1 CHANGES IN APE VERSION 2.5-1
6 o The new function stree generates trees with regular shapes.
8 o drop.tip(), extract.clade(), and root() now have an 'interactive'
9 option to make the operation on a plotted tree.
14 o rTraitDisc() did not use its 'freq' argument correctly (it was
15 multiplied with the rate matrix column-wise instead of row-wise).
17 o [node|tip|edge]labels(thermo = ) used to draw empty thermometers
18 with NA values. Nothing is drawn now like with 'text' or 'pch'.
19 The same bug occurred with the 'pie' option.
23 CHANGES IN APE VERSION 2.5
28 o The new function parafit by Pierre Legendre tests for the
29 coevolution between hosts and parasites. It has a companion
30 function, pcoa, that does principal coordinate decomposition.
31 The latter has a biplot method.
33 o The new function lmorigin by Pierre Legendre performs multiple
34 regression through the origin with testing by permutation.
36 o The new functions rTraitCont and rTraitDisc simulate continuous and
37 discrete traits under a wide range of evolutionary models.
39 o The new function delta.plot does a delta plot following Holland et
40 al. (2002, Mol. Biol. Evol. 12:2051).
42 o The new function edges draws additional branches between any nodes
43 and/or tips on a plotted tree.
45 o The new function fancyarrows enhances arrows from graphics with
46 triangle and harpoon heads; it can be called from edges().
48 o add.scale.bar() has a new option 'ask' to draw interactively.
50 o The branch length score replaces the geodesic distance in dist.topo.
52 o Three new data sets are included: the gopher-lice data (gopher.D),
53 SO2 air pollution in 41 US cities (lmorigin.ex1, from Sokal &
54 Rohlf 1995), and some host-parasite specificity data
55 (lmorigin.ex2, from Legendre & Desdevises 2009).
60 o add.scale.bar() drew the bar outside the plotting region with the
61 default options with unrooted or radial trees.
63 o dist.topo() made R stuck when the trees had different sizes (thanks
64 to Otto Cordero for the fix).
69 o The geodesic distance has been replaced by the branch length score
74 CHANGES IN APE VERSION 2.4-1
79 o rtree() and rcoal() now accept a numeric vector for the 'br'
82 o vcv() is a new generic function with methods for the classes "phylo"
83 and "corPhyl" so that it is possible to calculate the var-cov matrix
84 for "transformation models". vcv.phylo() can still be used for trees
85 of class "phylo"; its argument 'cor' has been renamed 'corr'.
90 o bind.tree() failed when 'y' had no root edge.
92 o read.nexus() shuffled tip labels when the trees have no branch
93 lengths and there is a TRANSLATE block.
95 o read.nexus() does not try to translate node labels if there is a
96 translation table in the NEXUS file. See ?read.nexus for a
97 clarification on this behaviour.
99 o plot.multiPhylo() crashed R when plotting a list of trees with
100 compressed tip labels.
102 o write.nexus() did not translate the taxa names when asked for.
104 o plot.phylo(type = "fan") did not rotate the tip labels correctly
105 when the tree has branch lengths.
107 o ace(type = "continuous", method = "ML") now avoids sigma² being
108 negative (which resulted in an error).
110 o nj() crashed with NA/NaN in the distance matrix: an error in now
115 CHANGES IN APE VERSION 2.4
120 o base.freq() has a new option 'freq' to return the counts; the
121 default is still to return the proportions.
126 o seg.sites() did not handle ambiguous nucleotides correctly: they
129 o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
130 the tree: the argument is now ignored.
132 o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
138 o Trying to plot a tree with a single tip now returns NULL with a
139 warning (it returned an error previously).
141 o The way lines representing nodes are coloured in phylograms has
142 been modified (as well as their widths and types) following some
143 users' request; this is only for dichotomous nodes.
145 o The argument 'adj' in [node][tip][edge]labels() now works when
146 using 'pie' or 'thermo'.
148 o A more informative message error is now returned by dist.dna() when
149 'model' is badly specified (partial matching of this argument is
152 o Deprecated functions are now listed in a help page: see
153 help("ape-defunct") with the quotes.
158 o The functions heterozygosity, nuc.div, theta.h, theta.k and
159 theta.s have been moved from ape to pegas.
161 o The functions mlphylo, DNAmodel and sh.test have been removed.
165 CHANGES IN APE VERSION 2.3-3
170 o add.scale.bar() always drew a horizontal bar.
172 o zoom() shuffled tips with unrooted trees.
174 o write.nexus() failed to write correctly trees with a "TipLabel"
177 o rcoal() failed to compute branch lengths with very large n.
179 o A small bug was fixed in compar.cheverud() (thanks to Michael
182 o seg.sites() failed when passing a vector.
184 o drop.tip() sometimes shuffled tip labels.
186 o root() shuffled node labels with 'resolve.root = TRUE'.
190 CHANGES IN APE VERSION 2.3-2
195 o all.equal.phylo() did not compare unrooted trees correctly.
197 o dist.topo(... method = "PH85") did not treat unrooted trees
198 correctly (thanks to Tim Wallstrom for the fix).
200 o root() sometimes failed to test for the monophyly of the
203 o extract.clade() sometimes included too many edges.
205 o vcv.phylo() did not work correctly when the tree is in
208 o nj() did not handle correctly distance matrices with many 0's.
209 The code has also been significantly improved: 7, 70, 160 times
210 faster with n = 100, 500, 1000, respectively.
214 CHANGES IN APE VERSION 2.3-1
219 o The new function is.monophyletic tests the monophyly of a group.
221 o There is now a c() method for lists of class "DNAbin".
223 o yule.cov() now fits the null model, and its help page has been
224 corrected with respect to this change.
226 o drop.tip() has a new option 'rooted' to force (or not) a tree
227 to be treated as (un)rooted.
232 o dist.gene() failed on most occasions with the default
233 pairwise.deletion = FALSE.
235 o read.tree() failed to read correctly the tree name(s).
237 o boot.phylo() now treats correctly data frames.
239 o del.gaps() did not copy the rownames of a matrix.
241 o A small bug was fixed in CDAM.global().
243 o ace() failed with large data sets. Thanks to Rich FitzJohn for
244 the fix. With other improvements, this function is now about 6
247 o write.tree() failed with objects of class "multiPhylo".
249 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
254 o [.multiPhylo and [.DNAbin now respect the original class.
