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 functions rTraitCont and rTraitDisc simulate continuous and
12 discrete traits under a wide range of evolutionary models.
14 o The new function delta.plot does a delta plot following Holland et
15 al. (2002, Mol. Biol. Evol. 12:2051).
17 o add.scale.bar() has a new option 'ask' to draw interactively.
19 o The branch length score replaces the geodesic distance in dist.topo.
24 o add.scale.bar() drew the bar outside the plotting region with the
25 default options with unrooted or radial trees.
27 o dist.topo() made R stuck when the trees had different sizes (thanks
28 to Otto Cordero for the fix).
32 CHANGES IN APE VERSION 2.4-1
37 o rtree() and rcoal() now accept a numeric vector for the 'br'
40 o vcv() is a new generic function with methods for the classes "phylo"
41 and "corPhyl" so that it is possible to calculate the var-cov matrix
42 for "transformation models". vcv.phylo() can still be used for trees
43 of class "phylo"; its argument 'cor' has been renamed 'corr'.
48 o bind.tree() failed when 'y' had no root edge.
50 o read.nexus() shuffled tip labels when the trees have no branch
51 lengths and there is a TRANSLATE block.
53 o read.nexus() does not try to translate node labels if there is a
54 translation table in the NEXUS file. See ?read.nexus for a
55 clarification on this behaviour.
57 o plot.multiPhylo() crashed R when plotting a list of trees with
58 compressed tip labels.
60 o write.nexus() did not translate the taxa names when asked for.
62 o plot.phylo(type = "fan") did not rotate the tip labels correctly
63 when the tree has branch lengths.
65 o ace(type = "continuous", method = "ML") now avoids sigma² being
66 negative (which resulted in an error).
68 o nj() crashed with NA/NaN in the distance matrix: an error in now
73 CHANGES IN APE VERSION 2.4
78 o base.freq() has a new option 'freq' to return the counts; the
79 default is still to return the proportions.
84 o seg.sites() did not handle ambiguous nucleotides correctly: they
87 o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
88 the tree: the argument is now ignored.
90 o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
96 o Trying to plot a tree with a single tip now returns NULL with a
97 warning (it returned an error previously).
99 o The way lines representing nodes are coloured in phylograms has
100 been modified (as well as their widths and types) following some
101 users' request; this is only for dichotomous nodes.
103 o The argument 'adj' in [node][tip][edge]labels() now works when
104 using 'pie' or 'thermo'.
106 o A more informative message error is now returned by dist.dna() when
107 'model' is badly specified (partial matching of this argument is
110 o Deprecated functions are now listed in a help page: see
111 help("ape-defunct") with the quotes.
116 o The functions heterozygosity, nuc.div, theta.h, theta.k and
117 theta.s have been moved from ape to pegas.
119 o The functions mlphylo, DNAmodel and sh.test have been removed.
123 CHANGES IN APE VERSION 2.3-3
128 o add.scale.bar() always drew a horizontal bar.
130 o zoom() shuffled tips with unrooted trees.
132 o write.nexus() failed to write correctly trees with a "TipLabel"
135 o rcoal() failed to compute branch lengths with very large n.
137 o A small bug was fixed in compar.cheverud() (thanks to Michael
140 o seg.sites() failed when passing a vector.
142 o drop.tip() sometimes shuffled tip labels.
144 o root() shuffled node labels with 'resolve.root = TRUE'.
148 CHANGES IN APE VERSION 2.3-2
153 o all.equal.phylo() did not compare unrooted trees correctly.
155 o dist.topo(... method = "PH85") did not treat unrooted trees
156 correctly (thanks to Tim Wallstrom for the fix).
158 o root() sometimes failed to test for the monophyly of the
161 o extract.clade() sometimes included too many edges.
163 o vcv.phylo() did not work correctly when the tree is in
166 o nj() did not handle correctly distance matrices with many 0's.
167 The code has also been significantly improved: 7, 70, 160 times
168 faster with n = 100, 500, 1000, respectively.
172 CHANGES IN APE VERSION 2.3-1
177 o The new function is.monophyletic tests the monophyly of a group.
179 o There is now a c() method for lists of class "DNAbin".
181 o yule.cov() now fits the null model, and its help page has been
182 corrected with respect to this change.
184 o drop.tip() has a new option 'rooted' to force (or not) a tree
185 to be treated as (un)rooted.
190 o dist.gene() failed on most occasions with the default
191 pairwise.deletion = FALSE.
193 o read.tree() failed to read correctly the tree name(s).
195 o boot.phylo() now treats correctly data frames.
197 o del.gaps() did not copy the rownames of a matrix.
199 o A small bug was fixed in CDAM.global().
201 o ace() failed with large data sets. Thanks to Rich FitzJohn for
202 the fix. With other improvements, this function is now about 6
205 o write.tree() failed with objects of class "multiPhylo".
207 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
212 o [.multiPhylo and [.DNAbin now respect the original class.
214 o Instances of the form class(phy) == "phylo" have been replaced
215 by inherits(phy, "phylo").
217 o rcoal() is now faster.
222 o klastorin() has been removed.
226 CHANGES IN APE VERSION 2.3
231 o The new functions CADM.global and CADM.post, contributed by
232 Pierre Legendre, test the congruence among several distance
235 o The new function yule.time fits a user-defined time-dependent
236 Yule model by maximum likelihood.
238 o The new function makeNodeLabel creates and/or modifies node
239 labels in a flexible way.
241 o read.tree() and write.tree() have been modified so that they can
242 handle individual tree names.
244 o plot.phylo() has a new argument 'edge.lty' that specifies the
245 types of lines used for the edges (plain, dotted, dashed, ...)
247 o phymltest() has been updated to work with PhyML 3.0.1.
252 o drop.tip() shuffled tip labels in some cases.
254 o drop.tip() did not handle node.label correctly.
256 o is.ultrametric() now checks the ordering of the edge matrix.
258 o ace() sometimes returned negative values of likelihoods of
259 ancestral states (thanks to Dan Rabosky for solving this long
265 o The data set xenarthra has been removed.
269 CHANGES IN APE VERSION 2.2-4
273 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
274 now fixed. (Thanks to Peter Wragg for the fix!)
