1 CHANGES IN APE VERSION 3.0-8
6 o The new function ewLasso tests whether an incomplete set of
7 distances uniquely determines the edge weights of a given
8 unrooted topology using the 'Lasso' method by Dress et
9 al. (2012, J. Math. Biol. 65:77).
11 o ace() gains a new option 'use.expm' to use expm() from the
12 package of the same name in place of matexpo().
17 o read.dna(, "fasta") may add '\r' in labels: this is fixed.
19 o prop.clades() returned wrong numbers when the tip labels of
20 'phy' are not in the same order than the list of trees (thanks
21 to Rupert Collins for the report).
23 o CADM.post() displayed "1" on the diagonal of the matrix of
24 Mantel p-values. It now displays "NA" on the diagonal,
25 indicating that no test of significance is computed between a
26 distance matrix and itself.
28 o rtree(n, rooted = FALSE) returned trees with an 'edge' matrix
29 stored as doubles instead of integers for n > 4.
34 o The files CDAM.global.R and CDAM.post.R have been renamed
35 CADM.global.R and CADM.post.R.
37 o ace() has a new default for its option 'method': this is "REML"
38 for continuous characters and "ML" for discrete ones.
40 o ape does not import gee anymore so the latter doesn't need to
45 CHANGES IN APE VERSION 3.0-7
50 o The new function chronos estimates chronograms by penalised
51 likelihood and maximum likelihood with a completely reworked
52 code and interface. There is a new function makeChronosCalib to
53 set the calibration points easily. chronos() will eventually
56 o The new function 'where' searches patterns in DNA sequences.
58 o pic() gains an option 'rescaled.tree = FALSE' to return the tree
59 with its branch lengths rescaled for the PIC calculation.
61 o clustal(), muscle(), and tcoffee() gain an option
62 'original.ordering = TRUE' to ease the comparisons of
65 o plot.phylo() has a new option, open.angle, used when plotting
68 o The new function read.FASTA reads FASTA files much faster and
69 more efficiently. It is called internally by read.dna(, "fasta")
70 or can be called directly.
75 o drop.tip() shuffled node labels on some trees.
77 o axisPhylo() now works correctly with circular trees, and gives a
78 sensible error message when type = "r" or "u".
83 o .compressTipLabel() is 10 times faster thanks to Joseph Brown.
85 o base.freq() is now faster with lists.
87 o as.matrix.DNAbin() should be faster and more efficient with
88 lists; it now accepts vectors.
92 CHANGES IN APE VERSION 3.0-6
97 o reorder.phylo() has a new order, "postorder", and a new option
98 index.only = TRUE to return only the vector of indices (the tree
99 is unmodified, see ?reorder.phylo for details).
101 o The three new functions node.depth.edgelength, node.height, and
102 node.height.clado make some internal code available from R. See
103 ?node.depth (which was already documented) for details.
108 o reorder(, "pruningwise") made R crash if the rows of the edge
109 matrix are in random order: this is now fixed.
111 o drop.tip() sometimes shuffled node labels (thanks to Rebecca
112 Best for the report).
114 o drop.tip(phy, "") returned a tree with zero-length tip labels:
115 it now returns the tree unchanged (thanks to Brian Anacker for
118 o plot.phylo() made R crash if the tree has zero-length tip
119 labels: it now returns NULL (thanks again to Brian Anacker).
124 o dist.nodes() is now 6 to 10 times faster.
126 o reorder(, "cladewise") is now faster. The change is not very
127 visible for small trees (n < 1000) but this can be more than
128 1000 faster for big trees (n >= 1e4).
130 o The attribute "order" of the objects of class "phylo" is now
131 strongly recommended, though not mandatory. Most functions in
132 ape should return a tree with this attribute correctly set.
134 o dbd() is now vectorized on both arguments 'x' (number of species
135 in clade) and 't' (clade age) to make likelihood calculations
140 CHANGES IN APE VERSION 3.0-5
145 o ace() should better catch errors when SEs cannot be computed.
150 o write.dna(format = "fasta") now conforms more closely to the
151 FASTA standard thanks to François Michonneau.
153 o print.DNAbin() does not print base compositions if there are more
154 than one million nucleotides.
158 CHANGES IN APE VERSION 3.0-4
163 o read.dna() failed to read Phylip files if the first line used
164 tabulations instead of white spaces.
166 o read.dna() failed to read Phylip or Clustal files with less than
167 10 nucleotides. (See other changes in this function below.)
171 o read.dna() now requires at least one space (or tab) between the
172 taxa names and the sequences (whatever the length of taxa
173 names). write.dna() now follows the same rule.
175 o The option 'seq.names' of read.dna has been removed.
177 o The files ape-defunct.R and ape-defunct.Rd, which have not been
178 modified for almost two years, have been removed.
180 o The C code of bionj() has been reworked: it is more stable (by
181 avoiding passing character strings), slightly faster (by about
182 20%), and numerically more accurate.
184 o The C code of fastme.*() has been slightly modified and should
185 be more stable by avoiding passing character strings (the
186 results are identical to the previous versions).
188 o The file src/newick.c has been removed.
192 CHANGES IN APE VERSION 3.0-3
197 o birthdeath() now catches errors and warnings much better so that
198 a result is returned in most cases.
203 o Because of problems with character string manipulation in C, the
204 examples in ?bionj and in ?fastme have been disallowed. In the
205 meantime, these functions might be unstable. This will be solved
206 for the next release.
210 CHANGES IN APE VERSION 3.0-2
215 o The new function alex (alignment explorator) zooms in a DNA
216 alignment and opens the result in a new window.
221 o compute.brtime() did not completely randomized the order of the
224 o write.nexus() did not work correctly with rooted trees (thanks
225 to Matt Johnson for the fix).
227 o mltt.plot(, backward = FALSE) did not set the x-axis correctly.
229 o A bug was introduced in prop.clades() with ape 3.0. The help page
230 has been clarified relative to the use of the option 'rooted'.
232 o mantel.test() printed a useless warning message.
234 o plot.phylo(, direction = "downward") ignored 'y.lim'.
236 o is.monophyletic() did not work correctly if 'tips' was not stored
239 o prop.part() could make R crash if the first tree had many
242 o njs(), bionjs(), and mvrs() now return an error if 'fs < 1'.
244 o SDM() did not work correctly. The code has also been generally
250 o The DESCRIPTION file has been updated.
252 o The option 'original.data' of write.nexus() has been removed.
254 o The files bionjs.c, mvr.c, mvrs.c, njs.c, triangMtd.c, and
255 triangMtds.c have been improved which should fix some bugs in
256 the corresponding functions.
258 o dist.gene() now coerces input data frame as matrix resulting in
259 much faster calculations (thanks to a suggestion by Markus
264 CHANGES IN APE VERSION 3.0-1
269 o dist.dna() has two new models: "indel" and "indelblock".
271 o bind.tree() now accepts 'position' > 0 when the trees have no
272 banch length permitting to create a node in 'x' when grafting
273 'y' (see ?bind.tree for details).
278 o cophyloplot( , rotate = TRUE) made R hanged after a few clicks.
279 Also the tree is no more plotted twice.
281 o read.GenBank() has been updated to work with EFetch 2.0.
283 o unroot() on trees in "pruningwise" order did not respect this
288 CHANGES IN APE VERSION 3.0
293 o The three functions dyule, dbd, and dbdTime calculate the
294 density probability (i.e., the distribution of the number of
295 species) for the Yule, the constant and the time-dependent
296 birth-beath models, respectively. These probabilities can be
297 conditional on no extinction and/or on a log-scale.
299 o plot.phylo() has a new option 'rotate.tree' to rotate unrooted,
300 fan, or radial trees around the center of the plot.
302 o boot.phylo() and prop.clades() have a new option rooted =
303 FALSE. Note that the behaviour of prop.part() is unchanged.
305 o edgelabels() has a new option 'date' to place labels on edges of
306 chronograms using the time scale (suggestion by Rob Lanfear).
311 o In chronopl(), the code setting the initial dates failed in
312 complicated settings (several dates known within intervals).
313 This has been generally improved and should result in faster
314 and more efficient convergence even in simple settings.
316 o mantel.test() sometimes returned P-values > 1 with the default
319 o extract.clade() sometimes shuffled some tip labels (thanks to
320 Ludovic Mallet and Mahendra Mariadassou for the fix).
322 o clustal() should now find by default the executable under Windows.
327 o The code of yule() has been simplified and is now much faster for
330 o The code of mantel.test() has been adjusted to be consistent
331 with common permutation tests.
333 o The C code of base.freq() has been improved and is now nearly 8
336 o The option 'original.data' of write.nexus() is now deprecated and
337 will be removed in a future release.
339 o The code of is.ultrametric() has been improved and is now 3 times
342 o The code of vcv.phylo() has been improved and is now 10 or 30
343 times faster for 100 or 1000 tips, respectively. Consequently,
344 fitting models with PGLS will be faster overall.
348 CHANGES IN APE VERSION 2.8
353 o Twelve new functions have been written by Andrei-Alin Popescu:
354 additive, ultrametric, is.compatible, arecompatible, mvr, mvrs,
355 njs, bionjs, SDM, treePop, triangMtd, triangMtd*.
