1 CHANGES IN APE VERSION 2.5-1
6 o rTraitDisc() did not use its 'freq' argument correctly (it was
7 multiplied with the rate matrix column-wise instead of row-wise).
11 CHANGES IN APE VERSION 2.5
16 o The new function parafit by Pierre Legendre tests for the
17 coevolution between hosts and parasites. It has a companion
18 function, pcoa, that does principal coordinate decomposition.
19 The latter has a biplot method.
21 o The new function lmorigin by Pierre Legendre performs multiple
22 regression through the origin with testing by permutation.
24 o The new functions rTraitCont and rTraitDisc simulate continuous and
25 discrete traits under a wide range of evolutionary models.
27 o The new function delta.plot does a delta plot following Holland et
28 al. (2002, Mol. Biol. Evol. 12:2051).
30 o The new function edges draws additional branches between any nodes
31 and/or tips on a plotted tree.
33 o The new function fancyarrows enhances arrows from graphics with
34 triangle and harpoon heads; it can be called from edges().
36 o add.scale.bar() has a new option 'ask' to draw interactively.
38 o The branch length score replaces the geodesic distance in dist.topo.
40 o Three new data sets are included: the gopher-lice data (gopher.D),
41 SO2 air pollution in 41 US cities (lmorigin.ex1, from Sokal &
42 Rohlf 1995), and some host-parasite specificity data
43 (lmorigin.ex2, from Legendre & Desdevises 2009).
48 o add.scale.bar() drew the bar outside the plotting region with the
49 default options with unrooted or radial trees.
51 o dist.topo() made R stuck when the trees had different sizes (thanks
52 to Otto Cordero for the fix).
57 o The geodesic distance has been replaced by the branch length score
62 CHANGES IN APE VERSION 2.4-1
67 o rtree() and rcoal() now accept a numeric vector for the 'br'
70 o vcv() is a new generic function with methods for the classes "phylo"
71 and "corPhyl" so that it is possible to calculate the var-cov matrix
72 for "transformation models". vcv.phylo() can still be used for trees
73 of class "phylo"; its argument 'cor' has been renamed 'corr'.
78 o bind.tree() failed when 'y' had no root edge.
80 o read.nexus() shuffled tip labels when the trees have no branch
81 lengths and there is a TRANSLATE block.
83 o read.nexus() does not try to translate node labels if there is a
84 translation table in the NEXUS file. See ?read.nexus for a
85 clarification on this behaviour.
87 o plot.multiPhylo() crashed R when plotting a list of trees with
88 compressed tip labels.
90 o write.nexus() did not translate the taxa names when asked for.
92 o plot.phylo(type = "fan") did not rotate the tip labels correctly
93 when the tree has branch lengths.
95 o ace(type = "continuous", method = "ML") now avoids sigma² being
96 negative (which resulted in an error).
98 o nj() crashed with NA/NaN in the distance matrix: an error in now
103 CHANGES IN APE VERSION 2.4
108 o base.freq() has a new option 'freq' to return the counts; the
109 default is still to return the proportions.
114 o seg.sites() did not handle ambiguous nucleotides correctly: they
117 o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
118 the tree: the argument is now ignored.
120 o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
126 o Trying to plot a tree with a single tip now returns NULL with a
127 warning (it returned an error previously).
129 o The way lines representing nodes are coloured in phylograms has
130 been modified (as well as their widths and types) following some
131 users' request; this is only for dichotomous nodes.
133 o The argument 'adj' in [node][tip][edge]labels() now works when
134 using 'pie' or 'thermo'.
136 o A more informative message error is now returned by dist.dna() when
137 'model' is badly specified (partial matching of this argument is
140 o Deprecated functions are now listed in a help page: see
141 help("ape-defunct") with the quotes.
146 o The functions heterozygosity, nuc.div, theta.h, theta.k and
147 theta.s have been moved from ape to pegas.
149 o The functions mlphylo, DNAmodel and sh.test have been removed.
153 CHANGES IN APE VERSION 2.3-3
158 o add.scale.bar() always drew a horizontal bar.
160 o zoom() shuffled tips with unrooted trees.
162 o write.nexus() failed to write correctly trees with a "TipLabel"
165 o rcoal() failed to compute branch lengths with very large n.
167 o A small bug was fixed in compar.cheverud() (thanks to Michael
170 o seg.sites() failed when passing a vector.
172 o drop.tip() sometimes shuffled tip labels.
174 o root() shuffled node labels with 'resolve.root = TRUE'.
178 CHANGES IN APE VERSION 2.3-2
183 o all.equal.phylo() did not compare unrooted trees correctly.
185 o dist.topo(... method = "PH85") did not treat unrooted trees
186 correctly (thanks to Tim Wallstrom for the fix).
188 o root() sometimes failed to test for the monophyly of the
191 o extract.clade() sometimes included too many edges.
193 o vcv.phylo() did not work correctly when the tree is in
196 o nj() did not handle correctly distance matrices with many 0's.
197 The code has also been significantly improved: 7, 70, 160 times
198 faster with n = 100, 500, 1000, respectively.
202 CHANGES IN APE VERSION 2.3-1
207 o The new function is.monophyletic tests the monophyly of a group.
209 o There is now a c() method for lists of class "DNAbin".
211 o yule.cov() now fits the null model, and its help page has been
212 corrected with respect to this change.
214 o drop.tip() has a new option 'rooted' to force (or not) a tree
215 to be treated as (un)rooted.
220 o dist.gene() failed on most occasions with the default
221 pairwise.deletion = FALSE.
223 o read.tree() failed to read correctly the tree name(s).
225 o boot.phylo() now treats correctly data frames.
227 o del.gaps() did not copy the rownames of a matrix.
229 o A small bug was fixed in CDAM.global().
231 o ace() failed with large data sets. Thanks to Rich FitzJohn for
232 the fix. With other improvements, this function is now about 6
235 o write.tree() failed with objects of class "multiPhylo".
237 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
242 o [.multiPhylo and [.DNAbin now respect the original class.
244 o Instances of the form class(phy) == "phylo" have been replaced
245 by inherits(phy, "phylo").
247 o rcoal() is now faster.
252 o klastorin() has been removed.
256 CHANGES IN APE VERSION 2.3
261 o The new functions CADM.global and CADM.post, contributed by
262 Pierre Legendre, test the congruence among several distance
265 o The new function yule.time fits a user-defined time-dependent
266 Yule model by maximum likelihood.
268 o The new function makeNodeLabel creates and/or modifies node
269 labels in a flexible way.
