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.
22 o add.scale.bar() drew the bar outside the plotting region with the
23 default options with unrooted or radial trees.
27 CHANGES IN APE VERSION 2.4-1
32 o rtree() and rcoal() now accept a numeric vector for the 'br'
35 o vcv() is a new generic function with methods for the classes "phylo"
36 and "corPhyl" so that it is possible to calculate the var-cov matrix
37 for "transformation models". vcv.phylo() can still be used for trees
38 of class "phylo"; its argument 'cor' has been renamed 'corr'.
43 o bind.tree() failed when 'y' had no root edge.
45 o read.nexus() shuffled tip labels when the trees have no branch
46 lengths and there is a TRANSLATE block.
48 o read.nexus() does not try to translate node labels if there is a
49 translation table in the NEXUS file. See ?read.nexus for a
50 clarification on this behaviour.
52 o plot.multiPhylo() crashed R when plotting a list of trees with
53 compressed tip labels.
55 o write.nexus() did not translate the taxa names when asked for.
57 o plot.phylo(type = "fan") did not rotate the tip labels correctly
58 when the tree has branch lengths.
60 o ace(type = "continuous", method = "ML") now avoids sigma² being
61 negative (which resulted in an error).
63 o nj() crashed with NA/NaN in the distance matrix: an error in now
68 CHANGES IN APE VERSION 2.4
73 o base.freq() has a new option 'freq' to return the counts; the
74 default is still to return the proportions.
79 o seg.sites() did not handle ambiguous nucleotides correctly: they
82 o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
83 the tree: the argument is now ignored.
85 o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
91 o Trying to plot a tree with a single tip now returns NULL with a
92 warning (it returned an error previously).
94 o The way lines representing nodes are coloured in phylograms has
95 been modified (as well as their widths and types) following some
96 users' request; this is only for dichotomous nodes.
98 o The argument 'adj' in [node][tip][edge]labels() now works when
99 using 'pie' or 'thermo'.
101 o A more informative message error is now returned by dist.dna() when
102 'model' is badly specified (partial matching of this argument is
105 o Deprecated functions are now listed in a help page: see
106 help("ape-defunct") with the quotes.
111 o The functions heterozygosity, nuc.div, theta.h, theta.k and
112 theta.s have been moved from ape to pegas.
114 o The functions mlphylo, DNAmodel and sh.test have been removed.
118 CHANGES IN APE VERSION 2.3-3
123 o add.scale.bar() always drew a horizontal bar.
125 o zoom() shuffled tips with unrooted trees.
127 o write.nexus() failed to write correctly trees with a "TipLabel"
130 o rcoal() failed to compute branch lengths with very large n.
132 o A small bug was fixed in compar.cheverud() (thanks to Michael
135 o seg.sites() failed when passing a vector.
137 o drop.tip() sometimes shuffled tip labels.
139 o root() shuffled node labels with 'resolve.root = TRUE'.
143 CHANGES IN APE VERSION 2.3-2
148 o all.equal.phylo() did not compare unrooted trees correctly.
150 o dist.topo(... method = "PH85") did not treat unrooted trees
151 correctly (thanks to Tim Wallstrom for the fix).
153 o root() sometimes failed to test for the monophyly of the
156 o extract.clade() sometimes included too many edges.
158 o vcv.phylo() did not work correctly when the tree is in
161 o nj() did not handle correctly distance matrices with many 0's.
162 The code has also been significantly improved: 7, 70, 160 times
163 faster with n = 100, 500, 1000, respectively.
167 CHANGES IN APE VERSION 2.3-1
172 o The new function is.monophyletic tests the monophyly of a group.
174 o There is now a c() method for lists of class "DNAbin".
176 o yule.cov() now fits the null model, and its help page has been
177 corrected with respect to this change.
179 o drop.tip() has a new option 'rooted' to force (or not) a tree
180 to be treated as (un)rooted.
185 o dist.gene() failed on most occasions with the default
186 pairwise.deletion = FALSE.
188 o read.tree() failed to read correctly the tree name(s).
190 o boot.phylo() now treats correctly data frames.
192 o del.gaps() did not copy the rownames of a matrix.
194 o A small bug was fixed in CDAM.global().
196 o ace() failed with large data sets. Thanks to Rich FitzJohn for
197 the fix. With other improvements, this function is now about 6
200 o write.tree() failed with objects of class "multiPhylo".
202 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
207 o [.multiPhylo and [.DNAbin now respect the original class.
209 o Instances of the form class(phy) == "phylo" have been replaced
210 by inherits(phy, "phylo").
212 o rcoal() is now faster.
217 o klastorin() has been removed.
221 CHANGES IN APE VERSION 2.3
226 o The new functions CADM.global and CADM.post, contributed by
227 Pierre Legendre, test the congruence among several distance
230 o The new function yule.time fits a user-defined time-dependent
231 Yule model by maximum likelihood.
233 o The new function makeNodeLabel creates and/or modifies node
234 labels in a flexible way.
236 o read.tree() and write.tree() have been modified so that they can
237 handle individual tree names.
239 o plot.phylo() has a new argument 'edge.lty' that specifies the
240 types of lines used for the edges (plain, dotted, dashed, ...)
242 o phymltest() has been updated to work with PhyML 3.0.1.
247 o drop.tip() shuffled tip labels in some cases.
249 o drop.tip() did not handle node.label correctly.
251 o is.ultrametric() now checks the ordering of the edge matrix.
253 o ace() sometimes returned negative values of likelihoods of
254 ancestral states (thanks to Dan Rabosky for solving this long
260 o The data set xenarthra has been removed.
264 CHANGES IN APE VERSION 2.2-4
268 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
269 now fixed. (Thanks to Peter Wragg for the fix!)
271 o A warning message occurred for no reason with ace(method="GLS").
276 o There is now a general help page displayed with '?ape'.
280 CHANGES IN APE VERSION 2.2-3
285 o The new function extract.clade extracts a clade from a tree by
286 specifying a node number or label.
288 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
289 operations of the same names.
291 o dist.dna() can now return the number of site differences by
292 specifying model="N".
297 o chronopl() did not work with CV = TRUE.