256 o Instances of the form class(phy) == "phylo" have been replaced
257 by inherits(phy, "phylo").
259 o rcoal() is now faster.
264 o klastorin() has been removed.
268 CHANGES IN APE VERSION 2.3
273 o The new functions CADM.global and CADM.post, contributed by
274 Pierre Legendre, test the congruence among several distance
277 o The new function yule.time fits a user-defined time-dependent
278 Yule model by maximum likelihood.
280 o The new function makeNodeLabel creates and/or modifies node
281 labels in a flexible way.
283 o read.tree() and write.tree() have been modified so that they can
284 handle individual tree names.
286 o plot.phylo() has a new argument 'edge.lty' that specifies the
287 types of lines used for the edges (plain, dotted, dashed, ...)
289 o phymltest() has been updated to work with PhyML 3.0.1.
294 o drop.tip() shuffled tip labels in some cases.
296 o drop.tip() did not handle node.label correctly.
298 o is.ultrametric() now checks the ordering of the edge matrix.
300 o ace() sometimes returned negative values of likelihoods of
301 ancestral states (thanks to Dan Rabosky for solving this long
307 o The data set xenarthra has been removed.
311 CHANGES IN APE VERSION 2.2-4
315 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
316 now fixed. (Thanks to Peter Wragg for the fix!)
318 o A warning message occurred for no reason with ace(method="GLS").
323 o There is now a general help page displayed with '?ape'.
327 CHANGES IN APE VERSION 2.2-3
332 o The new function extract.clade extracts a clade from a tree by
333 specifying a node number or label.
335 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
336 operations of the same names.
338 o dist.dna() can now return the number of site differences by
339 specifying model="N".
344 o chronopl() did not work with CV = TRUE.
346 o read.nexus() did not work correctly in some situations (trees on
347 multiple lines with different numbers of lines and/or with
348 comments inserted within the trees).
350 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
351 the number of lineages with non-binary trees.
356 o ape has now a namespace.
358 o drop.tip() has been improved: it should be much faster and work
359 better in some cases (e.g., see the example in ?zoom).
363 CHANGES IN APE VERSION 2.2-2
368 o dist.gene() has been substantially improved and gains an option
371 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
377 o prop.part() failed with a single tree with the default option
378 'check.labels = TRUE'.
380 o summary.DNAbin() failed to display correctly the summary of
381 sequence lengths with lists of sequences of 10,000 bases or more
382 (because summary.default uses 4 significant digits by default).
384 o read.nexus() failed to read a file with a single tree with line
385 breaks in the Newick string.
387 o del.gaps() returned a list of empty sequences when there were no
393 o phymltest() has been updated for PhyML 3.0 and gains an option
394 'append', whereas the option 'path2exec' has been removed.
396 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
397 which is returned unchanged (instead of an error).
399 o The data sets bird.orders and bird.families are now stored as
400 Newick strings; i.e., the command data(bird.orders) calls
405 CHANGES IN APE VERSION 2.2-1
410 o The new function makeLabel() helps to modify labels of trees,
411 lists of trees, or DNA sequences, with several utilities to
412 truncate and/or make them unique, substituting some
413 characters, and so on.
415 o The new function del.gaps() removes insertion gaps ("-") in a
416 set of DNA sequences.
418 o read.dna() can now read Clustal files (*.aln).
423 o root() failed with 'resolve.root = TRUE' when the root was
424 already the specified root.
426 o Several bugs were fixed in mlphylo().
428 o collapsed.singles() did not propagate the 'Nnode' and
429 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
431 o read.nexus() failed to remove correctly the comments within
434 o read.nexus() failed to read a file with a single tree and no
435 translation of tip labels.
437 o read.nexus() failed to place correctly tip labels when reading
438 a single tree with no edge lengths.
440 o A bug was fixed in sh.test().
445 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
448 o The option 'check.labels' of consensus() and prop.part() is now
451 o write.dna() now does not truncate names to 10 characters with
456 CHANGES IN APE VERSION 2.2
461 o Four new functions have been written by Damien de Vienne for the
462 graphical exploration of large trees (cophyloplot, subtrees,
463 subtreeplot), and to return the graphical coordinates of tree
466 o The new functions corPagel and corBlomberg implement the Pagel's
467 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
469 o chronopl() has been improved and gains several options: see its
470 help page for details.
472 o boot.phylo() has now an option 'trees' to possibly return the
473 bootstraped trees (the default is FALSE).
475 o prop.part() has been improved and should now be faster in all
481 o read.dna() failed if "?" occurred in the first 10 sites of the
484 o The x/y aspect of the plot is now respected when plotting a
485 circular tree (type = "r" or "f").
487 o Drawing the tip labels sometimes failed when plotting circular
490 o zoom() failed when tip labels were used instead of their numbers
491 (thanks to Yan Wong for the fix).
493 o drop.tip() failed with some trees (fixed by Yan Wong).
495 o seg.sites() failed with a list.
497 o consensus() failed in some cases. The function has been improved
498 as well and is faster.
502 CHANGES IN APE VERSION 2.1-3
507 o A bug in read.nexus() made the Windows R-GUI crash.
509 o An error was fixed in the computation of ancestral character
510 states by generalized least squares in ace().
512 o di2multi() did not modify node labels correctly.
514 o multi2di() failed if the tree had its attribute "order" set to
519 CHANGES IN APE VERSION 2.1-2
524 o There three new methods for the "multiPhylo" class: str, $,
527 o root() gains the options 'node' and 'resolve.root'
528 (FALSE by default) as well as its code being improved.
530 o mltt.plot() has now an option 'log' used in the same way
531 than in plot.default().
536 o mltt.plot() failed to display the legend with an unnamed
539 o nodelabels() with pies now correcly uses the argument
540 'cex' to draw symbols of different sizes (which has
541 worked already for thermometers).
543 o read.nexus() generally failed to read very big files.
548 o The argument 'family' of compar.gee() can now be a function
549 as well as a character string.
551 o read.tree() and read.nexus() now return an unnamed list if
554 o read.nexus() now returns a modified object of class "multiPhylo"
555 when there is a TRANSLATE block in the NEXUS file: the individual
556 trees have no 'tip.label' vector, but the list has a 'TipLabel'
557 attribute. The new methods '$' and '[[' set these elements
558 correctly when extracting trees.
562 CHANGES IN APE VERSION 2.1-1
567 o The new function rmtree generates lists of random trees.
