1 CHANGES IN APE VERSION 2.1-2
6 o root() gains the options 'node' and 'resolve.root'
7 (FALSE by default) as well as its code being improved.
11 CHANGES IN APE VERSION 2.1-1
16 o The new function rmtree generates lists of random trees.
18 o rcoal() now generates a genuine coalescent tree by default
19 (thanks to Vladimir Minin for the code).
24 o nuc.div() returned an incorrect value with the default
25 pairwise.deletion = FALSE.
30 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
31 have been improved so that they are stabler and faster.
33 o R packages used by ape are now loaded silently; lattice and gee
34 are loaded only when needed.
38 CHANGES IN APE VERSION 2.1
43 o The new function identify.phylo identifies clades on a plotted
46 o It is now possible to subset a list of trees (object of class
47 "multiPhylo") with "[" while keeping its class correct.
49 o The new function as.DNAbin.alignment converts DNA sequences
50 stored in the "alignment" format of the package seqinr into
51 an object of class "DNAbin".
53 o The new function weight.taxo2 helps to build similarity matrices
54 given two taxonomic levels (usually called by other functions).
56 o write.tree() can now take a list of trees (class "multiPhylo")
59 o plot.correlogram() and plot.correlogramList() have been
60 improved, and gain several options (see the help page for
61 details). A legend is now plotted by default.
66 o dist.dna() returned some incorrect values with `model = "JC69"'
67 and `pairwise.deletion = TRUE'. This affected only the
68 distances involving sequences with missing values. (Thanks
69 to Bruno Toupance for digging this bug out.)
71 o write.tree() failed with some trees: this is fixed by removing
72 the `multi.line' option (trees are now always printed on a
75 o read.nexus() did not correctly detect trees with multiple root
76 edges (see OTHER CHANGES).
81 o The code of mlphylo() has almost entirely rewritten, and should
82 much stabler now. The options have been also greatly simplified
83 (see ?mlphylo and ?DNAmodel for details).
85 o The internal function nTips has been renamed klastorin_nTips.
87 o The code of is.ultrametric() contained redundancies and has
90 o The code of Moran.I() and of correlogram.formula() have been
93 o read.tree() and read.nexus() now return an error when trying to
94 read a tree with multiple root edges (see BUG FIXES). The
95 correction applied in previous version did not work in all
98 o The class c("multi.tree", "phylo") has been renamed
104 o There is now a vignette in ape: see vignette("MoranI", "ape").
109 o as.matching() and as.phylo.matching() do not support branch
112 o correlogram.phylo() and discrete.dist() have been removed.
116 CHANGES IN APE VERSION 2.0-2
121 o The new function matexpo computes the exponential of a square
124 o The new function unique.multi.tree removes duplicate trees from
127 o yule() has a new option `use.root.edge = FALSE' that specifies
128 to ignore, by default, the root edge of the tree if it exists.
133 o which.edge() failed when the index of a single terminal edge was
136 o In diversi.time(), the values returned for model C were
139 o A bug was fixed in yule() that affected the calculation of the
140 likelihood in the presence of ties in the branching times.
142 o There was a bug in the C function mat_expo4x4 affecting the
143 calculations of the transition probabilities for models HKY and
146 o A small bug was fixed in as.matrix.DNAbin (thanks to James
149 o rtree() did not `shuffle' the tip labels by default, so only a
150 limited number of labelled topologies could be generated.
154 CHANGES IN APE VERSION 2.0-1
159 o The three new functions bionj, fastme.ols, and fastme.bal
160 perform phylogeny estimation by the BIONJ and fastME methods in
161 OLS and balanced versions. This is a port to R of previous
162 previous programs done by Vincent Lefort.
164 o The new function chronoMPL performs molecular dating with the
165 mean path lengths method of Britton et al. (2002, Mol. Phyl.
168 o The new function rotate, contributed by Christoph Heibl, swaps
169 two clades connected to the same node. It works also with
170 multichotomous nodes.
172 o The new `method' as.matrix.DNAbin() may be used to convert
173 easily DNA sequences stored in a list into a matrix while
174 keeping the names and the class.
179 o chronopl() failed when some branch lengths were equal to zero:
180 an error message is now returned.
182 o di2multi() failed when there was a series of consecutive edges
187 CHANGES IN APE VERSION 1.10-2
192 o plot.phylo() can now plot circular trees: the option is type =
193 "fan" or type = "f" (to avoid the ambiguity with type = "c").
195 o prop.part() has a new option `check.labels = FALSE' which allows
196 to considerably speed-up the calculations of bipartitions. As a
197 consequence, calculations of bootstrap values with boot.phylo()
198 should be much faster.
203 o read.GenBank() did not return correctly the list of species as
204 from ape 1.10: this is fixed in this version
206 o Applying as.phylo() on a tree of class "phylo" failed: the
207 object is now returned unchanged.
