1 CHANGES IN APE VERSION 2.2-2
6 o dist.gene() has been substantially improved and gains an option
12 o prop.part() failed with a single tree with the default option
13 'check.labels = TRUE'.
15 o summary.DNAbin() failed to display correctly the summary of
16 sequence lengths with lists of sequences of 10,000 bases or more
17 (because summary.default uses 4 significant digits by default).
19 o read.nexus() failed to read a file with a single tree with line
20 breaks in the Newick string.
22 o del.gaps() returned a list of empty sequences when there were no
28 o phymltest() has been updated for PhyML 3.0 and gains an option
29 'append', whereas the option 'path2exec' has been removed.
31 o rbind.DNAbin() now accepts a single matrix which is returned
32 unchanged instead of an error.
34 o The data sets bird.orders and bird.families are now stored as
35 Newick strings; i.e., the command data(bird.orders) calls
40 CHANGES IN APE VERSION 2.2-1
45 o The new function makeLabel() helps to modify labels of trees,
46 lists of trees, or DNA sequences, with several utilities to
47 truncate and/or make them unique, substituting some
48 characters, and so on.
50 o The new function del.gaps() removes insertion gaps ("-") in a
53 o read.dna() can now read Clustal files (*.aln).
58 o root() failed with 'resolve.root = TRUE' when the root was
59 already the specified root.
61 o Several bugs were fixed in mlphylo().
63 o collapsed.singles() did not propagate the 'Nnode' and
64 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
66 o read.nexus() failed to remove correctly the comments within
69 o read.nexus() failed to read a file with a single tree and no
70 translation of tip labels.
72 o read.nexus() failed to place correctly tip labels when reading
73 a single tree with no edge lengths.
75 o A bug was fixed in sh.test().
80 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
83 o The option 'check.labels' of consensus() and prop.part() is now
86 o write.dna() now does not truncate names to 10 characters with
91 CHANGES IN APE VERSION 2.2
96 o Four new functions have been written by Damien de Vienne for the
97 graphical exploration of large trees (cophyloplot, subtrees,
98 subtreeplot), and to return the graphical coordinates of tree
101 o The new functions corPagel and corBlomberg implement the Pagel's
102 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
104 o chronopl() has been improved and gains several options: see its
105 help page for details.
107 o boot.phylo() has now an option 'trees' to possibly return the
108 bootstraped trees (the default is FALSE).
110 o prop.part() has been improved and should now be faster in all
116 o read.dna() failed if "?" occurred in the first 10 sites of the
119 o The x/y aspect of the plot is now respected when plotting a
120 circular tree (type = "r" or "f").
122 o Drawing the tip labels sometimes failed when plotting circular
125 o zoom() failed when tip labels were used instead of their numbers
126 (thanks to Yan Wong for the fix).
128 o drop.tip() failed with some trees (fixed by Yan Wong).
130 o seg.sites() failed with a list.
132 o consensus() failed in some cases. The function has been improved
133 as well and is faster.
137 CHANGES IN APE VERSION 2.1-3
142 o A bug in read.nexus() made the Windows R-GUI crash.
144 o An error was fixed in the computation of ancestral character
145 states by generalized least squares in ace().
147 o di2multi() did not modify node labels correctly.
149 o multi2di() failed if the tree had its attribute "order" set to
154 CHANGES IN APE VERSION 2.1-2
159 o There three new methods for the "multiPhylo" class: str, $,
162 o root() gains the options 'node' and 'resolve.root'
163 (FALSE by default) as well as its code being improved.
165 o mltt.plot() has now an option 'log' used in the same way
166 than in plot.default().
171 o mltt.plot() failed to display the legend with an unnamed
174 o nodelabels() with pies now correcly uses the argument
175 'cex' to draw symbols of different sizes (which has
176 worked already for thermometers).
178 o read.nexus() generally failed to read very big files.
183 o The argument 'family' of compar.gee() can now be a function
184 as well as a character string.
186 o read.tree() and read.nexus() now return an unnamed list if
189 o read.nexus() now returns a modified object of class "multiPhylo"
190 when there is a TRANSLATE block in the NEXUS file: the individual
191 trees have no 'tip.label' vector, but the list has a 'TipLabel'
192 attribute. The new methods '$' and '[[' set these elements
193 correctly when extracting trees.
197 CHANGES IN APE VERSION 2.1-1
202 o The new function rmtree generates lists of random trees.
204 o rcoal() now generates a genuine coalescent tree by default
205 (thanks to Vladimir Minin for the code).
210 o nuc.div() returned an incorrect value with the default
211 pairwise.deletion = FALSE.
216 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
217 have been improved so that they are stabler and faster.
219 o R packages used by ape are now loaded silently; lattice and gee
220 are loaded only when needed.
224 CHANGES IN APE VERSION 2.1
229 o The new function identify.phylo identifies clades on a plotted
230 tree using the mouse.
232 o It is now possible to subset a list of trees (object of class
233 "multiPhylo") with "[" while keeping its class correct.
235 o The new function as.DNAbin.alignment converts DNA sequences
236 stored in the "alignment" format of the package seqinr into
237 an object of class "DNAbin".
239 o The new function weight.taxo2 helps to build similarity matrices
240 given two taxonomic levels (usually called by other functions).
