1 CHANGES IN APE VERSION 2.3
6 o The new functions CADM.global and CADM.post, contributed by
7 Pierre Legendre, test the congruence among several distance
10 o The new function yule.time fits a user-defined time-dependent
11 Yule model by maximum likelihood.
13 o The new function makeNodeLabel creates and/or modifies node
14 labels in a flexible way.
16 o read.tree() and write.tree() have been modified so that they can
17 handle individual tree names
22 o drop.tip() shuffled tip labels in some cases.
24 o drop.tip() did not handle node.label correctly.
26 o is.ultrametric() now checks the ordering of the edge matrix.
28 o ace() sometimes returned negative values of likelihoods of
29 ancestral states (thanks to Dan Rabosky for solving this long
35 o The data set xenarthra has been removed.
39 CHANGES IN APE VERSION 2.2-4
43 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
44 now fixed. (Thanks to Peter Wragg for the fix!)
46 o A warning message occurred for no reason with ace(method="GLS").
51 o There is now a general help page displayed with '?ape'
55 CHANGES IN APE VERSION 2.2-3
60 o The new function extract.clade extracts a clade from a tree by
61 specifying a node number or label.
63 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
64 operations of the same names.
66 o dist.dna() can now return the number of site differences by
72 o chronopl() did not work with CV = TRUE.
74 o read.nexus() did not work correctly in some situations (trees on
75 multiple lines with different numbers of lines and/or with
76 comments inserted within the trees).
78 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
79 the number of lineages with non-binary trees.
84 o ape has now a namespace.
86 o drip.tip() has been improved: it should be much faster and work
87 better in some cases (e.g., see the example in ?zoom).
91 CHANGES IN APE VERSION 2.2-2
96 o dist.gene() has been substantially improved and gains an option
99 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
105 o prop.part() failed with a single tree with the default option
106 'check.labels = TRUE'.
108 o summary.DNAbin() failed to display correctly the summary of
109 sequence lengths with lists of sequences of 10,000 bases or more
110 (because summary.default uses 4 significant digits by default).
112 o read.nexus() failed to read a file with a single tree with line
113 breaks in the Newick string.
115 o del.gaps() returned a list of empty sequences when there were no
121 o phymltest() has been updated for PhyML 3.0 and gains an option
122 'append', whereas the option 'path2exec' has been removed.
124 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
125 which is returned unchanged (instead of an error).
127 o The data sets bird.orders and bird.families are now stored as
128 Newick strings; i.e., the command data(bird.orders) calls
133 CHANGES IN APE VERSION 2.2-1
138 o The new function makeLabel() helps to modify labels of trees,
139 lists of trees, or DNA sequences, with several utilities to
140 truncate and/or make them unique, substituting some
141 characters, and so on.
143 o The new function del.gaps() removes insertion gaps ("-") in a
144 set of DNA sequences.
146 o read.dna() can now read Clustal files (*.aln).
151 o root() failed with 'resolve.root = TRUE' when the root was
152 already the specified root.
154 o Several bugs were fixed in mlphylo().
156 o collapsed.singles() did not propagate the 'Nnode' and
157 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
159 o read.nexus() failed to remove correctly the comments within
162 o read.nexus() failed to read a file with a single tree and no
163 translation of tip labels.
165 o read.nexus() failed to place correctly tip labels when reading
166 a single tree with no edge lengths.
168 o A bug was fixed in sh.test().
173 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
176 o The option 'check.labels' of consensus() and prop.part() is now
179 o write.dna() now does not truncate names to 10 characters with
184 CHANGES IN APE VERSION 2.2
189 o Four new functions have been written by Damien de Vienne for the
190 graphical exploration of large trees (cophyloplot, subtrees,
191 subtreeplot), and to return the graphical coordinates of tree
194 o The new functions corPagel and corBlomberg implement the Pagel's
195 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
197 o chronopl() has been improved and gains several options: see its
198 help page for details.
200 o boot.phylo() has now an option 'trees' to possibly return the
201 bootstraped trees (the default is FALSE).
203 o prop.part() has been improved and should now be faster in all
209 o read.dna() failed if "?" occurred in the first 10 sites of the
212 o The x/y aspect of the plot is now respected when plotting a
213 circular tree (type = "r" or "f").
215 o Drawing the tip labels sometimes failed when plotting circular
218 o zoom() failed when tip labels were used instead of their numbers
219 (thanks to Yan Wong for the fix).
221 o drop.tip() failed with some trees (fixed by Yan Wong).
223 o seg.sites() failed with a list.
225 o consensus() failed in some cases. The function has been improved
226 as well and is faster.
230 CHANGES IN APE VERSION 2.1-3
235 o A bug in read.nexus() made the Windows R-GUI crash.
237 o An error was fixed in the computation of ancestral character
238 states by generalized least squares in ace().
240 o di2multi() did not modify node labels correctly.
242 o multi2di() failed if the tree had its attribute "order" set to
247 CHANGES IN APE VERSION 2.1-2
252 o There three new methods for the "multiPhylo" class: str, $,
255 o root() gains the options 'node' and 'resolve.root'
256 (FALSE by default) as well as its code being improved.
258 o mltt.plot() has now an option 'log' used in the same way
259 than in plot.default().
264 o mltt.plot() failed to display the legend with an unnamed
267 o nodelabels() with pies now correcly uses the argument
268 'cex' to draw symbols of different sizes (which has
269 worked already for thermometers).
271 o read.nexus() generally failed to read very big files.
276 o The argument 'family' of compar.gee() can now be a function
277 as well as a character string.
