1 CHANGES IN APE VERSION 2.4-1
6 o bind.tree() failed when 'y' had no root edge.
8 o read.nexus() shuffled tip labels when the trees have no branch
9 lengths and there is a TRANSLATE block.
11 o plot.multiPhylo() crashed R when plotting a list of trees with
12 "compressed tip labels".
14 o write.nexus() did not translate the taxa names when asked for.
18 CHANGES IN APE VERSION 2.4
23 o base.freq() has a new option 'freq' to return the counts; the
24 default is still to return the proportions.
29 o seg.sites() did not handle ambiguous nucleotides correctly: they
32 o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
33 the tree: the argument is now ignored.
35 o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
41 o Trying to plot a tree with a single tip now returns NULL with a
42 warning (it returned an error previously).
44 o The way lines representing nodes are coloured in phylograms has
45 been modified (as well as their widths and types) following some
46 users' request; this is only for dichotomous nodes.
48 o The argument 'adj' in [node][tip][edge]labels() now works when
49 using 'pie' or 'thermo'.
51 o A more informative message error is now returned by dist.dna() when
52 'model' is badly specified (partial matching of this argument is
55 o Deprecated functions are now listed in a help page: see
56 help("ape-defunct") with the quotes.
61 o The functions heterozygosity, nuc.div, theta.h, theta.k and
62 theta.s have been moved from ape to pegas.
64 o The functions mlphylo, DNAmodel and sh.test have been removed.
68 CHANGES IN APE VERSION 2.3-3
73 o add.scale.bar() always drew a horizontal bar.
75 o zoom() shuffled tips with unrooted trees.
77 o write.nexus() failed to write correctly trees with a "TipLabel"
80 o rcoal() failed to compute branch lengths with very large n.
82 o A small bug was fixed in compar.cheverud() (thanks to Michael
85 o seg.sites() failed when passing a vector.
87 o drop.tip() sometimes shuffled tip labels.
89 o root() shuffled node labels with 'resolve.root = TRUE'.
93 CHANGES IN APE VERSION 2.3-2
98 o all.equal.phylo() did not compare unrooted trees correctly.
100 o dist.topo(... method = "PH85") did not treat unrooted trees
101 correctly (thanks to Tim Wallstrom for the fix).
103 o root() sometimes failed to test for the monophyly of the
106 o extract.clade() sometimes included too many edges.
108 o vcv.phylo() did not work correctly when the tree is in
111 o nj() did not handle correctly distance matrices with many 0's.
112 The code has also been significantly improved: 7, 70, 160 times
113 faster with n = 100, 500, 1000, respectively.
117 CHANGES IN APE VERSION 2.3-1
122 o The new function is.monophyletic tests the monophyly of a group.
124 o There is now a c() method for lists of class "DNAbin".
126 o yule.cov() now fits the null model, and its help page has been
127 corrected with respect to this change.
129 o drop.tip() has a new option 'rooted' to force (or not) a tree
130 to be treated as (un)rooted.
135 o dist.gene() failed on most occasions with the default
136 pairwise.deletion = FALSE.
138 o read.tree() failed to read correctly the tree name(s).
140 o boot.phylo() now treats correctly data frames.
142 o del.gaps() did not copy the rownames of a matrix.
144 o A small bug was fixed in CDAM.global().
146 o ace() failed with large data sets. Thanks to Rich FitzJohn for
147 the fix. With other improvements, this function is now about 6
150 o write.tree() failed with objects of class "multiPhylo".
152 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
157 o [.multiPhylo and [.DNAbin now respect the original class.
159 o Instances of the form class(phy) == "phylo" have been replaced
160 by inherits(phy, "phylo").
162 o rcoal() is now faster.
167 o klastorin() has been removed.
171 CHANGES IN APE VERSION 2.3
176 o The new functions CADM.global and CADM.post, contributed by
177 Pierre Legendre, test the congruence among several distance
180 o The new function yule.time fits a user-defined time-dependent
181 Yule model by maximum likelihood.
183 o The new function makeNodeLabel creates and/or modifies node
184 labels in a flexible way.
186 o read.tree() and write.tree() have been modified so that they can
187 handle individual tree names.
189 o plot.phylo() has a new argument 'edge.lty' that specifies the
190 types of lines used for the edges (plain, dotted, dashed, ...)
192 o phymltest() has been updated to work with PhyML 3.0.1.
197 o drop.tip() shuffled tip labels in some cases.
199 o drop.tip() did not handle node.label correctly.
201 o is.ultrametric() now checks the ordering of the edge matrix.
203 o ace() sometimes returned negative values of likelihoods of
204 ancestral states (thanks to Dan Rabosky for solving this long
210 o The data set xenarthra has been removed.
214 CHANGES IN APE VERSION 2.2-4
218 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
219 now fixed. (Thanks to Peter Wragg for the fix!)
221 o A warning message occurred for no reason with ace(method="GLS").
226 o There is now a general help page displayed with '?ape'.
230 CHANGES IN APE VERSION 2.2-3
235 o The new function extract.clade extracts a clade from a tree by
236 specifying a node number or label.
238 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
239 operations of the same names.
241 o dist.dna() can now return the number of site differences by
242 specifying model="N".
247 o chronopl() did not work with CV = TRUE.
249 o read.nexus() did not work correctly in some situations (trees on
250 multiple lines with different numbers of lines and/or with
251 comments inserted within the trees).
253 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
254 the number of lineages with non-binary trees.
259 o ape has now a namespace.
261 o drop.tip() has been improved: it should be much faster and work
262 better in some cases (e.g., see the example in ?zoom).
266 CHANGES IN APE VERSION 2.2-2
271 o dist.gene() has been substantially improved and gains an option
274 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
280 o prop.part() failed with a single tree with the default option
281 'check.labels = TRUE'.
283 o summary.DNAbin() failed to display correctly the summary of
284 sequence lengths with lists of sequences of 10,000 bases or more
285 (because summary.default uses 4 significant digits by default).
287 o read.nexus() failed to read a file with a single tree with line
288 breaks in the Newick string.
