1 CHANGES IN APE VERSION 2.2-3
6 o chronopl() did not work with CV = TRUE.
8 o read.nexus() did not work correctly in some situations (trees on
9 multiple lines with different numbers of lines and/or with
10 comments inserted within the trees).
14 CHANGES IN APE VERSION 2.2-2
19 o dist.gene() has been substantially improved and gains an option
22 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
28 o prop.part() failed with a single tree with the default option
29 'check.labels = TRUE'.
31 o summary.DNAbin() failed to display correctly the summary of
32 sequence lengths with lists of sequences of 10,000 bases or more
33 (because summary.default uses 4 significant digits by default).
35 o read.nexus() failed to read a file with a single tree with line
36 breaks in the Newick string.
38 o del.gaps() returned a list of empty sequences when there were no
44 o phymltest() has been updated for PhyML 3.0 and gains an option
45 'append', whereas the option 'path2exec' has been removed.
47 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
48 which is returned unchanged (instead of an error).
50 o The data sets bird.orders and bird.families are now stored as
51 Newick strings; i.e., the command data(bird.orders) calls
56 CHANGES IN APE VERSION 2.2-1
61 o The new function makeLabel() helps to modify labels of trees,
62 lists of trees, or DNA sequences, with several utilities to
63 truncate and/or make them unique, substituting some
64 characters, and so on.
66 o The new function del.gaps() removes insertion gaps ("-") in a
69 o read.dna() can now read Clustal files (*.aln).
74 o root() failed with 'resolve.root = TRUE' when the root was
75 already the specified root.
77 o Several bugs were fixed in mlphylo().
79 o collapsed.singles() did not propagate the 'Nnode' and
80 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
82 o read.nexus() failed to remove correctly the comments within
85 o read.nexus() failed to read a file with a single tree and no
86 translation of tip labels.
88 o read.nexus() failed to place correctly tip labels when reading
89 a single tree with no edge lengths.
91 o A bug was fixed in sh.test().
96 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
99 o The option 'check.labels' of consensus() and prop.part() is now
102 o write.dna() now does not truncate names to 10 characters with
107 CHANGES IN APE VERSION 2.2
112 o Four new functions have been written by Damien de Vienne for the
113 graphical exploration of large trees (cophyloplot, subtrees,
114 subtreeplot), and to return the graphical coordinates of tree
117 o The new functions corPagel and corBlomberg implement the Pagel's
118 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
120 o chronopl() has been improved and gains several options: see its
121 help page for details.
123 o boot.phylo() has now an option 'trees' to possibly return the
124 bootstraped trees (the default is FALSE).
126 o prop.part() has been improved and should now be faster in all
132 o read.dna() failed if "?" occurred in the first 10 sites of the
135 o The x/y aspect of the plot is now respected when plotting a
136 circular tree (type = "r" or "f").
138 o Drawing the tip labels sometimes failed when plotting circular
141 o zoom() failed when tip labels were used instead of their numbers
142 (thanks to Yan Wong for the fix).
144 o drop.tip() failed with some trees (fixed by Yan Wong).
146 o seg.sites() failed with a list.
148 o consensus() failed in some cases. The function has been improved
149 as well and is faster.
153 CHANGES IN APE VERSION 2.1-3
158 o A bug in read.nexus() made the Windows R-GUI crash.
160 o An error was fixed in the computation of ancestral character
161 states by generalized least squares in ace().
163 o di2multi() did not modify node labels correctly.
165 o multi2di() failed if the tree had its attribute "order" set to
170 CHANGES IN APE VERSION 2.1-2
175 o There three new methods for the "multiPhylo" class: str, $,
178 o root() gains the options 'node' and 'resolve.root'
179 (FALSE by default) as well as its code being improved.
181 o mltt.plot() has now an option 'log' used in the same way
182 than in plot.default().
187 o mltt.plot() failed to display the legend with an unnamed
190 o nodelabels() with pies now correcly uses the argument
191 'cex' to draw symbols of different sizes (which has
192 worked already for thermometers).
194 o read.nexus() generally failed to read very big files.
199 o The argument 'family' of compar.gee() can now be a function
200 as well as a character string.
202 o read.tree() and read.nexus() now return an unnamed list if
205 o read.nexus() now returns a modified object of class "multiPhylo"
206 when there is a TRANSLATE block in the NEXUS file: the individual
207 trees have no 'tip.label' vector, but the list has a 'TipLabel'
208 attribute. The new methods '$' and '[[' set these elements
209 correctly when extracting trees.
213 CHANGES IN APE VERSION 2.1-1
218 o The new function rmtree generates lists of random trees.
220 o rcoal() now generates a genuine coalescent tree by default
221 (thanks to Vladimir Minin for the code).
226 o nuc.div() returned an incorrect value with the default
227 pairwise.deletion = FALSE.
232 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
233 have been improved so that they are stabler and faster.
235 o R packages used by ape are now loaded silently; lattice and gee
236 are loaded only when needed.
240 CHANGES IN APE VERSION 2.1
245 o The new function identify.phylo identifies clades on a plotted
246 tree using the mouse.
248 o It is now possible to subset a list of trees (object of class
249 "multiPhylo") with "[" while keeping its class correct.
251 o The new function as.DNAbin.alignment converts DNA sequences
252 stored in the "alignment" format of the package seqinr into
253 an object of class "DNAbin".