211 CHANGES IN APE VERSION 1.10-1
216 o The three new functions Ntip, Nnode, and Nedge return, for a
217 given tree, the number of tips, nodes, or edges, respectively.
222 o read.nexus() did not set correctly the class of the returned
223 object when reading multiple trees.
225 o mllt.plot() failed with objects of class c("multi.tree",
228 o unroot() did not work correctly in most cases.
230 o reorder.phylo() made R freeze in some occasions.
232 o Plotting a tree in pruningwise order failed.
234 o When plotting an unrooted tree, the tip labels where not all
235 correctly positioned if the option `cex' was used.
239 CHANGES IN APE VERSION 1.10
244 o Five new `method' functions have been introduced to manipulate
245 DNA sequences in binary format (see below).
247 o Three new functions have been introduced to convert between the
248 new binary and the character formats.
250 o The new function as.alignment converts DNA sequences stored as
251 single characters into the class "alignment" used by the package
254 o read.dna() and read.GenBank() have a new argument `as.character'
255 controlling whether the sequences are returned in binary format
261 o root() failed when the tree had node labels: this is fixed.
263 o plot.phylo() did not correctly set the limits on the y-axis with
264 the default setting: this is fixed.
266 o dist.dna() returned a wrong result for the LogDet, paralinear,
267 and BH87 models with `pairwise.deletion = TRUE'.
272 o DNA sequences are now internally stored in a binary format. See
273 the document "A Bit-Level Coding Scheme for Nucleotides" for the
274 details. Most functions analyzing DNA functions have been
275 modified accordingly and are now much faster (dist.dna is now
276 ca. 60 times faster).
280 CHANGES IN APE VERSION 1.9-4
285 o A bug was fixed in edgelabels().
287 o as.phylo.hclust() did not work correctly when the object of
288 class "hclust" has its labels set to NULL: the returned tree has
289 now its tip labels set to "1", "2", ...
291 o consensus could fail if some tip labels are a subset of others
292 (e.g., "a" and "a_1"): this is now fixed.
294 o mlphylo() failed in most cases if some branch lengths of the
295 initial tree were greater than one: an error message is now
298 o mlphylo() failed in most cases when estimating the proportion of
299 invariants: this is fixed.
303 CHANGES IN APE VERSION 1.9-3
308 o The new function edgelabels adds labels on the edge of the tree
309 in the same way than nodelabels or tiplabels.
314 o multi2di() did not handle correctly branch lengths with the
315 default option `random = TRUE': this is now fixed.
317 o A bug was fixed in nuc.div() when using pairwise deletions.
319 o A bug occurred in the analysis of bipartitions with large
320 numbers of large trees, with consequences on prop.part,
321 prop.clades, and boot.phylo.
323 o The calculation of the Billera-Holmes-Vogtmann distance in
324 dist.topo was wrong: this has been fixed.
328 CHANGES IN APE VERSION 1.9-2
333 o The new function ladderize reorganizes the internal structure of
334 a tree to plot them left- or right-ladderized.
336 o The new function dist.nodes computes the patristic distances
337 between all nodes, internal and terminal, of a tree. It replaces
338 the option `full = TRUE' of cophenetic.phylo (see below).
343 o A bug was fixed in old2new.phylo().
345 o Some bugs were fixed in chronopl().
347 o The edge colours were not correctly displayed by plot.phylo
348 (thank you to Li-San Wang for the fix).
350 o cophenetic.phylo() failed with multichotomous trees: this is
356 o read.dna() now returns the sequences in a matrix if they are
357 aligned (interleaved or sequential format). Sequences in FASTA
358 format are still returned in a list.
360 o The option `full' of cophenetic.phylo() has been removed because
361 it could not be used from the generic.
366 o rotate() has been removed; this function did not work correctly
371 CHANGES IN APE VERSION 1.9-1
376 o Trees with a single tip were not read correctly in R as the
377 element `Nnode' was not set: this is fixed.
379 o unroot() did not set correctly the number of nodes of the
380 unrooted tree in most cases.
382 o read.GenBank() failed when fetching very long sequences,
383 particularly of the BX-series.
385 o A bug was introduced in read.tree() with ape 1.9: it has been
390 CHANGES IN APE VERSION 1.9
395 o There are two new print `methods' for trees of class "phylo" and
396 lists of trees of class "multi.tree", so that they are now
397 displayed in a compact and informative way.
399 o There are two new functions, old2new.phylo and new2old.phylo,
400 for converting between the old and new coding of the class
403 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
404 LogDet ("logdet"), and paralinear ("paralin").
406 o compute.brlen() has been extended: several methods are now
407 available to compute branch lengths.
409 o write.dna() can now handle matrices as well as lists.
