Nylander, allow to read and write molecular
1429 sequences in NEXUS files.
1431 o The new function reorder.phylo() reorders the internal structure
1432 of a tree of class "phylo". It is used as the generic, e.g.,
1435 o read.tree() and read.nexus() can now read trees with a single
1438 o The new data set `cynipids' supplies a set of protein sequences
1444 o The code of all.equal.phylo() has been completely rewritten
1445 (thanks to Benoît Durand) which fixes several bugs.
1447 o read.tree() and read.nexus() now checks the labels of the tree
1448 to remove or substitute any characters that are illegal in the
1449 Newick format (parentheses, etc.)
1451 o A negative P-value could be returned by mantel.test(): this is
1456 CHANGES IN APE VERSION 1.8-4
1461 o The new function sh.test() computes the Shimodaira-
1464 o The new function collapse.singles() removes the nodes with a
1465 single descendant from a tree.
1467 o plot.phylo() has a new argument `tip.color' to specify the
1468 colours of the tips.
1470 o mlphylo() has now an option `quiet' to control the display of
1471 the progress of the analysis (the default is FALSE).
1476 o read.dna() did not read correctly sequences in sequential format
1477 with leading alignment gaps "-": this is fixed.
1479 o ace() returned a list with no class so that the generic
1480 functions (anova, logLik, ...) could not be used directly. This
1481 is fixed as ace() now returns an object of class "ace".
1483 o anova.ace() had a small bug when computing the number of degrees
1484 of freedom: this is fixed.
1486 o mlphylo() did not work when the sequences were in a matrix or
1487 a data frame: this is fixed.
1489 o rtree() did not work correctly when trying to simulate an
1490 unrooted tree with two tips: an error message is now issued.
1495 o The algorithm of rtree() has been changed: it is now about 40,
1496 100, and 130 times faster for 10, 100, and 1000 tips,
1501 CHANGES IN APE VERSION 1.8-3
1506 o There are four new `method' functions to be used with the
1507 results of ace(): logLik(), deviance(), AIC(), and anova().
1509 o The plot method of phymltest has two new arguments: `main' to
1510 change the title, and `col' to control the colour of the
1511 segments showing the AIC values.
1513 o ace() has a new argument `ip' that gives the initial values used
1514 in the ML estimation with discrete characters (see the examples
1515 in ?ace). This function now returns a matrix giving the indices
1516 of the estimated rates when analysing discrete characters.
1518 o nodelabels() and tiplabels() have a new argument `pie' to
1519 represent proportions, with any number of categories, as
1520 piecharts. The use of the option `thermo' has been improved:
1521 there is now no limitation on the number of categories.
1526 o mlphylo() did not work with more than two partitions: this is
1529 o root() failed if the proposed outgroup was already an outgroup
1530 in the tree: this is fixed.
1532 o The `col' argument in nodelabels() and tiplabels() was not
1533 correctly passed when `text' was used: this is fixed.
1535 o Two bugs were fixed in mlphylo(): parameters were not always
1536 correctly output, and the estimation failed in some cases.
1538 o plot.phylo() was stuck when given a tree with a single tip: this
1539 is fixed and a message error is now returned.
1541 o An error was corrected in the help page of gammaStat regarding
1542 the calculation of P-values.
1544 o Using gls() could crash R when the number of species in the tree
1545 and in the variables were different: this is fixed.
1549 CHANGES IN APE VERSION 1.8-2
1554 o The new function mlphylo() fits a phylogenetic tree by maximum
1555 likelihood from DNA sequences. Its companion function DNAmodel()
1556 is used to define the substitution model which may include
1557 partitioning. There are methods for logLik(), deviance(), and
1558 AIC(), and the summary() method has been extended to display in
1559 a friendly way the results of this model fitting. Currently, the
1560 functionality is limited to estimating the substitution and
1561 associated parameters and computing the likelihood.
