1 CHANGES IN APE VERSION 2.4
6 o base.freq() has a new option 'freq' to return the counts; the
7 default is still to return the proportions.
12 o seg.sites() did not handle ambiguous nucleotides correctly: they
15 o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
16 the tree: the argument is now ignored.
18 o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
24 o Trying to plot a tree with a single tip now returns NULL with a
25 warning (it returned an error previously).
27 o The way lines representing nodes are coloured in phylograms has
28 been modified (as well as their widths and types) following some
29 users' request; this is only for dichotomous nodes.
31 o The argument 'adj' in [node][tip][edge]labels() now works when
32 using 'pie' or 'thermo'.
34 o A more informative message error is now returned by dist.dna() when
35 'model' is badly specified (partial matching of this argument is
38 o Deprecated functions are now listed in a help page: see
39 help("ape-defunct") with the quotes.
44 o The functions heterozygosity, nuc.div, theta.h, theta.k and
45 theta.s have been moved from ape to pegas.
47 o The functions mlphylo, DNAmodel and sh.test have been removed.
51 CHANGES IN APE VERSION 2.3-3
56 o add.scale.bar() always drew a horizontal bar.
58 o zoom() shuffled tips with unrooted trees.
60 o write.nexus() failed to write correctly trees with a "TipLabel"
63 o rcoal() failed to compute branch lengths with very large n.
65 o A small bug was fixed in compar.cheverud() (thanks to Michael
68 o seg.sites() failed when passing a vector.
70 o drop.tip() sometimes shuffled tip labels.
72 o root() shuffled node labels with 'resolve.root = TRUE'.
76 CHANGES IN APE VERSION 2.3-2
81 o all.equal.phylo() did not compare unrooted trees correctly.
83 o dist.topo(... method = "PH85") did not treat unrooted trees
84 correctly (thanks to Tim Wallstrom for the fix).
86 o root() sometimes failed to test for the monophyly of the
89 o extract.clade() sometimes included too many edges.
91 o vcv.phylo() did not work correctly when the tree is in
94 o nj() did not handle correctly distance matrices with many 0's.
95 The code has also been significantly improved: 7, 70, 160 times
96 faster with n = 100, 500, 1000, respectively.
100 CHANGES IN APE VERSION 2.3-1
105 o The new function is.monophyletic tests the monophyly of a group.
107 o There is now a c() method for lists of class "DNAbin".
109 o yule.cov() now fits the null model, and its help page has been
110 corrected with respect to this change.
112 o drop.tip() has a new option 'rooted' to force (or not) a tree
113 to be treated as (un)rooted.
118 o dist.gene() failed on most occasions with the default
119 pairwise.deletion = FALSE.
121 o read.tree() failed to read correctly the tree name(s).
123 o boot.phylo() now treats correctly data frames.
125 o del.gaps() did not copy the rownames of a matrix.
127 o A small bug was fixed in CDAM.global().
129 o ace() failed with large data sets. Thanks to Rich FitzJohn for
130 the fix. With other improvements, this function is now about 6
133 o write.tree() failed with objects of class "multiPhylo".
135 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
140 o [.multiPhylo and [.DNAbin now respect the original class.
142 o Instances of the form class(phy) == "phylo" have been replaced
143 by inherits(phy, "phylo").
145 o rcoal() is now faster.
150 o klastorin() has been removed.
154 CHANGES IN APE VERSION 2.3
159 o The new functions CADM.global and CADM.post, contributed by
160 Pierre Legendre, test the congruence among several distance
163 o The new function yule.time fits a user-defined time-dependent
164 Yule model by maximum likelihood.
166 o The new function makeNodeLabel creates and/or modifies node
167 labels in a flexible way.
169 o read.tree() and write.tree() have been modified so that they can
170 handle individual tree names.
172 o plot.phylo() has a new argument 'edge.lty' that specifies the
173 types of lines used for the edges (plain, dotted, dashed, ...)
175 o phymltest() has been updated to work with PhyML 3.0.1.
180 o drop.tip() shuffled tip labels in some cases.
182 o drop.tip() did not handle node.label correctly.
184 o is.ultrametric() now checks the ordering of the edge matrix.
186 o ace() sometimes returned negative values of likelihoods of
187 ancestral states (thanks to Dan Rabosky for solving this long
193 o The data set xenarthra has been removed.
197 CHANGES IN APE VERSION 2.2-4
201 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
202 now fixed. (Thanks to Peter Wragg for the fix!)
204 o A warning message occurred for no reason with ace(method="GLS").
209 o There is now a general help page displayed with '?ape'
213 CHANGES IN APE VERSION 2.2-3
218 o The new function extract.clade extracts a clade from a tree by
219 specifying a node number or label.
221 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
222 operations of the same names.
224 o dist.dna() can now return the number of site differences by
225 specifying model="N".
230 o chronopl() did not work with CV = TRUE.
232 o read.nexus() did not work correctly in some situations (trees on
233 multiple lines with different numbers of lines and/or with
234 comments inserted within the trees).
236 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
237 the number of lineages with non-binary trees.
242 o ape has now a namespace.
244 o drop.tip() has been improved: it should be much faster and work
245 better in some cases (e.g., see the example in ?zoom).
249 CHANGES IN APE VERSION 2.2-2
254 o dist.gene() has been substantially improved and gains an option
257 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
263 o prop.part() failed with a single tree with the default option
264 'check.labels = TRUE'.
266 o summary.DNAbin() failed to display correctly the summary of
267 sequence lengths with lists of sequences of 10,000 bases or more
268 (because summary.default uses 4 significant digits by default).
270 o read.nexus() failed to read a file with a single tree with line
271 breaks in the Newick string.
273 o del.gaps() returned a list of empty sequences when there were no
279 o phymltest() has been updated for PhyML 3.0 and gains an option
280 'append', whereas the option 'path2exec' has been removed.
282 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
283 which is returned unchanged (instead of an error).