357 o A new class "bitsplits" has been created by Andrei-Alin Popescu
358 to code splits (aka, bipartition).
360 o There is a new generic function as.bitsplits with a method to
361 convert from the class "prop.part" to the class "bitsplits".
363 o The new function ltt.coplot plots on the same scales a tree and
364 the derived LTT plot.
366 o ltt.plot() has two new options: backward and tol. It can now
367 handle non-ultrametic trees and its internal coding has been
368 improved. The coordinates of the plot can now be computed with
369 the new function ltt.plot.coords.
374 o prop.part() crashed if some trees had some multichotomies.
378 CHANGES IN APE VERSION 2.7-3
383 o The new function compute.brtime computes and sets branching times.
385 o mantel.test() has a new argument 'alternative' which is
386 "two-sided" by default. Previously, this test was one-tailed
387 with no possibility to change.
389 o ace() can now do REML estimation with continuous characters,
390 giving better estimates of the variance of the Brownian motion
396 o Branch lengths were wrongly updated with bind.tree(, where = <tip>,
397 position = 0). (Thanks to Liam Revell for digging this bug out.)
399 o Simulation of OU process with rTraitCont() did not work correctly.
400 This now uses formula from Gillespie (1996) reduced to a BM
401 process when alpha = 0 to avoid division by zero. The option
402 'linear' has been removed.
404 o Cross-validation in chronopl() did not work when 'age.max' was
407 o consensus(, p = 0.5) could return an incorrect tree if some
408 incompatible splits occur in 50% of the trees (especially with
409 small number of trees).
411 o c() with "multiPhylo" did not work correctly (thanks to Klaus
412 Schliep for the fix).
414 o root() failed in some cases with an outgroup made of several tips.
415 The help page has been clarified a bit.
419 CHANGES IN APE VERSION 2.7-2
424 o There is a new class "evonet" to code evolutionary networks, with
425 a constructor function evonet(), a print() and a plot() methods,
426 and four conversion methods to the classes "phylo", "networx",
427 "network", and "igraph".
429 o The new function rTraitMult does multivariate traits simulation
430 with user-defined models.
432 o plot.phylo() has a new option 'plot = TRUE'. If FALSE, the tree
433 is not plotted but the graphical device is set and the
434 coordinates are saved as usual.
436 o diversity.contrast.test() gains a fourth version of the test with
437 method = "logratio"; the literature citations have been clarified.
439 o add.scale.bar() has two new options, 'lwd' and 'lcol', to modify
440 the aspect of the bar.
442 o boot.phylo() now displays a progress bar by default (can be off
445 o There is a new predict() method for compar.gee().
450 o bionj() made R crash if distances were too large. It now returns
451 an error if at least one distance is greater than 100.
453 o drop.tip() returned a wrong tree if 'tip' was of zero length.
455 o read.nexus.data() failed with URLs.
457 o boot.phylo() returned overestimated support values in the
458 presence of identical or nearly identical sequences.
463 o The data bird.families, bird.orders, cynipids, and woodmouse are
464 now provided as .rda files.
468 CHANGES IN APE VERSION 2.7-1
473 o The new function trex does tree exploration with multiple
476 o The new function kronoviz plots several rooted (dated) trees on
479 o identify.phylo() has a new option 'quiet' (FALSE by default).
484 o A bug was introduced in read.nexus() in ape 2.7.
486 o image.DNAbin() did not colour correctly the bases if there were
489 o .compressTipLabel() failed with a list with a single tree.
491 o identify.phylo() returned a wrong answer when the x- and y-scales
494 o write.nexus() failed with lists of trees with compressed labels.
499 o identify.phylo() now returns NULL if the user right- (instead of
500 left-) clicks (an error was returned previously).
502 o read.nexus() should be robust to commands inserted in the TREES
507 CHANGES IN APE VERSION 2.7
512 o There is a new image() method for "DNAbin" objects: it plots DNA
513 alignments in a flexible and efficient way.
515 o Two new functions as.network.phylo and as.igraph.phylo convert
516 trees of class "phylo" into these respective network classes
517 defined in the packages of the same names.
519 o The three new functions clustal, muscle, and tcoffee perform
520 nucleotide sequence alignment by calling the external programs
523 o Four new functions, diversity.contrast.test, mcconwaysims.test,
524 richness.yule.test, and slowinskiguyer.test, implement various
525 tests of diversification shifts using sister-clade comparisons.
527 o base.freq() gains an option 'all' to count all the possible bases
528 including the ambiguous ones (defaults to FALSE).
530 o write.nexus() now writes tree names in the NEXUS file if given a
531 list of trees with names.
536 o prop.part() failed in some situations with unrooted trees.
538 o read.nexus() shuffled node labels when a TRANSLATE block was
541 o varCompPhylip() did not work if 'exec' was specified.
543 o bind.tree() shuffled node labels when position > 0 and 'where'
549 o BaseProportion in src/dist_dna.c has been modified.
551 o A number of functions in src/tree_build.c have been modified.
553 o The matching representation has now only two columns as the third
554 column was redundant.
558 CHANGES IN APE VERSION 2.6-3
563 o rTraitCont() and rTraitDisc() gains a '...' argument used with
564 user-defined models (suggestion by Gene Hunt).
569 o as.hclust.phylo() now returns an error with unrooted trees.
571 o as.hclust.phylo() failed with trees with node labels (thanks to
572 Jinlong Zhang for pointing this bug out).
574 o read.dna(, "fasta") failed if sequences were not all of the same
577 o plot.phylo() did not recycle values of 'font', 'cex' and
578 'tip.color' correctly when type = "fan" or "radial".
580 o plot.phylo() ignored 'label.offset' when type = "radial", "fan", or
581 "unrooted" with lab4ut = "axial" (the placement of tip labels still
582 needs to be improved with lab4ut = "horizontal").
587 o In drop.fossil() the default tol = 0 has been raised to 1e-8.
589 o The help command ?phylo now points to the man page of read.tree()
590 where this class is described. Similarly, ?matching points to the
591 man page of as.matching().
595 CHANGES IN APE VERSION 2.6-2
600 o Two new functions, pic.ortho and varCompPhylip, implements the
601 orthonormal contrasts of Felsenstein (2008, Am Nat, 171:713). The
602 second function requires Phylip to be installed on the computer.
604 o bd.ext() has a new option conditional = TRUE to use probabilities
605 conditioned on no extinction for the taxonomic data.
610 o write.tree() failed to output correctly tree names.
612 o dist.nodes() returned duplicated column(s) with unrooted and/or
613 multichotomous trees.
615 o mcmc.popsize() terminated unexpectedly if the progress bar was
618 o prop.part(x) made R frozen if 'x' is of class "multiPhylo".
620 o Compilation under Mandriva failed (thanks to Jos Käfer for the fix).
622 o drop.tip() shuffled tip labels with subtree = TRUE or trim.internal
625 o Objects returned by as.hclust.phylo() failed when analysed with
626 cutree() or rect.hclust().
628 o write.tree() did not output correctly node labels (thanks to Naim
629 Matasci and Jeremy Beaulieu for the fix).
631 o ace(type = "discrete") has been improved thanks to Naim Marasci and
636 CHANGES IN APE VERSION 2.6-1
641 o The new function speciesTree calculates the species tree from a set
642 of gene trees. Several methods are available including maximum tree
643 and shallowest divergence tree.
648 o A bug introduced in write.tree() with ape 2.6 has been fixed.
650 o as.list.DNAbin() did not work correctly with vectors.
652 o as.hclust.phylo() failed with trees with node labels (thanks to
653 Filipe Vieira for the fix).
657 CHANGES IN APE VERSION 2.6
662 o The new functions rlineage and rbdtree simulate phylogenies under
663 any user-defined time-dependent speciation-extinction model. They
664 use continuous time algorithms.
666 o The new function drop.fossil removes the extinct species from a
669 o The new function bd.time fits a user-defined time-dependent
670 birth-death model. It is a generalization of yule.time() taking
671 extinction into account.
673 o The new function MPR does most parsimonious reconstruction of
676 o The new function Ftab computes the contingency table of base
677 frequencies from a pair of sequences.
679 o There is now an 'as.list' method for the class "DNAbin".
681 o dist.dna() can compute the number of transitions or transversions
682 with the option model = "Ts" or model = "Tv", respectively.
684 o [node|tip|edge]labels() gain three options with default values to
685 control the aspect of thermometers: horiz = TRUE, width = NULL,
688 o compar.gee() has been improved with the new option 'corStruct' as an
689 alternative to 'phy' to specify the correlation structure, and
690 calculation of the QIC (Pan 2001, Biometrics). The display of the
691 results has also been improved.
693 o read.GenBank() has a new option 'gene.names' to return the name of
694 the gene (FALSE by default).
699 o extract.clade() sometimes shuffled the tip labels.
701 o plot.phylo(type = "unrooted") did not force asp = 1 (thanks to Klaus
704 o dist.dna(model = "logdet") used to divide distances by 4. The
705 documentation has been clarified on the formulae used.
710 o rTraitCont(model = "OU") has an option 'linear = TRUE' to possibly
711 change the parameterisation (see ?rTraitCont for details).