1563 o The new function drop1.compar.gee (used as, e.g., drop1(m))
1564 tests for single effects in GEE-based comparative method. A
1565 warning message is printed if there is not enough degrees of
1571 o An error message was sometimes issued by plot.multi.tree(),
1572 though with no consequence.
1576 CHANGES IN APE VERSION 1.8-1
1581 o There is a new plot method for lists of trees (objects of class
1582 "multi.tree"): it calls plot.phylo() internally and is
1583 documented on the same help page.
1588 o A bug was fixed in the C code that analyzes bipartitions: this
1589 has impact on several functions like prop.part, prop.clades,
1590 boot.phylo, or consensus.
1592 o root() did not work correctly when the specified outgroup had
1593 more than one element: this is fixed.
1595 o dist.dna() sometimes returned a warning inappropriately: this
1598 o If the distance object given to nj() had no rownames, nj()
1599 returned a tree with no tip labels: it now returns tips labelled
1600 "1", "2", ..., corresponding to the row numbers.
1605 o nj() has been slightly changed so that tips with a zero distance
1606 are first aggregated with zero-lengthed branches; the usual NJ
1607 procedure is then performed on a distance matrix without 0's.
1611 CHANGES IN APE VERSION 1.8
1616 o The new function chronopl() estimates dates using the penalized
1617 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1619 o The new function consensus() calculates the consensus tree of a
1622 o The new function evolve.phylo() simulates the evolution of
1623 continuous characters along a phylogeny under a Brownian model.
1625 o The new plot method for objects of class "ancestral" displays a
1626 tree together with ancestral values, as returned by the above
1629 o The new function as.phylo.formula() returns a phylogeny from a
1630 set of nested taxonomic variables given as a formula.
1632 o The new function read.caic() reads trees in CAIC format.
1634 o The new function tiplabels() allows to add labels to the tips
1635 of a tree using text or plotting symbols in a flexible way.
1637 o The new function unroot() unroots a phylogeny.
1639 o multi2di() has a new option, `random', which specifies whether
1640 to resolve the multichotomies randomly (the default) or not.
1642 o prop.part() now returns an object of class "prop.part" for which
1643 there are print (to display a partition in a more friendly way)
1644 and summary (to extract the numbers) methods.
1646 o plot.phylo() has a new option, `show.tip.label', specifying
1647 whether to print the labels of the tips. The default is TRUE.
1649 o The code of nj() has been replaced by a faster C code: it is now
1650 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1653 o write.nexus() now writes whether a tree is rooted or not.
1658 o Two bugs have been fixed in root(): unrooted trees are now
1659 handled corretly, and node labels are now output normally.
1661 o A bug was fixed in phymltest(): the executable couldn't be found
1664 o Three bug have been fixed in ace(): computing the likelihood of
1665 ancestral states of discrete characters failed, custom models
1666 did not work, and the function failed with a null gradient (a
1667 warning message is now returned; this latter bug was also
1668 present in yule.cov() as well and is now fixed).
1670 o pic() hanged out when missing data were present: a message error
1673 o A small bug was fixed in dist.dna() where the gamma correction
1674 was not always correctly dispatched.
1676 o plot.phylo() plotted correctly the root edge only when the tree
1677 was plotted rightwards: this works now for all directions.
1682 o dist.taxo() has been renamed as weight.taxo().
1684 o dist.phylo() has been replaced by the method cophenetic.phylo().
1686 o Various error and warning messages have been improved.
1690 CHANGES IN APE VERSION 1.7
1693 o The new function ace() estimates ancestral character states for
1694 continuous characters (with ML, GLS, and contrasts methods), and
1695 discrete characters (with ML only) for any number of states.
1697 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1698 of directional evolution for continuous characters. The user
1699 specifies the node(s) of the tree where the character optimum
1702 o The new function is.rooted() tests whether a tree (of class
1705 o The new function rcoal() generates random ultrametric trees with
1706 the possibility to specify the function that generates the
1707 inter-nodes distances.
1709 o The new function mrca() gives for all pairs of tips in a tree
1710 (and optionally nodes too) the most recent common ancestor.