279 o read.tree() and read.nexus() now return an unnamed list if
282 o read.nexus() now returns a modified object of class "multiPhylo"
283 when there is a TRANSLATE block in the NEXUS file: the individual
284 trees have no 'tip.label' vector, but the list has a 'TipLabel'
285 attribute. The new methods '$' and '[[' set these elements
286 correctly when extracting trees.
290 CHANGES IN APE VERSION 2.1-1
295 o The new function rmtree generates lists of random trees.
297 o rcoal() now generates a genuine coalescent tree by default
298 (thanks to Vladimir Minin for the code).
303 o nuc.div() returned an incorrect value with the default
304 pairwise.deletion = FALSE.
309 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
310 have been improved so that they are stabler and faster.
312 o R packages used by ape are now loaded silently; lattice and gee
313 are loaded only when needed.
317 CHANGES IN APE VERSION 2.1
322 o The new function identify.phylo identifies clades on a plotted
323 tree using the mouse.
325 o It is now possible to subset a list of trees (object of class
326 "multiPhylo") with "[" while keeping its class correct.
328 o The new function as.DNAbin.alignment converts DNA sequences
329 stored in the "alignment" format of the package seqinr into
330 an object of class "DNAbin".
332 o The new function weight.taxo2 helps to build similarity matrices
333 given two taxonomic levels (usually called by other functions).
335 o write.tree() can now take a list of trees (class "multiPhylo")
336 as its main argument.
338 o plot.correlogram() and plot.correlogramList() have been
339 improved, and gain several options (see the help page for
340 details). A legend is now plotted by default.
345 o dist.dna() returned some incorrect values with `model = "JC69"'
346 and `pairwise.deletion = TRUE'. This affected only the
347 distances involving sequences with missing values. (Thanks
348 to Bruno Toupance for digging this bug out.)
350 o write.tree() failed with some trees: this is fixed by removing
351 the `multi.line' option (trees are now always printed on a
354 o read.nexus() did not correctly detect trees with multiple root
355 edges (see OTHER CHANGES).
360 o The code of mlphylo() has been almost entirely rewritten, and
361 should be much stabler. The options have been also greatly
362 simplified (see ?mlphylo and ?DNAmodel for details).
364 o The internal function nTips has been renamed klastorin_nTips.
366 o The code of is.ultrametric() contained redundancies and has
369 o The code of Moran.I() and of correlogram.formula() have been
372 o read.tree() and read.nexus() now return an error when trying to
373 read a tree with multiple root edges (see BUG FIXES). The
374 correction applied in previous version did not work in all
377 o The class c("multi.tree", "phylo") has been renamed
383 o There is now a vignette in ape: see vignette("MoranI", "ape").
388 o as.matching() and as.phylo.matching() do not support branch
391 o correlogram.phylo() and discrete.dist() have been removed.
395 CHANGES IN APE VERSION 2.0-2
400 o The new function matexpo computes the exponential of a square
403 o The new function unique.multi.tree removes duplicate trees from
406 o yule() has a new option `use.root.edge = FALSE' that specifies
407 to ignore, by default, the root edge of the tree if it exists.
412 o which.edge() failed when the index of a single terminal edge was
415 o In diversi.time(), the values returned for model C were
418 o A bug was fixed in yule() that affected the calculation of the
419 likelihood in the presence of ties in the branching times.
421 o There was a bug in the C function mat_expo4x4 affecting the
422 calculations of the transition probabilities for models HKY and
425 o A small bug was fixed in as.matrix.DNAbin (thanks to James
428 o rtree() did not `shuffle' the tip labels by default, so only a
429 limited number of labelled topologies could be generated.
433 CHANGES IN APE VERSION 2.0-1
438 o The three new functions bionj, fastme.ols, and fastme.bal
439 perform phylogeny estimation by the BIONJ and fastME methods in
440 OLS and balanced versions. This is a port to R of previous
441 previous programs done by Vincent Lefort.
443 o The new function chronoMPL performs molecular dating with the
444 mean path lengths method of Britton et al. (2002, Mol. Phyl.
447 o The new function rotate, contributed by Christoph Heibl, swaps
448 two clades connected to the same node. It works also with
449 multichotomous nodes.
451 o The new `method' as.matrix.DNAbin() may be used to convert
452 easily DNA sequences stored in a list into a matrix while
453 keeping the names and the class.
458 o chronopl() failed when some branch lengths were equal to zero:
459 an error message is now returned.
461 o di2multi() failed when there was a series of consecutive edges
466 CHANGES IN APE VERSION 1.10-2
471 o plot.phylo() can now plot circular trees: the option is type =
472 "fan" or type = "f" (to avoid the ambiguity with type = "c").
474 o prop.part() has a new option `check.labels = FALSE' which allows
475 to considerably speed-up the calculations of bipartitions. As a
476 consequence, calculations of bootstrap values with boot.phylo()
477 should be much faster.
482 o read.GenBank() did not return correctly the list of species as
483 from ape 1.10: this is fixed in this version
485 o Applying as.phylo() on a tree of class "phylo" failed: the
486 object is now returned unchanged.
490 CHANGES IN APE VERSION 1.10-1
495 o The three new functions Ntip, Nnode, and Nedge return, for a
496 given tree, the number of tips, nodes, or edges, respectively.
501 o read.nexus() did not set correctly the class of the returned
502 object when reading multiple trees.
504 o mllt.plot() failed with objects of class c("multi.tree",
507 o unroot() did not work correctly in most cases.