276 o A warning message occurred for no reason with ace(method="GLS").
281 o There is now a general help page displayed with '?ape'.
285 CHANGES IN APE VERSION 2.2-3
290 o The new function extract.clade extracts a clade from a tree by
291 specifying a node number or label.
293 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
294 operations of the same names.
296 o dist.dna() can now return the number of site differences by
297 specifying model="N".
302 o chronopl() did not work with CV = TRUE.
304 o read.nexus() did not work correctly in some situations (trees on
305 multiple lines with different numbers of lines and/or with
306 comments inserted within the trees).
308 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
309 the number of lineages with non-binary trees.
314 o ape has now a namespace.
316 o drop.tip() has been improved: it should be much faster and work
317 better in some cases (e.g., see the example in ?zoom).
321 CHANGES IN APE VERSION 2.2-2
326 o dist.gene() has been substantially improved and gains an option
329 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
335 o prop.part() failed with a single tree with the default option
336 'check.labels = TRUE'.
338 o summary.DNAbin() failed to display correctly the summary of
339 sequence lengths with lists of sequences of 10,000 bases or more
340 (because summary.default uses 4 significant digits by default).
342 o read.nexus() failed to read a file with a single tree with line
343 breaks in the Newick string.
345 o del.gaps() returned a list of empty sequences when there were no
351 o phymltest() has been updated for PhyML 3.0 and gains an option
352 'append', whereas the option 'path2exec' has been removed.
354 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
355 which is returned unchanged (instead of an error).
357 o The data sets bird.orders and bird.families are now stored as
358 Newick strings; i.e., the command data(bird.orders) calls
363 CHANGES IN APE VERSION 2.2-1
368 o The new function makeLabel() helps to modify labels of trees,
369 lists of trees, or DNA sequences, with several utilities to
370 truncate and/or make them unique, substituting some
371 characters, and so on.
373 o The new function del.gaps() removes insertion gaps ("-") in a
374 set of DNA sequences.
376 o read.dna() can now read Clustal files (*.aln).
381 o root() failed with 'resolve.root = TRUE' when the root was
382 already the specified root.
384 o Several bugs were fixed in mlphylo().
386 o collapsed.singles() did not propagate the 'Nnode' and
387 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
389 o read.nexus() failed to remove correctly the comments within
392 o read.nexus() failed to read a file with a single tree and no
393 translation of tip labels.
395 o read.nexus() failed to place correctly tip labels when reading
396 a single tree with no edge lengths.
398 o A bug was fixed in sh.test().
403 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
406 o The option 'check.labels' of consensus() and prop.part() is now
409 o write.dna() now does not truncate names to 10 characters with
414 CHANGES IN APE VERSION 2.2
419 o Four new functions have been written by Damien de Vienne for the
420 graphical exploration of large trees (cophyloplot, subtrees,
421 subtreeplot), and to return the graphical coordinates of tree
424 o The new functions corPagel and corBlomberg implement the Pagel's
425 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
427 o chronopl() has been improved and gains several options: see its
428 help page for details.
430 o boot.phylo() has now an option 'trees' to possibly return the
431 bootstraped trees (the default is FALSE).
433 o prop.part() has been improved and should now be faster in all
439 o read.dna() failed if "?" occurred in the first 10 sites of the
442 o The x/y aspect of the plot is now respected when plotting a
443 circular tree (type = "r" or "f").
445 o Drawing the tip labels sometimes failed when plotting circular
448 o zoom() failed when tip labels were used instead of their numbers
449 (thanks to Yan Wong for the fix).
451 o drop.tip() failed with some trees (fixed by Yan Wong).
453 o seg.sites() failed with a list.
455 o consensus() failed in some cases. The function has been improved
456 as well and is faster.
460 CHANGES IN APE VERSION 2.1-3
465 o A bug in read.nexus() made the Windows R-GUI crash.
467 o An error was fixed in the computation of ancestral character
468 states by generalized least squares in ace().
470 o di2multi() did not modify node labels correctly.
472 o multi2di() failed if the tree had its attribute "order" set to
477 CHANGES IN APE VERSION 2.1-2
482 o There three new methods for the "multiPhylo" class: str, $,
485 o root() gains the options 'node' and 'resolve.root'
486 (FALSE by default) as well as its code being improved.
488 o mltt.plot() has now an option 'log' used in the same way
489 than in plot.default().
494 o mltt.plot() failed to display the legend with an unnamed
497 o nodelabels() with pies now correcly uses the argument
498 'cex' to draw symbols of different sizes (which has
499 worked already for thermometers).
501 o read.nexus() generally failed to read very big files.
506 o The argument 'family' of compar.gee() can now be a function
507 as well as a character string.
509 o read.tree() and read.nexus() now return an unnamed list if
512 o read.nexus() now returns a modified object of class "multiPhylo"
513 when there is a TRANSLATE block in the NEXUS file: the individual
514 trees have no 'tip.label' vector, but the list has a 'TipLabel'
515 attribute. The new methods '$' and '[[' set these elements
516 correctly when extracting trees.
520 CHANGES IN APE VERSION 2.1-1
525 o The new function rmtree generates lists of random trees.
527 o rcoal() now generates a genuine coalescent tree by default
528 (thanks to Vladimir Minin for the code).
533 o nuc.div() returned an incorrect value with the default
534 pairwise.deletion = FALSE.
539 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
540 have been improved so that they are stabler and faster.
542 o R packages used by ape are now loaded silently; lattice and gee
543 are loaded only when needed.
547 CHANGES IN APE VERSION 2.1
552 o The new function identify.phylo identifies clades on a plotted
553 tree using the mouse.
555 o It is now possible to subset a list of trees (object of class
556 "multiPhylo") with "[" while keeping its class correct.
558 o The new function as.DNAbin.alignment converts DNA sequences
559 stored in the "alignment" format of the package seqinr into
560 an object of class "DNAbin".
562 o The new function weight.taxo2 helps to build similarity matrices
563 given two taxonomic levels (usually called by other functions).
565 o write.tree() can now take a list of trees (class "multiPhylo")
566 as its main argument.
568 o plot.correlogram() and plot.correlogramList() have been
569 improved, and gain several options (see the help page for
570 details). A legend is now plotted by default.
