1 CHANGES IN APE VERSION 2.4-1
6 o rtree() and rcoal() now accept a numeric vector for the 'br'
12 o bind.tree() failed when 'y' had no root edge.
14 o read.nexus() shuffled tip labels when the trees have no branch
15 lengths and there is a TRANSLATE block.
17 o plot.multiPhylo() crashed R when plotting a list of trees with
18 "compressed tip labels".
20 o write.nexus() did not translate the taxa names when asked for.
22 o plot.phylo(type = "fan") did not rotate the tip labels correctly
23 when the tree has branch lengths.
27 CHANGES IN APE VERSION 2.4
32 o base.freq() has a new option 'freq' to return the counts; the
33 default is still to return the proportions.
38 o seg.sites() did not handle ambiguous nucleotides correctly: they
41 o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
42 the tree: the argument is now ignored.
44 o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
50 o Trying to plot a tree with a single tip now returns NULL with a
51 warning (it returned an error previously).
53 o The way lines representing nodes are coloured in phylograms has
54 been modified (as well as their widths and types) following some
55 users' request; this is only for dichotomous nodes.
57 o The argument 'adj' in [node][tip][edge]labels() now works when
58 using 'pie' or 'thermo'.
60 o A more informative message error is now returned by dist.dna() when
61 'model' is badly specified (partial matching of this argument is
64 o Deprecated functions are now listed in a help page: see
65 help("ape-defunct") with the quotes.
70 o The functions heterozygosity, nuc.div, theta.h, theta.k and
71 theta.s have been moved from ape to pegas.
73 o The functions mlphylo, DNAmodel and sh.test have been removed.
77 CHANGES IN APE VERSION 2.3-3
82 o add.scale.bar() always drew a horizontal bar.
84 o zoom() shuffled tips with unrooted trees.
86 o write.nexus() failed to write correctly trees with a "TipLabel"
89 o rcoal() failed to compute branch lengths with very large n.
91 o A small bug was fixed in compar.cheverud() (thanks to Michael
94 o seg.sites() failed when passing a vector.
96 o drop.tip() sometimes shuffled tip labels.
98 o root() shuffled node labels with 'resolve.root = TRUE'.
102 CHANGES IN APE VERSION 2.3-2
107 o all.equal.phylo() did not compare unrooted trees correctly.
109 o dist.topo(... method = "PH85") did not treat unrooted trees
110 correctly (thanks to Tim Wallstrom for the fix).
112 o root() sometimes failed to test for the monophyly of the
115 o extract.clade() sometimes included too many edges.
117 o vcv.phylo() did not work correctly when the tree is in
120 o nj() did not handle correctly distance matrices with many 0's.
121 The code has also been significantly improved: 7, 70, 160 times
122 faster with n = 100, 500, 1000, respectively.
126 CHANGES IN APE VERSION 2.3-1
131 o The new function is.monophyletic tests the monophyly of a group.
133 o There is now a c() method for lists of class "DNAbin".
135 o yule.cov() now fits the null model, and its help page has been
136 corrected with respect to this change.
138 o drop.tip() has a new option 'rooted' to force (or not) a tree
139 to be treated as (un)rooted.
144 o dist.gene() failed on most occasions with the default
145 pairwise.deletion = FALSE.
147 o read.tree() failed to read correctly the tree name(s).
149 o boot.phylo() now treats correctly data frames.
151 o del.gaps() did not copy the rownames of a matrix.
153 o A small bug was fixed in CDAM.global().
155 o ace() failed with large data sets. Thanks to Rich FitzJohn for
156 the fix. With other improvements, this function is now about 6
159 o write.tree() failed with objects of class "multiPhylo".
161 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
166 o [.multiPhylo and [.DNAbin now respect the original class.
168 o Instances of the form class(phy) == "phylo" have been replaced
169 by inherits(phy, "phylo").
171 o rcoal() is now faster.
176 o klastorin() has been removed.
180 CHANGES IN APE VERSION 2.3
185 o The new functions CADM.global and CADM.post, contributed by
186 Pierre Legendre, test the congruence among several distance
189 o The new function yule.time fits a user-defined time-dependent
190 Yule model by maximum likelihood.
192 o The new function makeNodeLabel creates and/or modifies node
193 labels in a flexible way.
195 o read.tree() and write.tree() have been modified so that they can
196 handle individual tree names.
198 o plot.phylo() has a new argument 'edge.lty' that specifies the
199 types of lines used for the edges (plain, dotted, dashed, ...)
201 o phymltest() has been updated to work with PhyML 3.0.1.
206 o drop.tip() shuffled tip labels in some cases.
208 o drop.tip() did not handle node.label correctly.
210 o is.ultrametric() now checks the ordering of the edge matrix.
212 o ace() sometimes returned negative values of likelihoods of
213 ancestral states (thanks to Dan Rabosky for solving this long
219 o The data set xenarthra has been removed.
223 CHANGES IN APE VERSION 2.2-4
227 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
228 now fixed. (Thanks to Peter Wragg for the fix!)
230 o A warning message occurred for no reason with ace(method="GLS").
235 o There is now a general help page displayed with '?ape'.
239 CHANGES IN APE VERSION 2.2-3
244 o The new function extract.clade extracts a clade from a tree by
245 specifying a node number or label.
247 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
248 operations of the same names.
250 o dist.dna() can now return the number of site differences by
251 specifying model="N".
256 o chronopl() did not work with CV = TRUE.
258 o read.nexus() did not work correctly in some situations (trees on
259 multiple lines with different numbers of lines and/or with
260 comments inserted within the trees).
262 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
263 the number of lineages with non-binary trees.
268 o ape has now a namespace.
270 o drop.tip() has been improved: it should be much faster and work
271 better in some cases (e.g., see the example in ?zoom).
275 CHANGES IN APE VERSION 2.2-2
280 o dist.gene() has been substantially improved and gains an option
283 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
289 o prop.part() failed with a single tree with the default option
290 'check.labels = TRUE'.
