1 CHANGES IN APE VERSION 2.4
6 o base.freq() has a new option 'freq' to return the counts; the
7 default is still to return the proportions.
12 o seg.sites() did not handle ambiguous nucleotides correctly: they are
18 o The functions heterozygosity, nuc.div, theta.h, theta.k and
19 theta.s have been moved from ape to pegas.
24 o Deprecated functions are now listed in a help page: see
25 help("ape-defunct"), with the quotes!
28 CHANGES IN APE VERSION 2.3-3
33 o add.scale.bar() always drew a horizontal bar.
35 o zoom() shuffled tips with unrooted trees.
37 o write.nexus() failed to write correctly trees with a "TipLabel"
40 o rcoal() failed to compute branch lengths with very large n.
42 o A small bug was fixed in compar.cheverud() (thanks to Michael
45 o seg.sites() failed when passing a vector.
47 o drop.tip() sometimes shuffled tip labels.
49 o root() shuffled node labels with 'resolve.root = TRUE'.
53 CHANGES IN APE VERSION 2.3-2
58 o all.equal.phylo() did not compare unrooted trees correctly.
60 o dist.topo(... method = "PH85") did not treat unrooted trees
61 correctly (thanks to Tim Wallstrom for the fix).
63 o root() sometimes failed to test for the monophyly of the
66 o extract.clade() sometimes included too many edges.
68 o vcv.phylo() did not work correctly when the tree is in
71 o nj() did not handle correctly distance matrices with many 0's.
72 The code has also been significantly improved: 7, 70, 160 times
73 faster with n = 100, 500, 1000, respectively.
77 CHANGES IN APE VERSION 2.3-1
82 o The new function is.monophyletic tests the monophyly of a group.
84 o There is now a c() method for lists of class "DNAbin".
86 o yule.cov() now fits the null model, and its help page has been
87 corrected with respect to this change.
89 o drop.tip() has a new option 'rooted' to force (or not) a tree
90 to be treated as (un)rooted.
95 o dist.gene() failed on most occasions with the default
96 pairwise.deletion = FALSE.
98 o read.tree() failed to read correctly the tree name(s).
100 o boot.phylo() now treats correctly data frames.
102 o del.gaps() did not copy the rownames of a matrix.
104 o A small bug was fixed in CDAM.global().
106 o ace() failed with large data sets. Thanks to Rich FitzJohn for
107 the fix. With other improvements, this function is now about 6
110 o write.tree() failed with objects of class "multiPhylo".
112 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
117 o [.multiPhylo and [.DNAbin now respect the original class.
119 o Instances of the form class(phy) == "phylo" have been replaced
120 by inherits(phy, "phylo").
122 o rcoal() is now faster.
127 o klastorin() has been removed.
131 CHANGES IN APE VERSION 2.3
136 o The new functions CADM.global and CADM.post, contributed by
137 Pierre Legendre, test the congruence among several distance
140 o The new function yule.time fits a user-defined time-dependent
141 Yule model by maximum likelihood.
143 o The new function makeNodeLabel creates and/or modifies node
144 labels in a flexible way.
146 o read.tree() and write.tree() have been modified so that they can
147 handle individual tree names.
149 o plot.phylo() has a new argument 'edge.lty' that specifies the
150 types of lines used for the edges (plain, dotted, dashed, ...)
152 o phymltest() has been updated to work with PhyML 3.0.1.
157 o drop.tip() shuffled tip labels in some cases.
159 o drop.tip() did not handle node.label correctly.
161 o is.ultrametric() now checks the ordering of the edge matrix.
163 o ace() sometimes returned negative values of likelihoods of
164 ancestral states (thanks to Dan Rabosky for solving this long
170 o The data set xenarthra has been removed.
174 CHANGES IN APE VERSION 2.2-4
178 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
179 now fixed. (Thanks to Peter Wragg for the fix!)
181 o A warning message occurred for no reason with ace(method="GLS").
186 o There is now a general help page displayed with '?ape'
190 CHANGES IN APE VERSION 2.2-3
195 o The new function extract.clade extracts a clade from a tree by
196 specifying a node number or label.
198 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
199 operations of the same names.
201 o dist.dna() can now return the number of site differences by
202 specifying model="N".
207 o chronopl() did not work with CV = TRUE.
209 o read.nexus() did not work correctly in some situations (trees on
210 multiple lines with different numbers of lines and/or with
211 comments inserted within the trees).
213 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
214 the number of lineages with non-binary trees.
219 o ape has now a namespace.
221 o drop.tip() has been improved: it should be much faster and work
222 better in some cases (e.g., see the example in ?zoom).
226 CHANGES IN APE VERSION 2.2-2
231 o dist.gene() has been substantially improved and gains an option
234 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
240 o prop.part() failed with a single tree with the default option
241 'check.labels = TRUE'.
243 o summary.DNAbin() failed to display correctly the summary of
244 sequence lengths with lists of sequences of 10,000 bases or more
245 (because summary.default uses 4 significant digits by default).
247 o read.nexus() failed to read a file with a single tree with line
248 breaks in the Newick string.
250 o del.gaps() returned a list of empty sequences when there were no
256 o phymltest() has been updated for PhyML 3.0 and gains an option
257 'append', whereas the option 'path2exec' has been removed.
259 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
260 which is returned unchanged (instead of an error).
262 o The data sets bird.orders and bird.families are now stored as
263 Newick strings; i.e., the command data(bird.orders) calls
268 CHANGES IN APE VERSION 2.2-1
273 o The new function makeLabel() helps to modify labels of trees,
274 lists of trees, or DNA sequences, with several utilities to
275 truncate and/or make them unique, substituting some
276 characters, and so on.
278 o The new function del.gaps() removes insertion gaps ("-") in a
279 set of DNA sequences.
281 o read.dna() can now read Clustal files (*.aln).
286 o root() failed with 'resolve.root = TRUE' when the root was
287 already the specified root.