575 o dist.dna() returned some incorrect values with `model = "JC69"'
576 and `pairwise.deletion = TRUE'. This affected only the
577 distances involving sequences with missing values. (Thanks
578 to Bruno Toupance for digging this bug out.)
580 o write.tree() failed with some trees: this is fixed by removing
581 the `multi.line' option (trees are now always printed on a
584 o read.nexus() did not correctly detect trees with multiple root
585 edges (see OTHER CHANGES).
590 o The code of mlphylo() has been almost entirely rewritten, and
591 should be much stabler. The options have been also greatly
592 simplified (see ?mlphylo and ?DNAmodel for details).
594 o The internal function nTips has been renamed klastorin_nTips.
596 o The code of is.ultrametric() contained redundancies and has
599 o The code of Moran.I() and of correlogram.formula() have been
602 o read.tree() and read.nexus() now return an error when trying to
603 read a tree with multiple root edges (see BUG FIXES). The
604 correction applied in previous version did not work in all
607 o The class c("multi.tree", "phylo") has been renamed
613 o There is now a vignette in ape: see vignette("MoranI", "ape").
618 o as.matching() and as.phylo.matching() do not support branch
621 o correlogram.phylo() and discrete.dist() have been removed.
625 CHANGES IN APE VERSION 2.0-2
630 o The new function matexpo computes the exponential of a square
633 o The new function unique.multi.tree removes duplicate trees from
636 o yule() has a new option `use.root.edge = FALSE' that specifies
637 to ignore, by default, the root edge of the tree if it exists.
642 o which.edge() failed when the index of a single terminal edge was
645 o In diversi.time(), the values returned for model C were
648 o A bug was fixed in yule() that affected the calculation of the
649 likelihood in the presence of ties in the branching times.
651 o There was a bug in the C function mat_expo4x4 affecting the
652 calculations of the transition probabilities for models HKY and
655 o A small bug was fixed in as.matrix.DNAbin (thanks to James
658 o rtree() did not `shuffle' the tip labels by default, so only a
659 limited number of labelled topologies could be generated.
663 CHANGES IN APE VERSION 2.0-1
668 o The three new functions bionj, fastme.ols, and fastme.bal
669 perform phylogeny estimation by the BIONJ and fastME methods in
670 OLS and balanced versions. This is a port to R of previous
671 previous programs done by Vincent Lefort.
673 o The new function chronoMPL performs molecular dating with the
674 mean path lengths method of Britton et al. (2002, Mol. Phyl.
677 o The new function rotate, contributed by Christoph Heibl, swaps
678 two clades connected to the same node. It works also with
679 multichotomous nodes.
681 o The new `method' as.matrix.DNAbin() may be used to convert
682 easily DNA sequences stored in a list into a matrix while
683 keeping the names and the class.
688 o chronopl() failed when some branch lengths were equal to zero:
689 an error message is now returned.
691 o di2multi() failed when there was a series of consecutive edges
696 CHANGES IN APE VERSION 1.10-2
701 o plot.phylo() can now plot circular trees: the option is type =
702 "fan" or type = "f" (to avoid the ambiguity with type = "c").
704 o prop.part() has a new option `check.labels = FALSE' which allows
705 to considerably speed-up the calculations of bipartitions. As a
706 consequence, calculations of bootstrap values with boot.phylo()
707 should be much faster.
712 o read.GenBank() did not return correctly the list of species as
713 from ape 1.10: this is fixed in this version
715 o Applying as.phylo() on a tree of class "phylo" failed: the
716 object is now returned unchanged.
720 CHANGES IN APE VERSION 1.10-1
725 o The three new functions Ntip, Nnode, and Nedge return, for a
726 given tree, the number of tips, nodes, or edges, respectively.
731 o read.nexus() did not set correctly the class of the returned
732 object when reading multiple trees.
734 o mllt.plot() failed with objects of class c("multi.tree",
737 o unroot() did not work correctly in most cases.
739 o reorder.phylo() made R freeze in some occasions.
741 o Plotting a tree in pruningwise order failed.
743 o When plotting an unrooted tree, the tip labels where not all
744 correctly positioned if the option `cex' was used.
748 CHANGES IN APE VERSION 1.10
753 o Five new `method' functions have been introduced to manipulate
754 DNA sequences in binary format (see below).
756 o Three new functions have been introduced to convert between the
757 new binary and the character formats.
759 o The new function as.alignment converts DNA sequences stored as
760 single characters into the class "alignment" used by the package
763 o read.dna() and read.GenBank() have a new argument `as.character'
764 controlling whether the sequences are returned in binary format
770 o root() failed when the tree had node labels: this is fixed.
772 o plot.phylo() did not correctly set the limits on the y-axis with
773 the default setting: this is fixed.
775 o dist.dna() returned a wrong result for the LogDet, paralinear,
776 and BH87 models with `pairwise.deletion = TRUE'.
781 o DNA sequences are now internally stored in a binary format. See
782 the document "A Bit-Level Coding Scheme for Nucleotides" for the
783 details. Most functions analyzing DNA functions have been
784 modified accordingly and are now much faster (dist.dna is now
785 ca. 60 times faster).
789 CHANGES IN APE VERSION 1.9-4
794 o A bug was fixed in edgelabels().
796 o as.phylo.hclust() did not work correctly when the object of
797 class "hclust" has its labels set to NULL: the returned tree has
798 now its tip labels set to "1", "2", ...
800 o consensus could fail if some tip labels are a subset of others
801 (e.g., "a" and "a_1"): this is now fixed.
803 o mlphylo() failed in most cases if some branch lengths of the
804 initial tree were greater than one: an error message is now
807 o mlphylo() failed in most cases when estimating the proportion of
808 invariants: this is fixed.
812 CHANGES IN APE VERSION 1.9-3
817 o The new function edgelabels adds labels on the edge of the tree
818 in the same way than nodelabels or tiplabels.
823 o multi2di() did not handle correctly branch lengths with the
824 default option `random = TRUE': this is now fixed.
826 o A bug was fixed in nuc.div() when using pairwise deletions.
828 o A bug occurred in the analysis of bipartitions with large
829 numbers of large trees, with consequences on prop.part,
830 prop.clades, and boot.phylo.