299 o read.nexus() did not work correctly in some situations (trees on
300 multiple lines with different numbers of lines and/or with
301 comments inserted within the trees).
303 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
304 the number of lineages with non-binary trees.
309 o ape has now a namespace.
311 o drop.tip() has been improved: it should be much faster and work
312 better in some cases (e.g., see the example in ?zoom).
316 CHANGES IN APE VERSION 2.2-2
321 o dist.gene() has been substantially improved and gains an option
324 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
330 o prop.part() failed with a single tree with the default option
331 'check.labels = TRUE'.
333 o summary.DNAbin() failed to display correctly the summary of
334 sequence lengths with lists of sequences of 10,000 bases or more
335 (because summary.default uses 4 significant digits by default).
337 o read.nexus() failed to read a file with a single tree with line
338 breaks in the Newick string.
340 o del.gaps() returned a list of empty sequences when there were no
346 o phymltest() has been updated for PhyML 3.0 and gains an option
347 'append', whereas the option 'path2exec' has been removed.
349 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
350 which is returned unchanged (instead of an error).
352 o The data sets bird.orders and bird.families are now stored as
353 Newick strings; i.e., the command data(bird.orders) calls
358 CHANGES IN APE VERSION 2.2-1
363 o The new function makeLabel() helps to modify labels of trees,
364 lists of trees, or DNA sequences, with several utilities to
365 truncate and/or make them unique, substituting some
366 characters, and so on.
368 o The new function del.gaps() removes insertion gaps ("-") in a
369 set of DNA sequences.
371 o read.dna() can now read Clustal files (*.aln).
376 o root() failed with 'resolve.root = TRUE' when the root was
377 already the specified root.
379 o Several bugs were fixed in mlphylo().
381 o collapsed.singles() did not propagate the 'Nnode' and
382 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
384 o read.nexus() failed to remove correctly the comments within
387 o read.nexus() failed to read a file with a single tree and no
388 translation of tip labels.
390 o read.nexus() failed to place correctly tip labels when reading
391 a single tree with no edge lengths.
393 o A bug was fixed in sh.test().
398 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
401 o The option 'check.labels' of consensus() and prop.part() is now
404 o write.dna() now does not truncate names to 10 characters with
409 CHANGES IN APE VERSION 2.2
414 o Four new functions have been written by Damien de Vienne for the
415 graphical exploration of large trees (cophyloplot, subtrees,
416 subtreeplot), and to return the graphical coordinates of tree
419 o The new functions corPagel and corBlomberg implement the Pagel's
420 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
422 o chronopl() has been improved and gains several options: see its
423 help page for details.
425 o boot.phylo() has now an option 'trees' to possibly return the
426 bootstraped trees (the default is FALSE).
428 o prop.part() has been improved and should now be faster in all
434 o read.dna() failed if "?" occurred in the first 10 sites of the
437 o The x/y aspect of the plot is now respected when plotting a
438 circular tree (type = "r" or "f").
440 o Drawing the tip labels sometimes failed when plotting circular
443 o zoom() failed when tip labels were used instead of their numbers
444 (thanks to Yan Wong for the fix).
446 o drop.tip() failed with some trees (fixed by Yan Wong).
448 o seg.sites() failed with a list.
450 o consensus() failed in some cases. The function has been improved
451 as well and is faster.
455 CHANGES IN APE VERSION 2.1-3
460 o A bug in read.nexus() made the Windows R-GUI crash.
462 o An error was fixed in the computation of ancestral character
463 states by generalized least squares in ace().
465 o di2multi() did not modify node labels correctly.
467 o multi2di() failed if the tree had its attribute "order" set to
472 CHANGES IN APE VERSION 2.1-2
477 o There three new methods for the "multiPhylo" class: str, $,
480 o root() gains the options 'node' and 'resolve.root'
481 (FALSE by default) as well as its code being improved.
483 o mltt.plot() has now an option 'log' used in the same way
484 than in plot.default().
489 o mltt.plot() failed to display the legend with an unnamed
492 o nodelabels() with pies now correcly uses the argument
493 'cex' to draw symbols of different sizes (which has
494 worked already for thermometers).
496 o read.nexus() generally failed to read very big files.
501 o The argument 'family' of compar.gee() can now be a function
502 as well as a character string.
504 o read.tree() and read.nexus() now return an unnamed list if
507 o read.nexus() now returns a modified object of class "multiPhylo"
508 when there is a TRANSLATE block in the NEXUS file: the individual
509 trees have no 'tip.label' vector, but the list has a 'TipLabel'
510 attribute. The new methods '$' and '[[' set these elements
511 correctly when extracting trees.
515 CHANGES IN APE VERSION 2.1-1
520 o The new function rmtree generates lists of random trees.
522 o rcoal() now generates a genuine coalescent tree by default
523 (thanks to Vladimir Minin for the code).
528 o nuc.div() returned an incorrect value with the default
529 pairwise.deletion = FALSE.
534 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
535 have been improved so that they are stabler and faster.
537 o R packages used by ape are now loaded silently; lattice and gee
538 are loaded only when needed.
542 CHANGES IN APE VERSION 2.1
547 o The new function identify.phylo identifies clades on a plotted
548 tree using the mouse.
550 o It is now possible to subset a list of trees (object of class
551 "multiPhylo") with "[" while keeping its class correct.
553 o The new function as.DNAbin.alignment converts DNA sequences
554 stored in the "alignment" format of the package seqinr into
555 an object of class "DNAbin".
557 o The new function weight.taxo2 helps to build similarity matrices
558 given two taxonomic levels (usually called by other functions).
560 o write.tree() can now take a list of trees (class "multiPhylo")
561 as its main argument.
563 o plot.correlogram() and plot.correlogramList() have been
564 improved, and gain several options (see the help page for
565 details). A legend is now plotted by default.
570 o dist.dna() returned some incorrect values with `model = "JC69"'
571 and `pairwise.deletion = TRUE'. This affected only the
572 distances involving sequences with missing values. (Thanks
573 to Bruno Toupance for digging this bug out.)
575 o write.tree() failed with some trees: this is fixed by removing
576 the `multi.line' option (trees are now always printed on a
579 o read.nexus() did not correctly detect trees with multiple root
580 edges (see OTHER CHANGES).