242 o write.tree() can now take a list of trees (class "multiPhylo")
243 as its main argument.
245 o plot.correlogram() and plot.correlogramList() have been
246 improved, and gain several options (see the help page for
247 details). A legend is now plotted by default.
252 o dist.dna() returned some incorrect values with `model = "JC69"'
253 and `pairwise.deletion = TRUE'. This affected only the
254 distances involving sequences with missing values. (Thanks
255 to Bruno Toupance for digging this bug out.)
257 o write.tree() failed with some trees: this is fixed by removing
258 the `multi.line' option (trees are now always printed on a
261 o read.nexus() did not correctly detect trees with multiple root
262 edges (see OTHER CHANGES).
267 o The code of mlphylo() has been almost entirely rewritten, and
268 should be much stabler. The options have been also greatly
269 simplified (see ?mlphylo and ?DNAmodel for details).
271 o The internal function nTips has been renamed klastorin_nTips.
273 o The code of is.ultrametric() contained redundancies and has
276 o The code of Moran.I() and of correlogram.formula() have been
279 o read.tree() and read.nexus() now return an error when trying to
280 read a tree with multiple root edges (see BUG FIXES). The
281 correction applied in previous version did not work in all
284 o The class c("multi.tree", "phylo") has been renamed
290 o There is now a vignette in ape: see vignette("MoranI", "ape").
295 o as.matching() and as.phylo.matching() do not support branch
298 o correlogram.phylo() and discrete.dist() have been removed.
302 CHANGES IN APE VERSION 2.0-2
307 o The new function matexpo computes the exponential of a square
310 o The new function unique.multi.tree removes duplicate trees from
313 o yule() has a new option `use.root.edge = FALSE' that specifies
314 to ignore, by default, the root edge of the tree if it exists.
319 o which.edge() failed when the index of a single terminal edge was
322 o In diversi.time(), the values returned for model C were
325 o A bug was fixed in yule() that affected the calculation of the
326 likelihood in the presence of ties in the branching times.
328 o There was a bug in the C function mat_expo4x4 affecting the
329 calculations of the transition probabilities for models HKY and
332 o A small bug was fixed in as.matrix.DNAbin (thanks to James
335 o rtree() did not `shuffle' the tip labels by default, so only a
336 limited number of labelled topologies could be generated.
340 CHANGES IN APE VERSION 2.0-1
345 o The three new functions bionj, fastme.ols, and fastme.bal
346 perform phylogeny estimation by the BIONJ and fastME methods in
347 OLS and balanced versions. This is a port to R of previous
348 previous programs done by Vincent Lefort.
350 o The new function chronoMPL performs molecular dating with the
351 mean path lengths method of Britton et al. (2002, Mol. Phyl.
354 o The new function rotate, contributed by Christoph Heibl, swaps
355 two clades connected to the same node. It works also with
356 multichotomous nodes.
358 o The new `method' as.matrix.DNAbin() may be used to convert
359 easily DNA sequences stored in a list into a matrix while
360 keeping the names and the class.
365 o chronopl() failed when some branch lengths were equal to zero:
366 an error message is now returned.
368 o di2multi() failed when there was a series of consecutive edges
373 CHANGES IN APE VERSION 1.10-2
378 o plot.phylo() can now plot circular trees: the option is type =
379 "fan" or type = "f" (to avoid the ambiguity with type = "c").
381 o prop.part() has a new option `check.labels = FALSE' which allows
382 to considerably speed-up the calculations of bipartitions. As a
383 consequence, calculations of bootstrap values with boot.phylo()
384 should be much faster.
389 o read.GenBank() did not return correctly the list of species as
390 from ape 1.10: this is fixed in this version
392 o Applying as.phylo() on a tree of class "phylo" failed: the
393 object is now returned unchanged.
397 CHANGES IN APE VERSION 1.10-1
402 o The three new functions Ntip, Nnode, and Nedge return, for a
403 given tree, the number of tips, nodes, or edges, respectively.
408 o read.nexus() did not set correctly the class of the returned
409 object when reading multiple trees.
411 o mllt.plot() failed with objects of class c("multi.tree",
414 o unroot() did not work correctly in most cases.
416 o reorder.phylo() made R freeze in some occasions.
418 o Plotting a tree in pruningwise order failed.
420 o When plotting an unrooted tree, the tip labels where not all
421 correctly positioned if the option `cex' was used.
425 CHANGES IN APE VERSION 1.10
430 o Five new `method' functions have been introduced to manipulate
431 DNA sequences in binary format (see below).
433 o Three new functions have been introduced to convert between the
434 new binary and the character formats.
436 o The new function as.alignment converts DNA sequences stored as
437 single characters into the class "alignment" used by the package
440 o read.dna() and read.GenBank() have a new argument `as.character'
441 controlling whether the sequences are returned in binary format
447 o root() failed when the tree had node labels: this is fixed.
449 o plot.phylo() did not correctly set the limits on the y-axis with
450 the default setting: this is fixed.
452 o dist.dna() returned a wrong result for the LogDet, paralinear,
453 and BH87 models with `pairwise.deletion = TRUE'.
458 o DNA sequences are now internally stored in a binary format. See
459 the document "A Bit-Level Coding Scheme for Nucleotides" for the
460 details. Most functions analyzing DNA functions have been
461 modified accordingly and are now much faster (dist.dna is now
462 ca. 60 times faster).