271 o read.tree() and write.tree() have been modified so that they can
272 handle individual tree names.
274 o plot.phylo() has a new argument 'edge.lty' that specifies the
275 types of lines used for the edges (plain, dotted, dashed, ...)
277 o phymltest() has been updated to work with PhyML 3.0.1.
282 o drop.tip() shuffled tip labels in some cases.
284 o drop.tip() did not handle node.label correctly.
286 o is.ultrametric() now checks the ordering of the edge matrix.
288 o ace() sometimes returned negative values of likelihoods of
289 ancestral states (thanks to Dan Rabosky for solving this long
295 o The data set xenarthra has been removed.
299 CHANGES IN APE VERSION 2.2-4
303 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
304 now fixed. (Thanks to Peter Wragg for the fix!)
306 o A warning message occurred for no reason with ace(method="GLS").
311 o There is now a general help page displayed with '?ape'.
315 CHANGES IN APE VERSION 2.2-3
320 o The new function extract.clade extracts a clade from a tree by
321 specifying a node number or label.
323 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
324 operations of the same names.
326 o dist.dna() can now return the number of site differences by
327 specifying model="N".
332 o chronopl() did not work with CV = TRUE.
334 o read.nexus() did not work correctly in some situations (trees on
335 multiple lines with different numbers of lines and/or with
336 comments inserted within the trees).
338 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
339 the number of lineages with non-binary trees.
344 o ape has now a namespace.
346 o drop.tip() has been improved: it should be much faster and work
347 better in some cases (e.g., see the example in ?zoom).
351 CHANGES IN APE VERSION 2.2-2
356 o dist.gene() has been substantially improved and gains an option
359 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
365 o prop.part() failed with a single tree with the default option
366 'check.labels = TRUE'.
368 o summary.DNAbin() failed to display correctly the summary of
369 sequence lengths with lists of sequences of 10,000 bases or more
370 (because summary.default uses 4 significant digits by default).
372 o read.nexus() failed to read a file with a single tree with line
373 breaks in the Newick string.
375 o del.gaps() returned a list of empty sequences when there were no
381 o phymltest() has been updated for PhyML 3.0 and gains an option
382 'append', whereas the option 'path2exec' has been removed.
384 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
385 which is returned unchanged (instead of an error).
387 o The data sets bird.orders and bird.families are now stored as
388 Newick strings; i.e., the command data(bird.orders) calls
393 CHANGES IN APE VERSION 2.2-1
398 o The new function makeLabel() helps to modify labels of trees,
399 lists of trees, or DNA sequences, with several utilities to
400 truncate and/or make them unique, substituting some
401 characters, and so on.
403 o The new function del.gaps() removes insertion gaps ("-") in a
404 set of DNA sequences.
406 o read.dna() can now read Clustal files (*.aln).
411 o root() failed with 'resolve.root = TRUE' when the root was
412 already the specified root.
414 o Several bugs were fixed in mlphylo().
416 o collapsed.singles() did not propagate the 'Nnode' and
417 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
419 o read.nexus() failed to remove correctly the comments within
422 o read.nexus() failed to read a file with a single tree and no
423 translation of tip labels.
425 o read.nexus() failed to place correctly tip labels when reading
426 a single tree with no edge lengths.
428 o A bug was fixed in sh.test().
433 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
436 o The option 'check.labels' of consensus() and prop.part() is now
439 o write.dna() now does not truncate names to 10 characters with
444 CHANGES IN APE VERSION 2.2
449 o Four new functions have been written by Damien de Vienne for the
450 graphical exploration of large trees (cophyloplot, subtrees,
451 subtreeplot), and to return the graphical coordinates of tree
454 o The new functions corPagel and corBlomberg implement the Pagel's
455 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
457 o chronopl() has been improved and gains several options: see its
458 help page for details.
460 o boot.phylo() has now an option 'trees' to possibly return the
461 bootstraped trees (the default is FALSE).
463 o prop.part() has been improved and should now be faster in all
469 o read.dna() failed if "?" occurred in the first 10 sites of the
472 o The x/y aspect of the plot is now respected when plotting a
473 circular tree (type = "r" or "f").
475 o Drawing the tip labels sometimes failed when plotting circular
478 o zoom() failed when tip labels were used instead of their numbers
479 (thanks to Yan Wong for the fix).
481 o drop.tip() failed with some trees (fixed by Yan Wong).
483 o seg.sites() failed with a list.
485 o consensus() failed in some cases. The function has been improved
486 as well and is faster.
490 CHANGES IN APE VERSION 2.1-3
495 o A bug in read.nexus() made the Windows R-GUI crash.
497 o An error was fixed in the computation of ancestral character
498 states by generalized least squares in ace().
500 o di2multi() did not modify node labels correctly.
502 o multi2di() failed if the tree had its attribute "order" set to
507 CHANGES IN APE VERSION 2.1-2
512 o There three new methods for the "multiPhylo" class: str, $,
515 o root() gains the options 'node' and 'resolve.root'
516 (FALSE by default) as well as its code being improved.
518 o mltt.plot() has now an option 'log' used in the same way
519 than in plot.default().
524 o mltt.plot() failed to display the legend with an unnamed
527 o nodelabels() with pies now correcly uses the argument
528 'cex' to draw symbols of different sizes (which has
529 worked already for thermometers).
531 o read.nexus() generally failed to read very big files.
536 o The argument 'family' of compar.gee() can now be a function
537 as well as a character string.
539 o read.tree() and read.nexus() now return an unnamed list if
542 o read.nexus() now returns a modified object of class "multiPhylo"
543 when there is a TRANSLATE block in the NEXUS file: the individual
544 trees have no 'tip.label' vector, but the list has a 'TipLabel'
545 attribute. The new methods '$' and '[[' set these elements
546 correctly when extracting trees.
550 CHANGES IN APE VERSION 2.1-1
555 o The new function rmtree generates lists of random trees.
557 o rcoal() now generates a genuine coalescent tree by default
558 (thanks to Vladimir Minin for the code).
563 o nuc.div() returned an incorrect value with the default
564 pairwise.deletion = FALSE.
569 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
570 have been improved so that they are stabler and faster.
