1 CHANGES IN APE VERSION 2.2-1
6 o The new function makeLabel() helps to modify labels of trees,
7 lists of trees, or DNA sequences, with several utilities to
8 truncate and/or make them unique, substituting some
11 o The new function del.gaps() removes insertion gaps ("-") in a
14 o read.dna() can now read Clustal files (*.aln).
19 o root() failed with 'resolve.root = TRUE' when the root was
20 already the specified root.
22 o Several bugs were fixed in mlphylo().
24 o collapsed.singles() did not propagate the 'Nnode' and
25 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
27 o read.nexus failed to remove correctly the comments within trees.
32 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
35 o The option 'check.labels' of consensus() and prop.part() is now
38 o write.dna() now does not truncate names to 10 characters with
43 CHANGES IN APE VERSION 2.2
48 o Four new functions have been written by Damien de Vienne for the
49 graphical exploration of large trees (cophyloplot, subtrees,
50 subtreeplot), and to return the graphical coordinates of tree
53 o The new functions corPagel and corBlomberg implement the Pagel's
54 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
56 o chronopl() has been improved and gains several options: see its
57 help page for details.
59 o boot.phylo() has now an option 'trees' to possibly return the
60 bootstraped trees (the default is FALSE).
62 o prop.part() has been improved and should now be faster in all
68 o read.dna() failed if "?" occurred in the first 10 sites of the
71 o The x/y aspect of the plot is now respected when plotting a
72 circular tree (type = "r" or "f").
74 o Drawing the tip labels sometimes failed when plotting circular
77 o zoom() failed when tip labels were used instead of their numbers
78 (thanks to Yan Wong for the fix).
80 o drop.tip() failed with some trees (fixed by Yan Wong).
82 o seg.sites() failed with a list.
84 o consensus() failed in some cases. The function has been improved
85 as well and is faster.
89 CHANGES IN APE VERSION 2.1-3
94 o A bug in read.nexus() made the Windows R-GUI crash.
96 o An error was fixed in the computation of ancestral character
97 states by generalized least squares in ace().
99 o di2multi() did not modify node labels correctly.
101 o multi2di() failed if the tree had its attribute "order" set to
106 CHANGES IN APE VERSION 2.1-2
111 o There three new methods for the "multiPhylo" class: str, $,
114 o root() gains the options 'node' and 'resolve.root'
115 (FALSE by default) as well as its code being improved.
117 o mltt.plot() has now an option 'log' used in the same way
118 than in plot.default().
123 o mltt.plot() failed to display the legend with an unnamed
126 o nodelabels() with pies now correcly uses the argument
127 'cex' to draw symbols of different sizes (which has
128 worked already for thermometers).
130 o read.nexus() generally failed to read very big files.
135 o The argument 'family' of compar.gee() can now be a function
136 as well as a character string.
138 o read.tree() and read.nexus() now return an unnamed list if
141 o read.nexus() now returns a modified object of class "multiPhylo"
142 when there is a TRANSLATE block in the NEXUS file: the individual
143 trees have no 'tip.label' vector, but the list has a 'TipLabel'
144 attribute. The new methods '$' and '[[' set these elements
145 correctly when extracting trees.
149 CHANGES IN APE VERSION 2.1-1
154 o The new function rmtree generates lists of random trees.
156 o rcoal() now generates a genuine coalescent tree by default
157 (thanks to Vladimir Minin for the code).
162 o nuc.div() returned an incorrect value with the default
163 pairwise.deletion = FALSE.
168 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
169 have been improved so that they are stabler and faster.
171 o R packages used by ape are now loaded silently; lattice and gee
172 are loaded only when needed.
176 CHANGES IN APE VERSION 2.1
181 o The new function identify.phylo identifies clades on a plotted
182 tree using the mouse.
184 o It is now possible to subset a list of trees (object of class
185 "multiPhylo") with "[" while keeping its class correct.
187 o The new function as.DNAbin.alignment converts DNA sequences
188 stored in the "alignment" format of the package seqinr into
189 an object of class "DNAbin".
191 o The new function weight.taxo2 helps to build similarity matrices
192 given two taxonomic levels (usually called by other functions).
194 o write.tree() can now take a list of trees (class "multiPhylo")
195 as its main argument.
197 o plot.correlogram() and plot.correlogramList() have been
198 improved, and gain several options (see the help page for
199 details). A legend is now plotted by default.
204 o dist.dna() returned some incorrect values with `model = "JC69"'
205 and `pairwise.deletion = TRUE'. This affected only the
206 distances involving sequences with missing values. (Thanks
207 to Bruno Toupance for digging this bug out.)
209 o write.tree() failed with some trees: this is fixed by removing
210 the `multi.line' option (trees are now always printed on a
213 o read.nexus() did not correctly detect trees with multiple root
214 edges (see OTHER CHANGES).
219 o The code of mlphylo() has almost entirely rewritten, and should
220 be much stabler. The options have been also greatly simplified
221 (see ?mlphylo and ?DNAmodel for details).
223 o The internal function nTips has been renamed klastorin_nTips.