292 o summary.DNAbin() failed to display correctly the summary of
293 sequence lengths with lists of sequences of 10,000 bases or more
294 (because summary.default uses 4 significant digits by default).
296 o read.nexus() failed to read a file with a single tree with line
297 breaks in the Newick string.
299 o del.gaps() returned a list of empty sequences when there were no
305 o phymltest() has been updated for PhyML 3.0 and gains an option
306 'append', whereas the option 'path2exec' has been removed.
308 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
309 which is returned unchanged (instead of an error).
311 o The data sets bird.orders and bird.families are now stored as
312 Newick strings; i.e., the command data(bird.orders) calls
317 CHANGES IN APE VERSION 2.2-1
322 o The new function makeLabel() helps to modify labels of trees,
323 lists of trees, or DNA sequences, with several utilities to
324 truncate and/or make them unique, substituting some
325 characters, and so on.
327 o The new function del.gaps() removes insertion gaps ("-") in a
328 set of DNA sequences.
330 o read.dna() can now read Clustal files (*.aln).
335 o root() failed with 'resolve.root = TRUE' when the root was
336 already the specified root.
338 o Several bugs were fixed in mlphylo().
340 o collapsed.singles() did not propagate the 'Nnode' and
341 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
343 o read.nexus() failed to remove correctly the comments within
346 o read.nexus() failed to read a file with a single tree and no
347 translation of tip labels.
349 o read.nexus() failed to place correctly tip labels when reading
350 a single tree with no edge lengths.
352 o A bug was fixed in sh.test().
357 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
360 o The option 'check.labels' of consensus() and prop.part() is now
363 o write.dna() now does not truncate names to 10 characters with
368 CHANGES IN APE VERSION 2.2
373 o Four new functions have been written by Damien de Vienne for the
374 graphical exploration of large trees (cophyloplot, subtrees,
375 subtreeplot), and to return the graphical coordinates of tree
378 o The new functions corPagel and corBlomberg implement the Pagel's
379 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
381 o chronopl() has been improved and gains several options: see its
382 help page for details.
384 o boot.phylo() has now an option 'trees' to possibly return the
385 bootstraped trees (the default is FALSE).
387 o prop.part() has been improved and should now be faster in all
393 o read.dna() failed if "?" occurred in the first 10 sites of the
396 o The x/y aspect of the plot is now respected when plotting a
397 circular tree (type = "r" or "f").
399 o Drawing the tip labels sometimes failed when plotting circular
402 o zoom() failed when tip labels were used instead of their numbers
403 (thanks to Yan Wong for the fix).
405 o drop.tip() failed with some trees (fixed by Yan Wong).
407 o seg.sites() failed with a list.
409 o consensus() failed in some cases. The function has been improved
410 as well and is faster.
414 CHANGES IN APE VERSION 2.1-3
419 o A bug in read.nexus() made the Windows R-GUI crash.
421 o An error was fixed in the computation of ancestral character
422 states by generalized least squares in ace().
424 o di2multi() did not modify node labels correctly.
426 o multi2di() failed if the tree had its attribute "order" set to
431 CHANGES IN APE VERSION 2.1-2
436 o There three new methods for the "multiPhylo" class: str, $,
439 o root() gains the options 'node' and 'resolve.root'
440 (FALSE by default) as well as its code being improved.
442 o mltt.plot() has now an option 'log' used in the same way
443 than in plot.default().
448 o mltt.plot() failed to display the legend with an unnamed
451 o nodelabels() with pies now correcly uses the argument
452 'cex' to draw symbols of different sizes (which has
453 worked already for thermometers).
455 o read.nexus() generally failed to read very big files.
460 o The argument 'family' of compar.gee() can now be a function
461 as well as a character string.
463 o read.tree() and read.nexus() now return an unnamed list if
466 o read.nexus() now returns a modified object of class "multiPhylo"
467 when there is a TRANSLATE block in the NEXUS file: the individual
468 trees have no 'tip.label' vector, but the list has a 'TipLabel'
469 attribute. The new methods '$' and '[[' set these elements
470 correctly when extracting trees.
474 CHANGES IN APE VERSION 2.1-1
479 o The new function rmtree generates lists of random trees.
481 o rcoal() now generates a genuine coalescent tree by default
482 (thanks to Vladimir Minin for the code).
487 o nuc.div() returned an incorrect value with the default
488 pairwise.deletion = FALSE.
493 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
494 have been improved so that they are stabler and faster.
496 o R packages used by ape are now loaded silently; lattice and gee
497 are loaded only when needed.
501 CHANGES IN APE VERSION 2.1
506 o The new function identify.phylo identifies clades on a plotted
507 tree using the mouse.
509 o It is now possible to subset a list of trees (object of class
510 "multiPhylo") with "[" while keeping its class correct.
512 o The new function as.DNAbin.alignment converts DNA sequences
513 stored in the "alignment" format of the package seqinr into
514 an object of class "DNAbin".
516 o The new function weight.taxo2 helps to build similarity matrices
517 given two taxonomic levels (usually called by other functions).
519 o write.tree() can now take a list of trees (class "multiPhylo")
520 as its main argument.
522 o plot.correlogram() and plot.correlogramList() have been
523 improved, and gain several options (see the help page for
524 details). A legend is now plotted by default.
529 o dist.dna() returned some incorrect values with `model = "JC69"'
530 and `pairwise.deletion = TRUE'. This affected only the
531 distances involving sequences with missing values. (Thanks
532 to Bruno Toupance for digging this bug out.)
534 o write.tree() failed with some trees: this is fixed by removing
535 the `multi.line' option (trees are now always printed on a
538 o read.nexus() did not correctly detect trees with multiple root
539 edges (see OTHER CHANGES).
544 o The code of mlphylo() has been almost entirely rewritten, and
545 should be much stabler. The options have been also greatly
546 simplified (see ?mlphylo and ?DNAmodel for details).
548 o The internal function nTips has been renamed klastorin_nTips.
