1 CHANGES IN APE VERSION 2.5-1
6 o The new function stree generates trees with regular shapes.
8 o It is now possible to bind two trees with x + y (see ?bind.tree for
11 o drop.tip(), extract.clade(), root(), and bind.tree() now have an
12 'interactive' option to make the operation on a plotted tree.
14 o cophyloplot() gains two new arguments 'lwd' and 'lty' for the
15 association links; they are recycled like 'col' (which wasn't before).
20 o rTraitDisc() did not use its 'freq' argument correctly (it was
21 multiplied with the rate matrix column-wise instead of row-wise).
23 o [node|tip|edge]labels(thermo = ) used to draw empty thermometers
24 with NA values. Nothing is drawn now like with 'text' or 'pch'.
25 The same bug occurred with the 'pie' option.
27 o A bug was fixed in compar.ou() and the help page was clarified.
29 o bind.tree() has been rewritten fixing several bugs and making it
32 o plot.phylo(type = "p") sometimes failed to colour correctly the
33 vertical lines representing the nodes.
35 o plot.phylo(direction = "l", x.lim = 30) failed to plot the branches
36 in the correct direction though the tip labels were displayed
42 o The c, cbind, and rbind methods for "DNAbin" objetcs now check that
43 the sequences are correctly stored (in a list for c, in a matrix
44 for the two other functions).
48 CHANGES IN APE VERSION 2.5
53 o The new function parafit by Pierre Legendre tests for the
54 coevolution between hosts and parasites. It has a companion
55 function, pcoa, that does principal coordinate decomposition.
56 The latter has a biplot method.
58 o The new function lmorigin by Pierre Legendre performs multiple
59 regression through the origin with testing by permutation.
61 o The new functions rTraitCont and rTraitDisc simulate continuous and
62 discrete traits under a wide range of evolutionary models.
64 o The new function delta.plot does a delta plot following Holland et
65 al. (2002, Mol. Biol. Evol. 12:2051).
67 o The new function edges draws additional branches between any nodes
68 and/or tips on a plotted tree.
70 o The new function fancyarrows enhances arrows from graphics with
71 triangle and harpoon heads; it can be called from edges().
73 o add.scale.bar() has a new option 'ask' to draw interactively.
75 o The branch length score replaces the geodesic distance in dist.topo.
77 o Three new data sets are included: the gopher-lice data (gopher.D),
78 SO2 air pollution in 41 US cities (lmorigin.ex1, from Sokal &
79 Rohlf 1995), and some host-parasite specificity data
80 (lmorigin.ex2, from Legendre & Desdevises 2009).
85 o add.scale.bar() drew the bar outside the plotting region with the
86 default options with unrooted or radial trees.
88 o dist.topo() made R stuck when the trees had different sizes (thanks
89 to Otto Cordero for the fix).
94 o The geodesic distance has been replaced by the branch length score
99 CHANGES IN APE VERSION 2.4-1
104 o rtree() and rcoal() now accept a numeric vector for the 'br'
107 o vcv() is a new generic function with methods for the classes "phylo"
108 and "corPhyl" so that it is possible to calculate the var-cov matrix
109 for "transformation models". vcv.phylo() can still be used for trees
110 of class "phylo"; its argument 'cor' has been renamed 'corr'.
115 o bind.tree() failed when 'y' had no root edge.
117 o read.nexus() shuffled tip labels when the trees have no branch
118 lengths and there is a TRANSLATE block.
120 o read.nexus() does not try to translate node labels if there is a
121 translation table in the NEXUS file. See ?read.nexus for a
122 clarification on this behaviour.
124 o plot.multiPhylo() crashed R when plotting a list of trees with
125 compressed tip labels.
127 o write.nexus() did not translate the taxa names when asked for.
129 o plot.phylo(type = "fan") did not rotate the tip labels correctly
130 when the tree has branch lengths.
132 o ace(type = "continuous", method = "ML") now avoids sigma² being
133 negative (which resulted in an error).
135 o nj() crashed with NA/NaN in the distance matrix: an error in now
140 CHANGES IN APE VERSION 2.4
145 o base.freq() has a new option 'freq' to return the counts; the
146 default is still to return the proportions.
151 o seg.sites() did not handle ambiguous nucleotides correctly: they
154 o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
155 the tree: the argument is now ignored.
157 o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
163 o Trying to plot a tree with a single tip now returns NULL with a
164 warning (it returned an error previously).
166 o The way lines representing nodes are coloured in phylograms has
167 been modified (as well as their widths and types) following some
168 users' request; this is only for dichotomous nodes.
170 o The argument 'adj' in [node][tip][edge]labels() now works when
171 using 'pie' or 'thermo'.
173 o A more informative message error is now returned by dist.dna() when
174 'model' is badly specified (partial matching of this argument is
177 o Deprecated functions are now listed in a help page: see
178 help("ape-defunct") with the quotes.
183 o The functions heterozygosity, nuc.div, theta.h, theta.k and
184 theta.s have been moved from ape to pegas.
186 o The functions mlphylo, DNAmodel and sh.test have been removed.
190 CHANGES IN APE VERSION 2.3-3
195 o add.scale.bar() always drew a horizontal bar.
197 o zoom() shuffled tips with unrooted trees.
199 o write.nexus() failed to write correctly trees with a "TipLabel"
202 o rcoal() failed to compute branch lengths with very large n.
204 o A small bug was fixed in compar.cheverud() (thanks to Michael
207 o seg.sites() failed when passing a vector.
209 o drop.tip() sometimes shuffled tip labels.
211 o root() shuffled node labels with 'resolve.root = TRUE'.
215 CHANGES IN APE VERSION 2.3-2
220 o all.equal.phylo() did not compare unrooted trees correctly.
222 o dist.topo(... method = "PH85") did not treat unrooted trees
223 correctly (thanks to Tim Wallstrom for the fix).
225 o root() sometimes failed to test for the monophyly of the
228 o extract.clade() sometimes included too many edges.
230 o vcv.phylo() did not work correctly when the tree is in
233 o nj() did not handle correctly distance matrices with many 0's.
234 The code has also been significantly improved: 7, 70, 160 times
235 faster with n = 100, 500, 1000, respectively.
239 CHANGES IN APE VERSION 2.3-1
244 o The new function is.monophyletic tests the monophyly of a group.
246 o There is now a c() method for lists of class "DNAbin".
248 o yule.cov() now fits the null model, and its help page has been
249 corrected with respect to this change.