572 o R packages used by ape are now loaded silently; lattice and gee
573 are loaded only when needed.
577 CHANGES IN APE VERSION 2.1
582 o The new function identify.phylo identifies clades on a plotted
583 tree using the mouse.
585 o It is now possible to subset a list of trees (object of class
586 "multiPhylo") with "[" while keeping its class correct.
588 o The new function as.DNAbin.alignment converts DNA sequences
589 stored in the "alignment" format of the package seqinr into
590 an object of class "DNAbin".
592 o The new function weight.taxo2 helps to build similarity matrices
593 given two taxonomic levels (usually called by other functions).
595 o write.tree() can now take a list of trees (class "multiPhylo")
596 as its main argument.
598 o plot.correlogram() and plot.correlogramList() have been
599 improved, and gain several options (see the help page for
600 details). A legend is now plotted by default.
605 o dist.dna() returned some incorrect values with `model = "JC69"'
606 and `pairwise.deletion = TRUE'. This affected only the
607 distances involving sequences with missing values. (Thanks
608 to Bruno Toupance for digging this bug out.)
610 o write.tree() failed with some trees: this is fixed by removing
611 the `multi.line' option (trees are now always printed on a
614 o read.nexus() did not correctly detect trees with multiple root
615 edges (see OTHER CHANGES).
620 o The code of mlphylo() has been almost entirely rewritten, and
621 should be much stabler. The options have been also greatly
622 simplified (see ?mlphylo and ?DNAmodel for details).
624 o The internal function nTips has been renamed klastorin_nTips.
626 o The code of is.ultrametric() contained redundancies and has
629 o The code of Moran.I() and of correlogram.formula() have been
632 o read.tree() and read.nexus() now return an error when trying to
633 read a tree with multiple root edges (see BUG FIXES). The
634 correction applied in previous version did not work in all
637 o The class c("multi.tree", "phylo") has been renamed
643 o There is now a vignette in ape: see vignette("MoranI", "ape").
648 o as.matching() and as.phylo.matching() do not support branch
651 o correlogram.phylo() and discrete.dist() have been removed.
655 CHANGES IN APE VERSION 2.0-2
660 o The new function matexpo computes the exponential of a square
663 o The new function unique.multi.tree removes duplicate trees from
666 o yule() has a new option `use.root.edge = FALSE' that specifies
667 to ignore, by default, the root edge of the tree if it exists.
672 o which.edge() failed when the index of a single terminal edge was
675 o In diversi.time(), the values returned for model C were
678 o A bug was fixed in yule() that affected the calculation of the
679 likelihood in the presence of ties in the branching times.
681 o There was a bug in the C function mat_expo4x4 affecting the
682 calculations of the transition probabilities for models HKY and
685 o A small bug was fixed in as.matrix.DNAbin (thanks to James
688 o rtree() did not `shuffle' the tip labels by default, so only a
689 limited number of labelled topologies could be generated.
693 CHANGES IN APE VERSION 2.0-1
698 o The three new functions bionj, fastme.ols, and fastme.bal
699 perform phylogeny estimation by the BIONJ and fastME methods in
700 OLS and balanced versions. This is a port to R of previous
701 previous programs done by Vincent Lefort.
703 o The new function chronoMPL performs molecular dating with the
704 mean path lengths method of Britton et al. (2002, Mol. Phyl.
707 o The new function rotate, contributed by Christoph Heibl, swaps
708 two clades connected to the same node. It works also with
709 multichotomous nodes.
711 o The new `method' as.matrix.DNAbin() may be used to convert
712 easily DNA sequences stored in a list into a matrix while
713 keeping the names and the class.
718 o chronopl() failed when some branch lengths were equal to zero:
719 an error message is now returned.
721 o di2multi() failed when there was a series of consecutive edges
726 CHANGES IN APE VERSION 1.10-2
731 o plot.phylo() can now plot circular trees: the option is type =
732 "fan" or type = "f" (to avoid the ambiguity with type = "c").
734 o prop.part() has a new option `check.labels = FALSE' which allows
735 to considerably speed-up the calculations of bipartitions. As a
736 consequence, calculations of bootstrap values with boot.phylo()
737 should be much faster.
742 o read.GenBank() did not return correctly the list of species as
743 from ape 1.10: this is fixed in this version
745 o Applying as.phylo() on a tree of class "phylo" failed: the
746 object is now returned unchanged.
750 CHANGES IN APE VERSION 1.10-1
755 o The three new functions Ntip, Nnode, and Nedge return, for a
756 given tree, the number of tips, nodes, or edges, respectively.
761 o read.nexus() did not set correctly the class of the returned
762 object when reading multiple trees.
764 o mllt.plot() failed with objects of class c("multi.tree",
767 o unroot() did not work correctly in most cases.
769 o reorder.phylo() made R freeze in some occasions.
771 o Plotting a tree in pruningwise order failed.
773 o When plotting an unrooted tree, the tip labels where not all
774 correctly positioned if the option `cex' was used.
778 CHANGES IN APE VERSION 1.10
783 o Five new `method' functions have been introduced to manipulate
784 DNA sequences in binary format (see below).
786 o Three new functions have been introduced to convert between the
787 new binary and the character formats.
789 o The new function as.alignment converts DNA sequences stored as
790 single characters into the class "alignment" used by the package
793 o read.dna() and read.GenBank() have a new argument `as.character'
794 controlling whether the sequences are returned in binary format
800 o root() failed when the tree had node labels: this is fixed.
802 o plot.phylo() did not correctly set the limits on the y-axis with
803 the default setting: this is fixed.
805 o dist.dna() returned a wrong result for the LogDet, paralinear,
806 and BH87 models with `pairwise.deletion = TRUE'.
811 o DNA sequences are now internally stored in a binary format. See
812 the document "A Bit-Level Coding Scheme for Nucleotides" for the
813 details. Most functions analyzing DNA functions have been
814 modified accordingly and are now much faster (dist.dna is now
815 ca. 60 times faster).
819 CHANGES IN APE VERSION 1.9-4
824 o A bug was fixed in edgelabels().
826 o as.phylo.hclust() did not work correctly when the object of
827 class "hclust" has its labels set to NULL: the returned tree has
828 now its tip labels set to "1", "2", ...
830 o consensus could fail if some tip labels are a subset of others
831 (e.g., "a" and "a_1"): this is now fixed.