289 o Several bugs were fixed in mlphylo().
291 o collapsed.singles() did not propagate the 'Nnode' and
292 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
294 o read.nexus() failed to remove correctly the comments within
297 o read.nexus() failed to read a file with a single tree and no
298 translation of tip labels.
300 o read.nexus() failed to place correctly tip labels when reading
301 a single tree with no edge lengths.
303 o A bug was fixed in sh.test().
308 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
311 o The option 'check.labels' of consensus() and prop.part() is now
314 o write.dna() now does not truncate names to 10 characters with
319 CHANGES IN APE VERSION 2.2
324 o Four new functions have been written by Damien de Vienne for the
325 graphical exploration of large trees (cophyloplot, subtrees,
326 subtreeplot), and to return the graphical coordinates of tree
329 o The new functions corPagel and corBlomberg implement the Pagel's
330 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
332 o chronopl() has been improved and gains several options: see its
333 help page for details.
335 o boot.phylo() has now an option 'trees' to possibly return the
336 bootstraped trees (the default is FALSE).
338 o prop.part() has been improved and should now be faster in all
344 o read.dna() failed if "?" occurred in the first 10 sites of the
347 o The x/y aspect of the plot is now respected when plotting a
348 circular tree (type = "r" or "f").
350 o Drawing the tip labels sometimes failed when plotting circular
353 o zoom() failed when tip labels were used instead of their numbers
354 (thanks to Yan Wong for the fix).
356 o drop.tip() failed with some trees (fixed by Yan Wong).
358 o seg.sites() failed with a list.
360 o consensus() failed in some cases. The function has been improved
361 as well and is faster.
365 CHANGES IN APE VERSION 2.1-3
370 o A bug in read.nexus() made the Windows R-GUI crash.
372 o An error was fixed in the computation of ancestral character
373 states by generalized least squares in ace().
375 o di2multi() did not modify node labels correctly.
377 o multi2di() failed if the tree had its attribute "order" set to
382 CHANGES IN APE VERSION 2.1-2
387 o There three new methods for the "multiPhylo" class: str, $,
390 o root() gains the options 'node' and 'resolve.root'
391 (FALSE by default) as well as its code being improved.
393 o mltt.plot() has now an option 'log' used in the same way
394 than in plot.default().
399 o mltt.plot() failed to display the legend with an unnamed
402 o nodelabels() with pies now correcly uses the argument
403 'cex' to draw symbols of different sizes (which has
404 worked already for thermometers).
406 o read.nexus() generally failed to read very big files.
411 o The argument 'family' of compar.gee() can now be a function
412 as well as a character string.
414 o read.tree() and read.nexus() now return an unnamed list if
417 o read.nexus() now returns a modified object of class "multiPhylo"
418 when there is a TRANSLATE block in the NEXUS file: the individual
419 trees have no 'tip.label' vector, but the list has a 'TipLabel'
420 attribute. The new methods '$' and '[[' set these elements
421 correctly when extracting trees.
425 CHANGES IN APE VERSION 2.1-1
430 o The new function rmtree generates lists of random trees.
432 o rcoal() now generates a genuine coalescent tree by default
433 (thanks to Vladimir Minin for the code).
438 o nuc.div() returned an incorrect value with the default
439 pairwise.deletion = FALSE.
444 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
445 have been improved so that they are stabler and faster.
447 o R packages used by ape are now loaded silently; lattice and gee
448 are loaded only when needed.
452 CHANGES IN APE VERSION 2.1
457 o The new function identify.phylo identifies clades on a plotted
458 tree using the mouse.
460 o It is now possible to subset a list of trees (object of class
461 "multiPhylo") with "[" while keeping its class correct.
463 o The new function as.DNAbin.alignment converts DNA sequences
464 stored in the "alignment" format of the package seqinr into
465 an object of class "DNAbin".
467 o The new function weight.taxo2 helps to build similarity matrices
468 given two taxonomic levels (usually called by other functions).
470 o write.tree() can now take a list of trees (class "multiPhylo")
471 as its main argument.
473 o plot.correlogram() and plot.correlogramList() have been
474 improved, and gain several options (see the help page for
475 details). A legend is now plotted by default.
480 o dist.dna() returned some incorrect values with `model = "JC69"'
481 and `pairwise.deletion = TRUE'. This affected only the
482 distances involving sequences with missing values. (Thanks
483 to Bruno Toupance for digging this bug out.)
485 o write.tree() failed with some trees: this is fixed by removing
486 the `multi.line' option (trees are now always printed on a
489 o read.nexus() did not correctly detect trees with multiple root
490 edges (see OTHER CHANGES).
495 o The code of mlphylo() has been almost entirely rewritten, and
496 should be much stabler. The options have been also greatly
497 simplified (see ?mlphylo and ?DNAmodel for details).
499 o The internal function nTips has been renamed klastorin_nTips.
501 o The code of is.ultrametric() contained redundancies and has
504 o The code of Moran.I() and of correlogram.formula() have been
507 o read.tree() and read.nexus() now return an error when trying to
508 read a tree with multiple root edges (see BUG FIXES). The
509 correction applied in previous version did not work in all
512 o The class c("multi.tree", "phylo") has been renamed
518 o There is now a vignette in ape: see vignette("MoranI", "ape").
523 o as.matching() and as.phylo.matching() do not support branch
526 o correlogram.phylo() and discrete.dist() have been removed.
530 CHANGES IN APE VERSION 2.0-2
535 o The new function matexpo computes the exponential of a square
538 o The new function unique.multi.tree removes duplicate trees from
541 o yule() has a new option `use.root.edge = FALSE' that specifies
542 to ignore, by default, the root edge of the tree if it exists.
547 o which.edge() failed when the index of a single terminal edge was
550 o In diversi.time(), the values returned for model C were
553 o A bug was fixed in yule() that affected the calculation of the
554 likelihood in the presence of ties in the branching times.