285 o The data sets bird.orders and bird.families are now stored as
286 Newick strings; i.e., the command data(bird.orders) calls
291 CHANGES IN APE VERSION 2.2-1
296 o The new function makeLabel() helps to modify labels of trees,
297 lists of trees, or DNA sequences, with several utilities to
298 truncate and/or make them unique, substituting some
299 characters, and so on.
301 o The new function del.gaps() removes insertion gaps ("-") in a
302 set of DNA sequences.
304 o read.dna() can now read Clustal files (*.aln).
309 o root() failed with 'resolve.root = TRUE' when the root was
310 already the specified root.
312 o Several bugs were fixed in mlphylo().
314 o collapsed.singles() did not propagate the 'Nnode' and
315 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
317 o read.nexus() failed to remove correctly the comments within
320 o read.nexus() failed to read a file with a single tree and no
321 translation of tip labels.
323 o read.nexus() failed to place correctly tip labels when reading
324 a single tree with no edge lengths.
326 o A bug was fixed in sh.test().
331 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
334 o The option 'check.labels' of consensus() and prop.part() is now
337 o write.dna() now does not truncate names to 10 characters with
342 CHANGES IN APE VERSION 2.2
347 o Four new functions have been written by Damien de Vienne for the
348 graphical exploration of large trees (cophyloplot, subtrees,
349 subtreeplot), and to return the graphical coordinates of tree
352 o The new functions corPagel and corBlomberg implement the Pagel's
353 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
355 o chronopl() has been improved and gains several options: see its
356 help page for details.
358 o boot.phylo() has now an option 'trees' to possibly return the
359 bootstraped trees (the default is FALSE).
361 o prop.part() has been improved and should now be faster in all
367 o read.dna() failed if "?" occurred in the first 10 sites of the
370 o The x/y aspect of the plot is now respected when plotting a
371 circular tree (type = "r" or "f").
373 o Drawing the tip labels sometimes failed when plotting circular
376 o zoom() failed when tip labels were used instead of their numbers
377 (thanks to Yan Wong for the fix).
379 o drop.tip() failed with some trees (fixed by Yan Wong).
381 o seg.sites() failed with a list.
383 o consensus() failed in some cases. The function has been improved
384 as well and is faster.
388 CHANGES IN APE VERSION 2.1-3
393 o A bug in read.nexus() made the Windows R-GUI crash.
395 o An error was fixed in the computation of ancestral character
396 states by generalized least squares in ace().
398 o di2multi() did not modify node labels correctly.
400 o multi2di() failed if the tree had its attribute "order" set to
405 CHANGES IN APE VERSION 2.1-2
410 o There three new methods for the "multiPhylo" class: str, $,
413 o root() gains the options 'node' and 'resolve.root'
414 (FALSE by default) as well as its code being improved.
416 o mltt.plot() has now an option 'log' used in the same way
417 than in plot.default().
422 o mltt.plot() failed to display the legend with an unnamed
425 o nodelabels() with pies now correcly uses the argument
426 'cex' to draw symbols of different sizes (which has
427 worked already for thermometers).
429 o read.nexus() generally failed to read very big files.
434 o The argument 'family' of compar.gee() can now be a function
435 as well as a character string.
437 o read.tree() and read.nexus() now return an unnamed list if
440 o read.nexus() now returns a modified object of class "multiPhylo"
441 when there is a TRANSLATE block in the NEXUS file: the individual
442 trees have no 'tip.label' vector, but the list has a 'TipLabel'
443 attribute. The new methods '$' and '[[' set these elements
444 correctly when extracting trees.
448 CHANGES IN APE VERSION 2.1-1
453 o The new function rmtree generates lists of random trees.
455 o rcoal() now generates a genuine coalescent tree by default
456 (thanks to Vladimir Minin for the code).
461 o nuc.div() returned an incorrect value with the default
462 pairwise.deletion = FALSE.
467 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
468 have been improved so that they are stabler and faster.
470 o R packages used by ape are now loaded silently; lattice and gee
471 are loaded only when needed.
475 CHANGES IN APE VERSION 2.1
480 o The new function identify.phylo identifies clades on a plotted
481 tree using the mouse.
483 o It is now possible to subset a list of trees (object of class
484 "multiPhylo") with "[" while keeping its class correct.
486 o The new function as.DNAbin.alignment converts DNA sequences
487 stored in the "alignment" format of the package seqinr into
488 an object of class "DNAbin".
490 o The new function weight.taxo2 helps to build similarity matrices
491 given two taxonomic levels (usually called by other functions).
493 o write.tree() can now take a list of trees (class "multiPhylo")
494 as its main argument.
496 o plot.correlogram() and plot.correlogramList() have been
497 improved, and gain several options (see the help page for
498 details). A legend is now plotted by default.
503 o dist.dna() returned some incorrect values with `model = "JC69"'
504 and `pairwise.deletion = TRUE'. This affected only the
505 distances involving sequences with missing values. (Thanks
506 to Bruno Toupance for digging this bug out.)
508 o write.tree() failed with some trees: this is fixed by removing
509 the `multi.line' option (trees are now always printed on a
512 o read.nexus() did not correctly detect trees with multiple root
513 edges (see OTHER CHANGES).
518 o The code of mlphylo() has been almost entirely rewritten, and
519 should be much stabler. The options have been also greatly
520 simplified (see ?mlphylo and ?DNAmodel for details).
522 o The internal function nTips has been renamed klastorin_nTips.
524 o The code of is.ultrametric() contained redundancies and has
527 o The code of Moran.I() and of correlogram.formula() have been
530 o read.tree() and read.nexus() now return an error when trying to
531 read a tree with multiple root edges (see BUG FIXES). The
532 correction applied in previous version did not work in all
535 o The class c("multi.tree", "phylo") has been renamed
541 o There is now a vignette in ape: see vignette("MoranI", "ape").
546 o as.matching() and as.phylo.matching() do not support branch
549 o correlogram.phylo() and discrete.dist() have been removed.