509 o reorder.phylo() made R freeze in some occasions.
511 o Plotting a tree in pruningwise order failed.
513 o When plotting an unrooted tree, the tip labels where not all
514 correctly positioned if the option `cex' was used.
518 CHANGES IN APE VERSION 1.10
523 o Five new `method' functions have been introduced to manipulate
524 DNA sequences in binary format (see below).
526 o Three new functions have been introduced to convert between the
527 new binary and the character formats.
529 o The new function as.alignment converts DNA sequences stored as
530 single characters into the class "alignment" used by the package
533 o read.dna() and read.GenBank() have a new argument `as.character'
534 controlling whether the sequences are returned in binary format
540 o root() failed when the tree had node labels: this is fixed.
542 o plot.phylo() did not correctly set the limits on the y-axis with
543 the default setting: this is fixed.
545 o dist.dna() returned a wrong result for the LogDet, paralinear,
546 and BH87 models with `pairwise.deletion = TRUE'.
551 o DNA sequences are now internally stored in a binary format. See
552 the document "A Bit-Level Coding Scheme for Nucleotides" for the
553 details. Most functions analyzing DNA functions have been
554 modified accordingly and are now much faster (dist.dna is now
555 ca. 60 times faster).
559 CHANGES IN APE VERSION 1.9-4
564 o A bug was fixed in edgelabels().
566 o as.phylo.hclust() did not work correctly when the object of
567 class "hclust" has its labels set to NULL: the returned tree has
568 now its tip labels set to "1", "2", ...
570 o consensus could fail if some tip labels are a subset of others
571 (e.g., "a" and "a_1"): this is now fixed.
573 o mlphylo() failed in most cases if some branch lengths of the
574 initial tree were greater than one: an error message is now
577 o mlphylo() failed in most cases when estimating the proportion of
578 invariants: this is fixed.
582 CHANGES IN APE VERSION 1.9-3
587 o The new function edgelabels adds labels on the edge of the tree
588 in the same way than nodelabels or tiplabels.
593 o multi2di() did not handle correctly branch lengths with the
594 default option `random = TRUE': this is now fixed.
596 o A bug was fixed in nuc.div() when using pairwise deletions.
598 o A bug occurred in the analysis of bipartitions with large
599 numbers of large trees, with consequences on prop.part,
600 prop.clades, and boot.phylo.
602 o The calculation of the Billera-Holmes-Vogtmann distance in
603 dist.topo was wrong: this has been fixed.
607 CHANGES IN APE VERSION 1.9-2
612 o The new function ladderize reorganizes the internal structure of
613 a tree to plot them left- or right-ladderized.
615 o The new function dist.nodes computes the patristic distances
616 between all nodes, internal and terminal, of a tree. It replaces
617 the option `full = TRUE' of cophenetic.phylo (see below).
622 o A bug was fixed in old2new.phylo().
624 o Some bugs were fixed in chronopl().
626 o The edge colours were not correctly displayed by plot.phylo
627 (thank you to Li-San Wang for the fix).
629 o cophenetic.phylo() failed with multichotomous trees: this is
635 o read.dna() now returns the sequences in a matrix if they are
636 aligned (interleaved or sequential format). Sequences in FASTA
637 format are still returned in a list.
639 o The option `full' of cophenetic.phylo() has been removed because
640 it could not be used from the generic.
645 o rotate() has been removed; this function did not work correctly
650 CHANGES IN APE VERSION 1.9-1
655 o Trees with a single tip were not read correctly in R as the
656 element `Nnode' was not set: this is fixed.
658 o unroot() did not set correctly the number of nodes of the
659 unrooted tree in most cases.
661 o read.GenBank() failed when fetching very long sequences,
662 particularly of the BX-series.
664 o A bug was introduced in read.tree() with ape 1.9: it has been
669 CHANGES IN APE VERSION 1.9
674 o There are two new print `methods' for trees of class "phylo" and
675 lists of trees of class "multi.tree", so that they are now
676 displayed in a compact and informative way.
678 o There are two new functions, old2new.phylo and new2old.phylo,
679 for converting between the old and new coding of the class
682 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
683 LogDet ("logdet"), and paralinear ("paralin").
685 o compute.brlen() has been extended: several methods are now
686 available to compute branch lengths.
688 o write.dna() can now handle matrices as well as lists.
693 o cophenetic.phylo() sometimes returned a wrong result with
694 multichotomous trees: this is fixed.
696 o rotate() failed when a single tip was specified: the tree is now
699 o ace() did not return the correct index matrix with custom
700 models: this is fixed.
702 o multi2di() did not work correctly when resolving multichotomies
703 randomly: the topology was always the same, only the arrangement
704 of clades was randomized: this is fixed. This function now
705 accepts trees with no branch lengths.
707 o The output of diversi.gof() was blurred by useless prints when a
708 user distribution was specified. This has been corrected, and
709 the help page of this function has been expanded.
714 o The internal structure of the class "phylo" has been changed:
715 see the document "Definition of Formats for Coding Phylogenetic
716 Trees in R" for the details. In addition, the code of most
717 functions has been improved.
719 o Several functions have been improved by replacing some R codes
720 by C codes: pic, plot.phylo, and reorder.phylo.
722 o There is now a citation information: see citation("ape") in R.
724 o write.tree() now does not add extra 0's to branch lengths so
725 that 1.23 is printed "1.23" by default, not "1.2300000000".
727 o The syntax of bind.tree() has been simplified. This function now
728 accepts trees with no branch lengths, and handles correctly node
731 o The option `as.numeric' of mrca() has been removed.
