1 CHANGES IN APE VERSION 3.0-7
6 o The new function chronos estimates chronograms by penalised
7 likelihood and maximum likelihood with a completely reworked
8 code and interface. There is a new function makeChronosCalib to
9 set the calibration points easily. chronos() will eventually
12 o The new function 'where' searches patterns in DNA sequences.
14 o pic() gains an option 'rescaled.tree = FALSE' to return the tree
15 with its branch lengths rescaled for the PIC calculation.
17 o clustal(), muscle(), and tcoffee() gain an option
18 'original.ordering = TRUE' to ease the comparisons of
21 o plot.phylo() has a new option, open.angle, used when plotting
24 o The new function read.FASTA reads FASTA files much faster and
25 more efficiently. It is called internally by read.dna(, "fasta")
26 or can be called directly.
31 o drop.tip() shuffled node labels on some trees.
33 o axisPhylo() now works correctly with circular trees, and gives a
34 sensible error message when type = "r" or "u".
39 o .compressTipLabel() is 10 times faster thanks to Joseph Brown.
41 o base.freq() is now faster with lists.
43 o as.matrix.DNAbin() should be faster and more efficient with
44 lists; it now accepts vectors.
46 o collapse.singles() is faster thanks to Klaus Schliep. This will
47 speed-up drop.tip() significantly.
51 CHANGES IN APE VERSION 3.0-6
56 o reorder.phylo() has a new order, "postorder", and a new option
57 index.only = TRUE to return only the vector of indices (the tree
58 is unmodified, see ?reorder.phylo for details).
60 o The three new functions node.depth.edgelength, node.height, and
61 node.height.clado make some internal code available from R. See
62 ?node.depth (which was already documented) for details.
67 o reorder(, "pruningwise") made R crash if the rows of the edge
68 matrix are in random order: this is now fixed.
70 o drop.tip() sometimes shuffled node labels (thanks to Rebecca
73 o drop.tip(phy, "") returned a tree with zero-length tip labels:
74 it now returns the tree unchanged (thanks to Brian Anacker for
77 o plot.phylo() made R crash if the tree has zero-length tip
78 labels: it now returns NULL (thanks again to Brian Anacker).
83 o dist.nodes() is now 6 to 10 times faster.
85 o reorder(, "cladewise") is now faster. The change is not very
86 visible for small trees (n < 1000) but this can be more than
87 1000 faster for big trees (n >= 1e4).
89 o The attribute "order" of the objects of class "phylo" is now
90 strongly recommended, though not mandatory. Most functions in
91 ape should return a tree with this attribute correctly set.
93 o dbd() is now vectorized on both arguments 'x' (number of species
94 in clade) and 't' (clade age) to make likelihood calculations
99 CHANGES IN APE VERSION 3.0-5
104 o ace() should better catch errors when SEs cannot be computed.
109 o write.dna(format = "fasta") now conforms more closely to the
110 FASTA standard thanks to François Michonneau.
112 o print.DNAbin() does not print base compositions if there are more
113 than one million nucleotides.
117 CHANGES IN APE VERSION 3.0-4
122 o read.dna() failed to read Phylip files if the first line used
123 tabulations instead of white spaces.
125 o read.dna() failed to read Phylip or Clustal files with less than
126 10 nucleotides. (See other changes in this function below.)
130 o read.dna() now requires at least one space (or tab) between the
131 taxa names and the sequences (whatever the length of taxa
132 names). write.dna() now follows the same rule.
134 o The option 'seq.names' of read.dna has been removed.
136 o The files ape-defunct.R and ape-defunct.Rd, which have not been
137 modified for almost two years, have been removed.
139 o The C code of bionj() has been reworked: it is more stable (by
140 avoiding passing character strings), slightly faster (by about
141 20%), and numerically more accurate.
143 o The C code of fastme.*() has been slightly modified and should
144 be more stable by avoiding passing character strings (the
145 results are identical to the previous versions).
147 o The file src/newick.c has been removed.
151 CHANGES IN APE VERSION 3.0-3
156 o birthdeath() now catches errors and warnings much better so that
157 a result is returned in most cases.
162 o Because of problems with character string manipulation in C, the
163 examples in ?bionj and in ?fastme have been disallowed. In the
164 meantime, these functions might be unstable. This will be solved
165 for the next release.
169 CHANGES IN APE VERSION 3.0-2
174 o The new function alex (alignment explorator) zooms in a DNA
175 alignment and opens the result in a new window.
180 o compute.brtime() did not completely randomized the order of the
183 o write.nexus() did not work correctly with rooted trees (thanks
184 to Matt Johnson for the fix).
186 o mltt.plot(, backward = FALSE) did not set the x-axis correctly.
188 o A bug was introduced in prop.clades() with ape 3.0. The help page
189 has been clarified relative to the use of the option 'rooted'.
191 o mantel.test() printed a useless warning message.
193 o plot.phylo(, direction = "downward") ignored 'y.lim'.
195 o is.monophyletic() did not work correctly if 'tips' was not stored
198 o prop.part() could make R crash if the first tree had many
201 o njs(), bionjs(), and mvrs() now return an error if 'fs < 1'.
203 o SDM() did not work correctly. The code has also been generally
209 o The DESCRIPTION file has been updated.
211 o The option 'original.data' of write.nexus() has been removed.
213 o The files bionjs.c, mvr.c, mvrs.c, njs.c, triangMtd.c, and
214 triangMtds.c have been improved which should fix some bugs in
215 the corresponding functions.
217 o dist.gene() now coerces input data frame as matrix resulting in
218 much faster calculations (thanks to a suggestion by Markus
223 CHANGES IN APE VERSION 3.0-1
228 o dist.dna() has two new models: "indel" and "indelblock".
230 o bind.tree() now accepts 'position' > 0 when the trees have no
231 banch length permitting to create a node in 'x' when grafting
232 'y' (see ?bind.tree for details).
237 o cophyloplot( , rotate = TRUE) made R hanged after a few clicks.
238 Also the tree is no more plotted twice.
240 o read.GenBank() has been updated to work with EFetch 2.0.
242 o unroot() on trees in "pruningwise" order did not respect this
247 CHANGES IN APE VERSION 3.0
252 o The three functions dyule, dbd, and dbdTime calculate the
253 density probability (i.e., the distribution of the number of
254 species) for the Yule, the constant and the time-dependent
255 birth-beath models, respectively. These probabilities can be
256 conditional on no extinction and/or on a log-scale.
258 o plot.phylo() has a new option 'rotate.tree' to rotate unrooted,
259 fan, or radial trees around the center of the plot.
261 o boot.phylo() and prop.clades() have a new option rooted =
262 FALSE. Note that the behaviour of prop.part() is unchanged.
264 o edgelabels() has a new option 'date' to place labels on edges of
265 chronograms using the time scale (suggestion by Rob Lanfear).
270 o In chronopl(), the code setting the initial dates failed in
271 complicated settings (several dates known within intervals).
272 This has been generally improved and should result in faster
273 and more efficient convergence even in simple settings.
275 o mantel.test() sometimes returned P-values > 1 with the default
278 o extract.clade() sometimes shuffled some tip labels (thanks to
279 Ludovic Mallet and Mahendra Mariadassou for the fix).
281 o clustal() should now find by default the executable under Windows.
286 o The code of yule() has been simplified and is now much faster for
289 o The code of mantel.test() has been adjusted to be consistent
290 with common permutation tests.
292 o The C code of base.freq() has been improved and is now nearly 8
295 o The option 'original.data' of write.nexus() is now deprecated and
296 will be removed in a future release.
298 o The code of is.ultrametric() has been improved and is now 3 times
301 o The code of vcv.phylo() has been improved and is now 10 or 30
302 times faster for 100 or 1000 tips, respectively. Consequently,
303 fitting models with PGLS will be faster overall.
307 CHANGES IN APE VERSION 2.8
312 o Twelve new functions have been written by Andrei-Alin Popescu:
313 additive, ultrametric, is.compatible, arecompatible, mvr, mvrs,
314 njs, bionjs, SDM, treePop, triangMtd, triangMtd*.
316 o A new class "bitsplits" has been created by Andrei-Alin Popescu
317 to code splits (aka, bipartition).
319 o There is a new generic function as.bitsplits with a method to
320 convert from the class "prop.part" to the class "bitsplits".
322 o The new function ltt.coplot plots on the same scales a tree and
323 the derived LTT plot.
325 o ltt.plot() has two new options: backward and tol. It can now
326 handle non-ultrametic trees and its internal coding has been
327 improved. The coordinates of the plot can now be computed with
328 the new function ltt.plot.coords.
333 o prop.part() crashed if some trees had some multichotomies.
337 CHANGES IN APE VERSION 2.7-3
342 o The new function compute.brtime computes and sets branching times.
344 o mantel.test() has a new argument 'alternative' which is
345 "two-sided" by default. Previously, this test was one-tailed
346 with no possibility to change.