553 CHANGES IN APE VERSION 2.0-2
558 o The new function matexpo computes the exponential of a square
561 o The new function unique.multi.tree removes duplicate trees from
564 o yule() has a new option `use.root.edge = FALSE' that specifies
565 to ignore, by default, the root edge of the tree if it exists.
570 o which.edge() failed when the index of a single terminal edge was
573 o In diversi.time(), the values returned for model C were
576 o A bug was fixed in yule() that affected the calculation of the
577 likelihood in the presence of ties in the branching times.
579 o There was a bug in the C function mat_expo4x4 affecting the
580 calculations of the transition probabilities for models HKY and
583 o A small bug was fixed in as.matrix.DNAbin (thanks to James
586 o rtree() did not `shuffle' the tip labels by default, so only a
587 limited number of labelled topologies could be generated.
591 CHANGES IN APE VERSION 2.0-1
596 o The three new functions bionj, fastme.ols, and fastme.bal
597 perform phylogeny estimation by the BIONJ and fastME methods in
598 OLS and balanced versions. This is a port to R of previous
599 previous programs done by Vincent Lefort.
601 o The new function chronoMPL performs molecular dating with the
602 mean path lengths method of Britton et al. (2002, Mol. Phyl.
605 o The new function rotate, contributed by Christoph Heibl, swaps
606 two clades connected to the same node. It works also with
607 multichotomous nodes.
609 o The new `method' as.matrix.DNAbin() may be used to convert
610 easily DNA sequences stored in a list into a matrix while
611 keeping the names and the class.
616 o chronopl() failed when some branch lengths were equal to zero:
617 an error message is now returned.
619 o di2multi() failed when there was a series of consecutive edges
624 CHANGES IN APE VERSION 1.10-2
629 o plot.phylo() can now plot circular trees: the option is type =
630 "fan" or type = "f" (to avoid the ambiguity with type = "c").
632 o prop.part() has a new option `check.labels = FALSE' which allows
633 to considerably speed-up the calculations of bipartitions. As a
634 consequence, calculations of bootstrap values with boot.phylo()
635 should be much faster.
640 o read.GenBank() did not return correctly the list of species as
641 from ape 1.10: this is fixed in this version
643 o Applying as.phylo() on a tree of class "phylo" failed: the
644 object is now returned unchanged.
648 CHANGES IN APE VERSION 1.10-1
653 o The three new functions Ntip, Nnode, and Nedge return, for a
654 given tree, the number of tips, nodes, or edges, respectively.
659 o read.nexus() did not set correctly the class of the returned
660 object when reading multiple trees.
662 o mllt.plot() failed with objects of class c("multi.tree",
665 o unroot() did not work correctly in most cases.
667 o reorder.phylo() made R freeze in some occasions.
669 o Plotting a tree in pruningwise order failed.
671 o When plotting an unrooted tree, the tip labels where not all
672 correctly positioned if the option `cex' was used.
676 CHANGES IN APE VERSION 1.10
681 o Five new `method' functions have been introduced to manipulate
682 DNA sequences in binary format (see below).
684 o Three new functions have been introduced to convert between the
685 new binary and the character formats.
687 o The new function as.alignment converts DNA sequences stored as
688 single characters into the class "alignment" used by the package
691 o read.dna() and read.GenBank() have a new argument `as.character'
692 controlling whether the sequences are returned in binary format
698 o root() failed when the tree had node labels: this is fixed.
700 o plot.phylo() did not correctly set the limits on the y-axis with
701 the default setting: this is fixed.
703 o dist.dna() returned a wrong result for the LogDet, paralinear,
704 and BH87 models with `pairwise.deletion = TRUE'.
709 o DNA sequences are now internally stored in a binary format. See
710 the document "A Bit-Level Coding Scheme for Nucleotides" for the
711 details. Most functions analyzing DNA functions have been
712 modified accordingly and are now much faster (dist.dna is now
713 ca. 60 times faster).
717 CHANGES IN APE VERSION 1.9-4
722 o A bug was fixed in edgelabels().
724 o as.phylo.hclust() did not work correctly when the object of
725 class "hclust" has its labels set to NULL: the returned tree has
726 now its tip labels set to "1", "2", ...
728 o consensus could fail if some tip labels are a subset of others
729 (e.g., "a" and "a_1"): this is now fixed.
731 o mlphylo() failed in most cases if some branch lengths of the
732 initial tree were greater than one: an error message is now
735 o mlphylo() failed in most cases when estimating the proportion of
736 invariants: this is fixed.
740 CHANGES IN APE VERSION 1.9-3
745 o The new function edgelabels adds labels on the edge of the tree
746 in the same way than nodelabels or tiplabels.
751 o multi2di() did not handle correctly branch lengths with the
752 default option `random = TRUE': this is now fixed.
754 o A bug was fixed in nuc.div() when using pairwise deletions.
756 o A bug occurred in the analysis of bipartitions with large
757 numbers of large trees, with consequences on prop.part,
758 prop.clades, and boot.phylo.
760 o The calculation of the Billera-Holmes-Vogtmann distance in
761 dist.topo was wrong: this has been fixed.
765 CHANGES IN APE VERSION 1.9-2
770 o The new function ladderize reorganizes the internal structure of
771 a tree to plot them left- or right-ladderized.
773 o The new function dist.nodes computes the patristic distances
774 between all nodes, internal and terminal, of a tree. It replaces
775 the option `full = TRUE' of cophenetic.phylo (see below).
780 o A bug was fixed in old2new.phylo().
782 o Some bugs were fixed in chronopl().
784 o The edge colours were not correctly displayed by plot.phylo
785 (thank you to Li-San Wang for the fix).
787 o cophenetic.phylo() failed with multichotomous trees: this is
793 o read.dna() now returns the sequences in a matrix if they are
794 aligned (interleaved or sequential format). Sequences in FASTA
795 format are still returned in a list.
797 o The option `full' of cophenetic.phylo() has been removed because
798 it could not be used from the generic.