733 o The unused options `format' and `rooted' of read.tree() have
736 o The unused option `format' of write.tree() has been removed.
738 o The use of node.depth() has been simplified.
742 CHANGES IN APE VERSION 1.8-5
747 o Two new functions read.nexus.data() and write.nexus.data(),
748 contributed by Johan Nylander, allow to read and write molecular
749 sequences in NEXUS files.
751 o The new function reorder.phylo() reorders the internal structure
752 of a tree of class "phylo". It is used as the generic, e.g.,
755 o read.tree() and read.nexus() can now read trees with a single
758 o The new data set `cynipids' supplies a set of protein sequences
764 o The code of all.equal.phylo() has been completely rewritten
765 (thanks to Benoît Durand) which fixes several bugs.
767 o read.tree() and read.nexus() now checks the labels of the tree
768 to remove or substitute any characters that are illegal in the
769 Newick format (parentheses, etc.)
771 o A negative P-value could be returned by mantel.test(): this is
776 CHANGES IN APE VERSION 1.8-4
781 o The new function sh.test() computes the Shimodaira-
784 o The new function collapse.singles() removes the nodes with a
785 single descendant from a tree.
787 o plot.phylo() has a new argument `tip.color' to specify the
790 o mlphylo() has now an option `quiet' to control the display of
791 the progress of the analysis (the default is FALSE).
796 o read.dna() did not read correctly sequences in sequential format
797 with leading alignment gaps "-": this is fixed.
799 o ace() returned a list with no class so that the generic
800 functions (anova, logLik, ...) could not be used directly. This
801 is fixed as ace() now returns an object of class "ace".
803 o anova.ace() had a small bug when computing the number of degrees
804 of freedom: this is fixed.
806 o mlphylo() did not work when the sequences were in a matrix or
807 a data frame: this is fixed.
809 o rtree() did not work correctly when trying to simulate an
810 unrooted tree with two tips: an error message is now issued.
815 o The algorithm of rtree() has been changed: it is now about 40,
816 100, and 130 times faster for 10, 100, and 1000 tips,
821 CHANGES IN APE VERSION 1.8-3
826 o There are four new `method' functions to be used with the
827 results of ace(): logLik(), deviance(), AIC(), and anova().
829 o The plot method of phymltest has two new arguments: `main' to
830 change the title, and `col' to control the colour of the
831 segments showing the AIC values.
833 o ace() has a new argument `ip' that gives the initial values used
834 in the ML estimation with discrete characters (see the examples
835 in ?ace). This function now returns a matrix giving the indices
836 of the estimated rates when analysing discrete characters.
838 o nodelabels() and tiplabels() have a new argument `pie' to
839 represent proportions, with any number of categories, as
840 piecharts. The use of the option `thermo' has been improved:
841 there is now no limitation on the number of categories.
846 o mlphylo() did not work with more than two partitions: this is
849 o root() failed if the proposed outgroup was already an outgroup
850 in the tree: this is fixed.
852 o The `col' argument in nodelabels() and tiplabels() was not
853 correctly passed when `text' was used: this is fixed.
855 o Two bugs were fixed in mlphylo(): parameters were not always
856 correctly output, and the estimation failed in some cases.
858 o plot.phylo() was stuck when given a tree with a single tip: this
859 is fixed and a message error is now returned.
861 o An error was corrected in the help page of gammaStat regarding
862 the calculation of P-values.
864 o Using gls() could crash R when the number of species in the tree
865 and in the variables were different: this is fixed.
869 CHANGES IN APE VERSION 1.8-2
874 o The new function mlphylo() fits a phylogenetic tree by maximum
875 likelihood from DNA sequences. Its companion function DNAmodel()
876 is used to define the substitution model which may include
877 partitioning. There are methods for logLik(), deviance(), and
878 AIC(), and the summary() method has been extended to display in
879 a friendly way the results of this model fitting. Currently, the
880 functionality is limited to estimating the substitution and
881 associated parameters and computing the likelihood.
883 o The new function drop1.compar.gee (used as, e.g., drop1(m))
884 tests for single effects in GEE-based comparative method. A
885 warning message is printed if there is not enough degrees of
891 o An error message was sometimes issued by plot.multi.tree(),
892 though with no consequence.
896 CHANGES IN APE VERSION 1.8-1
901 o There is a new plot method for lists of trees (objects of class
902 "multi.tree"): it calls plot.phylo() internally and is
903 documented on the same help page.
908 o A bug was fixed in the C code that analyzes bipartitions: this
909 has impact on several functions like prop.part, prop.clades,
910 boot.phylo, or consensus.
912 o root() did not work correctly when the specified outgroup had
913 more than one element: this is fixed.
915 o dist.dna() sometimes returned a warning inappropriately: this
918 o If the distance object given to nj() had no rownames, nj()
919 returned a tree with no tip labels: it now returns tips labelled
920 "1", "2", ..., corresponding to the row numbers.
925 o nj() has been slightly changed so that tips with a zero distance
926 are first aggregated with zero-lengthed branches; the usual NJ
927 procedure is then performed on a distance matrix without 0's.
931 CHANGES IN APE VERSION 1.8
936 o The new function chronopl() estimates dates using the penalized
937 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
939 o The new function consensus() calculates the consensus tree of a
942 o The new function evolve.phylo() simulates the evolution of
943 continuous characters along a phylogeny under a Brownian model.