569 o rcoal() now generates a genuine coalescent tree by default
570 (thanks to Vladimir Minin for the code).
575 o nuc.div() returned an incorrect value with the default
576 pairwise.deletion = FALSE.
581 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
582 have been improved so that they are stabler and faster.
584 o R packages used by ape are now loaded silently; lattice and gee
585 are loaded only when needed.
589 CHANGES IN APE VERSION 2.1
594 o The new function identify.phylo identifies clades on a plotted
595 tree using the mouse.
597 o It is now possible to subset a list of trees (object of class
598 "multiPhylo") with "[" while keeping its class correct.
600 o The new function as.DNAbin.alignment converts DNA sequences
601 stored in the "alignment" format of the package seqinr into
602 an object of class "DNAbin".
604 o The new function weight.taxo2 helps to build similarity matrices
605 given two taxonomic levels (usually called by other functions).
607 o write.tree() can now take a list of trees (class "multiPhylo")
608 as its main argument.
610 o plot.correlogram() and plot.correlogramList() have been
611 improved, and gain several options (see the help page for
612 details). A legend is now plotted by default.
617 o dist.dna() returned some incorrect values with `model = "JC69"'
618 and `pairwise.deletion = TRUE'. This affected only the
619 distances involving sequences with missing values. (Thanks
620 to Bruno Toupance for digging this bug out.)
622 o write.tree() failed with some trees: this is fixed by removing
623 the `multi.line' option (trees are now always printed on a
626 o read.nexus() did not correctly detect trees with multiple root
627 edges (see OTHER CHANGES).
632 o The code of mlphylo() has been almost entirely rewritten, and
633 should be much stabler. The options have been also greatly
634 simplified (see ?mlphylo and ?DNAmodel for details).
636 o The internal function nTips has been renamed klastorin_nTips.
638 o The code of is.ultrametric() contained redundancies and has
641 o The code of Moran.I() and of correlogram.formula() have been
644 o read.tree() and read.nexus() now return an error when trying to
645 read a tree with multiple root edges (see BUG FIXES). The
646 correction applied in previous version did not work in all
649 o The class c("multi.tree", "phylo") has been renamed
655 o There is now a vignette in ape: see vignette("MoranI", "ape").
660 o as.matching() and as.phylo.matching() do not support branch
663 o correlogram.phylo() and discrete.dist() have been removed.
667 CHANGES IN APE VERSION 2.0-2
672 o The new function matexpo computes the exponential of a square
675 o The new function unique.multi.tree removes duplicate trees from
678 o yule() has a new option `use.root.edge = FALSE' that specifies
679 to ignore, by default, the root edge of the tree if it exists.
684 o which.edge() failed when the index of a single terminal edge was
687 o In diversi.time(), the values returned for model C were
690 o A bug was fixed in yule() that affected the calculation of the
691 likelihood in the presence of ties in the branching times.
693 o There was a bug in the C function mat_expo4x4 affecting the
694 calculations of the transition probabilities for models HKY and
697 o A small bug was fixed in as.matrix.DNAbin (thanks to James
700 o rtree() did not `shuffle' the tip labels by default, so only a
701 limited number of labelled topologies could be generated.
705 CHANGES IN APE VERSION 2.0-1
710 o The three new functions bionj, fastme.ols, and fastme.bal
711 perform phylogeny estimation by the BIONJ and fastME methods in
712 OLS and balanced versions. This is a port to R of previous
713 previous programs done by Vincent Lefort.
715 o The new function chronoMPL performs molecular dating with the
716 mean path lengths method of Britton et al. (2002, Mol. Phyl.
719 o The new function rotate, contributed by Christoph Heibl, swaps
720 two clades connected to the same node. It works also with
721 multichotomous nodes.
723 o The new `method' as.matrix.DNAbin() may be used to convert
724 easily DNA sequences stored in a list into a matrix while
725 keeping the names and the class.
730 o chronopl() failed when some branch lengths were equal to zero:
731 an error message is now returned.
733 o di2multi() failed when there was a series of consecutive edges
738 CHANGES IN APE VERSION 1.10-2
743 o plot.phylo() can now plot circular trees: the option is type =
744 "fan" or type = "f" (to avoid the ambiguity with type = "c").
746 o prop.part() has a new option `check.labels = FALSE' which allows
747 to considerably speed-up the calculations of bipartitions. As a
748 consequence, calculations of bootstrap values with boot.phylo()
749 should be much faster.
754 o read.GenBank() did not return correctly the list of species as
755 from ape 1.10: this is fixed in this version
757 o Applying as.phylo() on a tree of class "phylo" failed: the
758 object is now returned unchanged.
762 CHANGES IN APE VERSION 1.10-1
767 o The three new functions Ntip, Nnode, and Nedge return, for a
768 given tree, the number of tips, nodes, or edges, respectively.
773 o read.nexus() did not set correctly the class of the returned
774 object when reading multiple trees.
776 o mllt.plot() failed with objects of class c("multi.tree",
779 o unroot() did not work correctly in most cases.
781 o reorder.phylo() made R freeze in some occasions.
783 o Plotting a tree in pruningwise order failed.
785 o When plotting an unrooted tree, the tip labels where not all
786 correctly positioned if the option `cex' was used.
790 CHANGES IN APE VERSION 1.10
795 o Five new `method' functions have been introduced to manipulate
796 DNA sequences in binary format (see below).
798 o Three new functions have been introduced to convert between the
799 new binary and the character formats.
801 o The new function as.alignment converts DNA sequences stored as
802 single characters into the class "alignment" used by the package
805 o read.dna() and read.GenBank() have a new argument `as.character'
806 controlling whether the sequences are returned in binary format
812 o root() failed when the tree had node labels: this is fixed.
814 o plot.phylo() did not correctly set the limits on the y-axis with
815 the default setting: this is fixed.
817 o dist.dna() returned a wrong result for the LogDet, paralinear,
818 and BH87 models with `pairwise.deletion = TRUE'.
823 o DNA sequences are now internally stored in a binary format. See
824 the document "A Bit-Level Coding Scheme for Nucleotides" for the
825 details. Most functions analyzing DNA functions have been
826 modified accordingly and are now much faster (dist.dna is now
827 ca. 60 times faster).
831 CHANGES IN APE VERSION 1.9-4
836 o A bug was fixed in edgelabels().
838 o as.phylo.hclust() did not work correctly when the object of
839 class "hclust" has its labels set to NULL: the returned tree has
840 now its tip labels set to "1", "2", ...
