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.
9 o mltt.plot() has now an option 'log' used in the same way
10 than in plot.default()
15 o mltt.plot() failed to display the legend with an unnamed
18 o nodelabels() with pies now correcly uses the argument
19 'cex' to draw symbols of different sizes (which has
20 worked already for thermometers).
25 o The argument 'family' of compar.gee() can now be a function
26 as well as a character string.
30 CHANGES IN APE VERSION 2.1-1
35 o The new function rmtree generates lists of random trees.
37 o rcoal() now generates a genuine coalescent tree by default
38 (thanks to Vladimir Minin for the code).
43 o nuc.div() returned an incorrect value with the default
44 pairwise.deletion = FALSE.
49 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
50 have been improved so that they are stabler and faster.
52 o R packages used by ape are now loaded silently; lattice and gee
53 are loaded only when needed.
57 CHANGES IN APE VERSION 2.1
62 o The new function identify.phylo identifies clades on a plotted
65 o It is now possible to subset a list of trees (object of class
66 "multiPhylo") with "[" while keeping its class correct.
68 o The new function as.DNAbin.alignment converts DNA sequences
69 stored in the "alignment" format of the package seqinr into
70 an object of class "DNAbin".
72 o The new function weight.taxo2 helps to build similarity matrices
73 given two taxonomic levels (usually called by other functions).
75 o write.tree() can now take a list of trees (class "multiPhylo")
78 o plot.correlogram() and plot.correlogramList() have been
79 improved, and gain several options (see the help page for
80 details). A legend is now plotted by default.
85 o dist.dna() returned some incorrect values with `model = "JC69"'
86 and `pairwise.deletion = TRUE'. This affected only the
87 distances involving sequences with missing values. (Thanks
88 to Bruno Toupance for digging this bug out.)
90 o write.tree() failed with some trees: this is fixed by removing
91 the `multi.line' option (trees are now always printed on a
94 o read.nexus() did not correctly detect trees with multiple root
95 edges (see OTHER CHANGES).
100 o The code of mlphylo() has almost entirely rewritten, and should
101 much stabler now. The options have been also greatly simplified
102 (see ?mlphylo and ?DNAmodel for details).
104 o The internal function nTips has been renamed klastorin_nTips.
106 o The code of is.ultrametric() contained redundancies and has
109 o The code of Moran.I() and of correlogram.formula() have been
112 o read.tree() and read.nexus() now return an error when trying to
113 read a tree with multiple root edges (see BUG FIXES). The
114 correction applied in previous version did not work in all
117 o The class c("multi.tree", "phylo") has been renamed
123 o There is now a vignette in ape: see vignette("MoranI", "ape").
128 o as.matching() and as.phylo.matching() do not support branch
131 o correlogram.phylo() and discrete.dist() have been removed.
135 CHANGES IN APE VERSION 2.0-2
140 o The new function matexpo computes the exponential of a square
143 o The new function unique.multi.tree removes duplicate trees from
146 o yule() has a new option `use.root.edge = FALSE' that specifies
147 to ignore, by default, the root edge of the tree if it exists.
152 o which.edge() failed when the index of a single terminal edge was
155 o In diversi.time(), the values returned for model C were
158 o A bug was fixed in yule() that affected the calculation of the
159 likelihood in the presence of ties in the branching times.
161 o There was a bug in the C function mat_expo4x4 affecting the
162 calculations of the transition probabilities for models HKY and
165 o A small bug was fixed in as.matrix.DNAbin (thanks to James
168 o rtree() did not `shuffle' the tip labels by default, so only a
169 limited number of labelled topologies could be generated.
173 CHANGES IN APE VERSION 2.0-1
178 o The three new functions bionj, fastme.ols, and fastme.bal
179 perform phylogeny estimation by the BIONJ and fastME methods in
180 OLS and balanced versions. This is a port to R of previous
181 previous programs done by Vincent Lefort.
183 o The new function chronoMPL performs molecular dating with the
184 mean path lengths method of Britton et al. (2002, Mol. Phyl.
187 o The new function rotate, contributed by Christoph Heibl, swaps
188 two clades connected to the same node. It works also with
189 multichotomous nodes.
191 o The new `method' as.matrix.DNAbin() may be used to convert
192 easily DNA sequences stored in a list into a matrix while
193 keeping the names and the class.
198 o chronopl() failed when some branch lengths were equal to zero:
199 an error message is now returned.
201 o di2multi() failed when there was a series of consecutive edges
206 CHANGES IN APE VERSION 1.10-2
211 o plot.phylo() can now plot circular trees: the option is type =
212 "fan" or type = "f" (to avoid the ambiguity with type = "c").
214 o prop.part() has a new option `check.labels = FALSE' which allows
215 to considerably speed-up the calculations of bipartitions. As a
216 consequence, calculations of bootstrap values with boot.phylo()
217 should be much faster.