832 o The calculation of the Billera-Holmes-Vogtmann distance in
833 dist.topo was wrong: this has been fixed.
837 CHANGES IN APE VERSION 1.9-2
842 o The new function ladderize reorganizes the internal structure of
843 a tree to plot them left- or right-ladderized.
845 o The new function dist.nodes computes the patristic distances
846 between all nodes, internal and terminal, of a tree. It replaces
847 the option `full = TRUE' of cophenetic.phylo (see below).
852 o A bug was fixed in old2new.phylo().
854 o Some bugs were fixed in chronopl().
856 o The edge colours were not correctly displayed by plot.phylo
857 (thank you to Li-San Wang for the fix).
859 o cophenetic.phylo() failed with multichotomous trees: this is
865 o read.dna() now returns the sequences in a matrix if they are
866 aligned (interleaved or sequential format). Sequences in FASTA
867 format are still returned in a list.
869 o The option `full' of cophenetic.phylo() has been removed because
870 it could not be used from the generic.
875 o rotate() has been removed; this function did not work correctly
880 CHANGES IN APE VERSION 1.9-1
885 o Trees with a single tip were not read correctly in R as the
886 element `Nnode' was not set: this is fixed.
888 o unroot() did not set correctly the number of nodes of the
889 unrooted tree in most cases.
891 o read.GenBank() failed when fetching very long sequences,
892 particularly of the BX-series.
894 o A bug was introduced in read.tree() with ape 1.9: it has been
899 CHANGES IN APE VERSION 1.9
904 o There are two new print `methods' for trees of class "phylo" and
905 lists of trees of class "multi.tree", so that they are now
906 displayed in a compact and informative way.
908 o There are two new functions, old2new.phylo and new2old.phylo,
909 for converting between the old and new coding of the class
912 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
913 LogDet ("logdet"), and paralinear ("paralin").
915 o compute.brlen() has been extended: several methods are now
916 available to compute branch lengths.
918 o write.dna() can now handle matrices as well as lists.
923 o cophenetic.phylo() sometimes returned a wrong result with
924 multichotomous trees: this is fixed.
926 o rotate() failed when a single tip was specified: the tree is now
929 o ace() did not return the correct index matrix with custom
930 models: this is fixed.
932 o multi2di() did not work correctly when resolving multichotomies
933 randomly: the topology was always the same, only the arrangement
934 of clades was randomized: this is fixed. This function now
935 accepts trees with no branch lengths.
937 o The output of diversi.gof() was blurred by useless prints when a
938 user distribution was specified. This has been corrected, and
939 the help page of this function has been expanded.
944 o The internal structure of the class "phylo" has been changed:
945 see the document "Definition of Formats for Coding Phylogenetic
946 Trees in R" for the details. In addition, the code of most
947 functions has been improved.
949 o Several functions have been improved by replacing some R codes
950 by C codes: pic, plot.phylo, and reorder.phylo.
952 o There is now a citation information: see citation("ape") in R.
954 o write.tree() now does not add extra 0's to branch lengths so
955 that 1.23 is printed "1.23" by default, not "1.2300000000".
957 o The syntax of bind.tree() has been simplified. This function now
958 accepts trees with no branch lengths, and handles correctly node
961 o The option `as.numeric' of mrca() has been removed.
963 o The unused options `format' and `rooted' of read.tree() have
966 o The unused option `format' of write.tree() has been removed.
968 o The use of node.depth() has been simplified.
972 CHANGES IN APE VERSION 1.8-5
977 o Two new functions read.nexus.data() and write.nexus.data(),
978 contributed by Johan Nylander, allow to read and write molecular
979 sequences in NEXUS files.
981 o The new function reorder.phylo() reorders the internal structure
982 of a tree of class "phylo". It is used as the generic, e.g.,
985 o read.tree() and read.nexus() can now read trees with a single
988 o The new data set `cynipids' supplies a set of protein sequences
994 o The code of all.equal.phylo() has been completely rewritten
995 (thanks to Benoît Durand) which fixes several bugs.
997 o read.tree() and read.nexus() now checks the labels of the tree
998 to remove or substitute any characters that are illegal in the
999 Newick format (parentheses, etc.)
1001 o A negative P-value could be returned by mantel.test(): this is
1006 CHANGES IN APE VERSION 1.8-4
1011 o The new function sh.test() computes the Shimodaira-
1014 o The new function collapse.singles() removes the nodes with a
1015 single descendant from a tree.
1017 o plot.phylo() has a new argument `tip.color' to specify the
1018 colours of the tips.
1020 o mlphylo() has now an option `quiet' to control the display of
1021 the progress of the analysis (the default is FALSE).
1026 o read.dna() did not read correctly sequences in sequential format
1027 with leading alignment gaps "-": this is fixed.
1029 o ace() returned a list with no class so that the generic
1030 functions (anova, logLik, ...) could not be used directly. This
1031 is fixed as ace() now returns an object of class "ace".
1033 o anova.ace() had a small bug when computing the number of degrees
1034 of freedom: this is fixed.
1036 o mlphylo() did not work when the sequences were in a matrix or
1037 a data frame: this is fixed.
1039 o rtree() did not work correctly when trying to simulate an
1040 unrooted tree with two tips: an error message is now issued.
1045 o The algorithm of rtree() has been changed: it is now about 40,
1046 100, and 130 times faster for 10, 100, and 1000 tips,
1051 CHANGES IN APE VERSION 1.8-3
1056 o There are four new `method' functions to be used with the
1057 results of ace(): logLik(), deviance(), AIC(), and anova().
1059 o The plot method of phymltest has two new arguments: `main' to
1060 change the title, and `col' to control the colour of the
1061 segments showing the AIC values.
1063 o ace() has a new argument `ip' that gives the initial values used
1064 in the ML estimation with discrete characters (see the examples
1065 in ?ace). This function now returns a matrix giving the indices
1066 of the estimated rates when analysing discrete characters.
1068 o nodelabels() and tiplabels() have a new argument `pie' to
1069 represent proportions, with any number of categories, as
1070 piecharts. The use of the option `thermo' has been improved:
1071 there is now no limitation on the number of categories.