1712 o nodelabels() has a new option `thermo' to plot proportions (up
1713 to three classes) on the nodes of a tree.
1715 o rtree() has been improved: it can now generate rooted or
1716 unrooted trees, and the mathematical function that generates the
1717 branch lengths may be specified by the user. The tip labels may
1718 be given directly in the call to rtree. The limit cases (n = 2,
1719 3) are now handled correctly.
1721 o dist.topo() has a new argument `method' with two choices: "PH85"
1722 for Penny and Henny's method (already available before and now
1723 the default), and "BHV01" for the geometric distance by Billera
1724 et al. (2001, Adv. Appl. Math. 27:733).
1726 o write.tree() has a new option, `digits', which specifies the
1727 number of digits to be printed in the Newick tree. By default
1728 digits = 10. The numbers are now always printed in decimal form
1729 (i.e., 1.0e-1 is now avoided).
1731 o dist.dna() can now compute the raw distances between pairs of
1732 DNA sequences by specifying model = "raw".
1734 o dist.phylo() has a new option `full' to possibly compute the
1735 distances among all tips and nodes of the tree. The default if
1741 o Several bugs were fixed in all.equal.phylo().
1743 o dist.dna() did not handle correctly gaps ("-") in alignments:
1744 they are now considered as missing data.
1746 o rotate() did not work if the tips were not ordered: this is
1749 o mantel.test() returned NA in some special cases: this is fixed
1750 and the function has been improved and is now faster.
1752 o A bug was fixed in diversi.gof() where the calculation of A² was
1755 o cherry() did not work correctly under some OSs (mainly Linux):
1758 o is.binary.tree() has been modified so that it works with both
1759 rooted and unrooted trees.
1761 o The documentation of theta.s() was not correct: this has been
1764 o plot.mst() did not work correctly: this is fixed.
1768 CHANGES IN APE VERSION 1.6
1773 o The new function dist.topo() computes the topological distances
1776 o The new function boot.phylo() performs a bootstrap analysis on
1777 phylogeny estimation.
1779 o The new functions prop.part() and prop.clades() analyse
1780 bipartitions from a series of trees.
1785 o read.GenBank() now uses the EFetch utility of NCBI instead of
1786 the usual Web interface: it is now much faster (e.g., 12 times
1787 faster to retrieve 8 sequences, 37 times for 60 sequences).
1792 o Several bugs were fixed in read.dna().
1794 o Several bugs were fixed in diversi.time().
1796 o is.binary.tree() did not work correctly if the tree has no edge
1797 lengths: this is fixed.
1799 o drop.tip() did not correctly propagated the `node.label' of a
1800 tree: this is fixed.
1804 CHANGES IN APE VERSION 1.5
1809 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1810 convert objects between the classes "phylo" and "matching". The
1811 latter implements the representation of binary trees introduced by
1812 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1813 as.matching() has been introduced as well.
1815 o Two new functions, multi2di() and di2multi(), allow to resolve
1816 and collapse multichotomies with branches of length zero.
1818 o The new function nuc.div() computes the nucleotide diversity
1819 from a sample a DNA sequences.
1821 o dist.dna() has been completely rewritten with a much faster
1822 (particularly for large data sets) C code. Eight models are
1823 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1824 option `method' has been renamed `model'). Computation of variance
1825 is available for all models. A gamma-correction is possible for
1826 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1827 to remove sites with missing data on a pairwise basis. The option
1828 `GCcontent' has been removed.
1830 o read.GenBank() has a new option (species.names) which specifies
1831 whether to return the species names of the organisms in addition
1832 to the accession numbers of the sequences (this is the default
1835 o write.nexus() can now write several trees in the same NEXUS file.
1837 o drop.tip() has a new option `root.edge' that allows to specify the
1838 new root edge if internal branches are trimmed.
1843 o as.phylo.hclust() failed if some labels had parentheses: this
1846 o Several bugs were fixed in all.equal.phylo(). This function now
1847 returns the logical TRUE if the trees are identical but with
1848 different representations (a report was printed previously).