290 o del.gaps() returned a list of empty sequences when there were no
296 o phymltest() has been updated for PhyML 3.0 and gains an option
297 'append', whereas the option 'path2exec' has been removed.
299 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
300 which is returned unchanged (instead of an error).
302 o The data sets bird.orders and bird.families are now stored as
303 Newick strings; i.e., the command data(bird.orders) calls
308 CHANGES IN APE VERSION 2.2-1
313 o The new function makeLabel() helps to modify labels of trees,
314 lists of trees, or DNA sequences, with several utilities to
315 truncate and/or make them unique, substituting some
316 characters, and so on.
318 o The new function del.gaps() removes insertion gaps ("-") in a
319 set of DNA sequences.
321 o read.dna() can now read Clustal files (*.aln).
326 o root() failed with 'resolve.root = TRUE' when the root was
327 already the specified root.
329 o Several bugs were fixed in mlphylo().
331 o collapsed.singles() did not propagate the 'Nnode' and
332 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
334 o read.nexus() failed to remove correctly the comments within
337 o read.nexus() failed to read a file with a single tree and no
338 translation of tip labels.
340 o read.nexus() failed to place correctly tip labels when reading
341 a single tree with no edge lengths.
343 o A bug was fixed in sh.test().
348 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
351 o The option 'check.labels' of consensus() and prop.part() is now
354 o write.dna() now does not truncate names to 10 characters with
359 CHANGES IN APE VERSION 2.2
364 o Four new functions have been written by Damien de Vienne for the
365 graphical exploration of large trees (cophyloplot, subtrees,
366 subtreeplot), and to return the graphical coordinates of tree
369 o The new functions corPagel and corBlomberg implement the Pagel's
370 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
372 o chronopl() has been improved and gains several options: see its
373 help page for details.
375 o boot.phylo() has now an option 'trees' to possibly return the
376 bootstraped trees (the default is FALSE).
378 o prop.part() has been improved and should now be faster in all
384 o read.dna() failed if "?" occurred in the first 10 sites of the
387 o The x/y aspect of the plot is now respected when plotting a
388 circular tree (type = "r" or "f").
390 o Drawing the tip labels sometimes failed when plotting circular
393 o zoom() failed when tip labels were used instead of their numbers
394 (thanks to Yan Wong for the fix).
396 o drop.tip() failed with some trees (fixed by Yan Wong).
398 o seg.sites() failed with a list.
400 o consensus() failed in some cases. The function has been improved
401 as well and is faster.
405 CHANGES IN APE VERSION 2.1-3
410 o A bug in read.nexus() made the Windows R-GUI crash.
412 o An error was fixed in the computation of ancestral character
413 states by generalized least squares in ace().
415 o di2multi() did not modify node labels correctly.
417 o multi2di() failed if the tree had its attribute "order" set to
422 CHANGES IN APE VERSION 2.1-2
427 o There three new methods for the "multiPhylo" class: str, $,
430 o root() gains the options 'node' and 'resolve.root'
431 (FALSE by default) as well as its code being improved.
433 o mltt.plot() has now an option 'log' used in the same way
434 than in plot.default().
439 o mltt.plot() failed to display the legend with an unnamed
442 o nodelabels() with pies now correcly uses the argument
443 'cex' to draw symbols of different sizes (which has
444 worked already for thermometers).
446 o read.nexus() generally failed to read very big files.
451 o The argument 'family' of compar.gee() can now be a function
452 as well as a character string.
454 o read.tree() and read.nexus() now return an unnamed list if
457 o read.nexus() now returns a modified object of class "multiPhylo"
458 when there is a TRANSLATE block in the NEXUS file: the individual
459 trees have no 'tip.label' vector, but the list has a 'TipLabel'
460 attribute. The new methods '$' and '[[' set these elements
461 correctly when extracting trees.
465 CHANGES IN APE VERSION 2.1-1
470 o The new function rmtree generates lists of random trees.
472 o rcoal() now generates a genuine coalescent tree by default
473 (thanks to Vladimir Minin for the code).
478 o nuc.div() returned an incorrect value with the default
479 pairwise.deletion = FALSE.
484 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
485 have been improved so that they are stabler and faster.
487 o R packages used by ape are now loaded silently; lattice and gee
488 are loaded only when needed.
492 CHANGES IN APE VERSION 2.1
497 o The new function identify.phylo identifies clades on a plotted
498 tree using the mouse.
500 o It is now possible to subset a list of trees (object of class
501 "multiPhylo") with "[" while keeping its class correct.
503 o The new function as.DNAbin.alignment converts DNA sequences
504 stored in the "alignment" format of the package seqinr into
505 an object of class "DNAbin".
507 o The new function weight.taxo2 helps to build similarity matrices
508 given two taxonomic levels (usually called by other functions).
510 o write.tree() can now take a list of trees (class "multiPhylo")
511 as its main argument.
513 o plot.correlogram() and plot.correlogramList() have been
514 improved, and gain several options (see the help page for
515 details). A legend is now plotted by default.
520 o dist.dna() returned some incorrect values with `model = "JC69"'
521 and `pairwise.deletion = TRUE'. This affected only the
522 distances involving sequences with missing values. (Thanks
523 to Bruno Toupance for digging this bug out.)
525 o write.tree() failed with some trees: this is fixed by removing
526 the `multi.line' option (trees are now always printed on a
529 o read.nexus() did not correctly detect trees with multiple root
530 edges (see OTHER CHANGES).
535 o The code of mlphylo() has been almost entirely rewritten, and
536 should be much stabler. The options have been also greatly
537 simplified (see ?mlphylo and ?DNAmodel for details).
539 o The internal function nTips has been renamed klastorin_nTips.
541 o The code of is.ultrametric() contained redundancies and has
544 o The code of Moran.I() and of correlogram.formula() have been
547 o read.tree() and read.nexus() now return an error when trying to
548 read a tree with multiple root edges (see BUG FIXES). The
549 correction applied in previous version did not work in all
552 o The class c("multi.tree", "phylo") has been renamed
558 o There is now a vignette in ape: see vignette("MoranI", "ape").
