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.
21 o Trying to plot a tree with a single tip now returns NULL with a
22 warning (it returned an error previously).
24 o The way lines representing nodes are coloured in phylograms has
25 been modified (as well as their widths and types) following some
26 users' request; this is only for dichotomous nodes.
28 o The argument 'adj' in [node][tip][edge]labels() now works when
29 using 'pie' or 'thermo'.
31 o Deprecated functions are now listed in a help page: see
32 help("ape-defunct") with the quotes.
37 o The functions heterozygosity, nuc.div, theta.h, theta.k and
38 theta.s have been moved from ape to pegas.
42 CHANGES IN APE VERSION 2.3-3
47 o add.scale.bar() always drew a horizontal bar.
49 o zoom() shuffled tips with unrooted trees.
51 o write.nexus() failed to write correctly trees with a "TipLabel"
54 o rcoal() failed to compute branch lengths with very large n.
56 o A small bug was fixed in compar.cheverud() (thanks to Michael
59 o seg.sites() failed when passing a vector.
61 o drop.tip() sometimes shuffled tip labels.
63 o root() shuffled node labels with 'resolve.root = TRUE'.
67 CHANGES IN APE VERSION 2.3-2
72 o all.equal.phylo() did not compare unrooted trees correctly.
74 o dist.topo(... method = "PH85") did not treat unrooted trees
75 correctly (thanks to Tim Wallstrom for the fix).
77 o root() sometimes failed to test for the monophyly of the
80 o extract.clade() sometimes included too many edges.
82 o vcv.phylo() did not work correctly when the tree is in
85 o nj() did not handle correctly distance matrices with many 0's.
86 The code has also been significantly improved: 7, 70, 160 times
87 faster with n = 100, 500, 1000, respectively.
91 CHANGES IN APE VERSION 2.3-1
96 o The new function is.monophyletic tests the monophyly of a group.
98 o There is now a c() method for lists of class "DNAbin".
100 o yule.cov() now fits the null model, and its help page has been
101 corrected with respect to this change.
103 o drop.tip() has a new option 'rooted' to force (or not) a tree
104 to be treated as (un)rooted.
109 o dist.gene() failed on most occasions with the default
110 pairwise.deletion = FALSE.
112 o read.tree() failed to read correctly the tree name(s).
114 o boot.phylo() now treats correctly data frames.
116 o del.gaps() did not copy the rownames of a matrix.
118 o A small bug was fixed in CDAM.global().
120 o ace() failed with large data sets. Thanks to Rich FitzJohn for
121 the fix. With other improvements, this function is now about 6
124 o write.tree() failed with objects of class "multiPhylo".
126 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
131 o [.multiPhylo and [.DNAbin now respect the original class.
133 o Instances of the form class(phy) == "phylo" have been replaced
134 by inherits(phy, "phylo").
136 o rcoal() is now faster.
141 o klastorin() has been removed.
145 CHANGES IN APE VERSION 2.3
150 o The new functions CADM.global and CADM.post, contributed by
151 Pierre Legendre, test the congruence among several distance
154 o The new function yule.time fits a user-defined time-dependent
155 Yule model by maximum likelihood.
157 o The new function makeNodeLabel creates and/or modifies node
158 labels in a flexible way.
160 o read.tree() and write.tree() have been modified so that they can
161 handle individual tree names.
163 o plot.phylo() has a new argument 'edge.lty' that specifies the
164 types of lines used for the edges (plain, dotted, dashed, ...)
166 o phymltest() has been updated to work with PhyML 3.0.1.
171 o drop.tip() shuffled tip labels in some cases.
173 o drop.tip() did not handle node.label correctly.
175 o is.ultrametric() now checks the ordering of the edge matrix.
177 o ace() sometimes returned negative values of likelihoods of
178 ancestral states (thanks to Dan Rabosky for solving this long
184 o The data set xenarthra has been removed.
188 CHANGES IN APE VERSION 2.2-4
192 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
193 now fixed. (Thanks to Peter Wragg for the fix!)
195 o A warning message occurred for no reason with ace(method="GLS").
200 o There is now a general help page displayed with '?ape'
204 CHANGES IN APE VERSION 2.2-3
209 o The new function extract.clade extracts a clade from a tree by
210 specifying a node number or label.
212 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
213 operations of the same names.
215 o dist.dna() can now return the number of site differences by
216 specifying model="N".
221 o chronopl() did not work with CV = TRUE.
223 o read.nexus() did not work correctly in some situations (trees on
224 multiple lines with different numbers of lines and/or with
225 comments inserted within the trees).
227 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
228 the number of lineages with non-binary trees.
233 o ape has now a namespace.
235 o drop.tip() has been improved: it should be much faster and work
236 better in some cases (e.g., see the example in ?zoom).
240 CHANGES IN APE VERSION 2.2-2
245 o dist.gene() has been substantially improved and gains an option
248 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
254 o prop.part() failed with a single tree with the default option
255 'check.labels = TRUE'.
257 o summary.DNAbin() failed to display correctly the summary of
258 sequence lengths with lists of sequences of 10,000 bases or more
259 (because summary.default uses 4 significant digits by default).
261 o read.nexus() failed to read a file with a single tree with line
262 breaks in the Newick string.
264 o del.gaps() returned a list of empty sequences when there were no
270 o phymltest() has been updated for PhyML 3.0 and gains an option
271 'append', whereas the option 'path2exec' has been removed.
273 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
274 which is returned unchanged (instead of an error).
276 o The data sets bird.orders and bird.families are now stored as
277 Newick strings; i.e., the command data(bird.orders) calls
282 CHANGES IN APE VERSION 2.2-1
287 o The new function makeLabel() helps to modify labels of trees,
288 lists of trees, or DNA sequences, with several utilities to
289 truncate and/or make them unique, substituting some
290 characters, and so on.
292 o The new function del.gaps() removes insertion gaps ("-") in a
293 set of DNA sequences.