255 o The new function weight.taxo2 helps to build similarity matrices
256 given two taxonomic levels (usually called by other functions).
258 o write.tree() can now take a list of trees (class "multiPhylo")
259 as its main argument.
261 o plot.correlogram() and plot.correlogramList() have been
262 improved, and gain several options (see the help page for
263 details). A legend is now plotted by default.
268 o dist.dna() returned some incorrect values with `model = "JC69"'
269 and `pairwise.deletion = TRUE'. This affected only the
270 distances involving sequences with missing values. (Thanks
271 to Bruno Toupance for digging this bug out.)
273 o write.tree() failed with some trees: this is fixed by removing
274 the `multi.line' option (trees are now always printed on a
277 o read.nexus() did not correctly detect trees with multiple root
278 edges (see OTHER CHANGES).
283 o The code of mlphylo() has been almost entirely rewritten, and
284 should be much stabler. The options have been also greatly
285 simplified (see ?mlphylo and ?DNAmodel for details).
287 o The internal function nTips has been renamed klastorin_nTips.
289 o The code of is.ultrametric() contained redundancies and has
292 o The code of Moran.I() and of correlogram.formula() have been
295 o read.tree() and read.nexus() now return an error when trying to
296 read a tree with multiple root edges (see BUG FIXES). The
297 correction applied in previous version did not work in all
300 o The class c("multi.tree", "phylo") has been renamed
306 o There is now a vignette in ape: see vignette("MoranI", "ape").
311 o as.matching() and as.phylo.matching() do not support branch
314 o correlogram.phylo() and discrete.dist() have been removed.
318 CHANGES IN APE VERSION 2.0-2
323 o The new function matexpo computes the exponential of a square
326 o The new function unique.multi.tree removes duplicate trees from
329 o yule() has a new option `use.root.edge = FALSE' that specifies
330 to ignore, by default, the root edge of the tree if it exists.
335 o which.edge() failed when the index of a single terminal edge was
338 o In diversi.time(), the values returned for model C were
341 o A bug was fixed in yule() that affected the calculation of the
342 likelihood in the presence of ties in the branching times.
344 o There was a bug in the C function mat_expo4x4 affecting the
345 calculations of the transition probabilities for models HKY and
348 o A small bug was fixed in as.matrix.DNAbin (thanks to James
351 o rtree() did not `shuffle' the tip labels by default, so only a
352 limited number of labelled topologies could be generated.
356 CHANGES IN APE VERSION 2.0-1
361 o The three new functions bionj, fastme.ols, and fastme.bal
362 perform phylogeny estimation by the BIONJ and fastME methods in
363 OLS and balanced versions. This is a port to R of previous
364 previous programs done by Vincent Lefort.
366 o The new function chronoMPL performs molecular dating with the
367 mean path lengths method of Britton et al. (2002, Mol. Phyl.
370 o The new function rotate, contributed by Christoph Heibl, swaps
371 two clades connected to the same node. It works also with
372 multichotomous nodes.
374 o The new `method' as.matrix.DNAbin() may be used to convert
375 easily DNA sequences stored in a list into a matrix while
376 keeping the names and the class.
381 o chronopl() failed when some branch lengths were equal to zero:
382 an error message is now returned.
384 o di2multi() failed when there was a series of consecutive edges
389 CHANGES IN APE VERSION 1.10-2
394 o plot.phylo() can now plot circular trees: the option is type =
395 "fan" or type = "f" (to avoid the ambiguity with type = "c").
397 o prop.part() has a new option `check.labels = FALSE' which allows
398 to considerably speed-up the calculations of bipartitions. As a
399 consequence, calculations of bootstrap values with boot.phylo()
400 should be much faster.
405 o read.GenBank() did not return correctly the list of species as
406 from ape 1.10: this is fixed in this version
408 o Applying as.phylo() on a tree of class "phylo" failed: the
409 object is now returned unchanged.
413 CHANGES IN APE VERSION 1.10-1
418 o The three new functions Ntip, Nnode, and Nedge return, for a
419 given tree, the number of tips, nodes, or edges, respectively.
424 o read.nexus() did not set correctly the class of the returned
425 object when reading multiple trees.
427 o mllt.plot() failed with objects of class c("multi.tree",
430 o unroot() did not work correctly in most cases.
432 o reorder.phylo() made R freeze in some occasions.
434 o Plotting a tree in pruningwise order failed.
436 o When plotting an unrooted tree, the tip labels where not all
437 correctly positioned if the option `cex' was used.
441 CHANGES IN APE VERSION 1.10
446 o Five new `method' functions have been introduced to manipulate
447 DNA sequences in binary format (see below).
449 o Three new functions have been introduced to convert between the
450 new binary and the character formats.
452 o The new function as.alignment converts DNA sequences stored as
453 single characters into the class "alignment" used by the package
456 o read.dna() and read.GenBank() have a new argument `as.character'
457 controlling whether the sequences are returned in binary format
463 o root() failed when the tree had node labels: this is fixed.
465 o plot.phylo() did not correctly set the limits on the y-axis with
466 the default setting: this is fixed.
468 o dist.dna() returned a wrong result for the LogDet, paralinear,
469 and BH87 models with `pairwise.deletion = TRUE'.