466 CHANGES IN APE VERSION 1.9-4
471 o A bug was fixed in edgelabels().
473 o as.phylo.hclust() did not work correctly when the object of
474 class "hclust" has its labels set to NULL: the returned tree has
475 now its tip labels set to "1", "2", ...
477 o consensus could fail if some tip labels are a subset of others
478 (e.g., "a" and "a_1"): this is now fixed.
480 o mlphylo() failed in most cases if some branch lengths of the
481 initial tree were greater than one: an error message is now
484 o mlphylo() failed in most cases when estimating the proportion of
485 invariants: this is fixed.
489 CHANGES IN APE VERSION 1.9-3
494 o The new function edgelabels adds labels on the edge of the tree
495 in the same way than nodelabels or tiplabels.
500 o multi2di() did not handle correctly branch lengths with the
501 default option `random = TRUE': this is now fixed.
503 o A bug was fixed in nuc.div() when using pairwise deletions.
505 o A bug occurred in the analysis of bipartitions with large
506 numbers of large trees, with consequences on prop.part,
507 prop.clades, and boot.phylo.
509 o The calculation of the Billera-Holmes-Vogtmann distance in
510 dist.topo was wrong: this has been fixed.
514 CHANGES IN APE VERSION 1.9-2
519 o The new function ladderize reorganizes the internal structure of
520 a tree to plot them left- or right-ladderized.
522 o The new function dist.nodes computes the patristic distances
523 between all nodes, internal and terminal, of a tree. It replaces
524 the option `full = TRUE' of cophenetic.phylo (see below).
529 o A bug was fixed in old2new.phylo().
531 o Some bugs were fixed in chronopl().
533 o The edge colours were not correctly displayed by plot.phylo
534 (thank you to Li-San Wang for the fix).
536 o cophenetic.phylo() failed with multichotomous trees: this is
542 o read.dna() now returns the sequences in a matrix if they are
543 aligned (interleaved or sequential format). Sequences in FASTA
544 format are still returned in a list.
546 o The option `full' of cophenetic.phylo() has been removed because
547 it could not be used from the generic.
552 o rotate() has been removed; this function did not work correctly
557 CHANGES IN APE VERSION 1.9-1
562 o Trees with a single tip were not read correctly in R as the
563 element `Nnode' was not set: this is fixed.
565 o unroot() did not set correctly the number of nodes of the
566 unrooted tree in most cases.
568 o read.GenBank() failed when fetching very long sequences,
569 particularly of the BX-series.
571 o A bug was introduced in read.tree() with ape 1.9: it has been
576 CHANGES IN APE VERSION 1.9
581 o There are two new print `methods' for trees of class "phylo" and
582 lists of trees of class "multi.tree", so that they are now
583 displayed in a compact and informative way.
585 o There are two new functions, old2new.phylo and new2old.phylo,
586 for converting between the old and new coding of the class
589 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
590 LogDet ("logdet"), and paralinear ("paralin").
592 o compute.brlen() has been extended: several methods are now
593 available to compute branch lengths.
595 o write.dna() can now handle matrices as well as lists.
600 o cophenetic.phylo() sometimes returned a wrong result with
601 multichotomous trees: this is fixed.
603 o rotate() failed when a single tip was specified: the tree is now
606 o ace() did not return the correct index matrix with custom
607 models: this is fixed.
609 o multi2di() did not work correctly when resolving multichotomies
610 randomly: the topology was always the same, only the arrangement
611 of clades was randomized: this is fixed. This function now
612 accepts trees with no branch lengths.
614 o The output of diversi.gof() was blurred by useless prints when a
615 user distribution was specified. This has been corrected, and
616 the help page of this function has been expanded.
621 o The internal structure of the class "phylo" has been changed:
622 see the document "Definition of Formats for Coding Phylogenetic
623 Trees in R" for the details. In addition, the code of most
624 functions has been improved.
626 o Several functions have been improved by replacing some R codes
627 by C codes: pic, plot.phylo, and reorder.phylo.
629 o There is now a citation information: see citation("ape") in R.
631 o write.tree() now does not add extra 0's to branch lengths so
632 that 1.23 is printed "1.23" by default, not "1.2300000000".
634 o The syntax of bind.tree() has been simplified. This function now
635 accepts trees with no branch lengths, and handles correctly node
638 o The option `as.numeric' of mrca() has been removed.
640 o The unused options `format' and `rooted' of read.tree() have
643 o The unused option `format' of write.tree() has been removed.
645 o The use of node.depth() has been simplified.
649 CHANGES IN APE VERSION 1.8-5
654 o Two new functions read.nexus.data() and write.nexus.data(),
655 contributed by Johan Nylander, allow to read and write molecular
656 sequences in NEXUS files.
658 o The new function reorder.phylo() reorders the internal structure
659 of a tree of class "phylo". It is used as the generic, e.g.,
662 o read.tree() and read.nexus() can now read trees with a single
665 o The new data set `cynipids' supplies a set of protein sequences
671 o The code of all.equal.phylo() has been completely rewritten
672 (thanks to Benoît Durand) which fixes several bugs.