414 o cophenetic.phylo() sometimes returned a wrong result with
415 multichotomous trees: this is fixed.
417 o rotate() failed when a single tip was specified: the tree is now
420 o ace() did not return the correct index matrix with custom
421 models: this is fixed.
423 o multi2di() did not work correctly when resolving multichotomies
424 randomly: the topology was always the same, only the arrangement
425 of clades was randomized: this is fixed. This function now
426 accepts trees with no branch lengths.
428 o The output of diversi.gof() was blurred by useless prints when a
429 user distribution was specified. This has been corrected, and
430 the help page of this function has been expanded.
435 o The internal structure of the class "phylo" has been changed:
436 see the document "Definition of Formats for Coding Phylogenetic
437 Trees in R" for the details. In addition, the code of most
438 functions has been improved.
440 o Several functions have been improved by replacing some R codes
441 by C codes: pic, plot.phylo, and reorder.phylo.
443 o There is now a citation information: see citation("ape") in R.
445 o write.tree() now does not add extra 0's to branch lengths so
446 that 1.23 is printed "1.23" by default, not "1.2300000000".
448 o The syntax of bind.tree() has been simplified. This function now
449 accepts trees with no branch lengths, and handles correctly node
452 o The option `as.numeric' of mrca() has been removed.
454 o The unused options `format' and `rooted' of read.tree() have
457 o The unused option `format' of write.tree() has been removed.
459 o The use of node.depth() has been simplified.
463 CHANGES IN APE VERSION 1.8-5
468 o Two new functions read.nexus.data() and write.nexus.data(),
469 contributed by Johan Nylander, allow to read and write molecular
470 sequences in NEXUS files.
472 o The new function reorder.phylo() reorders the internal structure
473 of a tree of class "phylo". It is used as the generic, e.g.,
476 o read.tree() and read.nexus() can now read trees with a single
479 o The new data set `cynipids' supplies a set of protein sequences
485 o The code of all.equal.phylo() has been completely rewritten
486 (thanks to Benoît Durand) which fixes several bugs.
488 o read.tree() and read.nexus() now checks the labels of the tree
489 to remove or substitute any characters that are illegal in the
490 Newick format (parentheses, etc.)
492 o A negative P-value could be returned by mantel.test(): this is
497 CHANGES IN APE VERSION 1.8-4
502 o The new function sh.test() computes the Shimodaira-
505 o The new function collapse.singles() removes the nodes with a
506 single descendant from a tree.
508 o plot.phylo() has a new argument `tip.color' to specify the
511 o mlphylo() has now an option `quiet' to control the display of
512 the progress of the analysis (the default is FALSE).
517 o read.dna() did not read correctly sequences in sequential format
518 with leading alignment gaps "-": this is fixed.
520 o ace() returned a list with no class so that the generic
521 functions (anova, logLik, ...) could not be used directly. This
522 is fixed as ace() now returns an object of class "ace".
524 o anova.ace() had a small bug when computing the number of degrees
525 of freedom: this is fixed.
527 o mlphylo() did not work when the sequences were in a matrix or
528 a data frame: this is fixed.
530 o rtree() did not work correctly when trying to simulate an
531 unrooted tree with two tips: an error message is now issued.
536 o The algorithm of rtree() has been changed: it is now about 40,
537 100, and 130 times faster for 10, 100, and 1000 tips,
542 CHANGES IN APE VERSION 1.8-3
547 o There are four new `method' functions to be used with the
548 results of ace(): logLik(), deviance(), AIC(), and anova().
550 o The plot method of phymltest has two new arguments: `main' to
551 change the title, and `col' to control the colour of the
552 segments showing the AIC values.
554 o ace() has a new argument `ip' that gives the initial values used
555 in the ML estimation with discrete characters (see the examples
556 in ?ace). This function now returns a matrix giving the indices
557 of the estimated rates when analysing discrete characters.
559 o nodelabels() and tiplabels() have a new argument `pie' to
560 represent proportions, with any number of categories, as
561 piecharts. The use of the option `thermo' has been improved:
562 there is now no limitation on the number of categories.
567 o mlphylo() did not work with more than two partitions: this is
570 o root() failed if the proposed outgroup was already an outgroup
571 in the tree: this is fixed.
573 o The `col' argument in nodelabels() and tiplabels() was not
574 correctly passed when `text' was used: this is fixed.
576 o Two bugs were fixed in mlphylo(): parameters were not always
577 correctly output, and the estimation failed in some cases.
579 o plot.phylo() was stuck when given a tree with a single tip: this
580 is fixed and a message error is now returned.
582 o An error was corrected in the help page of gammaStat regarding
583 the calculation of P-values.
585 o Using gls() could crash R when the number of species in the tree
586 and in the variables were different: this is fixed.