1076 o mlphylo() did not work with more than two partitions: this is
1079 o root() failed if the proposed outgroup was already an outgroup
1080 in the tree: this is fixed.
1082 o The `col' argument in nodelabels() and tiplabels() was not
1083 correctly passed when `text' was used: this is fixed.
1085 o Two bugs were fixed in mlphylo(): parameters were not always
1086 correctly output, and the estimation failed in some cases.
1088 o plot.phylo() was stuck when given a tree with a single tip: this
1089 is fixed and a message error is now returned.
1091 o An error was corrected in the help page of gammaStat regarding
1092 the calculation of P-values.
1094 o Using gls() could crash R when the number of species in the tree
1095 and in the variables were different: this is fixed.
1099 CHANGES IN APE VERSION 1.8-2
1104 o The new function mlphylo() fits a phylogenetic tree by maximum
1105 likelihood from DNA sequences. Its companion function DNAmodel()
1106 is used to define the substitution model which may include
1107 partitioning. There are methods for logLik(), deviance(), and
1108 AIC(), and the summary() method has been extended to display in
1109 a friendly way the results of this model fitting. Currently, the
1110 functionality is limited to estimating the substitution and
1111 associated parameters and computing the likelihood.
1113 o The new function drop1.compar.gee (used as, e.g., drop1(m))
1114 tests for single effects in GEE-based comparative method. A
1115 warning message is printed if there is not enough degrees of
1121 o An error message was sometimes issued by plot.multi.tree(),
1122 though with no consequence.
1126 CHANGES IN APE VERSION 1.8-1
1131 o There is a new plot method for lists of trees (objects of class
1132 "multi.tree"): it calls plot.phylo() internally and is
1133 documented on the same help page.
1138 o A bug was fixed in the C code that analyzes bipartitions: this
1139 has impact on several functions like prop.part, prop.clades,
1140 boot.phylo, or consensus.
1142 o root() did not work correctly when the specified outgroup had
1143 more than one element: this is fixed.
1145 o dist.dna() sometimes returned a warning inappropriately: this
1148 o If the distance object given to nj() had no rownames, nj()
1149 returned a tree with no tip labels: it now returns tips labelled
1150 "1", "2", ..., corresponding to the row numbers.
1155 o nj() has been slightly changed so that tips with a zero distance
1156 are first aggregated with zero-lengthed branches; the usual NJ
1157 procedure is then performed on a distance matrix without 0's.
1161 CHANGES IN APE VERSION 1.8
1166 o The new function chronopl() estimates dates using the penalized
1167 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1169 o The new function consensus() calculates the consensus tree of a
1172 o The new function evolve.phylo() simulates the evolution of
1173 continuous characters along a phylogeny under a Brownian model.
1175 o The new plot method for objects of class "ancestral" displays a
1176 tree together with ancestral values, as returned by the above
1179 o The new function as.phylo.formula() returns a phylogeny from a
1180 set of nested taxonomic variables given as a formula.
1182 o The new function read.caic() reads trees in CAIC format.
1184 o The new function tiplabels() allows to add labels to the tips
1185 of a tree using text or plotting symbols in a flexible way.
1187 o The new function unroot() unroots a phylogeny.
1189 o multi2di() has a new option, `random', which specifies whether
1190 to resolve the multichotomies randomly (the default) or not.
1192 o prop.part() now returns an object of class "prop.part" for which
1193 there are print (to display a partition in a more friendly way)
1194 and summary (to extract the numbers) methods.
1196 o plot.phylo() has a new option, `show.tip.label', specifying
1197 whether to print the labels of the tips. The default is TRUE.
1199 o The code of nj() has been replaced by a faster C code: it is now
1200 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1203 o write.nexus() now writes whether a tree is rooted or not.
1208 o Two bugs have been fixed in root(): unrooted trees are now
1209 handled corretly, and node labels are now output normally.
1211 o A bug was fixed in phymltest(): the executable couldn't be found
1214 o Three bug have been fixed in ace(): computing the likelihood of
1215 ancestral states of discrete characters failed, custom models
1216 did not work, and the function failed with a null gradient (a
1217 warning message is now returned; this latter bug was also
1218 present in yule.cov() as well and is now fixed).
1220 o pic() hanged out when missing data were present: a message error
1223 o A small bug was fixed in dist.dna() where the gamma correction
1224 was not always correctly dispatched.
1226 o plot.phylo() plotted correctly the root edge only when the tree
1227 was plotted rightwards: this works now for all directions.
1232 o dist.taxo() has been renamed as weight.taxo().
1234 o Various error and warning messages have been improved.
1238 CHANGES IN APE VERSION 1.7
1241 o The new function ace() estimates ancestral character states for
1242 continuous characters (with ML, GLS, and contrasts methods), and
1243 discrete characters (with ML only) for any number of states.
1245 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1246 of directional evolution for continuous characters. The user
1247 specifies the node(s) of the tree where the character optimum
1250 o The new function is.rooted() tests whether a tree (of class
1253 o The new function rcoal() generates random ultrametric trees with
1254 the possibility to specify the function that generates the
1255 inter-nodes distances.
1257 o The new function mrca() gives for all pairs of tips in a tree
1258 (and optionally nodes too) the most recent common ancestor.
1260 o nodelabels() has a new option `thermo' to plot proportions (up
1261 to three classes) on the nodes of a tree.
1263 o rtree() has been improved: it can now generate rooted or
1264 unrooted trees, and the mathematical function that generates the
1265 branch lengths may be specified by the user. The tip labels may
1266 be given directly in the call to rtree. The limit cases (n = 2,
1267 3) are now handled correctly.
1269 o dist.topo() has a new argument `method' with two choices: "PH85"
1270 for Penny and Henny's method (already available before and now
1271 the default), and "BHV01" for the geometric distance by Billera
1272 et al. (2001, Adv. Appl. Math. 27:733).
1274 o write.tree() has a new option, `digits', which specifies the
1275 number of digits to be printed in the Newick tree. By default
1276 digits = 10. The numbers are now always printed in decimal form
1277 (i.e., 1.0e-1 is now avoided).
1279 o dist.dna() can now compute the raw distances between pairs of
1280 DNA sequences by specifying model = "raw".
1282 o dist.phylo() has a new option `full' to possibly compute the
1283 distances among all tips and nodes of the tree. The default if
1289 o Several bugs were fixed in all.equal.phylo().