222 o read.GenBank() did not return correctly the list of species as
223 from ape 1.10: this is fixed in this version
225 o Applying as.phylo() on a tree of class "phylo" failed: the
226 object is now returned unchanged.
230 CHANGES IN APE VERSION 1.10-1
235 o The three new functions Ntip, Nnode, and Nedge return, for a
236 given tree, the number of tips, nodes, or edges, respectively.
241 o read.nexus() did not set correctly the class of the returned
242 object when reading multiple trees.
244 o mllt.plot() failed with objects of class c("multi.tree",
247 o unroot() did not work correctly in most cases.
249 o reorder.phylo() made R freeze in some occasions.
251 o Plotting a tree in pruningwise order failed.
253 o When plotting an unrooted tree, the tip labels where not all
254 correctly positioned if the option `cex' was used.
258 CHANGES IN APE VERSION 1.10
263 o Five new `method' functions have been introduced to manipulate
264 DNA sequences in binary format (see below).
266 o Three new functions have been introduced to convert between the
267 new binary and the character formats.
269 o The new function as.alignment converts DNA sequences stored as
270 single characters into the class "alignment" used by the package
273 o read.dna() and read.GenBank() have a new argument `as.character'
274 controlling whether the sequences are returned in binary format
280 o root() failed when the tree had node labels: this is fixed.
282 o plot.phylo() did not correctly set the limits on the y-axis with
283 the default setting: this is fixed.
285 o dist.dna() returned a wrong result for the LogDet, paralinear,
286 and BH87 models with `pairwise.deletion = TRUE'.
291 o DNA sequences are now internally stored in a binary format. See
292 the document "A Bit-Level Coding Scheme for Nucleotides" for the
293 details. Most functions analyzing DNA functions have been
294 modified accordingly and are now much faster (dist.dna is now
295 ca. 60 times faster).
299 CHANGES IN APE VERSION 1.9-4
304 o A bug was fixed in edgelabels().
306 o as.phylo.hclust() did not work correctly when the object of
307 class "hclust" has its labels set to NULL: the returned tree has
308 now its tip labels set to "1", "2", ...
310 o consensus could fail if some tip labels are a subset of others
311 (e.g., "a" and "a_1"): this is now fixed.
313 o mlphylo() failed in most cases if some branch lengths of the
314 initial tree were greater than one: an error message is now
317 o mlphylo() failed in most cases when estimating the proportion of
318 invariants: this is fixed.
322 CHANGES IN APE VERSION 1.9-3
327 o The new function edgelabels adds labels on the edge of the tree
328 in the same way than nodelabels or tiplabels.
333 o multi2di() did not handle correctly branch lengths with the
334 default option `random = TRUE': this is now fixed.
336 o A bug was fixed in nuc.div() when using pairwise deletions.
338 o A bug occurred in the analysis of bipartitions with large
339 numbers of large trees, with consequences on prop.part,
340 prop.clades, and boot.phylo.
342 o The calculation of the Billera-Holmes-Vogtmann distance in
343 dist.topo was wrong: this has been fixed.
347 CHANGES IN APE VERSION 1.9-2
352 o The new function ladderize reorganizes the internal structure of
353 a tree to plot them left- or right-ladderized.
355 o The new function dist.nodes computes the patristic distances
356 between all nodes, internal and terminal, of a tree. It replaces
357 the option `full = TRUE' of cophenetic.phylo (see below).
362 o A bug was fixed in old2new.phylo().
364 o Some bugs were fixed in chronopl().
366 o The edge colours were not correctly displayed by plot.phylo
367 (thank you to Li-San Wang for the fix).
369 o cophenetic.phylo() failed with multichotomous trees: this is
375 o read.dna() now returns the sequences in a matrix if they are
376 aligned (interleaved or sequential format). Sequences in FASTA
377 format are still returned in a list.
379 o The option `full' of cophenetic.phylo() has been removed because
380 it could not be used from the generic.
385 o rotate() has been removed; this function did not work correctly
390 CHANGES IN APE VERSION 1.9-1
395 o Trees with a single tip were not read correctly in R as the
396 element `Nnode' was not set: this is fixed.
398 o unroot() did not set correctly the number of nodes of the
399 unrooted tree in most cases.
401 o read.GenBank() failed when fetching very long sequences,
402 particularly of the BX-series.
404 o A bug was introduced in read.tree() with ape 1.9: it has been
409 CHANGES IN APE VERSION 1.9
414 o There are two new print `methods' for trees of class "phylo" and
415 lists of trees of class "multi.tree", so that they are now
416 displayed in a compact and informative way.
418 o There are two new functions, old2new.phylo and new2old.phylo,
419 for converting between the old and new coding of the class
422 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
423 LogDet ("logdet"), and paralinear ("paralin").
425 o compute.brlen() has been extended: several methods are now
426 available to compute branch lengths.
