1 CHANGES IN APE VERSION 2.1-1
6 o The new function rmtree generates lists of random trees.
8 o rcoal() now generates a genuine coalescent tree by default
9 (thanks to Vladimir Minin for the code).
14 o nuc.div() returned an incorrect value with the default
15 pairwise.deletion = FALSE.
20 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
21 have been improved so that they are stabler and faster.
23 o R packages used by ape are now loaded silently; lattice and gee
24 are loaded only when needed.
28 CHANGES IN APE VERSION 2.1
33 o The new function identify.phylo identifies clades on a plotted
36 o It is now possible to subset a list of trees (object of class
37 "multiPhylo") with "[" while keeping its class correct.
39 o The new function as.DNAbin.alignment converts DNA sequences
40 stored in the "alignment" format of the package seqinr into
41 an object of class "DNAbin".
43 o The new function weight.taxo2 helps to build similarity matrices
44 given two taxonomic levels (usually called by other functions).
46 o write.tree() can now take a list of trees (class "multiPhylo")
49 o plot.correlogram() and plot.correlogramList() have been
50 improved, and gain several options (see the help page for
51 details). A legend is now plotted by default.
56 o dist.dna() returned some incorrect values with `model = "JC69"'
57 and `pairwise.deletion = TRUE'. This affected only the
58 distances involving sequences with missing values. (Thanks
59 to Bruno Toupance for digging this bug out.)
61 o write.tree() failed with some trees: this is fixed by removing
62 the `multi.line' option (trees are now always printed on a
65 o read.nexus() did not correctly detect trees with multiple root
66 edges (see OTHER CHANGES).
71 o The code of mlphylo() has almost entirely rewritten, and should
72 much stabler now. The options have been also greatly simplified
73 (see ?mlphylo and ?DNAmodel for details).
75 o The internal function nTips has been renamed klastorin_nTips.
77 o The code of is.ultrametric() contained redundancies and has
80 o The code of Moran.I() and of correlogram.formula() have been
83 o read.tree() and read.nexus() now return an error when trying to
84 read a tree with multiple root edges (see BUG FIXES). The
85 correction applied in previous version did not work in all
88 o The class c("multi.tree", "phylo") has been renamed
94 o There is now a vignette in ape: see vignette("MoranI", "ape").
99 o as.matching() and as.phylo.matching() do not support branch
102 o correlogram.phylo() and discrete.dist() have been removed.
106 CHANGES IN APE VERSION 2.0-2
111 o The new function matexpo computes the exponential of a square
114 o The new function unique.multi.tree removes duplicate trees from
117 o yule() has a new option `use.root.edge = FALSE' that specifies
118 to ignore, by default, the root edge of the tree if it exists.
123 o which.edge() failed when the index of a single terminal edge was
126 o In diversi.time(), the values returned for model C were
129 o A bug was fixed in yule() that affected the calculation of the
130 likelihood in the presence of ties in the branching times.
132 o There was a bug in the C function mat_expo4x4 affecting the
133 calculations of the transition probabilities for models HKY and
136 o A small bug was fixed in as.matrix.DNAbin (thanks to James
139 o rtree() did not `shuffle' the tip labels by default, so only a
140 limited number of labelled topologies could be generated.
144 CHANGES IN APE VERSION 2.0-1
149 o The three new functions bionj, fastme.ols, and fastme.bal
150 perform phylogeny estimation by the BIONJ and fastME methods in
151 OLS and balanced versions. This is a port to R of previous
152 previous programs done by Vincent Lefort.
154 o The new function chronoMPL performs molecular dating with the
155 mean path lengths method of Britton et al. (2002, Mol. Phyl.
158 o The new function rotate, contributed by Christoph Heibl, swaps
159 two clades connected to the same node. It works also with
160 multichotomous nodes.
162 o The new `method' as.matrix.DNAbin() may be used to convert
163 easily DNA sequences stored in a list into a matrix while
164 keeping the names and the class.
169 o chronopl() failed when some branch lengths were equal to zero:
170 an error message is now returned.
172 o di2multi() failed when there was a series of consecutive edges
177 CHANGES IN APE VERSION 1.10-2
182 o plot.phylo() can now plot circular trees: the option is type =
183 "fan" or type = "f" (to avoid the ambiguity with type = "c").
185 o prop.part() has a new option `check.labels = FALSE' which allows
186 to considerably speed-up the calculations of bipartitions. As a
187 consequence, calculations of bootstrap values with boot.phylo()
188 should be much faster.
193 o read.GenBank() did not return correctly the list of species as
194 from ape 1.10: this is fixed in this version
196 o Applying as.phylo() on a tree of class "phylo" failed: the
197 object is now returned unchanged.