550 o The code of is.ultrametric() contained redundancies and has
553 o The code of Moran.I() and of correlogram.formula() have been
556 o read.tree() and read.nexus() now return an error when trying to
557 read a tree with multiple root edges (see BUG FIXES). The
558 correction applied in previous version did not work in all
561 o The class c("multi.tree", "phylo") has been renamed
567 o There is now a vignette in ape: see vignette("MoranI", "ape").
572 o as.matching() and as.phylo.matching() do not support branch
575 o correlogram.phylo() and discrete.dist() have been removed.
579 CHANGES IN APE VERSION 2.0-2
584 o The new function matexpo computes the exponential of a square
587 o The new function unique.multi.tree removes duplicate trees from
590 o yule() has a new option `use.root.edge = FALSE' that specifies
591 to ignore, by default, the root edge of the tree if it exists.
596 o which.edge() failed when the index of a single terminal edge was
599 o In diversi.time(), the values returned for model C were
602 o A bug was fixed in yule() that affected the calculation of the
603 likelihood in the presence of ties in the branching times.
605 o There was a bug in the C function mat_expo4x4 affecting the
606 calculations of the transition probabilities for models HKY and
609 o A small bug was fixed in as.matrix.DNAbin (thanks to James
612 o rtree() did not `shuffle' the tip labels by default, so only a
613 limited number of labelled topologies could be generated.
617 CHANGES IN APE VERSION 2.0-1
622 o The three new functions bionj, fastme.ols, and fastme.bal
623 perform phylogeny estimation by the BIONJ and fastME methods in
624 OLS and balanced versions. This is a port to R of previous
625 previous programs done by Vincent Lefort.
627 o The new function chronoMPL performs molecular dating with the
628 mean path lengths method of Britton et al. (2002, Mol. Phyl.
631 o The new function rotate, contributed by Christoph Heibl, swaps
632 two clades connected to the same node. It works also with
633 multichotomous nodes.
635 o The new `method' as.matrix.DNAbin() may be used to convert
636 easily DNA sequences stored in a list into a matrix while
637 keeping the names and the class.
642 o chronopl() failed when some branch lengths were equal to zero:
643 an error message is now returned.
645 o di2multi() failed when there was a series of consecutive edges
650 CHANGES IN APE VERSION 1.10-2
655 o plot.phylo() can now plot circular trees: the option is type =
656 "fan" or type = "f" (to avoid the ambiguity with type = "c").
658 o prop.part() has a new option `check.labels = FALSE' which allows
659 to considerably speed-up the calculations of bipartitions. As a
660 consequence, calculations of bootstrap values with boot.phylo()
661 should be much faster.
666 o read.GenBank() did not return correctly the list of species as
667 from ape 1.10: this is fixed in this version
669 o Applying as.phylo() on a tree of class "phylo" failed: the
670 object is now returned unchanged.
674 CHANGES IN APE VERSION 1.10-1
679 o The three new functions Ntip, Nnode, and Nedge return, for a
680 given tree, the number of tips, nodes, or edges, respectively.
685 o read.nexus() did not set correctly the class of the returned
686 object when reading multiple trees.
688 o mllt.plot() failed with objects of class c("multi.tree",
691 o unroot() did not work correctly in most cases.
693 o reorder.phylo() made R freeze in some occasions.
695 o Plotting a tree in pruningwise order failed.
697 o When plotting an unrooted tree, the tip labels where not all
698 correctly positioned if the option `cex' was used.
702 CHANGES IN APE VERSION 1.10
707 o Five new `method' functions have been introduced to manipulate
708 DNA sequences in binary format (see below).
710 o Three new functions have been introduced to convert between the
711 new binary and the character formats.
713 o The new function as.alignment converts DNA sequences stored as
714 single characters into the class "alignment" used by the package
717 o read.dna() and read.GenBank() have a new argument `as.character'
718 controlling whether the sequences are returned in binary format
724 o root() failed when the tree had node labels: this is fixed.
726 o plot.phylo() did not correctly set the limits on the y-axis with
727 the default setting: this is fixed.
729 o dist.dna() returned a wrong result for the LogDet, paralinear,
730 and BH87 models with `pairwise.deletion = TRUE'.
735 o DNA sequences are now internally stored in a binary format. See
736 the document "A Bit-Level Coding Scheme for Nucleotides" for the
737 details. Most functions analyzing DNA functions have been
738 modified accordingly and are now much faster (dist.dna is now
739 ca. 60 times faster).
743 CHANGES IN APE VERSION 1.9-4
748 o A bug was fixed in edgelabels().
750 o as.phylo.hclust() did not work correctly when the object of
751 class "hclust" has its labels set to NULL: the returned tree has
752 now its tip labels set to "1", "2", ...
754 o consensus could fail if some tip labels are a subset of others
755 (e.g., "a" and "a_1"): this is now fixed.
757 o mlphylo() failed in most cases if some branch lengths of the
758 initial tree were greater than one: an error message is now
761 o mlphylo() failed in most cases when estimating the proportion of
762 invariants: this is fixed.
766 CHANGES IN APE VERSION 1.9-3
771 o The new function edgelabels adds labels on the edge of the tree
772 in the same way than nodelabels or tiplabels.
777 o multi2di() did not handle correctly branch lengths with the
778 default option `random = TRUE': this is now fixed.
780 o A bug was fixed in nuc.div() when using pairwise deletions.
782 o A bug occurred in the analysis of bipartitions with large
783 numbers of large trees, with consequences on prop.part,
784 prop.clades, and boot.phylo.
786 o The calculation of the Billera-Holmes-Vogtmann distance in
787 dist.topo was wrong: this has been fixed.
791 CHANGES IN APE VERSION 1.9-2
796 o The new function ladderize reorganizes the internal structure of
797 a tree to plot them left- or right-ladderized.
799 o The new function dist.nodes computes the patristic distances
800 between all nodes, internal and terminal, of a tree. It replaces
801 the option `full = TRUE' of cophenetic.phylo (see below).
806 o A bug was fixed in old2new.phylo().
808 o Some bugs were fixed in chronopl().
810 o The edge colours were not correctly displayed by plot.phylo
811 (thank you to Li-San Wang for the fix).