225 o The code of is.ultrametric() contained redundancies and has
228 o The code of Moran.I() and of correlogram.formula() have been
231 o read.tree() and read.nexus() now return an error when trying to
232 read a tree with multiple root edges (see BUG FIXES). The
233 correction applied in previous version did not work in all
236 o The class c("multi.tree", "phylo") has been renamed
242 o There is now a vignette in ape: see vignette("MoranI", "ape").
247 o as.matching() and as.phylo.matching() do not support branch
250 o correlogram.phylo() and discrete.dist() have been removed.
254 CHANGES IN APE VERSION 2.0-2
259 o The new function matexpo computes the exponential of a square
262 o The new function unique.multi.tree removes duplicate trees from
265 o yule() has a new option `use.root.edge = FALSE' that specifies
266 to ignore, by default, the root edge of the tree if it exists.
271 o which.edge() failed when the index of a single terminal edge was
274 o In diversi.time(), the values returned for model C were
277 o A bug was fixed in yule() that affected the calculation of the
278 likelihood in the presence of ties in the branching times.
280 o There was a bug in the C function mat_expo4x4 affecting the
281 calculations of the transition probabilities for models HKY and
284 o A small bug was fixed in as.matrix.DNAbin (thanks to James
287 o rtree() did not `shuffle' the tip labels by default, so only a
288 limited number of labelled topologies could be generated.
292 CHANGES IN APE VERSION 2.0-1
297 o The three new functions bionj, fastme.ols, and fastme.bal
298 perform phylogeny estimation by the BIONJ and fastME methods in
299 OLS and balanced versions. This is a port to R of previous
300 previous programs done by Vincent Lefort.
302 o The new function chronoMPL performs molecular dating with the
303 mean path lengths method of Britton et al. (2002, Mol. Phyl.
306 o The new function rotate, contributed by Christoph Heibl, swaps
307 two clades connected to the same node. It works also with
308 multichotomous nodes.
310 o The new `method' as.matrix.DNAbin() may be used to convert
311 easily DNA sequences stored in a list into a matrix while
312 keeping the names and the class.
317 o chronopl() failed when some branch lengths were equal to zero:
318 an error message is now returned.
320 o di2multi() failed when there was a series of consecutive edges
325 CHANGES IN APE VERSION 1.10-2
330 o plot.phylo() can now plot circular trees: the option is type =
331 "fan" or type = "f" (to avoid the ambiguity with type = "c").
333 o prop.part() has a new option `check.labels = FALSE' which allows
334 to considerably speed-up the calculations of bipartitions. As a
335 consequence, calculations of bootstrap values with boot.phylo()
336 should be much faster.
341 o read.GenBank() did not return correctly the list of species as
342 from ape 1.10: this is fixed in this version
344 o Applying as.phylo() on a tree of class "phylo" failed: the
345 object is now returned unchanged.
349 CHANGES IN APE VERSION 1.10-1
354 o The three new functions Ntip, Nnode, and Nedge return, for a
355 given tree, the number of tips, nodes, or edges, respectively.
360 o read.nexus() did not set correctly the class of the returned
361 object when reading multiple trees.
363 o mllt.plot() failed with objects of class c("multi.tree",
366 o unroot() did not work correctly in most cases.
368 o reorder.phylo() made R freeze in some occasions.
370 o Plotting a tree in pruningwise order failed.
372 o When plotting an unrooted tree, the tip labels where not all
373 correctly positioned if the option `cex' was used.
377 CHANGES IN APE VERSION 1.10
382 o Five new `method' functions have been introduced to manipulate
383 DNA sequences in binary format (see below).
385 o Three new functions have been introduced to convert between the
386 new binary and the character formats.
388 o The new function as.alignment converts DNA sequences stored as
389 single characters into the class "alignment" used by the package
392 o read.dna() and read.GenBank() have a new argument `as.character'
393 controlling whether the sequences are returned in binary format
399 o root() failed when the tree had node labels: this is fixed.
401 o plot.phylo() did not correctly set the limits on the y-axis with
402 the default setting: this is fixed.
404 o dist.dna() returned a wrong result for the LogDet, paralinear,
405 and BH87 models with `pairwise.deletion = TRUE'.
410 o DNA sequences are now internally stored in a binary format. See
411 the document "A Bit-Level Coding Scheme for Nucleotides" for the
412 details. Most functions analyzing DNA functions have been
413 modified accordingly and are now much faster (dist.dna is now
414 ca. 60 times faster).
418 CHANGES IN APE VERSION 1.9-4
423 o A bug was fixed in edgelabels().
425 o as.phylo.hclust() did not work correctly when the object of
426 class "hclust" has its labels set to NULL: the returned tree has
427 now its tip labels set to "1", "2", ...
429 o consensus could fail if some tip labels are a subset of others
430 (e.g., "a" and "a_1"): this is now fixed.
432 o mlphylo() failed in most cases if some branch lengths of the
433 initial tree were greater than one: an error message is now
436 o mlphylo() failed in most cases when estimating the proportion of
437 invariants: this is fixed.
441 CHANGES IN APE VERSION 1.9-3
446 o The new function edgelabels adds labels on the edge of the tree
447 in the same way than nodelabels or tiplabels.