201 CHANGES IN APE VERSION 1.10-1
206 o The three new functions Ntip, Nnode, and Nedge return, for a
207 given tree, the number of tips, nodes, or edges, respectively.
212 o read.nexus() did not set correctly the class of the returned
213 object when reading multiple trees.
215 o mllt.plot() failed with objects of class c("multi.tree",
218 o unroot() did not work correctly in most cases.
220 o reorder.phylo() made R freeze in some occasions.
222 o Plotting a tree in pruningwise order failed.
224 o When plotting an unrooted tree, the tip labels where not all
225 correctly positioned if the option `cex' was used.
229 CHANGES IN APE VERSION 1.10
234 o Five new `method' functions have been introduced to manipulate
235 DNA sequences in binary format (see below).
237 o Three new functions have been introduced to convert between the
238 new binary and the character formats.
240 o The new function as.alignment converts DNA sequences stored as
241 single characters into the class "alignment" used by the package
244 o read.dna() and read.GenBank() have a new argument `as.character'
245 controlling whether the sequences are returned in binary format
251 o root() failed when the tree had node labels: this is fixed.
253 o plot.phylo() did not correctly set the limits on the y-axis with
254 the default setting: this is fixed.
256 o dist.dna() returned a wrong result for the LogDet, paralinear,
257 and BH87 models with `pairwise.deletion = TRUE'.
262 o DNA sequences are now internally stored in a binary format. See
263 the document "A Bit-Level Coding Scheme for Nucleotides" for the
264 details. Most functions analyzing DNA functions have been
265 modified accordingly and are now much faster (dist.dna is now
266 ca. 60 times faster).
270 CHANGES IN APE VERSION 1.9-4
275 o A bug was fixed in edgelabels().
277 o as.phylo.hclust() did not work correctly when the object of
278 class "hclust" has its labels set to NULL: the returned tree has
279 now its tip labels set to "1", "2", ...
281 o consensus could fail if some tip labels are a subset of others
282 (e.g., "a" and "a_1"): this is now fixed.
284 o mlphylo() failed in most cases if some branch lengths of the
285 initial tree were greater than one: an error message is now
288 o mlphylo() failed in most cases when estimating the proportion of
289 invariants: this is fixed.
293 CHANGES IN APE VERSION 1.9-3
298 o The new function edgelabels adds labels on the edge of the tree
299 in the same way than nodelabels or tiplabels.
304 o multi2di() did not handle correctly branch lengths with the
305 default option `random = TRUE': this is now fixed.
307 o A bug was fixed in nuc.div() when using pairwise deletions.
309 o A bug occurred in the analysis of bipartitions with large
310 numbers of large trees, with consequences on prop.part,
311 prop.clades, and boot.phylo.
313 o The calculation of the Billera-Holmes-Vogtmann distance in
314 dist.topo was wrong: this has been fixed.
318 CHANGES IN APE VERSION 1.9-2
323 o The new function ladderize reorganizes the internal structure of
324 a tree to plot them left- or right-ladderized.
326 o The new function dist.nodes computes the patristic distances
327 between all nodes, internal and terminal, of a tree. It replaces
328 the option `full = TRUE' of cophenetic.phylo (see below).
333 o A bug was fixed in old2new.phylo().
335 o Some bugs were fixed in chronopl().
337 o The edge colours were not correctly displayed by plot.phylo
338 (thank you to Li-San Wang for the fix).
340 o cophenetic.phylo() failed with multichotomous trees: this is
346 o read.dna() now returns the sequences in a matrix if they are
347 aligned (interleaved or sequential format). Sequences in FASTA
348 format are still returned in a list.
350 o The option `full' of cophenetic.phylo() has been removed because
351 it could not be used from the generic.
356 o rotate() has been removed; this function did not work correctly
361 CHANGES IN APE VERSION 1.9-1
366 o Trees with a single tip were not read correctly in R as the
367 element `Nnode' was not set: this is fixed.
369 o unroot() did not set correctly the number of nodes of the
370 unrooted tree in most cases.
372 o read.GenBank() failed when fetching very long sequences,
373 particularly of the BX-series.
375 o A bug was introduced in read.tree() with ape 1.9: it has been
380 CHANGES IN APE VERSION 1.9
385 o There are two new print `methods' for trees of class "phylo" and
386 lists of trees of class "multi.tree", so that they are now
387 displayed in a compact and informative way.
389 o There are two new functions, old2new.phylo and new2old.phylo,
390 for converting between the old and new coding of the class
393 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
394 LogDet ("logdet"), and paralinear ("paralin").
396 o compute.brlen() has been extended: several methods are now
397 available to compute branch lengths.
399 o write.dna() can now handle matrices as well as lists.
404 o cophenetic.phylo() sometimes returned a wrong result with
405 multichotomous trees: this is fixed.