813 o cophenetic.phylo() failed with multichotomous trees: this is
819 o read.dna() now returns the sequences in a matrix if they are
820 aligned (interleaved or sequential format). Sequences in FASTA
821 format are still returned in a list.
823 o The option `full' of cophenetic.phylo() has been removed because
824 it could not be used from the generic.
829 o rotate() has been removed; this function did not work correctly
834 CHANGES IN APE VERSION 1.9-1
839 o Trees with a single tip were not read correctly in R as the
840 element `Nnode' was not set: this is fixed.
842 o unroot() did not set correctly the number of nodes of the
843 unrooted tree in most cases.
845 o read.GenBank() failed when fetching very long sequences,
846 particularly of the BX-series.
848 o A bug was introduced in read.tree() with ape 1.9: it has been
853 CHANGES IN APE VERSION 1.9
858 o There are two new print `methods' for trees of class "phylo" and
859 lists of trees of class "multi.tree", so that they are now
860 displayed in a compact and informative way.
862 o There are two new functions, old2new.phylo and new2old.phylo,
863 for converting between the old and new coding of the class
866 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
867 LogDet ("logdet"), and paralinear ("paralin").
869 o compute.brlen() has been extended: several methods are now
870 available to compute branch lengths.
872 o write.dna() can now handle matrices as well as lists.
877 o cophenetic.phylo() sometimes returned a wrong result with
878 multichotomous trees: this is fixed.
880 o rotate() failed when a single tip was specified: the tree is now
883 o ace() did not return the correct index matrix with custom
884 models: this is fixed.
886 o multi2di() did not work correctly when resolving multichotomies
887 randomly: the topology was always the same, only the arrangement
888 of clades was randomized: this is fixed. This function now
889 accepts trees with no branch lengths.
891 o The output of diversi.gof() was blurred by useless prints when a
892 user distribution was specified. This has been corrected, and
893 the help page of this function has been expanded.
898 o The internal structure of the class "phylo" has been changed:
899 see the document "Definition of Formats for Coding Phylogenetic
900 Trees in R" for the details. In addition, the code of most
901 functions has been improved.
903 o Several functions have been improved by replacing some R codes
904 by C codes: pic, plot.phylo, and reorder.phylo.
906 o There is now a citation information: see citation("ape") in R.
908 o write.tree() now does not add extra 0's to branch lengths so
909 that 1.23 is printed "1.23" by default, not "1.2300000000".
911 o The syntax of bind.tree() has been simplified. This function now
912 accepts trees with no branch lengths, and handles correctly node
915 o The option `as.numeric' of mrca() has been removed.
917 o The unused options `format' and `rooted' of read.tree() have
920 o The unused option `format' of write.tree() has been removed.
922 o The use of node.depth() has been simplified.
926 CHANGES IN APE VERSION 1.8-5
931 o Two new functions read.nexus.data() and write.nexus.data(),
932 contributed by Johan Nylander, allow to read and write molecular
933 sequences in NEXUS files.
935 o The new function reorder.phylo() reorders the internal structure
936 of a tree of class "phylo". It is used as the generic, e.g.,
939 o read.tree() and read.nexus() can now read trees with a single
942 o The new data set `cynipids' supplies a set of protein sequences
948 o The code of all.equal.phylo() has been completely rewritten
949 (thanks to Benoît Durand) which fixes several bugs.
951 o read.tree() and read.nexus() now checks the labels of the tree
952 to remove or substitute any characters that are illegal in the
953 Newick format (parentheses, etc.)
955 o A negative P-value could be returned by mantel.test(): this is
960 CHANGES IN APE VERSION 1.8-4
965 o The new function sh.test() computes the Shimodaira-
968 o The new function collapse.singles() removes the nodes with a
969 single descendant from a tree.
971 o plot.phylo() has a new argument `tip.color' to specify the
974 o mlphylo() has now an option `quiet' to control the display of
975 the progress of the analysis (the default is FALSE).
980 o read.dna() did not read correctly sequences in sequential format
981 with leading alignment gaps "-": this is fixed.
983 o ace() returned a list with no class so that the generic
984 functions (anova, logLik, ...) could not be used directly. This
985 is fixed as ace() now returns an object of class "ace".
987 o anova.ace() had a small bug when computing the number of degrees
988 of freedom: this is fixed.
990 o mlphylo() did not work when the sequences were in a matrix or
991 a data frame: this is fixed.
993 o rtree() did not work correctly when trying to simulate an
994 unrooted tree with two tips: an error message is now issued.
999 o The algorithm of rtree() has been changed: it is now about 40,
1000 100, and 130 times faster for 10, 100, and 1000 tips,
1005 CHANGES IN APE VERSION 1.8-3
1010 o There are four new `method' functions to be used with the
1011 results of ace(): logLik(), deviance(), AIC(), and anova().
1013 o The plot method of phymltest has two new arguments: `main' to
1014 change the title, and `col' to control the colour of the
1015 segments showing the AIC values.
1017 o ace() has a new argument `ip' that gives the initial values used
1018 in the ML estimation with discrete characters (see the examples
1019 in ?ace). This function now returns a matrix giving the indices
1020 of the estimated rates when analysing discrete characters.
1022 o nodelabels() and tiplabels() have a new argument `pie' to
1023 represent proportions, with any number of categories, as
1024 piecharts. The use of the option `thermo' has been improved:
1025 there is now no limitation on the number of categories.
1030 o mlphylo() did not work with more than two partitions: this is
1033 o root() failed if the proposed outgroup was already an outgroup
1034 in the tree: this is fixed.
1036 o The `col' argument in nodelabels() and tiplabels() was not
1037 correctly passed when `text' was used: this is fixed.
1039 o Two bugs were fixed in mlphylo(): parameters were not always
1040 correctly output, and the estimation failed in some cases.
1042 o plot.phylo() was stuck when given a tree with a single tip: this
1043 is fixed and a message error is now returned.
1045 o An error was corrected in the help page of gammaStat regarding
1046 the calculation of P-values.
1048 o Using gls() could crash R when the number of species in the tree
1049 and in the variables were different: this is fixed.