842 o consensus could fail if some tip labels are a subset of others
843 (e.g., "a" and "a_1"): this is now fixed.
845 o mlphylo() failed in most cases if some branch lengths of the
846 initial tree were greater than one: an error message is now
849 o mlphylo() failed in most cases when estimating the proportion of
850 invariants: this is fixed.
854 CHANGES IN APE VERSION 1.9-3
859 o The new function edgelabels adds labels on the edge of the tree
860 in the same way than nodelabels or tiplabels.
865 o multi2di() did not handle correctly branch lengths with the
866 default option `random = TRUE': this is now fixed.
868 o A bug was fixed in nuc.div() when using pairwise deletions.
870 o A bug occurred in the analysis of bipartitions with large
871 numbers of large trees, with consequences on prop.part,
872 prop.clades, and boot.phylo.
874 o The calculation of the Billera-Holmes-Vogtmann distance in
875 dist.topo was wrong: this has been fixed.
879 CHANGES IN APE VERSION 1.9-2
884 o The new function ladderize reorganizes the internal structure of
885 a tree to plot them left- or right-ladderized.
887 o The new function dist.nodes computes the patristic distances
888 between all nodes, internal and terminal, of a tree. It replaces
889 the option `full = TRUE' of cophenetic.phylo (see below).
894 o A bug was fixed in old2new.phylo().
896 o Some bugs were fixed in chronopl().
898 o The edge colours were not correctly displayed by plot.phylo
899 (thank you to Li-San Wang for the fix).
901 o cophenetic.phylo() failed with multichotomous trees: this is
907 o read.dna() now returns the sequences in a matrix if they are
908 aligned (interleaved or sequential format). Sequences in FASTA
909 format are still returned in a list.
911 o The option `full' of cophenetic.phylo() has been removed because
912 it could not be used from the generic.
917 o rotate() has been removed; this function did not work correctly
922 CHANGES IN APE VERSION 1.9-1
927 o Trees with a single tip were not read correctly in R as the
928 element `Nnode' was not set: this is fixed.
930 o unroot() did not set correctly the number of nodes of the
931 unrooted tree in most cases.
933 o read.GenBank() failed when fetching very long sequences,
934 particularly of the BX-series.
936 o A bug was introduced in read.tree() with ape 1.9: it has been
941 CHANGES IN APE VERSION 1.9
946 o There are two new print `methods' for trees of class "phylo" and
947 lists of trees of class "multi.tree", so that they are now
948 displayed in a compact and informative way.
950 o There are two new functions, old2new.phylo and new2old.phylo,
951 for converting between the old and new coding of the class
954 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
955 LogDet ("logdet"), and paralinear ("paralin").
957 o compute.brlen() has been extended: several methods are now
958 available to compute branch lengths.
960 o write.dna() can now handle matrices as well as lists.
965 o cophenetic.phylo() sometimes returned a wrong result with
966 multichotomous trees: this is fixed.
968 o rotate() failed when a single tip was specified: the tree is now
971 o ace() did not return the correct index matrix with custom
972 models: this is fixed.
974 o multi2di() did not work correctly when resolving multichotomies
975 randomly: the topology was always the same, only the arrangement
976 of clades was randomized: this is fixed. This function now
977 accepts trees with no branch lengths.
979 o The output of diversi.gof() was blurred by useless prints when a
980 user distribution was specified. This has been corrected, and
981 the help page of this function has been expanded.
986 o The internal structure of the class "phylo" has been changed:
987 see the document "Definition of Formats for Coding Phylogenetic
988 Trees in R" for the details. In addition, the code of most
989 functions has been improved.
991 o Several functions have been improved by replacing some R codes
992 by C codes: pic, plot.phylo, and reorder.phylo.
994 o There is now a citation information: see citation("ape") in R.
996 o write.tree() now does not add extra 0's to branch lengths so
997 that 1.23 is printed "1.23" by default, not "1.2300000000".
999 o The syntax of bind.tree() has been simplified. This function now
1000 accepts trees with no branch lengths, and handles correctly node
1003 o The option `as.numeric' of mrca() has been removed.
1005 o The unused options `format' and `rooted' of read.tree() have
1008 o The unused option `format' of write.tree() has been removed.
1010 o The use of node.depth() has been simplified.
1014 CHANGES IN APE VERSION 1.8-5
1019 o Two new functions read.nexus.data() and write.nexus.data(),
1020 contributed by Johan Nylander, allow to read and write molecular
1021 sequences in NEXUS files.
1023 o The new function reorder.phylo() reorders the internal structure
1024 of a tree of class "phylo". It is used as the generic, e.g.,
1027 o read.tree() and read.nexus() can now read trees with a single
1030 o The new data set `cynipids' supplies a set of protein sequences
1036 o The code of all.equal.phylo() has been completely rewritten
1037 (thanks to Benoît Durand) which fixes several bugs.
1039 o read.tree() and read.nexus() now checks the labels of the tree
1040 to remove or substitute any characters that are illegal in the
1041 Newick format (parentheses, etc.)
1043 o A negative P-value could be returned by mantel.test(): this is
1048 CHANGES IN APE VERSION 1.8-4
1053 o The new function sh.test() computes the Shimodaira-
1056 o The new function collapse.singles() removes the nodes with a
1057 single descendant from a tree.
1059 o plot.phylo() has a new argument `tip.color' to specify the
1060 colours of the tips.
1062 o mlphylo() has now an option `quiet' to control the display of
1063 the progress of the analysis (the default is FALSE).
1068 o read.dna() did not read correctly sequences in sequential format
1069 with leading alignment gaps "-": this is fixed.
1071 o ace() returned a list with no class so that the generic
1072 functions (anova, logLik, ...) could not be used directly. This
1073 is fixed as ace() now returns an object of class "ace".
1075 o anova.ace() had a small bug when computing the number of degrees
1076 of freedom: this is fixed.
1078 o mlphylo() did not work when the sequences were in a matrix or
1079 a data frame: this is fixed.
1081 o rtree() did not work correctly when trying to simulate an
1082 unrooted tree with two tips: an error message is now issued.
1087 o The algorithm of rtree() has been changed: it is now about 40,
1088 100, and 130 times faster for 10, 100, and 1000 tips,
1093 CHANGES IN APE VERSION 1.8-3
1098 o There are four new `method' functions to be used with the
1099 results of ace(): logLik(), deviance(), AIC(), and anova().