713 o pic() now returns a vector with the node labels of the tree (if
716 o write.tree() and read.tree() have been substantially improved thanks
717 to contributions by Klaus Schliep.
721 CHANGES IN APE VERSION 2.5-3
726 o The new function mixedFontLabel helps to make labels with bits of
727 text to be plotted in different fonts.
729 o There are now replacement operators for [, [[, and $ for the class
730 "multiPhylo" (i.e., TREES[11:20] <- rmtree(10, 100)). They possibly
731 check that the tip labels are the same in all trees.
733 o Objects of class "multiPhylo" can be built with c(): there are
734 methods for the classes "phylo" and "multiPhylo".
736 o The internal functions .compressTipLabel and .uncompressTipLabel are
742 o bind.tree(x, y, where, position = 0) did not work correctly if 'y'
743 was a single-edge tree and 'where' was a tip.
745 o rTraitCont() did not use the square-root of branch lengths when
746 simulating a Brownian motion model.
750 CHANGES IN APE VERSION 2.5-2
755 o There is now a print method for results from ace().
757 o There is a labels() method for objects of class "DNAbin".
759 o read.dna() has a new option 'as.matrix' to possibly force sequences
760 in a FASTA file to be stored in a matrix (see ?read.dna for details).
765 o as.phylo.hclust() used to multiply edge lengths by 2.
767 o A minor bug was fixed in rTraitDisc().
769 o ace() sometimes failed (parameter value was NaN and the optimisation
775 o evolve.phylo() and plot.ancestral() have been removed.
777 o chronogram(), ratogram(), and NPRS.criterion() have been removed.
782 o nj() has been improved and is now about 30% faster.
784 o The default option 'drop' of [.DNAbin has been changed to FALSE to
785 avoid dropping rownames when selecting a single sequence.
787 o print.DNAbin() has been changed to summary.DNAbin() which has been
792 CHANGES IN APE VERSION 2.5-1
797 o The new function stree generates trees with regular shapes.
799 o It is now possible to bind two trees with x + y (see ?bind.tree for
802 o drop.tip(), extract.clade(), root(), and bind.tree() now have an
803 'interactive' option to make the operation on a plotted tree.
805 o cophyloplot() gains two new arguments 'lwd' and 'lty' for the
806 association links; they are recycled like 'col' (which wasn't before).
811 o rTraitDisc() did not use its 'freq' argument correctly (it was
812 multiplied with the rate matrix column-wise instead of row-wise).
814 o [node|tip|edge]labels(thermo = ) used to draw empty thermometers
815 with NA values. Nothing is drawn now like with 'text' or 'pch'.
816 The same bug occurred with the 'pie' option.
818 o A bug was fixed in compar.ou() and the help page was clarified.
820 o bind.tree() has been rewritten fixing several bugs and making it
823 o plot.phylo(type = "p") sometimes failed to colour correctly the
824 vertical lines representing the nodes.
826 o plot.phylo(direction = "l", x.lim = 30) failed to plot the branches
827 in the correct direction though the tip labels were displayed
833 o The c, cbind, and rbind methods for "DNAbin" objetcs now check that
834 the sequences are correctly stored (in a list for c, in a matrix
835 for the two other functions).
839 CHANGES IN APE VERSION 2.5
844 o The new function parafit by Pierre Legendre tests for the
845 coevolution between hosts and parasites. It has a companion
846 function, pcoa, that does principal coordinate decomposition.
847 The latter has a biplot method.
849 o The new function lmorigin by Pierre Legendre performs multiple
850 regression through the origin with testing by permutation.
852 o The new functions rTraitCont and rTraitDisc simulate continuous and
853 discrete traits under a wide range of evolutionary models.
855 o The new function delta.plot does a delta plot following Holland et
856 al. (2002, Mol. Biol. Evol. 12:2051).
858 o The new function edges draws additional branches between any nodes
859 and/or tips on a plotted tree.
861 o The new function fancyarrows enhances arrows from graphics with
862 triangle and harpoon heads; it can be called from edges().
864 o add.scale.bar() has a new option 'ask' to draw interactively.
866 o The branch length score replaces the geodesic distance in dist.topo.
868 o Three new data sets are included: the gopher-lice data (gopher.D),
869 SO2 air pollution in 41 US cities (lmorigin.ex1, from Sokal &
870 Rohlf 1995), and some host-parasite specificity data
871 (lmorigin.ex2, from Legendre & Desdevises 2009).
876 o add.scale.bar() drew the bar outside the plotting region with the
877 default options with unrooted or radial trees.
879 o dist.topo() made R stuck when the trees had different sizes (thanks
880 to Otto Cordero for the fix).
885 o The geodesic distance has been replaced by the branch length score
890 CHANGES IN APE VERSION 2.4-1
895 o rtree() and rcoal() now accept a numeric vector for the 'br'
898 o vcv() is a new generic function with methods for the classes "phylo"
899 and "corPhyl" so that it is possible to calculate the var-cov matrix
900 for "transformation models". vcv.phylo() can still be used for trees
901 of class "phylo"; its argument 'cor' has been renamed 'corr'.
906 o bind.tree() failed when 'y' had no root edge.
908 o read.nexus() shuffled tip labels when the trees have no branch
909 lengths and there is a TRANSLATE block.
911 o read.nexus() does not try to translate node labels if there is a
912 translation table in the NEXUS file. See ?read.nexus for a
913 clarification on this behaviour.
915 o plot.multiPhylo() crashed R when plotting a list of trees with
916 compressed tip labels.
918 o write.nexus() did not translate the taxa names when asked for.
920 o plot.phylo(type = "fan") did not rotate the tip labels correctly
921 when the tree has branch lengths.
923 o ace(type = "continuous", method = "ML") now avoids sigma² being
924 negative (which resulted in an error).
926 o nj() crashed with NA/NaN in the distance matrix: an error in now
931 CHANGES IN APE VERSION 2.4
936 o base.freq() has a new option 'freq' to return the counts; the
937 default is still to return the proportions.
942 o seg.sites() did not handle ambiguous nucleotides correctly: they
945 o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
946 the tree: the argument is now ignored.
948 o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
954 o Trying to plot a tree with a single tip now returns NULL with a
955 warning (it returned an error previously).
957 o The way lines representing nodes are coloured in phylograms has
958 been modified (as well as their widths and types) following some
959 users' request; this is only for dichotomous nodes.
961 o The argument 'adj' in [node][tip][edge]labels() now works when
962 using 'pie' or 'thermo'.
964 o A more informative message error is now returned by dist.dna() when
965 'model' is badly specified (partial matching of this argument is
968 o Deprecated functions are now listed in a help page: see
969 help("ape-defunct") with the quotes.
974 o The functions heterozygosity, nuc.div, theta.h, theta.k and
975 theta.s have been moved from ape to pegas.
977 o The functions mlphylo, DNAmodel and sh.test have been removed.
981 CHANGES IN APE VERSION 2.3-3
986 o add.scale.bar() always drew a horizontal bar.
988 o zoom() shuffled tips with unrooted trees.
990 o write.nexus() failed to write correctly trees with a "TipLabel"
993 o rcoal() failed to compute branch lengths with very large n.
995 o A small bug was fixed in compar.cheverud() (thanks to Michael
998 o seg.sites() failed when passing a vector.
1000 o drop.tip() sometimes shuffled tip labels.
1002 o root() shuffled node labels with 'resolve.root = TRUE'.
1006 CHANGES IN APE VERSION 2.3-2
1011 o all.equal.phylo() did not compare unrooted trees correctly.
1013 o dist.topo(... method = "PH85") did not treat unrooted trees
1014 correctly (thanks to Tim Wallstrom for the fix).
1016 o root() sometimes failed to test for the monophyly of the
1019 o extract.clade() sometimes included too many edges.
1021 o vcv.phylo() did not work correctly when the tree is in
1022 "pruningwise" order.
1024 o nj() did not handle correctly distance matrices with many 0's.
1025 The code has also been significantly improved: 7, 70, 160 times
1026 faster with n = 100, 500, 1000, respectively.
1030 CHANGES IN APE VERSION 2.3-1
1035 o The new function is.monophyletic tests the monophyly of a group.
1037 o There is now a c() method for lists of class "DNAbin".
1039 o yule.cov() now fits the null model, and its help page has been
1040 corrected with respect to this change.
1042 o drop.tip() has a new option 'rooted' to force (or not) a tree
1043 to be treated as (un)rooted.
1048 o dist.gene() failed on most occasions with the default
1049 pairwise.deletion = FALSE.
1051 o read.tree() failed to read correctly the tree name(s).
1053 o boot.phylo() now treats correctly data frames.
1055 o del.gaps() did not copy the rownames of a matrix.
1057 o A small bug was fixed in CDAM.global().
1059 o ace() failed with large data sets. Thanks to Rich FitzJohn for
1060 the fix. With other improvements, this function is now about 6
1063 o write.tree() failed with objects of class "multiPhylo".
1065 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
1070 o [.multiPhylo and [.DNAbin now respect the original class.
1072 o Instances of the form class(phy) == "phylo" have been replaced
1073 by inherits(phy, "phylo").