585 o The code of mlphylo() has been almost entirely rewritten, and
586 should be much stabler. The options have been also greatly
587 simplified (see ?mlphylo and ?DNAmodel for details).
589 o The internal function nTips has been renamed klastorin_nTips.
591 o The code of is.ultrametric() contained redundancies and has
594 o The code of Moran.I() and of correlogram.formula() have been
597 o read.tree() and read.nexus() now return an error when trying to
598 read a tree with multiple root edges (see BUG FIXES). The
599 correction applied in previous version did not work in all
602 o The class c("multi.tree", "phylo") has been renamed
608 o There is now a vignette in ape: see vignette("MoranI", "ape").
613 o as.matching() and as.phylo.matching() do not support branch
616 o correlogram.phylo() and discrete.dist() have been removed.
620 CHANGES IN APE VERSION 2.0-2
625 o The new function matexpo computes the exponential of a square
628 o The new function unique.multi.tree removes duplicate trees from
631 o yule() has a new option `use.root.edge = FALSE' that specifies
632 to ignore, by default, the root edge of the tree if it exists.
637 o which.edge() failed when the index of a single terminal edge was
640 o In diversi.time(), the values returned for model C were
643 o A bug was fixed in yule() that affected the calculation of the
644 likelihood in the presence of ties in the branching times.
646 o There was a bug in the C function mat_expo4x4 affecting the
647 calculations of the transition probabilities for models HKY and
650 o A small bug was fixed in as.matrix.DNAbin (thanks to James
653 o rtree() did not `shuffle' the tip labels by default, so only a
654 limited number of labelled topologies could be generated.
658 CHANGES IN APE VERSION 2.0-1
663 o The three new functions bionj, fastme.ols, and fastme.bal
664 perform phylogeny estimation by the BIONJ and fastME methods in
665 OLS and balanced versions. This is a port to R of previous
666 previous programs done by Vincent Lefort.
668 o The new function chronoMPL performs molecular dating with the
669 mean path lengths method of Britton et al. (2002, Mol. Phyl.
672 o The new function rotate, contributed by Christoph Heibl, swaps
673 two clades connected to the same node. It works also with
674 multichotomous nodes.
676 o The new `method' as.matrix.DNAbin() may be used to convert
677 easily DNA sequences stored in a list into a matrix while
678 keeping the names and the class.
683 o chronopl() failed when some branch lengths were equal to zero:
684 an error message is now returned.
686 o di2multi() failed when there was a series of consecutive edges
691 CHANGES IN APE VERSION 1.10-2
696 o plot.phylo() can now plot circular trees: the option is type =
697 "fan" or type = "f" (to avoid the ambiguity with type = "c").
699 o prop.part() has a new option `check.labels = FALSE' which allows
700 to considerably speed-up the calculations of bipartitions. As a
701 consequence, calculations of bootstrap values with boot.phylo()
702 should be much faster.
707 o read.GenBank() did not return correctly the list of species as
708 from ape 1.10: this is fixed in this version
710 o Applying as.phylo() on a tree of class "phylo" failed: the
711 object is now returned unchanged.
715 CHANGES IN APE VERSION 1.10-1
720 o The three new functions Ntip, Nnode, and Nedge return, for a
721 given tree, the number of tips, nodes, or edges, respectively.
726 o read.nexus() did not set correctly the class of the returned
727 object when reading multiple trees.
729 o mllt.plot() failed with objects of class c("multi.tree",
732 o unroot() did not work correctly in most cases.
734 o reorder.phylo() made R freeze in some occasions.
736 o Plotting a tree in pruningwise order failed.
738 o When plotting an unrooted tree, the tip labels where not all
739 correctly positioned if the option `cex' was used.
743 CHANGES IN APE VERSION 1.10
748 o Five new `method' functions have been introduced to manipulate
749 DNA sequences in binary format (see below).
751 o Three new functions have been introduced to convert between the
752 new binary and the character formats.
754 o The new function as.alignment converts DNA sequences stored as
755 single characters into the class "alignment" used by the package
758 o read.dna() and read.GenBank() have a new argument `as.character'
759 controlling whether the sequences are returned in binary format
765 o root() failed when the tree had node labels: this is fixed.
767 o plot.phylo() did not correctly set the limits on the y-axis with
768 the default setting: this is fixed.
770 o dist.dna() returned a wrong result for the LogDet, paralinear,
771 and BH87 models with `pairwise.deletion = TRUE'.
776 o DNA sequences are now internally stored in a binary format. See
777 the document "A Bit-Level Coding Scheme for Nucleotides" for the
778 details. Most functions analyzing DNA functions have been
779 modified accordingly and are now much faster (dist.dna is now
780 ca. 60 times faster).
784 CHANGES IN APE VERSION 1.9-4
789 o A bug was fixed in edgelabels().
791 o as.phylo.hclust() did not work correctly when the object of
792 class "hclust" has its labels set to NULL: the returned tree has
793 now its tip labels set to "1", "2", ...
795 o consensus could fail if some tip labels are a subset of others
796 (e.g., "a" and "a_1"): this is now fixed.
798 o mlphylo() failed in most cases if some branch lengths of the
799 initial tree were greater than one: an error message is now
802 o mlphylo() failed in most cases when estimating the proportion of
803 invariants: this is fixed.
807 CHANGES IN APE VERSION 1.9-3
812 o The new function edgelabels adds labels on the edge of the tree
813 in the same way than nodelabels or tiplabels.
818 o multi2di() did not handle correctly branch lengths with the
819 default option `random = TRUE': this is now fixed.
821 o A bug was fixed in nuc.div() when using pairwise deletions.
823 o A bug occurred in the analysis of bipartitions with large
824 numbers of large trees, with consequences on prop.part,
825 prop.clades, and boot.phylo.
827 o The calculation of the Billera-Holmes-Vogtmann distance in
828 dist.topo was wrong: this has been fixed.
832 CHANGES IN APE VERSION 1.9-2
837 o The new function ladderize reorganizes the internal structure of
838 a tree to plot them left- or right-ladderized.