590 CHANGES IN APE VERSION 1.8-2
595 o The new function mlphylo() fits a phylogenetic tree by maximum
596 likelihood from DNA sequences. Its companion function DNAmodel()
597 is used to define the substitution model which may include
598 partitioning. There are methods for logLik(), deviance(), and
599 AIC(), and the summary() method has been extended to display in
600 a friendly way the results of this model fitting. Currently, the
601 functionality is limited to estimating the substitution and
602 associated parameters and computing the likelihood.
604 o The new function drop1.compar.gee (used as, e.g., drop1(m))
605 tests for single effects in GEE-based comparative method. A
606 warning message is printed if there is not enough degrees of
612 o An error message was sometimes issued by plot.multi.tree(),
613 though with no consequence.
617 CHANGES IN APE VERSION 1.8-1
622 o There is a new plot method for lists of trees (objects of class
623 "multi.tree"): it calls plot.phylo() internally and is
624 documented on the same help page.
629 o A bug was fixed in the C code that analyzes bipartitions: this
630 has impact on several functions like prop.part, prop.clades,
631 boot.phylo, or consensus.
633 o root() did not work correctly when the specified outgroup had
634 more than one element: this is fixed.
636 o dist.dna() sometimes returned a warning inappropriately: this
639 o If the distance object given to nj() had no rownames, nj()
640 returned a tree with no tip labels: it now returns tips labelled
641 "1", "2", ..., corresponding to the row numbers.
646 o nj() has been slightly changed so that tips with a zero distance
647 are first aggregated with zero-lengthed branches; the usual NJ
648 procedure is then performed on a distance matrix without 0's.
652 CHANGES IN APE VERSION 1.8
657 o The new function chronopl() estimates dates using the penalized
658 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
660 o The new function consensus() calculates the consensus tree of a
663 o The new function evolve.phylo() simulates the evolution of
664 continuous characters along a phylogeny under a Brownian model.
666 o The new plot method for objects of class "ancestral" displays a
667 tree together with ancestral values, as returned by the above
670 o The new function as.phylo.formula() returns a phylogeny from a
671 set of nested taxonomic variables given as a formula.
673 o The new function read.caic() reads trees in CAIC format.
675 o The new function tiplabels() allows to add labels to the tips
676 of a tree using text or plotting symbols in a flexible way.
678 o The new function unroot() unroots a phylogeny.
680 o multi2di() has a new option, `random', which specifies whether
681 to resolve the multichotomies randomly (the default) or not.
683 o prop.part() now returns an object of class "prop.part" for which
684 there are print (to display a partition in a more friendly way)
685 and summary (to extract the numbers) methods.
687 o plot.phylo() has a new option, `show.tip.label', specifying
688 whether to print the labels of the tips. The default is TRUE.
690 o The code of nj() has been replaced by a faster C code: it is now
691 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
694 o write.nexus() now writes whether a tree is rooted or not.
699 o Two bugs have been fixed in root(): unrooted trees are now
700 handled corretly, and node labels are now output normally.
702 o A bug was fixed in phymltest(): the executable couldn't be found
705 o Three bug have been fixed in ace(): computing the likelihood of
706 ancestral states of discrete characters failed, custom models
707 did not work, and the function failed with a null gradient (a
708 warning message is now returned; this latter bug was also
709 present in yule.cov() as well and is now fixed).
711 o pic() hanged out when missing data were present: a message error
714 o A small bug was fixed in dist.dna() where the gamma correction
715 was not always correctly dispatched.
717 o plot.phylo() plotted correctly the root edge only when the tree
718 was plotted rightwards: this works now for all directions.
723 o dist.taxo() has been renamed as weight.taxo().
725 o Various error and warning messages have been improved.
729 CHANGES IN APE VERSION 1.7
732 o The new function ace() estimates ancestral character states for
733 continuous characters (with ML, GLS, and contrasts methods), and
734 discrete characters (with ML only) for any number of states.
736 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
737 of directional evolution for continuous characters. The user
738 specifies the node(s) of the tree where the character optimum
741 o The new function is.rooted() tests whether a tree (of class
744 o The new function rcoal() generates random ultrametric trees with
745 the possibility to specify the function that generates the
746 inter-nodes distances.
748 o The new function mrca() gives for all pairs of tips in a tree
749 (and optionally nodes too) the most recent common ancestor.
751 o nodelabels() has a new option `thermo' to plot proportions (up
752 to three classes) on the nodes of a tree.
754 o rtree() has been improved: it can now generate rooted or
755 unrooted trees, and the mathematical function that generates the
756 branch lengths may be specified by the user. The tip labels may
757 be given directly in the call to rtree. The limit cases (n = 2,
758 3) are now handled correctly.