556 o There was a bug in the C function mat_expo4x4 affecting the
557 calculations of the transition probabilities for models HKY and
560 o A small bug was fixed in as.matrix.DNAbin (thanks to James
563 o rtree() did not `shuffle' the tip labels by default, so only a
564 limited number of labelled topologies could be generated.
568 CHANGES IN APE VERSION 2.0-1
573 o The three new functions bionj, fastme.ols, and fastme.bal
574 perform phylogeny estimation by the BIONJ and fastME methods in
575 OLS and balanced versions. This is a port to R of previous
576 previous programs done by Vincent Lefort.
578 o The new function chronoMPL performs molecular dating with the
579 mean path lengths method of Britton et al. (2002, Mol. Phyl.
582 o The new function rotate, contributed by Christoph Heibl, swaps
583 two clades connected to the same node. It works also with
584 multichotomous nodes.
586 o The new `method' as.matrix.DNAbin() may be used to convert
587 easily DNA sequences stored in a list into a matrix while
588 keeping the names and the class.
593 o chronopl() failed when some branch lengths were equal to zero:
594 an error message is now returned.
596 o di2multi() failed when there was a series of consecutive edges
601 CHANGES IN APE VERSION 1.10-2
606 o plot.phylo() can now plot circular trees: the option is type =
607 "fan" or type = "f" (to avoid the ambiguity with type = "c").
609 o prop.part() has a new option `check.labels = FALSE' which allows
610 to considerably speed-up the calculations of bipartitions. As a
611 consequence, calculations of bootstrap values with boot.phylo()
612 should be much faster.
617 o read.GenBank() did not return correctly the list of species as
618 from ape 1.10: this is fixed in this version
620 o Applying as.phylo() on a tree of class "phylo" failed: the
621 object is now returned unchanged.
625 CHANGES IN APE VERSION 1.10-1
630 o The three new functions Ntip, Nnode, and Nedge return, for a
631 given tree, the number of tips, nodes, or edges, respectively.
636 o read.nexus() did not set correctly the class of the returned
637 object when reading multiple trees.
639 o mllt.plot() failed with objects of class c("multi.tree",
642 o unroot() did not work correctly in most cases.
644 o reorder.phylo() made R freeze in some occasions.
646 o Plotting a tree in pruningwise order failed.
648 o When plotting an unrooted tree, the tip labels where not all
649 correctly positioned if the option `cex' was used.
653 CHANGES IN APE VERSION 1.10
658 o Five new `method' functions have been introduced to manipulate
659 DNA sequences in binary format (see below).
661 o Three new functions have been introduced to convert between the
662 new binary and the character formats.
664 o The new function as.alignment converts DNA sequences stored as
665 single characters into the class "alignment" used by the package
668 o read.dna() and read.GenBank() have a new argument `as.character'
669 controlling whether the sequences are returned in binary format
675 o root() failed when the tree had node labels: this is fixed.
677 o plot.phylo() did not correctly set the limits on the y-axis with
678 the default setting: this is fixed.
680 o dist.dna() returned a wrong result for the LogDet, paralinear,
681 and BH87 models with `pairwise.deletion = TRUE'.
686 o DNA sequences are now internally stored in a binary format. See
687 the document "A Bit-Level Coding Scheme for Nucleotides" for the
688 details. Most functions analyzing DNA functions have been
689 modified accordingly and are now much faster (dist.dna is now
690 ca. 60 times faster).
694 CHANGES IN APE VERSION 1.9-4
699 o A bug was fixed in edgelabels().
701 o as.phylo.hclust() did not work correctly when the object of
702 class "hclust" has its labels set to NULL: the returned tree has
703 now its tip labels set to "1", "2", ...
705 o consensus could fail if some tip labels are a subset of others
706 (e.g., "a" and "a_1"): this is now fixed.
708 o mlphylo() failed in most cases if some branch lengths of the
709 initial tree were greater than one: an error message is now
712 o mlphylo() failed in most cases when estimating the proportion of
713 invariants: this is fixed.
717 CHANGES IN APE VERSION 1.9-3
722 o The new function edgelabels adds labels on the edge of the tree
723 in the same way than nodelabels or tiplabels.
728 o multi2di() did not handle correctly branch lengths with the
729 default option `random = TRUE': this is now fixed.
731 o A bug was fixed in nuc.div() when using pairwise deletions.
733 o A bug occurred in the analysis of bipartitions with large
734 numbers of large trees, with consequences on prop.part,
735 prop.clades, and boot.phylo.
737 o The calculation of the Billera-Holmes-Vogtmann distance in
738 dist.topo was wrong: this has been fixed.
742 CHANGES IN APE VERSION 1.9-2
747 o The new function ladderize reorganizes the internal structure of
748 a tree to plot them left- or right-ladderized.
750 o The new function dist.nodes computes the patristic distances
751 between all nodes, internal and terminal, of a tree. It replaces
752 the option `full = TRUE' of cophenetic.phylo (see below).
757 o A bug was fixed in old2new.phylo().
759 o Some bugs were fixed in chronopl().
761 o The edge colours were not correctly displayed by plot.phylo
762 (thank you to Li-San Wang for the fix).
764 o cophenetic.phylo() failed with multichotomous trees: this is
770 o read.dna() now returns the sequences in a matrix if they are
771 aligned (interleaved or sequential format). Sequences in FASTA
772 format are still returned in a list.
774 o The option `full' of cophenetic.phylo() has been removed because
775 it could not be used from the generic.
780 o rotate() has been removed; this function did not work correctly
785 CHANGES IN APE VERSION 1.9-1
790 o Trees with a single tip were not read correctly in R as the
791 element `Nnode' was not set: this is fixed.
793 o unroot() did not set correctly the number of nodes of the
794 unrooted tree in most cases.
796 o read.GenBank() failed when fetching very long sequences,
797 particularly of the BX-series.
