1 CHANGES IN APE VERSION 2.5
6 o The new function parafit by Pierre Legendre tests for the
7 coevolution between hosts and parasites. It has a companion
8 function, pcoa, that does principal coordinate decomposition.
9 The latter has a biplot method.
11 o The new function lmorigin by Pierre Legendre performs multiple
12 regression through the origin with testing by permutation.
14 o The new functions rTraitCont and rTraitDisc simulate continuous and
15 discrete traits under a wide range of evolutionary models.
17 o The new function delta.plot does a delta plot following Holland et
18 al. (2002, Mol. Biol. Evol. 12:2051).
20 o The new function edges draws additional branches between any nodes
21 and/or tips on a plotted tree.
23 o The new function fancyarrows enhances arrows from graphics with
24 triangle and harpoon heads; it can be called from edges().
26 o add.scale.bar() has a new option 'ask' to draw interactively.
28 o The branch length score replaces the geodesic distance in dist.topo.
33 o add.scale.bar() drew the bar outside the plotting region with the
34 default options with unrooted or radial trees.
36 o dist.topo() made R stuck when the trees had different sizes (thanks
37 to Otto Cordero for the fix).
41 CHANGES IN APE VERSION 2.4-1
46 o rtree() and rcoal() now accept a numeric vector for the 'br'
49 o vcv() is a new generic function with methods for the classes "phylo"
50 and "corPhyl" so that it is possible to calculate the var-cov matrix
51 for "transformation models". vcv.phylo() can still be used for trees
52 of class "phylo"; its argument 'cor' has been renamed 'corr'.
57 o bind.tree() failed when 'y' had no root edge.
59 o read.nexus() shuffled tip labels when the trees have no branch
60 lengths and there is a TRANSLATE block.
62 o read.nexus() does not try to translate node labels if there is a
63 translation table in the NEXUS file. See ?read.nexus for a
64 clarification on this behaviour.
66 o plot.multiPhylo() crashed R when plotting a list of trees with
67 compressed tip labels.
69 o write.nexus() did not translate the taxa names when asked for.
71 o plot.phylo(type = "fan") did not rotate the tip labels correctly
72 when the tree has branch lengths.
74 o ace(type = "continuous", method = "ML") now avoids sigma² being
75 negative (which resulted in an error).
77 o nj() crashed with NA/NaN in the distance matrix: an error in now
82 CHANGES IN APE VERSION 2.4
87 o base.freq() has a new option 'freq' to return the counts; the
88 default is still to return the proportions.
93 o seg.sites() did not handle ambiguous nucleotides correctly: they
96 o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
97 the tree: the argument is now ignored.
99 o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
105 o Trying to plot a tree with a single tip now returns NULL with a
106 warning (it returned an error previously).
108 o The way lines representing nodes are coloured in phylograms has
109 been modified (as well as their widths and types) following some
110 users' request; this is only for dichotomous nodes.
112 o The argument 'adj' in [node][tip][edge]labels() now works when
113 using 'pie' or 'thermo'.
115 o A more informative message error is now returned by dist.dna() when
116 'model' is badly specified (partial matching of this argument is
119 o Deprecated functions are now listed in a help page: see
120 help("ape-defunct") with the quotes.
125 o The functions heterozygosity, nuc.div, theta.h, theta.k and
126 theta.s have been moved from ape to pegas.
128 o The functions mlphylo, DNAmodel and sh.test have been removed.
132 CHANGES IN APE VERSION 2.3-3
137 o add.scale.bar() always drew a horizontal bar.
139 o zoom() shuffled tips with unrooted trees.
141 o write.nexus() failed to write correctly trees with a "TipLabel"
144 o rcoal() failed to compute branch lengths with very large n.
146 o A small bug was fixed in compar.cheverud() (thanks to Michael
149 o seg.sites() failed when passing a vector.
151 o drop.tip() sometimes shuffled tip labels.
153 o root() shuffled node labels with 'resolve.root = TRUE'.
157 CHANGES IN APE VERSION 2.3-2
162 o all.equal.phylo() did not compare unrooted trees correctly.
164 o dist.topo(... method = "PH85") did not treat unrooted trees
165 correctly (thanks to Tim Wallstrom for the fix).
167 o root() sometimes failed to test for the monophyly of the
170 o extract.clade() sometimes included too many edges.
172 o vcv.phylo() did not work correctly when the tree is in
175 o nj() did not handle correctly distance matrices with many 0's.
176 The code has also been significantly improved: 7, 70, 160 times
177 faster with n = 100, 500, 1000, respectively.
181 CHANGES IN APE VERSION 2.3-1
186 o The new function is.monophyletic tests the monophyly of a group.
188 o There is now a c() method for lists of class "DNAbin".
190 o yule.cov() now fits the null model, and its help page has been
191 corrected with respect to this change.
193 o drop.tip() has a new option 'rooted' to force (or not) a tree
194 to be treated as (un)rooted.
199 o dist.gene() failed on most occasions with the default
200 pairwise.deletion = FALSE.
202 o read.tree() failed to read correctly the tree name(s).
204 o boot.phylo() now treats correctly data frames.
206 o del.gaps() did not copy the rownames of a matrix.
208 o A small bug was fixed in CDAM.global().
210 o ace() failed with large data sets. Thanks to Rich FitzJohn for
211 the fix. With other improvements, this function is now about 6
214 o write.tree() failed with objects of class "multiPhylo".
216 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
221 o [.multiPhylo and [.DNAbin now respect the original class.
223 o Instances of the form class(phy) == "phylo" have been replaced
224 by inherits(phy, "phylo").
226 o rcoal() is now faster.
231 o klastorin() has been removed.
235 CHANGES IN APE VERSION 2.3
240 o The new functions CADM.global and CADM.post, contributed by
241 Pierre Legendre, test the congruence among several distance
244 o The new function yule.time fits a user-defined time-dependent
245 Yule model by maximum likelihood.
247 o The new function makeNodeLabel creates and/or modifies node
248 labels in a flexible way.
250 o read.tree() and write.tree() have been modified so that they can
251 handle individual tree names.
253 o plot.phylo() has a new argument 'edge.lty' that specifies the
254 types of lines used for the edges (plain, dotted, dashed, ...)
256 o phymltest() has been updated to work with PhyML 3.0.1.