407 o rotate() failed when a single tip was specified: the tree is now
410 o ace() did not return the correct index matrix with custom
411 models: this is fixed.
413 o multi2di() did not work correctly when resolving multichotomies
414 randomly: the topology was always the same, only the arrangement
415 of clades was randomized: this is fixed. This function now
416 accepts trees with no branch lengths.
418 o The output of diversi.gof() was blurred by useless prints when a
419 user distribution was specified. This has been corrected, and
420 the help page of this function has been expanded.
425 o The internal structure of the class "phylo" has been changed:
426 see the document "Definition of Formats for Coding Phylogenetic
427 Trees in R" for the details. In addition, the code of most
428 functions has been improved.
430 o Several functions have been improved by replacing some R codes
431 by C codes: pic, plot.phylo, and reorder.phylo.
433 o There is now a citation information: see citation("ape") in R.
435 o write.tree() now does not add extra 0's to branch lengths so
436 that 1.23 is printed "1.23" by default, not "1.2300000000".
438 o The syntax of bind.tree() has been simplified. This function now
439 accepts trees with no branch lengths, and handles correctly node
442 o The option `as.numeric' of mrca() has been removed.
444 o The unused options `format' and `rooted' of read.tree() have
447 o The unused option `format' of write.tree() has been removed.
449 o The use of node.depth() has been simplified.
453 CHANGES IN APE VERSION 1.8-5
458 o Two new functions read.nexus.data() and write.nexus.data(),
459 contributed by Johan Nylander, allow to read and write molecular
460 sequences in NEXUS files.
462 o The new function reorder.phylo() reorders the internal structure
463 of a tree of class "phylo". It is used as the generic, e.g.,
466 o read.tree() and read.nexus() can now read trees with a single
469 o The new data set `cynipids' supplies a set of protein sequences
475 o The code of all.equal.phylo() has been completely rewritten
476 (thanks to Benoît Durand) which fixes several bugs.
478 o read.tree() and read.nexus() now checks the labels of the tree
479 to remove or substitute any characters that are illegal in the
480 Newick format (parentheses, etc.)
482 o A negative P-value could be returned by mantel.test(): this is
487 CHANGES IN APE VERSION 1.8-4
492 o The new function sh.test() computes the Shimodaira-
495 o The new function collapse.singles() removes the nodes with a
496 single descendant from a tree.
498 o plot.phylo() has a new argument `tip.color' to specify the
501 o mlphylo() has now an option `quiet' to control the display of
502 the progress of the analysis (the default is FALSE).
507 o read.dna() did not read correctly sequences in sequential format
508 with leading alignment gaps "-": this is fixed.
510 o ace() returned a list with no class so that the generic
511 functions (anova, logLik, ...) could not be used directly. This
512 is fixed as ace() now returns an object of class "ace".
514 o anova.ace() had a small bug when computing the number of degrees
515 of freedom: this is fixed.
517 o mlphylo() did not work when the sequences were in a matrix or
518 a data frame: this is fixed.
520 o rtree() did not work correctly when trying to simulate an
521 unrooted tree with two tips: an error message is now issued.
526 o The algorithm of rtree() has been changed: it is now about 40,
527 100, and 130 times faster for 10, 100, and 1000 tips,
532 CHANGES IN APE VERSION 1.8-3
537 o There are four new `method' functions to be used with the
538 results of ace(): logLik(), deviance(), AIC(), and anova().
540 o The plot method of phymltest has two new arguments: `main' to
541 change the title, and `col' to control the colour of the
542 segments showing the AIC values.
544 o ace() has a new argument `ip' that gives the initial values used
545 in the ML estimation with discrete characters (see the examples
546 in ?ace). This function now returns a matrix giving the indices
547 of the estimated rates when analysing discrete characters.
549 o nodelabels() and tiplabels() have a new argument `pie' to
550 represent proportions, with any number of categories, as
551 piecharts. The use of the option `thermo' has been improved:
552 there is now no limitation on the number of categories.
557 o mlphylo() did not work with more than two partitions: this is
560 o root() failed if the proposed outgroup was already an outgroup
561 in the tree: this is fixed.
563 o The `col' argument in nodelabels() and tiplabels() was not
564 correctly passed when `text' was used: this is fixed.
566 o Two bugs were fixed in mlphylo(): parameters were not always
567 correctly output, and the estimation failed in some cases.
569 o plot.phylo() was stuck when given a tree with a single tip: this
570 is fixed and a message error is now returned.
572 o An error was corrected in the help page of gammaStat regarding
573 the calculation of P-values.
575 o Using gls() could crash R when the number of species in the tree
576 and in the variables were different: this is fixed.