452 o multi2di() did not handle correctly branch lengths with the
453 default option `random = TRUE': this is now fixed.
455 o A bug was fixed in nuc.div() when using pairwise deletions.
457 o A bug occurred in the analysis of bipartitions with large
458 numbers of large trees, with consequences on prop.part,
459 prop.clades, and boot.phylo.
461 o The calculation of the Billera-Holmes-Vogtmann distance in
462 dist.topo was wrong: this has been fixed.
466 CHANGES IN APE VERSION 1.9-2
471 o The new function ladderize reorganizes the internal structure of
472 a tree to plot them left- or right-ladderized.
474 o The new function dist.nodes computes the patristic distances
475 between all nodes, internal and terminal, of a tree. It replaces
476 the option `full = TRUE' of cophenetic.phylo (see below).
481 o A bug was fixed in old2new.phylo().
483 o Some bugs were fixed in chronopl().
485 o The edge colours were not correctly displayed by plot.phylo
486 (thank you to Li-San Wang for the fix).
488 o cophenetic.phylo() failed with multichotomous trees: this is
494 o read.dna() now returns the sequences in a matrix if they are
495 aligned (interleaved or sequential format). Sequences in FASTA
496 format are still returned in a list.
498 o The option `full' of cophenetic.phylo() has been removed because
499 it could not be used from the generic.
504 o rotate() has been removed; this function did not work correctly
509 CHANGES IN APE VERSION 1.9-1
514 o Trees with a single tip were not read correctly in R as the
515 element `Nnode' was not set: this is fixed.
517 o unroot() did not set correctly the number of nodes of the
518 unrooted tree in most cases.
520 o read.GenBank() failed when fetching very long sequences,
521 particularly of the BX-series.
523 o A bug was introduced in read.tree() with ape 1.9: it has been
528 CHANGES IN APE VERSION 1.9
533 o There are two new print `methods' for trees of class "phylo" and
534 lists of trees of class "multi.tree", so that they are now
535 displayed in a compact and informative way.
537 o There are two new functions, old2new.phylo and new2old.phylo,
538 for converting between the old and new coding of the class
541 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
542 LogDet ("logdet"), and paralinear ("paralin").
544 o compute.brlen() has been extended: several methods are now
545 available to compute branch lengths.
547 o write.dna() can now handle matrices as well as lists.
552 o cophenetic.phylo() sometimes returned a wrong result with
553 multichotomous trees: this is fixed.
555 o rotate() failed when a single tip was specified: the tree is now
558 o ace() did not return the correct index matrix with custom
559 models: this is fixed.
561 o multi2di() did not work correctly when resolving multichotomies
562 randomly: the topology was always the same, only the arrangement
563 of clades was randomized: this is fixed. This function now
564 accepts trees with no branch lengths.
566 o The output of diversi.gof() was blurred by useless prints when a
567 user distribution was specified. This has been corrected, and
568 the help page of this function has been expanded.
573 o The internal structure of the class "phylo" has been changed:
574 see the document "Definition of Formats for Coding Phylogenetic
575 Trees in R" for the details. In addition, the code of most
576 functions has been improved.
578 o Several functions have been improved by replacing some R codes
579 by C codes: pic, plot.phylo, and reorder.phylo.
581 o There is now a citation information: see citation("ape") in R.
583 o write.tree() now does not add extra 0's to branch lengths so
584 that 1.23 is printed "1.23" by default, not "1.2300000000".
586 o The syntax of bind.tree() has been simplified. This function now
587 accepts trees with no branch lengths, and handles correctly node
590 o The option `as.numeric' of mrca() has been removed.
592 o The unused options `format' and `rooted' of read.tree() have
595 o The unused option `format' of write.tree() has been removed.
597 o The use of node.depth() has been simplified.
601 CHANGES IN APE VERSION 1.8-5
606 o Two new functions read.nexus.data() and write.nexus.data(),
607 contributed by Johan Nylander, allow to read and write molecular
608 sequences in NEXUS files.
610 o The new function reorder.phylo() reorders the internal structure
611 of a tree of class "phylo". It is used as the generic, e.g.,
614 o read.tree() and read.nexus() can now read trees with a single
617 o The new data set `cynipids' supplies a set of protein sequences
623 o The code of all.equal.phylo() has been completely rewritten
624 (thanks to Benoît Durand) which fixes several bugs.
626 o read.tree() and read.nexus() now checks the labels of the tree
627 to remove or substitute any characters that are illegal in the
628 Newick format (parentheses, etc.)
630 o A negative P-value could be returned by mantel.test(): this is
635 CHANGES IN APE VERSION 1.8-4
640 o The new function sh.test() computes the Shimodaira-
643 o The new function collapse.singles() removes the nodes with a
644 single descendant from a tree.
646 o plot.phylo() has a new argument `tip.color' to specify the
649 o mlphylo() has now an option `quiet' to control the display of
650 the progress of the analysis (the default is FALSE).
655 o read.dna() did not read correctly sequences in sequential format
656 with leading alignment gaps "-": this is fixed.
658 o ace() returned a list with no class so that the generic
659 functions (anova, logLik, ...) could not be used directly. This
660 is fixed as ace() now returns an object of class "ace".