840 o The new function dist.nodes computes the patristic distances
841 between all nodes, internal and terminal, of a tree. It replaces
842 the option `full = TRUE' of cophenetic.phylo (see below).
847 o A bug was fixed in old2new.phylo().
849 o Some bugs were fixed in chronopl().
851 o The edge colours were not correctly displayed by plot.phylo
852 (thank you to Li-San Wang for the fix).
854 o cophenetic.phylo() failed with multichotomous trees: this is
860 o read.dna() now returns the sequences in a matrix if they are
861 aligned (interleaved or sequential format). Sequences in FASTA
862 format are still returned in a list.
864 o The option `full' of cophenetic.phylo() has been removed because
865 it could not be used from the generic.
870 o rotate() has been removed; this function did not work correctly
875 CHANGES IN APE VERSION 1.9-1
880 o Trees with a single tip were not read correctly in R as the
881 element `Nnode' was not set: this is fixed.
883 o unroot() did not set correctly the number of nodes of the
884 unrooted tree in most cases.
886 o read.GenBank() failed when fetching very long sequences,
887 particularly of the BX-series.
889 o A bug was introduced in read.tree() with ape 1.9: it has been
894 CHANGES IN APE VERSION 1.9
899 o There are two new print `methods' for trees of class "phylo" and
900 lists of trees of class "multi.tree", so that they are now
901 displayed in a compact and informative way.
903 o There are two new functions, old2new.phylo and new2old.phylo,
904 for converting between the old and new coding of the class
907 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
908 LogDet ("logdet"), and paralinear ("paralin").
910 o compute.brlen() has been extended: several methods are now
911 available to compute branch lengths.
913 o write.dna() can now handle matrices as well as lists.
918 o cophenetic.phylo() sometimes returned a wrong result with
919 multichotomous trees: this is fixed.
921 o rotate() failed when a single tip was specified: the tree is now
924 o ace() did not return the correct index matrix with custom
925 models: this is fixed.
927 o multi2di() did not work correctly when resolving multichotomies
928 randomly: the topology was always the same, only the arrangement
929 of clades was randomized: this is fixed. This function now
930 accepts trees with no branch lengths.
932 o The output of diversi.gof() was blurred by useless prints when a
933 user distribution was specified. This has been corrected, and
934 the help page of this function has been expanded.
939 o The internal structure of the class "phylo" has been changed:
940 see the document "Definition of Formats for Coding Phylogenetic
941 Trees in R" for the details. In addition, the code of most
942 functions has been improved.
944 o Several functions have been improved by replacing some R codes
945 by C codes: pic, plot.phylo, and reorder.phylo.
947 o There is now a citation information: see citation("ape") in R.
949 o write.tree() now does not add extra 0's to branch lengths so
950 that 1.23 is printed "1.23" by default, not "1.2300000000".
952 o The syntax of bind.tree() has been simplified. This function now
953 accepts trees with no branch lengths, and handles correctly node
956 o The option `as.numeric' of mrca() has been removed.
958 o The unused options `format' and `rooted' of read.tree() have
961 o The unused option `format' of write.tree() has been removed.
963 o The use of node.depth() has been simplified.
967 CHANGES IN APE VERSION 1.8-5
972 o Two new functions read.nexus.data() and write.nexus.data(),
973 contributed by Johan Nylander, allow to read and write molecular
974 sequences in NEXUS files.
976 o The new function reorder.phylo() reorders the internal structure
977 of a tree of class "phylo". It is used as the generic, e.g.,
980 o read.tree() and read.nexus() can now read trees with a single
983 o The new data set `cynipids' supplies a set of protein sequences
989 o The code of all.equal.phylo() has been completely rewritten
990 (thanks to Benoît Durand) which fixes several bugs.
992 o read.tree() and read.nexus() now checks the labels of the tree
993 to remove or substitute any characters that are illegal in the
994 Newick format (parentheses, etc.)
996 o A negative P-value could be returned by mantel.test(): this is
1001 CHANGES IN APE VERSION 1.8-4
1006 o The new function sh.test() computes the Shimodaira-
1009 o The new function collapse.singles() removes the nodes with a
1010 single descendant from a tree.
1012 o plot.phylo() has a new argument `tip.color' to specify the
1013 colours of the tips.
1015 o mlphylo() has now an option `quiet' to control the display of
1016 the progress of the analysis (the default is FALSE).
1021 o read.dna() did not read correctly sequences in sequential format
1022 with leading alignment gaps "-": this is fixed.
1024 o ace() returned a list with no class so that the generic
1025 functions (anova, logLik, ...) could not be used directly. This
1026 is fixed as ace() now returns an object of class "ace".
1028 o anova.ace() had a small bug when computing the number of degrees
1029 of freedom: this is fixed.
1031 o mlphylo() did not work when the sequences were in a matrix or
1032 a data frame: this is fixed.
1034 o rtree() did not work correctly when trying to simulate an
1035 unrooted tree with two tips: an error message is now issued.
1040 o The algorithm of rtree() has been changed: it is now about 40,
1041 100, and 130 times faster for 10, 100, and 1000 tips,
1046 CHANGES IN APE VERSION 1.8-3
1051 o There are four new `method' functions to be used with the
1052 results of ace(): logLik(), deviance(), AIC(), and anova().
1054 o The plot method of phymltest has two new arguments: `main' to
1055 change the title, and `col' to control the colour of the
1056 segments showing the AIC values.
1058 o ace() has a new argument `ip' that gives the initial values used
1059 in the ML estimation with discrete characters (see the examples
1060 in ?ace). This function now returns a matrix giving the indices
1061 of the estimated rates when analysing discrete characters.
1063 o nodelabels() and tiplabels() have a new argument `pie' to
1064 represent proportions, with any number of categories, as
1065 piecharts. The use of the option `thermo' has been improved:
1066 there is now no limitation on the number of categories.
1071 o mlphylo() did not work with more than two partitions: this is
1074 o root() failed if the proposed outgroup was already an outgroup
1075 in the tree: this is fixed.
1077 o The `col' argument in nodelabels() and tiplabels() was not
1078 correctly passed when `text' was used: this is fixed.
