1 CHANGES IN APE VERSION 2.5
6 o The new function parafit by Pierre Legendre tests for the
7 coevolution between hosts and parasites. It has a companion
8 function, pcoa, that does principal coordinate decomposition. The
9 latter has a biplot method.
11 o The new function lmorigin by Pierre Legendre performs multiple
12 regression through the origin with testing by permutation.
14 o The new functions rTraitCont and rTraitDisc simulate continuous and
15 discrete traits under a wide range of evolutionary models.
17 o The new function delta.plot does a delta plot following Holland et
18 al. (2002, Mol. Biol. Evol. 12:2051).
20 o add.scale.bar() has a new option 'ask' to draw interactively.
22 o The branch length score replaces the geodesic distance in dist.topo.
27 o add.scale.bar() drew the bar outside the plotting region with the
28 default options with unrooted or radial trees.
30 o dist.topo() made R stuck when the trees had different sizes (thanks
31 to Otto Cordero for the fix).
35 CHANGES IN APE VERSION 2.4-1
40 o rtree() and rcoal() now accept a numeric vector for the 'br'
43 o vcv() is a new generic function with methods for the classes "phylo"
44 and "corPhyl" so that it is possible to calculate the var-cov matrix
45 for "transformation models". vcv.phylo() can still be used for trees
46 of class "phylo"; its argument 'cor' has been renamed 'corr'.
51 o bind.tree() failed when 'y' had no root edge.
53 o read.nexus() shuffled tip labels when the trees have no branch
54 lengths and there is a TRANSLATE block.
56 o read.nexus() does not try to translate node labels if there is a
57 translation table in the NEXUS file. See ?read.nexus for a
58 clarification on this behaviour.
60 o plot.multiPhylo() crashed R when plotting a list of trees with
61 compressed tip labels.
63 o write.nexus() did not translate the taxa names when asked for.
65 o plot.phylo(type = "fan") did not rotate the tip labels correctly
66 when the tree has branch lengths.
68 o ace(type = "continuous", method = "ML") now avoids sigma² being
69 negative (which resulted in an error).
71 o nj() crashed with NA/NaN in the distance matrix: an error in now
76 CHANGES IN APE VERSION 2.4
81 o base.freq() has a new option 'freq' to return the counts; the
82 default is still to return the proportions.
87 o seg.sites() did not handle ambiguous nucleotides correctly: they
90 o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
91 the tree: the argument is now ignored.
93 o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
99 o Trying to plot a tree with a single tip now returns NULL with a
100 warning (it returned an error previously).
102 o The way lines representing nodes are coloured in phylograms has
103 been modified (as well as their widths and types) following some
104 users' request; this is only for dichotomous nodes.
106 o The argument 'adj' in [node][tip][edge]labels() now works when
107 using 'pie' or 'thermo'.
109 o A more informative message error is now returned by dist.dna() when
110 'model' is badly specified (partial matching of this argument is
113 o Deprecated functions are now listed in a help page: see
114 help("ape-defunct") with the quotes.
119 o The functions heterozygosity, nuc.div, theta.h, theta.k and
120 theta.s have been moved from ape to pegas.
122 o The functions mlphylo, DNAmodel and sh.test have been removed.
126 CHANGES IN APE VERSION 2.3-3
131 o add.scale.bar() always drew a horizontal bar.
133 o zoom() shuffled tips with unrooted trees.
135 o write.nexus() failed to write correctly trees with a "TipLabel"
138 o rcoal() failed to compute branch lengths with very large n.
140 o A small bug was fixed in compar.cheverud() (thanks to Michael
143 o seg.sites() failed when passing a vector.
145 o drop.tip() sometimes shuffled tip labels.
147 o root() shuffled node labels with 'resolve.root = TRUE'.
151 CHANGES IN APE VERSION 2.3-2
156 o all.equal.phylo() did not compare unrooted trees correctly.
158 o dist.topo(... method = "PH85") did not treat unrooted trees
159 correctly (thanks to Tim Wallstrom for the fix).
161 o root() sometimes failed to test for the monophyly of the
164 o extract.clade() sometimes included too many edges.
166 o vcv.phylo() did not work correctly when the tree is in
169 o nj() did not handle correctly distance matrices with many 0's.
170 The code has also been significantly improved: 7, 70, 160 times
171 faster with n = 100, 500, 1000, respectively.
175 CHANGES IN APE VERSION 2.3-1
180 o The new function is.monophyletic tests the monophyly of a group.
182 o There is now a c() method for lists of class "DNAbin".
184 o yule.cov() now fits the null model, and its help page has been
185 corrected with respect to this change.
187 o drop.tip() has a new option 'rooted' to force (or not) a tree
188 to be treated as (un)rooted.
193 o dist.gene() failed on most occasions with the default
194 pairwise.deletion = FALSE.
196 o read.tree() failed to read correctly the tree name(s).
198 o boot.phylo() now treats correctly data frames.
200 o del.gaps() did not copy the rownames of a matrix.
202 o A small bug was fixed in CDAM.global().
204 o ace() failed with large data sets. Thanks to Rich FitzJohn for
205 the fix. With other improvements, this function is now about 6
208 o write.tree() failed with objects of class "multiPhylo".
210 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
215 o [.multiPhylo and [.DNAbin now respect the original class.
217 o Instances of the form class(phy) == "phylo" have been replaced
218 by inherits(phy, "phylo").
220 o rcoal() is now faster.
225 o klastorin() has been removed.
229 CHANGES IN APE VERSION 2.3
234 o The new functions CADM.global and CADM.post, contributed by
235 Pierre Legendre, test the congruence among several distance
238 o The new function yule.time fits a user-defined time-dependent
239 Yule model by maximum likelihood.
241 o The new function makeNodeLabel creates and/or modifies node
242 labels in a flexible way.
244 o read.tree() and write.tree() have been modified so that they can
245 handle individual tree names.
247 o plot.phylo() has a new argument 'edge.lty' that specifies the
248 types of lines used for the edges (plain, dotted, dashed, ...)
250 o phymltest() has been updated to work with PhyML 3.0.1.
255 o drop.tip() shuffled tip labels in some cases.
257 o drop.tip() did not handle node.label correctly.
259 o is.ultrametric() now checks the ordering of the edge matrix.