295 o read.dna() can now read Clustal files (*.aln).
300 o root() failed with 'resolve.root = TRUE' when the root was
301 already the specified root.
303 o Several bugs were fixed in mlphylo().
305 o collapsed.singles() did not propagate the 'Nnode' and
306 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
308 o read.nexus() failed to remove correctly the comments within
311 o read.nexus() failed to read a file with a single tree and no
312 translation of tip labels.
314 o read.nexus() failed to place correctly tip labels when reading
315 a single tree with no edge lengths.
317 o A bug was fixed in sh.test().
322 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
325 o The option 'check.labels' of consensus() and prop.part() is now
328 o write.dna() now does not truncate names to 10 characters with
333 CHANGES IN APE VERSION 2.2
338 o Four new functions have been written by Damien de Vienne for the
339 graphical exploration of large trees (cophyloplot, subtrees,
340 subtreeplot), and to return the graphical coordinates of tree
343 o The new functions corPagel and corBlomberg implement the Pagel's
344 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
346 o chronopl() has been improved and gains several options: see its
347 help page for details.
349 o boot.phylo() has now an option 'trees' to possibly return the
350 bootstraped trees (the default is FALSE).
352 o prop.part() has been improved and should now be faster in all
358 o read.dna() failed if "?" occurred in the first 10 sites of the
361 o The x/y aspect of the plot is now respected when plotting a
362 circular tree (type = "r" or "f").
364 o Drawing the tip labels sometimes failed when plotting circular
367 o zoom() failed when tip labels were used instead of their numbers
368 (thanks to Yan Wong for the fix).
370 o drop.tip() failed with some trees (fixed by Yan Wong).
372 o seg.sites() failed with a list.
374 o consensus() failed in some cases. The function has been improved
375 as well and is faster.
379 CHANGES IN APE VERSION 2.1-3
384 o A bug in read.nexus() made the Windows R-GUI crash.
386 o An error was fixed in the computation of ancestral character
387 states by generalized least squares in ace().
389 o di2multi() did not modify node labels correctly.
391 o multi2di() failed if the tree had its attribute "order" set to
396 CHANGES IN APE VERSION 2.1-2
401 o There three new methods for the "multiPhylo" class: str, $,
404 o root() gains the options 'node' and 'resolve.root'
405 (FALSE by default) as well as its code being improved.
407 o mltt.plot() has now an option 'log' used in the same way
408 than in plot.default().
413 o mltt.plot() failed to display the legend with an unnamed
416 o nodelabels() with pies now correcly uses the argument
417 'cex' to draw symbols of different sizes (which has
418 worked already for thermometers).
420 o read.nexus() generally failed to read very big files.
425 o The argument 'family' of compar.gee() can now be a function
426 as well as a character string.
428 o read.tree() and read.nexus() now return an unnamed list if
431 o read.nexus() now returns a modified object of class "multiPhylo"
432 when there is a TRANSLATE block in the NEXUS file: the individual
433 trees have no 'tip.label' vector, but the list has a 'TipLabel'
434 attribute. The new methods '$' and '[[' set these elements
435 correctly when extracting trees.
439 CHANGES IN APE VERSION 2.1-1
444 o The new function rmtree generates lists of random trees.
446 o rcoal() now generates a genuine coalescent tree by default
447 (thanks to Vladimir Minin for the code).
452 o nuc.div() returned an incorrect value with the default
453 pairwise.deletion = FALSE.
458 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
459 have been improved so that they are stabler and faster.
461 o R packages used by ape are now loaded silently; lattice and gee
462 are loaded only when needed.
466 CHANGES IN APE VERSION 2.1
471 o The new function identify.phylo identifies clades on a plotted
472 tree using the mouse.
474 o It is now possible to subset a list of trees (object of class
475 "multiPhylo") with "[" while keeping its class correct.
477 o The new function as.DNAbin.alignment converts DNA sequences
478 stored in the "alignment" format of the package seqinr into
479 an object of class "DNAbin".
481 o The new function weight.taxo2 helps to build similarity matrices
482 given two taxonomic levels (usually called by other functions).
484 o write.tree() can now take a list of trees (class "multiPhylo")
485 as its main argument.
487 o plot.correlogram() and plot.correlogramList() have been
488 improved, and gain several options (see the help page for
489 details). A legend is now plotted by default.
494 o dist.dna() returned some incorrect values with `model = "JC69"'
495 and `pairwise.deletion = TRUE'. This affected only the
496 distances involving sequences with missing values. (Thanks
497 to Bruno Toupance for digging this bug out.)
499 o write.tree() failed with some trees: this is fixed by removing
500 the `multi.line' option (trees are now always printed on a
503 o read.nexus() did not correctly detect trees with multiple root
504 edges (see OTHER CHANGES).
509 o The code of mlphylo() has been almost entirely rewritten, and
510 should be much stabler. The options have been also greatly
511 simplified (see ?mlphylo and ?DNAmodel for details).
513 o The internal function nTips has been renamed klastorin_nTips.
515 o The code of is.ultrametric() contained redundancies and has
518 o The code of Moran.I() and of correlogram.formula() have been
521 o read.tree() and read.nexus() now return an error when trying to
522 read a tree with multiple root edges (see BUG FIXES). The
523 correction applied in previous version did not work in all
526 o The class c("multi.tree", "phylo") has been renamed
532 o There is now a vignette in ape: see vignette("MoranI", "ape").
537 o as.matching() and as.phylo.matching() do not support branch
540 o correlogram.phylo() and discrete.dist() have been removed.
544 CHANGES IN APE VERSION 2.0-2
549 o The new function matexpo computes the exponential of a square
552 o The new function unique.multi.tree removes duplicate trees from
555 o yule() has a new option `use.root.edge = FALSE' that specifies
556 to ignore, by default, the root edge of the tree if it exists.