1101 o The plot method of phymltest has two new arguments: `main' to
1102 change the title, and `col' to control the colour of the
1103 segments showing the AIC values.
1105 o ace() has a new argument `ip' that gives the initial values used
1106 in the ML estimation with discrete characters (see the examples
1107 in ?ace). This function now returns a matrix giving the indices
1108 of the estimated rates when analysing discrete characters.
1110 o nodelabels() and tiplabels() have a new argument `pie' to
1111 represent proportions, with any number of categories, as
1112 piecharts. The use of the option `thermo' has been improved:
1113 there is now no limitation on the number of categories.
1118 o mlphylo() did not work with more than two partitions: this is
1121 o root() failed if the proposed outgroup was already an outgroup
1122 in the tree: this is fixed.
1124 o The `col' argument in nodelabels() and tiplabels() was not
1125 correctly passed when `text' was used: this is fixed.
1127 o Two bugs were fixed in mlphylo(): parameters were not always
1128 correctly output, and the estimation failed in some cases.
1130 o plot.phylo() was stuck when given a tree with a single tip: this
1131 is fixed and a message error is now returned.
1133 o An error was corrected in the help page of gammaStat regarding
1134 the calculation of P-values.
1136 o Using gls() could crash R when the number of species in the tree
1137 and in the variables were different: this is fixed.
1141 CHANGES IN APE VERSION 1.8-2
1146 o The new function mlphylo() fits a phylogenetic tree by maximum
1147 likelihood from DNA sequences. Its companion function DNAmodel()
1148 is used to define the substitution model which may include
1149 partitioning. There are methods for logLik(), deviance(), and
1150 AIC(), and the summary() method has been extended to display in
1151 a friendly way the results of this model fitting. Currently, the
1152 functionality is limited to estimating the substitution and
1153 associated parameters and computing the likelihood.
1155 o The new function drop1.compar.gee (used as, e.g., drop1(m))
1156 tests for single effects in GEE-based comparative method. A
1157 warning message is printed if there is not enough degrees of
1163 o An error message was sometimes issued by plot.multi.tree(),
1164 though with no consequence.
1168 CHANGES IN APE VERSION 1.8-1
1173 o There is a new plot method for lists of trees (objects of class
1174 "multi.tree"): it calls plot.phylo() internally and is
1175 documented on the same help page.
1180 o A bug was fixed in the C code that analyzes bipartitions: this
1181 has impact on several functions like prop.part, prop.clades,
1182 boot.phylo, or consensus.
1184 o root() did not work correctly when the specified outgroup had
1185 more than one element: this is fixed.
1187 o dist.dna() sometimes returned a warning inappropriately: this
1190 o If the distance object given to nj() had no rownames, nj()
1191 returned a tree with no tip labels: it now returns tips labelled
1192 "1", "2", ..., corresponding to the row numbers.
1197 o nj() has been slightly changed so that tips with a zero distance
1198 are first aggregated with zero-lengthed branches; the usual NJ
1199 procedure is then performed on a distance matrix without 0's.
1203 CHANGES IN APE VERSION 1.8
1208 o The new function chronopl() estimates dates using the penalized
1209 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1211 o The new function consensus() calculates the consensus tree of a
1214 o The new function evolve.phylo() simulates the evolution of
1215 continuous characters along a phylogeny under a Brownian model.
1217 o The new plot method for objects of class "ancestral" displays a
1218 tree together with ancestral values, as returned by the above
1221 o The new function as.phylo.formula() returns a phylogeny from a
1222 set of nested taxonomic variables given as a formula.
1224 o The new function read.caic() reads trees in CAIC format.
1226 o The new function tiplabels() allows to add labels to the tips
1227 of a tree using text or plotting symbols in a flexible way.
1229 o The new function unroot() unroots a phylogeny.
1231 o multi2di() has a new option, `random', which specifies whether
1232 to resolve the multichotomies randomly (the default) or not.
1234 o prop.part() now returns an object of class "prop.part" for which
1235 there are print (to display a partition in a more friendly way)
1236 and summary (to extract the numbers) methods.
1238 o plot.phylo() has a new option, `show.tip.label', specifying
1239 whether to print the labels of the tips. The default is TRUE.
1241 o The code of nj() has been replaced by a faster C code: it is now
1242 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1245 o write.nexus() now writes whether a tree is rooted or not.
1250 o Two bugs have been fixed in root(): unrooted trees are now
1251 handled corretly, and node labels are now output normally.
1253 o A bug was fixed in phymltest(): the executable couldn't be found
1256 o Three bug have been fixed in ace(): computing the likelihood of
1257 ancestral states of discrete characters failed, custom models
1258 did not work, and the function failed with a null gradient (a
1259 warning message is now returned; this latter bug was also
1260 present in yule.cov() as well and is now fixed).
1262 o pic() hanged out when missing data were present: a message error
1265 o A small bug was fixed in dist.dna() where the gamma correction
1266 was not always correctly dispatched.
1268 o plot.phylo() plotted correctly the root edge only when the tree
1269 was plotted rightwards: this works now for all directions.
1274 o dist.taxo() has been renamed as weight.taxo().
1276 o dist.phylo() has been replaced by the method cophenetic.phylo().
1278 o Various error and warning messages have been improved.
1282 CHANGES IN APE VERSION 1.7
1285 o The new function ace() estimates ancestral character states for
1286 continuous characters (with ML, GLS, and contrasts methods), and
1287 discrete characters (with ML only) for any number of states.
1289 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1290 of directional evolution for continuous characters. The user
1291 specifies the node(s) of the tree where the character optimum
1294 o The new function is.rooted() tests whether a tree (of class
1297 o The new function rcoal() generates random ultrametric trees with
1298 the possibility to specify the function that generates the
1299 inter-nodes distances.
1301 o The new function mrca() gives for all pairs of tips in a tree
1302 (and optionally nodes too) the most recent common ancestor.
1304 o nodelabels() has a new option `thermo' to plot proportions (up
1305 to three classes) on the nodes of a tree.
1307 o rtree() has been improved: it can now generate rooted or
1308 unrooted trees, and the mathematical function that generates the
1309 branch lengths may be specified by the user. The tip labels may
1310 be given directly in the call to rtree. The limit cases (n = 2,
1311 3) are now handled correctly.