1075 o rcoal() is now faster.
1078 DEPRECATED & DEFUNCT
1080 o klastorin() has been removed.
1084 CHANGES IN APE VERSION 2.3
1089 o The new functions CADM.global and CADM.post, contributed by
1090 Pierre Legendre, test the congruence among several distance
1093 o The new function yule.time fits a user-defined time-dependent
1094 Yule model by maximum likelihood.
1096 o The new function makeNodeLabel creates and/or modifies node
1097 labels in a flexible way.
1099 o read.tree() and write.tree() have been modified so that they can
1100 handle individual tree names.
1102 o plot.phylo() has a new argument 'edge.lty' that specifies the
1103 types of lines used for the edges (plain, dotted, dashed, ...)
1105 o phymltest() has been updated to work with PhyML 3.0.1.
1110 o drop.tip() shuffled tip labels in some cases.
1112 o drop.tip() did not handle node.label correctly.
1114 o is.ultrametric() now checks the ordering of the edge matrix.
1116 o ace() sometimes returned negative values of likelihoods of
1117 ancestral states (thanks to Dan Rabosky for solving this long
1123 o The data set xenarthra has been removed.
1127 CHANGES IN APE VERSION 2.2-4
1131 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
1132 now fixed. (Thanks to Peter Wragg for the fix!)
1134 o A warning message occurred for no reason with ace(method="GLS").
1139 o There is now a general help page displayed with '?ape'.
1143 CHANGES IN APE VERSION 2.2-3
1148 o The new function extract.clade extracts a clade from a tree by
1149 specifying a node number or label.
1151 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
1152 operations of the same names.
1154 o dist.dna() can now return the number of site differences by
1155 specifying model="N".
1160 o chronopl() did not work with CV = TRUE.
1162 o read.nexus() did not work correctly in some situations (trees on
1163 multiple lines with different numbers of lines and/or with
1164 comments inserted within the trees).
1166 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
1167 the number of lineages with non-binary trees.
1172 o ape has now a namespace.
1174 o drop.tip() has been improved: it should be much faster and work
1175 better in some cases (e.g., see the example in ?zoom).
1179 CHANGES IN APE VERSION 2.2-2
1184 o dist.gene() has been substantially improved and gains an option
1185 'pairwise.deletion'.
1187 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
1193 o prop.part() failed with a single tree with the default option
1194 'check.labels = TRUE'.
1196 o summary.DNAbin() failed to display correctly the summary of
1197 sequence lengths with lists of sequences of 10,000 bases or more
1198 (because summary.default uses 4 significant digits by default).
1200 o read.nexus() failed to read a file with a single tree with line
1201 breaks in the Newick string.
1203 o del.gaps() returned a list of empty sequences when there were no
1209 o phymltest() has been updated for PhyML 3.0 and gains an option
1210 'append', whereas the option 'path2exec' has been removed.
1212 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
1213 which is returned unchanged (instead of an error).
1215 o The data sets bird.orders and bird.families are now stored as
1216 Newick strings; i.e., the command data(bird.orders) calls
1221 CHANGES IN APE VERSION 2.2-1
1226 o The new function makeLabel() helps to modify labels of trees,
1227 lists of trees, or DNA sequences, with several utilities to
1228 truncate and/or make them unique, substituting some
1229 characters, and so on.
1231 o The new function del.gaps() removes insertion gaps ("-") in a
1232 set of DNA sequences.
1234 o read.dna() can now read Clustal files (*.aln).
1239 o root() failed with 'resolve.root = TRUE' when the root was
1240 already the specified root.
1242 o Several bugs were fixed in mlphylo().
1244 o collapsed.singles() did not propagate the 'Nnode' and
1245 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
1247 o read.nexus() failed to remove correctly the comments within
1250 o read.nexus() failed to read a file with a single tree and no
1251 translation of tip labels.
1253 o read.nexus() failed to place correctly tip labels when reading
1254 a single tree with no edge lengths.
1256 o A bug was fixed in sh.test().
1261 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
1264 o The option 'check.labels' of consensus() and prop.part() is now
1267 o write.dna() now does not truncate names to 10 characters with
1272 CHANGES IN APE VERSION 2.2
1277 o Four new functions have been written by Damien de Vienne for the
1278 graphical exploration of large trees (cophyloplot, subtrees,
1279 subtreeplot), and to return the graphical coordinates of tree
1282 o The new functions corPagel and corBlomberg implement the Pagel's
1283 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
1285 o chronopl() has been improved and gains several options: see its
1286 help page for details.
1288 o boot.phylo() has now an option 'trees' to possibly return the
1289 bootstraped trees (the default is FALSE).
1291 o prop.part() has been improved and should now be faster in all
1297 o read.dna() failed if "?" occurred in the first 10 sites of the
1300 o The x/y aspect of the plot is now respected when plotting a
1301 circular tree (type = "r" or "f").
1303 o Drawing the tip labels sometimes failed when plotting circular
1306 o zoom() failed when tip labels were used instead of their numbers
1307 (thanks to Yan Wong for the fix).
1309 o drop.tip() failed with some trees (fixed by Yan Wong).
1311 o seg.sites() failed with a list.
1313 o consensus() failed in some cases. The function has been improved
1314 as well and is faster.
1318 CHANGES IN APE VERSION 2.1-3
1323 o A bug in read.nexus() made the Windows R-GUI crash.
1325 o An error was fixed in the computation of ancestral character
1326 states by generalized least squares in ace().
1328 o di2multi() did not modify node labels correctly.
1330 o multi2di() failed if the tree had its attribute "order" set to
1335 CHANGES IN APE VERSION 2.1-2
1340 o There three new methods for the "multiPhylo" class: str, $,
1343 o root() gains the options 'node' and 'resolve.root'
1344 (FALSE by default) as well as its code being improved.
1346 o mltt.plot() has now an option 'log' used in the same way
1347 than in plot.default().
1352 o mltt.plot() failed to display the legend with an unnamed
1355 o nodelabels() with pies now correcly uses the argument
1356 'cex' to draw symbols of different sizes (which has
1357 worked already for thermometers).
1359 o read.nexus() generally failed to read very big files.
1364 o The argument 'family' of compar.gee() can now be a function
1365 as well as a character string.
1367 o read.tree() and read.nexus() now return an unnamed list if
1368 'tree.names = NULL'.
1370 o read.nexus() now returns a modified object of class "multiPhylo"
1371 when there is a TRANSLATE block in the NEXUS file: the individual
1372 trees have no 'tip.label' vector, but the list has a 'TipLabel'
1373 attribute. The new methods '$' and '[[' set these elements
1374 correctly when extracting trees.
1378 CHANGES IN APE VERSION 2.1-1
1383 o The new function rmtree generates lists of random trees.
1385 o rcoal() now generates a genuine coalescent tree by default
1386 (thanks to Vladimir Minin for the code).
1391 o nuc.div() returned an incorrect value with the default
1392 pairwise.deletion = FALSE.
1397 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
1398 have been improved so that they are stabler and faster.
1400 o R packages used by ape are now loaded silently; lattice and gee
1401 are loaded only when needed.
1405 CHANGES IN APE VERSION 2.1
1410 o The new function identify.phylo identifies clades on a plotted
1411 tree using the mouse.
1413 o It is now possible to subset a list of trees (object of class
1414 "multiPhylo") with "[" while keeping its class correct.
1416 o The new function as.DNAbin.alignment converts DNA sequences
1417 stored in the "alignment" format of the package seqinr into
1418 an object of class "DNAbin".
1420 o The new function weight.taxo2 helps to build similarity matrices
1421 given two taxonomic levels (usually called by other functions).
1423 o write.tree() can now take a list of trees (class "multiPhylo")
1424 as its main argument.
1426 o plot.correlogram() and plot.correlogramList() have been
1427 improved, and gain several options (see the help page for
1428 details). A legend is now plotted by default.
1433 o dist.dna() returned some incorrect values with `model = "JC69"'
1434 and `pairwise.deletion = TRUE'. This affected only the
1435 distances involving sequences with missing values. (Thanks
1436 to Bruno Toupance for digging this bug out.)
1438 o write.tree() failed with some trees: this is fixed by removing
1439 the `multi.line' option (trees are now always printed on a
1442 o read.nexus() did not correctly detect trees with multiple root
1443 edges (see OTHER CHANGES).
1448 o The code of mlphylo() has been almost entirely rewritten, and
1449 should be much stabler. The options have been also greatly
1450 simplified (see ?mlphylo and ?DNAmodel for details).
1452 o The internal function nTips has been renamed klastorin_nTips.
1454 o The code of is.ultrametric() contained redundancies and has
1457 o The code of Moran.I() and of correlogram.formula() have been
1460 o read.tree() and read.nexus() now return an error when trying to
1461 read a tree with multiple root edges (see BUG FIXES). The
1462 correction applied in previous version did not work in all
1465 o The class c("multi.tree", "phylo") has been renamed
1471 o There is now a vignette in ape: see vignette("MoranI", "ape").
1474 DEPRECATED & DEFUNCT
1476 o as.matching() and as.phylo.matching() do not support branch
1479 o correlogram.phylo() and discrete.dist() have been removed.