561 o which.edge() failed when the index of a single terminal edge was
564 o In diversi.time(), the values returned for model C were
567 o A bug was fixed in yule() that affected the calculation of the
568 likelihood in the presence of ties in the branching times.
570 o There was a bug in the C function mat_expo4x4 affecting the
571 calculations of the transition probabilities for models HKY and
574 o A small bug was fixed in as.matrix.DNAbin (thanks to James
577 o rtree() did not `shuffle' the tip labels by default, so only a
578 limited number of labelled topologies could be generated.
582 CHANGES IN APE VERSION 2.0-1
587 o The three new functions bionj, fastme.ols, and fastme.bal
588 perform phylogeny estimation by the BIONJ and fastME methods in
589 OLS and balanced versions. This is a port to R of previous
590 previous programs done by Vincent Lefort.
592 o The new function chronoMPL performs molecular dating with the
593 mean path lengths method of Britton et al. (2002, Mol. Phyl.
596 o The new function rotate, contributed by Christoph Heibl, swaps
597 two clades connected to the same node. It works also with
598 multichotomous nodes.
600 o The new `method' as.matrix.DNAbin() may be used to convert
601 easily DNA sequences stored in a list into a matrix while
602 keeping the names and the class.
607 o chronopl() failed when some branch lengths were equal to zero:
608 an error message is now returned.
610 o di2multi() failed when there was a series of consecutive edges
615 CHANGES IN APE VERSION 1.10-2
620 o plot.phylo() can now plot circular trees: the option is type =
621 "fan" or type = "f" (to avoid the ambiguity with type = "c").
623 o prop.part() has a new option `check.labels = FALSE' which allows
624 to considerably speed-up the calculations of bipartitions. As a
625 consequence, calculations of bootstrap values with boot.phylo()
626 should be much faster.
631 o read.GenBank() did not return correctly the list of species as
632 from ape 1.10: this is fixed in this version
634 o Applying as.phylo() on a tree of class "phylo" failed: the
635 object is now returned unchanged.
639 CHANGES IN APE VERSION 1.10-1
644 o The three new functions Ntip, Nnode, and Nedge return, for a
645 given tree, the number of tips, nodes, or edges, respectively.
650 o read.nexus() did not set correctly the class of the returned
651 object when reading multiple trees.
653 o mllt.plot() failed with objects of class c("multi.tree",
656 o unroot() did not work correctly in most cases.
658 o reorder.phylo() made R freeze in some occasions.
660 o Plotting a tree in pruningwise order failed.
662 o When plotting an unrooted tree, the tip labels where not all
663 correctly positioned if the option `cex' was used.
667 CHANGES IN APE VERSION 1.10
672 o Five new `method' functions have been introduced to manipulate
673 DNA sequences in binary format (see below).
675 o Three new functions have been introduced to convert between the
676 new binary and the character formats.
678 o The new function as.alignment converts DNA sequences stored as
679 single characters into the class "alignment" used by the package
682 o read.dna() and read.GenBank() have a new argument `as.character'
683 controlling whether the sequences are returned in binary format
689 o root() failed when the tree had node labels: this is fixed.
691 o plot.phylo() did not correctly set the limits on the y-axis with
692 the default setting: this is fixed.
694 o dist.dna() returned a wrong result for the LogDet, paralinear,
695 and BH87 models with `pairwise.deletion = TRUE'.
700 o DNA sequences are now internally stored in a binary format. See
701 the document "A Bit-Level Coding Scheme for Nucleotides" for the
702 details. Most functions analyzing DNA functions have been
703 modified accordingly and are now much faster (dist.dna is now
704 ca. 60 times faster).
708 CHANGES IN APE VERSION 1.9-4
713 o A bug was fixed in edgelabels().
715 o as.phylo.hclust() did not work correctly when the object of
716 class "hclust" has its labels set to NULL: the returned tree has
717 now its tip labels set to "1", "2", ...
719 o consensus could fail if some tip labels are a subset of others
720 (e.g., "a" and "a_1"): this is now fixed.
722 o mlphylo() failed in most cases if some branch lengths of the
723 initial tree were greater than one: an error message is now
726 o mlphylo() failed in most cases when estimating the proportion of
727 invariants: this is fixed.
731 CHANGES IN APE VERSION 1.9-3
736 o The new function edgelabels adds labels on the edge of the tree
737 in the same way than nodelabels or tiplabels.
742 o multi2di() did not handle correctly branch lengths with the
743 default option `random = TRUE': this is now fixed.
745 o A bug was fixed in nuc.div() when using pairwise deletions.
747 o A bug occurred in the analysis of bipartitions with large
748 numbers of large trees, with consequences on prop.part,
749 prop.clades, and boot.phylo.
751 o The calculation of the Billera-Holmes-Vogtmann distance in
752 dist.topo was wrong: this has been fixed.
756 CHANGES IN APE VERSION 1.9-2
761 o The new function ladderize reorganizes the internal structure of
762 a tree to plot them left- or right-ladderized.
764 o The new function dist.nodes computes the patristic distances
765 between all nodes, internal and terminal, of a tree. It replaces
766 the option `full = TRUE' of cophenetic.phylo (see below).
771 o A bug was fixed in old2new.phylo().
773 o Some bugs were fixed in chronopl().
775 o The edge colours were not correctly displayed by plot.phylo
776 (thank you to Li-San Wang for the fix).
778 o cophenetic.phylo() failed with multichotomous trees: this is
784 o read.dna() now returns the sequences in a matrix if they are
785 aligned (interleaved or sequential format). Sequences in FASTA
786 format are still returned in a list.
788 o The option `full' of cophenetic.phylo() has been removed because
789 it could not be used from the generic.
794 o rotate() has been removed; this function did not work correctly
799 CHANGES IN APE VERSION 1.9-1
804 o Trees with a single tip were not read correctly in R as the
805 element `Nnode' was not set: this is fixed.
807 o unroot() did not set correctly the number of nodes of the
808 unrooted tree in most cases.