1080 o Two bugs were fixed in mlphylo(): parameters were not always
1081 correctly output, and the estimation failed in some cases.
1083 o plot.phylo() was stuck when given a tree with a single tip: this
1084 is fixed and a message error is now returned.
1086 o An error was corrected in the help page of gammaStat regarding
1087 the calculation of P-values.
1089 o Using gls() could crash R when the number of species in the tree
1090 and in the variables were different: this is fixed.
1094 CHANGES IN APE VERSION 1.8-2
1099 o The new function mlphylo() fits a phylogenetic tree by maximum
1100 likelihood from DNA sequences. Its companion function DNAmodel()
1101 is used to define the substitution model which may include
1102 partitioning. There are methods for logLik(), deviance(), and
1103 AIC(), and the summary() method has been extended to display in
1104 a friendly way the results of this model fitting. Currently, the
1105 functionality is limited to estimating the substitution and
1106 associated parameters and computing the likelihood.
1108 o The new function drop1.compar.gee (used as, e.g., drop1(m))
1109 tests for single effects in GEE-based comparative method. A
1110 warning message is printed if there is not enough degrees of
1116 o An error message was sometimes issued by plot.multi.tree(),
1117 though with no consequence.
1121 CHANGES IN APE VERSION 1.8-1
1126 o There is a new plot method for lists of trees (objects of class
1127 "multi.tree"): it calls plot.phylo() internally and is
1128 documented on the same help page.
1133 o A bug was fixed in the C code that analyzes bipartitions: this
1134 has impact on several functions like prop.part, prop.clades,
1135 boot.phylo, or consensus.
1137 o root() did not work correctly when the specified outgroup had
1138 more than one element: this is fixed.
1140 o dist.dna() sometimes returned a warning inappropriately: this
1143 o If the distance object given to nj() had no rownames, nj()
1144 returned a tree with no tip labels: it now returns tips labelled
1145 "1", "2", ..., corresponding to the row numbers.
1150 o nj() has been slightly changed so that tips with a zero distance
1151 are first aggregated with zero-lengthed branches; the usual NJ
1152 procedure is then performed on a distance matrix without 0's.
1156 CHANGES IN APE VERSION 1.8
1161 o The new function chronopl() estimates dates using the penalized
1162 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1164 o The new function consensus() calculates the consensus tree of a
1167 o The new function evolve.phylo() simulates the evolution of
1168 continuous characters along a phylogeny under a Brownian model.
1170 o The new plot method for objects of class "ancestral" displays a
1171 tree together with ancestral values, as returned by the above
1174 o The new function as.phylo.formula() returns a phylogeny from a
1175 set of nested taxonomic variables given as a formula.
1177 o The new function read.caic() reads trees in CAIC format.
1179 o The new function tiplabels() allows to add labels to the tips
1180 of a tree using text or plotting symbols in a flexible way.
1182 o The new function unroot() unroots a phylogeny.
1184 o multi2di() has a new option, `random', which specifies whether
1185 to resolve the multichotomies randomly (the default) or not.
1187 o prop.part() now returns an object of class "prop.part" for which
1188 there are print (to display a partition in a more friendly way)
1189 and summary (to extract the numbers) methods.
1191 o plot.phylo() has a new option, `show.tip.label', specifying
1192 whether to print the labels of the tips. The default is TRUE.
1194 o The code of nj() has been replaced by a faster C code: it is now
1195 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1198 o write.nexus() now writes whether a tree is rooted or not.
1203 o Two bugs have been fixed in root(): unrooted trees are now
1204 handled corretly, and node labels are now output normally.
1206 o A bug was fixed in phymltest(): the executable couldn't be found
1209 o Three bug have been fixed in ace(): computing the likelihood of
1210 ancestral states of discrete characters failed, custom models
1211 did not work, and the function failed with a null gradient (a
1212 warning message is now returned; this latter bug was also
1213 present in yule.cov() as well and is now fixed).
1215 o pic() hanged out when missing data were present: a message error
1218 o A small bug was fixed in dist.dna() where the gamma correction
1219 was not always correctly dispatched.
1221 o plot.phylo() plotted correctly the root edge only when the tree
1222 was plotted rightwards: this works now for all directions.
1227 o dist.taxo() has been renamed as weight.taxo().
1229 o Various error and warning messages have been improved.
1233 CHANGES IN APE VERSION 1.7
1236 o The new function ace() estimates ancestral character states for
1237 continuous characters (with ML, GLS, and contrasts methods), and
1238 discrete characters (with ML only) for any number of states.
1240 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1241 of directional evolution for continuous characters. The user
1242 specifies the node(s) of the tree where the character optimum
1245 o The new function is.rooted() tests whether a tree (of class
1248 o The new function rcoal() generates random ultrametric trees with
1249 the possibility to specify the function that generates the
1250 inter-nodes distances.
1252 o The new function mrca() gives for all pairs of tips in a tree
1253 (and optionally nodes too) the most recent common ancestor.
1255 o nodelabels() has a new option `thermo' to plot proportions (up
1256 to three classes) on the nodes of a tree.
1258 o rtree() has been improved: it can now generate rooted or
1259 unrooted trees, and the mathematical function that generates the
1260 branch lengths may be specified by the user. The tip labels may
1261 be given directly in the call to rtree. The limit cases (n = 2,
1262 3) are now handled correctly.
1264 o dist.topo() has a new argument `method' with two choices: "PH85"
1265 for Penny and Henny's method (already available before and now
1266 the default), and "BHV01" for the geometric distance by Billera
1267 et al. (2001, Adv. Appl. Math. 27:733).
1269 o write.tree() has a new option, `digits', which specifies the
1270 number of digits to be printed in the Newick tree. By default
1271 digits = 10. The numbers are now always printed in decimal form
1272 (i.e., 1.0e-1 is now avoided).
1274 o dist.dna() can now compute the raw distances between pairs of
1275 DNA sequences by specifying model = "raw".
1277 o dist.phylo() has a new option `full' to possibly compute the
1278 distances among all tips and nodes of the tree. The default if
1284 o Several bugs were fixed in all.equal.phylo().
1286 o dist.dna() did not handle correctly gaps ("-") in alignments:
1287 they are now considered as missing data.