1483 CHANGES IN APE VERSION 2.0-2
1488 o The new function matexpo computes the exponential of a square
1491 o The new function unique.multi.tree removes duplicate trees from
1494 o yule() has a new option `use.root.edge = FALSE' that specifies
1495 to ignore, by default, the root edge of the tree if it exists.
1500 o which.edge() failed when the index of a single terminal edge was
1503 o In diversi.time(), the values returned for model C were
1506 o A bug was fixed in yule() that affected the calculation of the
1507 likelihood in the presence of ties in the branching times.
1509 o There was a bug in the C function mat_expo4x4 affecting the
1510 calculations of the transition probabilities for models HKY and
1513 o A small bug was fixed in as.matrix.DNAbin (thanks to James
1516 o rtree() did not `shuffle' the tip labels by default, so only a
1517 limited number of labelled topologies could be generated.
1521 CHANGES IN APE VERSION 2.0-1
1526 o The three new functions bionj, fastme.ols, and fastme.bal
1527 perform phylogeny estimation by the BIONJ and fastME methods in
1528 OLS and balanced versions. This is a port to R of previous
1529 previous programs done by Vincent Lefort.
1531 o The new function chronoMPL performs molecular dating with the
1532 mean path lengths method of Britton et al. (2002, Mol. Phyl.
1535 o The new function rotate, contributed by Christoph Heibl, swaps
1536 two clades connected to the same node. It works also with
1537 multichotomous nodes.
1539 o The new `method' as.matrix.DNAbin() may be used to convert
1540 easily DNA sequences stored in a list into a matrix while
1541 keeping the names and the class.
1546 o chronopl() failed when some branch lengths were equal to zero:
1547 an error message is now returned.
1549 o di2multi() failed when there was a series of consecutive edges
1554 CHANGES IN APE VERSION 1.10-2
1559 o plot.phylo() can now plot circular trees: the option is type =
1560 "fan" or type = "f" (to avoid the ambiguity with type = "c").
1562 o prop.part() has a new option `check.labels = FALSE' which allows
1563 to considerably speed-up the calculations of bipartitions. As a
1564 consequence, calculations of bootstrap values with boot.phylo()
1565 should be much faster.
1570 o read.GenBank() did not return correctly the list of species as
1571 from ape 1.10: this is fixed in this version
1573 o Applying as.phylo() on a tree of class "phylo" failed: the
1574 object is now returned unchanged.
1578 CHANGES IN APE VERSION 1.10-1
1583 o The three new functions Ntip, Nnode, and Nedge return, for a
1584 given tree, the number of tips, nodes, or edges, respectively.
1589 o read.nexus() did not set correctly the class of the returned
1590 object when reading multiple trees.
1592 o mllt.plot() failed with objects of class c("multi.tree",
1595 o unroot() did not work correctly in most cases.
1597 o reorder.phylo() made R freeze in some occasions.
1599 o Plotting a tree in pruningwise order failed.
1601 o When plotting an unrooted tree, the tip labels where not all
1602 correctly positioned if the option `cex' was used.
1606 CHANGES IN APE VERSION 1.10
1611 o Five new `method' functions have been introduced to manipulate
1612 DNA sequences in binary format (see below).
1614 o Three new functions have been introduced to convert between the
1615 new binary and the character formats.
1617 o The new function as.alignment converts DNA sequences stored as
1618 single characters into the class "alignment" used by the package
1621 o read.dna() and read.GenBank() have a new argument `as.character'
1622 controlling whether the sequences are returned in binary format
1628 o root() failed when the tree had node labels: this is fixed.
1630 o plot.phylo() did not correctly set the limits on the y-axis with
1631 the default setting: this is fixed.
1633 o dist.dna() returned a wrong result for the LogDet, paralinear,
1634 and BH87 models with `pairwise.deletion = TRUE'.
1639 o DNA sequences are now internally stored in a binary format. See
1640 the document "A Bit-Level Coding Scheme for Nucleotides" for the
1641 details. Most functions analyzing DNA functions have been
1642 modified accordingly and are now much faster (dist.dna is now
1643 ca. 60 times faster).
1647 CHANGES IN APE VERSION 1.9-4
1652 o A bug was fixed in edgelabels().
1654 o as.phylo.hclust() did not work correctly when the object of
1655 class "hclust" has its labels set to NULL: the returned tree has
1656 now its tip labels set to "1", "2", ...
1658 o consensus could fail if some tip labels are a subset of others
1659 (e.g., "a" and "a_1"): this is now fixed.
1661 o mlphylo() failed in most cases if some branch lengths of the
1662 initial tree were greater than one: an error message is now
1665 o mlphylo() failed in most cases when estimating the proportion of
1666 invariants: this is fixed.
1670 CHANGES IN APE VERSION 1.9-3
1675 o The new function edgelabels adds labels on the edge of the tree
1676 in the same way than nodelabels or tiplabels.
1681 o multi2di() did not handle correctly branch lengths with the
1682 default option `random = TRUE': this is now fixed.
1684 o A bug was fixed in nuc.div() when using pairwise deletions.
1686 o A bug occurred in the analysis of bipartitions with large
1687 numbers of large trees, with consequences on prop.part,
1688 prop.clades, and boot.phylo.
1690 o The calculation of the Billera-Holmes-Vogtmann distance in
1691 dist.topo was wrong: this has been fixed.
1695 CHANGES IN APE VERSION 1.9-2
1700 o The new function ladderize reorganizes the internal structure of
1701 a tree to plot them left- or right-ladderized.
1703 o The new function dist.nodes computes the patristic distances
1704 between all nodes, internal and terminal, of a tree. It replaces
1705 the option `full = TRUE' of cophenetic.phylo (see below).
1710 o A bug was fixed in old2new.phylo().
1712 o Some bugs were fixed in chronopl().
1714 o The edge colours were not correctly displayed by plot.phylo
1715 (thank you to Li-San Wang for the fix).
1717 o cophenetic.phylo() failed with multichotomous trees: this is
1723 o read.dna() now returns the sequences in a matrix if they are
1724 aligned (interleaved or sequential format). Sequences in FASTA
1725 format are still returned in a list.
1727 o The option `full' of cophenetic.phylo() has been removed because
1728 it could not be used from the generic.
1731 DEPRECATED & DEFUNCT
1733 o rotate() has been removed; this function did not work correctly
1738 CHANGES IN APE VERSION 1.9-1
1743 o Trees with a single tip were not read correctly in R as the
1744 element `Nnode' was not set: this is fixed.
1746 o unroot() did not set correctly the number of nodes of the
1747 unrooted tree in most cases.
1749 o read.GenBank() failed when fetching very long sequences,
1750 particularly of the BX-series.
1752 o A bug was introduced in read.tree() with ape 1.9: it has been
1757 CHANGES IN APE VERSION 1.9
1762 o There are two new print `methods' for trees of class "phylo" and
1763 lists of trees of class "multi.tree", so that they are now
1764 displayed in a compact and informative way.
1766 o There are two new functions, old2new.phylo and new2old.phylo,
1767 for converting between the old and new coding of the class
1770 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
1771 LogDet ("logdet"), and paralinear ("paralin").
1773 o compute.brlen() has been extended: several methods are now
1774 available to compute branch lengths.
1776 o write.dna() can now handle matrices as well as lists.
1781 o cophenetic.phylo() sometimes returned a wrong result with
1782 multichotomous trees: this is fixed.
1784 o rotate() failed when a single tip was specified: the tree is now
1787 o ace() did not return the correct index matrix with custom
1788 models: this is fixed.
1790 o multi2di() did not work correctly when resolving multichotomies
1791 randomly: the topology was always the same, only the arrangement
1792 of clades was randomized: this is fixed. This function now
1793 accepts trees with no branch lengths.
1795 o The output of diversi.gof() was blurred by useless prints when a
1796 user distribution was specified. This has been corrected, and
1797 the help page of this function has been expanded.
1802 o The internal structure of the class "phylo" has been changed:
1803 see the document "Definition of Formats for Coding Phylogenetic
1804 Trees in R" for the details. In addition, the code of most
1805 functions has been improved.
1807 o Several functions have been improved by replacing some R codes
1808 by C codes: pic, plot.phylo, and reorder.phylo.
1810 o There is now a citation information: see citation("ape") in R.
1812 o write.tree() now does not add extra 0's to branch lengths so
1813 that 1.23 is printed "1.23" by default, not "1.2300000000".
1815 o The syntax of bind.tree() has been simplified. This function now
1816 accepts trees with no branch lengths, and handles correctly node
1819 o The option `as.numeric' of mrca() has been removed.
1821 o The unused options `format' and `rooted' of read.tree() have
1824 o The unused option `format' of write.tree() has been removed.
1826 o The use of node.depth() has been simplified.
1830 CHANGES IN APE VERSION 1.8-5
1835 o Two new functions read.nexus.data() and write.nexus.data(),
1836 contributed by Johan Nylander, allow to read and write molecular
1837 sequences in NEXUS files.