810 o read.GenBank() failed when fetching very long sequences,
811 particularly of the BX-series.
813 o A bug was introduced in read.tree() with ape 1.9: it has been
818 CHANGES IN APE VERSION 1.9
823 o There are two new print `methods' for trees of class "phylo" and
824 lists of trees of class "multi.tree", so that they are now
825 displayed in a compact and informative way.
827 o There are two new functions, old2new.phylo and new2old.phylo,
828 for converting between the old and new coding of the class
831 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
832 LogDet ("logdet"), and paralinear ("paralin").
834 o compute.brlen() has been extended: several methods are now
835 available to compute branch lengths.
837 o write.dna() can now handle matrices as well as lists.
842 o cophenetic.phylo() sometimes returned a wrong result with
843 multichotomous trees: this is fixed.
845 o rotate() failed when a single tip was specified: the tree is now
848 o ace() did not return the correct index matrix with custom
849 models: this is fixed.
851 o multi2di() did not work correctly when resolving multichotomies
852 randomly: the topology was always the same, only the arrangement
853 of clades was randomized: this is fixed. This function now
854 accepts trees with no branch lengths.
856 o The output of diversi.gof() was blurred by useless prints when a
857 user distribution was specified. This has been corrected, and
858 the help page of this function has been expanded.
863 o The internal structure of the class "phylo" has been changed:
864 see the document "Definition of Formats for Coding Phylogenetic
865 Trees in R" for the details. In addition, the code of most
866 functions has been improved.
868 o Several functions have been improved by replacing some R codes
869 by C codes: pic, plot.phylo, and reorder.phylo.
871 o There is now a citation information: see citation("ape") in R.
873 o write.tree() now does not add extra 0's to branch lengths so
874 that 1.23 is printed "1.23" by default, not "1.2300000000".
876 o The syntax of bind.tree() has been simplified. This function now
877 accepts trees with no branch lengths, and handles correctly node
880 o The option `as.numeric' of mrca() has been removed.
882 o The unused options `format' and `rooted' of read.tree() have
885 o The unused option `format' of write.tree() has been removed.
887 o The use of node.depth() has been simplified.
891 CHANGES IN APE VERSION 1.8-5
896 o Two new functions read.nexus.data() and write.nexus.data(),
897 contributed by Johan Nylander, allow to read and write molecular
898 sequences in NEXUS files.
900 o The new function reorder.phylo() reorders the internal structure
901 of a tree of class "phylo". It is used as the generic, e.g.,
904 o read.tree() and read.nexus() can now read trees with a single
907 o The new data set `cynipids' supplies a set of protein sequences
913 o The code of all.equal.phylo() has been completely rewritten
914 (thanks to Benoît Durand) which fixes several bugs.
916 o read.tree() and read.nexus() now checks the labels of the tree
917 to remove or substitute any characters that are illegal in the
918 Newick format (parentheses, etc.)
920 o A negative P-value could be returned by mantel.test(): this is
925 CHANGES IN APE VERSION 1.8-4
930 o The new function sh.test() computes the Shimodaira-
933 o The new function collapse.singles() removes the nodes with a
934 single descendant from a tree.
936 o plot.phylo() has a new argument `tip.color' to specify the
939 o mlphylo() has now an option `quiet' to control the display of
940 the progress of the analysis (the default is FALSE).
945 o read.dna() did not read correctly sequences in sequential format
946 with leading alignment gaps "-": this is fixed.
948 o ace() returned a list with no class so that the generic
949 functions (anova, logLik, ...) could not be used directly. This
950 is fixed as ace() now returns an object of class "ace".
952 o anova.ace() had a small bug when computing the number of degrees
953 of freedom: this is fixed.
955 o mlphylo() did not work when the sequences were in a matrix or
956 a data frame: this is fixed.
958 o rtree() did not work correctly when trying to simulate an
959 unrooted tree with two tips: an error message is now issued.
964 o The algorithm of rtree() has been changed: it is now about 40,
965 100, and 130 times faster for 10, 100, and 1000 tips,
970 CHANGES IN APE VERSION 1.8-3
975 o There are four new `method' functions to be used with the
976 results of ace(): logLik(), deviance(), AIC(), and anova().
978 o The plot method of phymltest has two new arguments: `main' to
979 change the title, and `col' to control the colour of the
980 segments showing the AIC values.
982 o ace() has a new argument `ip' that gives the initial values used
983 in the ML estimation with discrete characters (see the examples
984 in ?ace). This function now returns a matrix giving the indices
985 of the estimated rates when analysing discrete characters.
987 o nodelabels() and tiplabels() have a new argument `pie' to
988 represent proportions, with any number of categories, as
989 piecharts. The use of the option `thermo' has been improved:
990 there is now no limitation on the number of categories.
995 o mlphylo() did not work with more than two partitions: this is
998 o root() failed if the proposed outgroup was already an outgroup
999 in the tree: this is fixed.
1001 o The `col' argument in nodelabels() and tiplabels() was not
1002 correctly passed when `text' was used: this is fixed.
1004 o Two bugs were fixed in mlphylo(): parameters were not always
1005 correctly output, and the estimation failed in some cases.
1007 o plot.phylo() was stuck when given a tree with a single tip: this
1008 is fixed and a message error is now returned.
1010 o An error was corrected in the help page of gammaStat regarding
1011 the calculation of P-values.
1013 o Using gls() could crash R when the number of species in the tree
1014 and in the variables were different: this is fixed.
1018 CHANGES IN APE VERSION 1.8-2
1023 o The new function mlphylo() fits a phylogenetic tree by maximum
1024 likelihood from DNA sequences. Its companion function DNAmodel()
1025 is used to define the substitution model which may include
1026 partitioning. There are methods for logLik(), deviance(), and
1027 AIC(), and the summary() method has been extended to display in
1028 a friendly way the results of this model fitting. Currently, the
1029 functionality is limited to estimating the substitution and
1030 associated parameters and computing the likelihood.