833 o mlphylo() failed in most cases if some branch lengths of the
834 initial tree were greater than one: an error message is now
837 o mlphylo() failed in most cases when estimating the proportion of
838 invariants: this is fixed.
842 CHANGES IN APE VERSION 1.9-3
847 o The new function edgelabels adds labels on the edge of the tree
848 in the same way than nodelabels or tiplabels.
853 o multi2di() did not handle correctly branch lengths with the
854 default option `random = TRUE': this is now fixed.
856 o A bug was fixed in nuc.div() when using pairwise deletions.
858 o A bug occurred in the analysis of bipartitions with large
859 numbers of large trees, with consequences on prop.part,
860 prop.clades, and boot.phylo.
862 o The calculation of the Billera-Holmes-Vogtmann distance in
863 dist.topo was wrong: this has been fixed.
867 CHANGES IN APE VERSION 1.9-2
872 o The new function ladderize reorganizes the internal structure of
873 a tree to plot them left- or right-ladderized.
875 o The new function dist.nodes computes the patristic distances
876 between all nodes, internal and terminal, of a tree. It replaces
877 the option `full = TRUE' of cophenetic.phylo (see below).
882 o A bug was fixed in old2new.phylo().
884 o Some bugs were fixed in chronopl().
886 o The edge colours were not correctly displayed by plot.phylo
887 (thank you to Li-San Wang for the fix).
889 o cophenetic.phylo() failed with multichotomous trees: this is
895 o read.dna() now returns the sequences in a matrix if they are
896 aligned (interleaved or sequential format). Sequences in FASTA
897 format are still returned in a list.
899 o The option `full' of cophenetic.phylo() has been removed because
900 it could not be used from the generic.
905 o rotate() has been removed; this function did not work correctly
910 CHANGES IN APE VERSION 1.9-1
915 o Trees with a single tip were not read correctly in R as the
916 element `Nnode' was not set: this is fixed.
918 o unroot() did not set correctly the number of nodes of the
919 unrooted tree in most cases.
921 o read.GenBank() failed when fetching very long sequences,
922 particularly of the BX-series.
924 o A bug was introduced in read.tree() with ape 1.9: it has been
929 CHANGES IN APE VERSION 1.9
934 o There are two new print `methods' for trees of class "phylo" and
935 lists of trees of class "multi.tree", so that they are now
936 displayed in a compact and informative way.
938 o There are two new functions, old2new.phylo and new2old.phylo,
939 for converting between the old and new coding of the class
942 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
943 LogDet ("logdet"), and paralinear ("paralin").
945 o compute.brlen() has been extended: several methods are now
946 available to compute branch lengths.
948 o write.dna() can now handle matrices as well as lists.
953 o cophenetic.phylo() sometimes returned a wrong result with
954 multichotomous trees: this is fixed.
956 o rotate() failed when a single tip was specified: the tree is now
959 o ace() did not return the correct index matrix with custom
960 models: this is fixed.
962 o multi2di() did not work correctly when resolving multichotomies
963 randomly: the topology was always the same, only the arrangement
964 of clades was randomized: this is fixed. This function now
965 accepts trees with no branch lengths.
967 o The output of diversi.gof() was blurred by useless prints when a
968 user distribution was specified. This has been corrected, and
969 the help page of this function has been expanded.
974 o The internal structure of the class "phylo" has been changed:
975 see the document "Definition of Formats for Coding Phylogenetic
976 Trees in R" for the details. In addition, the code of most
977 functions has been improved.
979 o Several functions have been improved by replacing some R codes
980 by C codes: pic, plot.phylo, and reorder.phylo.
982 o There is now a citation information: see citation("ape") in R.
984 o write.tree() now does not add extra 0's to branch lengths so
985 that 1.23 is printed "1.23" by default, not "1.2300000000".
987 o The syntax of bind.tree() has been simplified. This function now
988 accepts trees with no branch lengths, and handles correctly node
991 o The option `as.numeric' of mrca() has been removed.
993 o The unused options `format' and `rooted' of read.tree() have
996 o The unused option `format' of write.tree() has been removed.
998 o The use of node.depth() has been simplified.
1002 CHANGES IN APE VERSION 1.8-5
1007 o Two new functions read.nexus.data() and write.nexus.data(),
1008 contributed by Johan Nylander, allow to read and write molecular
1009 sequences in NEXUS files.
1011 o The new function reorder.phylo() reorders the internal structure
1012 of a tree of class "phylo". It is used as the generic, e.g.,
1015 o read.tree() and read.nexus() can now read trees with a single
1018 o The new data set `cynipids' supplies a set of protein sequences
1024 o The code of all.equal.phylo() has been completely rewritten
1025 (thanks to Benoît Durand) which fixes several bugs.
1027 o read.tree() and read.nexus() now checks the labels of the tree
1028 to remove or substitute any characters that are illegal in the
1029 Newick format (parentheses, etc.)
1031 o A negative P-value could be returned by mantel.test(): this is
1036 CHANGES IN APE VERSION 1.8-4
1041 o The new function sh.test() computes the Shimodaira-
1044 o The new function collapse.singles() removes the nodes with a
1045 single descendant from a tree.
1047 o plot.phylo() has a new argument `tip.color' to specify the
1048 colours of the tips.
1050 o mlphylo() has now an option `quiet' to control the display of
1051 the progress of the analysis (the default is FALSE).
1056 o read.dna() did not read correctly sequences in sequential format
1057 with leading alignment gaps "-": this is fixed.
1059 o ace() returned a list with no class so that the generic
1060 functions (anova, logLik, ...) could not be used directly. This
1061 is fixed as ace() now returns an object of class "ace".
1063 o anova.ace() had a small bug when computing the number of degrees
1064 of freedom: this is fixed.
1066 o mlphylo() did not work when the sequences were in a matrix or
1067 a data frame: this is fixed.
1069 o rtree() did not work correctly when trying to simulate an
1070 unrooted tree with two tips: an error message is now issued.
1075 o The algorithm of rtree() has been changed: it is now about 40,
1076 100, and 130 times faster for 10, 100, and 1000 tips,
1081 CHANGES IN APE VERSION 1.8-3
1086 o There are four new `method' functions to be used with the
1087 results of ace(): logLik(), deviance(), AIC(), and anova().
1089 o The plot method of phymltest has two new arguments: `main' to
1090 change the title, and `col' to control the colour of the
1091 segments showing the AIC values.