580 CHANGES IN APE VERSION 1.8-2
585 o The new function mlphylo() fits a phylogenetic tree by maximum
586 likelihood from DNA sequences. Its companion function DNAmodel()
587 is used to define the substitution model which may include
588 partitioning. There are methods for logLik(), deviance(), and
589 AIC(), and the summary() method has been extended to display in
590 a friendly way the results of this model fitting. Currently, the
591 functionality is limited to estimating the substitution and
592 associated parameters and computing the likelihood.
594 o The new function drop1.compar.gee (used as, e.g., drop1(m))
595 tests for single effects in GEE-based comparative method. A
596 warning message is printed if there is not enough degrees of
602 o An error message was sometimes issued by plot.multi.tree(),
603 though with no consequence.
607 CHANGES IN APE VERSION 1.8-1
612 o There is a new plot method for lists of trees (objects of class
613 "multi.tree"): it calls plot.phylo() internally and is
614 documented on the same help page.
619 o A bug was fixed in the C code that analyzes bipartitions: this
620 has impact on several functions like prop.part, prop.clades,
621 boot.phylo, or consensus.
623 o root() did not work correctly when the specified outgroup had
624 more than one element: this is fixed.
626 o dist.dna() sometimes returned a warning inappropriately: this
629 o If the distance object given to nj() had no rownames, nj()
630 returned a tree with no tip labels: it now returns tips labelled
631 "1", "2", ..., corresponding to the row numbers.
636 o nj() has been slightly changed so that tips with a zero distance
637 are first aggregated with zero-lengthed branches; the usual NJ
638 procedure is then performed on a distance matrix without 0's.
642 CHANGES IN APE VERSION 1.8
647 o The new function chronopl() estimates dates using the penalized
648 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
650 o The new function consensus() calculates the consensus tree of a
653 o The new function evolve.phylo() simulates the evolution of
654 continuous characters along a phylogeny under a Brownian model.
656 o The new plot method for objects of class "ancestral" displays a
657 tree together with ancestral values, as returned by the above
660 o The new function as.phylo.formula() returns a phylogeny from a
661 set of nested taxonomic variables given as a formula.
663 o The new function read.caic() reads trees in CAIC format.
665 o The new function tiplabels() allows to add labels to the tips
666 of a tree using text or plotting symbols in a flexible way.
668 o The new function unroot() unroots a phylogeny.
670 o multi2di() has a new option, `random', which specifies whether
671 to resolve the multichotomies randomly (the default) or not.
673 o prop.part() now returns an object of class "prop.part" for which
674 there are print (to display a partition in a more friendly way)
675 and summary (to extract the numbers) methods.
677 o plot.phylo() has a new option, `show.tip.label', specifying
678 whether to print the labels of the tips. The default is TRUE.
680 o The code of nj() has been replaced by a faster C code: it is now
681 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
684 o write.nexus() now writes whether a tree is rooted or not.
689 o Two bugs have been fixed in root(): unrooted trees are now
690 handled corretly, and node labels are now output normally.
692 o A bug was fixed in phymltest(): the executable couldn't be found
695 o Three bug have been fixed in ace(): computing the likelihood of
696 ancestral states of discrete characters failed, custom models
697 did not work, and the function failed with a null gradient (a
698 warning message is now returned; this latter bug was also
699 present in yule.cov() as well and is now fixed).
701 o pic() hanged out when missing data were present: a message error
704 o A small bug was fixed in dist.dna() where the gamma correction
705 was not always correctly dispatched.
707 o plot.phylo() plotted correctly the root edge only when the tree
708 was plotted rightwards: this works now for all directions.
713 o dist.taxo() has been renamed as weight.taxo().
715 o Various error and warning messages have been improved.
719 CHANGES IN APE VERSION 1.7
722 o The new function ace() estimates ancestral character states for
723 continuous characters (with ML, GLS, and contrasts methods), and
724 discrete characters (with ML only) for any number of states.
726 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
727 of directional evolution for continuous characters. The user
728 specifies the node(s) of the tree where the character optimum
731 o The new function is.rooted() tests whether a tree (of class
734 o The new function rcoal() generates random ultrametric trees with
735 the possibility to specify the function that generates the
736 inter-nodes distances.
738 o The new function mrca() gives for all pairs of tips in a tree
739 (and optionally nodes too) the most recent common ancestor.
741 o nodelabels() has a new option `thermo' to plot proportions (up
742 to three classes) on the nodes of a tree.
744 o rtree() has been improved: it can now generate rooted or
745 unrooted trees, and the mathematical function that generates the
746 branch lengths may be specified by the user. The tip labels may
747 be given directly in the call to rtree. The limit cases (n = 2,
748 3) are now handled correctly.
750 o dist.topo() has a new argument `method' with two choices: "PH85"
751 for Penny and Henny's method (already available before and now
752 the default), and "BHV01" for the geometric distance by Billera
753 et al. (2001, Adv. Appl. Math. 27:733).