428 o write.dna() can now handle matrices as well as lists.
433 o cophenetic.phylo() sometimes returned a wrong result with
434 multichotomous trees: this is fixed.
436 o rotate() failed when a single tip was specified: the tree is now
439 o ace() did not return the correct index matrix with custom
440 models: this is fixed.
442 o multi2di() did not work correctly when resolving multichotomies
443 randomly: the topology was always the same, only the arrangement
444 of clades was randomized: this is fixed. This function now
445 accepts trees with no branch lengths.
447 o The output of diversi.gof() was blurred by useless prints when a
448 user distribution was specified. This has been corrected, and
449 the help page of this function has been expanded.
454 o The internal structure of the class "phylo" has been changed:
455 see the document "Definition of Formats for Coding Phylogenetic
456 Trees in R" for the details. In addition, the code of most
457 functions has been improved.
459 o Several functions have been improved by replacing some R codes
460 by C codes: pic, plot.phylo, and reorder.phylo.
462 o There is now a citation information: see citation("ape") in R.
464 o write.tree() now does not add extra 0's to branch lengths so
465 that 1.23 is printed "1.23" by default, not "1.2300000000".
467 o The syntax of bind.tree() has been simplified. This function now
468 accepts trees with no branch lengths, and handles correctly node
471 o The option `as.numeric' of mrca() has been removed.
473 o The unused options `format' and `rooted' of read.tree() have
476 o The unused option `format' of write.tree() has been removed.
478 o The use of node.depth() has been simplified.
482 CHANGES IN APE VERSION 1.8-5
487 o Two new functions read.nexus.data() and write.nexus.data(),
488 contributed by Johan Nylander, allow to read and write molecular
489 sequences in NEXUS files.
491 o The new function reorder.phylo() reorders the internal structure
492 of a tree of class "phylo". It is used as the generic, e.g.,
495 o read.tree() and read.nexus() can now read trees with a single
498 o The new data set `cynipids' supplies a set of protein sequences
504 o The code of all.equal.phylo() has been completely rewritten
505 (thanks to Benoît Durand) which fixes several bugs.
507 o read.tree() and read.nexus() now checks the labels of the tree
508 to remove or substitute any characters that are illegal in the
509 Newick format (parentheses, etc.)
511 o A negative P-value could be returned by mantel.test(): this is
516 CHANGES IN APE VERSION 1.8-4
521 o The new function sh.test() computes the Shimodaira-
524 o The new function collapse.singles() removes the nodes with a
525 single descendant from a tree.
527 o plot.phylo() has a new argument `tip.color' to specify the
530 o mlphylo() has now an option `quiet' to control the display of
531 the progress of the analysis (the default is FALSE).
536 o read.dna() did not read correctly sequences in sequential format
537 with leading alignment gaps "-": this is fixed.
539 o ace() returned a list with no class so that the generic
540 functions (anova, logLik, ...) could not be used directly. This
541 is fixed as ace() now returns an object of class "ace".
543 o anova.ace() had a small bug when computing the number of degrees
544 of freedom: this is fixed.
546 o mlphylo() did not work when the sequences were in a matrix or
547 a data frame: this is fixed.
549 o rtree() did not work correctly when trying to simulate an
550 unrooted tree with two tips: an error message is now issued.
555 o The algorithm of rtree() has been changed: it is now about 40,
556 100, and 130 times faster for 10, 100, and 1000 tips,
561 CHANGES IN APE VERSION 1.8-3
566 o There are four new `method' functions to be used with the
567 results of ace(): logLik(), deviance(), AIC(), and anova().
569 o The plot method of phymltest has two new arguments: `main' to
570 change the title, and `col' to control the colour of the
571 segments showing the AIC values.
573 o ace() has a new argument `ip' that gives the initial values used
574 in the ML estimation with discrete characters (see the examples
575 in ?ace). This function now returns a matrix giving the indices
576 of the estimated rates when analysing discrete characters.
578 o nodelabels() and tiplabels() have a new argument `pie' to
579 represent proportions, with any number of categories, as
580 piecharts. The use of the option `thermo' has been improved:
581 there is now no limitation on the number of categories.
586 o mlphylo() did not work with more than two partitions: this is
589 o root() failed if the proposed outgroup was already an outgroup
590 in the tree: this is fixed.
592 o The `col' argument in nodelabels() and tiplabels() was not
593 correctly passed when `text' was used: this is fixed.
595 o Two bugs were fixed in mlphylo(): parameters were not always
596 correctly output, and the estimation failed in some cases.
598 o plot.phylo() was stuck when given a tree with a single tip: this
599 is fixed and a message error is now returned.
601 o An error was corrected in the help page of gammaStat regarding
602 the calculation of P-values.