1093 o ace() has a new argument `ip' that gives the initial values used
1094 in the ML estimation with discrete characters (see the examples
1095 in ?ace). This function now returns a matrix giving the indices
1096 of the estimated rates when analysing discrete characters.
1098 o nodelabels() and tiplabels() have a new argument `pie' to
1099 represent proportions, with any number of categories, as
1100 piecharts. The use of the option `thermo' has been improved:
1101 there is now no limitation on the number of categories.
1106 o mlphylo() did not work with more than two partitions: this is
1109 o root() failed if the proposed outgroup was already an outgroup
1110 in the tree: this is fixed.
1112 o The `col' argument in nodelabels() and tiplabels() was not
1113 correctly passed when `text' was used: this is fixed.
1115 o Two bugs were fixed in mlphylo(): parameters were not always
1116 correctly output, and the estimation failed in some cases.
1118 o plot.phylo() was stuck when given a tree with a single tip: this
1119 is fixed and a message error is now returned.
1121 o An error was corrected in the help page of gammaStat regarding
1122 the calculation of P-values.
1124 o Using gls() could crash R when the number of species in the tree
1125 and in the variables were different: this is fixed.
1129 CHANGES IN APE VERSION 1.8-2
1134 o The new function mlphylo() fits a phylogenetic tree by maximum
1135 likelihood from DNA sequences. Its companion function DNAmodel()
1136 is used to define the substitution model which may include
1137 partitioning. There are methods for logLik(), deviance(), and
1138 AIC(), and the summary() method has been extended to display in
1139 a friendly way the results of this model fitting. Currently, the
1140 functionality is limited to estimating the substitution and
1141 associated parameters and computing the likelihood.
1143 o The new function drop1.compar.gee (used as, e.g., drop1(m))
1144 tests for single effects in GEE-based comparative method. A
1145 warning message is printed if there is not enough degrees of
1151 o An error message was sometimes issued by plot.multi.tree(),
1152 though with no consequence.
1156 CHANGES IN APE VERSION 1.8-1
1161 o There is a new plot method for lists of trees (objects of class
1162 "multi.tree"): it calls plot.phylo() internally and is
1163 documented on the same help page.
1168 o A bug was fixed in the C code that analyzes bipartitions: this
1169 has impact on several functions like prop.part, prop.clades,
1170 boot.phylo, or consensus.
1172 o root() did not work correctly when the specified outgroup had
1173 more than one element: this is fixed.
1175 o dist.dna() sometimes returned a warning inappropriately: this
1178 o If the distance object given to nj() had no rownames, nj()
1179 returned a tree with no tip labels: it now returns tips labelled
1180 "1", "2", ..., corresponding to the row numbers.
1185 o nj() has been slightly changed so that tips with a zero distance
1186 are first aggregated with zero-lengthed branches; the usual NJ
1187 procedure is then performed on a distance matrix without 0's.
1191 CHANGES IN APE VERSION 1.8
1196 o The new function chronopl() estimates dates using the penalized
1197 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1199 o The new function consensus() calculates the consensus tree of a
1202 o The new function evolve.phylo() simulates the evolution of
1203 continuous characters along a phylogeny under a Brownian model.
1205 o The new plot method for objects of class "ancestral" displays a
1206 tree together with ancestral values, as returned by the above
1209 o The new function as.phylo.formula() returns a phylogeny from a
1210 set of nested taxonomic variables given as a formula.
1212 o The new function read.caic() reads trees in CAIC format.
1214 o The new function tiplabels() allows to add labels to the tips
1215 of a tree using text or plotting symbols in a flexible way.
1217 o The new function unroot() unroots a phylogeny.
1219 o multi2di() has a new option, `random', which specifies whether
1220 to resolve the multichotomies randomly (the default) or not.
1222 o prop.part() now returns an object of class "prop.part" for which
1223 there are print (to display a partition in a more friendly way)
1224 and summary (to extract the numbers) methods.
1226 o plot.phylo() has a new option, `show.tip.label', specifying
1227 whether to print the labels of the tips. The default is TRUE.
1229 o The code of nj() has been replaced by a faster C code: it is now
1230 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1233 o write.nexus() now writes whether a tree is rooted or not.
1238 o Two bugs have been fixed in root(): unrooted trees are now
1239 handled corretly, and node labels are now output normally.
1241 o A bug was fixed in phymltest(): the executable couldn't be found
1244 o Three bug have been fixed in ace(): computing the likelihood of
1245 ancestral states of discrete characters failed, custom models
1246 did not work, and the function failed with a null gradient (a
1247 warning message is now returned; this latter bug was also
1248 present in yule.cov() as well and is now fixed).
1250 o pic() hanged out when missing data were present: a message error
1253 o A small bug was fixed in dist.dna() where the gamma correction
1254 was not always correctly dispatched.
1256 o plot.phylo() plotted correctly the root edge only when the tree
1257 was plotted rightwards: this works now for all directions.
1262 o dist.taxo() has been renamed as weight.taxo().
1264 o dist.phylo() has been replaced by the method cophenetic.phylo().
1266 o Various error and warning messages have been improved.
1270 CHANGES IN APE VERSION 1.7
1273 o The new function ace() estimates ancestral character states for
1274 continuous characters (with ML, GLS, and contrasts methods), and
1275 discrete characters (with ML only) for any number of states.
1277 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1278 of directional evolution for continuous characters. The user
1279 specifies the node(s) of the tree where the character optimum
1282 o The new function is.rooted() tests whether a tree (of class
1285 o The new function rcoal() generates random ultrametric trees with
1286 the possibility to specify the function that generates the
1287 inter-nodes distances.
1289 o The new function mrca() gives for all pairs of tips in a tree
1290 (and optionally nodes too) the most recent common ancestor.
1292 o nodelabels() has a new option `thermo' to plot proportions (up
1293 to three classes) on the nodes of a tree.
1295 o rtree() has been improved: it can now generate rooted or
1296 unrooted trees, and the mathematical function that generates the
1297 branch lengths may be specified by the user. The tip labels may
1298 be given directly in the call to rtree. The limit cases (n = 2,
1299 3) are now handled correctly.
1301 o dist.topo() has a new argument `method' with two choices: "PH85"
1302 for Penny and Henny's method (already available before and now
1303 the default), and "BHV01" for the geometric distance by Billera
1304 et al. (2001, Adv. Appl. Math. 27:733).