674 o read.tree() and read.nexus() now checks the labels of the tree
675 to remove or substitute any characters that are illegal in the
676 Newick format (parentheses, etc.)
678 o A negative P-value could be returned by mantel.test(): this is
683 CHANGES IN APE VERSION 1.8-4
688 o The new function sh.test() computes the Shimodaira-
691 o The new function collapse.singles() removes the nodes with a
692 single descendant from a tree.
694 o plot.phylo() has a new argument `tip.color' to specify the
697 o mlphylo() has now an option `quiet' to control the display of
698 the progress of the analysis (the default is FALSE).
703 o read.dna() did not read correctly sequences in sequential format
704 with leading alignment gaps "-": this is fixed.
706 o ace() returned a list with no class so that the generic
707 functions (anova, logLik, ...) could not be used directly. This
708 is fixed as ace() now returns an object of class "ace".
710 o anova.ace() had a small bug when computing the number of degrees
711 of freedom: this is fixed.
713 o mlphylo() did not work when the sequences were in a matrix or
714 a data frame: this is fixed.
716 o rtree() did not work correctly when trying to simulate an
717 unrooted tree with two tips: an error message is now issued.
722 o The algorithm of rtree() has been changed: it is now about 40,
723 100, and 130 times faster for 10, 100, and 1000 tips,
728 CHANGES IN APE VERSION 1.8-3
733 o There are four new `method' functions to be used with the
734 results of ace(): logLik(), deviance(), AIC(), and anova().
736 o The plot method of phymltest has two new arguments: `main' to
737 change the title, and `col' to control the colour of the
738 segments showing the AIC values.
740 o ace() has a new argument `ip' that gives the initial values used
741 in the ML estimation with discrete characters (see the examples
742 in ?ace). This function now returns a matrix giving the indices
743 of the estimated rates when analysing discrete characters.
745 o nodelabels() and tiplabels() have a new argument `pie' to
746 represent proportions, with any number of categories, as
747 piecharts. The use of the option `thermo' has been improved:
748 there is now no limitation on the number of categories.
753 o mlphylo() did not work with more than two partitions: this is
756 o root() failed if the proposed outgroup was already an outgroup
757 in the tree: this is fixed.
759 o The `col' argument in nodelabels() and tiplabels() was not
760 correctly passed when `text' was used: this is fixed.
762 o Two bugs were fixed in mlphylo(): parameters were not always
763 correctly output, and the estimation failed in some cases.
765 o plot.phylo() was stuck when given a tree with a single tip: this
766 is fixed and a message error is now returned.
768 o An error was corrected in the help page of gammaStat regarding
769 the calculation of P-values.
771 o Using gls() could crash R when the number of species in the tree
772 and in the variables were different: this is fixed.
776 CHANGES IN APE VERSION 1.8-2
781 o The new function mlphylo() fits a phylogenetic tree by maximum
782 likelihood from DNA sequences. Its companion function DNAmodel()
783 is used to define the substitution model which may include
784 partitioning. There are methods for logLik(), deviance(), and
785 AIC(), and the summary() method has been extended to display in
786 a friendly way the results of this model fitting. Currently, the
787 functionality is limited to estimating the substitution and
788 associated parameters and computing the likelihood.
790 o The new function drop1.compar.gee (used as, e.g., drop1(m))
791 tests for single effects in GEE-based comparative method. A
792 warning message is printed if there is not enough degrees of
798 o An error message was sometimes issued by plot.multi.tree(),
799 though with no consequence.
803 CHANGES IN APE VERSION 1.8-1
808 o There is a new plot method for lists of trees (objects of class
809 "multi.tree"): it calls plot.phylo() internally and is
810 documented on the same help page.
815 o A bug was fixed in the C code that analyzes bipartitions: this
816 has impact on several functions like prop.part, prop.clades,
817 boot.phylo, or consensus.
819 o root() did not work correctly when the specified outgroup had
820 more than one element: this is fixed.
822 o dist.dna() sometimes returned a warning inappropriately: this
825 o If the distance object given to nj() had no rownames, nj()
826 returned a tree with no tip labels: it now returns tips labelled
827 "1", "2", ..., corresponding to the row numbers.
832 o nj() has been slightly changed so that tips with a zero distance
833 are first aggregated with zero-lengthed branches; the usual NJ
834 procedure is then performed on a distance matrix without 0's.
838 CHANGES IN APE VERSION 1.8
843 o The new function chronopl() estimates dates using the penalized
844 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
846 o The new function consensus() calculates the consensus tree of a
849 o The new function evolve.phylo() simulates the evolution of
850 continuous characters along a phylogeny under a Brownian model.
852 o The new plot method for objects of class "ancestral" displays a
853 tree together with ancestral values, as returned by the above
856 o The new function as.phylo.formula() returns a phylogeny from a
857 set of nested taxonomic variables given as a formula.
859 o The new function read.caic() reads trees in CAIC format.
861 o The new function tiplabels() allows to add labels to the tips
862 of a tree using text or plotting symbols in a flexible way.
864 o The new function unroot() unroots a phylogeny.
866 o multi2di() has a new option, `random', which specifies whether
867 to resolve the multichotomies randomly (the default) or not.
869 o prop.part() now returns an object of class "prop.part" for which
870 there are print (to display a partition in a more friendly way)
871 and summary (to extract the numbers) methods.
873 o plot.phylo() has a new option, `show.tip.label', specifying
874 whether to print the labels of the tips. The default is TRUE.