1053 CHANGES IN APE VERSION 1.8-2
1058 o The new function mlphylo() fits a phylogenetic tree by maximum
1059 likelihood from DNA sequences. Its companion function DNAmodel()
1060 is used to define the substitution model which may include
1061 partitioning. There are methods for logLik(), deviance(), and
1062 AIC(), and the summary() method has been extended to display in
1063 a friendly way the results of this model fitting. Currently, the
1064 functionality is limited to estimating the substitution and
1065 associated parameters and computing the likelihood.
1067 o The new function drop1.compar.gee (used as, e.g., drop1(m))
1068 tests for single effects in GEE-based comparative method. A
1069 warning message is printed if there is not enough degrees of
1075 o An error message was sometimes issued by plot.multi.tree(),
1076 though with no consequence.
1080 CHANGES IN APE VERSION 1.8-1
1085 o There is a new plot method for lists of trees (objects of class
1086 "multi.tree"): it calls plot.phylo() internally and is
1087 documented on the same help page.
1092 o A bug was fixed in the C code that analyzes bipartitions: this
1093 has impact on several functions like prop.part, prop.clades,
1094 boot.phylo, or consensus.
1096 o root() did not work correctly when the specified outgroup had
1097 more than one element: this is fixed.
1099 o dist.dna() sometimes returned a warning inappropriately: this
1102 o If the distance object given to nj() had no rownames, nj()
1103 returned a tree with no tip labels: it now returns tips labelled
1104 "1", "2", ..., corresponding to the row numbers.
1109 o nj() has been slightly changed so that tips with a zero distance
1110 are first aggregated with zero-lengthed branches; the usual NJ
1111 procedure is then performed on a distance matrix without 0's.
1115 CHANGES IN APE VERSION 1.8
1120 o The new function chronopl() estimates dates using the penalized
1121 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1123 o The new function consensus() calculates the consensus tree of a
1126 o The new function evolve.phylo() simulates the evolution of
1127 continuous characters along a phylogeny under a Brownian model.
1129 o The new plot method for objects of class "ancestral" displays a
1130 tree together with ancestral values, as returned by the above
1133 o The new function as.phylo.formula() returns a phylogeny from a
1134 set of nested taxonomic variables given as a formula.
1136 o The new function read.caic() reads trees in CAIC format.
1138 o The new function tiplabels() allows to add labels to the tips
1139 of a tree using text or plotting symbols in a flexible way.
1141 o The new function unroot() unroots a phylogeny.
1143 o multi2di() has a new option, `random', which specifies whether
1144 to resolve the multichotomies randomly (the default) or not.
1146 o prop.part() now returns an object of class "prop.part" for which
1147 there are print (to display a partition in a more friendly way)
1148 and summary (to extract the numbers) methods.
1150 o plot.phylo() has a new option, `show.tip.label', specifying
1151 whether to print the labels of the tips. The default is TRUE.
1153 o The code of nj() has been replaced by a faster C code: it is now
1154 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1157 o write.nexus() now writes whether a tree is rooted or not.
1162 o Two bugs have been fixed in root(): unrooted trees are now
1163 handled corretly, and node labels are now output normally.
1165 o A bug was fixed in phymltest(): the executable couldn't be found
1168 o Three bug have been fixed in ace(): computing the likelihood of
1169 ancestral states of discrete characters failed, custom models
1170 did not work, and the function failed with a null gradient (a
1171 warning message is now returned; this latter bug was also
1172 present in yule.cov() as well and is now fixed).
1174 o pic() hanged out when missing data were present: a message error
1177 o A small bug was fixed in dist.dna() where the gamma correction
1178 was not always correctly dispatched.
1180 o plot.phylo() plotted correctly the root edge only when the tree
1181 was plotted rightwards: this works now for all directions.
1186 o dist.taxo() has been renamed as weight.taxo().
1188 o Various error and warning messages have been improved.
1192 CHANGES IN APE VERSION 1.7
1195 o The new function ace() estimates ancestral character states for
1196 continuous characters (with ML, GLS, and contrasts methods), and
1197 discrete characters (with ML only) for any number of states.
1199 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1200 of directional evolution for continuous characters. The user
1201 specifies the node(s) of the tree where the character optimum
1204 o The new function is.rooted() tests whether a tree (of class
1207 o The new function rcoal() generates random ultrametric trees with
1208 the possibility to specify the function that generates the
1209 inter-nodes distances.
1211 o The new function mrca() gives for all pairs of tips in a tree
1212 (and optionally nodes too) the most recent common ancestor.
1214 o nodelabels() has a new option `thermo' to plot proportions (up
1215 to three classes) on the nodes of a tree.
1217 o rtree() has been improved: it can now generate rooted or
1218 unrooted trees, and the mathematical function that generates the
1219 branch lengths may be specified by the user. The tip labels may
1220 be given directly in the call to rtree. The limit cases (n = 2,
1221 3) are now handled correctly.
1223 o dist.topo() has a new argument `method' with two choices: "PH85"
1224 for Penny and Henny's method (already available before and now
1225 the default), and "BHV01" for the geometric distance by Billera
1226 et al. (2001, Adv. Appl. Math. 27:733).
1228 o write.tree() has a new option, `digits', which specifies the
1229 number of digits to be printed in the Newick tree. By default
1230 digits = 10. The numbers are now always printed in decimal form
1231 (i.e., 1.0e-1 is now avoided).
1233 o dist.dna() can now compute the raw distances between pairs of
1234 DNA sequences by specifying model = "raw".
1236 o dist.phylo() has a new option `full' to possibly compute the
1237 distances among all tips and nodes of the tree. The default if
1243 o Several bugs were fixed in all.equal.phylo().
1245 o dist.dna() did not handle correctly gaps ("-") in alignments:
1246 they are now considered as missing data.
1248 o rotate() did not work if the tips were not ordered: this is
1251 o mantel.test() returned NA in some special cases: this is fixed
1252 and the function has been improved and is now faster.