803 o rotate() has been removed; this function did not work correctly
808 CHANGES IN APE VERSION 1.9-1
813 o Trees with a single tip were not read correctly in R as the
814 element `Nnode' was not set: this is fixed.
816 o unroot() did not set correctly the number of nodes of the
817 unrooted tree in most cases.
819 o read.GenBank() failed when fetching very long sequences,
820 particularly of the BX-series.
822 o A bug was introduced in read.tree() with ape 1.9: it has been
827 CHANGES IN APE VERSION 1.9
832 o There are two new print `methods' for trees of class "phylo" and
833 lists of trees of class "multi.tree", so that they are now
834 displayed in a compact and informative way.
836 o There are two new functions, old2new.phylo and new2old.phylo,
837 for converting between the old and new coding of the class
840 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
841 LogDet ("logdet"), and paralinear ("paralin").
843 o compute.brlen() has been extended: several methods are now
844 available to compute branch lengths.
846 o write.dna() can now handle matrices as well as lists.
851 o cophenetic.phylo() sometimes returned a wrong result with
852 multichotomous trees: this is fixed.
854 o rotate() failed when a single tip was specified: the tree is now
857 o ace() did not return the correct index matrix with custom
858 models: this is fixed.
860 o multi2di() did not work correctly when resolving multichotomies
861 randomly: the topology was always the same, only the arrangement
862 of clades was randomized: this is fixed. This function now
863 accepts trees with no branch lengths.
865 o The output of diversi.gof() was blurred by useless prints when a
866 user distribution was specified. This has been corrected, and
867 the help page of this function has been expanded.
872 o The internal structure of the class "phylo" has been changed:
873 see the document "Definition of Formats for Coding Phylogenetic
874 Trees in R" for the details. In addition, the code of most
875 functions has been improved.
877 o Several functions have been improved by replacing some R codes
878 by C codes: pic, plot.phylo, and reorder.phylo.
880 o There is now a citation information: see citation("ape") in R.
882 o write.tree() now does not add extra 0's to branch lengths so
883 that 1.23 is printed "1.23" by default, not "1.2300000000".
885 o The syntax of bind.tree() has been simplified. This function now
886 accepts trees with no branch lengths, and handles correctly node
889 o The option `as.numeric' of mrca() has been removed.
891 o The unused options `format' and `rooted' of read.tree() have
894 o The unused option `format' of write.tree() has been removed.
896 o The use of node.depth() has been simplified.
900 CHANGES IN APE VERSION 1.8-5
905 o Two new functions read.nexus.data() and write.nexus.data(),
906 contributed by Johan Nylander, allow to read and write molecular
907 sequences in NEXUS files.
909 o The new function reorder.phylo() reorders the internal structure
910 of a tree of class "phylo". It is used as the generic, e.g.,
913 o read.tree() and read.nexus() can now read trees with a single
916 o The new data set `cynipids' supplies a set of protein sequences
922 o The code of all.equal.phylo() has been completely rewritten
923 (thanks to Benoît Durand) which fixes several bugs.
925 o read.tree() and read.nexus() now checks the labels of the tree
926 to remove or substitute any characters that are illegal in the
927 Newick format (parentheses, etc.)
929 o A negative P-value could be returned by mantel.test(): this is
934 CHANGES IN APE VERSION 1.8-4
939 o The new function sh.test() computes the Shimodaira-
942 o The new function collapse.singles() removes the nodes with a
943 single descendant from a tree.
945 o plot.phylo() has a new argument `tip.color' to specify the
948 o mlphylo() has now an option `quiet' to control the display of
949 the progress of the analysis (the default is FALSE).
954 o read.dna() did not read correctly sequences in sequential format
955 with leading alignment gaps "-": this is fixed.
957 o ace() returned a list with no class so that the generic
958 functions (anova, logLik, ...) could not be used directly. This
959 is fixed as ace() now returns an object of class "ace".
961 o anova.ace() had a small bug when computing the number of degrees
962 of freedom: this is fixed.
964 o mlphylo() did not work when the sequences were in a matrix or
965 a data frame: this is fixed.
967 o rtree() did not work correctly when trying to simulate an
968 unrooted tree with two tips: an error message is now issued.
973 o The algorithm of rtree() has been changed: it is now about 40,
974 100, and 130 times faster for 10, 100, and 1000 tips,
979 CHANGES IN APE VERSION 1.8-3
984 o There are four new `method' functions to be used with the
985 results of ace(): logLik(), deviance(), AIC(), and anova().
987 o The plot method of phymltest has two new arguments: `main' to
988 change the title, and `col' to control the colour of the
989 segments showing the AIC values.
991 o ace() has a new argument `ip' that gives the initial values used
992 in the ML estimation with discrete characters (see the examples
993 in ?ace). This function now returns a matrix giving the indices
994 of the estimated rates when analysing discrete characters.
996 o nodelabels() and tiplabels() have a new argument `pie' to
997 represent proportions, with any number of categories, as
998 piecharts. The use of the option `thermo' has been improved:
999 there is now no limitation on the number of categories.
1004 o mlphylo() did not work with more than two partitions: this is
1007 o root() failed if the proposed outgroup was already an outgroup
1008 in the tree: this is fixed.
1010 o The `col' argument in nodelabels() and tiplabels() was not
1011 correctly passed when `text' was used: this is fixed.
1013 o Two bugs were fixed in mlphylo(): parameters were not always
1014 correctly output, and the estimation failed in some cases.
1016 o plot.phylo() was stuck when given a tree with a single tip: this
1017 is fixed and a message error is now returned.
1019 o An error was corrected in the help page of gammaStat regarding
1020 the calculation of P-values.
1022 o Using gls() could crash R when the number of species in the tree
1023 and in the variables were different: this is fixed.
1027 CHANGES IN APE VERSION 1.8-2
1032 o The new function mlphylo() fits a phylogenetic tree by maximum
1033 likelihood from DNA sequences. Its companion function DNAmodel()
1034 is used to define the substitution model which may include
1035 partitioning. There are methods for logLik(), deviance(), and
1036 AIC(), and the summary() method has been extended to display in
1037 a friendly way the results of this model fitting. Currently, the
1038 functionality is limited to estimating the substitution and
1039 associated parameters and computing the likelihood.