755 o write.tree() has a new option, `digits', which specifies the
756 number of digits to be printed in the Newick tree. By default
757 digits = 10. The numbers are now always printed in decimal form
758 (i.e., 1.0e-1 is now avoided).
760 o dist.dna() can now compute the raw distances between pairs of
761 DNA sequences by specifying model = "raw".
763 o dist.phylo() has a new option `full' to possibly compute the
764 distances among all tips and nodes of the tree. The default if
770 o Several bugs were fixed in all.equal.phylo().
772 o dist.dna() did not handle correctly gaps ("-") in alignments:
773 they are now considered as missing data.
775 o rotate() did not work if the tips were not ordered: this is
778 o mantel.test() returned NA in some special cases: this is fixed
779 and the function has been improved and is now faster.
781 o A bug was fixed in diversi.gof() where the calculation of A² was
784 o cherry() did not work correctly under some OSs (mainly Linux):
787 o is.binary.tree() has been modified so that it works with both
788 rooted and unrooted trees.
790 o The documentation of theta.s() was not correct: this has been
793 o plot.mst() did not work correctly: this is fixed.
797 CHANGES IN APE VERSION 1.6
802 o The new function dist.topo() computes the topological distances
805 o The new function boot.phylo() performs a bootstrap analysis on
806 phylogeny estimation.
808 o The new functions prop.part() and prop.clades() analyse
809 bipartitions from a series of trees.
814 o read.GenBank() now uses the EFetch utility of NCBI instead of
815 the usual Web interface: it is now much faster (e.g., 12 times
816 faster to retrieve 8 sequences, 37 times for 60 sequences).
821 o Several bugs were fixed in read.dna().
823 o Several bugs were fixed in diversi.time().
825 o is.binary.tree() did not work correctly if the tree has no edge
826 lengths: this is fixed.
828 o drop.tip() did not correctly propagated the `node.label' of a
833 CHANGES IN APE VERSION 1.5
838 o Two new functions, as.matching.phylo() and as.phylo.matching(),
839 convert objects between the classes "phylo" and "matching". The
840 latter implements the representation of binary trees introduced by
841 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
842 as.matching() has been introduced as well.
844 o Two new functions, multi2di() and di2multi(), allow to resolve
845 and collapse multichotomies with branches of length zero.
847 o The new function nuc.div() computes the nucleotide diversity
848 from a sample a DNA sequences.
850 o dist.dna() has been completely rewritten with a much faster
851 (particularly for large data sets) C code. Eight models are
852 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
853 option `method' has been renamed `model'). Computation of variance
854 is available for all models. A gamma-correction is possible for
855 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
856 to remove sites with missing data on a pairwise basis. The option
857 `GCcontent' has been removed.
859 o read.GenBank() has a new option (species.names) which specifies
860 whether to return the species names of the organisms in addition
861 to the accession numbers of the sequences (this is the default
864 o write.nexus() can now write several trees in the same NEXUS file.
866 o drop.tip() has a new option `root.edge' that allows to specify the
867 new root edge if internal branches are trimmed.
872 o as.phylo.hclust() failed if some labels had parentheses: this
875 o Several bugs were fixed in all.equal.phylo(). This function now
876 returns the logical TRUE if the trees are identical but with
877 different representations (a report was printed previously).
879 o read.GenBank() did not correctly handle ambiguous base codes:
885 o birthdeath() now returns an object of class "birthdeath" for
886 which there is a print method.
890 CHANGES IN APE VERSION 1.4
895 o The new function nj() performs phylogeny estimation with the
896 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
899 o The new function which.edge() identifies the edges of a tree
900 that belong to a group specified as a set of tips.
902 o The new function as.phylo.phylog() converts an object of class
903 "phylog" (from the package ade4) into an object of class
906 o The new function axisPhylo() draws axes on the side of a
909 o The new function howmanytrees() calculates the number of trees
910 in different cases and giving a number of tips.
912 o write.tree() has a new option `multi.line' (TRUE by default) to
913 write a Newick tree on several lines rather than on a single
916 o The functionalities of zoom() have been extended. Several
917 subtrees can be visualized at the same time, and they are marked
918 on the main tree with colors. The context of the subtrees can be
919 marked with the option `subtree' (see below).
921 o drop.tip() has a new option `subtree' (FALSE by default) which
922 specifies whether to output in the tree how many tips have been
925 o The arguments of add.scale.bar() have been redefined and have
926 now default values (see ?add.scale.bar for details). This
927 function now works even if the plotted tree has no edge length.
929 o plot.phylo() can now plot radial trees, but this does not take
930 edge lengths into account.