348 o ace() can now do REML estimation with continuous characters,
349 giving better estimates of the variance of the Brownian motion
355 o Branch lengths were wrongly updated with bind.tree(, where = <tip>,
356 position = 0). (Thanks to Liam Revell for digging this bug out.)
358 o Simulation of OU process with rTraitCont() did not work correctly.
359 This now uses formula from Gillespie (1996) reduced to a BM
360 process when alpha = 0 to avoid division by zero. The option
361 'linear' has been removed.
363 o Cross-validation in chronopl() did not work when 'age.max' was
366 o consensus(, p = 0.5) could return an incorrect tree if some
367 incompatible splits occur in 50% of the trees (especially with
368 small number of trees).
370 o c() with "multiPhylo" did not work correctly (thanks to Klaus
371 Schliep for the fix).
373 o root() failed in some cases with an outgroup made of several tips.
374 The help page has been clarified a bit.
378 CHANGES IN APE VERSION 2.7-2
383 o There is a new class "evonet" to code evolutionary networks, with
384 a constructor function evonet(), a print() and a plot() methods,
385 and four conversion methods to the classes "phylo", "networx",
386 "network", and "igraph".
388 o The new function rTraitMult does multivariate traits simulation
389 with user-defined models.
391 o plot.phylo() has a new option 'plot = TRUE'. If FALSE, the tree
392 is not plotted but the graphical device is set and the
393 coordinates are saved as usual.
395 o diversity.contrast.test() gains a fourth version of the test with
396 method = "logratio"; the literature citations have been clarified.
398 o add.scale.bar() has two new options, 'lwd' and 'lcol', to modify
399 the aspect of the bar.
401 o boot.phylo() now displays a progress bar by default (can be off
404 o There is a new predict() method for compar.gee().
409 o bionj() made R crash if distances were too large. It now returns
410 an error if at least one distance is greater than 100.
412 o drop.tip() returned a wrong tree if 'tip' was of zero length.
414 o read.nexus.data() failed with URLs.
416 o boot.phylo() returned overestimated support values in the
417 presence of identical or nearly identical sequences.
422 o The data bird.families, bird.orders, cynipids, and woodmouse are
423 now provided as .rda files.
427 CHANGES IN APE VERSION 2.7-1
432 o The new function trex does tree exploration with multiple
435 o The new function kronoviz plots several rooted (dated) trees on
438 o identify.phylo() has a new option 'quiet' (FALSE by default).
443 o A bug was introduced in read.nexus() in ape 2.7.
445 o image.DNAbin() did not colour correctly the bases if there were
448 o .compressTipLabel() failed with a list with a single tree.
450 o identify.phylo() returned a wrong answer when the x- and y-scales
453 o write.nexus() failed with lists of trees with compressed labels.
458 o identify.phylo() now returns NULL if the user right- (instead of
459 left-) clicks (an error was returned previously).
461 o read.nexus() should be robust to commands inserted in the TREES
466 CHANGES IN APE VERSION 2.7
471 o There is a new image() method for "DNAbin" objects: it plots DNA
472 alignments in a flexible and efficient way.
474 o Two new functions as.network.phylo and as.igraph.phylo convert
475 trees of class "phylo" into these respective network classes
476 defined in the packages of the same names.
478 o The three new functions clustal, muscle, and tcoffee perform
479 nucleotide sequence alignment by calling the external programs
482 o Four new functions, diversity.contrast.test, mcconwaysims.test,
483 richness.yule.test, and slowinskiguyer.test, implement various
484 tests of diversification shifts using sister-clade comparisons.
486 o base.freq() gains an option 'all' to count all the possible bases
487 including the ambiguous ones (defaults to FALSE).
489 o write.nexus() now writes tree names in the NEXUS file if given a
490 list of trees with names.
495 o prop.part() failed in some situations with unrooted trees.
497 o read.nexus() shuffled node labels when a TRANSLATE block was
500 o varCompPhylip() did not work if 'exec' was specified.
502 o bind.tree() shuffled node labels when position > 0 and 'where'
508 o BaseProportion in src/dist_dna.c has been modified.
510 o A number of functions in src/tree_build.c have been modified.
512 o The matching representation has now only two columns as the third
513 column was redundant.
517 CHANGES IN APE VERSION 2.6-3
522 o rTraitCont() and rTraitDisc() gains a '...' argument used with
523 user-defined models (suggestion by Gene Hunt).
528 o as.hclust.phylo() now returns an error with unrooted trees.
530 o as.hclust.phylo() failed with trees with node labels (thanks to
531 Jinlong Zhang for pointing this bug out).
533 o read.dna(, "fasta") failed if sequences were not all of the same
536 o plot.phylo() did not recycle values of 'font', 'cex' and
537 'tip.color' correctly when type = "fan" or "radial".
539 o plot.phylo() ignored 'label.offset' when type = "radial", "fan", or
540 "unrooted" with lab4ut = "axial" (the placement of tip labels still
541 needs to be improved with lab4ut = "horizontal").
546 o In drop.fossil() the default tol = 0 has been raised to 1e-8.
548 o The help command ?phylo now points to the man page of read.tree()
549 where this class is described. Similarly, ?matching points to the
550 man page of as.matching().
554 CHANGES IN APE VERSION 2.6-2
559 o Two new functions, pic.ortho and varCompPhylip, implements the
560 orthonormal contrasts of Felsenstein (2008, Am Nat, 171:713). The
561 second function requires Phylip to be installed on the computer.
563 o bd.ext() has a new option conditional = TRUE to use probabilities
564 conditioned on no extinction for the taxonomic data.
569 o write.tree() failed to output correctly tree names.
571 o dist.nodes() returned duplicated column(s) with unrooted and/or
572 multichotomous trees.
574 o mcmc.popsize() terminated unexpectedly if the progress bar was
577 o prop.part(x) made R frozen if 'x' is of class "multiPhylo".
579 o Compilation under Mandriva failed (thanks to Jos Käfer for the fix).
581 o drop.tip() shuffled tip labels with subtree = TRUE or trim.internal
584 o Objects returned by as.hclust.phylo() failed when analysed with
585 cutree() or rect.hclust().
587 o write.tree() did not output correctly node labels (thanks to Naim
588 Matasci and Jeremy Beaulieu for the fix).
590 o ace(type = "discrete") has been improved thanks to Naim Marasci and
595 CHANGES IN APE VERSION 2.6-1
600 o The new function speciesTree calculates the species tree from a set
601 of gene trees. Several methods are available including maximum tree
602 and shallowest divergence tree.
607 o A bug introduced in write.tree() with ape 2.6 has been fixed.
609 o as.list.DNAbin() did not work correctly with vectors.
611 o as.hclust.phylo() failed with trees with node labels (thanks to
612 Filipe Vieira for the fix).
616 CHANGES IN APE VERSION 2.6
621 o The new functions rlineage and rbdtree simulate phylogenies under
622 any user-defined time-dependent speciation-extinction model. They
623 use continuous time algorithms.
625 o The new function drop.fossil removes the extinct species from a
628 o The new function bd.time fits a user-defined time-dependent
629 birth-death model. It is a generalization of yule.time() taking
630 extinction into account.
632 o The new function MPR does most parsimonious reconstruction of
635 o The new function Ftab computes the contingency table of base
636 frequencies from a pair of sequences.
638 o There is now an 'as.list' method for the class "DNAbin".
640 o dist.dna() can compute the number of transitions or transversions
641 with the option model = "Ts" or model = "Tv", respectively.
643 o [node|tip|edge]labels() gain three options with default values to
644 control the aspect of thermometers: horiz = TRUE, width = NULL,
647 o compar.gee() has been improved with the new option 'corStruct' as an
648 alternative to 'phy' to specify the correlation structure, and
649 calculation of the QIC (Pan 2001, Biometrics). The display of the
650 results has also been improved.
652 o read.GenBank() has a new option 'gene.names' to return the name of
653 the gene (FALSE by default).
658 o extract.clade() sometimes shuffled the tip labels.
660 o plot.phylo(type = "unrooted") did not force asp = 1 (thanks to Klaus
663 o dist.dna(model = "logdet") used to divide distances by 4. The
664 documentation has been clarified on the formulae used.
669 o rTraitCont(model = "OU") has an option 'linear = TRUE' to possibly
670 change the parameterisation (see ?rTraitCont for details).
672 o pic() now returns a vector with the node labels of the tree (if
675 o write.tree() and read.tree() have been substantially improved thanks
676 to contributions by Klaus Schliep.
680 CHANGES IN APE VERSION 2.5-3
685 o The new function mixedFontLabel helps to make labels with bits of
686 text to be plotted in different fonts.
688 o There are now replacement operators for [, [[, and $ for the class
689 "multiPhylo" (i.e., TREES[11:20] <- rmtree(10, 100)). They possibly
690 check that the tip labels are the same in all trees.
692 o Objects of class "multiPhylo" can be built with c(): there are
693 methods for the classes "phylo" and "multiPhylo".
695 o The internal functions .compressTipLabel and .uncompressTipLabel are
701 o bind.tree(x, y, where, position = 0) did not work correctly if 'y'
702 was a single-edge tree and 'where' was a tip.