1041 o The new function drop1.compar.gee (used as, e.g., drop1(m))
1042 tests for single effects in GEE-based comparative method. A
1043 warning message is printed if there is not enough degrees of
1049 o An error message was sometimes issued by plot.multi.tree(),
1050 though with no consequence.
1054 CHANGES IN APE VERSION 1.8-1
1059 o There is a new plot method for lists of trees (objects of class
1060 "multi.tree"): it calls plot.phylo() internally and is
1061 documented on the same help page.
1066 o A bug was fixed in the C code that analyzes bipartitions: this
1067 has impact on several functions like prop.part, prop.clades,
1068 boot.phylo, or consensus.
1070 o root() did not work correctly when the specified outgroup had
1071 more than one element: this is fixed.
1073 o dist.dna() sometimes returned a warning inappropriately: this
1076 o If the distance object given to nj() had no rownames, nj()
1077 returned a tree with no tip labels: it now returns tips labelled
1078 "1", "2", ..., corresponding to the row numbers.
1083 o nj() has been slightly changed so that tips with a zero distance
1084 are first aggregated with zero-lengthed branches; the usual NJ
1085 procedure is then performed on a distance matrix without 0's.
1089 CHANGES IN APE VERSION 1.8
1094 o The new function chronopl() estimates dates using the penalized
1095 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1097 o The new function consensus() calculates the consensus tree of a
1100 o The new function evolve.phylo() simulates the evolution of
1101 continuous characters along a phylogeny under a Brownian model.
1103 o The new plot method for objects of class "ancestral" displays a
1104 tree together with ancestral values, as returned by the above
1107 o The new function as.phylo.formula() returns a phylogeny from a
1108 set of nested taxonomic variables given as a formula.
1110 o The new function read.caic() reads trees in CAIC format.
1112 o The new function tiplabels() allows to add labels to the tips
1113 of a tree using text or plotting symbols in a flexible way.
1115 o The new function unroot() unroots a phylogeny.
1117 o multi2di() has a new option, `random', which specifies whether
1118 to resolve the multichotomies randomly (the default) or not.
1120 o prop.part() now returns an object of class "prop.part" for which
1121 there are print (to display a partition in a more friendly way)
1122 and summary (to extract the numbers) methods.
1124 o plot.phylo() has a new option, `show.tip.label', specifying
1125 whether to print the labels of the tips. The default is TRUE.
1127 o The code of nj() has been replaced by a faster C code: it is now
1128 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1131 o write.nexus() now writes whether a tree is rooted or not.
1136 o Two bugs have been fixed in root(): unrooted trees are now
1137 handled corretly, and node labels are now output normally.
1139 o A bug was fixed in phymltest(): the executable couldn't be found
1142 o Three bug have been fixed in ace(): computing the likelihood of
1143 ancestral states of discrete characters failed, custom models
1144 did not work, and the function failed with a null gradient (a
1145 warning message is now returned; this latter bug was also
1146 present in yule.cov() as well and is now fixed).
1148 o pic() hanged out when missing data were present: a message error
1151 o A small bug was fixed in dist.dna() where the gamma correction
1152 was not always correctly dispatched.
1154 o plot.phylo() plotted correctly the root edge only when the tree
1155 was plotted rightwards: this works now for all directions.
1160 o dist.taxo() has been renamed as weight.taxo().
1162 o Various error and warning messages have been improved.
1166 CHANGES IN APE VERSION 1.7
1169 o The new function ace() estimates ancestral character states for
1170 continuous characters (with ML, GLS, and contrasts methods), and
1171 discrete characters (with ML only) for any number of states.
1173 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1174 of directional evolution for continuous characters. The user
1175 specifies the node(s) of the tree where the character optimum
1178 o The new function is.rooted() tests whether a tree (of class
1181 o The new function rcoal() generates random ultrametric trees with
1182 the possibility to specify the function that generates the
1183 inter-nodes distances.
1185 o The new function mrca() gives for all pairs of tips in a tree
1186 (and optionally nodes too) the most recent common ancestor.
1188 o nodelabels() has a new option `thermo' to plot proportions (up
1189 to three classes) on the nodes of a tree.
1191 o rtree() has been improved: it can now generate rooted or
1192 unrooted trees, and the mathematical function that generates the
1193 branch lengths may be specified by the user. The tip labels may
1194 be given directly in the call to rtree. The limit cases (n = 2,
1195 3) are now handled correctly.
1197 o dist.topo() has a new argument `method' with two choices: "PH85"
1198 for Penny and Henny's method (already available before and now
1199 the default), and "BHV01" for the geometric distance by Billera
1200 et al. (2001, Adv. Appl. Math. 27:733).
1202 o write.tree() has a new option, `digits', which specifies the
1203 number of digits to be printed in the Newick tree. By default
1204 digits = 10. The numbers are now always printed in decimal form
1205 (i.e., 1.0e-1 is now avoided).
1207 o dist.dna() can now compute the raw distances between pairs of
1208 DNA sequences by specifying model = "raw".
1210 o dist.phylo() has a new option `full' to possibly compute the
1211 distances among all tips and nodes of the tree. The default if
1217 o Several bugs were fixed in all.equal.phylo().
1219 o dist.dna() did not handle correctly gaps ("-") in alignments:
1220 they are now considered as missing data.
1222 o rotate() did not work if the tips were not ordered: this is
1225 o mantel.test() returned NA in some special cases: this is fixed
1226 and the function has been improved and is now faster.
1228 o A bug was fixed in diversi.gof() where the calculation of A² was
1231 o cherry() did not work correctly under some OSs (mainly Linux):
1234 o is.binary.tree() has been modified so that it works with both
1235 rooted and unrooted trees.
1237 o The documentation of theta.s() was not correct: this has been
1240 o plot.mst() did not work correctly: this is fixed.