760 o dist.topo() has a new argument `method' with two choices: "PH85"
761 for Penny and Henny's method (already available before and now
762 the default), and "BHV01" for the geometric distance by Billera
763 et al. (2001, Adv. Appl. Math. 27:733).
765 o write.tree() has a new option, `digits', which specifies the
766 number of digits to be printed in the Newick tree. By default
767 digits = 10. The numbers are now always printed in decimal form
768 (i.e., 1.0e-1 is now avoided).
770 o dist.dna() can now compute the raw distances between pairs of
771 DNA sequences by specifying model = "raw".
773 o dist.phylo() has a new option `full' to possibly compute the
774 distances among all tips and nodes of the tree. The default if
780 o Several bugs were fixed in all.equal.phylo().
782 o dist.dna() did not handle correctly gaps ("-") in alignments:
783 they are now considered as missing data.
785 o rotate() did not work if the tips were not ordered: this is
788 o mantel.test() returned NA in some special cases: this is fixed
789 and the function has been improved and is now faster.
791 o A bug was fixed in diversi.gof() where the calculation of A² was
794 o cherry() did not work correctly under some OSs (mainly Linux):
797 o is.binary.tree() has been modified so that it works with both
798 rooted and unrooted trees.
800 o The documentation of theta.s() was not correct: this has been
803 o plot.mst() did not work correctly: this is fixed.
807 CHANGES IN APE VERSION 1.6
812 o The new function dist.topo() computes the topological distances
815 o The new function boot.phylo() performs a bootstrap analysis on
816 phylogeny estimation.
818 o The new functions prop.part() and prop.clades() analyse
819 bipartitions from a series of trees.
824 o read.GenBank() now uses the EFetch utility of NCBI instead of
825 the usual Web interface: it is now much faster (e.g., 12 times
826 faster to retrieve 8 sequences, 37 times for 60 sequences).
831 o Several bugs were fixed in read.dna().
833 o Several bugs were fixed in diversi.time().
835 o is.binary.tree() did not work correctly if the tree has no edge
836 lengths: this is fixed.
838 o drop.tip() did not correctly propagated the `node.label' of a
843 CHANGES IN APE VERSION 1.5
848 o Two new functions, as.matching.phylo() and as.phylo.matching(),
849 convert objects between the classes "phylo" and "matching". The
850 latter implements the representation of binary trees introduced by
851 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
852 as.matching() has been introduced as well.
854 o Two new functions, multi2di() and di2multi(), allow to resolve
855 and collapse multichotomies with branches of length zero.
857 o The new function nuc.div() computes the nucleotide diversity
858 from a sample a DNA sequences.
860 o dist.dna() has been completely rewritten with a much faster
861 (particularly for large data sets) C code. Eight models are
862 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
863 option `method' has been renamed `model'). Computation of variance
864 is available for all models. A gamma-correction is possible for
865 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
866 to remove sites with missing data on a pairwise basis. The option
867 `GCcontent' has been removed.
869 o read.GenBank() has a new option (species.names) which specifies
870 whether to return the species names of the organisms in addition
871 to the accession numbers of the sequences (this is the default
874 o write.nexus() can now write several trees in the same NEXUS file.
876 o drop.tip() has a new option `root.edge' that allows to specify the
877 new root edge if internal branches are trimmed.
882 o as.phylo.hclust() failed if some labels had parentheses: this
885 o Several bugs were fixed in all.equal.phylo(). This function now
886 returns the logical TRUE if the trees are identical but with
887 different representations (a report was printed previously).
889 o read.GenBank() did not correctly handle ambiguous base codes:
895 o birthdeath() now returns an object of class "birthdeath" for
896 which there is a print method.
900 CHANGES IN APE VERSION 1.4
905 o The new function nj() performs phylogeny estimation with the
906 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
909 o The new function which.edge() identifies the edges of a tree
910 that belong to a group specified as a set of tips.
912 o The new function as.phylo.phylog() converts an object of class
913 "phylog" (from the package ade4) into an object of class
916 o The new function axisPhylo() draws axes on the side of a
919 o The new function howmanytrees() calculates the number of trees
920 in different cases and giving a number of tips.
922 o write.tree() has a new option `multi.line' (TRUE by default) to
923 write a Newick tree on several lines rather than on a single
926 o The functionalities of zoom() have been extended. Several
927 subtrees can be visualized at the same time, and they are marked
928 on the main tree with colors. The context of the subtrees can be
929 marked with the option `subtree' (see below).
931 o drop.tip() has a new option `subtree' (FALSE by default) which
932 specifies whether to output in the tree how many tips have been
935 o The arguments of add.scale.bar() have been redefined and have
936 now default values (see ?add.scale.bar for details). This
937 function now works even if the plotted tree has no edge length.
939 o plot.phylo() can now plot radial trees, but this does not take
940 edge lengths into account.