1313 o dist.topo() has a new argument `method' with two choices: "PH85"
1314 for Penny and Henny's method (already available before and now
1315 the default), and "BHV01" for the geometric distance by Billera
1316 et al. (2001, Adv. Appl. Math. 27:733).
1318 o write.tree() has a new option, `digits', which specifies the
1319 number of digits to be printed in the Newick tree. By default
1320 digits = 10. The numbers are now always printed in decimal form
1321 (i.e., 1.0e-1 is now avoided).
1323 o dist.dna() can now compute the raw distances between pairs of
1324 DNA sequences by specifying model = "raw".
1326 o dist.phylo() has a new option `full' to possibly compute the
1327 distances among all tips and nodes of the tree. The default if
1333 o Several bugs were fixed in all.equal.phylo().
1335 o dist.dna() did not handle correctly gaps ("-") in alignments:
1336 they are now considered as missing data.
1338 o rotate() did not work if the tips were not ordered: this is
1341 o mantel.test() returned NA in some special cases: this is fixed
1342 and the function has been improved and is now faster.
1344 o A bug was fixed in diversi.gof() where the calculation of A² was
1347 o cherry() did not work correctly under some OSs (mainly Linux):
1350 o is.binary.tree() has been modified so that it works with both
1351 rooted and unrooted trees.
1353 o The documentation of theta.s() was not correct: this has been
1356 o plot.mst() did not work correctly: this is fixed.
1360 CHANGES IN APE VERSION 1.6
1365 o The new function dist.topo() computes the topological distances
1368 o The new function boot.phylo() performs a bootstrap analysis on
1369 phylogeny estimation.
1371 o The new functions prop.part() and prop.clades() analyse
1372 bipartitions from a series of trees.
1377 o read.GenBank() now uses the EFetch utility of NCBI instead of
1378 the usual Web interface: it is now much faster (e.g., 12 times
1379 faster to retrieve 8 sequences, 37 times for 60 sequences).
1384 o Several bugs were fixed in read.dna().
1386 o Several bugs were fixed in diversi.time().
1388 o is.binary.tree() did not work correctly if the tree has no edge
1389 lengths: this is fixed.
1391 o drop.tip() did not correctly propagated the `node.label' of a
1392 tree: this is fixed.
1396 CHANGES IN APE VERSION 1.5
1401 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1402 convert objects between the classes "phylo" and "matching". The
1403 latter implements the representation of binary trees introduced by
1404 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1405 as.matching() has been introduced as well.
1407 o Two new functions, multi2di() and di2multi(), allow to resolve
1408 and collapse multichotomies with branches of length zero.
1410 o The new function nuc.div() computes the nucleotide diversity
1411 from a sample a DNA sequences.
1413 o dist.dna() has been completely rewritten with a much faster
1414 (particularly for large data sets) C code. Eight models are
1415 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1416 option `method' has been renamed `model'). Computation of variance
1417 is available for all models. A gamma-correction is possible for
1418 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1419 to remove sites with missing data on a pairwise basis. The option
1420 `GCcontent' has been removed.
1422 o read.GenBank() has a new option (species.names) which specifies
1423 whether to return the species names of the organisms in addition
1424 to the accession numbers of the sequences (this is the default
1427 o write.nexus() can now write several trees in the same NEXUS file.
1429 o drop.tip() has a new option `root.edge' that allows to specify the
1430 new root edge if internal branches are trimmed.
1435 o as.phylo.hclust() failed if some labels had parentheses: this
1438 o Several bugs were fixed in all.equal.phylo(). This function now
1439 returns the logical TRUE if the trees are identical but with
1440 different representations (a report was printed previously).
1442 o read.GenBank() did not correctly handle ambiguous base codes:
1448 o birthdeath() now returns an object of class "birthdeath" for
1449 which there is a print method.
1453 CHANGES IN APE VERSION 1.4
1458 o The new function nj() performs phylogeny estimation with the
1459 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1462 o The new function which.edge() identifies the edges of a tree
1463 that belong to a group specified as a set of tips.
1465 o The new function as.phylo.phylog() converts an object of class
1466 "phylog" (from the package ade4) into an object of class
1469 o The new function axisPhylo() draws axes on the side of a
1472 o The new function howmanytrees() calculates the number of trees
1473 in different cases and giving a number of tips.
1475 o write.tree() has a new option `multi.line' (TRUE by default) to
1476 write a Newick tree on several lines rather than on a single
1479 o The functionalities of zoom() have been extended. Several
1480 subtrees can be visualized at the same time, and they are marked
1481 on the main tree with colors. The context of the subtrees can be
1482 marked with the option `subtree' (see below).
1484 o drop.tip() has a new option `subtree' (FALSE by default) which
1485 specifies whether to output in the tree how many tips have been
1488 o The arguments of add.scale.bar() have been redefined and have
1489 now default values (see ?add.scale.bar for details). This
1490 function now works even if the plotted tree has no edge length.
1492 o plot.phylo() can now plot radial trees, but this does not take
1493 edge lengths into account.
1495 o In plot.phylo() with `type = "phylogram"', if the values of
1496 `edge.color' and `edge.width' are identical for sister-branches,
1497 they are propagated to the vertical line that link them.
1502 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1503 crashing. This is fixed.
1505 o In plot.phylo(), the options `edge.color' and `edge.width' are
1506 now properly recycled; their default values are now "black" and
1509 o A bug has been fixed in write.nexus().
1514 o The function node.depth.edgelength() has been removed and
1515 replaced by a C code.
1519 CHANGES IN APE VERSION 1.3-1
1524 o The new function nodelabels() allows to add labels to the nodes
1525 of a tree using text or plotting symbols in a flexible way.
1527 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1528 numeric values specifying the lower and upper limits on the x-
1529 and y-axes. This allows to leave some space on any side of the
1530 tree. If a single value is given, this is taken as the upper
1535 CHANGES IN APE VERSION 1.3
1540 o The new function phymltest() calls the software PHYML and fits
1541 28 models of DNA sequence evolution. There are a print method to
1542 display likelihood and AIC values, a summary method to compute
1543 the hierarchical likelihood ratio tests, and a plot method to
1544 display graphically the AIC values of each model.
1546 o The new function yule.cov() fits the Yule model with covariates,
1547 a model where the speciation rate is affected by several species
1548 traits through a generalized linear model. The parameters are
1549 estimated by maximum likelihood.