1254 o A bug was fixed in diversi.gof() where the calculation of A² was
1257 o cherry() did not work correctly under some OSs (mainly Linux):
1260 o is.binary.tree() has been modified so that it works with both
1261 rooted and unrooted trees.
1263 o The documentation of theta.s() was not correct: this has been
1266 o plot.mst() did not work correctly: this is fixed.
1270 CHANGES IN APE VERSION 1.6
1275 o The new function dist.topo() computes the topological distances
1278 o The new function boot.phylo() performs a bootstrap analysis on
1279 phylogeny estimation.
1281 o The new functions prop.part() and prop.clades() analyse
1282 bipartitions from a series of trees.
1287 o read.GenBank() now uses the EFetch utility of NCBI instead of
1288 the usual Web interface: it is now much faster (e.g., 12 times
1289 faster to retrieve 8 sequences, 37 times for 60 sequences).
1294 o Several bugs were fixed in read.dna().
1296 o Several bugs were fixed in diversi.time().
1298 o is.binary.tree() did not work correctly if the tree has no edge
1299 lengths: this is fixed.
1301 o drop.tip() did not correctly propagated the `node.label' of a
1302 tree: this is fixed.
1306 CHANGES IN APE VERSION 1.5
1311 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1312 convert objects between the classes "phylo" and "matching". The
1313 latter implements the representation of binary trees introduced by
1314 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1315 as.matching() has been introduced as well.
1317 o Two new functions, multi2di() and di2multi(), allow to resolve
1318 and collapse multichotomies with branches of length zero.
1320 o The new function nuc.div() computes the nucleotide diversity
1321 from a sample a DNA sequences.
1323 o dist.dna() has been completely rewritten with a much faster
1324 (particularly for large data sets) C code. Eight models are
1325 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1326 option `method' has been renamed `model'). Computation of variance
1327 is available for all models. A gamma-correction is possible for
1328 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1329 to remove sites with missing data on a pairwise basis. The option
1330 `GCcontent' has been removed.
1332 o read.GenBank() has a new option (species.names) which specifies
1333 whether to return the species names of the organisms in addition
1334 to the accession numbers of the sequences (this is the default
1337 o write.nexus() can now write several trees in the same NEXUS file.
1339 o drop.tip() has a new option `root.edge' that allows to specify the
1340 new root edge if internal branches are trimmed.
1345 o as.phylo.hclust() failed if some labels had parentheses: this
1348 o Several bugs were fixed in all.equal.phylo(). This function now
1349 returns the logical TRUE if the trees are identical but with
1350 different representations (a report was printed previously).
1352 o read.GenBank() did not correctly handle ambiguous base codes:
1358 o birthdeath() now returns an object of class "birthdeath" for
1359 which there is a print method.
1363 CHANGES IN APE VERSION 1.4
1368 o The new function nj() performs phylogeny estimation with the
1369 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1372 o The new function which.edge() identifies the edges of a tree
1373 that belong to a group specified as a set of tips.
1375 o The new function as.phylo.phylog() converts an object of class
1376 "phylog" (from the package ade4) into an object of class
1379 o The new function axisPhylo() draws axes on the side of a
1382 o The new function howmanytrees() calculates the number of trees
1383 in different cases and giving a number of tips.
1385 o write.tree() has a new option `multi.line' (TRUE by default) to
1386 write a Newick tree on several lines rather than on a single
1389 o The functionalities of zoom() have been extended. Several
1390 subtrees can be visualized at the same time, and they are marked
1391 on the main tree with colors. The context of the subtrees can be
1392 marked with the option `subtree' (see below).
1394 o drop.tip() has a new option `subtree' (FALSE by default) which
1395 specifies whether to output in the tree how many tips have been
1398 o The arguments of add.scale.bar() have been redefined and have
1399 now default values (see ?add.scale.bar for details). This
1400 function now works even if the plotted tree has no edge length.
1402 o plot.phylo() can now plot radial trees, but this does not take
1403 edge lengths into account.
1405 o In plot.phylo() with `type = "phylogram"', if the values of
1406 `edge.color' and `edge.width' are identical for sister-branches,
1407 they are propagated to the vertical line that link them.
1412 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1413 crashing. This is fixed.
1415 o In plot.phylo(), the options `edge.color' and `edge.width' are
1416 now properly recycled; their default values are now "black" and
1419 o A bug has been fixed in write.nexus().
1424 o The function node.depth.edgelength() has been removed and
1425 replaced by a C code.
1429 CHANGES IN APE VERSION 1.3-1
1434 o The new function nodelabels() allows to add labels to the nodes
1435 of a tree using text or plotting symbols in a flexible way.
1437 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1438 numeric values specifying the lower and upper limits on the x-
1439 and y-axes. This allows to leave some space on any side of the
1440 tree. If a single value is given, this is taken as the upper
1445 CHANGES IN APE VERSION 1.3
1450 o The new function phymltest() calls the software PHYML and fits
1451 28 models of DNA sequence evolution. There are a print method to
1452 display likelihood and AIC values, a summary method to compute
1453 the hierarchical likelihood ratio tests, and a plot method to
1454 display graphically the AIC values of each model.
1456 o The new function yule.cov() fits the Yule model with covariates,
1457 a model where the speciation rate is affected by several species
1458 traits through a generalized linear model. The parameters are
1459 estimated by maximum likelihood.
1461 o Three new functions, corBrownian(), corGrafen(), and
1462 corMartins(), compute the expected correlation structures among
1463 species given a phylogeny under different models of evolution.
1464 These can be used for GLS comparative phylogenetic methods (see
1465 the examples). There are coef() and corMatrix() methods and an
1466 Initialize.corPhyl() function associated.
1468 o The new function compar.cheverud() implements Cheverud et al.'s
1469 (1985; Evolution 39:1335) phylogenetic comparative method.
1471 o The new function varcomp() estimates variance components; it has
1474 o Two new functions, panel.superpose.correlogram() and
1475 plot.correlogramList(), allow to plot several phylogenetic
1478 o The new function node.leafnumber() computes the number of leaves
1479 of a subtree defined by a particular node.