261 o ace() sometimes returned negative values of likelihoods of
262 ancestral states (thanks to Dan Rabosky for solving this long
268 o The data set xenarthra has been removed.
272 CHANGES IN APE VERSION 2.2-4
276 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
277 now fixed. (Thanks to Peter Wragg for the fix!)
279 o A warning message occurred for no reason with ace(method="GLS").
284 o There is now a general help page displayed with '?ape'.
288 CHANGES IN APE VERSION 2.2-3
293 o The new function extract.clade extracts a clade from a tree by
294 specifying a node number or label.
296 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
297 operations of the same names.
299 o dist.dna() can now return the number of site differences by
300 specifying model="N".
305 o chronopl() did not work with CV = TRUE.
307 o read.nexus() did not work correctly in some situations (trees on
308 multiple lines with different numbers of lines and/or with
309 comments inserted within the trees).
311 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
312 the number of lineages with non-binary trees.
317 o ape has now a namespace.
319 o drop.tip() has been improved: it should be much faster and work
320 better in some cases (e.g., see the example in ?zoom).
324 CHANGES IN APE VERSION 2.2-2
329 o dist.gene() has been substantially improved and gains an option
332 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
338 o prop.part() failed with a single tree with the default option
339 'check.labels = TRUE'.
341 o summary.DNAbin() failed to display correctly the summary of
342 sequence lengths with lists of sequences of 10,000 bases or more
343 (because summary.default uses 4 significant digits by default).
345 o read.nexus() failed to read a file with a single tree with line
346 breaks in the Newick string.
348 o del.gaps() returned a list of empty sequences when there were no
354 o phymltest() has been updated for PhyML 3.0 and gains an option
355 'append', whereas the option 'path2exec' has been removed.
357 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
358 which is returned unchanged (instead of an error).
360 o The data sets bird.orders and bird.families are now stored as
361 Newick strings; i.e., the command data(bird.orders) calls
366 CHANGES IN APE VERSION 2.2-1
371 o The new function makeLabel() helps to modify labels of trees,
372 lists of trees, or DNA sequences, with several utilities to
373 truncate and/or make them unique, substituting some
374 characters, and so on.
376 o The new function del.gaps() removes insertion gaps ("-") in a
377 set of DNA sequences.
379 o read.dna() can now read Clustal files (*.aln).
384 o root() failed with 'resolve.root = TRUE' when the root was
385 already the specified root.
387 o Several bugs were fixed in mlphylo().
389 o collapsed.singles() did not propagate the 'Nnode' and
390 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
392 o read.nexus() failed to remove correctly the comments within
395 o read.nexus() failed to read a file with a single tree and no
396 translation of tip labels.
398 o read.nexus() failed to place correctly tip labels when reading
399 a single tree with no edge lengths.
401 o A bug was fixed in sh.test().
406 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
409 o The option 'check.labels' of consensus() and prop.part() is now
412 o write.dna() now does not truncate names to 10 characters with
417 CHANGES IN APE VERSION 2.2
422 o Four new functions have been written by Damien de Vienne for the
423 graphical exploration of large trees (cophyloplot, subtrees,
424 subtreeplot), and to return the graphical coordinates of tree
427 o The new functions corPagel and corBlomberg implement the Pagel's
428 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
430 o chronopl() has been improved and gains several options: see its
431 help page for details.
433 o boot.phylo() has now an option 'trees' to possibly return the
434 bootstraped trees (the default is FALSE).
436 o prop.part() has been improved and should now be faster in all
442 o read.dna() failed if "?" occurred in the first 10 sites of the
445 o The x/y aspect of the plot is now respected when plotting a
446 circular tree (type = "r" or "f").
448 o Drawing the tip labels sometimes failed when plotting circular
451 o zoom() failed when tip labels were used instead of their numbers
452 (thanks to Yan Wong for the fix).
454 o drop.tip() failed with some trees (fixed by Yan Wong).
456 o seg.sites() failed with a list.
458 o consensus() failed in some cases. The function has been improved
459 as well and is faster.
463 CHANGES IN APE VERSION 2.1-3
468 o A bug in read.nexus() made the Windows R-GUI crash.
470 o An error was fixed in the computation of ancestral character
471 states by generalized least squares in ace().
473 o di2multi() did not modify node labels correctly.
475 o multi2di() failed if the tree had its attribute "order" set to
480 CHANGES IN APE VERSION 2.1-2
485 o There three new methods for the "multiPhylo" class: str, $,
488 o root() gains the options 'node' and 'resolve.root'
489 (FALSE by default) as well as its code being improved.
491 o mltt.plot() has now an option 'log' used in the same way
492 than in plot.default().
497 o mltt.plot() failed to display the legend with an unnamed
500 o nodelabels() with pies now correcly uses the argument
501 'cex' to draw symbols of different sizes (which has
502 worked already for thermometers).
504 o read.nexus() generally failed to read very big files.
509 o The argument 'family' of compar.gee() can now be a function
510 as well as a character string.
512 o read.tree() and read.nexus() now return an unnamed list if
515 o read.nexus() now returns a modified object of class "multiPhylo"
516 when there is a TRANSLATE block in the NEXUS file: the individual
517 trees have no 'tip.label' vector, but the list has a 'TipLabel'
518 attribute. The new methods '$' and '[[' set these elements
519 correctly when extracting trees.
523 CHANGES IN APE VERSION 2.1-1
528 o The new function rmtree generates lists of random trees.
530 o rcoal() now generates a genuine coalescent tree by default
531 (thanks to Vladimir Minin for the code).
536 o nuc.div() returned an incorrect value with the default
537 pairwise.deletion = FALSE.
542 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
543 have been improved so that they are stabler and faster.
545 o R packages used by ape are now loaded silently; lattice and gee
546 are loaded only when needed.
550 CHANGES IN APE VERSION 2.1
555 o The new function identify.phylo identifies clades on a plotted
556 tree using the mouse.
558 o It is now possible to subset a list of trees (object of class
559 "multiPhylo") with "[" while keeping its class correct.
561 o The new function as.DNAbin.alignment converts DNA sequences
562 stored in the "alignment" format of the package seqinr into
563 an object of class "DNAbin".
565 o The new function weight.taxo2 helps to build similarity matrices
566 given two taxonomic levels (usually called by other functions).