932 o In plot.phylo() with `type = "phylogram"', if the values of
933 `edge.color' and `edge.width' are identical for sister-branches,
934 they are propagated to the vertical line that link them.
939 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
940 crashing. This is fixed.
942 o In plot.phylo(), the options `edge.color' and `edge.width' are
943 now properly recycled; their default values are now "black" and
946 o A bug has been fixed in write.nexus().
951 o The function node.depth.edgelength() has been removed and
952 replaced by a C code.
956 CHANGES IN APE VERSION 1.3-1
961 o The new function nodelabels() allows to add labels to the nodes
962 of a tree using text or plotting symbols in a flexible way.
964 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
965 numeric values specifying the lower and upper limits on the x-
966 and y-axes. This allows to leave some space on any side of the
967 tree. If a single value is given, this is taken as the upper
972 CHANGES IN APE VERSION 1.3
977 o The new function phymltest() calls the software PHYML and fits
978 28 models of DNA sequence evolution. There are a print method to
979 display likelihood and AIC values, a summary method to compute
980 the hierarchical likelihood ratio tests, and a plot method to
981 display graphically the AIC values of each model.
983 o The new function yule.cov() fits the Yule model with covariates,
984 a model where the speciation rate is affected by several species
985 traits through a generalized linear model. The parameters are
986 estimated by maximum likelihood.
988 o Three new functions, corBrownian(), corGrafen(), and
989 corMartins(), compute the expected correlation structures among
990 species given a phylogeny under different models of evolution.
991 These can be used for GLS comparative phylogenetic methods (see
992 the examples). There are coef() and corMatrix() methods and an
993 Initialize.corPhyl() function associated.
995 o The new function compar.cheverud() implements Cheverud et al.'s
996 (1985; Evolution 39:1335) phylogenetic comparative method.
998 o The new function varcomp() estimates variance components; it has
1001 o Two new functions, panel.superpose.correlogram() and
1002 plot.correlogramList(), allow to plot several phylogenetic
1005 o The new function node.leafnumber() computes the number of leaves
1006 of a subtree defined by a particular node.
1008 o The new function node.sons() gets all tags of son nodes from a
1011 o The new function compute.brlen() computes the branch lengths of
1012 a tree according to a specified method.
1014 o plot.phylo() has three new options: "cex" controls the size of
1015 the (tip and node) labels (thus it is no more needed to change
1016 the global graphical parameter), "direction" which allows to
1017 plot the tree rightwards, leftwards, upwards, or downwards, and
1018 "y.lim" which sets the upper limit on the y-axis.
1023 o Some functions which try to match tip labels and names of
1024 additional data (e.g. vector) are likely to fail if there are
1025 typing or syntax errors. If both series of names do not perfectly
1026 match, they are ignored and a warning message is now issued.
1027 These functions are bd.ext, compar.gee, pic. Their help pages
1028 have been clarified on this point.
1032 CHANGES IN APE VERSION 1.2-7
1037 o The new function root() reroots a phylogenetic tree with respect
1038 to a specified outgroup.
1040 o The new function rotate() rotates an internal branch of a tree.
1042 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1043 trees) controls the display of the tip labels in unrooted trees.
1044 This display has been greatly improved: the tip labels are now not
1045 expected to overlap with the tree (particularly if lab4ut =
1046 "axial"). In all cases, combining appropriate values of "lab4ut"
1047 and the font size (via "par(cex = )") should result in readable
1048 unrooted trees. See ?plot.phylo for some examples.
1050 o In drop.tip(), the argument `tip' can now be numeric or character.
1055 o drop.tip() did not work correctly with trees with no branch
1056 lengths: this is fixed.
1058 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1059 plotted with some line crossings: this is now fixed.
1063 CHANGES IN APE VERSION 1.2-6
1068 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1069 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1070 to implement comparative methods with an autocorrelation approach.
1072 o A new data set describing some life history traits of Carnivores
1078 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1083 o When plotting a tree with plot.phylo(), the new default of the
1084 option `label.offset' is now 0, so the labels are always visible.
1088 CHANGES IN APE VERSION 1.2-5
1093 o The new function bd.ext() fits a birth-death model with combined
1094 phylogenetic and taxonomic data, and estimates the corresponding
1095 speciation and extinction rates.
1100 o The package gee is no more required by ape but only suggested
1101 since only the function compar.gee() calls gee.
1105 CHANGES IN APE VERSION 1.2-4
1110 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1111 and lines.popsize) implementing a new approach for inferring the
1112 demographic history from genealogies using a reversible jump
1113 MCMC have been introduced.
1115 o The unit of time in the skyline plot and in the new plots can
1116 now be chosen to be actual years, rather than substitutions.
1120 CHANGES IN APE VERSION 1.2-3
1125 o The new function rtree() generates a random binary tree with or
1126 without branch lengths.