799 o A bug was introduced in read.tree() with ape 1.9: it has been
804 CHANGES IN APE VERSION 1.9
809 o There are two new print `methods' for trees of class "phylo" and
810 lists of trees of class "multi.tree", so that they are now
811 displayed in a compact and informative way.
813 o There are two new functions, old2new.phylo and new2old.phylo,
814 for converting between the old and new coding of the class
817 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
818 LogDet ("logdet"), and paralinear ("paralin").
820 o compute.brlen() has been extended: several methods are now
821 available to compute branch lengths.
823 o write.dna() can now handle matrices as well as lists.
828 o cophenetic.phylo() sometimes returned a wrong result with
829 multichotomous trees: this is fixed.
831 o rotate() failed when a single tip was specified: the tree is now
834 o ace() did not return the correct index matrix with custom
835 models: this is fixed.
837 o multi2di() did not work correctly when resolving multichotomies
838 randomly: the topology was always the same, only the arrangement
839 of clades was randomized: this is fixed. This function now
840 accepts trees with no branch lengths.
842 o The output of diversi.gof() was blurred by useless prints when a
843 user distribution was specified. This has been corrected, and
844 the help page of this function has been expanded.
849 o The internal structure of the class "phylo" has been changed:
850 see the document "Definition of Formats for Coding Phylogenetic
851 Trees in R" for the details. In addition, the code of most
852 functions has been improved.
854 o Several functions have been improved by replacing some R codes
855 by C codes: pic, plot.phylo, and reorder.phylo.
857 o There is now a citation information: see citation("ape") in R.
859 o write.tree() now does not add extra 0's to branch lengths so
860 that 1.23 is printed "1.23" by default, not "1.2300000000".
862 o The syntax of bind.tree() has been simplified. This function now
863 accepts trees with no branch lengths, and handles correctly node
866 o The option `as.numeric' of mrca() has been removed.
868 o The unused options `format' and `rooted' of read.tree() have
871 o The unused option `format' of write.tree() has been removed.
873 o The use of node.depth() has been simplified.
877 CHANGES IN APE VERSION 1.8-5
882 o Two new functions read.nexus.data() and write.nexus.data(),
883 contributed by Johan Nylander, allow to read and write molecular
884 sequences in NEXUS files.
886 o The new function reorder.phylo() reorders the internal structure
887 of a tree of class "phylo". It is used as the generic, e.g.,
890 o read.tree() and read.nexus() can now read trees with a single
893 o The new data set `cynipids' supplies a set of protein sequences
899 o The code of all.equal.phylo() has been completely rewritten
900 (thanks to Benoît Durand) which fixes several bugs.
902 o read.tree() and read.nexus() now checks the labels of the tree
903 to remove or substitute any characters that are illegal in the
904 Newick format (parentheses, etc.)
906 o A negative P-value could be returned by mantel.test(): this is
911 CHANGES IN APE VERSION 1.8-4
916 o The new function sh.test() computes the Shimodaira-
919 o The new function collapse.singles() removes the nodes with a
920 single descendant from a tree.
922 o plot.phylo() has a new argument `tip.color' to specify the
925 o mlphylo() has now an option `quiet' to control the display of
926 the progress of the analysis (the default is FALSE).
931 o read.dna() did not read correctly sequences in sequential format
932 with leading alignment gaps "-": this is fixed.
934 o ace() returned a list with no class so that the generic
935 functions (anova, logLik, ...) could not be used directly. This
936 is fixed as ace() now returns an object of class "ace".
938 o anova.ace() had a small bug when computing the number of degrees
939 of freedom: this is fixed.
941 o mlphylo() did not work when the sequences were in a matrix or
942 a data frame: this is fixed.
944 o rtree() did not work correctly when trying to simulate an
945 unrooted tree with two tips: an error message is now issued.
950 o The algorithm of rtree() has been changed: it is now about 40,
951 100, and 130 times faster for 10, 100, and 1000 tips,
956 CHANGES IN APE VERSION 1.8-3
961 o There are four new `method' functions to be used with the
962 results of ace(): logLik(), deviance(), AIC(), and anova().
964 o The plot method of phymltest has two new arguments: `main' to
965 change the title, and `col' to control the colour of the
966 segments showing the AIC values.
968 o ace() has a new argument `ip' that gives the initial values used
969 in the ML estimation with discrete characters (see the examples
970 in ?ace). This function now returns a matrix giving the indices
971 of the estimated rates when analysing discrete characters.
973 o nodelabels() and tiplabels() have a new argument `pie' to
974 represent proportions, with any number of categories, as
975 piecharts. The use of the option `thermo' has been improved:
976 there is now no limitation on the number of categories.
981 o mlphylo() did not work with more than two partitions: this is
984 o root() failed if the proposed outgroup was already an outgroup
985 in the tree: this is fixed.
987 o The `col' argument in nodelabels() and tiplabels() was not
988 correctly passed when `text' was used: this is fixed.
990 o Two bugs were fixed in mlphylo(): parameters were not always
991 correctly output, and the estimation failed in some cases.
993 o plot.phylo() was stuck when given a tree with a single tip: this
994 is fixed and a message error is now returned.
996 o An error was corrected in the help page of gammaStat regarding
997 the calculation of P-values.
999 o Using gls() could crash R when the number of species in the tree
1000 and in the variables were different: this is fixed.
1004 CHANGES IN APE VERSION 1.8-2
1009 o The new function mlphylo() fits a phylogenetic tree by maximum
1010 likelihood from DNA sequences. Its companion function DNAmodel()
1011 is used to define the substitution model which may include
1012 partitioning. There are methods for logLik(), deviance(), and
1013 AIC(), and the summary() method has been extended to display in
1014 a friendly way the results of this model fitting. Currently, the
1015 functionality is limited to estimating the substitution and
1016 associated parameters and computing the likelihood.