568 o write.tree() can now take a list of trees (class "multiPhylo")
569 as its main argument.
571 o plot.correlogram() and plot.correlogramList() have been
572 improved, and gain several options (see the help page for
573 details). A legend is now plotted by default.
578 o dist.dna() returned some incorrect values with `model = "JC69"'
579 and `pairwise.deletion = TRUE'. This affected only the
580 distances involving sequences with missing values. (Thanks
581 to Bruno Toupance for digging this bug out.)
583 o write.tree() failed with some trees: this is fixed by removing
584 the `multi.line' option (trees are now always printed on a
587 o read.nexus() did not correctly detect trees with multiple root
588 edges (see OTHER CHANGES).
593 o The code of mlphylo() has been almost entirely rewritten, and
594 should be much stabler. The options have been also greatly
595 simplified (see ?mlphylo and ?DNAmodel for details).
597 o The internal function nTips has been renamed klastorin_nTips.
599 o The code of is.ultrametric() contained redundancies and has
602 o The code of Moran.I() and of correlogram.formula() have been
605 o read.tree() and read.nexus() now return an error when trying to
606 read a tree with multiple root edges (see BUG FIXES). The
607 correction applied in previous version did not work in all
610 o The class c("multi.tree", "phylo") has been renamed
616 o There is now a vignette in ape: see vignette("MoranI", "ape").
621 o as.matching() and as.phylo.matching() do not support branch
624 o correlogram.phylo() and discrete.dist() have been removed.
628 CHANGES IN APE VERSION 2.0-2
633 o The new function matexpo computes the exponential of a square
636 o The new function unique.multi.tree removes duplicate trees from
639 o yule() has a new option `use.root.edge = FALSE' that specifies
640 to ignore, by default, the root edge of the tree if it exists.
645 o which.edge() failed when the index of a single terminal edge was
648 o In diversi.time(), the values returned for model C were
651 o A bug was fixed in yule() that affected the calculation of the
652 likelihood in the presence of ties in the branching times.
654 o There was a bug in the C function mat_expo4x4 affecting the
655 calculations of the transition probabilities for models HKY and
658 o A small bug was fixed in as.matrix.DNAbin (thanks to James
661 o rtree() did not `shuffle' the tip labels by default, so only a
662 limited number of labelled topologies could be generated.
666 CHANGES IN APE VERSION 2.0-1
671 o The three new functions bionj, fastme.ols, and fastme.bal
672 perform phylogeny estimation by the BIONJ and fastME methods in
673 OLS and balanced versions. This is a port to R of previous
674 previous programs done by Vincent Lefort.
676 o The new function chronoMPL performs molecular dating with the
677 mean path lengths method of Britton et al. (2002, Mol. Phyl.
680 o The new function rotate, contributed by Christoph Heibl, swaps
681 two clades connected to the same node. It works also with
682 multichotomous nodes.
684 o The new `method' as.matrix.DNAbin() may be used to convert
685 easily DNA sequences stored in a list into a matrix while
686 keeping the names and the class.
691 o chronopl() failed when some branch lengths were equal to zero:
692 an error message is now returned.
694 o di2multi() failed when there was a series of consecutive edges
699 CHANGES IN APE VERSION 1.10-2
704 o plot.phylo() can now plot circular trees: the option is type =
705 "fan" or type = "f" (to avoid the ambiguity with type = "c").
707 o prop.part() has a new option `check.labels = FALSE' which allows
708 to considerably speed-up the calculations of bipartitions. As a
709 consequence, calculations of bootstrap values with boot.phylo()
710 should be much faster.
715 o read.GenBank() did not return correctly the list of species as
716 from ape 1.10: this is fixed in this version
718 o Applying as.phylo() on a tree of class "phylo" failed: the
719 object is now returned unchanged.
723 CHANGES IN APE VERSION 1.10-1
728 o The three new functions Ntip, Nnode, and Nedge return, for a
729 given tree, the number of tips, nodes, or edges, respectively.
734 o read.nexus() did not set correctly the class of the returned
735 object when reading multiple trees.
737 o mllt.plot() failed with objects of class c("multi.tree",
740 o unroot() did not work correctly in most cases.
742 o reorder.phylo() made R freeze in some occasions.
744 o Plotting a tree in pruningwise order failed.
746 o When plotting an unrooted tree, the tip labels where not all
747 correctly positioned if the option `cex' was used.
751 CHANGES IN APE VERSION 1.10
756 o Five new `method' functions have been introduced to manipulate
757 DNA sequences in binary format (see below).
759 o Three new functions have been introduced to convert between the
760 new binary and the character formats.
762 o The new function as.alignment converts DNA sequences stored as
763 single characters into the class "alignment" used by the package
766 o read.dna() and read.GenBank() have a new argument `as.character'
767 controlling whether the sequences are returned in binary format
773 o root() failed when the tree had node labels: this is fixed.
775 o plot.phylo() did not correctly set the limits on the y-axis with
776 the default setting: this is fixed.
778 o dist.dna() returned a wrong result for the LogDet, paralinear,
779 and BH87 models with `pairwise.deletion = TRUE'.
784 o DNA sequences are now internally stored in a binary format. See
785 the document "A Bit-Level Coding Scheme for Nucleotides" for the
786 details. Most functions analyzing DNA functions have been
787 modified accordingly and are now much faster (dist.dna is now
788 ca. 60 times faster).
792 CHANGES IN APE VERSION 1.9-4
797 o A bug was fixed in edgelabels().
799 o as.phylo.hclust() did not work correctly when the object of
800 class "hclust" has its labels set to NULL: the returned tree has
801 now its tip labels set to "1", "2", ...
803 o consensus could fail if some tip labels are a subset of others
804 (e.g., "a" and "a_1"): this is now fixed.
806 o mlphylo() failed in most cases if some branch lengths of the
807 initial tree were greater than one: an error message is now
810 o mlphylo() failed in most cases when estimating the proportion of
811 invariants: this is fixed.
815 CHANGES IN APE VERSION 1.9-3
820 o The new function edgelabels adds labels on the edge of the tree
821 in the same way than nodelabels or tiplabels.
826 o multi2di() did not handle correctly branch lengths with the
827 default option `random = TRUE': this is now fixed.