1306 o write.tree() has a new option, `digits', which specifies the
1307 number of digits to be printed in the Newick tree. By default
1308 digits = 10. The numbers are now always printed in decimal form
1309 (i.e., 1.0e-1 is now avoided).
1311 o dist.dna() can now compute the raw distances between pairs of
1312 DNA sequences by specifying model = "raw".
1314 o dist.phylo() has a new option `full' to possibly compute the
1315 distances among all tips and nodes of the tree. The default if
1321 o Several bugs were fixed in all.equal.phylo().
1323 o dist.dna() did not handle correctly gaps ("-") in alignments:
1324 they are now considered as missing data.
1326 o rotate() did not work if the tips were not ordered: this is
1329 o mantel.test() returned NA in some special cases: this is fixed
1330 and the function has been improved and is now faster.
1332 o A bug was fixed in diversi.gof() where the calculation of A² was
1335 o cherry() did not work correctly under some OSs (mainly Linux):
1338 o is.binary.tree() has been modified so that it works with both
1339 rooted and unrooted trees.
1341 o The documentation of theta.s() was not correct: this has been
1344 o plot.mst() did not work correctly: this is fixed.
1348 CHANGES IN APE VERSION 1.6
1353 o The new function dist.topo() computes the topological distances
1356 o The new function boot.phylo() performs a bootstrap analysis on
1357 phylogeny estimation.
1359 o The new functions prop.part() and prop.clades() analyse
1360 bipartitions from a series of trees.
1365 o read.GenBank() now uses the EFetch utility of NCBI instead of
1366 the usual Web interface: it is now much faster (e.g., 12 times
1367 faster to retrieve 8 sequences, 37 times for 60 sequences).
1372 o Several bugs were fixed in read.dna().
1374 o Several bugs were fixed in diversi.time().
1376 o is.binary.tree() did not work correctly if the tree has no edge
1377 lengths: this is fixed.
1379 o drop.tip() did not correctly propagated the `node.label' of a
1380 tree: this is fixed.
1384 CHANGES IN APE VERSION 1.5
1389 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1390 convert objects between the classes "phylo" and "matching". The
1391 latter implements the representation of binary trees introduced by
1392 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1393 as.matching() has been introduced as well.
1395 o Two new functions, multi2di() and di2multi(), allow to resolve
1396 and collapse multichotomies with branches of length zero.
1398 o The new function nuc.div() computes the nucleotide diversity
1399 from a sample a DNA sequences.
1401 o dist.dna() has been completely rewritten with a much faster
1402 (particularly for large data sets) C code. Eight models are
1403 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1404 option `method' has been renamed `model'). Computation of variance
1405 is available for all models. A gamma-correction is possible for
1406 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1407 to remove sites with missing data on a pairwise basis. The option
1408 `GCcontent' has been removed.
1410 o read.GenBank() has a new option (species.names) which specifies
1411 whether to return the species names of the organisms in addition
1412 to the accession numbers of the sequences (this is the default
1415 o write.nexus() can now write several trees in the same NEXUS file.
1417 o drop.tip() has a new option `root.edge' that allows to specify the
1418 new root edge if internal branches are trimmed.
1423 o as.phylo.hclust() failed if some labels had parentheses: this
1426 o Several bugs were fixed in all.equal.phylo(). This function now
1427 returns the logical TRUE if the trees are identical but with
1428 different representations (a report was printed previously).
1430 o read.GenBank() did not correctly handle ambiguous base codes:
1436 o birthdeath() now returns an object of class "birthdeath" for
1437 which there is a print method.
1441 CHANGES IN APE VERSION 1.4
1446 o The new function nj() performs phylogeny estimation with the
1447 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1450 o The new function which.edge() identifies the edges of a tree
1451 that belong to a group specified as a set of tips.
1453 o The new function as.phylo.phylog() converts an object of class
1454 "phylog" (from the package ade4) into an object of class
1457 o The new function axisPhylo() draws axes on the side of a
1460 o The new function howmanytrees() calculates the number of trees
1461 in different cases and giving a number of tips.
1463 o write.tree() has a new option `multi.line' (TRUE by default) to
1464 write a Newick tree on several lines rather than on a single
1467 o The functionalities of zoom() have been extended. Several
1468 subtrees can be visualized at the same time, and they are marked
1469 on the main tree with colors. The context of the subtrees can be
1470 marked with the option `subtree' (see below).
1472 o drop.tip() has a new option `subtree' (FALSE by default) which
1473 specifies whether to output in the tree how many tips have been
1476 o The arguments of add.scale.bar() have been redefined and have
1477 now default values (see ?add.scale.bar for details). This
1478 function now works even if the plotted tree has no edge length.
1480 o plot.phylo() can now plot radial trees, but this does not take
1481 edge lengths into account.
1483 o In plot.phylo() with `type = "phylogram"', if the values of
1484 `edge.color' and `edge.width' are identical for sister-branches,
1485 they are propagated to the vertical line that link them.
1490 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1491 crashing. This is fixed.
1493 o In plot.phylo(), the options `edge.color' and `edge.width' are
1494 now properly recycled; their default values are now "black" and
1497 o A bug has been fixed in write.nexus().
1502 o The function node.depth.edgelength() has been removed and
1503 replaced by a C code.
1507 CHANGES IN APE VERSION 1.3-1
1512 o The new function nodelabels() allows to add labels to the nodes
1513 of a tree using text or plotting symbols in a flexible way.
1515 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1516 numeric values specifying the lower and upper limits on the x-
1517 and y-axes. This allows to leave some space on any side of the
1518 tree. If a single value is given, this is taken as the upper
1523 CHANGES IN APE VERSION 1.3
1528 o The new function phymltest() calls the software PHYML and fits
1529 28 models of DNA sequence evolution. There are a print method to
1530 display likelihood and AIC values, a summary method to compute
1531 the hierarchical likelihood ratio tests, and a plot method to
1532 display graphically the AIC values of each model.
1534 o The new function yule.cov() fits the Yule model with covariates,
1535 a model where the speciation rate is affected by several species
1536 traits through a generalized linear model. The parameters are
1537 estimated by maximum likelihood.
1539 o Three new functions, corBrownian(), corGrafen(), and
1540 corMartins(), compute the expected correlation structures among
1541 species given a phylogeny under different models of evolution.