251 o drop.tip() has a new option 'rooted' to force (or not) a tree
252 to be treated as (un)rooted.
257 o dist.gene() failed on most occasions with the default
258 pairwise.deletion = FALSE.
260 o read.tree() failed to read correctly the tree name(s).
262 o boot.phylo() now treats correctly data frames.
264 o del.gaps() did not copy the rownames of a matrix.
266 o A small bug was fixed in CDAM.global().
268 o ace() failed with large data sets. Thanks to Rich FitzJohn for
269 the fix. With other improvements, this function is now about 6
272 o write.tree() failed with objects of class "multiPhylo".
274 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
279 o [.multiPhylo and [.DNAbin now respect the original class.
281 o Instances of the form class(phy) == "phylo" have been replaced
282 by inherits(phy, "phylo").
284 o rcoal() is now faster.
289 o klastorin() has been removed.
293 CHANGES IN APE VERSION 2.3
298 o The new functions CADM.global and CADM.post, contributed by
299 Pierre Legendre, test the congruence among several distance
302 o The new function yule.time fits a user-defined time-dependent
303 Yule model by maximum likelihood.
305 o The new function makeNodeLabel creates and/or modifies node
306 labels in a flexible way.
308 o read.tree() and write.tree() have been modified so that they can
309 handle individual tree names.
311 o plot.phylo() has a new argument 'edge.lty' that specifies the
312 types of lines used for the edges (plain, dotted, dashed, ...)
314 o phymltest() has been updated to work with PhyML 3.0.1.
319 o drop.tip() shuffled tip labels in some cases.
321 o drop.tip() did not handle node.label correctly.
323 o is.ultrametric() now checks the ordering of the edge matrix.
325 o ace() sometimes returned negative values of likelihoods of
326 ancestral states (thanks to Dan Rabosky for solving this long
332 o The data set xenarthra has been removed.
336 CHANGES IN APE VERSION 2.2-4
340 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
341 now fixed. (Thanks to Peter Wragg for the fix!)
343 o A warning message occurred for no reason with ace(method="GLS").
348 o There is now a general help page displayed with '?ape'.
352 CHANGES IN APE VERSION 2.2-3
357 o The new function extract.clade extracts a clade from a tree by
358 specifying a node number or label.
360 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
361 operations of the same names.
363 o dist.dna() can now return the number of site differences by
364 specifying model="N".
369 o chronopl() did not work with CV = TRUE.
371 o read.nexus() did not work correctly in some situations (trees on
372 multiple lines with different numbers of lines and/or with
373 comments inserted within the trees).
375 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
376 the number of lineages with non-binary trees.
381 o ape has now a namespace.
383 o drop.tip() has been improved: it should be much faster and work
384 better in some cases (e.g., see the example in ?zoom).
388 CHANGES IN APE VERSION 2.2-2
393 o dist.gene() has been substantially improved and gains an option
396 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
402 o prop.part() failed with a single tree with the default option
403 'check.labels = TRUE'.
405 o summary.DNAbin() failed to display correctly the summary of
406 sequence lengths with lists of sequences of 10,000 bases or more
407 (because summary.default uses 4 significant digits by default).
409 o read.nexus() failed to read a file with a single tree with line
410 breaks in the Newick string.
412 o del.gaps() returned a list of empty sequences when there were no
418 o phymltest() has been updated for PhyML 3.0 and gains an option
419 'append', whereas the option 'path2exec' has been removed.
421 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
422 which is returned unchanged (instead of an error).
424 o The data sets bird.orders and bird.families are now stored as
425 Newick strings; i.e., the command data(bird.orders) calls
430 CHANGES IN APE VERSION 2.2-1
435 o The new function makeLabel() helps to modify labels of trees,
436 lists of trees, or DNA sequences, with several utilities to
437 truncate and/or make them unique, substituting some
438 characters, and so on.
440 o The new function del.gaps() removes insertion gaps ("-") in a
441 set of DNA sequences.
443 o read.dna() can now read Clustal files (*.aln).
448 o root() failed with 'resolve.root = TRUE' when the root was
449 already the specified root.
451 o Several bugs were fixed in mlphylo().
453 o collapsed.singles() did not propagate the 'Nnode' and
454 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
456 o read.nexus() failed to remove correctly the comments within
459 o read.nexus() failed to read a file with a single tree and no
460 translation of tip labels.
462 o read.nexus() failed to place correctly tip labels when reading
463 a single tree with no edge lengths.
465 o A bug was fixed in sh.test().
470 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
473 o The option 'check.labels' of consensus() and prop.part() is now
476 o write.dna() now does not truncate names to 10 characters with
481 CHANGES IN APE VERSION 2.2
486 o Four new functions have been written by Damien de Vienne for the
487 graphical exploration of large trees (cophyloplot, subtrees,
488 subtreeplot), and to return the graphical coordinates of tree
491 o The new functions corPagel and corBlomberg implement the Pagel's
492 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
494 o chronopl() has been improved and gains several options: see its
495 help page for details.
497 o boot.phylo() has now an option 'trees' to possibly return the
498 bootstraped trees (the default is FALSE).
500 o prop.part() has been improved and should now be faster in all
506 o read.dna() failed if "?" occurred in the first 10 sites of the
509 o The x/y aspect of the plot is now respected when plotting a
510 circular tree (type = "r" or "f").
512 o Drawing the tip labels sometimes failed when plotting circular
515 o zoom() failed when tip labels were used instead of their numbers
516 (thanks to Yan Wong for the fix).
518 o drop.tip() failed with some trees (fixed by Yan Wong).
520 o seg.sites() failed with a list.
522 o consensus() failed in some cases. The function has been improved
523 as well and is faster.
527 CHANGES IN APE VERSION 2.1-3
532 o A bug in read.nexus() made the Windows R-GUI crash.
534 o An error was fixed in the computation of ancestral character
535 states by generalized least squares in ace().
537 o di2multi() did not modify node labels correctly.
539 o multi2di() failed if the tree had its attribute "order" set to
544 CHANGES IN APE VERSION 2.1-2
549 o There three new methods for the "multiPhylo" class: str, $,
552 o root() gains the options 'node' and 'resolve.root'
553 (FALSE by default) as well as its code being improved.
555 o mltt.plot() has now an option 'log' used in the same way
556 than in plot.default().
561 o mltt.plot() failed to display the legend with an unnamed
564 o nodelabels() with pies now correcly uses the argument
565 'cex' to draw symbols of different sizes (which has
566 worked already for thermometers).
568 o read.nexus() generally failed to read very big files.