474 o DNA sequences are now internally stored in a binary format. See
475 the document "A Bit-Level Coding Scheme for Nucleotides" for the
476 details. Most functions analyzing DNA functions have been
477 modified accordingly and are now much faster (dist.dna is now
478 ca. 60 times faster).
482 CHANGES IN APE VERSION 1.9-4
487 o A bug was fixed in edgelabels().
489 o as.phylo.hclust() did not work correctly when the object of
490 class "hclust" has its labels set to NULL: the returned tree has
491 now its tip labels set to "1", "2", ...
493 o consensus could fail if some tip labels are a subset of others
494 (e.g., "a" and "a_1"): this is now fixed.
496 o mlphylo() failed in most cases if some branch lengths of the
497 initial tree were greater than one: an error message is now
500 o mlphylo() failed in most cases when estimating the proportion of
501 invariants: this is fixed.
505 CHANGES IN APE VERSION 1.9-3
510 o The new function edgelabels adds labels on the edge of the tree
511 in the same way than nodelabels or tiplabels.
516 o multi2di() did not handle correctly branch lengths with the
517 default option `random = TRUE': this is now fixed.
519 o A bug was fixed in nuc.div() when using pairwise deletions.
521 o A bug occurred in the analysis of bipartitions with large
522 numbers of large trees, with consequences on prop.part,
523 prop.clades, and boot.phylo.
525 o The calculation of the Billera-Holmes-Vogtmann distance in
526 dist.topo was wrong: this has been fixed.
530 CHANGES IN APE VERSION 1.9-2
535 o The new function ladderize reorganizes the internal structure of
536 a tree to plot them left- or right-ladderized.
538 o The new function dist.nodes computes the patristic distances
539 between all nodes, internal and terminal, of a tree. It replaces
540 the option `full = TRUE' of cophenetic.phylo (see below).
545 o A bug was fixed in old2new.phylo().
547 o Some bugs were fixed in chronopl().
549 o The edge colours were not correctly displayed by plot.phylo
550 (thank you to Li-San Wang for the fix).
552 o cophenetic.phylo() failed with multichotomous trees: this is
558 o read.dna() now returns the sequences in a matrix if they are
559 aligned (interleaved or sequential format). Sequences in FASTA
560 format are still returned in a list.
562 o The option `full' of cophenetic.phylo() has been removed because
563 it could not be used from the generic.
568 o rotate() has been removed; this function did not work correctly
573 CHANGES IN APE VERSION 1.9-1
578 o Trees with a single tip were not read correctly in R as the
579 element `Nnode' was not set: this is fixed.
581 o unroot() did not set correctly the number of nodes of the
582 unrooted tree in most cases.
584 o read.GenBank() failed when fetching very long sequences,
585 particularly of the BX-series.
587 o A bug was introduced in read.tree() with ape 1.9: it has been
592 CHANGES IN APE VERSION 1.9
597 o There are two new print `methods' for trees of class "phylo" and
598 lists of trees of class "multi.tree", so that they are now
599 displayed in a compact and informative way.
601 o There are two new functions, old2new.phylo and new2old.phylo,
602 for converting between the old and new coding of the class
605 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
606 LogDet ("logdet"), and paralinear ("paralin").
608 o compute.brlen() has been extended: several methods are now
609 available to compute branch lengths.
611 o write.dna() can now handle matrices as well as lists.
616 o cophenetic.phylo() sometimes returned a wrong result with
617 multichotomous trees: this is fixed.
619 o rotate() failed when a single tip was specified: the tree is now
622 o ace() did not return the correct index matrix with custom
623 models: this is fixed.
625 o multi2di() did not work correctly when resolving multichotomies
626 randomly: the topology was always the same, only the arrangement
627 of clades was randomized: this is fixed. This function now
628 accepts trees with no branch lengths.
630 o The output of diversi.gof() was blurred by useless prints when a
631 user distribution was specified. This has been corrected, and
632 the help page of this function has been expanded.
637 o The internal structure of the class "phylo" has been changed:
638 see the document "Definition of Formats for Coding Phylogenetic
639 Trees in R" for the details. In addition, the code of most
640 functions has been improved.
642 o Several functions have been improved by replacing some R codes
643 by C codes: pic, plot.phylo, and reorder.phylo.
645 o There is now a citation information: see citation("ape") in R.
647 o write.tree() now does not add extra 0's to branch lengths so
648 that 1.23 is printed "1.23" by default, not "1.2300000000".
650 o The syntax of bind.tree() has been simplified. This function now
651 accepts trees with no branch lengths, and handles correctly node
654 o The option `as.numeric' of mrca() has been removed.
656 o The unused options `format' and `rooted' of read.tree() have
659 o The unused option `format' of write.tree() has been removed.
661 o The use of node.depth() has been simplified.
665 CHANGES IN APE VERSION 1.8-5
670 o Two new functions read.nexus.data() and write.nexus.data(),
671 contributed by Johan Nylander, allow to read and write molecular
672 sequences in NEXUS files.
674 o The new function reorder.phylo() reorders the internal structure
675 of a tree of class "phylo". It is used as the generic, e.g.,
678 o read.tree() and read.nexus() can now read trees with a single
681 o The new data set `cynipids' supplies a set of protein sequences
687 o The code of all.equal.phylo() has been completely rewritten
688 (thanks to Benoît Durand) which fixes several bugs.