942 o In plot.phylo() with `type = "phylogram"', if the values of
943 `edge.color' and `edge.width' are identical for sister-branches,
944 they are propagated to the vertical line that link them.
949 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
950 crashing. This is fixed.
952 o In plot.phylo(), the options `edge.color' and `edge.width' are
953 now properly recycled; their default values are now "black" and
956 o A bug has been fixed in write.nexus().
961 o The function node.depth.edgelength() has been removed and
962 replaced by a C code.
966 CHANGES IN APE VERSION 1.3-1
971 o The new function nodelabels() allows to add labels to the nodes
972 of a tree using text or plotting symbols in a flexible way.
974 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
975 numeric values specifying the lower and upper limits on the x-
976 and y-axes. This allows to leave some space on any side of the
977 tree. If a single value is given, this is taken as the upper
982 CHANGES IN APE VERSION 1.3
987 o The new function phymltest() calls the software PHYML and fits
988 28 models of DNA sequence evolution. There are a print method to
989 display likelihood and AIC values, a summary method to compute
990 the hierarchical likelihood ratio tests, and a plot method to
991 display graphically the AIC values of each model.
993 o The new function yule.cov() fits the Yule model with covariates,
994 a model where the speciation rate is affected by several species
995 traits through a generalized linear model. The parameters are
996 estimated by maximum likelihood.
998 o Three new functions, corBrownian(), corGrafen(), and
999 corMartins(), compute the expected correlation structures among
1000 species given a phylogeny under different models of evolution.
1001 These can be used for GLS comparative phylogenetic methods (see
1002 the examples). There are coef() and corMatrix() methods and an
1003 Initialize.corPhyl() function associated.
1005 o The new function compar.cheverud() implements Cheverud et al.'s
1006 (1985; Evolution 39:1335) phylogenetic comparative method.
1008 o The new function varcomp() estimates variance components; it has
1011 o Two new functions, panel.superpose.correlogram() and
1012 plot.correlogramList(), allow to plot several phylogenetic
1015 o The new function node.leafnumber() computes the number of leaves
1016 of a subtree defined by a particular node.
1018 o The new function node.sons() gets all tags of son nodes from a
1021 o The new function compute.brlen() computes the branch lengths of
1022 a tree according to a specified method.
1024 o plot.phylo() has three new options: "cex" controls the size of
1025 the (tip and node) labels (thus it is no more needed to change
1026 the global graphical parameter), "direction" which allows to
1027 plot the tree rightwards, leftwards, upwards, or downwards, and
1028 "y.lim" which sets the upper limit on the y-axis.
1033 o Some functions which try to match tip labels and names of
1034 additional data (e.g. vector) are likely to fail if there are
1035 typing or syntax errors. If both series of names do not perfectly
1036 match, they are ignored and a warning message is now issued.
1037 These functions are bd.ext, compar.gee, pic. Their help pages
1038 have been clarified on this point.
1042 CHANGES IN APE VERSION 1.2-7
1047 o The new function root() reroots a phylogenetic tree with respect
1048 to a specified outgroup.
1050 o The new function rotate() rotates an internal branch of a tree.
1052 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1053 trees) controls the display of the tip labels in unrooted trees.
1054 This display has been greatly improved: the tip labels are now not
1055 expected to overlap with the tree (particularly if lab4ut =
1056 "axial"). In all cases, combining appropriate values of "lab4ut"
1057 and the font size (via "par(cex = )") should result in readable
1058 unrooted trees. See ?plot.phylo for some examples.
1060 o In drop.tip(), the argument `tip' can now be numeric or character.
1065 o drop.tip() did not work correctly with trees with no branch
1066 lengths: this is fixed.
1068 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1069 plotted with some line crossings: this is now fixed.
1073 CHANGES IN APE VERSION 1.2-6
1078 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1079 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1080 to implement comparative methods with an autocorrelation approach.
1082 o A new data set describing some life history traits of Carnivores
1088 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1093 o When plotting a tree with plot.phylo(), the new default of the
1094 option `label.offset' is now 0, so the labels are always visible.
1098 CHANGES IN APE VERSION 1.2-5
1103 o The new function bd.ext() fits a birth-death model with combined
1104 phylogenetic and taxonomic data, and estimates the corresponding
1105 speciation and extinction rates.
1110 o The package gee is no more required by ape but only suggested
1111 since only the function compar.gee() calls gee.
1115 CHANGES IN APE VERSION 1.2-4
1120 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1121 and lines.popsize) implementing a new approach for inferring the
1122 demographic history from genealogies using a reversible jump
1123 MCMC have been introduced.
1125 o The unit of time in the skyline plot and in the new plots can
1126 now be chosen to be actual years, rather than substitutions.