573 o The argument 'family' of compar.gee() can now be a function
574 as well as a character string.
576 o read.tree() and read.nexus() now return an unnamed list if
579 o read.nexus() now returns a modified object of class "multiPhylo"
580 when there is a TRANSLATE block in the NEXUS file: the individual
581 trees have no 'tip.label' vector, but the list has a 'TipLabel'
582 attribute. The new methods '$' and '[[' set these elements
583 correctly when extracting trees.
587 CHANGES IN APE VERSION 2.1-1
592 o The new function rmtree generates lists of random trees.
594 o rcoal() now generates a genuine coalescent tree by default
595 (thanks to Vladimir Minin for the code).
600 o nuc.div() returned an incorrect value with the default
601 pairwise.deletion = FALSE.
606 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
607 have been improved so that they are stabler and faster.
609 o R packages used by ape are now loaded silently; lattice and gee
610 are loaded only when needed.
614 CHANGES IN APE VERSION 2.1
619 o The new function identify.phylo identifies clades on a plotted
620 tree using the mouse.
622 o It is now possible to subset a list of trees (object of class
623 "multiPhylo") with "[" while keeping its class correct.
625 o The new function as.DNAbin.alignment converts DNA sequences
626 stored in the "alignment" format of the package seqinr into
627 an object of class "DNAbin".
629 o The new function weight.taxo2 helps to build similarity matrices
630 given two taxonomic levels (usually called by other functions).
632 o write.tree() can now take a list of trees (class "multiPhylo")
633 as its main argument.
635 o plot.correlogram() and plot.correlogramList() have been
636 improved, and gain several options (see the help page for
637 details). A legend is now plotted by default.
642 o dist.dna() returned some incorrect values with `model = "JC69"'
643 and `pairwise.deletion = TRUE'. This affected only the
644 distances involving sequences with missing values. (Thanks
645 to Bruno Toupance for digging this bug out.)
647 o write.tree() failed with some trees: this is fixed by removing
648 the `multi.line' option (trees are now always printed on a
651 o read.nexus() did not correctly detect trees with multiple root
652 edges (see OTHER CHANGES).
657 o The code of mlphylo() has been almost entirely rewritten, and
658 should be much stabler. The options have been also greatly
659 simplified (see ?mlphylo and ?DNAmodel for details).
661 o The internal function nTips has been renamed klastorin_nTips.
663 o The code of is.ultrametric() contained redundancies and has
666 o The code of Moran.I() and of correlogram.formula() have been
669 o read.tree() and read.nexus() now return an error when trying to
670 read a tree with multiple root edges (see BUG FIXES). The
671 correction applied in previous version did not work in all
674 o The class c("multi.tree", "phylo") has been renamed
680 o There is now a vignette in ape: see vignette("MoranI", "ape").
685 o as.matching() and as.phylo.matching() do not support branch
688 o correlogram.phylo() and discrete.dist() have been removed.
692 CHANGES IN APE VERSION 2.0-2
697 o The new function matexpo computes the exponential of a square
700 o The new function unique.multi.tree removes duplicate trees from
703 o yule() has a new option `use.root.edge = FALSE' that specifies
704 to ignore, by default, the root edge of the tree if it exists.
709 o which.edge() failed when the index of a single terminal edge was
712 o In diversi.time(), the values returned for model C were
715 o A bug was fixed in yule() that affected the calculation of the
716 likelihood in the presence of ties in the branching times.
718 o There was a bug in the C function mat_expo4x4 affecting the
719 calculations of the transition probabilities for models HKY and
722 o A small bug was fixed in as.matrix.DNAbin (thanks to James
725 o rtree() did not `shuffle' the tip labels by default, so only a
726 limited number of labelled topologies could be generated.
730 CHANGES IN APE VERSION 2.0-1
735 o The three new functions bionj, fastme.ols, and fastme.bal
736 perform phylogeny estimation by the BIONJ and fastME methods in
737 OLS and balanced versions. This is a port to R of previous
738 previous programs done by Vincent Lefort.
740 o The new function chronoMPL performs molecular dating with the
741 mean path lengths method of Britton et al. (2002, Mol. Phyl.
744 o The new function rotate, contributed by Christoph Heibl, swaps
745 two clades connected to the same node. It works also with
746 multichotomous nodes.
748 o The new `method' as.matrix.DNAbin() may be used to convert
749 easily DNA sequences stored in a list into a matrix while
750 keeping the names and the class.
755 o chronopl() failed when some branch lengths were equal to zero:
756 an error message is now returned.
758 o di2multi() failed when there was a series of consecutive edges
763 CHANGES IN APE VERSION 1.10-2
768 o plot.phylo() can now plot circular trees: the option is type =
769 "fan" or type = "f" (to avoid the ambiguity with type = "c").
771 o prop.part() has a new option `check.labels = FALSE' which allows
772 to considerably speed-up the calculations of bipartitions. As a
773 consequence, calculations of bootstrap values with boot.phylo()
774 should be much faster.
779 o read.GenBank() did not return correctly the list of species as
780 from ape 1.10: this is fixed in this version
782 o Applying as.phylo() on a tree of class "phylo" failed: the
783 object is now returned unchanged.
787 CHANGES IN APE VERSION 1.10-1
792 o The three new functions Ntip, Nnode, and Nedge return, for a
793 given tree, the number of tips, nodes, or edges, respectively.
798 o read.nexus() did not set correctly the class of the returned
799 object when reading multiple trees.
801 o mllt.plot() failed with objects of class c("multi.tree",
804 o unroot() did not work correctly in most cases.
806 o reorder.phylo() made R freeze in some occasions.
808 o Plotting a tree in pruningwise order failed.
810 o When plotting an unrooted tree, the tip labels where not all
811 correctly positioned if the option `cex' was used.
815 CHANGES IN APE VERSION 1.10
820 o Five new `method' functions have been introduced to manipulate
821 DNA sequences in binary format (see below).
823 o Three new functions have been introduced to convert between the
824 new binary and the character formats.
826 o The new function as.alignment converts DNA sequences stored as
827 single characters into the class "alignment" used by the package
830 o read.dna() and read.GenBank() have a new argument `as.character'
831 controlling whether the sequences are returned in binary format
837 o root() failed when the tree had node labels: this is fixed.
839 o plot.phylo() did not correctly set the limits on the y-axis with
840 the default setting: this is fixed.
842 o dist.dna() returned a wrong result for the LogDet, paralinear,
843 and BH87 models with `pairwise.deletion = TRUE'.