1850 o read.GenBank() did not correctly handle ambiguous base codes:
1856 o birthdeath() now returns an object of class "birthdeath" for
1857 which there is a print method.
1861 CHANGES IN APE VERSION 1.4
1866 o The new function nj() performs phylogeny estimation with the
1867 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1870 o The new function which.edge() identifies the edges of a tree
1871 that belong to a group specified as a set of tips.
1873 o The new function as.phylo.phylog() converts an object of class
1874 "phylog" (from the package ade4) into an object of class
1877 o The new function axisPhylo() draws axes on the side of a
1880 o The new function howmanytrees() calculates the number of trees
1881 in different cases and giving a number of tips.
1883 o write.tree() has a new option `multi.line' (TRUE by default) to
1884 write a Newick tree on several lines rather than on a single
1887 o The functionalities of zoom() have been extended. Several
1888 subtrees can be visualized at the same time, and they are marked
1889 on the main tree with colors. The context of the subtrees can be
1890 marked with the option `subtree' (see below).
1892 o drop.tip() has a new option `subtree' (FALSE by default) which
1893 specifies whether to output in the tree how many tips have been
1896 o The arguments of add.scale.bar() have been redefined and have
1897 now default values (see ?add.scale.bar for details). This
1898 function now works even if the plotted tree has no edge length.
1900 o plot.phylo() can now plot radial trees, but this does not take
1901 edge lengths into account.
1903 o In plot.phylo() with `type = "phylogram"', if the values of
1904 `edge.color' and `edge.width' are identical for sister-branches,
1905 they are propagated to the vertical line that link them.
1910 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1911 crashing. This is fixed.
1913 o In plot.phylo(), the options `edge.color' and `edge.width' are
1914 now properly recycled; their default values are now "black" and
1917 o A bug has been fixed in write.nexus().
1922 o The function node.depth.edgelength() has been removed and
1923 replaced by a C code.
1927 CHANGES IN APE VERSION 1.3-1
1932 o The new function nodelabels() allows to add labels to the nodes
1933 of a tree using text or plotting symbols in a flexible way.
1935 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1936 numeric values specifying the lower and upper limits on the x-
1937 and y-axes. This allows to leave some space on any side of the
1938 tree. If a single value is given, this is taken as the upper
1943 CHANGES IN APE VERSION 1.3
1948 o The new function phymltest() calls the software PHYML and fits
1949 28 models of DNA sequence evolution. There are a print method to
1950 display likelihood and AIC values, a summary method to compute
1951 the hierarchical likelihood ratio tests, and a plot method to
1952 display graphically the AIC values of each model.
1954 o The new function yule.cov() fits the Yule model with covariates,
1955 a model where the speciation rate is affected by several species
1956 traits through a generalized linear model. The parameters are
1957 estimated by maximum likelihood.
1959 o Three new functions, corBrownian(), corGrafen(), and
1960 corMartins(), compute the expected correlation structures among
1961 species given a phylogeny under different models of evolution.
1962 These can be used for GLS comparative phylogenetic methods (see
1963 the examples). There are coef() and corMatrix() methods and an
1964 Initialize.corPhyl() function associated.
1966 o The new function compar.cheverud() implements Cheverud et al.'s
1967 (1985; Evolution 39:1335) phylogenetic comparative method.
1969 o The new function varcomp() estimates variance components; it has
1972 o Two new functions, panel.superpose.correlogram() and
1973 plot.correlogramList(), allow to plot several phylogenetic
1976 o The new function node.leafnumber() computes the number of leaves
1977 of a subtree defined by a particular node.
1979 o The new function node.sons() gets all tags of son nodes from a
1982 o The new function compute.brlen() computes the branch lengths of
1983 a tree according to a specified method.
1985 o plot.phylo() has three new options: "cex" controls the size of
1986 the (tip and node) labels (thus it is no more needed to change
1987 the global graphical parameter), "direction" which allows to
1988 plot the tree rightwards, leftwards, upwards, or downwards, and
1989 "y.lim" which sets the upper limit on the y-axis.