1291 o dist.dna() did not handle correctly gaps ("-") in alignments:
1292 they are now considered as missing data.
1294 o rotate() did not work if the tips were not ordered: this is
1297 o mantel.test() returned NA in some special cases: this is fixed
1298 and the function has been improved and is now faster.
1300 o A bug was fixed in diversi.gof() where the calculation of A² was
1303 o cherry() did not work correctly under some OSs (mainly Linux):
1306 o is.binary.tree() has been modified so that it works with both
1307 rooted and unrooted trees.
1309 o The documentation of theta.s() was not correct: this has been
1312 o plot.mst() did not work correctly: this is fixed.
1316 CHANGES IN APE VERSION 1.6
1321 o The new function dist.topo() computes the topological distances
1324 o The new function boot.phylo() performs a bootstrap analysis on
1325 phylogeny estimation.
1327 o The new functions prop.part() and prop.clades() analyse
1328 bipartitions from a series of trees.
1333 o read.GenBank() now uses the EFetch utility of NCBI instead of
1334 the usual Web interface: it is now much faster (e.g., 12 times
1335 faster to retrieve 8 sequences, 37 times for 60 sequences).
1340 o Several bugs were fixed in read.dna().
1342 o Several bugs were fixed in diversi.time().
1344 o is.binary.tree() did not work correctly if the tree has no edge
1345 lengths: this is fixed.
1347 o drop.tip() did not correctly propagated the `node.label' of a
1348 tree: this is fixed.
1352 CHANGES IN APE VERSION 1.5
1357 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1358 convert objects between the classes "phylo" and "matching". The
1359 latter implements the representation of binary trees introduced by
1360 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1361 as.matching() has been introduced as well.
1363 o Two new functions, multi2di() and di2multi(), allow to resolve
1364 and collapse multichotomies with branches of length zero.
1366 o The new function nuc.div() computes the nucleotide diversity
1367 from a sample a DNA sequences.
1369 o dist.dna() has been completely rewritten with a much faster
1370 (particularly for large data sets) C code. Eight models are
1371 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1372 option `method' has been renamed `model'). Computation of variance
1373 is available for all models. A gamma-correction is possible for
1374 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1375 to remove sites with missing data on a pairwise basis. The option
1376 `GCcontent' has been removed.
1378 o read.GenBank() has a new option (species.names) which specifies
1379 whether to return the species names of the organisms in addition
1380 to the accession numbers of the sequences (this is the default
1383 o write.nexus() can now write several trees in the same NEXUS file.
1385 o drop.tip() has a new option `root.edge' that allows to specify the
1386 new root edge if internal branches are trimmed.
1391 o as.phylo.hclust() failed if some labels had parentheses: this
1394 o Several bugs were fixed in all.equal.phylo(). This function now
1395 returns the logical TRUE if the trees are identical but with
1396 different representations (a report was printed previously).
1398 o read.GenBank() did not correctly handle ambiguous base codes:
1404 o birthdeath() now returns an object of class "birthdeath" for
1405 which there is a print method.
1409 CHANGES IN APE VERSION 1.4
1414 o The new function nj() performs phylogeny estimation with the
1415 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1418 o The new function which.edge() identifies the edges of a tree
1419 that belong to a group specified as a set of tips.
1421 o The new function as.phylo.phylog() converts an object of class
1422 "phylog" (from the package ade4) into an object of class
1425 o The new function axisPhylo() draws axes on the side of a
1428 o The new function howmanytrees() calculates the number of trees
1429 in different cases and giving a number of tips.
1431 o write.tree() has a new option `multi.line' (TRUE by default) to
1432 write a Newick tree on several lines rather than on a single
1435 o The functionalities of zoom() have been extended. Several
1436 subtrees can be visualized at the same time, and they are marked
1437 on the main tree with colors. The context of the subtrees can be
1438 marked with the option `subtree' (see below).
1440 o drop.tip() has a new option `subtree' (FALSE by default) which
1441 specifies whether to output in the tree how many tips have been
1444 o The arguments of add.scale.bar() have been redefined and have
1445 now default values (see ?add.scale.bar for details). This
1446 function now works even if the plotted tree has no edge length.
1448 o plot.phylo() can now plot radial trees, but this does not take
1449 edge lengths into account.
1451 o In plot.phylo() with `type = "phylogram"', if the values of
1452 `edge.color' and `edge.width' are identical for sister-branches,
1453 they are propagated to the vertical line that link them.
1458 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1459 crashing. This is fixed.
1461 o In plot.phylo(), the options `edge.color' and `edge.width' are
1462 now properly recycled; their default values are now "black" and
1465 o A bug has been fixed in write.nexus().
1470 o The function node.depth.edgelength() has been removed and
1471 replaced by a C code.
1475 CHANGES IN APE VERSION 1.3-1
1480 o The new function nodelabels() allows to add labels to the nodes
1481 of a tree using text or plotting symbols in a flexible way.
1483 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1484 numeric values specifying the lower and upper limits on the x-
1485 and y-axes. This allows to leave some space on any side of the
1486 tree. If a single value is given, this is taken as the upper
1491 CHANGES IN APE VERSION 1.3
1496 o The new function phymltest() calls the software PHYML and fits
1497 28 models of DNA sequence evolution. There are a print method to
1498 display likelihood and AIC values, a summary method to compute
1499 the hierarchical likelihood ratio tests, and a plot method to
1500 display graphically the AIC values of each model.
1502 o The new function yule.cov() fits the Yule model with covariates,
1503 a model where the speciation rate is affected by several species
1504 traits through a generalized linear model. The parameters are
1505 estimated by maximum likelihood.
1507 o Three new functions, corBrownian(), corGrafen(), and
1508 corMartins(), compute the expected correlation structures among
1509 species given a phylogeny under different models of evolution.
1510 These can be used for GLS comparative phylogenetic methods (see
1511 the examples). There are coef() and corMatrix() methods and an
1512 Initialize.corPhyl() function associated.
1514 o The new function compar.cheverud() implements Cheverud et al.'s
1515 (1985; Evolution 39:1335) phylogenetic comparative method.