690 o read.tree() and read.nexus() now checks the labels of the tree
691 to remove or substitute any characters that are illegal in the
692 Newick format (parentheses, etc.)
694 o A negative P-value could be returned by mantel.test(): this is
699 CHANGES IN APE VERSION 1.8-4
704 o The new function sh.test() computes the Shimodaira-
707 o The new function collapse.singles() removes the nodes with a
708 single descendant from a tree.
710 o plot.phylo() has a new argument `tip.color' to specify the
713 o mlphylo() has now an option `quiet' to control the display of
714 the progress of the analysis (the default is FALSE).
719 o read.dna() did not read correctly sequences in sequential format
720 with leading alignment gaps "-": this is fixed.
722 o ace() returned a list with no class so that the generic
723 functions (anova, logLik, ...) could not be used directly. This
724 is fixed as ace() now returns an object of class "ace".
726 o anova.ace() had a small bug when computing the number of degrees
727 of freedom: this is fixed.
729 o mlphylo() did not work when the sequences were in a matrix or
730 a data frame: this is fixed.
732 o rtree() did not work correctly when trying to simulate an
733 unrooted tree with two tips: an error message is now issued.
738 o The algorithm of rtree() has been changed: it is now about 40,
739 100, and 130 times faster for 10, 100, and 1000 tips,
744 CHANGES IN APE VERSION 1.8-3
749 o There are four new `method' functions to be used with the
750 results of ace(): logLik(), deviance(), AIC(), and anova().
752 o The plot method of phymltest has two new arguments: `main' to
753 change the title, and `col' to control the colour of the
754 segments showing the AIC values.
756 o ace() has a new argument `ip' that gives the initial values used
757 in the ML estimation with discrete characters (see the examples
758 in ?ace). This function now returns a matrix giving the indices
759 of the estimated rates when analysing discrete characters.
761 o nodelabels() and tiplabels() have a new argument `pie' to
762 represent proportions, with any number of categories, as
763 piecharts. The use of the option `thermo' has been improved:
764 there is now no limitation on the number of categories.
769 o mlphylo() did not work with more than two partitions: this is
772 o root() failed if the proposed outgroup was already an outgroup
773 in the tree: this is fixed.
775 o The `col' argument in nodelabels() and tiplabels() was not
776 correctly passed when `text' was used: this is fixed.
778 o Two bugs were fixed in mlphylo(): parameters were not always
779 correctly output, and the estimation failed in some cases.
781 o plot.phylo() was stuck when given a tree with a single tip: this
782 is fixed and a message error is now returned.
784 o An error was corrected in the help page of gammaStat regarding
785 the calculation of P-values.
787 o Using gls() could crash R when the number of species in the tree
788 and in the variables were different: this is fixed.
792 CHANGES IN APE VERSION 1.8-2
797 o The new function mlphylo() fits a phylogenetic tree by maximum
798 likelihood from DNA sequences. Its companion function DNAmodel()
799 is used to define the substitution model which may include
800 partitioning. There are methods for logLik(), deviance(), and
801 AIC(), and the summary() method has been extended to display in
802 a friendly way the results of this model fitting. Currently, the
803 functionality is limited to estimating the substitution and
804 associated parameters and computing the likelihood.
806 o The new function drop1.compar.gee (used as, e.g., drop1(m))
807 tests for single effects in GEE-based comparative method. A
808 warning message is printed if there is not enough degrees of
814 o An error message was sometimes issued by plot.multi.tree(),
815 though with no consequence.
819 CHANGES IN APE VERSION 1.8-1
824 o There is a new plot method for lists of trees (objects of class
825 "multi.tree"): it calls plot.phylo() internally and is
826 documented on the same help page.
831 o A bug was fixed in the C code that analyzes bipartitions: this
832 has impact on several functions like prop.part, prop.clades,
833 boot.phylo, or consensus.
835 o root() did not work correctly when the specified outgroup had
836 more than one element: this is fixed.
838 o dist.dna() sometimes returned a warning inappropriately: this
841 o If the distance object given to nj() had no rownames, nj()
842 returned a tree with no tip labels: it now returns tips labelled
843 "1", "2", ..., corresponding to the row numbers.
848 o nj() has been slightly changed so that tips with a zero distance
849 are first aggregated with zero-lengthed branches; the usual NJ
850 procedure is then performed on a distance matrix without 0's.
854 CHANGES IN APE VERSION 1.8
859 o The new function chronopl() estimates dates using the penalized
860 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
862 o The new function consensus() calculates the consensus tree of a
865 o The new function evolve.phylo() simulates the evolution of
866 continuous characters along a phylogeny under a Brownian model.
868 o The new plot method for objects of class "ancestral" displays a
869 tree together with ancestral values, as returned by the above
872 o The new function as.phylo.formula() returns a phylogeny from a
873 set of nested taxonomic variables given as a formula.
875 o The new function read.caic() reads trees in CAIC format.
877 o The new function tiplabels() allows to add labels to the tips
878 of a tree using text or plotting symbols in a flexible way.
880 o The new function unroot() unroots a phylogeny.
882 o multi2di() has a new option, `random', which specifies whether
883 to resolve the multichotomies randomly (the default) or not.
885 o prop.part() now returns an object of class "prop.part" for which
886 there are print (to display a partition in a more friendly way)
887 and summary (to extract the numbers) methods.