848 o DNA sequences are now internally stored in a binary format. See
849 the document "A Bit-Level Coding Scheme for Nucleotides" for the
850 details. Most functions analyzing DNA functions have been
851 modified accordingly and are now much faster (dist.dna is now
852 ca. 60 times faster).
856 CHANGES IN APE VERSION 1.9-4
861 o A bug was fixed in edgelabels().
863 o as.phylo.hclust() did not work correctly when the object of
864 class "hclust" has its labels set to NULL: the returned tree has
865 now its tip labels set to "1", "2", ...
867 o consensus could fail if some tip labels are a subset of others
868 (e.g., "a" and "a_1"): this is now fixed.
870 o mlphylo() failed in most cases if some branch lengths of the
871 initial tree were greater than one: an error message is now
874 o mlphylo() failed in most cases when estimating the proportion of
875 invariants: this is fixed.
879 CHANGES IN APE VERSION 1.9-3
884 o The new function edgelabels adds labels on the edge of the tree
885 in the same way than nodelabels or tiplabels.
890 o multi2di() did not handle correctly branch lengths with the
891 default option `random = TRUE': this is now fixed.
893 o A bug was fixed in nuc.div() when using pairwise deletions.
895 o A bug occurred in the analysis of bipartitions with large
896 numbers of large trees, with consequences on prop.part,
897 prop.clades, and boot.phylo.
899 o The calculation of the Billera-Holmes-Vogtmann distance in
900 dist.topo was wrong: this has been fixed.
904 CHANGES IN APE VERSION 1.9-2
909 o The new function ladderize reorganizes the internal structure of
910 a tree to plot them left- or right-ladderized.
912 o The new function dist.nodes computes the patristic distances
913 between all nodes, internal and terminal, of a tree. It replaces
914 the option `full = TRUE' of cophenetic.phylo (see below).
919 o A bug was fixed in old2new.phylo().
921 o Some bugs were fixed in chronopl().
923 o The edge colours were not correctly displayed by plot.phylo
924 (thank you to Li-San Wang for the fix).
926 o cophenetic.phylo() failed with multichotomous trees: this is
932 o read.dna() now returns the sequences in a matrix if they are
933 aligned (interleaved or sequential format). Sequences in FASTA
934 format are still returned in a list.
936 o The option `full' of cophenetic.phylo() has been removed because
937 it could not be used from the generic.
942 o rotate() has been removed; this function did not work correctly
947 CHANGES IN APE VERSION 1.9-1
952 o Trees with a single tip were not read correctly in R as the
953 element `Nnode' was not set: this is fixed.
955 o unroot() did not set correctly the number of nodes of the
956 unrooted tree in most cases.
958 o read.GenBank() failed when fetching very long sequences,
959 particularly of the BX-series.
961 o A bug was introduced in read.tree() with ape 1.9: it has been
966 CHANGES IN APE VERSION 1.9
971 o There are two new print `methods' for trees of class "phylo" and
972 lists of trees of class "multi.tree", so that they are now
973 displayed in a compact and informative way.
975 o There are two new functions, old2new.phylo and new2old.phylo,
976 for converting between the old and new coding of the class
979 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
980 LogDet ("logdet"), and paralinear ("paralin").
982 o compute.brlen() has been extended: several methods are now
983 available to compute branch lengths.
985 o write.dna() can now handle matrices as well as lists.
990 o cophenetic.phylo() sometimes returned a wrong result with
991 multichotomous trees: this is fixed.
993 o rotate() failed when a single tip was specified: the tree is now
996 o ace() did not return the correct index matrix with custom
997 models: this is fixed.
999 o multi2di() did not work correctly when resolving multichotomies
1000 randomly: the topology was always the same, only the arrangement
1001 of clades was randomized: this is fixed. This function now
1002 accepts trees with no branch lengths.
1004 o The output of diversi.gof() was blurred by useless prints when a
1005 user distribution was specified. This has been corrected, and
1006 the help page of this function has been expanded.
1011 o The internal structure of the class "phylo" has been changed:
1012 see the document "Definition of Formats for Coding Phylogenetic
1013 Trees in R" for the details. In addition, the code of most
1014 functions has been improved.
1016 o Several functions have been improved by replacing some R codes
1017 by C codes: pic, plot.phylo, and reorder.phylo.
1019 o There is now a citation information: see citation("ape") in R.
1021 o write.tree() now does not add extra 0's to branch lengths so
1022 that 1.23 is printed "1.23" by default, not "1.2300000000".
1024 o The syntax of bind.tree() has been simplified. This function now
1025 accepts trees with no branch lengths, and handles correctly node
1028 o The option `as.numeric' of mrca() has been removed.
1030 o The unused options `format' and `rooted' of read.tree() have
1033 o The unused option `format' of write.tree() has been removed.
1035 o The use of node.depth() has been simplified.
1039 CHANGES IN APE VERSION 1.8-5
1044 o Two new functions read.nexus.data() and write.nexus.data(),
1045 contributed by Johan Nylander, allow to read and write molecular
1046 sequences in NEXUS files.
1048 o The new function reorder.phylo() reorders the internal structure
1049 of a tree of class "phylo". It is used as the generic, e.g.,
1052 o read.tree() and read.nexus() can now read trees with a single
1055 o The new data set `cynipids' supplies a set of protein sequences
1061 o The code of all.equal.phylo() has been completely rewritten
1062 (thanks to Benoît Durand) which fixes several bugs.
1064 o read.tree() and read.nexus() now checks the labels of the tree
1065 to remove or substitute any characters that are illegal in the
1066 Newick format (parentheses, etc.)
1068 o A negative P-value could be returned by mantel.test(): this is
1073 CHANGES IN APE VERSION 1.8-4
1078 o The new function sh.test() computes the Shimodaira-
1081 o The new function collapse.singles() removes the nodes with a
1082 single descendant from a tree.
1084 o plot.phylo() has a new argument `tip.color' to specify the
1085 colours of the tips.
1087 o mlphylo() has now an option `quiet' to control the display of
1088 the progress of the analysis (the default is FALSE).
1093 o read.dna() did not read correctly sequences in sequential format
1094 with leading alignment gaps "-": this is fixed.
1096 o ace() returned a list with no class so that the generic
1097 functions (anova, logLik, ...) could not be used directly. This
1098 is fixed as ace() now returns an object of class "ace".
1100 o anova.ace() had a small bug when computing the number of degrees
1101 of freedom: this is fixed.
1103 o mlphylo() did not work when the sequences were in a matrix or
1104 a data frame: this is fixed.