261 o drop.tip() shuffled tip labels in some cases.
263 o drop.tip() did not handle node.label correctly.
265 o is.ultrametric() now checks the ordering of the edge matrix.
267 o ace() sometimes returned negative values of likelihoods of
268 ancestral states (thanks to Dan Rabosky for solving this long
274 o The data set xenarthra has been removed.
278 CHANGES IN APE VERSION 2.2-4
282 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
283 now fixed. (Thanks to Peter Wragg for the fix!)
285 o A warning message occurred for no reason with ace(method="GLS").
290 o There is now a general help page displayed with '?ape'.
294 CHANGES IN APE VERSION 2.2-3
299 o The new function extract.clade extracts a clade from a tree by
300 specifying a node number or label.
302 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
303 operations of the same names.
305 o dist.dna() can now return the number of site differences by
306 specifying model="N".
311 o chronopl() did not work with CV = TRUE.
313 o read.nexus() did not work correctly in some situations (trees on
314 multiple lines with different numbers of lines and/or with
315 comments inserted within the trees).
317 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
318 the number of lineages with non-binary trees.
323 o ape has now a namespace.
325 o drop.tip() has been improved: it should be much faster and work
326 better in some cases (e.g., see the example in ?zoom).
330 CHANGES IN APE VERSION 2.2-2
335 o dist.gene() has been substantially improved and gains an option
338 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
344 o prop.part() failed with a single tree with the default option
345 'check.labels = TRUE'.
347 o summary.DNAbin() failed to display correctly the summary of
348 sequence lengths with lists of sequences of 10,000 bases or more
349 (because summary.default uses 4 significant digits by default).
351 o read.nexus() failed to read a file with a single tree with line
352 breaks in the Newick string.
354 o del.gaps() returned a list of empty sequences when there were no
360 o phymltest() has been updated for PhyML 3.0 and gains an option
361 'append', whereas the option 'path2exec' has been removed.
363 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
364 which is returned unchanged (instead of an error).
366 o The data sets bird.orders and bird.families are now stored as
367 Newick strings; i.e., the command data(bird.orders) calls
372 CHANGES IN APE VERSION 2.2-1
377 o The new function makeLabel() helps to modify labels of trees,
378 lists of trees, or DNA sequences, with several utilities to
379 truncate and/or make them unique, substituting some
380 characters, and so on.
382 o The new function del.gaps() removes insertion gaps ("-") in a
383 set of DNA sequences.
385 o read.dna() can now read Clustal files (*.aln).
390 o root() failed with 'resolve.root = TRUE' when the root was
391 already the specified root.
393 o Several bugs were fixed in mlphylo().
395 o collapsed.singles() did not propagate the 'Nnode' and
396 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
398 o read.nexus() failed to remove correctly the comments within
401 o read.nexus() failed to read a file with a single tree and no
402 translation of tip labels.
404 o read.nexus() failed to place correctly tip labels when reading
405 a single tree with no edge lengths.
407 o A bug was fixed in sh.test().
412 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
415 o The option 'check.labels' of consensus() and prop.part() is now
418 o write.dna() now does not truncate names to 10 characters with
423 CHANGES IN APE VERSION 2.2
428 o Four new functions have been written by Damien de Vienne for the
429 graphical exploration of large trees (cophyloplot, subtrees,
430 subtreeplot), and to return the graphical coordinates of tree
433 o The new functions corPagel and corBlomberg implement the Pagel's
434 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
436 o chronopl() has been improved and gains several options: see its
437 help page for details.
439 o boot.phylo() has now an option 'trees' to possibly return the
440 bootstraped trees (the default is FALSE).
442 o prop.part() has been improved and should now be faster in all
448 o read.dna() failed if "?" occurred in the first 10 sites of the
451 o The x/y aspect of the plot is now respected when plotting a
452 circular tree (type = "r" or "f").
454 o Drawing the tip labels sometimes failed when plotting circular
457 o zoom() failed when tip labels were used instead of their numbers
458 (thanks to Yan Wong for the fix).
460 o drop.tip() failed with some trees (fixed by Yan Wong).
462 o seg.sites() failed with a list.
464 o consensus() failed in some cases. The function has been improved
465 as well and is faster.
469 CHANGES IN APE VERSION 2.1-3
474 o A bug in read.nexus() made the Windows R-GUI crash.
476 o An error was fixed in the computation of ancestral character
477 states by generalized least squares in ace().
479 o di2multi() did not modify node labels correctly.
481 o multi2di() failed if the tree had its attribute "order" set to
486 CHANGES IN APE VERSION 2.1-2
491 o There three new methods for the "multiPhylo" class: str, $,
494 o root() gains the options 'node' and 'resolve.root'
495 (FALSE by default) as well as its code being improved.
497 o mltt.plot() has now an option 'log' used in the same way
498 than in plot.default().
503 o mltt.plot() failed to display the legend with an unnamed
506 o nodelabels() with pies now correcly uses the argument
507 'cex' to draw symbols of different sizes (which has
508 worked already for thermometers).
510 o read.nexus() generally failed to read very big files.
515 o The argument 'family' of compar.gee() can now be a function
516 as well as a character string.
518 o read.tree() and read.nexus() now return an unnamed list if
521 o read.nexus() now returns a modified object of class "multiPhylo"
522 when there is a TRANSLATE block in the NEXUS file: the individual
523 trees have no 'tip.label' vector, but the list has a 'TipLabel'
524 attribute. The new methods '$' and '[[' set these elements
525 correctly when extracting trees.
529 CHANGES IN APE VERSION 2.1-1
534 o The new function rmtree generates lists of random trees.
536 o rcoal() now generates a genuine coalescent tree by default
537 (thanks to Vladimir Minin for the code).
542 o nuc.div() returned an incorrect value with the default
543 pairwise.deletion = FALSE.
548 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
549 have been improved so that they are stabler and faster.
551 o R packages used by ape are now loaded silently; lattice and gee
552 are loaded only when needed.
556 CHANGES IN APE VERSION 2.1
561 o The new function identify.phylo identifies clades on a plotted
562 tree using the mouse.
564 o It is now possible to subset a list of trees (object of class
565 "multiPhylo") with "[" while keeping its class correct.
567 o The new function as.DNAbin.alignment converts DNA sequences
568 stored in the "alignment" format of the package seqinr into
569 an object of class "DNAbin".