1128 o Two new functions for drawing lineages-through-time (LTT) plots
1129 are provided: ltt.lines() adds a LTT curve to an existing plot,
1130 and mltt.plot() does a multiple LTT plot giving several trees as
1131 arguments (see `?ltt.plot' for details).
1136 o Some taxon names made R crashing when calling as.phylo.hclust():
1139 o dist.dna() returned an error with two identical DNA sequences
1140 (only using the Jukes-Cantor method returned 0): this is fixed.
1145 o The function dist.phylo() has been re-written using a different
1146 algorithm: it is now about four times faster.
1148 o The code of branching.times() has been improved: it is now about
1153 CHANGES IN APE VERSION 1.2-2
1158 o The new function seg.sites() finds the segregating sites in a
1159 sample of DNA sequences.
1164 o A bug introduced in read.tree() and in read.nexus() with version
1167 o A few errors were corrected and a few examples were added in the
1172 CHANGES IN APE VERSION 1.2-1
1177 o plot.phylo() can now draw the edge of the root of a tree if it
1178 has one (see the new option `root.edge', its default is FALSE).
1183 o A bug was fixed in read.nexus(): files with semicolons inside
1184 comment blocks were not read correctly.
1186 o The behaviour of read.tree() and read.nexus() was corrected so
1187 that tree files with badly represented root edges (e.g., with
1188 an extra pair of parentheses, see the help pages for details)
1189 are now correctly represented in the object of class "phylo";
1190 a warning message is now issued.
1194 CHANGES IN APE VERSION 1.2
1199 o plot.phylo() has been completely re-written and offers several
1200 new functionalities. Three types of trees can now be drawn:
1201 phylogram (as previously), cladogram, and unrooted tree; in
1202 all three types the branch lengths can be drawn using the edge
1203 lengths of the phylogeny or not (e.g., if the latter is absent).
1204 The vertical position of the nodes can be adjusted with two
1205 choices (see option `node.pos'). The code has been re-structured,
1206 and two new functions (potentially useful for developpers) are
1207 documented separately: node.depth.edgelength() and node.depth();
1208 see the respective help pages for details.
1210 o The new function zoom() allows to explore very large trees by
1211 focusing on a small portion of it.
1213 o The new function yule() fits by maximum likelihood the Yule model
1214 (birth-only process) to a phylogenetic tree.
1216 o Support for writing DNA sequences in FASTA format has been
1217 introduced in write.dna() (support for reading sequences in
1218 this format was introduced in read.dna() in version 1.1-2).
1219 The function has been completely re-written, fixing some bugs
1220 (see below); the default behaviour is no more to display the
1221 sequences on the standard output. Several options have been
1222 introduced to control the sequence printing in a flexible
1223 way. The help page has been extended.
1225 o A new data set is included: a supertree of bats in NEXUS format.
1230 o In theta.s(), the default of the option `variance' has
1231 been changed to `FALSE' (as was indicated in the help page).
1233 o Several bugs were fixed in the code of all.equal.phylo().
1235 o Several bugs were fixed in write.dna(), particularly this
1236 function did not work with `format = "interleaved"'.
1238 o Various errors were corrected in the help pages.
1243 o The argument names of as.hclust.phylo() have been changed
1244 from "(phy)" to "(x, ...)" to conform to the definition of
1245 the corresponding generic function.
1247 o gamma.stat() has been renamed gammaStat() to avoid confusion
1248 since gamma() is a generic function.
1252 CHANGES IN APE VERSION 1.1-3
1257 o base.freq() previously did not return a value of 0 for
1258 bases absent in the data (e.g., a vector of length 3 was
1259 returned if one base was absent). This is now fixed (a
1260 vector of length 4 is always returned).
1262 o Several bugs were fixed in read.nexus(), including that this
1263 function did not work in this absence of a "TRANSLATE"
1264 command in the NEXUS file, and that the commands were
1269 CHANGES IN APE VERSION 1.1-2
1274 o The Tamura and Nei (1993) model of DNA distance is now implemented
1275 in dist.dna(): five models are now available in this function.
1277 o A new data set is included: a set of 15 sequences of the
1278 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1284 o A bug in read.nexus() was fixed.
1286 o read.dna() previously did not work correctly in most cases.
1287 The function has been completely re-written and its help page
1288 has been considerably extended (see ?read.dna for details).
1289 Underscores (_) in taxon names are no more replaced with
1290 spaces (this behaviour was undocumented).
1292 o A bug was fixed in write.dna().
1296 CHANGES IN APE VERSION 1.1-1
1301 o A bug in read.tree() introduced in APE 1.1 was fixed.
1303 o A bug in compar.gee() resulted in an error when trying to fit
1304 a model with `family = "binomial"'. This is now fixed.