563 o as.matching() and as.phylo.matching() do not support branch
566 o correlogram.phylo() and discrete.dist() have been removed.
570 CHANGES IN APE VERSION 2.0-2
575 o The new function matexpo computes the exponential of a square
578 o The new function unique.multi.tree removes duplicate trees from
581 o yule() has a new option `use.root.edge = FALSE' that specifies
582 to ignore, by default, the root edge of the tree if it exists.
587 o which.edge() failed when the index of a single terminal edge was
590 o In diversi.time(), the values returned for model C were
593 o A bug was fixed in yule() that affected the calculation of the
594 likelihood in the presence of ties in the branching times.
596 o There was a bug in the C function mat_expo4x4 affecting the
597 calculations of the transition probabilities for models HKY and
600 o A small bug was fixed in as.matrix.DNAbin (thanks to James
603 o rtree() did not `shuffle' the tip labels by default, so only a
604 limited number of labelled topologies could be generated.
608 CHANGES IN APE VERSION 2.0-1
613 o The three new functions bionj, fastme.ols, and fastme.bal
614 perform phylogeny estimation by the BIONJ and fastME methods in
615 OLS and balanced versions. This is a port to R of previous
616 previous programs done by Vincent Lefort.
618 o The new function chronoMPL performs molecular dating with the
619 mean path lengths method of Britton et al. (2002, Mol. Phyl.
622 o The new function rotate, contributed by Christoph Heibl, swaps
623 two clades connected to the same node. It works also with
624 multichotomous nodes.
626 o The new `method' as.matrix.DNAbin() may be used to convert
627 easily DNA sequences stored in a list into a matrix while
628 keeping the names and the class.
633 o chronopl() failed when some branch lengths were equal to zero:
634 an error message is now returned.
636 o di2multi() failed when there was a series of consecutive edges
641 CHANGES IN APE VERSION 1.10-2
646 o plot.phylo() can now plot circular trees: the option is type =
647 "fan" or type = "f" (to avoid the ambiguity with type = "c").
649 o prop.part() has a new option `check.labels = FALSE' which allows
650 to considerably speed-up the calculations of bipartitions. As a
651 consequence, calculations of bootstrap values with boot.phylo()
652 should be much faster.
657 o read.GenBank() did not return correctly the list of species as
658 from ape 1.10: this is fixed in this version
660 o Applying as.phylo() on a tree of class "phylo" failed: the
661 object is now returned unchanged.
665 CHANGES IN APE VERSION 1.10-1
670 o The three new functions Ntip, Nnode, and Nedge return, for a
671 given tree, the number of tips, nodes, or edges, respectively.
676 o read.nexus() did not set correctly the class of the returned
677 object when reading multiple trees.
679 o mllt.plot() failed with objects of class c("multi.tree",
682 o unroot() did not work correctly in most cases.
684 o reorder.phylo() made R freeze in some occasions.
686 o Plotting a tree in pruningwise order failed.
688 o When plotting an unrooted tree, the tip labels where not all
689 correctly positioned if the option `cex' was used.
693 CHANGES IN APE VERSION 1.10
698 o Five new `method' functions have been introduced to manipulate
699 DNA sequences in binary format (see below).
701 o Three new functions have been introduced to convert between the
702 new binary and the character formats.
704 o The new function as.alignment converts DNA sequences stored as
705 single characters into the class "alignment" used by the package
708 o read.dna() and read.GenBank() have a new argument `as.character'
709 controlling whether the sequences are returned in binary format
715 o root() failed when the tree had node labels: this is fixed.
717 o plot.phylo() did not correctly set the limits on the y-axis with
718 the default setting: this is fixed.
720 o dist.dna() returned a wrong result for the LogDet, paralinear,
721 and BH87 models with `pairwise.deletion = TRUE'.
726 o DNA sequences are now internally stored in a binary format. See
727 the document "A Bit-Level Coding Scheme for Nucleotides" for the
728 details. Most functions analyzing DNA functions have been
729 modified accordingly and are now much faster (dist.dna is now
730 ca. 60 times faster).
734 CHANGES IN APE VERSION 1.9-4
739 o A bug was fixed in edgelabels().
741 o as.phylo.hclust() did not work correctly when the object of
742 class "hclust" has its labels set to NULL: the returned tree has
743 now its tip labels set to "1", "2", ...
745 o consensus could fail if some tip labels are a subset of others
746 (e.g., "a" and "a_1"): this is now fixed.
748 o mlphylo() failed in most cases if some branch lengths of the
749 initial tree were greater than one: an error message is now
752 o mlphylo() failed in most cases when estimating the proportion of
753 invariants: this is fixed.
757 CHANGES IN APE VERSION 1.9-3
762 o The new function edgelabels adds labels on the edge of the tree
763 in the same way than nodelabels or tiplabels.
768 o multi2di() did not handle correctly branch lengths with the
769 default option `random = TRUE': this is now fixed.
771 o A bug was fixed in nuc.div() when using pairwise deletions.
773 o A bug occurred in the analysis of bipartitions with large
774 numbers of large trees, with consequences on prop.part,
775 prop.clades, and boot.phylo.
777 o The calculation of the Billera-Holmes-Vogtmann distance in
778 dist.topo was wrong: this has been fixed.
782 CHANGES IN APE VERSION 1.9-2
787 o The new function ladderize reorganizes the internal structure of
788 a tree to plot them left- or right-ladderized.
790 o The new function dist.nodes computes the patristic distances
791 between all nodes, internal and terminal, of a tree. It replaces
792 the option `full = TRUE' of cophenetic.phylo (see below).
797 o A bug was fixed in old2new.phylo().
799 o Some bugs were fixed in chronopl().
801 o The edge colours were not correctly displayed by plot.phylo
802 (thank you to Li-San Wang for the fix).
804 o cophenetic.phylo() failed with multichotomous trees: this is
810 o read.dna() now returns the sequences in a matrix if they are
811 aligned (interleaved or sequential format). Sequences in FASTA
812 format are still returned in a list.