704 o rTraitCont() did not use the square-root of branch lengths when
705 simulating a Brownian motion model.
709 CHANGES IN APE VERSION 2.5-2
714 o There is now a print method for results from ace().
716 o There is a labels() method for objects of class "DNAbin".
718 o read.dna() has a new option 'as.matrix' to possibly force sequences
719 in a FASTA file to be stored in a matrix (see ?read.dna for details).
724 o as.phylo.hclust() used to multiply edge lengths by 2.
726 o A minor bug was fixed in rTraitDisc().
728 o ace() sometimes failed (parameter value was NaN and the optimisation
734 o evolve.phylo() and plot.ancestral() have been removed.
736 o chronogram(), ratogram(), and NPRS.criterion() have been removed.
741 o nj() has been improved and is now about 30% faster.
743 o The default option 'drop' of [.DNAbin has been changed to FALSE to
744 avoid dropping rownames when selecting a single sequence.
746 o print.DNAbin() has been changed to summary.DNAbin() which has been
751 CHANGES IN APE VERSION 2.5-1
756 o The new function stree generates trees with regular shapes.
758 o It is now possible to bind two trees with x + y (see ?bind.tree for
761 o drop.tip(), extract.clade(), root(), and bind.tree() now have an
762 'interactive' option to make the operation on a plotted tree.
764 o cophyloplot() gains two new arguments 'lwd' and 'lty' for the
765 association links; they are recycled like 'col' (which wasn't before).
770 o rTraitDisc() did not use its 'freq' argument correctly (it was
771 multiplied with the rate matrix column-wise instead of row-wise).
773 o [node|tip|edge]labels(thermo = ) used to draw empty thermometers
774 with NA values. Nothing is drawn now like with 'text' or 'pch'.
775 The same bug occurred with the 'pie' option.
777 o A bug was fixed in compar.ou() and the help page was clarified.
779 o bind.tree() has been rewritten fixing several bugs and making it
782 o plot.phylo(type = "p") sometimes failed to colour correctly the
783 vertical lines representing the nodes.
785 o plot.phylo(direction = "l", x.lim = 30) failed to plot the branches
786 in the correct direction though the tip labels were displayed
792 o The c, cbind, and rbind methods for "DNAbin" objetcs now check that
793 the sequences are correctly stored (in a list for c, in a matrix
794 for the two other functions).
798 CHANGES IN APE VERSION 2.5
803 o The new function parafit by Pierre Legendre tests for the
804 coevolution between hosts and parasites. It has a companion
805 function, pcoa, that does principal coordinate decomposition.
806 The latter has a biplot method.
808 o The new function lmorigin by Pierre Legendre performs multiple
809 regression through the origin with testing by permutation.
811 o The new functions rTraitCont and rTraitDisc simulate continuous and
812 discrete traits under a wide range of evolutionary models.
814 o The new function delta.plot does a delta plot following Holland et
815 al. (2002, Mol. Biol. Evol. 12:2051).
817 o The new function edges draws additional branches between any nodes
818 and/or tips on a plotted tree.
820 o The new function fancyarrows enhances arrows from graphics with
821 triangle and harpoon heads; it can be called from edges().
823 o add.scale.bar() has a new option 'ask' to draw interactively.
825 o The branch length score replaces the geodesic distance in dist.topo.
827 o Three new data sets are included: the gopher-lice data (gopher.D),
828 SO2 air pollution in 41 US cities (lmorigin.ex1, from Sokal &
829 Rohlf 1995), and some host-parasite specificity data
830 (lmorigin.ex2, from Legendre & Desdevises 2009).
835 o add.scale.bar() drew the bar outside the plotting region with the
836 default options with unrooted or radial trees.
838 o dist.topo() made R stuck when the trees had different sizes (thanks
839 to Otto Cordero for the fix).
844 o The geodesic distance has been replaced by the branch length score
849 CHANGES IN APE VERSION 2.4-1
854 o rtree() and rcoal() now accept a numeric vector for the 'br'
857 o vcv() is a new generic function with methods for the classes "phylo"
858 and "corPhyl" so that it is possible to calculate the var-cov matrix
859 for "transformation models". vcv.phylo() can still be used for trees
860 of class "phylo"; its argument 'cor' has been renamed 'corr'.
865 o bind.tree() failed when 'y' had no root edge.
867 o read.nexus() shuffled tip labels when the trees have no branch
868 lengths and there is a TRANSLATE block.
870 o read.nexus() does not try to translate node labels if there is a
871 translation table in the NEXUS file. See ?read.nexus for a
872 clarification on this behaviour.
874 o plot.multiPhylo() crashed R when plotting a list of trees with
875 compressed tip labels.
877 o write.nexus() did not translate the taxa names when asked for.
879 o plot.phylo(type = "fan") did not rotate the tip labels correctly
880 when the tree has branch lengths.
882 o ace(type = "continuous", method = "ML") now avoids sigma² being
883 negative (which resulted in an error).
885 o nj() crashed with NA/NaN in the distance matrix: an error in now
890 CHANGES IN APE VERSION 2.4
895 o base.freq() has a new option 'freq' to return the counts; the
896 default is still to return the proportions.
901 o seg.sites() did not handle ambiguous nucleotides correctly: they
904 o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
905 the tree: the argument is now ignored.
907 o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
913 o Trying to plot a tree with a single tip now returns NULL with a
914 warning (it returned an error previously).
916 o The way lines representing nodes are coloured in phylograms has
917 been modified (as well as their widths and types) following some
918 users' request; this is only for dichotomous nodes.
920 o The argument 'adj' in [node][tip][edge]labels() now works when
921 using 'pie' or 'thermo'.
923 o A more informative message error is now returned by dist.dna() when
924 'model' is badly specified (partial matching of this argument is
927 o Deprecated functions are now listed in a help page: see
928 help("ape-defunct") with the quotes.
933 o The functions heterozygosity, nuc.div, theta.h, theta.k and
934 theta.s have been moved from ape to pegas.
936 o The functions mlphylo, DNAmodel and sh.test have been removed.
940 CHANGES IN APE VERSION 2.3-3
945 o add.scale.bar() always drew a horizontal bar.
947 o zoom() shuffled tips with unrooted trees.
949 o write.nexus() failed to write correctly trees with a "TipLabel"
952 o rcoal() failed to compute branch lengths with very large n.
954 o A small bug was fixed in compar.cheverud() (thanks to Michael
957 o seg.sites() failed when passing a vector.
959 o drop.tip() sometimes shuffled tip labels.
961 o root() shuffled node labels with 'resolve.root = TRUE'.
965 CHANGES IN APE VERSION 2.3-2
970 o all.equal.phylo() did not compare unrooted trees correctly.
972 o dist.topo(... method = "PH85") did not treat unrooted trees
973 correctly (thanks to Tim Wallstrom for the fix).
975 o root() sometimes failed to test for the monophyly of the
978 o extract.clade() sometimes included too many edges.
980 o vcv.phylo() did not work correctly when the tree is in
983 o nj() did not handle correctly distance matrices with many 0's.
984 The code has also been significantly improved: 7, 70, 160 times
985 faster with n = 100, 500, 1000, respectively.
989 CHANGES IN APE VERSION 2.3-1
994 o The new function is.monophyletic tests the monophyly of a group.
996 o There is now a c() method for lists of class "DNAbin".
998 o yule.cov() now fits the null model, and its help page has been
999 corrected with respect to this change.
1001 o drop.tip() has a new option 'rooted' to force (or not) a tree
1002 to be treated as (un)rooted.
1007 o dist.gene() failed on most occasions with the default
1008 pairwise.deletion = FALSE.
1010 o read.tree() failed to read correctly the tree name(s).
1012 o boot.phylo() now treats correctly data frames.
1014 o del.gaps() did not copy the rownames of a matrix.
1016 o A small bug was fixed in CDAM.global().
1018 o ace() failed with large data sets. Thanks to Rich FitzJohn for
1019 the fix. With other improvements, this function is now about 6
1022 o write.tree() failed with objects of class "multiPhylo".
1024 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
1029 o [.multiPhylo and [.DNAbin now respect the original class.
1031 o Instances of the form class(phy) == "phylo" have been replaced
1032 by inherits(phy, "phylo").
1034 o rcoal() is now faster.
1037 DEPRECATED & DEFUNCT
1039 o klastorin() has been removed.
1043 CHANGES IN APE VERSION 2.3
1048 o The new functions CADM.global and CADM.post, contributed by
1049 Pierre Legendre, test the congruence among several distance
1052 o The new function yule.time fits a user-defined time-dependent
1053 Yule model by maximum likelihood.
1055 o The new function makeNodeLabel creates and/or modifies node
1056 labels in a flexible way.
1058 o read.tree() and write.tree() have been modified so that they can
1059 handle individual tree names.
1061 o plot.phylo() has a new argument 'edge.lty' that specifies the
1062 types of lines used for the edges (plain, dotted, dashed, ...)