1130 CHANGES IN APE VERSION 1.2-3
1135 o The new function rtree() generates a random binary tree with or
1136 without branch lengths.
1138 o Two new functions for drawing lineages-through-time (LTT) plots
1139 are provided: ltt.lines() adds a LTT curve to an existing plot,
1140 and mltt.plot() does a multiple LTT plot giving several trees as
1141 arguments (see `?ltt.plot' for details).
1146 o Some taxon names made R crashing when calling as.phylo.hclust():
1149 o dist.dna() returned an error with two identical DNA sequences
1150 (only using the Jukes-Cantor method returned 0): this is fixed.
1155 o The function dist.phylo() has been re-written using a different
1156 algorithm: it is now about four times faster.
1158 o The code of branching.times() has been improved: it is now about
1163 CHANGES IN APE VERSION 1.2-2
1168 o The new function seg.sites() finds the segregating sites in a
1169 sample of DNA sequences.
1174 o A bug introduced in read.tree() and in read.nexus() with version
1177 o A few errors were corrected and a few examples were added in the
1182 CHANGES IN APE VERSION 1.2-1
1187 o plot.phylo() can now draw the edge of the root of a tree if it
1188 has one (see the new option `root.edge', its default is FALSE).
1193 o A bug was fixed in read.nexus(): files with semicolons inside
1194 comment blocks were not read correctly.
1196 o The behaviour of read.tree() and read.nexus() was corrected so
1197 that tree files with badly represented root edges (e.g., with
1198 an extra pair of parentheses, see the help pages for details)
1199 are now correctly represented in the object of class "phylo";
1200 a warning message is now issued.
1204 CHANGES IN APE VERSION 1.2
1209 o plot.phylo() has been completely re-written and offers several
1210 new functionalities. Three types of trees can now be drawn:
1211 phylogram (as previously), cladogram, and unrooted tree; in
1212 all three types the branch lengths can be drawn using the edge
1213 lengths of the phylogeny or not (e.g., if the latter is absent).
1214 The vertical position of the nodes can be adjusted with two
1215 choices (see option `node.pos'). The code has been re-structured,
1216 and two new functions (potentially useful for developpers) are
1217 documented separately: node.depth.edgelength() and node.depth();
1218 see the respective help pages for details.
1220 o The new function zoom() allows to explore very large trees by
1221 focusing on a small portion of it.
1223 o The new function yule() fits by maximum likelihood the Yule model
1224 (birth-only process) to a phylogenetic tree.
1226 o Support for writing DNA sequences in FASTA format has been
1227 introduced in write.dna() (support for reading sequences in
1228 this format was introduced in read.dna() in version 1.1-2).
1229 The function has been completely re-written, fixing some bugs
1230 (see below); the default behaviour is no more to display the
1231 sequences on the standard output. Several options have been
1232 introduced to control the sequence printing in a flexible
1233 way. The help page has been extended.
1235 o A new data set is included: a supertree of bats in NEXUS format.
1240 o In theta.s(), the default of the option `variance' has
1241 been changed to `FALSE' (as was indicated in the help page).
1243 o Several bugs were fixed in the code of all.equal.phylo().
1245 o Several bugs were fixed in write.dna(), particularly this
1246 function did not work with `format = "interleaved"'.
1248 o Various errors were corrected in the help pages.
1253 o The argument names of as.hclust.phylo() have been changed
1254 from "(phy)" to "(x, ...)" to conform to the definition of
1255 the corresponding generic function.
1257 o gamma.stat() has been renamed gammaStat() to avoid confusion
1258 since gamma() is a generic function.
1262 CHANGES IN APE VERSION 1.1-3
1267 o base.freq() previously did not return a value of 0 for
1268 bases absent in the data (e.g., a vector of length 3 was
1269 returned if one base was absent). This is now fixed (a
1270 vector of length 4 is always returned).
1272 o Several bugs were fixed in read.nexus(), including that this
1273 function did not work in this absence of a "TRANSLATE"
1274 command in the NEXUS file, and that the commands were
1279 CHANGES IN APE VERSION 1.1-2
1284 o The Tamura and Nei (1993) model of DNA distance is now implemented
1285 in dist.dna(): five models are now available in this function.
1287 o A new data set is included: a set of 15 sequences of the
1288 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1294 o A bug in read.nexus() was fixed.
1296 o read.dna() previously did not work correctly in most cases.
1297 The function has been completely re-written and its help page
1298 has been considerably extended (see ?read.dna for details).
1299 Underscores (_) in taxon names are no more replaced with
1300 spaces (this behaviour was undocumented).
1302 o A bug was fixed in write.dna().
1306 CHANGES IN APE VERSION 1.1-1
1311 o A bug in read.tree() introduced in APE 1.1 was fixed.