571 o The new function weight.taxo2 helps to build similarity matrices
572 given two taxonomic levels (usually called by other functions).
574 o write.tree() can now take a list of trees (class "multiPhylo")
575 as its main argument.
577 o plot.correlogram() and plot.correlogramList() have been
578 improved, and gain several options (see the help page for
579 details). A legend is now plotted by default.
584 o dist.dna() returned some incorrect values with `model = "JC69"'
585 and `pairwise.deletion = TRUE'. This affected only the
586 distances involving sequences with missing values. (Thanks
587 to Bruno Toupance for digging this bug out.)
589 o write.tree() failed with some trees: this is fixed by removing
590 the `multi.line' option (trees are now always printed on a
593 o read.nexus() did not correctly detect trees with multiple root
594 edges (see OTHER CHANGES).
599 o The code of mlphylo() has been almost entirely rewritten, and
600 should be much stabler. The options have been also greatly
601 simplified (see ?mlphylo and ?DNAmodel for details).
603 o The internal function nTips has been renamed klastorin_nTips.
605 o The code of is.ultrametric() contained redundancies and has
608 o The code of Moran.I() and of correlogram.formula() have been
611 o read.tree() and read.nexus() now return an error when trying to
612 read a tree with multiple root edges (see BUG FIXES). The
613 correction applied in previous version did not work in all
616 o The class c("multi.tree", "phylo") has been renamed
622 o There is now a vignette in ape: see vignette("MoranI", "ape").
627 o as.matching() and as.phylo.matching() do not support branch
630 o correlogram.phylo() and discrete.dist() have been removed.
634 CHANGES IN APE VERSION 2.0-2
639 o The new function matexpo computes the exponential of a square
642 o The new function unique.multi.tree removes duplicate trees from
645 o yule() has a new option `use.root.edge = FALSE' that specifies
646 to ignore, by default, the root edge of the tree if it exists.
651 o which.edge() failed when the index of a single terminal edge was
654 o In diversi.time(), the values returned for model C were
657 o A bug was fixed in yule() that affected the calculation of the
658 likelihood in the presence of ties in the branching times.
660 o There was a bug in the C function mat_expo4x4 affecting the
661 calculations of the transition probabilities for models HKY and
664 o A small bug was fixed in as.matrix.DNAbin (thanks to James
667 o rtree() did not `shuffle' the tip labels by default, so only a
668 limited number of labelled topologies could be generated.
672 CHANGES IN APE VERSION 2.0-1
677 o The three new functions bionj, fastme.ols, and fastme.bal
678 perform phylogeny estimation by the BIONJ and fastME methods in
679 OLS and balanced versions. This is a port to R of previous
680 previous programs done by Vincent Lefort.
682 o The new function chronoMPL performs molecular dating with the
683 mean path lengths method of Britton et al. (2002, Mol. Phyl.
686 o The new function rotate, contributed by Christoph Heibl, swaps
687 two clades connected to the same node. It works also with
688 multichotomous nodes.
690 o The new `method' as.matrix.DNAbin() may be used to convert
691 easily DNA sequences stored in a list into a matrix while
692 keeping the names and the class.
697 o chronopl() failed when some branch lengths were equal to zero:
698 an error message is now returned.
700 o di2multi() failed when there was a series of consecutive edges
705 CHANGES IN APE VERSION 1.10-2
710 o plot.phylo() can now plot circular trees: the option is type =
711 "fan" or type = "f" (to avoid the ambiguity with type = "c").
713 o prop.part() has a new option `check.labels = FALSE' which allows
714 to considerably speed-up the calculations of bipartitions. As a
715 consequence, calculations of bootstrap values with boot.phylo()
716 should be much faster.
721 o read.GenBank() did not return correctly the list of species as
722 from ape 1.10: this is fixed in this version
724 o Applying as.phylo() on a tree of class "phylo" failed: the
725 object is now returned unchanged.
729 CHANGES IN APE VERSION 1.10-1
734 o The three new functions Ntip, Nnode, and Nedge return, for a
735 given tree, the number of tips, nodes, or edges, respectively.
740 o read.nexus() did not set correctly the class of the returned
741 object when reading multiple trees.
743 o mllt.plot() failed with objects of class c("multi.tree",
746 o unroot() did not work correctly in most cases.
748 o reorder.phylo() made R freeze in some occasions.
750 o Plotting a tree in pruningwise order failed.
752 o When plotting an unrooted tree, the tip labels where not all
753 correctly positioned if the option `cex' was used.
757 CHANGES IN APE VERSION 1.10
762 o Five new `method' functions have been introduced to manipulate
763 DNA sequences in binary format (see below).
765 o Three new functions have been introduced to convert between the
766 new binary and the character formats.
768 o The new function as.alignment converts DNA sequences stored as
769 single characters into the class "alignment" used by the package
772 o read.dna() and read.GenBank() have a new argument `as.character'
773 controlling whether the sequences are returned in binary format
779 o root() failed when the tree had node labels: this is fixed.
781 o plot.phylo() did not correctly set the limits on the y-axis with
782 the default setting: this is fixed.
784 o dist.dna() returned a wrong result for the LogDet, paralinear,
785 and BH87 models with `pairwise.deletion = TRUE'.
790 o DNA sequences are now internally stored in a binary format. See
791 the document "A Bit-Level Coding Scheme for Nucleotides" for the
792 details. Most functions analyzing DNA functions have been
793 modified accordingly and are now much faster (dist.dna is now
794 ca. 60 times faster).
798 CHANGES IN APE VERSION 1.9-4
803 o A bug was fixed in edgelabels().
805 o as.phylo.hclust() did not work correctly when the object of
806 class "hclust" has its labels set to NULL: the returned tree has
807 now its tip labels set to "1", "2", ...
809 o consensus could fail if some tip labels are a subset of others
810 (e.g., "a" and "a_1"): this is now fixed.
812 o mlphylo() failed in most cases if some branch lengths of the
813 initial tree were greater than one: an error message is now
816 o mlphylo() failed in most cases when estimating the proportion of
817 invariants: this is fixed.
821 CHANGES IN APE VERSION 1.9-3
826 o The new function edgelabels adds labels on the edge of the tree
827 in the same way than nodelabels or tiplabels.