945 o The new plot method for objects of class "ancestral" displays a
946 tree together with ancestral values, as returned by the above
949 o The new function as.phylo.formula() returns a phylogeny from a
950 set of nested taxonomic variables given as a formula.
952 o The new function read.caic() reads trees in CAIC format.
954 o The new function tiplabels() allows to add labels to the tips
955 of a tree using text or plotting symbols in a flexible way.
957 o The new function unroot() unroots a phylogeny.
959 o multi2di() has a new option, `random', which specifies whether
960 to resolve the multichotomies randomly (the default) or not.
962 o prop.part() now returns an object of class "prop.part" for which
963 there are print (to display a partition in a more friendly way)
964 and summary (to extract the numbers) methods.
966 o plot.phylo() has a new option, `show.tip.label', specifying
967 whether to print the labels of the tips. The default is TRUE.
969 o The code of nj() has been replaced by a faster C code: it is now
970 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
973 o write.nexus() now writes whether a tree is rooted or not.
978 o Two bugs have been fixed in root(): unrooted trees are now
979 handled corretly, and node labels are now output normally.
981 o A bug was fixed in phymltest(): the executable couldn't be found
984 o Three bug have been fixed in ace(): computing the likelihood of
985 ancestral states of discrete characters failed, custom models
986 did not work, and the function failed with a null gradient (a
987 warning message is now returned; this latter bug was also
988 present in yule.cov() as well and is now fixed).
990 o pic() hanged out when missing data were present: a message error
993 o A small bug was fixed in dist.dna() where the gamma correction
994 was not always correctly dispatched.
996 o plot.phylo() plotted correctly the root edge only when the tree
997 was plotted rightwards: this works now for all directions.
1002 o dist.taxo() has been renamed as weight.taxo().
1004 o Various error and warning messages have been improved.
1008 CHANGES IN APE VERSION 1.7
1011 o The new function ace() estimates ancestral character states for
1012 continuous characters (with ML, GLS, and contrasts methods), and
1013 discrete characters (with ML only) for any number of states.
1015 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1016 of directional evolution for continuous characters. The user
1017 specifies the node(s) of the tree where the character optimum
1020 o The new function is.rooted() tests whether a tree (of class
1023 o The new function rcoal() generates random ultrametric trees with
1024 the possibility to specify the function that generates the
1025 inter-nodes distances.
1027 o The new function mrca() gives for all pairs of tips in a tree
1028 (and optionally nodes too) the most recent common ancestor.
1030 o nodelabels() has a new option `thermo' to plot proportions (up
1031 to three classes) on the nodes of a tree.
1033 o rtree() has been improved: it can now generate rooted or
1034 unrooted trees, and the mathematical function that generates the
1035 branch lengths may be specified by the user. The tip labels may
1036 be given directly in the call to rtree. The limit cases (n = 2,
1037 3) are now handled correctly.
1039 o dist.topo() has a new argument `method' with two choices: "PH85"
1040 for Penny and Henny's method (already available before and now
1041 the default), and "BHV01" for the geometric distance by Billera
1042 et al. (2001, Adv. Appl. Math. 27:733).
1044 o write.tree() has a new option, `digits', which specifies the
1045 number of digits to be printed in the Newick tree. By default
1046 digits = 10. The numbers are now always printed in decimal form
1047 (i.e., 1.0e-1 is now avoided).
1049 o dist.dna() can now compute the raw distances between pairs of
1050 DNA sequences by specifying model = "raw".
1052 o dist.phylo() has a new option `full' to possibly compute the
1053 distances among all tips and nodes of the tree. The default if
1059 o Several bugs were fixed in all.equal.phylo().
1061 o dist.dna() did not handle correctly gaps ("-") in alignments:
1062 they are now considered as missing data.
1064 o rotate() did not work if the tips were not ordered: this is
1067 o mantel.test() returned NA in some special cases: this is fixed
1068 and the function has been improved and is now faster.
1070 o A bug was fixed in diversi.gof() where the calculation of A² was
1073 o cherry() did not work correctly under some OSs (mainly Linux):
1076 o is.binary.tree() has been modified so that it works with both
1077 rooted and unrooted trees.
1079 o The documentation of theta.s() was not correct: this has been
1082 o plot.mst() did not work correctly: this is fixed.
1086 CHANGES IN APE VERSION 1.6
1091 o The new function dist.topo() computes the topological distances
1094 o The new function boot.phylo() performs a bootstrap analysis on
1095 phylogeny estimation.
1097 o The new functions prop.part() and prop.clades() analyse
1098 bipartitions from a series of trees.
1103 o read.GenBank() now uses the EFetch utility of NCBI instead of
1104 the usual Web interface: it is now much faster (e.g., 12 times
1105 faster to retrieve 8 sequences, 37 times for 60 sequences).
1110 o Several bugs were fixed in read.dna().
1112 o Several bugs were fixed in diversi.time().
1114 o is.binary.tree() did not work correctly if the tree has no edge
1115 lengths: this is fixed.
1117 o drop.tip() did not correctly propagated the `node.label' of a
1118 tree: this is fixed.
1122 CHANGES IN APE VERSION 1.5
1127 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1128 convert objects between the classes "phylo" and "matching". The
1129 latter implements the representation of binary trees introduced by
1130 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1131 as.matching() has been introduced as well.
1133 o Two new functions, multi2di() and di2multi(), allow to resolve
1134 and collapse multichotomies with branches of length zero.
1136 o The new function nuc.div() computes the nucleotide diversity
1137 from a sample a DNA sequences.