814 o The option `full' of cophenetic.phylo() has been removed because
815 it could not be used from the generic.
820 o rotate() has been removed; this function did not work correctly
825 CHANGES IN APE VERSION 1.9-1
830 o Trees with a single tip were not read correctly in R as the
831 element `Nnode' was not set: this is fixed.
833 o unroot() did not set correctly the number of nodes of the
834 unrooted tree in most cases.
836 o read.GenBank() failed when fetching very long sequences,
837 particularly of the BX-series.
839 o A bug was introduced in read.tree() with ape 1.9: it has been
844 CHANGES IN APE VERSION 1.9
849 o There are two new print `methods' for trees of class "phylo" and
850 lists of trees of class "multi.tree", so that they are now
851 displayed in a compact and informative way.
853 o There are two new functions, old2new.phylo and new2old.phylo,
854 for converting between the old and new coding of the class
857 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
858 LogDet ("logdet"), and paralinear ("paralin").
860 o compute.brlen() has been extended: several methods are now
861 available to compute branch lengths.
863 o write.dna() can now handle matrices as well as lists.
868 o cophenetic.phylo() sometimes returned a wrong result with
869 multichotomous trees: this is fixed.
871 o rotate() failed when a single tip was specified: the tree is now
874 o ace() did not return the correct index matrix with custom
875 models: this is fixed.
877 o multi2di() did not work correctly when resolving multichotomies
878 randomly: the topology was always the same, only the arrangement
879 of clades was randomized: this is fixed. This function now
880 accepts trees with no branch lengths.
882 o The output of diversi.gof() was blurred by useless prints when a
883 user distribution was specified. This has been corrected, and
884 the help page of this function has been expanded.
889 o The internal structure of the class "phylo" has been changed:
890 see the document "Definition of Formats for Coding Phylogenetic
891 Trees in R" for the details. In addition, the code of most
892 functions has been improved.
894 o Several functions have been improved by replacing some R codes
895 by C codes: pic, plot.phylo, and reorder.phylo.
897 o There is now a citation information: see citation("ape") in R.
899 o write.tree() now does not add extra 0's to branch lengths so
900 that 1.23 is printed "1.23" by default, not "1.2300000000".
902 o The syntax of bind.tree() has been simplified. This function now
903 accepts trees with no branch lengths, and handles correctly node
906 o The option `as.numeric' of mrca() has been removed.
908 o The unused options `format' and `rooted' of read.tree() have
911 o The unused option `format' of write.tree() has been removed.
913 o The use of node.depth() has been simplified.
917 CHANGES IN APE VERSION 1.8-5
922 o Two new functions read.nexus.data() and write.nexus.data(),
923 contributed by Johan Nylander, allow to read and write molecular
924 sequences in NEXUS files.
926 o The new function reorder.phylo() reorders the internal structure
927 of a tree of class "phylo". It is used as the generic, e.g.,
930 o read.tree() and read.nexus() can now read trees with a single
933 o The new data set `cynipids' supplies a set of protein sequences
939 o The code of all.equal.phylo() has been completely rewritten
940 (thanks to Benoît Durand) which fixes several bugs.
942 o read.tree() and read.nexus() now checks the labels of the tree
943 to remove or substitute any characters that are illegal in the
944 Newick format (parentheses, etc.)
946 o A negative P-value could be returned by mantel.test(): this is
951 CHANGES IN APE VERSION 1.8-4
956 o The new function sh.test() computes the Shimodaira-
959 o The new function collapse.singles() removes the nodes with a
960 single descendant from a tree.
962 o plot.phylo() has a new argument `tip.color' to specify the
965 o mlphylo() has now an option `quiet' to control the display of
966 the progress of the analysis (the default is FALSE).
971 o read.dna() did not read correctly sequences in sequential format
972 with leading alignment gaps "-": this is fixed.
974 o ace() returned a list with no class so that the generic
975 functions (anova, logLik, ...) could not be used directly. This
976 is fixed as ace() now returns an object of class "ace".
978 o anova.ace() had a small bug when computing the number of degrees
979 of freedom: this is fixed.
981 o mlphylo() did not work when the sequences were in a matrix or
982 a data frame: this is fixed.
984 o rtree() did not work correctly when trying to simulate an
985 unrooted tree with two tips: an error message is now issued.
990 o The algorithm of rtree() has been changed: it is now about 40,
991 100, and 130 times faster for 10, 100, and 1000 tips,
996 CHANGES IN APE VERSION 1.8-3
1001 o There are four new `method' functions to be used with the
1002 results of ace(): logLik(), deviance(), AIC(), and anova().
1004 o The plot method of phymltest has two new arguments: `main' to
1005 change the title, and `col' to control the colour of the
1006 segments showing the AIC values.
1008 o ace() has a new argument `ip' that gives the initial values used
1009 in the ML estimation with discrete characters (see the examples
1010 in ?ace). This function now returns a matrix giving the indices
1011 of the estimated rates when analysing discrete characters.
1013 o nodelabels() and tiplabels() have a new argument `pie' to
1014 represent proportions, with any number of categories, as
1015 piecharts. The use of the option `thermo' has been improved:
1016 there is now no limitation on the number of categories.
1021 o mlphylo() did not work with more than two partitions: this is
1024 o root() failed if the proposed outgroup was already an outgroup
1025 in the tree: this is fixed.
1027 o The `col' argument in nodelabels() and tiplabels() was not
1028 correctly passed when `text' was used: this is fixed.
1030 o Two bugs were fixed in mlphylo(): parameters were not always
1031 correctly output, and the estimation failed in some cases.
1033 o plot.phylo() was stuck when given a tree with a single tip: this
1034 is fixed and a message error is now returned.
1036 o An error was corrected in the help page of gammaStat regarding
1037 the calculation of P-values.
1039 o Using gls() could crash R when the number of species in the tree
1040 and in the variables were different: this is fixed.