889 o plot.phylo() has a new option, `show.tip.label', specifying
890 whether to print the labels of the tips. The default is TRUE.
892 o The code of nj() has been replaced by a faster C code: it is now
893 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
896 o write.nexus() now writes whether a tree is rooted or not.
901 o Two bugs have been fixed in root(): unrooted trees are now
902 handled corretly, and node labels are now output normally.
904 o A bug was fixed in phymltest(): the executable couldn't be found
907 o Three bug have been fixed in ace(): computing the likelihood of
908 ancestral states of discrete characters failed, custom models
909 did not work, and the function failed with a null gradient (a
910 warning message is now returned; this latter bug was also
911 present in yule.cov() as well and is now fixed).
913 o pic() hanged out when missing data were present: a message error
916 o A small bug was fixed in dist.dna() where the gamma correction
917 was not always correctly dispatched.
919 o plot.phylo() plotted correctly the root edge only when the tree
920 was plotted rightwards: this works now for all directions.
925 o dist.taxo() has been renamed as weight.taxo().
927 o Various error and warning messages have been improved.
931 CHANGES IN APE VERSION 1.7
934 o The new function ace() estimates ancestral character states for
935 continuous characters (with ML, GLS, and contrasts methods), and
936 discrete characters (with ML only) for any number of states.
938 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
939 of directional evolution for continuous characters. The user
940 specifies the node(s) of the tree where the character optimum
943 o The new function is.rooted() tests whether a tree (of class
946 o The new function rcoal() generates random ultrametric trees with
947 the possibility to specify the function that generates the
948 inter-nodes distances.
950 o The new function mrca() gives for all pairs of tips in a tree
951 (and optionally nodes too) the most recent common ancestor.
953 o nodelabels() has a new option `thermo' to plot proportions (up
954 to three classes) on the nodes of a tree.
956 o rtree() has been improved: it can now generate rooted or
957 unrooted trees, and the mathematical function that generates the
958 branch lengths may be specified by the user. The tip labels may
959 be given directly in the call to rtree. The limit cases (n = 2,
960 3) are now handled correctly.
962 o dist.topo() has a new argument `method' with two choices: "PH85"
963 for Penny and Henny's method (already available before and now
964 the default), and "BHV01" for the geometric distance by Billera
965 et al. (2001, Adv. Appl. Math. 27:733).
967 o write.tree() has a new option, `digits', which specifies the
968 number of digits to be printed in the Newick tree. By default
969 digits = 10. The numbers are now always printed in decimal form
970 (i.e., 1.0e-1 is now avoided).
972 o dist.dna() can now compute the raw distances between pairs of
973 DNA sequences by specifying model = "raw".
975 o dist.phylo() has a new option `full' to possibly compute the
976 distances among all tips and nodes of the tree. The default if
982 o Several bugs were fixed in all.equal.phylo().
984 o dist.dna() did not handle correctly gaps ("-") in alignments:
985 they are now considered as missing data.
987 o rotate() did not work if the tips were not ordered: this is
990 o mantel.test() returned NA in some special cases: this is fixed
991 and the function has been improved and is now faster.
993 o A bug was fixed in diversi.gof() where the calculation of A² was
996 o cherry() did not work correctly under some OSs (mainly Linux):
999 o is.binary.tree() has been modified so that it works with both
1000 rooted and unrooted trees.
1002 o The documentation of theta.s() was not correct: this has been
1005 o plot.mst() did not work correctly: this is fixed.
1009 CHANGES IN APE VERSION 1.6
1014 o The new function dist.topo() computes the topological distances
1017 o The new function boot.phylo() performs a bootstrap analysis on
1018 phylogeny estimation.
1020 o The new functions prop.part() and prop.clades() analyse
1021 bipartitions from a series of trees.
1026 o read.GenBank() now uses the EFetch utility of NCBI instead of
1027 the usual Web interface: it is now much faster (e.g., 12 times
1028 faster to retrieve 8 sequences, 37 times for 60 sequences).
1033 o Several bugs were fixed in read.dna().
1035 o Several bugs were fixed in diversi.time().
1037 o is.binary.tree() did not work correctly if the tree has no edge
1038 lengths: this is fixed.
1040 o drop.tip() did not correctly propagated the `node.label' of a
1041 tree: this is fixed.
1045 CHANGES IN APE VERSION 1.5
1050 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1051 convert objects between the classes "phylo" and "matching". The
1052 latter implements the representation of binary trees introduced by
1053 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1054 as.matching() has been introduced as well.
1056 o Two new functions, multi2di() and di2multi(), allow to resolve
1057 and collapse multichotomies with branches of length zero.
1059 o The new function nuc.div() computes the nucleotide diversity
1060 from a sample a DNA sequences.
1062 o dist.dna() has been completely rewritten with a much faster
1063 (particularly for large data sets) C code. Eight models are
1064 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1065 option `method' has been renamed `model'). Computation of variance
1066 is available for all models. A gamma-correction is possible for
1067 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1068 to remove sites with missing data on a pairwise basis. The option
1069 `GCcontent' has been removed.
1071 o read.GenBank() has a new option (species.names) which specifies
1072 whether to return the species names of the organisms in addition
1073 to the accession numbers of the sequences (this is the default
1076 o write.nexus() can now write several trees in the same NEXUS file.
1078 o drop.tip() has a new option `root.edge' that allows to specify the
1079 new root edge if internal branches are trimmed.