832 o multi2di() did not handle correctly branch lengths with the
833 default option `random = TRUE': this is now fixed.
835 o A bug was fixed in nuc.div() when using pairwise deletions.
837 o A bug occurred in the analysis of bipartitions with large
838 numbers of large trees, with consequences on prop.part,
839 prop.clades, and boot.phylo.
841 o The calculation of the Billera-Holmes-Vogtmann distance in
842 dist.topo was wrong: this has been fixed.
846 CHANGES IN APE VERSION 1.9-2
851 o The new function ladderize reorganizes the internal structure of
852 a tree to plot them left- or right-ladderized.
854 o The new function dist.nodes computes the patristic distances
855 between all nodes, internal and terminal, of a tree. It replaces
856 the option `full = TRUE' of cophenetic.phylo (see below).
861 o A bug was fixed in old2new.phylo().
863 o Some bugs were fixed in chronopl().
865 o The edge colours were not correctly displayed by plot.phylo
866 (thank you to Li-San Wang for the fix).
868 o cophenetic.phylo() failed with multichotomous trees: this is
874 o read.dna() now returns the sequences in a matrix if they are
875 aligned (interleaved or sequential format). Sequences in FASTA
876 format are still returned in a list.
878 o The option `full' of cophenetic.phylo() has been removed because
879 it could not be used from the generic.
884 o rotate() has been removed; this function did not work correctly
889 CHANGES IN APE VERSION 1.9-1
894 o Trees with a single tip were not read correctly in R as the
895 element `Nnode' was not set: this is fixed.
897 o unroot() did not set correctly the number of nodes of the
898 unrooted tree in most cases.
900 o read.GenBank() failed when fetching very long sequences,
901 particularly of the BX-series.
903 o A bug was introduced in read.tree() with ape 1.9: it has been
908 CHANGES IN APE VERSION 1.9
913 o There are two new print `methods' for trees of class "phylo" and
914 lists of trees of class "multi.tree", so that they are now
915 displayed in a compact and informative way.
917 o There are two new functions, old2new.phylo and new2old.phylo,
918 for converting between the old and new coding of the class
921 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
922 LogDet ("logdet"), and paralinear ("paralin").
924 o compute.brlen() has been extended: several methods are now
925 available to compute branch lengths.
927 o write.dna() can now handle matrices as well as lists.
932 o cophenetic.phylo() sometimes returned a wrong result with
933 multichotomous trees: this is fixed.
935 o rotate() failed when a single tip was specified: the tree is now
938 o ace() did not return the correct index matrix with custom
939 models: this is fixed.
941 o multi2di() did not work correctly when resolving multichotomies
942 randomly: the topology was always the same, only the arrangement
943 of clades was randomized: this is fixed. This function now
944 accepts trees with no branch lengths.
946 o The output of diversi.gof() was blurred by useless prints when a
947 user distribution was specified. This has been corrected, and
948 the help page of this function has been expanded.
953 o The internal structure of the class "phylo" has been changed:
954 see the document "Definition of Formats for Coding Phylogenetic
955 Trees in R" for the details. In addition, the code of most
956 functions has been improved.
958 o Several functions have been improved by replacing some R codes
959 by C codes: pic, plot.phylo, and reorder.phylo.
961 o There is now a citation information: see citation("ape") in R.
963 o write.tree() now does not add extra 0's to branch lengths so
964 that 1.23 is printed "1.23" by default, not "1.2300000000".
966 o The syntax of bind.tree() has been simplified. This function now
967 accepts trees with no branch lengths, and handles correctly node
970 o The option `as.numeric' of mrca() has been removed.
972 o The unused options `format' and `rooted' of read.tree() have
975 o The unused option `format' of write.tree() has been removed.
977 o The use of node.depth() has been simplified.
981 CHANGES IN APE VERSION 1.8-5
986 o Two new functions read.nexus.data() and write.nexus.data(),
987 contributed by Johan Nylander, allow to read and write molecular
988 sequences in NEXUS files.
990 o The new function reorder.phylo() reorders the internal structure
991 of a tree of class "phylo". It is used as the generic, e.g.,
994 o read.tree() and read.nexus() can now read trees with a single
997 o The new data set `cynipids' supplies a set of protein sequences
1003 o The code of all.equal.phylo() has been completely rewritten
1004 (thanks to Benoît Durand) which fixes several bugs.
1006 o read.tree() and read.nexus() now checks the labels of the tree
1007 to remove or substitute any characters that are illegal in the
1008 Newick format (parentheses, etc.)
1010 o A negative P-value could be returned by mantel.test(): this is
1015 CHANGES IN APE VERSION 1.8-4
1020 o The new function sh.test() computes the Shimodaira-
1023 o The new function collapse.singles() removes the nodes with a
1024 single descendant from a tree.
1026 o plot.phylo() has a new argument `tip.color' to specify the
1027 colours of the tips.
1029 o mlphylo() has now an option `quiet' to control the display of
1030 the progress of the analysis (the default is FALSE).
1035 o read.dna() did not read correctly sequences in sequential format
1036 with leading alignment gaps "-": this is fixed.
1038 o ace() returned a list with no class so that the generic
1039 functions (anova, logLik, ...) could not be used directly. This
1040 is fixed as ace() now returns an object of class "ace".
1042 o anova.ace() had a small bug when computing the number of degrees
1043 of freedom: this is fixed.
1045 o mlphylo() did not work when the sequences were in a matrix or
1046 a data frame: this is fixed.
1048 o rtree() did not work correctly when trying to simulate an
1049 unrooted tree with two tips: an error message is now issued.
1054 o The algorithm of rtree() has been changed: it is now about 40,
1055 100, and 130 times faster for 10, 100, and 1000 tips,
1060 CHANGES IN APE VERSION 1.8-3
1065 o There are four new `method' functions to be used with the
1066 results of ace(): logLik(), deviance(), AIC(), and anova().
1068 o The plot method of phymltest has two new arguments: `main' to
1069 change the title, and `col' to control the colour of the
1070 segments showing the AIC values.
1072 o ace() has a new argument `ip' that gives the initial values used
1073 in the ML estimation with discrete characters (see the examples
1074 in ?ace). This function now returns a matrix giving the indices
1075 of the estimated rates when analysing discrete characters.