1106 o rtree() did not work correctly when trying to simulate an
1107 unrooted tree with two tips: an error message is now issued.
1112 o The algorithm of rtree() has been changed: it is now about 40,
1113 100, and 130 times faster for 10, 100, and 1000 tips,
1118 CHANGES IN APE VERSION 1.8-3
1123 o There are four new `method' functions to be used with the
1124 results of ace(): logLik(), deviance(), AIC(), and anova().
1126 o The plot method of phymltest has two new arguments: `main' to
1127 change the title, and `col' to control the colour of the
1128 segments showing the AIC values.
1130 o ace() has a new argument `ip' that gives the initial values used
1131 in the ML estimation with discrete characters (see the examples
1132 in ?ace). This function now returns a matrix giving the indices
1133 of the estimated rates when analysing discrete characters.
1135 o nodelabels() and tiplabels() have a new argument `pie' to
1136 represent proportions, with any number of categories, as
1137 piecharts. The use of the option `thermo' has been improved:
1138 there is now no limitation on the number of categories.
1143 o mlphylo() did not work with more than two partitions: this is
1146 o root() failed if the proposed outgroup was already an outgroup
1147 in the tree: this is fixed.
1149 o The `col' argument in nodelabels() and tiplabels() was not
1150 correctly passed when `text' was used: this is fixed.
1152 o Two bugs were fixed in mlphylo(): parameters were not always
1153 correctly output, and the estimation failed in some cases.
1155 o plot.phylo() was stuck when given a tree with a single tip: this
1156 is fixed and a message error is now returned.
1158 o An error was corrected in the help page of gammaStat regarding
1159 the calculation of P-values.
1161 o Using gls() could crash R when the number of species in the tree
1162 and in the variables were different: this is fixed.
1166 CHANGES IN APE VERSION 1.8-2
1171 o The new function mlphylo() fits a phylogenetic tree by maximum
1172 likelihood from DNA sequences. Its companion function DNAmodel()
1173 is used to define the substitution model which may include
1174 partitioning. There are methods for logLik(), deviance(), and
1175 AIC(), and the summary() method has been extended to display in
1176 a friendly way the results of this model fitting. Currently, the
1177 functionality is limited to estimating the substitution and
1178 associated parameters and computing the likelihood.
1180 o The new function drop1.compar.gee (used as, e.g., drop1(m))
1181 tests for single effects in GEE-based comparative method. A
1182 warning message is printed if there is not enough degrees of
1188 o An error message was sometimes issued by plot.multi.tree(),
1189 though with no consequence.
1193 CHANGES IN APE VERSION 1.8-1
1198 o There is a new plot method for lists of trees (objects of class
1199 "multi.tree"): it calls plot.phylo() internally and is
1200 documented on the same help page.
1205 o A bug was fixed in the C code that analyzes bipartitions: this
1206 has impact on several functions like prop.part, prop.clades,
1207 boot.phylo, or consensus.
1209 o root() did not work correctly when the specified outgroup had
1210 more than one element: this is fixed.
1212 o dist.dna() sometimes returned a warning inappropriately: this
1215 o If the distance object given to nj() had no rownames, nj()
1216 returned a tree with no tip labels: it now returns tips labelled
1217 "1", "2", ..., corresponding to the row numbers.
1222 o nj() has been slightly changed so that tips with a zero distance
1223 are first aggregated with zero-lengthed branches; the usual NJ
1224 procedure is then performed on a distance matrix without 0's.
1228 CHANGES IN APE VERSION 1.8
1233 o The new function chronopl() estimates dates using the penalized
1234 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1236 o The new function consensus() calculates the consensus tree of a
1239 o The new function evolve.phylo() simulates the evolution of
1240 continuous characters along a phylogeny under a Brownian model.
1242 o The new plot method for objects of class "ancestral" displays a
1243 tree together with ancestral values, as returned by the above
1246 o The new function as.phylo.formula() returns a phylogeny from a
1247 set of nested taxonomic variables given as a formula.
1249 o The new function read.caic() reads trees in CAIC format.
1251 o The new function tiplabels() allows to add labels to the tips
1252 of a tree using text or plotting symbols in a flexible way.
1254 o The new function unroot() unroots a phylogeny.
1256 o multi2di() has a new option, `random', which specifies whether
1257 to resolve the multichotomies randomly (the default) or not.
1259 o prop.part() now returns an object of class "prop.part" for which
1260 there are print (to display a partition in a more friendly way)
1261 and summary (to extract the numbers) methods.
1263 o plot.phylo() has a new option, `show.tip.label', specifying
1264 whether to print the labels of the tips. The default is TRUE.
1266 o The code of nj() has been replaced by a faster C code: it is now
1267 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1270 o write.nexus() now writes whether a tree is rooted or not.
1275 o Two bugs have been fixed in root(): unrooted trees are now
1276 handled corretly, and node labels are now output normally.
1278 o A bug was fixed in phymltest(): the executable couldn't be found
1281 o Three bug have been fixed in ace(): computing the likelihood of
1282 ancestral states of discrete characters failed, custom models
1283 did not work, and the function failed with a null gradient (a
1284 warning message is now returned; this latter bug was also
1285 present in yule.cov() as well and is now fixed).
1287 o pic() hanged out when missing data were present: a message error
1290 o A small bug was fixed in dist.dna() where the gamma correction
1291 was not always correctly dispatched.
1293 o plot.phylo() plotted correctly the root edge only when the tree
1294 was plotted rightwards: this works now for all directions.
1299 o dist.taxo() has been renamed as weight.taxo().
1301 o dist.phylo() has been replaced by the method cophenetic.phylo().
1303 o Various error and warning messages have been improved.
1307 CHANGES IN APE VERSION 1.7
1310 o The new function ace() estimates ancestral character states for
1311 continuous characters (with ML, GLS, and contrasts methods), and
1312 discrete characters (with ML only) for any number of states.
1314 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1315 of directional evolution for continuous characters. The user
1316 specifies the node(s) of the tree where the character optimum
1319 o The new function is.rooted() tests whether a tree (of class
1322 o The new function rcoal() generates random ultrametric trees with
1323 the possibility to specify the function that generates the
1324 inter-nodes distances.
1326 o The new function mrca() gives for all pairs of tips in a tree
1327 (and optionally nodes too) the most recent common ancestor.
1329 o nodelabels() has a new option `thermo' to plot proportions (up
1330 to three classes) on the nodes of a tree.