1289 o rotate() did not work if the tips were not ordered: this is
1292 o mantel.test() returned NA in some special cases: this is fixed
1293 and the function has been improved and is now faster.
1295 o A bug was fixed in diversi.gof() where the calculation of A² was
1298 o cherry() did not work correctly under some OSs (mainly Linux):
1301 o is.binary.tree() has been modified so that it works with both
1302 rooted and unrooted trees.
1304 o The documentation of theta.s() was not correct: this has been
1307 o plot.mst() did not work correctly: this is fixed.
1311 CHANGES IN APE VERSION 1.6
1316 o The new function dist.topo() computes the topological distances
1319 o The new function boot.phylo() performs a bootstrap analysis on
1320 phylogeny estimation.
1322 o The new functions prop.part() and prop.clades() analyse
1323 bipartitions from a series of trees.
1328 o read.GenBank() now uses the EFetch utility of NCBI instead of
1329 the usual Web interface: it is now much faster (e.g., 12 times
1330 faster to retrieve 8 sequences, 37 times for 60 sequences).
1335 o Several bugs were fixed in read.dna().
1337 o Several bugs were fixed in diversi.time().
1339 o is.binary.tree() did not work correctly if the tree has no edge
1340 lengths: this is fixed.
1342 o drop.tip() did not correctly propagated the `node.label' of a
1343 tree: this is fixed.
1347 CHANGES IN APE VERSION 1.5
1352 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1353 convert objects between the classes "phylo" and "matching". The
1354 latter implements the representation of binary trees introduced by
1355 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1356 as.matching() has been introduced as well.
1358 o Two new functions, multi2di() and di2multi(), allow to resolve
1359 and collapse multichotomies with branches of length zero.
1361 o The new function nuc.div() computes the nucleotide diversity
1362 from a sample a DNA sequences.
1364 o dist.dna() has been completely rewritten with a much faster
1365 (particularly for large data sets) C code. Eight models are
1366 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1367 option `method' has been renamed `model'). Computation of variance
1368 is available for all models. A gamma-correction is possible for
1369 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1370 to remove sites with missing data on a pairwise basis. The option
1371 `GCcontent' has been removed.
1373 o read.GenBank() has a new option (species.names) which specifies
1374 whether to return the species names of the organisms in addition
1375 to the accession numbers of the sequences (this is the default
1378 o write.nexus() can now write several trees in the same NEXUS file.
1380 o drop.tip() has a new option `root.edge' that allows to specify the
1381 new root edge if internal branches are trimmed.
1386 o as.phylo.hclust() failed if some labels had parentheses: this
1389 o Several bugs were fixed in all.equal.phylo(). This function now
1390 returns the logical TRUE if the trees are identical but with
1391 different representations (a report was printed previously).
1393 o read.GenBank() did not correctly handle ambiguous base codes:
1399 o birthdeath() now returns an object of class "birthdeath" for
1400 which there is a print method.
1404 CHANGES IN APE VERSION 1.4
1409 o The new function nj() performs phylogeny estimation with the
1410 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1413 o The new function which.edge() identifies the edges of a tree
1414 that belong to a group specified as a set of tips.
1416 o The new function as.phylo.phylog() converts an object of class
1417 "phylog" (from the package ade4) into an object of class
1420 o The new function axisPhylo() draws axes on the side of a
1423 o The new function howmanytrees() calculates the number of trees
1424 in different cases and giving a number of tips.
1426 o write.tree() has a new option `multi.line' (TRUE by default) to
1427 write a Newick tree on several lines rather than on a single
1430 o The functionalities of zoom() have been extended. Several
1431 subtrees can be visualized at the same time, and they are marked
1432 on the main tree with colors. The context of the subtrees can be
1433 marked with the option `subtree' (see below).
1435 o drop.tip() has a new option `subtree' (FALSE by default) which
1436 specifies whether to output in the tree how many tips have been
1439 o The arguments of add.scale.bar() have been redefined and have
1440 now default values (see ?add.scale.bar for details). This
1441 function now works even if the plotted tree has no edge length.
1443 o plot.phylo() can now plot radial trees, but this does not take
1444 edge lengths into account.
1446 o In plot.phylo() with `type = "phylogram"', if the values of
1447 `edge.color' and `edge.width' are identical for sister-branches,
1448 they are propagated to the vertical line that link them.
1453 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1454 crashing. This is fixed.
1456 o In plot.phylo(), the options `edge.color' and `edge.width' are
1457 now properly recycled; their default values are now "black" and
1460 o A bug has been fixed in write.nexus().
1465 o The function node.depth.edgelength() has been removed and
1466 replaced by a C code.
1470 CHANGES IN APE VERSION 1.3-1
1475 o The new function nodelabels() allows to add labels to the nodes
1476 of a tree using text or plotting symbols in a flexible way.
1478 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1479 numeric values specifying the lower and upper limits on the x-
1480 and y-axes. This allows to leave some space on any side of the
1481 tree. If a single value is given, this is taken as the upper
1486 CHANGES IN APE VERSION 1.3
1491 o The new function phymltest() calls the software PHYML and fits
1492 28 models of DNA sequence evolution. There are a print method to
1493 display likelihood and AIC values, a summary method to compute
1494 the hierarchical likelihood ratio tests, and a plot method to
1495 display graphically the AIC values of each model.
1497 o The new function yule.cov() fits the Yule model with covariates,
1498 a model where the speciation rate is affected by several species
1499 traits through a generalized linear model. The parameters are
1500 estimated by maximum likelihood.
1502 o Three new functions, corBrownian(), corGrafen(), and
1503 corMartins(), compute the expected correlation structures among
1504 species given a phylogeny under different models of evolution.
1505 These can be used for GLS comparative phylogenetic methods (see
1506 the examples). There are coef() and corMatrix() methods and an
1507 Initialize.corPhyl() function associated.
1509 o The new function compar.cheverud() implements Cheverud et al.'s
1510 (1985; Evolution 39:1335) phylogenetic comparative method.