1244 CHANGES IN APE VERSION 1.6
1249 o The new function dist.topo() computes the topological distances
1252 o The new function boot.phylo() performs a bootstrap analysis on
1253 phylogeny estimation.
1255 o The new functions prop.part() and prop.clades() analyse
1256 bipartitions from a series of trees.
1261 o read.GenBank() now uses the EFetch utility of NCBI instead of
1262 the usual Web interface: it is now much faster (e.g., 12 times
1263 faster to retrieve 8 sequences, 37 times for 60 sequences).
1268 o Several bugs were fixed in read.dna().
1270 o Several bugs were fixed in diversi.time().
1272 o is.binary.tree() did not work correctly if the tree has no edge
1273 lengths: this is fixed.
1275 o drop.tip() did not correctly propagated the `node.label' of a
1276 tree: this is fixed.
1280 CHANGES IN APE VERSION 1.5
1285 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1286 convert objects between the classes "phylo" and "matching". The
1287 latter implements the representation of binary trees introduced by
1288 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1289 as.matching() has been introduced as well.
1291 o Two new functions, multi2di() and di2multi(), allow to resolve
1292 and collapse multichotomies with branches of length zero.
1294 o The new function nuc.div() computes the nucleotide diversity
1295 from a sample a DNA sequences.
1297 o dist.dna() has been completely rewritten with a much faster
1298 (particularly for large data sets) C code. Eight models are
1299 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1300 option `method' has been renamed `model'). Computation of variance
1301 is available for all models. A gamma-correction is possible for
1302 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1303 to remove sites with missing data on a pairwise basis. The option
1304 `GCcontent' has been removed.
1306 o read.GenBank() has a new option (species.names) which specifies
1307 whether to return the species names of the organisms in addition
1308 to the accession numbers of the sequences (this is the default
1311 o write.nexus() can now write several trees in the same NEXUS file.
1313 o drop.tip() has a new option `root.edge' that allows to specify the
1314 new root edge if internal branches are trimmed.
1319 o as.phylo.hclust() failed if some labels had parentheses: this
1322 o Several bugs were fixed in all.equal.phylo(). This function now
1323 returns the logical TRUE if the trees are identical but with
1324 different representations (a report was printed previously).
1326 o read.GenBank() did not correctly handle ambiguous base codes:
1332 o birthdeath() now returns an object of class "birthdeath" for
1333 which there is a print method.
1337 CHANGES IN APE VERSION 1.4
1342 o The new function nj() performs phylogeny estimation with the
1343 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1346 o The new function which.edge() identifies the edges of a tree
1347 that belong to a group specified as a set of tips.
1349 o The new function as.phylo.phylog() converts an object of class
1350 "phylog" (from the package ade4) into an object of class
1353 o The new function axisPhylo() draws axes on the side of a
1356 o The new function howmanytrees() calculates the number of trees
1357 in different cases and giving a number of tips.
1359 o write.tree() has a new option `multi.line' (TRUE by default) to
1360 write a Newick tree on several lines rather than on a single
1363 o The functionalities of zoom() have been extended. Several
1364 subtrees can be visualized at the same time, and they are marked
1365 on the main tree with colors. The context of the subtrees can be
1366 marked with the option `subtree' (see below).
1368 o drop.tip() has a new option `subtree' (FALSE by default) which
1369 specifies whether to output in the tree how many tips have been
1372 o The arguments of add.scale.bar() have been redefined and have
1373 now default values (see ?add.scale.bar for details). This
1374 function now works even if the plotted tree has no edge length.
1376 o plot.phylo() can now plot radial trees, but this does not take
1377 edge lengths into account.
1379 o In plot.phylo() with `type = "phylogram"', if the values of
1380 `edge.color' and `edge.width' are identical for sister-branches,
1381 they are propagated to the vertical line that link them.
1386 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1387 crashing. This is fixed.
1389 o In plot.phylo(), the options `edge.color' and `edge.width' are
1390 now properly recycled; their default values are now "black" and
1393 o A bug has been fixed in write.nexus().
1398 o The function node.depth.edgelength() has been removed and
1399 replaced by a C code.
1403 CHANGES IN APE VERSION 1.3-1
1408 o The new function nodelabels() allows to add labels to the nodes
1409 of a tree using text or plotting symbols in a flexible way.
1411 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1412 numeric values specifying the lower and upper limits on the x-
1413 and y-axes. This allows to leave some space on any side of the
1414 tree. If a single value is given, this is taken as the upper
1419 CHANGES IN APE VERSION 1.3
1424 o The new function phymltest() calls the software PHYML and fits
1425 28 models of DNA sequence evolution. There are a print method to
1426 display likelihood and AIC values, a summary method to compute
1427 the hierarchical likelihood ratio tests, and a plot method to
1428 display graphically the AIC values of each model.
1430 o The new function yule.cov() fits the Yule model with covariates,
1431 a model where the speciation rate is affected by several species
1432 traits through a generalized linear model. The parameters are
1433 estimated by maximum likelihood.
1435 o Three new functions, corBrownian(), corGrafen(), and
1436 corMartins(), compute the expected correlation structures among
1437 species given a phylogeny under different models of evolution.
1438 These can be used for GLS comparative phylogenetic methods (see
1439 the examples). There are coef() and corMatrix() methods and an
1440 Initialize.corPhyl() function associated.
1442 o The new function compar.cheverud() implements Cheverud et al.'s
1443 (1985; Evolution 39:1335) phylogenetic comparative method.
1445 o The new function varcomp() estimates variance components; it has
1448 o Two new functions, panel.superpose.correlogram() and
1449 plot.correlogramList(), allow to plot several phylogenetic
1452 o The new function node.leafnumber() computes the number of leaves
1453 of a subtree defined by a particular node.
1455 o The new function node.sons() gets all tags of son nodes from a
1458 o The new function compute.brlen() computes the branch lengths of
1459 a tree according to a specified method.