604 o Using gls() could crash R when the number of species in the tree
605 and in the variables were different: this is fixed.
609 CHANGES IN APE VERSION 1.8-2
614 o The new function mlphylo() fits a phylogenetic tree by maximum
615 likelihood from DNA sequences. Its companion function DNAmodel()
616 is used to define the substitution model which may include
617 partitioning. There are methods for logLik(), deviance(), and
618 AIC(), and the summary() method has been extended to display in
619 a friendly way the results of this model fitting. Currently, the
620 functionality is limited to estimating the substitution and
621 associated parameters and computing the likelihood.
623 o The new function drop1.compar.gee (used as, e.g., drop1(m))
624 tests for single effects in GEE-based comparative method. A
625 warning message is printed if there is not enough degrees of
631 o An error message was sometimes issued by plot.multi.tree(),
632 though with no consequence.
636 CHANGES IN APE VERSION 1.8-1
641 o There is a new plot method for lists of trees (objects of class
642 "multi.tree"): it calls plot.phylo() internally and is
643 documented on the same help page.
648 o A bug was fixed in the C code that analyzes bipartitions: this
649 has impact on several functions like prop.part, prop.clades,
650 boot.phylo, or consensus.
652 o root() did not work correctly when the specified outgroup had
653 more than one element: this is fixed.
655 o dist.dna() sometimes returned a warning inappropriately: this
658 o If the distance object given to nj() had no rownames, nj()
659 returned a tree with no tip labels: it now returns tips labelled
660 "1", "2", ..., corresponding to the row numbers.
665 o nj() has been slightly changed so that tips with a zero distance
666 are first aggregated with zero-lengthed branches; the usual NJ
667 procedure is then performed on a distance matrix without 0's.
671 CHANGES IN APE VERSION 1.8
676 o The new function chronopl() estimates dates using the penalized
677 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
679 o The new function consensus() calculates the consensus tree of a
682 o The new function evolve.phylo() simulates the evolution of
683 continuous characters along a phylogeny under a Brownian model.
685 o The new plot method for objects of class "ancestral" displays a
686 tree together with ancestral values, as returned by the above
689 o The new function as.phylo.formula() returns a phylogeny from a
690 set of nested taxonomic variables given as a formula.
692 o The new function read.caic() reads trees in CAIC format.
694 o The new function tiplabels() allows to add labels to the tips
695 of a tree using text or plotting symbols in a flexible way.
697 o The new function unroot() unroots a phylogeny.
699 o multi2di() has a new option, `random', which specifies whether
700 to resolve the multichotomies randomly (the default) or not.
702 o prop.part() now returns an object of class "prop.part" for which
703 there are print (to display a partition in a more friendly way)
704 and summary (to extract the numbers) methods.
706 o plot.phylo() has a new option, `show.tip.label', specifying
707 whether to print the labels of the tips. The default is TRUE.
709 o The code of nj() has been replaced by a faster C code: it is now
710 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
713 o write.nexus() now writes whether a tree is rooted or not.
718 o Two bugs have been fixed in root(): unrooted trees are now
719 handled corretly, and node labels are now output normally.
721 o A bug was fixed in phymltest(): the executable couldn't be found
724 o Three bug have been fixed in ace(): computing the likelihood of
725 ancestral states of discrete characters failed, custom models
726 did not work, and the function failed with a null gradient (a
727 warning message is now returned; this latter bug was also
728 present in yule.cov() as well and is now fixed).
730 o pic() hanged out when missing data were present: a message error
733 o A small bug was fixed in dist.dna() where the gamma correction
734 was not always correctly dispatched.
736 o plot.phylo() plotted correctly the root edge only when the tree
737 was plotted rightwards: this works now for all directions.
742 o dist.taxo() has been renamed as weight.taxo().
744 o Various error and warning messages have been improved.
748 CHANGES IN APE VERSION 1.7
751 o The new function ace() estimates ancestral character states for
752 continuous characters (with ML, GLS, and contrasts methods), and
753 discrete characters (with ML only) for any number of states.
755 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
756 of directional evolution for continuous characters. The user
757 specifies the node(s) of the tree where the character optimum
760 o The new function is.rooted() tests whether a tree (of class
763 o The new function rcoal() generates random ultrametric trees with
764 the possibility to specify the function that generates the
765 inter-nodes distances.
767 o The new function mrca() gives for all pairs of tips in a tree
768 (and optionally nodes too) the most recent common ancestor.
770 o nodelabels() has a new option `thermo' to plot proportions (up
771 to three classes) on the nodes of a tree.
773 o rtree() has been improved: it can now generate rooted or
774 unrooted trees, and the mathematical function that generates the
775 branch lengths may be specified by the user. The tip labels may
776 be given directly in the call to rtree. The limit cases (n = 2,
777 3) are now handled correctly.