662 o anova.ace() had a small bug when computing the number of degrees
663 of freedom: this is fixed.
665 o mlphylo() did not work when the sequences were in a matrix or
666 a data frame: this is fixed.
668 o rtree() did not work correctly when trying to simulate an
669 unrooted tree with two tips: an error message is now issued.
674 o The algorithm of rtree() has been changed: it is now about 40,
675 100, and 130 times faster for 10, 100, and 1000 tips,
680 CHANGES IN APE VERSION 1.8-3
685 o There are four new `method' functions to be used with the
686 results of ace(): logLik(), deviance(), AIC(), and anova().
688 o The plot method of phymltest has two new arguments: `main' to
689 change the title, and `col' to control the colour of the
690 segments showing the AIC values.
692 o ace() has a new argument `ip' that gives the initial values used
693 in the ML estimation with discrete characters (see the examples
694 in ?ace). This function now returns a matrix giving the indices
695 of the estimated rates when analysing discrete characters.
697 o nodelabels() and tiplabels() have a new argument `pie' to
698 represent proportions, with any number of categories, as
699 piecharts. The use of the option `thermo' has been improved:
700 there is now no limitation on the number of categories.
705 o mlphylo() did not work with more than two partitions: this is
708 o root() failed if the proposed outgroup was already an outgroup
709 in the tree: this is fixed.
711 o The `col' argument in nodelabels() and tiplabels() was not
712 correctly passed when `text' was used: this is fixed.
714 o Two bugs were fixed in mlphylo(): parameters were not always
715 correctly output, and the estimation failed in some cases.
717 o plot.phylo() was stuck when given a tree with a single tip: this
718 is fixed and a message error is now returned.
720 o An error was corrected in the help page of gammaStat regarding
721 the calculation of P-values.
723 o Using gls() could crash R when the number of species in the tree
724 and in the variables were different: this is fixed.
728 CHANGES IN APE VERSION 1.8-2
733 o The new function mlphylo() fits a phylogenetic tree by maximum
734 likelihood from DNA sequences. Its companion function DNAmodel()
735 is used to define the substitution model which may include
736 partitioning. There are methods for logLik(), deviance(), and
737 AIC(), and the summary() method has been extended to display in
738 a friendly way the results of this model fitting. Currently, the
739 functionality is limited to estimating the substitution and
740 associated parameters and computing the likelihood.
742 o The new function drop1.compar.gee (used as, e.g., drop1(m))
743 tests for single effects in GEE-based comparative method. A
744 warning message is printed if there is not enough degrees of
750 o An error message was sometimes issued by plot.multi.tree(),
751 though with no consequence.
755 CHANGES IN APE VERSION 1.8-1
760 o There is a new plot method for lists of trees (objects of class
761 "multi.tree"): it calls plot.phylo() internally and is
762 documented on the same help page.
767 o A bug was fixed in the C code that analyzes bipartitions: this
768 has impact on several functions like prop.part, prop.clades,
769 boot.phylo, or consensus.
771 o root() did not work correctly when the specified outgroup had
772 more than one element: this is fixed.
774 o dist.dna() sometimes returned a warning inappropriately: this
777 o If the distance object given to nj() had no rownames, nj()
778 returned a tree with no tip labels: it now returns tips labelled
779 "1", "2", ..., corresponding to the row numbers.
784 o nj() has been slightly changed so that tips with a zero distance
785 are first aggregated with zero-lengthed branches; the usual NJ
786 procedure is then performed on a distance matrix without 0's.
790 CHANGES IN APE VERSION 1.8
795 o The new function chronopl() estimates dates using the penalized
796 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
798 o The new function consensus() calculates the consensus tree of a
801 o The new function evolve.phylo() simulates the evolution of
802 continuous characters along a phylogeny under a Brownian model.
804 o The new plot method for objects of class "ancestral" displays a
805 tree together with ancestral values, as returned by the above
808 o The new function as.phylo.formula() returns a phylogeny from a
809 set of nested taxonomic variables given as a formula.
811 o The new function read.caic() reads trees in CAIC format.
813 o The new function tiplabels() allows to add labels to the tips
814 of a tree using text or plotting symbols in a flexible way.
816 o The new function unroot() unroots a phylogeny.
818 o multi2di() has a new option, `random', which specifies whether
819 to resolve the multichotomies randomly (the default) or not.
821 o prop.part() now returns an object of class "prop.part" for which
822 there are print (to display a partition in a more friendly way)
823 and summary (to extract the numbers) methods.
825 o plot.phylo() has a new option, `show.tip.label', specifying
826 whether to print the labels of the tips. The default is TRUE.
828 o The code of nj() has been replaced by a faster C code: it is now
829 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
832 o write.nexus() now writes whether a tree is rooted or not.
837 o Two bugs have been fixed in root(): unrooted trees are now
838 handled corretly, and node labels are now output normally.
840 o A bug was fixed in phymltest(): the executable couldn't be found
843 o Three bug have been fixed in ace(): computing the likelihood of
844 ancestral states of discrete characters failed, custom models
845 did not work, and the function failed with a null gradient (a
846 warning message is now returned; this latter bug was also
847 present in yule.cov() as well and is now fixed).