1461 o plot.phylo() has three new options: "cex" controls the size of
1462 the (tip and node) labels (thus it is no more needed to change
1463 the global graphical parameter), "direction" which allows to
1464 plot the tree rightwards, leftwards, upwards, or downwards, and
1465 "y.lim" which sets the upper limit on the y-axis.
1470 o Some functions which try to match tip labels and names of
1471 additional data (e.g. vector) are likely to fail if there are
1472 typing or syntax errors. If both series of names do not perfectly
1473 match, they are ignored and a warning message is now issued.
1474 These functions are bd.ext, compar.gee, pic. Their help pages
1475 have been clarified on this point.
1479 CHANGES IN APE VERSION 1.2-7
1484 o The new function root() reroots a phylogenetic tree with respect
1485 to a specified outgroup.
1487 o The new function rotate() rotates an internal branch of a tree.
1489 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1490 trees) controls the display of the tip labels in unrooted trees.
1491 This display has been greatly improved: the tip labels are now not
1492 expected to overlap with the tree (particularly if lab4ut =
1493 "axial"). In all cases, combining appropriate values of "lab4ut"
1494 and the font size (via "par(cex = )") should result in readable
1495 unrooted trees. See ?plot.phylo for some examples.
1497 o In drop.tip(), the argument `tip' can now be numeric or character.
1502 o drop.tip() did not work correctly with trees with no branch
1503 lengths: this is fixed.
1505 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1506 plotted with some line crossings: this is now fixed.
1510 CHANGES IN APE VERSION 1.2-6
1515 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1516 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1517 to implement comparative methods with an autocorrelation approach.
1519 o A new data set describing some life history traits of Carnivores
1525 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1530 o When plotting a tree with plot.phylo(), the new default of the
1531 option `label.offset' is now 0, so the labels are always visible.
1535 CHANGES IN APE VERSION 1.2-5
1540 o The new function bd.ext() fits a birth-death model with combined
1541 phylogenetic and taxonomic data, and estimates the corresponding
1542 speciation and extinction rates.
1547 o The package gee is no more required by ape but only suggested
1548 since only the function compar.gee() calls gee.
1552 CHANGES IN APE VERSION 1.2-4
1557 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1558 and lines.popsize) implementing a new approach for inferring the
1559 demographic history from genealogies using a reversible jump
1560 MCMC have been introduced.
1562 o The unit of time in the skyline plot and in the new plots can
1563 now be chosen to be actual years, rather than substitutions.
1567 CHANGES IN APE VERSION 1.2-3
1572 o The new function rtree() generates a random binary tree with or
1573 without branch lengths.
1575 o Two new functions for drawing lineages-through-time (LTT) plots
1576 are provided: ltt.lines() adds a LTT curve to an existing plot,
1577 and mltt.plot() does a multiple LTT plot giving several trees as
1578 arguments (see `?ltt.plot' for details).
1583 o Some taxon names made R crashing when calling as.phylo.hclust():
1586 o dist.dna() returned an error with two identical DNA sequences
1587 (only using the Jukes-Cantor method returned 0): this is fixed.
1592 o The function dist.phylo() has been re-written using a different
1593 algorithm: it is now about four times faster.
1595 o The code of branching.times() has been improved: it is now about
1600 CHANGES IN APE VERSION 1.2-2
1605 o The new function seg.sites() finds the segregating sites in a
1606 sample of DNA sequences.
1611 o A bug introduced in read.tree() and in read.nexus() with version
1614 o A few errors were corrected and a few examples were added in the
1619 CHANGES IN APE VERSION 1.2-1
1624 o plot.phylo() can now draw the edge of the root of a tree if it
1625 has one (see the new option `root.edge', its default is FALSE).
1630 o A bug was fixed in read.nexus(): files with semicolons inside
1631 comment blocks were not read correctly.
1633 o The behaviour of read.tree() and read.nexus() was corrected so
1634 that tree files with badly represented root edges (e.g., with
1635 an extra pair of parentheses, see the help pages for details)
1636 are now correctly represented in the object of class "phylo";
1637 a warning message is now issued.
1641 CHANGES IN APE VERSION 1.2
1646 o plot.phylo() has been completely re-written and offers several
1647 new functionalities. Three types of trees can now be drawn:
1648 phylogram (as previously), cladogram, and unrooted tree; in
1649 all three types the branch lengths can be drawn using the edge
1650 lengths of the phylogeny or not (e.g., if the latter is absent).
1651 The vertical position of the nodes can be adjusted with two
1652 choices (see option `node.pos'). The code has been re-structured,
1653 and two new functions (potentially useful for developpers) are
1654 documented separately: node.depth.edgelength() and node.depth();
1655 see the respective help pages for details.
1657 o The new function zoom() allows to explore very large trees by
1658 focusing on a small portion of it.
1660 o The new function yule() fits by maximum likelihood the Yule model
1661 (birth-only process) to a phylogenetic tree.
1663 o Support for writing DNA sequences in FASTA format has been
1664 introduced in write.dna() (support for reading sequences in
1665 this format was introduced in read.dna() in version 1.1-2).
1666 The function has been completely re-written, fixing some bugs
1667 (see below); the default behaviour is no more to display the
1668 sequences on the standard output. Several options have been
1669 introduced to control the sequence printing in a flexible
1670 way. The help page has been extended.
1672 o A new data set is included: a supertree of bats in NEXUS format.
1677 o In theta.s(), the default of the option `variance' has
1678 been changed to `FALSE' (as was indicated in the help page).
1680 o Several bugs were fixed in the code of all.equal.phylo().
1682 o Several bugs were fixed in write.dna(), particularly this
1683 function did not work with `format = "interleaved"'.
1685 o Various errors were corrected in the help pages.
1690 o The argument names of as.hclust.phylo() have been changed
1691 from "(phy)" to "(x, ...)" to conform to the definition of
1692 the corresponding generic function.
1694 o gamma.stat() has been renamed gammaStat() to avoid confusion
1695 since gamma() is a generic function.