1481 o The new function node.sons() gets all tags of son nodes from a
1484 o The new function compute.brlen() computes the branch lengths of
1485 a tree according to a specified method.
1487 o plot.phylo() has three new options: "cex" controls the size of
1488 the (tip and node) labels (thus it is no more needed to change
1489 the global graphical parameter), "direction" which allows to
1490 plot the tree rightwards, leftwards, upwards, or downwards, and
1491 "y.lim" which sets the upper limit on the y-axis.
1496 o Some functions which try to match tip labels and names of
1497 additional data (e.g. vector) are likely to fail if there are
1498 typing or syntax errors. If both series of names do not perfectly
1499 match, they are ignored and a warning message is now issued.
1500 These functions are bd.ext, compar.gee, pic. Their help pages
1501 have been clarified on this point.
1505 CHANGES IN APE VERSION 1.2-7
1510 o The new function root() reroots a phylogenetic tree with respect
1511 to a specified outgroup.
1513 o The new function rotate() rotates an internal branch of a tree.
1515 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1516 trees) controls the display of the tip labels in unrooted trees.
1517 This display has been greatly improved: the tip labels are now not
1518 expected to overlap with the tree (particularly if lab4ut =
1519 "axial"). In all cases, combining appropriate values of "lab4ut"
1520 and the font size (via "par(cex = )") should result in readable
1521 unrooted trees. See ?plot.phylo for some examples.
1523 o In drop.tip(), the argument `tip' can now be numeric or character.
1528 o drop.tip() did not work correctly with trees with no branch
1529 lengths: this is fixed.
1531 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1532 plotted with some line crossings: this is now fixed.
1536 CHANGES IN APE VERSION 1.2-6
1541 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1542 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1543 to implement comparative methods with an autocorrelation approach.
1545 o A new data set describing some life history traits of Carnivores
1551 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1556 o When plotting a tree with plot.phylo(), the new default of the
1557 option `label.offset' is now 0, so the labels are always visible.
1561 CHANGES IN APE VERSION 1.2-5
1566 o The new function bd.ext() fits a birth-death model with combined
1567 phylogenetic and taxonomic data, and estimates the corresponding
1568 speciation and extinction rates.
1573 o The package gee is no more required by ape but only suggested
1574 since only the function compar.gee() calls gee.
1578 CHANGES IN APE VERSION 1.2-4
1583 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1584 and lines.popsize) implementing a new approach for inferring the
1585 demographic history from genealogies using a reversible jump
1586 MCMC have been introduced.
1588 o The unit of time in the skyline plot and in the new plots can
1589 now be chosen to be actual years, rather than substitutions.
1593 CHANGES IN APE VERSION 1.2-3
1598 o The new function rtree() generates a random binary tree with or
1599 without branch lengths.
1601 o Two new functions for drawing lineages-through-time (LTT) plots
1602 are provided: ltt.lines() adds a LTT curve to an existing plot,
1603 and mltt.plot() does a multiple LTT plot giving several trees as
1604 arguments (see `?ltt.plot' for details).
1609 o Some taxon names made R crashing when calling as.phylo.hclust():
1612 o dist.dna() returned an error with two identical DNA sequences
1613 (only using the Jukes-Cantor method returned 0): this is fixed.
1618 o The function dist.phylo() has been re-written using a different
1619 algorithm: it is now about four times faster.
1621 o The code of branching.times() has been improved: it is now about
1626 CHANGES IN APE VERSION 1.2-2
1631 o The new function seg.sites() finds the segregating sites in a
1632 sample of DNA sequences.
1637 o A bug introduced in read.tree() and in read.nexus() with version
1640 o A few errors were corrected and a few examples were added in the
1645 CHANGES IN APE VERSION 1.2-1
1650 o plot.phylo() can now draw the edge of the root of a tree if it
1651 has one (see the new option `root.edge', its default is FALSE).
1656 o A bug was fixed in read.nexus(): files with semicolons inside
1657 comment blocks were not read correctly.
1659 o The behaviour of read.tree() and read.nexus() was corrected so
1660 that tree files with badly represented root edges (e.g., with
1661 an extra pair of parentheses, see the help pages for details)
1662 are now correctly represented in the object of class "phylo";
1663 a warning message is now issued.
1667 CHANGES IN APE VERSION 1.2
1672 o plot.phylo() has been completely re-written and offers several
1673 new functionalities. Three types of trees can now be drawn:
1674 phylogram (as previously), cladogram, and unrooted tree; in
1675 all three types the branch lengths can be drawn using the edge
1676 lengths of the phylogeny or not (e.g., if the latter is absent).
1677 The vertical position of the nodes can be adjusted with two
1678 choices (see option `node.pos'). The code has been re-structured,
1679 and two new functions (potentially useful for developpers) are
1680 documented separately: node.depth.edgelength() and node.depth();
1681 see the respective help pages for details.
1683 o The new function zoom() allows to explore very large trees by
1684 focusing on a small portion of it.
1686 o The new function yule() fits by maximum likelihood the Yule model
1687 (birth-only process) to a phylogenetic tree.
1689 o Support for writing DNA sequences in FASTA format has been
1690 introduced in write.dna() (support for reading sequences in
1691 this format was introduced in read.dna() in version 1.1-2).
1692 The function has been completely re-written, fixing some bugs
1693 (see below); the default behaviour is no more to display the
1694 sequences on the standard output. Several options have been
1695 introduced to control the sequence printing in a flexible
1696 way. The help page has been extended.
1698 o A new data set is included: a supertree of bats in NEXUS format.
1703 o In theta.s(), the default of the option `variance' has
1704 been changed to `FALSE' (as was indicated in the help page).
1706 o Several bugs were fixed in the code of all.equal.phylo().
1708 o Several bugs were fixed in write.dna(), particularly this
1709 function did not work with `format = "interleaved"'.
1711 o Various errors were corrected in the help pages.
1716 o The argument names of as.hclust.phylo() have been changed
1717 from "(phy)" to "(x, ...)" to conform to the definition of
1718 the corresponding generic function.