849 o pic() hanged out when missing data were present: a message error
852 o A small bug was fixed in dist.dna() where the gamma correction
853 was not always correctly dispatched.
855 o plot.phylo() plotted correctly the root edge only when the tree
856 was plotted rightwards: this works now for all directions.
861 o dist.taxo() has been renamed as weight.taxo().
863 o Various error and warning messages have been improved.
867 CHANGES IN APE VERSION 1.7
870 o The new function ace() estimates ancestral character states for
871 continuous characters (with ML, GLS, and contrasts methods), and
872 discrete characters (with ML only) for any number of states.
874 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
875 of directional evolution for continuous characters. The user
876 specifies the node(s) of the tree where the character optimum
879 o The new function is.rooted() tests whether a tree (of class
882 o The new function rcoal() generates random ultrametric trees with
883 the possibility to specify the function that generates the
884 inter-nodes distances.
886 o The new function mrca() gives for all pairs of tips in a tree
887 (and optionally nodes too) the most recent common ancestor.
889 o nodelabels() has a new option `thermo' to plot proportions (up
890 to three classes) on the nodes of a tree.
892 o rtree() has been improved: it can now generate rooted or
893 unrooted trees, and the mathematical function that generates the
894 branch lengths may be specified by the user. The tip labels may
895 be given directly in the call to rtree. The limit cases (n = 2,
896 3) are now handled correctly.
898 o dist.topo() has a new argument `method' with two choices: "PH85"
899 for Penny and Henny's method (already available before and now
900 the default), and "BHV01" for the geometric distance by Billera
901 et al. (2001, Adv. Appl. Math. 27:733).
903 o write.tree() has a new option, `digits', which specifies the
904 number of digits to be printed in the Newick tree. By default
905 digits = 10. The numbers are now always printed in decimal form
906 (i.e., 1.0e-1 is now avoided).
908 o dist.dna() can now compute the raw distances between pairs of
909 DNA sequences by specifying model = "raw".
911 o dist.phylo() has a new option `full' to possibly compute the
912 distances among all tips and nodes of the tree. The default if
918 o Several bugs were fixed in all.equal.phylo().
920 o dist.dna() did not handle correctly gaps ("-") in alignments:
921 they are now considered as missing data.
923 o rotate() did not work if the tips were not ordered: this is
926 o mantel.test() returned NA in some special cases: this is fixed
927 and the function has been improved and is now faster.
929 o A bug was fixed in diversi.gof() where the calculation of A² was
932 o cherry() did not work correctly under some OSs (mainly Linux):
935 o is.binary.tree() has been modified so that it works with both
936 rooted and unrooted trees.
938 o The documentation of theta.s() was not correct: this has been
941 o plot.mst() did not work correctly: this is fixed.
945 CHANGES IN APE VERSION 1.6
950 o The new function dist.topo() computes the topological distances
953 o The new function boot.phylo() performs a bootstrap analysis on
954 phylogeny estimation.
956 o The new functions prop.part() and prop.clades() analyse
957 bipartitions from a series of trees.
962 o read.GenBank() now uses the EFetch utility of NCBI instead of
963 the usual Web interface: it is now much faster (e.g., 12 times
964 faster to retrieve 8 sequences, 37 times for 60 sequences).
969 o Several bugs were fixed in read.dna().
971 o Several bugs were fixed in diversi.time().
973 o is.binary.tree() did not work correctly if the tree has no edge
974 lengths: this is fixed.
976 o drop.tip() did not correctly propagated the `node.label' of a
981 CHANGES IN APE VERSION 1.5
986 o Two new functions, as.matching.phylo() and as.phylo.matching(),
987 convert objects between the classes "phylo" and "matching". The
988 latter implements the representation of binary trees introduced by
989 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
990 as.matching() has been introduced as well.
992 o Two new functions, multi2di() and di2multi(), allow to resolve
993 and collapse multichotomies with branches of length zero.
995 o The new function nuc.div() computes the nucleotide diversity
996 from a sample a DNA sequences.
998 o dist.dna() has been completely rewritten with a much faster
999 (particularly for large data sets) C code. Eight models are
1000 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1001 option `method' has been renamed `model'). Computation of variance
1002 is available for all models. A gamma-correction is possible for
1003 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1004 to remove sites with missing data on a pairwise basis. The option
1005 `GCcontent' has been removed.
1007 o read.GenBank() has a new option (species.names) which specifies
1008 whether to return the species names of the organisms in addition
1009 to the accession numbers of the sequences (this is the default
1012 o write.nexus() can now write several trees in the same NEXUS file.
1014 o drop.tip() has a new option `root.edge' that allows to specify the
1015 new root edge if internal branches are trimmed.
1020 o as.phylo.hclust() failed if some labels had parentheses: this
1023 o Several bugs were fixed in all.equal.phylo(). This function now
1024 returns the logical TRUE if the trees are identical but with
1025 different representations (a report was printed previously).
1027 o read.GenBank() did not correctly handle ambiguous base codes:
1033 o birthdeath() now returns an object of class "birthdeath" for
1034 which there is a print method.