779 o dist.topo() has a new argument `method' with two choices: "PH85"
780 for Penny and Henny's method (already available before and now
781 the default), and "BHV01" for the geometric distance by Billera
782 et al. (2001, Adv. Appl. Math. 27:733).
784 o write.tree() has a new option, `digits', which specifies the
785 number of digits to be printed in the Newick tree. By default
786 digits = 10. The numbers are now always printed in decimal form
787 (i.e., 1.0e-1 is now avoided).
789 o dist.dna() can now compute the raw distances between pairs of
790 DNA sequences by specifying model = "raw".
792 o dist.phylo() has a new option `full' to possibly compute the
793 distances among all tips and nodes of the tree. The default if
799 o Several bugs were fixed in all.equal.phylo().
801 o dist.dna() did not handle correctly gaps ("-") in alignments:
802 they are now considered as missing data.
804 o rotate() did not work if the tips were not ordered: this is
807 o mantel.test() returned NA in some special cases: this is fixed
808 and the function has been improved and is now faster.
810 o A bug was fixed in diversi.gof() where the calculation of A² was
813 o cherry() did not work correctly under some OSs (mainly Linux):
816 o is.binary.tree() has been modified so that it works with both
817 rooted and unrooted trees.
819 o The documentation of theta.s() was not correct: this has been
822 o plot.mst() did not work correctly: this is fixed.
826 CHANGES IN APE VERSION 1.6
831 o The new function dist.topo() computes the topological distances
834 o The new function boot.phylo() performs a bootstrap analysis on
835 phylogeny estimation.
837 o The new functions prop.part() and prop.clades() analyse
838 bipartitions from a series of trees.
843 o read.GenBank() now uses the EFetch utility of NCBI instead of
844 the usual Web interface: it is now much faster (e.g., 12 times
845 faster to retrieve 8 sequences, 37 times for 60 sequences).
850 o Several bugs were fixed in read.dna().
852 o Several bugs were fixed in diversi.time().
854 o is.binary.tree() did not work correctly if the tree has no edge
855 lengths: this is fixed.
857 o drop.tip() did not correctly propagated the `node.label' of a
862 CHANGES IN APE VERSION 1.5
867 o Two new functions, as.matching.phylo() and as.phylo.matching(),
868 convert objects between the classes "phylo" and "matching". The
869 latter implements the representation of binary trees introduced by
870 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
871 as.matching() has been introduced as well.
873 o Two new functions, multi2di() and di2multi(), allow to resolve
874 and collapse multichotomies with branches of length zero.
876 o The new function nuc.div() computes the nucleotide diversity
877 from a sample a DNA sequences.
879 o dist.dna() has been completely rewritten with a much faster
880 (particularly for large data sets) C code. Eight models are
881 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
882 option `method' has been renamed `model'). Computation of variance
883 is available for all models. A gamma-correction is possible for
884 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
885 to remove sites with missing data on a pairwise basis. The option
886 `GCcontent' has been removed.
888 o read.GenBank() has a new option (species.names) which specifies
889 whether to return the species names of the organisms in addition
890 to the accession numbers of the sequences (this is the default
893 o write.nexus() can now write several trees in the same NEXUS file.
895 o drop.tip() has a new option `root.edge' that allows to specify the
896 new root edge if internal branches are trimmed.
901 o as.phylo.hclust() failed if some labels had parentheses: this
904 o Several bugs were fixed in all.equal.phylo(). This function now
905 returns the logical TRUE if the trees are identical but with
906 different representations (a report was printed previously).
908 o read.GenBank() did not correctly handle ambiguous base codes:
914 o birthdeath() now returns an object of class "birthdeath" for
915 which there is a print method.
919 CHANGES IN APE VERSION 1.4
924 o The new function nj() performs phylogeny estimation with the
925 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
928 o The new function which.edge() identifies the edges of a tree
929 that belong to a group specified as a set of tips.
931 o The new function as.phylo.phylog() converts an object of class
932 "phylog" (from the package ade4) into an object of class
935 o The new function axisPhylo() draws axes on the side of a
938 o The new function howmanytrees() calculates the number of trees
939 in different cases and giving a number of tips.
941 o write.tree() has a new option `multi.line' (TRUE by default) to
942 write a Newick tree on several lines rather than on a single
945 o The functionalities of zoom() have been extended. Several
946 subtrees can be visualized at the same time, and they are marked
947 on the main tree with colors. The context of the subtrees can be
948 marked with the option `subtree' (see below).
950 o drop.tip() has a new option `subtree' (FALSE by default) which
951 specifies whether to output in the tree how many tips have been
954 o The arguments of add.scale.bar() have been redefined and have
955 now default values (see ?add.scale.bar for details). This
956 function now works even if the plotted tree has no edge length.