1699 CHANGES IN APE VERSION 1.1-3
1704 o base.freq() previously did not return a value of 0 for
1705 bases absent in the data (e.g., a vector of length 3 was
1706 returned if one base was absent). This is now fixed (a
1707 vector of length 4 is always returned).
1709 o Several bugs were fixed in read.nexus(), including that this
1710 function did not work in this absence of a "TRANSLATE"
1711 command in the NEXUS file, and that the commands were
1716 CHANGES IN APE VERSION 1.1-2
1721 o The Tamura and Nei (1993) model of DNA distance is now implemented
1722 in dist.dna(): five models are now available in this function.
1724 o A new data set is included: a set of 15 sequences of the
1725 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1731 o A bug in read.nexus() was fixed.
1733 o read.dna() previously did not work correctly in most cases.
1734 The function has been completely re-written and its help page
1735 has been considerably extended (see ?read.dna for details).
1736 Underscores (_) in taxon names are no more replaced with
1737 spaces (this behaviour was undocumented).
1739 o A bug was fixed in write.dna().
1743 CHANGES IN APE VERSION 1.1-1
1748 o A bug in read.tree() introduced in APE 1.1 was fixed.
1750 o A bug in compar.gee() resulted in an error when trying to fit
1751 a model with `family = "binomial"'. This is now fixed.
1755 CHANGES IN APE VERSION 1.1
1760 o The Klastorin (1982) method as suggested by Misawa and Tajima
1761 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1762 on the basis of phylogenetic trees has been implemented (see
1763 the function klastorin()).
1765 o Functions have been added to convert APE's "phylo" objects in
1766 "hclust" cluster objects and vice versa (see the help page of
1767 as.phylo for details).
1769 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1770 are introduced for the estimation of absolute evolutionary rates
1771 (ratogram) and dated clock-like trees (chronogram) from
1772 phylogenetic trees using the non-parametric rate smoothing approach
1773 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1775 o A summary method is now provided printing a summary information on a
1776 phylogenetic tree with, for instance, `summary(tree)'.
1778 o The behaviour of read.tree() was changed so that all spaces and
1779 tabulations in tree files are now ignored. Consequently, spaces in tip
1780 labels are no more allowed. Another side effect is that read.nexus()
1781 now does not replace the underscores (_) in tip labels with spaces
1782 (this behaviour was undocumented).
1784 o The function plot.phylo() has a new option (`underscore') which
1785 specifies whether the underscores in tip labels should be written on
1786 the plot as such or replaced with spaces (the default).
1788 o The function birthdeath() now computes 95% confidence intervals of
1789 the estimated parameters using profile likelihood.
1791 o Three new data sets are included: a gene tree estimated from 36
1792 landplant rbcL sequences, a gene tree estimated from 32 opsin
1793 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1798 o A bug was fixed in dist.gene() where nothing was returned.
1800 o A bug in plot.mst() was fixed.
1802 o A bug in vcv.phylo() resulted in false correlations when the
1803 option `cor = TRUE' was used (now fixed).
1807 CHANGES IN APE VERSION 1.0
1812 o Two new functions, read.dna() and write.dna(), read/write in a file
1813 DNA sequences in interleaved or in sequential format.
1815 o Two new functions, read.nexus() and write.nexus(), read/write trees
1818 o The new function bind.tree() allows to bind two trees together,
1819 possibly handling root edges to give internal branches.
1821 o The new function drop.tip() removes the tips in a phylogenetic tree,
1822 and trims (or not) the corresponding internal branches.
1824 o The new function is.ultrametric() tests if a tree is ultrametric.
1826 o The function plot.phylo() has more functionalities such as drawing the
1827 branches with different colours and/or different widths, showing the
1828 node labels, controling the position and font of the labels, rotating
1829 the labels, and controling the space around the plot.
1831 o The function read.tree() can now read trees with no branch length,
1832 such as "(a,b),c);". Consequently, the element `edge.length' in
1833 objects of class "phylo" is now optional.
1835 o The function write.tree() has a new default behaviour: if the default
1836 for the option `file' is used (i.e. file = ""), then a variable of
1837 mode character containing the tree in Newick format is returned which
1838 can thus be assigned (e.g., tree <- write.tree(phy)).
1840 o The function read.tree() has a new argument `text' which allows
1841 to read the tree in a variable of mode character.
1843 o A new data set is included: the phylogenetic relationships among
1844 the orders of birds from Sibley and Ahlquist (1990).
1848 CHANGES IN APE VERSION 0.2-1
1853 o Several bugs were fixed in the help pages.
1857 CHANGES IN APE VERSION 0.2
1862 o The function write.tree() writes phylogenetic trees (objects of class
1863 "phylo") in an ASCII file using the Newick parenthetic format.
1865 o The function birthdeath() fits a birth-death model to branching times
1866 by maximum likelihood, and estimates the corresponding speciation and
1869 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1872 o The function is.binary.tree() tests whether a phylogeny is binary.
1874 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1875 as well as some methods are introduced.
1877 o Several functions, including some generics and methods, for computing
1878 skyline plot estimates (classic and generalized) of effective
1879 population size through time are introduced and replace the function
1880 skyline.plot() in version 0.1.
1882 o Two data sets are now included: the phylogenetic relationships among
1883 the families of birds from Sibley and Ahlquist (1990), and an
1884 estimated clock-like phylogeny of HIV sequences sampled in the
1885 Democratic Republic of Congo.
1888 DEPRECATED & DEFUNCT
1890 o The function skyline.plot() in ape 0.1 has been deprecated and
1891 replaced by more elaborate functions (see above).
1896 o Two important bugs were fixed in plot.phylo(): phylogenies with
1897 multichotomies not at the root or not with only terminal branches,
1898 and phylogenies with a single node (i.e. only terminal branches)
1899 did not plot. These trees should be plotted correctly now.
1901 o Several bugs were fixed in diversi.time() in the computation of
1904 o Various errors were corrected in the help pages.
projects / ape.git / blob