1018 o The new function drop1.compar.gee (used as, e.g., drop1(m))
1019 tests for single effects in GEE-based comparative method. A
1020 warning message is printed if there is not enough degrees of
1026 o An error message was sometimes issued by plot.multi.tree(),
1027 though with no consequence.
1031 CHANGES IN APE VERSION 1.8-1
1036 o There is a new plot method for lists of trees (objects of class
1037 "multi.tree"): it calls plot.phylo() internally and is
1038 documented on the same help page.
1043 o A bug was fixed in the C code that analyzes bipartitions: this
1044 has impact on several functions like prop.part, prop.clades,
1045 boot.phylo, or consensus.
1047 o root() did not work correctly when the specified outgroup had
1048 more than one element: this is fixed.
1050 o dist.dna() sometimes returned a warning inappropriately: this
1053 o If the distance object given to nj() had no rownames, nj()
1054 returned a tree with no tip labels: it now returns tips labelled
1055 "1", "2", ..., corresponding to the row numbers.
1060 o nj() has been slightly changed so that tips with a zero distance
1061 are first aggregated with zero-lengthed branches; the usual NJ
1062 procedure is then performed on a distance matrix without 0's.
1066 CHANGES IN APE VERSION 1.8
1071 o The new function chronopl() estimates dates using the penalized
1072 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1074 o The new function consensus() calculates the consensus tree of a
1077 o The new function evolve.phylo() simulates the evolution of
1078 continuous characters along a phylogeny under a Brownian model.
1080 o The new plot method for objects of class "ancestral" displays a
1081 tree together with ancestral values, as returned by the above
1084 o The new function as.phylo.formula() returns a phylogeny from a
1085 set of nested taxonomic variables given as a formula.
1087 o The new function read.caic() reads trees in CAIC format.
1089 o The new function tiplabels() allows to add labels to the tips
1090 of a tree using text or plotting symbols in a flexible way.
1092 o The new function unroot() unroots a phylogeny.
1094 o multi2di() has a new option, `random', which specifies whether
1095 to resolve the multichotomies randomly (the default) or not.
1097 o prop.part() now returns an object of class "prop.part" for which
1098 there are print (to display a partition in a more friendly way)
1099 and summary (to extract the numbers) methods.
1101 o plot.phylo() has a new option, `show.tip.label', specifying
1102 whether to print the labels of the tips. The default is TRUE.
1104 o The code of nj() has been replaced by a faster C code: it is now
1105 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1108 o write.nexus() now writes whether a tree is rooted or not.
1113 o Two bugs have been fixed in root(): unrooted trees are now
1114 handled corretly, and node labels are now output normally.
1116 o A bug was fixed in phymltest(): the executable couldn't be found
1119 o Three bug have been fixed in ace(): computing the likelihood of
1120 ancestral states of discrete characters failed, custom models
1121 did not work, and the function failed with a null gradient (a
1122 warning message is now returned; this latter bug was also
1123 present in yule.cov() as well and is now fixed).
1125 o pic() hanged out when missing data were present: a message error
1128 o A small bug was fixed in dist.dna() where the gamma correction
1129 was not always correctly dispatched.
1131 o plot.phylo() plotted correctly the root edge only when the tree
1132 was plotted rightwards: this works now for all directions.
1137 o dist.taxo() has been renamed as weight.taxo().
1139 o Various error and warning messages have been improved.
1143 CHANGES IN APE VERSION 1.7
1146 o The new function ace() estimates ancestral character states for
1147 continuous characters (with ML, GLS, and contrasts methods), and
1148 discrete characters (with ML only) for any number of states.
1150 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1151 of directional evolution for continuous characters. The user
1152 specifies the node(s) of the tree where the character optimum
1155 o The new function is.rooted() tests whether a tree (of class
1158 o The new function rcoal() generates random ultrametric trees with
1159 the possibility to specify the function that generates the
1160 inter-nodes distances.
1162 o The new function mrca() gives for all pairs of tips in a tree
1163 (and optionally nodes too) the most recent common ancestor.
1165 o nodelabels() has a new option `thermo' to plot proportions (up
1166 to three classes) on the nodes of a tree.
1168 o rtree() has been improved: it can now generate rooted or
1169 unrooted trees, and the mathematical function that generates the
1170 branch lengths may be specified by the user. The tip labels may
1171 be given directly in the call to rtree. The limit cases (n = 2,
1172 3) are now handled correctly.
1174 o dist.topo() has a new argument `method' with two choices: "PH85"
1175 for Penny and Henny's method (already available before and now
1176 the default), and "BHV01" for the geometric distance by Billera
1177 et al. (2001, Adv. Appl. Math. 27:733).
1179 o write.tree() has a new option, `digits', which specifies the
1180 number of digits to be printed in the Newick tree. By default
1181 digits = 10. The numbers are now always printed in decimal form
1182 (i.e., 1.0e-1 is now avoided).
1184 o dist.dna() can now compute the raw distances between pairs of
1185 DNA sequences by specifying model = "raw".
1187 o dist.phylo() has a new option `full' to possibly compute the
1188 distances among all tips and nodes of the tree. The default if
1194 o Several bugs were fixed in all.equal.phylo().
1196 o dist.dna() did not handle correctly gaps ("-") in alignments:
1197 they are now considered as missing data.
1199 o rotate() did not work if the tips were not ordered: this is
1202 o mantel.test() returned NA in some special cases: this is fixed
1203 and the function has been improved and is now faster.
1205 o A bug was fixed in diversi.gof() where the calculation of A² was
1208 o cherry() did not work correctly under some OSs (mainly Linux):
1211 o is.binary.tree() has been modified so that it works with both
1212 rooted and unrooted trees.
1214 o The documentation of theta.s() was not correct: this has been
1217 o plot.mst() did not work correctly: this is fixed.
1221 CHANGES IN APE VERSION 1.6
1226 o The new function dist.topo() computes the topological distances
1229 o The new function boot.phylo() performs a bootstrap analysis on
1230 phylogeny estimation.