1332 o rtree() has been improved: it can now generate rooted or
1333 unrooted trees, and the mathematical function that generates the
1334 branch lengths may be specified by the user. The tip labels may
1335 be given directly in the call to rtree. The limit cases (n = 2,
1336 3) are now handled correctly.
1338 o dist.topo() has a new argument `method' with two choices: "PH85"
1339 for Penny and Henny's method (already available before and now
1340 the default), and "BHV01" for the geometric distance by Billera
1341 et al. (2001, Adv. Appl. Math. 27:733).
1343 o write.tree() has a new option, `digits', which specifies the
1344 number of digits to be printed in the Newick tree. By default
1345 digits = 10. The numbers are now always printed in decimal form
1346 (i.e., 1.0e-1 is now avoided).
1348 o dist.dna() can now compute the raw distances between pairs of
1349 DNA sequences by specifying model = "raw".
1351 o dist.phylo() has a new option `full' to possibly compute the
1352 distances among all tips and nodes of the tree. The default if
1358 o Several bugs were fixed in all.equal.phylo().
1360 o dist.dna() did not handle correctly gaps ("-") in alignments:
1361 they are now considered as missing data.
1363 o rotate() did not work if the tips were not ordered: this is
1366 o mantel.test() returned NA in some special cases: this is fixed
1367 and the function has been improved and is now faster.
1369 o A bug was fixed in diversi.gof() where the calculation of A² was
1372 o cherry() did not work correctly under some OSs (mainly Linux):
1375 o is.binary.tree() has been modified so that it works with both
1376 rooted and unrooted trees.
1378 o The documentation of theta.s() was not correct: this has been
1381 o plot.mst() did not work correctly: this is fixed.
1385 CHANGES IN APE VERSION 1.6
1390 o The new function dist.topo() computes the topological distances
1393 o The new function boot.phylo() performs a bootstrap analysis on
1394 phylogeny estimation.
1396 o The new functions prop.part() and prop.clades() analyse
1397 bipartitions from a series of trees.
1402 o read.GenBank() now uses the EFetch utility of NCBI instead of
1403 the usual Web interface: it is now much faster (e.g., 12 times
1404 faster to retrieve 8 sequences, 37 times for 60 sequences).
1409 o Several bugs were fixed in read.dna().
1411 o Several bugs were fixed in diversi.time().
1413 o is.binary.tree() did not work correctly if the tree has no edge
1414 lengths: this is fixed.
1416 o drop.tip() did not correctly propagated the `node.label' of a
1417 tree: this is fixed.
1421 CHANGES IN APE VERSION 1.5
1426 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1427 convert objects between the classes "phylo" and "matching". The
1428 latter implements the representation of binary trees introduced by
1429 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1430 as.matching() has been introduced as well.
1432 o Two new functions, multi2di() and di2multi(), allow to resolve
1433 and collapse multichotomies with branches of length zero.
1435 o The new function nuc.div() computes the nucleotide diversity
1436 from a sample a DNA sequences.
1438 o dist.dna() has been completely rewritten with a much faster
1439 (particularly for large data sets) C code. Eight models are
1440 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1441 option `method' has been renamed `model'). Computation of variance
1442 is available for all models. A gamma-correction is possible for
1443 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1444 to remove sites with missing data on a pairwise basis. The option
1445 `GCcontent' has been removed.
1447 o read.GenBank() has a new option (species.names) which specifies
1448 whether to return the species names of the organisms in addition
1449 to the accession numbers of the sequences (this is the default
1452 o write.nexus() can now write several trees in the same NEXUS file.
1454 o drop.tip() has a new option `root.edge' that allows to specify the
1455 new root edge if internal branches are trimmed.
1460 o as.phylo.hclust() failed if some labels had parentheses: this
1463 o Several bugs were fixed in all.equal.phylo(). This function now
1464 returns the logical TRUE if the trees are identical but with
1465 different representations (a report was printed previously).
1467 o read.GenBank() did not correctly handle ambiguous base codes:
1473 o birthdeath() now returns an object of class "birthdeath" for
1474 which there is a print method.
1478 CHANGES IN APE VERSION 1.4
1483 o The new function nj() performs phylogeny estimation with the
1484 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1487 o The new function which.edge() identifies the edges of a tree
1488 that belong to a group specified as a set of tips.
1490 o The new function as.phylo.phylog() converts an object of class
1491 "phylog" (from the package ade4) into an object of class
1494 o The new function axisPhylo() draws axes on the side of a
1497 o The new function howmanytrees() calculates the number of trees
1498 in different cases and giving a number of tips.
1500 o write.tree() has a new option `multi.line' (TRUE by default) to
1501 write a Newick tree on several lines rather than on a single
1504 o The functionalities of zoom() have been extended. Several
1505 subtrees can be visualized at the same time, and they are marked
1506 on the main tree with colors. The context of the subtrees can be
1507 marked with the option `subtree' (see below).
1509 o drop.tip() has a new option `subtree' (FALSE by default) which
1510 specifies whether to output in the tree how many tips have been
1513 o The arguments of add.scale.bar() have been redefined and have
1514 now default values (see ?add.scale.bar for details). This
1515 function now works even if the plotted tree has no edge length.
1517 o plot.phylo() can now plot radial trees, but this does not take
1518 edge lengths into account.
1520 o In plot.phylo() with `type = "phylogram"', if the values of
1521 `edge.color' and `edge.width' are identical for sister-branches,
1522 they are propagated to the vertical line that link them.
1527 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1528 crashing. This is fixed.
1530 o In plot.phylo(), the options `edge.color' and `edge.width' are
1531 now properly recycled; their default values are now "black" and
1534 o A bug has been fixed in write.nexus().
1539 o The function node.depth.edgelength() has been removed and
1540 replaced by a C code.
1544 CHANGES IN APE VERSION 1.3-1
1549 o The new function nodelabels() allows to add labels to the nodes
1550 of a tree using text or plotting symbols in a flexible way.
1552 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1553 numeric values specifying the lower and upper limits on the x-
1554 and y-axes. This allows to leave some space on any side of the
1555 tree. If a single value is given, this is taken as the upper
1560 CHANGES IN APE VERSION 1.3
1565 o The new function phymltest() calls the software PHYML and fits
1566 28 models of DNA sequence evolution. There are a print method to
1567 display likelihood and AIC values, a summary method to compute
1568 the hierarchical likelihood ratio tests, and a plot method to
1569 display graphically the AIC values of each model.