958 o plot.phylo() can now plot radial trees, but this does not take
959 edge lengths into account.
961 o In plot.phylo() with `type = "phylogram"', if the values of
962 `edge.color' and `edge.width' are identical for sister-branches,
963 they are propagated to the vertical line that link them.
968 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
969 crashing. This is fixed.
971 o In plot.phylo(), the options `edge.color' and `edge.width' are
972 now properly recycled; their default values are now "black" and
975 o A bug has been fixed in write.nexus().
980 o The function node.depth.edgelength() has been removed and
981 replaced by a C code.
985 CHANGES IN APE VERSION 1.3-1
990 o The new function nodelabels() allows to add labels to the nodes
991 of a tree using text or plotting symbols in a flexible way.
993 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
994 numeric values specifying the lower and upper limits on the x-
995 and y-axes. This allows to leave some space on any side of the
996 tree. If a single value is given, this is taken as the upper
1001 CHANGES IN APE VERSION 1.3
1006 o The new function phymltest() calls the software PHYML and fits
1007 28 models of DNA sequence evolution. There are a print method to
1008 display likelihood and AIC values, a summary method to compute
1009 the hierarchical likelihood ratio tests, and a plot method to
1010 display graphically the AIC values of each model.
1012 o The new function yule.cov() fits the Yule model with covariates,
1013 a model where the speciation rate is affected by several species
1014 traits through a generalized linear model. The parameters are
1015 estimated by maximum likelihood.
1017 o Three new functions, corBrownian(), corGrafen(), and
1018 corMartins(), compute the expected correlation structures among
1019 species given a phylogeny under different models of evolution.
1020 These can be used for GLS comparative phylogenetic methods (see
1021 the examples). There are coef() and corMatrix() methods and an
1022 Initialize.corPhyl() function associated.
1024 o The new function compar.cheverud() implements Cheverud et al.'s
1025 (1985; Evolution 39:1335) phylogenetic comparative method.
1027 o The new function varcomp() estimates variance components; it has
1030 o Two new functions, panel.superpose.correlogram() and
1031 plot.correlogramList(), allow to plot several phylogenetic
1034 o The new function node.leafnumber() computes the number of leaves
1035 of a subtree defined by a particular node.
1037 o The new function node.sons() gets all tags of son nodes from a
1040 o The new function compute.brlen() computes the branch lengths of
1041 a tree according to a specified method.
1043 o plot.phylo() has three new options: "cex" controls the size of
1044 the (tip and node) labels (thus it is no more needed to change
1045 the global graphical parameter), "direction" which allows to
1046 plot the tree rightwards, leftwards, upwards, or downwards, and
1047 "y.lim" which sets the upper limit on the y-axis.
1052 o Some functions which try to match tip labels and names of
1053 additional data (e.g. vector) are likely to fail if there are
1054 typing or syntax errors. If both series of names do not perfectly
1055 match, they are ignored and a warning message is now issued.
1056 These functions are bd.ext, compar.gee, pic. Their help pages
1057 have been clarified on this point.
1061 CHANGES IN APE VERSION 1.2-7
1066 o The new function root() reroots a phylogenetic tree with respect
1067 to a specified outgroup.
1069 o The new function rotate() rotates an internal branch of a tree.
1071 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1072 trees) controls the display of the tip labels in unrooted trees.
1073 This display has been greatly improved: the tip labels are now not
1074 expected to overlap with the tree (particularly if lab4ut =
1075 "axial"). In all cases, combining appropriate values of "lab4ut"
1076 and the font size (via "par(cex = )") should result in readable
1077 unrooted trees. See ?plot.phylo for some examples.
1079 o In drop.tip(), the argument `tip' can now be numeric or character.
1084 o drop.tip() did not work correctly with trees with no branch
1085 lengths: this is fixed.
1087 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1088 plotted with some line crossings: this is now fixed.
1092 CHANGES IN APE VERSION 1.2-6
1097 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1098 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1099 to implement comparative methods with an autocorrelation approach.
1101 o A new data set describing some life history traits of Carnivores
1107 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1112 o When plotting a tree with plot.phylo(), the new default of the
1113 option `label.offset' is now 0, so the labels are always visible.
1117 CHANGES IN APE VERSION 1.2-5
1122 o The new function bd.ext() fits a birth-death model with combined
1123 phylogenetic and taxonomic data, and estimates the corresponding
1124 speciation and extinction rates.
1129 o The package gee is no more required by ape but only suggested
1130 since only the function compar.gee() calls gee.
1134 CHANGES IN APE VERSION 1.2-4
1139 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1140 and lines.popsize) implementing a new approach for inferring the
1141 demographic history from genealogies using a reversible jump
1142 MCMC have been introduced.
1144 o The unit of time in the skyline plot and in the new plots can
1145 now be chosen to be actual years, rather than substitutions.