876 o The code of nj() has been replaced by a faster C code: it is now
877 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
880 o write.nexus() now writes whether a tree is rooted or not.
885 o Two bugs have been fixed in root(): unrooted trees are now
886 handled corretly, and node labels are now output normally.
888 o A bug was fixed in phymltest(): the executable couldn't be found
891 o Three bug have been fixed in ace(): computing the likelihood of
892 ancestral states of discrete characters failed, custom models
893 did not work, and the function failed with a null gradient (a
894 warning message is now returned; this latter bug was also
895 present in yule.cov() as well and is now fixed).
897 o pic() hanged out when missing data were present: a message error
900 o A small bug was fixed in dist.dna() where the gamma correction
901 was not always correctly dispatched.
903 o plot.phylo() plotted correctly the root edge only when the tree
904 was plotted rightwards: this works now for all directions.
909 o dist.taxo() has been renamed as weight.taxo().
911 o Various error and warning messages have been improved.
915 CHANGES IN APE VERSION 1.7
918 o The new function ace() estimates ancestral character states for
919 continuous characters (with ML, GLS, and contrasts methods), and
920 discrete characters (with ML only) for any number of states.
922 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
923 of directional evolution for continuous characters. The user
924 specifies the node(s) of the tree where the character optimum
927 o The new function is.rooted() tests whether a tree (of class
930 o The new function rcoal() generates random ultrametric trees with
931 the possibility to specify the function that generates the
932 inter-nodes distances.
934 o The new function mrca() gives for all pairs of tips in a tree
935 (and optionally nodes too) the most recent common ancestor.
937 o nodelabels() has a new option `thermo' to plot proportions (up
938 to three classes) on the nodes of a tree.
940 o rtree() has been improved: it can now generate rooted or
941 unrooted trees, and the mathematical function that generates the
942 branch lengths may be specified by the user. The tip labels may
943 be given directly in the call to rtree. The limit cases (n = 2,
944 3) are now handled correctly.
946 o dist.topo() has a new argument `method' with two choices: "PH85"
947 for Penny and Henny's method (already available before and now
948 the default), and "BHV01" for the geometric distance by Billera
949 et al. (2001, Adv. Appl. Math. 27:733).
951 o write.tree() has a new option, `digits', which specifies the
952 number of digits to be printed in the Newick tree. By default
953 digits = 10. The numbers are now always printed in decimal form
954 (i.e., 1.0e-1 is now avoided).
956 o dist.dna() can now compute the raw distances between pairs of
957 DNA sequences by specifying model = "raw".
959 o dist.phylo() has a new option `full' to possibly compute the
960 distances among all tips and nodes of the tree. The default if
966 o Several bugs were fixed in all.equal.phylo().
968 o dist.dna() did not handle correctly gaps ("-") in alignments:
969 they are now considered as missing data.
971 o rotate() did not work if the tips were not ordered: this is
974 o mantel.test() returned NA in some special cases: this is fixed
975 and the function has been improved and is now faster.
977 o A bug was fixed in diversi.gof() where the calculation of A² was
980 o cherry() did not work correctly under some OSs (mainly Linux):
983 o is.binary.tree() has been modified so that it works with both
984 rooted and unrooted trees.
986 o The documentation of theta.s() was not correct: this has been
989 o plot.mst() did not work correctly: this is fixed.
993 CHANGES IN APE VERSION 1.6
998 o The new function dist.topo() computes the topological distances
1001 o The new function boot.phylo() performs a bootstrap analysis on
1002 phylogeny estimation.
1004 o The new functions prop.part() and prop.clades() analyse
1005 bipartitions from a series of trees.
1010 o read.GenBank() now uses the EFetch utility of NCBI instead of
1011 the usual Web interface: it is now much faster (e.g., 12 times
1012 faster to retrieve 8 sequences, 37 times for 60 sequences).
1017 o Several bugs were fixed in read.dna().
1019 o Several bugs were fixed in diversi.time().
1021 o is.binary.tree() did not work correctly if the tree has no edge
1022 lengths: this is fixed.
1024 o drop.tip() did not correctly propagated the `node.label' of a
1025 tree: this is fixed.
1029 CHANGES IN APE VERSION 1.5
1034 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1035 convert objects between the classes "phylo" and "matching". The
1036 latter implements the representation of binary trees introduced by
1037 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1038 as.matching() has been introduced as well.
1040 o Two new functions, multi2di() and di2multi(), allow to resolve
1041 and collapse multichotomies with branches of length zero.
1043 o The new function nuc.div() computes the nucleotide diversity
1044 from a sample a DNA sequences.
1046 o dist.dna() has been completely rewritten with a much faster
1047 (particularly for large data sets) C code. Eight models are
1048 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1049 option `method' has been renamed `model'). Computation of variance
1050 is available for all models. A gamma-correction is possible for
1051 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1052 to remove sites with missing data on a pairwise basis. The option
1053 `GCcontent' has been removed.
1055 o read.GenBank() has a new option (species.names) which specifies
1056 whether to return the species names of the organisms in addition
1057 to the accession numbers of the sequences (this is the default
1060 o write.nexus() can now write several trees in the same NEXUS file.
1062 o drop.tip() has a new option `root.edge' that allows to specify the
1063 new root edge if internal branches are trimmed.