1032 o The new function drop1.compar.gee (used as, e.g., drop1(m))
1033 tests for single effects in GEE-based comparative method. A
1034 warning message is printed if there is not enough degrees of
1040 o An error message was sometimes issued by plot.multi.tree(),
1041 though with no consequence.
1045 CHANGES IN APE VERSION 1.8-1
1050 o There is a new plot method for lists of trees (objects of class
1051 "multi.tree"): it calls plot.phylo() internally and is
1052 documented on the same help page.
1057 o A bug was fixed in the C code that analyzes bipartitions: this
1058 has impact on several functions like prop.part, prop.clades,
1059 boot.phylo, or consensus.
1061 o root() did not work correctly when the specified outgroup had
1062 more than one element: this is fixed.
1064 o dist.dna() sometimes returned a warning inappropriately: this
1067 o If the distance object given to nj() had no rownames, nj()
1068 returned a tree with no tip labels: it now returns tips labelled
1069 "1", "2", ..., corresponding to the row numbers.
1074 o nj() has been slightly changed so that tips with a zero distance
1075 are first aggregated with zero-lengthed branches; the usual NJ
1076 procedure is then performed on a distance matrix without 0's.
1080 CHANGES IN APE VERSION 1.8
1085 o The new function chronopl() estimates dates using the penalized
1086 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1088 o The new function consensus() calculates the consensus tree of a
1091 o The new function evolve.phylo() simulates the evolution of
1092 continuous characters along a phylogeny under a Brownian model.
1094 o The new plot method for objects of class "ancestral" displays a
1095 tree together with ancestral values, as returned by the above
1098 o The new function as.phylo.formula() returns a phylogeny from a
1099 set of nested taxonomic variables given as a formula.
1101 o The new function read.caic() reads trees in CAIC format.
1103 o The new function tiplabels() allows to add labels to the tips
1104 of a tree using text or plotting symbols in a flexible way.
1106 o The new function unroot() unroots a phylogeny.
1108 o multi2di() has a new option, `random', which specifies whether
1109 to resolve the multichotomies randomly (the default) or not.
1111 o prop.part() now returns an object of class "prop.part" for which
1112 there are print (to display a partition in a more friendly way)
1113 and summary (to extract the numbers) methods.
1115 o plot.phylo() has a new option, `show.tip.label', specifying
1116 whether to print the labels of the tips. The default is TRUE.
1118 o The code of nj() has been replaced by a faster C code: it is now
1119 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1122 o write.nexus() now writes whether a tree is rooted or not.
1127 o Two bugs have been fixed in root(): unrooted trees are now
1128 handled corretly, and node labels are now output normally.
1130 o A bug was fixed in phymltest(): the executable couldn't be found
1133 o Three bug have been fixed in ace(): computing the likelihood of
1134 ancestral states of discrete characters failed, custom models
1135 did not work, and the function failed with a null gradient (a
1136 warning message is now returned; this latter bug was also
1137 present in yule.cov() as well and is now fixed).
1139 o pic() hanged out when missing data were present: a message error
1142 o A small bug was fixed in dist.dna() where the gamma correction
1143 was not always correctly dispatched.
1145 o plot.phylo() plotted correctly the root edge only when the tree
1146 was plotted rightwards: this works now for all directions.
1151 o dist.taxo() has been renamed as weight.taxo().
1153 o Various error and warning messages have been improved.
1157 CHANGES IN APE VERSION 1.7
1160 o The new function ace() estimates ancestral character states for
1161 continuous characters (with ML, GLS, and contrasts methods), and
1162 discrete characters (with ML only) for any number of states.
1164 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1165 of directional evolution for continuous characters. The user
1166 specifies the node(s) of the tree where the character optimum
1169 o The new function is.rooted() tests whether a tree (of class
1172 o The new function rcoal() generates random ultrametric trees with
1173 the possibility to specify the function that generates the
1174 inter-nodes distances.
1176 o The new function mrca() gives for all pairs of tips in a tree
1177 (and optionally nodes too) the most recent common ancestor.
1179 o nodelabels() has a new option `thermo' to plot proportions (up
1180 to three classes) on the nodes of a tree.
1182 o rtree() has been improved: it can now generate rooted or
1183 unrooted trees, and the mathematical function that generates the
1184 branch lengths may be specified by the user. The tip labels may
1185 be given directly in the call to rtree. The limit cases (n = 2,
1186 3) are now handled correctly.
1188 o dist.topo() has a new argument `method' with two choices: "PH85"
1189 for Penny and Henny's method (already available before and now
1190 the default), and "BHV01" for the geometric distance by Billera
1191 et al. (2001, Adv. Appl. Math. 27:733).
1193 o write.tree() has a new option, `digits', which specifies the
1194 number of digits to be printed in the Newick tree. By default
1195 digits = 10. The numbers are now always printed in decimal form
1196 (i.e., 1.0e-1 is now avoided).
1198 o dist.dna() can now compute the raw distances between pairs of
1199 DNA sequences by specifying model = "raw".
1201 o dist.phylo() has a new option `full' to possibly compute the
1202 distances among all tips and nodes of the tree. The default if
1208 o Several bugs were fixed in all.equal.phylo().
1210 o dist.dna() did not handle correctly gaps ("-") in alignments:
1211 they are now considered as missing data.
1213 o rotate() did not work if the tips were not ordered: this is
1216 o mantel.test() returned NA in some special cases: this is fixed
1217 and the function has been improved and is now faster.
1219 o A bug was fixed in diversi.gof() where the calculation of A² was
1222 o cherry() did not work correctly under some OSs (mainly Linux):
1225 o is.binary.tree() has been modified so that it works with both
1226 rooted and unrooted trees.
1228 o The documentation of theta.s() was not correct: this has been
1231 o plot.mst() did not work correctly: this is fixed.
1235 CHANGES IN APE VERSION 1.6
1240 o The new function dist.topo() computes the topological distances
1243 o The new function boot.phylo() performs a bootstrap analysis on
1244 phylogeny estimation.