1839 o The new function reorder.phylo() reorders the internal structure
1840 of a tree of class "phylo". It is used as the generic, e.g.,
1843 o read.tree() and read.nexus() can now read trees with a single
1846 o The new data set `cynipids' supplies a set of protein sequences
1852 o The code of all.equal.phylo() has been completely rewritten
1853 (thanks to Benoît Durand) which fixes several bugs.
1855 o read.tree() and read.nexus() now checks the labels of the tree
1856 to remove or substitute any characters that are illegal in the
1857 Newick format (parentheses, etc.)
1859 o A negative P-value could be returned by mantel.test(): this is
1864 CHANGES IN APE VERSION 1.8-4
1869 o The new function sh.test() computes the Shimodaira-
1872 o The new function collapse.singles() removes the nodes with a
1873 single descendant from a tree.
1875 o plot.phylo() has a new argument `tip.color' to specify the
1876 colours of the tips.
1878 o mlphylo() has now an option `quiet' to control the display of
1879 the progress of the analysis (the default is FALSE).
1884 o read.dna() did not read correctly sequences in sequential format
1885 with leading alignment gaps "-": this is fixed.
1887 o ace() returned a list with no class so that the generic
1888 functions (anova, logLik, ...) could not be used directly. This
1889 is fixed as ace() now returns an object of class "ace".
1891 o anova.ace() had a small bug when computing the number of degrees
1892 of freedom: this is fixed.
1894 o mlphylo() did not work when the sequences were in a matrix or
1895 a data frame: this is fixed.
1897 o rtree() did not work correctly when trying to simulate an
1898 unrooted tree with two tips: an error message is now issued.
1903 o The algorithm of rtree() has been changed: it is now about 40,
1904 100, and 130 times faster for 10, 100, and 1000 tips,
1909 CHANGES IN APE VERSION 1.8-3
1914 o There are four new `method' functions to be used with the
1915 results of ace(): logLik(), deviance(), AIC(), and anova().
1917 o The plot method of phymltest has two new arguments: `main' to
1918 change the title, and `col' to control the colour of the
1919 segments showing the AIC values.
1921 o ace() has a new argument `ip' that gives the initial values used
1922 in the ML estimation with discrete characters (see the examples
1923 in ?ace). This function now returns a matrix giving the indices
1924 of the estimated rates when analysing discrete characters.
1926 o nodelabels() and tiplabels() have a new argument `pie' to
1927 represent proportions, with any number of categories, as
1928 piecharts. The use of the option `thermo' has been improved:
1929 there is now no limitation on the number of categories.
1934 o mlphylo() did not work with more than two partitions: this is
1937 o root() failed if the proposed outgroup was already an outgroup
1938 in the tree: this is fixed.
1940 o The `col' argument in nodelabels() and tiplabels() was not
1941 correctly passed when `text' was used: this is fixed.
1943 o Two bugs were fixed in mlphylo(): parameters were not always
1944 correctly output, and the estimation failed in some cases.
1946 o plot.phylo() was stuck when given a tree with a single tip: this
1947 is fixed and a message error is now returned.
1949 o An error was corrected in the help page of gammaStat regarding
1950 the calculation of P-values.
1952 o Using gls() could crash R when the number of species in the tree
1953 and in the variables were different: this is fixed.
1957 CHANGES IN APE VERSION 1.8-2
1962 o The new function mlphylo() fits a phylogenetic tree by maximum
1963 likelihood from DNA sequences. Its companion function DNAmodel()
1964 is used to define the substitution model which may include
1965 partitioning. There are methods for logLik(), deviance(), and
1966 AIC(), and the summary() method has been extended to display in
1967 a friendly way the results of this model fitting. Currently, the
1968 functionality is limited to estimating the substitution and
1969 associated parameters and computing the likelihood.
1971 o The new function drop1.compar.gee (used as, e.g., drop1(m))
1972 tests for single effects in GEE-based comparative method. A
1973 warning message is printed if there is not enough degrees of
1979 o An error message was sometimes issued by plot.multi.tree(),
1980 though with no consequence.
1984 CHANGES IN APE VERSION 1.8-1
1989 o There is a new plot method for lists of trees (objects of class
1990 "multi.tree"): it calls plot.phylo() internally and is
1991 documented on the same help page.
1996 o A bug was fixed in the C code that analyzes bipartitions: this
1997 has impact on several functions like prop.part, prop.clades,
1998 boot.phylo, or consensus.
2000 o root() did not work correctly when the specified outgroup had
2001 more than one element: this is fixed.
2003 o dist.dna() sometimes returned a warning inappropriately: this
2006 o If the distance object given to nj() had no rownames, nj()
2007 returned a tree with no tip labels: it now returns tips labelled
2008 "1", "2", ..., corresponding to the row numbers.
2013 o nj() has been slightly changed so that tips with a zero distance
2014 are first aggregated with zero-lengthed branches; the usual NJ
2015 procedure is then performed on a distance matrix without 0's.
2019 CHANGES IN APE VERSION 1.8
2024 o The new function chronopl() estimates dates using the penalized
2025 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
2027 o The new function consensus() calculates the consensus tree of a
2030 o The new function evolve.phylo() simulates the evolution of
2031 continuous characters along a phylogeny under a Brownian model.
2033 o The new plot method for objects of class "ancestral" displays a
2034 tree together with ancestral values, as returned by the above
2037 o The new function as.phylo.formula() returns a phylogeny from a
2038 set of nested taxonomic variables given as a formula.
2040 o The new function read.caic() reads trees in CAIC format.
2042 o The new function tiplabels() allows to add labels to the tips
2043 of a tree using text or plotting symbols in a flexible way.
2045 o The new function unroot() unroots a phylogeny.
2047 o multi2di() has a new option, `random', which specifies whether
2048 to resolve the multichotomies randomly (the default) or not.
2050 o prop.part() now returns an object of class "prop.part" for which
2051 there are print (to display a partition in a more friendly way)
2052 and summary (to extract the numbers) methods.
2054 o plot.phylo() has a new option, `show.tip.label', specifying
2055 whether to print the labels of the tips. The default is TRUE.
2057 o The code of nj() has been replaced by a faster C code: it is now
2058 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
2061 o write.nexus() now writes whether a tree is rooted or not.
2066 o Two bugs have been fixed in root(): unrooted trees are now
2067 handled corretly, and node labels are now output normally.
2069 o A bug was fixed in phymltest(): the executable couldn't be found
2072 o Three bugs have been fixed in ace(): computing the likelihood of
2073 ancestral states of discrete characters failed, custom models
2074 did not work, and the function failed with a null gradient (a
2075 warning message is now returned; this latter bug was also
2076 present in yule.cov() as well and is now fixed).
2078 o pic() hanged out when missing data were present: an error is now
2081 o A small bug was fixed in dist.dna() where the gamma correction
2082 was not always correctly dispatched.
2084 o plot.phylo() plotted correctly the root edge only when the tree
2085 was plotted rightwards: this works now for all directions.
2090 o dist.taxo() has been renamed as weight.taxo().
2092 o dist.phylo() has been replaced by the method cophenetic.phylo().
2094 o Various error and warning messages have been improved.
2098 CHANGES IN APE VERSION 1.7
2101 o The new function ace() estimates ancestral character states for
2102 continuous characters (with ML, GLS, and contrasts methods), and
2103 discrete characters (with ML only) for any number of states.
2105 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
2106 of directional evolution for continuous characters. The user
2107 specifies the node(s) of the tree where the character optimum
2110 o The new function is.rooted() tests whether a tree (of class
2113 o The new function rcoal() generates random ultrametric trees with
2114 the possibility to specify the function that generates the
2115 inter-nodes distances.
2117 o The new function mrca() gives for all pairs of tips in a tree
2118 (and optionally nodes too) the most recent common ancestor.
2120 o nodelabels() has a new option `thermo' to plot proportions (up
2121 to three classes) on the nodes of a tree.
2123 o rtree() has been improved: it can now generate rooted or
2124 unrooted trees, and the mathematical function that generates the
2125 branch lengths may be specified by the user. The tip labels may
2126 be given directly in the call to rtree. The limit cases (n = 2,
2127 3) are now handled correctly.
2129 o dist.topo() has a new argument `method' with two choices: "PH85"
2130 for Penny and Henny's method (already available before and now
2131 the default), and "BHV01" for the geometric distance by Billera
2132 et al. (2001, Adv. Appl. Math. 27:733).
2134 o write.tree() has a new option, `digits', which specifies the
2135 number of digits to be printed in the Newick tree. By default
2136 digits = 10. The numbers are now always printed in decimal form
2137 (i.e., 1.0e-1 is now avoided).
2139 o dist.dna() can now compute the raw distances between pairs of
2140 DNA sequences by specifying model = "raw".
2142 o dist.phylo() has a new option `full' to possibly compute the
2143 distances among all tips and nodes of the tree. The default is
2149 o Several bugs were fixed in all.equal.phylo().
2151 o dist.dna() did not handle correctly gaps ("-") in alignments:
2152 they are now considered as missing data.
2154 o rotate() did not work if the tips were not ordered: this is
2157 o mantel.test() returned NA in some special cases: this is fixed
2158 and the function has been improved and is now faster.