1308 CHANGES IN APE VERSION 1.1
1313 o The Klastorin (1982) method as suggested by Misawa and Tajima
1314 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1315 on the basis of phylogenetic trees has been implemented (see
1316 the function klastorin()).
1318 o Functions have been added to convert APE's "phylo" objects in
1319 "hclust" cluster objects and vice versa (see the help page of
1320 as.phylo for details).
1322 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1323 are introduced for the estimation of absolute evolutionary rates
1324 (ratogram) and dated clock-like trees (chronogram) from
1325 phylogenetic trees using the non-parametric rate smoothing approach
1326 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1328 o A summary method is now provided printing a summary information on a
1329 phylogenetic tree with, for instance, `summary(tree)'.
1331 o The behaviour of read.tree() was changed so that all spaces and
1332 tabulations in tree files are now ignored. Consequently, spaces in tip
1333 labels are no more allowed. Another side effect is that read.nexus()
1334 now does not replace the underscores (_) in tip labels with spaces
1335 (this behaviour was undocumented).
1337 o The function plot.phylo() has a new option (`underscore') which
1338 specifies whether the underscores in tip labels should be written on
1339 the plot as such or replaced with spaces (the default).
1341 o The function birthdeath() now computes 95% confidence intervals of
1342 the estimated parameters using profile likelihood.
1344 o Three new data sets are included: a gene tree estimated from 36
1345 landplant rbcL sequences, a gene tree estimated from 32 opsin
1346 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1351 o A bug was fixed in dist.gene() where nothing was returned.
1353 o A bug in plot.mst() was fixed.
1355 o A bug in vcv.phylo() resulted in false correlations when the
1356 option `cor = TRUE' was used (now fixed).
1360 CHANGES IN APE VERSION 1.0
1365 o Two new functions, read.dna() and write.dna(), read/write in a file
1366 DNA sequences in interleaved or in sequential format.
1368 o Two new functions, read.nexus() and write.nexus(), read/write trees
1371 o The new function bind.tree() allows to bind two trees together,
1372 possibly handling root edges to give internal branches.
1374 o The new function drop.tip() removes the tips in a phylogenetic tree,
1375 and trims (or not) the corresponding internal branches.
1377 o The new function is.ultrametric() tests if a tree is ultrametric.
1379 o The function plot.phylo() has more functionalities such as drawing the
1380 branches with different colours and/or different widths, showing the
1381 node labels, controling the position and font of the labels, rotating
1382 the labels, and controling the space around the plot.
1384 o The function read.tree() can now read trees with no branch length,
1385 such as "(a,b),c);". Consequently, the element `edge.length' in
1386 objects of class "phylo" is now optional.
1388 o The function write.tree() has a new default behaviour: if the default
1389 for the option `file' is used (i.e. file = ""), then a variable of
1390 mode character containing the tree in Newick format is returned which
1391 can thus be assigned (e.g., tree <- write.tree(phy)).
1393 o The function read.tree() has a new argument `text' which allows
1394 to read the tree in a variable of mode character.
1396 o A new data set is included: the phylogenetic relationships among
1397 the orders of birds from Sibley and Ahlquist (1990).
1401 CHANGES IN APE VERSION 0.2-1
1406 o Several bugs were fixed in the help pages.
1410 CHANGES IN APE VERSION 0.2
1415 o The function write.tree() writes phylogenetic trees (objects of class
1416 "phylo") in an ASCII file using the Newick parenthetic format.
1418 o The function birthdeath() fits a birth-death model to branching times
1419 by maximum likelihood, and estimates the corresponding speciation and
1422 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1425 o The function is.binary.tree() tests whether a phylogeny is binary.
1427 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1428 as well as some methods are introduced.
1430 o Several functions, including some generics and methods, for computing
1431 skyline plot estimates (classic and generalized) of effective
1432 population size through time are introduced and replace the function
1433 skyline.plot() in version 0.1.
1435 o Two data sets are now included: the phylogenetic relationships among
1436 the families of birds from Sibley and Ahlquist (1990), and an
1437 estimated clock-like phylogeny of HIV sequences sampled in the
1438 Democratic Republic of Congo.
1441 DEPRECATED & DEFUNCT
1443 o The function skyline.plot() in ape 0.1 has been deprecated and
1444 replaced by more elaborate functions (see above).
1449 o Two important bugs were fixed in plot.phylo(): phylogenies with
1450 multichotomies not at the root or not with only terminal branches,
1451 and phylogenies with a single node (i.e. only terminal branches)
1452 did not plot. These trees should be plotted correctly now.
1454 o Several bugs were fixed in diversi.time() in the computation of
1457 o Various errors were corrected in the help pages.
projects / ape.git / blob