1084 o as.phylo.hclust() failed if some labels had parentheses: this
1087 o Several bugs were fixed in all.equal.phylo(). This function now
1088 returns the logical TRUE if the trees are identical but with
1089 different representations (a report was printed previously).
1091 o read.GenBank() did not correctly handle ambiguous base codes:
1097 o birthdeath() now returns an object of class "birthdeath" for
1098 which there is a print method.
1102 CHANGES IN APE VERSION 1.4
1107 o The new function nj() performs phylogeny estimation with the
1108 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1111 o The new function which.edge() identifies the edges of a tree
1112 that belong to a group specified as a set of tips.
1114 o The new function as.phylo.phylog() converts an object of class
1115 "phylog" (from the package ade4) into an object of class
1118 o The new function axisPhylo() draws axes on the side of a
1121 o The new function howmanytrees() calculates the number of trees
1122 in different cases and giving a number of tips.
1124 o write.tree() has a new option `multi.line' (TRUE by default) to
1125 write a Newick tree on several lines rather than on a single
1128 o The functionalities of zoom() have been extended. Several
1129 subtrees can be visualized at the same time, and they are marked
1130 on the main tree with colors. The context of the subtrees can be
1131 marked with the option `subtree' (see below).
1133 o drop.tip() has a new option `subtree' (FALSE by default) which
1134 specifies whether to output in the tree how many tips have been
1137 o The arguments of add.scale.bar() have been redefined and have
1138 now default values (see ?add.scale.bar for details). This
1139 function now works even if the plotted tree has no edge length.
1141 o plot.phylo() can now plot radial trees, but this does not take
1142 edge lengths into account.
1144 o In plot.phylo() with `type = "phylogram"', if the values of
1145 `edge.color' and `edge.width' are identical for sister-branches,
1146 they are propagated to the vertical line that link them.
1151 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1152 crashing. This is fixed.
1154 o In plot.phylo(), the options `edge.color' and `edge.width' are
1155 now properly recycled; their default values are now "black" and
1158 o A bug has been fixed in write.nexus().
1163 o The function node.depth.edgelength() has been removed and
1164 replaced by a C code.
1168 CHANGES IN APE VERSION 1.3-1
1173 o The new function nodelabels() allows to add labels to the nodes
1174 of a tree using text or plotting symbols in a flexible way.
1176 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1177 numeric values specifying the lower and upper limits on the x-
1178 and y-axes. This allows to leave some space on any side of the
1179 tree. If a single value is given, this is taken as the upper
1184 CHANGES IN APE VERSION 1.3
1189 o The new function phymltest() calls the software PHYML and fits
1190 28 models of DNA sequence evolution. There are a print method to
1191 display likelihood and AIC values, a summary method to compute
1192 the hierarchical likelihood ratio tests, and a plot method to
1193 display graphically the AIC values of each model.
1195 o The new function yule.cov() fits the Yule model with covariates,
1196 a model where the speciation rate is affected by several species
1197 traits through a generalized linear model. The parameters are
1198 estimated by maximum likelihood.
1200 o Three new functions, corBrownian(), corGrafen(), and
1201 corMartins(), compute the expected correlation structures among
1202 species given a phylogeny under different models of evolution.
1203 These can be used for GLS comparative phylogenetic methods (see
1204 the examples). There are coef() and corMatrix() methods and an
1205 Initialize.corPhyl() function associated.
1207 o The new function compar.cheverud() implements Cheverud et al.'s
1208 (1985; Evolution 39:1335) phylogenetic comparative method.
1210 o The new function varcomp() estimates variance components; it has
1213 o Two new functions, panel.superpose.correlogram() and
1214 plot.correlogramList(), allow to plot several phylogenetic
1217 o The new function node.leafnumber() computes the number of leaves
1218 of a subtree defined by a particular node.
1220 o The new function node.sons() gets all tags of son nodes from a
1223 o The new function compute.brlen() computes the branch lengths of
1224 a tree according to a specified method.
1226 o plot.phylo() has three new options: "cex" controls the size of
1227 the (tip and node) labels (thus it is no more needed to change
1228 the global graphical parameter), "direction" which allows to
1229 plot the tree rightwards, leftwards, upwards, or downwards, and
1230 "y.lim" which sets the upper limit on the y-axis.
1235 o Some functions which try to match tip labels and names of
1236 additional data (e.g. vector) are likely to fail if there are
1237 typing or syntax errors. If both series of names do not perfectly
1238 match, they are ignored and a warning message is now issued.
1239 These functions are bd.ext, compar.gee, pic. Their help pages
1240 have been clarified on this point.
1244 CHANGES IN APE VERSION 1.2-7
1249 o The new function root() reroots a phylogenetic tree with respect
1250 to a specified outgroup.
1252 o The new function rotate() rotates an internal branch of a tree.
1254 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1255 trees) controls the display of the tip labels in unrooted trees.
1256 This display has been greatly improved: the tip labels are now not
1257 expected to overlap with the tree (particularly if lab4ut =
1258 "axial"). In all cases, combining appropriate values of "lab4ut"
1259 and the font size (via "par(cex = )") should result in readable
1260 unrooted trees. See ?plot.phylo for some examples.
1262 o In drop.tip(), the argument `tip' can now be numeric or character.