1246 o The new functions prop.part() and prop.clades() analyse
1247 bipartitions from a series of trees.
1252 o read.GenBank() now uses the EFetch utility of NCBI instead of
1253 the usual Web interface: it is now much faster (e.g., 12 times
1254 faster to retrieve 8 sequences, 37 times for 60 sequences).
1259 o Several bugs were fixed in read.dna().
1261 o Several bugs were fixed in diversi.time().
1263 o is.binary.tree() did not work correctly if the tree has no edge
1264 lengths: this is fixed.
1266 o drop.tip() did not correctly propagated the `node.label' of a
1267 tree: this is fixed.
1271 CHANGES IN APE VERSION 1.5
1276 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1277 convert objects between the classes "phylo" and "matching". The
1278 latter implements the representation of binary trees introduced by
1279 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1280 as.matching() has been introduced as well.
1282 o Two new functions, multi2di() and di2multi(), allow to resolve
1283 and collapse multichotomies with branches of length zero.
1285 o The new function nuc.div() computes the nucleotide diversity
1286 from a sample a DNA sequences.
1288 o dist.dna() has been completely rewritten with a much faster
1289 (particularly for large data sets) C code. Eight models are
1290 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1291 option `method' has been renamed `model'). Computation of variance
1292 is available for all models. A gamma-correction is possible for
1293 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1294 to remove sites with missing data on a pairwise basis. The option
1295 `GCcontent' has been removed.
1297 o read.GenBank() has a new option (species.names) which specifies
1298 whether to return the species names of the organisms in addition
1299 to the accession numbers of the sequences (this is the default
1302 o write.nexus() can now write several trees in the same NEXUS file.
1304 o drop.tip() has a new option `root.edge' that allows to specify the
1305 new root edge if internal branches are trimmed.
1310 o as.phylo.hclust() failed if some labels had parentheses: this
1313 o Several bugs were fixed in all.equal.phylo(). This function now
1314 returns the logical TRUE if the trees are identical but with
1315 different representations (a report was printed previously).
1317 o read.GenBank() did not correctly handle ambiguous base codes:
1323 o birthdeath() now returns an object of class "birthdeath" for
1324 which there is a print method.
1328 CHANGES IN APE VERSION 1.4
1333 o The new function nj() performs phylogeny estimation with the
1334 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1337 o The new function which.edge() identifies the edges of a tree
1338 that belong to a group specified as a set of tips.
1340 o The new function as.phylo.phylog() converts an object of class
1341 "phylog" (from the package ade4) into an object of class
1344 o The new function axisPhylo() draws axes on the side of a
1347 o The new function howmanytrees() calculates the number of trees
1348 in different cases and giving a number of tips.
1350 o write.tree() has a new option `multi.line' (TRUE by default) to
1351 write a Newick tree on several lines rather than on a single
1354 o The functionalities of zoom() have been extended. Several
1355 subtrees can be visualized at the same time, and they are marked
1356 on the main tree with colors. The context of the subtrees can be
1357 marked with the option `subtree' (see below).
1359 o drop.tip() has a new option `subtree' (FALSE by default) which
1360 specifies whether to output in the tree how many tips have been
1363 o The arguments of add.scale.bar() have been redefined and have
1364 now default values (see ?add.scale.bar for details). This
1365 function now works even if the plotted tree has no edge length.
1367 o plot.phylo() can now plot radial trees, but this does not take
1368 edge lengths into account.
1370 o In plot.phylo() with `type = "phylogram"', if the values of
1371 `edge.color' and `edge.width' are identical for sister-branches,
1372 they are propagated to the vertical line that link them.
1377 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1378 crashing. This is fixed.
1380 o In plot.phylo(), the options `edge.color' and `edge.width' are
1381 now properly recycled; their default values are now "black" and
1384 o A bug has been fixed in write.nexus().
1389 o The function node.depth.edgelength() has been removed and
1390 replaced by a C code.
1394 CHANGES IN APE VERSION 1.3-1
1399 o The new function nodelabels() allows to add labels to the nodes
1400 of a tree using text or plotting symbols in a flexible way.
1402 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1403 numeric values specifying the lower and upper limits on the x-
1404 and y-axes. This allows to leave some space on any side of the
1405 tree. If a single value is given, this is taken as the upper
1410 CHANGES IN APE VERSION 1.3
1415 o The new function phymltest() calls the software PHYML and fits
1416 28 models of DNA sequence evolution. There are a print method to
1417 display likelihood and AIC values, a summary method to compute
1418 the hierarchical likelihood ratio tests, and a plot method to
1419 display graphically the AIC values of each model.
1421 o The new function yule.cov() fits the Yule model with covariates,
1422 a model where the speciation rate is affected by several species
1423 traits through a generalized linear model. The parameters are
1424 estimated by maximum likelihood.
1426 o Three new functions, corBrownian(), corGrafen(), and
1427 corMartins(), compute the expected correlation structures among
1428 species given a phylogeny under different models of evolution.
1429 These can be used for GLS comparative phylogenetic methods (see
1430 the examples). There are coef() and corMatrix() methods and an
1431 Initialize.corPhyl() function associated.
1433 o The new function compar.cheverud() implements Cheverud et al.'s
1434 (1985; Evolution 39:1335) phylogenetic comparative method.
1436 o The new function varcomp() estimates variance components; it has
1439 o Two new functions, panel.superpose.correlogram() and
1440 plot.correlogramList(), allow to plot several phylogenetic
1443 o The new function node.leafnumber() computes the number of leaves
1444 of a subtree defined by a particular node.
1446 o The new function node.sons() gets all tags of son nodes from a
1449 o The new function compute.brlen() computes the branch lengths of
1450 a tree according to a specified method.