1044 CHANGES IN APE VERSION 1.8-2
1049 o The new function mlphylo() fits a phylogenetic tree by maximum
1050 likelihood from DNA sequences. Its companion function DNAmodel()
1051 is used to define the substitution model which may include
1052 partitioning. There are methods for logLik(), deviance(), and
1053 AIC(), and the summary() method has been extended to display in
1054 a friendly way the results of this model fitting. Currently, the
1055 functionality is limited to estimating the substitution and
1056 associated parameters and computing the likelihood.
1058 o The new function drop1.compar.gee (used as, e.g., drop1(m))
1059 tests for single effects in GEE-based comparative method. A
1060 warning message is printed if there is not enough degrees of
1066 o An error message was sometimes issued by plot.multi.tree(),
1067 though with no consequence.
1071 CHANGES IN APE VERSION 1.8-1
1076 o There is a new plot method for lists of trees (objects of class
1077 "multi.tree"): it calls plot.phylo() internally and is
1078 documented on the same help page.
1083 o A bug was fixed in the C code that analyzes bipartitions: this
1084 has impact on several functions like prop.part, prop.clades,
1085 boot.phylo, or consensus.
1087 o root() did not work correctly when the specified outgroup had
1088 more than one element: this is fixed.
1090 o dist.dna() sometimes returned a warning inappropriately: this
1093 o If the distance object given to nj() had no rownames, nj()
1094 returned a tree with no tip labels: it now returns tips labelled
1095 "1", "2", ..., corresponding to the row numbers.
1100 o nj() has been slightly changed so that tips with a zero distance
1101 are first aggregated with zero-lengthed branches; the usual NJ
1102 procedure is then performed on a distance matrix without 0's.
1106 CHANGES IN APE VERSION 1.8
1111 o The new function chronopl() estimates dates using the penalized
1112 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1114 o The new function consensus() calculates the consensus tree of a
1117 o The new function evolve.phylo() simulates the evolution of
1118 continuous characters along a phylogeny under a Brownian model.
1120 o The new plot method for objects of class "ancestral" displays a
1121 tree together with ancestral values, as returned by the above
1124 o The new function as.phylo.formula() returns a phylogeny from a
1125 set of nested taxonomic variables given as a formula.
1127 o The new function read.caic() reads trees in CAIC format.
1129 o The new function tiplabels() allows to add labels to the tips
1130 of a tree using text or plotting symbols in a flexible way.
1132 o The new function unroot() unroots a phylogeny.
1134 o multi2di() has a new option, `random', which specifies whether
1135 to resolve the multichotomies randomly (the default) or not.
1137 o prop.part() now returns an object of class "prop.part" for which
1138 there are print (to display a partition in a more friendly way)
1139 and summary (to extract the numbers) methods.
1141 o plot.phylo() has a new option, `show.tip.label', specifying
1142 whether to print the labels of the tips. The default is TRUE.
1144 o The code of nj() has been replaced by a faster C code: it is now
1145 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1148 o write.nexus() now writes whether a tree is rooted or not.
1153 o Two bugs have been fixed in root(): unrooted trees are now
1154 handled corretly, and node labels are now output normally.
1156 o A bug was fixed in phymltest(): the executable couldn't be found
1159 o Three bug have been fixed in ace(): computing the likelihood of
1160 ancestral states of discrete characters failed, custom models
1161 did not work, and the function failed with a null gradient (a
1162 warning message is now returned; this latter bug was also
1163 present in yule.cov() as well and is now fixed).
1165 o pic() hanged out when missing data were present: a message error
1168 o A small bug was fixed in dist.dna() where the gamma correction
1169 was not always correctly dispatched.
1171 o plot.phylo() plotted correctly the root edge only when the tree
1172 was plotted rightwards: this works now for all directions.
1177 o dist.taxo() has been renamed as weight.taxo().
1179 o Various error and warning messages have been improved.
1183 CHANGES IN APE VERSION 1.7
1186 o The new function ace() estimates ancestral character states for
1187 continuous characters (with ML, GLS, and contrasts methods), and
1188 discrete characters (with ML only) for any number of states.
1190 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1191 of directional evolution for continuous characters. The user
1192 specifies the node(s) of the tree where the character optimum
1195 o The new function is.rooted() tests whether a tree (of class
1198 o The new function rcoal() generates random ultrametric trees with
1199 the possibility to specify the function that generates the
1200 inter-nodes distances.
1202 o The new function mrca() gives for all pairs of tips in a tree
1203 (and optionally nodes too) the most recent common ancestor.
1205 o nodelabels() has a new option `thermo' to plot proportions (up
1206 to three classes) on the nodes of a tree.
1208 o rtree() has been improved: it can now generate rooted or
1209 unrooted trees, and the mathematical function that generates the
1210 branch lengths may be specified by the user. The tip labels may
1211 be given directly in the call to rtree. The limit cases (n = 2,
1212 3) are now handled correctly.
1214 o dist.topo() has a new argument `method' with two choices: "PH85"
1215 for Penny and Henny's method (already available before and now
1216 the default), and "BHV01" for the geometric distance by Billera
1217 et al. (2001, Adv. Appl. Math. 27:733).
1219 o write.tree() has a new option, `digits', which specifies the
1220 number of digits to be printed in the Newick tree. By default
1221 digits = 10. The numbers are now always printed in decimal form
1222 (i.e., 1.0e-1 is now avoided).
1224 o dist.dna() can now compute the raw distances between pairs of
1225 DNA sequences by specifying model = "raw".
1227 o dist.phylo() has a new option `full' to possibly compute the
1228 distances among all tips and nodes of the tree. The default if
1234 o Several bugs were fixed in all.equal.phylo().
1236 o dist.dna() did not handle correctly gaps ("-") in alignments:
1237 they are now considered as missing data.
1239 o rotate() did not work if the tips were not ordered: this is
1242 o mantel.test() returned NA in some special cases: this is fixed
1243 and the function has been improved and is now faster.
1245 o A bug was fixed in diversi.gof() where the calculation of A² was
1248 o cherry() did not work correctly under some OSs (mainly Linux):
1251 o is.binary.tree() has been modified so that it works with both
1252 rooted and unrooted trees.