1139 o dist.dna() has been completely rewritten with a much faster
1140 (particularly for large data sets) C code. Eight models are
1141 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1142 option `method' has been renamed `model'). Computation of variance
1143 is available for all models. A gamma-correction is possible for
1144 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1145 to remove sites with missing data on a pairwise basis. The option
1146 `GCcontent' has been removed.
1148 o read.GenBank() has a new option (species.names) which specifies
1149 whether to return the species names of the organisms in addition
1150 to the accession numbers of the sequences (this is the default
1153 o write.nexus() can now write several trees in the same NEXUS file.
1155 o drop.tip() has a new option `root.edge' that allows to specify the
1156 new root edge if internal branches are trimmed.
1161 o as.phylo.hclust() failed if some labels had parentheses: this
1164 o Several bugs were fixed in all.equal.phylo(). This function now
1165 returns the logical TRUE if the trees are identical but with
1166 different representations (a report was printed previously).
1168 o read.GenBank() did not correctly handle ambiguous base codes:
1174 o birthdeath() now returns an object of class "birthdeath" for
1175 which there is a print method.
1179 CHANGES IN APE VERSION 1.4
1184 o The new function nj() performs phylogeny estimation with the
1185 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1188 o The new function which.edge() identifies the edges of a tree
1189 that belong to a group specified as a set of tips.
1191 o The new function as.phylo.phylog() converts an object of class
1192 "phylog" (from the package ade4) into an object of class
1195 o The new function axisPhylo() draws axes on the side of a
1198 o The new function howmanytrees() calculates the number of trees
1199 in different cases and giving a number of tips.
1201 o write.tree() has a new option `multi.line' (TRUE by default) to
1202 write a Newick tree on several lines rather than on a single
1205 o The functionalities of zoom() have been extended. Several
1206 subtrees can be visualized at the same time, and they are marked
1207 on the main tree with colors. The context of the subtrees can be
1208 marked with the option `subtree' (see below).
1210 o drop.tip() has a new option `subtree' (FALSE by default) which
1211 specifies whether to output in the tree how many tips have been
1214 o The arguments of add.scale.bar() have been redefined and have
1215 now default values (see ?add.scale.bar for details). This
1216 function now works even if the plotted tree has no edge length.
1218 o plot.phylo() can now plot radial trees, but this does not take
1219 edge lengths into account.
1221 o In plot.phylo() with `type = "phylogram"', if the values of
1222 `edge.color' and `edge.width' are identical for sister-branches,
1223 they are propagated to the vertical line that link them.
1228 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1229 crashing. This is fixed.
1231 o In plot.phylo(), the options `edge.color' and `edge.width' are
1232 now properly recycled; their default values are now "black" and
1235 o A bug has been fixed in write.nexus().
1240 o The function node.depth.edgelength() has been removed and
1241 replaced by a C code.
1245 CHANGES IN APE VERSION 1.3-1
1250 o The new function nodelabels() allows to add labels to the nodes
1251 of a tree using text or plotting symbols in a flexible way.
1253 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1254 numeric values specifying the lower and upper limits on the x-
1255 and y-axes. This allows to leave some space on any side of the
1256 tree. If a single value is given, this is taken as the upper
1261 CHANGES IN APE VERSION 1.3
1266 o The new function phymltest() calls the software PHYML and fits
1267 28 models of DNA sequence evolution. There are a print method to
1268 display likelihood and AIC values, a summary method to compute
1269 the hierarchical likelihood ratio tests, and a plot method to
1270 display graphically the AIC values of each model.
1272 o The new function yule.cov() fits the Yule model with covariates,
1273 a model where the speciation rate is affected by several species
1274 traits through a generalized linear model. The parameters are
1275 estimated by maximum likelihood.
1277 o Three new functions, corBrownian(), corGrafen(), and
1278 corMartins(), compute the expected correlation structures among
1279 species given a phylogeny under different models of evolution.
1280 These can be used for GLS comparative phylogenetic methods (see
1281 the examples). There are coef() and corMatrix() methods and an
1282 Initialize.corPhyl() function associated.
1284 o The new function compar.cheverud() implements Cheverud et al.'s
1285 (1985; Evolution 39:1335) phylogenetic comparative method.
1287 o The new function varcomp() estimates variance components; it has
1290 o Two new functions, panel.superpose.correlogram() and
1291 plot.correlogramList(), allow to plot several phylogenetic
1294 o The new function node.leafnumber() computes the number of leaves
1295 of a subtree defined by a particular node.
1297 o The new function node.sons() gets all tags of son nodes from a
1300 o The new function compute.brlen() computes the branch lengths of
1301 a tree according to a specified method.
1303 o plot.phylo() has three new options: "cex" controls the size of
1304 the (tip and node) labels (thus it is no more needed to change
1305 the global graphical parameter), "direction" which allows to
1306 plot the tree rightwards, leftwards, upwards, or downwards, and
1307 "y.lim" which sets the upper limit on the y-axis.
1312 o Some functions which try to match tip labels and names of
1313 additional data (e.g. vector) are likely to fail if there are
1314 typing or syntax errors. If both series of names do not perfectly
1315 match, they are ignored and a warning message is now issued.
1316 These functions are bd.ext, compar.gee, pic. Their help pages
1317 have been clarified on this point.
1321 CHANGES IN APE VERSION 1.2-7
1326 o The new function root() reroots a phylogenetic tree with respect
1327 to a specified outgroup.
1329 o The new function rotate() rotates an internal branch of a tree.
1331 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1332 trees) controls the display of the tip labels in unrooted trees.