1517 o The new function varcomp() estimates variance components; it has
1520 o Two new functions, panel.superpose.correlogram() and
1521 plot.correlogramList(), allow to plot several phylogenetic
1524 o The new function node.leafnumber() computes the number of leaves
1525 of a subtree defined by a particular node.
1527 o The new function node.sons() gets all tags of son nodes from a
1530 o The new function compute.brlen() computes the branch lengths of
1531 a tree according to a specified method.
1533 o plot.phylo() has three new options: "cex" controls the size of
1534 the (tip and node) labels (thus it is no more needed to change
1535 the global graphical parameter), "direction" which allows to
1536 plot the tree rightwards, leftwards, upwards, or downwards, and
1537 "y.lim" which sets the upper limit on the y-axis.
1542 o Some functions which try to match tip labels and names of
1543 additional data (e.g. vector) are likely to fail if there are
1544 typing or syntax errors. If both series of names do not perfectly
1545 match, they are ignored and a warning message is now issued.
1546 These functions are bd.ext, compar.gee, pic. Their help pages
1547 have been clarified on this point.
1551 CHANGES IN APE VERSION 1.2-7
1556 o The new function root() reroots a phylogenetic tree with respect
1557 to a specified outgroup.
1559 o The new function rotate() rotates an internal branch of a tree.
1561 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1562 trees) controls the display of the tip labels in unrooted trees.
1563 This display has been greatly improved: the tip labels are now not
1564 expected to overlap with the tree (particularly if lab4ut =
1565 "axial"). In all cases, combining appropriate values of "lab4ut"
1566 and the font size (via "par(cex = )") should result in readable
1567 unrooted trees. See ?plot.phylo for some examples.
1569 o In drop.tip(), the argument `tip' can now be numeric or character.
1574 o drop.tip() did not work correctly with trees with no branch
1575 lengths: this is fixed.
1577 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1578 plotted with some line crossings: this is now fixed.
1582 CHANGES IN APE VERSION 1.2-6
1587 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1588 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1589 to implement comparative methods with an autocorrelation approach.
1591 o A new data set describing some life history traits of Carnivores
1597 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1602 o When plotting a tree with plot.phylo(), the new default of the
1603 option `label.offset' is now 0, so the labels are always visible.
1607 CHANGES IN APE VERSION 1.2-5
1612 o The new function bd.ext() fits a birth-death model with combined
1613 phylogenetic and taxonomic data, and estimates the corresponding
1614 speciation and extinction rates.
1619 o The package gee is no more required by ape but only suggested
1620 since only the function compar.gee() calls gee.
1624 CHANGES IN APE VERSION 1.2-4
1629 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1630 and lines.popsize) implementing a new approach for inferring the
1631 demographic history from genealogies using a reversible jump
1632 MCMC have been introduced.
1634 o The unit of time in the skyline plot and in the new plots can
1635 now be chosen to be actual years, rather than substitutions.
1639 CHANGES IN APE VERSION 1.2-3
1644 o The new function rtree() generates a random binary tree with or
1645 without branch lengths.
1647 o Two new functions for drawing lineages-through-time (LTT) plots
1648 are provided: ltt.lines() adds a LTT curve to an existing plot,
1649 and mltt.plot() does a multiple LTT plot giving several trees as
1650 arguments (see `?ltt.plot' for details).
1655 o Some taxon names made R crashing when calling as.phylo.hclust():
1658 o dist.dna() returned an error with two identical DNA sequences
1659 (only using the Jukes-Cantor method returned 0): this is fixed.
1664 o The function dist.phylo() has been re-written using a different
1665 algorithm: it is now about four times faster.
1667 o The code of branching.times() has been improved: it is now about
1672 CHANGES IN APE VERSION 1.2-2
1677 o The new function seg.sites() finds the segregating sites in a
1678 sample of DNA sequences.
1683 o A bug introduced in read.tree() and in read.nexus() with version
1686 o A few errors were corrected and a few examples were added in the
1691 CHANGES IN APE VERSION 1.2-1
1696 o plot.phylo() can now draw the edge of the root of a tree if it
1697 has one (see the new option `root.edge', its default is FALSE).
1702 o A bug was fixed in read.nexus(): files with semicolons inside
1703 comment blocks were not read correctly.
1705 o The behaviour of read.tree() and read.nexus() was corrected so
1706 that tree files with badly represented root edges (e.g., with
1707 an extra pair of parentheses, see the help pages for details)
1708 are now correctly represented in the object of class "phylo";
1709 a warning message is now issued.
1713 CHANGES IN APE VERSION 1.2
1718 o plot.phylo() has been completely re-written and offers several
1719 new functionalities. Three types of trees can now be drawn:
1720 phylogram (as previously), cladogram, and unrooted tree; in
1721 all three types the branch lengths can be drawn using the edge
1722 lengths of the phylogeny or not (e.g., if the latter is absent).
1723 The vertical position of the nodes can be adjusted with two
1724 choices (see option `node.pos'). The code has been re-structured,
1725 and two new functions (potentially useful for developpers) are
1726 documented separately: node.depth.edgelength() and node.depth();
1727 see the respective help pages for details.
1729 o The new function zoom() allows to explore very large trees by
1730 focusing on a small portion of it.
1732 o The new function yule() fits by maximum likelihood the Yule model
1733 (birth-only process) to a phylogenetic tree.
1735 o Support for writing DNA sequences in FASTA format has been
1736 introduced in write.dna() (support for reading sequences in
1737 this format was introduced in read.dna() in version 1.1-2).
1738 The function has been completely re-written, fixing some bugs
1739 (see below); the default behaviour is no more to display the
1740 sequences on the standard output. Several options have been
1741 introduced to control the sequence printing in a flexible
1742 way. The help page has been extended.
1744 o A new data set is included: a supertree of bats in NEXUS format.
1749 o In theta.s(), the default of the option `variance' has
1750 been changed to `FALSE' (as was indicated in the help page).
1752 o Several bugs were fixed in the code of all.equal.phylo().
1754 o Several bugs were fixed in write.dna(), particularly this
1755 function did not work with `format = "interleaved"'.
1757 o Various errors were corrected in the help pages.