1064 o phymltest() has been updated to work with PhyML 3.0.1.
1069 o drop.tip() shuffled tip labels in some cases.
1071 o drop.tip() did not handle node.label correctly.
1073 o is.ultrametric() now checks the ordering of the edge matrix.
1075 o ace() sometimes returned negative values of likelihoods of
1076 ancestral states (thanks to Dan Rabosky for solving this long
1082 o The data set xenarthra has been removed.
1086 CHANGES IN APE VERSION 2.2-4
1090 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
1091 now fixed. (Thanks to Peter Wragg for the fix!)
1093 o A warning message occurred for no reason with ace(method="GLS").
1098 o There is now a general help page displayed with '?ape'.
1102 CHANGES IN APE VERSION 2.2-3
1107 o The new function extract.clade extracts a clade from a tree by
1108 specifying a node number or label.
1110 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
1111 operations of the same names.
1113 o dist.dna() can now return the number of site differences by
1114 specifying model="N".
1119 o chronopl() did not work with CV = TRUE.
1121 o read.nexus() did not work correctly in some situations (trees on
1122 multiple lines with different numbers of lines and/or with
1123 comments inserted within the trees).
1125 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
1126 the number of lineages with non-binary trees.
1131 o ape has now a namespace.
1133 o drop.tip() has been improved: it should be much faster and work
1134 better in some cases (e.g., see the example in ?zoom).
1138 CHANGES IN APE VERSION 2.2-2
1143 o dist.gene() has been substantially improved and gains an option
1144 'pairwise.deletion'.
1146 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
1152 o prop.part() failed with a single tree with the default option
1153 'check.labels = TRUE'.
1155 o summary.DNAbin() failed to display correctly the summary of
1156 sequence lengths with lists of sequences of 10,000 bases or more
1157 (because summary.default uses 4 significant digits by default).
1159 o read.nexus() failed to read a file with a single tree with line
1160 breaks in the Newick string.
1162 o del.gaps() returned a list of empty sequences when there were no
1168 o phymltest() has been updated for PhyML 3.0 and gains an option
1169 'append', whereas the option 'path2exec' has been removed.
1171 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
1172 which is returned unchanged (instead of an error).
1174 o The data sets bird.orders and bird.families are now stored as
1175 Newick strings; i.e., the command data(bird.orders) calls
1180 CHANGES IN APE VERSION 2.2-1
1185 o The new function makeLabel() helps to modify labels of trees,
1186 lists of trees, or DNA sequences, with several utilities to
1187 truncate and/or make them unique, substituting some
1188 characters, and so on.
1190 o The new function del.gaps() removes insertion gaps ("-") in a
1191 set of DNA sequences.
1193 o read.dna() can now read Clustal files (*.aln).
1198 o root() failed with 'resolve.root = TRUE' when the root was
1199 already the specified root.
1201 o Several bugs were fixed in mlphylo().
1203 o collapsed.singles() did not propagate the 'Nnode' and
1204 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
1206 o read.nexus() failed to remove correctly the comments within
1209 o read.nexus() failed to read a file with a single tree and no
1210 translation of tip labels.
1212 o read.nexus() failed to place correctly tip labels when reading
1213 a single tree with no edge lengths.
1215 o A bug was fixed in sh.test().
1220 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
1223 o The option 'check.labels' of consensus() and prop.part() is now
1226 o write.dna() now does not truncate names to 10 characters with
1231 CHANGES IN APE VERSION 2.2
1236 o Four new functions have been written by Damien de Vienne for the
1237 graphical exploration of large trees (cophyloplot, subtrees,
1238 subtreeplot), and to return the graphical coordinates of tree
1241 o The new functions corPagel and corBlomberg implement the Pagel's
1242 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
1244 o chronopl() has been improved and gains several options: see its
1245 help page for details.
1247 o boot.phylo() has now an option 'trees' to possibly return the
1248 bootstraped trees (the default is FALSE).
1250 o prop.part() has been improved and should now be faster in all
1256 o read.dna() failed if "?" occurred in the first 10 sites of the
1259 o The x/y aspect of the plot is now respected when plotting a
1260 circular tree (type = "r" or "f").
1262 o Drawing the tip labels sometimes failed when plotting circular
1265 o zoom() failed when tip labels were used instead of their numbers
1266 (thanks to Yan Wong for the fix).
1268 o drop.tip() failed with some trees (fixed by Yan Wong).
1270 o seg.sites() failed with a list.
1272 o consensus() failed in some cases. The function has been improved
1273 as well and is faster.
1277 CHANGES IN APE VERSION 2.1-3
1282 o A bug in read.nexus() made the Windows R-GUI crash.
1284 o An error was fixed in the computation of ancestral character
1285 states by generalized least squares in ace().
1287 o di2multi() did not modify node labels correctly.
1289 o multi2di() failed if the tree had its attribute "order" set to
1294 CHANGES IN APE VERSION 2.1-2
1299 o There three new methods for the "multiPhylo" class: str, $,
1302 o root() gains the options 'node' and 'resolve.root'
1303 (FALSE by default) as well as its code being improved.
1305 o mltt.plot() has now an option 'log' used in the same way
1306 than in plot.default().
1311 o mltt.plot() failed to display the legend with an unnamed
1314 o nodelabels() with pies now correcly uses the argument
1315 'cex' to draw symbols of different sizes (which has
1316 worked already for thermometers).
1318 o read.nexus() generally failed to read very big files.
1323 o The argument 'family' of compar.gee() can now be a function
1324 as well as a character string.
1326 o read.tree() and read.nexus() now return an unnamed list if
1327 'tree.names = NULL'.
1329 o read.nexus() now returns a modified object of class "multiPhylo"
1330 when there is a TRANSLATE block in the NEXUS file: the individual
1331 trees have no 'tip.label' vector, but the list has a 'TipLabel'
1332 attribute. The new methods '$' and '[[' set these elements
1333 correctly when extracting trees.
1337 CHANGES IN APE VERSION 2.1-1
1342 o The new function rmtree generates lists of random trees.
1344 o rcoal() now generates a genuine coalescent tree by default
1345 (thanks to Vladimir Minin for the code).
1350 o nuc.div() returned an incorrect value with the default
1351 pairwise.deletion = FALSE.
1356 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
1357 have been improved so that they are stabler and faster.
1359 o R packages used by ape are now loaded silently; lattice and gee
1360 are loaded only when needed.
1364 CHANGES IN APE VERSION 2.1
1369 o The new function identify.phylo identifies clades on a plotted
1370 tree using the mouse.
1372 o It is now possible to subset a list of trees (object of class
1373 "multiPhylo") with "[" while keeping its class correct.
1375 o The new function as.DNAbin.alignment converts DNA sequences
1376 stored in the "alignment" format of the package seqinr into
1377 an object of class "DNAbin".
1379 o The new function weight.taxo2 helps to build similarity matrices
1380 given two taxonomic levels (usually called by other functions).
1382 o write.tree() can now take a list of trees (class "multiPhylo")
1383 as its main argument.
1385 o plot.correlogram() and plot.correlogramList() have been
1386 improved, and gain several options (see the help page for
1387 details). A legend is now plotted by default.
1392 o dist.dna() returned some incorrect values with `model = "JC69"'
1393 and `pairwise.deletion = TRUE'. This affected only the
1394 distances involving sequences with missing values. (Thanks
1395 to Bruno Toupance for digging this bug out.)
1397 o write.tree() failed with some trees: this is fixed by removing
1398 the `multi.line' option (trees are now always printed on a
1401 o read.nexus() did not correctly detect trees with multiple root
1402 edges (see OTHER CHANGES).
1407 o The code of mlphylo() has been almost entirely rewritten, and
1408 should be much stabler. The options have been also greatly
1409 simplified (see ?mlphylo and ?DNAmodel for details).
1411 o The internal function nTips has been renamed klastorin_nTips.
1413 o The code of is.ultrametric() contained redundancies and has
1416 o The code of Moran.I() and of correlogram.formula() have been
1419 o read.tree() and read.nexus() now return an error when trying to
1420 read a tree with multiple root edges (see BUG FIXES). The
1421 correction applied in previous version did not work in all
1424 o The class c("multi.tree", "phylo") has been renamed
1430 o There is now a vignette in ape: see vignette("MoranI", "ape").
1433 DEPRECATED & DEFUNCT
1435 o as.matching() and as.phylo.matching() do not support branch
1438 o correlogram.phylo() and discrete.dist() have been removed.
1442 CHANGES IN APE VERSION 2.0-2
1447 o The new function matexpo computes the exponential of a square
1450 o The new function unique.multi.tree removes duplicate trees from
1453 o yule() has a new option `use.root.edge = FALSE' that specifies
1454 to ignore, by default, the root edge of the tree if it exists.
1459 o which.edge() failed when the index of a single terminal edge was
1462 o In diversi.time(), the values returned for model C were
1465 o A bug was fixed in yule() that affected the calculation of the
1466 likelihood in the presence of ties in the branching times.