1452 o plot.phylo() has three new options: "cex" controls the size of
1453 the (tip and node) labels (thus it is no more needed to change
1454 the global graphical parameter), "direction" which allows to
1455 plot the tree rightwards, leftwards, upwards, or downwards, and
1456 "y.lim" which sets the upper limit on the y-axis.
1461 o Some functions which try to match tip labels and names of
1462 additional data (e.g. vector) are likely to fail if there are
1463 typing or syntax errors. If both series of names do not perfectly
1464 match, they are ignored and a warning message is now issued.
1465 These functions are bd.ext, compar.gee, pic. Their help pages
1466 have been clarified on this point.
1470 CHANGES IN APE VERSION 1.2-7
1475 o The new function root() reroots a phylogenetic tree with respect
1476 to a specified outgroup.
1478 o The new function rotate() rotates an internal branch of a tree.
1480 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1481 trees) controls the display of the tip labels in unrooted trees.
1482 This display has been greatly improved: the tip labels are now not
1483 expected to overlap with the tree (particularly if lab4ut =
1484 "axial"). In all cases, combining appropriate values of "lab4ut"
1485 and the font size (via "par(cex = )") should result in readable
1486 unrooted trees. See ?plot.phylo for some examples.
1488 o In drop.tip(), the argument `tip' can now be numeric or character.
1493 o drop.tip() did not work correctly with trees with no branch
1494 lengths: this is fixed.
1496 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1497 plotted with some line crossings: this is now fixed.
1501 CHANGES IN APE VERSION 1.2-6
1506 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1507 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1508 to implement comparative methods with an autocorrelation approach.
1510 o A new data set describing some life history traits of Carnivores
1516 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1521 o When plotting a tree with plot.phylo(), the new default of the
1522 option `label.offset' is now 0, so the labels are always visible.
1526 CHANGES IN APE VERSION 1.2-5
1531 o The new function bd.ext() fits a birth-death model with combined
1532 phylogenetic and taxonomic data, and estimates the corresponding
1533 speciation and extinction rates.
1538 o The package gee is no more required by ape but only suggested
1539 since only the function compar.gee() calls gee.
1543 CHANGES IN APE VERSION 1.2-4
1548 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1549 and lines.popsize) implementing a new approach for inferring the
1550 demographic history from genealogies using a reversible jump
1551 MCMC have been introduced.
1553 o The unit of time in the skyline plot and in the new plots can
1554 now be chosen to be actual years, rather than substitutions.
1558 CHANGES IN APE VERSION 1.2-3
1563 o The new function rtree() generates a random binary tree with or
1564 without branch lengths.
1566 o Two new functions for drawing lineages-through-time (LTT) plots
1567 are provided: ltt.lines() adds a LTT curve to an existing plot,
1568 and mltt.plot() does a multiple LTT plot giving several trees as
1569 arguments (see `?ltt.plot' for details).
1574 o Some taxon names made R crashing when calling as.phylo.hclust():
1577 o dist.dna() returned an error with two identical DNA sequences
1578 (only using the Jukes-Cantor method returned 0): this is fixed.
1583 o The function dist.phylo() has been re-written using a different
1584 algorithm: it is now about four times faster.
1586 o The code of branching.times() has been improved: it is now about
1591 CHANGES IN APE VERSION 1.2-2
1596 o The new function seg.sites() finds the segregating sites in a
1597 sample of DNA sequences.
1602 o A bug introduced in read.tree() and in read.nexus() with version
1605 o A few errors were corrected and a few examples were added in the
1610 CHANGES IN APE VERSION 1.2-1
1615 o plot.phylo() can now draw the edge of the root of a tree if it
1616 has one (see the new option `root.edge', its default is FALSE).
1621 o A bug was fixed in read.nexus(): files with semicolons inside
1622 comment blocks were not read correctly.
1624 o The behaviour of read.tree() and read.nexus() was corrected so
1625 that tree files with badly represented root edges (e.g., with
1626 an extra pair of parentheses, see the help pages for details)
1627 are now correctly represented in the object of class "phylo";
1628 a warning message is now issued.
1632 CHANGES IN APE VERSION 1.2
1637 o plot.phylo() has been completely re-written and offers several
1638 new functionalities. Three types of trees can now be drawn:
1639 phylogram (as previously), cladogram, and unrooted tree; in
1640 all three types the branch lengths can be drawn using the edge
1641 lengths of the phylogeny or not (e.g., if the latter is absent).
1642 The vertical position of the nodes can be adjusted with two
1643 choices (see option `node.pos'). The code has been re-structured,
1644 and two new functions (potentially useful for developpers) are
1645 documented separately: node.depth.edgelength() and node.depth();
1646 see the respective help pages for details.
1648 o The new function zoom() allows to explore very large trees by
1649 focusing on a small portion of it.
1651 o The new function yule() fits by maximum likelihood the Yule model
1652 (birth-only process) to a phylogenetic tree.
1654 o Support for writing DNA sequences in FASTA format has been
1655 introduced in write.dna() (support for reading sequences in
1656 this format was introduced in read.dna() in version 1.1-2).
1657 The function has been completely re-written, fixing some bugs
1658 (see below); the default behaviour is no more to display the
1659 sequences on the standard output. Several options have been
1660 introduced to control the sequence printing in a flexible
1661 way. The help page has been extended.
1663 o A new data set is included: a supertree of bats in NEXUS format.
1668 o In theta.s(), the default of the option `variance' has
1669 been changed to `FALSE' (as was indicated in the help page).
1671 o Several bugs were fixed in the code of all.equal.phylo().
1673 o Several bugs were fixed in write.dna(), particularly this
1674 function did not work with `format = "interleaved"'.
1676 o Various errors were corrected in the help pages.
1681 o The argument names of as.hclust.phylo() have been changed
1682 from "(phy)" to "(x, ...)" to conform to the definition of
1683 the corresponding generic function.
1685 o gamma.stat() has been renamed gammaStat() to avoid confusion
1686 since gamma() is a generic function.