1994 o Some functions which try to match tip labels and names of
1995 additional data (e.g. vector) are likely to fail if there are
1996 typing or syntax errors. If both series of names do not perfectly
1997 match, they are ignored and a warning message is now issued.
1998 These functions are bd.ext, compar.gee, pic. Their help pages
1999 have been clarified on this point.
2003 CHANGES IN APE VERSION 1.2-7
2008 o The new function root() reroots a phylogenetic tree with respect
2009 to a specified outgroup.
2011 o The new function rotate() rotates an internal branch of a tree.
2013 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
2014 trees) controls the display of the tip labels in unrooted trees.
2015 This display has been greatly improved: the tip labels are now not
2016 expected to overlap with the tree (particularly if lab4ut =
2017 "axial"). In all cases, combining appropriate values of "lab4ut"
2018 and the font size (via "par(cex = )") should result in readable
2019 unrooted trees. See ?plot.phylo for some examples.
2021 o In drop.tip(), the argument `tip' can now be numeric or character.
2026 o drop.tip() did not work correctly with trees with no branch
2027 lengths: this is fixed.
2029 o A bug in plot.phylo(..., type = "unrooted") made some trees being
2030 plotted with some line crossings: this is now fixed.
2034 CHANGES IN APE VERSION 1.2-6
2039 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
2040 correlogram.phylo, dist.taxo, plot.correlogram) have been added
2041 to implement comparative methods with an autocorrelation approach.
2043 o A new data set describing some life history traits of Carnivores
2049 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
2054 o When plotting a tree with plot.phylo(), the new default of the
2055 option `label.offset' is now 0, so the labels are always visible.
2059 CHANGES IN APE VERSION 1.2-5
2064 o The new function bd.ext() fits a birth-death model with combined
2065 phylogenetic and taxonomic data, and estimates the corresponding
2066 speciation and extinction rates.
2071 o The package gee is no more required by ape but only suggested
2072 since only the function compar.gee() calls gee.
2076 CHANGES IN APE VERSION 1.2-4
2081 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
2082 and lines.popsize) implementing a new approach for inferring the
2083 demographic history from genealogies using a reversible jump
2084 MCMC have been introduced.
2086 o The unit of time in the skyline plot and in the new plots can
2087 now be chosen to be actual years, rather than substitutions.
2091 CHANGES IN APE VERSION 1.2-3
2096 o The new function rtree() generates a random binary tree with or
2097 without branch lengths.
2099 o Two new functions for drawing lineages-through-time (LTT) plots
2100 are provided: ltt.lines() adds a LTT curve to an existing plot,
2101 and mltt.plot() does a multiple LTT plot giving several trees as
2102 arguments (see `?ltt.plot' for details).
2107 o Some taxon names made R crashing when calling as.phylo.hclust():
2110 o dist.dna() returned an error with two identical DNA sequences
2111 (only using the Jukes-Cantor method returned 0): this is fixed.
2116 o The function dist.phylo() has been re-written using a different
2117 algorithm: it is now about four times faster.
2119 o The code of branching.times() has been improved: it is now about
2124 CHANGES IN APE VERSION 1.2-2
2129 o The new function seg.sites() finds the segregating sites in a
2130 sample of DNA sequences.
2135 o A bug introduced in read.tree() and in read.nexus() with version
2138 o A few errors were corrected and a few examples were added in the
2143 CHANGES IN APE VERSION 1.2-1
2148 o plot.phylo() can now draw the edge of the root of a tree if it
2149 has one (see the new option `root.edge', its default is FALSE).
2154 o A bug was fixed in read.nexus(): files with semicolons inside
2155 comment blocks were not read correctly.
2157 o The behaviour of read.tree() and read.nexus() was corrected so
2158 that tree files with badly represented root edges (e.g., with
2159 an extra pair of parentheses, see the help pages for details)
2160 are now correctly represented in the object of class "phylo";
2161 a warning message is now issued.