1068 o as.phylo.hclust() failed if some labels had parentheses: this
1071 o Several bugs were fixed in all.equal.phylo(). This function now
1072 returns the logical TRUE if the trees are identical but with
1073 different representations (a report was printed previously).
1075 o read.GenBank() did not correctly handle ambiguous base codes:
1081 o birthdeath() now returns an object of class "birthdeath" for
1082 which there is a print method.
1086 CHANGES IN APE VERSION 1.4
1091 o The new function nj() performs phylogeny estimation with the
1092 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1095 o The new function which.edge() identifies the edges of a tree
1096 that belong to a group specified as a set of tips.
1098 o The new function as.phylo.phylog() converts an object of class
1099 "phylog" (from the package ade4) into an object of class
1102 o The new function axisPhylo() draws axes on the side of a
1105 o The new function howmanytrees() calculates the number of trees
1106 in different cases and giving a number of tips.
1108 o write.tree() has a new option `multi.line' (TRUE by default) to
1109 write a Newick tree on several lines rather than on a single
1112 o The functionalities of zoom() have been extended. Several
1113 subtrees can be visualized at the same time, and they are marked
1114 on the main tree with colors. The context of the subtrees can be
1115 marked with the option `subtree' (see below).
1117 o drop.tip() has a new option `subtree' (FALSE by default) which
1118 specifies whether to output in the tree how many tips have been
1121 o The arguments of add.scale.bar() have been redefined and have
1122 now default values (see ?add.scale.bar for details). This
1123 function now works even if the plotted tree has no edge length.
1125 o plot.phylo() can now plot radial trees, but this does not take
1126 edge lengths into account.
1128 o In plot.phylo() with `type = "phylogram"', if the values of
1129 `edge.color' and `edge.width' are identical for sister-branches,
1130 they are propagated to the vertical line that link them.
1135 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1136 crashing. This is fixed.
1138 o In plot.phylo(), the options `edge.color' and `edge.width' are
1139 now properly recycled; their default values are now "black" and
1142 o A bug has been fixed in write.nexus().
1147 o The function node.depth.edgelength() has been removed and
1148 replaced by a C code.
1152 CHANGES IN APE VERSION 1.3-1
1157 o The new function nodelabels() allows to add labels to the nodes
1158 of a tree using text or plotting symbols in a flexible way.
1160 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1161 numeric values specifying the lower and upper limits on the x-
1162 and y-axes. This allows to leave some space on any side of the
1163 tree. If a single value is given, this is taken as the upper
1168 CHANGES IN APE VERSION 1.3
1173 o The new function phymltest() calls the software PHYML and fits
1174 28 models of DNA sequence evolution. There are a print method to
1175 display likelihood and AIC values, a summary method to compute
1176 the hierarchical likelihood ratio tests, and a plot method to
1177 display graphically the AIC values of each model.
1179 o The new function yule.cov() fits the Yule model with covariates,
1180 a model where the speciation rate is affected by several species
1181 traits through a generalized linear model. The parameters are
1182 estimated by maximum likelihood.
1184 o Three new functions, corBrownian(), corGrafen(), and
1185 corMartins(), compute the expected correlation structures among
1186 species given a phylogeny under different models of evolution.
1187 These can be used for GLS comparative phylogenetic methods (see
1188 the examples). There are coef() and corMatrix() methods and an
1189 Initialize.corPhyl() function associated.
1191 o The new function compar.cheverud() implements Cheverud et al.'s
1192 (1985; Evolution 39:1335) phylogenetic comparative method.
1194 o The new function varcomp() estimates variance components; it has
1197 o Two new functions, panel.superpose.correlogram() and
1198 plot.correlogramList(), allow to plot several phylogenetic
1201 o The new function node.leafnumber() computes the number of leaves
1202 of a subtree defined by a particular node.
1204 o The new function node.sons() gets all tags of son nodes from a
1207 o The new function compute.brlen() computes the branch lengths of
1208 a tree according to a specified method.
1210 o plot.phylo() has three new options: "cex" controls the size of
1211 the (tip and node) labels (thus it is no more needed to change
1212 the global graphical parameter), "direction" which allows to
1213 plot the tree rightwards, leftwards, upwards, or downwards, and
1214 "y.lim" which sets the upper limit on the y-axis.
1219 o Some functions which try to match tip labels and names of
1220 additional data (e.g. vector) are likely to fail if there are
1221 typing or syntax errors. If both series of names do not perfectly
1222 match, they are ignored and a warning message is now issued.
1223 These functions are bd.ext, compar.gee, pic. Their help pages
1224 have been clarified on this point.
1228 CHANGES IN APE VERSION 1.2-7
1233 o The new function root() reroots a phylogenetic tree with respect
1234 to a specified outgroup.
1236 o The new function rotate() rotates an internal branch of a tree.
1238 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1239 trees) controls the display of the tip labels in unrooted trees.
1240 This display has been greatly improved: the tip labels are now not
1241 expected to overlap with the tree (particularly if lab4ut =
1242 "axial"). In all cases, combining appropriate values of "lab4ut"
1243 and the font size (via "par(cex = )") should result in readable
1244 unrooted trees. See ?plot.phylo for some examples.
1246 o In drop.tip(), the argument `tip' can now be numeric or character.
1251 o drop.tip() did not work correctly with trees with no branch
1252 lengths: this is fixed.