829 o A bug was fixed in nuc.div() when using pairwise deletions.
831 o A bug occurred in the analysis of bipartitions with large
832 numbers of large trees, with consequences on prop.part,
833 prop.clades, and boot.phylo.
835 o The calculation of the Billera-Holmes-Vogtmann distance in
836 dist.topo was wrong: this has been fixed.
840 CHANGES IN APE VERSION 1.9-2
845 o The new function ladderize reorganizes the internal structure of
846 a tree to plot them left- or right-ladderized.
848 o The new function dist.nodes computes the patristic distances
849 between all nodes, internal and terminal, of a tree. It replaces
850 the option `full = TRUE' of cophenetic.phylo (see below).
855 o A bug was fixed in old2new.phylo().
857 o Some bugs were fixed in chronopl().
859 o The edge colours were not correctly displayed by plot.phylo
860 (thank you to Li-San Wang for the fix).
862 o cophenetic.phylo() failed with multichotomous trees: this is
868 o read.dna() now returns the sequences in a matrix if they are
869 aligned (interleaved or sequential format). Sequences in FASTA
870 format are still returned in a list.
872 o The option `full' of cophenetic.phylo() has been removed because
873 it could not be used from the generic.
878 o rotate() has been removed; this function did not work correctly
883 CHANGES IN APE VERSION 1.9-1
888 o Trees with a single tip were not read correctly in R as the
889 element `Nnode' was not set: this is fixed.
891 o unroot() did not set correctly the number of nodes of the
892 unrooted tree in most cases.
894 o read.GenBank() failed when fetching very long sequences,
895 particularly of the BX-series.
897 o A bug was introduced in read.tree() with ape 1.9: it has been
902 CHANGES IN APE VERSION 1.9
907 o There are two new print `methods' for trees of class "phylo" and
908 lists of trees of class "multi.tree", so that they are now
909 displayed in a compact and informative way.
911 o There are two new functions, old2new.phylo and new2old.phylo,
912 for converting between the old and new coding of the class
915 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
916 LogDet ("logdet"), and paralinear ("paralin").
918 o compute.brlen() has been extended: several methods are now
919 available to compute branch lengths.
921 o write.dna() can now handle matrices as well as lists.
926 o cophenetic.phylo() sometimes returned a wrong result with
927 multichotomous trees: this is fixed.
929 o rotate() failed when a single tip was specified: the tree is now
932 o ace() did not return the correct index matrix with custom
933 models: this is fixed.
935 o multi2di() did not work correctly when resolving multichotomies
936 randomly: the topology was always the same, only the arrangement
937 of clades was randomized: this is fixed. This function now
938 accepts trees with no branch lengths.
940 o The output of diversi.gof() was blurred by useless prints when a
941 user distribution was specified. This has been corrected, and
942 the help page of this function has been expanded.
947 o The internal structure of the class "phylo" has been changed:
948 see the document "Definition of Formats for Coding Phylogenetic
949 Trees in R" for the details. In addition, the code of most
950 functions has been improved.
952 o Several functions have been improved by replacing some R codes
953 by C codes: pic, plot.phylo, and reorder.phylo.
955 o There is now a citation information: see citation("ape") in R.
957 o write.tree() now does not add extra 0's to branch lengths so
958 that 1.23 is printed "1.23" by default, not "1.2300000000".
960 o The syntax of bind.tree() has been simplified. This function now
961 accepts trees with no branch lengths, and handles correctly node
964 o The option `as.numeric' of mrca() has been removed.
966 o The unused options `format' and `rooted' of read.tree() have
969 o The unused option `format' of write.tree() has been removed.
971 o The use of node.depth() has been simplified.
975 CHANGES IN APE VERSION 1.8-5
980 o Two new functions read.nexus.data() and write.nexus.data(),
981 contributed by Johan Nylander, allow to read and write molecular
982 sequences in NEXUS files.
984 o The new function reorder.phylo() reorders the internal structure
985 of a tree of class "phylo". It is used as the generic, e.g.,
988 o read.tree() and read.nexus() can now read trees with a single
991 o The new data set `cynipids' supplies a set of protein sequences
997 o The code of all.equal.phylo() has been completely rewritten
998 (thanks to Benoît Durand) which fixes several bugs.
1000 o read.tree() and read.nexus() now checks the labels of the tree
1001 to remove or substitute any characters that are illegal in the
1002 Newick format (parentheses, etc.)
1004 o A negative P-value could be returned by mantel.test(): this is
1009 CHANGES IN APE VERSION 1.8-4
1014 o The new function sh.test() computes the Shimodaira-
1017 o The new function collapse.singles() removes the nodes with a
1018 single descendant from a tree.
1020 o plot.phylo() has a new argument `tip.color' to specify the
1021 colours of the tips.
1023 o mlphylo() has now an option `quiet' to control the display of
1024 the progress of the analysis (the default is FALSE).
1029 o read.dna() did not read correctly sequences in sequential format
1030 with leading alignment gaps "-": this is fixed.
1032 o ace() returned a list with no class so that the generic
1033 functions (anova, logLik, ...) could not be used directly. This
1034 is fixed as ace() now returns an object of class "ace".
1036 o anova.ace() had a small bug when computing the number of degrees
1037 of freedom: this is fixed.
1039 o mlphylo() did not work when the sequences were in a matrix or
1040 a data frame: this is fixed.
1042 o rtree() did not work correctly when trying to simulate an
1043 unrooted tree with two tips: an error message is now issued.
1048 o The algorithm of rtree() has been changed: it is now about 40,
1049 100, and 130 times faster for 10, 100, and 1000 tips,
1054 CHANGES IN APE VERSION 1.8-3
1059 o There are four new `method' functions to be used with the
1060 results of ace(): logLik(), deviance(), AIC(), and anova().
1062 o The plot method of phymltest has two new arguments: `main' to
1063 change the title, and `col' to control the colour of the
1064 segments showing the AIC values.
1066 o ace() has a new argument `ip' that gives the initial values used
1067 in the ML estimation with discrete characters (see the examples
1068 in ?ace). This function now returns a matrix giving the indices
1069 of the estimated rates when analysing discrete characters.
1071 o nodelabels() and tiplabels() have a new argument `pie' to
1072 represent proportions, with any number of categories, as
1073 piecharts. The use of the option `thermo' has been improved:
1074 there is now no limitation on the number of categories.