1232 o The new functions prop.part() and prop.clades() analyse
1233 bipartitions from a series of trees.
1238 o read.GenBank() now uses the EFetch utility of NCBI instead of
1239 the usual Web interface: it is now much faster (e.g., 12 times
1240 faster to retrieve 8 sequences, 37 times for 60 sequences).
1245 o Several bugs were fixed in read.dna().
1247 o Several bugs were fixed in diversi.time().
1249 o is.binary.tree() did not work correctly if the tree has no edge
1250 lengths: this is fixed.
1252 o drop.tip() did not correctly propagated the `node.label' of a
1253 tree: this is fixed.
1257 CHANGES IN APE VERSION 1.5
1262 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1263 convert objects between the classes "phylo" and "matching". The
1264 latter implements the representation of binary trees introduced by
1265 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1266 as.matching() has been introduced as well.
1268 o Two new functions, multi2di() and di2multi(), allow to resolve
1269 and collapse multichotomies with branches of length zero.
1271 o The new function nuc.div() computes the nucleotide diversity
1272 from a sample a DNA sequences.
1274 o dist.dna() has been completely rewritten with a much faster
1275 (particularly for large data sets) C code. Eight models are
1276 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1277 option `method' has been renamed `model'). Computation of variance
1278 is available for all models. A gamma-correction is possible for
1279 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1280 to remove sites with missing data on a pairwise basis. The option
1281 `GCcontent' has been removed.
1283 o read.GenBank() has a new option (species.names) which specifies
1284 whether to return the species names of the organisms in addition
1285 to the accession numbers of the sequences (this is the default
1288 o write.nexus() can now write several trees in the same NEXUS file.
1290 o drop.tip() has a new option `root.edge' that allows to specify the
1291 new root edge if internal branches are trimmed.
1296 o as.phylo.hclust() failed if some labels had parentheses: this
1299 o Several bugs were fixed in all.equal.phylo(). This function now
1300 returns the logical TRUE if the trees are identical but with
1301 different representations (a report was printed previously).
1303 o read.GenBank() did not correctly handle ambiguous base codes:
1309 o birthdeath() now returns an object of class "birthdeath" for
1310 which there is a print method.
1314 CHANGES IN APE VERSION 1.4
1319 o The new function nj() performs phylogeny estimation with the
1320 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1323 o The new function which.edge() identifies the edges of a tree
1324 that belong to a group specified as a set of tips.
1326 o The new function as.phylo.phylog() converts an object of class
1327 "phylog" (from the package ade4) into an object of class
1330 o The new function axisPhylo() draws axes on the side of a
1333 o The new function howmanytrees() calculates the number of trees
1334 in different cases and giving a number of tips.
1336 o write.tree() has a new option `multi.line' (TRUE by default) to
1337 write a Newick tree on several lines rather than on a single
1340 o The functionalities of zoom() have been extended. Several
1341 subtrees can be visualized at the same time, and they are marked
1342 on the main tree with colors. The context of the subtrees can be
1343 marked with the option `subtree' (see below).
1345 o drop.tip() has a new option `subtree' (FALSE by default) which
1346 specifies whether to output in the tree how many tips have been
1349 o The arguments of add.scale.bar() have been redefined and have
1350 now default values (see ?add.scale.bar for details). This
1351 function now works even if the plotted tree has no edge length.
1353 o plot.phylo() can now plot radial trees, but this does not take
1354 edge lengths into account.
1356 o In plot.phylo() with `type = "phylogram"', if the values of
1357 `edge.color' and `edge.width' are identical for sister-branches,
1358 they are propagated to the vertical line that link them.
1363 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1364 crashing. This is fixed.
1366 o In plot.phylo(), the options `edge.color' and `edge.width' are
1367 now properly recycled; their default values are now "black" and
1370 o A bug has been fixed in write.nexus().
1375 o The function node.depth.edgelength() has been removed and
1376 replaced by a C code.
1380 CHANGES IN APE VERSION 1.3-1
1385 o The new function nodelabels() allows to add labels to the nodes
1386 of a tree using text or plotting symbols in a flexible way.
1388 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1389 numeric values specifying the lower and upper limits on the x-
1390 and y-axes. This allows to leave some space on any side of the
1391 tree. If a single value is given, this is taken as the upper
1396 CHANGES IN APE VERSION 1.3
1401 o The new function phymltest() calls the software PHYML and fits
1402 28 models of DNA sequence evolution. There are a print method to
1403 display likelihood and AIC values, a summary method to compute
1404 the hierarchical likelihood ratio tests, and a plot method to
1405 display graphically the AIC values of each model.
1407 o The new function yule.cov() fits the Yule model with covariates,
1408 a model where the speciation rate is affected by several species
1409 traits through a generalized linear model. The parameters are
1410 estimated by maximum likelihood.
1412 o Three new functions, corBrownian(), corGrafen(), and
1413 corMartins(), compute the expected correlation structures among
1414 species given a phylogeny under different models of evolution.
1415 These can be used for GLS comparative phylogenetic methods (see
1416 the examples). There are coef() and corMatrix() methods and an
1417 Initialize.corPhyl() function associated.
1419 o The new function compar.cheverud() implements Cheverud et al.'s
1420 (1985; Evolution 39:1335) phylogenetic comparative method.
1422 o The new function varcomp() estimates variance components; it has
1425 o Two new functions, panel.superpose.correlogram() and
1426 plot.correlogramList(), allow to plot several phylogenetic
1429 o The new function node.leafnumber() computes the number of leaves
1430 of a subtree defined by a particular node.
1432 o The new function node.sons() gets all tags of son nodes from a
1435 o The new function compute.brlen() computes the branch lengths of
1436 a tree according to a specified method.
1438 o plot.phylo() has three new options: "cex" controls the size of
1439 the (tip and node) labels (thus it is no more needed to change
1440 the global graphical parameter), "direction" which allows to
1441 plot the tree rightwards, leftwards, upwards, or downwards, and
1442 "y.lim" which sets the upper limit on the y-axis.