1149 CHANGES IN APE VERSION 1.2-3
1154 o The new function rtree() generates a random binary tree with or
1155 without branch lengths.
1157 o Two new functions for drawing lineages-through-time (LTT) plots
1158 are provided: ltt.lines() adds a LTT curve to an existing plot,
1159 and mltt.plot() does a multiple LTT plot giving several trees as
1160 arguments (see `?ltt.plot' for details).
1165 o Some taxon names made R crashing when calling as.phylo.hclust():
1168 o dist.dna() returned an error with two identical DNA sequences
1169 (only using the Jukes-Cantor method returned 0): this is fixed.
1174 o The function dist.phylo() has been re-written using a different
1175 algorithm: it is now about four times faster.
1177 o The code of branching.times() has been improved: it is now about
1182 CHANGES IN APE VERSION 1.2-2
1187 o The new function seg.sites() finds the segregating sites in a
1188 sample of DNA sequences.
1193 o A bug introduced in read.tree() and in read.nexus() with version
1196 o A few errors were corrected and a few examples were added in the
1201 CHANGES IN APE VERSION 1.2-1
1206 o plot.phylo() can now draw the edge of the root of a tree if it
1207 has one (see the new option `root.edge', its default is FALSE).
1212 o A bug was fixed in read.nexus(): files with semicolons inside
1213 comment blocks were not read correctly.
1215 o The behaviour of read.tree() and read.nexus() was corrected so
1216 that tree files with badly represented root edges (e.g., with
1217 an extra pair of parentheses, see the help pages for details)
1218 are now correctly represented in the object of class "phylo";
1219 a warning message is now issued.
1223 CHANGES IN APE VERSION 1.2
1228 o plot.phylo() has been completely re-written and offers several
1229 new functionalities. Three types of trees can now be drawn:
1230 phylogram (as previously), cladogram, and unrooted tree; in
1231 all three types the branch lengths can be drawn using the edge
1232 lengths of the phylogeny or not (e.g., if the latter is absent).
1233 The vertical position of the nodes can be adjusted with two
1234 choices (see option `node.pos'). The code has been re-structured,
1235 and two new functions (potentially useful for developpers) are
1236 documented separately: node.depth.edgelength() and node.depth();
1237 see the respective help pages for details.
1239 o The new function zoom() allows to explore very large trees by
1240 focusing on a small portion of it.
1242 o The new function yule() fits by maximum likelihood the Yule model
1243 (birth-only process) to a phylogenetic tree.
1245 o Support for writing DNA sequences in FASTA format has been
1246 introduced in write.dna() (support for reading sequences in
1247 this format was introduced in read.dna() in version 1.1-2).
1248 The function has been completely re-written, fixing some bugs
1249 (see below); the default behaviour is no more to display the
1250 sequences on the standard output. Several options have been
1251 introduced to control the sequence printing in a flexible
1252 way. The help page has been extended.
1254 o A new data set is included: a supertree of bats in NEXUS format.
1259 o In theta.s(), the default of the option `variance' has
1260 been changed to `FALSE' (as was indicated in the help page).
1262 o Several bugs were fixed in the code of all.equal.phylo().
1264 o Several bugs were fixed in write.dna(), particularly this
1265 function did not work with `format = "interleaved"'.
1267 o Various errors were corrected in the help pages.
1272 o The argument names of as.hclust.phylo() have been changed
1273 from "(phy)" to "(x, ...)" to conform to the definition of
1274 the corresponding generic function.
1276 o gamma.stat() has been renamed gammaStat() to avoid confusion
1277 since gamma() is a generic function.
1281 CHANGES IN APE VERSION 1.1-3
1286 o base.freq() previously did not return a value of 0 for
1287 bases absent in the data (e.g., a vector of length 3 was
1288 returned if one base was absent). This is now fixed (a
1289 vector of length 4 is always returned).
1291 o Several bugs were fixed in read.nexus(), including that this
1292 function did not work in this absence of a "TRANSLATE"
1293 command in the NEXUS file, and that the commands were
1298 CHANGES IN APE VERSION 1.1-2
1303 o The Tamura and Nei (1993) model of DNA distance is now implemented
1304 in dist.dna(): five models are now available in this function.
1306 o A new data set is included: a set of 15 sequences of the
1307 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1313 o A bug in read.nexus() was fixed.
1315 o read.dna() previously did not work correctly in most cases.
1316 The function has been completely re-written and its help page
1317 has been considerably extended (see ?read.dna for details).
1318 Underscores (_) in taxon names are no more replaced with
1319 spaces (this behaviour was undocumented).
1321 o A bug was fixed in write.dna().
1325 CHANGES IN APE VERSION 1.1-1
1330 o A bug in read.tree() introduced in APE 1.1 was fixed.