1720 o gamma.stat() has been renamed gammaStat() to avoid confusion
1721 since gamma() is a generic function.
1725 CHANGES IN APE VERSION 1.1-3
1730 o base.freq() previously did not return a value of 0 for
1731 bases absent in the data (e.g., a vector of length 3 was
1732 returned if one base was absent). This is now fixed (a
1733 vector of length 4 is always returned).
1735 o Several bugs were fixed in read.nexus(), including that this
1736 function did not work in this absence of a "TRANSLATE"
1737 command in the NEXUS file, and that the commands were
1742 CHANGES IN APE VERSION 1.1-2
1747 o The Tamura and Nei (1993) model of DNA distance is now implemented
1748 in dist.dna(): five models are now available in this function.
1750 o A new data set is included: a set of 15 sequences of the
1751 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1757 o A bug in read.nexus() was fixed.
1759 o read.dna() previously did not work correctly in most cases.
1760 The function has been completely re-written and its help page
1761 has been considerably extended (see ?read.dna for details).
1762 Underscores (_) in taxon names are no more replaced with
1763 spaces (this behaviour was undocumented).
1765 o A bug was fixed in write.dna().
1769 CHANGES IN APE VERSION 1.1-1
1774 o A bug in read.tree() introduced in APE 1.1 was fixed.
1776 o A bug in compar.gee() resulted in an error when trying to fit
1777 a model with `family = "binomial"'. This is now fixed.
1781 CHANGES IN APE VERSION 1.1
1786 o The Klastorin (1982) method as suggested by Misawa and Tajima
1787 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1788 on the basis of phylogenetic trees has been implemented (see
1789 the function klastorin()).
1791 o Functions have been added to convert APE's "phylo" objects in
1792 "hclust" cluster objects and vice versa (see the help page of
1793 as.phylo for details).
1795 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1796 are introduced for the estimation of absolute evolutionary rates
1797 (ratogram) and dated clock-like trees (chronogram) from
1798 phylogenetic trees using the non-parametric rate smoothing approach
1799 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1801 o A summary method is now provided printing a summary information on a
1802 phylogenetic tree with, for instance, `summary(tree)'.
1804 o The behaviour of read.tree() was changed so that all spaces and
1805 tabulations in tree files are now ignored. Consequently, spaces in tip
1806 labels are no more allowed. Another side effect is that read.nexus()
1807 now does not replace the underscores (_) in tip labels with spaces
1808 (this behaviour was undocumented).
1810 o The function plot.phylo() has a new option (`underscore') which
1811 specifies whether the underscores in tip labels should be written on
1812 the plot as such or replaced with spaces (the default).
1814 o The function birthdeath() now computes 95% confidence intervals of
1815 the estimated parameters using profile likelihood.
1817 o Three new data sets are included: a gene tree estimated from 36
1818 landplant rbcL sequences, a gene tree estimated from 32 opsin
1819 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1824 o A bug was fixed in dist.gene() where nothing was returned.
1826 o A bug in plot.mst() was fixed.
1828 o A bug in vcv.phylo() resulted in false correlations when the
1829 option `cor = TRUE' was used (now fixed).
1833 CHANGES IN APE VERSION 1.0
1838 o Two new functions, read.dna() and write.dna(), read/write in a file
1839 DNA sequences in interleaved or in sequential format.
1841 o Two new functions, read.nexus() and write.nexus(), read/write trees
1844 o The new function bind.tree() allows to bind two trees together,
1845 possibly handling root edges to give internal branches.
1847 o The new function drop.tip() removes the tips in a phylogenetic tree,
1848 and trims (or not) the corresponding internal branches.
1850 o The new function is.ultrametric() tests if a tree is ultrametric.
1852 o The function plot.phylo() has more functionalities such as drawing the
1853 branches with different colours and/or different widths, showing the
1854 node labels, controling the position and font of the labels, rotating
1855 the labels, and controling the space around the plot.
1857 o The function read.tree() can now read trees with no branch length,
1858 such as "(a,b),c);". Consequently, the element `edge.length' in
1859 objects of class "phylo" is now optional.
1861 o The function write.tree() has a new default behaviour: if the default
1862 for the option `file' is used (i.e. file = ""), then a variable of
1863 mode character containing the tree in Newick format is returned which
1864 can thus be assigned (e.g., tree <- write.tree(phy)).
1866 o The function read.tree() has a new argument `text' which allows
1867 to read the tree in a variable of mode character.
1869 o A new data set is included: the phylogenetic relationships among
1870 the orders of birds from Sibley and Ahlquist (1990).
1874 CHANGES IN APE VERSION 0.2-1
1879 o Several bugs were fixed in the help pages.
1883 CHANGES IN APE VERSION 0.2
1888 o The function write.tree() writes phylogenetic trees (objects of class
1889 "phylo") in an ASCII file using the Newick parenthetic format.
1891 o The function birthdeath() fits a birth-death model to branching times
1892 by maximum likelihood, and estimates the corresponding speciation and
1895 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1898 o The function is.binary.tree() tests whether a phylogeny is binary.
1900 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1901 as well as some methods are introduced.
1903 o Several functions, including some generics and methods, for computing
1904 skyline plot estimates (classic and generalized) of effective
1905 population size through time are introduced and replace the function
1906 skyline.plot() in version 0.1.
1908 o Two data sets are now included: the phylogenetic relationships among
1909 the families of birds from Sibley and Ahlquist (1990), and an
1910 estimated clock-like phylogeny of HIV sequences sampled in the
1911 Democratic Republic of Congo.
1914 DEPRECATED & DEFUNCT
1916 o The function skyline.plot() in ape 0.1 has been deprecated and
1917 replaced by more elaborate functions (see above).
1922 o Two important bugs were fixed in plot.phylo(): phylogenies with
1923 multichotomies not at the root or not with only terminal branches,
1924 and phylogenies with a single node (i.e. only terminal branches)
1925 did not plot. These trees should be plotted correctly now.
1927 o Several bugs were fixed in diversi.time() in the computation of
1930 o Various errors were corrected in the help pages.