1571 o The new function yule.cov() fits the Yule model with covariates,
1572 a model where the speciation rate is affected by several species
1573 traits through a generalized linear model. The parameters are
1574 estimated by maximum likelihood.
1576 o Three new functions, corBrownian(), corGrafen(), and
1577 corMartins(), compute the expected correlation structures among
1578 species given a phylogeny under different models of evolution.
1579 These can be used for GLS comparative phylogenetic methods (see
1580 the examples). There are coef() and corMatrix() methods and an
1581 Initialize.corPhyl() function associated.
1583 o The new function compar.cheverud() implements Cheverud et al.'s
1584 (1985; Evolution 39:1335) phylogenetic comparative method.
1586 o The new function varcomp() estimates variance components; it has
1589 o Two new functions, panel.superpose.correlogram() and
1590 plot.correlogramList(), allow to plot several phylogenetic
1593 o The new function node.leafnumber() computes the number of leaves
1594 of a subtree defined by a particular node.
1596 o The new function node.sons() gets all tags of son nodes from a
1599 o The new function compute.brlen() computes the branch lengths of
1600 a tree according to a specified method.
1602 o plot.phylo() has three new options: "cex" controls the size of
1603 the (tip and node) labels (thus it is no more needed to change
1604 the global graphical parameter), "direction" which allows to
1605 plot the tree rightwards, leftwards, upwards, or downwards, and
1606 "y.lim" which sets the upper limit on the y-axis.
1611 o Some functions which try to match tip labels and names of
1612 additional data (e.g. vector) are likely to fail if there are
1613 typing or syntax errors. If both series of names do not perfectly
1614 match, they are ignored and a warning message is now issued.
1615 These functions are bd.ext, compar.gee, pic. Their help pages
1616 have been clarified on this point.
1620 CHANGES IN APE VERSION 1.2-7
1625 o The new function root() reroots a phylogenetic tree with respect
1626 to a specified outgroup.
1628 o The new function rotate() rotates an internal branch of a tree.
1630 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1631 trees) controls the display of the tip labels in unrooted trees.
1632 This display has been greatly improved: the tip labels are now not
1633 expected to overlap with the tree (particularly if lab4ut =
1634 "axial"). In all cases, combining appropriate values of "lab4ut"
1635 and the font size (via "par(cex = )") should result in readable
1636 unrooted trees. See ?plot.phylo for some examples.
1638 o In drop.tip(), the argument `tip' can now be numeric or character.
1643 o drop.tip() did not work correctly with trees with no branch
1644 lengths: this is fixed.
1646 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1647 plotted with some line crossings: this is now fixed.
1651 CHANGES IN APE VERSION 1.2-6
1656 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1657 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1658 to implement comparative methods with an autocorrelation approach.
1660 o A new data set describing some life history traits of Carnivores
1666 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1671 o When plotting a tree with plot.phylo(), the new default of the
1672 option `label.offset' is now 0, so the labels are always visible.
1676 CHANGES IN APE VERSION 1.2-5
1681 o The new function bd.ext() fits a birth-death model with combined
1682 phylogenetic and taxonomic data, and estimates the corresponding
1683 speciation and extinction rates.
1688 o The package gee is no more required by ape but only suggested
1689 since only the function compar.gee() calls gee.
1693 CHANGES IN APE VERSION 1.2-4
1698 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1699 and lines.popsize) implementing a new approach for inferring the
1700 demographic history from genealogies using a reversible jump
1701 MCMC have been introduced.
1703 o The unit of time in the skyline plot and in the new plots can
1704 now be chosen to be actual years, rather than substitutions.
1708 CHANGES IN APE VERSION 1.2-3
1713 o The new function rtree() generates a random binary tree with or
1714 without branch lengths.
1716 o Two new functions for drawing lineages-through-time (LTT) plots
1717 are provided: ltt.lines() adds a LTT curve to an existing plot,
1718 and mltt.plot() does a multiple LTT plot giving several trees as
1719 arguments (see `?ltt.plot' for details).
1724 o Some taxon names made R crashing when calling as.phylo.hclust():
1727 o dist.dna() returned an error with two identical DNA sequences
1728 (only using the Jukes-Cantor method returned 0): this is fixed.
1733 o The function dist.phylo() has been re-written using a different
1734 algorithm: it is now about four times faster.
1736 o The code of branching.times() has been improved: it is now about
1741 CHANGES IN APE VERSION 1.2-2
1746 o The new function seg.sites() finds the segregating sites in a
1747 sample of DNA sequences.
1752 o A bug introduced in read.tree() and in read.nexus() with version
1755 o A few errors were corrected and a few examples were added in the
1760 CHANGES IN APE VERSION 1.2-1
1765 o plot.phylo() can now draw the edge of the root of a tree if it
1766 has one (see the new option `root.edge', its default is FALSE).
1771 o A bug was fixed in read.nexus(): files with semicolons inside
1772 comment blocks were not read correctly.
1774 o The behaviour of read.tree() and read.nexus() was corrected so
1775 that tree files with badly represented root edges (e.g., with
1776 an extra pair of parentheses, see the help pages for details)
1777 are now correctly represented in the object of class "phylo";
1778 a warning message is now issued.
1782 CHANGES IN APE VERSION 1.2
1787 o plot.phylo() has been completely re-written and offers several
1788 new functionalities. Three types of trees can now be drawn:
1789 phylogram (as previously), cladogram, and unrooted tree; in
1790 all three types the branch lengths can be drawn using the edge
1791 lengths of the phylogeny or not (e.g., if the latter is absent).
1792 The vertical position of the nodes can be adjusted with two
1793 choices (see option `node.pos'). The code has been re-structured,
1794 and two new functions (potentially useful for developpers) are
1795 documented separately: node.depth.edgelength() and node.depth();
1796 see the respective help pages for details.
1798 o The new function zoom() allows to explore very large trees by
1799 focusing on a small portion of it.
1801 o The new function yule() fits by maximum likelihood the Yule model
1802 (birth-only process) to a phylogenetic tree.
1804 o Support for writing DNA sequences in FASTA format has been
1805 introduced in write.dna() (support for reading sequences in
1806 this format was introduced in read.dna() in version 1.1-2).
1807 The function has been completely re-written, fixing some bugs
1808 (see below); the default behaviour is no more to display the
1809 sequences on the standard output. Several options have been
1810 introduced to control the sequence printing in a flexible
1811 way. The help page has been extended.
1813 o A new data set is included: a supertree of bats in NEXUS format.
1818 o In theta.s(), the default of the option `variance' has
1819 been changed to `FALSE' (as was indicated in the help page).