1762 o The argument names of as.hclust.phylo() have been changed
1763 from "(phy)" to "(x, ...)" to conform to the definition of
1764 the corresponding generic function.
1766 o gamma.stat() has been renamed gammaStat() to avoid confusion
1767 since gamma() is a generic function.
1771 CHANGES IN APE VERSION 1.1-3
1776 o base.freq() previously did not return a value of 0 for
1777 bases absent in the data (e.g., a vector of length 3 was
1778 returned if one base was absent). This is now fixed (a
1779 vector of length 4 is always returned).
1781 o Several bugs were fixed in read.nexus(), including that this
1782 function did not work in this absence of a "TRANSLATE"
1783 command in the NEXUS file, and that the commands were
1788 CHANGES IN APE VERSION 1.1-2
1793 o The Tamura and Nei (1993) model of DNA distance is now implemented
1794 in dist.dna(): five models are now available in this function.
1796 o A new data set is included: a set of 15 sequences of the
1797 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1803 o A bug in read.nexus() was fixed.
1805 o read.dna() previously did not work correctly in most cases.
1806 The function has been completely re-written and its help page
1807 has been considerably extended (see ?read.dna for details).
1808 Underscores (_) in taxon names are no more replaced with
1809 spaces (this behaviour was undocumented).
1811 o A bug was fixed in write.dna().
1815 CHANGES IN APE VERSION 1.1-1
1820 o A bug in read.tree() introduced in APE 1.1 was fixed.
1822 o A bug in compar.gee() resulted in an error when trying to fit
1823 a model with `family = "binomial"'. This is now fixed.
1827 CHANGES IN APE VERSION 1.1
1832 o The Klastorin (1982) method as suggested by Misawa and Tajima
1833 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1834 on the basis of phylogenetic trees has been implemented (see
1835 the function klastorin()).
1837 o Functions have been added to convert APE's "phylo" objects in
1838 "hclust" cluster objects and vice versa (see the help page of
1839 as.phylo for details).
1841 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1842 are introduced for the estimation of absolute evolutionary rates
1843 (ratogram) and dated clock-like trees (chronogram) from
1844 phylogenetic trees using the non-parametric rate smoothing approach
1845 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1847 o A summary method is now provided printing a summary information on a
1848 phylogenetic tree with, for instance, `summary(tree)'.
1850 o The behaviour of read.tree() was changed so that all spaces and
1851 tabulations in tree files are now ignored. Consequently, spaces in tip
1852 labels are no more allowed. Another side effect is that read.nexus()
1853 now does not replace the underscores (_) in tip labels with spaces
1854 (this behaviour was undocumented).
1856 o The function plot.phylo() has a new option (`underscore') which
1857 specifies whether the underscores in tip labels should be written on
1858 the plot as such or replaced with spaces (the default).
1860 o The function birthdeath() now computes 95% confidence intervals of
1861 the estimated parameters using profile likelihood.
1863 o Three new data sets are included: a gene tree estimated from 36
1864 landplant rbcL sequences, a gene tree estimated from 32 opsin
1865 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1870 o A bug was fixed in dist.gene() where nothing was returned.
1872 o A bug in plot.mst() was fixed.
1874 o A bug in vcv.phylo() resulted in false correlations when the
1875 option `cor = TRUE' was used (now fixed).
1879 CHANGES IN APE VERSION 1.0
1884 o Two new functions, read.dna() and write.dna(), read/write in a file
1885 DNA sequences in interleaved or in sequential format.
1887 o Two new functions, read.nexus() and write.nexus(), read/write trees
1890 o The new function bind.tree() allows to bind two trees together,
1891 possibly handling root edges to give internal branches.
1893 o The new function drop.tip() removes the tips in a phylogenetic tree,
1894 and trims (or not) the corresponding internal branches.
1896 o The new function is.ultrametric() tests if a tree is ultrametric.
1898 o The function plot.phylo() has more functionalities such as drawing the
1899 branches with different colours and/or different widths, showing the
1900 node labels, controling the position and font of the labels, rotating
1901 the labels, and controling the space around the plot.
1903 o The function read.tree() can now read trees with no branch length,
1904 such as "(a,b),c);". Consequently, the element `edge.length' in
1905 objects of class "phylo" is now optional.
1907 o The function write.tree() has a new default behaviour: if the default
1908 for the option `file' is used (i.e. file = ""), then a variable of
1909 mode character containing the tree in Newick format is returned which
1910 can thus be assigned (e.g., tree <- write.tree(phy)).
1912 o The function read.tree() has a new argument `text' which allows
1913 to read the tree in a variable of mode character.
1915 o A new data set is included: the phylogenetic relationships among
1916 the orders of birds from Sibley and Ahlquist (1990).
1920 CHANGES IN APE VERSION 0.2-1
1925 o Several bugs were fixed in the help pages.
1929 CHANGES IN APE VERSION 0.2
1934 o The function write.tree() writes phylogenetic trees (objects of class
1935 "phylo") in an ASCII file using the Newick parenthetic format.
1937 o The function birthdeath() fits a birth-death model to branching times
1938 by maximum likelihood, and estimates the corresponding speciation and
1941 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1944 o The function is.binary.tree() tests whether a phylogeny is binary.
1946 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1947 as well as some methods are introduced.
1949 o Several functions, including some generics and methods, for computing
1950 skyline plot estimates (classic and generalized) of effective
1951 population size through time are introduced and replace the function
1952 skyline.plot() in version 0.1.
1954 o Two data sets are now included: the phylogenetic relationships among
1955 the families of birds from Sibley and Ahlquist (1990), and an
1956 estimated clock-like phylogeny of HIV sequences sampled in the
1957 Democratic Republic of Congo.
1960 DEPRECATED & DEFUNCT
1962 o The function skyline.plot() in ape 0.1 has been deprecated and
1963 replaced by more elaborate functions (see above).
1968 o Two important bugs were fixed in plot.phylo(): phylogenies with
1969 multichotomies not at the root or not with only terminal branches,
1970 and phylogenies with a single node (i.e. only terminal branches)
1971 did not plot. These trees should be plotted correctly now.
1973 o Several bugs were fixed in diversi.time() in the computation of
1976 o Various errors were corrected in the help pages.