1468 o There was a bug in the C function mat_expo4x4 affecting the
1469 calculations of the transition probabilities for models HKY and
1472 o A small bug was fixed in as.matrix.DNAbin (thanks to James
1475 o rtree() did not `shuffle' the tip labels by default, so only a
1476 limited number of labelled topologies could be generated.
1480 CHANGES IN APE VERSION 2.0-1
1485 o The three new functions bionj, fastme.ols, and fastme.bal
1486 perform phylogeny estimation by the BIONJ and fastME methods in
1487 OLS and balanced versions. This is a port to R of previous
1488 previous programs done by Vincent Lefort.
1490 o The new function chronoMPL performs molecular dating with the
1491 mean path lengths method of Britton et al. (2002, Mol. Phyl.
1494 o The new function rotate, contributed by Christoph Heibl, swaps
1495 two clades connected to the same node. It works also with
1496 multichotomous nodes.
1498 o The new `method' as.matrix.DNAbin() may be used to convert
1499 easily DNA sequences stored in a list into a matrix while
1500 keeping the names and the class.
1505 o chronopl() failed when some branch lengths were equal to zero:
1506 an error message is now returned.
1508 o di2multi() failed when there was a series of consecutive edges
1513 CHANGES IN APE VERSION 1.10-2
1518 o plot.phylo() can now plot circular trees: the option is type =
1519 "fan" or type = "f" (to avoid the ambiguity with type = "c").
1521 o prop.part() has a new option `check.labels = FALSE' which allows
1522 to considerably speed-up the calculations of bipartitions. As a
1523 consequence, calculations of bootstrap values with boot.phylo()
1524 should be much faster.
1529 o read.GenBank() did not return correctly the list of species as
1530 from ape 1.10: this is fixed in this version
1532 o Applying as.phylo() on a tree of class "phylo" failed: the
1533 object is now returned unchanged.
1537 CHANGES IN APE VERSION 1.10-1
1542 o The three new functions Ntip, Nnode, and Nedge return, for a
1543 given tree, the number of tips, nodes, or edges, respectively.
1548 o read.nexus() did not set correctly the class of the returned
1549 object when reading multiple trees.
1551 o mllt.plot() failed with objects of class c("multi.tree",
1554 o unroot() did not work correctly in most cases.
1556 o reorder.phylo() made R freeze in some occasions.
1558 o Plotting a tree in pruningwise order failed.
1560 o When plotting an unrooted tree, the tip labels where not all
1561 correctly positioned if the option `cex' was used.
1565 CHANGES IN APE VERSION 1.10
1570 o Five new `method' functions have been introduced to manipulate
1571 DNA sequences in binary format (see below).
1573 o Three new functions have been introduced to convert between the
1574 new binary and the character formats.
1576 o The new function as.alignment converts DNA sequences stored as
1577 single characters into the class "alignment" used by the package
1580 o read.dna() and read.GenBank() have a new argument `as.character'
1581 controlling whether the sequences are returned in binary format
1587 o root() failed when the tree had node labels: this is fixed.
1589 o plot.phylo() did not correctly set the limits on the y-axis with
1590 the default setting: this is fixed.
1592 o dist.dna() returned a wrong result for the LogDet, paralinear,
1593 and BH87 models with `pairwise.deletion = TRUE'.
1598 o DNA sequences are now internally stored in a binary format. See
1599 the document "A Bit-Level Coding Scheme for Nucleotides" for the
1600 details. Most functions analyzing DNA functions have been
1601 modified accordingly and are now much faster (dist.dna is now
1602 ca. 60 times faster).
1606 CHANGES IN APE VERSION 1.9-4
1611 o A bug was fixed in edgelabels().
1613 o as.phylo.hclust() did not work correctly when the object of
1614 class "hclust" has its labels set to NULL: the returned tree has
1615 now its tip labels set to "1", "2", ...
1617 o consensus could fail if some tip labels are a subset of others
1618 (e.g., "a" and "a_1"): this is now fixed.
1620 o mlphylo() failed in most cases if some branch lengths of the
1621 initial tree were greater than one: an error message is now
1624 o mlphylo() failed in most cases when estimating the proportion of
1625 invariants: this is fixed.
1629 CHANGES IN APE VERSION 1.9-3
1634 o The new function edgelabels adds labels on the edge of the tree
1635 in the same way than nodelabels or tiplabels.
1640 o multi2di() did not handle correctly branch lengths with the
1641 default option `random = TRUE': this is now fixed.
1643 o A bug was fixed in nuc.div() when using pairwise deletions.
1645 o A bug occurred in the analysis of bipartitions with large
1646 numbers of large trees, with consequences on prop.part,
1647 prop.clades, and boot.phylo.
1649 o The calculation of the Billera-Holmes-Vogtmann distance in
1650 dist.topo was wrong: this has been fixed.
1654 CHANGES IN APE VERSION 1.9-2
1659 o The new function ladderize reorganizes the internal structure of
1660 a tree to plot them left- or right-ladderized.
1662 o The new function dist.nodes computes the patristic distances
1663 between all nodes, internal and terminal, of a tree. It replaces
1664 the option `full = TRUE' of cophenetic.phylo (see below).
1669 o A bug was fixed in old2new.phylo().
1671 o Some bugs were fixed in chronopl().
1673 o The edge colours were not correctly displayed by plot.phylo
1674 (thank you to Li-San Wang for the fix).
1676 o cophenetic.phylo() failed with multichotomous trees: this is
1682 o read.dna() now returns the sequences in a matrix if they are
1683 aligned (interleaved or sequential format). Sequences in FASTA
1684 format are still returned in a list.
1686 o The option `full' of cophenetic.phylo() has been removed because
1687 it could not be used from the generic.
1690 DEPRECATED & DEFUNCT
1692 o rotate() has been removed; this function did not work correctly
1697 CHANGES IN APE VERSION 1.9-1
1702 o Trees with a single tip were not read correctly in R as the
1703 element `Nnode' was not set: this is fixed.
1705 o unroot() did not set correctly the number of nodes of the
1706 unrooted tree in most cases.
1708 o read.GenBank() failed when fetching very long sequences,
1709 particularly of the BX-series.
1711 o A bug was introduced in read.tree() with ape 1.9: it has been
1716 CHANGES IN APE VERSION 1.9
1721 o There are two new print `methods' for trees of class "phylo" and
1722 lists of trees of class "multi.tree", so that they are now
1723 displayed in a compact and informative way.
1725 o There are two new functions, old2new.phylo and new2old.phylo,
1726 for converting between the old and new coding of the class
1729 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
1730 LogDet ("logdet"), and paralinear ("paralin").
1732 o compute.brlen() has been extended: several methods are now
1733 available to compute branch lengths.
1735 o write.dna() can now handle matrices as well as lists.
1740 o cophenetic.phylo() sometimes returned a wrong result with
1741 multichotomous trees: this is fixed.
1743 o rotate() failed when a single tip was specified: the tree is now
1746 o ace() did not return the correct index matrix with custom
1747 models: this is fixed.
1749 o multi2di() did not work correctly when resolving multichotomies
1750 randomly: the topology was always the same, only the arrangement
1751 of clades was randomized: this is fixed. This function now
1752 accepts trees with no branch lengths.
1754 o The output of diversi.gof() was blurred by useless prints when a
1755 user distribution was specified. This has been corrected, and
1756 the help page of this function has been expanded.
1761 o The internal structure of the class "phylo" has been changed:
1762 see the document "Definition of Formats for Coding Phylogenetic
1763 Trees in R" for the details. In addition, the code of most
1764 functions has been improved.
1766 o Several functions have been improved by replacing some R codes
1767 by C codes: pic, plot.phylo, and reorder.phylo.
1769 o There is now a citation information: see citation("ape") in R.
1771 o write.tree() now does not add extra 0's to branch lengths so
1772 that 1.23 is printed "1.23" by default, not "1.2300000000".
1774 o The syntax of bind.tree() has been simplified. This function now
1775 accepts trees with no branch lengths, and handles correctly node
1778 o The option `as.numeric' of mrca() has been removed.
1780 o The unused options `format' and `rooted' of read.tree() have
1783 o The unused option `format' of write.tree() has been removed.
1785 o The use of node.depth() has been simplified.
1789 CHANGES IN APE VERSION 1.8-5
1794 o Two new functions read.nexus.data() and write.nexus.data(),
1795 contributed by Johan Nylander, allow to read and write molecular
1796 sequences in NEXUS files.
1798 o The new function reorder.phylo() reorders the internal structure
1799 of a tree of class "phylo". It is used as the generic, e.g.,
1802 o read.tree() and read.nexus() can now read trees with a single
1805 o The new data set `cynipids' supplies a set of protein sequences
1811 o The code of all.equal.phylo() has been completely rewritten
1812 (thanks to Benoît Durand) which fixes several bugs.