1551 o Three new functions, corBrownian(), corGrafen(), and
1552 corMartins(), compute the expected correlation structures among
1553 species given a phylogeny under different models of evolution.
1554 These can be used for GLS comparative phylogenetic methods (see
1555 the examples). There are coef() and corMatrix() methods and an
1556 Initialize.corPhyl() function associated.
1558 o The new function compar.cheverud() implements Cheverud et al.'s
1559 (1985; Evolution 39:1335) phylogenetic comparative method.
1561 o The new function varcomp() estimates variance components; it has
1564 o Two new functions, panel.superpose.correlogram() and
1565 plot.correlogramList(), allow to plot several phylogenetic
1568 o The new function node.leafnumber() computes the number of leaves
1569 of a subtree defined by a particular node.
1571 o The new function node.sons() gets all tags of son nodes from a
1574 o The new function compute.brlen() computes the branch lengths of
1575 a tree according to a specified method.
1577 o plot.phylo() has three new options: "cex" controls the size of
1578 the (tip and node) labels (thus it is no more needed to change
1579 the global graphical parameter), "direction" which allows to
1580 plot the tree rightwards, leftwards, upwards, or downwards, and
1581 "y.lim" which sets the upper limit on the y-axis.
1586 o Some functions which try to match tip labels and names of
1587 additional data (e.g. vector) are likely to fail if there are
1588 typing or syntax errors. If both series of names do not perfectly
1589 match, they are ignored and a warning message is now issued.
1590 These functions are bd.ext, compar.gee, pic. Their help pages
1591 have been clarified on this point.
1595 CHANGES IN APE VERSION 1.2-7
1600 o The new function root() reroots a phylogenetic tree with respect
1601 to a specified outgroup.
1603 o The new function rotate() rotates an internal branch of a tree.
1605 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1606 trees) controls the display of the tip labels in unrooted trees.
1607 This display has been greatly improved: the tip labels are now not
1608 expected to overlap with the tree (particularly if lab4ut =
1609 "axial"). In all cases, combining appropriate values of "lab4ut"
1610 and the font size (via "par(cex = )") should result in readable
1611 unrooted trees. See ?plot.phylo for some examples.
1613 o In drop.tip(), the argument `tip' can now be numeric or character.
1618 o drop.tip() did not work correctly with trees with no branch
1619 lengths: this is fixed.
1621 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1622 plotted with some line crossings: this is now fixed.
1626 CHANGES IN APE VERSION 1.2-6
1631 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1632 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1633 to implement comparative methods with an autocorrelation approach.
1635 o A new data set describing some life history traits of Carnivores
1641 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1646 o When plotting a tree with plot.phylo(), the new default of the
1647 option `label.offset' is now 0, so the labels are always visible.
1651 CHANGES IN APE VERSION 1.2-5
1656 o The new function bd.ext() fits a birth-death model with combined
1657 phylogenetic and taxonomic data, and estimates the corresponding
1658 speciation and extinction rates.
1663 o The package gee is no more required by ape but only suggested
1664 since only the function compar.gee() calls gee.
1668 CHANGES IN APE VERSION 1.2-4
1673 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1674 and lines.popsize) implementing a new approach for inferring the
1675 demographic history from genealogies using a reversible jump
1676 MCMC have been introduced.
1678 o The unit of time in the skyline plot and in the new plots can
1679 now be chosen to be actual years, rather than substitutions.
1683 CHANGES IN APE VERSION 1.2-3
1688 o The new function rtree() generates a random binary tree with or
1689 without branch lengths.
1691 o Two new functions for drawing lineages-through-time (LTT) plots
1692 are provided: ltt.lines() adds a LTT curve to an existing plot,
1693 and mltt.plot() does a multiple LTT plot giving several trees as
1694 arguments (see `?ltt.plot' for details).
1699 o Some taxon names made R crashing when calling as.phylo.hclust():
1702 o dist.dna() returned an error with two identical DNA sequences
1703 (only using the Jukes-Cantor method returned 0): this is fixed.
1708 o The function dist.phylo() has been re-written using a different
1709 algorithm: it is now about four times faster.
1711 o The code of branching.times() has been improved: it is now about
1716 CHANGES IN APE VERSION 1.2-2
1721 o The new function seg.sites() finds the segregating sites in a
1722 sample of DNA sequences.
1727 o A bug introduced in read.tree() and in read.nexus() with version
1730 o A few errors were corrected and a few examples were added in the
1735 CHANGES IN APE VERSION 1.2-1
1740 o plot.phylo() can now draw the edge of the root of a tree if it
1741 has one (see the new option `root.edge', its default is FALSE).
1746 o A bug was fixed in read.nexus(): files with semicolons inside
1747 comment blocks were not read correctly.
1749 o The behaviour of read.tree() and read.nexus() was corrected so
1750 that tree files with badly represented root edges (e.g., with
1751 an extra pair of parentheses, see the help pages for details)
1752 are now correctly represented in the object of class "phylo";
1753 a warning message is now issued.
1757 CHANGES IN APE VERSION 1.2
1762 o plot.phylo() has been completely re-written and offers several
1763 new functionalities. Three types of trees can now be drawn:
1764 phylogram (as previously), cladogram, and unrooted tree; in
1765 all three types the branch lengths can be drawn using the edge
1766 lengths of the phylogeny or not (e.g., if the latter is absent).
1767 The vertical position of the nodes can be adjusted with two
1768 choices (see option `node.pos'). The code has been re-structured,
1769 and two new functions (potentially useful for developpers) are
1770 documented separately: node.depth.edgelength() and node.depth();
1771 see the respective help pages for details.
1773 o The new function zoom() allows to explore very large trees by
1774 focusing on a small portion of it.
1776 o The new function yule() fits by maximum likelihood the Yule model
1777 (birth-only process) to a phylogenetic tree.
1779 o Support for writing DNA sequences in FASTA format has been
1780 introduced in write.dna() (support for reading sequences in
1781 this format was introduced in read.dna() in version 1.1-2).
1782 The function has been completely re-written, fixing some bugs
1783 (see below); the default behaviour is no more to display the
1784 sequences on the standard output. Several options have been
1785 introduced to control the sequence printing in a flexible
1786 way. The help page has been extended.
1788 o A new data set is included: a supertree of bats in NEXUS format.
1793 o In theta.s(), the default of the option `variance' has
1794 been changed to `FALSE' (as was indicated in the help page).
1796 o Several bugs were fixed in the code of all.equal.phylo().