1077 o nodelabels() and tiplabels() have a new argument `pie' to
1078 represent proportions, with any number of categories, as
1079 piecharts. The use of the option `thermo' has been improved:
1080 there is now no limitation on the number of categories.
1085 o mlphylo() did not work with more than two partitions: this is
1088 o root() failed if the proposed outgroup was already an outgroup
1089 in the tree: this is fixed.
1091 o The `col' argument in nodelabels() and tiplabels() was not
1092 correctly passed when `text' was used: this is fixed.
1094 o Two bugs were fixed in mlphylo(): parameters were not always
1095 correctly output, and the estimation failed in some cases.
1097 o plot.phylo() was stuck when given a tree with a single tip: this
1098 is fixed and a message error is now returned.
1100 o An error was corrected in the help page of gammaStat regarding
1101 the calculation of P-values.
1103 o Using gls() could crash R when the number of species in the tree
1104 and in the variables were different: this is fixed.
1108 CHANGES IN APE VERSION 1.8-2
1113 o The new function mlphylo() fits a phylogenetic tree by maximum
1114 likelihood from DNA sequences. Its companion function DNAmodel()
1115 is used to define the substitution model which may include
1116 partitioning. There are methods for logLik(), deviance(), and
1117 AIC(), and the summary() method has been extended to display in
1118 a friendly way the results of this model fitting. Currently, the
1119 functionality is limited to estimating the substitution and
1120 associated parameters and computing the likelihood.
1122 o The new function drop1.compar.gee (used as, e.g., drop1(m))
1123 tests for single effects in GEE-based comparative method. A
1124 warning message is printed if there is not enough degrees of
1130 o An error message was sometimes issued by plot.multi.tree(),
1131 though with no consequence.
1135 CHANGES IN APE VERSION 1.8-1
1140 o There is a new plot method for lists of trees (objects of class
1141 "multi.tree"): it calls plot.phylo() internally and is
1142 documented on the same help page.
1147 o A bug was fixed in the C code that analyzes bipartitions: this
1148 has impact on several functions like prop.part, prop.clades,
1149 boot.phylo, or consensus.
1151 o root() did not work correctly when the specified outgroup had
1152 more than one element: this is fixed.
1154 o dist.dna() sometimes returned a warning inappropriately: this
1157 o If the distance object given to nj() had no rownames, nj()
1158 returned a tree with no tip labels: it now returns tips labelled
1159 "1", "2", ..., corresponding to the row numbers.
1164 o nj() has been slightly changed so that tips with a zero distance
1165 are first aggregated with zero-lengthed branches; the usual NJ
1166 procedure is then performed on a distance matrix without 0's.
1170 CHANGES IN APE VERSION 1.8
1175 o The new function chronopl() estimates dates using the penalized
1176 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1178 o The new function consensus() calculates the consensus tree of a
1181 o The new function evolve.phylo() simulates the evolution of
1182 continuous characters along a phylogeny under a Brownian model.
1184 o The new plot method for objects of class "ancestral" displays a
1185 tree together with ancestral values, as returned by the above
1188 o The new function as.phylo.formula() returns a phylogeny from a
1189 set of nested taxonomic variables given as a formula.
1191 o The new function read.caic() reads trees in CAIC format.
1193 o The new function tiplabels() allows to add labels to the tips
1194 of a tree using text or plotting symbols in a flexible way.
1196 o The new function unroot() unroots a phylogeny.
1198 o multi2di() has a new option, `random', which specifies whether
1199 to resolve the multichotomies randomly (the default) or not.
1201 o prop.part() now returns an object of class "prop.part" for which
1202 there are print (to display a partition in a more friendly way)
1203 and summary (to extract the numbers) methods.
1205 o plot.phylo() has a new option, `show.tip.label', specifying
1206 whether to print the labels of the tips. The default is TRUE.
1208 o The code of nj() has been replaced by a faster C code: it is now
1209 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1212 o write.nexus() now writes whether a tree is rooted or not.
1217 o Two bugs have been fixed in root(): unrooted trees are now
1218 handled corretly, and node labels are now output normally.
1220 o A bug was fixed in phymltest(): the executable couldn't be found
1223 o Three bug have been fixed in ace(): computing the likelihood of
1224 ancestral states of discrete characters failed, custom models
1225 did not work, and the function failed with a null gradient (a
1226 warning message is now returned; this latter bug was also
1227 present in yule.cov() as well and is now fixed).
1229 o pic() hanged out when missing data were present: a message error
1232 o A small bug was fixed in dist.dna() where the gamma correction
1233 was not always correctly dispatched.
1235 o plot.phylo() plotted correctly the root edge only when the tree
1236 was plotted rightwards: this works now for all directions.
1241 o dist.taxo() has been renamed as weight.taxo().
1243 o dist.phylo() has been replaced by the method cophenetic.phylo().
1245 o Various error and warning messages have been improved.
1249 CHANGES IN APE VERSION 1.7
1252 o The new function ace() estimates ancestral character states for
1253 continuous characters (with ML, GLS, and contrasts methods), and
1254 discrete characters (with ML only) for any number of states.
1256 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1257 of directional evolution for continuous characters. The user
1258 specifies the node(s) of the tree where the character optimum
1261 o The new function is.rooted() tests whether a tree (of class
1264 o The new function rcoal() generates random ultrametric trees with
1265 the possibility to specify the function that generates the
1266 inter-nodes distances.
1268 o The new function mrca() gives for all pairs of tips in a tree
1269 (and optionally nodes too) the most recent common ancestor.
1271 o nodelabels() has a new option `thermo' to plot proportions (up
1272 to three classes) on the nodes of a tree.
1274 o rtree() has been improved: it can now generate rooted or
1275 unrooted trees, and the mathematical function that generates the
1276 branch lengths may be specified by the user. The tip labels may
1277 be given directly in the call to rtree. The limit cases (n = 2,
1278 3) are now handled correctly.
1280 o dist.topo() has a new argument `method' with two choices: "PH85"
1281 for Penny and Henny's method (already available before and now
1282 the default), and "BHV01" for the geometric distance by Billera
1283 et al. (2001, Adv. Appl. Math. 27:733).
1285 o write.tree() has a new option, `digits', which specifies the
1286 number of digits to be printed in the Newick tree. By default
1287 digits = 10. The numbers are now always printed in decimal form
1288 (i.e., 1.0e-1 is now avoided).