1333 This display has been greatly improved: the tip labels are now not
1334 expected to overlap with the tree (particularly if lab4ut =
1335 "axial"). In all cases, combining appropriate values of "lab4ut"
1336 and the font size (via "par(cex = )") should result in readable
1337 unrooted trees. See ?plot.phylo for some examples.
1339 o In drop.tip(), the argument `tip' can now be numeric or character.
1344 o drop.tip() did not work correctly with trees with no branch
1345 lengths: this is fixed.
1347 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1348 plotted with some line crossings: this is now fixed.
1352 CHANGES IN APE VERSION 1.2-6
1357 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1358 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1359 to implement comparative methods with an autocorrelation approach.
1361 o A new data set describing some life history traits of Carnivores
1367 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1372 o When plotting a tree with plot.phylo(), the new default of the
1373 option `label.offset' is now 0, so the labels are always visible.
1377 CHANGES IN APE VERSION 1.2-5
1382 o The new function bd.ext() fits a birth-death model with combined
1383 phylogenetic and taxonomic data, and estimates the corresponding
1384 speciation and extinction rates.
1389 o The package gee is no more required by ape but only suggested
1390 since only the function compar.gee() calls gee.
1394 CHANGES IN APE VERSION 1.2-4
1399 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1400 and lines.popsize) implementing a new approach for inferring the
1401 demographic history from genealogies using a reversible jump
1402 MCMC have been introduced.
1404 o The unit of time in the skyline plot and in the new plots can
1405 now be chosen to be actual years, rather than substitutions.
1409 CHANGES IN APE VERSION 1.2-3
1414 o The new function rtree() generates a random binary tree with or
1415 without branch lengths.
1417 o Two new functions for drawing lineages-through-time (LTT) plots
1418 are provided: ltt.lines() adds a LTT curve to an existing plot,
1419 and mltt.plot() does a multiple LTT plot giving several trees as
1420 arguments (see `?ltt.plot' for details).
1425 o Some taxon names made R crashing when calling as.phylo.hclust():
1428 o dist.dna() returned an error with two identical DNA sequences
1429 (only using the Jukes-Cantor method returned 0): this is fixed.
1434 o The function dist.phylo() has been re-written using a different
1435 algorithm: it is now about four times faster.
1437 o The code of branching.times() has been improved: it is now about
1442 CHANGES IN APE VERSION 1.2-2
1447 o The new function seg.sites() finds the segregating sites in a
1448 sample of DNA sequences.
1453 o A bug introduced in read.tree() and in read.nexus() with version
1456 o A few errors were corrected and a few examples were added in the
1461 CHANGES IN APE VERSION 1.2-1
1466 o plot.phylo() can now draw the edge of the root of a tree if it
1467 has one (see the new option `root.edge', its default is FALSE).
1472 o A bug was fixed in read.nexus(): files with semicolons inside
1473 comment blocks were not read correctly.
1475 o The behaviour of read.tree() and read.nexus() was corrected so
1476 that tree files with badly represented root edges (e.g., with
1477 an extra pair of parentheses, see the help pages for details)
1478 are now correctly represented in the object of class "phylo";
1479 a warning message is now issued.
1483 CHANGES IN APE VERSION 1.2
1488 o plot.phylo() has been completely re-written and offers several
1489 new functionalities. Three types of trees can now be drawn:
1490 phylogram (as previously), cladogram, and unrooted tree; in
1491 all three types the branch lengths can be drawn using the edge
1492 lengths of the phylogeny or not (e.g., if the latter is absent).
1493 The vertical position of the nodes can be adjusted with two
1494 choices (see option `node.pos'). The code has been re-structured,
1495 and two new functions (potentially useful for developpers) are
1496 documented separately: node.depth.edgelength() and node.depth();
1497 see the respective help pages for details.
1499 o The new function zoom() allows to explore very large trees by
1500 focusing on a small portion of it.
1502 o The new function yule() fits by maximum likelihood the Yule model
1503 (birth-only process) to a phylogenetic tree.
1505 o Support for writing DNA sequences in FASTA format has been
1506 introduced in write.dna() (support for reading sequences in
1507 this format was introduced in read.dna() in version 1.1-2).
1508 The function has been completely re-written, fixing some bugs
1509 (see below); the default behaviour is no more to display the
1510 sequences on the standard output. Several options have been
1511 introduced to control the sequence printing in a flexible
1512 way. The help page has been extended.
1514 o A new data set is included: a supertree of bats in NEXUS format.
1519 o In theta.s(), the default of the option `variance' has
1520 been changed to `FALSE' (as was indicated in the help page).
1522 o Several bugs were fixed in the code of all.equal.phylo().
1524 o Several bugs were fixed in write.dna(), particularly this
1525 function did not work with `format = "interleaved"'.
1527 o Various errors were corrected in the help pages.
1532 o The argument names of as.hclust.phylo() have been changed
1533 from "(phy)" to "(x, ...)" to conform to the definition of
1534 the corresponding generic function.
1536 o gamma.stat() has been renamed gammaStat() to avoid confusion
1537 since gamma() is a generic function.
1541 CHANGES IN APE VERSION 1.1-3
1546 o base.freq() previously did not return a value of 0 for
1547 bases absent in the data (e.g., a vector of length 3 was
1548 returned if one base was absent). This is now fixed (a
1549 vector of length 4 is always returned).
1551 o Several bugs were fixed in read.nexus(), including that this
1552 function did not work in this absence of a "TRANSLATE"
1553 command in the NEXUS file, and that the commands were
1558 CHANGES IN APE VERSION 1.1-2
1563 o The Tamura and Nei (1993) model of DNA distance is now implemented
1564 in dist.dna(): five models are now available in this function.