1254 o The documentation of theta.s() was not correct: this has been
1257 o plot.mst() did not work correctly: this is fixed.
1261 CHANGES IN APE VERSION 1.6
1266 o The new function dist.topo() computes the topological distances
1269 o The new function boot.phylo() performs a bootstrap analysis on
1270 phylogeny estimation.
1272 o The new functions prop.part() and prop.clades() analyse
1273 bipartitions from a series of trees.
1278 o read.GenBank() now uses the EFetch utility of NCBI instead of
1279 the usual Web interface: it is now much faster (e.g., 12 times
1280 faster to retrieve 8 sequences, 37 times for 60 sequences).
1285 o Several bugs were fixed in read.dna().
1287 o Several bugs were fixed in diversi.time().
1289 o is.binary.tree() did not work correctly if the tree has no edge
1290 lengths: this is fixed.
1292 o drop.tip() did not correctly propagated the `node.label' of a
1293 tree: this is fixed.
1297 CHANGES IN APE VERSION 1.5
1302 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1303 convert objects between the classes "phylo" and "matching". The
1304 latter implements the representation of binary trees introduced by
1305 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1306 as.matching() has been introduced as well.
1308 o Two new functions, multi2di() and di2multi(), allow to resolve
1309 and collapse multichotomies with branches of length zero.
1311 o The new function nuc.div() computes the nucleotide diversity
1312 from a sample a DNA sequences.
1314 o dist.dna() has been completely rewritten with a much faster
1315 (particularly for large data sets) C code. Eight models are
1316 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1317 option `method' has been renamed `model'). Computation of variance
1318 is available for all models. A gamma-correction is possible for
1319 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1320 to remove sites with missing data on a pairwise basis. The option
1321 `GCcontent' has been removed.
1323 o read.GenBank() has a new option (species.names) which specifies
1324 whether to return the species names of the organisms in addition
1325 to the accession numbers of the sequences (this is the default
1328 o write.nexus() can now write several trees in the same NEXUS file.
1330 o drop.tip() has a new option `root.edge' that allows to specify the
1331 new root edge if internal branches are trimmed.
1336 o as.phylo.hclust() failed if some labels had parentheses: this
1339 o Several bugs were fixed in all.equal.phylo(). This function now
1340 returns the logical TRUE if the trees are identical but with
1341 different representations (a report was printed previously).
1343 o read.GenBank() did not correctly handle ambiguous base codes:
1349 o birthdeath() now returns an object of class "birthdeath" for
1350 which there is a print method.
1354 CHANGES IN APE VERSION 1.4
1359 o The new function nj() performs phylogeny estimation with the
1360 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1363 o The new function which.edge() identifies the edges of a tree
1364 that belong to a group specified as a set of tips.
1366 o The new function as.phylo.phylog() converts an object of class
1367 "phylog" (from the package ade4) into an object of class
1370 o The new function axisPhylo() draws axes on the side of a
1373 o The new function howmanytrees() calculates the number of trees
1374 in different cases and giving a number of tips.
1376 o write.tree() has a new option `multi.line' (TRUE by default) to
1377 write a Newick tree on several lines rather than on a single
1380 o The functionalities of zoom() have been extended. Several
1381 subtrees can be visualized at the same time, and they are marked
1382 on the main tree with colors. The context of the subtrees can be
1383 marked with the option `subtree' (see below).
1385 o drop.tip() has a new option `subtree' (FALSE by default) which
1386 specifies whether to output in the tree how many tips have been
1389 o The arguments of add.scale.bar() have been redefined and have
1390 now default values (see ?add.scale.bar for details). This
1391 function now works even if the plotted tree has no edge length.
1393 o plot.phylo() can now plot radial trees, but this does not take
1394 edge lengths into account.
1396 o In plot.phylo() with `type = "phylogram"', if the values of
1397 `edge.color' and `edge.width' are identical for sister-branches,
1398 they are propagated to the vertical line that link them.
1403 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1404 crashing. This is fixed.
1406 o In plot.phylo(), the options `edge.color' and `edge.width' are
1407 now properly recycled; their default values are now "black" and
1410 o A bug has been fixed in write.nexus().
1415 o The function node.depth.edgelength() has been removed and
1416 replaced by a C code.
1420 CHANGES IN APE VERSION 1.3-1
1425 o The new function nodelabels() allows to add labels to the nodes
1426 of a tree using text or plotting symbols in a flexible way.
1428 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1429 numeric values specifying the lower and upper limits on the x-
1430 and y-axes. This allows to leave some space on any side of the
1431 tree. If a single value is given, this is taken as the upper
1436 CHANGES IN APE VERSION 1.3
1441 o The new function phymltest() calls the software PHYML and fits
1442 28 models of DNA sequence evolution. There are a print method to
1443 display likelihood and AIC values, a summary method to compute
1444 the hierarchical likelihood ratio tests, and a plot method to
1445 display graphically the AIC values of each model.
1447 o The new function yule.cov() fits the Yule model with covariates,
1448 a model where the speciation rate is affected by several species
1449 traits through a generalized linear model. The parameters are
1450 estimated by maximum likelihood.
1452 o Three new functions, corBrownian(), corGrafen(), and
1453 corMartins(), compute the expected correlation structures among
1454 species given a phylogeny under different models of evolution.
1455 These can be used for GLS comparative phylogenetic methods (see
1456 the examples). There are coef() and corMatrix() methods and an
1457 Initialize.corPhyl() function associated.
1459 o The new function compar.cheverud() implements Cheverud et al.'s
1460 (1985; Evolution 39:1335) phylogenetic comparative method.
1462 o The new function varcomp() estimates variance components; it has
1465 o Two new functions, panel.superpose.correlogram() and
1466 plot.correlogramList(), allow to plot several phylogenetic
1469 o The new function node.leafnumber() computes the number of leaves
1470 of a subtree defined by a particular node.