1512 o The new function varcomp() estimates variance components; it has
1515 o Two new functions, panel.superpose.correlogram() and
1516 plot.correlogramList(), allow to plot several phylogenetic
1519 o The new function node.leafnumber() computes the number of leaves
1520 of a subtree defined by a particular node.
1522 o The new function node.sons() gets all tags of son nodes from a
1525 o The new function compute.brlen() computes the branch lengths of
1526 a tree according to a specified method.
1528 o plot.phylo() has three new options: "cex" controls the size of
1529 the (tip and node) labels (thus it is no more needed to change
1530 the global graphical parameter), "direction" which allows to
1531 plot the tree rightwards, leftwards, upwards, or downwards, and
1532 "y.lim" which sets the upper limit on the y-axis.
1537 o Some functions which try to match tip labels and names of
1538 additional data (e.g. vector) are likely to fail if there are
1539 typing or syntax errors. If both series of names do not perfectly
1540 match, they are ignored and a warning message is now issued.
1541 These functions are bd.ext, compar.gee, pic. Their help pages
1542 have been clarified on this point.
1546 CHANGES IN APE VERSION 1.2-7
1551 o The new function root() reroots a phylogenetic tree with respect
1552 to a specified outgroup.
1554 o The new function rotate() rotates an internal branch of a tree.
1556 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1557 trees) controls the display of the tip labels in unrooted trees.
1558 This display has been greatly improved: the tip labels are now not
1559 expected to overlap with the tree (particularly if lab4ut =
1560 "axial"). In all cases, combining appropriate values of "lab4ut"
1561 and the font size (via "par(cex = )") should result in readable
1562 unrooted trees. See ?plot.phylo for some examples.
1564 o In drop.tip(), the argument `tip' can now be numeric or character.
1569 o drop.tip() did not work correctly with trees with no branch
1570 lengths: this is fixed.
1572 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1573 plotted with some line crossings: this is now fixed.
1577 CHANGES IN APE VERSION 1.2-6
1582 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1583 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1584 to implement comparative methods with an autocorrelation approach.
1586 o A new data set describing some life history traits of Carnivores
1592 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1597 o When plotting a tree with plot.phylo(), the new default of the
1598 option `label.offset' is now 0, so the labels are always visible.
1602 CHANGES IN APE VERSION 1.2-5
1607 o The new function bd.ext() fits a birth-death model with combined
1608 phylogenetic and taxonomic data, and estimates the corresponding
1609 speciation and extinction rates.
1614 o The package gee is no more required by ape but only suggested
1615 since only the function compar.gee() calls gee.
1619 CHANGES IN APE VERSION 1.2-4
1624 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1625 and lines.popsize) implementing a new approach for inferring the
1626 demographic history from genealogies using a reversible jump
1627 MCMC have been introduced.
1629 o The unit of time in the skyline plot and in the new plots can
1630 now be chosen to be actual years, rather than substitutions.
1634 CHANGES IN APE VERSION 1.2-3
1639 o The new function rtree() generates a random binary tree with or
1640 without branch lengths.
1642 o Two new functions for drawing lineages-through-time (LTT) plots
1643 are provided: ltt.lines() adds a LTT curve to an existing plot,
1644 and mltt.plot() does a multiple LTT plot giving several trees as
1645 arguments (see `?ltt.plot' for details).
1650 o Some taxon names made R crashing when calling as.phylo.hclust():
1653 o dist.dna() returned an error with two identical DNA sequences
1654 (only using the Jukes-Cantor method returned 0): this is fixed.
1659 o The function dist.phylo() has been re-written using a different
1660 algorithm: it is now about four times faster.
1662 o The code of branching.times() has been improved: it is now about
1667 CHANGES IN APE VERSION 1.2-2
1672 o The new function seg.sites() finds the segregating sites in a
1673 sample of DNA sequences.
1678 o A bug introduced in read.tree() and in read.nexus() with version
1681 o A few errors were corrected and a few examples were added in the
1686 CHANGES IN APE VERSION 1.2-1
1691 o plot.phylo() can now draw the edge of the root of a tree if it
1692 has one (see the new option `root.edge', its default is FALSE).
1697 o A bug was fixed in read.nexus(): files with semicolons inside
1698 comment blocks were not read correctly.
1700 o The behaviour of read.tree() and read.nexus() was corrected so
1701 that tree files with badly represented root edges (e.g., with
1702 an extra pair of parentheses, see the help pages for details)
1703 are now correctly represented in the object of class "phylo";
1704 a warning message is now issued.
1708 CHANGES IN APE VERSION 1.2
1713 o plot.phylo() has been completely re-written and offers several
1714 new functionalities. Three types of trees can now be drawn:
1715 phylogram (as previously), cladogram, and unrooted tree; in
1716 all three types the branch lengths can be drawn using the edge
1717 lengths of the phylogeny or not (e.g., if the latter is absent).
1718 The vertical position of the nodes can be adjusted with two
1719 choices (see option `node.pos'). The code has been re-structured,
1720 and two new functions (potentially useful for developpers) are
1721 documented separately: node.depth.edgelength() and node.depth();
1722 see the respective help pages for details.
1724 o The new function zoom() allows to explore very large trees by
1725 focusing on a small portion of it.
1727 o The new function yule() fits by maximum likelihood the Yule model
1728 (birth-only process) to a phylogenetic tree.
1730 o Support for writing DNA sequences in FASTA format has been
1731 introduced in write.dna() (support for reading sequences in
1732 this format was introduced in read.dna() in version 1.1-2).
1733 The function has been completely re-written, fixing some bugs
1734 (see below); the default behaviour is no more to display the
1735 sequences on the standard output. Several options have been
1736 introduced to control the sequence printing in a flexible
1737 way. The help page has been extended.
1739 o A new data set is included: a supertree of bats in NEXUS format.
1744 o In theta.s(), the default of the option `variance' has
1745 been changed to `FALSE' (as was indicated in the help page).
1747 o Several bugs were fixed in the code of all.equal.phylo().
1749 o Several bugs were fixed in write.dna(), particularly this
1750 function did not work with `format = "interleaved"'.
1752 o Various errors were corrected in the help pages.
1757 o The argument names of as.hclust.phylo() have been changed
1758 from "(phy)" to "(x, ...)" to conform to the definition of
1759 the corresponding generic function.