1254 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1255 plotted with some line crossings: this is now fixed.
1259 CHANGES IN APE VERSION 1.2-6
1264 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1265 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1266 to implement comparative methods with an autocorrelation approach.
1268 o A new data set describing some life history traits of Carnivores
1274 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1279 o When plotting a tree with plot.phylo(), the new default of the
1280 option `label.offset' is now 0, so the labels are always visible.
1284 CHANGES IN APE VERSION 1.2-5
1289 o The new function bd.ext() fits a birth-death model with combined
1290 phylogenetic and taxonomic data, and estimates the corresponding
1291 speciation and extinction rates.
1296 o The package gee is no more required by ape but only suggested
1297 since only the function compar.gee() calls gee.
1301 CHANGES IN APE VERSION 1.2-4
1306 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1307 and lines.popsize) implementing a new approach for inferring the
1308 demographic history from genealogies using a reversible jump
1309 MCMC have been introduced.
1311 o The unit of time in the skyline plot and in the new plots can
1312 now be chosen to be actual years, rather than substitutions.
1316 CHANGES IN APE VERSION 1.2-3
1321 o The new function rtree() generates a random binary tree with or
1322 without branch lengths.
1324 o Two new functions for drawing lineages-through-time (LTT) plots
1325 are provided: ltt.lines() adds a LTT curve to an existing plot,
1326 and mltt.plot() does a multiple LTT plot giving several trees as
1327 arguments (see `?ltt.plot' for details).
1332 o Some taxon names made R crashing when calling as.phylo.hclust():
1335 o dist.dna() returned an error with two identical DNA sequences
1336 (only using the Jukes-Cantor method returned 0): this is fixed.
1341 o The function dist.phylo() has been re-written using a different
1342 algorithm: it is now about four times faster.
1344 o The code of branching.times() has been improved: it is now about
1349 CHANGES IN APE VERSION 1.2-2
1354 o The new function seg.sites() finds the segregating sites in a
1355 sample of DNA sequences.
1360 o A bug introduced in read.tree() and in read.nexus() with version
1363 o A few errors were corrected and a few examples were added in the
1368 CHANGES IN APE VERSION 1.2-1
1373 o plot.phylo() can now draw the edge of the root of a tree if it
1374 has one (see the new option `root.edge', its default is FALSE).
1379 o A bug was fixed in read.nexus(): files with semicolons inside
1380 comment blocks were not read correctly.
1382 o The behaviour of read.tree() and read.nexus() was corrected so
1383 that tree files with badly represented root edges (e.g., with
1384 an extra pair of parentheses, see the help pages for details)
1385 are now correctly represented in the object of class "phylo";
1386 a warning message is now issued.
1390 CHANGES IN APE VERSION 1.2
1395 o plot.phylo() has been completely re-written and offers several
1396 new functionalities. Three types of trees can now be drawn:
1397 phylogram (as previously), cladogram, and unrooted tree; in
1398 all three types the branch lengths can be drawn using the edge
1399 lengths of the phylogeny or not (e.g., if the latter is absent).
1400 The vertical position of the nodes can be adjusted with two
1401 choices (see option `node.pos'). The code has been re-structured,
1402 and two new functions (potentially useful for developpers) are
1403 documented separately: node.depth.edgelength() and node.depth();
1404 see the respective help pages for details.
1406 o The new function zoom() allows to explore very large trees by
1407 focusing on a small portion of it.
1409 o The new function yule() fits by maximum likelihood the Yule model
1410 (birth-only process) to a phylogenetic tree.
1412 o Support for writing DNA sequences in FASTA format has been
1413 introduced in write.dna() (support for reading sequences in
1414 this format was introduced in read.dna() in version 1.1-2).
1415 The function has been completely re-written, fixing some bugs
1416 (see below); the default behaviour is no more to display the
1417 sequences on the standard output. Several options have been
1418 introduced to control the sequence printing in a flexible
1419 way. The help page has been extended.
1421 o A new data set is included: a supertree of bats in NEXUS format.
1426 o In theta.s(), the default of the option `variance' has
1427 been changed to `FALSE' (as was indicated in the help page).
1429 o Several bugs were fixed in the code of all.equal.phylo().
1431 o Several bugs were fixed in write.dna(), particularly this
1432 function did not work with `format = "interleaved"'.
1434 o Various errors were corrected in the help pages.
1439 o The argument names of as.hclust.phylo() have been changed
1440 from "(phy)" to "(x, ...)" to conform to the definition of
1441 the corresponding generic function.
1443 o gamma.stat() has been renamed gammaStat() to avoid confusion
1444 since gamma() is a generic function.
1448 CHANGES IN APE VERSION 1.1-3
1453 o base.freq() previously did not return a value of 0 for
1454 bases absent in the data (e.g., a vector of length 3 was
1455 returned if one base was absent). This is now fixed (a
1456 vector of length 4 is always returned).
1458 o Several bugs were fixed in read.nexus(), including that this
1459 function did not work in this absence of a "TRANSLATE"
1460 command in the NEXUS file, and that the commands were
1465 CHANGES IN APE VERSION 1.1-2
1470 o The Tamura and Nei (1993) model of DNA distance is now implemented
1471 in dist.dna(): five models are now available in this function.