1079 o mlphylo() did not work with more than two partitions: this is
1082 o root() failed if the proposed outgroup was already an outgroup
1083 in the tree: this is fixed.
1085 o The `col' argument in nodelabels() and tiplabels() was not
1086 correctly passed when `text' was used: this is fixed.
1088 o Two bugs were fixed in mlphylo(): parameters were not always
1089 correctly output, and the estimation failed in some cases.
1091 o plot.phylo() was stuck when given a tree with a single tip: this
1092 is fixed and a message error is now returned.
1094 o An error was corrected in the help page of gammaStat regarding
1095 the calculation of P-values.
1097 o Using gls() could crash R when the number of species in the tree
1098 and in the variables were different: this is fixed.
1102 CHANGES IN APE VERSION 1.8-2
1107 o The new function mlphylo() fits a phylogenetic tree by maximum
1108 likelihood from DNA sequences. Its companion function DNAmodel()
1109 is used to define the substitution model which may include
1110 partitioning. There are methods for logLik(), deviance(), and
1111 AIC(), and the summary() method has been extended to display in
1112 a friendly way the results of this model fitting. Currently, the
1113 functionality is limited to estimating the substitution and
1114 associated parameters and computing the likelihood.
1116 o The new function drop1.compar.gee (used as, e.g., drop1(m))
1117 tests for single effects in GEE-based comparative method. A
1118 warning message is printed if there is not enough degrees of
1124 o An error message was sometimes issued by plot.multi.tree(),
1125 though with no consequence.
1129 CHANGES IN APE VERSION 1.8-1
1134 o There is a new plot method for lists of trees (objects of class
1135 "multi.tree"): it calls plot.phylo() internally and is
1136 documented on the same help page.
1141 o A bug was fixed in the C code that analyzes bipartitions: this
1142 has impact on several functions like prop.part, prop.clades,
1143 boot.phylo, or consensus.
1145 o root() did not work correctly when the specified outgroup had
1146 more than one element: this is fixed.
1148 o dist.dna() sometimes returned a warning inappropriately: this
1151 o If the distance object given to nj() had no rownames, nj()
1152 returned a tree with no tip labels: it now returns tips labelled
1153 "1", "2", ..., corresponding to the row numbers.
1158 o nj() has been slightly changed so that tips with a zero distance
1159 are first aggregated with zero-lengthed branches; the usual NJ
1160 procedure is then performed on a distance matrix without 0's.
1164 CHANGES IN APE VERSION 1.8
1169 o The new function chronopl() estimates dates using the penalized
1170 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1172 o The new function consensus() calculates the consensus tree of a
1175 o The new function evolve.phylo() simulates the evolution of
1176 continuous characters along a phylogeny under a Brownian model.
1178 o The new plot method for objects of class "ancestral" displays a
1179 tree together with ancestral values, as returned by the above
1182 o The new function as.phylo.formula() returns a phylogeny from a
1183 set of nested taxonomic variables given as a formula.
1185 o The new function read.caic() reads trees in CAIC format.
1187 o The new function tiplabels() allows to add labels to the tips
1188 of a tree using text or plotting symbols in a flexible way.
1190 o The new function unroot() unroots a phylogeny.
1192 o multi2di() has a new option, `random', which specifies whether
1193 to resolve the multichotomies randomly (the default) or not.
1195 o prop.part() now returns an object of class "prop.part" for which
1196 there are print (to display a partition in a more friendly way)
1197 and summary (to extract the numbers) methods.
1199 o plot.phylo() has a new option, `show.tip.label', specifying
1200 whether to print the labels of the tips. The default is TRUE.
1202 o The code of nj() has been replaced by a faster C code: it is now
1203 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1206 o write.nexus() now writes whether a tree is rooted or not.
1211 o Two bugs have been fixed in root(): unrooted trees are now
1212 handled corretly, and node labels are now output normally.
1214 o A bug was fixed in phymltest(): the executable couldn't be found
1217 o Three bug have been fixed in ace(): computing the likelihood of
1218 ancestral states of discrete characters failed, custom models
1219 did not work, and the function failed with a null gradient (a
1220 warning message is now returned; this latter bug was also
1221 present in yule.cov() as well and is now fixed).
1223 o pic() hanged out when missing data were present: a message error
1226 o A small bug was fixed in dist.dna() where the gamma correction
1227 was not always correctly dispatched.
1229 o plot.phylo() plotted correctly the root edge only when the tree
1230 was plotted rightwards: this works now for all directions.
1235 o dist.taxo() has been renamed as weight.taxo().
1237 o dist.phylo() has been replaced by the method cophenetic.phylo().
1239 o Various error and warning messages have been improved.
1243 CHANGES IN APE VERSION 1.7
1246 o The new function ace() estimates ancestral character states for
1247 continuous characters (with ML, GLS, and contrasts methods), and
1248 discrete characters (with ML only) for any number of states.
1250 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1251 of directional evolution for continuous characters. The user
1252 specifies the node(s) of the tree where the character optimum
1255 o The new function is.rooted() tests whether a tree (of class
1258 o The new function rcoal() generates random ultrametric trees with
1259 the possibility to specify the function that generates the
1260 inter-nodes distances.
1262 o The new function mrca() gives for all pairs of tips in a tree
1263 (and optionally nodes too) the most recent common ancestor.
1265 o nodelabels() has a new option `thermo' to plot proportions (up
1266 to three classes) on the nodes of a tree.
1268 o rtree() has been improved: it can now generate rooted or
1269 unrooted trees, and the mathematical function that generates the
1270 branch lengths may be specified by the user. The tip labels may
1271 be given directly in the call to rtree. The limit cases (n = 2,
1272 3) are now handled correctly.
1274 o dist.topo() has a new argument `method' with two choices: "PH85"
1275 for Penny and Henny's method (already available before and now
1276 the default), and "BHV01" for the geometric distance by Billera
1277 et al. (2001, Adv. Appl. Math. 27:733).
1279 o write.tree() has a new option, `digits', which specifies the
1280 number of digits to be printed in the Newick tree. By default
1281 digits = 10. The numbers are now always printed in decimal form
1282 (i.e., 1.0e-1 is now avoided).