1290 o dist.dna() can now compute the raw distances between pairs of
1291 DNA sequences by specifying model = "raw".
1293 o dist.phylo() has a new option `full' to possibly compute the
1294 distances among all tips and nodes of the tree. The default if
1300 o Several bugs were fixed in all.equal.phylo().
1302 o dist.dna() did not handle correctly gaps ("-") in alignments:
1303 they are now considered as missing data.
1305 o rotate() did not work if the tips were not ordered: this is
1308 o mantel.test() returned NA in some special cases: this is fixed
1309 and the function has been improved and is now faster.
1311 o A bug was fixed in diversi.gof() where the calculation of A² was
1314 o cherry() did not work correctly under some OSs (mainly Linux):
1317 o is.binary.tree() has been modified so that it works with both
1318 rooted and unrooted trees.
1320 o The documentation of theta.s() was not correct: this has been
1323 o plot.mst() did not work correctly: this is fixed.
1327 CHANGES IN APE VERSION 1.6
1332 o The new function dist.topo() computes the topological distances
1335 o The new function boot.phylo() performs a bootstrap analysis on
1336 phylogeny estimation.
1338 o The new functions prop.part() and prop.clades() analyse
1339 bipartitions from a series of trees.
1344 o read.GenBank() now uses the EFetch utility of NCBI instead of
1345 the usual Web interface: it is now much faster (e.g., 12 times
1346 faster to retrieve 8 sequences, 37 times for 60 sequences).
1351 o Several bugs were fixed in read.dna().
1353 o Several bugs were fixed in diversi.time().
1355 o is.binary.tree() did not work correctly if the tree has no edge
1356 lengths: this is fixed.
1358 o drop.tip() did not correctly propagated the `node.label' of a
1359 tree: this is fixed.
1363 CHANGES IN APE VERSION 1.5
1368 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1369 convert objects between the classes "phylo" and "matching". The
1370 latter implements the representation of binary trees introduced by
1371 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1372 as.matching() has been introduced as well.
1374 o Two new functions, multi2di() and di2multi(), allow to resolve
1375 and collapse multichotomies with branches of length zero.
1377 o The new function nuc.div() computes the nucleotide diversity
1378 from a sample a DNA sequences.
1380 o dist.dna() has been completely rewritten with a much faster
1381 (particularly for large data sets) C code. Eight models are
1382 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1383 option `method' has been renamed `model'). Computation of variance
1384 is available for all models. A gamma-correction is possible for
1385 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1386 to remove sites with missing data on a pairwise basis. The option
1387 `GCcontent' has been removed.
1389 o read.GenBank() has a new option (species.names) which specifies
1390 whether to return the species names of the organisms in addition
1391 to the accession numbers of the sequences (this is the default
1394 o write.nexus() can now write several trees in the same NEXUS file.
1396 o drop.tip() has a new option `root.edge' that allows to specify the
1397 new root edge if internal branches are trimmed.
1402 o as.phylo.hclust() failed if some labels had parentheses: this
1405 o Several bugs were fixed in all.equal.phylo(). This function now
1406 returns the logical TRUE if the trees are identical but with
1407 different representations (a report was printed previously).
1409 o read.GenBank() did not correctly handle ambiguous base codes:
1415 o birthdeath() now returns an object of class "birthdeath" for
1416 which there is a print method.
1420 CHANGES IN APE VERSION 1.4
1425 o The new function nj() performs phylogeny estimation with the
1426 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1429 o The new function which.edge() identifies the edges of a tree
1430 that belong to a group specified as a set of tips.
1432 o The new function as.phylo.phylog() converts an object of class
1433 "phylog" (from the package ade4) into an object of class
1436 o The new function axisPhylo() draws axes on the side of a
1439 o The new function howmanytrees() calculates the number of trees
1440 in different cases and giving a number of tips.
1442 o write.tree() has a new option `multi.line' (TRUE by default) to
1443 write a Newick tree on several lines rather than on a single
1446 o The functionalities of zoom() have been extended. Several
1447 subtrees can be visualized at the same time, and they are marked
1448 on the main tree with colors. The context of the subtrees can be
1449 marked with the option `subtree' (see below).
1451 o drop.tip() has a new option `subtree' (FALSE by default) which
1452 specifies whether to output in the tree how many tips have been
1455 o The arguments of add.scale.bar() have been redefined and have
1456 now default values (see ?add.scale.bar for details). This
1457 function now works even if the plotted tree has no edge length.
1459 o plot.phylo() can now plot radial trees, but this does not take
1460 edge lengths into account.
1462 o In plot.phylo() with `type = "phylogram"', if the values of
1463 `edge.color' and `edge.width' are identical for sister-branches,
1464 they are propagated to the vertical line that link them.
1469 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1470 crashing. This is fixed.
1472 o In plot.phylo(), the options `edge.color' and `edge.width' are
1473 now properly recycled; their default values are now "black" and
1476 o A bug has been fixed in write.nexus().
1481 o The function node.depth.edgelength() has been removed and
1482 replaced by a C code.
1486 CHANGES IN APE VERSION 1.3-1
1491 o The new function nodelabels() allows to add labels to the nodes
1492 of a tree using text or plotting symbols in a flexible way.
1494 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1495 numeric values specifying the lower and upper limits on the x-
1496 and y-axes. This allows to leave some space on any side of the
1497 tree. If a single value is given, this is taken as the upper
1502 CHANGES IN APE VERSION 1.3
1507 o The new function phymltest() calls the software PHYML and fits
1508 28 models of DNA sequence evolution. There are a print method to
1509 display likelihood and AIC values, a summary method to compute
1510 the hierarchical likelihood ratio tests, and a plot method to
1511 display graphically the AIC values of each model.
1513 o The new function yule.cov() fits the Yule model with covariates,
1514 a model where the speciation rate is affected by several species
1515 traits through a generalized linear model. The parameters are
1516 estimated by maximum likelihood.
1518 o Three new functions, corBrownian(), corGrafen(), and
1519 corMartins(), compute the expected correlation structures among
1520 species given a phylogeny under different models of evolution.