1038 CHANGES IN APE VERSION 1.4
1043 o The new function nj() performs phylogeny estimation with the
1044 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1047 o The new function which.edge() identifies the edges of a tree
1048 that belong to a group specified as a set of tips.
1050 o The new function as.phylo.phylog() converts an object of class
1051 "phylog" (from the package ade4) into an object of class
1054 o The new function axisPhylo() draws axes on the side of a
1057 o The new function howmanytrees() calculates the number of trees
1058 in different cases and giving a number of tips.
1060 o write.tree() has a new option `multi.line' (TRUE by default) to
1061 write a Newick tree on several lines rather than on a single
1064 o The functionalities of zoom() have been extended. Several
1065 subtrees can be visualized at the same time, and they are marked
1066 on the main tree with colors. The context of the subtrees can be
1067 marked with the option `subtree' (see below).
1069 o drop.tip() has a new option `subtree' (FALSE by default) which
1070 specifies whether to output in the tree how many tips have been
1073 o The arguments of add.scale.bar() have been redefined and have
1074 now default values (see ?add.scale.bar for details). This
1075 function now works even if the plotted tree has no edge length.
1077 o plot.phylo() can now plot radial trees, but this does not take
1078 edge lengths into account.
1080 o In plot.phylo() with `type = "phylogram"', if the values of
1081 `edge.color' and `edge.width' are identical for sister-branches,
1082 they are propagated to the vertical line that link them.
1087 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1088 crashing. This is fixed.
1090 o In plot.phylo(), the options `edge.color' and `edge.width' are
1091 now properly recycled; their default values are now "black" and
1094 o A bug has been fixed in write.nexus().
1099 o The function node.depth.edgelength() has been removed and
1100 replaced by a C code.
1104 CHANGES IN APE VERSION 1.3-1
1109 o The new function nodelabels() allows to add labels to the nodes
1110 of a tree using text or plotting symbols in a flexible way.
1112 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1113 numeric values specifying the lower and upper limits on the x-
1114 and y-axes. This allows to leave some space on any side of the
1115 tree. If a single value is given, this is taken as the upper
1120 CHANGES IN APE VERSION 1.3
1125 o The new function phymltest() calls the software PHYML and fits
1126 28 models of DNA sequence evolution. There are a print method to
1127 display likelihood and AIC values, a summary method to compute
1128 the hierarchical likelihood ratio tests, and a plot method to
1129 display graphically the AIC values of each model.
1131 o The new function yule.cov() fits the Yule model with covariates,
1132 a model where the speciation rate is affected by several species
1133 traits through a generalized linear model. The parameters are
1134 estimated by maximum likelihood.
1136 o Three new functions, corBrownian(), corGrafen(), and
1137 corMartins(), compute the expected correlation structures among
1138 species given a phylogeny under different models of evolution.
1139 These can be used for GLS comparative phylogenetic methods (see
1140 the examples). There are coef() and corMatrix() methods and an
1141 Initialize.corPhyl() function associated.
1143 o The new function compar.cheverud() implements Cheverud et al.'s
1144 (1985; Evolution 39:1335) phylogenetic comparative method.
1146 o The new function varcomp() estimates variance components; it has
1149 o Two new functions, panel.superpose.correlogram() and
1150 plot.correlogramList(), allow to plot several phylogenetic
1153 o The new function node.leafnumber() computes the number of leaves
1154 of a subtree defined by a particular node.
1156 o The new function node.sons() gets all tags of son nodes from a
1159 o The new function compute.brlen() computes the branch lengths of
1160 a tree according to a specified method.
1162 o plot.phylo() has three new options: "cex" controls the size of
1163 the (tip and node) labels (thus it is no more needed to change
1164 the global graphical parameter), "direction" which allows to
1165 plot the tree rightwards, leftwards, upwards, or downwards, and
1166 "y.lim" which sets the upper limit on the y-axis.
1171 o Some functions which try to match tip labels and names of
1172 additional data (e.g. vector) are likely to fail if there are
1173 typing or syntax errors. If both series of names do not perfectly
1174 match, they are ignored and a warning message is now issued.
1175 These functions are bd.ext, compar.gee, pic. Their help pages
1176 have been clarified on this point.
1180 CHANGES IN APE VERSION 1.2-7
1185 o The new function root() reroots a phylogenetic tree with respect
1186 to a specified outgroup.
1188 o The new function rotate() rotates an internal branch of a tree.
1190 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1191 trees) controls the display of the tip labels in unrooted trees.
1192 This display has been greatly improved: the tip labels are now not
1193 expected to overlap with the tree (particularly if lab4ut =
1194 "axial"). In all cases, combining appropriate values of "lab4ut"
1195 and the font size (via "par(cex = )") should result in readable
1196 unrooted trees. See ?plot.phylo for some examples.
1198 o In drop.tip(), the argument `tip' can now be numeric or character.
1203 o drop.tip() did not work correctly with trees with no branch
1204 lengths: this is fixed.
1206 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1207 plotted with some line crossings: this is now fixed.
1211 CHANGES IN APE VERSION 1.2-6
1216 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1217 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1218 to implement comparative methods with an autocorrelation approach.