1284 o dist.dna() can now compute the raw distances between pairs of
1285 DNA sequences by specifying model = "raw".
1287 o dist.phylo() has a new option `full' to possibly compute the
1288 distances among all tips and nodes of the tree. The default if
1294 o Several bugs were fixed in all.equal.phylo().
1296 o dist.dna() did not handle correctly gaps ("-") in alignments:
1297 they are now considered as missing data.
1299 o rotate() did not work if the tips were not ordered: this is
1302 o mantel.test() returned NA in some special cases: this is fixed
1303 and the function has been improved and is now faster.
1305 o A bug was fixed in diversi.gof() where the calculation of A² was
1308 o cherry() did not work correctly under some OSs (mainly Linux):
1311 o is.binary.tree() has been modified so that it works with both
1312 rooted and unrooted trees.
1314 o The documentation of theta.s() was not correct: this has been
1317 o plot.mst() did not work correctly: this is fixed.
1321 CHANGES IN APE VERSION 1.6
1326 o The new function dist.topo() computes the topological distances
1329 o The new function boot.phylo() performs a bootstrap analysis on
1330 phylogeny estimation.
1332 o The new functions prop.part() and prop.clades() analyse
1333 bipartitions from a series of trees.
1338 o read.GenBank() now uses the EFetch utility of NCBI instead of
1339 the usual Web interface: it is now much faster (e.g., 12 times
1340 faster to retrieve 8 sequences, 37 times for 60 sequences).
1345 o Several bugs were fixed in read.dna().
1347 o Several bugs were fixed in diversi.time().
1349 o is.binary.tree() did not work correctly if the tree has no edge
1350 lengths: this is fixed.
1352 o drop.tip() did not correctly propagated the `node.label' of a
1353 tree: this is fixed.
1357 CHANGES IN APE VERSION 1.5
1362 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1363 convert objects between the classes "phylo" and "matching". The
1364 latter implements the representation of binary trees introduced by
1365 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1366 as.matching() has been introduced as well.
1368 o Two new functions, multi2di() and di2multi(), allow to resolve
1369 and collapse multichotomies with branches of length zero.
1371 o The new function nuc.div() computes the nucleotide diversity
1372 from a sample a DNA sequences.
1374 o dist.dna() has been completely rewritten with a much faster
1375 (particularly for large data sets) C code. Eight models are
1376 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1377 option `method' has been renamed `model'). Computation of variance
1378 is available for all models. A gamma-correction is possible for
1379 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1380 to remove sites with missing data on a pairwise basis. The option
1381 `GCcontent' has been removed.
1383 o read.GenBank() has a new option (species.names) which specifies
1384 whether to return the species names of the organisms in addition
1385 to the accession numbers of the sequences (this is the default
1388 o write.nexus() can now write several trees in the same NEXUS file.
1390 o drop.tip() has a new option `root.edge' that allows to specify the
1391 new root edge if internal branches are trimmed.
1396 o as.phylo.hclust() failed if some labels had parentheses: this
1399 o Several bugs were fixed in all.equal.phylo(). This function now
1400 returns the logical TRUE if the trees are identical but with
1401 different representations (a report was printed previously).
1403 o read.GenBank() did not correctly handle ambiguous base codes:
1409 o birthdeath() now returns an object of class "birthdeath" for
1410 which there is a print method.
1414 CHANGES IN APE VERSION 1.4
1419 o The new function nj() performs phylogeny estimation with the
1420 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1423 o The new function which.edge() identifies the edges of a tree
1424 that belong to a group specified as a set of tips.
1426 o The new function as.phylo.phylog() converts an object of class
1427 "phylog" (from the package ade4) into an object of class
1430 o The new function axisPhylo() draws axes on the side of a
1433 o The new function howmanytrees() calculates the number of trees
1434 in different cases and giving a number of tips.
1436 o write.tree() has a new option `multi.line' (TRUE by default) to
1437 write a Newick tree on several lines rather than on a single
1440 o The functionalities of zoom() have been extended. Several
1441 subtrees can be visualized at the same time, and they are marked
1442 on the main tree with colors. The context of the subtrees can be
1443 marked with the option `subtree' (see below).
1445 o drop.tip() has a new option `subtree' (FALSE by default) which
1446 specifies whether to output in the tree how many tips have been
1449 o The arguments of add.scale.bar() have been redefined and have
1450 now default values (see ?add.scale.bar for details). This
1451 function now works even if the plotted tree has no edge length.
1453 o plot.phylo() can now plot radial trees, but this does not take
1454 edge lengths into account.
1456 o In plot.phylo() with `type = "phylogram"', if the values of
1457 `edge.color' and `edge.width' are identical for sister-branches,
1458 they are propagated to the vertical line that link them.
1463 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1464 crashing. This is fixed.
1466 o In plot.phylo(), the options `edge.color' and `edge.width' are
1467 now properly recycled; their default values are now "black" and
1470 o A bug has been fixed in write.nexus().
1475 o The function node.depth.edgelength() has been removed and
1476 replaced by a C code.
1480 CHANGES IN APE VERSION 1.3-1
1485 o The new function nodelabels() allows to add labels to the nodes
1486 of a tree using text or plotting symbols in a flexible way.
1488 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1489 numeric values specifying the lower and upper limits on the x-
1490 and y-axes. This allows to leave some space on any side of the
1491 tree. If a single value is given, this is taken as the upper
1496 CHANGES IN APE VERSION 1.3
1501 o The new function phymltest() calls the software PHYML and fits
1502 28 models of DNA sequence evolution. There are a print method to
1503 display likelihood and AIC values, a summary method to compute
1504 the hierarchical likelihood ratio tests, and a plot method to
1505 display graphically the AIC values of each model.
1507 o The new function yule.cov() fits the Yule model with covariates,
1508 a model where the speciation rate is affected by several species
1509 traits through a generalized linear model. The parameters are
1510 estimated by maximum likelihood.
1512 o Three new functions, corBrownian(), corGrafen(), and
1513 corMartins(), compute the expected correlation structures among
1514 species given a phylogeny under different models of evolution.
1515 These can be used for GLS comparative phylogenetic methods (see
1516 the examples). There are coef() and corMatrix() methods and an
1517 Initialize.corPhyl() function associated.
1519 o The new function compar.cheverud() implements Cheverud et al.'s
1520 (1985; Evolution 39:1335) phylogenetic comparative method.