1521 These can be used for GLS comparative phylogenetic methods (see
1522 the examples). There are coef() and corMatrix() methods and an
1523 Initialize.corPhyl() function associated.
1525 o The new function compar.cheverud() implements Cheverud et al.'s
1526 (1985; Evolution 39:1335) phylogenetic comparative method.
1528 o The new function varcomp() estimates variance components; it has
1531 o Two new functions, panel.superpose.correlogram() and
1532 plot.correlogramList(), allow to plot several phylogenetic
1535 o The new function node.leafnumber() computes the number of leaves
1536 of a subtree defined by a particular node.
1538 o The new function node.sons() gets all tags of son nodes from a
1541 o The new function compute.brlen() computes the branch lengths of
1542 a tree according to a specified method.
1544 o plot.phylo() has three new options: "cex" controls the size of
1545 the (tip and node) labels (thus it is no more needed to change
1546 the global graphical parameter), "direction" which allows to
1547 plot the tree rightwards, leftwards, upwards, or downwards, and
1548 "y.lim" which sets the upper limit on the y-axis.
1553 o Some functions which try to match tip labels and names of
1554 additional data (e.g. vector) are likely to fail if there are
1555 typing or syntax errors. If both series of names do not perfectly
1556 match, they are ignored and a warning message is now issued.
1557 These functions are bd.ext, compar.gee, pic. Their help pages
1558 have been clarified on this point.
1562 CHANGES IN APE VERSION 1.2-7
1567 o The new function root() reroots a phylogenetic tree with respect
1568 to a specified outgroup.
1570 o The new function rotate() rotates an internal branch of a tree.
1572 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1573 trees) controls the display of the tip labels in unrooted trees.
1574 This display has been greatly improved: the tip labels are now not
1575 expected to overlap with the tree (particularly if lab4ut =
1576 "axial"). In all cases, combining appropriate values of "lab4ut"
1577 and the font size (via "par(cex = )") should result in readable
1578 unrooted trees. See ?plot.phylo for some examples.
1580 o In drop.tip(), the argument `tip' can now be numeric or character.
1585 o drop.tip() did not work correctly with trees with no branch
1586 lengths: this is fixed.
1588 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1589 plotted with some line crossings: this is now fixed.
1593 CHANGES IN APE VERSION 1.2-6
1598 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1599 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1600 to implement comparative methods with an autocorrelation approach.
1602 o A new data set describing some life history traits of Carnivores
1608 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1613 o When plotting a tree with plot.phylo(), the new default of the
1614 option `label.offset' is now 0, so the labels are always visible.
1618 CHANGES IN APE VERSION 1.2-5
1623 o The new function bd.ext() fits a birth-death model with combined
1624 phylogenetic and taxonomic data, and estimates the corresponding
1625 speciation and extinction rates.
1630 o The package gee is no more required by ape but only suggested
1631 since only the function compar.gee() calls gee.
1635 CHANGES IN APE VERSION 1.2-4
1640 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1641 and lines.popsize) implementing a new approach for inferring the
1642 demographic history from genealogies using a reversible jump
1643 MCMC have been introduced.
1645 o The unit of time in the skyline plot and in the new plots can
1646 now be chosen to be actual years, rather than substitutions.
1650 CHANGES IN APE VERSION 1.2-3
1655 o The new function rtree() generates a random binary tree with or
1656 without branch lengths.
1658 o Two new functions for drawing lineages-through-time (LTT) plots
1659 are provided: ltt.lines() adds a LTT curve to an existing plot,
1660 and mltt.plot() does a multiple LTT plot giving several trees as
1661 arguments (see `?ltt.plot' for details).
1666 o Some taxon names made R crashing when calling as.phylo.hclust():
1669 o dist.dna() returned an error with two identical DNA sequences
1670 (only using the Jukes-Cantor method returned 0): this is fixed.
1675 o The function dist.phylo() has been re-written using a different
1676 algorithm: it is now about four times faster.
1678 o The code of branching.times() has been improved: it is now about
1683 CHANGES IN APE VERSION 1.2-2
1688 o The new function seg.sites() finds the segregating sites in a
1689 sample of DNA sequences.
1694 o A bug introduced in read.tree() and in read.nexus() with version
1697 o A few errors were corrected and a few examples were added in the
1702 CHANGES IN APE VERSION 1.2-1
1707 o plot.phylo() can now draw the edge of the root of a tree if it
1708 has one (see the new option `root.edge', its default is FALSE).
1713 o A bug was fixed in read.nexus(): files with semicolons inside
1714 comment blocks were not read correctly.
1716 o The behaviour of read.tree() and read.nexus() was corrected so
1717 that tree files with badly represented root edges (e.g., with
1718 an extra pair of parentheses, see the help pages for details)
1719 are now correctly represented in the object of class "phylo";
1720 a warning message is now issued.
1724 CHANGES IN APE VERSION 1.2
1729 o plot.phylo() has been completely re-written and offers several
1730 new functionalities. Three types of trees can now be drawn:
1731 phylogram (as previously), cladogram, and unrooted tree; in
1732 all three types the branch lengths can be drawn using the edge
1733 lengths of the phylogeny or not (e.g., if the latter is absent).
1734 The vertical position of the nodes can be adjusted with two
1735 choices (see option `node.pos'). The code has been re-structured,
1736 and two new functions (potentially useful for developpers) are
1737 documented separately: node.depth.edgelength() and node.depth();
1738 see the respective help pages for details.
1740 o The new function zoom() allows to explore very large trees by
1741 focusing on a small portion of it.
1743 o The new function yule() fits by maximum likelihood the Yule model
1744 (birth-only process) to a phylogenetic tree.
1746 o Support for writing DNA sequences in FASTA format has been
1747 introduced in write.dna() (support for reading sequences in
1748 this format was introduced in read.dna() in version 1.1-2).
1749 The function has been completely re-written, fixing some bugs
1750 (see below); the default behaviour is no more to display the
1751 sequences on the standard output. Several options have been
1752 introduced to control the sequence printing in a flexible
1753 way. The help page has been extended.
1755 o A new data set is included: a supertree of bats in NEXUS format.
1760 o In theta.s(), the default of the option `variance' has
1761 been changed to `FALSE' (as was indicated in the help page).
1763 o Several bugs were fixed in the code of all.equal.phylo().
1765 o Several bugs were fixed in write.dna(), particularly this
1766 function did not work with `format = "interleaved"'.