1814 o read.tree() and read.nexus() now checks the labels of the tree
1815 to remove or substitute any characters that are illegal in the
1816 Newick format (parentheses, etc.)
1818 o A negative P-value could be returned by mantel.test(): this is
1823 CHANGES IN APE VERSION 1.8-4
1828 o The new function sh.test() computes the Shimodaira-
1831 o The new function collapse.singles() removes the nodes with a
1832 single descendant from a tree.
1834 o plot.phylo() has a new argument `tip.color' to specify the
1835 colours of the tips.
1837 o mlphylo() has now an option `quiet' to control the display of
1838 the progress of the analysis (the default is FALSE).
1843 o read.dna() did not read correctly sequences in sequential format
1844 with leading alignment gaps "-": this is fixed.
1846 o ace() returned a list with no class so that the generic
1847 functions (anova, logLik, ...) could not be used directly. This
1848 is fixed as ace() now returns an object of class "ace".
1850 o anova.ace() had a small bug when computing the number of degrees
1851 of freedom: this is fixed.
1853 o mlphylo() did not work when the sequences were in a matrix or
1854 a data frame: this is fixed.
1856 o rtree() did not work correctly when trying to simulate an
1857 unrooted tree with two tips: an error message is now issued.
1862 o The algorithm of rtree() has been changed: it is now about 40,
1863 100, and 130 times faster for 10, 100, and 1000 tips,
1868 CHANGES IN APE VERSION 1.8-3
1873 o There are four new `method' functions to be used with the
1874 results of ace(): logLik(), deviance(), AIC(), and anova().
1876 o The plot method of phymltest has two new arguments: `main' to
1877 change the title, and `col' to control the colour of the
1878 segments showing the AIC values.
1880 o ace() has a new argument `ip' that gives the initial values used
1881 in the ML estimation with discrete characters (see the examples
1882 in ?ace). This function now returns a matrix giving the indices
1883 of the estimated rates when analysing discrete characters.
1885 o nodelabels() and tiplabels() have a new argument `pie' to
1886 represent proportions, with any number of categories, as
1887 piecharts. The use of the option `thermo' has been improved:
1888 there is now no limitation on the number of categories.
1893 o mlphylo() did not work with more than two partitions: this is
1896 o root() failed if the proposed outgroup was already an outgroup
1897 in the tree: this is fixed.
1899 o The `col' argument in nodelabels() and tiplabels() was not
1900 correctly passed when `text' was used: this is fixed.
1902 o Two bugs were fixed in mlphylo(): parameters were not always
1903 correctly output, and the estimation failed in some cases.
1905 o plot.phylo() was stuck when given a tree with a single tip: this
1906 is fixed and a message error is now returned.
1908 o An error was corrected in the help page of gammaStat regarding
1909 the calculation of P-values.
1911 o Using gls() could crash R when the number of species in the tree
1912 and in the variables were different: this is fixed.
1916 CHANGES IN APE VERSION 1.8-2
1921 o The new function mlphylo() fits a phylogenetic tree by maximum
1922 likelihood from DNA sequences. Its companion function DNAmodel()
1923 is used to define the substitution model which may include
1924 partitioning. There are methods for logLik(), deviance(), and
1925 AIC(), and the summary() method has been extended to display in
1926 a friendly way the results of this model fitting. Currently, the
1927 functionality is limited to estimating the substitution and
1928 associated parameters and computing the likelihood.
1930 o The new function drop1.compar.gee (used as, e.g., drop1(m))
1931 tests for single effects in GEE-based comparative method. A
1932 warning message is printed if there is not enough degrees of
1938 o An error message was sometimes issued by plot.multi.tree(),
1939 though with no consequence.
1943 CHANGES IN APE VERSION 1.8-1
1948 o There is a new plot method for lists of trees (objects of class
1949 "multi.tree"): it calls plot.phylo() internally and is
1950 documented on the same help page.
1955 o A bug was fixed in the C code that analyzes bipartitions: this
1956 has impact on several functions like prop.part, prop.clades,
1957 boot.phylo, or consensus.
1959 o root() did not work correctly when the specified outgroup had
1960 more than one element: this is fixed.
1962 o dist.dna() sometimes returned a warning inappropriately: this
1965 o If the distance object given to nj() had no rownames, nj()
1966 returned a tree with no tip labels: it now returns tips labelled
1967 "1", "2", ..., corresponding to the row numbers.
1972 o nj() has been slightly changed so that tips with a zero distance
1973 are first aggregated with zero-lengthed branches; the usual NJ
1974 procedure is then performed on a distance matrix without 0's.
1978 CHANGES IN APE VERSION 1.8
1983 o The new function chronopl() estimates dates using the penalized
1984 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1986 o The new function consensus() calculates the consensus tree of a
1989 o The new function evolve.phylo() simulates the evolution of
1990 continuous characters along a phylogeny under a Brownian model.
1992 o The new plot method for objects of class "ancestral" displays a
1993 tree together with ancestral values, as returned by the above
1996 o The new function as.phylo.formula() returns a phylogeny from a
1997 set of nested taxonomic variables given as a formula.
1999 o The new function read.caic() reads trees in CAIC format.
2001 o The new function tiplabels() allows to add labels to the tips
2002 of a tree using text or plotting symbols in a flexible way.
2004 o The new function unroot() unroots a phylogeny.
2006 o multi2di() has a new option, `random', which specifies whether
2007 to resolve the multichotomies randomly (the default) or not.
2009 o prop.part() now returns an object of class "prop.part" for which
2010 there are print (to display a partition in a more friendly way)
2011 and summary (to extract the numbers) methods.
2013 o plot.phylo() has a new option, `show.tip.label', specifying
2014 whether to print the labels of the tips. The default is TRUE.
2016 o The code of nj() has been replaced by a faster C code: it is now
2017 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
2020 o write.nexus() now writes whether a tree is rooted or not.
2025 o Two bugs have been fixed in root(): unrooted trees are now
2026 handled corretly, and node labels are now output normally.
2028 o A bug was fixed in phymltest(): the executable couldn't be found
2031 o Three bugs have been fixed in ace(): computing the likelihood of
2032 ancestral states of discrete characters failed, custom models
2033 did not work, and the function failed with a null gradient (a
2034 warning message is now returned; this latter bug was also
2035 present in yule.cov() as well and is now fixed).
2037 o pic() hanged out when missing data were present: an error is now
2040 o A small bug was fixed in dist.dna() where the gamma correction
2041 was not always correctly dispatched.
2043 o plot.phylo() plotted correctly the root edge only when the tree
2044 was plotted rightwards: this works now for all directions.
2049 o dist.taxo() has been renamed as weight.taxo().
2051 o dist.phylo() has been replaced by the method cophenetic.phylo().
2053 o Various error and warning messages have been improved.
2057 CHANGES IN APE VERSION 1.7
2060 o The new function ace() estimates ancestral character states for
2061 continuous characters (with ML, GLS, and contrasts methods), and
2062 discrete characters (with ML only) for any number of states.
2064 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
2065 of directional evolution for continuous characters. The user
2066 specifies the node(s) of the tree where the character optimum
2069 o The new function is.rooted() tests whether a tree (of class
2072 o The new function rcoal() generates random ultrametric trees with
2073 the possibility to specify the function that generates the
2074 inter-nodes distances.
2076 o The new function mrca() gives for all pairs of tips in a tree
2077 (and optionally nodes too) the most recent common ancestor.
2079 o nodelabels() has a new option `thermo' to plot proportions (up
2080 to three classes) on the nodes of a tree.
2082 o rtree() has been improved: it can now generate rooted or
2083 unrooted trees, and the mathematical function that generates the
2084 branch lengths may be specified by the user. The tip labels may
2085 be given directly in the call to rtree. The limit cases (n = 2,
2086 3) are now handled correctly.
2088 o dist.topo() has a new argument `method' with two choices: "PH85"
2089 for Penny and Henny's method (already available before and now
2090 the default), and "BHV01" for the geometric distance by Billera
2091 et al. (2001, Adv. Appl. Math. 27:733).
2093 o write.tree() has a new option, `digits', which specifies the
2094 number of digits to be printed in the Newick tree. By default
2095 digits = 10. The numbers are now always printed in decimal form
2096 (i.e., 1.0e-1 is now avoided).
2098 o dist.dna() can now compute the raw distances between pairs of
2099 DNA sequences by specifying model = "raw".
2101 o dist.phylo() has a new option `full' to possibly compute the
2102 distances among all tips and nodes of the tree. The default is
2108 o Several bugs were fixed in all.equal.phylo().
2110 o dist.dna() did not handle correctly gaps ("-") in alignments:
2111 they are now considered as missing data.
2113 o rotate() did not work if the tips were not ordered: this is
2116 o mantel.test() returned NA in some special cases: this is fixed
2117 and the function has been improved and is now faster.
2119 o A bug was fixed in diversi.gof() where the calculation of A² was
2122 o cherry() did not work correctly under some OSs (mainly Linux):
2125 o is.binary.tree() has been modified so that it works with both
2126 rooted and unrooted trees.
2128 o The documentation of theta.s() was not correct: this has been
2131 o plot.mst() did not work correctly: this is fixed.