1522 o The new function varcomp() estimates variance components; it has
1525 o Two new functions, panel.superpose.correlogram() and
1526 plot.correlogramList(), allow to plot several phylogenetic
1529 o The new function node.leafnumber() computes the number of leaves
1530 of a subtree defined by a particular node.
1532 o The new function node.sons() gets all tags of son nodes from a
1535 o The new function compute.brlen() computes the branch lengths of
1536 a tree according to a specified method.
1538 o plot.phylo() has three new options: "cex" controls the size of
1539 the (tip and node) labels (thus it is no more needed to change
1540 the global graphical parameter), "direction" which allows to
1541 plot the tree rightwards, leftwards, upwards, or downwards, and
1542 "y.lim" which sets the upper limit on the y-axis.
1547 o Some functions which try to match tip labels and names of
1548 additional data (e.g. vector) are likely to fail if there are
1549 typing or syntax errors. If both series of names do not perfectly
1550 match, they are ignored and a warning message is now issued.
1551 These functions are bd.ext, compar.gee, pic. Their help pages
1552 have been clarified on this point.
1556 CHANGES IN APE VERSION 1.2-7
1561 o The new function root() reroots a phylogenetic tree with respect
1562 to a specified outgroup.
1564 o The new function rotate() rotates an internal branch of a tree.
1566 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1567 trees) controls the display of the tip labels in unrooted trees.
1568 This display has been greatly improved: the tip labels are now not
1569 expected to overlap with the tree (particularly if lab4ut =
1570 "axial"). In all cases, combining appropriate values of "lab4ut"
1571 and the font size (via "par(cex = )") should result in readable
1572 unrooted trees. See ?plot.phylo for some examples.
1574 o In drop.tip(), the argument `tip' can now be numeric or character.
1579 o drop.tip() did not work correctly with trees with no branch
1580 lengths: this is fixed.
1582 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1583 plotted with some line crossings: this is now fixed.
1587 CHANGES IN APE VERSION 1.2-6
1592 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1593 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1594 to implement comparative methods with an autocorrelation approach.
1596 o A new data set describing some life history traits of Carnivores
1602 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1607 o When plotting a tree with plot.phylo(), the new default of the
1608 option `label.offset' is now 0, so the labels are always visible.
1612 CHANGES IN APE VERSION 1.2-5
1617 o The new function bd.ext() fits a birth-death model with combined
1618 phylogenetic and taxonomic data, and estimates the corresponding
1619 speciation and extinction rates.
1624 o The package gee is no more required by ape but only suggested
1625 since only the function compar.gee() calls gee.
1629 CHANGES IN APE VERSION 1.2-4
1634 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1635 and lines.popsize) implementing a new approach for inferring the
1636 demographic history from genealogies using a reversible jump
1637 MCMC have been introduced.
1639 o The unit of time in the skyline plot and in the new plots can
1640 now be chosen to be actual years, rather than substitutions.
1644 CHANGES IN APE VERSION 1.2-3
1649 o The new function rtree() generates a random binary tree with or
1650 without branch lengths.
1652 o Two new functions for drawing lineages-through-time (LTT) plots
1653 are provided: ltt.lines() adds a LTT curve to an existing plot,
1654 and mltt.plot() does a multiple LTT plot giving several trees as
1655 arguments (see `?ltt.plot' for details).
1660 o Some taxon names made R crashing when calling as.phylo.hclust():
1663 o dist.dna() returned an error with two identical DNA sequences
1664 (only using the Jukes-Cantor method returned 0): this is fixed.
1669 o The function dist.phylo() has been re-written using a different
1670 algorithm: it is now about four times faster.
1672 o The code of branching.times() has been improved: it is now about
1677 CHANGES IN APE VERSION 1.2-2
1682 o The new function seg.sites() finds the segregating sites in a
1683 sample of DNA sequences.
1688 o A bug introduced in read.tree() and in read.nexus() with version
1691 o A few errors were corrected and a few examples were added in the
1696 CHANGES IN APE VERSION 1.2-1
1701 o plot.phylo() can now draw the edge of the root of a tree if it
1702 has one (see the new option `root.edge', its default is FALSE).
1707 o A bug was fixed in read.nexus(): files with semicolons inside
1708 comment blocks were not read correctly.
1710 o The behaviour of read.tree() and read.nexus() was corrected so
1711 that tree files with badly represented root edges (e.g., with
1712 an extra pair of parentheses, see the help pages for details)
1713 are now correctly represented in the object of class "phylo";
1714 a warning message is now issued.
1718 CHANGES IN APE VERSION 1.2
1723 o plot.phylo() has been completely re-written and offers several
1724 new functionalities. Three types of trees can now be drawn:
1725 phylogram (as previously), cladogram, and unrooted tree; in
1726 all three types the branch lengths can be drawn using the edge
1727 lengths of the phylogeny or not (e.g., if the latter is absent).
1728 The vertical position of the nodes can be adjusted with two
1729 choices (see option `node.pos'). The code has been re-structured,
1730 and two new functions (potentially useful for developpers) are
1731 documented separately: node.depth.edgelength() and node.depth();
1732 see the respective help pages for details.
1734 o The new function zoom() allows to explore very large trees by
1735 focusing on a small portion of it.
1737 o The new function yule() fits by maximum likelihood the Yule model
1738 (birth-only process) to a phylogenetic tree.
1740 o Support for writing DNA sequences in FASTA format has been
1741 introduced in write.dna() (support for reading sequences in
1742 this format was introduced in read.dna() in version 1.1-2).
1743 The function has been completely re-written, fixing some bugs
1744 (see below); the default behaviour is no more to display the
1745 sequences on the standard output. Several options have been
1746 introduced to control the sequence printing in a flexible
1747 way. The help page has been extended.
1749 o A new data set is included: a supertree of bats in NEXUS format.
1754 o In theta.s(), the default of the option `variance' has
1755 been changed to `FALSE' (as was indicated in the help page).
1757 o Several bugs were fixed in the code of all.equal.phylo().
1759 o Several bugs were fixed in write.dna(), particularly this
1760 function did not work with `format = "interleaved"'.