2160 o A bug was fixed in diversi.gof() where the calculation of A² was
2163 o cherry() did not work correctly under some OSs (mainly Linux):
2166 o is.binary.tree() has been modified so that it works with both
2167 rooted and unrooted trees.
2169 o The documentation of theta.s() was not correct: this has been
2172 o plot.mst() did not work correctly: this is fixed.
2176 CHANGES IN APE VERSION 1.6
2181 o The new function dist.topo() computes the topological distances
2184 o The new function boot.phylo() performs a bootstrap analysis on
2185 phylogeny estimation.
2187 o The new functions prop.part() and prop.clades() analyse
2188 bipartitions from a series of trees.
2193 o read.GenBank() now uses the EFetch utility of NCBI instead of
2194 the usual Web interface: it is now much faster (e.g., 12 times
2195 faster to retrieve 8 sequences, 37 times for 60 sequences).
2200 o Several bugs were fixed in read.dna().
2202 o Several bugs were fixed in diversi.time().
2204 o is.binary.tree() did not work correctly if the tree has no edge
2205 lengths: this is fixed.
2207 o drop.tip() did not correctly propagated the `node.label' of a
2208 tree: this is fixed.
2212 CHANGES IN APE VERSION 1.5
2217 o Two new functions, as.matching.phylo() and as.phylo.matching(),
2218 convert objects between the classes "phylo" and "matching". The
2219 latter implements the representation of binary trees introduced by
2220 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
2221 as.matching() has been introduced as well.
2223 o Two new functions, multi2di() and di2multi(), allow to resolve
2224 and collapse multichotomies with branches of length zero.
2226 o The new function nuc.div() computes the nucleotide diversity
2227 from a sample a DNA sequences.
2229 o dist.dna() has been completely rewritten with a much faster
2230 (particularly for large data sets) C code. Eight models are
2231 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
2232 option `method' has been renamed `model'). Computation of variance
2233 is available for all models. A gamma-correction is possible for
2234 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
2235 to remove sites with missing data on a pairwise basis. The option
2236 `GCcontent' has been removed.
2238 o read.GenBank() has a new option (species.names) which specifies
2239 whether to return the species names of the organisms in addition
2240 to the accession numbers of the sequences (this is the default
2243 o write.nexus() can now write several trees in the same NEXUS file.
2245 o drop.tip() has a new option `root.edge' that allows to specify the
2246 new root edge if internal branches are trimmed.
2251 o as.phylo.hclust() failed if some labels had parentheses: this
2254 o Several bugs were fixed in all.equal.phylo(). This function now
2255 returns the logical TRUE if the trees are identical but with
2256 different representations (a report was printed previously).
2258 o read.GenBank() did not correctly handle ambiguous base codes:
2264 o birthdeath() now returns an object of class "birthdeath" for
2265 which there is a print method.
2269 CHANGES IN APE VERSION 1.4
2274 o The new function nj() performs phylogeny estimation with the
2275 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
2278 o The new function which.edge() identifies the edges of a tree
2279 that belong to a group specified as a set of tips.
2281 o The new function as.phylo.phylog() converts an object of class
2282 "phylog" (from the package ade4) into an object of class
2285 o The new function axisPhylo() draws axes on the side of a
2288 o The new function howmanytrees() calculates the number of trees
2289 in different cases and giving a number of tips.
2291 o write.tree() has a new option `multi.line' (TRUE by default) to
2292 write a Newick tree on several lines rather than on a single
2295 o The functionalities of zoom() have been extended. Several
2296 subtrees can be visualized at the same time, and they are marked
2297 on the main tree with colors. The context of the subtrees can be
2298 marked with the option `subtree' (see below).
2300 o drop.tip() has a new option `subtree' (FALSE by default) which
2301 specifies whether to output in the tree how many tips have been
2304 o The arguments of add.scale.bar() have been redefined and have
2305 now default values (see ?add.scale.bar for details). This
2306 function now works even if the plotted tree has no edge length.
2308 o plot.phylo() can now plot radial trees, but this does not take
2309 edge lengths into account.
2311 o In plot.phylo() with `type = "phylogram"', if the values of
2312 `edge.color' and `edge.width' are identical for sister-branches,
2313 they are propagated to the vertical line that link them.
2318 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
2319 crashing. This is fixed.
2321 o In plot.phylo(), the options `edge.color' and `edge.width' are
2322 now properly recycled; their default values are now "black" and
2325 o A bug has been fixed in write.nexus().
2330 o The function node.depth.edgelength() has been removed and
2331 replaced by a C code.
2335 CHANGES IN APE VERSION 1.3-1
2340 o The new function nodelabels() allows to add labels to the nodes
2341 of a tree using text or plotting symbols in a flexible way.
2343 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
2344 numeric values specifying the lower and upper limits on the x-
2345 and y-axes. This allows to leave some space on any side of the
2346 tree. If a single value is given, this is taken as the upper
2351 CHANGES IN APE VERSION 1.3
2356 o The new function phymltest() calls the software PHYML and fits
2357 28 models of DNA sequence evolution. There are a print method to
2358 display likelihood and AIC values, a summary method to compute
2359 the hierarchical likelihood ratio tests, and a plot method to
2360 display graphically the AIC values of each model.
2362 o The new function yule.cov() fits the Yule model with covariates,
2363 a model where the speciation rate is affected by several species
2364 traits through a generalized linear model. The parameters are
2365 estimated by maximum likelihood.
2367 o Three new functions, corBrownian(), corGrafen(), and
2368 corMartins(), compute the expected correlation structures among
2369 species given a phylogeny under different models of evolution.
2370 These can be used for GLS comparative phylogenetic methods (see
2371 the examples). There are coef() and corMatrix() methods and an
2372 Initialize.corPhyl() function associated.
2374 o The new function compar.cheverud() implements Cheverud et al.'s
2375 (1985; Evolution 39:1335) phylogenetic comparative method.
2377 o The new function varcomp() estimates variance components; it has
2380 o Two new functions, panel.superpose.correlogram() and
2381 plot.correlogramList(), allow to plot several phylogenetic
2384 o The new function node.leafnumber() computes the number of leaves
2385 of a subtree defined by a particular node.
2387 o The new function node.sons() gets all tags of son nodes from a
2390 o The new function compute.brlen() computes the branch lengths of
2391 a tree according to a specified method.
2393 o plot.phylo() has three new options: "cex" controls the size of
2394 the (tip and node) labels (thus it is no more needed to change
2395 the global graphical parameter), "direction" which allows to
2396 plot the tree rightwards, leftwards, upwards, or downwards, and
2397 "y.lim" which sets the upper limit on the y-axis.
2402 o Some functions which try to match tip labels and names of
2403 additional data (e.g. vector) are likely to fail if there are
2404 typing or syntax errors. If both series of names do not perfectly
2405 match, they are ignored and a warning message is now issued.
2406 These functions are bd.ext, compar.gee, pic. Their help pages
2407 have been clarified on this point.
2411 CHANGES IN APE VERSION 1.2-7
2416 o The new function root() reroots a phylogenetic tree with respect
2417 to a specified outgroup.
2419 o The new function rotate() rotates an internal branch of a tree.
2421 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
2422 trees) controls the display of the tip labels in unrooted trees.
2423 This display has been greatly improved: the tip labels are now not
2424 expected to overlap with the tree (particularly if lab4ut =
2425 "axial"). In all cases, combining appropriate values of "lab4ut"
2426 and the font size (via "par(cex = )") should result in readable
2427 unrooted trees. See ?plot.phylo for some examples.
2429 o In drop.tip(), the argument `tip' can now be numeric or character.
2434 o drop.tip() did not work correctly with trees with no branch
2435 lengths: this is fixed.
2437 o A bug in plot.phylo(..., type = "unrooted") made some trees being
2438 plotted with some line crossings: this is now fixed.
2442 CHANGES IN APE VERSION 1.2-6
2447 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
2448 correlogram.phylo, dist.taxo, plot.correlogram) have been added
2449 to implement comparative methods with an autocorrelation approach.
2451 o A new data set describing some life history traits of Carnivores
2457 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
2462 o When plotting a tree with plot.phylo(), the new default of the
2463 option `label.offset' is now 0, so the labels are always visible.
2467 CHANGES IN APE VERSION 1.2-5
2472 o The new function bd.ext() fits a birth-death model with combined
2473 phylogenetic and taxonomic data, and estimates the corresponding
2474 speciation and extinction rates.
2479 o The package gee is no more required by ape but only suggested
2480 since only the function compar.gee() calls gee.
2484 CHANGES IN APE VERSION 1.2-4
2489 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
2490 and lines.popsize) implementing a new approach for inferring the
2491 demographic history from genealogies using a reversible jump
2492 MCMC have been introduced.
2494 o The unit of time in the skyline plot and in the new plots can
2495 now be chosen to be actual years, rather than substitutions.
2499 CHANGES IN APE VERSION 1.2-3
2504 o The new function rtree() generates a random binary tree with or
2505 without branch lengths.
2507 o Two new functions for drawing lineages-through-time (LTT) plots
2508 are provided: ltt.lines() adds a LTT curve to an existing plot,
2509 and mltt.plot() does a multiple LTT plot giving several trees as
2510 arguments (see `?ltt.plot' for details).