1332 o A bug in compar.gee() resulted in an error when trying to fit
1333 a model with `family = "binomial"'. This is now fixed.
1337 CHANGES IN APE VERSION 1.1
1342 o The Klastorin (1982) method as suggested by Misawa and Tajima
1343 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1344 on the basis of phylogenetic trees has been implemented (see
1345 the function klastorin()).
1347 o Functions have been added to convert APE's "phylo" objects in
1348 "hclust" cluster objects and vice versa (see the help page of
1349 as.phylo for details).
1351 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1352 are introduced for the estimation of absolute evolutionary rates
1353 (ratogram) and dated clock-like trees (chronogram) from
1354 phylogenetic trees using the non-parametric rate smoothing approach
1355 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1357 o A summary method is now provided printing a summary information on a
1358 phylogenetic tree with, for instance, `summary(tree)'.
1360 o The behaviour of read.tree() was changed so that all spaces and
1361 tabulations in tree files are now ignored. Consequently, spaces in tip
1362 labels are no more allowed. Another side effect is that read.nexus()
1363 now does not replace the underscores (_) in tip labels with spaces
1364 (this behaviour was undocumented).
1366 o The function plot.phylo() has a new option (`underscore') which
1367 specifies whether the underscores in tip labels should be written on
1368 the plot as such or replaced with spaces (the default).
1370 o The function birthdeath() now computes 95% confidence intervals of
1371 the estimated parameters using profile likelihood.
1373 o Three new data sets are included: a gene tree estimated from 36
1374 landplant rbcL sequences, a gene tree estimated from 32 opsin
1375 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1380 o A bug was fixed in dist.gene() where nothing was returned.
1382 o A bug in plot.mst() was fixed.
1384 o A bug in vcv.phylo() resulted in false correlations when the
1385 option `cor = TRUE' was used (now fixed).
1389 CHANGES IN APE VERSION 1.0
1394 o Two new functions, read.dna() and write.dna(), read/write in a file
1395 DNA sequences in interleaved or in sequential format.
1397 o Two new functions, read.nexus() and write.nexus(), read/write trees
1400 o The new function bind.tree() allows to bind two trees together,
1401 possibly handling root edges to give internal branches.
1403 o The new function drop.tip() removes the tips in a phylogenetic tree,
1404 and trims (or not) the corresponding internal branches.
1406 o The new function is.ultrametric() tests if a tree is ultrametric.
1408 o The function plot.phylo() has more functionalities such as drawing the
1409 branches with different colours and/or different widths, showing the
1410 node labels, controling the position and font of the labels, rotating
1411 the labels, and controling the space around the plot.
1413 o The function read.tree() can now read trees with no branch length,
1414 such as "(a,b),c);". Consequently, the element `edge.length' in
1415 objects of class "phylo" is now optional.
1417 o The function write.tree() has a new default behaviour: if the default
1418 for the option `file' is used (i.e. file = ""), then a variable of
1419 mode character containing the tree in Newick format is returned which
1420 can thus be assigned (e.g., tree <- write.tree(phy)).
1422 o The function read.tree() has a new argument `text' which allows
1423 to read the tree in a variable of mode character.
1425 o A new data set is included: the phylogenetic relationships among
1426 the orders of birds from Sibley and Ahlquist (1990).
1430 CHANGES IN APE VERSION 0.2-1
1435 o Several bugs were fixed in the help pages.
1439 CHANGES IN APE VERSION 0.2
1444 o The function write.tree() writes phylogenetic trees (objects of class
1445 "phylo") in an ASCII file using the Newick parenthetic format.
1447 o The function birthdeath() fits a birth-death model to branching times
1448 by maximum likelihood, and estimates the corresponding speciation and
1451 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1454 o The function is.binary.tree() tests whether a phylogeny is binary.
1456 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1457 as well as some methods are introduced.
1459 o Several functions, including some generics and methods, for computing
1460 skyline plot estimates (classic and generalized) of effective
1461 population size through time are introduced and replace the function
1462 skyline.plot() in version 0.1.
1464 o Two data sets are now included: the phylogenetic relationships among
1465 the families of birds from Sibley and Ahlquist (1990), and an
1466 estimated clock-like phylogeny of HIV sequences sampled in the
1467 Democratic Republic of Congo.
1470 DEPRECATED & DEFUNCT
1472 o The function skyline.plot() in ape 0.1 has been deprecated and
1473 replaced by more elaborate functions (see above).
1478 o Two important bugs were fixed in plot.phylo(): phylogenies with
1479 multichotomies not at the root or not with only terminal branches,
1480 and phylogenies with a single node (i.e. only terminal branches)
1481 did not plot. These trees should be plotted correctly now.
1483 o Several bugs were fixed in diversi.time() in the computation of
1486 o Various errors were corrected in the help pages.
projects / ape.git / blob