1473 o A new data set is included: a set of 15 sequences of the
1474 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1480 o A bug in read.nexus() was fixed.
1482 o read.dna() previously did not work correctly in most cases.
1483 The function has been completely re-written and its help page
1484 has been considerably extended (see ?read.dna for details).
1485 Underscores (_) in taxon names are no more replaced with
1486 spaces (this behaviour was undocumented).
1488 o A bug was fixed in write.dna().
1492 CHANGES IN APE VERSION 1.1-1
1497 o A bug in read.tree() introduced in APE 1.1 was fixed.
1499 o A bug in compar.gee() resulted in an error when trying to fit
1500 a model with `family = "binomial"'. This is now fixed.
1504 CHANGES IN APE VERSION 1.1
1509 o The Klastorin (1982) method as suggested by Misawa and Tajima
1510 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1511 on the basis of phylogenetic trees has been implemented (see
1512 the function klastorin()).
1514 o Functions have been added to convert APE's "phylo" objects in
1515 "hclust" cluster objects and vice versa (see the help page of
1516 as.phylo for details).
1518 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1519 are introduced for the estimation of absolute evolutionary rates
1520 (ratogram) and dated clock-like trees (chronogram) from
1521 phylogenetic trees using the non-parametric rate smoothing approach
1522 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1524 o A summary method is now provided printing a summary information on a
1525 phylogenetic tree with, for instance, `summary(tree)'.
1527 o The behaviour of read.tree() was changed so that all spaces and
1528 tabulations in tree files are now ignored. Consequently, spaces in tip
1529 labels are no more allowed. Another side effect is that read.nexus()
1530 now does not replace the underscores (_) in tip labels with spaces
1531 (this behaviour was undocumented).
1533 o The function plot.phylo() has a new option (`underscore') which
1534 specifies whether the underscores in tip labels should be written on
1535 the plot as such or replaced with spaces (the default).
1537 o The function birthdeath() now computes 95% confidence intervals of
1538 the estimated parameters using profile likelihood.
1540 o Three new data sets are included: a gene tree estimated from 36
1541 landplant rbcL sequences, a gene tree estimated from 32 opsin
1542 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1547 o A bug was fixed in dist.gene() where nothing was returned.
1549 o A bug in plot.mst() was fixed.
1551 o A bug in vcv.phylo() resulted in false correlations when the
1552 option `cor = TRUE' was used (now fixed).
1556 CHANGES IN APE VERSION 1.0
1561 o Two new functions, read.dna() and write.dna(), read/write in a file
1562 DNA sequences in interleaved or in sequential format.
1564 o Two new functions, read.nexus() and write.nexus(), read/write trees
1567 o The new function bind.tree() allows to bind two trees together,
1568 possibly handling root edges to give internal branches.
1570 o The new function drop.tip() removes the tips in a phylogenetic tree,
1571 and trims (or not) the corresponding internal branches.
1573 o The new function is.ultrametric() tests if a tree is ultrametric.
1575 o The function plot.phylo() has more functionalities such as drawing the
1576 branches with different colours and/or different widths, showing the
1577 node labels, controling the position and font of the labels, rotating
1578 the labels, and controling the space around the plot.
1580 o The function read.tree() can now read trees with no branch length,
1581 such as "(a,b),c);". Consequently, the element `edge.length' in
1582 objects of class "phylo" is now optional.
1584 o The function write.tree() has a new default behaviour: if the default
1585 for the option `file' is used (i.e. file = ""), then a variable of
1586 mode character containing the tree in Newick format is returned which
1587 can thus be assigned (e.g., tree <- write.tree(phy)).
1589 o The function read.tree() has a new argument `text' which allows
1590 to read the tree in a variable of mode character.
1592 o A new data set is included: the phylogenetic relationships among
1593 the orders of birds from Sibley and Ahlquist (1990).
1597 CHANGES IN APE VERSION 0.2-1
1602 o Several bugs were fixed in the help pages.
1606 CHANGES IN APE VERSION 0.2
1611 o The function write.tree() writes phylogenetic trees (objects of class
1612 "phylo") in an ASCII file using the Newick parenthetic format.
1614 o The function birthdeath() fits a birth-death model to branching times
1615 by maximum likelihood, and estimates the corresponding speciation and
1618 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1621 o The function is.binary.tree() tests whether a phylogeny is binary.
1623 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1624 as well as some methods are introduced.
1626 o Several functions, including some generics and methods, for computing
1627 skyline plot estimates (classic and generalized) of effective
1628 population size through time are introduced and replace the function
1629 skyline.plot() in version 0.1.
1631 o Two data sets are now included: the phylogenetic relationships among
1632 the families of birds from Sibley and Ahlquist (1990), and an
1633 estimated clock-like phylogeny of HIV sequences sampled in the
1634 Democratic Republic of Congo.
1637 DEPRECATED & DEFUNCT
1639 o The function skyline.plot() in ape 0.1 has been deprecated and
1640 replaced by more elaborate functions (see above).
1645 o Two important bugs were fixed in plot.phylo(): phylogenies with
1646 multichotomies not at the root or not with only terminal branches,
1647 and phylogenies with a single node (i.e. only terminal branches)
1648 did not plot. These trees should be plotted correctly now.
1650 o Several bugs were fixed in diversi.time() in the computation of
1653 o Various errors were corrected in the help pages.