1472 o The new function node.sons() gets all tags of son nodes from a
1475 o The new function compute.brlen() computes the branch lengths of
1476 a tree according to a specified method.
1478 o plot.phylo() has three new options: "cex" controls the size of
1479 the (tip and node) labels (thus it is no more needed to change
1480 the global graphical parameter), "direction" which allows to
1481 plot the tree rightwards, leftwards, upwards, or downwards, and
1482 "y.lim" which sets the upper limit on the y-axis.
1487 o Some functions which try to match tip labels and names of
1488 additional data (e.g. vector) are likely to fail if there are
1489 typing or syntax errors. If both series of names do not perfectly
1490 match, they are ignored and a warning message is now issued.
1491 These functions are bd.ext, compar.gee, pic. Their help pages
1492 have been clarified on this point.
1496 CHANGES IN APE VERSION 1.2-7
1501 o The new function root() reroots a phylogenetic tree with respect
1502 to a specified outgroup.
1504 o The new function rotate() rotates an internal branch of a tree.
1506 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1507 trees) controls the display of the tip labels in unrooted trees.
1508 This display has been greatly improved: the tip labels are now not
1509 expected to overlap with the tree (particularly if lab4ut =
1510 "axial"). In all cases, combining appropriate values of "lab4ut"
1511 and the font size (via "par(cex = )") should result in readable
1512 unrooted trees. See ?plot.phylo for some examples.
1514 o In drop.tip(), the argument `tip' can now be numeric or character.
1519 o drop.tip() did not work correctly with trees with no branch
1520 lengths: this is fixed.
1522 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1523 plotted with some line crossings: this is now fixed.
1527 CHANGES IN APE VERSION 1.2-6
1532 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1533 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1534 to implement comparative methods with an autocorrelation approach.
1536 o A new data set describing some life history traits of Carnivores
1542 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1547 o When plotting a tree with plot.phylo(), the new default of the
1548 option `label.offset' is now 0, so the labels are always visible.
1552 CHANGES IN APE VERSION 1.2-5
1557 o The new function bd.ext() fits a birth-death model with combined
1558 phylogenetic and taxonomic data, and estimates the corresponding
1559 speciation and extinction rates.
1564 o The package gee is no more required by ape but only suggested
1565 since only the function compar.gee() calls gee.
1569 CHANGES IN APE VERSION 1.2-4
1574 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1575 and lines.popsize) implementing a new approach for inferring the
1576 demographic history from genealogies using a reversible jump
1577 MCMC have been introduced.
1579 o The unit of time in the skyline plot and in the new plots can
1580 now be chosen to be actual years, rather than substitutions.
1584 CHANGES IN APE VERSION 1.2-3
1589 o The new function rtree() generates a random binary tree with or
1590 without branch lengths.
1592 o Two new functions for drawing lineages-through-time (LTT) plots
1593 are provided: ltt.lines() adds a LTT curve to an existing plot,
1594 and mltt.plot() does a multiple LTT plot giving several trees as
1595 arguments (see `?ltt.plot' for details).
1600 o Some taxon names made R crashing when calling as.phylo.hclust():
1603 o dist.dna() returned an error with two identical DNA sequences
1604 (only using the Jukes-Cantor method returned 0): this is fixed.
1609 o The function dist.phylo() has been re-written using a different
1610 algorithm: it is now about four times faster.
1612 o The code of branching.times() has been improved: it is now about
1617 CHANGES IN APE VERSION 1.2-2
1622 o The new function seg.sites() finds the segregating sites in a
1623 sample of DNA sequences.
1628 o A bug introduced in read.tree() and in read.nexus() with version
1631 o A few errors were corrected and a few examples were added in the
1636 CHANGES IN APE VERSION 1.2-1
1641 o plot.phylo() can now draw the edge of the root of a tree if it
1642 has one (see the new option `root.edge', its default is FALSE).
1647 o A bug was fixed in read.nexus(): files with semicolons inside
1648 comment blocks were not read correctly.
1650 o The behaviour of read.tree() and read.nexus() was corrected so
1651 that tree files with badly represented root edges (e.g., with
1652 an extra pair of parentheses, see the help pages for details)
1653 are now correctly represented in the object of class "phylo";
1654 a warning message is now issued.
1658 CHANGES IN APE VERSION 1.2
1663 o plot.phylo() has been completely re-written and offers several
1664 new functionalities. Three types of trees can now be drawn:
1665 phylogram (as previously), cladogram, and unrooted tree; in
1666 all three types the branch lengths can be drawn using the edge
1667 lengths of the phylogeny or not (e.g., if the latter is absent).
1668 The vertical position of the nodes can be adjusted with two
1669 choices (see option `node.pos'). The code has been re-structured,
1670 and two new functions (potentially useful for developpers) are
1671 documented separately: node.depth.edgelength() and node.depth();
1672 see the respective help pages for details.
1674 o The new function zoom() allows to explore very large trees by
1675 focusing on a small portion of it.
1677 o The new function yule() fits by maximum likelihood the Yule model
1678 (birth-only process) to a phylogenetic tree.
1680 o Support for writing DNA sequences in FASTA format has been
1681 introduced in write.dna() (support for reading sequences in
1682 this format was introduced in read.dna() in version 1.1-2).
1683 The function has been completely re-written, fixing some bugs
1684 (see below); the default behaviour is no more to display the
1685 sequences on the standard output. Several options have been
1686 introduced to control the sequence printing in a flexible
1687 way. The help page has been extended.
1689 o A new data set is included: a supertree of bats in NEXUS format.
1694 o In theta.s(), the default of the option `variance' has
1695 been changed to `FALSE' (as was indicated in the help page).
1697 o Several bugs were fixed in the code of all.equal.phylo().
1699 o Several bugs were fixed in write.dna(), particularly this
1700 function did not work with `format = "interleaved"'.
1702 o Various errors were corrected in the help pages.
1707 o The argument names of as.hclust.phylo() have been changed
1708 from "(phy)" to "(x, ...)" to conform to the definition of
1709 the corresponding generic function.