1566 o A new data set is included: a set of 15 sequences of the
1567 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1573 o A bug in read.nexus() was fixed.
1575 o read.dna() previously did not work correctly in most cases.
1576 The function has been completely re-written and its help page
1577 has been considerably extended (see ?read.dna for details).
1578 Underscores (_) in taxon names are no more replaced with
1579 spaces (this behaviour was undocumented).
1581 o A bug was fixed in write.dna().
1585 CHANGES IN APE VERSION 1.1-1
1590 o A bug in read.tree() introduced in APE 1.1 was fixed.
1592 o A bug in compar.gee() resulted in an error when trying to fit
1593 a model with `family = "binomial"'. This is now fixed.
1597 CHANGES IN APE VERSION 1.1
1602 o The Klastorin (1982) method as suggested by Misawa and Tajima
1603 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1604 on the basis of phylogenetic trees has been implemented (see
1605 the function klastorin()).
1607 o Functions have been added to convert APE's "phylo" objects in
1608 "hclust" cluster objects and vice versa (see the help page of
1609 as.phylo for details).
1611 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1612 are introduced for the estimation of absolute evolutionary rates
1613 (ratogram) and dated clock-like trees (chronogram) from
1614 phylogenetic trees using the non-parametric rate smoothing approach
1615 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1617 o A summary method is now provided printing a summary information on a
1618 phylogenetic tree with, for instance, `summary(tree)'.
1620 o The behaviour of read.tree() was changed so that all spaces and
1621 tabulations in tree files are now ignored. Consequently, spaces in tip
1622 labels are no more allowed. Another side effect is that read.nexus()
1623 now does not replace the underscores (_) in tip labels with spaces
1624 (this behaviour was undocumented).
1626 o The function plot.phylo() has a new option (`underscore') which
1627 specifies whether the underscores in tip labels should be written on
1628 the plot as such or replaced with spaces (the default).
1630 o The function birthdeath() now computes 95% confidence intervals of
1631 the estimated parameters using profile likelihood.
1633 o Three new data sets are included: a gene tree estimated from 36
1634 landplant rbcL sequences, a gene tree estimated from 32 opsin
1635 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1640 o A bug was fixed in dist.gene() where nothing was returned.
1642 o A bug in plot.mst() was fixed.
1644 o A bug in vcv.phylo() resulted in false correlations when the
1645 option `cor = TRUE' was used (now fixed).
1649 CHANGES IN APE VERSION 1.0
1654 o Two new functions, read.dna() and write.dna(), read/write in a file
1655 DNA sequences in interleaved or in sequential format.
1657 o Two new functions, read.nexus() and write.nexus(), read/write trees
1660 o The new function bind.tree() allows to bind two trees together,
1661 possibly handling root edges to give internal branches.
1663 o The new function drop.tip() removes the tips in a phylogenetic tree,
1664 and trims (or not) the corresponding internal branches.
1666 o The new function is.ultrametric() tests if a tree is ultrametric.
1668 o The function plot.phylo() has more functionalities such as drawing the
1669 branches with different colours and/or different widths, showing the
1670 node labels, controling the position and font of the labels, rotating
1671 the labels, and controling the space around the plot.
1673 o The function read.tree() can now read trees with no branch length,
1674 such as "(a,b),c);". Consequently, the element `edge.length' in
1675 objects of class "phylo" is now optional.
1677 o The function write.tree() has a new default behaviour: if the default
1678 for the option `file' is used (i.e. file = ""), then a variable of
1679 mode character containing the tree in Newick format is returned which
1680 can thus be assigned (e.g., tree <- write.tree(phy)).
1682 o The function read.tree() has a new argument `text' which allows
1683 to read the tree in a variable of mode character.
1685 o A new data set is included: the phylogenetic relationships among
1686 the orders of birds from Sibley and Ahlquist (1990).
1690 CHANGES IN APE VERSION 0.2-1
1695 o Several bugs were fixed in the help pages.
1699 CHANGES IN APE VERSION 0.2
1704 o The function write.tree() writes phylogenetic trees (objects of class
1705 "phylo") in an ASCII file using the Newick parenthetic format.
1707 o The function birthdeath() fits a birth-death model to branching times
1708 by maximum likelihood, and estimates the corresponding speciation and
1711 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1714 o The function is.binary.tree() tests whether a phylogeny is binary.
1716 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1717 as well as some methods are introduced.
1719 o Several functions, including some generics and methods, for computing
1720 skyline plot estimates (classic and generalized) of effective
1721 population size through time are introduced and replace the function
1722 skyline.plot() in version 0.1.
1724 o Two data sets are now included: the phylogenetic relationships among
1725 the families of birds from Sibley and Ahlquist (1990), and an
1726 estimated clock-like phylogeny of HIV sequences sampled in the
1727 Democratic Republic of Congo.
1730 DEPRECATED & DEFUNCT
1732 o The function skyline.plot() in ape 0.1 has been deprecated and
1733 replaced by more elaborate functions (see above).
1738 o Two important bugs were fixed in plot.phylo(): phylogenies with
1739 multichotomies not at the root or not with only terminal branches,
1740 and phylogenies with a single node (i.e. only terminal branches)
1741 did not plot. These trees should be plotted correctly now.
1743 o Several bugs were fixed in diversi.time() in the computation of
1746 o Various errors were corrected in the help pages.
projects / ape.git / blob