1542 These can be used for GLS comparative phylogenetic methods (see
1543 the examples). There are coef() and corMatrix() methods and an
1544 Initialize.corPhyl() function associated.
1546 o The new function compar.cheverud() implements Cheverud et al.'s
1547 (1985; Evolution 39:1335) phylogenetic comparative method.
1549 o The new function varcomp() estimates variance components; it has
1552 o Two new functions, panel.superpose.correlogram() and
1553 plot.correlogramList(), allow to plot several phylogenetic
1556 o The new function node.leafnumber() computes the number of leaves
1557 of a subtree defined by a particular node.
1559 o The new function node.sons() gets all tags of son nodes from a
1562 o The new function compute.brlen() computes the branch lengths of
1563 a tree according to a specified method.
1565 o plot.phylo() has three new options: "cex" controls the size of
1566 the (tip and node) labels (thus it is no more needed to change
1567 the global graphical parameter), "direction" which allows to
1568 plot the tree rightwards, leftwards, upwards, or downwards, and
1569 "y.lim" which sets the upper limit on the y-axis.
1574 o Some functions which try to match tip labels and names of
1575 additional data (e.g. vector) are likely to fail if there are
1576 typing or syntax errors. If both series of names do not perfectly
1577 match, they are ignored and a warning message is now issued.
1578 These functions are bd.ext, compar.gee, pic. Their help pages
1579 have been clarified on this point.
1583 CHANGES IN APE VERSION 1.2-7
1588 o The new function root() reroots a phylogenetic tree with respect
1589 to a specified outgroup.
1591 o The new function rotate() rotates an internal branch of a tree.
1593 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1594 trees) controls the display of the tip labels in unrooted trees.
1595 This display has been greatly improved: the tip labels are now not
1596 expected to overlap with the tree (particularly if lab4ut =
1597 "axial"). In all cases, combining appropriate values of "lab4ut"
1598 and the font size (via "par(cex = )") should result in readable
1599 unrooted trees. See ?plot.phylo for some examples.
1601 o In drop.tip(), the argument `tip' can now be numeric or character.
1606 o drop.tip() did not work correctly with trees with no branch
1607 lengths: this is fixed.
1609 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1610 plotted with some line crossings: this is now fixed.
1614 CHANGES IN APE VERSION 1.2-6
1619 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1620 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1621 to implement comparative methods with an autocorrelation approach.
1623 o A new data set describing some life history traits of Carnivores
1629 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1634 o When plotting a tree with plot.phylo(), the new default of the
1635 option `label.offset' is now 0, so the labels are always visible.
1639 CHANGES IN APE VERSION 1.2-5
1644 o The new function bd.ext() fits a birth-death model with combined
1645 phylogenetic and taxonomic data, and estimates the corresponding
1646 speciation and extinction rates.
1651 o The package gee is no more required by ape but only suggested
1652 since only the function compar.gee() calls gee.
1656 CHANGES IN APE VERSION 1.2-4
1661 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1662 and lines.popsize) implementing a new approach for inferring the
1663 demographic history from genealogies using a reversible jump
1664 MCMC have been introduced.
1666 o The unit of time in the skyline plot and in the new plots can
1667 now be chosen to be actual years, rather than substitutions.
1671 CHANGES IN APE VERSION 1.2-3
1676 o The new function rtree() generates a random binary tree with or
1677 without branch lengths.
1679 o Two new functions for drawing lineages-through-time (LTT) plots
1680 are provided: ltt.lines() adds a LTT curve to an existing plot,
1681 and mltt.plot() does a multiple LTT plot giving several trees as
1682 arguments (see `?ltt.plot' for details).
1687 o Some taxon names made R crashing when calling as.phylo.hclust():
1690 o dist.dna() returned an error with two identical DNA sequences
1691 (only using the Jukes-Cantor method returned 0): this is fixed.
1696 o The function dist.phylo() has been re-written using a different
1697 algorithm: it is now about four times faster.
1699 o The code of branching.times() has been improved: it is now about
1704 CHANGES IN APE VERSION 1.2-2
1709 o The new function seg.sites() finds the segregating sites in a
1710 sample of DNA sequences.
1715 o A bug introduced in read.tree() and in read.nexus() with version
1718 o A few errors were corrected and a few examples were added in the
1723 CHANGES IN APE VERSION 1.2-1
1728 o plot.phylo() can now draw the edge of the root of a tree if it
1729 has one (see the new option `root.edge', its default is FALSE).
1734 o A bug was fixed in read.nexus(): files with semicolons inside
1735 comment blocks were not read correctly.
1737 o The behaviour of read.tree() and read.nexus() was corrected so
1738 that tree files with badly represented root edges (e.g., with
1739 an extra pair of parentheses, see the help pages for details)
1740 are now correctly represented in the object of class "phylo";
1741 a warning message is now issued.
1745 CHANGES IN APE VERSION 1.2
1750 o plot.phylo() has been completely re-written and offers several
1751 new functionalities. Three types of trees can now be drawn:
1752 phylogram (as previously), cladogram, and unrooted tree; in
1753 all three types the branch lengths can be drawn using the edge
1754 lengths of the phylogeny or not (e.g., if the latter is absent).
1755 The vertical position of the nodes can be adjusted with two
1756 choices (see option `node.pos'). The code has been re-structured,
1757 and two new functions (potentially useful for developpers) are
1758 documented separately: node.depth.edgelength() and node.depth();
1759 see the respective help pages for details.
1761 o The new function zoom() allows to explore very large trees by
1762 focusing on a small portion of it.
1764 o The new function yule() fits by maximum likelihood the Yule model
1765 (birth-only process) to a phylogenetic tree.
1767 o Support for writing DNA sequences in FASTA format has been
1768 introduced in write.dna() (support for reading sequences in
1769 this format was introduced in read.dna() in version 1.1-2).
1770 The function has been completely re-written, fixing some bugs
1771 (see below); the default behaviour is no more to display the
1772 sequences on the standard output. Several options have been
1773 introduced to control the sequence printing in a flexible
1774 way. The help page has been extended.
1776 o A new data set is included: a supertree of bats in NEXUS format.
1781 o In theta.s(), the default of the option `variance' has
1782 been changed to `FALSE' (as was indicated in the help page).
1784 o Several bugs were fixed in the code of all.equal.phylo().