2165 CHANGES IN APE VERSION 1.2
2170 o plot.phylo() has been completely re-written and offers several
2171 new functionalities. Three types of trees can now be drawn:
2172 phylogram (as previously), cladogram, and unrooted tree; in
2173 all three types the branch lengths can be drawn using the edge
2174 lengths of the phylogeny or not (e.g., if the latter is absent).
2175 The vertical position of the nodes can be adjusted with two
2176 choices (see option `node.pos'). The code has been re-structured,
2177 and two new functions (potentially useful for developpers) are
2178 documented separately: node.depth.edgelength() and node.depth();
2179 see the respective help pages for details.
2181 o The new function zoom() allows to explore very large trees by
2182 focusing on a small portion of it.
2184 o The new function yule() fits by maximum likelihood the Yule model
2185 (birth-only process) to a phylogenetic tree.
2187 o Support for writing DNA sequences in FASTA format has been
2188 introduced in write.dna() (support for reading sequences in
2189 this format was introduced in read.dna() in version 1.1-2).
2190 The function has been completely re-written, fixing some bugs
2191 (see below); the default behaviour is no more to display the
2192 sequences on the standard output. Several options have been
2193 introduced to control the sequence printing in a flexible
2194 way. The help page has been extended.
2196 o A new data set is included: a supertree of bats in NEXUS format.
2201 o In theta.s(), the default of the option `variance' has
2202 been changed to `FALSE' (as was indicated in the help page).
2204 o Several bugs were fixed in the code of all.equal.phylo().
2206 o Several bugs were fixed in write.dna(), particularly this
2207 function did not work with `format = "interleaved"'.
2209 o Various errors were corrected in the help pages.
2214 o The argument names of as.hclust.phylo() have been changed
2215 from "(phy)" to "(x, ...)" to conform to the definition of
2216 the corresponding generic function.
2218 o gamma.stat() has been renamed gammaStat() to avoid confusion
2219 since gamma() is a generic function.
2223 CHANGES IN APE VERSION 1.1-3
2228 o base.freq() previously did not return a value of 0 for
2229 bases absent in the data (e.g., a vector of length 3 was
2230 returned if one base was absent). This is now fixed (a
2231 vector of length 4 is always returned).
2233 o Several bugs were fixed in read.nexus(), including that this
2234 function did not work in this absence of a "TRANSLATE"
2235 command in the NEXUS file, and that the commands were
2240 CHANGES IN APE VERSION 1.1-2
2245 o The Tamura and Nei (1993) model of DNA distance is now implemented
2246 in dist.dna(): five models are now available in this function.
2248 o A new data set is included: a set of 15 sequences of the
2249 cytochrome b mitochondrial gene of the woodmouse (Apodemus
2255 o A bug in read.nexus() was fixed.
2257 o read.dna() previously did not work correctly in most cases.
2258 The function has been completely re-written and its help page
2259 has been considerably extended (see ?read.dna for details).
2260 Underscores (_) in taxon names are no more replaced with
2261 spaces (this behaviour was undocumented).
2263 o A bug was fixed in write.dna().
2267 CHANGES IN APE VERSION 1.1-1
2272 o A bug in read.tree() introduced in APE 1.1 was fixed.
2274 o A bug in compar.gee() resulted in an error when trying to fit
2275 a model with `family = "binomial"'. This is now fixed.
2279 CHANGES IN APE VERSION 1.1
2284 o The Klastorin (1982) method as suggested by Misawa and Tajima
2285 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
2286 on the basis of phylogenetic trees has been implemented (see
2287 the function klastorin()).
2289 o Functions have been added to convert APE's "phylo" objects in
2290 "hclust" cluster objects and vice versa (see the help page of
2291 as.phylo for details).
2293 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
2294 are introduced for the estimation of absolute evolutionary rates
2295 (ratogram) and dated clock-like trees (chronogram) from
2296 phylogenetic trees using the non-parametric rate smoothing approach
2297 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
2299 o A summary method is now provided printing a summary information on a
2300 phylogenetic tree with, for instance, `summary(tree)'.