2515 o Some taxon names made R crashing when calling as.phylo.hclust():
2518 o dist.dna() returned an error with two identical DNA sequences
2519 (only using the Jukes-Cantor method returned 0): this is fixed.
2524 o The function dist.phylo() has been re-written using a different
2525 algorithm: it is now about four times faster.
2527 o The code of branching.times() has been improved: it is now about
2532 CHANGES IN APE VERSION 1.2-2
2537 o The new function seg.sites() finds the segregating sites in a
2538 sample of DNA sequences.
2543 o A bug introduced in read.tree() and in read.nexus() with version
2546 o A few errors were corrected and a few examples were added in the
2551 CHANGES IN APE VERSION 1.2-1
2556 o plot.phylo() can now draw the edge of the root of a tree if it
2557 has one (see the new option `root.edge', its default is FALSE).
2562 o A bug was fixed in read.nexus(): files with semicolons inside
2563 comment blocks were not read correctly.
2565 o The behaviour of read.tree() and read.nexus() was corrected so
2566 that tree files with badly represented root edges (e.g., with
2567 an extra pair of parentheses, see the help pages for details)
2568 are now correctly represented in the object of class "phylo";
2569 a warning message is now issued.
2573 CHANGES IN APE VERSION 1.2
2578 o plot.phylo() has been completely re-written and offers several
2579 new functionalities. Three types of trees can now be drawn:
2580 phylogram (as previously), cladogram, and unrooted tree; in
2581 all three types the branch lengths can be drawn using the edge
2582 lengths of the phylogeny or not (e.g., if the latter is absent).
2583 The vertical position of the nodes can be adjusted with two
2584 choices (see option `node.pos'). The code has been re-structured,
2585 and two new functions (potentially useful for developpers) are
2586 documented separately: node.depth.edgelength() and node.depth();
2587 see the respective help pages for details.
2589 o The new function zoom() allows to explore very large trees by
2590 focusing on a small portion of it.
2592 o The new function yule() fits by maximum likelihood the Yule model
2593 (birth-only process) to a phylogenetic tree.
2595 o Support for writing DNA sequences in FASTA format has been
2596 introduced in write.dna() (support for reading sequences in
2597 this format was introduced in read.dna() in version 1.1-2).
2598 The function has been completely re-written, fixing some bugs
2599 (see below); the default behaviour is no more to display the
2600 sequences on the standard output. Several options have been
2601 introduced to control the sequence printing in a flexible
2602 way. The help page has been extended.
2604 o A new data set is included: a supertree of bats in NEXUS format.
2609 o In theta.s(), the default of the option `variance' has
2610 been changed to `FALSE' (as was indicated in the help page).
2612 o Several bugs were fixed in the code of all.equal.phylo().
2614 o Several bugs were fixed in write.dna(), particularly this
2615 function did not work with `format = "interleaved"'.
2617 o Various errors were corrected in the help pages.
2622 o The argument names of as.hclust.phylo() have been changed
2623 from "(phy)" to "(x, ...)" to conform to the definition of
2624 the corresponding generic function.
2626 o gamma.stat() has been renamed gammaStat() to avoid confusion
2627 since gamma() is a generic function.
2631 CHANGES IN APE VERSION 1.1-3
2636 o base.freq() previously did not return a value of 0 for
2637 bases absent in the data (e.g., a vector of length 3 was
2638 returned if one base was absent). This is now fixed (a
2639 vector of length 4 is always returned).
2641 o Several bugs were fixed in read.nexus(), including that this
2642 function did not work in this absence of a "TRANSLATE"
2643 command in the NEXUS file, and that the commands were
2648 CHANGES IN APE VERSION 1.1-2
2653 o The Tamura and Nei (1993) model of DNA distance is now implemented
2654 in dist.dna(): five models are now available in this function.
2656 o A new data set is included: a set of 15 sequences of the
2657 cytochrome b mitochondrial gene of the woodmouse (Apodemus
2663 o A bug in read.nexus() was fixed.
2665 o read.dna() previously did not work correctly in most cases.
2666 The function has been completely re-written and its help page
2667 has been considerably extended (see ?read.dna for details).
2668 Underscores (_) in taxon names are no more replaced with
2669 spaces (this behaviour was undocumented).
2671 o A bug was fixed in write.dna().
2675 CHANGES IN APE VERSION 1.1-1
2680 o A bug in read.tree() introduced in APE 1.1 was fixed.
2682 o A bug in compar.gee() resulted in an error when trying to fit
2683 a model with `family = "binomial"'. This is now fixed.
2687 CHANGES IN APE VERSION 1.1
2692 o The Klastorin (1982) method as suggested by Misawa and Tajima
2693 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
2694 on the basis of phylogenetic trees has been implemented (see
2695 the function klastorin()).
2697 o Functions have been added to convert APE's "phylo" objects in
2698 "hclust" cluster objects and vice versa (see the help page of
2699 as.phylo for details).
2701 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
2702 are introduced for the estimation of absolute evolutionary rates
2703 (ratogram) and dated clock-like trees (chronogram) from
2704 phylogenetic trees using the non-parametric rate smoothing approach
2705 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
2707 o A summary method is now provided printing a summary information on a
2708 phylogenetic tree with, for instance, `summary(tree)'.
2710 o The behaviour of read.tree() was changed so that all spaces and
2711 tabulations in tree files are now ignored. Consequently, spaces in tip
2712 labels are no more allowed. Another side effect is that read.nexus()
2713 now does not replace the underscores (_) in tip labels with spaces
2714 (this behaviour was undocumented).
2716 o The function plot.phylo() has a new option (`underscore') which
2717 specifies whether the underscores in tip labels should be written on
2718 the plot as such or replaced with spaces (the default).
2720 o The function birthdeath() now computes 95% confidence intervals of
2721 the estimated parameters using profile likelihood.
2723 o Three new data sets are included: a gene tree estimated from 36
2724 landplant rbcL sequences, a gene tree estimated from 32 opsin
2725 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
2730 o A bug was fixed in dist.gene() where nothing was returned.
2732 o A bug in plot.mst() was fixed.
2734 o A bug in vcv.phylo() resulted in false correlations when the
2735 option `cor = TRUE' was used (now fixed).
2739 CHANGES IN APE VERSION 1.0
2744 o Two new functions, read.dna() and write.dna(), read/write in a file
2745 DNA sequences in interleaved or in sequential format.
2747 o Two new functions, read.nexus() and write.nexus(), read/write trees
2750 o The new function bind.tree() allows to bind two trees together,
2751 possibly handling root edges to give internal branches.
2753 o The new function drop.tip() removes the tips in a phylogenetic tree,
2754 and trims (or not) the corresponding internal branches.
2756 o The new function is.ultrametric() tests if a tree is ultrametric.
2758 o The function plot.phylo() has more functionalities such as drawing the
2759 branches with different colours and/or different widths, showing the
2760 node labels, controling the position and font of the labels, rotating
2761 the labels, and controling the space around the plot.
2763 o The function read.tree() can now read trees with no branch length,
2764 such as "(a,b),c);". Consequently, the element `edge.length' in
2765 objects of class "phylo" is now optional.
2767 o The function write.tree() has a new default behaviour: if the default
2768 for the option `file' is used (i.e. file = ""), then a variable of
2769 mode character containing the tree in Newick format is returned which
2770 can thus be assigned (e.g., tree <- write.tree(phy)).
2772 o The function read.tree() has a new argument `text' which allows
2773 to read the tree in a variable of mode character.
2775 o A new data set is included: the phylogenetic relationships among
2776 the orders of birds from Sibley and Ahlquist (1990).
2780 CHANGES IN APE VERSION 0.2-1
2785 o Several bugs were fixed in the help pages.
2789 CHANGES IN APE VERSION 0.2
2794 o The function write.tree() writes phylogenetic trees (objects of class
2795 "phylo") in an ASCII file using the Newick parenthetic format.
2797 o The function birthdeath() fits a birth-death model to branching times
2798 by maximum likelihood, and estimates the corresponding speciation and
2801 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
2804 o The function is.binary.tree() tests whether a phylogeny is binary.
2806 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
2807 as well as some methods are introduced.
2809 o Several functions, including some generics and methods, for computing
2810 skyline plot estimates (classic and generalized) of effective
2811 population size through time are introduced and replace the function
2812 skyline.plot() in version 0.1.
2814 o Two data sets are now included: the phylogenetic relationships among
2815 the families of birds from Sibley and Ahlquist (1990), and an
2816 estimated clock-like phylogeny of HIV sequences sampled in the
2817 Democratic Republic of Congo.
2820 DEPRECATED & DEFUNCT
2822 o The function skyline.plot() in ape 0.1 has been deprecated and
2823 replaced by more elaborate functions (see above).
2828 o Two important bugs were fixed in plot.phylo(): phylogenies with
2829 multichotomies not at the root or not with only terminal branches,
2830 and phylogenies with a single node (i.e. only terminal branches)
2831 did not plot. These trees should be plotted correctly now.
2833 o Several bugs were fixed in diversi.time() in the computation of
2836 o Various errors were corrected in the help pages.
projects / ape.git / blob