1768 o Various errors were corrected in the help pages.
1773 o The argument names of as.hclust.phylo() have been changed
1774 from "(phy)" to "(x, ...)" to conform to the definition of
1775 the corresponding generic function.
1777 o gamma.stat() has been renamed gammaStat() to avoid confusion
1778 since gamma() is a generic function.
1782 CHANGES IN APE VERSION 1.1-3
1787 o base.freq() previously did not return a value of 0 for
1788 bases absent in the data (e.g., a vector of length 3 was
1789 returned if one base was absent). This is now fixed (a
1790 vector of length 4 is always returned).
1792 o Several bugs were fixed in read.nexus(), including that this
1793 function did not work in this absence of a "TRANSLATE"
1794 command in the NEXUS file, and that the commands were
1799 CHANGES IN APE VERSION 1.1-2
1804 o The Tamura and Nei (1993) model of DNA distance is now implemented
1805 in dist.dna(): five models are now available in this function.
1807 o A new data set is included: a set of 15 sequences of the
1808 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1814 o A bug in read.nexus() was fixed.
1816 o read.dna() previously did not work correctly in most cases.
1817 The function has been completely re-written and its help page
1818 has been considerably extended (see ?read.dna for details).
1819 Underscores (_) in taxon names are no more replaced with
1820 spaces (this behaviour was undocumented).
1822 o A bug was fixed in write.dna().
1826 CHANGES IN APE VERSION 1.1-1
1831 o A bug in read.tree() introduced in APE 1.1 was fixed.
1833 o A bug in compar.gee() resulted in an error when trying to fit
1834 a model with `family = "binomial"'. This is now fixed.
1838 CHANGES IN APE VERSION 1.1
1843 o The Klastorin (1982) method as suggested by Misawa and Tajima
1844 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1845 on the basis of phylogenetic trees has been implemented (see
1846 the function klastorin()).
1848 o Functions have been added to convert APE's "phylo" objects in
1849 "hclust" cluster objects and vice versa (see the help page of
1850 as.phylo for details).
1852 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1853 are introduced for the estimation of absolute evolutionary rates
1854 (ratogram) and dated clock-like trees (chronogram) from
1855 phylogenetic trees using the non-parametric rate smoothing approach
1856 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1858 o A summary method is now provided printing a summary information on a
1859 phylogenetic tree with, for instance, `summary(tree)'.
1861 o The behaviour of read.tree() was changed so that all spaces and
1862 tabulations in tree files are now ignored. Consequently, spaces in tip
1863 labels are no more allowed. Another side effect is that read.nexus()
1864 now does not replace the underscores (_) in tip labels with spaces
1865 (this behaviour was undocumented).
1867 o The function plot.phylo() has a new option (`underscore') which
1868 specifies whether the underscores in tip labels should be written on
1869 the plot as such or replaced with spaces (the default).
1871 o The function birthdeath() now computes 95% confidence intervals of
1872 the estimated parameters using profile likelihood.
1874 o Three new data sets are included: a gene tree estimated from 36
1875 landplant rbcL sequences, a gene tree estimated from 32 opsin
1876 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1881 o A bug was fixed in dist.gene() where nothing was returned.
1883 o A bug in plot.mst() was fixed.
1885 o A bug in vcv.phylo() resulted in false correlations when the
1886 option `cor = TRUE' was used (now fixed).
1890 CHANGES IN APE VERSION 1.0
1895 o Two new functions, read.dna() and write.dna(), read/write in a file
1896 DNA sequences in interleaved or in sequential format.
1898 o Two new functions, read.nexus() and write.nexus(), read/write trees
1901 o The new function bind.tree() allows to bind two trees together,
1902 possibly handling root edges to give internal branches.
1904 o The new function drop.tip() removes the tips in a phylogenetic tree,
1905 and trims (or not) the corresponding internal branches.
1907 o The new function is.ultrametric() tests if a tree is ultrametric.
1909 o The function plot.phylo() has more functionalities such as drawing the
1910 branches with different colours and/or different widths, showing the
1911 node labels, controling the position and font of the labels, rotating
1912 the labels, and controling the space around the plot.
1914 o The function read.tree() can now read trees with no branch length,
1915 such as "(a,b),c);". Consequently, the element `edge.length' in
1916 objects of class "phylo" is now optional.
1918 o The function write.tree() has a new default behaviour: if the default
1919 for the option `file' is used (i.e. file = ""), then a variable of
1920 mode character containing the tree in Newick format is returned which
1921 can thus be assigned (e.g., tree <- write.tree(phy)).
1923 o The function read.tree() has a new argument `text' which allows
1924 to read the tree in a variable of mode character.
1926 o A new data set is included: the phylogenetic relationships among
1927 the orders of birds from Sibley and Ahlquist (1990).
1931 CHANGES IN APE VERSION 0.2-1
1936 o Several bugs were fixed in the help pages.
1940 CHANGES IN APE VERSION 0.2
1945 o The function write.tree() writes phylogenetic trees (objects of class
1946 "phylo") in an ASCII file using the Newick parenthetic format.
1948 o The function birthdeath() fits a birth-death model to branching times
1949 by maximum likelihood, and estimates the corresponding speciation and
1952 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1955 o The function is.binary.tree() tests whether a phylogeny is binary.
1957 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1958 as well as some methods are introduced.
1960 o Several functions, including some generics and methods, for computing
1961 skyline plot estimates (classic and generalized) of effective
1962 population size through time are introduced and replace the function
1963 skyline.plot() in version 0.1.
1965 o Two data sets are now included: the phylogenetic relationships among
1966 the families of birds from Sibley and Ahlquist (1990), and an
1967 estimated clock-like phylogeny of HIV sequences sampled in the
1968 Democratic Republic of Congo.
1971 DEPRECATED & DEFUNCT
1973 o The function skyline.plot() in ape 0.1 has been deprecated and
1974 replaced by more elaborate functions (see above).
1979 o Two important bugs were fixed in plot.phylo(): phylogenies with
1980 multichotomies not at the root or not with only terminal branches,
1981 and phylogenies with a single node (i.e. only terminal branches)
1982 did not plot. These trees should be plotted correctly now.
1984 o Several bugs were fixed in diversi.time() in the computation of
1987 o Various errors were corrected in the help pages.
projects / ape.git / blob