1762 o Various errors were corrected in the help pages.
1767 o The argument names of as.hclust.phylo() have been changed
1768 from "(phy)" to "(x, ...)" to conform to the definition of
1769 the corresponding generic function.
1771 o gamma.stat() has been renamed gammaStat() to avoid confusion
1772 since gamma() is a generic function.
1776 CHANGES IN APE VERSION 1.1-3
1781 o base.freq() previously did not return a value of 0 for
1782 bases absent in the data (e.g., a vector of length 3 was
1783 returned if one base was absent). This is now fixed (a
1784 vector of length 4 is always returned).
1786 o Several bugs were fixed in read.nexus(), including that this
1787 function did not work in this absence of a "TRANSLATE"
1788 command in the NEXUS file, and that the commands were
1793 CHANGES IN APE VERSION 1.1-2
1798 o The Tamura and Nei (1993) model of DNA distance is now implemented
1799 in dist.dna(): five models are now available in this function.
1801 o A new data set is included: a set of 15 sequences of the
1802 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1808 o A bug in read.nexus() was fixed.
1810 o read.dna() previously did not work correctly in most cases.
1811 The function has been completely re-written and its help page
1812 has been considerably extended (see ?read.dna for details).
1813 Underscores (_) in taxon names are no more replaced with
1814 spaces (this behaviour was undocumented).
1816 o A bug was fixed in write.dna().
1820 CHANGES IN APE VERSION 1.1-1
1825 o A bug in read.tree() introduced in APE 1.1 was fixed.
1827 o A bug in compar.gee() resulted in an error when trying to fit
1828 a model with `family = "binomial"'. This is now fixed.
1832 CHANGES IN APE VERSION 1.1
1837 o The Klastorin (1982) method as suggested by Misawa and Tajima
1838 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1839 on the basis of phylogenetic trees has been implemented (see
1840 the function klastorin()).
1842 o Functions have been added to convert APE's "phylo" objects in
1843 "hclust" cluster objects and vice versa (see the help page of
1844 as.phylo for details).
1846 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1847 are introduced for the estimation of absolute evolutionary rates
1848 (ratogram) and dated clock-like trees (chronogram) from
1849 phylogenetic trees using the non-parametric rate smoothing approach
1850 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1852 o A summary method is now provided printing a summary information on a
1853 phylogenetic tree with, for instance, `summary(tree)'.
1855 o The behaviour of read.tree() was changed so that all spaces and
1856 tabulations in tree files are now ignored. Consequently, spaces in tip
1857 labels are no more allowed. Another side effect is that read.nexus()
1858 now does not replace the underscores (_) in tip labels with spaces
1859 (this behaviour was undocumented).
1861 o The function plot.phylo() has a new option (`underscore') which
1862 specifies whether the underscores in tip labels should be written on
1863 the plot as such or replaced with spaces (the default).
1865 o The function birthdeath() now computes 95% confidence intervals of
1866 the estimated parameters using profile likelihood.
1868 o Three new data sets are included: a gene tree estimated from 36
1869 landplant rbcL sequences, a gene tree estimated from 32 opsin
1870 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1875 o A bug was fixed in dist.gene() where nothing was returned.
1877 o A bug in plot.mst() was fixed.
1879 o A bug in vcv.phylo() resulted in false correlations when the
1880 option `cor = TRUE' was used (now fixed).
1884 CHANGES IN APE VERSION 1.0
1889 o Two new functions, read.dna() and write.dna(), read/write in a file
1890 DNA sequences in interleaved or in sequential format.
1892 o Two new functions, read.nexus() and write.nexus(), read/write trees
1895 o The new function bind.tree() allows to bind two trees together,
1896 possibly handling root edges to give internal branches.
1898 o The new function drop.tip() removes the tips in a phylogenetic tree,
1899 and trims (or not) the corresponding internal branches.
1901 o The new function is.ultrametric() tests if a tree is ultrametric.
1903 o The function plot.phylo() has more functionalities such as drawing the
1904 branches with different colours and/or different widths, showing the
1905 node labels, controling the position and font of the labels, rotating
1906 the labels, and controling the space around the plot.
1908 o The function read.tree() can now read trees with no branch length,
1909 such as "(a,b),c);". Consequently, the element `edge.length' in
1910 objects of class "phylo" is now optional.
1912 o The function write.tree() has a new default behaviour: if the default
1913 for the option `file' is used (i.e. file = ""), then a variable of
1914 mode character containing the tree in Newick format is returned which
1915 can thus be assigned (e.g., tree <- write.tree(phy)).
1917 o The function read.tree() has a new argument `text' which allows
1918 to read the tree in a variable of mode character.
1920 o A new data set is included: the phylogenetic relationships among
1921 the orders of birds from Sibley and Ahlquist (1990).
1925 CHANGES IN APE VERSION 0.2-1
1930 o Several bugs were fixed in the help pages.
1934 CHANGES IN APE VERSION 0.2
1939 o The function write.tree() writes phylogenetic trees (objects of class
1940 "phylo") in an ASCII file using the Newick parenthetic format.
1942 o The function birthdeath() fits a birth-death model to branching times
1943 by maximum likelihood, and estimates the corresponding speciation and
1946 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1949 o The function is.binary.tree() tests whether a phylogeny is binary.
1951 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1952 as well as some methods are introduced.
1954 o Several functions, including some generics and methods, for computing
1955 skyline plot estimates (classic and generalized) of effective
1956 population size through time are introduced and replace the function
1957 skyline.plot() in version 0.1.
1959 o Two data sets are now included: the phylogenetic relationships among
1960 the families of birds from Sibley and Ahlquist (1990), and an
1961 estimated clock-like phylogeny of HIV sequences sampled in the
1962 Democratic Republic of Congo.
1965 DEPRECATED & DEFUNCT
1967 o The function skyline.plot() in ape 0.1 has been deprecated and
1968 replaced by more elaborate functions (see above).
1973 o Two important bugs were fixed in plot.phylo(): phylogenies with
1974 multichotomies not at the root or not with only terminal branches,
1975 and phylogenies with a single node (i.e. only terminal branches)
1976 did not plot. These trees should be plotted correctly now.
1978 o Several bugs were fixed in diversi.time() in the computation of
1981 o Various errors were corrected in the help pages.