1798 o Several bugs were fixed in write.dna(), particularly this
1799 function did not work with `format = "interleaved"'.
1801 o Various errors were corrected in the help pages.
1806 o The argument names of as.hclust.phylo() have been changed
1807 from "(phy)" to "(x, ...)" to conform to the definition of
1808 the corresponding generic function.
1810 o gamma.stat() has been renamed gammaStat() to avoid confusion
1811 since gamma() is a generic function.
1815 CHANGES IN APE VERSION 1.1-3
1820 o base.freq() previously did not return a value of 0 for
1821 bases absent in the data (e.g., a vector of length 3 was
1822 returned if one base was absent). This is now fixed (a
1823 vector of length 4 is always returned).
1825 o Several bugs were fixed in read.nexus(), including that this
1826 function did not work in this absence of a "TRANSLATE"
1827 command in the NEXUS file, and that the commands were
1832 CHANGES IN APE VERSION 1.1-2
1837 o The Tamura and Nei (1993) model of DNA distance is now implemented
1838 in dist.dna(): five models are now available in this function.
1840 o A new data set is included: a set of 15 sequences of the
1841 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1847 o A bug in read.nexus() was fixed.
1849 o read.dna() previously did not work correctly in most cases.
1850 The function has been completely re-written and its help page
1851 has been considerably extended (see ?read.dna for details).
1852 Underscores (_) in taxon names are no more replaced with
1853 spaces (this behaviour was undocumented).
1855 o A bug was fixed in write.dna().
1859 CHANGES IN APE VERSION 1.1-1
1864 o A bug in read.tree() introduced in APE 1.1 was fixed.
1866 o A bug in compar.gee() resulted in an error when trying to fit
1867 a model with `family = "binomial"'. This is now fixed.
1871 CHANGES IN APE VERSION 1.1
1876 o The Klastorin (1982) method as suggested by Misawa and Tajima
1877 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1878 on the basis of phylogenetic trees has been implemented (see
1879 the function klastorin()).
1881 o Functions have been added to convert APE's "phylo" objects in
1882 "hclust" cluster objects and vice versa (see the help page of
1883 as.phylo for details).
1885 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1886 are introduced for the estimation of absolute evolutionary rates
1887 (ratogram) and dated clock-like trees (chronogram) from
1888 phylogenetic trees using the non-parametric rate smoothing approach
1889 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1891 o A summary method is now provided printing a summary information on a
1892 phylogenetic tree with, for instance, `summary(tree)'.
1894 o The behaviour of read.tree() was changed so that all spaces and
1895 tabulations in tree files are now ignored. Consequently, spaces in tip
1896 labels are no more allowed. Another side effect is that read.nexus()
1897 now does not replace the underscores (_) in tip labels with spaces
1898 (this behaviour was undocumented).
1900 o The function plot.phylo() has a new option (`underscore') which
1901 specifies whether the underscores in tip labels should be written on
1902 the plot as such or replaced with spaces (the default).
1904 o The function birthdeath() now computes 95% confidence intervals of
1905 the estimated parameters using profile likelihood.
1907 o Three new data sets are included: a gene tree estimated from 36
1908 landplant rbcL sequences, a gene tree estimated from 32 opsin
1909 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1914 o A bug was fixed in dist.gene() where nothing was returned.
1916 o A bug in plot.mst() was fixed.
1918 o A bug in vcv.phylo() resulted in false correlations when the
1919 option `cor = TRUE' was used (now fixed).
1923 CHANGES IN APE VERSION 1.0
1928 o Two new functions, read.dna() and write.dna(), read/write in a file
1929 DNA sequences in interleaved or in sequential format.
1931 o Two new functions, read.nexus() and write.nexus(), read/write trees
1934 o The new function bind.tree() allows to bind two trees together,
1935 possibly handling root edges to give internal branches.
1937 o The new function drop.tip() removes the tips in a phylogenetic tree,
1938 and trims (or not) the corresponding internal branches.
1940 o The new function is.ultrametric() tests if a tree is ultrametric.
1942 o The function plot.phylo() has more functionalities such as drawing the
1943 branches with different colours and/or different widths, showing the
1944 node labels, controling the position and font of the labels, rotating
1945 the labels, and controling the space around the plot.
1947 o The function read.tree() can now read trees with no branch length,
1948 such as "(a,b),c);". Consequently, the element `edge.length' in
1949 objects of class "phylo" is now optional.
1951 o The function write.tree() has a new default behaviour: if the default
1952 for the option `file' is used (i.e. file = ""), then a variable of
1953 mode character containing the tree in Newick format is returned which
1954 can thus be assigned (e.g., tree <- write.tree(phy)).
1956 o The function read.tree() has a new argument `text' which allows
1957 to read the tree in a variable of mode character.
1959 o A new data set is included: the phylogenetic relationships among
1960 the orders of birds from Sibley and Ahlquist (1990).
1964 CHANGES IN APE VERSION 0.2-1
1969 o Several bugs were fixed in the help pages.
1973 CHANGES IN APE VERSION 0.2
1978 o The function write.tree() writes phylogenetic trees (objects of class
1979 "phylo") in an ASCII file using the Newick parenthetic format.
1981 o The function birthdeath() fits a birth-death model to branching times
1982 by maximum likelihood, and estimates the corresponding speciation and
1985 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1988 o The function is.binary.tree() tests whether a phylogeny is binary.
1990 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1991 as well as some methods are introduced.
1993 o Several functions, including some generics and methods, for computing
1994 skyline plot estimates (classic and generalized) of effective
1995 population size through time are introduced and replace the function
1996 skyline.plot() in version 0.1.
1998 o Two data sets are now included: the phylogenetic relationships among
1999 the families of birds from Sibley and Ahlquist (1990), and an
2000 estimated clock-like phylogeny of HIV sequences sampled in the
2001 Democratic Republic of Congo.
2004 DEPRECATED & DEFUNCT
2006 o The function skyline.plot() in ape 0.1 has been deprecated and
2007 replaced by more elaborate functions (see above).
2012 o Two important bugs were fixed in plot.phylo(): phylogenies with
2013 multichotomies not at the root or not with only terminal branches,
2014 and phylogenies with a single node (i.e. only terminal branches)
2015 did not plot. These trees should be plotted correctly now.
2017 o Several bugs were fixed in diversi.time() in the computation of
2020 o Various errors were corrected in the help pages.
projects / ape.git / blob