2135 CHANGES IN APE VERSION 1.6
2140 o The new function dist.topo() computes the topological distances
2143 o The new function boot.phylo() performs a bootstrap analysis on
2144 phylogeny estimation.
2146 o The new functions prop.part() and prop.clades() analyse
2147 bipartitions from a series of trees.
2152 o read.GenBank() now uses the EFetch utility of NCBI instead of
2153 the usual Web interface: it is now much faster (e.g., 12 times
2154 faster to retrieve 8 sequences, 37 times for 60 sequences).
2159 o Several bugs were fixed in read.dna().
2161 o Several bugs were fixed in diversi.time().
2163 o is.binary.tree() did not work correctly if the tree has no edge
2164 lengths: this is fixed.
2166 o drop.tip() did not correctly propagated the `node.label' of a
2167 tree: this is fixed.
2171 CHANGES IN APE VERSION 1.5
2176 o Two new functions, as.matching.phylo() and as.phylo.matching(),
2177 convert objects between the classes "phylo" and "matching". The
2178 latter implements the representation of binary trees introduced by
2179 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
2180 as.matching() has been introduced as well.
2182 o Two new functions, multi2di() and di2multi(), allow to resolve
2183 and collapse multichotomies with branches of length zero.
2185 o The new function nuc.div() computes the nucleotide diversity
2186 from a sample a DNA sequences.
2188 o dist.dna() has been completely rewritten with a much faster
2189 (particularly for large data sets) C code. Eight models are
2190 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
2191 option `method' has been renamed `model'). Computation of variance
2192 is available for all models. A gamma-correction is possible for
2193 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
2194 to remove sites with missing data on a pairwise basis. The option
2195 `GCcontent' has been removed.
2197 o read.GenBank() has a new option (species.names) which specifies
2198 whether to return the species names of the organisms in addition
2199 to the accession numbers of the sequences (this is the default
2202 o write.nexus() can now write several trees in the same NEXUS file.
2204 o drop.tip() has a new option `root.edge' that allows to specify the
2205 new root edge if internal branches are trimmed.
2210 o as.phylo.hclust() failed if some labels had parentheses: this
2213 o Several bugs were fixed in all.equal.phylo(). This function now
2214 returns the logical TRUE if the trees are identical but with
2215 different representations (a report was printed previously).
2217 o read.GenBank() did not correctly handle ambiguous base codes:
2223 o birthdeath() now returns an object of class "birthdeath" for
2224 which there is a print method.
2228 CHANGES IN APE VERSION 1.4
2233 o The new function nj() performs phylogeny estimation with the
2234 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
2237 o The new function which.edge() identifies the edges of a tree
2238 that belong to a group specified as a set of tips.
2240 o The new function as.phylo.phylog() converts an object of class
2241 "phylog" (from the package ade4) into an object of class
2244 o The new function axisPhylo() draws axes on the side of a
2247 o The new function howmanytrees() calculates the number of trees
2248 in different cases and giving a number of tips.
2250 o write.tree() has a new option `multi.line' (TRUE by default) to
2251 write a Newick tree on several lines rather than on a single
2254 o The functionalities of zoom() have been extended. Several
2255 subtrees can be visualized at the same time, and they are marked
2256 on the main tree with colors. The context of the subtrees can be
2257 marked with the option `subtree' (see below).
2259 o drop.tip() has a new option `subtree' (FALSE by default) which
2260 specifies whether to output in the tree how many tips have been
2263 o The arguments of add.scale.bar() have been redefined and have
2264 now default values (see ?add.scale.bar for details). This
2265 function now works even if the plotted tree has no edge length.
2267 o plot.phylo() can now plot radial trees, but this does not take
2268 edge lengths into account.
2270 o In plot.phylo() with `type = "phylogram"', if the values of
2271 `edge.color' and `edge.width' are identical for sister-branches,
2272 they are propagated to the vertical line that link them.
2277 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
2278 crashing. This is fixed.
2280 o In plot.phylo(), the options `edge.color' and `edge.width' are
2281 now properly recycled; their default values are now "black" and
2284 o A bug has been fixed in write.nexus().
2289 o The function node.depth.edgelength() has been removed and
2290 replaced by a C code.
2294 CHANGES IN APE VERSION 1.3-1
2299 o The new function nodelabels() allows to add labels to the nodes
2300 of a tree using text or plotting symbols in a flexible way.
2302 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
2303 numeric values specifying the lower and upper limits on the x-
2304 and y-axes. This allows to leave some space on any side of the
2305 tree. If a single value is given, this is taken as the upper
2310 CHANGES IN APE VERSION 1.3
2315 o The new function phymltest() calls the software PHYML and fits
2316 28 models of DNA sequence evolution. There are a print method to
2317 display likelihood and AIC values, a summary method to compute
2318 the hierarchical likelihood ratio tests, and a plot method to
2319 display graphically the AIC values of each model.
2321 o The new function yule.cov() fits the Yule model with covariates,
2322 a model where the speciation rate is affected by several species
2323 traits through a generalized linear model. The parameters are
2324 estimated by maximum likelihood.
2326 o Three new functions, corBrownian(), corGrafen(), and
2327 corMartins(), compute the expected correlation structures among
2328 species given a phylogeny under different models of evolution.
2329 These can be used for GLS comparative phylogenetic methods (see
2330 the examples). There are coef() and corMatrix() methods and an
2331 Initialize.corPhyl() function associated.
2333 o The new function compar.cheverud() implements Cheverud et al.'s
2334 (1985; Evolution 39:1335) phylogenetic comparative method.
2336 o The new function varcomp() estimates variance components; it has
2339 o Two new functions, panel.superpose.correlogram() and
2340 plot.correlogramList(), allow to plot several phylogenetic
2343 o The new function node.leafnumber() computes the number of leaves
2344 of a subtree defined by a particular node.
2346 o The new function node.sons() gets all tags of son nodes from a
2349 o The new function compute.brlen() computes the branch lengths of
2350 a tree according to a specified method.
2352 o plot.phylo() has three new options: "cex" controls the size of
2353 the (tip and node) labels (thus it is no more needed to change
2354 the global graphical parameter), "direction" which allows to
2355 plot the tree rightwards, leftwards, upwards, or downwards, and
2356 "y.lim" which sets the upper limit on the y-axis.
2361 o Some functions which try to match tip labels and names of
2362 additional data (e.g. vector) are likely to fail if there are
2363 typing or syntax errors. If both series of names do not perfectly
2364 match, they are ignored and a warning message is now issued.
2365 These functions are bd.ext, compar.gee, pic. Their help pages
2366 have been clarified on this point.
2370 CHANGES IN APE VERSION 1.2-7
2375 o The new function root() reroots a phylogenetic tree with respect
2376 to a specified outgroup.
2378 o The new function rotate() rotates an internal branch of a tree.
2380 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
2381 trees) controls the display of the tip labels in unrooted trees.
2382 This display has been greatly improved: the tip labels are now not
2383 expected to overlap with the tree (particularly if lab4ut =
2384 "axial"). In all cases, combining appropriate values of "lab4ut"
2385 and the font size (via "par(cex = )") should result in readable
2386 unrooted trees. See ?plot.phylo for some examples.
2388 o In drop.tip(), the argument `tip' can now be numeric or character.
2393 o drop.tip() did not work correctly with trees with no branch
2394 lengths: this is fixed.
2396 o A bug in plot.phylo(..., type = "unrooted") made some trees being
2397 plotted with some line crossings: this is now fixed.
2401 CHANGES IN APE VERSION 1.2-6
2406 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
2407 correlogram.phylo, dist.taxo, plot.correlogram) have been added
2408 to implement comparative methods with an autocorrelation approach.
2410 o A new data set describing some life history traits of Carnivores
2416 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
2421 o When plotting a tree with plot.phylo(), the new default of the
2422 option `label.offset' is now 0, so the labels are always visible.
2426 CHANGES IN APE VERSION 1.2-5
2431 o The new function bd.ext() fits a birth-death model with combined
2432 phylogenetic and taxonomic data, and estimates the corresponding
2433 speciation and extinction rates.
2438 o The package gee is no more required by ape but only suggested
2439 since only the function compar.gee() calls gee.
2443 CHANGES IN APE VERSION 1.2-4
2448 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
2449 and lines.popsize) implementing a new approach for inferring the
2450 demographic history from genealogies using a reversible jump
2451 MCMC have been introduced.
2453 o The unit of time in the skyline plot and in the new plots can
2454 now be chosen to be actual years, rather than substitutions.
2458 CHANGES IN APE VERSION 1.2-3
2463 o The new function rtree() generates a random binary tree with or
2464 without branch lengths.
2466 o Two new functions for drawing lineages-through-time (LTT) plots
2467 are provided: ltt.lines() adds a LTT curve to an existing plot,
2468 and mltt.plot() does a multiple LTT plot giving several trees as
2469 arguments (see `?ltt.plot' for details).
2474 o Some taxon names made R crashing when calling as.phylo.hclust():
2477 o dist.dna() returned an error with two identical DNA sequences
2478 (only using the Jukes-Cantor method returned 0): this is fixed.