1786 o Several bugs were fixed in write.dna(), particularly this
1787 function did not work with `format = "interleaved"'.
1789 o Various errors were corrected in the help pages.
1794 o The argument names of as.hclust.phylo() have been changed
1795 from "(phy)" to "(x, ...)" to conform to the definition of
1796 the corresponding generic function.
1798 o gamma.stat() has been renamed gammaStat() to avoid confusion
1799 since gamma() is a generic function.
1803 CHANGES IN APE VERSION 1.1-3
1808 o base.freq() previously did not return a value of 0 for
1809 bases absent in the data (e.g., a vector of length 3 was
1810 returned if one base was absent). This is now fixed (a
1811 vector of length 4 is always returned).
1813 o Several bugs were fixed in read.nexus(), including that this
1814 function did not work in this absence of a "TRANSLATE"
1815 command in the NEXUS file, and that the commands were
1820 CHANGES IN APE VERSION 1.1-2
1825 o The Tamura and Nei (1993) model of DNA distance is now implemented
1826 in dist.dna(): five models are now available in this function.
1828 o A new data set is included: a set of 15 sequences of the
1829 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1835 o A bug in read.nexus() was fixed.
1837 o read.dna() previously did not work correctly in most cases.
1838 The function has been completely re-written and its help page
1839 has been considerably extended (see ?read.dna for details).
1840 Underscores (_) in taxon names are no more replaced with
1841 spaces (this behaviour was undocumented).
1843 o A bug was fixed in write.dna().
1847 CHANGES IN APE VERSION 1.1-1
1852 o A bug in read.tree() introduced in APE 1.1 was fixed.
1854 o A bug in compar.gee() resulted in an error when trying to fit
1855 a model with `family = "binomial"'. This is now fixed.
1859 CHANGES IN APE VERSION 1.1
1864 o The Klastorin (1982) method as suggested by Misawa and Tajima
1865 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1866 on the basis of phylogenetic trees has been implemented (see
1867 the function klastorin()).
1869 o Functions have been added to convert APE's "phylo" objects in
1870 "hclust" cluster objects and vice versa (see the help page of
1871 as.phylo for details).
1873 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1874 are introduced for the estimation of absolute evolutionary rates
1875 (ratogram) and dated clock-like trees (chronogram) from
1876 phylogenetic trees using the non-parametric rate smoothing approach
1877 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1879 o A summary method is now provided printing a summary information on a
1880 phylogenetic tree with, for instance, `summary(tree)'.
1882 o The behaviour of read.tree() was changed so that all spaces and
1883 tabulations in tree files are now ignored. Consequently, spaces in tip
1884 labels are no more allowed. Another side effect is that read.nexus()
1885 now does not replace the underscores (_) in tip labels with spaces
1886 (this behaviour was undocumented).
1888 o The function plot.phylo() has a new option (`underscore') which
1889 specifies whether the underscores in tip labels should be written on
1890 the plot as such or replaced with spaces (the default).
1892 o The function birthdeath() now computes 95% confidence intervals of
1893 the estimated parameters using profile likelihood.
1895 o Three new data sets are included: a gene tree estimated from 36
1896 landplant rbcL sequences, a gene tree estimated from 32 opsin
1897 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1902 o A bug was fixed in dist.gene() where nothing was returned.
1904 o A bug in plot.mst() was fixed.
1906 o A bug in vcv.phylo() resulted in false correlations when the
1907 option `cor = TRUE' was used (now fixed).
1911 CHANGES IN APE VERSION 1.0
1916 o Two new functions, read.dna() and write.dna(), read/write in a file
1917 DNA sequences in interleaved or in sequential format.
1919 o Two new functions, read.nexus() and write.nexus(), read/write trees
1922 o The new function bind.tree() allows to bind two trees together,
1923 possibly handling root edges to give internal branches.
1925 o The new function drop.tip() removes the tips in a phylogenetic tree,
1926 and trims (or not) the corresponding internal branches.
1928 o The new function is.ultrametric() tests if a tree is ultrametric.
1930 o The function plot.phylo() has more functionalities such as drawing the
1931 branches with different colours and/or different widths, showing the
1932 node labels, controling the position and font of the labels, rotating
1933 the labels, and controling the space around the plot.
1935 o The function read.tree() can now read trees with no branch length,
1936 such as "(a,b),c);". Consequently, the element `edge.length' in
1937 objects of class "phylo" is now optional.
1939 o The function write.tree() has a new default behaviour: if the default
1940 for the option `file' is used (i.e. file = ""), then a variable of
1941 mode character containing the tree in Newick format is returned which
1942 can thus be assigned (e.g., tree <- write.tree(phy)).
1944 o The function read.tree() has a new argument `text' which allows
1945 to read the tree in a variable of mode character.
1947 o A new data set is included: the phylogenetic relationships among
1948 the orders of birds from Sibley and Ahlquist (1990).
1952 CHANGES IN APE VERSION 0.2-1
1957 o Several bugs were fixed in the help pages.
1961 CHANGES IN APE VERSION 0.2
1966 o The function write.tree() writes phylogenetic trees (objects of class
1967 "phylo") in an ASCII file using the Newick parenthetic format.
1969 o The function birthdeath() fits a birth-death model to branching times
1970 by maximum likelihood, and estimates the corresponding speciation and
1973 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1976 o The function is.binary.tree() tests whether a phylogeny is binary.
1978 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1979 as well as some methods are introduced.
1981 o Several functions, including some generics and methods, for computing
1982 skyline plot estimates (classic and generalized) of effective
1983 population size through time are introduced and replace the function
1984 skyline.plot() in version 0.1.
1986 o Two data sets are now included: the phylogenetic relationships among
1987 the families of birds from Sibley and Ahlquist (1990), and an
1988 estimated clock-like phylogeny of HIV sequences sampled in the
1989 Democratic Republic of Congo.
1992 DEPRECATED & DEFUNCT
1994 o The function skyline.plot() in ape 0.1 has been deprecated and
1995 replaced by more elaborate functions (see above).
2000 o Two important bugs were fixed in plot.phylo(): phylogenies with
2001 multichotomies not at the root or not with only terminal branches,
2002 and phylogenies with a single node (i.e. only terminal branches)
2003 did not plot. These trees should be plotted correctly now.
2005 o Several bugs were fixed in diversi.time() in the computation of
2008 o Various errors were corrected in the help pages.
projects / ape.git / blob