2302 o The behaviour of read.tree() was changed so that all spaces and
2303 tabulations in tree files are now ignored. Consequently, spaces in tip
2304 labels are no more allowed. Another side effect is that read.nexus()
2305 now does not replace the underscores (_) in tip labels with spaces
2306 (this behaviour was undocumented).
2308 o The function plot.phylo() has a new option (`underscore') which
2309 specifies whether the underscores in tip labels should be written on
2310 the plot as such or replaced with spaces (the default).
2312 o The function birthdeath() now computes 95% confidence intervals of
2313 the estimated parameters using profile likelihood.
2315 o Three new data sets are included: a gene tree estimated from 36
2316 landplant rbcL sequences, a gene tree estimated from 32 opsin
2317 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
2322 o A bug was fixed in dist.gene() where nothing was returned.
2324 o A bug in plot.mst() was fixed.
2326 o A bug in vcv.phylo() resulted in false correlations when the
2327 option `cor = TRUE' was used (now fixed).
2331 CHANGES IN APE VERSION 1.0
2336 o Two new functions, read.dna() and write.dna(), read/write in a file
2337 DNA sequences in interleaved or in sequential format.
2339 o Two new functions, read.nexus() and write.nexus(), read/write trees
2342 o The new function bind.tree() allows to bind two trees together,
2343 possibly handling root edges to give internal branches.
2345 o The new function drop.tip() removes the tips in a phylogenetic tree,
2346 and trims (or not) the corresponding internal branches.
2348 o The new function is.ultrametric() tests if a tree is ultrametric.
2350 o The function plot.phylo() has more functionalities such as drawing the
2351 branches with different colours and/or different widths, showing the
2352 node labels, controling the position and font of the labels, rotating
2353 the labels, and controling the space around the plot.
2355 o The function read.tree() can now read trees with no branch length,
2356 such as "(a,b),c);". Consequently, the element `edge.length' in
2357 objects of class "phylo" is now optional.
2359 o The function write.tree() has a new default behaviour: if the default
2360 for the option `file' is used (i.e. file = ""), then a variable of
2361 mode character containing the tree in Newick format is returned which
2362 can thus be assigned (e.g., tree <- write.tree(phy)).
2364 o The function read.tree() has a new argument `text' which allows
2365 to read the tree in a variable of mode character.
2367 o A new data set is included: the phylogenetic relationships among
2368 the orders of birds from Sibley and Ahlquist (1990).
2372 CHANGES IN APE VERSION 0.2-1
2377 o Several bugs were fixed in the help pages.
2381 CHANGES IN APE VERSION 0.2
2386 o The function write.tree() writes phylogenetic trees (objects of class
2387 "phylo") in an ASCII file using the Newick parenthetic format.
2389 o The function birthdeath() fits a birth-death model to branching times
2390 by maximum likelihood, and estimates the corresponding speciation and
2393 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
2396 o The function is.binary.tree() tests whether a phylogeny is binary.
2398 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
2399 as well as some methods are introduced.
2401 o Several functions, including some generics and methods, for computing
2402 skyline plot estimates (classic and generalized) of effective
2403 population size through time are introduced and replace the function
2404 skyline.plot() in version 0.1.
2406 o Two data sets are now included: the phylogenetic relationships among
2407 the families of birds from Sibley and Ahlquist (1990), and an
2408 estimated clock-like phylogeny of HIV sequences sampled in the
2409 Democratic Republic of Congo.
2412 DEPRECATED & DEFUNCT
2414 o The function skyline.plot() in ape 0.1 has been deprecated and
2415 replaced by more elaborate functions (see above).
2420 o Two important bugs were fixed in plot.phylo(): phylogenies with
2421 multichotomies not at the root or not with only terminal branches,
2422 and phylogenies with a single node (i.e. only terminal branches)
2423 did not plot. These trees should be plotted correctly now.
2425 o Several bugs were fixed in diversi.time() in the computation of
2428 o Various errors were corrected in the help pages.