2483 o The function dist.phylo() has been re-written using a different
2484 algorithm: it is now about four times faster.
2486 o The code of branching.times() has been improved: it is now about
2491 CHANGES IN APE VERSION 1.2-2
2496 o The new function seg.sites() finds the segregating sites in a
2497 sample of DNA sequences.
2502 o A bug introduced in read.tree() and in read.nexus() with version
2505 o A few errors were corrected and a few examples were added in the
2510 CHANGES IN APE VERSION 1.2-1
2515 o plot.phylo() can now draw the edge of the root of a tree if it
2516 has one (see the new option `root.edge', its default is FALSE).
2521 o A bug was fixed in read.nexus(): files with semicolons inside
2522 comment blocks were not read correctly.
2524 o The behaviour of read.tree() and read.nexus() was corrected so
2525 that tree files with badly represented root edges (e.g., with
2526 an extra pair of parentheses, see the help pages for details)
2527 are now correctly represented in the object of class "phylo";
2528 a warning message is now issued.
2532 CHANGES IN APE VERSION 1.2
2537 o plot.phylo() has been completely re-written and offers several
2538 new functionalities. Three types of trees can now be drawn:
2539 phylogram (as previously), cladogram, and unrooted tree; in
2540 all three types the branch lengths can be drawn using the edge
2541 lengths of the phylogeny or not (e.g., if the latter is absent).
2542 The vertical position of the nodes can be adjusted with two
2543 choices (see option `node.pos'). The code has been re-structured,
2544 and two new functions (potentially useful for developpers) are
2545 documented separately: node.depth.edgelength() and node.depth();
2546 see the respective help pages for details.
2548 o The new function zoom() allows to explore very large trees by
2549 focusing on a small portion of it.
2551 o The new function yule() fits by maximum likelihood the Yule model
2552 (birth-only process) to a phylogenetic tree.
2554 o Support for writing DNA sequences in FASTA format has been
2555 introduced in write.dna() (support for reading sequences in
2556 this format was introduced in read.dna() in version 1.1-2).
2557 The function has been completely re-written, fixing some bugs
2558 (see below); the default behaviour is no more to display the
2559 sequences on the standard output. Several options have been
2560 introduced to control the sequence printing in a flexible
2561 way. The help page has been extended.
2563 o A new data set is included: a supertree of bats in NEXUS format.
2568 o In theta.s(), the default of the option `variance' has
2569 been changed to `FALSE' (as was indicated in the help page).
2571 o Several bugs were fixed in the code of all.equal.phylo().
2573 o Several bugs were fixed in write.dna(), particularly this
2574 function did not work with `format = "interleaved"'.
2576 o Various errors were corrected in the help pages.
2581 o The argument names of as.hclust.phylo() have been changed
2582 from "(phy)" to "(x, ...)" to conform to the definition of
2583 the corresponding generic function.
2585 o gamma.stat() has been renamed gammaStat() to avoid confusion
2586 since gamma() is a generic function.
2590 CHANGES IN APE VERSION 1.1-3
2595 o base.freq() previously did not return a value of 0 for
2596 bases absent in the data (e.g., a vector of length 3 was
2597 returned if one base was absent). This is now fixed (a
2598 vector of length 4 is always returned).
2600 o Several bugs were fixed in read.nexus(), including that this
2601 function did not work in this absence of a "TRANSLATE"
2602 command in the NEXUS file, and that the commands were
2607 CHANGES IN APE VERSION 1.1-2
2612 o The Tamura and Nei (1993) model of DNA distance is now implemented
2613 in dist.dna(): five models are now available in this function.
2615 o A new data set is included: a set of 15 sequences of the
2616 cytochrome b mitochondrial gene of the woodmouse (Apodemus
2622 o A bug in read.nexus() was fixed.
2624 o read.dna() previously did not work correctly in most cases.
2625 The function has been completely re-written and its help page
2626 has been considerably extended (see ?read.dna for details).
2627 Underscores (_) in taxon names are no more replaced with
2628 spaces (this behaviour was undocumented).
2630 o A bug was fixed in write.dna().
2634 CHANGES IN APE VERSION 1.1-1
2639 o A bug in read.tree() introduced in APE 1.1 was fixed.
2641 o A bug in compar.gee() resulted in an error when trying to fit
2642 a model with `family = "binomial"'. This is now fixed.
2646 CHANGES IN APE VERSION 1.1
2651 o The Klastorin (1982) method as suggested by Misawa and Tajima
2652 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
2653 on the basis of phylogenetic trees has been implemented (see
2654 the function klastorin()).
2656 o Functions have been added to convert APE's "phylo" objects in
2657 "hclust" cluster objects and vice versa (see the help page of
2658 as.phylo for details).
2660 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
2661 are introduced for the estimation of absolute evolutionary rates
2662 (ratogram) and dated clock-like trees (chronogram) from
2663 phylogenetic trees using the non-parametric rate smoothing approach
2664 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
2666 o A summary method is now provided printing a summary information on a
2667 phylogenetic tree with, for instance, `summary(tree)'.
2669 o The behaviour of read.tree() was changed so that all spaces and
2670 tabulations in tree files are now ignored. Consequently, spaces in tip
2671 labels are no more allowed. Another side effect is that read.nexus()
2672 now does not replace the underscores (_) in tip labels with spaces
2673 (this behaviour was undocumented).
2675 o The function plot.phylo() has a new option (`underscore') which
2676 specifies whether the underscores in tip labels should be written on
2677 the plot as such or replaced with spaces (the default).
2679 o The function birthdeath() now computes 95% confidence intervals of
2680 the estimated parameters using profile likelihood.
2682 o Three new data sets are included: a gene tree estimated from 36
2683 landplant rbcL sequences, a gene tree estimated from 32 opsin
2684 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
2689 o A bug was fixed in dist.gene() where nothing was returned.
2691 o A bug in plot.mst() was fixed.
2693 o A bug in vcv.phylo() resulted in false correlations when the
2694 option `cor = TRUE' was used (now fixed).
2698 CHANGES IN APE VERSION 1.0
2703 o Two new functions, read.dna() and write.dna(), read/write in a file
2704 DNA sequences in interleaved or in sequential format.
2706 o Two new functions, read.nexus() and write.nexus(), read/write trees
2709 o The new function bind.tree() allows to bind two trees together,
2710 possibly handling root edges to give internal branches.
2712 o The new function drop.tip() removes the tips in a phylogenetic tree,
2713 and trims (or not) the corresponding internal branches.
2715 o The new function is.ultrametric() tests if a tree is ultrametric.
2717 o The function plot.phylo() has more functionalities such as drawing the
2718 branches with different colours and/or different widths, showing the
2719 node labels, controling the position and font of the labels, rotating
2720 the labels, and controling the space around the plot.
2722 o The function read.tree() can now read trees with no branch length,
2723 such as "(a,b),c);". Consequently, the element `edge.length' in
2724 objects of class "phylo" is now optional.
2726 o The function write.tree() has a new default behaviour: if the default
2727 for the option `file' is used (i.e. file = ""), then a variable of
2728 mode character containing the tree in Newick format is returned which
2729 can thus be assigned (e.g., tree <- write.tree(phy)).
2731 o The function read.tree() has a new argument `text' which allows
2732 to read the tree in a variable of mode character.
2734 o A new data set is included: the phylogenetic relationships among
2735 the orders of birds from Sibley and Ahlquist (1990).
2739 CHANGES IN APE VERSION 0.2-1
2744 o Several bugs were fixed in the help pages.
2748 CHANGES IN APE VERSION 0.2
2753 o The function write.tree() writes phylogenetic trees (objects of class
2754 "phylo") in an ASCII file using the Newick parenthetic format.
2756 o The function birthdeath() fits a birth-death model to branching times
2757 by maximum likelihood, and estimates the corresponding speciation and
2760 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
2763 o The function is.binary.tree() tests whether a phylogeny is binary.
2765 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
2766 as well as some methods are introduced.
2768 o Several functions, including some generics and methods, for computing
2769 skyline plot estimates (classic and generalized) of effective
2770 population size through time are introduced and replace the function
2771 skyline.plot() in version 0.1.
2773 o Two data sets are now included: the phylogenetic relationships among
2774 the families of birds from Sibley and Ahlquist (1990), and an
2775 estimated clock-like phylogeny of HIV sequences sampled in the
2776 Democratic Republic of Congo.
2779 DEPRECATED & DEFUNCT
2781 o The function skyline.plot() in ape 0.1 has been deprecated and
2782 replaced by more elaborate functions (see above).
2787 o Two important bugs were fixed in plot.phylo(): phylogenies with
2788 multichotomies not at the root or not with only terminal branches,
2789 and phylogenies with a single node (i.e. only terminal branches)
2790 did not plot. These trees should be plotted correctly now.
2792 o Several bugs were fixed in diversi.time() in the computation of
2795 o Various errors were corrected in the help pages.
projects / ape.git / blob