1447 o Some functions which try to match tip labels and names of
1448 additional data (e.g. vector) are likely to fail if there are
1449 typing or syntax errors. If both series of names do not perfectly
1450 match, they are ignored and a warning message is now issued.
1451 These functions are bd.ext, compar.gee, pic. Their help pages
1452 have been clarified on this point.
1456 CHANGES IN APE VERSION 1.2-7
1461 o The new function root() reroots a phylogenetic tree with respect
1462 to a specified outgroup.
1464 o The new function rotate() rotates an internal branch of a tree.
1466 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1467 trees) controls the display of the tip labels in unrooted trees.
1468 This display has been greatly improved: the tip labels are now not
1469 expected to overlap with the tree (particularly if lab4ut =
1470 "axial"). In all cases, combining appropriate values of "lab4ut"
1471 and the font size (via "par(cex = )") should result in readable
1472 unrooted trees. See ?plot.phylo for some examples.
1474 o In drop.tip(), the argument `tip' can now be numeric or character.
1479 o drop.tip() did not work correctly with trees with no branch
1480 lengths: this is fixed.
1482 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1483 plotted with some line crossings: this is now fixed.
1487 CHANGES IN APE VERSION 1.2-6
1492 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1493 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1494 to implement comparative methods with an autocorrelation approach.
1496 o A new data set describing some life history traits of Carnivores
1502 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1507 o When plotting a tree with plot.phylo(), the new default of the
1508 option `label.offset' is now 0, so the labels are always visible.
1512 CHANGES IN APE VERSION 1.2-5
1517 o The new function bd.ext() fits a birth-death model with combined
1518 phylogenetic and taxonomic data, and estimates the corresponding
1519 speciation and extinction rates.
1524 o The package gee is no more required by ape but only suggested
1525 since only the function compar.gee() calls gee.
1529 CHANGES IN APE VERSION 1.2-4
1534 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1535 and lines.popsize) implementing a new approach for inferring the
1536 demographic history from genealogies using a reversible jump
1537 MCMC have been introduced.
1539 o The unit of time in the skyline plot and in the new plots can
1540 now be chosen to be actual years, rather than substitutions.
1544 CHANGES IN APE VERSION 1.2-3
1549 o The new function rtree() generates a random binary tree with or
1550 without branch lengths.
1552 o Two new functions for drawing lineages-through-time (LTT) plots
1553 are provided: ltt.lines() adds a LTT curve to an existing plot,
1554 and mltt.plot() does a multiple LTT plot giving several trees as
1555 arguments (see `?ltt.plot' for details).
1560 o Some taxon names made R crashing when calling as.phylo.hclust():
1563 o dist.dna() returned an error with two identical DNA sequences
1564 (only using the Jukes-Cantor method returned 0): this is fixed.
1569 o The function dist.phylo() has been re-written using a different
1570 algorithm: it is now about four times faster.
1572 o The code of branching.times() has been improved: it is now about
1577 CHANGES IN APE VERSION 1.2-2
1582 o The new function seg.sites() finds the segregating sites in a
1583 sample of DNA sequences.
1588 o A bug introduced in read.tree() and in read.nexus() with version
1591 o A few errors were corrected and a few examples were added in the
1596 CHANGES IN APE VERSION 1.2-1
1601 o plot.phylo() can now draw the edge of the root of a tree if it
1602 has one (see the new option `root.edge', its default is FALSE).
1607 o A bug was fixed in read.nexus(): files with semicolons inside
1608 comment blocks were not read correctly.
1610 o The behaviour of read.tree() and read.nexus() was corrected so
1611 that tree files with badly represented root edges (e.g., with
1612 an extra pair of parentheses, see the help pages for details)
1613 are now correctly represented in the object of class "phylo";
1614 a warning message is now issued.
1618 CHANGES IN APE VERSION 1.2
1623 o plot.phylo() has been completely re-written and offers several
1624 new functionalities. Three types of trees can now be drawn:
1625 phylogram (as previously), cladogram, and unrooted tree; in
1626 all three types the branch lengths can be drawn using the edge
1627 lengths of the phylogeny or not (e.g., if the latter is absent).
1628 The vertical position of the nodes can be adjusted with two
1629 choices (see option `node.pos'). The code has been re-structured,
1630 and two new functions (potentially useful for developpers) are
1631 documented separately: node.depth.edgelength() and node.depth();
1632 see the respective help pages for details.
1634 o The new function zoom() allows to explore very large trees by
1635 focusing on a small portion of it.
1637 o The new function yule() fits by maximum likelihood the Yule model
1638 (birth-only process) to a phylogenetic tree.
1640 o Support for writing DNA sequences in FASTA format has been
1641 introduced in write.dna() (support for reading sequences in
1642 this format was introduced in read.dna() in version 1.1-2).
1643 The function has been completely re-written, fixing some bugs
1644 (see below); the default behaviour is no more to display the
1645 sequences on the standard output. Several options have been
1646 introduced to control the sequence printing in a flexible
1647 way. The help page has been extended.
1649 o A new data set is included: a supertree of bats in NEXUS format.
1654 o In theta.s(), the default of the option `variance' has
1655 been changed to `FALSE' (as was indicated in the help page).
1657 o Several bugs were fixed in the code of all.equal.phylo().
1659 o Several bugs were fixed in write.dna(), particularly this
1660 function did not work with `format = "interleaved"'.
1662 o Various errors were corrected in the help pages.
1667 o The argument names of as.hclust.phylo() have been changed
1668 from "(phy)" to "(x, ...)" to conform to the definition of
1669 the corresponding generic function.
1671 o gamma.stat() has been renamed gammaStat() to avoid confusion
1672 since gamma() is a generic function.