1313 o A bug in compar.gee() resulted in an error when trying to fit
1314 a model with `family = "binomial"'. This is now fixed.
1318 CHANGES IN APE VERSION 1.1
1323 o The Klastorin (1982) method as suggested by Misawa and Tajima
1324 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1325 on the basis of phylogenetic trees has been implemented (see
1326 the function klastorin()).
1328 o Functions have been added to convert APE's "phylo" objects in
1329 "hclust" cluster objects and vice versa (see the help page of
1330 as.phylo for details).
1332 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1333 are introduced for the estimation of absolute evolutionary rates
1334 (ratogram) and dated clock-like trees (chronogram) from
1335 phylogenetic trees using the non-parametric rate smoothing approach
1336 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1338 o A summary method is now provided printing a summary information on a
1339 phylogenetic tree with, for instance, `summary(tree)'.
1341 o The behaviour of read.tree() was changed so that all spaces and
1342 tabulations in tree files are now ignored. Consequently, spaces in tip
1343 labels are no more allowed. Another side effect is that read.nexus()
1344 now does not replace the underscores (_) in tip labels with spaces
1345 (this behaviour was undocumented).
1347 o The function plot.phylo() has a new option (`underscore') which
1348 specifies whether the underscores in tip labels should be written on
1349 the plot as such or replaced with spaces (the default).
1351 o The function birthdeath() now computes 95% confidence intervals of
1352 the estimated parameters using profile likelihood.
1354 o Three new data sets are included: a gene tree estimated from 36
1355 landplant rbcL sequences, a gene tree estimated from 32 opsin
1356 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1361 o A bug was fixed in dist.gene() where nothing was returned.
1363 o A bug in plot.mst() was fixed.
1365 o A bug in vcv.phylo() resulted in false correlations when the
1366 option `cor = TRUE' was used (now fixed).
1370 CHANGES IN APE VERSION 1.0
1375 o Two new functions, read.dna() and write.dna(), read/write in a file
1376 DNA sequences in interleaved or in sequential format.
1378 o Two new functions, read.nexus() and write.nexus(), read/write trees
1381 o The new function bind.tree() allows to bind two trees together,
1382 possibly handling root edges to give internal branches.
1384 o The new function drop.tip() removes the tips in a phylogenetic tree,
1385 and trims (or not) the corresponding internal branches.
1387 o The new function is.ultrametric() tests if a tree is ultrametric.
1389 o The function plot.phylo() has more functionalities such as drawing the
1390 branches with different colours and/or different widths, showing the
1391 node labels, controling the position and font of the labels, rotating
1392 the labels, and controling the space around the plot.
1394 o The function read.tree() can now read trees with no branch length,
1395 such as "(a,b),c);". Consequently, the element `edge.length' in
1396 objects of class "phylo" is now optional.
1398 o The function write.tree() has a new default behaviour: if the default
1399 for the option `file' is used (i.e. file = ""), then a variable of
1400 mode character containing the tree in Newick format is returned which
1401 can thus be assigned (e.g., tree <- write.tree(phy)).
1403 o The function read.tree() has a new argument `text' which allows
1404 to read the tree in a variable of mode character.
1406 o A new data set is included: the phylogenetic relationships among
1407 the orders of birds from Sibley and Ahlquist (1990).
1411 CHANGES IN APE VERSION 0.2-1
1416 o Several bugs were fixed in the help pages.
1420 CHANGES IN APE VERSION 0.2
1425 o The function write.tree() writes phylogenetic trees (objects of class
1426 "phylo") in an ASCII file using the Newick parenthetic format.
1428 o The function birthdeath() fits a birth-death model to branching times
1429 by maximum likelihood, and estimates the corresponding speciation and
1432 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1435 o The function is.binary.tree() tests whether a phylogeny is binary.
1437 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1438 as well as some methods are introduced.
1440 o Several functions, including some generics and methods, for computing
1441 skyline plot estimates (classic and generalized) of effective
1442 population size through time are introduced and replace the function
1443 skyline.plot() in version 0.1.
1445 o Two data sets are now included: the phylogenetic relationships among
1446 the families of birds from Sibley and Ahlquist (1990), and an
1447 estimated clock-like phylogeny of HIV sequences sampled in the
1448 Democratic Republic of Congo.
1451 DEPRECATED & DEFUNCT
1453 o The function skyline.plot() in ape 0.1 has been deprecated and
1454 replaced by more elaborate functions (see above).
1459 o Two important bugs were fixed in plot.phylo(): phylogenies with
1460 multichotomies not at the root or not with only terminal branches,
1461 and phylogenies with a single node (i.e. only terminal branches)
1462 did not plot. These trees should be plotted correctly now.
1464 o Several bugs were fixed in diversi.time() in the computation of
1467 o Various errors were corrected in the help pages.
projects / ape.git / blob