1821 o Several bugs were fixed in the code of all.equal.phylo().
1823 o Several bugs were fixed in write.dna(), particularly this
1824 function did not work with `format = "interleaved"'.
1826 o Various errors were corrected in the help pages.
1831 o The argument names of as.hclust.phylo() have been changed
1832 from "(phy)" to "(x, ...)" to conform to the definition of
1833 the corresponding generic function.
1835 o gamma.stat() has been renamed gammaStat() to avoid confusion
1836 since gamma() is a generic function.
1840 CHANGES IN APE VERSION 1.1-3
1845 o base.freq() previously did not return a value of 0 for
1846 bases absent in the data (e.g., a vector of length 3 was
1847 returned if one base was absent). This is now fixed (a
1848 vector of length 4 is always returned).
1850 o Several bugs were fixed in read.nexus(), including that this
1851 function did not work in this absence of a "TRANSLATE"
1852 command in the NEXUS file, and that the commands were
1857 CHANGES IN APE VERSION 1.1-2
1862 o The Tamura and Nei (1993) model of DNA distance is now implemented
1863 in dist.dna(): five models are now available in this function.
1865 o A new data set is included: a set of 15 sequences of the
1866 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1872 o A bug in read.nexus() was fixed.
1874 o read.dna() previously did not work correctly in most cases.
1875 The function has been completely re-written and its help page
1876 has been considerably extended (see ?read.dna for details).
1877 Underscores (_) in taxon names are no more replaced with
1878 spaces (this behaviour was undocumented).
1880 o A bug was fixed in write.dna().
1884 CHANGES IN APE VERSION 1.1-1
1889 o A bug in read.tree() introduced in APE 1.1 was fixed.
1891 o A bug in compar.gee() resulted in an error when trying to fit
1892 a model with `family = "binomial"'. This is now fixed.
1896 CHANGES IN APE VERSION 1.1
1901 o The Klastorin (1982) method as suggested by Misawa and Tajima
1902 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1903 on the basis of phylogenetic trees has been implemented (see
1904 the function klastorin()).
1906 o Functions have been added to convert APE's "phylo" objects in
1907 "hclust" cluster objects and vice versa (see the help page of
1908 as.phylo for details).
1910 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1911 are introduced for the estimation of absolute evolutionary rates
1912 (ratogram) and dated clock-like trees (chronogram) from
1913 phylogenetic trees using the non-parametric rate smoothing approach
1914 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1916 o A summary method is now provided printing a summary information on a
1917 phylogenetic tree with, for instance, `summary(tree)'.
1919 o The behaviour of read.tree() was changed so that all spaces and
1920 tabulations in tree files are now ignored. Consequently, spaces in tip
1921 labels are no more allowed. Another side effect is that read.nexus()
1922 now does not replace the underscores (_) in tip labels with spaces
1923 (this behaviour was undocumented).
1925 o The function plot.phylo() has a new option (`underscore') which
1926 specifies whether the underscores in tip labels should be written on
1927 the plot as such or replaced with spaces (the default).
1929 o The function birthdeath() now computes 95% confidence intervals of
1930 the estimated parameters using profile likelihood.
1932 o Three new data sets are included: a gene tree estimated from 36
1933 landplant rbcL sequences, a gene tree estimated from 32 opsin
1934 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1939 o A bug was fixed in dist.gene() where nothing was returned.
1941 o A bug in plot.mst() was fixed.
1943 o A bug in vcv.phylo() resulted in false correlations when the
1944 option `cor = TRUE' was used (now fixed).
1948 CHANGES IN APE VERSION 1.0
1953 o Two new functions, read.dna() and write.dna(), read/write in a file
1954 DNA sequences in interleaved or in sequential format.
1956 o Two new functions, read.nexus() and write.nexus(), read/write trees
1959 o The new function bind.tree() allows to bind two trees together,
1960 possibly handling root edges to give internal branches.
1962 o The new function drop.tip() removes the tips in a phylogenetic tree,
1963 and trims (or not) the corresponding internal branches.
1965 o The new function is.ultrametric() tests if a tree is ultrametric.
1967 o The function plot.phylo() has more functionalities such as drawing the
1968 branches with different colours and/or different widths, showing the
1969 node labels, controling the position and font of the labels, rotating
1970 the labels, and controling the space around the plot.
1972 o The function read.tree() can now read trees with no branch length,
1973 such as "(a,b),c);". Consequently, the element `edge.length' in
1974 objects of class "phylo" is now optional.
1976 o The function write.tree() has a new default behaviour: if the default
1977 for the option `file' is used (i.e. file = ""), then a variable of
1978 mode character containing the tree in Newick format is returned which
1979 can thus be assigned (e.g., tree <- write.tree(phy)).
1981 o The function read.tree() has a new argument `text' which allows
1982 to read the tree in a variable of mode character.
1984 o A new data set is included: the phylogenetic relationships among
1985 the orders of birds from Sibley and Ahlquist (1990).
1989 CHANGES IN APE VERSION 0.2-1
1994 o Several bugs were fixed in the help pages.
1998 CHANGES IN APE VERSION 0.2
2003 o The function write.tree() writes phylogenetic trees (objects of class
2004 "phylo") in an ASCII file using the Newick parenthetic format.
2006 o The function birthdeath() fits a birth-death model to branching times
2007 by maximum likelihood, and estimates the corresponding speciation and
2010 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
2013 o The function is.binary.tree() tests whether a phylogeny is binary.
2015 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
2016 as well as some methods are introduced.
2018 o Several functions, including some generics and methods, for computing
2019 skyline plot estimates (classic and generalized) of effective
2020 population size through time are introduced and replace the function
2021 skyline.plot() in version 0.1.
2023 o Two data sets are now included: the phylogenetic relationships among
2024 the families of birds from Sibley and Ahlquist (1990), and an
2025 estimated clock-like phylogeny of HIV sequences sampled in the
2026 Democratic Republic of Congo.
2029 DEPRECATED & DEFUNCT
2031 o The function skyline.plot() in ape 0.1 has been deprecated and
2032 replaced by more elaborate functions (see above).
2037 o Two important bugs were fixed in plot.phylo(): phylogenies with
2038 multichotomies not at the root or not with only terminal branches,
2039 and phylogenies with a single node (i.e. only terminal branches)
2040 did not plot. These trees should be plotted correctly now.
2042 o Several bugs were fixed in diversi.time() in the computation of
2045 o Various errors were corrected in the help pages.
projects / ape.git / blob