1267 o drop.tip() did not work correctly with trees with no branch
1268 lengths: this is fixed.
1270 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1271 plotted with some line crossings: this is now fixed.
1275 CHANGES IN APE VERSION 1.2-6
1280 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1281 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1282 to implement comparative methods with an autocorrelation approach.
1284 o A new data set describing some life history traits of Carnivores
1290 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1295 o When plotting a tree with plot.phylo(), the new default of the
1296 option `label.offset' is now 0, so the labels are always visible.
1300 CHANGES IN APE VERSION 1.2-5
1305 o The new function bd.ext() fits a birth-death model with combined
1306 phylogenetic and taxonomic data, and estimates the corresponding
1307 speciation and extinction rates.
1312 o The package gee is no more required by ape but only suggested
1313 since only the function compar.gee() calls gee.
1317 CHANGES IN APE VERSION 1.2-4
1322 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1323 and lines.popsize) implementing a new approach for inferring the
1324 demographic history from genealogies using a reversible jump
1325 MCMC have been introduced.
1327 o The unit of time in the skyline plot and in the new plots can
1328 now be chosen to be actual years, rather than substitutions.
1332 CHANGES IN APE VERSION 1.2-3
1337 o The new function rtree() generates a random binary tree with or
1338 without branch lengths.
1340 o Two new functions for drawing lineages-through-time (LTT) plots
1341 are provided: ltt.lines() adds a LTT curve to an existing plot,
1342 and mltt.plot() does a multiple LTT plot giving several trees as
1343 arguments (see `?ltt.plot' for details).
1348 o Some taxon names made R crashing when calling as.phylo.hclust():
1351 o dist.dna() returned an error with two identical DNA sequences
1352 (only using the Jukes-Cantor method returned 0): this is fixed.
1357 o The function dist.phylo() has been re-written using a different
1358 algorithm: it is now about four times faster.
1360 o The code of branching.times() has been improved: it is now about
1365 CHANGES IN APE VERSION 1.2-2
1370 o The new function seg.sites() finds the segregating sites in a
1371 sample of DNA sequences.
1376 o A bug introduced in read.tree() and in read.nexus() with version
1379 o A few errors were corrected and a few examples were added in the
1384 CHANGES IN APE VERSION 1.2-1
1389 o plot.phylo() can now draw the edge of the root of a tree if it
1390 has one (see the new option `root.edge', its default is FALSE).
1395 o A bug was fixed in read.nexus(): files with semicolons inside
1396 comment blocks were not read correctly.
1398 o The behaviour of read.tree() and read.nexus() was corrected so
1399 that tree files with badly represented root edges (e.g., with
1400 an extra pair of parentheses, see the help pages for details)
1401 are now correctly represented in the object of class "phylo";
1402 a warning message is now issued.
1406 CHANGES IN APE VERSION 1.2
1411 o plot.phylo() has been completely re-written and offers several
1412 new functionalities. Three types of trees can now be drawn:
1413 phylogram (as previously), cladogram, and unrooted tree; in
1414 all three types the branch lengths can be drawn using the edge
1415 lengths of the phylogeny or not (e.g., if the latter is absent).
1416 The vertical position of the nodes can be adjusted with two
1417 choices (see option `node.pos'). The code has been re-structured,
1418 and two new functions (potentially useful for developpers) are
1419 documented separately: node.depth.edgelength() and node.depth();
1420 see the respective help pages for details.
1422 o The new function zoom() allows to explore very large trees by
1423 focusing on a small portion of it.
1425 o The new function yule() fits by maximum likelihood the Yule model
1426 (birth-only process) to a phylogenetic tree.
1428 o Support for writing DNA sequences in FASTA format has been
1429 introduced in write.dna() (support for reading sequences in
1430 this format was introduced in read.dna() in version 1.1-2).
1431 The function has been completely re-written, fixing some bugs
1432 (see below); the default behaviour is no more to display the
1433 sequences on the standard output. Several options have been
1434 introduced to control the sequence printing in a flexible
1435 way. The help page has been extended.
1437 o A new data set is included: a supertree of bats in NEXUS format.
1442 o In theta.s(), the default of the option `variance' has
1443 been changed to `FALSE' (as was indicated in the help page).
1445 o Several bugs were fixed in the code of all.equal.phylo().
1447 o Several bugs were fixed in write.dna(), particularly this
1448 function did not work with `format = "interleaved"'.
1450 o Various errors were corrected in the help pages.
1455 o The argument names of as.hclust.phylo() have been changed
1456 from "(phy)" to "(x, ...)" to conform to the definition of
1457 the corresponding generic function.
1459 o gamma.stat() has been renamed gammaStat() to avoid confusion
1460 since gamma() is a generic function.
1464 CHANGES IN APE VERSION 1.1-3
1469 o base.freq() previously did not return a value of 0 for
1470 bases absent in the data (e.g., a vector of length 3 was
1471 returned if one base was absent). This is now fixed (a
1472 vector of length 4 is always returned).
1474 o Several bugs were fixed in read.nexus(), including that this
1475 function did not work in this absence of a "TRANSLATE"
1476 command in the NEXUS file, and that the commands were
1481 CHANGES IN APE VERSION 1.1-2
1486 o The Tamura and Nei (1993) model of DNA distance is now implemented
1487 in dist.dna(): five models are now available in this function.