1690 CHANGES IN APE VERSION 1.1-3
1695 o base.freq() previously did not return a value of 0 for
1696 bases absent in the data (e.g., a vector of length 3 was
1697 returned if one base was absent). This is now fixed (a
1698 vector of length 4 is always returned).
1700 o Several bugs were fixed in read.nexus(), including that this
1701 function did not work in this absence of a "TRANSLATE"
1702 command in the NEXUS file, and that the commands were
1707 CHANGES IN APE VERSION 1.1-2
1712 o The Tamura and Nei (1993) model of DNA distance is now implemented
1713 in dist.dna(): five models are now available in this function.
1715 o A new data set is included: a set of 15 sequences of the
1716 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1722 o A bug in read.nexus() was fixed.
1724 o read.dna() previously did not work correctly in most cases.
1725 The function has been completely re-written and its help page
1726 has been considerably extended (see ?read.dna for details).
1727 Underscores (_) in taxon names are no more replaced with
1728 spaces (this behaviour was undocumented).
1730 o A bug was fixed in write.dna().
1734 CHANGES IN APE VERSION 1.1-1
1739 o A bug in read.tree() introduced in APE 1.1 was fixed.
1741 o A bug in compar.gee() resulted in an error when trying to fit
1742 a model with `family = "binomial"'. This is now fixed.
1746 CHANGES IN APE VERSION 1.1
1751 o The Klastorin (1982) method as suggested by Misawa and Tajima
1752 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1753 on the basis of phylogenetic trees has been implemented (see
1754 the function klastorin()).
1756 o Functions have been added to convert APE's "phylo" objects in
1757 "hclust" cluster objects and vice versa (see the help page of
1758 as.phylo for details).
1760 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1761 are introduced for the estimation of absolute evolutionary rates
1762 (ratogram) and dated clock-like trees (chronogram) from
1763 phylogenetic trees using the non-parametric rate smoothing approach
1764 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1766 o A summary method is now provided printing a summary information on a
1767 phylogenetic tree with, for instance, `summary(tree)'.
1769 o The behaviour of read.tree() was changed so that all spaces and
1770 tabulations in tree files are now ignored. Consequently, spaces in tip
1771 labels are no more allowed. Another side effect is that read.nexus()
1772 now does not replace the underscores (_) in tip labels with spaces
1773 (this behaviour was undocumented).
1775 o The function plot.phylo() has a new option (`underscore') which
1776 specifies whether the underscores in tip labels should be written on
1777 the plot as such or replaced with spaces (the default).
1779 o The function birthdeath() now computes 95% confidence intervals of
1780 the estimated parameters using profile likelihood.
1782 o Three new data sets are included: a gene tree estimated from 36
1783 landplant rbcL sequences, a gene tree estimated from 32 opsin
1784 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1789 o A bug was fixed in dist.gene() where nothing was returned.
1791 o A bug in plot.mst() was fixed.
1793 o A bug in vcv.phylo() resulted in false correlations when the
1794 option `cor = TRUE' was used (now fixed).
1798 CHANGES IN APE VERSION 1.0
1803 o Two new functions, read.dna() and write.dna(), read/write in a file
1804 DNA sequences in interleaved or in sequential format.
1806 o Two new functions, read.nexus() and write.nexus(), read/write trees
1809 o The new function bind.tree() allows to bind two trees together,
1810 possibly handling root edges to give internal branches.
1812 o The new function drop.tip() removes the tips in a phylogenetic tree,
1813 and trims (or not) the corresponding internal branches.
1815 o The new function is.ultrametric() tests if a tree is ultrametric.
1817 o The function plot.phylo() has more functionalities such as drawing the
1818 branches with different colours and/or different widths, showing the
1819 node labels, controling the position and font of the labels, rotating
1820 the labels, and controling the space around the plot.
1822 o The function read.tree() can now read trees with no branch length,
1823 such as "(a,b),c);". Consequently, the element `edge.length' in
1824 objects of class "phylo" is now optional.
1826 o The function write.tree() has a new default behaviour: if the default
1827 for the option `file' is used (i.e. file = ""), then a variable of
1828 mode character containing the tree in Newick format is returned which
1829 can thus be assigned (e.g., tree <- write.tree(phy)).
1831 o The function read.tree() has a new argument `text' which allows
1832 to read the tree in a variable of mode character.
1834 o A new data set is included: the phylogenetic relationships among
1835 the orders of birds from Sibley and Ahlquist (1990).
1839 CHANGES IN APE VERSION 0.2-1
1844 o Several bugs were fixed in the help pages.
1848 CHANGES IN APE VERSION 0.2
1853 o The function write.tree() writes phylogenetic trees (objects of class
1854 "phylo") in an ASCII file using the Newick parenthetic format.
1856 o The function birthdeath() fits a birth-death model to branching times
1857 by maximum likelihood, and estimates the corresponding speciation and
1860 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1863 o The function is.binary.tree() tests whether a phylogeny is binary.
1865 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1866 as well as some methods are introduced.
1868 o Several functions, including some generics and methods, for computing
1869 skyline plot estimates (classic and generalized) of effective
1870 population size through time are introduced and replace the function
1871 skyline.plot() in version 0.1.
1873 o Two data sets are now included: the phylogenetic relationships among
1874 the families of birds from Sibley and Ahlquist (1990), and an
1875 estimated clock-like phylogeny of HIV sequences sampled in the
1876 Democratic Republic of Congo.
1879 DEPRECATED & DEFUNCT
1881 o The function skyline.plot() in ape 0.1 has been deprecated and
1882 replaced by more elaborate functions (see above).
1887 o Two important bugs were fixed in plot.phylo(): phylogenies with
1888 multichotomies not at the root or not with only terminal branches,
1889 and phylogenies with a single node (i.e. only terminal branches)
1890 did not plot. These trees should be plotted correctly now.
1892 o Several bugs were fixed in diversi.time() in the computation of
1895 o Various errors were corrected in the help pages.
projects / ape.git / blob