1220 o A new data set describing some life history traits of Carnivores
1226 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1231 o When plotting a tree with plot.phylo(), the new default of the
1232 option `label.offset' is now 0, so the labels are always visible.
1236 CHANGES IN APE VERSION 1.2-5
1241 o The new function bd.ext() fits a birth-death model with combined
1242 phylogenetic and taxonomic data, and estimates the corresponding
1243 speciation and extinction rates.
1248 o The package gee is no more required by ape but only suggested
1249 since only the function compar.gee() calls gee.
1253 CHANGES IN APE VERSION 1.2-4
1258 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1259 and lines.popsize) implementing a new approach for inferring the
1260 demographic history from genealogies using a reversible jump
1261 MCMC have been introduced.
1263 o The unit of time in the skyline plot and in the new plots can
1264 now be chosen to be actual years, rather than substitutions.
1268 CHANGES IN APE VERSION 1.2-3
1273 o The new function rtree() generates a random binary tree with or
1274 without branch lengths.
1276 o Two new functions for drawing lineages-through-time (LTT) plots
1277 are provided: ltt.lines() adds a LTT curve to an existing plot,
1278 and mltt.plot() does a multiple LTT plot giving several trees as
1279 arguments (see `?ltt.plot' for details).
1284 o Some taxon names made R crashing when calling as.phylo.hclust():
1287 o dist.dna() returned an error with two identical DNA sequences
1288 (only using the Jukes-Cantor method returned 0): this is fixed.
1293 o The function dist.phylo() has been re-written using a different
1294 algorithm: it is now about four times faster.
1296 o The code of branching.times() has been improved: it is now about
1301 CHANGES IN APE VERSION 1.2-2
1306 o The new function seg.sites() finds the segregating sites in a
1307 sample of DNA sequences.
1312 o A bug introduced in read.tree() and in read.nexus() with version
1315 o A few errors were corrected and a few examples were added in the
1320 CHANGES IN APE VERSION 1.2-1
1325 o plot.phylo() can now draw the edge of the root of a tree if it
1326 has one (see the new option `root.edge', its default is FALSE).
1331 o A bug was fixed in read.nexus(): files with semicolons inside
1332 comment blocks were not read correctly.
1334 o The behaviour of read.tree() and read.nexus() was corrected so
1335 that tree files with badly represented root edges (e.g., with
1336 an extra pair of parentheses, see the help pages for details)
1337 are now correctly represented in the object of class "phylo";
1338 a warning message is now issued.
1342 CHANGES IN APE VERSION 1.2
1347 o plot.phylo() has been completely re-written and offers several
1348 new functionalities. Three types of trees can now be drawn:
1349 phylogram (as previously), cladogram, and unrooted tree; in
1350 all three types the branch lengths can be drawn using the edge
1351 lengths of the phylogeny or not (e.g., if the latter is absent).
1352 The vertical position of the nodes can be adjusted with two
1353 choices (see option `node.pos'). The code has been re-structured,
1354 and two new functions (potentially useful for developpers) are
1355 documented separately: node.depth.edgelength() and node.depth();
1356 see the respective help pages for details.
1358 o The new function zoom() allows to explore very large trees by
1359 focusing on a small portion of it.
1361 o The new function yule() fits by maximum likelihood the Yule model
1362 (birth-only process) to a phylogenetic tree.
1364 o Support for writing DNA sequences in FASTA format has been
1365 introduced in write.dna() (support for reading sequences in
1366 this format was introduced in read.dna() in version 1.1-2).
1367 The function has been completely re-written, fixing some bugs
1368 (see below); the default behaviour is no more to display the
1369 sequences on the standard output. Several options have been
1370 introduced to control the sequence printing in a flexible
1371 way. The help page has been extended.
1373 o A new data set is included: a supertree of bats in NEXUS format.
1378 o In theta.s(), the default of the option `variance' has
1379 been changed to `FALSE' (as was indicated in the help page).
1381 o Several bugs were fixed in the code of all.equal.phylo().
1383 o Several bugs were fixed in write.dna(), particularly this
1384 function did not work with `format = "interleaved"'.
1386 o Various errors were corrected in the help pages.
1391 o The argument names of as.hclust.phylo() have been changed
1392 from "(phy)" to "(x, ...)" to conform to the definition of
1393 the corresponding generic function.
1395 o gamma.stat() has been renamed gammaStat() to avoid confusion
1396 since gamma() is a generic function.
1400 CHANGES IN APE VERSION 1.1-3
1405 o base.freq() previously did not return a value of 0 for
1406 bases absent in the data (e.g., a vector of length 3 was
1407 returned if one base was absent). This is now fixed (a
1408 vector of length 4 is always returned).
1410 o Several bugs were fixed in read.nexus(), including that this
1411 function did not work in this absence of a "TRANSLATE"
1412 command in the NEXUS file, and that the commands were
1417 CHANGES IN APE VERSION 1.1-2
1422 o The Tamura and Nei (1993) model of DNA distance is now implemented
1423 in dist.dna(): five models are now available in this function.
1425 o A new data set is included: a set of 15 sequences of the
1426 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1432 o A bug in read.nexus() was fixed.
1434 o read.dna() previously did not work correctly in most cases.