1676 CHANGES IN APE VERSION 1.1-3
1681 o base.freq() previously did not return a value of 0 for
1682 bases absent in the data (e.g., a vector of length 3 was
1683 returned if one base was absent). This is now fixed (a
1684 vector of length 4 is always returned).
1686 o Several bugs were fixed in read.nexus(), including that this
1687 function did not work in this absence of a "TRANSLATE"
1688 command in the NEXUS file, and that the commands were
1693 CHANGES IN APE VERSION 1.1-2
1698 o The Tamura and Nei (1993) model of DNA distance is now implemented
1699 in dist.dna(): five models are now available in this function.
1701 o A new data set is included: a set of 15 sequences of the
1702 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1708 o A bug in read.nexus() was fixed.
1710 o read.dna() previously did not work correctly in most cases.
1711 The function has been completely re-written and its help page
1712 has been considerably extended (see ?read.dna for details).
1713 Underscores (_) in taxon names are no more replaced with
1714 spaces (this behaviour was undocumented).
1716 o A bug was fixed in write.dna().
1720 CHANGES IN APE VERSION 1.1-1
1725 o A bug in read.tree() introduced in APE 1.1 was fixed.
1727 o A bug in compar.gee() resulted in an error when trying to fit
1728 a model with `family = "binomial"'. This is now fixed.
1732 CHANGES IN APE VERSION 1.1
1737 o The Klastorin (1982) method as suggested by Misawa and Tajima
1738 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1739 on the basis of phylogenetic trees has been implemented (see
1740 the function klastorin()).
1742 o Functions have been added to convert APE's "phylo" objects in
1743 "hclust" cluster objects and vice versa (see the help page of
1744 as.phylo for details).
1746 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1747 are introduced for the estimation of absolute evolutionary rates
1748 (ratogram) and dated clock-like trees (chronogram) from
1749 phylogenetic trees using the non-parametric rate smoothing approach
1750 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1752 o A summary method is now provided printing a summary information on a
1753 phylogenetic tree with, for instance, `summary(tree)'.
1755 o The behaviour of read.tree() was changed so that all spaces and
1756 tabulations in tree files are now ignored. Consequently, spaces in tip
1757 labels are no more allowed. Another side effect is that read.nexus()
1758 now does not replace the underscores (_) in tip labels with spaces
1759 (this behaviour was undocumented).
1761 o The function plot.phylo() has a new option (`underscore') which
1762 specifies whether the underscores in tip labels should be written on
1763 the plot as such or replaced with spaces (the default).
1765 o The function birthdeath() now computes 95% confidence intervals of
1766 the estimated parameters using profile likelihood.
1768 o Three new data sets are included: a gene tree estimated from 36
1769 landplant rbcL sequences, a gene tree estimated from 32 opsin
1770 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1775 o A bug was fixed in dist.gene() where nothing was returned.
1777 o A bug in plot.mst() was fixed.
1779 o A bug in vcv.phylo() resulted in false correlations when the
1780 option `cor = TRUE' was used (now fixed).
1784 CHANGES IN APE VERSION 1.0
1789 o Two new functions, read.dna() and write.dna(), read/write in a file
1790 DNA sequences in interleaved or in sequential format.
1792 o Two new functions, read.nexus() and write.nexus(), read/write trees
1795 o The new function bind.tree() allows to bind two trees together,
1796 possibly handling root edges to give internal branches.
1798 o The new function drop.tip() removes the tips in a phylogenetic tree,
1799 and trims (or not) the corresponding internal branches.
1801 o The new function is.ultrametric() tests if a tree is ultrametric.
1803 o The function plot.phylo() has more functionalities such as drawing the
1804 branches with different colours and/or different widths, showing the
1805 node labels, controling the position and font of the labels, rotating
1806 the labels, and controling the space around the plot.
1808 o The function read.tree() can now read trees with no branch length,
1809 such as "(a,b),c);". Consequently, the element `edge.length' in
1810 objects of class "phylo" is now optional.
1812 o The function write.tree() has a new default behaviour: if the default
1813 for the option `file' is used (i.e. file = ""), then a variable of
1814 mode character containing the tree in Newick format is returned which
1815 can thus be assigned (e.g., tree <- write.tree(phy)).
1817 o The function read.tree() has a new argument `text' which allows
1818 to read the tree in a variable of mode character.
1820 o A new data set is included: the phylogenetic relationships among
1821 the orders of birds from Sibley and Ahlquist (1990).
1825 CHANGES IN APE VERSION 0.2-1
1830 o Several bugs were fixed in the help pages.
1834 CHANGES IN APE VERSION 0.2
1839 o The function write.tree() writes phylogenetic trees (objects of class
1840 "phylo") in an ASCII file using the Newick parenthetic format.
1842 o The function birthdeath() fits a birth-death model to branching times
1843 by maximum likelihood, and estimates the corresponding speciation and
1846 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1849 o The function is.binary.tree() tests whether a phylogeny is binary.
1851 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1852 as well as some methods are introduced.
1854 o Several functions, including some generics and methods, for computing
1855 skyline plot estimates (classic and generalized) of effective
1856 population size through time are introduced and replace the function
1857 skyline.plot() in version 0.1.
1859 o Two data sets are now included: the phylogenetic relationships among
1860 the families of birds from Sibley and Ahlquist (1990), and an
1861 estimated clock-like phylogeny of HIV sequences sampled in the
1862 Democratic Republic of Congo.
1865 DEPRECATED & DEFUNCT
1867 o The function skyline.plot() in ape 0.1 has been deprecated and
1868 replaced by more elaborate functions (see above).
1873 o Two important bugs were fixed in plot.phylo(): phylogenies with
1874 multichotomies not at the root or not with only terminal branches,
1875 and phylogenies with a single node (i.e. only terminal branches)
1876 did not plot. These trees should be plotted correctly now.
1878 o Several bugs were fixed in diversi.time() in the computation of
1881 o Various errors were corrected in the help pages.
projects / ape.git / blob