1489 o A new data set is included: a set of 15 sequences of the
1490 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1496 o A bug in read.nexus() was fixed.
1498 o read.dna() previously did not work correctly in most cases.
1499 The function has been completely re-written and its help page
1500 has been considerably extended (see ?read.dna for details).
1501 Underscores (_) in taxon names are no more replaced with
1502 spaces (this behaviour was undocumented).
1504 o A bug was fixed in write.dna().
1508 CHANGES IN APE VERSION 1.1-1
1513 o A bug in read.tree() introduced in APE 1.1 was fixed.
1515 o A bug in compar.gee() resulted in an error when trying to fit
1516 a model with `family = "binomial"'. This is now fixed.
1520 CHANGES IN APE VERSION 1.1
1525 o The Klastorin (1982) method as suggested by Misawa and Tajima
1526 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1527 on the basis of phylogenetic trees has been implemented (see
1528 the function klastorin()).
1530 o Functions have been added to convert APE's "phylo" objects in
1531 "hclust" cluster objects and vice versa (see the help page of
1532 as.phylo for details).
1534 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1535 are introduced for the estimation of absolute evolutionary rates
1536 (ratogram) and dated clock-like trees (chronogram) from
1537 phylogenetic trees using the non-parametric rate smoothing approach
1538 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1540 o A summary method is now provided printing a summary information on a
1541 phylogenetic tree with, for instance, `summary(tree)'.
1543 o The behaviour of read.tree() was changed so that all spaces and
1544 tabulations in tree files are now ignored. Consequently, spaces in tip
1545 labels are no more allowed. Another side effect is that read.nexus()
1546 now does not replace the underscores (_) in tip labels with spaces
1547 (this behaviour was undocumented).
1549 o The function plot.phylo() has a new option (`underscore') which
1550 specifies whether the underscores in tip labels should be written on
1551 the plot as such or replaced with spaces (the default).
1553 o The function birthdeath() now computes 95% confidence intervals of
1554 the estimated parameters using profile likelihood.
1556 o Three new data sets are included: a gene tree estimated from 36
1557 landplant rbcL sequences, a gene tree estimated from 32 opsin
1558 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1563 o A bug was fixed in dist.gene() where nothing was returned.
1565 o A bug in plot.mst() was fixed.
1567 o A bug in vcv.phylo() resulted in false correlations when the
1568 option `cor = TRUE' was used (now fixed).
1572 CHANGES IN APE VERSION 1.0
1577 o Two new functions, read.dna() and write.dna(), read/write in a file
1578 DNA sequences in interleaved or in sequential format.
1580 o Two new functions, read.nexus() and write.nexus(), read/write trees
1583 o The new function bind.tree() allows to bind two trees together,
1584 possibly handling root edges to give internal branches.
1586 o The new function drop.tip() removes the tips in a phylogenetic tree,
1587 and trims (or not) the corresponding internal branches.
1589 o The new function is.ultrametric() tests if a tree is ultrametric.
1591 o The function plot.phylo() has more functionalities such as drawing the
1592 branches with different colours and/or different widths, showing the
1593 node labels, controling the position and font of the labels, rotating
1594 the labels, and controling the space around the plot.
1596 o The function read.tree() can now read trees with no branch length,
1597 such as "(a,b),c);". Consequently, the element `edge.length' in
1598 objects of class "phylo" is now optional.
1600 o The function write.tree() has a new default behaviour: if the default
1601 for the option `file' is used (i.e. file = ""), then a variable of
1602 mode character containing the tree in Newick format is returned which
1603 can thus be assigned (e.g., tree <- write.tree(phy)).
1605 o The function read.tree() has a new argument `text' which allows
1606 to read the tree in a variable of mode character.
1608 o A new data set is included: the phylogenetic relationships among
1609 the orders of birds from Sibley and Ahlquist (1990).
1613 CHANGES IN APE VERSION 0.2-1
1618 o Several bugs were fixed in the help pages.
1622 CHANGES IN APE VERSION 0.2
1627 o The function write.tree() writes phylogenetic trees (objects of class
1628 "phylo") in an ASCII file using the Newick parenthetic format.
1630 o The function birthdeath() fits a birth-death model to branching times
1631 by maximum likelihood, and estimates the corresponding speciation and
1634 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1637 o The function is.binary.tree() tests whether a phylogeny is binary.
1639 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1640 as well as some methods are introduced.
1642 o Several functions, including some generics and methods, for computing
1643 skyline plot estimates (classic and generalized) of effective
1644 population size through time are introduced and replace the function
1645 skyline.plot() in version 0.1.
1647 o Two data sets are now included: the phylogenetic relationships among
1648 the families of birds from Sibley and Ahlquist (1990), and an
1649 estimated clock-like phylogeny of HIV sequences sampled in the
1650 Democratic Republic of Congo.
1653 DEPRECATED & DEFUNCT
1655 o The function skyline.plot() in ape 0.1 has been deprecated and
1656 replaced by more elaborate functions (see above).
1661 o Two important bugs were fixed in plot.phylo(): phylogenies with
1662 multichotomies not at the root or not with only terminal branches,
1663 and phylogenies with a single node (i.e. only terminal branches)
1664 did not plot. These trees should be plotted correctly now.
1666 o Several bugs were fixed in diversi.time() in the computation of
1669 o Various errors were corrected in the help pages.
projects / ape.git / blob