1711 o gamma.stat() has been renamed gammaStat() to avoid confusion
1712 since gamma() is a generic function.
1716 CHANGES IN APE VERSION 1.1-3
1721 o base.freq() previously did not return a value of 0 for
1722 bases absent in the data (e.g., a vector of length 3 was
1723 returned if one base was absent). This is now fixed (a
1724 vector of length 4 is always returned).
1726 o Several bugs were fixed in read.nexus(), including that this
1727 function did not work in this absence of a "TRANSLATE"
1728 command in the NEXUS file, and that the commands were
1733 CHANGES IN APE VERSION 1.1-2
1738 o The Tamura and Nei (1993) model of DNA distance is now implemented
1739 in dist.dna(): five models are now available in this function.
1741 o A new data set is included: a set of 15 sequences of the
1742 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1748 o A bug in read.nexus() was fixed.
1750 o read.dna() previously did not work correctly in most cases.
1751 The function has been completely re-written and its help page
1752 has been considerably extended (see ?read.dna for details).
1753 Underscores (_) in taxon names are no more replaced with
1754 spaces (this behaviour was undocumented).
1756 o A bug was fixed in write.dna().
1760 CHANGES IN APE VERSION 1.1-1
1765 o A bug in read.tree() introduced in APE 1.1 was fixed.
1767 o A bug in compar.gee() resulted in an error when trying to fit
1768 a model with `family = "binomial"'. This is now fixed.
1772 CHANGES IN APE VERSION 1.1
1777 o The Klastorin (1982) method as suggested by Misawa and Tajima
1778 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1779 on the basis of phylogenetic trees has been implemented (see
1780 the function klastorin()).
1782 o Functions have been added to convert APE's "phylo" objects in
1783 "hclust" cluster objects and vice versa (see the help page of
1784 as.phylo for details).
1786 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1787 are introduced for the estimation of absolute evolutionary rates
1788 (ratogram) and dated clock-like trees (chronogram) from
1789 phylogenetic trees using the non-parametric rate smoothing approach
1790 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1792 o A summary method is now provided printing a summary information on a
1793 phylogenetic tree with, for instance, `summary(tree)'.
1795 o The behaviour of read.tree() was changed so that all spaces and
1796 tabulations in tree files are now ignored. Consequently, spaces in tip
1797 labels are no more allowed. Another side effect is that read.nexus()
1798 now does not replace the underscores (_) in tip labels with spaces
1799 (this behaviour was undocumented).
1801 o The function plot.phylo() has a new option (`underscore') which
1802 specifies whether the underscores in tip labels should be written on
1803 the plot as such or replaced with spaces (the default).
1805 o The function birthdeath() now computes 95% confidence intervals of
1806 the estimated parameters using profile likelihood.
1808 o Three new data sets are included: a gene tree estimated from 36
1809 landplant rbcL sequences, a gene tree estimated from 32 opsin
1810 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1815 o A bug was fixed in dist.gene() where nothing was returned.
1817 o A bug in plot.mst() was fixed.
1819 o A bug in vcv.phylo() resulted in false correlations when the
1820 option `cor = TRUE' was used (now fixed).
1824 CHANGES IN APE VERSION 1.0
1829 o Two new functions, read.dna() and write.dna(), read/write in a file
1830 DNA sequences in interleaved or in sequential format.
1832 o Two new functions, read.nexus() and write.nexus(), read/write trees
1835 o The new function bind.tree() allows to bind two trees together,
1836 possibly handling root edges to give internal branches.
1838 o The new function drop.tip() removes the tips in a phylogenetic tree,
1839 and trims (or not) the corresponding internal branches.
1841 o The new function is.ultrametric() tests if a tree is ultrametric.
1843 o The function plot.phylo() has more functionalities such as drawing the
1844 branches with different colours and/or different widths, showing the
1845 node labels, controling the position and font of the labels, rotating
1846 the labels, and controling the space around the plot.
1848 o The function read.tree() can now read trees with no branch length,
1849 such as "(a,b),c);". Consequently, the element `edge.length' in
1850 objects of class "phylo" is now optional.
1852 o The function write.tree() has a new default behaviour: if the default
1853 for the option `file' is used (i.e. file = ""), then a variable of
1854 mode character containing the tree in Newick format is returned which
1855 can thus be assigned (e.g., tree <- write.tree(phy)).
1857 o The function read.tree() has a new argument `text' which allows
1858 to read the tree in a variable of mode character.
1860 o A new data set is included: the phylogenetic relationships among
1861 the orders of birds from Sibley and Ahlquist (1990).
1865 CHANGES IN APE VERSION 0.2-1
1870 o Several bugs were fixed in the help pages.
1874 CHANGES IN APE VERSION 0.2
1879 o The function write.tree() writes phylogenetic trees (objects of class
1880 "phylo") in an ASCII file using the Newick parenthetic format.
1882 o The function birthdeath() fits a birth-death model to branching times
1883 by maximum likelihood, and estimates the corresponding speciation and
1886 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1889 o The function is.binary.tree() tests whether a phylogeny is binary.
1891 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1892 as well as some methods are introduced.
1894 o Several functions, including some generics and methods, for computing
1895 skyline plot estimates (classic and generalized) of effective
1896 population size through time are introduced and replace the function
1897 skyline.plot() in version 0.1.
1899 o Two data sets are now included: the phylogenetic relationships among
1900 the families of birds from Sibley and Ahlquist (1990), and an
1901 estimated clock-like phylogeny of HIV sequences sampled in the
1902 Democratic Republic of Congo.
1905 DEPRECATED & DEFUNCT
1907 o The function skyline.plot() in ape 0.1 has been deprecated and
1908 replaced by more elaborate functions (see above).
1913 o Two important bugs were fixed in plot.phylo(): phylogenies with
1914 multichotomies not at the root or not with only terminal branches,
1915 and phylogenies with a single node (i.e. only terminal branches)
1916 did not plot. These trees should be plotted correctly now.
1918 o Several bugs were fixed in diversi.time() in the computation of
1921 o Various errors were corrected in the help pages.