1435 The function has been completely re-written and its help page
1436 has been considerably extended (see ?read.dna for details).
1437 Underscores (_) in taxon names are no more replaced with
1438 spaces (this behaviour was undocumented).
1440 o A bug was fixed in write.dna().
1444 CHANGES IN APE VERSION 1.1-1
1449 o A bug in read.tree() introduced in APE 1.1 was fixed.
1451 o A bug in compar.gee() resulted in an error when trying to fit
1452 a model with `family = "binomial"'. This is now fixed.
1456 CHANGES IN APE VERSION 1.1
1461 o The Klastorin (1982) method as suggested by Misawa and Tajima
1462 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1463 on the basis of phylogenetic trees has been implemented (see
1464 the function klastorin()).
1466 o Functions have been added to convert APE's "phylo" objects in
1467 "hclust" cluster objects and vice versa (see the help page of
1468 as.phylo for details).
1470 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1471 are introduced for the estimation of absolute evolutionary rates
1472 (ratogram) and dated clock-like trees (chronogram) from
1473 phylogenetic trees using the non-parametric rate smoothing approach
1474 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1476 o A summary method is now provided printing a summary information on a
1477 phylogenetic tree with, for instance, `summary(tree)'.
1479 o The behaviour of read.tree() was changed so that all spaces and
1480 tabulations in tree files are now ignored. Consequently, spaces in tip
1481 labels are no more allowed. Another side effect is that read.nexus()
1482 now does not replace the underscores (_) in tip labels with spaces
1483 (this behaviour was undocumented).
1485 o The function plot.phylo() has a new option (`underscore') which
1486 specifies whether the underscores in tip labels should be written on
1487 the plot as such or replaced with spaces (the default).
1489 o The function birthdeath() now computes 95% confidence intervals of
1490 the estimated parameters using profile likelihood.
1492 o Three new data sets are included: a gene tree estimated from 36
1493 landplant rbcL sequences, a gene tree estimated from 32 opsin
1494 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1499 o A bug was fixed in dist.gene() where nothing was returned.
1501 o A bug in plot.mst() was fixed.
1503 o A bug in vcv.phylo() resulted in false correlations when the
1504 option `cor = TRUE' was used (now fixed).
1508 CHANGES IN APE VERSION 1.0
1513 o Two new functions, read.dna() and write.dna(), read/write in a file
1514 DNA sequences in interleaved or in sequential format.
1516 o Two new functions, read.nexus() and write.nexus(), read/write trees
1519 o The new function bind.tree() allows to bind two trees together,
1520 possibly handling root edges to give internal branches.
1522 o The new function drop.tip() removes the tips in a phylogenetic tree,
1523 and trims (or not) the corresponding internal branches.
1525 o The new function is.ultrametric() tests if a tree is ultrametric.
1527 o The function plot.phylo() has more functionalities such as drawing the
1528 branches with different colours and/or different widths, showing the
1529 node labels, controling the position and font of the labels, rotating
1530 the labels, and controling the space around the plot.
1532 o The function read.tree() can now read trees with no branch length,
1533 such as "(a,b),c);". Consequently, the element `edge.length' in
1534 objects of class "phylo" is now optional.
1536 o The function write.tree() has a new default behaviour: if the default
1537 for the option `file' is used (i.e. file = ""), then a variable of
1538 mode character containing the tree in Newick format is returned which
1539 can thus be assigned (e.g., tree <- write.tree(phy)).
1541 o The function read.tree() has a new argument `text' which allows
1542 to read the tree in a variable of mode character.
1544 o A new data set is included: the phylogenetic relationships among
1545 the orders of birds from Sibley and Ahlquist (1990).
1549 CHANGES IN APE VERSION 0.2-1
1554 o Several bugs were fixed in the help pages.
1558 CHANGES IN APE VERSION 0.2
1563 o The function write.tree() writes phylogenetic trees (objects of class
1564 "phylo") in an ASCII file using the Newick parenthetic format.
1566 o The function birthdeath() fits a birth-death model to branching times
1567 by maximum likelihood, and estimates the corresponding speciation and
1570 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1573 o The function is.binary.tree() tests whether a phylogeny is binary.
1575 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1576 as well as some methods are introduced.
1578 o Several functions, including some generics and methods, for computing
1579 skyline plot estimates (classic and generalized) of effective
1580 population size through time are introduced and replace the function
1581 skyline.plot() in version 0.1.
1583 o Two data sets are now included: the phylogenetic relationships among
1584 the families of birds from Sibley and Ahlquist (1990), and an
1585 estimated clock-like phylogeny of HIV sequences sampled in the
1586 Democratic Republic of Congo.
1589 DEPRECATED & DEFUNCT
1591 o The function skyline.plot() in ape 0.1 has been deprecated and
1592 replaced by more elaborate functions (see above).
1597 o Two important bugs were fixed in plot.phylo(): phylogenies with
1598 multichotomies not at the root or not with only terminal branches,
1599 and phylogenies with a single node (i.e. only terminal branches)
1600 did not plot. These trees should be plotted correctly now.
1602 o Several bugs were fixed in diversi.time() in the computation of
1605 o Various errors were corrected in the help pages.
projects / ape.git / blob