1761 o gamma.stat() has been renamed gammaStat() to avoid confusion
1762 since gamma() is a generic function.
1766 CHANGES IN APE VERSION 1.1-3
1771 o base.freq() previously did not return a value of 0 for
1772 bases absent in the data (e.g., a vector of length 3 was
1773 returned if one base was absent). This is now fixed (a
1774 vector of length 4 is always returned).
1776 o Several bugs were fixed in read.nexus(), including that this
1777 function did not work in this absence of a "TRANSLATE"
1778 command in the NEXUS file, and that the commands were
1783 CHANGES IN APE VERSION 1.1-2
1788 o The Tamura and Nei (1993) model of DNA distance is now implemented
1789 in dist.dna(): five models are now available in this function.
1791 o A new data set is included: a set of 15 sequences of the
1792 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1798 o A bug in read.nexus() was fixed.
1800 o read.dna() previously did not work correctly in most cases.
1801 The function has been completely re-written and its help page
1802 has been considerably extended (see ?read.dna for details).
1803 Underscores (_) in taxon names are no more replaced with
1804 spaces (this behaviour was undocumented).
1806 o A bug was fixed in write.dna().
1810 CHANGES IN APE VERSION 1.1-1
1815 o A bug in read.tree() introduced in APE 1.1 was fixed.
1817 o A bug in compar.gee() resulted in an error when trying to fit
1818 a model with `family = "binomial"'. This is now fixed.
1822 CHANGES IN APE VERSION 1.1
1827 o The Klastorin (1982) method as suggested by Misawa and Tajima
1828 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1829 on the basis of phylogenetic trees has been implemented (see
1830 the function klastorin()).
1832 o Functions have been added to convert APE's "phylo" objects in
1833 "hclust" cluster objects and vice versa (see the help page of
1834 as.phylo for details).
1836 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1837 are introduced for the estimation of absolute evolutionary rates
1838 (ratogram) and dated clock-like trees (chronogram) from
1839 phylogenetic trees using the non-parametric rate smoothing approach
1840 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1842 o A summary method is now provided printing a summary information on a
1843 phylogenetic tree with, for instance, `summary(tree)'.
1845 o The behaviour of read.tree() was changed so that all spaces and
1846 tabulations in tree files are now ignored. Consequently, spaces in tip
1847 labels are no more allowed. Another side effect is that read.nexus()
1848 now does not replace the underscores (_) in tip labels with spaces
1849 (this behaviour was undocumented).
1851 o The function plot.phylo() has a new option (`underscore') which
1852 specifies whether the underscores in tip labels should be written on
1853 the plot as such or replaced with spaces (the default).
1855 o The function birthdeath() now computes 95% confidence intervals of
1856 the estimated parameters using profile likelihood.
1858 o Three new data sets are included: a gene tree estimated from 36
1859 landplant rbcL sequences, a gene tree estimated from 32 opsin
1860 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1865 o A bug was fixed in dist.gene() where nothing was returned.
1867 o A bug in plot.mst() was fixed.
1869 o A bug in vcv.phylo() resulted in false correlations when the
1870 option `cor = TRUE' was used (now fixed).
1874 CHANGES IN APE VERSION 1.0
1879 o Two new functions, read.dna() and write.dna(), read/write in a file
1880 DNA sequences in interleaved or in sequential format.
1882 o Two new functions, read.nexus() and write.nexus(), read/write trees
1885 o The new function bind.tree() allows to bind two trees together,
1886 possibly handling root edges to give internal branches.
1888 o The new function drop.tip() removes the tips in a phylogenetic tree,
1889 and trims (or not) the corresponding internal branches.
1891 o The new function is.ultrametric() tests if a tree is ultrametric.
1893 o The function plot.phylo() has more functionalities such as drawing the
1894 branches with different colours and/or different widths, showing the
1895 node labels, controling the position and font of the labels, rotating
1896 the labels, and controling the space around the plot.
1898 o The function read.tree() can now read trees with no branch length,
1899 such as "(a,b),c);". Consequently, the element `edge.length' in
1900 objects of class "phylo" is now optional.
1902 o The function write.tree() has a new default behaviour: if the default
1903 for the option `file' is used (i.e. file = ""), then a variable of
1904 mode character containing the tree in Newick format is returned which
1905 can thus be assigned (e.g., tree <- write.tree(phy)).
1907 o The function read.tree() has a new argument `text' which allows
1908 to read the tree in a variable of mode character.
1910 o A new data set is included: the phylogenetic relationships among
1911 the orders of birds from Sibley and Ahlquist (1990).
1915 CHANGES IN APE VERSION 0.2-1
1920 o Several bugs were fixed in the help pages.
1924 CHANGES IN APE VERSION 0.2
1929 o The function write.tree() writes phylogenetic trees (objects of class
1930 "phylo") in an ASCII file using the Newick parenthetic format.
1932 o The function birthdeath() fits a birth-death model to branching times
1933 by maximum likelihood, and estimates the corresponding speciation and
1936 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1939 o The function is.binary.tree() tests whether a phylogeny is binary.
1941 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1942 as well as some methods are introduced.
1944 o Several functions, including some generics and methods, for computing
1945 skyline plot estimates (classic and generalized) of effective
1946 population size through time are introduced and replace the function
1947 skyline.plot() in version 0.1.
1949 o Two data sets are now included: the phylogenetic relationships among
1950 the families of birds from Sibley and Ahlquist (1990), and an
1951 estimated clock-like phylogeny of HIV sequences sampled in the
1952 Democratic Republic of Congo.
1955 DEPRECATED & DEFUNCT
1957 o The function skyline.plot() in ape 0.1 has been deprecated and
1958 replaced by more elaborate functions (see above).
1963 o Two important bugs were fixed in plot.phylo(): phylogenies with
1964 multichotomies not at the root or not with only terminal branches,
1965 and phylogenies with a single node (i.e. only terminal branches)
1966 did not plot. These trees should be plotted correctly now.
1968 o Several bugs were fixed in diversi.time() in the computation of
1971 o Various errors were corrected in the help pages.
projects / ape.git / blob